Matthew Anderson

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded.

Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.

The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the mutational signatures they harbour, including a deficiency in G:C > T:A base excision repair due to inactivation of MUTYH, which encodes a DNA glycosylase. Clinically sporadic PanNETs contain a larger-than-expected proportion of germline mutations, including previously unreported mutations in the DNA repair genes MUTYH, CHEK2 and BRCA2. Together with mutations in MEN1 and VHL, these mutations occur in 17% of patients. Somatic mutations, including point mutations and gene fusions, were commonly found in genes involved in four main pathways: chromatin remodelling, DNA damage repair, activation of mTOR signalling (including previously undescribed EWSR1 gene fusions), and telomere maintenance. In addition, our gene expression analyses identified a subgroup of tumours associated with hypoxia and HIF signalling. The genomes of 102 primary pancreatic neuroendocrine tumours have been sequenced, revealing mutations in genes with functions such as chromatin remodelling, DNA damage repair, mTOR activation and telomere maintenance, and a greater-than-expected contribution from germ line mutations. Pancreatic neuroendocrine tumours (PanNETs) are the second most common epithelial neoplasm of the pancreas. Aldo Scarpa, Sean Grimmond and colleagues report whole-genome sequencing of 102 primary PanNETs and present analysis of their mutational signatures as part of the International Cancer Genome Consortium. They find frequent mutations in genes with functions that include chromatin remodelling, DNA damage repair, activation of mTOR signalling, and telomere maintenance. They also identify mutational signatures, including one resulting from inactivation of the DNA repair gene MUTYH, and report a larger than expected germline contribution to PanNET development.

Post-traumatic osteoarthritis (PTOA) is a common consequence of traumatic joint injury, with 50% of anterior cruciate ligament (ACL) rupture patients developing PTOA within 10-20 years. Currently accepted mouse models of PTOA initiate symptoms using various methods, none of which faithfully mimic clinically-relevant injury conditions. In this study we characterize a novel non-invasive mouse model of PTOA that injures the ACL with a single load of tibial compression overload. We utilize this model to determine the time course of articular cartilage and subchondral bone changes following knee injury.Mice were euthanized 1, 3, 7, 14, 28, or 56 days after non-invasive knee injury. Knees were scanned using micro-computed tomography (μCT) in order to quantify subchondral trabecular bone, subchondral bone plate, and non-native bone formation (heterotopic ossification). Development of osteoarthritis (OA) was graded using the osteoarthritis research society international (OARSI) scale on histological sections of injured and uninjured knees.Following injury we observed a rapid loss of trabecular bone in injured knees compared to uninjured knees by 7 days post-injury, followed by a partial recovery of trabecular bone to a new steady state by 28 days post-injury. We also observed considerable non-native bone formation by 56 days post-injury. Grading of histological sections revealed deterioration of articular cartilage by 56 days post-injury, consistent with development of mild OA.This study establishes a novel mouse model of PTOA, and describes the time course of musculoskeletal changes following knee injury, helping to establish the window of opportunity for preventative treatment.

Pancreatic cancer is molecularly diverse, with few effective therapies. Increased mutation burden and defective DNA repair are associated with response to immune checkpoint inhibitors in several other cancer types. We interrogated 385 pancreatic cancer genomes to define hypermutation and its causes. Mutational signatures inferring defects in DNA repair were enriched in those with the highest mutation burdens. Mismatch repair deficiency was identified in 1% of tumors harboring different mechanisms of somatic inactivation of MLH1 and MSH2. Defining mutation load in individual pancreatic cancers and the optimal assay for patient selection may inform clinical trial design for immunotherapy in pancreatic cancer. Pancreatic cancer is molecularly diverse, with few effective therapies. Increased mutation burden and defective DNA repair are associated with response to immune checkpoint inhibitors in several other cancer types. We interrogated 385 pancreatic cancer genomes to define hypermutation and its causes. Mutational signatures inferring defects in DNA repair were enriched in those with the highest mutation burdens. Mismatch repair deficiency was identified in 1% of tumors harboring different mechanisms of somatic inactivation of MLH1 and MSH2. Defining mutation load in individual pancreatic cancers and the optimal assay for patient selection may inform clinical trial design for immunotherapy in pancreatic cancer. Pancreatic ductal adenocarcinoma has a 5-year survival of <5%, with therapies offering only incremental benefit,1Vogelzang N.J. et al.J Clin Oncol. 2012; 30: 88-109Crossref PubMed Scopus (85) Google Scholar potentially due to the diversity of its genomic landscape.2Bailey P. et al.Nature. 2016; 531: 47-52Crossref PubMed Scopus (1973) Google Scholar, 3Biankin A.V. et al.Nature. 2012; 491: 399-405Crossref PubMed Scopus (1379) Google Scholar, 4Waddell N. et al.Nature. 2015; 518: 495-501Crossref PubMed Scopus (1466) Google Scholar Recent reports link high mutation burden with response to immune checkpoint inhibitors in several cancer types.5Le D.T. et al.N Engl J Med. 2015; 372: 2509-2520Crossref PubMed Scopus (6099) Google Scholar Defining tumors that are hypermutated with an increased mutation burden and understanding the underlying mechanisms in pancreatic cancer has the potential to advance therapeutic development, particularly for immunotherapeutic strategies. Whole genome sequencing (WGS, n = 180) and whole exome sequencing (n = 205) of 385 unselected predominantly sporadic pancreatic ductal adenocarcinoma (Supplementary Table 1) defined a mean mutation load of 1.8 and 1.1 mutation per megabase (Mb), respectively (Supplementary Table 2). Outlier analysis identified 20 tumors with the highest mutation burden (5.2%, 15 WGS and 5 exome) (Table 1 and Supplementary Figure 1A), 5 of which were considered extreme outliers and classified as hypermutated as they contained ≥12 somatic mutations/Mb, the defined threshold for hypermutation in colorectal cancer.6Cancer Genome Atlas NetworkNature. 2012; 487: 330-337Crossref PubMed Scopus (5894) Google Scholar Immunohistochemistry for mismatch repair (MMR) proteins (MSH2, MSH6, MLH1, and PMS2) identified 4 MMR-deficient tumors, all of which were hypermutated (n = 180, Figure 1).Table 1Clinical and Histologic Features and Proposed Etiology for Highly Mutated Pancreatic Ductal Adenocarcinoma Tumors (n = 20)Sample IDPersonal and family history of malignancyHistologyMutation load, mutations/MbIHC resultMSIsensor scoreKRAS mutationPredominant mutation signature (mutations/Mb)SV subtype (no. of events)Proposed etiologyHypermutation (extreme outliers) ICGC_0076aSample sequenced by WGS, other samples by exome sequencing.NoneMixed signet ring, mucinous and papillary adenocarcinoma38.55Absent MLH1 and PMS228.3p.G12VMMR (18.3)Scattered (131)MMR deficiency: >280 kb somatic homozygous deletion over MSH2. ICGC_0297aSample sequenced by WGS, other samples by exome sequencing.NoneUndifferentiated adenocarcinoma60.62Absent MSH2 and MSH627.33WTMMR (33.4)Scattered (75)MMR deficiency: Somatic MLH1 promoter hypermethylation. ICGC_0548aSample sequenced by WGS, other samples by exome sequencing.NoneDuctal adenocarcinoma, moderately differentiated30.13Absent MSH2 and MSH617.47WTMMR (16.6)Stable (49)MMR deficiency: >27 kb somatic inversion rearrangement disrupting MSH2. ICGC_0328aSample sequenced by WGS, other samples by exome sequencing.NoneDuctal adenocarcinoma16.63Normal3.2p.G12DUnknown (11.9)Scattered (110)Cell line with signature: etiology unknown. ICGC_00901 FDR, father CRCDuctal adenocarcinoma, moderately differentiated12.9Absent MSH2 and MSH60.21p.G12CNANAMMR deficiency: somatic MSH2 splice site c.2006G>A.Highly mutated tumors ICGC_0054aSample sequenced by WGS, other samples by exome sequencing.NoneDuctal adenocarcinoma, poorly differentiated6.52Normal0.01p.G12VHR deficiency (1.3)Unstable (310)HR deficiency: no germline or somatic cause found. ICGC_0290aSample sequenced by WGS, other samples by exome sequencing.NoneDuctal adenocarcinoma, poorly differentiated6.54Not available0.07p.G12VHR deficiency (3.1)Unstable (558)HR deficiency: Germline BRCA2 mutation c.7180A>T, p.A2394*. Somatic CN-LOH. ICGC_0215aSample sequenced by WGS, other samples by exome sequencing.2 FDR lung cancer, 2 FDR prostate cancer. Previous CRC and melanomaDuctal adenocarcinoma, moderately differentiated6.27Normal0.01p.G12VHR deficiency (1.9)Scattered (111)HR deficiency: Germline ATM mutation c.7539_7540delAT, p.Y2514*. Somatic CN-LOH. ICGC_0324NoneDuctal adenocarcinoma, moderately differentiated6.24Normal0p.G12DNANAUndefined ICGC_0034aSample sequenced by WGS, other samples by exome sequencing.NoneDuctal adenocarcinoma, poorly differentiated6.09Normal4.02p.G12DHR deficiency (3.4)Unstable (366)HR deficiency: Germline BRCA2 mutation c.5237_5238insT, p.N1747*. Somatic CN-LOH. ICGC_0131aSample sequenced by WGS, other samples by exome sequencing.Lung cancer after PCDuctal adenocarcinoma, moderately differentiated5.63Normal0p.G12DT>G at TT sites (3.0)Focal (147)T>G at TT sites signature: etiology potentially associated with DNA oxidation ICGC_0006aSample sequenced by WGS, other samples by exome sequencing.1 FDR, father lung cancerAdenocarcinoma arising from IPMN, moderately differentiated5.29Normal0.01p.G12DHR deficiency (1.2)Unstable (211)HR deficiency: Somatic BRCA2 c.5351dupA, p.N1784KfsTer3. Somatic CN-LOH. ICGC_0321aSample sequenced by WGS, other samples by exome sequencing.2 FDR, mother and cousin breast cancerDuctal adenocarcinoma, poorly differentiated4.79Not available0p.G12DHR deficiency (2.1)Unstable (286)HR deficiency: Germline BRCA2 c.6699delT, p.F2234LfsTer7. Somatic CN loss- 1 copy. ICGC_0309aSample sequenced by WGS, other samples by exome sequencing.NoneAdenocarcinoma arising from IPMN, moderately differentiated4.74Normal0.03p.G12VT>G at TT sites (3.1)Unstable (232)T>G at TT sites signature: etiology potentially associated with DNA oxidation ICGC_0005aSample sequenced by WGS, other samples by exome sequencing.1 FDR, mother CRCDuctal adenocarcinoma, poorly differentiated4.72Not available1p.G12VHR deficiency (1.1)Focal (95)HR deficiency: No germline or somatic cause found. ICGC_0016aSample sequenced by WGS, other samples by exome sequencing.NoneDuctal adenocarcinoma, poorly differentiated4.61Normal3.03p.G12VHR deficiency (1.7)Unstable (447)HR deficiency: potentially linked to Somatic RPA1 c.273G>T, p.R91S ICGC_00461 FDR, brother PCDuctal adenocarcinoma, poorly differentiated4.3Normal0p.Q61HNANAUndefined GARV_0668aSample sequenced by WGS, other samples by exome sequencing.NoneDuctal adenocarcinoma, poorly differentiated4.3Not available2.19p.G12VHR deficiency (1.6)Unstable (464)HR deficiency: Germline BRCA2 c.7068_7069delTC, p.L2357VfsTer2. Somatic CN loss - 1 copy. ICGC_0291NoneDuctal adenocarcinoma, well differentiated3.84Not available0.03p.G12RNANAHR deficiency: Somatic BRCA2 c.7283T>A, p.L2428*. ICGC_0256NoneDuctal adenocarcinoma, poorly differentiated3.72Not available0.06p.G12DNANAUndefinedCRC, colorectal cancer; FDR, first-degree relative; IHC, immunohistochemistry; IPMN, intraductal papillary mucinous neoplasm; CN-LOH, copy neutral loss of heterozygosity; CN, copy number; PC, pancreatic cancer; NA, not applicable to exome data.a Sample sequenced by WGS, other samples by exome sequencing. Open table in a new tab CRC, colorectal cancer; FDR, first-degree relative; IHC, immunohistochemistry; IPMN, intraductal papillary mucinous neoplasm; CN-LOH, copy neutral loss of heterozygosity; CN, copy number; PC, pancreatic cancer; NA, not applicable to exome data. KRAS mutation status and histopathologic characteristics have been associated with MMR-deficient pancreatic tumors.7Goggins M. et al.Am J Pathol. 1998; 152: 1501-1507PubMed Google Scholar Of the 4 MMR-deficient tumors in our cohort, 2 were KRAS wild-type; 3 had undifferentiated to moderately differentiated histology and one had a signet-ring component. These features were not predictive of MMR deficiency in our cohort, as 11 additional non−MMR-deficient tumors had a signet-ring cell component or colloid morphology, and 131 of 347 assessable tumors had poorly or undifferentiated histology. Mutational signature analysis can detect MMR deficiency indirectly based on the pattern of somatic mutations.8Alexandrov L.B. et al.Nature. 2013; 500: 415-421Crossref PubMed Scopus (6213) Google Scholar An MMR-deficient signature dominated the MMR-deficient tumors (with WGS), and was minimal in MMR intact tumors (Supplementary Figure 1). In addition, microsatellite instability (MSI), a hallmark of MMR deficiency in colorectal cancer, was detected in all three MMR deficient tumors with WGS using MSIsensor9Niu B. Ye K. et al.Bioinformatics. 2014; 30: 1015-1016Crossref PubMed Scopus (294) Google Scholar (Supplementary Table 2). MSI was not identified for the fourth MMR deficient sample potentially due to the reduced number of microsatellite loci in exome data. The underlying causes of MMR deficiency in the 4 cases were private somatic events. For 2 cases, MSH2 was disrupted by different structural rearrangements, 1 case contained a missense MSH2 mutation and the last, methylation of the MLH1 promoter (Figure 1). The missense mutation caused an MSH2 splice acceptor site mutation that alters the same nucleotide results in a pathogenic skipping of exon 13 in germline studies.10Thompson B.A. et al.Nat Genet. 2014; 46: 107-115Crossref PubMed Scopus (346) Google Scholar Hypermethylation of the MLH1 promoter is the predominant mechanism of MSI in sporadic colon cancer.11Boland C.R. et al.Gastroenterology. 2010; 138: 2073-2087 e3Abstract Full Text Full Text PDF PubMed Scopus (1359) Google Scholar The remaining hypermutated tumor contained an intact MMR pathway, and was a cell line (ATCC, CRL-2551) with an unidentified mutational signature, therefore the high mutation burden in this sample may be the result of long-term cell culture. The 15 samples (11 WGS and 4 exome) identified in the outlier analysis with high mutation burden, but not hypermutated (∼4 to 12 mutations/Mb) contained no evidence of MMR deficiency. Mutational signature analysis of the WGS samples indicated homologous recombination (HR) repair deficiency as the most substantial (range, 1.0–3.4 mutations/Mb) contributor to the mutation burden for 8 WGS mutation load outlier tumors. In support of a HR defect4Waddell N. et al.Nature. 2015; 518: 495-501Crossref PubMed Scopus (1466) Google Scholar; 7 of these tumors contained high levels of genomic instability with >200 structural variants and mutations in genes involved in HR were present for 6 of 8 cases (Supplementary Table 2). In addition, 1 case that had undergone exome sequencing had a somatic BRCA2 nonsense mutation that likely contributed to HR deficiency in this case. A mutational signature associated with T>G mutations at TT sites previously described in other cancers, including esophageal cancer12Nones K. Waddell N. Wayte N. et al.Nat Commun. 2014; : 5Google Scholar was the major contributor (>3 mutations/Mb) in 2 samples. For these 2 and the remaining 4 cases, no potential causative event could be identified. Although germline defects in MMR genes are well reported in pancreatic cancer13Grant R.C. Selander I. et al.Gastroenterology. 2015; 148: 556-564Abstract Full Text Full Text PDF PubMed Scopus (211) Google Scholar in our cohort, they did not contribute to MMR deficiency even in those with familial pancreatic cancer or a personal or family history of Lynch-related tumors. A germline truncating variant was detected in PMS2 in 1 case, but did not have loss of the second allele, had normal immunohistochemistry staining and did not display a MMR mutational signature (Supplementary Table 2). MMR deficiency is important in the evolution in a small, but meaningful proportion of pancreatic cancers with a prevalence of 1% (4 of 385) in our cohort. This is consistent with recent studies using the Bethesda polymerase chain reaction panel,14Laghi L. et al.PLoS One. 2012; 7: e46002Crossref PubMed Scopus (55) Google Scholar and with previous estimates of MSI prevalence of 2%−3%.15Nakata B. et al.Clin Cancer Res. 2002; 8: 2536-2540PubMed Google Scholar However, in tumors with low epithelial content that underwent exome sequencing, the sensitivity of somatic mutation detection is reduced, which will affect mutation burden and signature analysis. While cognizant of small numbers, immunohistochemistry was the most accurate in defining MMR due to multiple genomic mechanisms of MMR gene inactivation. Multiple methods to define MMR deficiency may be required for clinical trials that aim to recruit MMR-deficient participants to assess the potential efficacy of checkpoint inhibitors or other therapies in pancreatic cancer. Homologous recombination-deficient tumors, and those with a novel signature seen in esophageal cancer had an increased mutation burden, and need further evaluation as potential patient selection markers for clinical trials of checkpoint inhibitor and other therapies that target tumors with a high mutation burden. The authors would like to thank Cathy Axford, Deborah Gwynne, Mary-Anne Brancato, Clare Watson, Michelle Thomas, Gerard Hammond, and Doug Stetner for central coordination of the Australian Pancreatic Cancer Genome Initiative, data management, and quality control; Mona Martyn-Smith, Lisa Braatvedt, Henry Tang, Virginia Papangelis, and Maria Beilin for biospecimen acquisition; and Sonia Grimaldi and Giada Bonizzato of the ARC-Net Biobank for biospecimen acquisition. For a full list of contributors see Australian Pancreatic Cancer Genome Initiative: http://www.pancreaticcancer.net.au/apgi/collaborators. The cohort consisted of 385 patients with histologically verified pancreatic exocrine carcinoma, prospectively recruited between 2006 and 2013 through the Australian Pancreatic Cancer Genome Initiative (www.pancreaticcancer.net.au) as part of the International Cancer Genome Consortium.1Hudson T.J. et al.Nature. 2010; 464: 993-998Crossref PubMed Scopus (1689) Google Scholar Ethical approval was granted at all treating institutions and individual patients provided informed consent upon entry to the study. The clinicopathologic information for the cohort is described in (Supplementary Table 1), and the global mutation profile has previously been reported for some of these tumors (Supplementary Table 2). Tumor and normal DNA were extracted after histologic review from fresh frozen tissue samples collected at the time of surgical resection or biopsy, as described previously.2Biankin A.V. et al.Nature. 2012; 491: 399-405Crossref PubMed Scopus (1513) Google Scholar Tumor cellularity was determined from single-nucleotide polymorphism array data using qpure.3Song S. et al.PLoS One. 2012; 7: e45835Crossref PubMed Scopus (85) Google Scholar Tumors with epithelial content ≥40% underwent WGS lower cellularity tumors underwent whole exome sequencing. DNA from patient-derived pancreas cell lines and matched normal was also extracted. Exome and WGS were performed using paired 100-bp reads on the Illumina HiSeq 2000, as described previously.2Biankin A.V. et al.Nature. 2012; 491: 399-405Crossref PubMed Scopus (1513) Google Scholar, 4Waddell N. et al.Nature. 2015; 518: 495-501Crossref PubMed Scopus (1686) Google Scholar Regions of germline and somatic copy number change were detected using Illumina SNP BeadChips with GAP.5Popova T. et al.Genome Biol. 2009; 10 (R128−R128)Crossref PubMed Scopus (151) Google Scholar Somatic structural variants were identified from WGS reads using the qSV tool.4Waddell N. et al.Nature. 2015; 518: 495-501Crossref PubMed Scopus (1686) Google Scholar, 6Patch A.M. et al.Nature. 2015; 521: 489-494Crossref PubMed Scopus (930) Google Scholar Single nucleotide variants were called using 2 variant callers: qSNP7Kassahn K.S. et al.PLoS One. 2013; 8: e74380Crossref PubMed Scopus (52) Google Scholar and GATK.8McKenna A. et al.Genome Res. 2010; 20: 1297-1303Crossref PubMed Scopus (14755) Google Scholar Mutations identified by both callers or, those that were unique to a caller but verified by an orthogonal sequencing approach, were considered high confidence and used in all subsequent analyses. Small indels (<200 bp) were identified using Pindel9Ye K. et al.Bioinformatics. 2009; 25: 2865-2871Crossref PubMed Scopus (1391) Google Scholar and each indel was visually inspected in the Integrative Genome Browser. The distribution of the total number of small somatic mutations (coding and noncoding single nucleotide and indel variants) identified per megabase for exome and WGS sequence data were analyzed separately. The group of samples with high mutation load, at the top of each distribution, were defined as the upper distribution outliers for mutations per megabase, that is, ≥75th centile + (1.5× interquartile range). The threshold for detecting outliers in the exome and WGS groups was 3.4 and 4.2 mutations/Mb, respectively. From within the highly mutated set of tumors, hypermutated samples were identified as those with a mutation rate exceeding the thresholds for extreme distribution outliers (≥75th centile + [5× interquartile range]) of 7.4 and 8.1 mutations/Mb for exome and WGS sequencing, respectively. MSIsensor was used to detect microsatellite instability by directly comparing microsatellite repeat lengths between paired normal and tumor sequencing data.10Niu B. et al.Bioinformatics. 2014; 30: 1015-1016Crossref PubMed Scopus (378) Google Scholar A MSIsensor score of >3.5% of somatic microsatellites with repeat length shifts was the detection threshold used to indicate microsatellite instability as published for endometrial cancer.10Niu B. et al.Bioinformatics. 2014; 30: 1015-1016Crossref PubMed Scopus (378) Google Scholar This correlated well with the 5 and 7 microsatellite panels recommended in the Bethesda guidelines.10Niu B. et al.Bioinformatics. 2014; 30: 1015-1016Crossref PubMed Scopus (378) Google Scholar, 11Umar A. et al.J Natl Cancer Inst. 2004; 96: 261-268Crossref PubMed Scopus (2461) Google Scholar Tissue microarrays were constructed using at least three 1-mm formalin-fixed, paraffin-embedded tumor cores. Immunohistochemistry for MSH6 and PMS2 proteins was performed on tissue microarray sections as a screen for MMR deficiency due to MMR proteins forming heterodimers with concordant mismatch repair loss (ie, loss of MLH1 and PMS2 or loss of MSH2 and MSH6).12Hall G. et al.Pathology. 2010; 42: 409-413Abstract Full Text PDF PubMed Scopus (98) Google Scholar Immunohistochemistry on full tumor sections for MSH2, MLH1, MSH6, and PMS2 was performed in those with abnormal staining in core sections. The immunohistochemistry was performed as described previously12Hall G. et al.Pathology. 2010; 42: 409-413Abstract Full Text PDF PubMed Scopus (98) Google Scholar and scored by a senior pathologist. Somatic mutational signatures were extracted from the whole genome sequenced samples using the framework described previously.13Alexandrov L.B. et al.Cell Rep. 2013; 3: 246-259Abstract Full Text Full Text PDF PubMed Scopus (734) Google Scholar High confidence somatic substitutions were classified by the substitution change and sequence context, that is, the type of immediately neighboring bases to the variant. The framework processes the counts of somatic mutations at each context within each sample using non-negative factorization to produce the different signature profiles that are present in the data. The profiles identified were matched against reported signatures from the Cancer of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk/cosmic/signatures). The major contributory signatures, defined as the mutational signature with the highest number of contributing somatic substitution variants, is reported for highly mutated whole genome samples. Bisulfite-converted whole-genome amplified DNA was hybridized to Infinium Human Methylation 450K Beadchips according to the manufacturers protocol (Illumina). Methylation arrays were performed on DNA from 174 pancreatic ductal adenocarcinoma samples, which were compared to DNA from 29 adjacent nonmalignant pancreata. A subset of the methylation data has been published previously.14Nones K. et al.Int J Cancer. 2014; 135: 1110-1118Crossref PubMed Scopus (156) Google Scholar We examined the data for evidence of tumor-specific hypermethylation of the promoter region of MLH1 and MSH2 genes. The methylation array data have been deposited into the International Cancer Genome Consortium data portal (dcc.icgc.org, project PACA-AU). Download .xlsx (.08 MB) Help with xlsx files Supplementary Tables 1 and 2

