bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Covid-19 on the human central olfactory system: a natural pre-post experiment
Authors: Thunell Evelina , Peter Moa G. , Lenoir Vincent , Andersson Patrik , Landis Basile N. , Becker Minerva , Lundström Johan N. 
Published: December 2021

ABSTRACTReduced olfactory function is the symptom with the highest prevalence in COVID-19 with nearly 70% of individuals with COVID-19 experiencing partial or total loss of their sense of smell at some point during the disease. The exact cause is not known but beyond peripheral damage, studies have demonstrated insults to both the olfactory bulb and central olfactory brain areas. However, these studies often lack both baseline pre-COVID-19 assessments and a control group and could therefore simply reflect preexisting risk factors. Right before the COVID-19 outbreak, we completed an olfactory focused study including structural MR brain images and a full clinical olfactory test. Opportunistically, we invited participants back one year later, including 9 participants who had experienced mild to medium COVID-19 (C19+) and 12 that had not (C19-), thereby creating a pre-post controlled natural experiment with a control group. Despite C19+ participants reporting subjective olfactory dysfunction, few showed signs of objectively altered function one year later. Critically, all but one individual in the C19+ group had reduced olfactory bulb volume with an average volume reduction of 14.3%, but this did not amount to a significant between group difference compared to the control group (2.3% reduction) using inference statistics. No morphological differences in cerebral olfactory areas were found but we found stronger functional connectivity between olfactory brain areas in the C19+ croup at the post measure. Taken together, these data suggest that COVID-19 might cause a long-term reduction in olfactory bulb volume but with no discernible differences in cerebral olfactory regions.
Evolution of COVID-19 Health Disparities in Arizona
Authors: Shen Felix L. , Shu Jingmin , Lee Matthew , Oh Hyunsung , Marsiglia Flavio , Li Ming , Runger George , Liu Li 
Published: December 2021

ABSTRACTObjectiveCOVID-19 burdens are disproportionally high in underserved and vulnerable groups in Arizona. As the pandemic progresses, it is unclear if the disparities have evolved. In this study, we aim to elicit the dynamic landscape of COVID-19 disparities at the community level and identify newly emerged vulnerable subpopulations.Materials and MethodsWe compiled biweekly COVID-19 case counts of 274 zip code tabulation areas (ZCTAs) in Arizona from October 21, 2020, to November 25, 2021, during which the COVID-19 growth rate has changed significantly. Within each growth period, we detected health disparities by testing associations between the growth rate of COVID-19 cases in a ZCTA and the population composition of race/ethnicity, income, employment, and age. We then compared the associations between periods to discover temporal patterns of health disparities.ResultsHigh percentage of Latinx or Black residents, high poverty rate, and young median age were risk factors of high cumulative COVID-19 case counts in a ZCTA. However, the impact of these factors on the growth rate of new COVID-19 cases varied. While high percentage of Black residents and young median age remained as risk factors of fast COVID-19 growth rate, high poverty rate became a protective factor. The association between the percentage of Latinx residents and the COVID-19 growth rate converted from positive to negative during summer 2021. The unemployment rate emerged as a new risk factor of fast COVID-19 growth rate after September 2021. Based on these findings, we identified 37 ZCTAs that are highly vulnerable to fast escalation of COVID-19 cases.Discussion and ConclusionAs the pandemic progresses, disadvantaged communities continue suffering from escalated risk of COVID-19 infection. But the vulnerabilities have evolved. While the disparities related to Latinx ethnicity improved gradually, those related to Black ethnicity and young communities aggravated. The struggle of financially disadvantaged communities continued, although the burden had shifted from those living under the poverty line to those with a high unemployment rate. It is necessary to adjust current resource allocations and design and deploy new interventions to address emerging needs.
Design of Epitope Based Peptide Vaccine against Brucella Abortus OmpW Family Protein using Immunoinformatics
Authors: Elhag Mustafa , Abdelmoneim Abdelrahman Hamza , Sati Anfal Osama , Saadaldin Moaaz Mohammed , Ahmad Nagla Mohammad , Hassan Mohammed A. 
Published: December 2021

