bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validating a semi-quantitative method to assess the degree of methylene blue staining in sentinel lymph nodes
Authors: Ram Ann Steffi , Oblak Michelle L , Matuszewska Kathy , Singh Ameet , Petrik Jim 
Published: March 2020

AbstractPurposeTo develop a digital algorithm and validate a semi-quantitative scoring method for surface methylene blue (MB) staining in whole lymph nodes (LN).MethodsLymph nodes from canine models undergoing sentinel lymph node (SLN) mapping were prospectively assessedex vivoand photographed. Two blinded observers evaluated all images and assigned a semi-quantitative score based on surface staining (0 – no blue stain, 1 – 1-50% stained, 2 – 51-100% stained). A standard reference for degree of blue staining was based on signal-to-background ratios using computer-based imaging software with an output measurement of percentage of staining of the LN. Agreement between observers was assessed using the Kappa coefficient.Results124 lymph nodes were included and demonstrated strong agreement (K = 0.8007, p < 0.0001) between results of semi-quantitative scoring and image analysis. Also, strong interobserver and intraobserver agreement was observed for the scoring system (K = 0.8051, p < 0.0001 and K = 0.9493, p < 0.0001, respectively).DiscussionAgreement between the observer-based scoring system and imaging software illustrates a validated method in assessing MB staining, without the need for analysis software. The use of a semi-quantitative scoring system shows promise for a simple, objective assessment of MB staining in surgery and for future study. Lymph nodes can have variable surface colour, which can make assessment of blue staining challenging for novice observers in certain cases. This study describes a digital algorithm for quantitative analysis of blue staining in LN thereby providing a novel and objective reporting mechanism in scientific research involving SLN mapping.
Differential transcript usage unravels gene expression alterations in Alzheimer’s disease human brains
Authors: Marques-Coelho Diego , da Cruz Carvalho Lukas Iohan , de Farias Ana Raquel Melo ,   NeuroCEB Brain Bank, Lambert Jean-Charles , Costa Marcos Romualdo 
Published: March 2020

AbstractAlzheimer’s disease (AD) is the leading cause of dementia in aging individuals. However pathophysiological processes involved in the brain are still poorly understood. Among numerous strategies, a comprehensive overview of gene expression alterations in the diseased brain has been proposed to help for a better understanding of the disease processes. In this work, we probed the differential expression of genes in different brain regions of healthy and AD adult subjects using data from three large studies: MAYO Clinic; Mount Sinai Brain Bank (MSBB) and ROSMAP. Using a combination of differential expression of gene (DEG) and isoform switch analyses we provide a detailed landscape of gene expression alterations in the temporal and frontal lobes, harboring brain areas affected at early and late stages of the AD pathology, respectively. Next, we took advantage of an indirect approach to assign the complex gene expression changes revealed in bulk RNAseq to individual cell types of the adult brain. This strategy allowed us to identify cell type/subtype specific isoform switches in AD brains previously overlooked. This was the case, for example, for the AD causal gene APP and the risk gene BIN1, which presented isoform switches with potential functional consequences in neuronal cells. Altogether, our work proposes a novel integrative strategy to analyze RNAseq data in AD based on both gene/transcript expression and regional/cell-type specificities.
MATHEMATICAL PREDICTIONS FOR COVID-19 AS A GLOBAL PANDEMIC
Authors: Okhuese Victor Alexander 
Published: March 2020

ABSTRACTThis study shows that the disease free equilibrium (E0) for COVID-19 coronavirus does not satisfy the criteria for a locally or globally asymptotic stability. This implies that as a pandemic as declared by WHO (2020) the COVID-19 coronavirus does not have a curative vaccine yet and precautionary measures are advised through quarantine and observatory procedures. Also, the Basic Reproductive number (R0 < 1) by Equation (33) shows that there is a chance of decline of secondary infections when the ratio between the incidence rate in the population and the total number of infected population quarantined with observatory procedure.The effort to evaluate the disease equilibrium shows that unless there is a dedicated effort from government, decision makers and stakeholders, the world would hardly be reed of the COVID-19 coronavirus and further spread is eminent and the rate of infection will continue to increase despite the increased rate of recovery because of the absence of vaccine at the moment.
Neural Correlates of Positive and Negative Valence System Dysfunction in Adolescents Revealed by Data-Driven Parcellation and Resting-State Network Modeling
Authors: Gabbay Vilma , Liu Qi , DeWitt Samuel J. , Mehra Lushna M. , Alonso Carmen M. , Ely Benjamin A. 
Published: March 2020

