bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full stomachs at empty tides: tidal cycle affects feeding activity and diet of the sandy beach gastropod Olivella minuta
Authors: Checon Helio H , Silva Mariana O , Corte Guilherme N , Yokoyama Leonardo Q , Teodósio M Alexandra , Turra Alexander 
Published: May 2020

ABSTRACTOlivella minuta is an abundant neogastropod on sandy beaches from Texas (USA) to southern Brazil. This study aimed to characterize and compare the feeding activity and diet of a Brazilian population of O. minuta in different tidal zones (intertidal and subtidal), and different tidal levels (high and low tides), with three combinations of tidal zone and level being studied (intertidal during low tide, intertidal during high tide and subtidal). The results showed that diet composition was generally similar among tidal conditions, with O. minuta being a generalist, feeding on 45 different food items. Feeding activity, however, was higher in the intertidal during low tide, whereas the richness and diversity of food items were higher in the intertidal during high tide. The higher feeding activity of O. minuta during low tide may be linked to a lower risk of predation; at low tide organisms may be able to feed for a longer time, and this may be particularly true on beaches with fine sand, where water retention is higher than that on beaches with coarse sand. The higher diversity of food items consumed in the intertidal during high tide is likely related to the increased prevalence of planktonic food during high tide. Our results indicate that tidal zone and level may strongly influence the feeding activity of coastal soft-bottom species and that species may show higher feeding activity during low tide. Given the current loss of intertidal habitats due to anthropogenic activity and climate-change associated factors, our study has important implications, highlighting the importance of intertidal areas for the ecology and conservation of sandy beach species.
Distortions in Production Networks*
Authors: Bigio Saki , La’O Jennifer 
Published: May 2020

Abstract
How does an economy’s production structure determine its macroeconomic response to sectoral distortions? We study a static, multisector framework in which production is organized in an input-output network and production decisions are distorted. Sectoral distortions manifest at the aggregate level via two channels: total factor productivity (TFP) and the labor wedge. We show that near efficiency, distortions have zero first-order effects on TFP and nonzero first-order effects on the labor wedge, and that a sufficient statistic for the latter are the Domar weights. We thereby provide a Hulten-like theorem for the aggregate effects of sectoral distortions. A quantitative application of the model to the 2008–09 financial crisis suggests that the U.S. input-output structure amplified financial distortions by roughly a factor of two during the crisis.
Functional Pathway Identification With CRISPR/Cas9 Genome-wide Gene Disruption in Human Dopaminergic Neuronal Cells Following Chronic Treatment With Dieldrin
Authors: Russo Max , Sobh Amin , Zhang Ping , Loguinov Alex , Tagmount Abderrahmane , Vulpe Chris D , Liu Bin 
Published: May 2020

AbstractOrganochlorine pesticides, once widely used, are extremely persistent and bio-accumulative in the environment. Epidemiological studies have implicated that environmental exposure to organochlorine pesticides including dieldrin is a risk factor for the development of Parkinson’s disease. However, the pertinent mechanisms of action remain poorly understood. In this study, we carried out a genome-wide (Brunello library, 19 114 genes, 76 411 sgRNAs) CRISPR/Cas9 screen in human dopaminergic SH-SY5Y neuronal cells exposed to a chronic treatment (30 days) with dieldrin to identify cellular pathways that are functionally related to the chronic cellular toxicity. Our results indicate that dieldrin toxicity was enhanced by gene disruption of specific components of the ubiquitin proteasome system as well as, surprisingly, the protein degradation pathways previously implicated in inherited forms of Parkinson’s disease, centered on Parkin. In addition, disruption of regulatory components of the mTOR pathway which integrates cellular responses to both intra- and extracellular signals and is a central regulator for cell metabolism, growth, proliferation, and survival, led to increased sensitivity to dieldrin-induced cellular toxicity. This study is one of the first to apply a genome-wide CRISPR/Cas9-based functional gene disruption screening approach in an adherent neuronal cell line to globally decipher cellular mechanisms that contribute to environmental toxicant-induced neurotoxicity and provides novel insight into the dopaminergic neurotoxicity associated with chronic exposure to dieldrin.
Characterization of SARS-CoV-2 viral diversity within and across hosts
Authors: Sashittal Palash , Luo Yunan , Peng Jian , El-Kebir Mohammed 
Published: May 2020

