bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental and social analysis as risk factors for the spread of the novel coronavirus (SARS-CoV-2) using remote sensing, GIS and analytical hierarchy process (AHP): Case of Peru
Authors: Badillo-Rivera Edwin , Fow-Esteves Anthony , Alata-López Fernando , Virú-Vásquez Paul , Medina-Acuña Martha 
Published: June 2020

ABSTRACTThe novel coronavirus disease (COVID-19) generated by the SARS-CoV-2 virus was originated in the city of Wuhan (China) in December 2019, the virus began to spread in other regions of China until it spread to the rest of the world. In this research, an analysis was made of environmental factors (tropospheric column of NO2, vertical airflow, percentage of solid waste disposed of in open dumps and percentage of the population without any mechanism of faeces disposal) and social factors (levels of monetary poverty, percentage of the number of hospitals per population and vulnerable population) that could directly and indirectly affect the spread of SARS-CoV-2 virus in the regions of Peru. Remote sensing techniques, geographic information systems and an analysis under the multi-parametric statistical approach proposed by Saaty were used to determine which regions present greater susceptibility, vulnerability and risk of spreading the SARS-CoV-2 virus. The results show that the prevalence of high values of tropospheric NO2and values close to 0 Pa/s of the vertical airflow were directly related to the number of positive cases by COVID-19. In addition, it was found that 68% of the regions of Peru are at a “high” and “very high” risk of spreading SARS-CoV-2 virus, and most of them are in northern and central Peru (Callao, Tumbes, Piura, Loreto, Lambayeque, Huancavelica, Amazonas, Cajamarca, Ucayali, Huanuco and among others), therefore, special care should be taken with the measures adopted after social isolation in order to avoid the resurgence and collapse of the of health systems. It concludes that public policies on air quality management, integrated solid waste management and sanitation services should be improved in order to reduce the risk of spreading the SARS-CoV-2 virus. This research can be replicated on a longer scale, including more variables.HIGHLITGHS68% of the regions are at a “high” and “very high” risk of spreading of SARS-CoV-2Tropospheric NO2 concentration and number of cases of COVID-19 are related directlyCases of COVID-19 are linked to tropospheric NO2 and vertical airflow to 0 Pa/sEnvironmental and social factors are analyzed together in the regions of Peru
Lineage and Spatial Mapping of Glioblastoma-associated Immunity
Authors: Ravi Vidhya M. , Neidert Nicolas , Will Paulina , Joseph Kevin , Maier Julian P. , Kückelhaus Jan , Vollmer Lea , Goeldner Jonathan M , Behringer Simon P. , Scherer Florian , Boerries Melanie , Follo Marie , Weiss Tobias , Delev Daniel , Kernbach Julius , Franco Pamela , Schallner Nils , Dierks Christine , Carro Maria Stella , Hofmann Ulrich G. , Fung Christian , Beck Jürgen , Sankowski Roman , Prinz Marco , Schnell Oliver , Henrik Heiland Dieter 
Published: June 2020

SummaryThe diversity of molecular states and cellular plasticity of immune cells in the glioblastoma environment is still poorly understood. Here, we performed scRNA sequencing of the immune compartment and mapped potential cellular interactions leading to an immunosuppressive microenvironment and dysfunction of T cells. Through inferring the dynamic adaptation during T cell activation, we identified three different terminal states with unique transcriptional programs. Modeling of driver genes for terminal T cell fate identified IL-10 signaling alterations in a subpopulation of HAVCR2(+) T cells. To explore in depth cellular interactions, we established anin-silicomodel by the integration of spatial transcriptomic and scRNA-sequencing, and identified a subset of HMOX1+myeloid cells defined by IL10 release leading to T cell exhaustion. We found a spatial overlap between HMOX(+) myeloid and HAVCR2(+) T cells, suggesting that myeloid-lymphoid interaction causes immunosuppression present in tumor regions with enriched mesenchymal gene expression. Using human neocortical GBM model, coupled with patient-derived T cells, we confirmed that the functional interaction between myeloid and lymphoid cells, leads to a dysfunctional state of T cells. This IL-10 driven T cell exhaustion was found to be rescued by JAK/STAT inhibition. A comprehensive understanding of the cellular states and plasticity of lymphoid cells in GBM will aid towards successful immunotherapeutic approaches.
Brain Tumor IDH, 1p/19q, and MGMT Molecular Classification Using MRI-based Deep Learning: Effect of Motion and Motion Correction
Authors: Nalawade Sahil S. , Yu Fang F. , Bangalore Yogananda Chandan Ganesh , Murugesan Gowtham K. , Shah Bhavya R. , Pinho Marco C. , Wagner Benjamin C. , Mickey Bruce , Patel Toral R. , Fei Baowei , Madhuranthakam Ananth J. , Maldjian Joseph A. 
Published: June 2020

