Stephen W. Peterson

The taxonomic history of anamorphic species attributed to Penicillium subgenus Biverticillium is reviewed, along with evidence supporting their relationship with teleomorphic species classified in Talaromyces. To supplement previous conclusions based on ITS, SSU and/or LSU sequencing that Talaromyces and subgenus Biverticillium comprise a monophyletic group that is distinct from Penicillium at the generic level, the phylogenetic relationships of these two groups with other genera of Trichocomaceae was further studied by sequencing a part of the RPB1 (RNA polymerase II largest subunit) gene. Talaromyces species and most species of Penicillium subgenus Biverticilliumsensu Pitt reside in a monophyletic clade distant from species of other subgenera of Penicillium. For detailed phylogenetic analysis of species relationships, the ITS region (incl. 5.8S nrDNA) was sequenced for the available type strains and/or representative isolates of Talaromyces and related biverticillate anamorphic species. Extrolite profiles were compiled for all type strains and many supplementary cultures. All evidence supports our conclusions that Penicillium subgenus Biverticillium is distinct from other subgenera in Penicillium and should be taxonomically unified with the Talaromyces species that reside in the same clade. Following the concepts of nomenclatural priority and single name nomenclature, we transfer all accepted species of Penicillium subgenus Biverticillium to Talaromyces. A holomorphic generic diagnosis for the expanded concept of Talaromyces, including teleomorph and anamorph characters, is provided. A list of accepted Talaromyces names and newly combined Penicillium names is given. Species of biotechnological and medical importance, such as P. funiculosum and P. marneffei, are now combined in Talaromyces. Excluded species and taxa that need further taxonomic study are discussed. An appendix lists other generic names, usually considered synonyms of Penicillium sensu lato that were considered prior to our adoption of the name Talaromyces.Taxonomic novelties:New species - Talaromyces apiculatus Samson, Yilmaz & Frisvad, sp. nov. New combinationsand names - Talaromyces aculeatus (Raper & Fennell) Samson, Yilmaz, Frisvad & Seifert, T. albobiverticillius (H.-M. Hsieh, Y.-M. Ju & S.-Y. Hsieh) Samson, Yilmaz, Frisvad & Seifert, T. allahabadensis (B.S. Mehrotra & D. Kumar) Samson, Yilmaz & Frisvad, T. aurantiacus (J.H. Mill., Giddens & A.A. Foster) Samson, Yilmaz, & Frisvad, T. boninensis (Yaguchi & Udagawa) Samson, Yilmaz, & Frisvad, T. brunneus (Udagawa) Samson, Yilmaz & Frisvad, T. calidicanius (J.L. Chen) Samson, Yilmaz & Frisvad, T. cecidicola (Seifert, Hoekstra & Frisvad) Samson, Yilmaz, Frisvad & Seifert, T. coalescens (Quintan.) Samson, Yilmaz & Frisvad, T. dendriticus (Pitt) Samson, Yilmaz, Frisvad & Seifert, T. diversus (Raper & Fennell) Samson, Yilmaz & Frisvad, T. duclauxii (Delacr.) Samson, Yilmaz, Frisvad & Seifert, T. echinosporus (Nehira) Samson, Yilmaz & Frisvad, comb. nov. T. erythromellis (A.D. Hocking) Samson, Yilmaz, Frisvad & Seifert, T. funiculosus (Thom) Samson, Yilmaz, Frisvad & Seifert, T. islandicus (Sopp) Samson, Yilmaz, Frisvad & Seifert, T. loliensis (Pitt) Samson, Yilmaz & Frisvad, T. marneffei (Segretain, Capponi & Sureau) Samson, Yilmaz, Frisvad & Seifert, T. minioluteus (Dierckx) Samson, Yilmaz, Frisvad & Seifert, T. palmae (Samson, Stolk & Frisvad) Samson, Yilmaz, Frisvad & Seifert, T. panamensis (Samson, Stolk & Frisvad) Samson, Yilmaz, Frisvad & Seifert, T. paucisporus (Yaguchi, Someya & Udagawa) Samson & Houbraken T. phialosporus (Udagawa) Samson, Yilmaz & Frisvad, T. piceus (Raper & Fennell) Samson, Yilmaz, Frisvad & Seifert, T. pinophilus (Hedgcock) Samson, Yilmaz, Frisvad & Seifert, T. pittii (Quintan.) Samson, Yilmaz, Frisvad & Seifert, T. primulinus (Pitt) Samson, Yilmaz & Frisvad, T. proteolyticus (Kamyschko) Samson, Yilmaz & Frisvad, T. pseudostromaticus (Hodges, G.M. Warner, Rogerson) Samson, Yilmaz, Frisvad & Seifert, T. purpurogenus (Stoll) Samson, Yilmaz, Frisvad & Seifert, T. rademirici (Quintan.) Samson, Yilmaz & Frisvad, T. radicus (A.D. Hocking & Whitelaw) Samson, Yilmaz, Frisvad & Seifert, T. ramulosus (Visagie & K. Jacobs) Samson, Yilmaz, Frisvad & Seifert, T. rubicundus (J.H. Mill., Giddens & A.A. Foster) Samson, Yilmaz, Frisvad & Seifert, T. rugulosus (Thom) Samson, Yilmaz, Frisvad & Seifert, T. sabulosus (Pitt & A.D. Hocking) Samson, Yilmaz & Frisvad, T. siamensis (Manoch & C. Ramírez) Samson, Yilmaz & Frisvad, T. sublevisporus (Yaguchi & Udagawa) Samson, Yilmaz & Frisvad, T. variabilis (Sopp) Samson, Yilmaz, Frisvad & Seifert, T. varians (G. Sm.) Samson, Yilmaz & Frisvad, T. verruculosus (Peyronel) Samson, Yilmaz, Frisvad & Seifert, T. viridulus Samson, Yilmaz & Frisvad.

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.

A large aggregate collection of clinical isolates of aspergilli (n = 218) from transplant patients with proven or probable invasive aspergillosis was available from the Transplant-Associated Infection Surveillance Network, a 6-year prospective surveillance study. To determine the Aspergillus species distribution in this collection, isolates were subjected to comparative sequence analyses by use of the internal transcribed spacer and beta-tubulin regions. Aspergillus fumigatus was the predominant species recovered, followed by A. flavus and A. niger. Several newly described species were identified, including A. lentulus and A. calidoustus; both species had high in vitro MICs to multiple antifungal drugs. Aspergillus tubingensis, a member of the A. niger species complex, is described from clinical specimens; all A. tubingensis isolates had low in vitro MICs to antifungal drugs.

Novel species of fungi described in the present study include the following from Australia: Vermiculariopsiella eucalypti, Mulderomyces natalis (incl. Mulderomyces gen. nov.), Fusicladium paraamoenum, Neotrimmatostroma paraexcentricum, and Pseudophloeospora eucalyptorum on leaves of Eucalyptus spp., Anungitea grevilleae (on leaves of Grevillea sp.), Pyrenochaeta acaciae (on leaves of Acacia sp.), and Brunneocarpos banksiae (incl. Brunneocarpos gen. nov.) on cones of Banksia attenuata. Novel foliicolous taxa from South Africa include Neosulcatispora strelitziae (on Strelitzia nicolai), Colletotrichum ledebouriae (on Ledebouria floridunda), Cylindrosympodioides brabejum (incl. Cylindrosympodioides gen. nov.) on Brabejum stellatifolium, Sclerostagonospora ericae (on Erica sp.), Setophoma cyperi (on Cyperus sphaerocephala), and Phaeosphaeria breonadiae (on Breonadia microcephala). Novelties described from Robben Island (South Africa) include Wojnowiciella cissampeli and Diaporthe cissampeli (both on Cissampelos capensis), Phaeotheca salicorniae (on Salicornia meyeriana), Paracylindrocarpon aloicola (incl. Paracylindrocarpon gen. nov.) on Aloe sp., and Libertasomyces myopori (incl. Libertasomyces gen. nov.) on Myoporum serratum. Several novelties are recorded from La Réunion (France), namely Phaeosphaeriopsis agapanthi (on Agapanthus sp.), Roussoella solani (on Solanum mauritianum), Vermiculariopsiella acaciae (on Acacia heterophylla), Dothiorella acacicola (on Acacia mearnsii), Chalara clidemiae (on Clidemia hirta), Cytospora tibouchinae (on Tibouchina semidecandra), Diaporthe ocoteae (on Ocotea obtusata), Castanediella eucalypticola, Phaeophleospora eucalypticola and Fusicladium eucalypticola (on Eucalyptus robusta), Lareunionomyces syzygii (incl. Lareunionomyces gen. nov.) and Parawiesneriomyces syzygii (incl. Parawiesneriomyces gen. nov.) on leaves of Syzygium jambos. Novel taxa from the USA include Meristemomyces arctostaphylos (on Arctostaphylos patula), Ochroconis dracaenae (on Dracaena reflexa), Rasamsonia columbiensis (air of a hotel conference room), Paecilomyces tabacinus (on Nicotiana tabacum), Toxicocladosporium hominis (from human broncoalveolar lavage fluid), Nothophoma macrospora (from respiratory secretion of a patient with pneumonia), and Penidiellopsis radicularis (incl. Penidiellopsis gen. nov.) from a human nail. Novel taxa described from Malaysia include Prosopidicola albizziae (on Albizzia falcataria), Proxipyricularia asari (on Asarum sp.), Diaporthe passifloricola (on Passiflora foetida), Paramycoleptodiscus albizziae (incl. Paramycoleptodiscus gen. nov.) on Albizzia falcataria, and Malaysiasca phaii (incl. Malaysiasca gen. nov.) on Phaius reflexipetalus. Two species are newly described from human patients in the Czech Republic, namely Microascus longicollis (from toenails of patient with suspected onychomycosis), and Chrysosporium echinulatum (from sole skin of patient). Furthermore, Alternaria quercicola is described on leaves of Quercus brantii (Iran), Stemphylium beticola on leaves of Beta vulgaris (The Netherlands), Scleroderma capeverdeanum on soil (Cape Verde Islands), Scleroderma dunensis on soil, and Blastobotrys meliponae from bee honey (Brazil), Ganoderma mbrekobenum on angiosperms (Ghana), Geoglossum raitviirii and Entoloma kruticianum on soil (Russia), Priceomyces vitoshaensis on Pterostichus melas (Carabidae) (Bulgaria) is the only one for which the family is listed, Ganoderma ecuadoriense on decaying wood (Ecuador), Thyrostroma cornicola on Cornus officinalis (Korea), Cercophora vinosa on decorticated branch of Salix sp. (France), Coprinus pinetorum, Coprinus littoralis and Xerocomellus poederi on soil (Spain). Two new genera from Colombia include Helminthosporiella and Uwemyces on leaves of Elaeis oleifera. Two species are described from India, namely Russula intervenosa (ectomycorrhizal with Shorea robusta), and Crinipellis odorata (on bark of Mytragyna parviflora). Novelties from Thailand include Cyphellophora gamsii (on leaf litter), Pisolithus aureosericeus and Corynascus citrinus (on soil). Two species are newly described from Citrus in Italy, namely Dendryphiella paravinosa on Citrus sinensis, and Ramularia citricola on Citrus floridana. Morphological and culture characteristics along with ITS nrDNA barcodes are provided for all taxa.

Novel species of fungi described in this study include those from various countries as follows: Angola, Gnomoniopsis angolensis and Pseudopithomyces angolensis on unknown host plants. Australia, Dothiora corymbiae on Corymbia citriodora, Neoeucasphaeria eucalypti (incl. Neoeucasphaeria gen. nov.) on Eucalyptus sp., Fumagopsis stellae on Eucalyptus sp., Fusculina eucalyptorum (incl. Fusculinaceae fam. nov.) on Eucalyptus socialis, Harknessia corymbiicola on Corymbia maculata, Neocelosporiumeucalypti (incl. Neocelosporium gen. nov., Neocelosporiaceae fam. nov. and Neocelosporiales ord. nov.) on Eucalyptus cyanophylla, Neophaeomoniella corymbiae on Corymbia citriodora, Neophaeomoniella eucalyptigena on Eucalyptus pilularis, Pseudoplagiostoma corymbiicola on Corymbia citriodora, Teratosphaeria gracilis on Eucalyptus gracilis, Zasmidium corymbiae on Corymbia citriodora.Brazil, Calonectria hemileiae on pustules of Hemileia vastatrix formed on leaves of Coffea arabica, Calvatia caatinguensis on soil, Cercospora solani-betacei on Solanum betaceum, Clathrus natalensis on soil, Diaporthe poincianellae on Poincianella pyramidalis, Geastrum piquiriunense on soil, Geosmithia carolliae on wing of Carollia perspicillata, Henningsia resupinata on wood, Penicillium guaibinense from soil, Periconia caespitosa from leaf litter, Pseudocercospora styracina on Styrax sp., Simplicillium filiforme as endophyte from Citrullus lanatus, Thozetella pindobacuensis on leaf litter, Xenosonderheniacoussapoae on Coussapoa floccosa.Canary Islands (Spain), Orbilia amarilla on Euphorbia canariensis.Cape Verde Islands, Xylodon jacobaeus on Eucalyptus camaldulensis.Chile, Colletotrichum arboricola on Fuchsia magellanica.Costa Rica, Lasiosphaeria miniovina on tree branch. Ecuador, Ganoderma chocoense on tree trunk. France, Neofitzroyomycesnerii (incl. Neofitzroyomyces gen. nov.) on Nerium oleander.Ghana, Castanediella tereticornis on Eucalyptus tereticornis, Falcocladium africanum on Eucalyptus brassiana, Rachicladosporium corymbiae on Corymbia citriodora.Hungary, Entoloma silvae-frondosae in Carpinus betulus-Pinus sylvestris mixed forest. Iran, Pseudopyricularia persiana on Cyperus sp.Italy, Inocybe roseascens on soil in mixed forest. Laos, Ophiocordyceps houaynhangensis on Coleoptera larva. Malaysia, Monilochaetes melastomae on Melastoma sp. Mexico, Absidia terrestris from soil. Netherlands, Acaulium pannemaniae, Conioscypha boutwelliae, Fusicolla septimanifiniscientiae, Gibellulopsis simonii, Lasionectria hilhorstii, Lectera nordwiniana,Leptodiscella rintelii, Parasarocladium debruynii and Sarocladium dejongiae (incl. Sarocladiaceae fam. nov.) from soil. New Zealand, Gnomoniopsis rosae on Rosa sp. and Neodevriesia metrosideri on Metrosideros sp. Puerto Rico, Neodevriesia coccolobae on Coccoloba uvifera, Neodevriesia tabebuiae and Alfaria tabebuiae on Tabebuia chrysantha. Russia, Amanita paludosa on bogged soil in mixed deciduous forest, Entoloma tiliae in forest of Tilia × europaea, Kwoniella endophytica on Pyrus communis.South Africa, Coniella diospyri on Diospyros mespiliformis, Neomelanconiella combreti (incl. Neomelanconiellaceae fam. nov. and Neomelanconiella gen. nov.) on Combretum sp., Polyphialoseptoria natalensis on unidentified plant host, Pseudorobillarda bolusanthi on Bolusanthus speciosus, Thelonectria pelargonii on Pelargonium sp. Spain, Vermiculariopsiella lauracearum and Anungitopsis lauri on Laurus novocanariensis, Geosmithia xerotolerans from a darkened wall of a house, Pseudopenidiella gallaica on leaf litter. Thailand, Corynespora thailandica on wood, Lareunionomyces loeiensis on leaf litter, Neocochlearomyceschromolaenae (incl. Neocochlearomyces gen. nov.) on Chromolaena odorata, Neomyrmecridium septatum (incl. Neomyrmecridium gen. nov.), Pararamichloridium caricicola on Carex sp., Xenodactylaria thailandica (incl. Xenodactylariaceae fam. nov. and Xenodactylaria gen. nov.), Neomyrmecridium asiaticum and Cymostachys thailandica from unidentified vine. USA, Carolinigaster bonitoi (incl. Carolinigaster gen. nov.) from soil, Penicillium fortuitum from house dust, Phaeotheca shathenatiana (incl. Phaeothecaceae fam. nov.) from twig and cone litter, Pythium wohlseniorum from stream water, Superstratomyces tardicrescens from human eye, Talaromyces iowaense from office air. Vietnam, Fistulinella olivaceoalba on soil. Morphological and culture characteristics along with DNA barcodes are provided.