SUMMARYIn light of the current COVID-19 pandemic, there is an urgent need to accurately infer the evolutionary and transmission history of the virus to inform real-time outbreak management, public health policies and mitigation strategies. Current phylogenetic and phylodynamic approaches typically use consensus sequences, essentially assuming the presence of a single viral strain per host. Here, we analyze 621 bulk RNA sequencing samples and 7,540 consensus sequences from COVID-19 patients, and identify multiple strains of the virus, SARS-CoV-2, in four major clades that are prevalent within and across hosts. In particular, we find evidence for (i) within-host diversity across phylogenetic clades, (ii) putative cases of recombination, multi-strain and/or superinfections as well as (iii) distinct strain profiles across geographical locations and time. Our findings and algorithms will facilitate more detailed evolutionary analyses and contact tracing that specifically account for within-host viral diversity in the ongoing COVID-19 pandemic as well as future pandemics.
Beneficial effect of corticosteroids in severe COVID-19 pneumonia: a propensity score matching analysis
Authors: Chroboczek Tomasz , Lacoste Marie , Wackenheim Chloe , Challan-Belval Thibaut , Amar Benjamin , Boisson Thomas , Hubac Jason , Leduc Dominique , Masse Colleen , Dechaene Victor , Touhiri-Maximin Laetitia , Megessier Sandrine , Lassale Camille 
Published: May 2020

AbstractBackgroundSince December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for Coronavirus Disease 2019 (COVID-19), is spreading worldwide, causing significant morbidity and mortality. No specific treatment has yet clearly shown to improve the disease’s evolution. Validated therapeutic options are urgently needed.MethodsIn this retrospective study, we aimed to evaluate determinants of the prognosis of the disease in 70 patients with COVID-19 severe pneumonia (i.e. requiring at least 3 liters of oxygen) hospitalized between 10 March and 9 April, 2020, in the Centre Hospitalier Alpes Léman, France. The main outcome was oro-tracheal intubation and the exposure of interest was corticotherapy. Since this was not a randomized trial, we used propensity score matching to estimate average treatment effect.ResultsThere was evidence that corticotherapy lowered the risk of intubation with a risk difference of −47.1% (95% confidence interval −71.8% to −22.5%).ConclusionCorticosteroid, a well-known, easily available, and cheap treatment, could be an important tool in management of severe COVID-19 patients with respiratory failure. Not only could it provide an individual benefit, but also, in the setting of the COVID-19 ongoing pandemic, lower the burden on our vulnerable healthcare systems.Key pointsBy propensity score matching analysis, the average treatment effect of corticosteroids on 70 patients with severe COVID-19 pneumonia was estimated. Corticosteroid therapy lowered the risk of intubation with a risk difference of −47.1% (95% confidence interval −71.8% to −22.5%).
Mathematical model of COVID-19 spread in Turkey and South Africa: Theory, methods and applications
Authors: Atangana Abdon , İğret Araz Seda 
Published: May 2020