AbstractDeep learning has shown promise for predicting glioma molecular profiles using MR images. Before clinical implementation, ensuring robustness to real-world problems, such as patient motion, is crucial. We sought to evaluate the effects of motion artifact on glioma marker classifier performance and develop a deep learning motion correction network to restore classification accuracies. T2w images and molecular information were retrieved from the TCIA and TCGA databases. Three-fold cross-validation was used to train and test the motion correction network on artifact-corrupted images. We then compared the performance of three glioma marker classifiers (IDH mutation, 1p/19q codeletion, and MGMT methylation) using motion-corrupted and motion-corrected images. Glioma marker classifier performance decreased markedly with increasing motion corruption. Applying motion correction effectively restored classification accuracy for even the most motion-corrupted images. For IDH classification, an accuracy of 99% was achieved, representing a new benchmark in non-invasive image-based IDH classification and exceeding the original performance of the network. Robust motion correction can enable high accuracy in deep learning MRI-based molecular marker classification rivaling tissue-based characterization.STATEMENT OF SIGNIFICANCEDeep learning networks have shown promise for predicting molecular profiles of gliomas using MR images. We demonstrate that patient motion artifact, which is frequently encountered in the clinic, can significantly impair the performance of these algorithms. The application of robust motion correction algorithms can restore the performance of these networks, rivaling tissue-based characterization.
Haplotype-Resolved Assembly for Synthetic Long Reads Using a Trio-Binning Strategy
Authors: Xu Mengyang , Guo Lidong , Du Xiao , Li Lei , Deng Li , Wang Ou , Ni Ming , Yang Huanming , Xu Xun , Liu Xin , Huang Jie , Fan Guangyi 
Published: June 2020

ABSTRACTThe accuracy and completeness of genome haplotyping are crucial for characterizing the relationship between human disease susceptibility and genetic variations, especially for the heterozygous variations. However, most of current variations are unphased genotypes, and the construction of long-range haplotypes remains challenging. We introduced ade novohaplotype-resolved assembly tool, HAST that exports two haplotypes of a diploid species for synthetic long reads with trio binning. It generates parental distinguishingk-mer libraries, partitions reads from the offspring according to the unique markers, and individually assembles them to resolve the haplotyping problem. Based on the stLFR co-barcoding data of an Asian as well as his parental massive parallel sequencing data, we utilized HAST to recover both haplotypes with a scaffold N50 of >11 Mb and an assembly accuracy of 99.99995% (Q63). The complete and accurate employment of long-range haplotyping information provided sub-chromosome level phase blocks (N50 ∼13 Mb) with 99.6% precision and 94.1% recall on average. We suggest that the accurate and efficient approach accomplishes the regeneration of the haplotype chromosomes with trio binning, thus promoting the determination of haplotype phase, the heterosis of crossbreeding, and the formation of autopolyploid and allopolyploid.
Trends and gaps in the use of citizen science derived data as input for species distribution models: a quantitative review
Authors: Feldman Mariano J. , Imbeau Louis , Marchand Philippe , Mazerolle Marc J. , Darveau Marcel , Fenton Nicole J. 
Published: June 2020

