bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agreement between ranking metrics in network meta-analysis: an empirical study
Authors: Chiocchia Virginia , Nikolakopoulou Adriani , Papakonstantinou Theodoros , Egger Matthias , Salanti Georgia 
Published: February 2020

ABSTRACTObjectiveTo empirically explore the level of agreement of the treatment hierarchies from different ranking metrics in network meta-analysis (NMA) and to investigate how network characteristics influence the agreement.DesignEmpirical evaluation from re-analysis of network meta-analyses.Data232 networks of four or more interventions from randomised controlled trials, published between 1999 and 2015.MethodsWe calculated treatment hierarchies from several ranking metrics: relative treatment effects, probability of producing the best value (pBV) and the surface under the cumulative ranking curve (SUCRA). We estimated the level of agreement between the treatment hierarchies using different measures: Kendall’sτand Spearman’sρcorrelation; and the YilmazτAPand Average Overlap, to give more weight to the top of the rankings. Finally, we assessed how the amount of the information present in a network affects the agreement between treatment hierarchies, using the average variance, the relative range of variance, and the total sample size over the number of interventions of a network.ResultsOverall, the pairwise agreement was high for all treatment hierarchies obtained by the different ranking metrics. The highest agreement was observed between SUCRA and the relative treatment effect for both correlation and top-weighted measures whose medians were all equal to one. The agreement between rankings decreased for networks with less precise estimates and the hierarchies obtained frompBVappeared to be the most sensitive to large differences in the variance estimates. However, such large differences were rare.ConclusionsDifferent ranking metrics address different treatment hierarchy problems, however they produced similar rankings in the published networks. Researchers reporting NMA results can use the ranking metric they prefer, unless there are imprecise estimates or large imbalances in the variance estimates. In this case treatment hierarchies based on both probabilistic and non-probabilistic ranking metrics should be presented.STRENGTH AND LIMITATIONS OF THIS STUDYTo our knowledge, this is the first empirical study exploring the level of agreement of the treatment hierarchies from different ranking metrics in network meta-analysis (NMA).The study also explores how agreement is influenced by network characteristics.More than 200 published NMAs were re-analysed and three different ranking metrics calculated using both frequentist and Bayesian approaches.Other potential factors not investigated in this study could influence the agreement between hierarchies.
Ophthalmologic evidence against the interpersonal transmission of 2019 novel coronavirus through conjunctiva
Authors: Zhou Yunyun , Zeng Yuyang , Tong Yongqing , Chen Changzheng 
Published: February 2020

AbstractBackgroundThe emerging 2019 novel coronavirus (2019-nCoV) has pushed several countries into state of emergency all over the world. The possible transmission of 2019-nCoV by conjunctiva is controversial and has substantial public health implications.MethodsA retrospective cohort study was initiated to investigate the possible transmission of 2019-nCoV through aerosol contact with conjunctiva. We enrolled 67 cases of confirmed or suspected cases of novel coronavirus pneumonia (NCP) during 17–28 Jan 2020. Nasopharyngeal and conjunctival swabs were collected for real time RT-PCR analysis to detect 2019-nCoV.Results63 patients were identified as laboratory-confirmed NCP and the remaining four were suspected NCP. Conjunctival swab samples from one NCP patient yielded positive PCR results and two NCP patients yielded probable positive PCR results. None of the three patients had ocular symptoms. The only one NCP patient with conjunctivitis as the first symptom had negative conjunctival sac 2019-nCoV test. Conjunctival swab samples from the four suspected cases of NCIP were negative.Conclusion2019-nCoV can be detected in the conjunctival sac of patients with NCP. Through clinical analysis, viral transmission via the conjunctival route was not supported by the data. Good clinical protection can effectively cut off the transmission path.
Healthcare-resource-adjusted vulnerabilities towards the 2019-nCoV epidemic across China
Authors: Zhou Hanchu , Yang Jiannan , Tang Kaicheng , Zhang Qingpeng , Cao Zhidong , Pfeiffer Dirk , Zeng Daniel Dajun 
Published: February 2020

