bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential Neutralizing Antibodies Discovered for Novel Corona Virus Using Machine Learning
Authors: Magar Rishikesh , Yadav Prakarsh , Farimani Amir Barati 
Published: March 2020

AbstractThe fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. Recent outbreak of novel coronavirus infected and killed thousands of people in the world. Rapid methods in finding peptides or antibody sequences that can inhibit the viral epitopes of COVID-19 will save the life of thousands. In this paper, we devised a machine learning (ML) model to predict the possible inhibitory synthetic antibodies for Corona virus. We collected 1933 virus-antibody sequences and their clinical patient neutralization response and trained an ML model to predict the antibody response. Using graph featurization with variety of ML methods, we screened thousands of hypothetical antibody sequences and found 8 stable antibodies that potentially inhibit COVID-19. We combined bioinformatics, structural biology, and Molecular Dynamics (MD) simulations to verify the stability of the candidate antibodies that can inhibit the Corona virus.
Monocular vision is intrinsically unstable: a side-effect of binocular homeostasis
Authors: Reynaud Alexandre , Blaize Kévin , Chavane Frédéric , Hess Robert F. 
Published: March 2020

AbstractIt is now accepted that short-term deprivation of one eye in adults results in not only a post-deprivation strengthening of the vision in the previously deprived eye but also a deterioration in the vision of the previously non-patched eye. Such monocular deprivation of 1-2 hours induces changes that last approximately 30-90 minutes. There is some support for this neuroplastic effect being the consequence of a change in the contrast gain within the binocular circuity. What is not known is when these changes in gain are initiated. One possibility is that they are initiated only once the patch is removed. The other possibility is that they are the result of a slow build up from the moment the patch is first applied.In this study, we measure monocular contrast detection thresholds of the non-deprived eye over time during the deprivation of the other eye. We show that contrast threshold increases over time during the deprivation of the other eye. This observation suggest that the patching effect is mediated by a slow build up over the deprivation period: reducing the vision of the non-deprived eye and enhancing the vision of the deprived eye reflecting reciprocal changes in sensitivity. These results highlight a hitherto unknown feature of human vision, namely that monocular visionper seis intrinsically unstable which is a consequence of the reciprocal inhibitory circuits that homeostatically regulate binocular vision. This questions a whole corpus of studies of visual function that rely on the assumption that monocular vision is intrinsically stable.
Scientometric Trends for Coronaviruses and Other Emerging Viral Infections
Authors: Kagan Dima , Moran-Gilad Jacob , Fire Michael 
Published: March 2020

AbstractCOVID-19 is the most rapidly expanding coronavirus outbreak in the past two decades. To provide a swift response to a novel outbreak, prior knowledge from similar outbreaks is essential. Here, we study the volume of research conducted on previous coronavirus outbreaks, specifically SARS and MERS, relative to other infectious diseases by analyzing over 35 million papers from the last 20 years. Our results demonstrate that previous coronavirus outbreaks have been understudied compared to other viruses. We also show that the research volume of emerging infectious diseases is very high after an outbreak and drops drastically upon the containment of the disease. This can yield inadequate research and limited investment in gaining a full understanding of novel coronavirus management and prevention. Independent of the outcome of the current COVID-19 outbreak, we believe that measures should be taken to encourage sustained research in the field.
Development and utilization of an intelligent application for aiding COVID-19 diagnosis
Authors: Meng Zirui , Wang Minjin , Song Huan , Guo Shuo , Zhou Yanbing , Li Weimin , Zhou Yongzhao , Li Mengjiao , Song Xingbo , Zhou Yi , Li Qingfeng , Lu Xiaojun , Ying Binwu 
Published: March 2020

ABSTRACTBackgroundCOVID-19 has been spreading globally since emergence, but the diagnostic resources are relatively insufficient.ResultsIn order to effectively relieve the resource deficiency of diagnosing COVID-19, we developed a machine learning-based diagnosis model on basis of laboratory examinations indicators from a total of 620 samples, and subsequently implemented it as a COVID-19 diagnosis aid APP to facilitate promotion.ConclusionsExternal validation showed satisfiable model prediction performance (i.e., the positive predictive value and negative predictive value was 86.35% and 84.62%, respectively), which guarantees the promising use of this tool for extensive screening.
Consumption of Cattle Hide Singed with Scrap Tyre is Detrimental to the Liver, Heart and Kidney of Rats
Authors: Woko Eze. C. , Ibegbulem C.O. , Alisi Chinwe. S. 
Published: March 2020

