bluuebunny/crossref_metadata_2025_split huggingface dataset:
BET Protein Inhibition Prolongs Cardiac Transplant Survival via Enhanced Myocardial Autophagy
Authors: Chen Juntao , Miao Xiaolong , Liu Chen , Liu Baoqing , Wu Xiaoying , Kong Deqiang , Sun Qiming , Gong Weihua 
Published: May 2020

Background.
Graft rejection continues to be a major barrier to long-term engraftment after transplantation. Autophagy plays an important role in cardiac injury pathogenesis. The bromodomain and extraterminal protein inhibitor (S)-tert-butyl2-(4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)acetate (JQ1) inhibits inflammatory responses. However, the beneficial effect of JQ1 on transplant and the potential role of autophagy in the protective effect of graft survival are yet to be investigated.

Methods.
Syngeneic or allogeneic heterotopic heart transplantation was performed using C57BL/6 or BALB/c donors for C57BL/6 recipients through different treatments. Some mice were used to observe the survival of the grafts. The other mice were euthanized on the third, fifth, and seventh days after surgery. The graft samples were taken for cytokines and autophagy pathway analyses.

Results.
Our study revealed that JQ1 treatment prolonged cardiac allograft survival. JQ1 increased the expression levels of liver kinase beta 1, autophagy-specific gene 5, and microtubule-associated protein light chain3-II (LC3-II) and potentiated the phosphorylation of AMP-activated protein kinase, unc-51-like kinase 1 (ULK1), and autophagy-specific gene 14 in allografts. A conditional autophagy-specific gene 5 deletion donor was utilized to abrogate the effect induced by JQ1. The combined use of JQ1 with bafilomycin A1 partially reversed the effect of JQ1, suggesting that autophagy is involved in the signaling pathway in graft survival. JQ1 downregulated the expression of inflammatory cytokines, such as interleukin-6, interleukin-1β, tumor necrosis factor-α, and interferon-γ, which was abrogated when autophagy was inhibited.

Conclusions.
JQ1 prolonged cardiac allograft survival by potentiating myocardial autophagy through the liver kinase beta 1–AMP-activated protein kinase–ULK1 signaling pathway and inhibiting the subsequent release of inflammatory cytokines. This result might provide novel insights for extending transplant survival.
Predictive value of Altmetric Score on prospective citation and bibliometric impact: rise of a new argot
Authors: Robinson David BT , Powell Arfon GMT , Waterman Jennifer , Hopkins Luke , James Osian P , Egan Richard J , Lewis Wyn G 
Published: May 2020

AbstractBackgroundBibliometric and Altmetric analyses provide important but alternative perspectives regarding research article impact. This study aimed to establish whether Altmetric Score (AS) was associated with citation rate, independent of bibliometrics.MethodCitations for a previously reported cohort of 100 most cited articles associated with the keyword “Surgery” (2018, Powellet al), were collected and a three-year interval Citation Gain (iCG) evaluated. Previous citation count, Citation Rate Index (CRI), AS, five-year Impact Factor, and Oxford Centre for Evidence Based Medicine (OCEBM) levels were used to classify citation rate prospect.ResultsDuring follow-up, the median iCG was 161 (IQR 83–281), with 73 and 62 articles receiving an increase in CRI and AS, respectively. Median CRI and AS increase were 2.8 (−0.1–7.7) and 3 (0–4), respectively. Receiver-Operator-Characteristic (ROC) analysis revealed that CRI (AUC 0.86 (95% CI 0.79–0.93), p<0.001) and AS (Area Under Curve (AUC) 0.65 (95% CI 0.55–0.76), p=0.008) were associated with higher iCG. AS critical threshold ≥ 2.0 was associated with better iCG when dichotomised at iCG median (OR=4.94, 95% CI 1.99–12.26, p=0.001) and iCG Upper Quartile (UQ, OR=4.13, 95% CI 1.60–10.66, p=0.003). Multivariable analysis identified that only CRI was independently associated with iCG when dichotomised at the median (OR 18.22, 95% CI 6.70–49.55, p<0.001) and UQ (OR 19.30, 95% CI 4.23–88.15, p<0.001).ConclusionCitation Rate Indices and Altmetric Scores are important predictors of interval Citation Gain, and better at predicting future citations than the historical and established Impact Factor and OCEBM quality of evidence descriptors.
Global Analysis of an SEIRS Model for COVID-19 Capturing Saturated Incidence with Treatment Response
Authors: Oluyori David A. , Adebayo Helen O. , Pérez Ángel G. C. 
Published: May 2020