Novel species of fungi described in this study include those from various countries as follows: Australia, Chaetopsina eucalypti on Eucalyptus leaf litter, Colletotrichum cobbittiense from Cordyline stricta × C. australis hybrid, Cyanodermella banksiae on Banksia ericifolia subsp. macrantha, Discosia macrozamiae on Macrozamia miquelii, Elsinoë banksiigena on Banksia marginata, Elsinoë elaeocarpi on Elaeocarpus sp., Elsinoë leucopogonis on Leucopogon sp., Helminthosporium livistonae on Livistona australis, Idriellomyces eucalypti (incl. Idriellomyces gen. nov.) on Eucalyptus obliqua, Lareunionomyces eucalypti on Eucalyptus sp., Myrotheciomyces corymbiae (incl. Myrotheciomyces gen. nov., Myrotheciomycetaceae fam. nov.), Neolauriomyces eucalypti (incl. Neolauriomyces gen. nov., Neolauriomycetaceae fam. nov.) on Eucalyptus sp., Nullicamyces eucalypti (incl. Nullicamyces gen. nov.) on Eucalyptus leaf litter, Oidiodendron eucalypti on Eucalyptus maidenii, Paracladophialophora cyperacearum (incl. Paracladophialophoraceae fam. nov.) and Periconia cyperacearum on leaves of Cyperaceae, Porodiplodia livistonae (incl. Porodiplodia gen. nov., Porodiplodiaceae fam. nov.) on Livistona australis, Sporidesmium melaleucae (incl. Sporidesmiales ord. nov.) on Melaleuca sp., Teratosphaeria sieberi on Eucalyptus sieberi, Thecaphora australiensis in capsules of a variant of Oxalis exilis.Brazil, Aspergillus serratalhadensis from soil, Diaporthe pseudoinconspicua from Poincianella pyramidalis, Fomitiporella pertenuis on dead wood, Geastrum magnosporum on soil, Marquesius aquaticus (incl. Marquesius gen. nov.) from submerged decaying twig and leaves of unidentified plant, Mastigosporella pigmentata from leaves of Qualea parviflorae, Mucor souzae from soil, Mycocalia aquaphila on decaying wood from tidal detritus, Preussia citrullina as endophyte from leaves of Citrullus lanatus, Queiroziella brasiliensis (incl. Queiroziella gen. nov.) as epiphytic yeast on leaves of Portea leptantha, Quixadomyces cearensis (incl. Quixadomyces gen. nov.) on decaying bark, Xylophallus clavatus on rotten wood. Canada, Didymella cari on Carum carvi and Coriandrum sativum.Chile, Araucasphaeria foliorum (incl. Araucasphaeria gen. nov.) on Araucaria araucana, Aspergillus tumidus from soil, Lomentospora valparaisensis from soil. Colombia, Corynespora pseudocassiicola on Byrsonima sp., Eucalyptostroma eucalyptorum on Eucalyptus pellita, Neometulocladosporiella eucalypti (incl. Neometulocladosporiella gen. nov.) on Eucalyptus grandis × urophylla, Tracylla eucalypti (incl. Tracyllaceae fam. nov., Tracyllalales ord. nov.) on Eucalyptus urophylla.Cyprus, Gyromitra anthracobia (incl. Gyromitra subg. Pseudoverpa) on burned soil. Czech Republic, Lecanicillium restrictum from the surface of the wooden barrel, Lecanicillium testudineum from scales of Trachemys scripta elegans. Ecuador, Entoloma yanacolor and Saproamanita quitensis on soil. France, Lentithecium carbonneanum from submerged decorticated Populus branch. Hungary, Pleuromyces hungaricus (incl. Pleuromyces gen. nov.) from a large Fagus sylvatica log. Iran, Zymoseptoria crescenta on Aegilops triuncialis.Malaysia, Ochroconis musicola on Musa sp. Mexico, Cladosporium michoacanense from soil. New Zealand, Acrodontium metrosideri on Metrosideros excelsa, Polynema podocarpi on Podocarpus totara, Pseudoarthrographis phlogis (incl. Pseudoarthrographis gen. nov.) on Phlox subulata.Nigeria, Coprinopsis afrocinerea on soil. Pakistan, Russula mansehraensis on soil under Pinus roxburghii.Russia, Baorangia alexandri on soil in deciduous forests with Quercus mongolica.South Africa, Didymocyrtis brachylaenae on Brachylaena discolor.Spain, Alfaria dactylis from fruit of Phoenix dactylifera, Dothiora infuscans from a blackened wall, Exophiala nidicola from the nest of an unidentified bird, Matsushimaea monilioides from soil, Terfezia morenoi on soil. United Arab Emirates, Tirmania honrubiae on soil. USA, Arxotrichum wyomingense (incl. Arxotrichum gen. nov.) from soil, Hongkongmyces snookiorum from submerged detritus from a fresh water fen, Leratiomyces tesquorum from soil, Talaromyces tabacinus on leaves of Nicotiana tabacum.Vietnam, Afroboletus vietnamensis on soil in an evergreen tropical forest, Colletotrichum condaoense from Ipomoea pes-caprae. Morphological and culture characteristics along with DNA barcodes are provided.

The species recognition and identification of aspergilli and their teleomorphs is discussed. A historical overview of the taxonomic concepts starting with the monograph of Raper & Fennell (1965) is given. A list of taxa described since 2000 is provided. Physiological characters, particularly growth rates and the production of extrolites, often show differences that reflect phylogenetic species boundaries and greater emphasis should be placed on extrolite profiles and growth characteristics in species descriptions. Multilocus sequence-based phylogenetic analyses have emerged as the primary tool for inferring phylogenetic species boundaries and relationships within subgenera and sections. A four locus DNA sequence study covering all major lineages in Aspergillus using genealogical concordance theory resulted in a species recognition system that agrees in part with phenotypic studies and reveals the presence of many undescribed species not resolved by phenotype. The use of as much data from as many sources as possible in making taxonomic decisions is advocated. For species identification, DNA barcoding uses a short genetic marker in an organism"s DNA to quickly and easily identify it to a particular species. Partial cytochrome oxidase subunit 1 sequences, which are used for barcoding animal species, were found to have limited value for species identification among black aspergilli. The various possibilities are discussed and at present partial beta-tubulin or calmodulin are the most promising loci for Aspergillus identification. For characterising Aspergillus species one application would be to produce a multilocus phylogeny, with the goal of having a firm understanding of the evolutionary relationships among species across the entire genus. DNA chip technologies are discussed as possibilities for an accurate multilocus barcoding tool for the genus Aspergillus.

The taxonomy of Aspergillus section Fumigati with its teleomorph genus Neosartorya is revised. The species concept is based on phenotypic (morphology and extrolite profiles) and molecular (beta-tubulin and calmodulin gene sequences) characters in a polyphasic approach. Four new taxa are proposed: N. australensis N. ferenczii, N. papuaensis and N. warcupii. All newly described and accepted species are illustrated. The section consists of 33 taxa: 10 strictly anamorphic Aspergillus species and 23 Neosartorya species. Four other Neosartorya species described previously were not available for this monograph, and consequently are relegated to the category of doubtful species.

We characterized sleep disorder rates in temporomandibular joint disorder (TMD) and evaluated possible associations between sleep disorders and laboratory measures of pain sensitivity.Research diagnostic examinations were conducted, followed by two consecutive overnight polysomnographic studies with morning and evening assessments of pain threshold.Orofacial pain clinic and inpatient sleep research facility.Fifty-three patients meeting research diagnostic criteria for myofascial TMD.N/A.We determined sleep disorder diagnostic rates and conducted algometric measures of pressure pain threshold on the masseter and forearm. Heat pain threshold was measured on the forearm; 75% met self-report criteria for sleep bruxism, but only 17% met PSG criteria for active sleep bruxism. Two or more sleep disorders were diagnosed in 43% of patients. Insomnia disorder (36%) and sleep apnea (28.4%) demonstrated the highest frequencies. Primary insomnia (PI) (26%) comprised the largest subcategory of insomnia. Even after controlling for multiple potential confounds, PI was associated with reduced mechanical and thermal pain thresholds at all sites (P < 0.05). Conversely, the respiratory disturbance index was associated with increased mechanical pain thresholds on the forearm (P < 0.05).High rates of PI and sleep apnea highlight the need to refer TMD patients complaining of sleep disturbance for polysomnographic evaluation. The association of PI and hyperalgesia at a nonorofacial site suggests that PI may be linked with central sensitivity and could play an etiologic role in idiopathic pain disorders. The association between sleep disordered breathing and hypoalgesia requires further study and may provide novel insight into the complex interactions between sleep and pain-regulatory processes.

The entomopathogenic fungus Beauveria bassiana was established in coffee seedlings after fungal spore suspensions were applied as foliar sprays, stem injections, or soil drenches. Direct injection yielded the highest post-inoculation recovery of endophytic B. bassiana. Establishment, based on percent recovery of B. bassiana, decreased as time post-inoculation increased in all treatments. Several other endophytes were isolated from the seedlings and could have negatively influenced establishment of B. bassiana. The recovery of B. bassiana from sites distant from the point of inoculation indicates that the fungus has the potential to move throughout the plant.

A recent report of an aflatoxin producing isolate of Aspergillus tamarii prompted a taxonomic re-examination of aflatoxigenic and non-aflatoxigenic isolates identified as A. tamarii as well as the closely related A. caelatus. Representatives of each species, including atypical isolates, were compared morphologically, for mycotoxin production, and for divergence in ITS, 28S, β-tubulin and calmodulin gene sequences. Because of genetic, morphological, and mycotoxin differences, the aflatoxin producing isolates of A. tamarii are given species rank as Aspergillus pseudotamarii sp. nov.

Coffee (Coffea arabica) plant tissues were surface-sterilized and fungal endophytes isolated using standard techniques, followed by DNA extraction and sequencing of the internal transcribed spacer region (ITS). A total of 843 fungal isolates were recovered and sequenced (Colombia, 267; Hawai'i, 393; Mexico, 109; Puerto Rico, 74) yielding 257 unique ITS genotypes (Colombia, 113; Hawai'i, 126; Mexico, 32; Puerto Rico, 40). The most abundant taxa were Colletotrichum, Fusarium, Penicillium, and Xylariaceae. Overall, 220 genotypes were detected in only one of the countries sampled; only two genotypes were found in all four countries. Endophytes were also isolated from Coffea canephora, Coffea congensis, Coffea liberica, Coffea macrocarpa, Coffea racemosa, and Coffea stenophylla in Hawai'i. The high biodiversity of fungal endophytes in coffee plants may indicate that most of these are "accidental tourists" with no role in the plant, in contrast to endophytes that could be defined as "influential passengers" and whose role in the plant has been elucidated. This study, the most comprehensive analysis of fungal endophytes associated with a single host species, demonstrates that coffee plants serve as a reservoir for a wide variety of fungal endophytes that can be isolated from various plant tissues, including the seed, and illustrates the different fungal communities encountered by C. arabica in different coffee-growing regions of the world.

DNA sequences were determined for beta tubulin (BT2), calmodulin (CF), ITS and lsu rDNA (ID) and RNA polymerase II (RPB2) from ca. 460 Aspergillus isolates. RPB2 and rDNA sequences were combined and analyzed to determine relationships in the genus and in the family Trichocomaceae. Eupenicillium species form a statistically supported clade with origins among the Aspergillus clades. A. crystallinus, A. malodoratus and H. paradoxus are members of the Eupenicillium clade. A. zonatus, A. clavatoflvus and W. spinulosa occur in a clade along with Hamigera sp. Other than these exceptional species, Aspergillus species and sections occur on three strongly supported clades that descend from a polytomy. Section Versicolores as a monophyletic group includes only A. versicolor and A. sydowii and is superfluous. The other sections were retained but modified. All four loci were used in genealogical concordance analysis of species boundaries. Fennellia flavipes and F. nivea are not conspecific with their supposed anamorphs A. flavipes and A. nivea. Synonymies were found for some species and more than 20 undescribed taxa were identified in genealogical concordance analysis. Newly discovered taxa will be described elsewhere. Possibly paralogous gene fragments were amplified with the BT2 primers in sections Nidulantes, Usti and Nigri. Use of nonhomologous sequences in genealogical concordance analysis could lead to false conclusions and so BT2 sequences were not used in analysis of those sections.

Recent research suggests bi-directional interactions between the experience of pain and the process of sleep; pain interferes with the ability to obtain sleep, and disrupted sleep contributes to enhanced pain perception. Our group recently reported, in a controlled experimental study, that sleep fragmentation among healthy adults resulted in subsequent decrements in endogenous pain inhibition. The present report follows up that observation by extending this line of research to a sample of patients experiencing persistent pain. Patients with chronic temporomandibular joint disorder (TMD) pain were studied using polysomnography and psychophysical evaluation of pain responses. We assessed whether individual differences in sleep continuity and/or architecture were related to diffuse noxious inhibitory controls (DNIC), a measure of central nervous system pain inhibition. Among 53 TMD patients, higher sleep efficiency and longer total sleep time were positively associated with better functioning of DNIC (r=0.42-0.44, p<0.01; ps<0.05 for the multivariate analyses). These results suggest the possibility that disrupted sleep may serve as a risk factor for inadequate pain-inhibitory processing and hint that aggressive efforts to treat sleep disturbance early in the course of a pain condition might be beneficial in reducing the severity or impact of clinical pain.

