bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron Subvariant BA.2 in a Single-Source Community Outbreak
Authors: Cheng Vincent Chi Chung , Ip Jonathan Daniel , Chu Allen Wing Ho , Tam Anthony Raymond , Chan Wan Mui , Abdullah Syed Muhammad Umer , Chan Brian Pui Chun , Wong Shuk Ching , Kwan Mike Yat Wah , Chua Gilbert T , Ip Patrick , Chan Jacky Man Chun , Lam Bosco Hoi Shiu , To Wing Kin , Chuang Vivien Wai Man , Yuen Kwok Yung , Hung Ivan Fan Ngai , To Kelvin Kai Wang 
Published: March 2022

Abstract

Background
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant BA.2 sublineage has increased rapidly in Europe and Asia since January 2022. Here, we report the epidemiological and genomic analysis of a large single-source BA.2 outbreak in a housing estate.

Methods
We analyzed the epidemiological information on a community outbreak of BA.2 (STY outbreak). We performed whole viral genome sequencing using the Oxford Nanopore MinION device. We calculated the doubling time of the outbreak within a housing estate.

Results
The STY outbreak involved a total of 768 individuals as of 5 February 2022, including 432 residents, visitors, or staff (56.3%) from a single housing estate (KC Estate). The outbreak at the KC Estate had a short doubling time of 1.28 days (95% confidence interval: .560–1.935). The outbreak was promptly controlled with the lockdown of 3 buildings within the housing estate. Whole-genome sequencing was performed for 133 patients in the STY outbreak, including 106 residents of the KC Estate. All 133 sequences from the STY outbreak belonged to the BA.2 sublineage, and phylogenetic analysis showed that these sequences cluster together. All individuals in the STY cluster had the unique mutation C12525T.

Conclusions
Our study highlights the exceptionally high transmissibility of the Omicron variant BA.2 sublineage in Hong Kong, where stringent measures are implemented as part of the elimination strategy. Continual genomic surveillance is crucial in monitoring the emergence of epidemiologically important Omicron sublineages.
Reproductive Ecology ofDrosophila obscura: A Cold Adapted Species
Authors: Canal Domenech Berta , Seipelt Aileen , Fricke Claudia 
Published: March 2022

AbstractThe study of insect reproductive ecology is essential to determine species distributions and fate under changing environments. Species adapted to harsh environments are good examples to investigate the reproductive mechanisms that allow them to cope with the challenging conditions. We here focus on studying for the first time the reproductive ecology of a cold-adapted Drosophila obscura (Diptera: Drosophilidae) strain collected in Finland (subarctic climate region). We tested several reproductive traits such as fertility and fecundity to observe the onset of reproduction and gauge when sexual maturity is reached in both males and females. We combined these measures with an analysis of changes of their reproductive organs shortly after eclosion. We found that males matured several days before females and that this process was underpinned by female egg maturation and male accessory gland growth, while sperm was already present in two-day old males. This delayed maturation is not observed to the same extent in other closely related species and might be a signature of exposure to harsh environments. Whether this delay is an adaptation to cope with variation in resource availability or prolonged unfavorable temperatures is though not clear. Finally, our study adds to the set of reproductive mechanisms used by cold adapted species and the information presented here contributes to understanding the breadth of Drosophila reproductive ecology.
Importance of genetic testing in unexplained cardiac arrest
Authors: Grondin Steffany , Davies Brianna , Cadrin-Tourigny Julia , Steinberg Christian , Cheung Christopher C , Jorda Paloma , Healey Jeffrey S , Green Martin S , Sanatani Shubhayan , Alqarawi Wael , Angaran Paul , Arbour Laura , Antiperovitch Pavel , Khan Habib , Leather Richard , Guerra Peter G , Rivard Lena , Simpson Christopher S , Gardner Martin , MacIntyre Ciorsti , Seifer Colette , Fournier Anne , Joza Jacqueline , Gollob Michael H , Lettre Guillaume , Talajic Mario , Laksman Zachary W , Roberts Jason D , Krahn Andrew D , Tadros Rafik 
Published: March 2022

Abstract

Aims
Genetic testing is recommended in specific inherited heart diseases but its role remains unclear and it is not currently recommended in unexplained cardiac arrest (UCA). We sought to assess the yield and clinical utility of genetic testing in UCA using whole-exome sequencing (WES).

