bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid evaluation of neutralizing antibodies in COVID-19 patients
Authors: Zhang Pingping , Li Baisheng , Min Wei , Wang Xiaohui , Li Zhencui , Zhao Yong , Zhang Huan , Jiang Min , Zheng Huanying , Yang Chao , Zhang Wei , Zuo Le , Gao Qi , Yang Zhengrong , Li Yanzhao , Feng Tiejian , Lin Changqing , Hu Qinghua , Song Tie , Yang Ruifu 
Published: September 2020

AbstractThe ongoing coronavirus disease 2019 (COVID-19) pandemic calls for a method to rapidly and conveniently evaluate neutralizing antibody (NAb) activity in patients. Here, an up-conversion phosphor technology-based point-of-care testing (UPT-POCT) and a microneutralization assay were employed to detect total antibodies against the receptor-binding domain of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) spike protein and NAb activity in COVID-19 patients’ sera, respectively, in order to determine if UPT-POCT could be used as a surrogate method for rapid evaluation of serum NAb activity in COVID-19 patients. In total, 519 serum samples from 213 recovered and 99 polymerase chain reaction re-positive (RP) COVID-19 patients were used in this report. We found that UPT-POCT reporting values correlated highly with NAb titers from 1:4 to 1:1024, with a correlation coefficientr= 0.9654 (P< 0.001), as well as protection rate against RP (r = 0.9886, P < 0.0001). As a significant point for reducing re-positive rate, UPT-POCT values of 4.380 ± 2.677, corresponding to NAb titer of 1:64, may be appropriate as an indicator for evaluating high efficiency of protection. This study demonstrates that the quantitative lateral flow based UPT-POCT, could be used to rapidly evaluate NAb titer, which is of importance for assessing vaccine immunization efficacy, herd immunity, and screening patient plasma for high NAbs.
Tumour volume distribution can yield information on tumour growth and tumour control
Authors: Schneider Uwe , Besserer Jürgen 
Published: September 2020

AbstractBackgroundIt is shown that tumour volume distributions, can yield information on two aspects of cancer research: tumour induction and tumour control.Materials and methodsFrom the hypothesis that the intrinsic distribution of breast cancer volumes follows an exponential distribution, firstly the probability density function of tumour growth time was deduced via a mathematical transformation of the probability density functions of tumour volumes. In a second step, the distribution of tumour volumes was used to model the variation of the clonogenic cell number between patients in order to determine tumour control probabilities for radiotherapy patients.ResultsDistribution of lag times, i.e. the time from the appearance of the first fully malignant cell until a clinicaly observable cancer, can be used to deduce the probability of tumour induction as a function of patient age. The integration of the volume variation with a Poisson-TCP model results in a logistic function which explains population-averaged survival data of radiotherapy patients.ConclusionsThe inclusion of tumour volume distributions into the TCP formalism enables a direct link to be deduced between a cohort TCP model (logistic) and a TCP model for individual patients (Poisson). The TCP model can be applied to non-uniform tumour dose distributions.
Non-alcoholic fatty liver disease (NAFLD) and risk of hospitalization for Covid-19
Authors: Bramante Carolyn T. , Tignanelli Christopher J. , Dutta Nirjhar , Jones Emma , Tamaritz Leonardo , Clark Jeanne , Melton-Meaux Genevieve , Usher Michael , Ikramuddin Sayeed 
Published: September 2020