ABSTRACT The rapid identification of bacteria and fungi directly from the blood of patients with suspected bloodstream infections aids in diagnosis and guides treatment decisions. The development of an automated, rapid, and sensitive molecular technology capable of detecting the diverse agents of such infections at low titers has been challenging, due in part to the high background of genomic DNA in blood. PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) allows for the rapid and accurate identification of microorganisms but with a sensitivity of about 50% compared to that of culture when using 1-ml whole-blood specimens. Here, we describe a new integrated specimen preparation technology that substantially improves the sensitivity of PCR/ESI-MS analysis. An efficient lysis method and automated DNA purification system were designed for processing 5 ml of whole blood. In addition, PCR amplification formulations were optimized to tolerate high levels of human DNA. An analysis of 331 specimens collected from patients with suspected bloodstream infections resulted in 35 PCR/ESI-MS-positive specimens (10.6%) compared to 18 positive by culture (5.4%). PCR/ESI-MS was 83% sensitive and 94% specific compared to culture. Replicate PCR/ESI-MS testing from a second aliquot of the PCR/ESI-MS-positive/culture-negative specimens corroborated the initial findings in most cases, resulting in increased sensitivity (91%) and specificity (99%) when confirmed detections were considered true positives. The integrated solution described here has the potential to provide rapid detection and identification of organisms responsible for bloodstream infections.

Novel species of fungi described in this study include those from various countries as follows: Antarctica: Cadophora antarctica from soil. Australia: Alfaria dandenongensis on Cyperaceae, Amphosoma persooniae on Persoonia sp., Anungitea nullicana on Eucalyptus sp., Bagadiella eucalypti on Eucalyptus globulus, Castanediella eucalyptigena on Eucalyptus sp., Cercospora dianellicola on Dianella sp., Cladoriella kinglakensis on Eucalyptus regnans, Cladoriella xanthorrhoeae (incl. Cladoriellaceae fam. nov. and Cladoriellales ord. nov.) on Xanthorrhoea sp., Cochlearomyces eucalypti (incl. Cochlearomyces gen. nov. and Cochlearomycetaceae fam. nov.) on Eucalyptus obliqua, Codinaea lambertiae on Lambertia formosa, Diaporthe obtusifoliae on Acacia obtusifolia, Didymella acaciae on Acacia melanoxylon, Dothidea eucalypti on Eucalyptus dalrympleana, Fitzroyomyces cyperi (incl. Fitzroyomyces gen. nov.) on Cyperaceae, Murramarangomyces corymbiae (incl. Murramarangomyces gen. nov., Murramarangomycetaceae fam. nov. and Murramarangomycetales ord. nov.) on Corymbia maculata, Neoanungitea eucalypti (incl. Neoanungitea gen. nov.) on Eucalyptus obliqua, Neoconiothyrium persooniae (incl. Neoconiothyrium gen. nov.) on Persoonia laurina subsp. laurina, Neocrinula lambertiae (incl. Neocrinulaceae fam. nov.) on Lambertia sp., Ochroconis podocarpi on Podocarpus grayae, Paraphysalospora eucalypti (incl. Paraphysalospora gen. nov.) on Eucalyptus sieberi, Pararamichloridium livistonae (incl. Pararamichloridium gen. nov., Pararamichloridiaceae fam. nov. and Pararamichloridiales ord. nov.) on Livistona sp., Pestalotiopsis dianellae on Dianella sp., Phaeosphaeria gahniae on Gahnia aspera, Phlogicylindrium tereticornis on Eucalyptus tereticornis, Pleopassalora acaciae on Acacia obliquinervia, Pseudodactylaria xanthorrhoeae (incl. Pseudodactylaria gen. nov., Pseudodactylariaceae fam. nov. and Pseudodactylariales ord. nov.) on Xanthorrhoea sp., Pseudosporidesmium lambertiae (incl. Pseudosporidesmiaceae fam. nov.) on Lambertia formosa, Saccharata acaciae on Acacia sp., Saccharata epacridis on Epacris sp., Saccharata hakeigena on Hakea sericea, Seiridium persooniae on Persoonia sp., Semifissispora tooloomensis on Eucalyptus dunnii, Stagonospora lomandrae on Lomandra longifolia, Stagonospora victoriana on Poaceae, Subramaniomyces podocarpi on Podocarpus elatus, Sympoventuria melaleucae on Melaleuca sp., Sympoventuria regnans on Eucalyptus regnans, Trichomerium eucalypti on Eucalyptus tereticornis, Vermiculariopsiella eucalypticola on Eucalyptus dalrympleana, Verrucoconiothyrium acaciae on Acacia falciformis, Xenopassalora petrophiles (incl. Xenopassalora gen. nov.) on Petrophile sp., Zasmidium dasypogonis on Dasypogon sp., Zasmidium gahniicola on Gahnia sieberiana.Brazil: Achaetomium lippiae on Lippia gracilis, Cyathus isometricus on decaying wood, Geastrum caririense on soil, Lycoperdon demoulinii (incl. Lycoperdon subg. Arenicola) on soil, Megatomentella cristata (incl. Megatomentella gen. nov.) on unidentified plant, Mutinus verrucosus on soil, Paraopeba schefflerae (incl. Paraopeba gen. nov.) on Schefflera morototoni, Phyllosticta catimbauensis on Mandevilla catimbauensis, Pseudocercospora angularis on Prunus persica, Pseudophialophora sorghi on Sorghum bicolor, Spumula piptadeniae on Piptadenia paniculata.Bulgaria: Yarrowia parophonii from gut of Parophonus hirsutulus. Croatia: Pyrenopeziza velebitica on Lonicera borbasiana.Cyprus: Peziza halophila on coastal dunes. Czech Republic: Aspergillus contaminans from human fingernail. Ecuador: Cuphophyllus yacurensis on forest soil, Ganoderma podocarpense on fallen tree trunk. England: Pilidium anglicum (incl. Chaetomellales ord. nov.) on Eucalyptus sp. France: Planamyces parisiensis (incl. Planamyces gen. nov.) on wood inside a house. French Guiana: Lactifluus ceraceus on soil. Germany: Talaromyces musae on Musa sp. India: Hyalocladosporiella cannae on Canna indica, Nothophoma raii from soil. Italy: Setophaeosphaeria citri on Citrus reticulata, Yuccamyces citri on Citrus limon.Japan: Glutinomyces brunneus (incl. Glutinomyces gen. nov.) from roots of Quercus sp. Netherlands (all from soil): Collariella hilkhuijsenii, Fusarium petersiae, Gamsia kooimaniorum, Paracremonium binnewijzendii, Phaeoisaria annesophieae, Plectosphaerella niemeijerarum, Striaticonidium deklijnearum, Talaromyces annesophieae, Umbelopsis wiegerinckiae, Vandijckella johannae (incl. Vandijckella gen. nov. and Vandijckellaceae fam. nov.), Verhulstia trisororum (incl. Verhulstia gen. nov.). New Zealand: Lasiosphaeria similisorbina on decorticated wood. Papua New Guinea: Pseudosubramaniomyces gen. nov. (based on Pseudosubramaniomyces fusisaprophyticus comb. nov.). Slovakia: Hemileucoglossum pusillum on soil. South Africa: Tygervalleyomyces podocarpi (incl. Tygervalleyomyces gen. nov.) on Podocarpus falcatus.Spain: Coniella heterospora from herbivorous dung, Hymenochaete macrochloae on Macrochloa tenacissima, Ramaria cistophila on shrubland of Cistus ladanifer.Thailand: Polycephalomyces phaothaiensis on Coleoptera larvae, buried in soil. Uruguay: Penicillium uruguayense from soil. Vietnam: Entoloma nigrovelutinum on forest soil, Volvariella morozovae on wood of unknown tree. Morphological and culture characteristics along with DNA barcodes are provided.

ß-tubulin, calmodulin, internal transcribed spacer and partial Isu-rDNA, RNA polymerase 2, DNA replication licensing factor Mcm7, and pre-rRNA processing protein Tsr1 were amplified and sequenced from numerous isolates belonging to Aspergillus sect, versicolor. The isolates were analyzed phylogenetically using the concordance model to establish species boundaries. Aspergillus austroafricanus, A. creber, A. cvjetkovicii, A. fructus, A. jensenii, A. puulaauensis, A. subversicolor, A. tennesseensis and A. venenatus are described as new species and A. amoenus, A. protuberus, A. sydowii, A. tabacinus and A. versicolor are accepted as distinct species on the basis of molecular and phenotypic differences. PCR primer pairs used to detect A. versicolor in sick building syndrome studies have a positive reaction for all of the newly described species except A. subversicolor.

In this work, we investigate the use of a three-stage Compton camera to measure secondary prompt gamma rays emitted from patients treated with proton beam radiotherapy. The purpose of this study was (1) to develop an optimal three-stage Compton camera specifically designed to measure prompt gamma rays emitted from tissue and (2) to determine the feasibility of using this optimized Compton camera design to measure and image prompt gamma rays emitted during proton beam irradiation. The three-stage Compton camera was modeled in Geant4 as three high-purity germanium detector stages arranged in parallel-plane geometry. Initially, an isotropic gamma source ranging from 0 to 15 MeV was used to determine lateral width and thickness of the detector stages that provided the optimal detection efficiency. Then, the gamma source was replaced by a proton beam irradiating a tissue phantom to calculate the overall efficiency of the optimized camera for detecting emitted prompt gammas. The overall calculated efficiencies varied from ∼10−6 to 10−3 prompt gammas detected per proton incident on the tissue phantom for several variations of the optimal camera design studied. Based on the overall efficiency results, we believe it feasible that a three-stage Compton camera could detect a sufficient number of prompt gammas to allow measurement and imaging of prompt gamma emission during proton radiotherapy.

Section Terrei of Aspergillus was studied using a polyphasic approach including sequence analysis of parts of the β-tubulin and calmodulin genes and the ITS region, macro-and micromorphological analyses and examination of extrolite profiles to describe three new species in this section.Based on phylogenetic analysis of calmodulin and β-tubulin sequences seven lineages were observed among isolates that have previously been treated as A. terreus and its subspecies by Raper & Fennell (1965) and others.Aspergillus alabamensis, A. terreus var.floccosus, A. terreus var.africanus, A. terreus var.aureus, A. hortai and A. terreus NRRL 4017 all represent distinct lineages from the A. terreus clade.Among them, A. terreus var.floccosus, A. terreus NRRL 4017 and A. terreus var.aureus could also be distinguished from A. terreus by using ITS sequence data.New names are proposed for A. terreus var.floccosus, A. terreus var.africanus, A. terreus var.aureus, while Aspergillus hortai is recognised at species level.Aspergillus terreus NRRL 4017 is described as the new species A. pseudoterreus.Also included in section Terrei are some species formerly placed in sections Flavipedes and Versicolores.A. clade including the type isolate of A. niveus (CBS 115.27) constitutes a lineage closely related to A. carneus.Fennellia nivea, the hypothesized teleomorph is not related to this clade.Aspergillus allahabadii, A. niveus var.indicus, and two species originally placed in section Versicolores, A. ambiguus and A. microcysticus, also form well-defined lineages on all trees.Species in Aspergillus section Terrei are producers of a diverse array of secondary metabolites.However, many of the species in the section produce different combinations of the following metabolites: acetylaranotin, asperphenamate, aspochalamins, aspulvinones, asteltoxin, asterric acid, asterriquinones, aszonalenins, atrovenetins, butyrolactones, citreoisocoumarins, citreoviridins, citrinins, decaturins, fulvic acid, geodins, gregatins, mevinolins, serantrypinone, terreic acid (only the precursor 3,6-dihydroxytoluquinone found), terreins, terrequinones, terretonins and territrems.The cholesterol-lowering agent mevinolin was found in A. terreus and A. neoafricanus only.The hepatotoxic extrolite citrinin was found in eight species: A.

We tested the ability of a single Compton camera (CC) to produce 3-dimensional (3D) images of prompt gammas (PGs) emitted during the irradiation of a tissue-equivalent plastic phantom with proton pencil beams for clinical doses delivered at clinical dose rates. PG measurements were made with a small prototype CC placed at three different locations along the proton beam path. We evaluated the ability of the CC to produce images at each location for two clinical scenarios: (1) the delivery of a single 2 Gy pencil beam from a hypo-fractionated treatment (~9 × 108 protons), and (2) a single pencil beam from a standard treatment (~1 × 108 protons). Additionally, the data measured at each location were combined to simulate measurements with a larger scale, clinical CC and its ability to image shifts in the Bragg peak (BP) range for both clinical scenarios. With our prototype CC, the location of the distal end of the BP could be seen with the CC placed up to 4 cm proximal or distal to the BP distal falloff. Using the data from the simulated full scale clinical CC, 3D images of the PG emission were produced with the delivery of as few as 1 × 108 protons, and shifts in the proton beam range as small as 2 mm could be detected for delivery of a 2 Gy spot. From these results we conclude that 3D PG imaging for proton range verification under clinical beam delivery conditions is possible with a single CC.

Aspergillus section Aspergillus contains economically important, xerophilic fungi that are widely distributed in nature and the human environment and are known for their ability to grow on substrates with low water activity. The taxa were revised based on sequence data from four loci, PCR fingerprinting, micro- and macromorphology, and physiology. The number of taxa was reduced to 17 species, all of which can be distinguished with sequence data from either the caM or RPB2 locus. The original description of A. proliferans was supplemented by a description of its teleomorph. This species seems to be relatively common and often has been confused with A. glaucus. In addition, green sporulating isolates of A. niveoglaucus isolated from food and several other substrates are indistinguishable in phenotype from A. glaucus. A dichotomous key based on ascospore size and ornamentation and the ability to grow at specific combinations of temperature and water activity is provided for identification of species. In response to recent changes in the botanical code, we transferred the Eurotium species to Aspergillus and selected one name for each species.

Aspergillus section Restricti together with sister section Aspergillus (formerly Eurotium) comprises xerophilic species, that are able to grow on substrates with low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus Aspergillus and applied a multidisciplinary approach for definition of species boundaries in sect. Restricti. The monophyly of sections Aspergillus and Restricti was tested on a set of 102 isolates comprising all currently accepted species and was strongly supported by Maximum likelihood (ML) and Bayesian inferrence (BI) analysis based on β-tubulin (benA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) loci. More than 300 strains belonging to sect. Restricti from various isolation sources and four continents were characterized by DNA sequencing, and 193 isolates were selected for phylogenetic analyses and phenotypic studies. Species delimitation methods based on multispecies coalescent model were employed on DNA sequences from four loci, i.e., ID region of rDNA (ITS + 28S), CaM, benA and RPB2, and supported recognition of 21 species, including 14 new. All these species were also strongly supported in ML and BI analyses. All recognised species can be reliably identified by all four examined genetic loci. Phenotype analysis was performed to support the delimitation of new species and includes colony characteristics on seven cultivation media incubated at several temperatures, growth on an osmotic gradient (six media with NaCl concentration from 0 to 25 %) and analysis of morphology including scanning electron microscopy. The micromorphology of conidial heads, vesicle dimensions, temperature profiles and growth parameters in osmotic gradient were useful criteria for species identification. The vast majority of species in sect. Restricti produce asperglaucide, asperphenamate or both in contrast to species in sect. Aspergillus. Mycophenolic acid was detected for the first time in at least six members of the section. The ascomata of A. halophilicus do not contain auroglaucin, epiheveadride or flavoglaucin which are common in sect. Aspergillus, but shares the echinulins with sect. Aspergillus.