AbstractBrucella abortus is a small aerobic, non-spore-forming, non-motile intracellular coccobacilli localized in the reproductive organs of host animals and causes acute or chronic disorders. It infects approximately 200 cases per 100,000 of the population and has become endemic in many countries. OmpW family protein is an outer membrane protein involved in the initial interaction between the pathogen and it’s host. This study predicts an effective epitope-based vaccine against OmpW family protein of Brucella abortus using immunoinformatics tools. Sequences were obtained from NCBI and prediction tests were accomplished to analyze possible epitopes for B and T cells. Seven B cell epitopes passed the antigenicity, accessibility and hydrophilicity tests. Forty-three MHC I epitopes were the most promising, while 438 from MHC II. For the population coverage, the epitopes covered 99.97% of the alleles worldwide excluding certain MHC II alleles. We recommend invivo and invitro studies to prove it’s effectiveness.
Genome assembly, transcriptome and SNP database for chum salmon (Oncorhynchus keta)
Authors: Rondeau Eric B. , Christensen Kris A. , Sakhrani Dionne , Biagi Carlo A. , Wetklo Mike , Johnson Hollie A. , Despins Cody A. , Leggatt Rosalind A. , Minkley David R. , Withler Ruth E. , Beacham Terry D. , Koop Ben F. , Devlin Robert H. 
Published: December 2021

AbstractChum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous Pacific salmonids,. Chum salmon is the second largest of the Pacific salmon, behind Chinook salmon, and considered the most plentiful Pacific salmon by overall biomass. This species is of significant commercial and economic importance: on average the commercial chum salmon fishery has the second highest processed value of the Pacific salmon within British Columbia. The aim of this work was to establish genomic baseline resources for this species. Our first step to accomplish this goal was to generate a chum salmon reference genome assembly from a doubled-haploid chum salmon. Gene annotation of this genome was facilitated by an extensive RNA-seq database we were able to create from multiple tissues. Range-wide resequencing of chum salmon genomes allowed us to categorize genome-wide geographic variation, which in turn reinforced the idea that genetic differentiation was best described on a regional, rather than at a stock-specific, level. Within British Columbia, chum salmon regional groupings were described at the conservation unit (CU) level, and there may be substructure within particular CUs. Genome wide associations of phenotypic sex to SNP genetic markers identified two clear peaks, a very strong peak on Linkage Group 15, and another on Linkage Group 3. With these new resources, we were better able to characterize the sex-determining region and gain further insights into sex determination in chum salmon and the general biology of this species.
Recommendations for clinical interpretation of variants found in non-coding regions of the genome
Authors: Ellingford Jamie M , Ahn Joo Wook , Bagnall Richard D , Baralle Diana , Barton Stephanie , Campbell Chris , Downes Kate , Ellard Sian , Duff-Farrier Celia , FitzPatrick David R , Ingles Jodie , Krishnan Neesha , Lord Jenny , Martin Hilary C , Newman William G , O’Donnell-Luria Anne , Ramsden Simon C , Rehm Heidi L , Richardson Ebony , Singer-Berk Moriel , Taylor Jenny C , Williams Maggie , Wood Jordan C , Wright Caroline F , Harrison Steven M , Whiffin Nicola 
Published: December 2021

ABSTRACTPurposeThe majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts.MethodsWe convened a panel of clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups.ResultsWe discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for these variants.ConclusionThese recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.
Vaccine effectiveness against hospital admission in South African health care workers who received a homologous booster of Ad26.COV2 during an Omicron COVID19 wave: Preliminary Results of the Sisonke 2 Study
Authors: Gray Glenda E , Collie Shirley , Garrett Nigel , Goga Ameena , Champion Jared , Zylstra Matthew , Reddy Tarylee , Yende Nonhlanhla , Seocharan Ishen , Takalani Azwi , Sanne Ian , Mayat Fatima , Odhiambo Jacky , Bamford Lesley , Moultrie Harry , Fairall Lara , Bekker Linda-Gail 
Published: December 2021