AbstractBackgroundCovid-19 disease causes significant morbidity and mortality through increase inflammation and thrombosis. Non-alcoholic fatty liver disease and non-alcoholic steatohepatitis are states of chronic inflammation and indicate advanced metabolic disease. We sought to understand the risk of hospitalization for Covid-19 associated with NAFLD/NASH.MethodsRetrospective analysis of electronic medical record data of 6,700 adults with a positive SARS-CoV-2 PCR from March 1, 2020 to Aug 25, 2020. Logistic regression and competing risk were used to assess odds of being hospitalized. Additional adjustment was added to assess risk of hospitalization among patients with a prescription for metformin use within the 3 months prior to the SARS-CoV-2 PCR result, history of home glucagon-like-peptide 1 receptor agonist (GLP-1 RA) use, and history of metabolic and bariatric surgery (MBS). Interactions were assessed by gender and race.ResultsA history of NAFLD/NASH was associated with increased odds of admission for Covid-19: logistic regression OR 2.04 (1.55, 2.96, p<0.01), competing risks OR 1.43 (1.09-1.88, p<0.01); and each additional year of having NAFLD/NASH was associated with a significant increased risk of being hospitalized for Covid-19, OR 1.86 (1.43-2.42, p<0.01). After controlling for NAFLD/NASH, persons with obesity had decreased odds of hospitalization for Covid-19, OR 0.41 (0.34-0.49, p<0.01). NAFLD/NASH increased risk of hospitalization in men and women, and in all racial/ethnic subgroups. Mediation treatments for metabolic syndrome were associated with non-significant reduced risk of admission: OR 0.42 (0.18-1.01, p=0.05) for home metformin use and OR 0.40 (0.14-1.17, p=0.10) for home GLP-1RA use. MBS was associated with a significant decreased risk of admission: OR 0.22 (0.05-0.98, p<0.05).ConclusionsNAFLD/NASH is a significant risk factor for hospitalization for Covid-19, and appears to account for risk attributed to obesity. Treatments for metabolic disease mitigated risks from NAFLD/NASH. More research is needed to confirm risk associated with visceral adiposity, and patients should be screened for and informed of treatments for metabolic syndrome.Key QuestionsQuestionDoes NAFLD/NASH independently increase risk for poor outcomes from Covid-19?FindingsIn this observational study, a history of NAFLD/NASH was associated with a significantly increased odds of hospitalization. Metabolic surgery was protective against admission in persons with NAFLD/NASH and Covid-19. Metformin and glucagon like peptide 1 receptor agonists were associated with non-significant protecting against admission.MeaningTreatment for metabolic syndrome greatly reduce the elevated risk of hospitalization for Covid-19 among persons with NAFLD/NASH.
Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Authors: Lee Hye Kyung , Knabl Ludwig , Pipperger Lisa , Volland Andre , Furth Priscilla A. , Kang Keunsoo , Smith Harold E. , Ludwig Knabl , Bellmann Romuald , Bernhard Christina , Kaiser Norbert , Gänzer Hannes , Ströhle Mathias , Walser Andreas , Laer Dorothee von , Hennighausen Lothar 
Published: September 2020

AbstractTo investigate prevalence of ongoing activation of inflammation following asymptomatic SARS-CoV-2 infection we characterized immune cell transcriptomes from 43 asymptomatic seropositive and 52 highly exposed seronegative individuals with few underlying health issues following a community superspreading event. Four mildly symptomatic seropositive individuals examined three weeks after infection as positive controls demonstrated immunological activation. Approximately four to six weeks following the event, the two asymptomatic groups showed no significant differences. Two seropositive patients with underlying genetic disease impacting immunological activation were included (Cystic Fibrosis (CF), Nuclear factor-kappa B Essential Modulator (NEMO) deficiency). CF, but not NEMO, associated with significant immune transcriptome differences including some associated with severe SARS-CoV-2 infection (IL1B, IL17A, respective receptors). All subjects remained in their usual state of health from event through five-month follow-up. Here, asymptomatic infection resolved without evidence of prolonged immunological activation. Inclusion of subjects with underlying genetic disease illustrated the pathophysiological importance of context on impact of immunological response.
Transcriptome analysis of growth variation in early juvenile stage sandfishHolothuria scabra
Authors: Ordoñez June Feliciano F. , Galindez Gihanna Gaye ST. , Ravago-Gotanco Rachel 
Published: September 2020

AbstractThe sandfishHolothuria scabrais a high-value tropical sea cucumber species representing a major mariculture prospect across the Indo-Pacific. Advancements in culture technology, rearing, and processing present options for augmenting capture production, stock restoration, and sustainable livelihood activities from hatchery-produced sandfish. Further improvements in mariculture production may be gained from the application of genomic technologies to improve performance traits such as growth. In this study, we performedde novotranscriptome assembly and characterization of fast- and slow-growing juvenileH. scabrafrom three Philippine populations. Analyses revealed 66 unigenes that were consistently differentially regulated in fast-growing sandfish and found to be associated with immune response and metabolism. Further, we identified microsatellite and single nucleotide polymorphism markers potentially associated with fast growth. These findings provide insight on potential genomic determinants underlying growth regulation in early juvenile sandfish which will be useful for further functional studies.HighlightsThe study explores the genomic basis of growth variation in juvenile sandfish by examining gene expression profiles of fast- and slow-growing early juvenile stages from three hatchery populations using RNA-seq.Sixty-six differentially regulated unigenes potentially related to growth variation are associated with several biological and molecular processes, including carbohydrate binding, extracellular matrix organization, fatty-acid metabolism, and metabolite and solute transport.A large number of potential microsatellite and growth category-associated SNP markers have been identified.
High species turnover shapes anuran community composition in ponds along an urban-rural gradient
Authors: Ganci Carolina Cunha , Provete Diogo B. , Püttker Thomas , Lindenmayer David , Almeida-Gomes Mauricio 
Published: September 2020