AbstractA new aflatoxigenic species of Aspergillus, A. bombycis, was discovered during isolation of fungi from insect frass collected in silkworm rearing houses in Japan. The new species resembles A. flavus, but produces B and G aflatoxins. It is distinguished from A. flavus and A. nomius by differences in growth rates at 37 and 42 C, from A. nomius by roughness of the stipe, and from both of these species by differences in the nucleotide sequences in the beta-tubulin, calmodulin, norsolorinic acid reductase, ITS, and lsu-rDNA genes. Aspergillus bombycis is known from nine isolates, eight collected in silkworm-rearing houses in Japan and one collected in a silk-worm rearing house in Indonesia. Phylogenetic analysis of the DNA sequences shows that A. bombycis is a phylogenetically distinct species which is most closely related to A. nomius and which belongs in Aspergillus section Flavi. Analysis by partition homogeneity did not reveal evidence of genetic recombination in A. bombycis, but in A. nomius the patterns of polymorphisms in different genes strongly suggest cryptic genetic recombination.Key Words: aflatoxinfungimolecular systematicsribosomal DNA sequence

The genetic and implicit taxonomic resolution provided by ribosomal RNA sequence divergence was estimated from comparisons of sibling yeast species. Two regions of the large subunit (25S) rRNA and four regions of the small subunit (18S) rRNA comprising a total of 855 nucleotides were examined in all strains. Within these regions, no nucleotide differences were detected between strains of the same species. The sibling species pairs Pichia mississippiensis/P. amylophila, P. americana/P. bimundalis, and Issatchenkia scutulata and its variety exigua could be separated from each other by differences in a ca. 200-base region of the large subunit rRNA. Sequence differences within the sibling species complex composed of Saccharomyces bayanus, S. pastorianius (S. carlsbergensis), and S. cerevisiae were consistent with the prior proposal that S. pastorianus is a partial amphidiploid formed by a rare mating between the other two Saccharomyces species. From these data, the highly variable region identified in the 25S subunit rRNA appears suitable for rapid separation of nearly all species by oligonucleotide probe technology.

In this paper, we present the results of a preliminary study of secondary 'prompt' gamma-ray emission produced by proton–nuclear interactions within tissue during proton radiotherapy. Monte Carlo simulations were performed for mono-energetic proton beams, ranging from 2.5 MeV to 250 MeV, irradiating elemental and tissue targets. Calculations of the emission spectra from different biological tissues and their elemental components were made. Also, prompt gamma rays emitted during delivery of a clinical proton spread-out Bragg peak (SOBP) in a homogeneous water phantom and a water phantom containing heterogeneous tissue inserts were calculated to study the correlation between prompt gamma-ray production and proton dose delivery. The results show that the prompt gamma-ray spectra differ significantly for each type of tissue studied. The relative intensity of the characteristic gamma rays emitted from a given tissue was shown to be proportional to the concentration of each element in that tissue. A strong correlation was found between the delivered SOBP dose distribution and the characteristic prompt gamma-ray production. Based on these results, we discuss the potential use of prompt gamma-ray emission as a method to verify the accuracy and efficacy of doses delivered with proton radiotherapy.

In this paper, we present results of initial measurements and calculations of prompt gamma ray spectra (produced by proton–nucleus interactions) emitted from tissue equivalent phantoms during irradiations with proton beams. Measurements of prompt gamma ray spectra were made using a high-purity germanium detector shielded either with lead (passive shielding), or a Compton suppression system (active shielding). Calculations of the spectra were performed using a model of both the passive and active shielding experimental setups developed using the Geant4 Monte Carlo toolkit. From the measured spectra it was shown that it is possible to distinguish the characteristic emission lines from the major elemental constituent atoms (C, O, Ca) in the irradiated phantoms during delivery of proton doses similar to those delivered during patient treatment. Also, the Monte Carlo spectra were found to be in very good agreement with the measured spectra providing an initial validation of our model for use in further studies of prompt gamma ray emission during proton therapy.

Aspergillus section Flavipedes contains species found worldwide in soils and rhizospheres, indoor and cave environments, as endophytes, food contaminants and occasionally as human pathogens. They produce many extensively studied bioactive secondary metabolites and biotechnologically relevant enzymes. The taxa were revised based on phylogenetic analysis of sequences from four loci (β-tubulin, calmodulin, RPB2, ITS rDNA), two PCR fingerprinting methods, micro- and macromorphology and physiology. Section Flavipedes includes three known and seven new species: A. ardalensis, A. frequens, A. luppii, A. mangaliensis, A. movilensis, A. polyporicola and A. spelaeus. The name A. neoflavipes was proposed for Fennellia flavipes a distinct species from its supposed asexual state A. flavipes. Aspergillus iizukae, A. frequens and A. mangaliensis are the most common and widely distributed species, whereas A. flavipes s. str. is rare. A dichotomous key based on the combination of morphology and physiology is provided for all recognized species. Aspergillus section Jani is established to contain A. janus and A. brevijanus, species previously classified as members of sect. Versicolores, Terrei or Flavipedes. This new section is strongly supported by phylogenetic data and morphology. Section Jani species produce three types of conidiophores and conidia, and colonies have green and white sectors making them distinctive. Accessory conidia found in pathogenic A. terreus were found in all members of sects. Flavipedes and Jani. Our data indicated that A. frequens is a clinically relevant and produces accessory conidia during infection.

Aspergillus section Fumigati contains 12 clinically relevant species. Among these Aspergillus species, A. fumigatus is the most frequent agent of invasive aspergillosis, followed by A. lentulus and A. viridinutans. Genealogical concordance and mating experiments were performed to examine the relationship between phylogenetic distance and mating success in these three heterothallic species. Analyses of 19 isolates from section Fumigati revealed the presence of three previously unrecognized species within the broadly circumscribed species A. viridinutans. A single mating type was found in the new species Aspergillus pseudofelis and Aspergillus pseudoviridinutans, but in Aspergillus parafelis, both mating types were present. Reciprocal interspecific pairings of all species in the study showed that the only successful crosses occurred with the MAT1-2 isolates of both A. parafelis and A. pseudofelis. The MAT1-2 isolate of A. parafelis was fertile when paired with the MAT1-1 isolates of A. fumigatus, A. viridinutans, A. felis, A. pseudoviridinutans, and A. wyomingensis but was not fertile with the MAT1-1 isolate of A. lentulus. The MAT1-2 isolates of A. pseudofelis were fertile when paired with the MAT1-1 isolate of A. felis but not with any of the other species. The general infertility in the interspecies crossings suggests that genetically unrelated species are also biologically incompatible, with the MAT1-2 isolates of A. parafelis and A. pseudofelis being the exception. Our findings underscore the importance of genealogical concordance analysis for species circumscription, as well as for accurate species identification, since misidentification of morphologically similar pathogens with differences in innate drug resistance may be of grave consequences for disease management.

Poly(β-L-malic acid) (PMA) is a natural biopolyester that has pharmaceutical applications and other potential uses. In this study, we examined PMA production by 56 strains of the fungus Aureobasidium pullulans representing genetically diverse phylogenetic clades. Thirty-six strains were isolated from various locations in Iceland and Thailand. All strains from Iceland belonged to a newly recognized clade 13, while strains from Thailand were distributed among 8 other clades, including a novel clade 14. Thirty of these isolates, along with 26 previously described strains, were examined for PMA production in medium containing 5% glucose. Most strains produced at least 4 g PMA/L, and several strains in clades 9, 11, and 13 made 9-11 g PMA/L. Strains also produced both pullulan and heavy oil, but PMA isolated by differential precipitation in ethanol exhibited up to 72% purity with no more than 12% contamination by pullulan. The molecular weight of PMA from A. pullulans ranged from 5.1 to 7.9 kDa. Results indicate that certain genetic groups of A. pullulans are promising for the production of PMA.

In this paper, we study the feasibility of using the stochastic origin ensemble (SOE) algorithm for reconstructing images of secondary gammas emitted during proton radiotherapy from data measured with a three-stage Compton camera. The purpose of this study was to evaluate the quality of the images of the gamma rays emitted during proton irradiation produced using the SOE algorithm and to measure how well the images reproduce the distal falloff of the beam. For our evaluation, we performed a Monte Carlo simulation of an ideal three-stage Compton camera positioned above and orthogonal to a proton pencil beam irradiating a tissue phantom. Scattering of beam protons with nuclei in the phantom produces secondary gamma rays, which are detected by the Compton camera and used as input to the SOE algorithm. We studied the SOE reconstructed images as a function of the number of iterations, the voxel probability parameter, and the number of detected gammas used by the SOE algorithm. We quantitatively evaluated the capabilities of the SOE algorithm by calculating and comparing the normalized mean square error (NMSE) of SOE reconstructed images. We also studied the ability of the SOE reconstructed images to predict the distal falloff of the secondary gamma production in the irradiated tissue. Our results show that the images produced with the SOE algorithm converge in ~10,000 iterations, with little improvement to the image NMSE for iterations above this number. We found that the statistical noise of the images is inversely proportional to the ratio of the number of gammas detected to the SOE voxel probability parameter value. In our study, the SOE predicted distal falloff of the reconstructed images agrees with the Monte Carlo calculated distal falloff of the gamma emission profile in the phantom to within ±0.6 mm for the positions of maximum emission (100%) and 90%, 50% and 20% distal falloff of the gamma emission profile. We conclude that the SOE algorithm is an effective method for reconstructing images of a proton pencil beam from the data collected by an ideal Compton camera and that these images accurately model the distal falloff of secondary gamma emission during proton irradiation.

Bloodstream infection (BSI) and sepsis are rising in incidence throughout the developed world. The spread of multi-drug resistant organisms presents increasing challenges to treatment. Surviving BSI is dependent on rapid and accurate identification of causal organisms, and timely application of appropriate antibiotics. Current culture-based methods used to detect and identify agents of BSI are often too slow to impact early therapy and may fail to detect relevant organisms in many positive cases. Existing methods for direct molecular detection of microbial DNA in blood are limited in either sensitivity (likely the result of small sample volumes) or in breadth of coverage, often because the PCR primers and probes used target only a few specific pathogens. There is a clear unmet need for a sensitive molecular assay capable of identifying the diverse bacteria and yeast associated with BSI directly from uncultured whole blood samples. We have developed a method of extracting DNA from larger volumes of whole blood (5 ml per sample), amplifying multiple widely conserved bacterial and fungal genes using a mismatch- and background-tolerant PCR chemistry, and identifying hundreds of diverse organisms from the amplified fragments on the basis of species-specific genetic signatures using electrospray ionization mass spectrometry (PCR/ESI-MS). We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. The assay generated matching results in 80% of culture-positive cases (86% when common contaminants were excluded from the analysis), and twice the total number of positive detections. The described method is capable of providing organism identifications directly from uncultured blood in less than 8 hours. Disclaimer: The IRIDICA BAC BSI Assay is not available in the United States.

Phylogenetic relationships among heterobasidiomycetous yeasts, including anamorphic and teleomorphic taxa, have been compared from the sequence similarity of small (18S) and large (25S) subunit ribosomal RNA. Species examined were Cystofilobasidium capitatum, Filobasidiella neoformans, Filobasidium floriforme, Leucosporidium scottii, Malassezia furfur, M. pachydermatis, Phaffia rhodozyma, Rhodosporidium toruloides, Sporidiobolus johnsonii, Sterigmatosporidium polymorphum, Trichosporon beigelii, T. cutaneum and T. pullulans. The taxa cluster into three main groups. One group contains the nonteliospore forming genera Sterigmatosporidium, Filobasidiella, Filobasidium and the anamorphic species T. beigelii and T. cutaneum. The teliospore formers Leucosporidium, Rhodosporidium and Sporidiobolus, all of which have simple septal pores, cluster into a single group, despite the heterogeneity of carotenoid formation. By contrast, C. capitatum appears separate, not only from Rhodosporidium, but also from the Filobasidiaceae with which it shares a primitive dolipore septum. The uniqueness of the genus Malassezia among yeasts is confirmed, and one might predict from nucleotide sequence similarity that teleomorphs of those lipophilic organisms would form teliospores whereas Trichosporon beigelii and T. cutaneum appear related to the family Filobasidiaceae.

Tissues from Coffea arabica, C. congensis, C. dewevrei and C. liberica collected in Colombia, Hawaii and at a local plant nursery in Maryland were sampled for the presence of fungal endophytes. Surface sterilized tissues including roots, leaves, stems and various berry parts were plated on yeast-malt agar. DNA was extracted from a set of isolates visually recognized as Penicillium, and the internal transcribed spacer region and partial LSU-rDNA was amplified and sequenced. Comparison of DNA sequences with GenBank and unpublished sequences revealed the presence of 11 known Penicillium species: P. brevicompactum, P. brocae, P. cecidicola, P. citrinum, P. coffeae, P. crustosum, P. janthinellum, P. olsonii, P. oxalicum, P. sclerotiorum and P. steckii as well as two possibly undescribed species near P. diversum and P. roseopurpureum. Ochratoxin A was produced by only four isolates, one isolate each of P. brevicompactum, P. crustosum, P. olsonii and P. oxalicum. The role these endophytes play in the biology of the coffee plant remains enigmatic.

Phylogenetic analyses of sequences generated from portions of three genes coding for the proteins enolase (enoA), beta-tubulin (benA), and calmodulin (calM) of a large number of isolates within the section Terrei, genus Aspergillus, revealed the presence of a new cryptic species within this section, Aspergillus alabamensis. Most members of this new cryptic species were recovered as colonizing isolates from immunocompetent patient populations, had decreased in vitro susceptibilities to the antifungal drug amphotericin B, and were morphologically similar to but genetically distinct from Aspergillus terreus isolates.

Aureobasidium pullulans is the source of the commercially valuable polysaccharide pullulan and the enzyme xylanase. Isolates are typically off-white to pale pink or black on solid media, while some tropical isolates have been described as 'color variants' with bright pigments of red, yellow or purple. We sequenced 5 loci (internal transcribed spacer, intergenic spacer 1, translation elongation factor-1 alpha, beta tubulin, and RNA polymerase II) from 45 new isolates from Thailand. Based on the phylogenetic analyses, isolates were classified into 12 clades. Each clade showed different colors on different culture media including two clades with 'color variants' and some clades exhibited high levels of pullulan production or xylanase activity. Colony characteristics do not correlate perfectly with DNA sequence phylogeny or the physiological characters, but DNA sequence differences rapidly identify isolates with genetic novelty.

