bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chest Computed Tomography for the Diagnosis of Patients with Coronavirus Disease 2019 (COVID-19): A Rapid Review and Meta-Analysis
Authors: Lv Meng , Wang Mengshu , Yang Nan , Luo Xufei , Li Wei , Chen Xin , Liu Yunlan , Ren Mengjuan , Zhang Xianzhuo , Wang Ling , Ma Yanfang , Lei Junqiang , Fukuoka Toshio , Ahn Hyeong Sik , Lee Myeong Soo , Luo Zhengxiu , Chen Yaolong , Liu Enmei , Tian Jinhui , Wang Xiaohui 
Published: April 2020

AbstractBackgroundThe outbreak of the coronavirus disease 2019 (COVID-19) has had a massive impact on the whole world. Computed tomography (CT) has been widely used in the diagnosis of this novel pneumonia. This study aims to understand the role of CT for the diagnosis and the main imaging manifestations of patients with COVID-19.MethodsWe conducted a rapid review and meta-analysis on studies about the use of chest CT for the diagnosis of COVID-19. We comprehensively searched databases and preprint servers on chest CT for patients with COVID-19 between 1 January 2020 and 31 March 2020. The primary outcome was the sensitivity of chest CT imaging. We also conducted subgroup analyses and evaluated the quality of evidence using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach.ResultsA total of 104 studies with 5694 patients were included. Using RT-PCR results as reference, a meta-analysis based on 64 studies estimated the sensitivity of chest CT imaging in COVID-19 was 99% (95% CI, 0.97-1.00). If case reports were excluded, the sensitivity in case series was 96% (95% CI, 0.93-0.99). The sensitivity of CT scan in confirmed patients under 18 years old was only 66% (95% CI, 0.11-1.00). The most common imaging manifestation was ground-glass opacities (GGO) which was found in 75% (95% CI, 0.68-0.82) of the patients. The pooled probability of bilateral involvement was 84% (95% CI, 0.81-0.88). The most commonly involved lobes were the right lower lobe (84%, 95% CI, 0.78-0.90) and left lower lobe (81%, 95% CI, 0.74-0.87). The quality of evidence was low across all outcomes.ConclusionsIn conclusion, this meta-analysis indicated that chest CT scan had a high sensitivity in diagnosis of patients with COVID-19. Therefore, CT can potentially be used to assist in the diagnosis of COVID-19.
The end of the social confinement in Spain and the COVID-19 re-emergence risk
Authors: López Leonardo , Rodó Xavier 
Published: April 2020

ABSTRACTAfter the spread of SARS-CoV-2 epidemic out of China, the world approaches the 2 million declared infected cases and death toll rises well above the 100 thousand. The course of pandemic evolution has shown great differences among countries and not much is yet known about the level of generated immunity, which might appear not to be long-lasting. In this situation, management of a recurrent disease seems to be a plausible scenario that countries worldwide will have to face, before effective drugs or a vaccine appear. Spain in Europe, appears to be the first country deciding to partly lift the strict social distancing regulations imposed. Whether this action may lead to further epidemic recrudescence, to a following second wave of cases or conversely, help return to previous normality, is a subject of great debate and interest to all other countries affected by COVID-19. Here we applied a modified SEIR compartmental model accounting for the spread of infection during the latent period, in which we had also incorporated effects of social confinement. We now modify this previous model configuration to mimic potential post-confinement scenarios, by simulating from instant massive liberation of different portions of the confined population, up to a more gradual incorporation of people to work. Results show how current lockdown conditions should be extended at least two weeks more to prevent a new escalation in cases and deaths, as well as a larger second wave occurring in just a few months. Conversely, best-case scenario in terms of lower COVID-19 incidence and casualties should gradually incorporate workers back in a daily proportion at most 30 percent higher than that of previous confinement. The former should begin not earlier than by the end of April and it would represent approximately 600 thousand people or a 3.75% rate for the whole of Spain.
How high and long will the COVID-19 wave be? A data-driven approach to model and predict the COVID-19 epidemic and the required capacity for the German health system
Authors: Klabunde Thomas , Giegerich Clemens 
Published: April 2020