AbstractObjectiveAdolescence is a period of rapid brain development when symptoms of mood, anxiety, and other disorders often first emerge, suggesting disruptions in maturing reward circuitry may play a role in mental illness onset. Here, we characterized associations between resting-state network properties and psychiatric symptomatology in medication-free adolescents with a wide range of symptom severity.MethodsAdolescents (age 12-20) with mood and/or anxiety symptoms (n=68) and healthy controls (n=19) completed diagnostic interviews, depression/anhedonia/anxiety questionnaires, and 3T resting-state fMRI (10min/2.3mm/TR=1s). Data were preprocessed (HCP Pipelines), aligned (MSMAll), and parcellated into 750 nodes encompassing the entire cortex/subcortex (Cole-Anticevic Brain-wide Network Partition). Weighted graph theoretical metrics (Strength Centrality=CStr; Eigenvector Centrality=CEig; Local Efficiency=ELoc) were estimated withinWhole Brainand task-derivedReward Anticipation/Attainment/Prediction Errornetworks. Associations with clinical status and symptoms were assessed non-parametrically (two-tailedpFWE<0.05).ResultsRelative to controls, clinical adolescents had increased ventral striatum CEigwithin theReward Attainmentnetwork. Across subjects, depression correlated with subgenual cingulate CStrand ELoc, anhedonia correlated with ventromedial prefrontal CStrand lateral amygdala ELoc, and anxiety negatively correlated with parietal operculum CEigand medial amygdala ELocwithin theWhole Brainnetwork.ConclusionsUsing a data-driven analysis approach, high-quality parcellation, and clinically diverse adolescent cohort, we found that symptoms within positive and negative valence system constructs differentially associated with resting-state network abnormalities: depression and anhedonia, as well as clinical status, involved greater influence and communication efficiency in prefrontal and limbic reward areas, whereas anxiety was linked to reduced influence/efficiency in amygdala and cortical regions involved in stimulus monitoring.
A comparative analysis reveals irreproducibility in searches of scientific literature
Authors: Pozsgai Gábor , Lövei Gábor L. , Vasseur Liette , Gurr Geoff , Batáry Péter , Korponai János , Littlewood Nick A. , Liu Jian , Móra Arnold , Obrycki John , Reynolds Olivia , Stockan Jenni A. , VanVolkenburg Heather , Zhang Jie , Zhou Wenwu , You Minsheng 
Published: March 2020

AbstractRepeatability is the cornerstone of science and it is particularly important for systematic reviews. However, little is known on how database and search engine choices influence replicability. Here, we present a comparative analysis of time-synchronized searches at different locations in the world, revealing a large variation among the hits obtained within each of the several search terms using different search engines. We found that PubMed and Scopus returned geographically consistent results to identical search strings, Google Scholar and Web of Science varied substantially both in the number of returned hits and in the list of individual articles depending on the search location and computing environment. To maintain scientific integrity and consistency, especially in systematic reviews, action is needed from both the scientific community and scientific search platforms to increase search consistency. Researchers are encouraged to report the search location, and database providers should make search algorithms transparent and revise access rules to titles behind paywalls.
Validation of chronic restraint stress model in rats for the study of depression using longitudinal multimodal MR imaging
Authors: Seewoo Bhedita J , Hennessy Lauren A , Feindel Kirk W , Etherington Sarah J , Croarkin Paul E , Rodger Jennifer 
Published: March 2020

