Wei Li

We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.

Olaparib is an oral poly(adenosine diphosphate-ribose) polymerase inhibitor that has promising antitumor activity in patients with metastatic breast cancer and a germline BRCA mutation.We conducted a randomized, open-label, phase 3 trial in which olaparib monotherapy was compared with standard therapy in patients with a germline BRCA mutation and human epidermal growth factor receptor type 2 (HER2)-negative metastatic breast cancer who had received no more than two previous chemotherapy regimens for metastatic disease. Patients were randomly assigned, in a 2:1 ratio, to receive olaparib tablets (300 mg twice daily) or standard therapy with single-agent chemotherapy of the physician's choice (capecitabine, eribulin, or vinorelbine in 21-day cycles). The primary end point was progression-free survival, which was assessed by blinded independent central review and was analyzed on an intention-to-treat basis.Of the 302 patients who underwent randomization, 205 were assigned to receive olaparib and 97 were assigned to receive standard therapy. Median progression-free survival was significantly longer in the olaparib group than in the standard-therapy group (7.0 months vs. 4.2 months; hazard ratio for disease progression or death, 0.58; 95% confidence interval, 0.43 to 0.80; P<0.001). The response rate was 59.9% in the olaparib group and 28.8% in the standard-therapy group. The rate of grade 3 or higher adverse events was 36.6% in the olaparib group and 50.5% in the standard-therapy group, and the rate of treatment discontinuation due to toxic effects was 4.9% and 7.7%, respectively.Among patients with HER2-negative metastatic breast cancer and a germline BRCA mutation, olaparib monotherapy provided a significant benefit over standard therapy; median progression-free survival was 2.8 months longer and the risk of disease progression or death was 42% lower with olaparib monotherapy than with standard therapy. (Funded by AstraZeneca; OlympiAD ClinicalTrials.gov number, NCT02000622 .).

Transfer learning, where a model is first pre-trained on a data-rich task before being fine-tuned on a downstream task, has emerged as a powerful technique in natural language processing (NLP). The effectiveness of transfer learning has given rise to a diversity of approaches, methodology, and practice. In this paper, we explore the landscape of transfer learning techniques for NLP by introducing a unified framework that converts all text-based language problems into a text-to-text format. Our systematic study compares pre-training objectives, architectures, unlabeled data sets, transfer approaches, and other factors on dozens of language understanding tasks. By combining the insights from our exploration with scale and our new ``Colossal Clean Crawled Corpus'', we achieve state-of-the-art results on many benchmarks covering summarization, question answering, text classification, and more. To facilitate future work on transfer learning for NLP, we release our data set, pre-trained models, and code.

Person re-identification is to match pedestrian images from disjoint camera views detected by pedestrian detectors. Challenges are presented in the form of complex variations of lightings, poses, viewpoints, blurring effects, image resolutions, camera settings, occlusions and background clutter across camera views. In addition, misalignment introduced by the pedestrian detector will affect most existing person re-identification methods that use manually cropped pedestrian images and assume perfect detection. In this paper, we propose a novel filter pairing neural network (FPNN) to jointly handle misalignment, photometric and geometric transforms, occlusions and background clutter. All the key components are jointly optimized to maximize the strength of each component when cooperating with others. In contrast to existing works that use handcrafted features, our method automatically learns features optimal for the re-identification task from data. The learned filter pairs encode photometric transforms. Its deep architecture makes it possible to model a mixture of complex photometric and geometric transforms. We build the largest benchmark re-id dataset with 13, 164 images of 1, 360 pedestrians. Unlike existing datasets, which only provide manually cropped pedestrian images, our dataset provides automatically detected bounding boxes for evaluation close to practical applications. Our neural network significantly outperforms state-of-the-art methods on this dataset.

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Acute ischemic stroke caused by internal carotid artery (ICA) occlusion usually has a poor prognosis, especially the T occlusion cases without functional collaterals. The efficacy of intravenous (IV) or intra-arterial (IA) thrombolysis with recombinant tissue plasminogen activator (rt-PA) remains ambiguous in these patients. Eendovascular recanalization of the occluded carotid has been attempted in recent years as a potential strategy. However, the different etiologies of ICA occlusion pose a significant challenge to neurointerventionists. Recently, several endovascular evolvements have been reported in treating carotid occlusion-related stroke. This review summarizes the current status of treatment for acute ICA occlusion.

Abstract Motivation: RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses. However, QC is a time-consuming and complex task, due to the massive size and versatile nature of RNA-seq data. Therefore, a convenient and comprehensive QC tool to assess RNA-seq quality is sorely needed. Results: We developed the RSeQC package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models. Most modules in RSeQC take advantage of R scripts for visualization, and they are notably efficient in dealing with large BAM/SAM files containing hundreds of millions of alignments. Availability and implementation: RSeQC is written in Python and C. Source code and a comprehensive user's manual are freely available at: http://code.google.com/p/rseqc/. Contact: WL1@bcm.edu Supplementary Information: Supplementary data are available at Bioinformatics online.

Narrow bandgap conjugated polymers in combination with fullerene acceptors are under intense investigation in the field of organic photovoltaics (OPVs). The open circuit voltage, and thereby the power conversion efficiency, of the devices is related to the offset of the frontier orbital energy levels of the donor and acceptor components, which are widely determined by cyclic voltammetry. Inconsistencies have appeared in the use of the ferrocenium/ferrocene (Fc + /Fc) redox couple, as well as the values used for the absolute potentials of standard electrodes, which can complicate the comparison of materials properties and determination of structure/property relationships.

Afatinib-an oral irreversible ErbB family blocker-improves progression-free survival compared with pemetrexed and cisplatin for first-line treatment of patients with EGFR mutation-positive advanced non-small-cell lung cancer (NSCLC). We compared afatinib with gemcitabine and cisplatin-a chemotherapy regimen widely used in Asia-for first-line treatment of Asian patients with EGFR mutation-positive advanced NSCLC.This open-label, randomised phase 3 trial was done at 36 centres in China, Thailand, and South Korea. After central testing for EGFR mutations, treatment-naive patients (stage IIIB or IV cancer [American Joint Committee on Cancer version 6], performance status 0-1) were randomly assigned (2:1) to receive either oral afatinib (40 mg per day) or intravenous gemcitabine 1000 mg/m(2) on day 1 and day 8 plus cisplatin 75 mg/m(2) on day 1 of a 3-week schedule for up to six cycles. Randomisation was done centrally with a random number-generating system and an interactive internet and voice-response system. Randomisation was stratified by EGFR mutation (Leu858Arg, exon 19 deletions, or other; block size three). Clinicians and patients were not masked to treatment assignment, but the independent central imaging review group were. Treatment continued until disease progression, intolerable toxic effects, or withdrawal of consent. The primary endpoint was progression-free survival assessed by independent central review (intention-to-treat population). This study is registered with ClinicalTrials.gov, NCT01121393.910 patients were screened and 364 were randomly assigned (242 to afatinib, 122 to gemcitabine and cisplatin). Median progression-free survival was significantly longer in the afatinib group (11·0 months, 95% CI 9·7-13·7) than in the gemcitabine and cisplatin group (5·6 months, 5·1-6·7; hazard ratio 0·28, 95% CI 0·20-0·39; p<0·0001). The most common treatment-related grade 3 or 4 adverse events in the afatinib group were rash or acne (35 [14·6%] of 239 patients), diarrhoea (13 [5·4%]), and stomatitis or mucositis (13 [5·4%]), compared with neutropenia (30 [26·5%] of 113 patients), vomiting (22 [19·5%]), and leucopenia (17 [15·0%]) in the gemcitabine and cisplatin group. Treatment-related serious adverse events occurred in 15 (6·3%) patients in the afatinib group and nine (8·0%) patients in the gemcitabine and cisplatin group.First-line afatinib significantly improves progression-free survival with a tolerable and manageable safety profile in Asian patients with EGFR mutation-positive advanced lung NSCLC. Afatinib should be considered as a first-line treatment option for this patient population.Boehringer Ingelheim.

We propose the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. MAGeCK demonstrates better performance compared with existing methods, identifies both positively and negatively selected genes simultaneously, and reports robust results across different experimental conditions. Using public datasets, MAGeCK identified novel essential genes and pathways, including EGFR in vemurafenib-treated A375 cells harboring a BRAF mutation. MAGeCK also detected cell type-specific essential genes, including BCR and ABL1, in KBM7 cells bearing a BCR-ABL fusion, and IGF1R in HL-60 cells, which depends on the insulin signaling pathway for proliferation.

Thousands of novel transcripts have been identified using deep transcriptome sequencing. This discovery of large and ‘hidden’ transcriptome rejuvenates the demand for methods that can rapidly distinguish between coding and noncoding RNA. Here, we present a novel alignment-free method, Coding Potential Assessment Tool (CPAT), which rapidly recognizes coding and noncoding transcripts from a large pool of candidates. To this end, CPAT uses a logistic regression model built with four sequence features: open reading frame size, open reading frame coverage, Fickett TESTCODE statistic and hexamer usage bias. CPAT software outperformed (sensitivity: 0.96, specificity: 0.97) other state-of-the-art alignment-based software such as Coding-Potential Calculator (sensitivity: 0.99, specificity: 0.74) and Phylo Codon Substitution Frequencies (sensitivity: 0.90, specificity: 0.63). In addition to high accuracy, CPAT is approximately four orders of magnitude faster than Coding-Potential Calculator and Phylo Codon Substitution Frequencies, enabling its users to process thousands of transcripts within seconds. The software accepts input sequences in either FASTA- or BED-formatted data files. We also developed a web interface for CPAT that allows users to submit sequences and receive the prediction results almost instantly.

Hypoxia-inducible factor-1 (HIF-1) has been recognized as an important cancer drug target. Many recent studies have provided convincing evidences of strong correlation between elevated levels of HIF-1 and tumor metastasis, angiogenesis, poor patient prognosis as well as tumor resistance therapy. It was found that hypoxia (low O2 levels) is a common character in many types of solid tumors. As an adaptive response to hypoxic stress, hypoxic tumor cells activate several survival pathways to carry out their essential biological processes in different ways compared with normal cells. Recent advances in cancer biology at the cellular and molecular levels highlighted the HIF-1α pathway as a crucial survival pathway for which novel strategies of cancer therapy could be developed. However, targeting the HIF-1α pathway has been a challenging but promising progresses have been made in the past twenty years. This review summarizes the role and regulation of the HIF-1α in cancer, and recent therapeutic approaches targeting this important pathway.

Reduced muscular strength, as measured by grip strength, has been associated with an increased risk of all-cause and cardiovascular mortality. Grip strength is appealing as a simple, quick, and inexpensive means of stratifying an individual's risk of cardiovascular death. However, the prognostic value of grip strength with respect to the number and range of populations and confounders is unknown. The aim of this study was to assess the independent prognostic importance of grip strength measurement in socioculturally and economically diverse countries.The Prospective Urban-Rural Epidemiology (PURE) study is a large, longitudinal population study done in 17 countries of varying incomes and sociocultural settings. We enrolled an unbiased sample of households, which were eligible if at least one household member was aged 35-70 years and if household members intended to stay at that address for another 4 years. Participants were assessed for grip strength, measured using a Jamar dynamometer. During a median follow-up of 4.0 years (IQR 2.9-5.1), we assessed all-cause mortality, cardiovascular mortality, non-cardiovascular mortality, myocardial infarction, stroke, diabetes, cancer, pneumonia, hospital admission for pneumonia or chronic obstructive pulmonary disease (COPD), hospital admission for any respiratory disease (including COPD, asthma, tuberculosis, and pneumonia), injury due to fall, and fracture. Study outcomes were adjudicated using source documents by a local investigator, and a subset were adjudicated centrally.Between January, 2003, and December, 2009, a total of 142,861 participants were enrolled in the PURE study, of whom 139,691 with known vital status were included in the analysis. During a median follow-up of 4.0 years (IQR 2.9-5.1), 3379 (2%) of 139,691 participants died. After adjustment, the association between grip strength and each outcome, with the exceptions of cancer and hospital admission due to respiratory illness, was similar across country-income strata. Grip strength was inversely associated with all-cause mortality (hazard ratio per 5 kg reduction in grip strength 1.16, 95% CI 1.13-1.20; p<0.0001), cardiovascular mortality (1.17, 1.11-1.24; p<0.0001), non-cardiovascular mortality (1.17, 1.12-1.21; p<0.0001), myocardial infarction (1.07, 1.02-1.11; p=0.002), and stroke (1.09, 1.05-1.15; p<0.0001). Grip strength was a stronger predictor of all-cause and cardiovascular mortality than systolic blood pressure. We found no significant association between grip strength and incident diabetes, risk of hospital admission for pneumonia or COPD, injury from fall, or fracture. In high-income countries, the risk of cancer and grip strength were positively associated (0.916, 0.880-0.953; p<0.0001), but this association was not found in middle-income and low-income countries.This study suggests that measurement of grip strength is a simple, inexpensive risk-stratifying method for all-cause death, cardiovascular death, and cardiovascular disease. Further research is needed to identify determinants of muscular strength and to test whether improvement in strength reduces mortality and cardiovascular disease.Full funding sources listed at end of paper (see Acknowledgments).

Most patients with small-cell lung cancer (SCLC) have extensive-stage disease at presentation, and prognosis remains poor. Recently, immunotherapy has demonstrated clinical activity in extensive-stage SCLC (ES-SCLC). The CASPIAN trial assessed durvalumab, with or without tremelimumab, in combination with etoposide plus either cisplatin or carboplatin (platinum-etoposide) in treatment-naive patients with ES-SCLC.This randomised, open-label, phase 3 trial was done at 209 sites across 23 countries. Eligible patients were adults with untreated ES-SCLC, with WHO performance status 0 or 1 and measurable disease as per Response Evaluation Criteria in Solid Tumors, version 1.1. Patients were randomly assigned (in a 1:1:1 ratio) to durvalumab plus platinum-etoposide; durvalumab plus tremelimumab plus platinum-etoposide; or platinum-etoposide alone. All drugs were administered intravenously. Platinum-etoposide consisted of etoposide 80-100 mg/m2 on days 1-3 of each cycle with investigator's choice of either carboplatin area under the curve 5-6 mg/mL per min or cisplatin 75-80 mg/m2 (administered on day 1 of each cycle). Patients received up to four cycles of platinum-etoposide plus durvalumab 1500 mg with or without tremelimumab 75 mg every 3 weeks followed by maintenance durvalumab 1500 mg every 4 weeks in the immunotherapy groups and up to six cycles of platinum-etoposide every 3 weeks plus prophylactic cranial irradiation (investigator's discretion) in the platinum-etoposide group. The primary endpoint was overall survival in the intention-to-treat population. We report results for the durvalumab plus platinum-etoposide group versus the platinum-etoposide group from a planned interim analysis. Safety was assessed in all patients who received at least one dose of their assigned study treatment. This study is registered at ClinicalTrials.gov, NCT03043872, and is ongoing.Patients were enrolled between March 27, 2017, and May 29, 2018. 268 patients were allocated to the durvalumab plus platinum-etoposide group and 269 to the platinum-etoposide group. Durvalumab plus platinum-etoposide was associated with a significant improvement in overall survival, with a hazard ratio of 0·73 (95% CI 0·59-0·91; p=0·0047]); median overall survival was 13·0 months (95% CI 11·5-14·8) in the durvalumab plus platinum-etoposide group versus 10·3 months (9·3-11·2) in the platinum-etoposide group, with 34% (26·9-41·0) versus 25% (18·4-31·6) of patients alive at 18 months. Any-cause adverse events of grade 3 or 4 occurred in 163 (62%) of 265 treated patients in the durvalumab plus platinum-etoposide group and 166 (62%) of 266 in the platinum-etoposide group; adverse events leading to death occurred in 13 (5%) and 15 (6%) patients.First-line durvalumab plus platinum-etoposide significantly improved overall survival in patients with ES-SCLC versus a clinically relevant control group. Safety findings were consistent with the known safety profiles of all drugs received.AstraZeneca.

