bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 Testing Disparities in Massachusetts
Authors: Dryden-Peterson Scott , Velásquez Gustavo E. , Stopka Thomas J. , Davey Sonya , Lockman Shahin , Ojikutu Bisola 
Published: November 2020

AbstractObjectiveEarly deficiencies in testing capacity contributed to poor control of transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the context of marked improvement in SARS-CoV-2 testing infrastructure, we sought to examine the alignment of testing with epidemic intensity to mitigate subsequent waves of COVID-19 in Massachusetts.MethodsWe compiled publicly available weekly SARS-CoV-2 molecular testing data for period (May 27 to October 14, 2020) following the initial COVID-19 wave. We defined testing intensity as weekly SARS-CoV-2 tests performed per 100,000 population and used weekly test positivity (percent of tests positive) as a measure of epidemic intensity. We considered optimal alignment of testing resources to be matching community ranks of testing and positivity. In communities with a lower rank of testing than positivity in a given week, the testing gap was calculated as the additional tests required to achieve matching ranks. Multivariable Poisson modeling was utilized to assess for trends and association with community characteristics.ResultsDuring the observation period, 4,262,000 tests were reported in Massachusetts and the misalignment of testing with epidemic intensity increased. The weekly testing gap increased 9.0% per week (adjusted rate ratio [aRR]: 1.090, 95% confidence interval [CI]: 1.08-1.10). Increasing levels of community socioeconomic vulnerability (aRR: 1.35 per quartile increase, 95% CI: 1.23-1.50) and the highest quartile of minority and language vulnerability (aRR: 1.46, 95% CI 0.96-1.49) were associated with increased testing gaps, but the latter association was not statistically significant. Presence of large university student population (>10% of population) was associated with a marked decrease in testing gap (aRR 0.21, 95% CI: 0.12-0.38).ConclusionThese analyses indicate that despite objectives to promote equity and enhance epidemic control in vulnerable communities, testing resources across Massachusetts have been disproportionally allocated to more affluent communities. Worsening structural inequities in access to SARS-CoV-2 testing increase the risk for another intense wave of COVID-19 in Massachusetts, particularly among vulnerable communities.
Altered Resting State Brain Networks and Cognition in Familial Adenomatous Polyposis
Authors: Cali Ryan J. , Nephew Benjamin C. , Moore Constance M. , Chumachenko Serhiy , Sala Ana Cecilia , Cintron Beatriz , Luciano Carlos , King Jean A. , Hooper Stephen R. , Giardiello Francis M. , Cruz-Correa Marcia 
Published: November 2020

AbstractFamilial Adenomatous Polyposis (FAP) is an autosomal dominant disorder caused by mutation of the APC gene presenting with numerous colorectal adenomatous polyps and a near 100% risk of colon cancer. Preliminary research findings from our group indicate that FAP patients experience significant deficits across many cognitive domains. In the current study, fMRI brain metrics in a FAP population and matched controls were used to further the mechanistic understanding of reported cognitive deficits. This research identified and characterized any possible differences in resting brain networks and associations between neural network changes and cognition from 34 participants (18 FAP patients, 16 healthy controls). Functional connectivity analysis was performed using FSL with independent component analysis (ICA) to identify functional networks. Significant differences between cases and controls were observed in 8 well-established resting state networks. With the addition of an aggregate cognitive measure as a covariate, these differences were virtually non-existent, indicating a strong correlation between cognition and brain activity at the network level. The data indicate robust and pervasive effects on functional neural network activity among FAP patients and these effects are likely involved in cognitive deficits associated with this disease.
The duration, dynamics and determinants of SARS-CoV-2 antibody responses in individual healthcare workers
Authors: Lumley Sheila F , Wei Jia , O’Donnell Denise , Stoesser Nicole E , Matthews Philippa C , Howarth Alison , Hatch Stephanie B , Marsden Brian D , Cox Stuart , James Tim , Peck Liam , Ritter Thomas , de Toledo Zoe , Cornall Richard J , Jones E Yvonne , Stuart David I , Screaton Gavin , Ebner Daniel , Hoosdally Sarah , Crook Derrick W ,   Oxford University Hospitals Staff Testing Group, Conlon Christopher P , Pouwels Koen B , Walker A Sarah , Peto Tim EA , Walker Timothy M , Jeffery Katie , Eyre David W 
Published: November 2020