AbstractSequel to V. A. Okhuese [Mathematical Predictions for COVID-19 as a Global Pandemic, medRxiv, 2020, https://doi.org/10.1101/2020.03.19.20038794], who studied the dynamics of COVID-19 using an SEIRUS model. We consider an SEIRS model capturing saturated incidence with treatment response. In this theoretical model, we assumed that the treatment response is proportional to the number of infected as long as the incidence cases are within the capacity of the healthcare system, after which the value becomes constant, when the number of confirmed cases exceed the carrying capacity of the available medical facilities. Thus, we obtain the reproduction number stating that when R0 is less than a critical value R, the disease-free equilibrium is globally asymptotically stable. Also, we studied the existence of the local and global stability of the disease-free and endemic equilibria and found that the kind of treatment response and inhibitory measures deployed in tackling the COVID-19 pandemic determines whether the disease will die out or become endemic.
Empirical Assessment of COVID-19 Crisis Standards of Care Guidelines
Authors: Jezmir Julia L. , Bharadwaj Maheetha , Kishore Sandeep P. , Winkler Marisa , Diephuis Bradford , Kim Edy Y. , Feldman William B. 
Published: May 2020

AbstractBackgroundSeveral states have released Crisis Standards of Care (CSC) guidelines for the allocation of scarce critical care resources. Most guidelines rely on Sequential Organ Failure Assessment (SOFA) scores to maximize lives saved, but states have adopted different stances on whether to maximize long-term outcomes (life-years saved) by accounting for patient comorbidities.MethodsWe compared 4 representative state guidelines with varying approaches to comorbidities and analyzed how CSC prioritization correlates with clinical outcomes. We included 27 laboratory-confirmed COVID-19 patients admitted to ICUs at Brigham and Women’s Hospital from March 12 to April 3, 2020. We compared prioritization algorithms from New York, which assigns priority based on SOFA alone; Maryland, which uses SOFA plus severe comorbidities; Pennsylvania, which uses SOFA plus major and severe comorbidities; and Colorado, which uses SOFA plus a modified Charlson comorbidity index.ResultsIn pairwise comparisons across all possible pairs, we found that state guidelines frequently resulted in tie-breakers based on age or lottery: New York 100% of the time (100% resolved by lottery), Pennsylvania 86% of the time (18% by lottery), Maryland 93% of the time (35% by lottery), and Colorado: 32% of the time (10% by lottery). The prioritization algorithm with the strongest correlation with 14-day outcomes was Colorado (rs = −0.483. p = 0.011) followed by Maryland (rs = −0. 394, p =0.042), Pennsylvania (rs = −0.382, p = 0.049), and New York (rs = 0). An alternative model using raw SOFA scores alone was moderately correlated with outcomes (rs = −0.448, p = 0.019).ConclusionsState guidelines for scarce resource allocation frequently resulted in identical priority scores, requiring tie-breakers based on age or lottery. These findings suggest that state CSC guidelines should be further assessed empirically to understand whether they meet their goals.
Plasma and Fecal Metabolite Profiles in Autism Spectrum Disorder
Authors: Needham Brittany D. , Adame Mark D. , Serena Gloria , Rose Destanie R. , Preston Gregory M. , Conrad Mary C. , Campbell A. Stewart , Donabedian David H. , Fasano Alessio , Ashwood Paul , Mazmanian Sarkis K. 
Published: May 2020

ABSTRACTAutism Spectrum Disorder (ASD) is a neurodevelopmental condition with hallmark behavioral manifestations including impaired social communication and restricted repetitive behavior. In addition, many affected individuals display metabolic imbalances, immune dysregulation, gastrointestinal (GI) dysfunction, and altered gut microbiome compositions. We sought to better understand non-behavioral features of ASD by determining molecular signatures in peripheral tissues. Herein, we present the untargeted metabolome of 231 plasma and 97 fecal samples from a large cohort of children with ASD and typically developing (TD) controls. Differences in lipid, amino acid, and xenobiotic metabolism discriminate ASD and TD samples. We reveal correlations between specific metabolite profiles and clinical behavior scores, and identify metabolites particularly associated with GI dysfunction in ASD. These findings support a connection between GI physiology, metabolism, and complex behavioral traits, and may advance discovery and development of molecular biomarkers for ASD.
Genome-wide effects of the antimicrobial peptide apidaecin on translation termination
Authors: Mangano Kyle , Florin Tanja , Shao Xinhao , Klepacki Dorota , Chelysheva Irina , Ignatova Zoya , Gao Yu , Mankin Alexander S. , Vázquez-Laslop Nora 
Published: May 2020