Célia Soaresa, Paula Rodriguesb, Stephen W. Petersonc, Nelson Lima & Armando Venâncio*aa Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057, Braga, Portugalb Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal, and CIMO-Escola Superior Agrária de Bragança, Campus Santa Apolónia, 5301-855 Bragança, Portugalc Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, US Department of Agriculture 1815 North University Street Peoria, Illinois 61604

ABSTRACT Emmonsia crescens , an agent of adiaspiromycosis, Blastomyces dermatitidis , the agent of blastomycosis, and Histoplasma capsulatum , the agent of histoplasmosis, are known to form meiotic (sexual) stages in the ascomycete genus Ajellomyces ( Onygenaceae , Onygenales ), but no sexual stage is known for E. parva , the type species of the genus Emmonsia . To evaluate relationships among members of the putative Ajellomyces clade, large-subunit ribosomal and internal transcribed spacer region DNA sequences were determined from PCR-amplified DNA fragments. Sequences were analyzed phylogenetically to evaluate the genetic variation within the genus Emmonsia and evolutionary relationships to other taxa. E. crescens and E. parva are distinct species. E. crescens isolates are placed into two groups that correlate with their continents of origin. Considerable variation occurred among isolates previously classified as E. parva . Most isolates are placed into two closely related groups, but the remaining isolates, including some from human sources, are phylogenetically distinct and represent undescribed species. Strains of B. dermatitidis are a sister species of E. parva . Paracoccidioides brasiliensis and Histoplasma capsulatum are ancestral to most Emmonsia isolates, and P. brasiliensis , which has no known teleomorph, falls within the Ajellomyces clade.

Maintaining and preserving fungal cultures are essential elements of systematics and biodiversity studies. Because fungi are such a diverse group, several methods of cultivation and preservation are required to ensure the viability and morphological, physiological, and genetic integrity of the cultures over time. The cost and convenience of each method, however, also must be considered. We encourage the reader to investigate the excellent papers on fungal preservation by Fennell 1960), Smith and Onions (1994), Smith (1991), and Simione and Brown (1991). The primary methods of culture preservation are continuous growth, drying, and freezing. Continuous growth methods, in which cultures are grown on agar, typically are used for short-term storage. Such cultures are stored at temperatures of from 5°-20°C, or they may be frozen to increase the interval between subcultures. The methods are simple and inexpensive because specialized equipment is not required. Drying is the most useful method of preservation for cultures that produce spores or other resting structures. Silica gel, glass beads, and soil are substrata commonly used in drying. Fungi have been stored successfully on silica gel for up to 11 years (Smith and Onions 1983). Drying methods are technically simple and also do not require expensive equipment. Freezing methods, including cryopreservation, are versatile and widely applicable. Most fungi can be preserved, with or without cryoprotectants, in liquid nitrogen or in standard home freezers. With freezedrying, or lyophilization, the fungal cultures are frozen and subsequently dried under vacuum. The method is highly successful with cultures that produce mitospores. Freeze-drying and freezing below -1 35°C are excellent methods for permanent preservation, and we highly recommend them. However, both methods require specialized and expensive equipment, as described in the next section (see “Liquid Nitrogen” and “Lyophilization” under “Long-term Preservation,” later in this chapter). The choice of preservation method depends on the species of concern, the resources available, and the goal

Re-examination of some species in the genus Neosartorya was prompted by the receipt of a Neosartorya strain isolated at autopsy from a fungal lesion occurring in human neck vertebrae (although the fungal lesion was not the proximal cause of death). The ascospore morphology of this clinical strain did not match that of any species description, but was identical to that of a strain of Aspergillus fischeri var. thermomutatus ex type. Examination of type material of A. fischeri var. thermomutatus showed that this taxon had been inadequately described. The anamorph is raised to species rank as Aspergillus thermomutatus, and the teleomorph is described as the new species Neosartorya pseudofischeri. Genetic similarity studies were conducted to aid in determining the correct taxonomic rank of the organism.

Eighty years ago, Alexander Fleming described the antibiotic effects of a fungus that had contaminated his bacterial culture, kick starting the antimicrobial revolution. The fungus was later ascribed to a putatively globally distributed asexual species, Penicillium chrysogenum. Recently, the species has been shown to be genetically diverse, and possess mating-type genes. Here, phylogenetic and population genetic analyses show that this apparently ubiquitous fungus is actually composed of at least two genetically distinct species with only slight differences detected in physiology. We found each species in air and dust samples collected in and around St Mary's Hospital where Fleming worked. Genotyping of 30 markers across the genome showed that preserved fungal material from Fleming's laboratory was nearly identical to derived strains currently in culture collections and in the same distinct species as a wild progenitor strain of current penicillin producing industrial strains rather than the type species P. chrysogenum. Global samples of the two most common species were found to possess mating-type genes in a near 1:1 ratio, and show evidence of recombination with little geographic population subdivision evident. However, no hybridization was detected between the species despite an estimated time of divergence of less than 1MYA. Growth studies showed significant interspecific inhibition by P. chrysogenum of the other common species, suggesting that competition may facilitate species maintenance despite globally overlapping distributions. Results highlight under-recognized diversity even among the best-known fungal groups and the potential for speciation despite overlapping distribution.

Aspergillus floridensis and A. trinidadensis spp. nov. are described as novel uniseriate species of Aspergillus section Nigri isolated from air samples. To describe the species we used phenotypes from 7-d Czapek yeast extract agar culture (CYA), creatine agar culture (CREA) and malt extract agar culture (MEA), with support by molecular analysis of the β-tubulin, calmodulin, RNA polymerase II (RPB2), and translation elongation factor-alpha (TEF) gene amplified and sequenced from 56 air isolates and one isolate from almonds belonging to Aspergillus sectionNigri.Aspergillus floridensis is closely related to A. aculeatus, and A. trinidadensis is closely related to A. aculeatinus. Aspergillus brunneoviolaceus (syn. A. fijiensis) and A. uvarum are reported for the first time from the USA and from the indoor air environment. The newly described species do not produce ochratoxin A.

The most common cause of invasive aspergillosis (IA) in patients with chronic granulomatous disease (CGD) is Aspergillus fumigatus followed by A. nidulans; other aspergilli rarely cause the disease. Here we review two clinical cases of fatal IA in CGD patients and describe a new etiologic agent of IA refractory to antifungal therapy. Unlike typical IA caused by A. fumigatus, the disease caused by the new species was chronic and spread from the lung to multiple adjacent organs. Mycological characteristics and the phylogenetic relationship with other aspergilli based on the sequence analysis of Mcm7, RPB2, and Tsr1 indicated that the new species, which we named as A. tanneri, belongs to Aspergillus section Circumdati. The species has a higher amphotericin B, voriconazole, and itraconazole MIC and causes more chronic infection in CGD mice than A. fumigatus. This is the first report documenting IA in CGD patients caused by a species belonging to the Aspergillus section Circumdati that is inherently resistant to azoles and amphotericin B. Unlike the results seen with many members of Aspergillus section Circumdati, ochratoxin was not detected in filtrates of cultures grown in various media. Our phenotypic and genetic characterization of the new species and the case reports will assist future diagnosis of infection caused by A. tanneri and lead to more appropriate patient management.

Prompt gamma rays emitted from biological tissues during proton irradiation carry dosimetric and spectroscopic information that can assist with treatment verification and provide an indication of the biological response of the irradiated tissues. Compton cameras are capable of determining the origin and energy of gamma rays. However, prompt gamma monitoring during proton therapy requires new Compton camera designs that perform well at the high gamma energies produced when tissues are bombarded with therapeutic protons. In this study we optimize the materials and geometry of a three-stage Compton camera for prompt gamma detection and calculate the theoretical efficiency of such a detector. The materials evaluated in this study include germanium, bismuth germanate (BGO), NaI, xenon, silicon and lanthanum bromide (LaBr(3)). For each material, the dimensions of each detector stage were optimized to produce the maximum number of relevant interactions. These results were used to predict the efficiency of various multi-material cameras. The theoretical detection efficiencies of the most promising multi-material cameras were then calculated for the photons emitted from a tissue-equivalent phantom irradiated by therapeutic proton beams ranging from 50 to 250 MeV. The optimized detector stages had a lateral extent of 10 × 10 cm(2) with the thickness of the initial two stages dependent on the detector material. The thickness of the third stage was fixed at 10 cm regardless of material. The most efficient single-material cameras were composed of germanium (3 cm) and BGO (2.5 cm). These cameras exhibited efficiencies of 1.15 × 10(-4) and 9.58 × 10(-5) per incident proton, respectively. The most efficient multi-material camera design consisted of two initial stages of germanium (3 cm) and a final stage of BGO, resulting in a theoretical efficiency of 1.26 × 10(-4) per incident proton.

Detection of pathogens in bloodstream infections is important for directing antimicrobial treatment, but current culture-based approaches can be problematic. Broad-range PCR assays which target conserved genomic motifs for postamplification amplicon analysis permit detection of sepsis-causing pathogens. Comparison of different broad-range assays is important for informing future implementation strategies. In this study, we compared positive-blood-culture bottles processed by PCR coupled to high-resolution melting curve analysis (PCR/HRMA) and PCR coupled to electrospray ionization-mass spectrometry (PCR/ESI-MS) to microbiology culture results. Genus-level concordance was 90% (confidence interval [CI], 80 to 96%) for PCR/HRMA and 94% (CI, 85 to 98%) for PCR/ESI-MS. Species-level concordance was 90% (CI, 80 to 96%) for PCR/HRMA and 86% (CI, 75 to 93%) for PCR/ESI-MS. Unlike PCR/HRMA, PCR/ESI-MS was able to resolve polymicrobial samples. Our results demonstrated that the two assays have similar overall concordance rates but may have different roles as potential adjunctive tests with standard blood culture, since each method has different capabilities, advantages, and disadvantages.

We studied the application of a deep, fully connected Neural Network (NN) to process prompt gamma (PG) data measured by a Compton camera (CC) during the delivery of clinical proton radiotherapy beams. The network identifies 1) recorded “bad” PG events arising from background noise during the measurement, and 2) the correct ordering of PG interactions in the CC to help improve the fidelity of “good” data used for image reconstruction. PG emission from a tissue-equivalent target during irradiation with a 150 MeV proton beam delivered at clinical dose rates was measured with a prototype CC. Images were reconstructed from both the raw measured data and the measured data that was further processed with a neural network (NN) trained to identify “good” and “bad” PG events and predict the ordering of individual interactions within the good PG events. We determine if NN processing of the CC data could improve the reconstructed PG images to a level in which they could provide clinically useful information about the in vivo range and range shifts of the proton beams delivered at full clinical dose rates. Results showed that a deep, fully connected NN improved the achievable contrast to noise ratio (CNR) in our images by more than a factor of 8x. This allowed the path, range, and lateral width of the clinical proton beam within a tissue equivalent target to easily be identified from the PG images, even at the highest dose rates of a 150 MeV proton beam used for clinical treatments. On average, shifts in the beam range as small as 3 mm could be identified. However, when limited by the amount of PG data measured with our prototype CC during the delivery of a single proton pencil beam (∼1 × 10 9 protons), the uncertainty in the reconstructed PG images limited the identification of range shift to ∼5 mm. Substantial improvements in CC images were obtained during clinical beam delivery through NN pre-processing of the measured PG data. We believe this shows the potential of NNs to help improve and push CC-based PG imaging toward eventual clinical application for proton RT treatment delivery verification.

Penicillium coffeae is described as a novel endophyte isolated from a Coffea arabica L. plant in Hawaii. The species is slow growing with short, vesiculate, monoverticillate conidiophores. Phylogenetic analysis using three loci shows that P. coffeae forms a strongly supported clade with P. fellutanum, P. charlesii, P. chermesinum, P. indicum, P. phoeniceum and P. brocae. Phenotypic ally these species are quite similar but can be distinguished. The EF-1α gene from P. fellutanum, P. charlesii, P. chermesinum and P. indicum lack introns, P. coffeae and P. phoeniceum have a previously unknown intron at codon 20 and P. brocae and P. thiersii isolates have a single intron at codon 26. The most parsimonious interpretation of intron changes on the strongly supported phylogenetic tree requires the gain of a novel intron at position 20 and loss of intron 26 to arrive at the current distribution of introns in this gene. This is one of only a few examples of intron gain in genes.

Penicillium coffeae is described as a novel endophyte isolated from a Coffea arabica L. plant in Hawaii. The species is slow growing with short, vesiculate, monoverticillate conidiophores. Phylogenetic analysis using three loci shows that P. coffeae forms a strongly supported clade with P. fellutanum, P. charlesii, P. chermesinum, P. indicum, P. phoeniceum and P. brocae. Phenotypic ally these species are quite similar but can be distinguished. The EF-1α gene from P. fellutanum, P. charlesii, P. chermesinum and P. indicum lack introns, P. coffeae and P. phoeniceum have a previously unknown intron at codon 20 and P. brocae and P. thiersii isolates have a single intron at codon 26. The most parsimonious interpretation of intron changes on the strongly supported phylogenetic tree requires the gain of a novel intron at position 20 and loss of intron 26 to arrive at the current distribution of introns in this gene. This is one of only a few examples of intron gain in genes.

Aureobasidium thailandense sp. nov. is described from cultures of material collected on leaves and wooden surfaces in Thailand and the type isolate is NRRL 58539(T). Phylogenetically it is distinct from other species of the genus Aureobasidium. Phenotypically it is distinguished by its cardinal growth temperatures, salt tolerance and production of reddish brown hyphal pigmentation in PDA cultures, but micro-morphologically it is not clearly distinguishable from Aureobasidium pullulans. Unlike A. pullulans, A. thailandense sp. nov. produces a non-pullulan extracellular polysaccharide whose characteristics are unknown. The two known isolates of A. thailandense sp. nov. possess an approx. 500 bp type I intron in the 18S rRNA gene that is present in ITS amplifications using primers ITS4 and ITS5. A. pullulans isolates uniformly lack this intron.

A sclerotium-forming member of Aspergillus section Nigri was sampled from a population in a single field in North Carolina, USA, and identified as A. tubingensis based on genealogical concordance analysis. Aspergillus tubingensis was shown to be heterothallic, with individual strains containing either a MAT1-1 or MAT1-2 mating-type gene. Strains of opposite mating type were crossed on mixed cereal agar and incubated for 5–6 months. Stromata typically formed 1–2 indehiscent ascocarps containing asci and ascospores within the pseudo-parenchymatous matrix in a manner similar to the Petromyces sexual stage from section Flavi, which is closely related to section Nigri. Ascospores of A. tubingensis differed from those of section Flavi species in the reticulate ornamentation of ascospores and the presence of two crests that form an equatorial furrow. Sexual reproduction in A. tubingensis may be useful for enhancing enzyme and organic acid production through recombination-mediated genetic engineering of industrial strains.

The identity of nine clinical isolates recovered from Czech patients and presumptively identified as Aspergillus sp. section Candidi based on colony morphology was revised using sequences of β-tubulin, calmodulin gene sequence, and internal transcribed spacer rDNA. Six isolates were from suspected and proven onychomycosis, one from otitis externa, and two associated with probable invasive aspergillosis. The results showed that one Aspergillus candidus isolate was the cause of otitis externa, and both isolates obtained from sputa of patients with probable invasive aspergillosis were reidentified as A. carneus (sect. Terrei) and A. flavus (sect. Flavi). Three isolates from nail scrapings were identified as A. tritici, a verified agent of nondermatophyte onychomycosis. One isolate from toenail was determined to be A. candidus and the two isolates belonged to a hitherto undescribed species, Aspergillus pragensis sp. nov. This species is well supported by phylogenetic analysis based on β-tubulin and calmodulin gene and is distinguishable from other members of sect. Candidi by red-brown reverse on malt extract agar, slow growth on Czapek-Dox agar and inability to grow at 37°C. A secondary metabolite analysis was also provided with comparison of metabolite spectrum to other species. Section Candidi now encompasses five species for which a dichotomous key based on colony characteristics is provided. All clinical isolates were tested for susceptibilities to selected antifungal agents using the Etest and disc diffusion method. Overall sect. Candidi members are highly susceptible to common antifungals.

