bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Assembly of the Canadian two-row Malting Barley cultivar AAC Synergy
Authors: Xu Wayne , Tucker James R , Bekele Wubishet A , You Frank M , Fu Yong-Bi , Khanal Raja , Yao Zhen , Singh Jaswinder , Boyle Brian , Beattie Aaron D , Belzile François , Mascher Martin , Tinker Nicholas A , Badea Ana 
Published: February 2021

AbstractBarley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb, and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (&lt; 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.
X-linked meiotic drive can boost population size and persistence
Authors: Mackintosh Carl , Pomiankowski Andrew , Scott Michael F 
Published: February 2021

AbstractX-linked meiotic drivers cause X-bearing sperm to be produced in excess by male carriers, leading to female-biased sex ratios. Here, we find general conditions for the spread and fixation of X-linked alleles. Our conditions show that the spread of X-linked alleles depends on sex-specific selection and transmission rather than the time spent in each sex. Applying this logic to meiotic drive, we show that polymorphism is heavily dependent on sperm competition induced both by female and male mating behavior and the degree of compensation to gamete loss in the ejaculate size of drive males. We extend these evolutionary models to investigate the demographic consequences of biased sex ratios. Our results suggest driving X-alleles that invade and reach polymorphism (or fix and do not bias segregation excessively) will boost population size and persistence time by increasing population productivity, demonstrating the potential for selfish genetic elements to move sex ratios closer to the population-level optimum. However, when the spread of drive causes strong sex-ratio bias, it can lead to populations with so few males that females remain unmated, cannot produce offspring, and go extinct. This outcome is exacerbated when the male mating rate is low. We suggest that researchers should consider the potential for ecologically beneficial side effects of selfish genetic elements, especially in light of proposals to use meiotic drive for biological control.
Characterizing the genetic basis of copper toxicity in Drosophila reveals a complex pattern of allelic, regulatory, and behavioral variation
Authors: Everman Elizabeth R , Cloud-Richardson Kristen M , Macdonald Stuart J 
Published: February 2021

Abstract
A range of heavy metals are required for normal cell function and homeostasis. However, the anthropogenic release of metal compounds into soil and water sources presents a pervasive health threat. Copper is one of many heavy metals that negatively impacts diverse organisms at a global scale. Using a combination of quantitative trait locus (QTL) mapping and RNA sequencing in the Drosophila Synthetic Population Resource, we demonstrate that resistance to the toxic effects of ingested copper in D. melanogaster is genetically complex and influenced by allelic and expression variation at multiple loci. QTL mapping identified several QTL that account for a substantial fraction of heritability. Additionally, we find that copper resistance is impacted by variation in behavioral avoidance of copper and may be subject to life-stage specific regulation. Gene expression analysis further demonstrated that resistant and sensitive strains are characterized by unique expression patterns. Several of the candidate genes identified via QTL mapping and RNAseq have known copper-specific functions (e.g., Ccs, Sod3, CG11825), and others are involved in the regulation of other heavy metals (e.g., Catsup, whd). We validated several of these candidate genes with RNAi suggesting they contribute to variation in adult copper resistance. Our study illuminates the interconnected roles that allelic and expression variation, organism life stage, and behavior play in copper resistance, allowing a deeper understanding of the diverse mechanisms through which metal pollution can negatively impact organisms.
Proteome-Wide Analysis Using SOMAscan Identifies and Validates Chitinase-3-Like Protein 1 as a Risk and Disease Marker of Delirium Among Older Adults Undergoing Major Elective Surgery
Authors: Vasunilashorn Sarinnapha M , Dillon Simon T , Chan Noel Y , Fong Tamara G , Joseph Marie , Tripp Bridget , Xie Zhongcong , Ngo Long H , Lee Chun Geun , Elias Jack A , Otu Hasan H , Inouye Sharon K , Marcantonio Edward R , Libermann Towia A 
Published: February 2021

Abstract

Background
Delirium (an acute change in cognition) is a common, morbid, and costly syndrome seen primarily in aging adults. Despite increasing knowledge of its epidemiology, delirium remains a clinical diagnosis with no established biomarkers to guide diagnosis or management. Advances in proteomics now provide opportunities to identify novel markers of risk and disease progression for postoperative delirium and its associated long-term consequences (eg, long-term cognitive decline and Alzheimer’s disease [AD]).