Transfer learning, where a model is first pre-trained on a data-rich task before being fine-tuned on a downstream task, has emerged as a powerful technique in natural language processing (NLP). The effectiveness of transfer learning has given rise to a diversity of approaches, methodology, and practice. In this paper, we explore the landscape of transfer learning techniques for NLP by introducing a unified framework that converts all text-based language problems into a text-to-text format. Our systematic study compares pre-training objectives, architectures, unlabeled data sets, transfer approaches, and other factors on dozens of language understanding tasks. By combining the insights from our exploration with scale and our new ``Colossal Clean Crawled Corpus'', we achieve state-of-the-art results on many benchmarks covering summarization, question answering, text classification, and more. To facilitate future work on transfer learning for NLP, we release our data set, pre-trained models, and code.

Estrogen plays an essential physiologic role in reproduction and a pathologic one in breast cancer. The completion of the human genome has allowed the identification of the expressed regions of protein-coding genes; however, little is known concerning the organization of their cis-regulatory elements. We have mapped the association of the estrogen receptor (ER) with the complete nonrepetitive sequence of human chromosomes 21 and 22 by combining chromatin immunoprecipitation (ChIP) with tiled microarrays. ER binds selectively to a limited number of sites, the majority of which are distant from the transcription start sites of regulated genes. The unbiased sequence interrogation of the genuine chromatin binding sites suggests that direct ER binding requires the presence of Forkhead factor binding in close proximity. Furthermore, knockdown of FoxA1 expression blocks the association of ER with chromatin and estrogen-induced gene expression demonstrating the necessity of FoxA1 in mediating an estrogen response in breast cancer cells.

In response to environmental stress, the related RNA-binding proteins TIA-1 and TIAR colocalize with poly(A)+ RNA at cytoplasmic foci that resemble the stress granules (SGs) that harbor untranslated mRNAs in heat shocked plant cells (Nover et al. 1989; Nover et al. 1983; Scharf et al. 1998). The accumulation of untranslated mRNA at SGs is reversible in cells that recover from a sublethal stress, but irreversible in cells subjected to a lethal stress. We have found that the assembly of TIA-1/R+ SGs is initiated by the phosphorylation of eIF-2α. A phosphomimetic eIF-2α mutant (S51D) induces the assembly of SGs, whereas a nonphosphorylatable eIF-2α mutant (S51A) prevents the assembly of SGs. The ability of a TIA-1 mutant lacking its RNA-binding domains to function as a transdominant inhibitor of SG formation suggests that this RNA-binding protein acts downstream of the phosphorylation of eIF-2α to promote the sequestration of untranslated mRNAs at SGs. The assembly and disassembly of SGs could regulate the duration of stress- induced translational arrest in cells recovering from environmental stress.

Reliable prediction of antibody, or B-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. A correlation between antigenicity, solvent accessibility, and flexibility in proteins was demonstrated. Subsequently, Thornton and colleagues proposed a method for identifying continuous epitopes in the protein regions protruding from the protein's globular surface. The aim of this work was to implement that method as a web-tool and evaluate its performance on discontinuous epitopes known from the structures of antibody-protein complexes.Here we present ElliPro, a web-tool that implements Thornton's method and, together with a residue clustering algorithm, the MODELLER program and the Jmol viewer, allows the prediction and visualization of antibody epitopes in a given protein sequence or structure. ElliPro has been tested on a benchmark dataset of discontinuous epitopes inferred from 3D structures of antibody-protein complexes. In comparison with six other structure-based methods that can be used for epitope prediction, ElliPro performed the best and gave an AUC value of 0.732, when the most significant prediction was considered for each protein. Since the rank of the best prediction was at most in the top three for more than 70% of proteins and never exceeded five, ElliPro is considered a useful research tool for identifying antibody epitopes in protein antigens. ElliPro is available at http://tools.immuneepitope.org/tools/ElliPro.The results from ElliPro suggest that further research on antibody epitopes considering more features that discriminate epitopes from non-epitopes may further improve predictions. As ElliPro is based on the geometrical properties of protein structure and does not require training, it might be more generally applied for predicting different types of protein-protein interactions.

Existing person re-identification (re-id) methods either assume the availability of well-aligned person bounding box images as model input or rely on constrained attention selection mechanisms to calibrate misaligned images. They are therefore sub-optimal for re-id matching in arbitrarily aligned person images potentially with large human pose variations and unconstrained auto-detection errors. In this work, we show the advantages of jointly learning attention selection and feature representation in a Convolutional Neural Network (CNN) by maximising the complementary information of different levels of visual attention subject to re-id discriminative learning constraints. Specifically, we formulate a novel Harmonious Attention CNN (HA-CNN) model for joint learning of soft pixel attention and hard regional attention along with simultaneous optimisation of feature representations, dedicated to optimise person re-id in uncontrolled (misaligned) images. Extensive comparative evaluations validate the superiority of this new HA-CNN model for person re-id over a wide variety of state-of-the-art methods on three large-scale benchmarks including CUHK03, Market-1501, and DukeMTMC-ReID.

The ability to detect light over a broad spectral range is central to practical optoelectronic applications and has been successfully demonstrated with photodetectors of two-dimensional layered crystals such as graphene and MoS2. However, polarization sensitivity within such a photodetector remains elusive. Here, we demonstrate a broadband photodetector using a layered black phosphorus transistor that is polarization-sensitive over a bandwidth from ∼400 nm to 3,750 nm. The polarization sensitivity is due to the strong intrinsic linear dichroism, which arises from the in-plane optical anisotropy of this material. In this transistor geometry, a perpendicular built-in electric field induced by gating can spatially separate the photogenerated electrons and holes in the channel, effectively reducing their recombination rate and thus enhancing the performance for linear dichroism photodetection. The use of anisotropic layered black phosphorus in polarization-sensitive photodetection might provide new functionalities in novel optical and optoelectronic device applications.

Searching for superconducting materials with high transition temperature (TC) is one of the most exciting and challenging fields in physics and materials science. Although superconductivity has been discovered for more than 100 years, the copper oxides are so far the only materials with TC above 77 K, the liquid nitrogen boiling point. Here we report an interface engineering method for dramatically raising the TC of superconducting films. We find that one unit-cell (UC) thick films of FeSe grown on SrTiO3 (STO) substrates by molecular beam epitaxy (MBE) show signatures of superconducting transition above 50 K by transport measurement. A superconducting gap as large as 20 meV of the 1 UC films observed by scanning tunneling microcopy (STM) suggests that the superconductivity could occur above 77 K. The occurrence of superconductivity is further supported by the presence of superconducting vortices under magnetic field. Our work not only demonstrates a powerful way for finding new superconductors and for raising TC, but also provides a well-defined platform for systematic study of the mechanism of unconventional superconductivity by using different superconducting materials and substrates.

Abstract Solution-processed planar perovskite devices are highly desirable in a wide variety of optoelectronic applications; however, they are prone to hysteresis and current instabilities. Here we report the first perovskite–PCBM hybrid solid with significantly reduced hysteresis and recombination loss achieved in a single step. This new material displays an efficient electrically coupled microstructure: PCBM is homogeneously distributed throughout the film at perovskite grain boundaries. The PCBM passivates the key PbI 3 − antisite defects during the perovskite self-assembly, as revealed by theory and experiment. Photoluminescence transient spectroscopy proves that the PCBM phase promotes electron extraction. We showcase this mixed material in planar solar cells that feature low hysteresis and enhanced photovoltage. Using conductive AFM studies, we reveal the memristive properties of perovskite films. We close by positing that PCBM, by tying up both halide-rich antisites and unincorporated halides, reduces electric field-induced anion migration that may give rise to hysteresis and unstable diode behaviour.

Models for many natural language tasks benefit from the flexibility to use overlapping, non-independent features. For example, the need for labeled data can be drastically reduced by taking advantage of domain knowledge in the form of word lists, part-of-speech tags, character n-grams, and capitalization patterns. While it is difficult to capture such inter-dependent features with a generative probabilistic model, conditionally-trained models, such as conditional maximum entropy models, handle them well. There has been significant work with such models for greedy sequence modeling in NLP (Ratnaparkhi, 1996; Borthwick et al., 1998).

Bisulfite sequencing is a powerful technique to study DNA cytosine methylation. Bisulfite treatment followed by PCR amplification specifically converts unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect the methylation status of every cytosine in the genome. However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation.We developed an efficient bisulfite reads mapping algorithm BSMAP to address the above issues. BSMAP combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping. Compared with existing bisulfite mapping approaches, BSMAP is faster, more sensitive and more flexible.BSMAP is the first general-purpose bisulfite mapping software. It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage. It is freely available under GPL v3 license at http://code.google.com/p/bsmap/.

Loss of the de novo DNA methyltransferases Dnmt3a and Dnmt3b in embryonic stem cells obstructs differentiation; however, the role of these enzymes in somatic stem cells is largely unknown. Using conditional ablation, we show that Dnmt3a loss progressively impairs hematopoietic stem cell (HSC) differentiation over serial transplantation, while simultaneously expanding HSC numbers in the bone marrow. Dnmt3a-null HSCs show both increased and decreased methylation at distinct loci, including substantial CpG island hypermethylation. Dnmt3a-null HSCs upregulate HSC multipotency genes and downregulate differentiation factors, and their progeny exhibit global hypomethylation and incomplete repression of HSC-specific genes. These data establish Dnmt3a as a critical participant in the epigenetic silencing of HSC regulatory genes, thereby enabling efficient differentiation.

Among breast cancers without human epidermal growth factor receptor 2 (HER2) amplification, overexpression, or both, a large proportion express low levels of HER2 that may be targetable. Currently available HER2-directed therapies have been ineffective in patients with these "HER2-low" cancers.We conducted a phase 3 trial involving patients with HER2-low metastatic breast cancer who had received one or two previous lines of chemotherapy. (Low expression of HER2 was defined as a score of 1+ on immunohistochemical [IHC] analysis or as an IHC score of 2+ and negative results on in situ hybridization.) Patients were randomly assigned in a 2:1 ratio to receive trastuzumab deruxtecan or the physician's choice of chemotherapy. The primary end point was progression-free survival in the hormone receptor-positive cohort. The key secondary end points were progression-free survival among all patients and overall survival in the hormone receptor-positive cohort and among all patients.Of 557 patients who underwent randomization, 494 (88.7%) had hormone receptor-positive disease and 63 (11.3%) had hormone receptor-negative disease. In the hormone receptor-positive cohort, the median progression-free survival was 10.1 months in the trastuzumab deruxtecan group and 5.4 months in the physician's choice group (hazard ratio for disease progression or death, 0.51; P<0.001), and overall survival was 23.9 months and 17.5 months, respectively (hazard ratio for death, 0.64; P = 0.003). Among all patients, the median progression-free survival was 9.9 months in the trastuzumab deruxtecan group and 5.1 months in the physician's choice group (hazard ratio for disease progression or death, 0.50; P<0.001), and overall survival was 23.4 months and 16.8 months, respectively (hazard ratio for death, 0.64; P = 0.001). Adverse events of grade 3 or higher occurred in 52.6% of the patients who received trastuzumab deruxtecan and 67.4% of those who received the physician's choice of chemotherapy. Adjudicated, drug-related interstitial lung disease or pneumonitis occurred in 12.1% of the patients who received trastuzumab deruxtecan; 0.8% had grade 5 events.In this trial involving patients with HER2-low metastatic breast cancer, trastuzumab deruxtecan resulted in significantly longer progression-free and overall survival than the physician's choice of chemotherapy. (Funded by Daiichi Sankyo and AstraZeneca; DESTINY-Breast04 ClinicalTrials.gov number, NCT03734029.).

Monkeys serve as important model species for studying human diseases and developing therapeutic strategies, yet the application of monkeys in biomedical researches has been significantly hindered by the difficulties in producing animals genetically modified at the desired target sites. Here, we first applied the CRISPR/Cas9 system, a versatile tool for editing the genes of different organisms, to target monkey genomes. By coinjection of Cas9 mRNA and sgRNAs into one-cell-stage embryos, we successfully achieve precise gene targeting in cynomolgus monkeys. We also show that this system enables simultaneous disruption of two target genes (Ppar-γ and Rag1) in one step, and no off-target mutagenesis was detected by comprehensive analysis. Thus, coinjection of one-cell-stage embryos with Cas9 mRNA and sgRNAs is an efficient and reliable approach for gene-modified cynomolgus monkey generation.

SNF'ing out antitumor immunity Immune checkpoint inhibitors induce durable tumor regressions in some, but not all, cancer patients. Understanding the mechanisms that determine tumor sensitivity to these drugs could potentially expand the number of patients who benefit (see the Perspective by Ghorani and Quezada). Pan et al. discovered that tumor cells in which a specific SWI/SNF chromatin remodeling complex had been experimentally inactivated were more sensitive to T cell–mediated killing. The cells were more responsive to interferon-γ, leading to increased secretion of cytokines that promote antitumor immunity. Miao et al. examined the genomic features of tumors from patients with metastatic renal cell carcinoma who had been treated with immune checkpoint inhibitors. Tumors harboring inactivating mutations in PBRM1 , which encodes a subunit of the same SWI/SNF complex, were more likely to respond to the drugs. Science , this issue p. 770 , p. 801 ; see also p. 745

Complex organisms require tissue-specific transcriptional programs, yet little is known about how these are established. The transcription factor FoxA1 is thought to contribute to gene regulation through its ability to act as a pioneer factor binding to nucleosomal DNA. Through genome-wide positional analyses, we demonstrate that FoxA1 cell type-specific functions rely primarily on differential recruitment to chromatin predominantly at distant enhancers rather than proximal promoters. This differential recruitment leads to cell type-specific changes in chromatin structure and functional collaboration with lineage-specific transcription factors. Despite the ability of FoxA1 to bind nucleosomes, its differential binding to chromatin sites is dependent on the distribution of histone H3 lysine 4 dimethylation. Together, our results suggest that methylation of histone H3 lysine 4 is part of the epigenetic signature that defines lineage-specific FoxA1 recruitment sites in chromatin. FoxA1 translates this epigenetic signature into changes in chromatin structure thereby establishing lineage-specific transcriptional enhancers and programs.

Hybrid organic–inorganic perovskites (HOIPs) can have a diverse range of compositions including halides, azides, formates, dicyanamides, cyanides and dicyanometallates. These materials have several common features, including their classical ABX3 perovskite architecture and the presence of organic amine cations that occupy the A-sites. Current research in HOIPs tends to focus on metal halide HOIPs, which show promise for use in solar cells and optoelectronic devices; however, the other subclasses also exhibit a diverse range of physical properties. In this Review, we summarize the chemical variability and structural diversity of all known HOIP subclasses. We also present a comprehensive account of their intriguing physical properties, including photovoltaic and optoelectronic properties, dielectricity, magnetism, ferroelectricity, ferroelasticity and multiferroicity. Moreover, we discuss the current challenges and future opportunities in this exciting field. Hybrid organic–inorganic perovskites (HOIPs) comprise a diverse range of chemical compositions from halides and azides to formates, dicyanamides, cyanides and dicyanometallates. In this Review, advances in the synthesis, structures and properties of all HOIP subclasses are summarized and their future opportunities are discussed.