Abstract There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naïve Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation. Pilot clinical validation of our method correctly identified the etiologic organisms at the species-level in 59 culture-positive mono-bacterial blood culture samples with 90% accuracy. Our findings suggest that broad bacterial sequences may be simply, reliably and automatically profiled by ITS HRM assay for clinical adoption.

Abstract Invasive aspergillosis (IA) is the most serious mold infection encountered in patients with iatrogenic immunosuppression. IA is also a major cause of mortality and morbidity in individuals with primary immunodeficiency (PID). Although Aspergillus fumigatus is the most common etiologic agent of IA reported in PID patients, followed by A. nidulans, multiple poorly recognized Aspergillus species such as A. udagawae, A. quadrilineatus, A. pseudoviridinutans, A. tanneri, A. subramanianii, and A. fumisynnematus have been reported almost exclusively from patients with inborn defects in host antifungal defense pathways. Infection in PID patients exhibits patterns of disease progression distinct from those in iatrogenic immunosuppression. Specifically, the disease can be extrapulmonary and chronic with a tendency to disseminate in a contiguous manner across anatomical planes. It is also more refractory to standard antifungal therapy. This synopsis summarizes our understanding of emerging rare Aspergillus species that primarily affect patients with PIDs but not those with acquired immunodeficiencies.

Compton-based prompt gamma (PG) imaging is being investigated by several groups as a potential solution for in vivo range monitoring in proton therapy. The performance of this technique depends on the detector system as well as the ability of the reconstruction method to obtain good spatial resolution to establish a quantitative correlation between the PG emission and the proton beam range in the patient. To evaluate the feasibility of PG imaging for range monitoring, we quantitatively evaluated the emission distributions reconstructed by a Maximum Likelihood Expectation Maximization (MLEM) and a Stochastic Origin Ensemble (SOE) algorithm. To this end, we exploit experimental and Monte Carlo (MC) simulation data acquired with the Polaris-J Compton Camera (CC) prototype. The differences between the proton beam range (RD) defined as the 80% distal dose fall-off and the PG range (RPG), obtained by fitting the distal end of the reconstructed profile with a sigmoid function, were quantified. A comparable performance of both reconstruction algorithms was found. For both experimental and simulated irradiation scenarios, the correlation between RD and RPG was within 5 mm. These values were consistent with the ground truth distance (RD-RPGg≈ 3 mm) calculated by using the expected PG emission available from MC simulation. Furthermore, shifts of 3 mm in the proton beam range were resolved with the MLEM algorithm by calculating the relative difference between the RPG for each reconstructed profile. In non-homogeneous targets, the spatial changes in the PG emission due to the different materials could not be fully resolved from the reconstructed profiles; however, the fall-off region still resembled the ground truth emission. For this scenario, the PG correlation (RD-RPG) varied from 0.1 mm to 4 mm, which is close to the ground truth correlation (3 mm). This work provides a framework for the evaluation of the range monitoring capabilities of a CC device for PG imaging. The two investigated image reconstruction algorithms showed a comparable and consistent performance for homogeneous and heterogeneous targets.

Large subunit ribosomal DNA from Aspergillus species in sections Cremei, Wentii, and some morphologically related species in subgenus Circumdati, was amplified using PCR techniques. The nucleotide sequences were determined from the amplified DNA and phylogenetic species relationships were inferred from parsimony analysis of the data. On the basis of the analysis, section Wentii is abandoned. All species formerly assigned to section Wentii are phylogenetically related to species in other sections of subgenus Circumdati (e.g. sections Cremei, Flavi). Aspergillus gorakhpurensis (section Sparsi), A. dimorphicus (section Circumdati) and A. pulvinus (section Versicolores) are transferred to section Cremei. Genetic and morphological analysis support these changes in Aspergillus subgeneric classification. A key to the species in the modified section Cremei is provided.

Penicillium brevicompactum and other isolates with the compact, complex conidiogenous apparatus typical of the species were sequenced in one ribosomal and two protein coding regions. The aligned DNA sequences were analyzed by maximum parsimony and the data from different loci were tested for compatibility using the partition homogeneity test. Analysis of each of the three loci revealed three clades corresponding to P. brevicompactum, P. olsonii and P. biourgeianum. Using the phylogenetic species concept and the genetic isolation of the clades, P. hagemi, P. patrismei, P. stoloniferum, and P. griseobrunneum are all synonyms of P. brevicompactum. P. volgaense is a synonym of Penicillium olsonii, while P. biourgeianum is a distinct species closely related to P. brevicompactum and P. olsonii. Phenotypic distinctions between the species are mostly based on colony characteristics such as colour. P. bialowiezenze, often treated as a synonym of P. brevicompactum, is most closely related to P. polonicum.

Despite several studies reporting Penicillium as one of the most frequent fungal genera in cork planks, the isolates were rarely identified to species level. We conducted a detailed study to identify Penicillium species from the field to the factory environment prior to and after boiling the cork planks. A total of 84 samples were analyzed. Of the 486 Penicillium isolates phenotypically identified, 32 representative or unusual strains were selected for identification by multilocus DNA sequence type. Cork proved to be a rich source of Penicillium biodiversity. A total of 30 taxa were recognized from cork including rarely seen species and 6 phylogenetically unique groups. Spores of some species lodged deep in cork can survive the boiling process. P. glabrum, P. glandicola and P. toxicarium, species with high CFU numbers in the field, are still frequently present in cork after boiling. Other species are killed by the boiling treatment and replaced by Penicillium species originating from the factory environment. Species known to contribute to cork taint were isolated at all stages. Good manufacturing practices are necessary at all stages in the preparation of cork planks to minimize the load of Penicillium species that produce cork taint.

The purpose of this study is to validate the accuracy of a Monte Carlo calculation model of a proton magnetic beam scanning delivery nozzle developed using the Geant4 toolkit. The Monte Carlo model was used to produce depth dose and lateral profiles, which were compared to data measured in the clinical scanning treatment nozzle at several energies. Comparisons were also made between measured and simulated off-axis profiles to test the accuracy of the model's magnetic steering. Comparison of the 80% distal dose fall-off values for the measured and simulated depth dose profiles agreed to within 1 mm for the beam energies evaluated. Agreement of the full width at half maximum values for the measured and simulated lateral fluence profiles was within 1.3 mm for all energies. The position of measured and simulated spot positions for the magnetically steered beams agreed to within 0.7 mm of each other. Based on these results, we found that the Geant4 Monte Carlo model of the beam scanning nozzle has the ability to accurately predict depth dose profiles, lateral profiles perpendicular to the beam axis and magnetic steering of a proton beam during beam scanning proton therapy.

During the course of mold surveys, a set of Talaromyces isolates were obtained that did not fit any described species. Phenotypic examination of these isolates showed that they were similar to T. piceus but differed in some growth characteristics. Multilocus DNA sequence data were obtained for the new isolates and some related species in the broader, more inclusive clade, and the data were analyzed using genealogical concordance. The new isolates are described as Talaromyces columbinus. From analysis of the related species, Penicillium rugulosum var. atricolum is given species status in Talaromyces as T. atricola. Penicillium tardum and P. chrysitis were showed to be synonyms of T. rugulosus. Penicillium scorteum and T. phialosporus were showed to be conspecific and under the rule of priority T. scorteus is the proper name for isolates previously known as T. phialosporus. Talaromyces wortmanii was showed to be distinct from Penicillium concavorugulosum and T. variabilis but the relationship of the latter two species remains unresolved. Examination of ITS sequences from GenBank showed that T. columbinus has previously been reported from human lung infections under the name Penicillium piceum.

The authors investigated how the characteristics of the detectors used in a three-stage Compton camera (CC) affect the CC's ability to accurately measure the emission distribution and energy spectrum of prompt gammas (PG) emitted by nuclear de-excitations during proton therapy. The detector characteristics they studied included the material (high-purity germanium [HPGe] and cadmium zinc telluride [CZT]), Doppler broadening (DB), and resolution (lateral, depth, and energy).The authors simulated three-stage HPGe and CZT CCs of various configurations, detecting gammas from point sources with energies ranging from 0.511 to 7.12 MeV. They also simulated a proton pencil beam irradiating a tissue target to study how the detector characteristics affect the PG data measured by CCs in a clinical proton therapy setting. They used three figures of merit: the distance of closest approach (DCA) and the point of closest approach (PCA) between the measured and actual position of the PG emission origin, and the calculated energy resolution.For CCs with HPGe detectors, DB caused the DCA to be greater than 3 mm for 14% of the 6.13 MeV gammas and 20% of the 0.511 MeV gammas. For CCs with CZT detectors, DB caused the DCA to be greater than 3 mm for 18% of the 6.13 MeV gammas and 25% of the 0.511 MeV gammas. The full width at half maximum (FWHM) of the PCA in the ẑ direction for HPGe and CZT detectors ranged from 1.3 to 0.4 mm for gammas with incident energy ranging from 0.511 to 7.12 MeV. For CCs composed of HPGe detectors, the resolution of incident gamma energy calculated by the CC ranged from 6% to 1% for gammas with true incident energies from 0.511 to 7.12 MeV. For CCs composed of CZT detectors, the resolution of gamma energy calculated by the CC ranged from 10% to 1% for gammas with true incident energies from 0.511 to 7.12 MeV. For HPGe and CZT CCs in which all detector effect were included, the DCA was less than 3 mm for 75% and 68% of the detected gammas, respectively, and restricting gammas to those having energy greater than 2.0 MeV increased these percentages to 83% and 77% for HPGe and CZT, respectively. Distributions of the true gamma origins and the PCA after detector characteristics had been included showed good agreement on beam range and some loss of resolution for the lateral profile of the PG emission. Characteristic energy lines were evident in the calculated gamma energy spectrum.The authors found the following: (1) DB is the dominant source of spatial and energy resolution loss in the CCs at all energy levels; (2) the largest difference in the spatial resolution of HPGe and CZT CCs is that the spatial resolution distributions of CZT have broader tails. The differences in the FWHM of these distributions are small; (3) the energy resolution of both HPGe and CZT three-stage CCs is adequate for PG spectroscopy; and (4) restricting the gammas to those having energy greater than 2.0 MeV can improve the achievable image resolution.

Two new and phylogenetically closely related species in Aspergillus section Fumigati are described and illustrated. Homothallic Aspergillus waksmanii sp. nov. was isolated from New Jersey soil (USA) and is represented by the ex-type isolate NRRL 179(T) ( = CCF 4266(T) = Thom 4138.HS2(T) = IBT 31900(T)). Aspergillus marvanovae sp. nov. was isolated from water with high boracic acid anions content in Dukovany nuclear power station (Czech Republic). The sexual stage of this species is unknown, but the MAT1-1 locus was successfully amplified suggesting that the species is probably heterothallic and teleomorphic but is represented by only the ex-type isolate CCM 8003(T) ( = CCF 4037(T) = NRRL 62486(T) = IBT 31279(T) = IFM 60873(T)). Both species can be distinguished from all previously described species in section Fumigati based on morphology, maximum growth temperature, sequence data from five unlinked loci and unique secondary metabolites profiles.

Avellanin C, an inhibitor of quorum-sensing signaling in Staphylococcus aureus , from Hamigera ingelheimensis

A set of isolates very similar to or potentially conspecific with an unidentified Penicillium isolate NRRL 735, was assembled using a BLAST search of ITS similarity among described (GenBank) and undescribed Penicillium isolates in our laboratories. DNA was amplified from six loci of the assembled isolates and sequenced. Two species in section Cinnamopurpurea are self-compatible sexual species, but the asexual species had polymorphic loci suggestive of sexual reproduction and variation in conidium size suggestive of ploidy level differences typical of heterothallism. Accordingly we use genealogical concordance analysis, a technique valid only in heterothallic organisms, for putatively asexual species. Seven new species were revealed in the analysis and are described here. Extrolite analysis showed that two of the new species, P. colei and P. monsserratidens produce the mycotoxin citreoviridin that has demonstrated pharmacological activity against human lung tumors. These isolates could provide leads in pharmaceutical research.

Tissues from Coffea arabica, C. congensis, C. dewevrei and C. liberica collected in Colombia, Hawaii and at a local plant nursery in Maryland were sampled for the presence of fungal endophytes. Surface sterilized tissues including roots, leaves, stems and various berry parts were plated on yeast-malt agar. DNA was extracted from a set of isolates visually recognized as Penicillium, and the internal transcribed spacer region and partial LSU-rDNA was amplified and sequenced. Comparison of DNA sequences with GenBank and unpublished sequences revealed the presence of 11 known Penicillium species: P. brevicompactum, P. brocae, P. cecidicola, P. citrinum, P. coffeae, P. crustosum, P. janthinellum, P. olsonii, P. oxalicum, P. sclerotiorum and P. steckii as well as two possibly undescribed species near P. diversum and P. roseopurpureum. Ochratoxin A was produced by only four isolates, one isolate each of P. brevicompactum, P. crustosum, P. olsonii and P. oxalicum. The role these endophytes play in the biology of the coffee plant remains enigmatic.

Genus Hamigera was erected for Talaro-myces species that make asci singly instead of in chains. Initially it contained two species, H. avellanea and H. striata. We describe six new species in the genus, H. fusca, H. inflata, H. insecticola, H. pallida, H. paravellanea and H. terricola. Merimbla ingelheimensis is a distinct anamorphic species in the Hamigera clade. None of our DNA sequence data (BT2, calmodulin, ITS, 1su rDNA, RPB2, Tsr1 and Mcm7) supported the placement of H. striata in the same clade as H. avellanea, thus we accepted Talaromyces striatus. In addition to Hamigera species we examined the phylogenetic disposition of Warcupiella spinulosa, Penicillium megasporum, Penicillium arenicola and Merimbla humicoloides. Despite nominal similarity of some of these species to Merimbla, none of these species are part of the Hamigera clade and M. humicoloides is placed in Penicillium to have a monophyletic genus Hamigera.