AbstractPrior research suggests that the neurobiological underpinnings of depression include disruptions in functional connectivity, neurometabolite levels, and hippocampal volume. This study examined the validity of a chronic restraint stress (CRS) paradigm in male Sprague Dawley rats for the study of depression using longitudinal behavioural tests and multiple 9.4 T MRI modalities (resting-state functional MRI, proton magnetic resonance spectroscopy, and volumetric studies). In the CRS protocol, rats were placed in individual transparent tubes for 2.5 h daily over 13 days. Elevated plus-maze test (EPM) and forced swim test (FST) confirmed the presence of anxiety-like and depression-like behaviours respectively post-restraint. Brain changes were also detected by MR. The rs-fMRI data revealed hypoconnectivity within the salience and interoceptive networks and hyperconnectivity of several brain regions to the cingulate cortex. The1H-MRS data revealed decreased sensorimotor cortical glutamate, glutamine and combined glutamate-glutamine levels. Volumetric analysis of T2-weighted images revealed decreased hippocampal volume, which was also correlated with salience network connectivity. Depression-like behaviours were correlated with salience and interoceptive network connectivity, glutamate and combined glutamate-glutamine levels and hippocampal volume. Anxiety-like behaviours were correlated with both hippocampus connectivity and interoceptive network connectivity. The present findings identify significant changes in brain connectivity, neurometabolites and structure that are correlated with abnormal behaviour in CRS rats. Importantly, these changes parallel those found in human depression, suggesting that the CRS rodent model has utility for translational studies and novel intervention development for depression.
Effects of Blood Sugar Levels, Kidney Disease and Medication on Anaemia Status of Type 2 Diabetes Mellitus Patients
Authors: Mulavu Malala , Zulu Mildred , Sinkala Musalula , Munsaka Sody , Okuku Pauline , Nkhoma Panji 
Published: March 2020

ABSTRACTIntroductionLifestyle-related diseases like type 2 diabetes mellitus, have emerged as a significant public health problem due to rapid urbanization and industrialization. In 2018, the prevalence of type 2 diabetes mellitus was estimated to be 500 million cases worldwide and was comparable between high- and low-income countries. Diabetes leads to multiple complications, including end-stage renal disease, cardiovascular disease, infection, and death. Anaemia in diabetic individuals has severe adverse effects on the quality of life and is associated with disease progression. A cross-sectional study was conducted that included 101 participants. The study aimed to determine the prevalence of anaemia and kidney disease and their interplay with medication and/or blood glucose levels in T2D patients.Resultsseventy-one per cent of participants were females. Majority of patients 62% were on Insulin, 30% on metformin, 7% on a combination of metformin and glimepiride and 1% on glimepiride. Ninety-five (94%) of the participants were HIV negative. The prevalence of anaemia among the participants was 23% out of which 56% had moderate anaemia, and 44% had mild anaemia. Twenty-one per cent (21%) of the participants had high creatinine levels signifying impaired kidney function or kidney disease. Anaemia was significantly associated with kidney function, fasting blood glucose and use of metformin; p = 0.042 beta = 2.5, p = 0.025 beta = 2.7 and p = 0.040 beta = −2.5 respectively.ConclusionThe study found the prevalence of anaemia of 23%, which was of moderate public health concern. Also, the prevalence of kidney disease was high in patients with Type 2 Diabetes Mellitus. It also found that kidney disease and high blood glucose levels increase the chances of developing anaemia. However, we found that metformin had a protective role against the development of anaemia in Type 2 Diabetes Mellitus patients.
On a non-standard two-species stochastic competing system and a related degenerate parabolic equation
Authors: Yoshioka H. , Yoshioka Y. 
Published: March 2020

AbstractWe propose and analyse a new stochastic competing two-species population dynamics model. Competing algae population dynamics in river environment, important engineering problems, motivate this model. It is a system of stochastic differential equations (SDEs) and has a characteristic that the two populations are competing with each other through the environmental capacities. Unique existence of the uniformly bounded strong solution is proven and an attractor is identified. The Kolmogorov backward equation associated with the population dynamics is formulated and its unique solvability in a Banach space with a weighted norm is discussed. Our mathematical analysis results can be effectively utilized for a base-stone of modelling, analysis, and control of the competing population dynamics.
Convergence within divergence: insights of wheat adaptation fromTriticumpopulation sequencing
Authors: Zhou Yao , Zhao Xuebo , Li Yiwen , Xu Jun , Bi Aoyue , Kang Lipeng , Chen Haofeng , Wang Ying , Wang Yuan-ge , Liu Sanyang , Jiao Chengzhi , Lu Hongfeng , Wang Jing , Yin Changbin , Jiao Yuling , Lu Fei 
Published: March 2020