The precise control of the size, morphology, surface chemistry, and assembly process of each component is important to construction of integrated functional nanocomposites. We report here the fabrication of multifunctional microspheres which possess a core of nonporous silica-protected magnetite particles, transition layer of active gold nanoparticles, and an outer shell of ordered mesoporous silica with perpendicularly aligned pore channels. The well-designed microspheres have high magnetization (18.6 emu/g), large surface area (236 m(2)/g), highly open mesopores (approximately 2.2 nm), and stably confined but accessible Au nanoparticles and, as a result, show high performance in catalytic reduction of 4-nitrophenol (with conversion of 95% in 12 min), styrene epoxidation with high conversion (72%) and selectivity (80%), especially convenient magnetic separability, long life and good reusability. The unique nanostructure makes the microsphere to be a novel stable and approachable catalyst system for various catalytic industry processes.

Mesoporous TiO2 has gained increasing interest because of its outstanding properties and promising applications in a wide range of fields. Herein, we report the facile synthesis of ordered mesoporous black TiO2 (OMBT) materials, which exhibit excellent photocatalytic hydrogen evolution performances. In this case, the employment of a thermally stable and high-surface-area mesoporous TiO2 as the hydrogenation precursor is the key for fabricating the OMBT materials, which not only facilitate H2 gas diffusion into TiO2 and interaction with their structures but also maintain the ordered mesoporous structures as well as inhibit the phase transformation (from anatase to rutile) and crystal growth during hydrogenation at 500 °C. The resultant OMBT materials possess a relatively high surface area of ∼124 m2 g–1 and a large pore size and pore volume of ∼9.6 nm and 0.24 cm3 g–1, respectively. More importantly, the OMBT materials can extend the photoresponse from ultraviolet to visible and infrared light regions and exhibit a high solar-driven hydrogen production rate (136.2 μmol h–1), which is almost two times as high as that of pristine mesoporous TiO2 (76.6 μmol h–1).

TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ‘User Comments’ may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.

Nitrous oxide (N2O), like carbon dioxide, is a long-lived greenhouse gas that accumulates in the atmosphere. Over the past 150 years, increasing atmospheric N2O concentrations have contributed to stratospheric ozone depletion1 and climate change2, with the current rate of increase estimated at 2 per cent per decade. Existing national inventories do not provide a full picture of N2O emissions, owing to their omission of natural sources and limitations in methodology for attributing anthropogenic sources. Here we present a global N2O inventory that incorporates both natural and anthropogenic sources and accounts for the interaction between nitrogen additions and the biochemical processes that control N2O emissions. We use bottom-up (inventory, statistical extrapolation of flux measurements, process-based land and ocean modelling) and top-down (atmospheric inversion) approaches to provide a comprehensive quantification of global N2O sources and sinks resulting from 21 natural and human sectors between 1980 and 2016. Global N2O emissions were 17.0 (minimum-maximum estimates: 12.2-23.5) teragrams of nitrogen per year (bottom-up) and 16.9 (15.9-17.7) teragrams of nitrogen per year (top-down) between 2007 and 2016. Global human-induced emissions, which are dominated by nitrogen additions to croplands, increased by 30% over the past four decades to 7.3 (4.2-11.4) teragrams of nitrogen per year. This increase was mainly responsible for the growth in the atmospheric burden. Our findings point to growing N2O emissions in emerging economies-particularly Brazil, China and India. Analysis of process-based model estimates reveals an emerging N2O-climate feedback resulting from interactions between nitrogen additions and climate change. The recent growth in N2O emissions exceeds some of the highest projected emission scenarios3,4, underscoring the urgency to mitigate N2O emissions.

CTCF and the associated cohesin complex play a central role in insulator function and higher-order chromatin organization of mammalian genomes. Recent studies identified a correlation between the orientation of CTCF-binding sites (CBSs) and chromatin loops. To test the functional significance of this observation, we combined CRISPR/Cas9-based genomic-DNA-fragment editing with chromosome-conformation-capture experiments to show that the location and relative orientations of CBSs determine the specificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and β-globin as model genes. Inversion of CBS elements within the Pcdh enhancer reconfigures the topology of chromatin loops between the distal enhancer and target promoters and alters gene-expression patterns. Thus, although enhancers can function in an orientation-independent manner in reporter assays, in the native chromosome context, the orientation of at least some enhancers carrying CBSs can determine both the architecture of topological chromatin domains and enhancer/promoter specificity. These findings reveal how 3D chromosome architecture can be encoded by linear genome sequences.

The evolution of prostate cancer from an androgen-dependent state to one that is androgen-independent marks its lethal progression. The androgen receptor (AR) is essential in both, though its function in androgen-independent cancers is poorly understood. We have defined the direct AR-dependent target genes in both androgen-dependent and -independent cancer cells by generating AR-dependent gene expression profiles and AR cistromes. In contrast to what is found in androgen-dependent cells, AR selectively upregulates M-phase cell-cycle genes in androgen-independent cells, including UBE2C, a gene that inactivates the M-phase checkpoint. We find that epigenetic marks at the UBE2C enhancer, notably histone H3K4 methylation and FoxA1 transcription factor binding, are present in androgen-independent cells and direct AR-enhancer binding and UBE2C activation. Thus, the role of AR in androgen-independent cancer cells is not to direct the androgen-dependent gene expression program without androgen, but rather to execute a distinct program resulting in androgen-independent growth.

A mobile ad hoc network consists of a collection of wireless mobile nodes that are capable of communicating with each other without the use of a network infrastructure or any centralized administration. MANET is an emerging research area with practical applications. However, wireless MANET is particularly vulnerable due to its fundamental characteristics, such as open medium, dynamic topology, distributed cooperation, and constrained capability. Routing plays an important role in the security of the entire network. In general, routing security in wireless MANETs appears to be a problem that is not trivial to solve. In this article we study the routing security issues of MANETs, and analyze in detail one type of attack-the "black hole" problem-that can easily be employed against the MANETs. We also propose a solution for the black hole problem for ad hoc on-demand distance vector routing protocol.

Although some patients with adult congenital heart disease (ACHD) report limitations in exercise capacity, we hypothesized that depressed exercise capacity may be more widespread than superficially evident during clinical consultation and could be a means of assessing risk.Cardiopulmonary exercise testing was performed in 335 consecutive ACHD patients (age, 33+/-13 years), 40 non-congenital heart failure patients (age, 58+/-15 years), and 11 young (age, 29+/-5 years) and 12 older (age, 59+/-9 years) healthy subjects. Peak oxygen consumption (peak VO2) was reduced in ACHD patients compared with healthy subjects of similar age (21.7+/-8.5 versus 45.1+/-8.6; P<0.001). No significant difference in peak VO2 was found between ACHD and heart failure patients of corresponding NYHA class (P=NS for each NYHA class). Within ACHD subgroups, peak VO2 gradually declined from aortic coarctation (28.7+/-10.4) to Eisenmenger (11.5+/-3.6) patients (P<0.001). Multivariable correlates of peak VO2 were peak heart rate (r=0.33), forced expiratory volume (r=0.33), pulmonary hypertension (r=-0.26), gender (r=-0.23), and body mass index (r=-0.19). After a median follow-up of 10 months, 62 patients (18.5%) were hospitalized or had died. On multivariable Cox analysis, peak VO2 predicted hospitalization or death (hazard ratio, 0.937; P=0.01) and was related to the frequency and duration of hospitalization (P=0.01 for each).Exercise capacity is depressed in ACHD patients (even in allegedly asymptomatic patients) on a par with chronic heart failure subjects. Lack of heart rate response to exercise, pulmonary arterial hypertension, and impaired pulmonary function are important correlates of exercise capacity, as is underlying cardiac anatomy. Poor exercise capacity identifies ACHD patients at risk for hospitalization or death.