In animals with multiple-partner mating systems, the gametes of two or more males must compete to fertilize a given set of ova. Here we show that the volume of the midpiece in individual sperm is significantly greater in primate species in which the females mate with multiple partners, and in which males have larger testes in relation to their body weight, than in those species that mate with only one partner and have relatively small testes. Our results indicate that sexual selection by sperm competition has influenced the evolution of a specific component of male-gamete morphology, the volume of the sperm midpiece.

There is a pressing need for patient-derived cell models of brain diseases that are relevant and robust enough to produce the large quantities of cells required for molecular and functional analyses. We describe here a new cell model based on patient-derived cells from the human olfactory mucosa, the organ of smell, which regenerates throughout life from neural stem cells. Olfactory mucosa biopsies were obtained from healthy controls and patients with either schizophrenia, a neurodevelopmental psychiatric disorder, or Parkinson's disease, a neurodegenerative disease. Biopsies were dissociated and grown as neurospheres in defined medium. Neurosphere-derived cell lines were grown in serum-containing medium as adherent monolayers and stored frozen. By comparing 42 patient and control cell lines we demonstrated significant disease-specific alterations in gene expression, protein expression and cell function, including dysregulated neurodevelopmental pathways in schizophrenia and dysregulated mitochondrial function, oxidative stress and xenobiotic metabolism in Parkinson's disease. The study has identified new candidate genes and cell pathways for future investigation. Fibroblasts from schizophrenia patients did not show these differences. Olfactory neurosphere-derived cells have many advantages over embryonic stem cells and induced pluripotent stem cells as models for brain diseases. They do not require genetic reprogramming and they can be obtained from adults with complex genetic diseases. They will be useful for understanding disease aetiology, for diagnostics and for drug discovery.

Morphogenesis of mammalian facial processes requires coordination of cellular proliferation, migration, and apoptosis to develop intricate features. Cleft lip and/or palate (CL/P), the most frequent human craniofacial birth defect, can be caused by perturbation of any of these programs. Mutations of WNT, P63, and IRF6 yield CL/P in humans and mice; however, how these genes are regulated remains elusive. We generated mouse lines lacking Pbx genes in cephalic ectoderm and demonstrated that they exhibit fully penetrant CL/P and perturbed Wnt signaling. We also characterized a midfacial regulatory element that Pbx proteins bind to control the expression of Wnt9b-Wnt3, which in turn regulates p63. Altogether, we establish a Pbx-dependent Wnt-p63-Irf6 regulatory module in midfacial ectoderm that is conserved within mammals. Dysregulation of this network leads to localized suppression of midfacial apoptosis and CL/P. Ectopic Wnt ectodermal expression in Pbx mutants rescues the clefting, opening avenues for tissue repair.

