182 Works

Data from: Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses

Benjamin Roche, John M. Drake, Justin Brown, David E. Stallknecht, Trevor Bedford & Pejman Rohani
Avian influenza viruses (AIVs) have been pivotal to the origination of human pandemic strains. Despite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of AIVs in wild birds, where major pools of genetic diversity are generated and maintained. Here, we present comparative phylodynamic analyses of human and AIVs in North America, demonstrating (i) significantly higher standing genetic diversity and (ii) phylogenetic trees with a weaker...

Data from: Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation

Duncan K. Ralph, & Frederick A. Matsen
VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D,...

Data from: Purifying selection maintains dosage-sensitive genes during degeneration of the threespine stickleback Y chromosome

Michael A. White, Jun Kitano & Catherine L. Peichel
Sex chromosomes are subject to unique evolutionary forces that cause suppression of recombination, leading to sequence degeneration and the formation of heteromorphic chromosome pairs (i.e., XY or ZW). Although progress has been made in characterizing the outcomes of these evolutionary processes on vertebrate sex chromosomes, it is still unclear how recombination suppression and sequence divergence typically occur and how gene dosage imbalances are resolved in the heterogametic sex. The threespine stickleback fish (Gasterosteus aculeatus) is...

Data from: The impacts of Wolbachia and the microbiome on mate choice in Drosophila melanogaster

Devin Arbuthnott, Tera C. Levin & Daniel E. L. Promislow
Symbionts and parasites can manipulate their hosts’ reproduction to their own benefit, profoundly influencing patterns of mate choice and evolution of the host population. Wolbachia is one of the most widespread symbionts among arthropods, and one that alters its hosts’ reproduction in diverse and dramatic ways. While we are beginning to appreciate how Wolbachia's extreme manipulations of host reproduction can influence species diversification and reproductive isolation, we understand little about how symbionts and Wolbachia, in...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: Caenorhabditis elegans genes affecting interindividual variation in life-span biomarker gene expression

Alexander Mendenhall, Matthew M. Crane, Patricia M. Tedesco, Thomas E. Johnson & Roger Brent
Genetically identical organisms grown in homogenous environments differ in quantitative phenotypes. Differences in one such trait, expression of a single biomarker gene, can identify isogenic cells or organisms that later manifest different fates. For example, in isogenic populations of young adult Caenorhabditis elegans, differences in Green Fluorescent Protein (GFP) expressed from the hsp-16.2 promoter predict differences in life span. Thus, it is of interest to determine how interindividual differences in biomarker gene expression arise. Prior...

Data from: Single‐cell profiling screen identifies microtubule‐dependent reduction of variability in signaling

C. Gustavo Pesce, William J. Peria, Stefan Zdraljevic, Daniel Rockwell, Richard C. Yu, Alejandro Colman-Lerner, Roger Brent, Alan Bush & María Victoria Repetto
Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell‐to‐cell variability in signal strength and cellular response. Here, we screened 1,141 non‐essential genes to identify 50 “variability genes”. Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct “axes” of system behavior. Three genes affected...

Application of simultaneous selective pressures slows adaptation

Lauren Merlo, Kathleen Sprouffske, Taylor Howard, Kristin Gardiner, Aleah Caulin, Steven Blum, Perry Evans, Antonio Bedalov, Paul Sniegowski & Carlo Maley
Background and objectives: Beneficial mutations that arise in an evolving asexual population may compete or interact in ways that alter the overall rate of adaptation through mechanisms such as clonal or functional interference. The application of multiple selective pressures simultaneously may allow for a greater number of adaptive mutations, increasing the opportunities for competition between selectively advantageous alterations, and thereby reducing the rate of adaptation. Methodology: We evolved a strain of Saccharomyces cerevisiae that could...

Additional file 4 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 4. Concentration and forest plots for each individual immune mediator. Concentration plots - Each symbol shows the concentration of the indicated immune mediator in a single sample. Each study is plotted separately. Lines connect samples from the same participant; in some cases participants provided multiple samples in the same phase, in which case multiple symbols within the same phase may be connected. Pale grey symbols are below the lower limit of detection and...

Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Abstract Background Hormonal changes during the menstrual cycle play a key role in shaping immunity in the cervicovaginal tract. Cervicovaginal fluid contains cytokines, chemokines, immunoglobulins, and other immune mediators. Many studies have shown that the concentrations of these immune mediators change throughout the menstrual cycle, but the studies have often shown inconsistent results. Our understanding of immunological correlates of the menstrual cycle remains limited and could be improved by meta-analysis of the available evidence. Methods...