AbstractThe presence of essential amino acids in meat makes it a complete protein, this makes meat a highly sort after source of protein in the human diet. The World’s demand for animal-derived protein has been projected to double by 2050. As a result there is a resultant increase in livestock industries to meet this demand. While meat is generally consumed as a source of protein, processed cattle hide popularly known as “Kanda”in southeastern Nigeria is consumed as a substitute for meat though it may not necessarily provide the same level of nutritional value with meat. The method of processing this food delicacy (Kanda) by singeing with scrap tyre or firewood has opened the door for heavy metal and or polycyclic aromatic hydrocarbon (PAHs) contamination, thereby putting unsuspecting consumers at health risk. This study therefore investigated the effects of consuming scrap tyre-singed cattle hide and firewood singed cattle hide on the kidney, liver and heart of male Wistar rats. Consuming singed cattle hides significantly elevated some serum marker enzymes important in kidney, liver and heart damage i.e alanine and aspartate aminotransferases, alkaline phosphatase, creatine kinase, and lactate dehydrogenase, with the groups that were fed with the hide singed with scrap tyre showing severe elevations. Consuming the singedKandaalso significantly decreased the serum concentrations of K+, Na+, Cl−, and significantly increased HCO3−and urea concentration. An examination of the organ tissues also revealed serious morphological changes. In conclusion, consuming singedKandahad detrimental effects on the vital organs studied.
SSP: An R package to estimate sampling effort in studies of ecological communities
Authors: Guerra-Castro Edlin J. , Cajas Juan Carlos , Simões Nuno , Cruz-Motta Juan J , Mascaró Maite 
Published: March 2020

ABSTRACTSSP(simulation-based sampling protocol) is an R package that uses simulation of ecological data and dissimilarity-based multivariate standard error (MultSE) as an estimator of precision to evaluate the adequacy of different sampling efforts for studies that will test hypothesis using permutational multivariate analysis of variance. The procedure consists in simulating several extensive data matrixes that mimic some of the relevant ecological features of the community of interest using a pilot data set. For each simulated data, several sampling efforts are repeatedly executed andMultSEcalculated. The mean value, 0.025 and 0.975 quantiles ofMultSEfor each sampling effort across all simulated data are then estimated and standardized regarding the lowest sampling effort. The optimal sampling effort is identified as that in which the increase in sampling effort do not improve the precision beyond a threshold value (e.g. 2.5 %). The performance ofSSPwas validated using real data, and in all examples the simulated data mimicked well the real data, allowing to evaluate the relationshipMultSE–nbeyond the sampling size of the pilot studies.SSPcan be used to estimate sample size in a wide range of situations, ranging from simple (e.g. single site) to more complex (e.g. several sites for different habitats) experimental designs. The latter constitutes an important advantage, since it offers new possibilities for complex sampling designs, as it has been advised for multi-scale studies in ecology.
Insulin-Like Growth Factor I Modulates Sleep Through Hypothalamic Orexin Neurons
Authors: Zegarra-Valdivia Jonathan A. , Pignatelli Jaime , de Sevilla Maria Estrella Fernandez , Fernandez Ana M. , Munive Victor , Martinez-Rachadell Laura , Nuñez Angel , Aleman Ignacio Torres 
Published: March 2020