AbstractBiochemical studies suggested that the antimicrobial peptide apidaecin (Api) inhibits protein synthesis by binding in the nascent peptide exit tunnel and trapping the release factor associated with a terminating ribosome. The mode of Api action in bacterial cells had remained unknown. Here, genome-wide analysis revealed that Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing ribosomes. By sequestering the available release factors, Api promotes pervasive stop codon bypass, leading to expression of proteins with C-terminal extensions. Api-mediated translation arrest leads to futile activation of the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may facilitate development of new medicines and research tools for genome exploration.
An updated global COI barcode reference data set for Fall Armyworm (Spodoptera frugiperda) and first record of this species in Bhutan
Authors: Mahat Kiran , Mitchell Andrew , Zangpo Tshelthrim 
Published: May 2020

AbstractWe report the first detection of Fall Armyworm (FAW),Spodoptera frugiperda(Smith, 1797), in Bhutan. FAW feeds on more than 300 plant species and is a serious pest of many. It has been spreading through Africa since 2016 and Asia since 2018. In Bhutan, this species was first detected in maize fields in the western part of the country in September 2019 and subsequently found infesting maize crop in southern parts of the country in December 2019 and April 2020. Using morphological and molecular techniques the presence of the first invading populations ofS. frugiperdain Bhutan is confirmed through this study. We present an updated reference DNA barcode data set for FAW comprising 374 sequences, which can be used to reliably identify this serious pest species, and discuss some of the reasons why such compiled reference data sets are necessary, despite the publicly availability of the underlying data. We also report on a second armyworm species, the Northern Armyworm,Mythimna separata(Walker, 1865), in rice, maize and other crops in eighteen districts of Bhutan.
Workstation benchmark of Spark Capable Genome Analysis ToolKit 4 Variant Calling
Authors: Hansen Marcus H. , Simonsen Anita T. , Ommen Hans B. , Nyvold Charlotte G. 
Published: May 2020

AbstractBackgroundRapid and practical DNA-sequencing processing has become essential for modern biomedical laboratories, especially in the field of cancer, pathology and genetics. While sequencing turn-over time has been, and still is, a bottleneck in research and diagnostics, the field of bioinformatics is moving at a rapid pace – both in terms of hardware and software development. Here, we benchmarked the local performance of three of the most important Spark-enabled Genome analysis toolkit 4 (GATK4) tools in a targeted sequencing workflow: Duplicate marking, base quality score recalibration (BQSR) and variant calling on targeted DNA sequencing using a modest hyperthreading 12-core single CPU and a high-speed PCI express solid-state drive.ResultsCompared to the previous GATK version the performance of Spark-enabled BQSR and HaplotypeCaller is shifted towards a more efficient usage of the available cores on CPU and outperforms the earlier GATK3.8 version with an order of magnitude reduction in processing time to analysis ready variants, whereas MarkDuplicateSpark was found to be thrice as fast. Furthermore, HaploTypeCallerSpark and BQSRPipelineSpark were significantly faster than the equivalent GATK4 standard tools with a combined ∼86% reduction in execution time, reaching a median rate of ten million processed bases per second, and duplicate marking was reduced ∼42%. The called variants were found to be in close agreement between the Spark and non-Spark versions, with an overall concordance of 98%. In this setup, the tools were also highly efficient when compared execution on a small 72 virtual CPU/18-node Google Cloud cluster.ConclusionIn conclusion, GATK4 offers practical parallelization possibilities for DNA sequence processing, and the Spark-enabled tools optimize performance and utilization of local CPUs. Spark utilizing GATK variant calling is several times faster than previous GATK3.8 multithreading with the same multi-core, single CPU, configuration. The improved opportunities for parallel computations not only hold implications for high-performance cluster, but also for modest laboratory or research workstations for targeted sequencing analysis, such as exome, panel or amplicon sequencing.
OPTIONAL VACCINE UTILIZATION HAS A MALE GENDER PREFERENCE – A RECORD BASED ANALYSIS FROM A TERTIARY CARE CENTRE OF EASTERN INDIA
Authors: Panigrahi Sandeep Kumar , Maiti Anumita , Epari Venkatarao 
Published: May 2020

