Improved Performance of Gene Set Analysis on Genome-Wide Transcriptomics Data When Using Gene Activity State Estimates

Gene set analysis methods continue to be a popular and powerful method of evaluating genome-wide transcriptomics data. These approach require a priori grouping of genes into biologically meaningful sets, and then conducting downstream analyses at the set (instead of gene) level of analysis. Gene set analysis methods have been shown to yield more powerful statistical conclusions than single-gene analyses due to both reduced multiple testing penalties and potentially larger observed effects due to the aggregation of effects across multiple genes in the set. Traditionally, gene set analysis methods have been applied directly to normalized, log-transformed, transcriptomics data. Recently, efforts have been made to transform transcriptomics data to scales yielding more biologically interpretable results. For example, recently proposed models transform log-transformed transcriptomics data to a confidence metric (ranging between 0 and 100%) that a gene is active (roughly speaking, that the gene product is part of an active cellular mechanism). In this manuscript, we demonstrate, on both real and simulated transcriptomics data, that tests for differential expression between sets of genes using are typically more powerful when using gene activity state estimates as opposed to log-transformed gene expression data. Our analysis suggests further exploration of techniques to transform transcriptomics data to meaningful quantities for improved downstream inference

Radio galaxy zoo EMU: towards a semantic radio galaxy morphology taxonomy

© 2023 The Author(s). Published by Oxford University Press on behalf of Royal Astronomical Society. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/)We present a novel natural language processing (NLP) approach to deriving plain English descriptors for science cases otherwise restricted by obfuscating technical terminology. We address the limitations of common radio galaxy morphology classifications by applying this approach. We experimentally derive a set of semantic tags for the Radio Galaxy Zoo EMU (Evolutionary Map of the Universe) project and the wider astronomical community. We collect 8486 plain English annotations of radio galaxy morphology, from which we derive a taxonomy of tags. The tags are plain English. The result is an extensible framework, which is more flexible, more easily communicated, and more sensitive to rare feature combinations, which are indescribable using the current framework of radio astronomy classifications.Peer reviewe

Structure of Herpes Simplex Virus Glycoprotein D Bound to the Human Receptor Nectin-1

Binding of herpes simplex virus (HSV) glycoprotein D (gD) to a cell surface receptor is required to trigger membrane fusion during entry into host cells. Nectin-1 is a cell adhesion molecule and the main HSV receptor in neurons and epithelial cells. We report the structure of gD bound to nectin-1 determined by x-ray crystallography to 4.0 Å resolution. The structure reveals that the nectin-1 binding site on gD differs from the binding site of the HVEM receptor. A surface on the first Ig-domain of nectin-1, which mediates homophilic interactions of Ig-like cell adhesion molecules, buries an area composed by residues from both the gD N- and C-terminal extensions. Phenylalanine 129, at the tip of the loop connecting β-strands F and G of nectin-1, protrudes into a groove on gD, which is otherwise occupied by C-terminal residues in the unliganded gD and by N-terminal residues in the gD/HVEM complex. Notably, mutation of Phe129 to alanine prevents nectin-1 binding to gD and HSV entry. Together these data are consistent with previous studies showing that gD disrupts the normal nectin-1 homophilic interactions. Furthermore, the structure of the complex supports a model in which gD-receptor binding triggers HSV entry through receptor-mediated displacement of the gD C-terminal region

Pseudorhabdosynochus species (Monogenoidea, Diplectanidae) parasitizing groupers (Serranidae, Epinephelinae, Epinephelini) in the western Atlantic Ocean and adjacent waters, with descriptions of 13 new species