Background:Operative treatment of mechanical ankle instability is indicated for patients with multiple sprains and continued episodes of instability. Open repair of the lateral ankle ligaments involves exposure of the attenuated ligaments and advancement back to their anatomic insertions on the fibula using bone tunnels or suture implants. Hypothesis:Open and arthroscopic fixation are equal in strength to failure for anatomic Broström repair. Methods:Seven matched pairs of human cadaveric ankle specimens were randomized into 2 groups of anatomic Broström repair: open or arthroscopic. The calcaneofibular ligament and anterior talofibular ligament were excised from their origin on the fibula. In the open repair group, 2 suture anchors were used to reattach the ligaments to their anatomic origins. In the arthroscopic repair group, identical suture anchors were used for repair via an arthroscopic technique. The ligaments were cyclically loaded 20 times and then tested to failure. Torque to failure, degrees to failure, initial stiffness, and working stiffness were measured. A matched-pair analysis was performed. Power analysis of 0.8 demonstrated that 7 pairs needed to show a difference of 30%, with a 15% standard error at a significance level of α = .05. Results:There was no difference in the degrees to failure, torque to failure, or stiffness for the repaired ligament complex. Nine of 14 specimens failed at the suture anchor. Conclusion:There is no statistical difference in strength or stiffness of a traditional open repair as compared with an arthroscopic anatomic repair of the lateral ligaments of the ankle. Clinical Relevance:An arthroscopic technique can be considered for lateral ligament stabilization in patients with mild to moderate mechanical instability.

Abstract Treatment options for patients with brain metastases ( BMs ) have limited efficacy and the mortality rate is virtually 100%. Targeted therapy is critically under‐utilized, and our understanding of mechanisms underpinning metastatic outgrowth in the brain is limited. To address these deficiencies, we investigated the genomic and transcriptomic landscapes of 36 BMs from breast, lung, melanoma and oesophageal cancers, using DNA copy‐number analysis and exome‐ and RNA ‐sequencing. The key findings were as follows. (a) Identification of novel candidates with possible roles in BM development, including the significantly mutated genes DSC2 , ST7 , PIK3R1 and SMC5 , and the DNA repair, ERBB – HER signalling, axon guidance and protein kinase‐A signalling pathways. (b) Mutational signature analysis was applied to successfully identify the primary cancer type for two BMs with unknown origins. (c) Actionable genomic alterations were identified in 31/36 BMs (86%); in one case we retrospectively identified ERBB2 amplification representing apparent HER2 status conversion, then confirmed progressive enrichment for HER2 ‐positivity across four consecutive metastatic deposits by IHC and SISH , resulting in the deployment of HER2 ‐targeted therapy for the patient. (d) In the ERBB / HER pathway, ERBB2 expression correlated with ERBB3 ( r 2 = 0.496; p &lt; 0.0001) and HER3 and HER4 were frequently activated in an independent cohort of 167 archival BM from seven primary cancer types: 57.6% and 52.6% of cases were phospho‐ HER3 Y1222 or phospho‐ HER4 Y1162 membrane‐positive, respectively. The HER3 ligands NRG1 / 2 were barely detectable by RNAseq , with NRG1 (8p12) genomic loss in 63.6% breast cancer‐ BMs , suggesting a microenvironmental source of ligand. In summary, this is the first study to characterize the genomic landscapes of BM . The data revealed novel candidates, potential clinical applications for genomic profiling of resectable BMs , and highlighted the possibility of therapeutically targeting HER3 , which is broadly over‐expressed and activated in BMs , independent of primary site and systemic therapy. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.

The mammalian lung forms its elaborate tree-like structure following a largely stereotypical branching sequence. While a number of genes have been identified to play essential roles in lung branching, what coordinates the choice between branch growth and new branch formation has not been elucidated. Here we show that loss of FGF-activated transcription factor genes, Etv4 and Etv5 (collectively Etv), led to prolonged branch tip growth and delayed new branch formation. Unexpectedly, this phenotype is more similar to mutants with increased rather than decreased FGF activity. Indeed, an increased Fgf10 expression is observed, and reducing Fgf10 dosage can attenuate the Etv mutant phenotype. Further evidence indicates that ETV inhibits Fgf10 via directly promoting Shh expression. SHH in turn inhibits local Fgf10 expression and redirects growth, thereby initiating new branches. Together, our findings establish ETV as a key node in the FGF-ETV-SHH inhibitory feedback loop that dictates branching periodicity.

Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.

Abstract Large and medium‐bodied rainforest canopy mammals are typically surveyed using line transects, but these are labour intensive and usually ignore nocturnal species. Camera traps have become the preferred tool for assessing terrestrial mammal communities, but have rarely been used for arboreal species. Here, we compare the efficiency of arboreal camera trapping with line transects for inventorying medium and large‐sized arboreal mammals, and assess the viability of using camera traps in trees to model habitat occupancy. We installed 42 camera traps, spaced 2 km apart, in the canopy of the Maijuna‐Kichwa Regional Conservation Area, Peru and walked 2014 km of diurnal line transects on 22 trails at the same site. We compared the efficiency of each method using species accumulation curves. We applied a multi‐species occupancy model, while examining the effect of camera height on detection probabilities, including the distance from a village and from a river as covariates to examine variability in habitat occupancy. In 3147 camera days, 18 species of arboreal medium and large‐sized mammals were detected by cameras, while 11 species were recorded on line transects. Ten of these species were detected by both methods. Diurnal species were detected more quickly and with less effort using arboreal camera trapping than using diurnal line transects at the same site, although some species were more easily detected during line transects. Habitat occupancy was positively correlated with distance from the village for two species, and negatively correlated with distance from the river for one. Detection probabilities increased modestly with camera height. Practical limitations of arboreal camera trapping include the requirement for specialized climbing techniques, as well as increased potential for false triggers, requiring extended processing time. Arboreal camera trapping is an efficient method for inventorying arboreal mammals and a viable option for studying their distribution relative to environmental or anthropogenic variables when abundance or density estimates are not required.

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.

This paper presents and discusses algorithms, hardware, and software architecture developed by the TEAM CoSTAR (Collaborative SubTerranean Autonomous Robots), competing in the DARPA Subterranean Challenge. Specifically, it presents the techniques utilized within the Tunnel (2019) and Urban (2020) competitions, where CoSTAR achieved 2nd and 1st place, respectively. We also discuss CoSTAR's demonstrations in Martian-analog surface and subsurface (lava tubes) exploration. The paper introduces our autonomy solution, referred to as NeBula (Networked Belief-aware Perceptual Autonomy). NeBula is an uncertainty-aware framework that aims at enabling resilient and modular autonomy solutions by performing reasoning and decision making in the belief space (space of probability distributions over the robot and world states). We discuss various components of the NeBula framework, including: (i) geometric and semantic environment mapping; (ii) a multi-modal positioning system; (iii) traversability analysis and local planning; (iv) global motion planning and exploration behavior; (i) risk-aware mission planning; (vi) networking and decentralized reasoning; and (vii) learning-enabled adaptation. We discuss the performance of NeBula on several robot types (e.g. wheeled, legged, flying), in various environments. We discuss the specific results and lessons learned from fielding this solution in the challenging courses of the DARPA Subterranean Challenge competition.

This study examines the question of whether multipartner matings by female primates, with resulting sperm competition among males, may have favored the evolution of biochemical mechanisms to enhance seminal coagulationand copulatory plug formation. Comparative ratings of seminal coagulation (using a four-point scale where 1 = no coagulation and 4 = copulatory plug formation) were obtained for 40 species representing 26 primate genera. Coagulation ratings were highest (mean = 3.64) in those genera where females commonly mate with multiple partners, and lowest (mean = 2.09) in genera where females are primarily monogamous or belong to polygynous (one male) units(p < 0.0001). This result remained significant (p < 0.001) after the use of comparative analysis of independent contrasts (CAIC) to control for possible phylogenetic biases in the data set. Results indicate that sexual selection has played an important role in the evolution of seminal coagulation, and copulatory plug function, in primates.

On a quantitative, whole-body basis, little is known about the amount of linoleate that is converted to arachidonate or the partitioning of linoleate and its longer-chain derivatives among lean and fat tissues. The aim of the present study was to examine linoleate balance and organ partitioning in rats consuming a low but adequate level of linoleate. Weanling male Sprague-Dawley rats were given free access to a semipurified diet containing 2.3% of energy as linoleate. Food intake, fecal output and body weight gain were measured for 26 d. Whole-body fatty acid balance analysis showed that 75.5% of the linoleate consumed disappeared (apparently by β-oxidation), 18.7% was accumulated as linoleate, 3.0% was converted to (n-6) longer-chain polyunsaturated fatty acids, and 1.2% was excreted in the feces. Visceral fat contained 64% of the accumulated linoleate, and 23% was in lean tissues. Comparable values for α-linolenate were as follows: disappearance (84.9%), accumulation (10.9%), excretion in the feces (2.2%), and conversion to (n-3) longer-chain polyunsaturated fatty acids (1.4%). Visceral fat contained 67% of the accumulated α-linolenate, and 23% was in lean tissues. Visceral fat also accumulated 26% of newly synthesized (n-6) longer-chain polyunsaturated fatty acids and 31% of the (n-3) longer-chain polyunsaturated fatty acids. Thus, only 6.5% of dietary linoleate consumed at a low but adequate level for rats appeared in lean tissues as linoleate or its fatty acid metabolites; the rest was β-oxidized or stored in fat, mostly in visceral fat. These results lead us to speculate whether losses through β-oxidation contribute to the recommended intake for linoleate in growing rats.

Sperm competition involves competition between the gametes of two or more males of a species for fertilization of a given set of ova. Sperm competition is widespread among mammals, as in many other groups of vertebrates. Effects of sexual selection, via sperm competition, upon the evolution of reproductive physiology and behavior are much better understood in invertebrates (and especially in insects) than is the case for mammals. However, if the reproductive organs of male mammals are viewed as an integrated system for production and delivery of spermatozoa (and accessory glandular secretions) to females, then it is logical to assume that sperm competition might influence the evolution of all parts of the system, as well as associated physiological mechanisms (e.g., testicular endocrinology) and behavior (e.g., copulatory patterns). Here we analyze and review relationships between mating systems, relative testes sizes and sperm morphology, phallic morphology, circulating testosterone levels and sexual behavior in male mammals.

Abstract Men and women at Northwest University (n = 631), Xi'an, China, were asked to rate the attractiveness of male or female figures manipulated to vary somatotype, waist‐to‐hip ratio (WHR), secondary sexual traits, and other features. In study 1, women rated the average masculine somatotype as most attractive, followed by the mesomorphic (muscular), ectomorphic (slim), and endomorphic (heavily built) somatotypes, in descending order of preference. In study 2, the amount and distribution of masculine trunk (chest and abdominal) hair were altered progressively in a series of front‐posed figures. Women rated figures with no or little trunk hair as most attractive. Study 3 assessed the attractiveness of front‐posed male figures which varied only in length of their nonerect penis. Numerical ratings for this trait were low, but moderate lengthening of the penis (22% or 33% above average) resulted in a significant increase in scores for attractiveness. In study 4, Chinese men rated the attractiveness of back‐posed female images varying in waist‐to‐hip ratio (WHR from 0.5–1.0). The 0.6 WHR figure was most preferred, followed by 0.7, while figures with higher ratios (0.9 or 1.0) were significantly less attractive. Study 5 rated the attractiveness of female skin color: men expressed a marked preference for images which were lighter in color, as compared to images of average or darker skin colors. These results, the first of their kind reported for a Chinese population, support the view that sexual selection has influenced the evolution of human physique and sexual attractiveness in men and women. Am. J. Hum. Biol. 19:88–95, 2007. © 2006 Wiley‐Liss, Inc.

Abstract Post‐traumatic osteoarthritis (PTOA) is a common long‐term consequence of joint injuries such as anterior cruciate ligament (ACL) rupture. In this study we used a tibial compression overload mouse model to compare knee injury induced at low speed (1 mm/s), which creates an avulsion fracture, to injury induced at high speed (500 mm/s), which induces midsubstance tear of the ACL. Mice were sacrificed at 0 days, 10 days, 12 weeks, or 16 weeks post‐injury, and joints were analyzed with micro‐computed tomography, whole joint histology, and biomechanical laxity testing. Knee injury with both injury modes caused considerable trabecular bone loss by 10 days post‐injury, with the Low Speed Injury group (avulsion) exhibiting a greater amount of bone loss than the High Speed Injury group (midsubstance tear). Immediately after injury, both injury modes resulted in greater than twofold increases in total AP joint laxity relative to control knees. By 12 and 16 weeks post‐injury, total AP laxity was restored to uninjured control values, possibly due to knee stabilization via osteophyte formation. This model presents an opportunity to explore fundamental questions regarding the role of bone turnover in PTOA, and the findings of this study support a biomechanical mechanism of osteophyte formation following injury. © 2013 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 32:79–88, 2014.

Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising from PCR, sequencing errors or mis-mapping. Tumor cellularity or purity, sub-clonality and copy number changes also confound the identification of true somatic events against a background of germline variants. We have developed a heuristic strategy and software (http://www.qcmg.org/bioinformatics/qsnp/) for somatic mutation calling in samples with low tumor content and we show the superior sensitivity and precision of our approach using a previously sequenced cell line, a series of tumor/normal admixtures, and 3,253 putative somatic SNVs verified on an orthogonal platform.