Additional file 1 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 1. Supporting methods documents. PRISMA-P and PRISMA-IPD checklists, database search strategies, manuscript screening form, risk of bias instrument, and strength of evidence tool.

Additional file 2 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 2. Amendments to the pre-registered protocol.

Whole-genome resequencing of Dorper and Hu sheep to reveal selection signatures associated with important traits

Xiaoyang Lv, Weihao Chen, Shanhe Wang, Xiukai Cao, Zehu Yuan, Tesfaye Getachew, Joram M. Mwacharo, Aynalem Haile & Wei Sun
Dorper and Hu sheep exhibit different characteristics in terms of reproduction, growth, and meat quality. Comparison of the genomes of two breeds help to reveal important genomic information. In this study, whole genome resequencing of 30 individuals (Dorper, DB and Hu sheep, HY) identified 15,108,125 single nucleotide polymorphisms (SNPs). Population differentiation (Fst) and cross population extended haplotype homozygosity (XP-EHH) were performed for selective signal analysis. In total, 106 and 515 overlapped genes were present in...

Additional file 3 of Relationship between metabolically healthy obesity and the development of hypertension: a nationwide population-based study

Yue Yuan, Wei Sun & Xiangqing Kong
Additional file 3: Table S3. Adjusted odds ratios and 95% confidence intervals of the association of metabolic health and general obesity with prehypertension and hypertension by different age periods.

sj-png-2-eso-10.1177_23969873221127738 – Supplemental material for General anesthesia versus conscious sedation during endovascular treatment in posterior circulation large vessel occlusion: A systematic review and meta-analysis

Mikel Terceño, Saima Bashir, Juan Cienfuegos, Alan Murillo, Víctor Augusto Vera-Monge, Laura Pardo, Montserrat Reina, Carme Gubern-Mérida, Dolors Puigoriol-Illamola, Laia Carballo, Anna Costa, Maria Buxó, Joaquín Serena & Yolanda Silva
Supplemental material, sj-png-2-eso-10.1177_23969873221127738 for General anesthesia versus conscious sedation during endovascular treatment in posterior circulation large vessel occlusion: A systematic review and meta-analysis by Mikel Terceño, Saima Bashir, Juan Cienfuegos, Alan Murillo, Víctor Augusto Vera-Monge, Laura Pardo, Montserrat Reina, Carme Gubern-Mérida, Dolors Puigoriol-Illamola, Laia Carballo, Anna Costa, Maria Buxó, Joaquín Serena and Yolanda Silva in European Stroke Journal

China’s terrestrial ecosystem carbon balance during the 20th century: an analysis with a process-based biogeochemistry model

Yanyu Lu, Yao Huang, Qianlai Zhuang, Wei Sun, Shutao Chen & Jun Lu
Abstract Background China’s terrestrial ecosystems play a pronounced role in the global carbon cycle. Here we combine spatially-explicit information on vegetation, soil, topography, climate and land use change with a process-based biogeochemistry model to quantify the responses of terrestrial carbon cycle in China during the 20th century. Results At a century scale, China’s terrestrial ecosystems have acted as a carbon sink averaging at 96 Tg C yr− 1, with large inter-annual and decadal variabilities. The...

Additional file 2 of Evaluate the immune-related eRNA models and signature score to predict the response to immunotherapy in thyroid carcinoma

Pu Wu, Jinyuan Shi, Zhiyuan Wang, Wei Sun & Hao Zhang
Additional file 2: Figure S2. The diagnostic values of 9 eRNAs for THCA patients.

Clostridium subterminale infection in a patient with diffuse large B-cell lymphoma and haemophagocytic syndrome: A case report and literature review

Ying Zhou, Sheng Wang & Xing-bei Weng
Although uncommon, infection caused by Clostridium subterminale may be life threatening particularly in immunocompromised patients. We report here a rare presentation of a patient with diffuse large B-cell lymphoma and haemophagocytic syndrome associated with C. subterminale bacteraemia. The management of the patient is described as well as a review of medical literature. Infection by Clostridium species, including C. subterminale, should be considered in a febrile patient with a haematologic malignancy. The case highlights the importance...

sj-pdf-1-imr-10.1177_03000605221129558 - Supplemental material for Clostridium subterminale infection in a patient with diffuse large B-cell lymphoma and haemophagocytic syndrome: A case report and literature review

Ying Zhou, Sheng Wang & Xing-bei Weng
Supplemental material, sj-pdf-1-imr-10.1177_03000605221129558 for Clostridium subterminale infection in a patient with diffuse large B-cell lymphoma and haemophagocytic syndrome: A case report and literature review by Ying Zhou, Sheng Wang, Xing-bei Weng in Journal of International Medical Research

Additional file 2 of A standardized nomenclature for mammalian histone genes

Ruth L. Seal, Paul Denny, Elspeth A. Bruford, Anna K. Gribkova, David Landsman, William F. Marzluff, Monica McAndrews, Anna R. Panchenko, Alexey K. Shaytan & Paul B. Talbert
Additional file 2. List of human histone proteins from the Histone Sequence Database for every histone gene, the available set of transcript and coding sequence GENCODE annotations were obtained from the Ensembl 105 database. Next, only protein-coding transcripts identical between Ensembl automated annotation and HAVANA manual curation were retained. In those cases where several transcripts of one gene correspond to the same amino acid protein sequence, only one record was retained with preference given to...