Article15 August 2001free access Regulation of elongation factor 2 kinase by p90RSK1 and p70 S6 kinase Xuemin Wang Xuemin Wang Division of Molecular Physiology, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK Search for more papers by this author Wei Li Wei Li Division of Molecular Physiology, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK Search for more papers by this author Michayla Williams Michayla Williams MRC Protein Phosphorylation Unit, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK Search for more papers by this author Naohiro Terada Naohiro Terada Department of Pathology, University of Florida College of Medicine, Gainesville, FL, 32610-0275 USA Search for more papers by this author Dario R. Alessi Dario R. Alessi MRC Protein Phosphorylation Unit, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK Search for more papers by this author Christopher G. Proud Corresponding Author Christopher G. Proud Division of Molecular Physiology, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK Search for more papers by this author Xuemin Wang Xuemin Wang Division of Molecular Physiology, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK Search for more papers by this author Wei Li Wei Li Division of Molecular Physiology, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK Search for more papers by this author Michayla Williams Michayla Williams MRC Protein Phosphorylation Unit, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK Search for more papers by this author Naohiro Terada Naohiro Terada Department of Pathology, University of Florida College of Medicine, Gainesville, FL, 32610-0275 USA Search for more papers by this author Dario R. Alessi Dario R. Alessi MRC Protein Phosphorylation Unit, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK Search for more papers by this author Christopher G. Proud Corresponding Author Christopher G. Proud Division of Molecular Physiology, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK Search for more papers by this author Author Information Xuemin Wang1, Wei Li1, Michayla Williams2, Naohiro Terada3, Dario R. Alessi2 and Christopher G. Proud 1 1Division of Molecular Physiology, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK 2MRC Protein Phosphorylation Unit, School of Life Sciences, MSI/WTB Complex, University of Dundee, Dundee, DD1 5EH UK 3Department of Pathology, University of Florida College of Medicine, Gainesville, FL, 32610-0275 USA *Corresponding author. E-mail: [email protected] The EMBO Journal (2001)20:4370-4379https://doi.org/10.1093/emboj/20.16.4370 PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Elongation factor 2 kinase (eEF2k) phosphorylates and inactivates eEF2. Insulin induces dephosphorylation of eEF2 and inactivation of eEF2 kinase, and these effects are blocked by rapamycin, which inhibits the mammalian target of rapamycin, mTOR. However, the signalling mechanisms underlying these effects are unknown. Regulation of eEF2 phosphorylation and eEF2k activity is lost in cells in which phosphoinositide-dependent kinase 1 (PDK1) has been genetically knocked out. This is not due to loss of mTOR function since phosphorylation of another target of mTOR, initiation factor 4E-binding protein 1, is not defective. PDK1 is required for activation of members of the AGC kinase family; we show that two such kinases, p70 S6 kinase (regulated via mTOR) and p90RSK1 (activated by Erk), phosphorylate eEF2k at a conserved serine and inhibit its activity. In response to insulin-like growth factor 1, which activates p70 S6 kinase but not Erk, regulation of eEF2 is blocked by rapamycin. In contrast, regulation of eEF2 by stimuli that activate Erk is insensitive to rapamycin, but blocked by inhibitors of MEK/Erk signalling, consistent with the involvement of p90RSK1. Introduction The control of mRNA translation in mammalian cells involves regulated phosphorylation of a number of components of the translational machinery (Proud and Denton, 1997; Rhoads, 1999). Phosphorylation of several of these proteins is under the control of the mammalian target of rapamycin, mTOR. These include: (i) the 70 kDa protein kinase (p70 S6k), which acts on ribosomal protein S6 and may be involved in controlling the translation of the set of mRNAs in mammalian cells that encode ribosomal proteins (Fumagalli and Thomas, 2000; Meyuhas and Hornstein, 2000); (ii) the initiation factor 4E binding protein, 4E-BP1, which regulates the formation of the eIF4F complexes that are required for the initiation of cap-dependent mRNA translation (Raught et al., 2000); and (iii) elongation factor 2 (eEF2), which mediates the translocation step of elongation (Redpath et al., 1996). The phosphorylation states of each of these proteins are regulated by insulin in a rapamycin-sensitive manner, demonstrating that signalling to these proteins requires mTOR activity. However, the molecular mechanisms linking them to mTOR remain obscure. mTOR is structurally related to lipid kinases, but displays protein rather than lipid kinase activity (Brunn et al., 1997; Burnett et al., 1998; Thomas and Hall, 1997; Isotani et al., 1999). It appears to play an important role not only in insulin and mitogen signalling, but also in the regulation of cellular function in response to nutritional cues (Kimball and Jefferson, 2000). p70 S6k exists as at least two isoforms, encoded by different genes, in mammalian cells (Gout et al., 1998; Shima et al., 1998). The β-isoform was discovered only recently and shows both similarities to, and certain differences from, p70 S6kα (Gout et al., 1998; Shima et al., 1998; Lee-Fruman et al., 1999; Martin et al., 2001). p70 S6kα has been the subject of detailed investigation (Fumagalli and Thomas, 2000). Activation of p70 S6kα involves its phosphorylation on multiple sites (reviewed in Fumagalli and Thomas, 2000). The regulation of p70 S6kα involves inputs from signalling events linked to phosphatidylinositol 3-kinase (PI 3-kinase) that are not yet fully understood. Thr229 (a site conserved in p70 S6kβ) is phosphorylated by phosphoinositide-dependent kinase-1 (PDK1) (Alessi et al., 1998; Gout et al., 1998; Pullen et al., 1998; Shima et al., 1998; Balendran et al., 1999). mTOR has been reported to phosphorylate Thr389 and some of the Ser-Pro or Thr-Pro sites in the C-terminus of p70 S6kα (Burnett et al., 1998; Isotani et al., 1999). PDK1 also plays an important role in the regulation of other members of the so-called AGC family by phosphorylating residues in their ‘T-loop’ that are required for their activation, such as members of the protein kinase C (PKC) family (Chou et al., 1998; Dutil et al., 1998; Toker and Newton, 2000) and p90RSK1 (Jensen et al., 1999; Richards et al., 1999). Kinases acting at other sites in p70 S6kα remain to be identified. 4E-BP1 also undergoes phosphorylation at multiple sites in vivo, although again it is not known which kinases act on them. It is clear that rapamycin blocks phosphorylation of the sites that are important in regulating its association with eIF4E (Raught et al., 2000). Binding of 4E-BP1 to eIF4E blocks its ability to form functional initiation complexes with eIF4G, a scaffolding protein that also interacts with eIF4A and eIF3, the latter mediating interactions with the 40S ribosomal subunit (Raught et al., 2000). The signalling events that lie upstream of 4E-BP1 remain unclear; some reports have suggested that they involve PKB (Gingras et al., 1998). It has also been suggested that PKB plays a role in regulating mTOR itself (Scott et al., 1998; Navé et al., 1999). eEF2 is inactivated by phosphorylation at Thr56 (reviewed in Proud, 2000). It undergoes dephosphorylation in response to insulin or serum in a rapamycin-sensitive manner (Redpath et al., 1996; Diggle et al., 1998; Wang et al., 2000), and this correlates with activation of elongation, which is also sensitive to rapamycin. Dephosphorylation of eEF2 in response to insulin or serum involves the inactivation of the kinase that phosphorylates eEF2 (Redpath et al., 1996; Wang et al., 2000), a highly specific enzyme that does not belong to the main kinase superfamily (Ryazanov et al., 1999). The regulation of eEF2 kinase (eEF2k) by insulin or mitogens is poorly understood and, in particular, it is not known how mTOR-dependent signalling is coupled to the regulation of its activity. Here we have made use of cells engineered to lack specific protein kinases to explore the signalling pathways by which these mTOR-sensitive translational regulators are controlled. Our data demonstrate that PDK1, and therefore PKB, are not required for basal phosphorylation of 4E-BP1 or, by implication, the basal activity of mTOR, which appears to be maintained by amino acids in the cells' growth medium. Most importantly, we demonstrate that PDK1 is required for the regulation of the phosphorylation of eEF2, and show that eEF2k is regulated by phosphorylation by two PDK1-dependent protein kinases, p70 S6k and p90RSK. These studies identify novel signalling connections involved in regulating mRNA translation. Results PDK1 is required for the regulation of the phosphorylation of eEF2 eEF2 is a target for mTOR signalling and is involved in regulating translation elongation (Proud, 2000). To study its phosphorylation, we used an antibody that detects eEF2 only when it is phosphorylated at Thr56. Serum-starved cells displayed significant phosphorylation of eEF2 and this was higher in the PDK1−/− than in the PDK1+/+ cells (Figure 1A). Treatment of almost (80%) confluent PDK1+/+ cells with insulin-like growth factor 1 (IGF1) elicited a decrease in the level of phosphorylation of eEF2 (Figure 1A). In contrast, IGF1 had no effect on eEF2 phosphorylation in PDK1−/− cells. PDK1−/− cells subjected to mild serum starvation showed high levels of eEF2 phosphorylation, which were not increased further either by rapamycin (Figure 1A) or by amino acid withdrawal (not shown). In PDK1+/+ cells that were less confluent, the initial level of eEF2 phosphorylation was submaximal, as confirmed by the increase seen when such cells were treated with rapamycin (Figure 1B). Withdrawal of amino acids from such cells led to increased phosphorylation of eEF2, similar to that observed after addition of rapamycin (Figure 1B). In contrast, in PDK1−/− cells, neither amino acid withdrawal nor rapamycin caused any further increase in eEF2 phosphorylation (Figure 1B). Figure 1.Regulation of eEF2 and eEF2k in ES cells. (A) ES cells (PDK1+/+ or PDK1−/− as indicated, >80% confluent) were serum starved for 3 h and then treated with rapamycin (Rap) and/or IGF1 (40 min) as shown. Samples were subjected to SDS–PAGE and western blotting. Upper section: antibody against eEF2 phosphorylated at Thr56; lower section: blot with antibody detecting eEF2 irrespective of its phosphorylation state (loading control). (B) PDK+/+ or PDK1−/− ES cells (∼70% confluent) were serum starved for 3 h and then treated with rapamycin (Rap), IGF1 (20 min) or transferred to D-PBS/glucose for 1 h (-AA). Samples were subjected to SDS–PAGE/blotting with anti-(P)eEF2 antiserum or anti-eEF2. (C) Cell treatments as in (A). eEF2k activity was assayed in cell extracts using purified eEF2 as substrate. This figure is an autoradiograph. Signals were quantified by densitometry, activity for the control being set at 100. Con indicates control (untreated) cells. Download figure Download PowerPoint To explore this further, we measured the activity of eEF2k in extracts of both cell lines before and after treatment with IGF1, using purified rabbit muscle eEF2 as substrate. IGF1 clearly decreased the activity of eEF2k in PDK1+/+ cells and this was inhibited by rapamycin (Figure 1C). In contrast, in PDK1−/− cells, IGF1 had no effect on eEF2k activity (Figure 1C). These data strongly imply that PDK1 is required for the regulation of eEF2k, either directly or through its action on another protein kinase, e.g. a member of the AGC family of kinases. eEF2k does not belong to this group of enzymes (Ryazanov et al., 1999) and we found no significant phosphorylation of recombinant eEF2k by PDK1 in vitro (data not shown). This is consistent with the lack, within the sequence of eEF2k, of a consensus site for PDK1. It seemed possible, therefore, that disruption of PDK1 might interfere with the function and/or regulation of mTOR; indeed, it has been suggested that PKB may play a role in the control of mTOR activity (Scott et al., 1998; Navé et al., 1999) or the regulation of other targets of mTOR signalling (Burgering and Coffer, 1995; Gingras et al., 1998; Kitamura et al., 1998). 4E-BP1 is highly phosphorylated in PDK1−/− cells To assess whether mTOR was functional in PDK1−/− cells, we examined the phosphorylation of another target of mTOR signalling, 4E-BP1. Its phosphorylation state can be assessed by its mobility on SDS–PAGE, where more highly phosphorylated forms migrate more slowly. Extracts from PDK1+/+ or PDK1−/− embryonic stem (ES) cells (which had been starved of serum for 4 h) were subjected to SDS–PAGE and western blotting using anti-4E-BP1 antiserum. From this analysis, it is clear that 4E-BP1 is as highly phosphorylated in PDK1−/− cells as it is in PDK1+/+ cells (Figure 2A). As expected, pre-treatment of ES cells with rapamycin caused a shift in the migration of 4E-BP1 towards more mobile species in both cases. In other cell types, removal of amino acids induces dephosphorylation of 4E-BP1. To study this in ES cells, they were transferred to medium lacking amino acids for 1 h. This also resulted in a marked decrease in 4E-BP1 phosphorylation (Figure 2A). These data indicate that mTOR signalling is active in PDK1−/− cells, being maintained by the amino acids in the medium. These data thus demonstrate that neither PDK1 nor PKB is required for basal mTOR activity or for signalling downstream of mTOR to 4E-BP1. Figure 2.4E-BP1 undergoes rapamycin-sensitive phosphorylation in PDK1−/− cells. (A) ES cells (PDK1+/+ or PDK1−/− as indicated) were treated with IGF1 (40 min) or transferred to amino acid-free medium (-AA; 1 h). Where shown (Rap), cells were pre-treated with rapamycin for 1 h. Extracts were subjected to immunoblotting using an antibody against 4E-BP1 that detects the protein irrespective of its phosphoryl ation state. Positions of the three electrophoretically distinct forms of 4E-BP1 (α–γ in order of increasing phosphorylation) are indicated. (B) Cell treatments as in (A) (but no amino acid withdrawal experiments). Cell extracts were subjected to affinity chromatography on m7GTP–Sepharose and the bound material was subjected to SDS–PAGE/western blotting using antisera for 4E-BP1, eIF4E and eIF4G (positions indicated). (C) ES cells were treated as in (B) and samples were analysed by SDS–PAGE/western blotting using phosphospecific antisera for the indicated sites in 4E-BP1. Con indicates control (untreated) cells. Download figure Download PowerPoint Treatment of PDK1+/+ ES cells with IGF1 caused a small shift in the migration of 4E-BP1 towards the most phosphorylated γ-species (Figure 2A). This effect was blocked by either of two inhibitors of PI 3-kinase: LY294002 and wortmannin (data not shown). In contrast, IGF1 did not affect the mobility of 4E-BP1 in PDK−/− cells. These observations are consistent with the suggested role for PKB (Gingras et al., 1998) in the stimulation of 4E-BP1 phosphorylation by insulin. To assess whether IGF1 affected binding of 4E-BP1 to eIF4E, the latter was isolated from cell extracts on m7GTP–Sepharose, and the bound material was subjected to SDS–PAGE and western blotting to detect bound 4E-BP1 or eIF4G. Consistent with the high initial state of phosphorylation of 4E-BP1 in ES cells, relatively little was bound to eIF4E in serum-starved controls. Rapamycin treatment (Figure 2B) or withdrawal of amino acids (not shown) markedly increased the amount of 4E-BP1 bound to eIF4E in parallel with the decrease in its phosphorylation documented in Figure 2A (Figure 2B). In agreement with the low level of 4E-BP1 binding to eIF4E, the amount of eIF4G associated with eIF4E was high even in serum-starved controls (Figure 2B), for both control and knockout cells. Rapamycin treatment (Figure 2B) caused almost complete loss of eIF4G bound to eIF4E. The high basal level of eIF4F complexes resembles the situation in CHO cells (Campbell et al., 1999), where this also appears to be maintained by amino acids in the medium. Earlier reports suggested that the effects of amino acids on intracellular signalling pathways require PI 3-kinase (Wang et al., 1998; Peyrollier et al., 2000). However, the present data show that the effects of amino acids on mTOR-dependent eIF4F assembly are independent of PDK1. This concurs with earlier data (Campbell et al., 1999; Kimball and Jefferson, 2000; Peyrollier et al., 2000) indicating that amino acids do not activate PKB. Basal eIF4F formation is clearly also independent of PKB and other AGC kinases regulated by PDK1. Phosphorylation of 4E-BP1 is complex, with up to six sites of phosphorylation that have differing effects upon the mobility of 4E-BP1 and its ability to bind eIF4E (Lawrence and Abraham, 1997; Mothe-Satney et al., 2000a,b; Raught et al., 2000). In order to study the phosphorylation of specific sites in 4E-BP1, we made use of antisera specific for these sites. Antisera are available for Thr36/45 (antibody cannot distinguish between these sites; Mothe-Satney et al., 2000b), Ser64 and Thr69, but not for Ser82 or Ser112. For the four sites studied, phosphorylation appeared similar in PDK−/− and PDK1+/+ cells (Figure 2C). Phosphorylation of Ser64 was markedly suppressed by rapamycin. This site is only phosphorylated in the γ-species of 4E-BP1, suggesting that its phosphorylation contributes to or causes the mobility shift from β to γ (see also Mothe-Satney et al., 2000a,b). Using the anti-(P)Thr69 or anti-(P)Thr36/45 antisera, two bands (β and γ) are observed in some cases and one in others (in rapamycin-treated cells), so this makes changes in overall intensity rather harder to discern here. However, it does appear that rapamycin also suppresses the phosphorylation of these sites (Figure 2C). Treatment of ES cells with IGF1 caused little, if any, change in the phosphorylation of any of these sites (Figure 2C). The above data indicate that mTOR signalling, e.g. in response to amino acids, is functional in cells lacking PDK1 and thus that neither PDK1 nor any of the AGC family kinases that it regulates is required for mTOR function or for its control by amino acids. Consistent with this, Hara and colleagues have found that mTOR activity (measured in vitro against p70 S6kα or 4E-BP1) is identical in extracts from PDK1+/+ or PDK1−/− cells (K.Hara, D.Alessi and K.Yonezawa, in preparation). Analysis of the phosphorylation of ribosomal protein S6 and GSK3 confirmed that the PDK1−/− cells used here are devoid of PKB and S6 kinase activity, although p70 S6kα appeared to be partially phosphorylated in these cells (see Supplementary data available at The EMBO Journal Online). eEF2k is phosphorylated at Ser366 by p70 S6kα and p90RSK1 Since the above data for 4E-BP1 indicate that there is no defect in mTOR signalling in PDK1−/− cells, it appeared likely that the absence of regulation of eEF2 and eEF2k in such cells was due to a role for a PDK1-activated member of the AGC kinase family in the control of eEF2k. To study the phosphorylation of eEF2k by different members of the subfamily of AGC kinases, we expressed human eEF2k in Escherichia coli as a glutathione S-transferase (GST) fusion protein. p90RSK1 and p70 S6kα readily phosphorylated GST–eEF2k, but PKA, PKB and MSK1 (all tested at 1 U/ml) only showed low or very low activity against GST–eEF2k (Figure 3A). Control experiments showed that, under the same conditions, the BAD [Bcl-2/Bcl-X(L)-antagonist, causing cell death] was phosphorylated with similar efficiency by PKA, p90RSK1, PKB and MSK1 (Lizcano et al., 2000), whereas the transcription factor CREB was phosphorylated to a similar extent by MSK1 and PKA, but at a vastly lower rate by p90RSK1 (Deak et al., 1998; Figure 3A). p70 S6kα and p90RSK1 (at 1 U/ml) each phosphorylated GST–eEF2k to 0.5–0.8 mol of phosphate/mol of protein after 60 min (Figure 3B and data not shown). Tryptic digestion of GST–eEF2k labelled in vitro by p70 S6kα and p90RSK1, followed by HPLC, revealed one major tryptic phosphopeptide, P1, eluting at 28% acetonitrile (Figure 3C and E). Phosphoamino acid analysis revealed that P1 contained only phosphoserine. During solid-phase sequencing, 32P radioactivity was released after the third cycle of Edman degradation (Figure 3D and F). The molecular mass of P1 determined by MALDI-TOF mass spectrometry (4608.9) was identical to that expected for the monophosphorylated tryptic phosphopeptide comprising residues 364–374. This was confirmed by gas-phase Edman sequencing of P1 (data not shown; sequence given in Figure 4D and F). These data demonstrate that p70 S6kα and p90RSK1 each phosphorylate human eEF2k at Ser366. This residue lies in a consensus sequence for these kinases, i.e. RXRXXS, and it, and the sequence immediately adjacent to it, are conserved in the three known sequences for mammalian eEF2k (Figure 4A). The main exception is that while the residue immediately C-terminal to Ser366 is Gly in rat and human eEF2k, it is replaced by Ser in mouse. Figure 3.Phosphorylation of eEF2k at Ser366 by AGC kinases. (A) GST–eEF2k, GST–CREB, GST–BAD and histone 2B (H2B) were incubated with the indicated AGC kinases in the presence of [γ-32P]ATP, and phosphorylation was analysed as described in Materials and methods. Similar results were obtained in two separate experiments. (B) GST–eEF2k was incubated with [γ-32P]ATP in the presence or absence of p70 S6kα, and after the times indicated reactions were terminated and the phosphorylation of eEF2k was determined. The stoichiometry of GST–eEF2k phosphorylation at each time point was measured. (C and E) GST–eEF2k that had been phosphorylated with p70 S6kα or p90RSK1 was digested with trypsin and chromatographed on a Vydac 218TP54 C18 column (Separations Group, Hesperia, CA) equilibrated in 0.1% (by vol) TFA in water. The column was developed with CH3CN (dashed line) at 0.8 ml/min and fractions (0.4 ml) were collected. Eighty per cent of the radioactivity applied to the column eluted with the major 32P-containing peptide (P1) at 28% CH3CN. (D and F) An aliquot of the 32P-labelled P1 peptide (from eEF2k phosphorylated by p70 S6kα or p90RSK1, respectively) was subjected to solid-phase Edman degradation. Release of 32P radioactivity was measured after each cycle. Sequences determined by gas-phase Edman degradation are indicated in (D) and (F). Download figure Download PowerPoint Figure 4.Phosphorylation of eEF2k at Ser366 inhibits its activity. (A) Sequence alignment around Ser366. The sequences from rat (Rn), mouse (Mm) and human (Hs) eEF2k around the equivalent of Ser366 (indicated by the arrow: human protein; 365 in rodents) are shown. (B) Wild-type (wt) or mutant (S366A) eEF2k proteins were expressed as GST fusions in E.coli and incubated with p70 S6kα in vitro in the presence of [γ-32P]ATP/MgCl2 for the times indicated. Samples were analysed by SDS–PAGE followed by autoradiography. The figure shows an autoradiograph. (C) Wild-type GST–eEF2k was pre-treated with (lower section) or without (upper section) p70 S6kα for 30 min in the presence of ATP/MgCl2. eEF2, CaCl2 (final concentration 100 μM), CaM and [γ-32P]ATP were then added, and the incubation was continued for the times indicated. Samples were analysed by SDS–PAGE/autoradiography to assess incorporation of radiolabel into eEF2. (D) Wild-type (wt) eEF2k or eEF2k in which Ser366 was mutated to Ala or Glu was expressed in E.coli and their activities were assessed using eEF2 as substrate in incubations containing [γ-32P]ATP/MgCl2, CaM and the indicated final concentrations of CaCl2 (upper section). eEF2k (wt or mutant as indicated) was pre-incubated with ATP/MgCl2 and with (lower section) or without (upper section) p70 S6kα in the absence of Ca ions or CaM prior to assay against eEF2 under the conditions described above. Samples were analysed by SDS–PAGE and autoradiography to assess incorporation of label into eEF2. Download figure Download PowerPoint Mutant eEF2k proteins in which Ser366 was mutated to Ala (which cannot be phosphorylated) or Glu (an acidic residue that may mimic phosphoserine) were not phosphorylated by p70 S6kα (Figure 4B and data not shown), demonstrating that Ser366 is the only significant site of phosphorylation for p70 S6kα in eEF2k. Phosphorylation of eEF2k by p70 S6kα inhibits its activity To assess whether phosphorylation by p70 S6kα affected the activity of eEF2k, GST–eEF2k was pre-incubated with or without p70 S6kα, and its activity against eEF2 was assayed at a free calcium ion concentration similar to that used in our standard assays (100 μM). eEF2k activity was clearly decreased following pre-treatment with p70 S6kα [the activity of the phosphorylated enzyme was 39.8 ± 2.6% of the unphosphorylated control (n = 5)]. To examine the effect of phosphorylation on eEF2k activity at Ca2+ ion concentrations similar to those occurring in vivo, we repeated the experiments performing the assays at three different Ca2+ concentrations: 0.5, 1 and 10 μM (Figure 4D). Pre-treatment of eEF2k [but not eEF2k(S366A)] with p70 S6kα resulted in a very marked decrease in its activity when assayed at low calcium as compared with the control, i.e. eEF2k incubated only with ATP-Mg (Figure 4D, compare upper and lower sections). Mutation of Ser366 to Glu decreased eEF2k activity at low calcium in a similar way to phosphorylation of the wild-type enzyme by p70 S6kα (Figure 4D), and may also decrease its activity at high Ca2+ concentrations. Taken together, these data show that eEF2k is phosphorylated by p70 S6k at Ser366 and that this markedly inhibits its activity, especially at low micromolar calcium concentrations. This provides a mechanism by which insulin and other agents that activate p70 S6k may switch off eEF2k in an mTOR-dependent manner. IGF1-induced eEF2 dephosphorylation is compromised in p70 S6kα−/− cells To assess the role of p70 S6kα in regulating eEF2 phosphorylation in intact cells, we made use of ES cells in which both copies of the gene for p70 S6kα have been disrupted (p70 S6kα−/− cells; Kawasome et al., 1998), using the corresponding p70 S6kα+/+ cells as control. Western blot analysis revealed a clear signal for p70 S6kα in p70 S6kα+/+ cells, and in these cells IGF1 increase the phosphorylation of p70 S6kα, as shown by retardation of its mobility on SDS–PAGE (Figure 5A). As anticipated, there was no detectable p70 S6kα in the p70 S6kα−/− cells (Figure 5A). These cells also lack p70 S6kα activity (data not shown). Consistent with this, while IGF1 or serum caused a marked rapamycin-sensitive increase in the phosphorylation of ribosomal protein S6 in p70 S6kα+/+ cells, the signal was very substantially reduced in the p70 S6kα−/− cells (Figure 5A, lower section). However, serum or IGF1 still elicited a small but reproducible increase in S6 phosphorylation in these cells. Two isoforms of p70 S6k exist in mammals, encoded by different genes, so it seemed possible that the p70 S6kα−/− cells expressed some p70 S6kβ+/+, which was responsible for the residual phosphorylation of S6. Immunoblotting using an antibody specific for p70 S6kβ revealed similar levels of this kinase in p70 S6kα−/− and p70 S6kα+/+ cells (Figure 5B). Figure 5.Regulation of S6 phosphorylation, eEF2 and eEF2k in p70 S6kα+/+ and p70S6kα−/− ES cells. (A) ES cells (p70 S6kα+/+ or p70 S6kα−/− as indicated) were treated with rapamycin (Rap), serum (40 min) or IGF1 (times in minutes). Samples were analysed by SDS–PAGE, followed by western blotting with an antibody against p70 S6kα (upper section) or S6 [Ser235(P)]. The band running just below the position of p70 S6α in the samples from the p70 S6kα−/− cells represents a non-specific cross-reaction (band is also visible in other lanes). (B) Extracts of p70 S6kα+/+ or p70 S6kα−/− cells were subjected to SDS–PAGE and western blotting using antiserum for p70 S6kβ (position indicated). (C) ES cells were treated with rapamycin (Rap) and/or IGF1. Samples were prepared and analysed by SDS–PAGE/western blotting using antisera for phosphorylated eEF2 (upper part) or eEF2 irrespective of its state of phosphorylation (loading control, lower part). (D) ES cells were treated with rapamycin (Rap), serum or IGF1. Cell lysates were prepared and assayed for eEF2k activity using eEF2 as substrate. Signals were quantified by densitometry, activity for the control being set at 100 in each case. (E) Recombinant eEF2k or S366A mutant was incubated with p70 S6kα or p70 S6kβ and [γ-32P]ATP as indicated. Samples were analysed by SDS–PAGE and autoradiography. Con indicates control (untreated) cells. Download figure Download PowerPoint In p70 S6kα+/+ cells, IGF1 induced the dephosphorylation of eEF2 (Figure 5C). In contrast, IGF1 had little, if any, effect on the level of phosphorylation of eEF2 in p70 S6k−/− cells (Figure 5C). Thus, loss of p70 S6kα grea