AbstractA comprehensive study about the spread of COVID-19 cases in Turkey and South Africa has been presented in this paper. An exhaustive statistical analysis encompassing arithmetic, geometric, harmonic means, standard deviation, skewness, variance, Pearson and Spearman correlation was derived from the data collected from Turkey and South Africa within the period of 11 March 2020 to 3 May 2020 and 05 March and 3 of May respectively. It was observed that in the case of Turkey, a negative Spearman correlation for the number of infected class and a positive Spearman correlation for both the number of deaths and recoveries were obtained. This implied that the daily infections could decrease, while the daily deaths and number of recovered people could increase under current conditions. In the case of South Africa, a negative Spearman correlation for both daily deaths and daily infected people was obtained, indicating that these numbers may decrease if the current conditions are maintained. The utilization of a statistical technique predicted the daily number of infected, recovered and dead people for each country; and three results were obtained for Turkey, namely an upper boundary, a prediction from current situation and lower boundary. The prediction shows that Turkey may register in the near future approximately more than 6000 new infections in a day as worst case scenario; and less than 300 cases in the perfect scenario. However, the country could register in the near future a daily number of 27000 people recovered from COVID-19 in the perfect scenario; and less than 5000 people in a worst scenario. Moreover, Turkey in a worst-case scenario could record a high number of approximately 200 deaths per day; and less than 150 deaths in a perfect scenario. Similarly, in the case of South Africa, the prediction results show that in the near future the country could register about 500 new infected cases daily and more than 25 deaths in the worst scenario; while in a perfect scenario less than 50 new infected and zero death cases could be recorded. The histograms of the daily number of newly infected, recovered and death showed a sign of lognormal and normal distribution, which is presented using the Bell curving method parameters estimation. A new mathematical model COVID-19 comprised of nine classes was suggested; of which a formula of the reproductive number, well-poseness of the solutions and the stability analysis were presented in details. The suggested model was further extended to the scope of nonlocal operators for each case; whereby the Atangana-Seda numerical method was used to provide numerical solutions, and simulations were performed for different non-integer numbers. Additionally, sections devoted to control optimal and others dedicated to compare cases between Turkey and South Africa with the aim to comprehend why there are less numbers of deaths and infected people in South Africa than Turkey were presented in details.
Epidemiological, socio-demographic and clinical features of the early phase of the COVID-19 epidemic in Ecuador
Authors: Ortiz-Prado Esteban , Simbaña-Rivera Katherine , Diaz Ana Maria , Barreto Alejandra , Moyano Carla , Arcos Vannesa , Vásconez-González Eduardo , Paz Clara , Simbaña-Guaycha Fernanda , Molestina-Luzuriaga Martin , Fernández-Naranjo Raúl , Feijoo Javier , Henriquez Aquiles R. , Adana Lila , López Cortés Andrés , Fletcher Isabel , Lowe Rachel , Gómez-Barreno Lenin 
Published: May 2020

AbstractBackgroundThe SARS-CoV-2 virus has spread rapidly around the globe. Nevertheless, there is limited information describing the characteristics and outcomes of COVID-19 patients in Latin America.MethodsWe conducted a cross-sectional analysis of 9,468 confirmed COVID-19 cases reported in Ecuador. We calculated overall incidence, mortality, case fatality rates, disability adjusted life years, attack and crude mortality rates, as well as relative risk and relative odds of death, adjusted for age, sex and presence of comorbidities.ResultsA total of 9,468 positive COVID-19 cases and 474 deaths were included in the analysis. Men accounted for 55.4% (n = 5, 247) of cases and women for 44.6% (n = 4, 221). We found the presence of comorbidities, being male and older than 65 years were important determinants of mortality. Coastal regions were most affected by COVID-19, with higher mortality rates than the highlands. Fatigue was reported in 53.2% of the patients, followed by headache (43%), dry cough (41.7%), ageusia (37.1%) and anosmia (36.1%).ConclusionWe present the first analysis of the burden of COVID-19 in Ecuador. Our findings show that men are at higher risk of dying from COVID-19 than women, and risk increases with age and the presence of comorbidities. We also found that blue-collar workers and the unemployed are at greater risk of dying. These early observations offer clinical insights for the medical community to help improve patient care and for public health officials to strengthen Ecuador’s response to the outbreak.
Three pictures of COVID-19 behavior in Italy: similar growth and different degrowth
Authors: Feoli A. , Iannella A. L. , Benedetto E. 
Published: May 2020

AbstractIn this short note, we present an analysis of the data regarding Coronavirus (COVID-19) in Italy. We have used the official database provided by the Italian Civil Protection. Since the total number of people infected by the virus is uncertain, we have considered the trend of ICU patients, ICU patients plus deaths, and finally the sum of hospitalized patients plus the deceased. The growth of the corresponding curves is similar for all the three graphs while the trend after the turning point is completely different. We find that the curve of ICU patients can be a useful tool to monitor the behavior of epidemic and a model to predict the future evolution of COVID-19.
Model-based Cellular Kinetic Analysis of Chimeric Antigen Receptor-T Cells in Humans
Authors: Liu Can , Ayyar Vivaswath S. , Zheng Xirong , Chen Wenbo , Zheng Songmao , Mody Hardik , Wang Weirong , Heald Donald , Singh Aman P. , Cao Yanguang 
Published: May 2020

