bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 detection by nasal strips: a superior tool for surveillance of pediatric populations
Authors: Chan Renee WY , Chan Kate C , Chan Kathy YY , Lui Grace CY , Tsun Joseph GS , Wong Rity YK , Yu Michelle WL , Wang Maggie HT , Chan Paul KS , Lam Hugh Simon , Li Albert M 
Published: November 2020

AbstractBackgroundDeep throat saliva (DTS) and pooled nasopharyngeal swab and throat swab (NPSTS) are utilized for viral detection. DTS is challenging for children. Swabbing the respiratory mucosa requires trained personnel and may trigger sneezing and coughing, which generate droplets. A reliable, simple and safe sampling method applicable to a wide age range is required for community-based surveillance.MethodsWe introduced nasal strip as an easy and low-risk collection method. Asymptomatic and symptomatic SARS-CoV-2 infected patients (n = 38) were recruited. Nasal epithelial lining fluid (NELF) (n = 43) strip paired with nasal swab (n = 13) were collected by a healthcare worker to compare with NPSTS (n = 21) or DTS (n =22) collected within 24 hours as reference. All samples were subjected to viral RNA quantitation by real-time PCR targeting the nucleoprotein gene.ResultsComparable Ct values were observed between paired nasal strip and nasal swab samples. The agreement between nasal strip samples and NPSTS was 94.44% and 100% for NPSTS positive and negative samples. Higher viral RNA concentration was detected in nasal strips than DTS samples. False-negative results were recorded in six DTS specimens, of which four were from children. Storage at room temperature up to 72 (n = 3) hours did not affect diagnostic yield of nasal strips.ConclusionsNasal strip is a reliable and non-invasive sampling method for SARS-CoV-2 detection, and viral detection remains stable for at least 72 hours. It can be used as an alternative tool for community-based surveillance.
Causal contribution of malignancy to anomalous baroreflex functionality in patients with cancer: An overlooked aspect of cardio-oncology
Authors: Fang Chi , Tsai Ching-Yi , Chien Chih-Yen , Chan Samuel H.H. 
Published: November 2020

AbstractThe current trend in cardio-oncology places major emphasis on circulatory toxicity induced by cancer therapy. Whether malignancy itself is a direct contributing factor to cardiovascular dysfunctions and baroreflex dysregulation in patients with cancer, however, has rarely appeared in literature. The present study addressed this largely overlooked aspect of cardio-oncology by evaluating blood pressure, heart rate and baroreflex functionality before and after curative surgery in patients with oral cavity squamous cell carcinoma (OSCC). We found that these patients exhibited reduced baroreflex-mediated sympathetic vasomotor tone and augmented cardiac vagal baroreflex, and such inherent anomalies were readily reversed to levels of healthy controls after surgical removal of the primary tumor. It is concluded that by being more prone to hypotension and bradycardia, anomalous baroreflex functionality causally induced by malignancy predisposes patients with cancer to detrimental cardiovascular abnormalities that may be further exacerbated by cancer therapy.
Predicting the Effect of Malaria Control Strategies Using Mathematical Modeling Approach
Authors: Eguda Felix Yakubu , Abah Samuel Eneojo , Andrawus James , Atuba Sunday , Abba Aliyu 
Published: November 2020

AbstractMalaria is a life-threatening disease which has caused enormous public health challenge. A mathematical model describing the dynamics of malaria between the human and vector population is formulated to understand the important parameters in the transmission and develop effective prevention and control strategies. We analysed the model and found that the model has a disease-free equilibrium (DFE) which is locally and globally asymptotically stable if the effective reproduction number can be brought below unity. Our model shows that the infectivity of mildly infected children and adults amplifies the disease burden in a population. It was shown that the model does not undergo the phenomenon of backward bifurcation so long as the recovered children and adults do not lose their acquired immunity and if the infection of mildly infected adult is not high enough to infect susceptible mosquitoes. However, control strategies involving mosquito reduction through high rate of application of insecticide will serve as an effective malaria control strategy. It is further shown that whenever the effective reproduction number is greater than unity the model has a unique endemic equilibrium which is globally stable for the case when there is loss of acquired immunity in children and adults. Numerical simulations show that the presence of all the control strategies is more effective in preventing mild malaria cases in adult and children as compared to severe malaria cases in adult and children.
Sample pooling, a population screening strategy for SARS-CoV2 to prevent future outbreak and mitigate the “second-wave” of infection of the virus
Authors: Sawarkar S. , Victor A. , Viotti M. , Haran S. , Verma S. , Griffin D. , Sams J. 
Published: November 2020