Methods and results
Survivors of UCA requiring external defibrillation were included from the Cardiac Arrest Survivor with Preserved Ejection fraction Registry. Whole-exome sequencing was performed, followed by assessment of rare variants in previously reported cardiovascular disease genes. A total of 228 UCA survivors (mean age at arrest 39 ± 13 years) were included. The majority were males (66%) and of European ancestry (81%). Following advanced clinical testing at baseline, the likely aetiology of cardiac arrest was determined in 21/228 (9%) cases. Whole-exome sequencing identified a pathogenic or likely pathogenic (P/LP) variant in 23/228 (10%) of UCA survivors overall, increasing the proportion of ‘explained’ cases from 9% only following phenotyping to 18% when combining phenotyping with WES. Notably, 13 (57%) of the 23 P/LP variants identified were located in genes associated with cardiomyopathy, in the absence of a diagnosis of cardiomyopathy at the time of arrest.

Conclusions
Genetic testing identifies a disease-causing variant in 10% of apparent UCA survivors. The majority of disease-causing variants was located in cardiomyopathy-associated genes, highlighting the arrhythmogenic potential of such variants in the absence of an overt cardiomyopathy diagnosis. The present study supports the use of genetic testing including assessment of arrhythmia and cardiomyopathy genes in survivors of UCA.
Strong Parallel Differential Gene Expression Induced by Hatchery Rearing Weakly Associated with Methylation Signals in Adult Coho Salmon (O. kisutch)
Authors: Leitwein Maeva , Wellband Kyle , Cayuela Hugo , Le Luyer Jérémy , Mohns Kayla , Withler Ruth , Bernatchez Louis 
Published: March 2022

AbstractHuman activities and resource exploitation led to a massive decline of wild salmonid populations, consequently, numerous conservation programs have been developed to supplement wild populations. However, many studies documented reduced fitness of hatchery-born relative to wild fish. Here, by using both RNA sequencing and Whole Genome Bisulfite Sequencing of hatchery and wild-born adult Coho salmon (Oncorhynchus kisutch) originating from two previously studied river systems, we show that early-life hatchery-rearing environment-induced significant and parallel gene expression differentiation is maintained until Coho come back to their natal river for reproduction. A total of 3,643 genes differentially expressed and 859 coexpressed genes were downregulated in parallel in hatchery-born fish from both rivers relative to their wild congeners. Among those genes, 26 displayed a significant relationship between gene expression and the median gene body methylation and 669 single CpGs displayed a significant correlation between methylation level and the associated gene expression. The link between methylation and gene expression was weak suggesting that DNA methylation is not the only player in mediating hatchery-related expression differences. Yet, significant gene expression differentiation was observed despite 18 months spent in a common environment (i.e., the sea). Finally, the differentiation is observed in parallel in two different river systems, highlighting the fact that early-life environment may account for at least some of the reduced fitness of the hatchery salmon in the wild. These results illustrate the relevance and importance of considering both epigenome and transcriptome to evaluate the costs and benefits of large-scale supplementation programs.
Carbohydrate Structure Database oligosaccharide conformation tool
Authors: Scherbinina Sofya I , Frank Martin , Toukach Philip V 
Published: March 2022

Abstract
Population analysis in terms of glycosidic torsion angles is frequently used to reveal preferred conformers of glycans. However, due to high structural diversity and flexibility of carbohydrates, conformational characterization of complex glycans can be a challenging task. Herein, we present a conformation module of oligosaccharide fragments occurring in natural glycan structures developed on the platform of the Carbohydrate Structure Database. Currently, this module deposits free energy surface and conformer abundance maps plotted as a function of glycosidic torsions for 194 “inter”residue bonds. Data are automatically and continuously derived from explicit-solvent molecular dynamics (MD) simulations. The module was also supplemented with high-temperature MD data of saccharides (2,403 maps) provided by GlycoMapsDB (hosted by GLYCOSCIENCES.de project). Conformational data defined by up to 4 torsional degrees of freedom can be freely explored using a web interface of the module available at http://csdb.glycoscience.ru/database/core/search_conf.html.
Mitochondrial DNA variants segregate during human preimplantation development into genetically different cell lineages that are maintained postnatally
Authors: Mertens Joke , Regin Marius , De Munck Neelke , Couvreu de Deckersberg Edouard , Belva Florence , Sermon Karen , Tournaye Herman , Blockeel Christophe , Van de Velde Hilde , Spits Claudia 
Published: March 2022