AbstractWe integrate the human movement and healthcare resource data to identify cities with high vulnerability towards the 2019-nCoV epidemic with respect to available health resources. The results inform public health responses in multiple ways.
TheSeminavis robustagenome provides insights into the evolutionary adaptations of benthic diatoms
Authors: Osuna-Cruz Cristina Maria , Bilcke Gust , Vancaester Emmelien , De Decker Sam , Poulsen Nicole , Bulankova Petra , Verhelst Bram , Audoor Sien , Stojanovova Darja , Pargana Aikaterini , Russo Monia , Stock Frederike , Cirri Emilio , Brembu Tore , Pohnert Georg , Winge Per , Bones Atle M. , Piganeu Gwenael , Ferrante Maria Immacolata , Mock Thomas , Sterck Lieven , Sabbe Koen , De Veylder Lieven , Vyverman Wim , Vandepoele Klaas 
Published: February 2020

AbstractBenthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatomSeminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer new insights on the genetic diversity and gene functions in benthic diatoms.
Aerial attack strategies of bat-hunting hawks, and the dilution effect of swarming
Authors: Brighton Caroline H. , Zusi Lillias , McGowan Kathryn , Kinniry Morgan , Kloepper Laura N. , Taylor Graham K. 
Published: February 2020

AbstractAggregation behaviors can often reduce predation risk, whether through dilution, confusion, or vigilance effects, but these effects are challenging to measure under natural conditions, involving strong interactions between the behaviors of predators and prey. Here we study aerial predation of massive swarms of Brazilian free-tailed batsTadarida brasiliensisby Swainson’s hawksButeo swainsoni, testing how the behavioral strategies of predator and prey influence catch success and predation risk. The hawks achieved high overall catch success, but they were no more successful against lone bats than against bats flying in column formation. There was therefore no evidence of any net vigilance or confusion effect, and hawks attacking the column benefitted from the opportunity to make several attempted grabs. Even so, the bats’ overall risk of predation was an order of magnitude higher when flying alone. Attacks on lone bats (∼10% of attacks) were greatly overrepresented relative to the proportion of bats classified as flying alone (∼0.2%), so dilution is both necessary and sufficient to explain the higher survival rates of bats flying in the column. From the hawks’ perspective, their odds of catching a bat more than trebled if the attack involved a stoop rather than level flight, or a rolling rather than pitching grab maneuver. These behavioral tactics were independently deployed in nearly three-quarters of all attacks. Hence, whereas the survival rate of a bat depends principally on whether it flies alone or in a group, the catch success of a hawk depends principally on how it maneuvers to attack.Lay summaryBats emerging by daylight from a massive desert roost are able to minimise their predation risk by maintaining tight column formation, because the hawks that attack them target stragglers disproportionately often. Whereas the predation risk of a bat therefore depends on how it maintains its position within the swarm, the catch success of a hawk depends on how it maneuvers to attack. Catch success is maximised by executing a stooping dive or a rolling grab.
Structural insights into secretory immunoglobulin A and its interaction with a pneumococcal adhesin
Authors: Wang Yuxin , Wang Guopeng , Li Yaxin , Shen Hao , Chu Huarui , Gao Ning , Xiao Junyu 
Published: February 2020

AbstractSecretory Immunoglobulin A (SIgA) is the most abundant antibody at the mucosal surface. SIgA possesses two additional subunits besides IgA: the joining chain (J-chain) and secretory component (SC). SC is the ectodomain of the polymeric immunoglobulin receptor (pIgR), which functions to transport IgA to the mucosa. The underlying mechanism of how the J-chain and pIgR/SC facilitates the assembly and secretion of SIgA remains to be understood. During the infection ofStreptococcus pneumoniae, a pneumococcal adhesin SpsA hijacks SIgA and unliganded pIgR/SC to evade host defense and gain entry to human cells. How SpsA specifically targets SIgA and pIgR/SC also remains unclear. Here we report a cryo-electron microscopy structure of the Fc region of human IgA1 (Fcα) in complex with J-chain and SC (Fcα-J-SC), which reveals the organization principle of SIgA. We also present the structure of Fcα-J-SC in complex with SpsA, which uncovers the specific interaction between SpsA and human pIgR/SC. These results advance the molecular understanding of SIgA and shed light on the pathogenesis ofS. pneumoniae.
To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multiple-task deep neural networks
Authors: Sun Zhe , Zheng Shuangjia , Zhao Huiying , Niu Zhangming , Lu Yutong , Pan Yi , Yang Yuedong 
Published: February 2020