AbstractBackground and objectiveIn March 2020 the SARS-CoV-2 outbreak has been declared as global pandemic. Most countries have implemented numerous “social distancing” measures in order to limit its transmission and control the outbreak. This study aims to describe the impact of these control measures on the spread of the disease for Italy and Germany, forecast the epidemic trend of COVID-19 in both countries and estimate the medical capacity requirements in terms of hospital beds and intensive care units (ICUs) for optimal clinical treatment of severe and critical COVID-19 patients, for the Germany health system.MethodsWe used an exponential decline function to model the trajectory of the daily growth rate of infections in Italy and Germany. A linear regression of the logarithmic growth rate functions of different stages allowed to describe the impact of the “social distancing” measures leading to a faster decline of the growth rate in both countries. We used the linear model to predict the number of diagnosed and fatal COVID-19 cases from April 10th until May 31st. For Germany we estimated the required daily number of hospital beds and intensive care units (ICU) using clinical observations on the average lengths of a hospital stay for the severe and critical COVID-19 patients.ResultsAnalyzing the data from Germany and Italy allowed us to identify changes in the trajectory of the growth rate of infection most likely resulted from the various “social distancing” measures implemented. In Italy a stronger decline in the growth rate was observed around the week of March 17th, whereas for Germany the stronger decline occurred approximately a week later (the week of March 23rd). Under the assumption that the impact of the measures will last, the total size of the outbreak can be estimated to 155,000 cases in Germany (range 140,000-180,000) and to 185,000 cases in Italy (range 175,000-200,000). For Germany the total number of deaths until May 31st is calculated to 3,850 (range 3,500-4,450). Based on the projected number of new COVID-19 cases we expect that the hospital capacity requirements for severe and critical cases in Germany will decline from the 2nd week of April onwards from 13,500 to ∼2500 hospital beds (range 1500-4300) and from 2500 to ∼500 ICU beds in early May (range 300-800).ConclusionsThe modeling effort presented here provides a valuable framework to capture the impact of the “social distancing” measures on the COVID-19 epidemic in European countries and to forecast the future trend of daily COVID-19 cases. It provides a tool for medical authorities in Germany and other countries to help inform the required hospital capacity of the health care system. Germany appears to be in the middle of the (first) COVID-19 outbreak wave and the German health system is well prepared to handle it with the available capacities.
Landscapes of transposable elements inApisspecies by meta-analysis
Authors: Yokoi Kakeru , Kimura Kiyoshi , Bono Hidemasa 
Published: April 2020

AbstractTransposable elements (TEs) are grouped into several classes with diverse sequences. Owing to their diversity, studies involving the detection, classification, and annotation of TEs are difficult tasks. Moreover, simple comparisons of TEs among different species with different methods can lead to misinterpretations. The genome data of several honey bee (Apis) species are available in public databases. Therefore, we conducted a meta-analysis of TEs, using 11 sets of genome data forApisspecies, in order to establish the basal TE data (termed here as the ‘landscape of TEs’). Consensus TE sequences were constructed and their distributions in theApisgenomes were determined. Our results showed that TEs from several limited families mainly consisted ofApisTEs and that more DNA/TcMar-Mariner consensus sequences and copies were present in allApisgenomes tested. In addition, more consensus sequences and copy numbers of DNA/TcMar-Mariner were detected inApis melliferathan in otherApisspecies. These results suggest that TcMar-Mariner might exertA. mellifera-specific effects on the hostA. melliferaspecies. In conclusion, our unified approach enabled comparison ofApisgenome sequences to determine the TE landscape, which provide novel evolutionary insights intoApisspecies.Simple SummaryStudies on the detection of transposable elements and their annotations have posed several challenges. For example, simple comparisons of transposable elements in different species using different methods can lead to misinterpretations. Thus, assembling data for transposable elements analyzed by unified methods is important for comparison purposes. Therefore, we performed a meta-analysis of transposable elements identified using genome datasets from 5Apisspecies (11 sets of genome data) and specific software to detect the transposable elements, which revealed the landscapes of transposable elements. We examined the types and locations of transposable elements in theApisgenomes. The landscapes of transposable elements showed that several limited transposable element families consisted mainly ofApis-associated transposable elements. These limited families include DNA/TcMar-Mariner and DNA/CMC-EnSpm. In addition, more DNA/TcMar-Mariner consensus sequences and copies were detected inApis melliferathan in otherApisspecies. These data suggest that TcMar-Mariner might exertA. mellifera-specific effects in the hostA. melliferaspecies. Our landscape data provide new insights intoApistransposable elements; furthermore, detailed analyses of our data could pave the way for new biological insights in this field.
Prostacyclin Promotes Degenerative Pathology in a Model of Alzheimer’s disease
Authors: Womack Tasha R. , Vollert Craig , Nwoko Odochi , Schmitt Monika , Montazari Sagi , Beckett Tina , Mayerich David , Murphy Michael Paul , Eriksen Jason L. 
Published: April 2020

