cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14046854.v1
title: Delimitation and phylogeny of <i>Dictyochaeta</i>, and introduction of <i>Achrochaeta</i> and <i>Tubulicolla</i>, genera nova

description: <i>Dictyochaeta</i> (Chaetosphaeriaceae) is a phialidic dematiaceous hyphomycete with teleomorphs classified in <i>Chaetosphaeria</i>. It is associated with significant variability of asexual morphological traits, which led to its broad delimitation. In the present study, six loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), nuc 18S rDNA (18S), nuc 28S rDNA (28S), DNA-directed RNA polymerase II second largest subunit gene (<i>RPB2</i>), translation elongation factor 1-α (<i>TEF1-α</i>), and β-tubulin (<i>TUB2</i>), along with comparative morphological and cultivation studies, are used to reevaluate the concept of <i>Dictyochaeta</i> and establish species boundaries. Based on revised species, morphological characteristics of conidia (shape, septation, absence or presence of setulae), collarettes (shape), and setae (presence or absence) and an extension of the conidiogenous cell proved to be important at the generic level. The dual DNA barcoding using ITS and <i>TEF1-α</i>, together with <i>TUB2</i>, facilitated accurate identification of <i>Dictyochaeta</i> species. Thirteen species are accepted, of which seven are characterized in this study; an identification key is provided. It was revealed that <i>D. fuegiana</i>, the type species, is a complex of three distinct species including <i>D. querna</i> and the newly described <i>D. stratosa</i>. Besides, a new species, <i>D. detriticola</i>, and two new combinations, <i>D. callimorpha</i> and <i>D. montana</i>, are proposed. An epitype of <i>D. montana</i> is selected. <i>Dictyochaeta</i> includes saprobes on decaying wood, bark, woody fruits, and fallen leaves. <i>Dictyochaeta</i> is shown to be distantly related to the morphologically similar <i>Codinaea</i>, which is resolved as paraphyletic. <i>Chaetosphaeria talbotii</i> with a <i>Dictyochaeta</i> anamorph represents a novel lineage in the Chaetosphaeriaceae; it is segregated from <i>Dictyochaeta</i>, and a new genus <i>Achrochaeta</i> is proposed. Multigene phylogenetic analysis revealed that <i>D. cylindrospora</i> belongs to the Vermiculariopsiellales, and a new genus <i>Tubulicolla</i> is introduced.
DOI: 10.6084/m9.figshare.13554725
title: Phylogenetic revision of South American Teloschistaceae (lichenized Ascomycota, Teloschistales) reveals three new genera and species

description: Members of the poorly investigated family Teloschistaceae in South America, mostly from Bolivia and Peru, were examined using molecular and morphological data here for the first time. In recent phylogenetic reclassifications of Teloschistaceae, South American representatives were poorly represented but shown to belong to subfamilies Teloschistoideae and Xanthorioideae. In this study, we expanded the sampling of South American taxa and investigated mainly the lobate, sublobate, and squamulose members of <i>Caloplaca</i> s.l., using morphological characters and a molecular phylogeny based on a combined three-locus data set (one mitochondrial and two nuclear loci). Building upon new phylogenies at the family and subfamily levels (Teloschistoideae), we propose here three new genera: <i>Andina, Aridoplaca</i>, and <i>Cinnabaria</i>, with the type species <i>Andina citrinoides, Aridoplaca peltata</i>, and <i>Cinnabaria boliviana</i>. We also propose to reduce <i>Tarasginia</i> to synonymy with <i>Sirenophila</i> and <i>Tayloriellina</i> to synonymy with <i>Villophora</i> and introduce three new combinations: <i>Dufourea ottolangei, D. volkmarwirthii</i>, and <i>Villophora erythrosticta. Scutaria andina</i> is reported as new to Bolivia. A critical revision of the subfamily Brownlielloideae confirmed recent findings that it is an artifactual taxon based on a “chimeric” data set, with the type genus being part of Teloschistoideae.
DOI: 10.6084/m9.figshare.13554725.v1
title: Phylogenetic revision of South American Teloschistaceae (lichenized Ascomycota, Teloschistales) reveals three new genera and species