Abstract Fracture healing involves rapid stem and progenitor cell migration, homing, and differentiation. SDF‐1 (CXCL12) is considered a master regulator of CXCR4‐positive stem and progenitor cell trafficking to sites of ischemic (hypoxic) injury and regulates their subsequent differentiation into mature reparative cells. In this study, we investigated the role of SDF‐1/CXCR4 signaling in fracture healing where vascular disruption results in hypoxia and SDF‐1 expression. Mice were injected with AMD3100, a CXCR4 antagonist, or vehicle twice daily until euthanasia with the intent to impair stem cell homing to the fracture site and/or their differentiation. Fracture healing was evaluated using micro‐computed tomography, histology, quantitative PCR, and mechanical testing. AMD3100 administration resulted in a significantly reduced hyaline cartilage volume (day 14), callus volume (day 42) and mineralized bone volume (day 42) and reduced expression of genes associated with endochondral ossification including collagen Type 1 alpha 1, collagen Type 2 alpha 1, vascular endothelial growth factor, Annexin A5, nitric oxide synthase 2, and mechanistic target of rapamycin. Our data suggest that the SDF‐1/CXCR4 signaling plays a central role in bone healing possibly by regulating the recruitment and/or differentiation of stem and progenitor cells. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:1853–1859, 2012

Previous studies in animal models of osteoarthritis suggest that alendronate (ALN) has antiresorptive and chondroprotective effects, and can reduce osteophyte formation. However, these studies used non-physiologic injury methods, and did not investigate early time points during which bone is rapidly remodeled prior to cartilage degeneration. The current study utilized a non-invasive model of knee injury in mice to investigate the effect of ALN treatment on subchondral bone changes, articular cartilage degeneration, and osteophyte formation following injury.Non-invasive knee injury via tibial compression overload or sham injury was performed on a total of 90 mice. Mice were treated with twice weekly subcutaneous injections of low-dose ALN (40 μg/kg/dose), high-dose ALN (1,000 μg/kg/dose), or vehicle, starting immediately after injury until sacrifice at 7, 14 or 56 days. Trabecular bone of the femoral epiphysis, subchondral cortical bone, and osteophyte volume were quantified using micro-computed tomography (μCT). Whole-joint histology was performed at all time points to analyze articular cartilage and joint degeneration. Blood was collected at sacrifice, and serum was analyzed for biomarkers of bone formation and resorption.μCT analysis revealed significant loss of trabecular bone from the femoral epiphysis 7 and 14 days post-injury, which was effectively prevented by high-dose ALN treatment. High-dose ALN treatment was also able to reduce subchondral bone thickening 56 days post-injury, and was able to partially preserve articular cartilage 14 days post-injury. However, ALN treatment was not able to reduce osteophyte formation at 56 days post-injury, nor was it able to prevent articular cartilage and joint degeneration at this time point. Analysis of serum biomarkers revealed an increase in bone resorption at 7 and 14 days post-injury, with no change in bone formation at any time points.High-dose ALN treatment was able to prevent early trabecular bone loss and cartilage degeneration following non-invasive knee injury, but was not able to mitigate long-term joint degeneration. These data contribute to understanding the effect of bisphosphonates on the development of osteoarthritis, and may support the use of anti-resorptive drugs to prevent joint degeneration following injury, although further investigation is warranted.

The alignment of the lower extremity has important implications in the development of knee arthritis. The effect of incremental rotations of the limb on common parameters of alignment has not been studied. The purpose of the study was to (1) determine the standardized neutral position measurements of alignment and (2) determine the effect of rotation on commonly used measurements of alignment.Eighty-seven full length CT angiography studies (49 males and 38 females, average age 66 years old) were included. Three-dimensional models were created using a rendering software program and placed on a virtual plane. An image of the extremity was obtained. Thirty scans were randomly selected, and those models were rotated in 3° intervals around the longitudinal axis and additional images were obtained.In the neutral position, the mechanical lateral distal femoral articular angle (mLDFA) was 85.6 ± 2.3°, medial proximal tibial angle (MPTA) was 86.1 ± 2.8°, and mechanical tibiofemoral angle (mTFA) was -0.7 ± 3.1°. Females had a more valgus alignment with a mTFA of 0.5 ± 2.9° while males had a more varus alignment with a mTFA of -1.7 ± 2.9°. The anatomic tibiofemoral angle (aTFA) was 4.8 ± 2.6°, the anatomic lateral distal femoral angle (aLDFA) measured 80.2 ± 2.2°, and the anatomical-mechanical angle (AMA) was 5.4 ± 0.7°. The prevalence of constitutional varus was 18%. The effect of rotation on the rotated scans led to statistically significant differences relative to the 0° measurement for all measurements. These effects may be small, and their clinical importance is unknown.This study provides new information on standardized measures of lower extremity alignment and the relationship between discreet axial rotations of the entire lower extremity and these parameters.

Abstract Sperm competition occurs when the gametes of two, or more, males compete for opportunities to fertilize a given set of ova. This study examined whether mammalian sperm morphology could be affected by sexual selection. Comparisons were made of linear and volumetric measurements of the sperm head, midpiece and flagellum for 123 species representing 71 genera of mammals having either single partner mating systems or multiple partner mating systems. Sperm midpiece volume was found to be significantly larger in those species were females mate with more than one male during a single peri‐ovulatory period. A positive correlation was also found between relative testes sizes and sperm midpiece volumes, while no relationship was found with any other sperm measure. These results indicate that, within mammals, the evolution of sperm midpiece volume has been affected by selection pressures resulting from sperm competition. The significance of these findings may relate to the density of mitochondria within the sperm midpiece. The mitochondria provide the energy required for sperm motility, in the absence of glycolytic support. A higher mitochondrial loading may therefore be associated with enhanced sperm motility.

The study of Parkinson's disease (PD), like other complex neurodegenerative disorders, is limited by access to brain tissue from patients with a confirmed diagnosis. Alternatively the study of peripheral tissues may offer some insight into the molecular basis of disease susceptibility and progression, but this approach still relies on brain tissue to benchmark relevant molecular changes against. Several studies have reported whole-genome expression profiling in post-mortem brain but reported concordance between these analyses is lacking. Here we apply a standardised pathway analysis to seven independent case-control studies, and demonstrate increased concordance between data sets. Moreover data convergence increased when the analysis was limited to the five substantia nigra (SN) data sets; this highlighted the down regulation of dopamine receptor signaling and insulin-like growth factor 1 (IGF1) signaling pathways. We also show that case-control comparisons of affected post mortem brain tissue are more likely to reflect terminal cytoarchitectural differences rather than primary pathogenic mechanisms. The implementation of a correction factor for dopaminergic neuronal loss predictably resulted in the loss of significance of the dopamine signaling pathway while axon guidance pathways increased in significance. Interestingly the IGF1 signaling pathway was also over-represented when data from non-SN areas, unaffected or only terminally affected in PD, were considered. Our findings suggest that there is greater concordance in PD whole-genome expression profiling when standardised pathway membership rather than ranked gene list is used for comparison.

This study assesses the information search and evaluation behavior of professional and non-professional financial analysts. These groups were analyzed because they are demonstrably interested in financial analysis. The study compares problem-solving behavior during the analysis of an initial public offering of an equity security, using a process tracing technique. General results of the study suggest that professionals tend to treat data in different ways to non-professionals. Principal differences include strategy selection, weights attached to data and final conclusions. However, professionals also seem to use different data than that generally proposed in fundamental analysis texts.

During vertebrate axis extension, adjacent tissue layers undergo profound morphological changes: within the neuroepithelium, neural tube closure and neural crest formation are occurring, while within the paraxial mesoderm somites are segmenting from the presomitic mesoderm (PSM). Little is known about the signals between these tissues that regulate their coordinated morphogenesis. Here, we analyze the posterior axis truncation of mouse Fgf3 null homozygotes and demonstrate that the earliest role of PSM-derived FGF3 is to regulate BMP signals in the adjacent neuroepithelium. FGF3 loss causes elevated BMP signals leading to increased neuroepithelium proliferation, delay in neural tube closure and premature neural crest specification. We demonstrate that elevated BMP4 depletes PSM progenitors in vitro, phenocopying the Fgf3 mutant, suggesting that excessive BMP signals cause the Fgf3 axis defect. To test this in vivo we increased BMP signaling in Fgf3 mutants by removing one copy of Noggin, which encodes a BMP antagonist. In such mutants, all parameters of the Fgf3 phenotype were exacerbated: neural tube closure delay, premature neural crest specification, and premature axis termination. Conversely, genetically decreasing BMP signaling in Fgf3 mutants, via loss of BMP receptor activity, alleviates morphological defects. Aberrant apoptosis is observed in the Fgf3 mutant tailbud. However, we demonstrate that cell death does not cause the Fgf3 phenotype: blocking apoptosis via deletion of pro-apoptotic genes surprisingly increases all Fgf3 defects including causing spina bifida. We demonstrate that this counterintuitive consequence of blocking apoptosis is caused by the increased survival of BMP-producing cells in the neuroepithelium. Thus, we show that FGF3 in the caudal vertebrate embryo regulates BMP signaling in the neuroepithelium, which in turn regulates neural tube closure, neural crest specification and axis termination. Uncovering this FGF3-BMP signaling axis is a major advance toward understanding how these tissue layers interact during axis extension with important implications in human disease.

Embryonic morphogenesis of a complex organism requires proper regulation of patterning and directional growth. Planar cell polarity (PCP) signaling is emerging as a crucial evolutionarily conserved mechanism whereby directional information is conveyed. PCP is thought to be established by global cues, and recent studies have revealed an instructive role of a Wnt signaling gradient in epithelial tissues of both invertebrates and vertebrates. However, it remains unclear whether Wnt/PCP signaling is regulated in a coordinated manner with embryonic patterning during morphogenesis. Here, in mouse developing limbs, we find that apical ectoderm ridge-derived Fgfs required for limb patterning regulate PCP along the proximal-distal axis in a Wnt5a-dependent manner. We demonstrate with genetic evidence that the Wnt5a gradient acts as a global cue that is instructive in establishing PCP in the limb mesenchyme, and that Wnt5a also plays a permissive role to allow Fgf signaling to orient PCP. Our results indicate that limb morphogenesis is regulated by coordination of directional growth and patterning through integration of Wnt5a and Fgf signaling.

The positional information theory proposes that a coordinate system provides information to embryonic cells about their position and orientation along a patterning axis. Cells interpret this information to produce the appropriate pattern. During development, morphogens and interpreter transcription factors provide this information. We report a gradient of Meis homeodomain transcription factors along the mouse limb bud proximo-distal (PD) axis antiparallel to and shaped by the inhibitory action of distal fibroblast growth factor (FGF). Elimination of Meis results in premature limb distalization and HoxA expression, proximalization of PD segmental borders, and phocomelia. Our results show that Meis transcription factors interpret FGF signaling to convey positional information along the limb bud PD axis. These findings establish a new model for the generation of PD identities in the vertebrate limb and provide a molecular basis for the interpretation of FGF signal gradients during axial patterning.

During vertebrate development, the presomitic mesoderm (PSM) periodically segments into somites, which will form the segmented vertebral column and associated muscle, connective tissue, and dermis. The periodicity of somitogenesis is regulated by a segmentation clock of oscillating Notch activity. Here, we examined mouse mutants lacking only Fgf4 or Fgf8 , which we previously demonstrated act redundantly to prevent PSM differentiation. Fgf8 is not required for somitogenesis, but Fgf4 mutants display a range of vertebral defects. We analyzed Fgf4 mutants by quantifying mRNAs fluorescently labeled by hybridization chain reaction within Imaris-based volumetric tissue subsets. These data indicate that FGF4 maintains Hes7 levels and normal oscillatory patterns. To support our hypothesis that FGF4 regulates somitogenesis through Hes7 , we demonstrate genetic synergy between Hes7 and Fgf4 , but not with Fgf8 . Our data indicate that Fgf4 is potentially important in a spectrum of human Segmentation Defects of the Vertebrae caused by defective Notch oscillations.

The heart develops in a synchronized sequence of proliferation and differentiation of cardiac progenitor cells (CPCs) from two anatomically distinct pools of cells, the first heart field (FHF) and second heart field (SHF). Congenital heart defects arise upon dysregulation of these processes, many of which are restricted to derivatives of the FHF or SHF. Of the conserved set of signaling pathways that regulate development, the Wnt signaling pathway has long been known for its importance in SHF development. The source of such Wnts has remained elusive, though it has been postulated that these Wnts are secreted from ectodermal or endodermal sources. The central question remains unanswered: Where do these Wnts come from? Here, we show that CPCs autoregulate SHF development via Wnt through genetic manipulation of a key Wnt export protein (Wls), scRNA-seq analysis of CPCs, and use of our precardiac organoid system. Through this, we identify dysregulated developmental trajectories of anterior SHF cell fate, leading to a striking single ventricle phenotype in knockout embryos. We then applied our findings to our precardiac organoid model and found that Wnt2 is sufficient to restore SHF cell fate in our model of disrupted endogenous Wnt signaling. In this study, we provide a basis for SHF cell fate decision-proliferation vs. differentiation-autoregulated by CPCs through Wnt.

Aortic arch malformations are common congenital disorders that are frequently of unknown etiology. To gain insight into the factors that guide branchial aortic arch development, we examined the process by which these vessels assemble in wild type zebrafish embryos and in kurzschlusstr12 (kus tr12) mutants. In wild type embryos, each branchial aortic arch first appears as an island of angioblasts in the lateral pharyngeal mesoderm, then elaborates by angiogenesis to connect to the lateral dorsal aorta and ventral aorta. In kustr12 mutants, angioblast formation and initial sprouting are normal, but aortic arches 5 and 6 fail to form a lumenized connection to the lateral dorsal aorta. Blood enters these blind-ending vessels from the ventral aorta, distending the arteries and precipitating fusion with an adjacent vein. This arteriovenous malformation (AVM), which shunts nearly all blood directly back to the heart, is not exclusively genetically programmed, as its formation correlates with blood flow and aortic arch enlargement. By positional cloning, we have identified a nonsense mutation in unc45a in kus tr12 mutants. Our results are the first to ascribe a role for Unc45a, a putative myosin chaperone, in vertebrate development, and identify a novel mechanism by which an AVM can form.

The study of axis extension and somitogenesis has been greatly advanced through the use of genetic tools such as the TCre mouse line. In this line, Cre is controlled by a fragment of the T (Brachyury) promoter that is active in progenitor cells that reside within the primitive streak and tail bud and which give rise to lineages emerging from these tissues as the embryonic axis extends. However, because TCre-mediated recombination occurs early in development, gene inactivation can result in an axis truncation that precludes the study of gene function in later or more posterior tissues. To address this limitation, we have generated an inducible TCre transgenic mouse line, called TCreERT2, that provides temporal control, through tamoxifen administration, in all cells emerging from the primitive streak or tail bud throughout development. TCreERT2 activity is mostly silent in the absence of tamoxifen and, in its presence, results in near complete recombination of emerging mesoderm from E7.5 through E13.5. We demonstrate the utility of the TCreERT2 line for determining rate of posterior axis extension and somite formation, thus providing the first in vivo tool for such measurements. To test the usefulness of TCreERT2 for genetic manipulation, we demonstrate that an early deletion of ß-Catenin via TCreERT2 induction phenocopies the TCre-mediated deletion of ß-Catenin defect, whereas a later induction bypasses this early phenotype and produces a similar defect in more caudal tissues. TCreERT2 provides a useful and novel tool for the control of gene expression of emerging embryonic lineages throughout development.