AbstractFollowing the results of the ENSEMBLE 2 study, which demonstrated improved vaccine efficacy of a two-dose regimen of Ad26.COV.2 vaccine given 2 months apart, we expanded the Sisonke study which had provided single dose Ad26.COV.2 vaccine to almost 500 000 health care workers (HCW) in South Africa to include a booster dose of the Ad26.COV.2. Sisonke 2 enrolled 227 310 HCW from the 8 November to the 17 December 2021. Enrolment commenced before the onset of the Omicron driven fourth wave in South Africa affording us an opportunity to evaluate early VE in preventing hospital admissions of a homologous boost of the Ad26.COV.2 vaccine given 6-9 months after the initial vaccination in HCW.We estimated vaccine effectiveness (VE) of the Ad26.COV2.S vaccine booster in 69 092 HCW as compared to unvaccinated individuals enrolled in the same managed care organization using a test negative design. We compared VE against COVID19 admission for omicron during the period 15 November to 20 December 2021. After adjusting for confounders, we observed that VE for hospitalisation increased over time since booster dose, from 63% (95%CI 31-81%); to 84% (95% CI 67-92%) and then 85% (95% CI: 54-95%), 0-13 days, 14-27 days, and 1-2 months post-boost.We provide the first evidence of the effectiveness of a homologous Ad26.COV.2 vaccine boost given 6-9 months after the initial single vaccination series during a period of omicron variant circulation. This data is important given the increased reliance on the Ad26.COV.2 vaccine in Africa.
Immunogenicity and safety of an inactivated SARS-CoV-2 vaccine (BBV152) in children from 2 to 18 years of age: an open-label, age-de-escalation phase 2/3 study
Authors: Vadrevu Krishna Mohan , Reddy Siddharth , Jogdand Harsh , Ganneru Brunda , Mirza Nizam , Tripathy V.N. , Singh Chandramani , Khalatkar Vasant , Prasanth Siddaiah , Rai Sanjay , Ella Raches , Blackwelder William , Prasad Sai , Ella Krishna 
Published: December 2021

ABSTRACTBackgroundWe assessed the safety, reactogenicity, and immunogenicity of BBV152 in an open-label age de-escalation study in three age cohorts of children from 18 years of age down to 2 years of age.MethodsThis was a phase 2/3 open-label, multi-centre study done across six hospitals in India. All children received two 0.5mL doses of BBV152 (Covaxin®, Bharat Biotech International Ltd., Hyderabad, India), which is the same formulation indicated in adults. Participants were monitored for adverse events, and post-vaccination blood draws were collected to assess neutralising antibodies. A total of 526 children were enrolled into Group 1 (ages 12 through 18 years, n=176), Group 2 (ages 6 through 12 years, n=175), Group 3 (ages 2 through 6 years, n=175).FindingsThere were no serious adverse events, deaths, or withdrawals due to an adverse event during the study. Vaccination with BBV152 was generally well tolerated, with no substantial difference in reactogenicity profiles between the different age groups. Similar immune responses were measured as microneutralisation (MNT) antibody titers in all three age groups. Vaccine-induced MNT responses in all groups were comparable to BEI reference sera run in the same assay. Seroconversion (measured by Plaque Reduction Neutralization Test (PRNT)) achieved high levels (95-98%) in all three groups four weeks after the second vaccination. The PRNT GMT ratio was 1·76 (95%CI: 1.32 – 2.33) (GMT all children subgroup / GMT in adults) had a lower limit ≥ 1, indicating superior antibodies in children when compared to adults. Vaccine responses were skewed towards a Th1 response with IgG1/IgG4 ratios above 1.InterpretationBBV152 is well tolerated and immunogenic in children from 18 years down to 2 years of age. Immunogenicity analysis (by PRNT) shows superior antibody responses were observed in children compared to adults, suggesting that BBV152 will also be efficacious in this age group.
Neutralizing antibody responses to SARS-CoV-2: a population based seroepidemiological analysis in Delhi, India
Authors: Sharma Pragya , Gupta Ekta , Basu Saurav , Aggarwal Reshu , Mishra Suruchi , Kale Pratibha , Mundeja Nutan , Charan B S , Singh Gautam Kumar , Singh Mongjam Meghachandra 
Published: December 2021