description: Members of the poorly investigated family Teloschistaceae in South America, mostly from Bolivia and Peru, were examined using molecular and morphological data here for the first time. In recent phylogenetic reclassifications of Teloschistaceae, South American representatives were poorly represented but shown to belong to subfamilies Teloschistoideae and Xanthorioideae. In this study, we expanded the sampling of South American taxa and investigated mainly the lobate, sublobate, and squamulose members of <i>Caloplaca</i> s.l., using morphological characters and a molecular phylogeny based on a combined three-locus data set (one mitochondrial and two nuclear loci). Building upon new phylogenies at the family and subfamily levels (Teloschistoideae), we propose here three new genera: <i>Andina, Aridoplaca</i>, and <i>Cinnabaria</i>, with the type species <i>Andina citrinoides, Aridoplaca peltata</i>, and <i>Cinnabaria boliviana</i>. We also propose to reduce <i>Tarasginia</i> to synonymy with <i>Sirenophila</i> and <i>Tayloriellina</i> to synonymy with <i>Villophora</i> and introduce three new combinations: <i>Dufourea ottolangei, D. volkmarwirthii</i>, and <i>Villophora erythrosticta. Scutaria andina</i> is reported as new to Bolivia. A critical revision of the subfamily Brownlielloideae confirmed recent findings that it is an artifactual taxon based on a “chimeric” data set, with the type genus being part of Teloschistoideae.
DOI: 10.6084/m9.figshare.13754774
title: <i>Xylaria necrophora</i>, sp. nov., is an emerging root-associated pathogen responsible for taproot decline of soybean in the southern United States

description: Taproot decline (TRD) is a disease of soybean that has been reported recently from the southern United States (U.S.). Symptoms of TRD include foliar interveinal chlorosis followed by necrosis. Darkened, charcoal-colored areas of thin stromatic tissue are evident on the taproot and lateral roots along with areas of necrosis within the root and white mycelia within the pith. Upright stromata typical of <i>Xylaria</i> can be observed on crop debris and emerging from infested roots in fields where taproot decline is present, but these have not been determined to contain fertile perithecia. Symptomatic plant material was collected across the known range of the disease in the southern U.S., and the causal agent was isolated from roots. Four loci, ⍺-actin (<i>ACT</i>), β-tubulin (<i>TUB2</i>), the nuclear rDNA internal transcribed spacers (nrITS), and the RNA polymerase subunit II (<i>RPB2</i>), were sequenced from representative isolates. Both maximum likelihood and Bayesian phylogenetic analyses showed consistent clustering of representative TRD isolates in a highly supported clade within the <i>Xylaria arbuscula</i> species complex in the “HY” clade of the family Xylariaceae, distinct from any previously described taxa. In order to understand the origin of this pathogen, we sequenced herbarium specimens previously determined to be “<i>Xylaria arbuscula</i>” based on morphology and xylariaceous endophytes collected in the southern U.S. Some historical specimens from U.S. herbaria collected in the southern region as saprophytes as well as a single specimen from Martinique clustered within the “TRD” clade in phylogenetic analyses, suggesting a possible shift in lifestyle. The remaining specimens that clustered within the family Xylariaceae, but outside of the “TRD” clade, are reported. Both morphological evidence and molecular evidence indicate that the TRD pathogen is a novel species, which is described as <i>Xylaria necrophora</i>.
DOI: 10.6084/m9.figshare.14046854
title: Delimitation and phylogeny of <i>Dictyochaeta</i>, and introduction of <i>Achrochaeta</i> and <i>Tubulicolla</i>, genera nova

description: <i>Dictyochaeta</i> (Chaetosphaeriaceae) is a phialidic dematiaceous hyphomycete with teleomorphs classified in <i>Chaetosphaeria</i>. It is associated with significant variability of asexual morphological traits, which led to its broad delimitation. In the present study, six loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), nuc 18S rDNA (18S), nuc 28S rDNA (28S), DNA-directed RNA polymerase II second largest subunit gene (<i>RPB2</i>), translation elongation factor 1-α (<i>TEF1-α</i>), and β-tubulin (<i>TUB2</i>), along with comparative morphological and cultivation studies, are used to reevaluate the concept of <i>Dictyochaeta</i> and establish species boundaries. Based on revised species, morphological characteristics of conidia (shape, septation, absence or presence of setulae), collarettes (shape), and setae (presence or absence) and an extension of the conidiogenous cell proved to be important at the generic level. The dual DNA barcoding using ITS and <i>TEF1-α</i>, together with <i>TUB2</i>, facilitated accurate identification of <i>Dictyochaeta</i> species. Thirteen species are accepted, of which seven are characterized in this study; an identification key is provided. It was revealed that <i>D. fuegiana</i>, the type species, is a complex of three distinct species including <i>D. querna</i> and the newly described <i>D. stratosa</i>. Besides, a new species, <i>D. detriticola</i>, and two new combinations, <i>D. callimorpha</i> and <i>D. montana</i>, are proposed. An epitype of <i>D. montana</i> is selected. <i>Dictyochaeta</i> includes saprobes on decaying wood, bark, woody fruits, and fallen leaves. <i>Dictyochaeta</i> is shown to be distantly related to the morphologically similar <i>Codinaea</i>, which is resolved as paraphyletic. <i>Chaetosphaeria talbotii</i> with a <i>Dictyochaeta</i> anamorph represents a novel lineage in the Chaetosphaeriaceae; it is segregated from <i>Dictyochaeta</i>, and a new genus <i>Achrochaeta</i> is proposed. Multigene phylogenetic analysis revealed that <i>D. cylindrospora</i> belongs to the Vermiculariopsiellales, and a new genus <i>Tubulicolla</i> is introduced.
DOI: 10.6084/m9.figshare.14186441
title: Framing Survey Raw Analysis and Summary Data