Mammalian stress granules (SGs) harbor untranslated mRNAs that accumulate in cells exposed to environmental stress. Drugs that stabilize polysomes (emetine) inhibit the assembly of SGs, whereas drugs that destabilize polysomes (puromycin) promote the assembly of SGs. Moreover, emetine dissolves preformed SGs as it promotes the assembly of polysomes, suggesting that these mRNP species (i.e., SGs and polysomes) exist in equilibrium. We used green flourescent protein–tagged SG-associated RNA-binding proteins (specifically, TIA-1 and poly[A] binding protein [PABP-I]) to monitor SG assembly, disassembly, and turnover in live cells. Fluorescence recovery after photobleaching shows that both TIA-1 and PABP-I rapidly and continuously shuttle in and out of SGs, indicating that the assembly of SGs is a highly dynamic process. This unexpected result leads us to propose that mammalian SGs are sites at which untranslated mRNAs are sorted and processed for either reinitiation, degradation, or packaging into stable nonpolysomal mRNP complexes. A truncation mutant of TIA-1 (TIA-1ΔRRM), which acts as a transdominant inhibitor of SG assembly, promotes the expression of cotransfected reporter genes in COS transfectants, suggesting that this process of mRNA triage might, directly or indirectly, influence protein expression.

Mesenchymal stem cells (MSCs) have been considered as an attractive tool for the therapy of diseases. Exosomes excreted from MSCs can reduce myocardial ischemia/reperfusion damage and protect against acute tubular injury. However, whether MSC-derived exosomes can relieve liver fibrosis and its mechanism remain unknown. Previous work showed that human umbilical cord-MSCs (hucMSCs) transplanted into acutely injured and fibrotic livers could restore liver function and improve liver fibrosis. In this study, it was found that transplantation of exosomes derived from hucMSC (hucMSC-Ex) reduced the surface fibrous capsules and got their textures soft, alleviated hepatic inflammation and collagen deposition in carbon tetrachloride (CCl4)-induced fibrotic liver. hucMSC-Ex also significantly recovered serum aspartate aminotransferase (AST) activity, decreased collagen type I and III, transforming growth factor (TGF)-β1 and phosphorylation Smad2 expression in vivo. In further experiments, we found that epithelial-to-mesenchymal transition (EMT)-associated markers E-cadherin-positive cells increased and N-cadherin- and vimentin-positive cells decreased after hucMSC-Ex transplantation. Furthermore, the human liver cell line HL7702 underwent typical EMT after induction with recombinant human TGF-β1, and then hucMSC-Ex treatment reversed spindle-shaped and EMT-associated markers expression in vitro. Taken together, these results suggest that hucMSC-Ex could ameliorate CCl4-induced liver fibrosis by inhibiting EMT and protecting hepatocytes. This provides a novel approach for the treatment of fibrotic liver disease.

Cell-surface-localized plant immune receptors, such as FLS2, detect pathogen-associated molecular patterns (PAMPs) and initiate PAMP-triggered immunity (PTI) through poorly understood signal-transduction pathways. The pathogenic Pseudomonas syringae effector AvrPphB, a cysteine protease, cleaves the Arabidopsis receptor-like cytoplasmic kinase PBS1 to trigger cytoplasmic immune receptor RPS5-specified effector-triggered immunity (ETI). Analyzing the function of AvrPphB in plants lacking RPS5, we find that AvrPphB can inhibit PTI by cleaving additional PBS1-like (PBL) kinases, including BIK1, PBL1, and PBL2. In unstimulated plants, BIK1 and PBL1 interact with FLS2 and are rapidly phosphorylated upon FLS2 activation by its ligand flg22. Genetic and molecular analyses indicate that BIK1, and possibly PBL1, PBL2, and PBS1, integrate immune signaling from multiple immune receptors. Whereas AvrPphB-mediated degradation of one of these kinases, PBS1, is monitored by RPS5 to initiate ETI, this pathogenic effector targets other PBL kinases for PTI inhibition.

Polymeric carbon nitride (C3N4) has emerged as the most promising candidate for metal-free photocatalysts but is plagued by low activity due to the poor quantum efficiency and low specific surface area. Exfoliation of bulk crystals into ultrathin nanosheets has proven to be an effective and widely used strategy for enabling high photocatalytic performances; however, this process is complicated, time-consuming, and costly. Here, we report a simple bottom-up method to synthesize porous few-layer C3N4, which involves molecule self-assembly into layered precursors, alcohol molecules intercalation, and subsequent thermal-induced exfoliation and polycondensation. The as-prepared few-layer C3N4 expose more active sites and greatly enhance the separation of charge carriers, thus exhibiting a 26-fold higher hydrogen evolution activity than bulk counterpart. Furthermore, we find that both the high activity and selectivity for the oxidative coupling of amines to imines can be obtained under visible light that surpass those of other metal-free photocatalysts so far.

Specificity of protein ubiquitylation is conferred by E3 ubiquitin (Ub) ligases. We have annotated ∼617 putative E3s and substrate-recognition subunits of E3 complexes encoded in the human genome. The limited knowledge of the function of members of the large E3 superfamily prompted us to generate genome-wide E3 cDNA and RNAi expression libraries designed for functional screening. An imaging-based screen using these libraries to identify E3s that regulate mitochondrial dynamics uncovered MULAN/FLJ12875, a RING finger protein whose ectopic expression and knockdown both interfered with mitochondrial trafficking and morphology. We found that MULAN is a mitochondrial protein – two transmembrane domains mediate its localization to the organelle's outer membrane. MULAN is oriented such that its E3-active, C-terminal RING finger is exposed to the cytosol, where it has access to other components of the Ub system. Both an intact RING finger and the correct subcellular localization were required for regulation of mitochondrial dynamics, suggesting that MULAN's downstream effectors are proteins that are either integral to, or associated with, mitochondria and that become modified with Ub. Interestingly, MULAN had previously been identified as an activator of NF-κB, thus providing a link between mitochondrial dynamics and mitochondria-to-nucleus signaling. These findings suggest the existence of a new, Ub-mediated mechanism responsible for integration of mitochondria into the cellular environment.

Nitrogen-doped graphene sheets were prepared through a hydrothermal reduction of colloidal dispersions of graphite oxide in the presence of hydrazine and ammonia at pH of 10. The effect of hydrothermal temperature on the structure, morphology, and surface chemistry of as-prepared graphene sheets were investigated though XRD, N(2) adsorption, solid-state (13)C NMR, SEM, TEM, and XPS characterizations. Oxygen reduction and nitrogen doping were achieved simultaneously under the hydrothermal reaction. Up to 5% nitrogen-doped graphene sheets with slightly wrinkled and folded feature were obtained at the relative low hydrothermal temperature. With the increase of hydrothermal temperature, the nitrogen content decreased slightly and more pyridinic N incorporated into the graphene network. Meanwhile, a jellyfish-like graphene structure was formed by self-organization of graphene sheets at the hydrothermal temperature of 160 °C. Further increase of the temperature to 200 °C, graphene sheets could self-aggregate into agglomerate particles but still contained doping level of 4 wt % N. The unique hydrothermal environment should play an important role in the nitrogen doping and the jellyfish-like graphene formation. This simple hydrothermal method could provide the synthesis of nitrogen-doped graphene sheets in large scale for various practical applications.

<h2>Summary</h2><h3>Background</h3> In December, 2019, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. The number of affected pregnant women is increasing, but scarce information is available about the clinical features of COVID-19 in pregnancy. This study aimed to clarify the clinical features and obstetric and neonatal outcomes of pregnant patients with COVID-19. <h3>Methods</h3> In this retrospective, single-centre study, we included all pregnant women with COVID-19 who were admitted to Tongji Hospital in Wuhan, China. Clinical features, treatments, and maternal and fetal outcomes were assessed. <h3>Findings</h3> Seven patients, admitted to Tongji Hospital from Jan 1, to Feb 8, 2020, were included in our study. The mean age of the patients was 32 years (range 29–34 years) and the mean gestational age was 39 weeks plus 1 day (range 37 weeks to 41 weeks plus 2 days). Clinical manifestations were fever (six [86%] patients), cough (one [14%] patient), shortness of breath (one [14%] patient), and diarrhoea (one [14%] patient). All the patients had caesarean section within 3 days of clinical presentation with an average gestational age of 39 weeks plus 2 days. The final date of follow-up was Feb 12, 2020. The outcomes of the pregnant women and neonates were good. Three neonates were tested for SARS-CoV-2 and one neonate was infected with SARS-CoV-2 36 h after birth. <h3>Interpretation</h3> The maternal, fetal, and neonatal outcomes of patients who were infected in late pregnancy appeared very good, and these outcomes were achieved with intensive, active management that might be the best practice in the absence of more robust data. The clinical characteristics of these patients with COVID-19 during pregnancy were similar to those of non-pregnant adults with COVID-19 that have been reported in the literature. <h3>Funding</h3> National Natural Science Foundation of China, Hubei Provincial Natural Science Foundation of China.

A reciprocal relationship exists between persistent pain and negative affective states such as fear, anxiety, and depression. Accumulating evidence points to the amygdala as an important site of such interaction. Whereas a key role of the amygdala in the neuronal mechanisms of emotionality and affective disorders has been well established, the concept of the amygdala as an important contributor to pain and its emotional component is still emerging. This article will review and discuss evidence from anatomical, neuroimaging, behavioral, electrophysiological, pharmacological, and biochemical data that implicate the amygdala in pain modulation and emotional responses to pain. The latero-capsular division of the central nucleus of the amygdala is now defined as the "nociceptive amygdala" and integrates nociceptive information with poly-modal information about the internal and external bodily environment. Dependent on environmental conditions and affective states, the amygdala appears to play a dual facilitatory and inhibitory role in the modulation of pain behavior and nociceptive processing at different levels of the pain neuraxis. Only recently, electrophysiological, pharmacological, and biochemical neuroplastic changes were shown in the nociceptive amygdala in persistent pain. It is conceivable, however, that amygdala plasticity plays an important role in emotional pain behavior and its modulation by affective state.

As synthesised ZIF-8 nanoparticles (size ∼ 60 nm and specific surface area ∼ 1300–1600 m2 g−1) were directly incorporated into a model polymer matrix (Matrimid® 5218) by solution mixing. This produces flexible transparent membranes with excellent dispersion of nanoparticles (up to loadings of 30 wt%) with good adhesion within the polymer matrix, as confirmed by scanning electron microscopy, dynamic mechanical thermal analysis and gas sorption studies. Pure gas (H2, CO2, O2, N2 and CH4) permeation tests showed enhanced permeability of the mixed matrix membrane with negligible losses in selectivity. Positron annihilation lifetime spectroscopy (PALS) indicated that an increase in the free volume of the polymer with ZIF-8 loading together with the free diffusion of gas through the cages of ZIF-8 contributed to an increase in gas permeability of the composite membrane. The gas transport properties of the composite membranes were well predicted by a Maxwell model whilst the processing strategy reported can be extended to fabricate other polymer nanocomposite membranes intended for a wide range of emerging energy applications.