AbstractBackgroundSARS-CoV-2 IgG antibody measurements can be used to estimate the proportion of a population exposed or infected and may be informative about the risk of future infection. Previous estimates of the duration of antibody responses vary.MethodsWe present 6 months of data from a longitudinal seroprevalence study of 3217 UK healthcare workers (HCWs). Serial measurements of IgG antibodies to SARS-CoV-2 nucleocapsid were obtained. Bayesian mixed linear models were used to investigate antibody waning and associations with age, gender, ethnicity, previous symptoms and PCR results.ResultsIn this cohort of working age HCWs, antibody levels rose to a peak at 24 (95% credibility interval, CrI 19-31) days post-first positive PCR test, before beginning to fall. Considering 452 IgG seropositive HCWs over a median of 121 days (maximum 171 days) from their maximum positive IgG titre, the mean estimated antibody half-life was 85 (95%CrI, 81-90) days. The estimated mean time to loss of a positive antibody result was 137 (95%CrI 127-148) days. We observed variation between individuals; higher maximum observed IgG titres were associated with longer estimated antibody half-lives. Increasing age, Asian ethnicity and prior self-reported symptoms were independently associated with higher maximum antibody levels, and increasing age and a positive PCR test undertaken for symptoms with longer antibody half-lives.ConclusionIgG antibody levels to SARS-CoV-2 nucleocapsid wane within months, and faster in younger adults and those without symptoms. Ongoing longitudinal studies are required to track the long-term duration of antibody levels and their association with immunity to SARS-CoV-2 reinfection.SummarySerially measured SARS-CoV-2 anti-nucleocapsid IgG titres from 452 seropositive healthcare workers demonstrate levels fall by half in 85 days. From a peak result, detectable antibodies last a mean 137 days. Levels fall faster in younger adults and following asymptomatic infection.
Racial disparities in the prevalence of vaccine and non-vaccine HPV types and multiple HPV infection between Asia and Africa: A systematic review
Authors: Okoye Jude Ogechukwu , Okekpa Simon Imakwu , Chukwukelu Chiemeka Franklin , Onyekachi-Umeh Ifeoma Nora , Ngokere Anthony Ajuluchukwu 
Published: November 2020

SummaryBackgroundCervical Cancer is the 6th most common and 3rd most deadly cancer among women. Despite the fact that majority of the countries in Asia and Africa have similar economy and low life expectancy, the mean age standardized incidence rate (ASIR) of cervical cancer is substantially higher in Africa than Asia. Thus, this study aimed to identify the correlates of the higher ASIR rates in Africa relative to Asia.MethodsPeer-reviewed articles published between 2004 and 2017 were selected using the PRISMA standard. Sources of articles include Google Scholar, Scopus, PubMed Central, and EMBASE. Search keywords included: HPV genotypes, cervical cancer, HPV vaccine, and multiple infection in Africa and Asia.ResultA total of 29 and 17 full-length articles were selected from Africa and Asia respectively. Based on estimates in the general population, the incidence of high-risk HPV (hrHPV) types in Africa and Asia was 3.5 and 1.0 respectively. The prevalence of HPV infection was higher in Africa than in Asia (p< 0.001). The prevalence of HPV infection between 2004-2009 and 2010-2017 decreased in Africa but increased in Asia. More so, the prevalence of multiple HPV and non-vaccine HPV infection were higher in Africa than Asia (p< 0.001). The prevalent HPV types in Africa were HPV16, HPV18, and HPV52, while that of Asia were HPV16, HPV52, and HPV58, in descending order of prevalence. This study revealed that nonavalent HPV vaccine could prevent the development of 69.3% and 83.2% of HPV associated cervical abnormalities in Africa and Asia, respectively.ConclusionThis study revealed higher prevalence of HPV infection and multiple HPV infection in Africa compared with Asia, which could be responsible for the higher ASIR in Africa. It suggests that nonavalent vaccination including cervical screening using Pap smear could prevent over 90% of the cervical abnormalities in Africa.
Immunopeptidomics for Dummies: Detailed Experimental Protocols and Rapid, User-Friendly Visualization of MHC I and II Ligand Datasets with MhcVizPipe
Authors: Kovalchik Kevin A. , Wessling Laura , Saab Frederic , Ma Qing , Despault Jérôme , Kubiniok Peter , Hamelin David , Faridi Pouya , Li Chen , Purcell Anthony , Tognetti Marco , Reiter Lukas , Bruderer Roland , Lanoix Joël , Bonneil Éric , Courcelles Mathieu , Thibault Pierre , Caron Etienne , Sirois Isabelle 
Published: November 2020