ProblemHow do we manage treatment and stabilization in clinical settings and static population communities like assisted living facility settings of their patient or resident populations during and post the SARS-CoV-2 pandemic?ScopeThis proposal explores the possible and predicted changes to standard operating procedures to the facility management and associated landscape and focuses on series of deployments, during and post peak SARS-CoV-2 activity, and will outline possible models for the current medical facility model that we operate with. This article primarily focuses on non-emergency facility management.Assumptions and understanding of the fieldWith a reduction in the numbers nationally, patients are highly motivated and likely to seek non-emergency and planned medical procedural treatment as early as possible as social distancing measures are eased and restrictions on non-urgent procedures are lifted.Conclusions and next stepsAn initial pan-national shutdown and suspension of services was necessary in an effort to ensure that essential medical services and resources were not strained. The authors feel that a strategic resumption of regular non-emergency treatments around the United States and continued provision of services at care facilities is possible with innovative testing strategies like pooled screening of large populations at a manageable price point. Moreover, pooling as a strategy when used widely, would be extremely effective at predicting outbreaks of the virus and as an effect help in mitigating the spread of the virus in its “second-wave”. We have developed one such innovative pooling strategy that can be easily deployed across laboratories and reduce the cost of population wide COVID-19 testing significantly
Clinical validation of Whole Genome Sequencing for cancer diagnostics
Authors: Roepman Paul , Bruijn Ewart de , Lieshout Stef van , Schoenmaker Lieke , Boelens Mirjam C , Dubbink Hendrikus J , Geurts-Giele Willemina RR , Groenendijk Floris H , Huibers Manon MH , EG Kranendonk Mariëtte , Roemer Margaretha GM , Samsom Kris G , Steehouwer Marloes , Leng Wendy WJ de , Hoischen Alexander , Ylstra Bauke , Monkhorst Kim , van der Hoeven Jacobus JM , Cuppen Edwin 
Published: November 2020

AbstractWhole genome sequencing (WGS) using fresh frozen tissue and matched blood samples from cancer patients is becoming in reach as the most complete genetic tumor test. With a trend towards the availability of small biopsies and the need to screen an increasing number of (complex) biomarkers, the use of a single all-inclusive test is preferred over multiple consecutive assays. To meet high-quality diagnostics standards, we optimized and clinically validated WGS sample and data processing procedures resulting in a technical success rate of 95.6% for fresh-frozen samples with sufficient (≥20%) tumor content.Independent validation of identified biomarkers against commonly used diagnostic assays showed a high sensitivity (recall) (98.5%) and precision (positive predictive value) (97.8%) for detection of somatic SNV and indels (across 22 genes), and high concordance for detection of gene amplification (97.0%, EGRF and MET) as well as somatic complete loss (100%, CDKN2A/p16). Gene fusion analysis showed a concordance of 91.3% between DNA-based WGS and an orthogonal RNA-based gene fusion assay. Microsatellite (in)stability assessment showed a sensitivity of 100% with a precision of 94%, and virus detection (HPV) an accuracy of 100% compared to standard testing.In conclusion, whole genome sequencing has a >95% sensitivity and precision compared to routinely used DNA techniques in diagnostics and all relevant mutation types can be detected reliably in a single assay.
Service user experiences of community services for Complex Emotional Needs: A qualitative thematic synthesis
Authors: Rains Luke Sheridan , Echave Athena , Rees Jessica , Scott Hannah Rachel , Lever-Taylor Billie , Broeckelmann Eva , Steare Thomas , Barnett Phoebe , Cooper Chris , Jeynes Tamar , Russell Jessica , Oram Sian , Rowe Sarah , Johnson Sonia 
Published: November 2020