description: Data Analysis for survey responses gathered via Prolific platform to test 5 framing variations for AMR narrative. Raw responses and pivoted summary data.
DOI: 10.6084/m9.figshare.14186441.v2
title: Framing Survey Raw Analysis and Summary Data

description: Data Analysis for survey responses gathered via Prolific platform to test 5 framing variations for AMR narrative. Raw responses and pivoted summary data.
DOI: 10.6084/m9.figshare.14186441.v1
title: Framing Survey Analysis Data.xlsx

description: Data Analysis for survey responses gathered via Prolific platform to test 5 framing variations for AMR narrative
DOI: 10.6084/m9.figshare.3997821.v2
title: On the Reproducibility of Psychological Science

description: Investigators from a large consortium of scientists recently performed a multi-year study in which they replicated 100 psychology experiments. Although statistically significant results were reported in 97% of the original studies, statistical significance was achieved in only 36% of the replicated studies. This article presents a reanalysis of these data based on a formal statistical model that accounts for publication bias by treating outcomes from unpublished studies as missing data, while simultaneously estimating the distribution of effect sizes for those studies that tested nonnull effects. The resulting model suggests that more than 90% of tests performed in eligible psychology experiments tested negligible effects, and that publication biases based on <i>p</i>-values caused the observed rates of nonreproducibility. The results of this reanalysis provide a compelling argument for both increasing the threshold required for declaring scientific discoveries and for adopting statistical summaries of evidence that account for the high proportion of tested hypotheses that are false. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1627948.v1
title: <b>Non-Local Priors for High-Dimensional Estimation</b>

description: Jointly achieving parsimony and good predictive power in high dimensions is a main challenge in statistics. Non-local priors (NLPs) possess appealing properties for model choice, but their use for estimation has not been studied in detail. We show that for regular models NLP-based Bayesian model averaging (BMA) shrink spurious parameters either at fast polynomial or quasi-exponential rates as the sample size <i>n</i> increases, while non-spurious parameter estimates are not shrunk. We extend some results to linear models with dimension <i>p</i> growing with <i>n</i>. Coupled with our theoretical investigations, we outline the constructive representation of NLPs as mixtures of truncated distributions that enables simple posterior sampling and extending NLPs beyond previous proposals. Our results show notable high-dimensional estimation for linear models with <i>p</i> &gt; &gt;<i>n</i> at low computational cost. NLPs provided lower estimation error than benchmark and hyper-g priors, SCAD and LASSO in simulations, and in gene expression data achieved higher cross-validated <i>R</i><sup>2</sup> with less predictors. Remarkably, these results were obtained without pre-screening variables. Our findings contribute to the debate of whether different priors should be used for estimation and model selection, showing that selection priors may actually be desirable for high-dimensional estimation.
DOI: 10.6084/m9.figshare.2069686.v1
title: A multi-resolution approximation for massive spatial datasets

description: Automated sensing instruments on satellites and aircraft have enabled the collection of massive amounts of high-resolution observations of spatial fields over large spatial regions. If these datasets can be efficiently exploited, they can provide new insights on a wide variety of issues. However, traditional spatial-statistical techniques such as kriging are not computationally feasible for big datasets. We propose a multi-resolution approximation (<i>M</i>-RA) of Gaussian processes observed at irregular locations in space. The <i>M</i>-RA process is specified as a linear combination of basis functions at multiple levels of spatial resolution, which can capture spatial structure from very fine to very large scales. The basis functions are automatically chosen to approximate a given covariance function, which can be nonstationary. All computations involving the <i>M</i>-RA, including parameter inference and prediction, are highly scalable for massive datasets. Crucially, the inference algorithms can also be parallelized to take full advantage of large distributed-memory computing environments. In comparisons using simulated data and a large satellite dataset, the <i>M</i>-RA outperforms a related state-of-the-art method.
DOI: 10.6084/m9.figshare.2069721.v2
title: <b>Covariance Regression Analysis</b>