The purpose of this study was to determine how the characteristics of the data acquisition (DAQ) electronics of a Compton camera (CC) affect the quality of the recorded prompt gamma (PG) interaction data and the reconstructed images, during clinical proton beam delivery. We used the Monte-Carlo-plus-Detector-Effect (MCDE) model to simulate the delivery of a 150 MeV clinical proton pencil beam to a tissue-equivalent plastic phantom. With the MCDE model we analyzed how the recorded PG interaction data changed as two characteristics of the DAQ electronics of a CC were changed: (1) the number of data readout channels; and (2) the active charge collection, readout, and reset time. As the proton beam dose rate increased, the number of recorded PG single-, double-, and triple-scatter events decreased by a factor of 60× for the current DAQ configuration of the CC. However, as the DAQ readout channels were increased and the readout/reset timing decreased, the number of recorded events decreased by <5× at the highest clinical dose rate. The increased number of readout channels and reduced readout/reset timing also resulted in higher quality recorded data. That is, a higher percentage of the recorded double- and triple-scatters were "true" events (caused by a single incident gamma) and not "false" events (caused by multiple incident gammas). The increase in the number and the quality of recorded data allowed higher quality PG images to be reconstructed even at the highest clinical dose rates.

AbstractAbstractA new aflatoxigenic species of Aspergillus, A. bombycis, was discovered during isolation of fungi from insect frass collected in silkworm rearing houses in Japan. The new species resembles A. flavus, but produces B and G aflatoxins. It is distinguished from A. flavus and A. nomius by differences in growth rates at 37 and 42 C, from A. nomius by roughness of the stipe, and from both of these species by differences in the nucleotide sequences in the beta-tubulin, calmodulin, norsolorinic acid reductase, ITS, and lsu-rDNA genes. Aspergillus bombycis is known from nine isolates, eight collected in silkworm-rearing houses in Japan and one collected in a silk-worm rearing house in Indonesia. Phylogenetic analysis of the DNA sequences shows that A. bombycis is a phylogenetically distinct species which is most closely related to A. nomius and which belongs in Aspergillus section Flavi. Analysis by partition homogeneity did not reveal evidence of genetic recombination in A. bombycis, but in A. nomius the patterns of polymorphisms in different genes strongly suggest cryptic genetic recombination.Key Words: aflatoxinfungimolecular systematicsribosomal DNA sequence

The first case of osteomyelitis caused by Neosartorya pseudofischeri is reported. The patient, a 77-year-old male with a history of silicosis and tuberculosis, on X-ray examination revealed lytic lesions of L2 and L3 vertebrae suspicious for metastatic lesions. Histologic examination of biopsy specimens from vertebral bodies showed short, distorted, extra- and intracellular, hyaline hyphal fragments. The culture from the biopsy tissue produced numerous, evanescent asci containing eight ellipsoidal ascospores with two distinctive equatorial bands ca. 1 micron wide. When examined by a scanning electron microscope, ascospores exhibited a convex surface ornamented with raised flaps of tissue, in shape resembling triangular projections or long ridge lines. The conidial state (anamorph) was identified as Aspergillus thermomutatus on the basis of conidial columns which were smaller and less tightly packed as well as of a lighter shade of green than those observed in Aspergillus fumigatus. On the basis of the morphologic features of the ascospores, the teleomorph was identified as N. pseudofischeri.

Agriculture, Aflatoxins, and Aspergillus P.J. Cotty, et al. Biosynthesis of Aspergillus Toxins-Non-Aflatoxins M.O. Moss. The Molecular Genetics of Aflatoxin Biosynthesis J.W. Bennett, et al. Aspergillus Toxins in Animal Feeding Stuffs K.A. Scudamore. Aspergilli in Feeds and Seeds J. Lacey. Antiinsectan Effects of Aspergillus Metabolites D.T. Wicklow, et al. Aspergillus Spoilage B. Flannigan, A.R. Pearce. Industrial Fermentation and Aspergillus A.G. Brooke. Regulation of Organic Acid Production by Aspergilli C.P. Kubichek, et al. Aspergillus Enzymes and Industrial Uses K. Oxenbol. Industrial Aspects of Soy Sauce and B.J. Fermentation Using Aspergillus K.E. Aidoo, et al. Aspergillus and Fermented Foods P.E. Cook, G. Campbell-Platt. The ARpI Aspergillus Replicating Plasmid J. Clutterbuck, et al. 15 additional articles. Index.

Field surveys were carried out in coffee plantations in Chiapas, Mexico, to collect and identify fungi associated with the cuticle, gut, faeces and galleries of the coffee berry borer, Hypothenemus hampei. Insects and coffee berries containing galleries were collected in three coffee farms at different altitudes: Rosario Izapa (425 m), La Alianza (700 m) and Monteperla (950 m). An additional sample consisting of coffee berry borers reared in the laboratory on meridic diets was also included. Results show that there is a great diversity of fungi associated with this insect. 212 cultures, including 40 species distributed in 22 genera, were isolated. The recovery of fungi from the galleries was markedly less than from the borer's body. Three of the isolated species were undescribed; two belonging to the Penicillium and one to Hanseniaspora. Most of the species were collected from the cuticle of the insect, and the presence of fungi was not correlated with altitude. Fusarium, Penicillium, Candida and Aspergillus were the dominant genera with percentage abundance of 26.4, 18.7, 13.4 and 12.5%, respectively. The present study provides a detailed description of the mycobiota associated with H. hampei and represents a significant advance in the understanding of the relationship among this insect and the fungi associated with it.

Two new Penicillium species were isolated from peanut-field soils in Georgia. The species were noted particularly because they sporulated on the conidial heads of Aspergillus species. Phenotypic descriptions were prepared with standard media. LSU-rDNA sequences were determined for the new species and compared to existing homologous sequences from Penicillium species with parsimony analysis. The monoverticillate species, P. parvulum, was related most closely to E. cinnamopurpureum, while the furcate species, P. georgiense, appeared in the tree near P. thiersii. Because P. parvulum was closely related to E. cinnamopurpureum additional loci were sequenced (beta-tubulin and calmodulin) for these and some other closely related species to establish the status of the species through genealogical concordance. Some proposed synonymies from prior studies were examined and resolved.

Schizophyllan is a homoglucan produced by the fungus Schizophyllum commune, with a β-1,3-linked backbone and β-1,6-linked side chains of single glucose units at every other residue. Schizophyllan is commercially produced for pharmaceutical and cosmetics uses. However, surprisingly little information is available on the biodegradation of schizophyllan. Enzymes that attack schizophyllan could be useful for controlled modifications of the polymer for novel applications. Enrichment cultures were used to isolate 20 novel fungal strains from soil samples, capable of growing on schizophyllan as a sole carbon source. Three additional strains were isolated as contaminants of stored schizophyllan solutions. Strains showing the highest levels of β-glucanase activity were identified as Penicillium simplicissimum, Penicillium crustosum, and Hypocrea nigricans. β-glucanases also showed activity against the similar β-glucans, laminarin and curdlan. By comparison, commercial β-glucanase from Trichoderma longibrachiatum and laminarinase from Trichoderma sp. showed lower specific activities toward schizophyllan than most of the novel isolates. β-glucanases from P. simplicissimum and H. nigricans exhibited temperature optima of 60 °C and 50 °C against schizophyllan, respectively, with broad pH optima around pH 5.0. Partial purifications of β-glucanase from P. simplicissimum and P. crustosum demonstrated the presence of multiple active endoglucanase species, including a 20–25 kD enzyme from P. simplicissimum.

Secondary metabolite phenotypes in nine species of the Hamigera clade were analysed to assess their correlations to a multi-gene species-level phylogeny. High-pressure-liquid-chromatography-based chemical analysis revealed three distinctive patterns of secondary metabolite production: (1) the nine species could be divided into two groups on the basis of production of the sesquiterpene tricinonoic acid; (2) the tricinonoic acid-producing group produced two cyclic peptides avellanins A and B; (3) the tricinonoic acid-non-producing group could be further divided into two groups according to the production of avellanins A and B. The chemical phenotype was consistent with the phylogeny of the species, although metabolite patterns were not diagnostic at the species level. In addition, the taxonomy of the Hamigera clade was updated with the new combination Hamigera ingelheimensis proposed for Merimbla ingelheimensis, so that all species in the clade are now in the same genus.

A Compton imaging method for medical applications that includes new energy determination and data filtering techniques has been tested using several point sources with known emission lines. Using a prototype Compton camera, a distance-of-closest approach technique has been employed to determine the initial energy of the incoming γs and to ensure the reconstructed source position is within an acceptable distance from the known γ source location. Further analysis is done by implementing a Compton line filtering technique, keeping only those interactions whose deposited energy in the first interaction matches the theoretical energy deposition predicted by the Compton equation. Using this new event filtering method, we see improvements in the full width at half maximum in the lateral profiles of γ point sources of up to 70% over standard Compton imaging methods, as well as achievable spatial resolutions in the reconstructed images of better than 2 mm. In addition, this new Compton imaging method was able to reconstruct an extended source of γ rays emitted during irradiation of a water tank with a clinical proton radiotherapy beam.

Infections caused by Penicillium species are rare in dogs, and the prognosis in these cases is poor. An unknown species of Penicillium was isolated from a bone lesion in a young dog with osteomyelitis of the right ilium. Extensive diagnostic evaluation did not reveal evidence of dissemination. Resolution of lameness and clinical stability of disease were achieved with intravenous phospholipid-complexed amphotericin B initially, followed by long-term combination therapy with terbinafine and ketoconazole. A detailed morphological and molecular characterization of the mold was undertaken. Sequence analysis of the internal transcribed spacer revealed the isolate to be closely related to Penicillium menonorum and Penicillium pimiteouiense. Additional sequence analysis of β-tubulin, calmodulin, minichromosome maintenance factor, DNA-dependent RNA polymerase, and pre-rRNA processing protein revealed the isolate to be a novel species; the name Penicillium canis sp. nov. is proposed. Morphologically, smooth, ovoid conidia, a greenish gray colony color, slow growth on all media, and a failure to form ascomata distinguish this species from closely related Penicillium species.

A multilocus phylogenetic study was carried out to assess species identity of a set of 34 clinical isolates from Aspergillus section Circumdati from the United States and to determine their in vitro antifungal susceptibility against eight antifungal drugs. The genetic markers used were the internal transcribed spacer (ITS) region, and fragments of the beta-tubulin (BenA), calmodulin (CaM), and RNA polymerase II second largest subunit (RPB2) genes. The drugs tested were amphotericin B, itraconazole, posaconazole, voriconazole, anidulafungin, caspofungin, micafungin, and terbinafine. The most common species sampled was A. westerdijkiae (29.4%), followed by a novel species, which was described here as A. pseudosclerotiorum (23.5%). Other species identified were A. sclerotiorum (17.6%), A. ochraceus (8.8%), A. subramanianii (8.8%), and A. insulicola and A. ochraceopetaliformis, with two isolates (5.9%) of each. The drugs that showed the most potent activity were caspofungin, micafungin, and terbinafine, while amphotericin B showed the least activity.

A sample of isolates from Talaromyces pinophilus (55 isolates) and closely related species (76 isolates) was sequenced at four loci, the data were analyzed using maximum likelihood analysis and the GCPSR. The isolates were subjected to growth studies on the recommended media for description of Talaromyces species. On the basis of the combined data, five new species were segregated out of T. pinophilus and placed in newly described species. The T. pinophilus species complex contains ten species. The three other new species, Talaromyces argentinensis, T. californicus and T. louisianensis were not a part of the T. pinophilus species complex but occurred in Talaromyces sect. Talaromyces. T. argentinensis produces a teleomorphic state and is phylogenetically and morphologically distinct from other Talaromyces species.

Aspergillus section Nidulantes encompasses almost 80 homothallic and anamorphic species, mostly isolated from soil, plant material, or the indoor environment. Some species are clinically relevant or produce mycotoxins. This study reevaluated the species boundaries within several clades of section Nidulantes. Five data sets were assembled, each containing presumptive new species and their closest relatives, and phylogenetic and phenotypic analyses were performed. We tested the hypotheses that the newly isolated or reexamined strains constitute separate species (splitting approach) or should be treated as part of broadly defined species (lumping approach). Four DNA sequence loci were amplified, internal transcribed spacer (ITS) and large subunit (LSU) regions of the rDNA and partial sequences of the β-tubulin (benA), calmodulin (CaM), and RNA polymerase II second largest subunit (RPB2) genes. The latter three loci were used for the phylogenetic analysis and served as input for single-locus (GMYC, bGMYC, PTP, and bPTP) and multilocus (STACEY and BP&P) species delimitation analyses. The phenotypic analysis comprised macro- and micromorphology (including scanning electron microscopy) and comparison of cardinal growth temperatures. The phylogenetic analysis supported the splitting hypothesis in all cases, and based on the combined approach, we propose six new species, four that are homothallic and two anamorphic. Four new species were isolated from the indoor environment (Jamaica, Trinidad and Tobago, USA), one originated from soil (Australia), and one from a kangaroo rat cheek pouch (USA).

This paper describes a realistic simulation of a Compton-camera (CC) based prompt-gamma (PG) imaging system for proton range verification for a range of clinical dose rates, and its comparison to PG measured data with a pre-clinical CC. We used a Monte Carlo plus Detector Effects (MCDE) model to simulate the production of prompt gamma-rays (PG) and their energy depositions in the CC. With Monte Carlo, we simulated PG emission resulting from irradiation of a high density polyethylene phantom with a 150 MeV proton pencil beam at dose rates of 5.0 × 108, 2.6 × 109, and 4.6 × 109 p+ s-1. Realistic detector timing effects (e.g. delayed triggering time, event-coincidence, dead time, etc,) were added in post-processing to allow for flexible count rate variations. We acquired PG emission measurements with our pre-clinical CC during irradiation with a clinical 150 MeV proton pencil beam at the same dose rates. For simulations and measurements, three primary changes could be seen in the PG emission data as the dose rate increased: (1) reduction in the total number of detected events due to increased dead-time percentage; (2) increase in false-coincidence events (i.e. multiple PGs interacting, rather than a single PG scatter); and (3) loss of distinct PG emission peaks in the energy spectrum. We used the MCDE model to estimate the quality of our measured PG data, primarily with regards to true and false double-scatters and triple-scatters recorded by the CC. The simulation results showed that of the recorded double-scatter PG interactions 22%, 57%, and 70% were false double-scatters and for triple-scatter interactions 3%, 21%, and 35% were false events at 5.0 × 108, 2.6 × 109, and 4.6 × 109 p+ s-1, respectively. These false scatter events represent noise in the data, and the high percentage of these events in the data represents a major limitation in our ability to produce usable PG images with our prototype CC.

We have measured the γ-ray line production cross sections in proton-induced nuclear reactions on various target nuclei (12C, 16O, 24Mg, 28Si, 56Fe) of chemical elements abundant in astrophysical sites (solar flares, the interstellar medium, cosmic compact objects) over the incident energy range of Ep = 30 – 200 MeV. We carried out experimental campaigns in joint collaboration at the K = 200 separated sector cyclotron of iThemba LABS using a high-energy resolution, high-efficiency detection array composed of 8 Compton-suppressed clover detectors comprising 32 HP-Ge crystals for recording the γ-ray energy spectra. In the current paper, we focus on γ-ray de-excitation lines produced in proton irradiations of natC and Mylar targets, in particular, on the prominent 4.439 and 6.129 MeV lines of 12C and 16O which are among the strongest lines emitted in solar flares and in interactions of low-energy cosmic rays (LECRs) with the gas and dust of the inner galaxy. We report new γ-ray production experimental cross section data for ten nuclear γ-ray lines that we compare to previous low-energy data sets from the literature, to the predictions of the TALYS code of nuclear reactions and to a semi-empirical compilation. In the first approach, performing calculations with default input parameters of TALYS we observed substantial deviations between the predicted cross sections and experimental data. Then, using modified optical model potential (OMP) and nuclear level deformation parameters as input data we generated theoretical excitation functions for the above two main lines fully consistent with experimental data. In contrast, the experimental data sets for the other eight analyzed lines from the two proton-irradiated targets exhibit significant deviations with the predicted cross section values. We also report line-shape experimental data for the line complex observed at Eγ = 4.44 MeV in irradiations of the two targets. Finally, we emphasize the astrophysical implications of our results.