Methods
In a nested matched case–control study (18 delirium/no-delirium pairs) within the Successful Aging after Elective Surgery study (N = 556), we evaluated the association of 1305 plasma proteins preoperatively [PREOP] and on postoperative day 2 [POD2]) with delirium using SOMAscan. Generalized linear models were applied to enzyme-linked immunosorbant assay (ELISA) validation data of one protein across the full cohort. Multi-protein modeling included delirium biomarkers identified in prior work (C-reactive protein, interleukin-6 [IL6]).

Results
We identified chitinase-3-like-protein-1 (CHI3L1/YKL-40) as the sole delirium-associated protein in both a PREOP and a POD2 predictor model, a finding confirmed by ELISA. Multi-protein modeling found high PREOP CHI3L1/YKL-40 and POD2 IL6 increased the risk of delirium (relative risk [95% confidence interval] Quartile [Q]4 vs Q1: 2.4[1.2–5.0] and 2.1[1.1–4.1], respectively).

Conclusions
Our identification of CHI3L1/YKL-40 in postoperative delirium parallels reports of CHI3L1/YKL-40 and its association with aging, mortality, and age-related conditions including AD onset and progression. This highlights the type 2 innate immune response, involving CHI3L1/YKL-40, as an underlying mechanism of postoperative delirium, a common, morbid, and costly syndrome that threatens the independence of older adults.
Metre-scale stress heterogeneities and stress redistribution drive complex fracture slip and fracture growth during a hydraulic stimulation experiment
Authors: Villiger Linus , Gischig Valentin Samuel , Kwiatek Grzegorz , Krietsch Hannes , Doetsch Joseph , Jalali Mohammadreza , Amann Florian , Giardini Domenico , Wiemer Stefan 
Published: February 2021

SUMMARYWe investigated the induced seismicity, source mechanisms and mechanical responses of a decametre-scale hydraulic stimulation of a pre-existing shear zone in crystalline rock, at the Grimsel Test Site, Switzerland. The analysis reveals the metre-scale complexity of hydraulic stimulation, which remains hidden at the reservoir-scale. High earthquake location accuracy allowed the separation of four distinct clusters, of which three were attributed to the stimulation of fractures in the damage zone of the shear zone. The source mechanism of the larger-magnitude seismicity varied by cluster, and suggests a heterogeneous stress field already prevailing before stimulation, which is further modified during stimulation. In the course of the experiment, stress redistribution led to the aseismic initiation of a tensile-dominated fracture, which induced seismicity in the fourth of the identified seismic clusters. The streaky pattern of seismicity separated by zones without seismicity suggests fluid flow in conduits along existing fracture planes. The observed submetre scale complexity questions the forecasting ability of induced seismic hazard at the reservoir scale from small-scale experiments.
On the Assembly Map for Complex Semisimple Quantum Groups
Authors: Voigt Christian 
Published: February 2021

AbstractWe show that complex semisimple quantum groups, that is, Drinfeld doubles of $q$-deformations of compact semisimple Lie groups, satisfy a categorical version of the Baum–Connes conjecture with trivial coefficients. Our approach, based on homological algebra in triangulated categories, is compatible with the previously studied deformation picture of the assembly map and allows us to define an assembly map with arbitrary coefficients for these quantum groups.
Refiguring Christianity and Black Atlantic Religion: Representation, Essentialism, and Christian Variation in the Southern Caribbean
Authors: Thornton Brendan Jamal 
Published: February 2021