ABSTRACTImmunopeptidomics refers to the science of investigating the composition and dynamics of peptides presented by major histocompatibility complex (MHC) class I and class II molecules using mass spectrometry (MS). Here, we aim to provide a technical report to any non-expert in the field wishing to establish and/or optimize an immunopeptidomic workflow with relatively limited computational knowledge and resources. To this end, we thoroughly describe step-by-step instructions to isolate MHC class I and II-associated peptides from various biological sources, including mouse and human biospecimens. Most notably, we created MhcVizPipe (MVP) (https://github.com/CaronLab/MhcVizPipe), a new and easy-to-use open-source software tool to rapidly assess the quality and the specific enrichment of immunopeptidomic datasets upon the establishment of new workflows. In fact, MVP enables intuitive visualization of multiple immunopeptidomic datasets upon testing sample preparation protocols and new antibodies for the isolation of MHC class I and II peptides. In addition, MVP enables the identification of unexpected binding motifs and facilitates the analysis of non-canonical MHC peptides. We anticipate that the experimental and bioinformatic resources provided herein will represent a great starting point for any non-expert and will therefore foster the accessibility and expansion of the field to ultimately boost its maturity and impact.
Reaction-Diffusion Model of Cortical Atrophy Spread during Early Stages of Alzheimer’s Disease
Authors: Kulason Sue , Miller Michael I , Trouvé Alain ,   Alzheimer’s Disease Neuroimaging Initiative
Published: November 2020

1.AbstractThis study introduces a reaction-diffusion model of atrophy spread across the rhinal cortex during early stages of Alzheimer’s disease. Our finite elements model of atrophy spread is motivated by histological evidence of a spatio-temporally specific pattern of neurofibrillary tau accumulation, and evidence of grey matter atrophy correlating with sites of neurofibrillary tau accumulation. The goal is to estimate disease-related parameters such as the origin of atrophy, the speed at which atrophy spreads, and the stage of the disease. We solve a constrained optimization problem using the adjoint state method and gradient descent to match modeled cortical thickness to observed cortical thickness as calculated from 3T MRI scans. Simulation testing shows that disease-related parameters can be estimated accurately with as little as 2 years of annual observations, depending on the stage of the disease. Case studies of 3 subjects suggests that we can pinpoint the origin of atrophy to the anterior transentorhinal cortex, and that the speed of atrophy spread is less than 1 mm per year. In the future, this type of modeling could be useful to stage the progression of the disease prior to the onset of clinical symptoms.2.Author SummaryMisfolded tau proteins are associated with Alzheimer’s disease. They are known to accumulate and spread across the rhinal cortex, which is an area of the temporal lobe. Recent imaging studies suggest that we can detect grey matter thinning that occurs in pattern similar to tau spread. In this study, we introduce a model of disease spread to examine where thinning begins, how fast it spreads, and the stage of the disease. The results show that the origin of thinning corresponds with the earliest known location of tau accumulation, and spreads at a rate of less than 1 mm per year. Future work may focus on staging the progression of the disease using this type of model.
Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model
Authors: Goryachev A.N. , Kalantarov S.A. , Severova A.G. , Goryacheva A.S. 
Published: November 2020