ABSTRACTChimeric antigen receptor (CAR)-T cell therapy has achieved considerable success in treating B-cell hematologic malignancies. However, the challenges of extending CAR-T therapy to other tumor types, particularly solid tumors, remain appreciable. There are substantial variabilities in CAR-T cellular kinetics across CAR-designs, CAR-T products, dosing regimens, patient responses, disease types, tumor burdens, and lymphodepletion conditions. As a “living drug”, CAR-T cellular kinetics typically exhibit four distinct phases: distribution, expansion, contraction, and persistence. The cellular kinetics of CAR-T may correlate with patient responses, but which factors determine CAR-T cellular kinetics remain poorly defined. Herein, we developed a cellular kinetic model to retrospectively characterize CAR-T kinetics in 217 patients from 7 trials and compared CAR-T kinetics across response status, patient populations, and tumor types. Based on our analysis results, CAR-T cells exhibited a significantly higher cell proliferation rate and capacity but a lower contraction rate in patients who responded to treatment. CAR-T cells proliferate to a higher degree in hematologic malignancies than in solid tumors. Within the assessed dose ranges (107–109 cells), CAR-T doses were weakly correlated with CAR-T cellular kinetics and patient response status. In conclusion, the developed CAR-T cellular kinetic model adequately characterized the multiphasic CAR-T cellular kinetics and supported systematic evaluations of the potential influencing factors, which can have significant implications for the development of more effective CAR-T therapies.
Brief sensory deprivation triggers cell type-specific structural and functional plasticity in olfactory bulb neurons
Authors: Galliano Elisa , Hahn Christiane , Browne Lorcan , Villamayor Paula R. , Grubb Matthew S. 
Published: May 2020

ABSTRACTCan alterations in experience trigger different plastic modifications in neuronal structure and function, and if so, how do they integrate at the cellular level? To address this question, we interrogated circuitry in the mouse olfactory bulb responsible for the earliest steps in odour processing. We induced experience-dependent plasticity in mice by blocking one nostril for a day, a minimally-invasive manipulation which leaves the sensory organ undamaged and is akin to the natural transient blockage suffered during common mild rhinal infections. We found that such brief sensory deprivation produced structural and functional plasticity in one highly specialised bulbar cell type: axon-bearing dopaminergic neurons in the glomerular layer. After 24h naris occlusion, the axon initial segment (AIS) in bulbar dopaminergic neurons became significantly shorter, a structural modification that was also associated with a decrease in intrinsic excitability. These effects were specific to the AIS-positive dopaminergic subpopulation, because no experience-dependent alterations in intrinsic excitability were observed in AIS-negative dopaminergic cells. Moreover, 24h naris occlusion produced no structural changes at the AIS of bulbar excitatory neurons – mitral/tufted and external tufted cells – nor did it alter their intrinsic excitability. By targeting excitability in one specialised dopaminergic subpopulation, experience-dependent plasticity in early olfactory networks might act to fine-tune sensory processing in the face of continually fluctuating inputs.
PhotoModPlus: A webserver for photosynthetic protein prediction from a genome neighborhood feature
Authors: Sangphukieo Apiwat , Laomettachit Teeraphan , Ruengjitchatchawalya Marasri 
Published: May 2020