Joint injuries initiate a surge of inflammatory cytokines and proteases that contribute to cartilage and subchondral bone degeneration. Detecting these early processes in animal models of post-traumatic osteoarthritis (PTOA) typically involves ex vivo analysis of blood serum or synovial fluid biomarkers, or histological analysis of the joint. In this study, we used in vivo fluorescence reflectance imaging (FRI) to quantify protease, matrix metalloproteinase (MMP), and Cathepsin K activity in mice following anterior cruciate ligament (ACL) rupture. We hypothesized that these processes would be elevated at early time points following joint injury, but would return to control levels at later time points.Mice were injured via tibial compression overload, and FRI was performed at time points from 1 to 56 days after injury using commercially available activatable fluorescent tracers to quantify protease, MMP, and cathepsin K activity in injured vs uninjured knees. PTOA was assessed at 56 days post-injury using micro-computed tomography and whole-joint histology.Protease activity, MMP activity, and cathepsin K activity were all significantly increased in injured knees relative to uninjured knees at all time points, peaking at 1-7 days post-injury, then decreasing at later time points while still remaining elevated relative to controls.This study establishes FRI as a reliable method for in vivo quantification of early biological processes in a translatable mouse model of PTOA, and provides crucial information about the time course of inflammation and biological activity following joint injury. These data may inform future studies aimed at targeting these early processes to inhibit PTOA development.

ABSTRACT Osteophytes are a typical radiographic finding during osteoarthritis (OA). Osteophytes are thought to form in response to joint instability; however, the time course of osteophyte formation and joint stabilization following joint injury is not well understood. In this study, we investigated the time course of osteophyte formation and joint function following non‐invasive knee injury in mice. We hypothesized that initial joint instability following knee injury would initiate osteophyte formation, which would in turn restabilize the joint and reduce range of motion (ROM). Mice were subjected to non‐invasive anterior cruciate ligament (ACL) rupture. Anterior–posterior (AP) joint laxity, ROM, and chondro/osteophyte formation were measured immediately after injury, and 2, 4, 6, and 8 weeks post‐injury. Chondrophyte areas at each time point were measured with histology, while mineralized osteophyte volume was determined using micro‐computed tomography. Immediately after ACL rupture, AP joint laxity was increased twofold, while ROM was increased 11.7%. Chondrophytes appeared by 2 weeks post‐injury, corresponding with a decrease in AP joint laxity and ROM. By 8 weeks post‐injury, considerable osteophyte formation was observed around the joint, AP joint laxity returned to control levels, and joint ROM decreased to 61% of control values. These data support a role for chondro/osteophytes in joint restabilization after injury, and provide crucial insight into the time course and pathology of joint degeneration during OA development in the mouse. Statement of Clinical Significance: Results from this study increase understanding of conditions leading to osteophyte formation.© 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:466–473, 2017.

Development of osteoarthritis commonly involves degeneration of epiphyseal trabecular bone. In previous studies, we observed 30-44% loss of epiphyseal trabecular bone (BV/TV) from the distal femur within 1 week following non-invasive knee injury in mice. Mechanical unloading (disuse) may contribute to this bone loss; however, it is unclear to what extent the injured limb is unloaded following injury, and whether disuse can fully account for the observed magnitude of bone loss. In this study, we investigated the contribution of mechanical unloading to trabecular bone changes observed following non-invasive knee injury in mice (female C57BL/6N). We investigated changes in gait during treadmill walking, and changes in voluntary activity level using Open Field analysis at 4, 14, 28, and 42 days post-injury. We also quantified epiphyseal trabecular bone using μCT and weighed lower-limb muscles to quantify atrophy following knee injury in both ground control and hindlimb unloaded (HLU) mice. Gait analysis revealed a slightly altered stride pattern in the injured limb, with a decreased stance phase and increased swing phase. However, Open Field analysis revealed no differences in voluntary movement between injured and sham mice at any time point. Both knee injury and HLU resulted in comparable magnitudes of trabecular bone loss; however, HLU resulted in considerably more muscle loss than knee injury, suggesting another mechanism contributing to bone loss following injury. Altogether, these data suggest that mechanical unloading likely contributes to trabecular bone loss following non-invasive knee injury, but the magnitude of this bone loss cannot be fully explained by disuse. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1680-1687, 2016.

Highly efficient forward and reverse on-DNA amide couplings were developed exploiting hydrophobic linkers in combination with the micelle forming surfactant TPGS-750M. The method is highly effective for a wide range of substrates in the synthesis of DNA-encoded libraries.

We compare the behavior of laboratory markets populated by experienced commodity and stock traders with the behavior of markets populated by MBA student traders. Unlike previous research, subject experience is a treatment variable in our experiment. Trading experience is found to be an important determinant of how well market outcomes approximate equilibrium predictions. Markets with student traders exhibit biases consistent with the prior literature; bias levels in markets with experienced traders are substantially reduced and trend toward zero. These market level results are confirmed with individual level tests. However, we cannot unambiguously determine whether the market outcomes with experienced traders are better organized using Bayes′ rule or by a heuristic-base rate neglect.

Abstract Two central concerns for elephant husbandry and management are whether zoological enclosures are appropriately sized and the degree to which naturalistic exercise and activity are observed in such enclosures. In order to address these issues, accurate data on the daily walking distance of elephants both in situ and ex situ are necessary. We used an accelerometer, a pedometer that measures step count and activity level, to estimate walking distance in African elephants ( Loxodonta africana ) at the San Diego Zoo's Wild Animal Park. The accelerometer was worn simultaneously with a GPS unit that recorded actual walking distance. Estimates of walking distance were extrapolated from the accelerometer and compared with actual distances determined by GPS data. The accelerometer was found to overestimate step count, and subsequently walking distance, by including false counts of steps. Extrapolating walking distance based upon stride length measurements did not match actual GPS walking distance. However, activity level output from the accelerometer significantly correlated with actual GPS walking distance. In addition, we report that the rate of movement is comparable to that reported in other zoological settings. We provide a linear regression equation that can be utilized by other institutions to estimate daily walking distance of elephants in their collection who are outfitted with accelerometers. Zoo Biol 30:579–591, 2011. © 2010 Wiley Periodicals, Inc.

During vertebrate embryogenesis the interdigital mesenchyme is removed by programmed cell death (PCD), except in species with webbed limbs. Although bone morphogenetic proteins (BMPs) have long been known to be players in this process, it is unclear if they play a direct role in the interdigital mesenchyme or if they only act indirectly, by affecting fibroblast growth factor (FGF) signaling. A series of genetic studies have shown that BMPs act indirectly by regulating the withdrawal of FGF activity from the apical ectodermal ridge (AER); this FGF activity acts as a cell survival factor for the underlying mesenchyme. Other studies using exogenous factors to inhibit BMP activity in explanted mouse limbs suggest that BMPs do not act directly in the mesenchyme. To address the question of whether BMPs act directly, we used an interdigit-specific Cre line to inactivate several genes that encode components of the BMP signaling pathway, without perturbing the normal downregulation of AER-FGF activity. Of three Bmps expressed in the interdigital mesenchyme, Bmp7 is necessary for PCD, but Bmp2 and Bmp4 both have redundant roles, with Bmp2 being the more prominent player. Removing BMP signals to the interdigit by deleting the receptor gene, Bmpr1a, causes a loss of PCD and syndactyly, thereby unequivocally proving that BMPs are direct triggers of PCD in this tissue. We present a model in which two events must occur for normal interdigital PCD: the presence of a BMP death trigger and the absence of an FGF survival activity. We demonstrate that neither event is required for formation of the interdigital vasculature, which is necessary for PCD. However, both events converge on the production of reactive oxygen species that activate PCD.

Lead halide perovskites have a rich landscape of structural and optical properties, which can be explored and possibly controlled by applying high pressure. Despite several reports on high-pressure studies of CsPbBr3 nanocrystals (NCs), there have so far been no studies under pressure that incorporate planar defects. CsPbBr3 NCs with Ruddlesden–Popper (RP) faults, formed via post-synthetic fusion growth, are significantly larger in size than as-synthesized NCs and display exceptional emission stability. Here, we compare synchrotron-based high-pressure X-ray diffraction and photoluminescence (PL) properties of CsPbBr3 (without RP) and RP-CsPbBr3 (with RP) and resolve their crystal structure under pressure for the first time. CsPbBr3 undergoes a phase transition from the orthorhombic Pnma phase at ambient pressure to the cubic Pm3̅m phase at 1.7 GPa, and RP-CsPbBr3 transforms from Pnma to the monoclinic P21/m phase at 0.74 GPa in addition to several isostructural transitions. Density-functional calculations predict a narrowing of the band gap with pressure, concomitant with the PL energies. The RP-CsPbBr3 NCs exhibit enhanced PL intensity at 1 GPa and show band gap opening at high pressures. This study opens new strategies for not only tuning just the structural properties but also tuning planar defects in alkali halide lead crystals for improved optical properties.

Abstract The host microbiome in the gut and tumors have been shown to affect tumor growth and therapeutic response in cancer. Furthermore, the presence of specific fungal taxa are associated with tumor hypoxia, tumor progression, therapeutic response, and clinical outcomes in colorectal cancer (CRC). Preliminary data from our group found that the presence of Candida species increased tumor hypoxia and decreased overall survival in CRC. However, whether intratumoral Candida drive, support, or simply inhabit tumors with poor prognoses remains unclear. Here, we investigate a casual role for Candida albicans in tumor progression and therapy response using a syngeneic mouse model of microsatellite-instability high (MSI-H) colorectal cancer. We subcutaneously implanted MC38 colorectal cancer cells into C57BL/6 mice and then orally gavaged these mice with C. albicans, Saccharomyces cerevisiae, or PBS. The site of tumor formation was locally irradiated once (7.5 Gy), and growth of the tumor was measured over time. Differences in tumor volume were assessed by longitudinal mixed-effect models. Tumor sections were stained for fungi using calcofluor white (CFW) and underwent bulk RNA sequencing to detect differential gene expression, which were interpreted using gene set enrichment analysis (GSEA). Mice gavaged with C. albicans showed decreased response to radiation compared to mice gavaged with either S. cerevisiae (p&amp;lt;0.05) or PBS (p&amp;lt;0.001). Additionally, hyphae were observed in murine tumors gavaged with C. albicans, suggesting translocation of gavaged C. albicans from the gut to tumors. Further, tumors from mice gavaged with C. albicans displayed unique gene expression profiles, including decreased interferon alpha and IL-6 and STAT3 signaling, decreased oxidative phosphorylation, and decreased apoptosis-related gene expression. Here, we show that C. albicans may confer resistance to radiation therapy and affects immune and cancer cell activity in the MC38 (MSI-H) syngeneic in vivo model of colorectal cancer. Further, we show that hyphal fungi can be visualized in heterotopic murine tumors from our C. albicans gavage condition. These data establish that fungi can translocate from the gut to distal tumor sites, and that upon translocation, changes in gene expression and therapy response are observed. Future directions will explore the mechanism by which these effects occur and whether these findings can be leveraged to improve radiotherapy outcomes. Citation Format: Dennis J. Grencewicz, Alexander Loncar, Rebecca Hoyd, Aaditya Pallerla, Nyelia Williams, Martin Benej, McKenzie Kreamer, Yogita Mehra, Shiva Jahanbakhshi, Matthew Anderson, Nicholas Denko, Daniel Spakowicz. Gavage with Candida albicans leads to fungal colonization of colorectal tumors and decreased response to radiotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1282.

Abstract Oviduct length was measured in 48 species representing 33 genera of mammals in order to examine possible relationships between female morphology and the occurrence of sperm competition due to matings with multiple males. Multiple regression analyses revealed that residuals of oviduct length were positively correlated both with residuals of testes weight and with sperm midpiece volume in the genera and species studied. These correlations remained significant after application of comparative analysis of independent contrasts to control for possible phylogenetic biases in the data set. These results indicate that sexual selection (relating to sperm competition and cryptic female choice) has influenced co‐evolution of oviduct length, testes size and sperm morphology in mammals.

DNA-encoded libraries (DELs) have become a leading technology for hit identification in drug discovery projects as large, diverse libraries can be generated. DELs are commonly synthesised via split-and-pool methodology; thus, chemical transformations utilised must be highly efficient, proceeding with high conversions. Reactions performed in DEL synthesis also require a broad substrate scope to produce diverse, drug-like libraries. Many pharmaceutical compounds incorporate multiple C-N bonds, over a quarter of which are synthesised via reductive aminations. However, few on-DNA reductive amination procedures have been developed. Herein is reported the application of the micelle-forming surfactant, TPGS-750-M, to the on-DNA reductive amination of DNA-conjugated amines, yielding highly efficient conversions with a broad range of aldehydes, including medicinally relevant heterocyclic and aliphatic substrates. The procedure is compatible with DNA amplification and sequencing, demonstrating its applicability to DEL synthesis.

Background: There is a known shortage of nursing faculty in academia. Understanding factors influencing the shortage will help to develop strategies to reduce it. Purpose: The purpose was to identify the underlying factors influencing the decisions of current and former nursing faculty to leave or consider leaving their teaching roles. Methods: A cross-sectional state-level survey was distributed to licensed registered nurses and advanced practice registered nurses. The survey covered demographics, employment status, compensation, tenure, mentorship experiences, and significant factors affecting their decision-making. Results: Of 496 nursing faculty responses (221 current, 275 former), low compensation, unrealistic workload, retirement, lack of appreciation, and personal/family issues were noted as significant reasons for leaving or considering departure. Conclusions: The study gives voice to various factors influencing nursing faculty’s intention to leave and emphasizes the need to address issues of compensation, workload, and mentorship to mitigate faculty shortages.