description: This article introduces covariance regression analysis for a <i>p</i>-dimensional response vector. The proposed method explores the regression relationship between the <i>p</i>-dimensional covariance matrix and auxiliary information. We study three types of estimators: maximum likelihood, ordinary least squares, and feasible generalized least squares estimators. Then, we demonstrate that these regression estimators are consistent and asymptotically normal. Furthermore, we obtain the high dimensional and large sample properties of the corresponding covariance matrix estimators. Simulation experiments are presented to demonstrate the performance of both regression and covariance matrix estimates. An example is analyzed from the Chinese stock market to illustrate the usefulness of the proposed covariance regression model.
DOI: 10.6084/m9.figshare.14672016
title: cdg2013

description: GWAS summary statistics from the Psychiatric Genomics Consortium (PGC)
DOI: 10.25345/c52530
title: MassIVE MSV000087521 - Synergistic PIM kinase and proteasome inhibition in MYC-overexpressing triple-negative breast cancer
title: Triple-negative breast cancer (TNBC) is the breast cancer (BC) subtype with the poorest outcome. The PIM family of kinases has recently emerged as a factor that is both overexpressed in TNBC samples and associated with poor outcomes. Preclinical data suggest that TNBC that exhibits an elevated MYC oncoprotein expression (MYC+TNBC), accounting for 50% of TNBC cases, is sensitive to PIM inhibition. However, ongoing clinical observations indicate that the efficacy of PIM inhibitors as single agents may be limited in solid tumors, suggesting the need for combination therapies. We conducted drug combination screens to identify a combination that targets PIM and the 20S proteasome (the PIMi/20Si combination) as the most synergistic combination. Following the screening, we used a chemical genetic approach to reveal that the mechanisms of drug synergy involve disruption of protein homeostasis and obstruction of an adaptive resistance mechanism associated with proteasome inhibition. Thus, the PIMi/20Si combination could represent a rational combination therapy against MYC+ TNBC that is readily translatable to early-stage clinical investigations.
DOI: 10.6084/m9.figshare.11354360
title: <i>Fusarium xyrophilum</i>, sp. nov., a member of the <i>Fusarium fujikuroi</i> species complex recovered from pseudoflowers on yellow-eyed grass (<i>Xyris</i> spp.) from Guyana

description: We report on the discovery and characterization of a novel <i>Fusarium</i> species that produced yellow-orange pseudoflowers on <i>Xyris</i> spp. (yellow-eyed grass; Xyridaceae) growing in the savannas of the Pakaraima Mountains of western Guyana. The petaloid fungal structures produced on infected plants mimic host flowers in gross morphology. Molecular phylogenetic analyses of full-length <i>RPB1</i> (RNA polymerase largest subunit), <i>RPB2</i> (RNA polymerase second largest subunit), and <i>TEF1</i> (elongation factor 1-α) DNA sequences mined from genome sequences resolved the fungus, described herein as <i>F. xyrophilum</i>, sp. nov., as sister to <i>F. pseudocircinatum</i> within the African clade of the <i>F. fujikuroi</i> species complex. Results of a polymerase chain reaction (PCR) assay for mating type idiomorph revealed that single-conidial isolates of <i>F. xyrophilum</i> had only one of the <i>MAT</i> idiomorphs (<i>MAT1-1</i> or <i>MAT1-2</i>), which suggests that the fungus may have a heterothallic sexual reproductive mode. BLASTn searches of whole-genome sequence of three strains of <i>F. xyrophilum</i> indicated that it has the genetic potential to produce secondary metabolites, including phytohormones, pigments, and mycotoxins. However, a polyketide-derived pigment, 8-<i>O</i>-methylbostrycoidin, was the only metabolite detected in cracked maize kernel cultures. When grown on carnation leaf agar, <i>F. xyrophilum</i> is phenotypically distinct from other described <i>Fusarium</i> species in that it produces aseptate microconidia on erect indeterminate synnemata that are up to 2 mm tall and it does not produce multiseptate macroconidia.
DOI: 10.6084/m9.figshare.11388705
title: Genera of Inocybaceae: New skin for the old ceremony