ABSTRACTBackground And ObjectivesOptional vaccines find an important place in immunization today. This study attempts to find out the trend of optional vaccine utilization, over the past three years in the immunization clinic of a tertiary care centre and to find out the association of gender disparity with the utilization of these vaccines.MethodsThe retrospective study was conducted during October to December 2016 using the register based secondary data of October 2013 to September 2016. Month wise utilization of optional vaccines (Pneumococcal, influenza, typhoid, varicella, hepatitis A and MMR) and measles was captured. Analysis was done using Stata 12.1 SE.ResultsAn increasing trend of utilization was seen for all vaccines including optional vaccines. The mean doses received by male children was significantly more for all optional vaccines (unlike all vaccines taken together) as well as for individual vaccines like Pneumococcal, influenza, typhoid, MMR, hepatitis A (p<0.05), but not for varicella and measles vaccine (p>0.05).ConclusionGender disparity (preference for male children) was present for all optional vaccines except varicella, and not in case of measles vaccine used in universal immunization program selected as control.Author’s noteWhat is already known on this subjectDifferences in uptake are related to various factors in national immunization program of India.Optional vaccines are not a part of the national immunization program,There is no clarity regarding pattern and trend of use and gender differences, if any for optional vaccines.What this study addsTrend of optional vaccine uptake is on the rise reflecting increasing demand among parents.Gender differences do not exist for vaccines covered under national immunization program, as seen for Measles vaccine, probably because of universalization.Preference for male children exists for most of the optional vaccines (even for MMR) probably because of the cost involved.Gender disparity was absent in Varicella, probably because of fear of parents for scar marks on face of their girl child.
Metamorphosis of COVID-19 Pandemic
Authors: Saif Farhan 
Published: May 2020

AbstractWe show phase-wise growth of COVID 19 pandemic and explain it by comparing real time data with Discrete Generalized Growth model and Discrete Generalized Richard Model. The comparison of COVID 19 is made for China, Italy, Japan and the USA. The mathematical techniques makes it possible to calculate the rate of exponential growth of active cases, estimates the size of the outbreak, and measures the deviation from the exponential growth indicating slowing down effect. The phase-wise pandemic evolution following the real time data of active cases defines the impact-point when the preventive steps, taken to eradicate the pandemic, becomes effective. The study is important to devise the measures to handle emerging threat of similar COVID-19 outbreaks in other countries, especially in the absence of a medicine.
Cadherin-11 is required for neural crest determination and survival
Authors: Manohar Subrajaa , Camacho Alberto , Rogers Crystal D. 
Published: May 2020

AbstractNeural crest (NC) cells are multipotent embryonic cells that form melanocytes, craniofacial bone and cartilage, and the peripheral nervous system in vertebrates. NC cells express many cadherin proteins, which control their specification, epithelial to mesenchymal transition (EMT), migration, and mesenchymal to epithelial transition. Abnormal NC development leads to congenital defects including craniofacial clefts as well as NC-derived cancers. Here, we identify the role of the type II cadherin protein, Cadherin-11 (CDH11), in early chicken NC development. CDH11 is crucial for NC cell migration in amphibian embryos and is linked to cell survival, proliferation, and migration in cancer cells. It has been linked to the complex neurocristopathy disorder, Elsahy‐Waters Syndrome, in humans. Using immunohistochemistry (IHC), we determined that CDH11 protein has dynamic expression that is first co-localized with neural progenitors in early embryos and subsequently upregulated specifically in NC cells as they are specified in the dorsal neural tube prior to migration. We identified that loss of CDH11 led to a reduction of bonafide NC cells in the dorsal neural tube combined with defects in cell migration and survival. Loss of CDH11 increased p53-mediated programmed-cell death, and blocking the p53 pathway rescued the NC phenotype. Our findings demonstrate an early requirement for CDH11 in NC development, and may increase our understanding of early cadherin-related NC developmental defects.SummaryChicken Cadherin-11 (CDH11), which is expressed in neural crest (NC) cells prior to NC cell migration, is necessary for the determination and survival of the premigratory NC population.
Multi-Antigenic Virus-like Particle of SARS CoV-2 produced inSaccharomyces cerevisiaeas a vaccine candidate
Authors: Arora Kajal , Rastogi Ruchir , Arora Nupur Mehrotra , Parashar Deepak , Paliwal Jeny , Naqvi Aelia , Srivastava Apoorva , Singh Sudhir Kumar , Kalyanaraman Sriganesh , Potdar Swaroop , Kumar Devanand , Arya Vidya Bhushan , Bansal Sarthi , Rautray Satabdi , Singh Indrajeet , Fengade Pankaj Surendra , Kumar Bibekanand , Kundu Prabuddha Kumar 
Published: May 2020