Ovarian cancers (OVCAs) and endometrial cancers (EMCAs) with CCNE1-amplification are often resistant to standard of care treatment and represent an unmet clinical need. Previously, synthetic-lethal screening identified loss of the CDK1 regulator, PKMYT1, as synthetically lethal with CCNE1-amplification. We hypothesized that CCNE1-amplification associated replication stress will be more effectively targeted by combining the PKMYT1 inhibitor, lunresertib (RP-6306), with the ATR inhibitor, camonsertib (RP-3500/RG6526). Low dose combination RP-6306 with RP-3500 synergistically increased cytotoxicity more in CCNE1 amplified compared to non-amplified cells. Combination treatment produced durable antitumor activity and increased survival in CCNE1 amplified patient-derived and cell line-derived xenografts. Mechanistically, low doses of RP-6306 with RP-3500 increase CDK1 activation more so than monotherapy, triggering rapid and robust induction of premature mitosis, DNA damage and apoptosis in a CCNE1-dependent manner. These findings suggest that targeting CDK1 activity by combining RP-6306 with RP-3500 is a novel therapeutic approach to treat CCNE1-amplifed OVCAs and EMCAs.

The aim of this study is to gauge the current social climate in neurosurgical residency training and attitudes regarding sexual orientation and gender identity.We conducted a cross-sectional study through a 35-question questionnaire distributed to roughly 1700 residents at all U.S. neurosurgical residency programs.A total of 107 responses were obtained. Seventeen residents (16%) identified as being an LGBTQ+ individual. The majority (76%) of LGBTQ+ residents were concerned about how their sexual orientation would be perceived while applying to programs, and 47% endorsed purposefully concealing sexual orientation at work for fear of rejection or reprisal. More than half (56%) of those surveyed have witnessed homophobic/transphobic remarks by patients. While at work, 29% of LGBTQ+ individuals stated they are uncomfortable being open with their sexual orientation, and 3 LGBTQ+ individuals admitted being the target of direct homophobic/transphobic comments.This is the first study to our knowledge that has been conducted assessing the presence, perception, and treatment of LGBTQ+ trainees in neurosurgical residency. Our study outlines the challenges LGBTQ+ individuals face when applying to neurosurgical programs, which involves the perception of their sexual orientation, their witnessed instances of homophobic and transphobic comments by coworkers and patients, and their hesitation with discussing their social lives compared with their non-LGBTQ+ peers at work for fear of judgment or reprisal. Ongoing research is needed to address these issues to obtain workplace respect and fairness in this population and thus create an accepting atmosphere and achieve social justice in neurosurgery training.

The current experiment investigated ontogenetic forgetting on a novel object-recognition task similar to that of Besheer and Bevins. 18-day-old pups (n = 49) and adult (n = 29) rats were tested at two retention intervals (1 min. or 120 min.). By employing exclusion criteria which demanded minimum amounts of object exploration at training and test, the performance of 18-day-old pups but not that of adults was significantly impaired at 120 min. relative to 1 min. Analysis indicated that the ontogeny of the learning and memory measured in novel object recognition follows a developmental trend similar to that of other forms of learning, with older animals remembering more and thus performing better than younger animals. Unfortunately, given the extreme variability inherent to the task and large N necessary to achieve significance, the use of this task in studies of learning, memory, and development is discouraged.

Abstract Sperm competition occurs when the gametes of or more males compete for opportunities to fertilize a given set of ova. Previous studies have demonstrated that certain morphological characteristics are affected by sperm competition intensity (e.g. relative testes size and sperm midpiece volume). This study examined whether aspects of sperm energetics may also be affected by sexual selection. We compared the membrane potential of mitochondria in live sperm between H. sapiens (single partner mating system) and P. troglodytes (multiple partner mating system). Flow cytometry of sperm stained with the carbocyanine fluorescent dye JC‐1 (an assay for mitochondrial membrane potential) revealed marked differences in red fluorescence intensity. P. troglodytes sperm showed significantly higher mitochondrial membrane potential. Mitochondria provide a substantial part of the energy required for sperm motility. A higher mitochondrial loading may therefore be associated with enhanced sperm motility and/or longevity. Additionally, examination of JC‐1 red fluorescence levels before and after in vitro capacitation revealed further differences. Whereas chimpanzee sperm showed maintenance of membrane potential after capacitation (in some cases even an increase), sperm from humans consistently showed reduction in membrane potential. These results indicate that the sperm of human beings and chimpanzees exhibit marked differences in mitochondrial function, which are affected by selection pressures relating to sperm competition and that these pressures differ significantly between humans and chimpanzees. Am J Phys Anthropol 2007. © 2007 Wiley‐Liss, Inc.

A series of observational studies of captive Caribbean flamingos Phoenicopterus ruber were conducted to determine why flamingos rest on one leg. While frequently asked by the general public, this basic question has remained unanswered by the scientific community. Here we suggest that the latency of flamingos to initiate forward locomotion following resting on one leg is significantly longer than following resting on two, discounting the possibility that unipedal resting reduces muscle fatigue or enhances predatory escape. Additionally, we demonstrate that flamingos do not display lateral preferences at the individual or group levels when resting on one leg, with each bird dividing its resting time across both legs. We show that while flamingos prefer resting on one leg to two regardless of location, the percentage of birds resting on one leg is significantly higher among birds standing in the water than among those on land. Finally, we demonstrate a negative relationship between temperature and the percentage of observed birds resting on one leg, such that resting on one leg decreases as temperature rises. Results strongly suggest that unipedal resting aids flamingos in thermoregulation.

When flamingos rest, they typically lay their heads along their backs. In order to achieve this positioning they curve their necks to either the right or left of their midline. Previously we have shown both individual and flock-level laterality of preferred neck-resting direction, with most birds preferring to rest their necks to their right (Anderson, Williams, & O'Brien, 2009). As laterality has been shown to play a role in social cohesion (e.g., Rogers & Workman, 1989) and aggression (e.g., Vallortigara, Cozzutti, Tommasi, & Rogers, 2001), here we attempted to determine whether a flamingo's preferred neck-resting direction could be used to predict involvement in aggressive encounters. Results replicated the earlier flock-level preference for neck resting towards the right, and indicated that those flamingos preferring the left were more likely to be involved in aggressive encounters.

The use of tracking devices (e.g., VHF radio collars, GPS collars, ear transmitters) enables researchers to assess activity budgets, species-specific movement patterns, effects of environmental enrichment, and exercise levels in zoo animals. The fundamental assumption in these studies of tagged animals is that attachable tracking devices have negligible effects on the animals’ behavior. The present study examined solitary and social behavior rates, as well as overall activity budgets, in eight African elephants living at the San Diego Zoo Safari Park, Escondido, CA, USA. Each elephant was trained over several months to wear leather collars affixed with GPS units encased in watertight plastic containers. Behavioral data collected while the GPS collars were worn (16 daylight hours, 16 night hours) were compared to behavioral data when the GPS collars were not worn (16 daylight hours, 16 night hours) throughout June and July 2010. No significant differences (P < 0.05) in behavior rates or average percent of observation time the subjects were recorded in particular states were found. During the morning hours, while the collars were both worn and not worn, feeding was the most common behavior state (M = 44.7 ± 3.8%, M = 49.3 ± 15.3%), followed by resting (M = 35.5 ± 10%, M = 37.3 ± 12%) and walking (M = 10 ± 3.1%, M = 8.7 ± 1.9%). During the evening hours, feeding remained the most common behavior state for both worn and not worn conditions (M = 66.1 ± 12.3%, M = 63.3 ± 13.7%), followed by resting (M = 17.6 ± 7.7%, M = 19.4 ± 9.5%), and sleeping (M = 8.1 ± 8.9%, M = 7.8 ± 8.1%). This distribution of daily behavior state is similar to previous activity budgets examined in other zoo elephant herds. These results suggest that, with adequate training, GPS collars may have minimal impact on the behavior of zoo elephants.

Nature 521, 489–494 (2015); doi: 10.1038/nature14410 In this Article, the affiliations of authors Michael Quinn and Orla McNally should read “22Department of Obstetrics and Gynaecology, The University of Melbourne, and The Royal Women’s Hospital, Parkville, Victoria 3052, Australia”. Their affiliations have been corrected in the HTML and PDF versions online.

Berlyne [Berlyne, D.E., 1950. Novelty and curiosity as determinants of exploratory behaviour. Brit. J. Psychol. 41, 68–80] first illustrated that rats prefer to explore novel objects over ones with which they have had previous experience. Recently, variants on this novel object recognition (NOR) task have become widely popular and have been employed in numerous neuroscience and behavioral pharmacological studies investigating memory processes. Given this popularity, a thorough understanding of the various behavioral processes involved in novelty reaction and preference is essential. The current study compared the effects of spaced and massed initial stimulus exposures upon later object exploration and novel stimulus preference in Long-Evans rats. Results illustrated that a distributed initial stimulus familiarization procedure promoted greater novel object preference than did a massed procedure, and suggest that the novel object recognition task is sensitive to spacing effects in a similar fashion to more traditional learning paradigms. The mechanisms underlying such spacing effects are briefly discussed.

Objectives: To develop and validate a translatable and reproducible rodent critical-sized defect (CSD) model and to determine the optimal dose of recombinant human bone morphogenetic protein (BMP)-7 required to consistently heal the CSD in the new model. Methods: Rats with 6-mm CSDs stabilized with a commercial radiolucent plate and screws with angular stability were randomly assigned to 4 treatment groups with varied doses of recombinant human BMP-7 (25, 50, 75, and 100 μg) on absorbable collagen sponge and a single control group (absorbable collagen sponge alone). Bone formation was evaluated by radiographs, micro-computed tomography, histology, and biomechanics. Results: All the rats treated with 100 μg of BMP-7 with CSDs were united by 4 weeks and all 75- and 50-μg-group rats united by 6 weeks. None of the animals in the 25-μg BMP-7 group or the control group were healed at the time of killing. Bone volume, bone mineral density, the ratio of bone volume to total volume, stiffness, and ultimate load to failure were maximal in the 50-μg group. Total callus volume progressively increased with increasing BMP dose. Histologic analysis demonstrated increased callus width with increasing BMP-7 doses above 50 μg, but the bone seemed structurally abnormal. Conclusions: There was a 100% union rate in the 50-, 75-, and 100-μg BMP-7–treated groups. None of the control or 25-μg-dose rats united. The biomechanical data demonstrated that 50 μg of BMP-7 produced the highest mechanical strength in the bone regenerate. These data also suggest that administration of BMP-7 above 50 μg does not improve bone regeneration and actually seems to produce lower quality bone with diminished biomechanical properties.

Little information is available on the functional activity of leukocytes after arthroplasty or the expansion of populations with immune suppressive properties during the acute post-operative period. Synovial fluid and matched pre- and post-surgical blood samples were collected from total hip and knee arthroplasty patients (THA and TKA, respectively) to examine the impact of surgery on peripheral blood leukocyte frequency, bactericidal activity, and inflammatory mediator expression. For spinal surgeries, inflammatory mediator production by peripheral blood mononuclear cells (PBMCs) pre- and post-surgery was examined. An expansion of immune suppressive granulocytic myeloid-derived suppressor cells (G-MDSCs) was observed following arthroplasty, which correlated with significantly increased serum interleukin-10 (IL-10) levels. Analysis of synovial fluid from THA and TKAs revealed reduced granulocyte colony-stimulating factor (G-CSF) and soluble CD40 ligand (sCD40L) and increased interleukin-6 (IL-6), monocyte chemoattractant protein 2 (CCL2) and Fms-like tyrosine kinase 3 ligand (Flt-3L) compared to pre- and post-surgical serum. For the spinal surgery cohort, stimulation of PBMCs isolated post-surgery with bacterial antigens produced significantly less pro-inflammatory (IL-1α, IL-1β, interleukin-1 receptor antagonist (IL-1RA), IL-12p40, growth-related oncogene-α/GRO-α (CXCL1) and 6Ckine (CCL21)) and more anti-inflammatory/tissue repair mediators (IL-10, G-CSF and granulocyte-macrophage colony-stimulating factor (GM-CSF)) compared to PBMCs recovered before surgery. The observed bias towards systemic anti-inflammatory changes without concomitant increases in pro-inflammatory responses may influence susceptibility to infection following orthopaedic surgery in the context of underlying co-morbidities or risk factors.

The effects of age on the forgetting of stimulus attributes in a differential fear-conditioning paradigm were examined with 18- and 70-day-old rats tested in either the original conditions or shifted stimulating conditions at one of three retention intervals (1, 48, and 120 h). Adults displayed significant shifts at each retention interval, with those tested in the original context displaying greater fear than those tested in the shifted conditions. By contrast, by 48 h the 18-day-olds had forgotten the specific attributes of the training situation and began treating the two stimulating conditions as functionally equivalent (Experiment 1). In Experiment 2, we tracked the ontogenetic emergence of adult-like memory for stimulus attributes and found a dramatic increase in memory capability by 25 days of age. Experiment 3 illustrated that the forgotten memory attributes of infants may be retrieved by administering a 90-sec cuing treatment 10 min prior to the 48-h test Implications for the phenomenon of infantile amnesia are discussed.

Striking secondary traits, such as brightly colored sexual skin, capes of hair, beards, and other facial adornments occur in adult males of many anthropoid primate species. This review focuses upon the role of selection in the evolution of these traits. A quantitative approach is used to measure sexually dimorphic characters and to compare their development in the monogamous, polygynous, and multimale-multifemale mating systems of monkeys, apes, and human beings.

When resting, flamingos often lay their heads along their backs. While in this position they must curve their necks to either the right or left of their midline. Observations of captive Caribbean flamingos at the Philadelphia Zoo (Philadelphia, PA, USA) were conducted in order to determine if individual birds would display consistent preferences in neck-resting position over multiple observations. While individual birds were shown to vary greatly in regards to the strength and direction of their preferences, a significant flock-level preference towards neck resting to the right was obtained. Analysis of individual flamingos revealed that 5 out of 17 birds displayed preferences that significantly differed from chance, with each of these birds preferring to rest their necks to the right. From the present data we can conclude that flamingos display behavioural laterality of neck-resting position at both the level of the group and that of the individual.