SummaryData on potential effectiveness and prospects of treatment of new coronavirus infection of COVID-19 caused by virus SARS-CoV-2 with the help of antisense oligonucleotides acting against RNA of virus on an in vitro model are given. The ability of antisense oligonucleotides to suppress viral replication in diseases caused by coronaviruses using the example of SARS and MERS is shown. The identity of the initial regulatory section of RNA of various coronaviruses was found within 50 - 100 nucleotides from the 5’-end, which allows using antisense suppression of this RNA fragment. A new RNA fragment of the virus present in all samples of coronovirus SARS-CoV-2 has been identified, the suppression of which with the help of an antisense oligonucleotide can be effective in the treatment of COVID-19. The study of the synthesized antisense oligonucleotide 5’ - AGCCGAGTGACAGCC ACACAG, complementary to the selected virus RNA sequence, was carried out. The low toxicity of the preparations of this group in the cell culture study and the ability to reduce viral load at high doses according to real time-PCR data are shown. The cytopathogenic dose exceeds 2 mg / ml. At a dosage of 1 mg / ml, viral replication is reduced by 5-13 times. Conclusions are made about the prospects of this direction and the feasibility of using the inhalation way of drug administration into the body.
Metabolomics shows the Australian dingo has a unique plasma profile
Authors: Yadav Sonu , Pickford Russell , Zammit Robert A. , Ballard J. William O. 
Published: November 2020

AbstractDingoes have not been artificially selected in the past 3,500 years. They occupy a wide range of the Australian mainland and play a crucial role as an apex predator with a generalist omnivorous feeding behaviour. In contrast, humans have selected breed dogs for novel and desirable traits. First, we explore whether the distinct evolutionary histories of dingoes and domestic dogs can lead to plasma metabolomic differences. We study metabolite composition differences between dingoes (n=15) and two domestic dog breeds (Basenji n= 9 and German Shepherd Dog: GSD n=10). After accounting for within group variation, 62 significant metabolite differences were detected between dingoes and domestic dogs, with a greater number of differences in protein (n= 14) and lipid metabolites (n= 12). Most differences were observed between dingoes and domestic dogs and fewest between the domestic dog breeds. Second, we investigate variation between pure dingoes (n=10) and dingo-dog hybrids (n=10) as hybridisation is common. We detected no significant differences in metabolite levels between dingoes and dingo-dog hybrids after Bonferroni correction. However, power analyses reported that increasing the sample size to 15 could result in differences in uridine 5’-diphosphogalactose (UDPgal) levels related to galactose metabolism. We suggest this may be related to an increase inAmylase 2Bcopy number in hybrids. Our study illustrates that the dingo metabolome is significantly different from domestic dog breeds and hybridisation is likely to influence carbohydrate metabolism.
Descending and ascending signals that maintain rhythmic walking pattern in the cricket
Authors: Naniwa Keisuke , Aonuma Hitoshi 
Published: November 2020

AbstractThe cricket is one of the model animals used to investigate the neuronal mechanisms underlying adaptive locomotion. An intact cricket walks with a tripod gait, similar to other insects. The motor control center of the leg movements is located in the thoracic ganglia. In this study, we investigated the walking gait patterns of crickets whose ventral nerve cords were surgically cut to gain an understanding of how the descending signals from the head ganglia and ascending signals from the abdominal nervous system into the thoracic ganglia mediate the initiation and coordination of the walking gait pattern. Crickets whose paired connectives between the brain and subesophageal ganglion (SEG) were cut exhibited a tripod gait pattern. However, when one side of the connectives between the brain and SEG was cut, the crickets continued to turn in the opposite direction to the connective cut. Crickets whose paired connectives between the SEG and prothoracic ganglion were cut did not walk, whereas the crickets exhibited an ordinal tripod gait pattern when one side of the connectives was intact. Crickets whose paired connectives between the metathoracic ganglion and abdominal ganglia were cut initiated walking, although the gait was not a coordinated tripod pattern, whereas the crickets exhibited a tripod gait when one side of the connectives was intact. These results suggest that the brain plays an inhibitory role in initiating leg movements, and that both the descending signals from the head ganglia and the ascending signals from the abdominal nervous system are both important in initiating and coordinating insect walking gait patterns.
A global indicator of utilised wildlife populations: regional trends and the impact of management
Authors: McRae Louise , Freeman Robin , Geldmann Jonas , Moss Grace B. , Kjær-Hansen Louise , Burgess Neil D. 
Published: November 2020