AbstractHumans present remarkable diversity in their mitochondrial DNA (mtDNA) in terms of variants across individuals as well as across tissues and even cells within one person. We have investigated the timing of the first appearance of this variant-driven mosaicism. For this, we deep-sequenced the mtDNA of 254 oocytes from 85 donors, 158 single blastomeres of 25 day-3 embryos, 17 inner cell mass and trophectoderm samples of 7 day-5 blastocysts, 142 bulk DNA and 68 single cells of different adult tissues. We found that day-3 embryos present blastomeres that carry variants only detected in that cell, showing that mtDNA mosaicism arises very early in human development. We classified the mtDNA variants based on their recurrence or uniqueness across different samples. Recurring variants had higher heteroplasmic loads and more frequently resulted in synonymous changes or were located in non-coding regions than variants unique to one oocyte or single embryonic cell. These differences were maintained through development, suggesting that the mtDNA mosaicism arising in the embryo is maintained into adulthood. We observed a decline in potentially pathogenic variants between day 3 and day 5 of development, suggesting early selection. We propose a model in which closely clustered mitochondria carrying specific mtDNA variants in the ooplasm are asymmetrically distributed throughout the cell divisions of the preimplantation embryo, resulting in the earliest form of mtDNA mosaicism in human development.
Neutralizing Activities Against the Omicron Variant After a Heterologous Booster in Healthy Adults Receiving Two Doses of CoronaVac Vaccination
Authors: Assawakosri Suvichada , Kanokudom Sitthichai , Suntronwong Nungruthai , Auphimai Chompoonut , Nilyanimit Pornjarim , Vichaiwattana Preeyaporn , Thongmee Thanunrat , Duangchinda Thaneeya , Chantima Warangkana , Pakchotanon Pattarakul , Srimuan Donchida , Thatsanatorn Thaksaporn , Klinfueng Sirapa , Yorsaeng Ritthideach , Sudhinaraset Natthinee , Wanlapakorn Nasamon , Mongkolsapaya Juthathip , Honsawek Sittisak , Poovorawan Yong 
Published: March 2022

Abstract

Background
The use of an inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine (CoronaVac) against SARS-CoV-2 is implemented worldwide. However, waning immunity and breakthrough infections have been observed. Therefore, we hypothesized that the heterologous booster might improve the protection against the delta and omicron variants.

Methods
A total of 224 individuals who completed the 2-dose CoronaVac for 6 months were included. We studied reactogenicity and immunogenicity after a heterologous booster with the inactivated vaccine (BBIBP), the viral vector vaccine (AZD1222), and the messenger ribonucleic acid (mRNA) vaccine (both BNT162B2 and mRNA-1273). We also determined immunogenicity at 3- and 6-month boosting intervals.

Results
The solicited adverse events were mild to moderate and well tolerated. Total receptor binding domain (RBD) immunoglobulin (Ig), anti-RBD IgG, focus reduction neutralization test (FRNT50) against delta and omicron variants, and T-cell response were highest in the mRNA-1273 group followed by the BNT162b2, AZD1222, and BBIBP groups, respectively. We also witnessed a higher total Ig anti-RBD in the long-interval than in the short-interval group.

Conclusions
All 4 booster vaccines significantly increased binding and neutralizing antibodies in individuals immunized with 2 doses of CoronaVac. The present evidence may benefit vaccine strategies to thwart variants of concern, including the omicron variant.
44 Evaluation of the Relationship Between Hair Coat Shedding Ability and Apparent Digestibility in Angus Cattle
Authors: Loftin Margaret P , Burnett Randy H , Smith Trent , Rude Brian J 
Published: March 2022