The present study sought to determine the effects of decreased peripheral sensory nerve function on skeletal development and bone metabolism in mice.C57BL/6 neonatal mice were treated with capsaicin to induce peripheral sensory nerve degeneration, and compared to vehicle-treated controls at 4, 8 and 12 weeks of age. Changes in bone structure were assessed using micro-computed tomography, mechanical properties and fracture resistance were assessed using three-point bending of radii, and bone turnover was assessed using dynamic histomorphometry and serum biomarkers.Capsaicin treatment resulted in small but significant decreases in bone structure, particularly affecting trabecular bone. Capsaicin-treated mice exhibited lower trabecular thickness at the femoral metaphysis and L5 vertebral body compared with vehicle-treated mice. However, capsaicin- and vehicle-treated mice had similar mechanical properties and bone turnover rates.Neonatal capsaicin treatment affected trabecular bone during development; however these small changes may not be meaningful with respect to bone strength under normal loading conditions. It is possible that capsaicin-sensitive neurons may be more important for bone under stress conditions such as increased mechanical loading or injury. Future studies will investigate this potential role of peripheral sensory nerves in bone adaptation.

Primates are frequently hunted in Amazonia. Assessing the sustainability of hunting is essential to conservation planning. The most-used sustainability model, the 'Production Model', and more recent spatial models, rely on basic reproductive parameters for accuracy. These parameters are often crudely estimated. To date, parameters used for the Amazon's most-hunted primate, the woolly monkey (Lagothrix spp.), come from captive populations in the 1960s, when captive births were rare. Furthermore, woolly monkeys have since been split into five species. We provide reproductive parameters calculated by examining the reproductive organs of female Poeppig's woolly monkeys (Lagothrix poeppigii), collected by hunters as part of their normal subsistence activity. Production was 0.48-0.54 young per female per year, and an interbirth interval of 22.3 to 25.2 months, similar to parameters from captive populations. However, breeding was seasonal, which imposes limits on the maximum reproductive rate attainable. We recommend the use of spatial models over the Production Model, since they are less sensitive to error in estimated reproductive rates. Further refinements to reproductive parameters are needed for most primate taxa. Methods like ours verify the suitability of captive reproductive rates for sustainability analysis and population modelling for populations under differing conditions of hunting pressure and seasonality. Without such research, population modelling is based largely on guesswork.

Caribbean flamingo social structure, how pair bonds affect the structure of the flock, and how social stress affects health measured by heterophil to lymphocyte ratios (H/L) were investigated at the Philadelphia Zoo. It was hypothesized that a hierarchy may become apparent by analyzing agonistic interactions and that paired individuals would share similar places within the hierarchy. Furthermore, it was hypothesized that a negative relationship between H/L ratio and dominance would exist. Forty observations were conducted and in 70% of interactions instigating bird(s) won the encounter, suggesting either some advantage for instigating birds or a prior expectation of an encounter's outcome based upon an understanding of the flock's hierarchy. The flock possessed a semi-linear hierarchy (in terms of wins/losses) and birds with higher pair-bond strengths maintained dominant positions, suggesting that pair-bonding may help individuals become more successful in agonistic encounters. Birds who won more often had higher lymphocytes percentages and analyses suggested a trend indicating dominant birds may be less stressed. A semi-linear hierarchy was also found in terms of initiation/being targeted, and a bird's rank on the dominance (wins/losses) and initiate/target hierarchies were positively correlated, suggesting that subdominant birds were targeted by dominant birds more frequently than vice versa.

In order to examine age-related changes in long-trace conditioning, five age groups (0.25, 1, 1.5, 2, and 2.5 years) of Wistar-derived female albino rats were subjected to taste-aversion conditioning at one of five conditioned stimulus-conditioned stimulus (CS-US) intervals (0, 45, 90, 180, and 360 min). Age differences in the strength of the aversion were evident at CS-US intervals greater than 0 min and the strength of the aversion was directly related to age. An aversion was conditioned in only the two oldest age groups when the CS-US interval was 360 min. The age differences in taste-aversion and the superior long-trace conditioning in old-age rats were attributed to factors that accompany aging, for example, the gradual slowing down of a metabolic pacemaker.

White blood cell (WBC) and red blood cell (RBC) counts were examined in a sample comprising 762 specimens, representing 25 genera and 38 species of captive non-human primates. Animals suffering from illnesses exhibited higher WBC counts than healthy specimens sampled during routine health checks. Analysis of basal WBC counts in healthy animals confirmed a positive correlation between higher cell counts and occurrences of multiple partner mating. This finding remained statistically significant after use of comparative analysis of independent contrasts (CAIC) to control for possible phylogenetic biases in the dataset. These findings were confirmed when using relative testis size as an independent index of mating system. By contrast, RBC counts were not significantly affected by health or correlated with mating systems. These studies confirm a correlation between WBC counts and primate mating systems, and extend the findings to include a positive correlation between WBC counts and relative testis size. However, the findings do not prove that a causal relationship between these variables exists. Further research is required to establish the evolutionary causation of basal WBC counts in primates.

This study sought to examine the relationship between weather and aggression in Caribbean flamingos by utilising a novel observation method. Previous research has shown evidence of increased levels of aggression during periods of warmer weather in a wide range of species including humans. We observed the captive flock of Caribbean flamingos at the Smithsonian National Zoological Park (Washington, DC, USA) by means of a web cam, and correlated the observed instances of aggression with eight different weather variables gathered via www.weather.com . Results evidenced significant positive correlations between aggression and several variables including: temperature [ r (38) = 0.31, P = 0.048], “feels like” [ r (38) = 0.31, P = 0.049], and UV-index [ r (38) = 0.35, P = 0.025]; and a multiple linear regression (stepwise) suggested that UV-index is a significant predictor of aggressive instances, thus highlighting the relationship between such environmental factors and flamingo aggression. Evidence has been found of a relationships between UV light and aggression in other species, and the results of the present study suggest a similar relationship in flamingos. Employing webcams may allow researchers to obtain larger samples to be included in the study of aggression or to examine this and other behaviors in a wider variety of captive animals.

Large-scale high performance computing systems generate, update, and retrieve enormous amounts of data over their lifetimes from various types of persistent storage. Without appropriate abstractions and associated user interfaces, governing and coordinating access to this information would not be practically feasible. File systems provide high-level semantics that hide the details of directly accessing storage devices at the block level. One of the most widespread input/output interfaces in use today is defined by the Portable Operating System Interface standard, discussed in this chapter along with usage examples. Parallel access to shared data in distributed environments introduces additional challenges that are addressed by distributed and parallel file systems. These are exemplified by the Network File System, the General Parallel File System, and the Lustre parallel file system.

Sexual selection has had profound effects at the copulatory and postcopulatory levels, upon the evolution of reproductive anatomy, physiology, and patterns of mating behavior. This review deals with the effects of sexual selection upon the evolution of relative testes sizes, sperm morphology, seminal vesicular function, penile morphology, and copulatory behavior in the Order Primates. The concept of cryptic female choice is also discussed, and its potential value in understanding how co-evolution of genital morphologies may have occurred in primates and inother animals.

Abstract Much controversy surrounds the welfare of elephants within zoological institutions. Among the many concerns are lack of exercise and the prevention of sedentary health and welfare issues due to smaller exhibits in comparison to the home-range sizes for elephants in Africa and Asia. While many scientists have used GPS to examine distances travelled by wild elephants, there is currently little information on distance travelled by elephants within zoological institutions. In the wild, it is necessary to chemically immobilise elephants using a dart gun in order to put on or take off collars which are used to acquire GPS data. Within a zoological institution, elephants can be trained to wear a collar with a GPS device but this training can be time consuming and also dangerous depending on the level of expertise of animal care staff. However, training an elephant within a zoological institution to wear an anklet outfitted with a GPS device can be much safer and less time consuming. The purpose of the current research was to validate methods for examining the walking rates of elephants in a zoological facility. This included testing GPS units, examining walking rates of eight elephants at the San Diego Zoo Safari Park using collars and conducting trials on a subset of elephants wearing both a collar and anklet outfitted with GPS devices to determine reliability. The average distance travelled by eight African elephants (Loxodonta africana) within a 24-h period was 8.65 (± 0.64) km which corresponds to a rate of 0.360 (± 0.033) kph. Trials comparing anklets to collars were found to be highly reliable except on days when weather conditions were overcast or there was rainfall at the park. The methods used for the current study can be utilised in future studies to examine walking rates as a component of animal welfare for elephants or other large mammals within zoological institutions.

The closure of the embryonic ventral body wall in amniotes is an important morphogenetic event and is essential for life. Defects in human ventral wall closure are a major class of birth defect and a significant health burden. Despite this, very little is understood about how the ventral body wall is formed. Here we show that fibroblast growth factor (FGF) ligands FGF8, FGF17 and FGF18 are essential for this process. Conditional mutants for these genes display subtle migratory defects in the abdominal muscles of the ventral body wall and an enlarged umbilical ring, through which the internal organs are extruded. By refining where and when these genes are required using different Cre lines, we show that Fgf8 and Fgf17 are required in the presomitic mesoderm while Fgf18 is required in the somites. These studies identify complex and multifactorial origins of ventral wall defects and has important implications for understanding their origins during embryonic development.

The enteric nervous system (ENS), a collection of neural cells contained in the wall of the gut, is of fundamental importance to gastrointestinal and systemic health. According to the prevailing paradigm, the ENS arises from progenitor cells migrating from the neural crest and remains largely unchanged thereafter. Here, we show that the lineage composition of maturing ENS changes with time, with a decline in the canonical lineage of neural-crest derived neurons and their replacement by a newly identified lineage of mesoderm-derived neurons. Single cell transcriptomics and immunochemical approaches establish a distinct expression profile of mesoderm-derived neurons. The dynamic balance between the proportions of neurons from these two different lineages in the post-natal gut is dependent on the availability of their respective trophic signals, GDNF-RET and HGF-MET. With increasing age, the mesoderm-derived neurons become the dominant form of neurons in the ENS, a change associated with significant functional effects on intestinal motility which can be reversed by GDNF supplementation. Transcriptomic analyses of human gut tissues show reduced GDNF-RET signaling in patients with intestinal dysmotility which is associated with reduction in neural crest-derived neuronal markers and concomitant increase in transcriptional patterns specific to mesoderm-derived neurons. Normal intestinal function in the adult gastrointestinal tract therefore appears to require an optimal balance between these two distinct lineages within the ENS.

Total shoulder arthroplasty (TSA) with a nonspherical humeral head component and inlay glenoid is a successful bone-preserving treatment for glenohumeral arthritis. This study aimed to describe the 90-day complication profile of TSA with this prosthesis and compare major and minor complication and readmission rates between inpatient- and outpatient-procedure patients.A retrospective review was performed of a consecutive cohort of patients undergoing TSA with a nonspherical humeral head and inlay glenoid in the inpatient and outpatient settings by a single surgeon between 2017 and 2022. Age, sex, body mass index, American Society of Anesthesiologists (ASA) score, Charlson Comorbidity Index (CCI), and 90-day complication and readmission rates were compared between inpatient and outpatient groups.One hundred eighteen TSAs in 111 patients were identified. Mean age was 64.9 years (range, 39-90) and 65% of patients were male. Ninety-four (80%) and 24 (20%) patients underwent outpatient and inpatient procedures, respectively. Four complications (3.4%) were recorded: axillary nerve stretch injury, isolated ipsilateral arm deep venous thrombosis (DVT), ipsilateral arm DVT with pulmonary embolism requiring readmission, and gastrointestinal bleed requiring readmission. There were no reoperations or other complications. Outpatients were younger with lower ASA and CCI scores than inpatients; however, there was no difference in complications (1/24 vs. 3/94, P=1.00) or readmissions (1/24 vs. 1/94, P=0.37) between these two groups.TSA with a nonspherical humeral head and inlay glenoid can be performed safely in both inpatient and outpatient settings. Rates of early complications and readmissions were low with no difference according to surgical setting. Level of evidence: IV.

Abstract Sperm competition is widespread, resulting in sexual selection when the gametes of two or more males compete for access to a given set of ova. This study shows, for the first time, that sexual selection has influenced the evolution of the mammalian vas deferens – that is, the muscular duct which rapidly transports spermatozoa from the cauda epididymis to the ampulla during sexual activity. Morphometric studies of 103 species, representing 70 genera of mammals, show that the vas deferens is on average 33% shorter and its muscular walls are 45% thicker, in those forms where sperm competition pressures are greatest. The outer and inner longitudinal muscle layers of the vas are thickened under these conditions, whereas the central, circular muscle layer is significantly reduced. Thus, mammals that have multiple partner mating systems, and large testes in relation to body weight, have shorter and more muscular vasa deferentia than mammals where single partner mating systems, and smaller relative testes sizes, are the norm. These differences are statistically significant after application of procedures to correct for possible phylogenetic biases in the data set. Sperm competition has played an important role in the evolution of the mammalian vasa deferentia, favouring muscular specializations that enhance sperm transport.

Previous research has suggested that the duration of stressful video material is estimated to be longer than one containing less stressful material. The current study sought to examine what effects viewing news coverage of the September 11th 2001 terrorist attacks might have on estimated duration of exposure. 16 participants were recruited from Saint Joseph's College of Maine psychology courses and viewed two 3-min. video clips. One clip contained coverage of the 9-11 terrorist attacks; the other, a nonstressful control, was taken from a familiar segment of The Wizard of Oz. Participants estimated the length of the clip and rated stress experienced while viewing the clip. Analysis showed the September 11th footage was rated as more stressful and was estimated as longer than the control clip.

This corrects the article DOI: 10.1038/nature21063.

Lateralization is defined as a behavior or mental process displayed by an animal in wh ich there is a distinctive side preference. Caribbean flamingos have been shown to display lateralization in neck resting behavior (Anderson, Williams, & OBrien, 2009), and relationships between this side preference and aggression (Anderson, Williams, & Bono, 2010) and pair-bonding (Williams & Anderson, 2012) have been previously found. The pre sent study investigated whether Caribbean flamingos display lateral behavioral preferences in foot scratching and two types of stamp-feeding behavior, and examined the relationship, if any, between these lateral behaviors and both pair-bonding and aggression. Four of the birds displayed an individual-level lateral preference on one of the two feeding behaviors. Foot scratching preference was related to age such that older birds tended to utilize the right foot more for scratching. Results also suggested that birds who scratch with the left foot are mo re likely to be involved in, to be targeted in, and to lose fights, suggesting that lateral foot usage during scratching may be somehow related to social behaviors in this species, but as significant lateral scratching preferences were not found, such results must be viewed with caution. The lateral feeding behaviors did not appear to be significantly related to social cohesion.