description: A six-gene phylogeny of the Inocybaceae is presented to address classification of major clades within the family. Seven genera are recognized that establish a global overview of phylogenetic relationships in the Inocybaceae. Two genera—<i>Nothocybe</i> and <i>Pseudosperma—</i>are described as new. Two subgenera of <i>Inocybe</i>—subg. <i>Inosperma</i> and subg. <i>Mallocybe—</i>are elevated to generic rank. These four new genera, together with the previously described <i>Auritella, Tubariomyces</i>, and now <i>Inocybe</i> sensu stricto, constitute the Inocybaceae, an ectomycorrhizal lineage of Agaricales that associates with at least 23 plant families worldwide. <i>Pseudosperma, Nothocybe</i>, and <i>Inocybe</i> are recovered as a strongly supported inclusive clade within the family. The genus <i>Nothocybe</i>, represented by a single species from tropical India, is strongly supported as the sister lineage to <i>Inocybe</i>, a hyperdiverse genus containing hundreds of species and global distribution. Two additional inclusive clades, including <i>Inosperma, Tubariomyces, Auritella</i>, and <i>Mallocybe</i>, and a nested grouping of <i>Auritella, Mallocybe</i>, and <i>Tubariomyces</i>, are recovered but with marginal statistical support. Overall, the six-gene data set provides a more robust phylogenetic estimate of relationships within the family than do single-gene and single-gene-region estimates. In addition, Africa, India, and Australia are characterized by the most genera in the family, with South America containing the fewest number of genera. A total of 180 names are recombined or proposed as new in <i>Inosperma, Mallocybe</i>, and <i>Pseudosperma</i>. A key to genera of Inocybaceae is provided.
DOI: 10.6084/m9.figshare.11530779
title: Phylogeny and taxonomy of <i>Ceriporia</i> and other related taxa and description of three new species

description: Species of <i>Ceriporia</i> (Irpicaceae, Basidiomycota) are saprotrophs or endophytes in forest ecosystems. To evaluate the taxonomy and generic relationships of <i>Ceriporia</i> and other related taxa, we used morphology and multigene phylogenetic analyses based on sequence data from nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) region, nuc 28S rDNA (28S), and RNA polymerase II largest subunit (<i>rpb1</i>). Our results show that <i>Ceriporia</i> sensu lato is polyphyletic and distributed across multiple clades in the Irpicaceae, Phanerochaetaceae, and Meruliaceae. Some species previously considered in <i>Ceriporia</i> are now recovered in <i>Meruliopsis</i>, resulting in four new combinations: <i>M. albomellea, M. crassitunicata, M. nanlingensis</i>, and <i>M. pseudocystidiata</i>. Two new species of <i>Meruliopsis</i> are described: <i>M. leptocystidiata</i> from northeast China and South Korea and <i>M. parvispora</i> from Taiwan. <i>Ceriporia arbuscula</i> is described as a new species from Taiwan. <i>Ceriporia mellita</i> and <i>Meruliopsis nanlingensis</i> are newly recorded from Japan and Taiwan, and <i>M. taxicola</i> is recorded from Taiwan for the first time.
DOI: 10.6084/m9.figshare.11506281.v1
title: Revision of leccinoid fungi, with emphasis on North American taxa, based on molecular and morphological data

description: The leccinoid fungi are boletes and related sequestrate mushrooms (Boletaceae, Basidiomycota) that have traditionally been placed in <i>Leccinum, Boletus, Leccinellum</i>, and a handful of other less familiar genera. These mushrooms generally feature scabers or scaber-like dots on the surface of the stipe, and they are often fairly tall and slender when compared with other boletes. They are ectomycorrhizal fungi and appear to be fairly strictly associated with specific trees or groups of related trees. In the present study, we investigate the phylogenetic relationships among the leccinoid fungi and other members of the family Boletaceae using portions of three loci from nuc 28S rDNA (28S), translation elongation factor 1-α (<i>TEF1</i>), and the RNA polymerase II second-largest subunit (<i>RPB2</i>). Two DNA data sets (combined 28S-<i>TEF1</i> and 28S-<i>TEF1-RPB2</i>), comprising sequences from nearly 270 voucher specimens, were evaluated using two different phylogenetic analyses (maximum likelihood and Bayesian inference). Five major clades were obtained, and leccinoid fungi appeared in four of them. Taxonomic proposals supported by our results, representing a broadly circumscribed <i>Leccinum</i> that includes several sequestrate genera, along with <i>Leccinellum</i>, are made.