AbstractAlthough metabolic and sleep disturbances are commonly associated, the underlying processes are not yet fully defined. Insulin-like growth factor-I (IGF-I), an anabolic hormone that shows a circadian pattern in the circulation and activity-dependent entrance in the brain, is associated to sleep regulation along evolution. However, its role in this universal homeostatic process remains poorly understood. We now report that the activity of orexin neurons, a discrete cell population in the lateral hypothalamus that is involved in the circadian sleep/wake cycle and arousal, is modulated by circulating IGF-I. Furthermore, mice with blunted IGF-I receptor activity in orexin neurons have lower levels of orexin in the hypothalamus, show altered electrocorticographic patterns with predominant slow wave activity, reduced onset-sleep latency, and less transitions between sleep and awake stages. Collectively, these results extend the role of this pleiotropic growth factor to shaping sleep architecture through regulation of orexin neurons. We speculate that poor sleep quality associated to diverse conditions may be related to disturbed brain IGF-I input to orexin neurons.
Siderophores provoke extracellular superoxide production by carbon-starvingArthrobacterstrains when carbon sources recover
Authors: Ning Xue , Liang Jinsong , Men Yujie , Chang Yangyang , Bai Yaohui , Liu Huijuan , Wang Aijie , Zhang Tong , Qu Jiuhui 
Published: March 2020

ABSTRACTSuperoxide and other reactive oxygen species (ROS) in the environment shape microbial communities1and drive transformation of metals2,3and inorganic/organic matter4,5. Taxonomically diverse bacteria and phytoplankton can produce extracellular superoxide during laboratory cultivation6-11. Understanding the physiological reasons for extracellular superoxide production by aerobes in the environment is a crucial question yet not fully solved. Here, we showed that iron-starvingArthrobactersp. QXT-31 (referred to asA.QXT-31 hereafter) secreted a type of siderophore (deferoxamine, DFO), which provoked extracellular superoxide production by carbon-starvingA.QXT-31 when carbon sources were recovered. Several other siderophores also demonstrated similar effects. RNA-Seq data hinted that DFO stripped iron from iron-bearing proteins in the electron transfer chain (ETC) of metabolically activeA.QXT-31, resulting in electron leakage from the electron-rich (resulting from carbons source metabolism) ETC and superoxide production. Considering that most aerobes secrete siderophore(s)12and often suffer from carbon starvation in the environment, certain aerobes are expected to produce extracellular superoxide when carbon source(s) recover/fluctuate, thus influencing the microbial community and cycling of many elements. In addition, an artificial iron-chelator (diethylenetriamine pentaacetic acid, DTPA) was widely used in microbial superoxide quantification. Our results showed that DTPA provoked superoxide production byA. QXT-31 and highlighted its potential interference in microbial superoxide quantification.
The BBSome assembly is spatially controlled by BBS1 and BBS4 in human cells
Authors: Prasai Avishek , Cernohorska Marketa Schmidt , Ruppova Klara , Niederlova Veronika , Andelova Monika , Draber Peter , Stepanek Ondrej , Huranova Martina 
Published: March 2020

AbstractBardet-Biedl Syndrome (BBS) is a pleiotropic ciliopathy caused by dysfunction of primary cilia. Most BBS patients carry mutations in one of eight genes encoding for subunits of a protein complex, BBSome, which mediates the trafficking of ciliary cargoes. Although, the structure of the BBSome has been resolved recently, the mechanism of assembly of this complicated complex in living cells is poorly understood. We generated a large library of human retinal epithelial cell lines deficient in particular BBSome subunit and expressing another subunit tagged with a fluorescent protein. We performed a comprehensive analysis of these cell lines using biochemical and microscopy approaches. Our data revealed that the BBSome formation is a sequential process including a step of the pre-BBSome assembly at pericentriolar satellites nucleated by BBS4, followed by the translocation of the BBSome into the ciliary base mediated by BBS1.
MiR-146a controls age related bone loss
Authors: Saferding Victoria , Hofmann Melanie , Brunner Julia S. , Niederreiter Birgit , Timmen Melanie , Magilnick Nathaniel , Hayer Silvia , Heller Gerwin , Steiner Günter , Stange Richard , Boldin Mark , Schabbauer Gernot , Weigl Moritz , Hackl Matthias , Grillari Johannes , Smolen Josef S. , Blüml Stephan 
Published: March 2020