AbstractThe rapid expansion of urban areas in which natural and semi-natural areas are replaced by human infrastructure, such as buildings and streets, is a major threat to biodiversity worldwide. However, little is known about how the structure of biotic communities is affected by urbanization in the tropics. Here, we tested the effect of land use types in urban and peri-urban areas on frog species richness and community composition in central Brazil. We selected 20 ponds differing in size and surrounding levels of urbanization as well as natural forest cover. We then used a Poisson GLM and a distance-based Redundancy Analysis (db-RDA) to relate species richness and community composition, respectively, to environmental variables. Variation in species richness was best explained by pond size (positive effect) and amount of urbanization (negative effect) in the surrounding 500 m. Community composition was mainly driven by species turnover than by nestedness, with db-RDA showing that turnover was explained primarily by urban infrastructure and forest cover. Our results indicate that urbanization negatively influences species richness. Moreover, as the amount of urbanization increased, several species were replaced by others taxa that appear better adapted to urban environments. Our results indicate that maintaining large ponds with surrounding native vegetation in urban environments might be an effective strategy for conserving frog communities.
Meaningful Associations in the Adolescent Brain Cognitive Development Study
Authors: Dick Anthony Steven , Lopez Daniel A. , Watts Ashley L. , Heeringa Steven , Reuter Chase , Bartsch Hauke , Fan Chun Chieh , Kennedy David N. , Palmer Clare , Marshall Andrew , Haist Frank , Hawes Samuel , Nichols Thomas E. , Barch Deanna M. , Jernigan Terry L. , Garavan Hugh , Grant Steven , Pariyadath Vani , Hoffman Elizabeth , Neale Michael , Stuart Elizabeth A. , Paulus Martin P. , Sher Kenneth J. , Thompson Wesley K. 
Published: September 2020

AbstractThe Adolescent Brain Cognitive Development (ABCD) Study is the largest single-cohort prospective longitudinal study of neurodevelopment and children’s health in the United States. A cohort of n= 11,880 children aged 9-10 years (and their parents/guardians) were recruited across 22 sites and are being followed with in-person visits on an annual basis for at least 10 years. The study approximates the US population on several key sociodemographic variables, including sex, race, ethnicity, household income, and parental education. Data collected include assessments of health, mental health, substance use, culture and environment and neurocognition, as well as geocoded exposures, structural and functional magnetic resonance imaging (MRI), and whole-genome genotyping. Here, we describe the ABCD Study aims and design, as well as issues surrounding estimation of meaningful associations using its data, including population inferences, hypothesis testing, power and precision, control of covariates, interpretation of associations, and recommended best practices for reproducible research, analytical procedures and reporting of results.
Molecular Mechanism of Nuclear Tau Accumulation and its Role in Protein Synthesis
Authors: Portillo Miguel , Eremenko Ekaterina , Kaluski Shai , Onn Lior , Stein Daniel , Slobodnik Zeev , Ueberham Uwe , Einav Monica , Brückner Martina K. , Arendt Thomas , Toiber Debra 
Published: September 2020