AbstractCitizen science (CS) currently refers to some level of volunteer participation in any discipline of scientific research. Over the last two decades, nature-based CS has flourished due to innovative technology, novel devices, and widespread digital platforms used to collect and classify species occurrence data. For scientists, CS offers a low-cost approach of collecting species occurrence information at large spatial scales that otherwise would be prohibitively expensive. We examined the trends and gaps linked to the use of CS as a source of data for species distribution models (SDMs), in order to propose guidelines and highlight solutions. We conducted a quantitative literature review of 224 peer-reviewed articles to measure how the representation of different taxa, regions, and data types have changed in SDM publications since the 2010s. Our review shows that the number of papers using CS for SDMs has increased at approximately double the rate of the overall number of SDM papers. However, disparities in taxonomic and geographic coverage remain in studies using CS. Western Europe and North America were the regions with the most coverage (71.2%). Papers on birds (51.2%) and mammals (26.2%) outnumbered other taxa. Among invertebrates, flying insects including Lepidoptera and Odonata received the most attention. Compared to studies on animal taxa, papers on plants using CS data remain rare. Although the aims and scope of SDM papers are diverse, conservation remained the central theme of SDM using CS data. We present examples of the use of CS and highlight recommendations to motivate further research, such as combining multiple data sources and promoting local and traditional knowledge. We hope our findings will strengthen citizen-researchers partnerships to better inform SDMs, especially for less-studied taxa and regions. Researchers stand to benefit from the large quantity of data available from CS sources to improve global predictions of species distributions.
Hemodynamic and electromechanical effects of paraquat in rat heart
Authors: Lin Chih-Chuan , Hsu Kuang-Hung , Chang Gwo-Jyh 
Published: June 2020

AbstractParaquat (PQ) is a highly lethal herbicide. Ingestion of large quantities of PQ usually results in cardiovascular collapse and eventually death. However, the mechanism of acute PQ poisoning induced cardiotoxicity is poorly understood. Therefore, the purpose of the present study was to aim to investigate the mechanisms of PQ induced cardiotoxicity by examining the effects of PQ on hemodynamics in vivo, as well as in vitro on isolated hearts and ventricular myocytes in rats. Intravenous administration of PQ (100 or 180 mg/kg) in anesthetized rats induced dose-dependent decreases in heart rate, blood pressure, and cardiac contractility (left ventricular [LV] dP/dtmax). Furthermore, it prolonged the rate-corrected QT (QTc) interval. In Langendorff-perfused isolated hearts, PQ (33 or 60 μM) decreased LV pressure and contractility (LV dP/dtmaxin isolated ventricular myocytes), PQ (10–60 μM) decreased the amplitude of Ca2+transients and cell shortening in a concentration-dependent manner. Patch-clamp experiments demonstrated that PQ decreased the amplitude and availability of the transient outward K+channel (Ito) and altered its gating kinetics. These results suggest that PQ-induced cardiotoxicity results mainly from diminished Ca2+transients and inhibited K+channels, which lead to the suppression of LV contractile force and prolongation of the QTc interval.
Autophagy in T cells from aged donors is maintained by spermidine, and correlates with function and vaccine responses
Authors: Alsaleh Ghada , Panse Isabel , Swadling Leo , Zhang Hanlin , Meyer Alain , Lord Janet , Barnes Eleanor , Klenerman Paul , Green Christopher , Simon Anna Katharina 
Published: June 2020

AbstractOlder adults are at high risk for infectious diseases such as the recent COVID-19 and vaccination seems to be the only long-term solution to the pandemic. While most vaccines are less efficacious in older adults, little is known about the molecular mechanisms that underpin this. Autophagy, a major degradation pathway and one of the few processes known to prevent aging, is critical for the maintenance of immune memory in mice. Here, we show induction of autophagy is specifically induced in human vaccine-induced antigen-specific T cellsin vivo. Reduced IFNγ secretion by vaccine-induced T cells in older vaccinees correlates with low autophagy. We demonstrate in human cohorts that levels of the endogenous autophagy-inducing metabolite spermidine, fall with age and supplementing itin vitrorecovers autophagy and T cell function. Finally, our data show that endogenous spermidine maintains autophagy via the translation factor eIF5A and transcription factor TFEB. With these findings we have uncovered novel targets and biomarkers for the development of anti-aging drugs for human T cells, providing evidence for the use of spermidine in improving vaccine immunogenicity in the aged human population.
Modelling parameter uncertainty reveals bushmeat yields versus survival trade-offs in heavily-hunted duikerCephalophusspp.
Authors: Barychka Tatsiana , Purves Drew W. , Milner-Gulland E.J. , Mace Georgina M. 
Published: June 2020