Graphene is an optical material of unusual characteristics because of its linearly dispersive conduction and valence bands and the strong interband transitions. It allows broadband light-matter interactions with ultrafast responses and can be readily pasted to surfaces of functional structures for photonic and optoelectronic applications. Recently, graphene-based optical modulators have been demonstrated with electrical tuning of the Fermi level of graphene. Their operation bandwidth, however, was limited to about 1 GHz by the response of the driving electrical circuit. Clearly, this can be improved by an all-optical approach. Here, we show that a graphene-clad microfiber all-optical modulator can achieve a modulation depth of 38% and a response time of ∼ 2.2 ps, limited only by the intrinsic carrier relaxation time of graphene. This modulator is compatible with current high-speed fiber-optic communication networks and may open the door to meet future demand of ultrafast optical signal processing.

Androgen receptor (AR) is a ligand-dependent transcription factor that plays a key role in prostate cancer. Little is known about the nature of AR cis-regulatory sites in the human genome. We have mapped the AR binding regions on two chromosomes in human prostate cancer cells by combining chromatin immunoprecipitation (ChIP) with tiled oligonucleotide microarrays. We find that the majority of AR binding regions contain noncanonical AR-responsive elements (AREs). Importantly, we identify a noncanonical ARE as a cis-regulatory target of AR action in TMPRSS2, a gene fused to ETS transcription factors in the majority of prostate cancers. In addition, through the presence of enriched DNA-binding motifs, we find other transcription factors including GATA2 and Oct1 that cooperate in mediating the androgen response. These collaborating factors, together with AR, form a regulatory hierarchy that governs androgen-dependent gene expression and prostate cancer growth and offer potential new opportunities for therapeutic intervention.

Tubulin dynamics is a promising target for new chemotherapeutic agents. The colchicine binding site is one of the most important pockets for potential tubulin polymerization destabilizers. Colchicine binding site inhibitors (CBSI) exert their biological effects by inhibiting tubulin assembly and suppressing microtubule formation. A large number of molecules interacting with the colchicine binding site have been designed and synthesized with significant structural diversity. CBSIs have been modified as to chemical structure as well as pharmacokinetic properties, and tested in order to find a highly potent, low toxicity agent for treatment of cancers. CBSIs are believed to act by a common mechanism via binding to the colchicine site on tubulin. The present review is a synopsis of compounds that have been reported in the past decade that have provided an increase in our understanding of the actions of CBSIs.

Diabetic cardiomyopathy is related directly to hyperglycemia. Cell death such as apoptosis plays a critical role in cardiac pathogenesis. Whether hyperglycemia induces myocardial apoptosis, leading to diabetic cardiomyopathy, remains unclear. We tested the hypothesis that apoptotic cell death occurs in the diabetic myocardium through mitochondrial cytochrome c-mediated caspase-3 activation pathway. Diabetic mice produced by streptozotocin and H9c2 cardiac myoblast cells exposed to high levels of glucose were used. In the hearts of diabetic mice, apoptotic cell death occurred as detected by terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay. Correspondingly, caspase-3 activation as determined by enzymatic assay and mitochondrial cytochrome c release detected by Western blotting analysis were observed. Supplementation of insulin inhibited diabetes-induced myocardial apoptosis as well as suppressed hyperglycemia. To explore whether apoptosis in diabetic hearts is related directly to hyperglycemia, we exposed cardiac myoblast H9c2 cells to high levels of glucose (22 and 33 mmol/l) in cultures. Apoptotic cell death was detected by TUNEL assay and DAPI nuclear staining. Caspase-3 activation with a concomitant mitochondrial cytochrome c release was also observed. Apoptosis or activation of caspase-3 was not observed in the cultures exposed to the same concentrations of mannitol. Inhibition of caspase-3 with a specific inhibitor, Ac-DEVD-cmk, suppressed apoptosis induced by high levels of glucose. In addition, reactive oxygen species (ROS) generation was detected in the cells exposed to high levels of glucose. These results suggest that hyperglycemia directly induces apoptotic cell death in the myocardium in vivo. Hyperglycemia-induced myocardial apoptosis is mediated, at least in part, by activation of the cytochrome c-activated caspase-3 pathway, which may be triggered by ROS derived from high levels of glucose.

Jasmonate (JA) and ethylene (ET) are two major plant hormones that synergistically regulate plant development and tolerance to necrotrophic fungi. Both JA and ET induce the expression of several pathogenesis-related genes, while blocking either signaling pathway abolishes the induction of these genes by JA and ET alone or in combination. However, the molecular basis of JA/ET coaction and signaling interdependency is largely unknown. Here, we report that two Arabidopsis ET-stabilized transcription factors (EIN3 and EIL1) integrate ET and JA signaling in the regulation of gene expression, root development, and necrotrophic pathogen defense. Further studies reveal that JA enhances the transcriptional activity of EIN3/EIL1 by removal of JA-Zim domain (JAZ) proteins, which physically interact with and repress EIN3/EIL1. In addition, we find that JAZ proteins recruit an RPD3-type histone deacetylase (HDA6) as a corepressor that modulates histone acetylation, represses EIN3/EIL1-dependent transcription, and inhibits JA signaling. Our studies identify EIN3/EIL1 as a key integration node whose activation requires both JA and ET signaling, and illustrate transcriptional derepression as a common mechanism to integrate diverse signaling pathways in the regulation of plant development and defense.

Abstract Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single‐nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal‐transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem–loop structure holds the fluorescence‐donor and fluorescence‐acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein–DNA interaction studies, and protein recognition.

Donor-acceptor conjugated polymers PBDT-DTBT and PBDT-DTNT, based on 2,1,3-benzothiadiazole (BT) and naphtho[1,2-c:5,6-c]bis[1,2,5]thiadiazole (NT), have been designed and synthesized for polymer solar cells. NT contains two fused 1,2,5-thiadiazole rings that lower the band gap, enhance the interchain packing, and improve the charge mobility of the resulting polymer. Consequently, the NT-based polymer PBDT-DTNT exhibited considerably better photovoltaic performance with a power conversion efficiency (PCE) of 6.00% when compared with the BT-based polymer PBDT-DTBT, which gave a PCE of 2.11% under identical device configurations.

The roles and regulatory mechanisms of ferroptosis (a non-apoptotic form of cell death) in cancer remain unclear. The tumour suppressor BRCA1-associated protein 1 (BAP1) encodes a nuclear deubiquitinating enzyme to reduce histone 2A ubiquitination (H2Aub) on chromatin. Here, integrated transcriptomic, epigenomic and cancer genomic analyses link BAP1 to metabolism-related biological processes, and identify cystine transporter SLC7A11 as a key BAP1 target gene in human cancers. Functional studies reveal that BAP1 decreases H2Aub occupancy on the SLC7A11 promoter and represses SLC7A11 expression in a deubiquitinating-dependent manner, and that BAP1 inhibits cystine uptake by repressing SLC7A11 expression, leading to elevated lipid peroxidation and ferroptosis. Furthermore, we show that BAP1 inhibits tumour development partly through SLC7A11 and ferroptosis, and that cancer-associated BAP1 mutants lose their abilities to repress SLC7A11 and to promote ferroptosis. Together, our results uncover a previously unappreciated epigenetic mechanism coupling ferroptosis to tumour suppression.

Late morbidity and mortality remain problematic after repair of tetralogy of Fallot (TOF). We hypothesized that fibrosis detected by late gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) would be present in adults with repaired TOF and would be related to adverse markers of outcome.LGE was scored in the right and left ventricles (RV and LV) of 92 adult patients who had undergone TOF repair. RV LGE was seen in all patients at surgical sites located in the outflow tract (99%) or the site of ventricular septal defect patching (98%) and in the inferior RV insertion point (79%) and trabeculated myocardium (24%). LV LGE (53%) was located at the apex consistent with apical vent insertion (49%), in the inferior or lateral wall consistent with infarction (5%), or in other areas (8%). Patients with supramedian RV LGE score were older (38 versus 27 years, P<0.001) and more symptomatic (38% versus 8% in New York Heart Association class II or greater, P=0.001), had increased levels of atrial natriuretic peptide (7.3 versus 4.9 pmol/L, P=0.041), and had a trend to higher brain natriuretic peptide (12.3 versus 7.2 pmol/L, P=0.086), exercise intolerance (maximum VO2 24 versus 28 mL.min(-1).kg(-1), P=0.021), RV dysfunction (RV end-systolic volume 61 versus 55 mL/m2, P=0.018; RV ejection fraction 50% versus 56%, P=0.007), and clinical arrhythmia (26% versus 10%, P=0.039). Non-apical vent LV LGE also correlated with markers of adverse outcome. In a multivariate model, RV LGE remained a predictor of arrhythmia.RV and LV LGE were common after TOF repair and were related to adverse clinical markers, including ventricular dysfunction, exercise intolerance, and neurohormonal activation. Furthermore, RV LGE was significantly associated with clinical arrhythmia.

Platinum-Free Diesel The efficiency advantages inherent in diesel-based combustion engines are counterbalanced by the production of pollutants such as nitrogen oxides (NO x ). Currently, expensive precious metals, such as platinum, are required to remove these pollutants. Kim et al. (p. 1624 ; see the Perspective by Parks ) show that a strontium-doped perovskite catalyst, prepared from more abundant (and cheaper) elements, may help to lower the cost of NO x treatments and thus ultimately make diesel a more cost-effective automotive fuel. Under conditions realistically simulating exhaust streams, the catalyst rivaled platinum in accelerating NO x decomposition.

Most existing person re-identification (re-id) methods require supervised model learning from a separate large set of pairwise labelled training data for every single camera pair. This significantly limits their scalability and usability in real-world large scale deployments with the need for performing re-id across many camera views. To address this scalability problem, we develop a novel deep learning method for transferring the labelled information of an existing dataset to a new unseen (unlabelled) target domain for person re-id without any supervised learning in the target domain. Specifically, we introduce an Transferable Joint Attribute-Identity Deep Learning (TJ-AIDL) for simultaneously learning an attribute-semantic and identity-discriminative feature representation space transferrable to any new (unseen) target domain for re-id tasks without the need for collecting new labelled training data from the target domain (i.e. unsupervised learning in the target domain). Extensive comparative evaluations validate the superiority of this new TJ-AIDL model for unsupervised person re-id over a wide range of state-of-the-art methods on four challenging benchmarks including VIPeR, PRID, Market-1501, and DukeMTMC-ReID.

Environmental stress-induced phosphorylation of eIF2alpha inhibits protein translation by reducing the availability of eIF2-GTP-tRNA(i)Met, the ternary complex that joins initiator tRNA(Met) to the 43S preinitiation complex. The resulting untranslated mRNA is dynamically routed to discrete cytoplasmic foci known as stress granules (SGs), a process requiring the related RNA-binding proteins TIA-1 and TIAR. SGs appear to be in equilibrium with polysomes, but the nature of this relationship is obscure. We now show that most components of the 48S preinitiation complex (i.e., small, but not large, ribosomal subunits, eIF3, eIF4E, eIF4G) are coordinately recruited to SGs in arsenite-stressed cells. In contrast, eIF2 is not a component of newly assembled SGs. Cells expressing a phosphomimetic mutant (S51D) of eIF2alpha assemble SGs of similar composition, confirming that the recruitment of these factors is a direct consequence of blocked translational initiation and not due to other effects of arsenite. Surprisingly, phospho-eIF2alpha is recruited to SGs that are disassembling in cells recovering from arsenite-induced stress. We discuss these results in the context of a translational checkpoint model wherein TIA and eIF2 are functional antagonists of translational initiation, and in which lack of ternary complex drives SG assembly.

Sulfur-doped disordered carbon exhibits high capacity and excellent cyclability as an anode for sodium ion batteries.

Latent Dirichlet allocation (LDA) and other related topic models are increasingly popular tools for summarization and manifold discovery in discrete data. However, LDA does not capture correlations between topics. In this paper, we introduce the pachinko allocation model (PAM), which captures arbitrary, nested, and possibly sparse correlations between topics using a directed acyclic graph (DAG). The leaves of the DAG represent individual words in the vocabulary, while each interior node represents a correlation among its children, which may be words or other interior nodes (topics). PAM provides a flexible alternative to recent work by Blei and Lafferty (2006), which captures correlations only between pairs of topics. Using text data from newsgroups, historic NIPS proceedings and other research paper corpora, we show improved performance of PAM in document classification, likelihood of held-out data, the ability to support finer-grained topics, and topical keyword coherence.

To investigate the cell-intrinsic aging mechanisms that erode the function of somatic stem cells during aging, we have conducted a comprehensive integrated genomic analysis of young and aged cells. We profiled the transcriptome, DNA methylome, and histone modifications of young and old murine hematopoietic stem cells (HSCs). Transcriptome analysis indicated reduced TGF-β signaling and perturbation of genes involved in HSC proliferation and differentiation. Aged HSCs exhibited broader H3K4me3 peaks across HSC identity and self-renewal genes and showed increased DNA methylation at transcription factor binding sites associated with differentiation-promoting genes combined with a reduction at genes associated with HSC maintenance. Altogether, these changes reinforce HSC self-renewal and diminish differentiation, paralleling phenotypic HSC aging behavior. Ribosomal biogenesis emerged as a particular target of aging with increased transcription of ribosomal protein and RNA genes and hypomethylation of rRNA genes. This data set will serve as a reference for future epigenomic analysis of stem cell aging.

The CRISPR/Cas9 system has revolutionized mammalian somatic cell genetics. Genome-wide functional screens using CRISPR/Cas9-mediated knockout or dCas9 fusion-mediated inhibition/activation (CRISPRi/a) are powerful techniques for discovering phenotype-associated gene function. We systematically assessed the DNA sequence features that contribute to single guide RNA (sgRNA) efficiency in CRISPR-based screens. Leveraging the information from multiple designs, we derived a new sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments. Our model confirmed known features and suggested new features including a preference for cytosine at the cleavage site. The model was experimentally validated for sgRNA-mediated mutation rate and protein knockout efficiency. Tested on independent data sets, the model achieved significant results in both positive and negative selection conditions and outperformed existing models. We also found that the sequence preference for CRISPRi/a is substantially different from that for CRISPR/Cas9 knockout and propose a new model for predicting sgRNA efficiency in CRISPRi/a experiments. These results facilitate the genome-wide design of improved sgRNA for both knockout and CRISPRi/a studies.

Rational design and controllable synthesis of TiO2 based materials with unique microstructure, high reactivity, and excellent electrochemical performance for lithium ion batteries are crucially desired. In this paper, we developed a versatile route to synthesize hollow TiO2/graphitic carbon (H-TiO2/GC) spheres with superior electrochemical performance. The as-prepared mesoporous H-TiO2/GC hollow spheres present a high specific surface area (298 m2 g–1), a high pore volume (0.31 cm3 g–1), a large pore size (∼5 nm), well-defined hollow structure (monodispersed size of 600 nm and inner diameter of ∼400 nm, shell thickness of 100 nm), and small nanocrystals of anatase TiO2 (∼8 nm) conformably encapsulated in ultrathin graphitic carbon layers. As a result, the H-TiO2/GC hollow spheres achieve excellent electrochemical reactivity and stability as an anode material for lithium ion batteries. A high specific capacity of 137 mAh g–1 can be achieved up to 1000 cycles at a current density of 1 A g–1 (5 C). We believe that the mesoporous H-TiO2/GC hollow spheres are expected to be applied as a high-performance electrode material for next generation lithium ion batteries.

Standardized sampling from many sites worldwide was used to address an important ecological problem.