AbstractBread wheat expanded its habitats from a small core area of the Fertile Crescent to global environments within ∼10,000 years. Genetic mechanisms of this remarkable evolutionary success are not well understood. By whole-genome sequencing of populations from 25 subspecies within generaTriticumandAegilops, we identified composite introgression from these wild populations contributing 13%∼36% of the bread wheat genome, which tremendously increased the genetic diversity of bread wheat and allowed its divergent adaptation. Meanwhile, convergent adaption to human selection showed 2- to 16-fold enrichment relative to random expectation inTriticumspecies despite their drastic differences in ploidy levels and growing zones, indicating the vital importance of adaptive constraints in the success of bread wheat. These results showed the genetic necessities of wheat as a global crop and provided new perspectives on leveraging adaptation success across species for crop improvement.
In response to Liet al.: Linker histones function inDrosophilaembryogenesis
Authors: Carbonell Albert , Henn Lazslo , Pérez-Roldán Juan , Tamirisa Srividya , Szabó Anikó , Boros Imre M. , Azorín Fernando 
Published: March 2020

ABSTRACTIn an earlier paper (Pérez-Montero et al., 2013), we reported that the embryonic linker histone ofDrosophiladBigH1 was essential for earlyDrosophilaembryogenesis since embryos homozygous for thebigH1100mutation showed strong defects and did not survive beyond zygotic genome activation (ZGA) at cellularization. Recent results challenge these observations since nullbigH1mutations generated by CRISPR/Cas9 methodology turn out to be homozygous viable, as reported in Liet al. (2019) and here. In this regard, Liet al. described a novel mechanism by which lack of dBigH1 is compensated by the early expression of maternal dH1. Here, we confirm this observation and show that such compensatory mechanism is not activated inbigH1100embryos.
Predicting the number of reported and unreported cases for the COVID-19 epidemic in South Korea, Italy, France and Germany
Authors: Magal P. , Webb G. 
Published: March 2020

AbstractWe model the COVID-19 coronavirus epidemic in South Korea, Italy, France, and Germany. We use early reported case data to predict the cumulative number of reported cases to a final size. The key features of our model are the timing of implementation of major public policies restricting social movement, the identification and isolation of unreported cases, and the impact of asymptomatic infectious cases.
A green tea polyphenol Epigallocatechin-3-gallate modulates Tau Post-translational modifications and cytoskeletal network
Authors: Sonawane Shweta Kishor , Chinnathambi Subashchandrabose 
Published: March 2020

AbstractBackgroundAlzheimer’s disease is a type of dementia denoted by progressive neuronal death due to the accumulation of proteinaceous aggregates of Tau. Post-translational modifications like hyperphosphorylation, truncation, glycation,etc. play a pivotal role in Tau pathogenesis. Glycation of Tau aids in paired helical filament formation and abates its microtubule-binding function. The chemical modulators of Tau PTMs, such as kinase inhibitors and antibody-based therapeutics, have been developed, but natural compounds, as modulators of Tau PTMs are not much explored.MethodsWe applied biophysical and biophysical techniques like fluorescence kinetics, SDS-PAGE, western blot analysis and transmission electron microscopy to investigate the impact of EGCG on Tau glycationin vitro. The effect of glycation on cytoskeleton instability and its EGCG-mediated rescue were studied by immunofluorescence in neuroblastoma cells.ResultsEGCG inhibited methyl glyoxal (MG)-induced Tau glycationin vitro. EGCG potently inhibited MG-induced advanced glycation endproducts formation in neuroblastoma cells as well modulated the localization of AT100 phosphorylated Tau in the cells. In addition to preventing the glycation, EGCG enhanced actin-rich neuritic extensions and rescued actin and tubulin cytoskeleton severely disrupted by MG. EGCG maintained the integrity of the Microtubule Organizing Center (MTOC) stabilized microtubules by Microtubule-associated protein RP/EB family member 1 (EB1).ConclusionsWe report EGCG, a green tea polyphenol, as a modulator ofin vitromethylglyoxal-induced Tau glycation and its impact on reducing advanced glycation end products in neuroblastoma cells. We unravel unprecedented function of EGCG in remodeling neuronal cytoskeletal integrity.
Solving thewhereproblem and quantifying geometric variation in neuroanatomy using generative diffeomorphic mapping
Authors: Tward Daniel J , Gray Bryson D P , Li Xu , Huo Bingxing , Banerjee Samik , Savoia Stephen , Mezias Christopher , Das Sukhendu , Miller Michael I , Mitra Partha P 
Published: March 2020