AbstractThis article considers the analytic categories scholars use to conceptualize religious difference in the Caribbean and addresses the relatively sparse theorizing of Christianity in the study of so-called syncretic or creole religions of the African diaspora. I take the Spiritual Baptists of Trinidad and Tobago as a case study to shed light on the significant divergences between vernacular definitions of Christianity and those designations scholars use to parse and make sense of Afro-Creole diversity. I am especially interested in what is at stake analytically. Spiritual Baptists challenge conventional articulations of Christian orthodoxy and Black Atlantic religiosity by reconciling a “fundamentalist” Christian identity with an especially fluid cosmopolitan eclecticism. Drawing on comprehensive ethnographic research, I show how the unique permutations of creole variation within Spiritual Baptist faith unsettle deterministic equations of race and religion and contest the often manufactured oppositions between Christianity and African religion.
Collective assessment of antimicrobial susceptibility among the most common Gram-negative respiratory pathogens driving therapy in the ICU
Authors: Moise Pamela A , Gonzalez Marcela , Alekseeva Irina , Lopez Diego , Akrich Brune , DeRyke C Andrew , Chen Wei-Ting , Pavia Jacqueline , Palermo Brandon , Hackel Meredith , Motyl Mary 
Published: February 2021

Abstract

Objectives
To describe the pathogen predominance and to evaluate the probability of covering the most common Gram-negative pathogens collectively in both empirical and early adjustment prescribing scenarios in ICU patients with respiratory infections.

Methods
Data were collected from an international cohort of hospitals as part of the SMART Surveillance Program (2018). Susceptibility testing (mg/L) was performed by broth microdilution methods.

Results
7171 Gram-negative respiratory isolates from adult ICU patients across 209 hospitals from 56 different countries were studied. Overall, the most common ICU respiratory pathogens isolated were Pseudomonas aeruginosa (25%), Klebsiella pneumoniae (18%), Acinetobacter baumannii (14%), and Escherichia coli (11%), with inter-regional differences among these pathogens. Among Enterobacterales, 36% were ESBL positive. When the collective susceptibility profile of this set of pathogens (P. aeruginosa plus Enterobacterales; comprising 78% of all organisms isolated) was performed, ceftolozane/tazobactam (84%), followed by meropenem (81%), provided the most reliable in vitro activity in the empirical prescribing scenario compared with other β-lactam antibiotics. P. aeruginosa co-resistance was common among first-line β-lactam antibiotics. If P. aeruginosa was non-susceptible to piperacillin/tazobactam, less than one-third were susceptible to meropenem or ceftazidime. In contrast, ceftolozane/tazobactam offered in vitro coverage in over two-thirds of these resistant pathogens.

Conclusions
Ceftolozane/tazobactam demonstrated high cumulative susceptibility levels and in vitro activity in both empirical and adjustment antibiotic prescribing scenarios. High frequency of co-resistance undermines reliable coverage for Gram-negative pathogens already resistant to first-line agents. Ceftolozane/tazobactam would offer additional coverage in this setting.
Changes in genomic predictions when new information is added
Authors: Hidalgo Jorge , Lourenco Daniela , Tsuruta Shogo , Masuda Yutaka , Miller Stephen , Bermann Matias , Garcia Andre L S , Misztal Ignacy 
Published: February 2021