AbstractReliably predicting sustainable exploitation levels for many tropical species subject to hunting remains a difficult task, largely because of the inherent uncertainty associated with estimating parameters related to both population dynamics and hunting pressure. Here, we investigate a modelling approach to support decisions in bushmeat management which explicitly considers parameter uncertainty. We apply the approach to duikerCephalophusspp., assuming either a constant quota-based, or a constant proportional harvesting, strategy. Within each strategy, we evaluate different hunting levels in terms of both average yield and survival probability, over different time horizons. Under quota-based harvesting, considering uncertainty revealed a trade-off between yield and extinction probability that was not evident when ignoring uncertainty. The highest yield was returned by a quota that implied a 40% extinction risk, whereas limiting extinction risk to 10% reduced yield by 50%-70%. By contrast, under proportional harvesting, there was no trade-off between yield and extinction probability. The maximum proportion returned a yield comparable with the maximum possible under quota-based harvesting, but with extinction risk below 10%. However, proportional harvesting can be harder to implement in practice because it depends on an estimate of population size. In both harvesting approaches, predicted yields were highly right-skewed with median yields differing from mean yields, implying that decision outcomes depend on attitude to risk. The analysis shows how an explicit consideration of all available information, including uncertainty, can, as part of a wider process involving multiple stakeholders, help inform harvesting policies.
Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations
Authors: Hemez Colin , Clarelli Fabrizio , Palmer Adam C. , Chindelevitch Leonid , Cohen Theodore , Abel zur Wiesch Pia 
Published: June 2020

AbstractAntibiotic-resistant pathogens are a major public health threat. A deeper understanding of how an antibiotic’s mechanism of action influences the emergence of resistance would aid in the design of new drugs and help to preserve the effectiveness of existing ones. To this end, we developed a model that links bacterial population dynamics with antibiotic-target binding kinetics. Our approach allows us to derive mechanistic insights on drug activity from population-scale experimental data and to quantify the interplay between drug mechanism and resistance selection. We find that whether a drug acts as a bacteriostatic or bactericidal agent has little influence on resistance selection. We also show that heterogeneous drug-target binding within a population enables resistant bacteria to evolve fitness-improving secondary mutations even when drug doses remain above the resistant strain’s minimum inhibitory concentration. Our work suggests that antibiotic doses beyond this “secondary mutation selection window” could safeguard against the emergence of high-fitness resistant strains during treatment.
Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection
Authors: Ding Jun , Lugo-Martinez Jose , Yuan Ye , Huang Jessie , Hume Adam J. , Suder Ellen L. , Mühlberger Elke , Kotton Darrell N. , Bar-Joseph Ziv 
Published: June 2020

AbstractSeveral molecular datasets have been recently compiled to characterize the activity of SARS-CoV-2 within human cells. Here we extend computational methods to integrate several different types of sequence, functional and interaction data to reconstruct networks and pathways activated by the virus in host cells. We identify key proteins in these networks and further intersect them with genes differentially expressed at conditions that are known to impact viral activity. Several of the top ranked genes do not directly interact with virus proteins. We experimentally tested treatments for a number of the predicted targets. We show that blocking one of the predicted indirect targets significantly reduces viral loads in stem cell-derived alveolar epithelial type II cells (iAT2s).Software and interactive visualizationhttps://github.com/phoenixding/sdremsc
Neonatal hyperoxia inhibits proliferation of atrial cardiomyocytes by suppressing fatty acid synthesis
Authors: Cohen Ethan David , Yee Min , Porter George A. , McDavid Andrew N. , Brookes Paul S. , Pryhuber Gloria S. , O’Reilly Michael A. 
Published: June 2020