AbstractIdentification of photosynthetic proteins and their functions is essential for understanding and improving photosynthetic efficiency. We present here a new webserver called PhotoModPlus as a platform to predict photosynthetic proteins via genome neighborhood networks (GNN) and a machine learning method. GNN facilitates users to visualize the overview of the conserved neighboring genes from multiple photosynthetic prokaryotic genomes and provides functional guidance to the query input. We also integrated a newly developed machine learning model for predicting photosynthesis-specific functions based on 24 prokaryotic photosynthesis-related GO terms, namely PhotoModGO, into the webserver. The new model was developed using a multi-label classification approach and genome neighborhood features. The performance of the new model was up to 0.872 of F1 measure, which was better than the sequence-based approaches evaluated by nested five-fold cross-validation. Finally, we demonstrated the applications of the webserver and the new model in the identification of novel photosynthetic proteins. The server was user-friendly designed and compatible with all devices and available athttp://bicep.kmutt.ac.th/photomodorhttp://bicep2.kmutt.ac.th/photomod.
Acute effects of prolactin on hypothalamic prolactin receptor expressing neurones in the mouse
Authors: Georgescu T. , Ladyman S.R. , Brown R.S.E. , Grattan D.R. 
Published: May 2020

AbstractThe anterior pituitary hormone, prolactin, is a fundamental regulator of lactation, and also plays a role in many other physiological processes including maternal behaviour, reproduction, immune response and even energy balance. Indeed, prolactin receptors (Prlr) are widely distributed throughout the body, including a number of different brain regions, further attesting to its pleiotropic nature. Within the brain, previous research has identified key areas upon which prolactin exerts effects on gene transcription through the canonical JAK2/STAT5 pathway downstream of the Prlr. In some neurones, however, such as the tuberoinfundibular dopamine neurones that control prolactin secretion, prolactin can also exert rapid actions to stimulate neuronal activity. While prolactin-induced activation of STAT5 has been described in a wide variety of brain regions, its capacity for acute modulation of electrical properties of many Prlr-expressing neurones remains to be elucidated. To investigate how widespread these rapid actions of prolactin are in various Prlr-expressing neurones, we utilised a transgenic mouse line in which Cre recombinase is specifically expressed in the coding region of the prolactin long form receptor gene (Prlr-iCre). This mouse line was crossed with a Cre-dependent calcium indicator (GCaMP6f) transgenic mouse, allowing us to visually monitor the electrical activity of Prlr-expressing neurones inex vivo200μm brain slice preparations. Here, we survey hypothalamic regions implicated in prolactin’s diverse physiological functions such as: the arcuate (ARC) and paraventricular nuclei of the hypothalamus (PVN), and the medial preoptic area (MPOA). We observe that in both males and virgin and lactating females, bath application of prolactin is able to induce electrical changes in a subset of Prlr-expressing cells in all of these brain regions. The effects we detected ranged from rapid or sustained increases in intracellular calcium to inhibitory effects, indicating a heterogeneous nature of these Prlr-expressing populations. These results enhance our understanding of mechanisms by which prolactin acts on hypothalamic neurones and provide insights into how prolactin might influence neuronal circuits in the mouse brain.
Reduced purine biosynthesis in humans after their divergence from Neandertals
Authors: Stepanova Vita , Moczulska Kaja Ewa , Vacano Guido N. , Ju Xiang-chun , Riesenberg Stephan , Macak Dominik , Maricic Tomislav , Dombrowski Linda , Schörnig Maria , Anastassiadis Konstantinos , Baker Oliver , Naumann Ronald , Khrameeva Ekaterina , Vanushkina Anna , Stekolschikova Elena , Kurochkin Ilia , Mazzarino Randall , Duval Nathan , Zubkov Dmitri , Giavalisco Patrick , Wilkinson Terry G. , Patterson David , Khaitovich Philipp , Pääbo Svante 
Published: May 2020

AbstractWe analyze the metabolomes of humans, chimpanzees and macaques in muscle, kidney and three different regions of the brain. Whereas several compounds in amino acid metabolism occur at either higher or lower concentrations in humans than in the other primates, metabolites in oxidative phosphorylation and purine biosynthesis are consistently present in lower concentrations in the brains of humans. In particular, metabolites downstream of adenylosuccinate lyase, which catalyzes two reactions in purine synthesis, occur at lower concentrations in humans. This enzyme carries an amino acid substitution that is present in all humans today but absent in Neandertals. By introducing the modern human substitution into the genomes of mice, as well as the ancestral, Neandertal-like substitution into the genomes of human cells, we show that this amino acid substitution is responsible for much or all of the reduction ofde novosynthesis of purines in humans.