ABSTRACTWe conducted this study to estimate seroprevalence of neutralizing antibodies in the general population and to further correlate it with the IgG SARS-CoV-2 IgG levels. This present cross-sectional analysis was conducted as a sequel to a state level community-based seroepidemiological study in Delhi, India. A total of 2564 seropositive samples were selected from 25622 seropositive samples through simple random sampling. Neutralizing capacity was estimated by performing a surrogate virus neutralization test with the sVNT (GenScript) assay. Neutralizing antibody against the SARS-CoV-2 virus was operationally considered as detected when the signal inhibition was ≥30%.A total of 2233 (87.1%, 95% C.I. 85.7, 88.3) of the 2564 SARS-CoV-2 seropositive samples had detectable neutralizing antibodies. On bi-variate analysis but not on adjusted analysis, Covid-19 vaccination showed a statistically significant association with the presence of neutralizing antibodies (p<0.001). The signal/ cut off (S/CO) of SARS-CoV-2 IgG ranged from 1.00 to 22.8 (median 11.40). In samples with S/CO ≥4.00, the neutralizing antibodies ranged from 94.5 to 100%, while in samples with S/CO <4.00, it ranged from 52.0 to 79.2%. The neutralizing antibody seroprevalence strongly correlated with the S/CO range (r=0.62, p=0.002). In conclusion, in populations with high SARS-CoV-2 seroprevalence, neutralizing antibodies are generated in nearly 9 of 10 seropositive individuals.
SoyFGB v2.0: a unique access to variations of Chinese Soybean Gene Bank (CNSGB) germplasm
Authors: Zheng Tianqing , Li Yinghui , Li Yanfei , Zhang Shengrui , Wang Chunchao , Zhang Fan , Zhang Lina , Wu Xiangyun , Tian Yu , Jiang Shan , Xu Jianlong , Qiu Lijuan 
Published: December 2021

SummaryIn Chinese National Soybean GeneBank (CNSGB), we have collected more than 30,000 soybean accessions. However, data sharing for soybean remains an especially ‘sensitive’ question, and how to share the genome variations within rule frame has been bothering the soybean germplasm workers for a long time.Here we release a big data source named Soybean Functional Genomics & Breeding database (SoyFGB v2.0) (https://sfgb.rmbreeding.cn/), which embed a core collection of 2,214 soybean resequencing genome (2K-SG) from the CNSGB germplasm. This source presents a unique example which may help elucidating the following three major functions for multiple genome data mining with general interests for plant researchers. 1) On-line analysis tools are provided by the ‘Analysis’ module for haplotype mining in high-throughput genotyped germplasms with different methods. 2) Variations for 2K-SG are provided in SoyFGB v2.0 by Browse module which contains two functions of ‘SNP’ and ‘InDel’. Together with the ‘Gene (SNP & InDel)’ function embedded in Search module, the genotypic information of 2K-SG for targeting gene / region is accessible. 3) Scaled phenotype data of 42 traits, including 9 quality and 33 quantitative traits are provided by SoyFGB v2.0. With the scaled-phenotype data search and seed request tools under a control list, the germplasm information could be shared without direct downloading the unpublished phenotypic data or information of sensitive germplasms.In a word, the mode of data mining and sharing underlies SoyFGB v2.0 may inspire more ideas for works on genome resources of not only soybean but also the other plants.
Perception and propagation of activity through the cortical hierarchy is determined by neural variability
Authors: Rowland James M. , van der Plas Thijs L. , Loidolt Matthias , Lees Robert M. , Keeling Joshua , Dehning Jonas , Akam Thomas , Priesemann Viola , Packer Adam M. 
Published: December 2021