ABSTRACTPreterm birth increases the risk for pulmonary hypertension and heart failure in adulthood. Oxygen therapy can damage the immature cardiopulmonary system and may be partially responsible for the cardiovascular disease in adults born preterm. We previously showed that exposing newborn mice to hyperoxia causes pulmonary hypertension by 1 year of age that is preceded by a poorly understood loss of pulmonary vein cardiomyocyte proliferation. We now show that hyperoxia also inhibits the proliferation of left atrial cardiomyocytes and causes diastolic heart failure by thinning the walls of the left atrium and disrupting its ability to pump effectively. Transcriptomic profiling showed that neonatal hyperoxia permanently suppressed fatty acid synthase (Fasn), stearoyl-CoA desaturase 1 (Scd1) and other fatty acid synthesis genes in the atria of mice, the HL-1 line of mouse atrial cardiomyocytes and left atrial tissue explanted from human infants. SuppressingFasnorScd1reduced HL-1 cell proliferation while overexpressing these genes maintained their expansion in hyperoxic conditions, suggesting hyperoxia directly inhibits atrial cardiomyocyte proliferation by repressingFasnandScd1. Pharmacologic interventions that restoreFasn, Scd1and other fatty acid synthesis genes in atrial cardiomyocytes may thus provide a way of ameliorating the adverse effects of supplemental oxygen on preterm infants.
Transport mechanism of the neuronal excitatory amino acid transporter
Authors: Qiu Biao , Matthies Doreen , Fortea Eva , Yu Zhiheng , Boudker Olga 
Published: June 2020

AbstractHuman excitatory amino acid transporter 3 (hEAAT3) mediates glutamate uptake in neurons, intestine, and kidney. Here, we report Cryo-EM structures of hEAAT3 in several functional states where the transporter is empty, bound to coupled sodium ions only, or fully loaded with three sodium ions, a proton, and the substrate aspartate. The structures suggest that hEAAT3 operates by an elevator mechanism involving three functionally independent subunits. When the substrate-binding site is near the cytoplasm, it has a remarkably low affinity for the substrate, perhaps facilitating its release and allowing for the rapid transport turnover. The mechanism of the coupled uptake of the sodium ions and the substrate is conserved across evolutionarily distant families and is augmented by coupling to protons in EAATs. The structures further suggest a mechanism by which conserved glutamate mediates proton symport.
Neural population dynamics underlying expected value computation
Authors: Yamada Hiroshi , Imaizumi Yuri , Matsumoto Masayuki 
Published: June 2020

AbstractComputation of expected values, i.e., probability times magnitude, seems to be a dynamic integrative process performed in the brain for efficient economic behavior. However, neural dynamics underlying this computation remain largely unknown. We examined (1) whether four core reward-related regions detect and integrate the probability and magnitude cued by numerical symbols and (2) whether these regions have distinct dynamics in the integrative process. Extractions of mechanistic structure of neural population signal demonstrated that expected-value signals simultaneously arose in central part of orbitofrontal cortex (cOFC, area 13m) and ventral striatum (VS). These expected-value signals were incredibly stable in contrast to weak and/or fluctuated signals in dorsal striatum and medial OFC. Notably, temporal dynamics of these stable expected-value signals were unambiguously distinct: sharp and gradual signal evolutions in cOFC and VS, respectively. These intimate dynamics suggest that cOFC and VS compute the expected-values with unique time constants, as distinct, partially overlapping processes.
Scale-dependent influences of distance and vegetation on the composition of aboveground and belowground tropical fungal communities
Authors: Boraks Andre , Plunkett Gregory M. , Doro Thomas , Alo Frazer , Sam Chanel , Tuiwawa Marika , Ticktin Tamara , Amend Anthony S. 
Published: June 2020

AbstractFungi provide essential ecosystem services and engage in a variety of symbiotic relationships with trees. In this study, we investigate the spatial relationship of trees and fungi at a community level. We characterized the spatial dynamics for above- and belowground fungi using a series of forest monitoring plots, at nested spatial scales, located in the tropical South Pacific. Fungal communities exhibited strong distance decay of similarity across our entire sampling range (3–110,000 m), and also at small spatial scales (< 50 m). Unexpectedly, this pattern was inverted at an intermediate scale (3.7–26 km). At large scales (80–110 km), belowground and aboveground fungal communities responded inversely to increasing geographic distance.Aboveground fungal communityturnover (beta diversity) was best explained, at all scales, by geographic distance. In contrast,belowground fungal communityturnover was best explained by geographic distance at small scales, and tree community composition at large scales. We demonstrate scale-dependent spatial dynamics of fungal communities, synchronous spatial dynamics for trees and fungi, and the varying influence of habitat versus geographic distance in structuring Soil,Selaginella sp.,and Understory fungal communities.