AbstractBackgroundThere is a recognised need to develop clear service models and pathways to provide high quality care in the community for people with complex emotional needs, who may have been given a “personality disorder” diagnosis. Services should be informed by the views of people with these experiences.AimsTo systematically review and synthesise qualitative studies on service user experiences of community mental health care for Complex Emotional Needs.MethodsWe searched six bibliographic databases for papers published since 2003. We included peer reviewed studies reporting data on service user experiences and views about good care from community-based mental health services for adults with CEN, including generic mental health services and specialist “personality disorder” services. Studies using any qualitative method were included and thematic synthesis used to identify over-arching themes.ResultsForty-seven papers were included. Main themes were: 1) The need for a long-term perspective on treatment journeys; 2) The need for individualised and holistic care; 3) Large variations in accessibility and quality of mental health services; 4) The centrality of therapeutic relationships; 5) Impacts of ‘personality disorder’ diagnosis. Themes tended to recur across studies from different countries and years.DiscussionRecurrent major themes included wanting support that is individualised and holistic, provides continuity over long journeys towards recovery, and that is delivered by empathetic and well-informed clinicians who are hopeful but realistic about the prospects of treatment. Care that met these simple and clearly stated priorities tended to be restricted to often limited periods of treatment by specialist “personality disorder” services: generic and primary care services were often reported as far from adequate. There is an urgent need to co-design and test strategies for improving long-term support and treatment care for people with “personality disorders” throughout the mental health care system.
OmicPioneer-sc: an integrated, interactive visualization environment for single-cell sequencing data
Authors: Weinstein John N. , Rohrdanz Mary A. , Stucky Mark , Melott James , Ma Jun , Mohanty Vakul , Manyam Ganiraju , Wakefield Christopher , Chen Ken , Navin Nicholas E. , Ryan Michael C. , Akbani Rehan , Broom Bradley M. 
Published: November 2020

AbstractOmicPioneer-sc is an open-source data visualization/analysis package that integrates dimensionality-reduction plots (DRPs) such as t-SNE and UMAP with Next-Generation Clustered Heat Maps (NGCHMs) and Pathway Visualization Modules (PVMs) in a seamless, highly interactive exploratory environment. It includes fluent zooming and navigation, a statistical toolkit, dozens of link-outs to external public bioinformatic resources, high-resolution graphics that meet the requirements of all major journals, and the ability to store all metadata needed to reproduce the visualizations at a later time. A user-friendly, multi-panel graphical interface enables non-informaticians to interact with the system without programming, asking and answering questions that require navigation among the three types of modules or extension from them to the Gene Ontology or information on therapies. The visual integration can be useful for detective work to identify and annotate cell-types for color-coding of the DRPs, and multiple NGCHMs can be layered on top of each other (with toggling among them) as an aid to multi-omic analysis. The tools are available in containerized form with APIs to facilitate incorporation as a plug-in to other bioinformatic environments. The capabilities of OmicPioneer-sc are illustrated here through application to a single-cell RNA-seq airway dataset pertinent to the biology of both cancer and COVID-19.[Supplemental material is available for this article.]
Canopy micrometeorology monitoring in diverse climates innovatively improves the evaluation heat-induced sterility of rice under climate change
Authors: Yoshimoto Mayumi , Fukuoka Minehiko , Tsujimoto Yasuhiro , Matsui Tsutomu , Kobayasi Kazuhiro , Saito Kazuki , van Oort Pepijn A.J. , Inusah Baba I.Y , Vijayalakshmi Chenniappan , Vijayalakshmi Dhashnamurthi , Weerakoon W.M.W. , Chandradasa Silva , Daw Tin Tin Myint , Daw Zar Chi Phyo , Tian Xiaohai , Lur Huu-Sheng , Yang Chwen-Ming , Tarpley Lee , Manigbas Norvie L. , Hasegawa Toshihiro 
Published: November 2020