Abstract
The objective of this study was to evaluate winter hair coat shedding ability in conjunction with apparent forage digestibility. Data were collected on fall calving purebred Angus females with calves from March until July in 2019 (n = 10) and 2020 (n = 31). Dams were observed once monthly by two trained technicians for winter hair coat shedding and were given a visual score of 1 to 5 with 1 indicating complete shed and 5 indicating no shed. Month of first shed (MFS) was determined when a female reached an average hair shedding score of 3.5 for any given month. Fecal samples were collected during the grazing months of March, May, and July for 5 consecutive days and were then analyzed via proximate analysis to calculate apparent digestibility of crude protein (CP), acid detergent fiber (ADF), neutral detergent fiber (NDF), ash, and dry matter percentage (DM) of forage. Data were analyzed using repeated measures of the MIXED procedure of SAS with a significance declared at P ≤ 0.05. The model included MFS, month, and MFS by month interaction with year and ambient temperature as a covariate with cow ID nested within MFS Interactions of MFS by month were observed for CP, ADF, NDF, ash, and DM. Females with a MFS in May or June showed decreased CP apparent digestibility during the month of May when compared with cows reaching a MFS in April or July (P = 0.04). For DM in July, females with an MFS in June and July were similar but decreased when compared to females with an MFS in April and May (P = 0.015). Interpretation of these results show no clear trend of an association between hair shedding ability and apparent digestibility. Further research into this area is important in understanding changes in overall cow performance due to adaptability.
139 Determination of Population, Demographics, and Location of Equids in Tennessee Using Coggins Test Records and United States Department of Agriculture Census Data
Authors: Berger Amy M , Schneider Liesel G , Horsman Matt , Beaty Samantha , Ivey Jennie L 
Published: March 2022

Abstract
Knowledge of equine populations and demographics is of vital importance to educational, economic, and health aspects within Tennessee. While the United States Department of Agriculture (USDA) census assesses equids on operations making a set amount of income per year, this method alone may not effectively capture the recreational-use equine population. This study aimed to develop a novel approach of characterizing the population, demographics, and location of equids in Tennessee through annual Coggins test reports and to determine how Coggins test data compared to the USDA census population data. Information was collected from the 2018 Coggins tests (n = 31195), provided by the Tennessee Department of Agriculture, including sex, age, breed, owner location, equid location, and reason for testing. The equine population and location of equids per county (n = 86928) were collected from USDA census data. Statistical analysis was performed using the frequency procedure and means procedure in SAS 9.4. The middle region of Tennessee represented the highest proportion of equids in both the Coggins (60.32%, n = 18816) and USDA (52.05%, n = 45244) data. The counties with the highest proportion of equids from the Coggins data were Putnam (10.21%, n = 3186), Bedford (5.33%, n = 1664), and Shelby (4.18%, n = 1304) whereas the USDA data showed Bedford (4.41%, n = 3832), Williamson (3.38%, n = 2941), and Wilson (3.04%, n = 2643) as the most populated. Per the Coggins data where sex was reported (n = 31073), 48.46% (n = 15059) of the equids were geldings and 51.44% (n = 15983) were mares. Reported breeds within Coggins data (n = 31043) indicated the highest proportion of non-mixed breeds were Quarter Horses (28.20%, n = 8755), Tennessee Walking Horses (22.20%, n = 6892), and Spotted Saddle Horses (7.46%, n = 2316). While neither method fully captures the entire population of the equine industry, assessing both data sets may be helpful in developing targeted strategies for educational programming, population or disease models, and marketing campaigns.
24 Prevalence, Usage, and Perceptions of Pulsed Electromagnetic Field Therapy (PEMF) in the Equine Industry
Authors: Rostad Delaney R , Ivey Jennie L 
Published: March 2022

Abstract
The use of alternative therapies in the equine industry is increasing in popularity and spans manual manipulation to more progressive forms of technology. Pulsed electromagnetic field therapy (PEMF) has shown to reduce pain and increase range of motion within human and canine medicine. Often, PEMF is touted to improve performance and reduce stress prior to competition, yet little information exists on effectiveness, perceptions, treatment protocols, and therapeutic response within equids. Our objective was to assess how PEMF is administered and perceived therapy impact on equine patients. An online survey (Qualtrics) was disseminated to United States residents over 18 years of age and deemed exempt by the institutional review board. Data were analyzed using the frequency procedure in SAS (v9.4). Three groups within the equine industry were targeted: equine owners and leasers (OL, n = 350); trainers, coaches, grooms, and jockeys (TC, n = 80); and administrators of PEMF therapy (AD, n = 237). Across all survey respondents (n = 355), 86% (n = 305) exercise or ride their horses and 85.08% (n = 268) of individuals who ride have used PEMF therapy on their performance horse. Among TC, 96.25% (n = 77) respondents reported the use of PEMF therapy on a horse under their care. Whole body therapy was the most commonly reported location for PEMF by OL (91.6%, n = 240) and AD (96.12%, n = 223), followed by back and loin(47.33%, 124) for OL and front legs (56.47%, n = 131) for AD. Most frequent session length reported by OL was 45-90 minutes (30.96%, n = 61). Within 1 day of treatment, the majority of AD (n = 85, 40.28%) and OL (n = 104, 39.54%) perceived the greatest effects of PEMF therapy. Use and positive perception of PEMF in the equine industry is evident; however, more research is needed to elicit therapeutic effects for performance animals.
27 Transcriptome Comparison of Parthenogenetic vs. Biparental Embryos in Beef Cattle
Authors: Singleton Sarah A , Franco-Johannsen Gessica , Dalmaso Gabriela , Ortega M Sofia , Pohler Ky G 
Published: March 2022