Seventeen of twenty-three species of groupers collected from the western Atlantic Ocean and adjacent waters were infected with 19 identified species (13 new) of Pseudorhabdosynochus Yamaguti, 1958 (Dactylogyridea, Diplectanidae); specimens of the Spanish flag Gonioplectrus hispanus, coney Cephalopholis fulva, marbled grouper Dermatolepis inermis, mutton hamlet Alphestes afer, and misty grouper Hyporthodus mystacinus were not infected; the yellowmouth grouper Mycteroperca interstitialis and yellowfin grouper Mycteroperca venenosa were infected with unidentified species of Pseudorhabdosynochus; the Atlantic creolefish Paranthias furcifer was infected with an unidentified species of Diplectanidae that could not be accommodated in Pseudorhabdosynochus. The following species of Pseudorhabdosynochus are described or redescribed based entirely or in part on new collections: Pseudorhabdosynochus americanus (Price, 1937) Kritsky & Beverley-Burton, 1986 from Atlantic goliath grouper Epinephelus itajara; Pseudorhabdosynochus yucatanensis Vidal-Martínez, Aguirre-Macedo & Mendoza-Franco, 1997 and Pseudorhabdosynochus justinella n. sp. from red grouper Epinephelus morio; Pseudorhabdosynochus kritskyi Dyer, Williams & Bunkley-Williams, 1995 from gag Mycteroperca microlepis; Pseudorhabdosynochus capurroi Vidal-Martínez & Mendoza-Franco, 1998 from black grouper Mycteroperca bonaci; Pseudorhabdosynochus hyphessometochus n. sp. from Mycteroperca interstitialis; Pseudorhabdosynochus sulamericanus Santos, Buchmann & Gibson, 2000 from snowy grouper Hyporthodus niveatus and Warsaw grouper Hyporthodus nigritus (new host record); Pseudorhabdosynochus firmicoleatus n. sp. from yellowedge grouper Hyporthodus flavolimbatus and snowy grouper H. niveatus; Pseudorhabdosynochus mcmichaeli n. sp., Pseudorhabdosynochus contubernalis n. sp., and Pseudorhabdosynochus vascellum n. sp. from scamp Mycteroperca phenax; Pseudorhabdosynochus meganmarieae n. sp. from graysby Cephalopholis cruentata; Pseudorhabdosynochus beverleyburtonae (Oliver, 1984) Kritsky & Beverley-Burton, 1986 from dusky grouper Mycteroperca marginata; Pseudorhabdosynochus mizellei n. sp. from red hind Epinephelus guttatus; Pseudorhabdosynochus williamsi n. sp. from rock hind Epinephelus adscensionis; Pseudorhabdosynochus bunkleywilliamsae n. sp. from Nassau grouper Epinephelus striatus; Pseudorhabdosynochus mycteropercae n. sp. from tiger grouper Mycteroperca tigris; and Pseudorhabdosynochus tumeovagina n. sp. from speckled hind Epinephelus drummondhayi. Pseudorhabdosynochus woodi n. sp. from red hind Epinephelus guttatus is described based on specimens from the US National Parasite Collection (USNPC). Drawings of the haptoral and copulatory sclerites of the type specimens in the USNPC of Pseudorhabdosynochus monaensis Dyer, Williams & Bunkley-Williams, 1994 from rock hind Epinephelus adscensionis are presented. Finally, a note confirming Pseudorhabdosynochus epinepheli Yamaguti, 1958 rather than its senior synonym Pseudorhabdosynochus epinepheli (Yamaguti, 1938) Kritsky & Beverley-Burton, 1986 as the type species of Pseudorhabdosynochus is provided

From Preserving the Past to Preserving the Future: The Data-PASS Project and the Challenges of Preserving Digital Social Science Data

Social science data are an unusual part of the past, present, and future of digital preservation. They are both an unqualified success, due to long-lived and sustainable archival organizations, and in need of further development because not all digital content is being preserved. This article is about the Data Preservation Alliance for the Social Sciences (Data-PASS), a project supported by the National Digital Information Infrastructure and Preservation Program (NDIIPP), which is a partnership of five major U.S. social science data archives. Broadly speaking, Data-PASS has the goal of ensuring that at-risk social science data are identified, acquired, and preserved, and that we have a future-oriented organization that could collaborate on those preservation tasks for the future. Throughout the life of the Data-PASS project we have worked to identify digital materials that have never been systematically archived, and to appraise and acquire them. As the project has progressed, however, it has increasingly turned its attention from identifying and acquiring legacy and at-risk social science data to identifying ongoing and future research projects that will produce data. This article is about the project???s history, with an emphasis of the issues that underlay the transition from looking backward to looking forward.published or submitted for publicatio

Nanotubes as polymers

AbstractIn this review, we show that the structure and behavior of single-walled nanotubes (SWNTs) are essentially polymeric; in fact, many have referred to SWNTs as “the ultimate polymer”. The classification of SWNTS as polymers is explored by comparing the structure, properties, phase behavior, rheology, processing, and applications of SWNTs with those of rigid-rod polymers. Special attention is given to research efforts focusing on the use of SWNTs as molecular composites (also termed nanocomposites) with SWNTs as the filler and flexible polymer chains as the host. This perspective of “SWNTs as polymers” allows the methods, applications, and theoretical framework of polymer science to be appropriated and applied to nanotubes