AbstractBone loss is one of the consequences of aging, leading to diseases such as osteoporosis and increased susceptibility to fragility fractures and therefore considerable morbidity and mortality in humans. Here we identify microRNA 146a as an essential epigenetic switch controlling bone loss with age. Mice deficient in miR-146a show regular development of their skeleton. However, while WT mice start to lose bone with age, animals deficient in miR-146a continue to accrue bone throughout their life span. Increased bone mass is due to increased generation and activity of osteoblasts in miR-146a deficient mice as a result of sustained activation of bone anabolic Wnt signaling during aging. Deregulation of the miR-146a target genes Wnt1 and Wnt5a parallel bone accrual and osteoblast generation, which is accompanied by reduced development of bone marrow adiposity. Furthermore, miR-146a deficient mice are protected from ovariectomy induced bone loss. In humans, levels of miR-146a are increased in patients suffering fragility fractures in comparison to those who do not.These data identify miR-146a as a crucial epigenetic temporal regulator which essentially controls bone homeostasis during aging by regulating bone anabolic Wnt signaling. Therefore, miR-146a might be a powerful therapeutic target to prevent age related bone dysfunction such as the development of bone marrow adiposity and osteoporosis.
The evolving systemic biomarker milieu in obese ZSF1 rat model of human cardiometabolic syndrome: Characterization of the model and cardioprotective effect of GDF15
Authors: Stolina Marina , Luo Xin , Dwyer Denise , Han Chun-Ya , Chen Rhonda , Zhang Ying , Xiong YuMei , Chen Yinhong , Yin Jun , Ason Brandon , Hale Clarence , Véniant Murielle M. 
Published: March 2020

AbstractCardiometabolic syndrome has become a global health issue. Heart failure is a common comorbidity of cardiometabolic syndrome. Successful drug development to prevent cardiometabolic syndrome and associated comorbidities requires preclinical models predictive of human conditions. To characterize the heart failure component of cardiometabolic syndrome, cardiometabolic, metabolic, and renal biomarkers were evaluated in obese and lean ZSF1 20-to 22-week-old male rats. Cardiac function, exercise capacity, and left ventricular gene expression were also analyzed. Obese ZSF1 rats exhibited multiple features of human cardiometabolic syndrome by pathological changes in systemic renal, metabolic, and cardiovascular disease circulating biomarkers. Hemodynamic assessment, echocardiography, and decreased exercise capacity confirmed heart failure with preserved ejection fraction. RNA-seq results demonstrated changes in left ventricular gene expression associated with fatty acid and branched chain amino acid metabolism, cardiomyopathy, cardiac hypertrophy, and heart failure. Twelve weeks of growth differentiation factor 15 (GDF15) treatment significantly decreased body weight, food intake, blood glucose, and triglycerides and improved exercise capacity in obese ZSF1 males. Systemic cardiovascular injury markers were significantly lower in GDF15-treated obese ZSF1 rats. Obese ZSF1 male rats represent a preclinical model for human cardiometabolic syndrome with established heart failure with preserved ejection fraction. GDF15 treatment mediated dietary response and demonstrated a cardioprotective effect in obese ZSF1 rats.
Direct and indirect nutritional factors that determine reproductive performance of heifer and primiparous cows
Authors: Eloy Lidiane R. , Bremm Carolina , Lobato José F. P. , Pötter Luciana , Laca Emilio A. 
Published: March 2020

AbstractPregnancy rate is a major determinant of population dynamics of wild ungulates and of productivity of livestock systems. Allocation of feeding resources, including stocking rates, prior to and during the breeding season is a crucial determinant of this vital rate. Thus, quantification of effects and interaction among multiple factors that affect pregnancy rate is essential for management and conservation of pasture-based systems. Pregnancy rate of 2982 heifers and primiparous cows was studied as a function of animal category, average daily gain during the breeding season, stocking rate, pasture type and body weight at the beginning of the breeding season. Data were obtained from 43 experiments conducted in commercial ranches and research stations in the Pampas region between 1976 and 2015. Stocking rate ranged from 200 to 464 kg live weight/ha, which brackets values for most of the grazinglands in similar regions. Age at breeding was 14-36 months (24.6 ± 7.5 months); initial breeding weights were 129-506 kg and 194-570 kg for heifers and primiparous cows. Pregnancy rate was modeled with an apriori set of explanatory variables where proximate variables (breed, body weight at start of breeding, weight gain during breeding and category) were included first and subsequently modeled as functions of other variables (pasture type, supplementation and stocking rate). This modeling approach allowed detection of direct and indirect effects (through nutrition and body weight) of factors that affect pregnancy rate. Taurine (Bos taurusbreeds, N = 1058) had higher pregnancy rate thanB. TaurusxB. indicuscrossbreed (N = 1924) females. Pregnancy rate of heifers and primiparous cows grazing in natural grasslands decreased with increasing stocking rate, but no effect of stocking rate was detected in cultivated and improved pastures. Pregnancy rate increased with increasing average daily gain during the breeding season. Use of cultivated or improved natural pastures promotes higher pregnancy rate, as well as allows higher in stocking rate at the regional level. Body weight at the start of the breeding season is the primary determinant of pregnancy rates in heifer and primiparous cows.
Kinetochore protein Spindly controls microtubule polarity inDrosophilaaxons
Authors: Castillo Urko del , Müller Hans-Arno J. , Gelfand Vladimir I. 
Published: March 2020