AbstractThe sustainable use of wildlife is a core aspiration of biodiversity conservation but is the subject of intense debate in the scientific literature as to how, and whether, species are best used and managed. While both positive and negative outcomes of sustainable use are known for specific taxa or local case studies, a global and regional picture of trends in wildlife populations in use is lacking. We use a global data set of over 11,000 time-series to derive indices of ‘utilised’ and ‘not utilised’ wildlife populations and assess global and regional changes, principally for mammals, birds and fishes. We also assess whether ‘management’ makes a measurable difference to wildlife population trends, especially for the utilised species populations. Our results show that wildlife population trends globally are negative, but with utilised populations tending to decline more rapidly, especially in Africa and the Americas. Crucially, where utilised populations are managed, using a variety of mechanisms, there is a positive impact on the trend. It is therefore true that use of species can both be a driver of negative population trends, or a driver of species recovery, with numerous species and population specific case examples making up these broader trends. This work is relevant to the evidence base for the IPBES Sustainable Use Assessment, and to the development of indicators of sustainable use of species under the post-2020 Global Biodiversity Framework being developed under the Convention on Biological Diversity.
Computational prediction of SARS-CoV-2 encoded miRNAs and their putative host targets
Authors: Verma Sonia , Dwivedy Abhisek , Kumar Neeraj , Biswal Bichitra K. 
Published: November 2020

AbstractOver the past two decades, there has been a continued research on the role of small non-coding RNAs including microRNAs (miRNAs) in various diseases. Studies have shown that viruses modulate the host cellular machinery and hijack its metabolic and immune signalling pathways by miRNA mediated gene silencing. Given the immensity of coronavirus disease 19 (COVID-19) pandemic and the strong association of viral encoded miRNAs with their pathogenesis, it is important to study Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) miRNAs. To address this unexplored area, we identified 8 putative novel miRNAs from SARS-CoV-2 genome and explored their possible human gene targets. A significant proportion of these targets populated key immune and metabolic pathways such as MAPK signalling pathway, maturity-onset diabetes, Insulin signalling pathway, endocytosis, RNA transport, TGF-β signalling pathway, to name a few. The data from this work is backed up by recently reported high-throughput transcriptomics datasets obtains from SARS-CoV-2 infected samples. Analysis of these datasets reveal that a significant proportion of the target human genes were down-regulated upon SARS-CoV-2 infection. The current study brings to light probable host metabolic and immune pathways susceptible to viral miRNA mediated silencing in a SARS-CoV-2 infection, and discusses its effects on the host pathophysiology.
Rice rhizospheric microbes confer limited Arsenic protection under high Arsenic conditions
Authors: Gundlah-Mooney Victoria , Bais Harsh P. 
Published: November 2020

AbstractRice (Oryza sativa) is a staple food crop worldwide and plays a critical role in ensuring food security as the global population continues to expand exponentially. Groundwater contamination with Arsenite [As(III)], a naturally occurring inorganic form of arsenic (As), leads to uptake and accumulation within rice plants. As a result, grain yield is lowered, the overall plant health is diminished, and there is a risk of arsenic toxicity from grain consumption. It was previously shown that a novel bacterial strain from the rice rhizosphere may reduce As accumulation in rice plants exposed to low levels of environmental As. We hypothesized that different rice varieties may exhibit varying responses to high As levels, resulting in differences in As uptake and toxicity. Utilizing the natural rice rhizospheric microbes, we initiated a set of hydroponic experiments with two rice varieties, Nipponbare (As tolerant) and IR66 (As susceptible). Rice varieties exposed to high As(III) concentration (50 μM) showed changes in both aboveground and belowground traits. As-tolerant Nipponbare varieties show grain production at high As(III) concentrations compared to the As-susceptible IR66 variety. Supplementation of natural rice rhizospheric microbes as single inoculums showed varied responses in both As-tolerant and As-susceptible varieties. Three natural rice rhizospheric microbesPantoeasps (EA106),Pseudomonas corrugata(EA104), andArthrobacter oxydans(EA201) were selected based on previously reported high Iron (Fe)-siderophore activity and were used for the hydroponic experiments as well as a non-rice rhizospheric strain,Bacillus subtilisUD1022. Interestingly, treatment with two strains (EA104 and EA201) led to reduction in As(III) uptake in shoots, roots, and grains and the degree of reduction of As(III) was pronounced in As-susceptible IR66 varieties. Non-rice rhizospheric UD1022 showed subtle protection against high As toxicity. High As(III) treatment led to lack or delay of flowering and seed setting in the As-susceptible IR66 variety. The data presented here may further the understanding of how beneficial microbes in the rhizosphere may help rice plants cope with high concentrations of As in the soil or groundwater.