AbstractSeveral neurodegenerative diseases present Tau accumulation as the main pathological marker. Tau post-translational modifications such as phosphorylation and acetylation are increased in neurodegenerative patients. Here, we show that Tau hyper-acetylation at residue 174 increases its own nuclear presence and is the result of DNA damage signaling or the lack of SIRT6, both causative of neurodegeneration. Tau-K174ac is deacetylated in the nucleus by SIRT6. However, lack of SIRT6 or chronic DNA damage result in nuclear Tau-K174ac accumulation. Once there, it induces global changes in gene expression affecting protein translation, synthesis and energy production. Tau-K174Q expressing cells showed changes in the nucleolus increasing their intensity and number, as well as in rRNA synthesis leading to an increase in protein translation and ATP reduction. Concomitantly, AD patients showed increased Nucleolin and a decrease in SIRT6 levels. AD patients present increased levels of nuclear Tau, particularly Tau-K174ac. Our results suggest that increased Tau-K174ac in AD patients is the result of DNA damage signaling and SIRT6 depletion. We propose that Tau-K174ac toxicity is due to its increased stability, nuclear accumulation and nucleolar dysfunction.
Social groups buffer maternal loss in mountain gorillas
Authors: Morrison Robin E , Eckardt Winnie , Colchero Fernando , Vecellio Veronica , Stoinski Tara S 
Published: September 2020

AbstractMothers are crucial for mammals’ survival before nutritional independence, but many social mammals reside with their mothers long after. In these species the social adversity caused by maternal loss later in life can dramatically reduce fitness. However, in some human populations these negative consequences appear to be overcome by care from other group members. We investigated the consequences of maternal loss in mountain gorillas and found no discernible fitness costs to maternal loss through survival, age at first birth or survival of first offspring through infancy. Social network analysis revealed that maternal loss led to strengthened relationships with other group members, particularly the dominant male and age-mates. In contrast to most social mammals, where maternal loss causes considerable social adversity, in mountain gorillas, as in certain human populations, this may be buffered by relationships within cohesive social groups, breaking the link between maternal loss, increased social adversity and decreased fitness.
Optimising biomedical relationship extraction with BioBERT
Authors: Giles Oliver , Karlsson Anneli , Masiala Spyroula , White Simon , Cesareni Gianni , Perfetto Livia , Mullen Joe , Hughes Michael , Harland Lee , Malone James 
Published: September 2020

AbstractText mining is widely used within the life sciences as an evidence stream for inferring relationships between biological entities. In most cases, conventional string matching is used to identify cooccurrences of given entities within sentences. This limits the utility of text mining results, as they tend to contain significant noise due to weak inclusion criteria. We show that, in the indicative case of protein-protein interactions (PPIs), the majority of sentences containing cooccurrences (∽75%) do not describe any causal relationship. We further demonstrate the feasibility of fine tuning a strong domain-specific language model, BioBERT, to analyse sentences containing cooccurrences and accurately (F1 score: 88.95%) identify functional links between proteins. These strong results come in spite of the deep complexity of the language involved, which limits the accuracy even of expert curators. We establish guidelines for best practices in data creation to this end, including an examination of inter-annotator agreement, of semisupervision, and of rules based alternatives to manual curation, and explore the potential for downstream use of the model to accelerate curation of interactions in the SIGNOR database of causal protein interactions and the IntAct database of experimental evidence for physical protein interactions.
Peripapillary Perfused Capillary Density in True Versus Pseudoexfoliation Syndrome: An OCTA Study
Authors: Tangtammaruk Phantaraporn , Petpiroon Purit , Supakonatanasan Wasu , Teekhasaenee Chaiwat , Suwan Yanin 
Published: September 2020

AbstractPurposeTo compare peripapillary perfused capillary density (PCD) among eyes with true exfoliation syndrome (TEX), eyes with pseudoexfoliation syndrome (PEX), and healthy control eyes.Materials and MethodsIn this observational cross-sectional study, eyes with and without TEX or PEX were assessed by optical coherence tomography angiography (OCTA) imaging. Bilateral OCTA images (4.5 · 4.5 mm2) centered at the optic nerve head were obtained using a commercial spectral domain OCTA system. Optic nerve head perfusion was quantified using the split-spectrum amplitude decorrelation angiography algorithm. Categorical and continuous variables were compared using the chi-squared test and one-way analysis of variance, respectively. The generalized estimating equation was used to adjust for confounding factors and determine inter-ocular associations.ResultsWe enrolled 39 eyes with TEX, 31 eyes with PEX, and 32 control eyes. There were no significant differences among the three groups regarding age, intraocular pressure, cup-to-disc ratio, blood pressure, or axial length (all p>0.05). There were significant differences in global PCD among the three groups (p=0.01). There were significant differences in annular PCD between the TEX and PEX groups (p=0.027).ConclusionsWhile both global and annular PCDs did not differ between the TEX and control groups, greater loss of annular PCD in the PEX group than in the TEX and control groups suggests more pronounced microvascular disturbance in PEX.Synopsis/PrecisGreater microvascular attenuation in PEX compared with TEX and normal control measured by OCTA.
iBRAB:in silicobased-designed Broad-spectrum Fab against H1N1 Influenza A Virus
Authors: Do Phuc-Chau , Nguyen Trung H. , Vo Uyen T.M. , Le Ly 
Published: September 2020