AbstractThis study is the first and unique of open-field studies to assess the determination process of heat-induced spikelet sterility (HISS) of rice by using the same variety and the same monitoring system, MINCER (Micrometeorological Instrument for Near Canopy Environment of Rice), covering the major-rice growing regions from Sub-Saharan Africa, South, Southeast, and East Asia, and USA. Applying the observation data from the monitoring network, MINCERnet, to the canopy heat balance model, IM2PACT, it was quantitatively corroborated in open-field conditions worldwide that the canopy and panicle transpiration and their evaporative cooling effect played a great role on the micrometeorological gap between the ambient air temperature and the panicle temperature, and that the sterility rate due to HISS in open-fields can be evaluated accurately in diverse climates by the mean panicle temperature at flowering hours in the flowering period. The heat balance structure suggested that the risk of HISS should be higher in high humidity climates rather than in dry climates also in the future, which lead to the importance of the humidity accuracy as well as of the air temperature in climate scenarios and their spatial downscaling for future prediction of rice heat stress and production. Applying the heat-tolerant variety was suggested to be able to keep the sterility due to HISS low in all climates. It is needed of the approach using the panicle temperature as indicator of HISS by intervening sub-model and/or monitoring of micrometeorology inside the canopy to reduce uncertainties in future rice yield prediction under various adaptation measures.
Trade-offs between risks of predation and starvation in larvae make the shelf break an optimal spawning location for Atlantic Bluefin tuna
Authors: Shropshire Taylor A. , Morey Steven L. , Chassignet Eric P. , Coles Victoria J. , Karnauskas Mandy , Malca Estrella , Laiz-Carrión Raúl , Fiksen Øyvind , Reglero Patricia , Shiroza Akihiro , Quintanilla Hervas José M. , Gerard Trika , Lamkin John T. , Stukel Michael R. 
Published: November 2020

ABSTRACTAtlantic Bluefin tuna (ABT) (Thunnus thynnus) travel long distances to spawn in oligotrophic regions of the Gulf of Mexico. To estimate regional larval ABT mortality, we developed a spatially-explicit, Lagrangian, individual-based model that simulates dispersal, growth, and mortality within realistic predator and prey fields during the spawning periods from 1993-2012. Modelled larval ABT experience high mortality in the first week of feeding with an average mortality rate of 0.53 ± 0.26 d−1prior to postflexion. Survival ranged from 0.12%–0.32% suggesting that recruitment may vary by a factor of 2.7 due to early life stage mortality alone. Starvation is the dominant source of mortality driven by the early critical period; however, survival is ultimately limited by predation on older individuals. As a result, first-feeding larvae survive better in the more food-rich areas on the shelf, while larger larvae survive better in the open ocean with fewer predators, making the shelf break an optimal spawning area. Our findings support the hypothesis that ABT spawn in oligotrophic regions to minimize predation on their larvae. Ocean modeling tools presented in this study may help facilitate an ecosystem-based management approach to improve future stock assessment models by better resolving the stock-recruitment relationship.
Structural basis for repurpose and design of nucleoside drugs for treating COVID-19
Authors: Yin Wanchao , Luan Xiaodong , Li Zhihai , Xie Yuanchao , Zhou Ziwei , Liu Jia , Gao Minqi , Wang Xiaoxi , Zhou Fulai , Wang Qingxia , Wang Qingxing , Shen Dandan , Zhang Yan , Tian Guanghui , Aisa Haji A. , Hu Tianwen , Wei Daibao , Jiang Yi , Xiao Gengfu , Jiang Hualiang , Zhang Leike , Yu Xuekui , Shen Jingshan , Zhang Shuyang , Xu H. Eric 
Published: November 2020

SARS-CoV-2 has caused a global pandemic of COVID-19 that urgently needs an effective treatment. Nucleoside analog drugs including favipiravir have been repurposed for COVID-19 despite of unclear mechanism of their inhibition of the viral RNA polymerase (RdRp). Here we report the cryo-EM structures of the viral RdRp in complex with favipiravir and two other nucleoside inhibitor drugs ribavirin and penciclovir. Ribavirin and the ribosylated form of favipiravir share a similar ribose scaffold that is distinct from penciclovir. However, the structures reveal that all three inhibitors are covalently linked to the primer strand in a monophosphate form despite the different chemical scaffolds between favipiravir and penciclovir. Surprisingly, the base moieties of these inhibitors can form mismatched pairs with the template strand. Moreover, in view of the clinical disadvantages of remdesivir mainly associated with its prodrug form, we designed several orally-available remdesivir parent nucleoside derivatives, including VV16 that showed 5-fold more potent than remdesivir in inhibition of viral replication. Together, these results demonstrate an unexpected promiscuity of the viral RNA polymerase and provide a basis for repurpose and design of nucleotide analog drugs for COVID-19.One Sentence SummaryCryo-EM structures of the RNA polymerase of SARS-CoV-2 reveals the basis for repurposing of old nucleotide drugs to treat COVID-19.
Beyond linearity in neuroimaging: Capturing nonlinear relationships with application to longitudinal studies
Authors: Chen Gang , Nash Tiffany A. , Reding Katherine M. , Kohn Philip D. , Wei Shau-Ming , Gregory Michael D. , Eisenberg Daniel P. , Cox Robert W. , Berman Karen F. , Kippenhan J. Shane 
Published: November 2020