AbstractSpike, Envelope and Membrane proteins from the SARS CoV-2 virus surface coat are important vaccine targets. We hereby report recombinant co-expression of the three proteins (Spike, Envelope and Membrane) in a engineeredSaccharomyces cerevisiaeplatform (D-Crypt™) and their self-assembly as Virus-like particle (VLP). This design as a multi-antigenic VLP for SARS CoV-2 has the potential to be a scalable vaccine candidate. The VLP is confirmed by transmission electron microscopy (TEM) images of the SARS CoV-2, along with supportive HPLC, Dynamic Light Scattering (DLS) and allied analytical data. The images clearly outline the presence of a “Corona” like morphology, and uniform size distribution.
Expanding Biomaterial Surface Topographical Design Space through Natural Surface Reproduction
Authors: Vermeulen Steven , Honig Floris , Vasilevich Aliaksei , Roumans Nadia , Carlier Aurélie , Romero Manuel , Williams Paul , Uquillas Jorge Alfredo , de Boer Jan 
Published: May 2020

AbstractSurface topography guides cell behavior and is a tool to endow biomaterials with bioactive properties. The large number of possible designs makes it challenging to find the optimal surface structure to induce a specific cell response. The TopoChip platform is currently the largest collection of topographies with 2176 in silico designed micro-topographies. Still, it is exploring only a small part of the design space due to the boundary conditions of the design algorithm and the surface engineering strategy. Inspired by the diversity of natural surfaces, we assessed to what extend we could expand the topographical design space and consequently the resulting cellular responses using natural surfaces. To this end, we replicated twenty-six plant and insect surfaces in polystyrene and quantified their surface properties using white light interferometry, image analysis and principle component analysis. Next, we quantified mesenchymal stem cell morphology and the pattern ofPseudomonas aeruginosacolonization and compared it to previous data from TopoChip screens. Our data show that natural surfaces extended the TopoChip design space. Moreover, the natural surfaces induced MSC morphologies and bacterial attachment patterns not previously observed on the TopoChip. In the future, we will train our design algorithms with the results obtained by natural surface imprint experiments to further explore the design space and bio-active properties of surface topography.
Novel insights into the structure and transport mechanisms of TAPT1
Authors: Parvez Md Sorwer Alam , Rahman Mohammad Mahfujur , Morshed Md Niaz , Rahman Dolilur , Anwar Saeed , Coucke Paul J. , Hosen Mohammad Jakir 
Published: May 2020

AbstractTransmembrane anterior-posterior transformation protein 1 (TAPT1), encoded by theTAPT1gene expressed in the basal ciliary body, plays a crucial role in cilia formation as well as axial skeletal patterning. Mutations in this gene have been reported to cause several ciliopathies and osteo-related diseases. Unfortunately, the cellular and molecular pathogenic mechanisms are still unclear also due to the lack of X-ray crystallographic structure and further characterization of TAPT1 protein. In this study, we attempted to characterize this protein byin silicotechniques. A 3D structure of TAPT1 was generated by theab initiomethod, which was further used for the analysis of the substrate-binding site, to determine pore size and for the prediction of the possible substrate(s). Validation by using different software packages revealed a reliable 3D model of TAPT1. Topology modeling revealed that TAPT1 has eight transmembrane helices with a total number of 27 helices in secondary structure. The amino acid residues H235, R323, K443, N446, S447, L450, K453, S454, Y457, K511, N513, D533, K535, D536, and T538 were found to form the pore surface as well as involved in the binding interaction with the substrate(s). This study predicted flavonoids as the possible substrate for TAPT1, which could further be confirmed by ingenuity pathway analysis. Moreover, our analysis indicated that TAPT1 might localize in the mitochondrial membrane in addition to the ciliary basal body. Our study gives novel insights for TAPT1 structure and its function.