Aspergillus tamarii is known to produce mycotoxins such as cyclopiazonic acid (CPA) and kojic acid (KA). Recently we isolated several cultures of A. tamarii from Japanese tea fields and found one of the isolates "No.19", and single-spore cultures (NRRL 25517, 25518, 25519) derived from this isolate, produced substantial quantities of aflatoxin B1 and B2. Here we report the results of a limited survey of 15 A. tamarii strains isolated from Japanese tea fields, one strain from silk worm excrement and 29 strains received from culture collections. Most A. tamarii isolates produced CPA and KA but only the strains derived from isolate "No.19" and strain NRRL 443 produced aflatoxin B1 and B2. Each aflatoxin-producing strain of A. tamarii showed yellow-green colors in young colonies and did not darken in age, suggestive of the "bronze series". The relation between the levels of CPA or KA production by the individual strains was very weak.

Penicillium brocae is a new monoverticillate species isolated from coffee berry borers collected at coffee plantations in Mexico near Cacahoatán, Chiapas, and from borers reared on artificial diets at ECOSUR laboratory facilities in Tapachula, Chiapas. Phenotypically, it is in Penicillium series Implicatum, but because it does not conform to known species we have described it as new. ITS and large subunit rDNA were sequenced and compared to determine the phylogenetic position of this species. It is most closely related to Penicillium adametzii. Penicillium brocae has only been found in association with the coffee berry borer and is one of several fungi that grow in coffee berry borer galleries. Penicillium brocae may provide the exogenous sterols necessary for the coffee berry borer's development and thus be mutualistically associated with the insect.

The phylogeny of the genus Aspergillus and its teleomorphs is discussed based on multilocus sequence data. DNA sequence analysis was used to formulate a nucleotide sequence framework of the genus and to analyse character changes in relationship to the phylogeny hypothesised from the DNA sequence analysis. The sequence data used to delineate subgeneric taxa included partial calmodulin, rDNA and RNA polymerase gene sequences. In our phylogenic structure of Aspergillus extrolite data of the various Aspergillus taxa collected from ex-type cultures and numerous other isolates are also discussed. A new subgeneric classification is proposed which includes 8 subgenera and 22 sections within the genus Aspergillus. Characteristics of these taxa are briefly discussed in this chapter.

During proton beam radiotherapy, discrete secondary prompt gamma rays are induced by inelastic nuclear reactions between protons and nuclei in the human body. In recent years, the Geant4 Monte Carlo toolkit has played an important role in the development of a device for real time dose range verification purposes using prompt gamma radiation. Unfortunately the default physics models in Geant4 do not reliably replicate the measured prompt gamma emission. Determining a suitable physics model for low energy proton inelastic interactions will boost the accuracy of prompt gamma simulations. Among the built-in physics models, we found that the precompound model with a modified initial exciton state of 2 (1 particle, 1 hole) produced more accurate discrete gamma lines from the most important elements found within the body such as 16O, 12C and 14N when comparing them with the available gamma production cross section data. Using the modified physics model, we investigated the prompt gamma spectra produced in a water phantom by a 200 MeV pencil beam of protons. The spectra were attained using a LaBr3 detector with a time-of-flight (TOF) window and BGO active shield to reduce the secondary neutron and gamma background. The simulations show that a 2 ns TOF window could reduce 99% of the secondary neutron flux hitting the detector. The results show that using both timing and active shielding can remove up to 85% of the background radiation which includes a 33% reduction by BGO subtraction.

Talaromyces strains isolated from maize seeds and the built environment were examined taxonomically because they could not be identified as previously described species. Using phenotypic analysis, DNA sequencing, and phylogenetic and concordance analyses, the authors discovered and described 10 new species in sect. Islandici and 1 new species in sect. Subinflati. Taxonomic novelties in sect. Islandici are Talaromyces delawarensis, T. herodensis, T. juglandicola, T. kilbournensis, T. novojersensis, T. ricevillensis, T. rogersiae, T. siglerae, T. subtropicalis, and T. tiftonensis, and the species from sect. Subinflata is T. tzapotlensis. The isolate of T. siglerae is unusual in Talaromyces because it produced a Sagenomella-like anamorph, but phylogenetic analysis placed it in Talaromyces. Talaromyces rotundus is known from a few isolates, but searches with internal transcribed spacer (ITS) sequences in GenBank revealed that it is commonly endolichenous with Lasallia hispanica. Talaromyces wortmannii also has a role as an endophyte of the aquatic plant Persicaria amphibia, based on ITS sequence records from GenBank.

The purpose of this study was to determine the types, proportions, and energies of secondary particle interactions in a Compton camera (CC) during the delivery of clinical proton beams. The delivery of clinical proton pencil beams ranging from 70 to 200 MeV incident on a water phantom was simulated using Geant4 software (version 10.4). The simulation included a CC similar to the configuration of a Polaris J3 CC designed to image prompt gammas (PGs) emitted during proton beam irradiation for the purpose of in vivo range verification. The interaction positions and energies of secondary particles in each CC detector module were scored. For a 150-MeV proton beam, a total of 156,688(575) secondary particles per 108 protons, primarily composed of gamma rays (46.31%), neutrons (41.37%), and electrons (8.88%), were found to reach the camera modules, and 79.37% of these particles interacted with the modules. Strategies for using CCs for proton range verification should include methods of reducing the large neutron backgrounds and low-energy non-PG radiation. The proportions of interaction types by module from this study may provide information useful for background suppression.

Formal response organizations perform rapid damage assessments after natural and human-induced disasters to measure the extent of damage to infrastructures such as roads, bridges, and buildings. This time-critical task, when performed using traditional approaches such as experts surveying the disaster areas, poses serious challenges and delays response. This paper presents an AI-based system that leverages citizen science to collect damage images reported on social media and perform rapid damage assessment in real-time. Several image processing models in the system tackle non-trivial challenges posed by social media as a data source, such as high-volume of redundant and irrelevant content. The system determines the severity of damage using a state-of-the-art computer vision model. Together with a response organization in the US, we deployed the system to identify damage reports during a major real-world disaster. We observe that almost 42% of the images are unique, 28% relevant, and more importantly, only 10% of them contain either mild or severe damage. Experts from our partner organization provided feedback on the system's mistakes, which we used to perform additional experiments to retrain the models. Consequently, the retrained models based on expert feedback on the target domain data helped us achieve significant performance improvements.

We describe three new fungicolous species on the basis of phenotypic and phylogenetic differences from known species. Penicillium thiersii, P. angulare and Penicillium decaturense are described. Penicillium thiersii phenotypically is identified on the basis of several characteristics including growth rates, vesicle size and condium shape and roughening. Penicillium angulare is related most closely to P. adametzioides but differs from it by restricted growth rates and conidiophores greater than 60 μm in length. Penicillium decaturense is related most closely to P. miczynskii but differs from that species by growth rate, minimum growth temperature and pigment production on MEA. Multilocus phylogenetic analysis confirmed the genetic distinctiveness of P. decaturense and the closely related species P. miczynskii, P. chrzaszczii and P. manginii. Penicillium rivolii is a synonym of P. waksmanii on the basis of this analysis. Analysis of the EF-1α gene shows rapid changes of position, number and length of introns between the species, suggesting a recent evolutionary origin for the introns.

The purpose of this work was to develop a method to calculate and study the impact of fluctuations in the magnetic field strengths within the steering magnets in a proton scanning beam treatment nozzle on the dose delivered to the patient during a proton therapy treatment. First, an analytical relationship between magnetic field uncertainties in the steering magnets and the resulting lateral displacements in the position of the delivered scanned beam “dose spot” was established. Next, using a simple 3D dose calculation code and data from a validated Monte Carlo model of the proton scanning beam treatment nozzle, the uniform dose delivery to a 3D treatment volume was calculated. The dose distribution was then recalculated using the calculated lateral displacements due to magnetic field fluctuations to the proton pencil beam position. Using these two calculated dose distributions, the clinical effects of the magnetic field fluctuations were determined. A deliberate displacement of four adjacent spots either toward or away from each other was used to determine the “maximum” dose impact, while a random displacement of all spots was used to establish a more realistic clinical dose impact. Changes in the dose volume histogram (DVH) and the presence of hot and cold spots in the treatment volume were used to quantify the impact of dose-spot displacement. A general analytical relationship between magnetic field uncertainty and final dose-spot position is presented. This analytical relationship was developed such that it can be applied to study magnetic beam steering for any scanned beam nozzle design. Using this relationship the authors found for the example beam steering nozzle used in this study that deliberate lateral displacements of 0.5 mm or random lateral displacements of up to 1.0 mm produced a noticeable dose impact (5% hot spot) in the treatment volume. A noticeable impact (3% decrease in treatment volume coverage) on the DVH was observed for random displacements of up to 1.5 mm. For the scanning nozzle studied in this work, these displacement values correlated with an uncertainty value of 2.04% in the magnetic field values of the nozzle steering magnets. The authors conclude that fluctuations in the dose-spot delivery caused by uncertainty in the magnet fields used for beam steering could have clinically significant effects on the delivered dose distribution. Due to differences in the design and implementation of proton beam scanning nozzles at different treatment facilities, the effects of magnetic field fluctuations of dose delivery should be evaluated and understood for each specific nozzle design during clinical commissioning of the treatment nozzle.

Penicillium menonorum is described as a new monoverticillate, non-vesiculate species that resembles P. restrictum and P. pimiteouiense. On the basis of phylogenetic analysis of DNA sequences from four loci, P. menonorum occurs in a clade with P. pimiteouiense, P. vinaceum, P. guttulosum, P. rubidurum, and P. parvum. Genealogical concordance analysis was applied to P. pimiteouiense and P. parvum, substantiating the phenotypically defined species. The species P. rubidurum, P. guttulosum, and P. menonorum were on distinct branches statistically excluded from inclusion in other species and have distinct phenotypes.

ABSTRACT Electrospray ionization mass spectrometry (ESI-MS) analysis of reverse transcription (RT)-PCR amplicons from human respiratory samples allows for broad pathogen identification approximately 8 h after collection. We investigated the performance characteristics of a high-throughput RT-PCR-coupled ESI-MS assay for distinguishing biothreat (BT) agents from common bacterial, fungal, and viral respiratory pathogens in bronchoalveolar lavage (BAL) fluid specimens from subjects with suspected respiratory infections. In a retrospective case series, 202 BAL fluid specimens were collected at the Johns Hopkins Hospital between August 2010 and February 2011 from patients with suspected acute respiratory infections. Samples were processed using standard bacterial, viral, and fungal testing in the clinical microbiology laboratory as part of routine care and then were blindly spiked with either water or nucleic acids from BT organisms ( Bacillus anthracis , Yersinia pestis , Francisella tularensis , Brucella spp., Burkholderia spp., and Rickettsia prowazekii ) and tested by RT-PCR–ESI-MS. The sensitivities and specificities of RT-PCR–ESI-MS versus standard clinical methods were as follows: for mock BT DNA, 98.5% sensitivity (95% confidence interval [CI], 94.2 to 99.7%) and 100% specificity (95% CI, 93.1 to 100.0%); for bacterial pathogens, 81.8% sensitivity (95% CI, 74.3 to 87.6%) and 73.6% specificity (95% CI, 64.2 to 81.4%); for viral pathogens, 93.3% sensitivity (95% CI, 66.0 to 99.7%) and 97.3% specificity (95% CI, 89.7 to 99.5%); for fungal pathogens, 42.6% sensitivity (95% CI, 29.5 to 56.7%) and 97.8% specificity (95% CI, 91.8 to 99.6%). Our data suggest that RT-PCR–ESI-MS is a useful adjunct to standard culture protocols for rapid detection of both BT and common respiratory pathogens; further study is required for assay validation, especially for fungal detection, and potential implementation.

We describe two new terverticillate Penicillium species isolated from grapes on the basis of phenotypic and phylogenetic differences from known species. The strains were isolated in the course of a study to establish the mycobiota of grapes in Portugal. Penicillium astrolabium is phenotypically similar to P. olsonii but differs from it by two cultural characters, growth rates and the colony reverse color. P. neocrassum is similar to P. brevicompactum but is readily distinguished by sclerotia production. Phylogenetically P. astrolabium and P. neocrassum are placed respectively in the P. olsonii and P. brevicompactum clade. Multilocus analysis confirmed the genetic distinctiveness of both species. The parsimony trees obtained for ITS-lsu rDNA region and two protein coding genes, calmodulin and beta-tubulin, show congruence for all the species in the Olsonii series: P. brevicompactum, P. bialowiezense, P. olsonii, P. astrolabium and P. neocrassum, indicating that these taxa are genetically well isolated.

Three amino acid-derived compounds, haenamindole (1) and 2'-epi-fumiquinazolines C (2) and D (3), were isolated from cultures of a fungicolous isolate of Penicillium lanosum (MYC-1813=NRRL 66231). Compound 1 was also encountered in cultures of P. corylophilum (MYC-418=NRRL 28126). Structure elucidation of these metabolites was based mainly on high resolution mass spectrometry and NMR data analysis. Haenamindole (1) was found to be a recently reported diketopiperazine-type metabolite that incorporates an unusual β-Phe unit. Analysis of X-ray crystallographic data and the products of acid hydrolysis of 1 enabled a conclusive, slightly modified stereochemical assignment for haenamindole. Fumiquinazoline analog 2 is a new natural product, while related compound 3 has been previously reported only as a product of an in vitro enzymatic step and of a genetically engineered fungal culture. Compounds 1 and 3 showed antiinsectan activity against the fall armyworm Spodoptera frugiperda.

Penicillium brocae is a new monoverticillate species isolated from coffee berry borers collected at coffee plantations in Mexico near Cacahoatán, Chiapas, and from borers reared on artificial diets at ECOSUR laboratory facilities in Tapachula, Chiapas. Phenotypically, it is in Penicillium series Implicatum, but because it does not conform to known species we have described it as new. ITS and large subunit rDNA were sequenced and compared to determine the phylogenetic position of this species. It is most closely related to Penicillium adametzii. Penicillium brocae has only been found in association with the coffee berry borer and is one of several fungi that grow in coffee berry borer galleries. Penicillium brocae may provide the exogenous sterols necessary for the coffee berry borer's development and thus be mutualistically associated with the insect.