Image phase from gradient echo MRI provides a unique contrast that reflects brain tissue composition variations, such as iron and myelin distribution. Phase imaging is emerging as a powerful tool for the investigation of functional brain anatomy and disease diagnosis. However, the quantitative value of phase is compromised by its nonlocal and orientation dependent properties. There is an increasing need for reliable quantification of magnetic susceptibility, the intrinsic property of tissue. In this study, we developed a novel and accurate susceptibility mapping method that is also phase-wrap insensitive. The proposed susceptibility mapping method utilized two complementary equations: (1) the Fourier relationship of phase and magnetic susceptibility; and (2) the first-order partial derivative of the first equation in the spatial frequency domain. In numerical simulation, this method reconstructed the susceptibility map almost free of streaking artifact. Further, the iterative implementation of this method allowed for high quality reconstruction of susceptibility maps of human brain in vivo. The reconstructed susceptibility map provided excellent contrast of iron-rich deep nuclei and white matter bundles from surrounding tissues. Further, it also revealed anisotropic magnetic susceptibility in brain white matter. Hence, the proposed susceptibility mapping method may provide a powerful tool for the study of brain physiology and pathophysiology. Further elucidation of anisotropic magnetic susceptibility in vivo may allow us to gain more insight into the white matter micro-architectures.

Sirtuin proteins regulate diverse cellular pathways that influence genomic stability, metabolism and ageing. SIRT7 is a mammalian sirtuin whose biochemical activity, molecular targets and physiological functions have been unclear. Here we show that SIRT7 is an NAD(+)-dependent H3K18Ac (acetylated lysine 18 of histone H3) deacetylase that stabilizes the transformed state of cancer cells. Genome-wide binding studies reveal that SIRT7 binds to promoters of a specific set of gene targets, where it deacetylates H3K18Ac and promotes transcriptional repression. The spectrum of SIRT7 target genes is defined in part by its interaction with the cancer-associated E26 transformed specific (ETS) transcription factor ELK4, and comprises numerous genes with links to tumour suppression. Notably, selective hypoacetylation of H3K18Ac has been linked to oncogenic transformation, and in patients is associated with aggressive tumour phenotypes and poor prognosis. We find that deacetylation of H3K18Ac by SIRT7 is necessary for maintaining essential features of human cancer cells, including anchorage-independent growth and escape from contact inhibition. Moreover, SIRT7 is necessary for a global hypoacetylation of H3K18Ac associated with cellular transformation by the viral oncoprotein E1A. Finally, SIRT7 depletion markedly reduces the tumorigenicity of human cancer cell xenografts in mice. Together, our work establishes SIRT7 as a highly selective H3K18Ac deacetylase and demonstrates a pivotal role for SIRT7 in chromatin regulation, cellular transformation programs and tumour formation in vivo.

<h3>Background & Aims</h3> Liver enzyme abnormalities are common in patients with coronavirus disease 2019 (COVID-19). Whether or not severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can lead to liver damage <i>per se</i> remains unknown. Herein, we reported the clinical characteristics and liver pathological manifestations of COVID-19 patients with liver enzyme abnormalities. <h3>Methods</h3> We analyzed 156 patients diagnosed with COVID-19 from 2 designated centers in China and compared clinical features between patients with or without elevated aminotransferases. Postmortem liver biopsies were obtained from 2 cases who had elevated aminotransferases. We investigated the patterns of liver impairment by electron microscopy, immunohistochemistry, TUNEL assay and pathological studies. <h3>Results</h3> Sixty-four out of 156 (41.0%) patients with COVID-19 had elevated aminotransferases. The median levels of alanine aminotransferase were 50 U/L <i>vs.</i> 19 U/L, respectively, aspartate aminotransferase were 45.5 U/L <i>vs.</i> 24 U/L, respectively in abnormal and normal aminotransferase groups. Liver enzyme abnormalities were associated with disease severity, as well as a series of laboratory tests including higher alveolar-arterial oxygen partial pressure difference, higher gamma-glutamyltransferase, lower albumin, decreased CD4+ T cells and B lymphocytes. Ultrastructural examination identified typical coronavirus particles, characterized by spike structures, in the cytoplasm of hepatocytes in 2 COVID-19 cases. SARS-CoV-2-infected hepatocytes displayed conspicuous mitochondrial swelling, endoplasmic reticulum dilatation and glycogen granule decrease. Histologically, massive hepatic apoptosis and some binuclear hepatocytes were observed. Taken together, both ultrastructural and histological evidence indicated a typical lesion of viral infection. Immunohistochemical results showed scarce CD4+ and CD8+ lymphocytes. No obvious eosinophil infiltration, cholestasis, fibrin deposition, granuloma, massive central necrosis, or interface hepatitis were observed. <h3>Conclusions</h3> SARS-CoV-2 infection in the liver directly contributes to hepatic impairment in patients with COVID-19. Hence, a surveillance of viral clearance in liver and long-term outcome of COVID-19 is required. <h3>Lay summary</h3> Liver enzyme abnormalities are common in patients with coronavirus disease 2019 (COVID-19). We reported the clinical characteristics and liver pathological manifestations of COVID-19 patients with elevated liver enzymes. Our findings suggested that SARS-CoV-2 infection of the liver is a crucial factor contributing to hepatic impairment in patients with COVID-19.

Transfer learning, where a model is first pre-trained on a data-rich task before being fine-tuned on a downstream task, has emerged as a powerful technique in natural language processing (NLP). The effectiveness of transfer learning has given rise to a diversity of approaches, methodology, and practice. In this paper, we explore the landscape of transfer learning techniques for NLP by introducing a unified framework that converts all text-based language problems into a text-to-text format. Our systematic study compares pre-training objectives, architectures, unlabeled data sets, transfer approaches, and other factors on dozens of language understanding tasks. By combining the insights from our exploration with scale and our new ``Colossal Clean Crawled Corpus'', we achieve state-of-the-art results on many benchmarks covering summarization, question answering, text classification, and more. To facilitate future work on transfer learning for NLP, we release our data set, pre-trained models, and code.

To sleep, perchance to remember Many researchers believe sleep helps us consolidate our memories, but no one knows quite how. Yang et al. investigated the precise role of sleep in changing mouse brain structures (see the Perspective by Euston and Steenland). When mice learned motor tasks, small protuberances—or “spines”—formed on some of the dendritic branches of specific brain neurons. These spines represent the physical correlate of a memory. But the neurons grew and retained these spines better when the mice slept after learning the task. Neurons that fired during learning fired again during subsequent slow-wave sleep, allowing the mice to conserve the newly formed spines—and memories. Science , this issue p. 1173 ; see also p. 1087

In this paper, collaborative representation is proposed for anomaly detection in hyperspectral imagery. The algorithm is directly based on the concept that each pixel in background can be approximately represented by its spatial neighborhoods, while anomalies cannot. The representation is assumed to be the linear combination of neighboring pixels, and the collaboration of representation is reinforced by l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -norm minimization of the representation weight vector. To adjust the contribution of each neighboring pixel, a distance-weighted regularization matrix is included in the optimization problem, which has a simple and closed-form solution. By imposing the sum-to-one constraint to the weight vector, the stability of the solution can be enhanced. The major advantage of the proposed algorithm is the capability of adaptively modeling the background even when anomalous pixels are involved. A kernel extension of the proposed approach is also studied. Experimental results indicate that our proposed detector may outperform the traditional detection methods such as the classic Reed-Xiaoli (RX) algorithm, the kernel RX algorithm, and the state-of-the-art robust principal component analysis based and sparse-representation-based anomaly detectors, with low computational cost.

Efficacy indices do not contain the same information although they are all combinations of the same two quantities. Therefore, one should choose the proper index. Actually, none is entirely appropriate. Each more or less meets the specifications, depending on the underlying effect model for the therapy considered. However, one can say that the absolute benefit is more appropriate from the patient's point of view, the relative from the scientific point of view and the number of patients to treat from the policy maker's point of view. Nevertheless, this classification needs to be considered with caution. Finally, it emerges from the review that none is fully relevant to express the efficacy of a therapy, even in the most suitable condition, the acute illness.

MicroRNAs (miRNAs) are a large new class of small non-coding RNAs. To date, hundreds of microRNAs have been identified in plants. MicroRNAs play important roles in post-transcriptional gene regulation by targeting mRNAs for cleavage or repressing translation. To better understand microRNA function, we have used an oligonucleotide microarray to monitor rice (Oryza sativa) microRNA expression profile under drought stress. Two drought-induced microRNAs were identified. Furthermore, miR-169g was confirmed as the only member induced by drought among the miR-169 family and the induction of miR-169g was more prominent in roots than in shoots. Sequence analysis revealed occurrence of two proximate DREs (dehydration-responsive element) in the upstream of the MIR-169g, suggesting that miR-169g expression may be regulated directly by CBF/DREBs.

RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO). DeepCNF not only models complex sequence–structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels. Our experimental results show that, tested on CASP10, CASP11 and the other benchmarks, this server can obtain ∼84% Q3 accuracy for 3-state SS, ∼72% Q8 accuracy for 8-state SS, ∼66% Q3 accuracy for 3-state solvent accessibility, and ∼0.89 area under the ROC curve (AUC) for disorder prediction.

Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation. We demonstrate an independent and rapid evolution of the tea caffeine synthesis pathway relative to cacao and coffee. A comparative study among 25 Camellia species revealed that higher expression levels of most flavonoid- and caffeine- but not theanine-related genes contribute to the increased production of catechins and caffeine and thus enhance tea-processing suitability and tea quality. These novel findings pave the way for further metabolomic and functional genomic refinement of characteristic biosynthesis pathways and will help develop a more diversified set of tea flavors that would eventually satisfy and attract more tea drinkers worldwide.

Myeloperoxidase, secreted by activated phagocytes, produces the powerful cytotoxin hypochlorous acid from H2O2 and Cl-. We show that the enzyme can also employ H2O2 to oxidize L-tyrosine to tyrosyl radical, yielding the stable cross-linked product dityrosine. Dityrosine synthesis by the myeloperoxidase-H2O2 system did not require halide and was partially inhibited by Cl-. At physiological concentrations of Cl-, L-tyrosine, and other plasma amino acids, purified myeloperoxidase utilized 26% of the H2O2 in the reaction mixture to form dityrosine. Aminotriazole, cyanide, and azide inhibited the reaction. Phorbol ester-stimulated human neutrophils and monocyte-derived macrophages similarly generated dityrosine from L-tyrosine by a pathway inhibited by catalase, aminotriazole, and azide. The requirement for H2O2 and the inhibition by heme poisons suggest that activated phagocytes synthesize dityrosine by a peroxidative mechanism. These results indicate that L-tyrosine can compete effectively with Cl- as a substrate for myeloperoxidase and raise the possibility that formation of tyrosyl radical may play a role in the phagocyte inflammatory response. Because dityrosine is protease-resistant, stable to acid hydrolysis, and intensely fluorescent, its identification in tissues may pinpoint targets where phagocytes inflict oxidative damage in vivo.

We have observed that Au nanorods (NRs) have distinct effects on cell viability via killing cancer cells while posing negligible impact on normal cells and mesenchymal stem cells. Obvious differences in cellular uptake, intracellular trafficking, and susceptibility of lysosome to Au NRs by different types of cells resulted in selective accumulation of Au NRs in the mitochondria of cancer cells. Their long-term retention decreased mitochondrial membrane potential and increased reactive oxygen species level that enhances the likelihood of cell death. These findings thus provide guidance for the design of organelle-targeted nanomaterials in tumor therapy.

Background— Adult congenital heart disease (ACHD) patients have ongoing morbidity and reduced long-term survival. Recently, the importance of specialized follow-up at tertiary ACHD centers has been highlighted. We aimed to assess survival prospects and clarify causes of death in a large cohort of patients at a single, tertiary center. Methods and Results— We included 6969 adult patients (age 29.9±15.4 years) under follow-up at our institution between 1991 and 2013. Causes of death were ascertained from official death certificates. Survival was compared with the expected survival in the general age- and sex-matched population, and standardized mortality rates were calculated. Over a median follow-up time of 9.1 years (interquartile range, 5.2–14.5), 524 patients died. Leading causes of death were chronic heart failure (42%), pneumonia (10%), sudden-cardiac death (7%), cancer (6%), and hemorrhage (5%), whereas perioperative mortality was comparatively low. Isolated simple defects exhibited mortality rates similar to those in the general population, whereas patients with Eisenmenger syndrome, complex congenital heart disease, and Fontan physiology had much poorer long-term survival ( P &lt;0.0001 for all). The probability of cardiac death decreased with increasing patient’s age, whereas the proportion of patients dying from noncardiac causes, such as cancer, increased. Conclusions— ACHD patients continue to be afflicted by increased mortality in comparision with the general population as they grow older. Highest mortality rates were observed among patients with complex ACHD, Fontan physiology, and Eisenmenger syndrome. Our data provide an overview over causes of mortality and especially the spectrum of noncardiac causes of death in contemporary ACHD patients.

Rubidium (Rb) is explored as an alternative cation to use in a novel multication method with the formamidinium/methylammonium/cesium (Cs) system to obtain 1.73 eV bangap perovskite cells with negligible hysteresis and steady state efficiency as high as 17.4%. The study shows the beneficial effect of Rb in improving the crystallinity and suppressing defect migration in the perovskite material. The light stability of the cells examined under continuous illumination of 12 h is improved upon the addition of Cs and Rb. After several cycles of 12 h light–dark, the cell retains 90% of its initial efficiency. In parallel, sputtered transparent conducting oxide thin films are developed to be used as both rear and front transparent contacts on quartz substrate with less than 5% parasitic absorption of near infrared wavelengths. Using these developments, semi‐transparent perovskite cells are fabricated with steady state efficiency of up to 16.0% and excellent average transparency of ≈84% between 720 and 1100 nm. In a tandem configuration using a 23.9% silicon cell, 26.4% efficiency (10.4% from the silicon cell) in a mechanically stacked tandem configuration is demonstrated which is very close to the current record for a single junction silicon cell of 26.6%.

The reprogramming of parental methylomes is essential for embryonic development. In mammals, paternal 5-methylcytosines (5mCs) have been proposed to be actively converted to oxidized bases. These paternal oxidized bases and maternal 5mCs are believed to be passively diluted by cell divisions. By generating single-base resolution, allele-specific DNA methylomes from mouse gametes, early embryos, and primordial germ cell (PGC), as well as single-base-resolution maps of oxidized cytosine bases for early embryos, we report the existence of 5hmC and 5fC in both maternal and paternal genomes and find that 5mC or its oxidized derivatives, at the majority of demethylated CpGs, are converted to unmodified cytosines independent of passive dilution from gametes to four-cell embryos. Therefore, we conclude that paternal methylome and at least a significant proportion of maternal methylome go through active demethylation during embryonic development. Additionally, all the known imprinting control regions (ICRs) were classified into germ-line or somatic ICRs.

Microplastics are widely identified in aquatic environments, but their impacts on phytoplankton have not been extensively studied. Here, the responses of Chlorella pyrenoidosa under polystyrene (PS) microplastics exposure were studied across its whole growth period, with microplastic sizes of 0.1 and 1.0 μm and 3 concentration gradients each, which covered (10 and 50 mg/L) and exceeded (100 mg/L) its environmental concentrations, respectively. PS microplastics caused dose-dependent adverse effects on Chlorella pyrenoidosa growth from the lag to the earlier logarithmic phases, but exhibited slight difference in the maximal inhibition ratio (approximately 38%) with respect to the two microplastic sizes. In addition to the reduced photosynthetic activity of Chlorella pyrenoidosa, unclear pyrenoids, distorted thylakoids and damaged cell membrane were observed, attributing to the physical damage and oxidative stress caused by microplastics. However, from the end of the logarithmic to the stationary phase, Chlorella pyrenoidosa could reduce the adverse effects of microplastics jointly through cell wall thickening, algae homo-aggregation and algae-microplastics hetero-aggregation, hence triggering an increase of algal photosynthetic activity and its growth, and cell structures turned to normal. Our study confirmed that PS microplastics can impair but then enhance algae growth, which will be helpful in understanding the ecological risks of microplastics.