Abstract
This experiment aimed to determine differences in circulating pregnancy-associated glycoprotein (PAG) concentrations, differentially expressed genes (DEGs), and comparative gene ontology profiles between parthenogenetic embryos (PA; absence of paternal genetics) and biparental control embryos (CON). PA embryos were produced in vitro using a validated chemical activation method, and CON embryos were produced in vitro using industry standard techniques. A blood sample was collected on day 31, and PAG concentrations were determined by an in-house ELISA. Transrectal ultrasonography was performed daily to monitor conceptus development. Cows (n = 30) were synchronized, underwent embryo transfer [ET; 7 days after onset of estrus (day 0)] and were euthanized at approximately day 31 of gestation. Tissues from endometrium (EM), trophectoderm (TE), and corpus luteum (CL) were collected and sequenced from both groups (3 PA; 3 CON). Average PAG concentrations between PA and CON on day 31 were 0.81±0.44 ng/mL and 5.23±0.44 ng/mL (P = 0.01), respectively. When comparing PA to CON, there were 969 DEG in the EM (599 genes upregulated; 269 genes downregulated; 101 nonannotated genes) and 250 DEG in the TE (163 genes upregulated; 47 downregulated; 40 nonannotated genes). Comparative gene ontology profiles between DEGs showed an upregulation in immune system-associated activities and extracellular matrix interactions and a downregulation in redox reactions and proteolytic activities involving PAGs for PA as compared to CON. Similarly, the TE comparisons showed an upregulation in prolactin (PRL) inhibiting pathways and a downregulation in structural molecule activity and signaling for PA as compared to CON. The DEGs observed in PAs show significant decreases in conceptus-derived products and gene ontology profiles associated with pregnancy. Overall, these findings demonstrate that uniparental embryos can be a useful model to better understand pregnancy development and loss in cattle.
13 Influence of Prenatal Exposure to Endophyte-infected Tall Fescue on Glucose Metabolism in Weaned Steer Calves
Authors: Benefield R F , Hubbell D S , Galloway D L , Looney C R , Powell J G , Kegley E B , Littlejohn B P 
Published: March 2022

Abstract
The objective was to evaluate the influence of prenatal exposure to endophyte-infected tall fescue (toxic fescue) on postweaning glucose metabolism in crossbred steers. Pregnant multiparous cows (n = 36) were maintained on replicated novel or toxic fescue pastures throughout gestation and bermudagrass pastures following calving. From the subsequent calf crop, weaned steers (257±28 d of age) of similar body weight (234±32 kg Toxic; 236±44 kg Novel) were randomly selected (n = 8 Toxic; n = 7 Novel) for a glucose tolerance test. Steers were fitted with jugular vein catheters and fasted for a minimum of 12 h before intravenous administration of a 50% dextrose solution (0.5 mL/kg of body weight). Blood was collected at -10, 0, 10, 20, 30, 45, 60, 90, 120, and 150 min (0 min=glucose administration). Plasma glucose and serum insulin were determined by hexokinase colorimetric assay and radioimmunoassay, respectively. Glucose, insulin, and the insulin to glucose (I:G) ratio were analyzed using MIXED procedures of SAS specific for repeated measures with treatment as a fixed effect and sire as random. All other variables were analyzed using MIXED procedures of SAS with treatment as a fixed effect and sire as random. As expected, glucose, insulin, and the I:G ratio increased in response to glucose administration (time P &lt; 0.01). There was no effect of treatment (P &gt; 0.39) or the treatment by time interaction (P &gt; 0.19) for glucose, insulin, or the I:G ratio. However, Toxic steers exhibited numerically increased glucose, decreased insulin, and decreased I:G ratios relative to Novel steers following glucose administration. There was no difference (P &gt; 0.13) in baseline, peak, time at peak, or time at return to baseline concentrations for insulin or glucose. While prenatal exposure to toxic fescue did not influence glucose or insulin homeostasis in response to exogenous glucose administration in this preliminary study, numerical differences warrant future evaluation with increased animal numbers.