Summary The fibroblast growth factor (FGF) family consists of 22 ligands in mice and humans. FGF signaling is vital for embryogenesis and, when dysregulated, can cause disease. Loss‐of‐function genetic analysis in the mouse has been crucial for understanding FGF function. Such analysis has revealed that multiple Fgfs sometimes function redundantly. Exploring such redundancy between Fgf3 and Fgf4 is currently impossible because both genes are located on chromosome 7, about 18.5 kb apart, making the frequency of interallelic cross‐over between existing mutant alleles too infrequent to be practicable. Therefore, we retargeted Fgf3 and Fgf4 in cis , generating an Fgf3 null allele and a conditional Fgf4 allele, subject to Cre inactivation. To increase the frequency of cis targeting, we used an F1 embryonic stem cell line that contained 129/SvJae (129) and C57BL/6J (B6) chromosomes and targeting constructs isogenic to the 129 chromosome. We confirmed cis targeting by assaying for B6/129 allele‐specific single‐nucleotide polymorphisms. We demonstrated the utility of the Fgf3 Δ ‐Fgf4 flox ‐ cis mouse line by showing that the caudal axis extension defects found in the Fgf3 mutants worsen when Fgf4 is also inactivated. This Fgf3 Δ ‐Fgf4 flox ‐ cis line will be useful to study redundancy of these genes in a variety of tissues and stages in development. genesis 54:91–98, 2016. Published 2016. This article is a US Government work and is in the public domain in the USA.

Cohn and Umans proposed a framework for developing fast matrix multiplication algorithms based on the embedding computation in certain groups algebras. In subsequent work with Kleinberg and Szegedy, they connected this to the search for combinatorial objects called strong uniquely solvable puzzles (strong USPs). We begin a systematic computer-aided search for these objects. We develop and implement constraint-based algorithms build on reductions to $\mathrm{SAT}$ and $\mathrm{IP}$ to verify that puzzles are strong USPs, and to search for large strong USPs. We produce tight bounds on the maximum size of a strong USP for width $k \le 5$, construct puzzles of small width that are larger than previous work, and improve the upper bounds on strong USP size for $k \le 12$. Although our work only deals with puzzles of small-constant width, the strong USPs we find imply matrix multiplication algorithms that run in $O(n^\omega)$ time with exponent $\omega \le 2.66$. While our algorithms do not beat the fastest algorithms, our work provides evidence and, perhaps, a path to finding families of strong USPs that imply matrix multiplication algorithms that are more efficient than those currently known.

We advance the Cohn-Umans framework for developing fast matrix multiplication algorithms. We introduce, analyze, and search for a new subclass of strong uniquely solvable puzzles (SUSP), which we call simplifiable SUSPs. We show that these puzzles are efficiently verifiable, which remains an open question for general SUSPs. We also show that individual simplifiable SUSPs can achieve the same strength of bounds on the matrix multiplication exponent $\omega$ that infinite families of SUSPs can. We report on the construction, by computer search, of larger SUSPs than previously known for small width. This, combined with our tighter analysis, strengthens the upper bound on the matrix multiplication exponent from $2.66$ to $2.505$ obtainable via this computational approach, and nears the results of the handcrafted constructions of Cohn et al.

To see if the neural representation of the conditioned stimulus (CS) is available to old-age rats beyond the time it is available to young adults, the intensity of the unconditioned stimulus (US) and the length of the CS-US interval were systematically varied in a trace conditioning experiment. Results indicated that increasing US intensity extends the interval over which trace conditioning is evident in old-age rats but not in young adults, suggesting that trace decay occurs more rapidly in young rats. Results were interpreted in terms of age differences in the workings of hypothesized biochemical timing mechanisms that may directly influence the ability to associate stimuli over trace intervals in conditioned taste-aversion procedures.

Conditioned flavor aversion was examined in Wistar-derived albino rats that were immersed in cold water for 0, 2.5, 5, or 10 min immediately following 10-min exposure to a.1% saccharin solution and given an intraperitoneal (i.p.) injection of 0.15 M lithium chloride (LiCl) either 90, 135, 180, or 225 min later. Cold water immersion for 2.5, 5, and 10 min led to body temperature decreases of approximately 4.5, 7, and 10 degrees C, respectively. Rats whose body temperatures were not reduced (0 min immersion) showed no saccharin aversion when the LiCl was delayed 90 min. Rats whose body temperatures were reduced 4.5, 7, and 10 degrees C displayed conditioned aversions at LiCl delays up to 135, 180, and 225 min, respectively. These results were interpreted in terms of a cold-induced slowing of a biochemical clock that may uniquely govern specific timing processes involved in associative learning over long delays, such as long-trace conditioned flavor aversion, learned safety, and certain types of learning that involve an extensive time lapse (e.g., extinction of fear).

The effect of tail-pinch stress interpolated between the saccharin conditioned stimulus (CS) and the illness-inducing unconditioned stimulus (US) during long-trace taste-aversion conditioning was examined in young- and old adult rats with a two-cylinder (saccharin versus water) test. A 2 x 2 x 4 factorial ANOVA was performed on percent-preference-for-saccharin data, with age (young, old), stress condition (stressed, non-stressed), and CS-US interval (22.5-, 45-, 90-, and 180-min) being the factors under consideration. The ANOVA yielded only significant main effects of stress condition and CS-US interval. These findings indicate that stress weakens the CS-US association as evidenced by a higher percent preference for saccharin in the stressed rats than in non-stressed rats at all CS-US intervals. A comparison of the stressed and non-stressed conditioned rats with pseudo-conditioned controls showed that the non-stressed rats formed strong aversions up to the 45-min CS-US interval whereas the stressed rats showed no conditioning beyond the 22.5 min CS-US interval, indicating that stress decreases the effective CS-US interval. Results were interpreted in terms of time-contraction and an internal biological countdown timer hypothesized to govern processes involved in associative learning over long delays.

Abstract When flamingos rest, they typically lay their head on their back and curve their neck to either the right or left of their body, with both individual and population-level lateral preferences for rightward neck resting when preferences are tracked over time (Anderson, Williams, & O'Brien, 2009). The present study attempted to replicate these previous neck-resting preferences, to examine how they changed over time, and to examine the possibility of a relationship between lateral neck-resting preference and pair bonding in captive Caribbean flamingos (Phoenicopterus ruber) housed at the Philadelphia Zoo (Philadelphia, PA, USA). Results successfully replicated the individual- and population-level lateral preferences for rightward neck resting, and demonstrated that these preferences were stable over time. Moreover, individual flamingos that demonstrated stronger pair bond strengths tended to differ less from their partners in terms of neck-resting preference than did those birds displaying weaker pair bond strengths, suggesting a relationship between laterality and social cohesion. Keywords: FlamingosPair bondLateralityResting behaviourView correction statement:Corrigendum Acknowledgements We would like to thank the Philadelphia Zoo for allowing the continued observation of their flamingos. In particular we express our thanks to Dr Aliza Baltz, Curator of Birds, who has provided much assistance during our studies. Gratitude is also owed to Dr Judith Chapman for her helpful suggestions over the course of this project, and to Lorraine Calabro for collecting some of the observations.

Background Baptisia is commonly found in residential gardens as an ornamental plant, in municipal “rain gardens” for water control, as well as in native and restored prairie habitat. Cytisine, an alkaloid with nicotinic acetylcholine receptor agonist properties, is a component of Baptisia. Case Report Two patients poisoned after simultaneously ingesting Baptisia plant material are presented. In addition to findings of generalized nicotinic agonist toxicity, including generalized weakness and gastrointestinal symptoms, profound ataxia was present in both, consistent with recently described nicotinic subunit activity in the cerebellum. Why Should an Emergency Physician Be Aware of This? Baptisia, a native prairie plant commonly found in restored prairie habitats and public spaces, has striking “look-alike” characteristics, in its immature state, to asparagus. As future exposures by foraging citizens will be likely, awareness of this relationship and the toxic manifestations of cytisine will be useful.

The present study sought to explore the possibility that lateral behaviour in captive Caribbean flamingos (Phoenicopterus ruber) housed at the Philadelphia Zoo (Philadelphia, PA) could be used to predict a variety of physiological measures of health obtained via complete blood counts (CBC) and plasma biochemistry analyses that were performed as part of the flock's annual physical examination. Consistent with previous research, evidence of rightward lateral neck-resting preferences were obtained, no evidence was found for the existence of leg stance preferences, and neck-resting and leg stance preferences were shown to be unrelated. Both lateral neck-resting preferences and lateral support leg preference were shown to be related to a variety of measures from the CBC and plasma biochemistry analyses. While several general trends emerged in regards to the CBC variables, the relationships between the lateral behaviours and those variables generated via plasma biochemistry analyses proved to be fewer and somewhat less consistent. Birds with rightward neck-resting preferences and birds with leftward support leg preferences generally appeared to be healthier and less stressed according to the CBC measures; however, the validity of lateral leg stance preference as a predictor of health and wellbeing is questionable given the lack of statistically significant leg stance preferences.

One of the most widely used parallel programming models today is MapReduce. MapReduce is easy both to learn and use, and is especially useful in analyzing large datasets. While it is not suitable for several classes of scientific computing operations that are better served by message-passing interface or OpenMP, such as numerical linear algebra or finite element and finite difference computations, MapReduce's utility in workflows frequently called “big data” has made it a mainstay in high performance computing. This chapter introduces the MapReduce programming model and the Hadoop open-source framework which supports it.

The strong spin–orbit coupling (SOC) in lead halide perovskites, when inversion symmetry is lifted, has provided opportunities for investigating the Rashba effect in these systems. Moreover, the strong orbital moment, which, in turn, impacts the spin-pair in singlet and triplet electronic states, plays a significant role in enhancing the optoelectronic properties in the presence of external magnetic fields in lead halide perovskites. Here, we investigate the effect of weak magnetic fields (&amp;lt;1 T) on the photoluminescence (PL) properties of CsPbBr3 nanocrystals with and without Ruddlesden–Popper (RP) faults and single crystals of CH3NH3PbBr3. Along with an enhancement in the PL intensity as a function of an external magnetic field, which is observed in both lead bromide perovskites, the PL emission red-shifts in CsPbBr3 nanocrystals. Density-functional theory calculations of the electronic band-edge in CsPbBr3 show almost no change in the energy gap as a function of the external magnetic field. The experimental results, thus, suggest the role of mixing of the triplet and singlet excitonic states under weak magnetic fields. This is further deduced from an enhancement in PL lifetimes as a function of the field in CsPbBr3. In CH3NH3PbBr3, an increase in PL intensity is observed under weak magnetic fields; however, no changes in the peak energy or PL lifetimes are observed. The internal magnetic fields due to SOC are characterized for all three samples and found to be the highest for CsPbBr3 nanocrystals with RP faults.

Physician burnout is a major problem in the United States. Small studies suggest scribes can improve clinician satisfaction, but scribe programs have not been evaluated using separate control groups or structured measures of electronic health record (EHR) use.We conducted a pre-post, non-randomized controlled evaluation of a remote scribe pilot program introduced in September 2019 in an academic primary care practice. Scribes were paired with physicians via an audio-only cellphone connection to hear and document in real-time. Physician wellness was measured with the 10-item Mini-Z and 16-item Professional Fulfillment Index. EHR use was measured using vendor-derived platforms that provide routine EHR-related data.37 of 38 scribe users (97.4%) and 68 of 160 potential control physicians (42.5%) completed both pre and post intervention questionnaires. Compared with controls, scribe users had improvements in Mini-Z wellness metrics including Joyful Workplace (mean improvement 2.83, 95%CI 0.60, 5.06) and a single-item dichotomized burnout measure (OR 0.15, 95%CI 0.03, 0.71). There were significant reductions among scribe users compared to controls in total EHR time per 8 scheduled hours (-1.14 h, 95%CI -1.55, -0.72), and an increase in the percentage of orders with team contribution (10.4%, 95%CI 5.2, 15.6). These findings remained significant in adjusted analyses.A remote scribe program was associated with improvements in physician wellness and reduced EHR use. Healthcare organizations can consider scribe programs to help improve wellness among their physician workforce.

DNA-Encoded Libraries (DELs) use chemical reactions to build organic moieties on the coding DNA strand. Accordingly, the generation of a DEL requires robust chemical transformations that are compatible with DNA and the aqueous conditions required for its solubilisation. Reactions that damage DNA cannot be employed, neither can reactions that are hindered by the functionality in DNA (Malone and Paegel, ACS Comb Sci 18(4):182–187, 2016). The nature of DEL synthesis imposes further restrictions: reactions must be compatible with split-and-pool, and reactions must proceed predominantly to the desired product without excessive side products. A broad substrate scope is required using accessible reagents. As a consequence, a great deal of effort has been expended in developing synthetic methodologies that are DNA-compatible, in order to increase the chemical space DELs can cover. These are, most often, adaptations of off-DNA synthesis methods extended to a DEL setting. The range of reactions available to DEL chemists is ever-expanding, covering an extensive range of reactions including, but not limited to amide couplings, cycloadditions, heterocycle syntheses, nucleophilic additions, reductive aminations, SNAr reactions, and a wide variety of metal-catalysed cross-couplings, such as Suzuki-Miyaura, Buchwald-Hartwig, and Sonogashira couplings (Kunig et al., Biol Chem 399 (7):691–710, 2018; Shi et al., RSC Adv 11(4):2359–2376, 2021; Castan et al., Bioorg Med Chem 43:116273, 2021; Fair et al., Bioorg Med Chem Lett 51:128339, 2021). This synthetic toolkit is not all-encompassing; however, new methodologies towards DEL-compatible chemical reactions are constantly being elucidated, broadening the available tools towards DEL synthesis. Herein, recent advances towards DNA-compatible synthetic methods are outlined, comprising DNA damage assessment procedures, technologies to prevent this damage, and applications of these techniques to DEL generation.