Sorting molecules with DNA robots Single-stranded DNA robots can move over the surface of a DNA origami sheet and sort molecular cargoes. Thubagere et al. developed a simple algorithm for recognizing two types of molecular cargoes and their drop-off destinations on the surface (see the Perspective by Reif). The DNA robot, which has three modular functional domains, repeatedly picks up the two types of molecules and then places them at their target destinations. No additional power is required because the DNA robot does this by random walking across the origami surface. Science , this issue p. eaan6558 ; see also p. 1095

Alternative polyadenylation (APA) is a pervasive mechanism in the regulation of most human genes, and its implication in diseases including cancer is only beginning to be appreciated. Since conventional APA profiling has not been widely adopted, global cancer APA studies are very limited. Here we develop a novel bioinformatics algorithm (DaPars) for the de novo identification of dynamic APAs from standard RNA-seq. When applied to 358 TCGA Pan-Cancer tumour/normal pairs across seven tumour types, DaPars reveals 1,346 genes with recurrent and tumour-specific APAs. Most APA genes (91%) have shorter 3′-untranslated regions (3′ UTRs) in tumours that can avoid microRNA-mediated repression, including glutaminase (GLS), a key metabolic enzyme for tumour proliferation. Interestingly, selected APA events add strong prognostic power beyond common clinical and molecular variables, suggesting their potential as novel prognostic biomarkers. Finally, our results implicate CstF64, an essential polyadenylation factor, as a master regulator of 3′-UTR shortening across multiple tumour types. Alternative polyadenylation (APA) has been implicated in diverse physiological and pathological conditions including cancer. The authors present a new algorithm, DaPars, for APA analysis using available RNA-seq data and suggest CstF64 as a master regulator of 3′-UTR shortening across multiple tumour types.

Angewandte Chemie International EditionVolume 52, Issue 31 p. 8151-8155 Communication Simple and Green Synthesis of Nitrogen-Doped Photoluminescent Carbonaceous Nanospheres for Bioimaging† Wei Li, Wei Li Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/ These authors contributed equally to this work.Search for more papers by this authorZehui Zhang, Zehui Zhang State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433 (P. R. China) These authors contributed equally to this work.Search for more papers by this authorBiao Kong, Biao Kong Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorShanshan Feng, Shanshan Feng Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorDr. Jinxiu Wang, Dr. Jinxiu Wang Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorDr. Lingzhi Wang, Dr. Lingzhi Wang Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorJianping Yang, Jianping Yang Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorDr. Fan Zhang, Dr. Fan Zhang Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorProf. Dr. Peiyi Wu, Corresponding Author Prof. Dr. Peiyi Wu [email protected] State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433 (P. R. China) Peiyi Wu, State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433 (P. R. China) Dongyuan Zhao, Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorProf. Dr. Dongyuan Zhao, Corresponding Author Prof. Dr. Dongyuan Zhao [email protected] Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/ Peiyi Wu, State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433 (P. R. China) Dongyuan Zhao, Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this author Wei Li, Wei Li Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/ These authors contributed equally to this work.Search for more papers by this authorZehui Zhang, Zehui Zhang State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433 (P. R. China) These authors contributed equally to this work.Search for more papers by this authorBiao Kong, Biao Kong Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorShanshan Feng, Shanshan Feng Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorDr. Jinxiu Wang, Dr. Jinxiu Wang Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorDr. Lingzhi Wang, Dr. Lingzhi Wang Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorJianping Yang, Jianping Yang Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorDr. Fan Zhang, Dr. Fan Zhang Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorProf. Dr. Peiyi Wu, Corresponding Author Prof. Dr. Peiyi Wu [email protected] State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433 (P. R. China) Peiyi Wu, State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433 (P. R. China) Dongyuan Zhao, Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this authorProf. Dr. Dongyuan Zhao, Corresponding Author Prof. Dr. Dongyuan Zhao [email protected] Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/ Peiyi Wu, State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433 (P. R. China) Dongyuan Zhao, Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, (P. R. China) http://www.mesogroup.fudan.edu.cn/Search for more papers by this author First published: 20 June 2013 https://doi.org/10.1002/anie.201303927Citations: 404 † This work was supported by the State Key Basic Research Program of the PRC (2012CB224805, 2013CB934104), and the NSF of China (21210004). Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Graphical Abstract From silk to spheres: A large-scale synthesis of water-soluble nitrogen-doped polymer-like carbonaceous nanospheres with a uniform size of ca. 70 nm, through a simple and green hydrothermal process employing cocoon silk in water, has been developed. The resultant nanospheres show excellent photoluminescent properties, exhibit low toxicity, and are biocompatible for in vivo imaging. References 1L. Dai, Angew. Chem. 2011, 123, 4840; Angew. Chem. Int. Ed. 2011, 50, 4744. 2M. Prato, J. Mater. Chem. 1997, 7, 1097. 3J. Liang, Y. Jiao, M. Jaroniec, S. Z. Qiao, Angew. Chem. 2012, 124, 11664; Angew. Chem. Int. Ed. 2012, 51, 11496. 4 4aW. Li, F. Zhang, Y. Q. Dou, Z. X. Wu, H. J. Liu, X. F. Qian, D. Gu, Y. Y. Xia, B. Tu, D. Y. Zhao, Adv. Energy Mater. 2011, 1, 382; 4bW. Li, D. Y. Zhao, Chem. Commun. 2013, 49, 943. 5 5aL. Cao, M. J. Meziani, S. Sahu, Y. P. Sun, Acc. Chem. Res. 2013, 46, 171; 5bS. N. Baker, G. A. Baker, Angew. Chem. 2010, 122, 6876; Angew. 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A nanotube material is obtained by the reaction of polycrystalline TiO2 with concentrated NaOH solution for 20 h at 110 °C. From the contents of Na, Ti and the structural water determined, it is concluded that the nanotube material is Na2Ti2O4(OH)2, rather than TiO2, TiOx or H2TiO3. After treating with an HCl solution of pH 1, nanotube Na2Ti2O4(OH)2 can be converted to nanotube H2Ti2O4(OH)2. The crystalline structure of such nanotube materials belongs to an orthorhombic crystalline system. TEM results indicate that nanotube Na2Ti2O4(OH)2 is formed in the reaction stage of TiO2 with concentrated NaOH solution. The formation process is discussed.

Diabetes mellitus (DM) is a primary risk factor for cardiovascular disease. Although recent studies have demonstrated an important role for extracellular matrix metalloproteinases (MMPs) in atherosclerosis, little is known about the effects of hyperglycemia on MMP regulation in vascular cells. Gelatin zymography and Western blot analysis revealed that the activity and expression of 92-kDa (MMP-9) gelatinase, but not of 72 kDa (MMP-2) gelatinase, were significantly increased in vascular tissue and plasma of two distinct rodent models of DM. Bovine aortic endothelial cells (BAECs) grown in culture did not express MMP-9 constitutively; however, chronic (2-week) incubation with high glucose medium induced MMP-9 promoter activity, mRNA and protein expression, and gelatinase activity in BAECs. On the other hand, high glucose culture did not change MMP-9 activity from vascular smooth muscle cells or macrophages. Electron paramagnetic resonance studies indicate that BAECs chronically grown in high glucose conditions produce 70% more ROS than do control cells. Enhanced MMP-9 activity was significantly reduced by treatment with the antioxidants polyethylene glycol-superoxide dismutase and N-acetyl-L-cysteine but not by inhibitors of protein kinase C. In conclusion, vascular MMP-9 activity is increased in DM, in part because of enhanced elaboration from vascular endothelial cells, and oxidative stress plays an important role. This novel mechanism of redox-sensitive MMP-9 expression by hyperglycemia may provide a rationale for antioxidant therapy to modulate diabetic vascular complications.

Cisplatin-based adjuvant chemotherapy is the standard of care for patients with resected stage II-IIIA non-small-cell lung cancer (NSCLC). RADIANT and SELECT trial data suggest patients with EGFR-mutant stage IB-IIIA resected NSCLC could benefit from adjuvant EGFR tyrosine kinase inhibitor treatment. We aimed to compare the efficacy of adjuvant gefitinib versus vinorelbine plus cisplatin in patients with completely resected EGFR-mutant stage II-IIIA (N1-N2) NSCLC.We did a randomised, open-label, phase 3 trial at 27 centres in China. We enrolled patients aged 18-75 years with completely resected (R0), stage II-IIIA (N1-N2), EGFR-mutant (exon 19 deletion or exon 21 Leu858Arg) NSCLC. Patients were stratified by N stage and EGFR mutation status and randomised (1:1) by Pocock and Simon minimisation with a random element to either gefitinib (250 mg once daily) for 24 months or intravenous vinorelbine (25 mg/m2 on days 1 and 8) plus intravenous cisplatin (75 mg/m2 on day 1) every 3 weeks for four cycles. The primary endpoint was disease-free survival in the intention-to-treat population, which comprised all randomised patients; the safety population included all randomised patients who received at least one dose of study medication. Enrolment to the study is closed but survival follow-up is ongoing. The study is registered with ClinicalTrials.gov, number NCT01405079.Between Sept 19, 2011, and April 24, 2014, 483 patients were screened and 222 patients were randomised, 111 to gefitinib and 111 to vinorelbine plus cisplatin. Median follow-up was 36·5 months (IQR 23·8-44·8). Median disease-free survival was significantly longer with gefitinib (28·7 months [95% CI 24·9-32·5]) than with vinorelbine plus cisplatin (18·0 months [13·6-22·3]; hazard ratio [HR] 0·60, 95% CI 0·42-0·87; p=0·0054). In the safety population, the most commonly reported grade 3 or worse adverse events in the gefitinib group (n=106) were raised alanine aminotransferase and asparate aminotransferase (two [2%] patients with each event vs none with vinorelbine plus cisplatin). In the vinorelbine plus cisplatin group (n=87), the most frequently reported grade 3 or worse adverse events were neutropenia (30 [34%] patients vs none with gefitinib), leucopenia (14 [16%] vs none), and vomiting (eight [9%] vs none). Serious adverse events were reported for seven (7%) patients who received gefitinib and 20 (23%) patients who received vinorelbine plus cisplatin. No interstitial lung disease was noted with gefitinib. No deaths were treatment related.Adjuvant gefitinib led to significantly longer disease-free survival compared with that for vinorelbine plus cisplatin in patients with completely resected stage II-IIIA (N1-N2) EGFR-mutant NSCLC. Based on the superior disease-free survival, reduced toxicity, and improved quality of life, adjuvant gefitinib could be a potential treatment option compared with adjuvant chemotherapy in these patients. However, the duration of benefit with gefitinib after 24 months might be limited and overall survival data are not yet mature.Guangdong Provincial Key Laboratory of Lung Cancer Translational Medicine; National Health and Family Planning Commission of People's Republic of China; Guangzhou Science and Technology Bureau; AstraZeneca China.

Unlike an intercalation cathode, which has an intrinsic host structure made of redox metal sites allowing the transport of Li+/e−, sulfur as a conversion cathode requires an additional host to store and immobilize the mobile redox centers, polysulfides. Metal–organic frameworks (MOFs) as a class of highly porous and well-defined crystalline materials are a promising platform to search for an effective host through rational design. With the appropriate selection of an electrolyte and a cutoff voltage range, sulfur stored in an appropriate MOF host can take advantage of both intercalation (fast and stable) and conversion (high energy density) cathodes. Herein, we describe a fast cathode with long cycle life based on sulfur and ZIF-8 nanocrystals. With 30 wt% sulfur loading in the electrode, it achieves remarkable discharge capacities of 1055 mA h g−1 (based on sulfur) at 0.1 C and 710 mA h g−1 at 1 C. The decay over 300 cycles at 0.5 C is 0.08% per cycle, prominent in long-cycle Li–S batteries. By comparing with another three distinct MOFs, MIL-53 (Al), NH2-MIL-53 (Al) and HKUST-1, as well as two sets of ZIF-8 with particle sizes in the micrometer range, it reveals that (i) the small particle size of the MOF host is appreciable to achieve a high capacity and (ii) small apertures, associated with functionalities in the open framework that have affinity with the polysulfide anions, can help achieve a stable cycling. We believe that the findings are general and applicable for the rational design of new hosts for sulfur in other porous material families to produce more effective and stable Li–S batteries.

Convolutional neural network (CNN) is of great interest in machine learning and has demonstrated excellent performance in hyperspectral image classification. In this paper, we propose a classification framework, called diverse region-based CNN, which can encode semantic context-aware representation to obtain promising features. With merging a diverse set of discriminative appearance factors, the resulting CNN-based representation exhibits spatial-spectral context sensitivity that is essential for accurate pixel classification. The proposed method exploiting diverse region-based inputs to learn contextual interactional features is expected to have more discriminative power. The joint representation containing rich spectral and spatial information is then fed to a fully connected network and the label of each pixel vector is predicted by a softmax layer. Experimental results with widely used hyperspectral image data sets demonstrate that the proposed method can surpass any other conventional deep learning-based classifiers and other state-of-the-art classifiers.

Hyperspectral imagery typically provides a wealth of information captured in a wide range of the electromagnetic spectrum for each pixel in the image; however, when used in statistical pattern-classification tasks, the resulting high-dimensional feature spaces often tend to result in ill-conditioned formulations. Popular dimensionality-reduction techniques such as principal component analysis, linear discriminant analysis, and their variants typically assume a Gaussian distribution. The quadratic maximum-likelihood classifier commonly employed for hyperspectral analysis also assumes single-Gaussian class-conditional distributions. Departing from this single-Gaussian assumption, a classification paradigm designed to exploit the rich statistical structure of the data is proposed. The proposed framework employs local Fisher's discriminant analysis to reduce the dimensionality of the data while preserving its multimodal structure, while a subsequent Gaussian mixture model or support vector machine provides effective classification of the reduced-dimension multimodal data. Experimental results on several different multiple-class hyperspectral-classification tasks demonstrate that the proposed approach significantly outperforms several traditional alternatives.

Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training.Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

Abstract Photocatalytic hydrogen production using semiconductors is identified as one of the most promising routes for sustainable energy; however, it is challenging to harvest the full solar spectrum in a particulate photocatalyst for high activity. Herein, a hierarchical hollow black TiO 2 /MoS 2 /CdS tandem heterojunction photocatalyst, which allows broad‐spectrum absorption, thus delivering enhanced hydrogen evolution performance is designed and synthesized. The MoS 2 nanosheets not only function as a cost‐effective cocatalyst but also act as a bridge to connect two light‐harvesting semiconductors into a tandem heterojunction where the CdS nanoparticles and black TiO 2 spheres absorb UV and visible light on both sides efficiently, coupling with the MoS 2 cocatalyst into a particulate photocatalyst system. Consequently, the photocatalytic hydrogen rate of the black TiO 2 /MoS 2 /CdS tandem heterojunction is as high as 179 µmol h −1 per 20 mg photocatalyst under visible‐light irradiation, which is almost 3 times higher than that of black TiO 2 /MoS 2 heterojunctions (57.2 µmol h −1 ). Most importantly, the stability of CdS nanoparticles in the black TiO 2 /MoS 2 /CdS tandem heterojunction is greatly improved compared to MoS 2 /CdS because of the formation of tandem heterojunctions and the strong UV‐absorbing effect of black TiO 2 . Such a tandem architectural design provides new ways for synthesizing particulate photocatalysts with high efficiencies.

The stacking fault energy (SFE) of paramagnetic FeCrCoNiMn high entropy alloy is investigated as a function of temperature via ab initio calculations. We divide the SFE into three major contributions: chemical, magnetic and strain parts. Structural energies, local magnetic moments and elastic moduli are used to estimate the effect of temperature on each term. The present results explain the recently reported twinning observed below room-temperature and predict the occurrence of the hexagonal phase at cryogenic conditions.