AbstractThe ubiquitous adoption of linearity for quantitative explanatory variables in statistical modeling is likely attributable to its advantages of straightforward interpretation and computational feasibility. The linearity assumption may be a reasonable approximation especially when the variable is confined within a narrow range, but it can be problematic when the variable’s effect is non-monotonic or complex. Furthermore, visualization and model assessment of a linear fit are usually omitted because of challenges at the whole brain level in neuroimaging. By adopting a principle of learning from the data in the presence of uncertainty to resolve the problematic aspects of conventional polynomial fitting, we introduce a flexible and adaptive approach of multilevel smoothing splines (MSS) to capture any nonlinearity of a quantitative explanatory variable for population-level neuroimaging data analysis. With no prior knowledge regarding the underlying relationship other than a parsimonious assumption about the extent of smoothness (e.g., no sharp corners), we express the unknown relationship with a sufficient number of smoothing splines and use the data to adaptively determine the specifics of the nonlinearity. In addition to introducing the theoretical framework of MSS as an efficient approach with a counterbalance between flexibility and stability, we strive to (a) lay out the specific schemes for population-level nonlinear analyses that may involve task (e.g., contrasting conditions) and subject-grouping (e.g., patients vs controls) factors; (b) provide modeling accommodations to adaptively reveal, estimate and compare any nonlinear effects of an explanatory variable across the brain, or to more accurately account for the effects (including nonlinear effects) of a quantitative confound; (c) offer the associated program 3dMSS to the neuroimaging community for whole-brain voxel-wise analysis as part of the AFNI suite; and (d) demonstrate the modeling approach and visualization processes with a longitudinal dataset of structural MRI scans.
Chemical signatures of human odour generate a unique neural code in the brain ofAedes aegyptimosquitoes
Authors: Zhao Zhilei , Zung Jessica L. , Kriete Alexis L. , Iqbal Azwad , Younger Meg A. , Matthews Benjamin J. , Merhof Dorit , Thiberge Stephan , Strauch Martin , McBride Carolyn S. 
Published: November 2020

AbstractA globally invasive form of the mosquitoAedes aegyptispecializes in biting humans, making it an efficient vector of dengue, yellow fever, Zika, and chikungunya viruses. Host-seeking females strongly prefer human odour over the odour of non-human animals, but exactly how they distinguish the two is not known. Vertebrate odours are complex blends of volatile chemicals with many shared components, making discrimination an interesting sensory coding challenge. Here we show that human and animal odour blends evoke activity in unique combinations of olfactory glomeruli within theAedes aegyptiantennal lobe. Human blends consistently activate a ‘universal’ glomerulus, which is equally responsive to diverse animal and nectar-related blends, and a more selective ‘human-sensitive’ glomerulus. This dual signal robustly distinguishes humans from animals across concentrations, individual humans, and diverse animal species. Remarkably, the human-sensitive glomerulus is narrowly tuned to the long-chain aldehydes decanal and undecanal, which we show are consistently enriched in (though not specific to) human odour and which likely originate from unique human skin lipids. We propose a model of host-odour coding wherein normalization of activity in the human-sensitive glomerulus by that in the broadly-tuned universal glomerulus generates a robust discriminatory signal of the relative concentration of long-chain aldehydes in a host odour blend. Our work demonstrates how animal brains may distil complex odour stimuli of innate biological relevance into simple neural codes and reveals novel targets for the design of next-generation mosquito-control strategies.