AbstractAlzheimer’s disease (AD) is a progressive neurodegenerative disorder that is the most common cause of dementia in aged populations. A substantial amount of data demonstrates that chronic neuroinflammation can accelerate neurodegenerative pathologies, while epidemiological and experimental evidence suggests that the use of anti-inflammatory agents may be neuroprotective. In AD, chronic neuroinflammation results in the upregulation of cyclooxygenase and increased production of prostaglandin H2, a precursor for many vasoactive prostanoids. While it is well-established that many prostaglandins can modulate the progression of neurodegenerative disorders, the role of prostacyclin (PGI2) in the brain is poorly understood. We have conducted studies to assess the effect of elevated prostacyclin biosynthesis in a mouse model of AD. Upregulated prostacyclin expression significantly worsened multiple measures associated with amyloid disease pathologies. Mice overexpressing both amyloid and PGI2exhibited impaired learning and memory and increased anxiety-like behavior compared with non-transgenic and PGI2control mice. PGI2overexpression accelerated the development of amyloid accumulation in the brain and selectively increased the production of soluble amyloid-β 42. PGI2damaged the microvasculature through alterations in vascular length and branching; amyloid expression exacerbated these effects. Our findings demonstrate that chronic prostacyclin expression plays a novel and unexpected role that hastens the development of the AD phenotype.
α-Linolenic acid modulates phagocytosis of extracellular Tau and induces microglial migration
Authors: Desale Smita Eknath , Chinnathambi Subashchandrabose 
Published: April 2020

AbstractThe seeding effect of extracellular Tau species is an emerging aspect to study the Tauopathies in Alzheimer’s disease. Tau seeds enhance the propagation of disease along with its contribution to microglia-mediated inflammation. Omega-3 fatty acids are known to exert the anti-inflammatory property to microglia by modulating cell membrane compositions that influence various receptors expression and signaling cascade. The immunomodulatory function of omega-3 fatty acids exerts anti-inflammatory properties to microglia. Owing to the imparted anti-inflammatory nature enhance phagocytosis and increased migration property has been observed in microglia. The increased phagocytosis of extracellular Tau monomer and aggregates has been observed upon ALA exposure to microglia cells. The intracellular degradation of internalized Tau species was targeted by early and late endosomal markers Rab5 and Rab7. The increased levels of LAMP-2A and colocalization with internalized Tau indicated the degradationvialysosome. These results indicate the degradation of internalized Tau species in the presence of ALA instead of getting accumulated in the cell. The enhanced migratory ability of microglia in the presence of ALA induces the MTOC repolarization. Tau seeds greatly contribute to the spread of disease, one way to reduce the spreading is to reduce the presence of extracellular Tau seed. Microglia could be influenced to reduce extracellular Tau seed with dietary fatty acids. Our results suggest that dietary fatty acids ALA significantly enhances phagocytosis and intracellular degradation of internalized Tau. Enhanced migration supports the phagocytosis process. Our approach provides insights into the beneficial role of ALA as an anti-inflammatory dietary supplement to treat AD.
Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genusFicus(Moraceae)
Authors: Rasplus Jean-Yves , Rodriguez Lillian Jennifer , Sauné Laure , Peng Yang-Qiong , Bain Anthony , Kjellberg Finn , Harrison Rhett D. , Pereira Rodrigo A.S. , Ubaidillah Rosichon , Tollon-Cordet Christine , Gautier Mathieu , Rossi Jean-Pierre , Cruaud Astrid 
Published: April 2020