AbstractThe brains of higher organisms are composed of anatomically and functionally distinct regions performing specialised tasks; but regions do not operate in isolation. Orchestration of complex behaviours requires communication between brain regions, but how neural activity dynamics are organised to facilitate reliable transmission is not well understood. We studied this process directly by generating neural activity that propagates between brain regions and drives behaviour, allowing us to assess how populations of neurons in sensory cortex cooperate to transmit information. We achieved this by imaging two hierarchically organised and densely interconnected regions, the primary and secondary somatosensory cortex (S1 and S2) in mice while performing two-photon photostimulation of S1 neurons and assigning behavioural salience to the photostimulation. We found that the probability of perception is determined not only by the strength of the photostimulation signal, but also by the variability of S1 neural activity. Therefore, maximising the signal-to-noise ratio of the stimulus representation in cortex relative to the noise or variability in cortex is critical to facilitate activity propagation and perception. Further, we show that propagated, behaviourally salient activity elicits balanced, persistent, and generalised activation of the downstream region. Hence, our work adds to existing understanding of cortical function by identifying how population activity is formatted to ensure robust transmission of information, allowing specialised brain regions to communicate and coordinate behaviour.
Increased resistance of SARS-CoV-2 Omicron Variant to Neutralization by Vaccine-Elicited and Therapeutic Antibodies
Authors: Tada Takuya , Zhou Hao , Dcosta Belinda M. , Samanovic Marie I. , Chivukula Vidya , Herati Ramin S. , Hubbard Stevan R. , Mulligan Mark J. , Landau Nathaniel R. 
Published: December 2021

SummaryCurrently authorized vaccines for SARS-CoV-2 have been highly successful in preventing infection and lessening disease severity. The vaccines maintain effectiveness against SARS-CoV-2 Variants of Concern but the heavily mutated, highly transmissible Omicron variant poses an obstacle both to vaccine protection and monoclonal antibody therapies. Analysis of the neutralization of Omicron spike protein-pseudotyped lentiviruses showed a 26-fold relative resistance (compared to D614G) to neutralization by convalescent sera and 26-34-fold resistance to Pfizer BNT162b2 and Moderna vaccine-elicited antibodies following two immunizations. A booster immunization increased neutralizing titers against Omicron by 6-8-fold. Previous SARS-CoV-2 infection followed by vaccination resulted in the highest neutralizing titers against Omicron. Regeneron REGN10933 and REGN10987, and Lilly LY-CoV555 and LY-CoV016 monoclonal antibodies were ineffective against Omicron, while Sotrovimab was partially effective. The results highlight the benefit of a booster immunization in providing protection against Omicron but demonstrate the challenge to monoclonal antibody therapies.
Precise measurement of nanoscopic septin ring structures in deep learning-assisted quantitative superresolution microscopy
Authors: Zehtabian Amin , Müller Paul Markus , Goisser Maximilian , Obendorf Leon , Jänisch Lea , Hümpfer Nadja , Rentsch Jakob , Ewers Helge 
Published: December 2021

AbstractThe combination of image analysis and fluorescence superresolution microscopy methods allows for unprecedented insight into the organization of macromolecular assemblies in cells. Advances in deep learning-based object recognition enables the automated processing of large amounts of data, resulting in high accuracy through averaging. However, while the analysis of highly symmetric structures of constant size allows for a resolution approaching the dimensions of structural biology, deep learning methods are prone to different forms of bias. A biased recognition of structures may prohibit the development of readouts for processes that involve significant changes in size or shape of amorphous macromolecular complexes. What is required to overcome this problem is a detailed investigation of potential sources of bias and the rigorous testing of trained models using real or simulated data covering a wide dynamic range of possible results. Here we combine single molecule localization-based superresolution microscopy of septin ring structures with the training of several different deep learning models for a quantitative investigation of bias resulting from different training approaches and finally quantitative changes in septin ring structures. We find that trade-off exists between measurement accuracy and the dynamic range of recognized phenotypes. Using our trained models, we furthermore find that septin ring size can be explained by the number of subunits they are assembled from alone. Our work provides a new experimental system for the investigation of septin polymerization.