Record of American Democracy, State Level MCD-Group Data for MO

The Record of American Democracy (ROAD) data provide election returns, socioeconomic summaries, and demographic details about the American public at unusually low levels of geographic aggregation. The NSF-supported ROAD project spans every state in the country from 1984 through 1990 (including some off-year elections). These data enable research on topics such as electoral behavior, the political characteristics of local community context, electoral geography, the role of minority groups in elections and legislative redistricting, split ticket voting and divided government, and elections under federalism. Another set of files has added to these roughly 30-40 political variables an additional 3,725 variables merged from the 1990 United States Census for 47,327 aggregate units called MCD Groups. The MCD Group is a construct for purposes of this data collection. It is based on a merging of the electoral precincts and Census Minor Civil Divisions (MCDs). An MCD is about the size of a city or town. An MCD Group is smaller than or equal to a county and (except in California) is greater than or equal to the size of an MCD. The MCD Group units completely tile the United States landmass. This particular study contains the files for the State Level MCD Group Data for the state of Missouri. Documentation and frequently asked questions are available online at the ROAD Website. A downloadable PDF codebook is also available in the files section of this study. <br /

Record of American Democracy, State Level MCD-Group Data for IN

The Record of American Democracy (ROAD) data provide election returns, socioeconomic summaries, and demographic details about the American public at unusually low levels of geographic aggregation. The NSF-supported ROAD project spans every state in the country from 1984 through 1990 (including some off-year elections). These data enable research on topics such as electoral behavior, the political characteristics of local community context, electoral geography, the role of minority groups in elections and legislative redistricting, split ticket voting and divided government, and elections under federalism. Another set of files has added to these roughly 30-40 political variables an additional 3,725 variables merged from the 1990 United States Census for 47,327 aggregate units called MCD Groups. The MCD Group is a construct for purposes of this data collection. It is based on a merging of the electoral precincts and Census Minor Civil Divisions (MCDs). An MCD is about the size of a city or town. An MCD Group is smaller than or equal to a county and (except in California) is greater than or equal to the size of an MCD. The MCD Group units completely tile the United States landmass. This particular study contains the files for the State Level MCD Group Data for the state of Indiana. Documentation and frequently asked questions are available online at the ROAD Website. A downloadable PDF codebook is also available in the files section of this study. <br /

Record of American Democracy, All pkey Data Files

The Record of American Democracy (ROAD) data provide election, socioeconomic summaries, and demographic details about thepublic at unusually low levels of geographic aggregation.NSF-supported ROAD project spans every state in the country1984 through 1990 (including some off-year elections). Theseenable research on topics such as electoral behavior, thecharacteristics of local community context, electoral, the role of minority groups in elections and legislative, split ticket voting and divided government, andunder federalism. This study comprises allof the publicdtat files for this study. Documentation and frequently asked questions are available online at the ROAD Website. A downloadable PDF codebook is also available in the files section of this study. <br /

Record of American Democracy, State Level MCD-Group Data for PA

The Record of American Democracy (ROAD) data provide election returns, socioeconomic summaries, and demographic details about the American public at unusually low levels of geographic aggregation. The NSF-supported ROAD project spans every state in the country from 1984 through 1990 (including some off-year elections). These data enable research on topics such as electoral behavior, the political characteristics of local community context, electoral geography, the role of minority groups in elections and legislative redistricting, split ticket voting and divided government, and elections under federalism. Another set of files has added to these roughly 30-40 political variables an additional 3,725 variables merged from the 1990 United States Census for 47,327 aggregate units called MCD Groups. The MCD Group is a construct for purposes of this data collection. It is based on a merging of the electoral precincts and Census Minor Civil Divisions (MCDs). An MCD is about the size of a city or town. An MCD Group is smaller than or equal to a county and (except in California) is greater than or equal to the size of an MCD. The MCD Group units completely tile the United States landmass. This particular study contains the files for the State Level MCD Group Data for the state of Pennsylvania. Documentation and frequently asked questions are available online at the ROAD Website. A downloadable PDF codebook is also available in the files section of this study. <br /