Additional file 1 of Colorectal cancer incidences in Lynch syndrome: a comparison of results from the prospective lynch syndrome database and the international mismatch repair consortium

Pål Møller, Toni Seppälä, James G. Dowty, Saskia Haupt, Mev Dominguez-Valentin, Lone Sunde, Inge Bernstein, Christoph Engel, Stefan Aretz, Maartje Nielsen, Gabriel Capella, Dafydd Gareth Evans, John Burn, Elke Holinski-Feder, Lucio Bertario, Bernardo Bonanni, Annika Lindblom, Zohar Levi, Finlay Macrae, Ingrid Winship, John-Paul Plazzer, Rolf Sijmons, Luigi Laghi, Adriana Della Valle, Karl Heinimann … & Mark A. Jenkins
Additional file 1.

Additional file 9 of Genome-wide identification of key enzyme-encoding genes and the catalytic roles of two 2-oxoglutarate-dependent dioxygenase involved in flavonoid biosynthesis in Cannabis sativa L.

Xuewen Zhu, Yaolei Mi, Xiangxiao Meng, Yiming Zhang, Weiqiang Chen, Xue Cao, Huihua Wan, Wei Yang, Jun Li, Sifan Wang, Zhichao Xu, Atia Tul Wahab, Shilin Chen & Wei Sun
Additional file 9: Figure S4. Cis-acting elements within the promoters of CsFLS2 and CsFLS3.

Additional file 1 of Genome-wide identification of key enzyme-encoding genes and the catalytic roles of two 2-oxoglutarate-dependent dioxygenase involved in flavonoid biosynthesis in Cannabis sativa L.

Xuewen Zhu, Yaolei Mi, Xiangxiao Meng, Yiming Zhang, Weiqiang Chen, Xue Cao, Huihua Wan, Wei Yang, Jun Li, Sifan Wang, Zhichao Xu, Atia Tul Wahab, Shilin Chen & Wei Sun
Additional file 1: Table S1. Physical characteristics of the major enzyme-encoding genes of flavonoid metabolic pathway in C. sativa.

Genome-wide identification of key enzyme-encoding genes and the catalytic roles of two 2-oxoglutarate-dependent dioxygenase involved in flavonoid biosynthesis in Cannabis sativa L.

Xuewen Zhu, Yaolei Mi, Xiangxiao Meng, Yiming Zhang, Weiqiang Chen, Xue Cao, Huihua Wan, Wei Yang, Jun Li, Sifan Wang, Zhichao Xu, Atia Tul Wahab, Shilin Chen & Wei Sun
Abstract Background Flavonoids are necessary for plant growth and resistance to adversity and stress. They are also an essential nutrient for human diet and health. Among the metabolites produced in Cannabis sativa (C. sativa), phytocannabinoids have undergone extensive research on their structures, biosynthesis, and biological activities. Besides the phytocannabinoids, C. sativa is also rich in terpenes, alkaloids, and flavonoids, although little research has been conducted in this area. Results In this study, we identified 11...

Reproduction Materials for: Change in Plasma Alpha-tocopherol Associations with Attenuated Pulmonary Function Decline and with CYP4F2 Missense Variation

Jiayi Xu, Kristin Guertin, Nathan Gaddis, Anne H. Agular, Robert S. Parker, Jared M. Feldman, Alan R. Kristal, Kathryn B. Arnold, Phyllis J. Goodman, Catherine M. Tangen, Dana Hancock & Patricia A. Cassano
**PI-Provided Abstract:** Background: Vitamin E (vitE) is hypothesized to attenuate age-related decline in pulmonary function. Objective: We investigated the association between change in plasma vitE (∆vitE) and pulmonary function decline (forced expiratory volume in the first second [FEV1]) and examined genetic and non-genetic factors associated with ∆vitE. Design: We studied 1,144 men randomized to vitE in the Selenium and Vitamin E Cancer Prevention Trial. ∆vitE was the difference between baseline and year 3 vitE concentrations...

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