ABSTRACTDespite their ecological and evolutionary importance as key components of tropical ecosystems, the phylogeny of fig trees is still unresolved. We use restriction-site-associated DNA (RAD) sequencing (ca420kb) and 102 morphological characters to elucidate the relationships between 70 species ofFicusrepresenting all known subgenera and sections and five outgroups. We compare morphological and molecular results to highlight discrepancies and reveal possible inference bias. We analyse marker and taxon properties that may bias molecular inferences, with existing softwares and a new approach based on iterative principal component analysis to reduce variance between clusters of samples. For the first time, with both molecular and morphological data, we recover a monophyletic subgenusUrostigmaand a clade with all gynodioecious fig trees. However, our analyses show that it is not possible to homogenize evolutionary rates and GC content for all taxa prior to phylogenetic inference and that four competing positions for the root of the molecular tree are possible. The placement of the long-branched sectionPharmacosyceaas sister to all other fig trees is not supported by morphological data and considered as a result of a long branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides the genusFicusinto monoeciousversusgynodioecious species appears most likely. Active pollination is inferred as the ancestral state for all topologies, ambiguity remains for ancestral breeding system including for the favored topology, and it appears most likely that the ancestor of fig trees was a freestanding tree. Increasing sampling may improve results and would be at least as relevant as maximizing the number of sequenced regions given the strong heterogeneity in evolutionary rates, and to a lesser extent, base composition among species. Despite morphological plasticity and frequent homoplasy of multiple characters, we advocate giving a central role to morphology in our understanding of the evolution ofFicus, especially as it can help detect insidious systematic errors that tend to become more pronounced with larger molecular data sets.
Introduction of a leaky stop codon as molecular tool inChlamydomonas reinhardtii
Authors: Caspari Oliver D 
Published: April 2020

AbstractExpression of proteins in the chloroplast or mitochondria of the model green algaChlamydomonas reinhardtiican be achieved by directly inserting transgenes into organellar genomes, or through nuclear expression and post-translational import. A number of tools have been developed in the literature for achieving high expression levels from the nuclear genome despite messy genomic integration and widespread silencing of transgenes. Here, recent advances in the field are combined and two systems of bicistronic expression, based on ribosome reinitiation or ribosomal skip induced by a viral 2A sequence, are compared side-by-side. Further, the small subunit of Rubisco (RBCS) was developed as a functional nuclear reporter for successful chloroplast import and restoration of photosynthesis: To be able to combine RBCS with a Venus fluorescent reporter without compromising photosynthetic activity, a leaky stop codon is introduced as a novel molecular tool that allows the simultaneous expression of functional and fluorescently tagged versions of the protein from a single construct.
Uncovering of cytochrome P450 anatomy by SecStrAnnotator
Authors: Midlik Adam , Navrátilová Veronika , Moturu Taraka Ramji , Koča Jaroslav , Svobodová Radka , Berka Karel 
Published: April 2020

AbstractProtein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand.We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs) – a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals an anomalous group of bacterial CYPs with some typically eukaryotic features. Application of our workflow to other families could produce equally surprising findings.
DTA expression in mTas1r3+ cells lead to male infertility
Authors: Li Feng , Niu Bowen , Liu Lingling 
Published: April 2020