Abstract
The stability of genomic evaluations depends on the amount of data and population parameters. When the dataset is large enough to estimate the value of nearly all independent chromosome segments (~10K in American Angus cattle), the accuracy and persistency of breeding values will be high. The objective of this study was to investigate changes in estimated breeding values (EBV) and genomic EBV (GEBV) across monthly evaluations for 1 yr in a large genotyped population of beef cattle. The American Angus data used included 8.2 million records for birth weight, 8.9 for weaning weight, and 4.4 for postweaning gain. A total of 10.1 million animals born until December 2017 had pedigree information, and 484,074 were genotyped. A truncated dataset included animals born until December 2016. To mimic a scenario with monthly evaluations, 2017 data were added 1 mo at a time to estimate EBV using best linear unbiased prediction (BLUP) and GEBV using single-step genomic BLUP with the algorithm for proven and young (APY) with core group fixed for 1 yr or updated monthly. Predictions from monthly evaluations in 2017 were contrasted with the predictions of the evaluation in December 2016 or the previous month for all genotyped animals born until December 2016 with or without their own phenotypes or progeny phenotypes. Changes in EBV and GEBV were similar across traits, and only results for weaning weight are presented. Correlations between evaluations from December 2016 and the 12 consecutive evaluations were ≥0.97 for EBV and ≥0.99 for GEBV. Average absolute changes for EBV were about two times smaller than for GEBV, except for animals with new progeny phenotypes (≤0.12 and ≤0.11 additive genetic SD [SDa] for EBV and GEBV). The maximum absolute changes for EBV (≤2.95 SDa) were greater than for GEBV (≤1.59 SDa). The average(maximum) absolute GEBV changes for young animals from December 2016 to January and December 2017 ranged from 0.05(0.25) to 0.10(0.53) SDa. Corresponding ranges for animals with new progeny phenotypes were from 0.05(0.88) to 0.11(1.59) SDa for GEBV changes. The average absolute change in EBV(GEBV) from December 2016 to December 2017 for sires with ≤50 progeny phenotypes was 0.26(0.14) and for sires with &gt;50 progeny phenotypes was 0.25(0.16) SDa. Updating the core group in APY without adding data created an average absolute change of 0.07 SDa in GEBV. Genomic evaluations in large genotyped populations are as stable and persistent as the traditional genetic evaluations, with less extreme changes.
Dietary conjugated linoleic acid supplementation alters skeletal muscle mitochondria and antioxidant status in young horses
Authors: Mrugala Daria , Leatherwood Jessica L , Morris Elizabeth F , Dickson Emily C , Latham Christine M , Owen Randi N , Beverly Marcy M , Kelley Stanley F , White-Springer Sarah H 
Published: February 2021

Abstract
Conjugated linoleic acid (CLA) improves oxidative stress and mitochondrial biogenesis in various species but has not been thoroughly investigated in horses. We collected blood and muscle samples from lightly exercising horses before and 6 and 12 wk after receiving either soybean oil (CON; n = 5) or CLA (CLA; n = 5) supplementation. Samples were analyzed for markers of mitochondrial characteristics, antioxidant status, oxidative stress, and muscle damage. Data were analyzed using a linear model with repeated measures. In the triceps brachii (TB), citrate synthase (CS) activity was higher in CON than CLA horses (P = 0.003) but was unaffected by diet in the gluteus medius (GM). Integrative (relative to mg protein) cytochrome c oxidase (CCO) activity was higher in TB than the GM (P &lt; 0.0001), while intrinsic (relative to CS) CCO was lower in the TB than the GM (P = 0.02) and tended to be lower in CON than CLA horses (P = 0.06). Neither CS nor integrative CCO activities were affected by time. In the GM, superoxide dismutase activity tended to increase in CON through week 12 (P = 0.10). Over both muscle groups, glutathione peroxidase activity tended to be higher in CON compared with CLA at week 12 (P = 0.06). Malondialdehyde was higher in the TB than the GM (P = 0.0004) but was unaffected by diet, while serum creatine kinase activity tended to be lower in CLA than CON horses (P = 0.07). These results suggest that CLA supplementation may lead to mitochondrial adaptations and prevent myofiber perturbation in skeletal muscle of young, lightly exercised horses.
Collecting people: bluestocking sociability and the assembling of knowledge
Authors: Eger Elizabeth 
Published: February 2021