AbstractMicrotubule polarity in axons and dendrites defines the direction of intracellular transport in neurons. Axons contain arrays of uniformly polarized microtubules with plus-ends facing the tips of the processes (plus-end-out), while dendrites contain microtubules with minus-end-out orientation. It has been shown that cytoplasmic dynein, targeted to cortical actin, removes minus-end-out microtubules from axons. Here we have identified Spindly, a protein known for recruitment of dynein to kinetochores in mitosis, as a key factor required for dynein-dependent microtubule sorting in axons ofDrosophilaneurons. Depletion of Spindly affects polarity of axonal microtubulesin vivoand in primary neuronal cultures. In addition to these defects, depletion of Spindly in neurons causes major collapse of axonal patterning in the third-instar larval brain as well as severe coordination impairment in adult flies. These defects can be fully rescued by full-length Spindly, but not by variants with mutations in its dynein-binding site. Biochemical analysis demonstrated that Spindly binds F-actin, suggesting that Spindly serves as a link between dynein and cortical actin in axons. Therefore, Spindly plays a critical role during neurodevelopment by mediating dynein-driven sorting of axonal microtubules.Significance StatementNeurons send and receive electrical signals through long microtubule-filled neurites called axons and dendrites. One of the main structural differences between axons and dendrites is how their microtubules are organized. Axons contains microtubules with their plus-ends out while microtubules in dendrites are organized with mixed or plus-end-in orientation. Dynein, the main minus-end microtubule motor, anchored to cortical actin filaments in the axons is responsible for the uniform microtubule polarity in axons. However, it is unknown how dynein is recruited to the actin cortex in axons. The major finding of this work is that Spindly, a protein involved in anchoring dynein to kinetochores during cell division, has a second important function in interphase cells recruiting dynein to the actin cortex in axons.
SGK1 Signaling Promotes Glucose Metabolism and Survival in Extracellular Matrix Detached Cells
Authors: Mason Joshua A. , Cockfield Jordan A. , Pape Daniel J. , Meissner Hannah , Sokolowski Michael , White Taylor C. , Valentín López José C. , Liu Juan , Liu Xiaojing , Martínez-Reyes Inmaculada , Chandel Navdeep S. , Locasale Jason W. , Schafer Zachary T. 
Published: March 2020

SummaryLoss of integrin-mediated attachment to extracellular matrix (ECM) proteins can trigger a variety of cellular changes that impact cell viability. Foremost among these is the activation of anoikis, caspase-mediated cell death induced by ECM-detachment. In addition to anoikis, loss of ECM-attachment causes profound alterations in cellular metabolism that can lead to anoikis-independent cell death. Here, we describe a surprising role for serum and glucocorticoid kinase-1 (SGK1) in the promotion of energy production when cells are detached. Our data demonstrate that SGK1 activation is necessary and sufficient for ATP generation during ECM-detachment and anchorage-independent growth. More specifically, SGK1 promotes a substantial elevation in glucose uptake due to elevated GLUT1 transcription. In addition, carbon flux into the pentose phosphate pathway (PPP) is necessary to accommodate elevated glucose uptake and PPP-mediated glyceraldehyde-3-phosphate (G3P) is necessary for ATP production. Thus, our data unmask SGK1 as master regulator of glucose metabolism and cell survival during ECM-detached conditions.