ABSTRACTA current focus of research in neuroscience is to enumerate, map and annotate neuronal cell types in whole vertebrate brains using different modalities of data acquisition. Mapping these molecular and anatomical datasets into a common reference space remains a key challenge. While several brain-to-atlas mapping workflows exist, they do not adequately address challenges of modern high throughput neuroimaging, including multimodal and multiscale signals, missing data or non reference signals, and geometric quantification of individual variation. Our solution is to implement a generative statistical model that describes the likelihood of imaging data given a sequence of transforms of an atlas image, and a framework for maximum a posteriori estimation of unknown parameters capturing the issues listed above. The key idea in our approach is to minimize the difference between synthetic image volumes and real data over these parameter.Rather than merely using mappings as a “normalization” step, we implement tools for using their local metric changes as an opportunity for geometric quantification of technical and biological sources of variation in an unprecedented manner. While the framework is used to compute pairwise mappings, our approach particularly allows for easy compositions across chains of multimodality datasets. We apply these methods across a broad range of datasets including various combinations of in-vivo and ex-vivo MRI, 3D STP and fMOST data sets, 2D serial histology sections, and brains processed for snRNAseq with tissue partially removed. We show biological utility by quantifying cell density and diffeomorphic characterization of brain shape fluctuations across biological covariates. We note that the magnitude of individual variation is often greater than differences between different sample preparation techniques.To facilitate community accessibility, we implement our algorithm as open source, include a web based framework, and implement input and output dataset standards. Our work establishes a quantitative, scalable and streamlined workflow for unifying a broad spectrum of multi-modal whole-brain light microscopic data volumes into a coordinate-based atlas framework. This work enables large scale integration of whole brain data sets that are essential in modern neuroscience.
Hypertension and Diabetes Delay the Viral Clearance in COVID-19 Patients
Authors: Chen Xiaoping , Hu Wenjia , Ling Jiaxin , Mo Pingzheng , Zhang Yongxi , Jiang Qunqun , Ma Zhiyong , Cao Qian , Deng Liping , Song Shihui , Zheng Ruiying , Gao Shicheng , Ke Hengning , Gui Xien , Lundkvist Åke , Li Jinlin , Lindahl Johanna F , Xiong Yong 
Published: March 2020

AbstractObjectivesComorbidities have significant indications for the disease outcome of COVID-19, however which underlying diseases that contribute the most to aggravate the conditions of COVID-19 patients is still largely unknown. SARS-CoV-2 viral clearance is a golden standard for defining the recovery of COVID-19 infections. To dissect the underlying diseases that could impact on viral clearance, we enrolled 106 COVID-19 patients who were hospitalized in the Zhongnan Hospital of Wuhan University, Wuhan, China between Jan 5 and Feb 25, 2020.MethodologyWe comprehensively analyzed demographic, clinical and laboratory data, as well as patient treatment records. Survival analyses with Kaplan-Meier and Cox regression modelling were employed to identify factors influencing the viral clearance negatively.ResultsWe found that increasing age, male gender, and angiotensin-converting enzyme 2 (ACE2) associated factors (including hypertension, diabetes, and cardiovascular diseases) adversely affected the viral clearance. Furthermore, analysis by a random forest survival model pointed out hypertension, cortisone treatment, gender, and age as the four most important variables.ConclusionsWe conclude that patients at old age, males, and/or having diseases associated with high expression of ACE2 will have worse prognosis during a COVID-19 infections.