Abstract
This essay explores the relationship between knowledge and sociability in eighteenth-century England through a discussion of two female collectors and their collections. The friendship between Elizabeth Montagu (1718–1800) and Margaret Cavendish Bentinck, Duchess of Portland (1715–1785) was founded upon a shared enthusiasm for the art of conversation and the ambition to create communities of learning in which both sexes could flourish. The duchess’s natural history collection at Bulstrode Park and Montagu’s London salon, adorned with its own combination of nature and art, are compared as parallel sites that attracted visitors from a diverse range of professions, nationalities and political persuasions. For elite women, sociability and the assembling of people were integral to the pursuit and display of knowledge. The work of Mrs Montagu and the duchess as collectors reveals the complex relationship between science, sociability and aesthetics that characterizes the history of collections.
The Role of Predation in Determining Traits of Aedes aegypti (Diptera: Culicidae) and Infection With Zika Virus
Authors: Bellamy Shawna , Alto Barry W 
Published: February 2021

Abstract
Non-lethal predator-prey interactions during the immature stages can cause significant changes to mosquito life history traits and their ability to transmit pathogens as adults. Treatment manipulations using mosquitoes Aedes aegypti (L.) and Toxoryhnchites rutilus (Coquillett) were performed during the immature stages to explore the potential impacts of non-lethal interactions on adult susceptibility to infection, disseminated infection and saliva infection of Ae. aegypti following ingestion of Zika virus-infected blood. Treatments inducing density reduction resulted in reduced development time and survivorship to adulthood. However, effects of treatment did not alter infection, dissemination, or saliva infection. These observations indicate that, while non-lethal predation may impact some traits that influence population dynamics and transmission of pathogens, there were no direct effects on mosquito-arbovirus interactions.
Summer Bat Habitat Use and Forest Characteristics in Managed Northeastern Forests
Authors: Gallagher Megan E , Farrell Shannon L , Germain René H , Rojas Vanessa G 
Published: February 2021

AbstractThere has been limited research investigating summer habitat use of bats in managed forests in the northeastern United States. Consequently, there is limited knowledge to inform forest managers seeking to maintain or enhance bat habitat, particularly for several federally threatened, endangered, or candidate species. In summer 2017–2018, we conducted repeated acoustic surveys to determine what forest characteristics are associated with bat habitat use in managed forests in the Adirondack region of upstate New York. We modeled detection corrected probability of occupancy for bats in three phonic groups: high, mid, and low frequency. Across all phonic groups, probability of occupancy increased with decreasing canopy cover. High-, mid-, and low-frequency bats were more likely to use recently harvested sites (&lt;10 years since harvest). High-frequency bats also used mature stands. Midfrequency bats demonstrated a preference for further distances from forest roads, whereas low-frequency bats preferred areas with a higher percentage of clutter. Our results suggest that tending and regenerating even-aged forest management practices can provide habitat for foraging bats in the Adirondacks.
Avleddha: an example of Griko in popular music
Authors: Souli Dafni , Dilucca Maddalena 
Published: February 2021

Abstract
This paper is part of a wider study about a corpus of songs, collected in the three different languages spoken in Salento (Puglia- South Italy): Italian (with regional variety), Griko and Salentino dialect. We analyze all the discography (texts and music of songs) of Avleddha, one of the most famous popular bands, founded in the early ‘90s in the Grecìa Salentina. This corpus is compared to other 80 songs, that includes English, Italian and popular music. We use Principal Component Analysis and techniques of sound analysis (spectrograms) we demonstrate that songs of the four bands are well separated from a point of view of complexity of the texts and music. The aim of this study is to characterize Avleddha’s music with reference to the other group of songs. We show that it is closer to the tradition of Salento popular music, but is able to maintain an original fingerprint, that makes it unique in its field. In this research the description of language systems at morphosyntactic level is not present, but we present a novel quantitative approach to reveal features both generic and specific in corpora of popular music.