AbstractInfluenza virus A is a significant agent involved in the outbreak of worldwide epidemics, causing millions of fatalities around the world by respiratory diseases and seasonal illness. Many projects had been conducting to investigate recovered infected patients for therapeutic vaccines that have broad-spectrum activity. With the aid of the computational approach in biology, the designation for a vaccine model is more accessible. We developed anin silicoprotocol callediBRAB to design a broad-reactive Fab on a wide range of influenza A virus. The Fab model was constructed based on sequences and structure of available broad-spectrum Abs or Fabs against a wide range of H1N1 influenza A virus. As a result, the proposed Fab model followediBRAB has good binding affinity over 27 selected HA of different strains of H1 influenza A virus, including wild-type and mutated ones. The examination also took by computational tools to fasten the procedure. This protocol could be applied for a fast designed therapeutic vaccine against different types of threats.
Estimating partial body ionizing radiation exposure by automated cytogenetic biodosimetry
Authors: Shirley Ben C. , Knoll Joan H.M. , Moquet Jayne , Ainsbury Elizabeth , Duy Pham Ngoc , Norton Farrah , Wilkins Ruth C. , Rogan Peter K. 
Published: September 2020

AbstractPurposeInhomogeneous exposures to ionizing radiation can be detected and quantified with the Dicentric Chromosome Assay (DCA) of metaphase cells. Complete automation of interpretation of the DCA for whole body irradiation has significantly improved throughput without compromising accuracy, however low levels of residual false positive dicentric chromosomes (DCs) have confounded its application for partial body exposure determination.Materials and MethodsWe describe a method of estimating and correcting for false positive DCs in digitally processed images of metaphase cells. Nearly all DCs detected in unirradiated calibration samples are introduced by digital image processing. DC frequencies of irradiated calibration samples and those exposed to unknown radiation levels are corrected subtracting this false positive fraction from each. In partial body exposures, the fraction of cells exposed, and radiation dose can be quantified after applying this modification of the contaminated Poisson method.ResultsDose estimates of three partially irradiated samples diverged 0.2 to 2.5 Gy from physical doses and irradiated cell fractions deviated by 2.3-15.8% from the known levels. Synthetic partial body samples comprised of unirradiated and 3 Gy samples from 4 laboratories were correctly discriminated as inhomogeneous by multiple criteria. Root mean squared errors of these dose estimates ranged from 0.52 to 1.14 Gy2and from 8.1 to 33.3%2for the fraction of cells irradiated.ConclusionsAutomated DCA can differentiate whole-from partial-body radiation exposures and provides timely quantification of estimated whole-body equivalent dose.Biographical NoteBen Shirley M.Sc. is Chief Software Architect, CytoGnomix Inc. Canada; Joan Knoll Ph.D. Dipl.ABMGG, FCCMG is Professor in Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, Canada and cofounder, CytoGnomix Inc.; Jayne Moquet Ph.D. is Principal Radiation Protection Scientist in the Cytogenetics Group, Public Health England; Elizabeth Ainsbury Ph.D. is Head, Cytogenetics Group and the Chromosome Dosimetry Service, Public Health England; Pham Ngoc Duy M.Sc. is deputy director of Biotechnology Center, Dalat Nuclear Research Institute, Vietnam; Farrah Norton M.Sc.is Research Scientist and Lead of the Biodosimetry emergency response and research capability at Canadian Nuclear Laboratories; Ruth Wilkins, Ph.D. is Research Scientist and Chief of the Ionizing Radiation Health Sciences Division at Health Canada, Ontario, Canada; and Peter K. Rogan Ph.D. is Professor of Biochemistry and Oncology, Schulich School of Medicine and Dentistry, University of Western Ontario, Canada, and President, CytoGnomix Inc.