AbstractTAS1R taste receptors and their associated heterotrimeric G protein gustducin are strongly expressed in testis and sperm, but their functions and distribution in these tissues were unknown. Using transgenic mouse models, we show that taste signal transduction cascades (mTas1r3-Gnat3-Trmp5) are observed in testis form GFP transgenic mice. It is mTas1rs and mTas2rs, not Gnat3, that was expressed in leydig and sertoli cells. The pattern of mTas1r3 expression was different from that of mTas2r105 expression in seminiferous epithelium. Analysis of the seminiferous epithelium cycle show that both mTas1r3 and mTas2r105 is expressed in the spermatid stage, but mTas2r5 expression is found in spermatocyte stage. Conditional deletion of mTas1r3+ cells leads to male infertility, but do not affect the expression of taste signal transduction cascade during the spermatogenesis. The current results indicate a critical role for mTas1r3+ cell in sperm development and maturation.
IGF-1 facilitates extinction of conditioned fear
Authors: Noriega-Prieto José A. , Maglio Laura E. , Maroto Irene B. , Martin-Cortecero Jesús , Muñoz-Callejas Antonio , Callejo-Móstoles Marta , de Sevilla David Fernández 
Published: April 2020

SUMMARYInsulin-like growth factor-1 (IGF-1) plays a key role in synaptic plasticity, degenerative diseases, spatial learning, and anxiety-like behavioral processes. While IGF-1 regulates neuronal activity in many areas of the brain, its effect on synaptic plasticity and animal behavior dependent on the prefrontal cortex remain unexplored. Here, we show that IGF-1 induces a long-lasting depression of the medium and slow post-spike afterhyperpolarization (mAHP and sAHP), increasing the excitability of layer 5 pyramidal neurons of the infralimbic cortex. Besides, IGF-1 mediates a long-term depression of both inhibitory and excitatory synaptic transmission that results in a longterm potentiation of the postsynaptic potentials. We demonstrate that these synaptic and intrinsic regulatory processes mediated by IGF-1 favor the fear extinction memory. These results show novel functional consequences of IGF-1 signaling on animal behavior tasks dependent on the prefrontal cortex, revealing IGF-1 as a key element in the control of the fear extinction memory.Impact StatementIGF-1 modulates the neuronal firing and synaptic plasticity in infralimbic cortex, favoring the extinction memory
Severe asthma is associated with a remodeling of the pulmonary arteries in horses
Authors: Ceriotti Serena , Bullone Michela , Leclere Mathilde , Ferrucci Francesco , Lavoie Jean-Pierre 
Published: April 2020

AbstractPulmonary hypertension andcor pulmonaleare complications of severe equine asthma, as a consequence of pulmonary hypoxic vasoconstriction. However, as pulmonary hypertension is only partially reversible by oxygen administration, other etiological factors are likely involved. In human chronic obstructive pulmonary disease, pulmonary artery remodeling contributes to the development of pulmonary hypertension. In rodent models, pulmonary vascular remodeling is present as a consequence of allergic airway inflammation. The present study investigated the presence of remodeling of the pulmonary arteries in severe equine asthma, its distribution throughout the lungs, and its reversibility following long-term antigen avoidance strategies and inhaled corticosteroid administration. Using histomorphometry, the total wall area of pulmonary arteries from different regions of the lung of asthmatic horses and controls was measured. The smooth muscle mass of pulmonary arteries was also estimated on lung sections stained for α-smooth muscle actin. Reversibility of vascular changes in asthmatic horses was assessed after 1 year of antigen avoidance alone or treatment with inhaled fluticasone. Pulmonary arteries showed increased wall area in apical and caudodorsal lung regions of asthmatic horses in both exacerbation and remission. The pulmonary arteries smooth muscle mass was similarly increased. Both treatments reversed the increase in wall area. However, normalization of the vascular smooth muscle mass was observed only after treatment with antigen avoidance, but not with fluticasone. In conclusion, severe equine asthma is associated with remodeling of the pulmonary arteries consisting in an increased smooth muscle mass. The resulting narrowing of the artery lumen could enhance hypoxic vasoconstriction, contributing to pulmonary hypertension. Vascular smooth muscle mass normalization is better achieved by antigen avoidance than with inhaled corticosteroids.