AbstractMotivationThe interactions of proteins with DNA, RNA, peptide, and carbohydrate play key roles in various biological processes. The studies of uncharacterized protein–molecules interactions could be aided by accurate predictions of residues that bind with partner molecules. However, the existing methods for predicting binding residues on proteins remain of relatively low accuracies due to the limited number of complex structures in databases. As different types of molecules partially share chemical mechanisms, the predictions for each molecular type should benefit from the binding information with other molecules types.ResultsIn this study, we employed a multiple task deep learning strategy to develop a new sequence-based method for simultaneously predicting binding residues/sites with multiple important molecule types named MTDsite. By combining four training sets for DNA, RNA, peptide, and carbohydrate-binding proteins, our method yielded accurate and robust predictions with AUC values of 0.852, 0836, 0.758, and 0.776 on their respective independent test sets, which are 0.52 to 6.6% better than other state-of-the-art methods. More importantly, this study provides a new strategy to improve predictions by combining multiple similar tasks.Availabilityhttp://biomed.nscc-gz.cn/server/MTDsite/Contactyangyd25@mail.sysu.edu.cn
Expression ofdlxgenes in the normal and regenerating brain of adult zebrafish
Authors: Weinschutz Mendes Hellen , Taktek Mariam , Duret Thomas , Ekker Marc 
Published: February 2020

AbstractDysfunctions in the GABAergic system lead to various pathological conditions and impaired inhibitory function is one of the causes behind neuropathies characterized by neuronal hyper excitability. TheDlxhomeobox genes are involved in the development of nervous system, neural crest, brachial arches and developing appendages.Dlxgenes also take part in neuronal migration and differentiation during development, more precisely, in the migration and differentiation of GABAergic neurons. Functional analysis ofdlxgenes has mainly been carried out in developing zebrafish embryos and larvae; however information regarding the expression and roles of these genes in the adult zebrafish brain is still lacking. The extensive neurogenesis that takes place in the brain of adult zebrafish makes them a good model for the visualization of mechanisms involvingdlxgenes during adulthood in physiological conditions and during regeneration of the nervous system. We have identified the adult brain regions where transcripts ofdlx1a, dlx2a, dlx5aanddlx6agenes are normally found and have confirmed that within telencephalic domains, there is high overlapping expression of the fourdlxparalogs with a marker for GABAergic neurons. Co-localization analyses carried with the Tg(dlx6a-1.4kbdlx5a/dlx6a:GFP) reporter line have also shown that in some areas of the diencephalon, cells expressing thedlx5a/6abigene may have a neural stem cell identity by co-localizing with a Sox2 antibody. Furthermore, investigations in a response to stab wound lesions, have demonstrated a possible participation of thedlx5a/6abigene, most likely, ofdlx5aduring the regeneration of the adult zebrafish brain. These data suggest a possible participation ofdlx-expressing cells during brain regeneration in adult zebrafish and also provide information on the role ofdlxgenes under normal physiological conditions in adults.
Site wind right: Identifying low-impact wind development areas in the Central United States
Authors: Hise Chris , Obermeyer Brian , Ahlering Marissa , Wilkinson Jessica , Fargione Joseph 
Published: February 2020

AbstractTo help avoid the most catastrophic effects of climate change, society needs to achieve net-zero greenhouse gas emissions by mid-century. Wind energy provides a clean, renewable source of electricity; however, improperly sited wind facilities pose known threats to wildlife populations and contribute to degradation of natural habitats. To support a rapid transition to low-carbon energy while protecting imperiled species, we identified potential low-impact areas for wind development in a 17-state region of the central U.S. By combining maps of sensitive habitats and species with wind speed and land use information, we demonstrate that there is significant potential to develop wind energy in the Great Plains while avoiding significant negative impacts to wildlife. These low-impact areas have the potential to yield approximately 1,099-1,832 GW of wind capacity. This is equivalent to 10-18 times current U.S. installed wind capacity. Our analysis demonstrates that ambitious low-carbon energy goals are achievable on sites with minimal risk of wildlife conflict.
Correlation between the immuno-virological response and the nutritional profile of treatment-experienced HIV-infected patients in the East region of Cameroon
Authors: Aissatou Abba , Fokam Joseph , Kamgaing Rachel Simo , Yimga Junie Flore , Ka’e Aude Christelle , Nka Alex Durand , Tommo Tchouaket Michel Carlos , Chenwi Ambe Collins , Jagni Semengue Ezechiel Ngoufack , Ndjolo Alexis , Sosso Samuel Martin 
Published: February 2020

AbstractBackgroundHIV management remains concerning and even more challenging in the frame of comorbidities like malnutrition that favors disease progression and mortality in resource-limited settings (RLS).ObjectiveTo evaluate the correlation between immuno-virological responses and the nutritional profile of HIV-infected individuals receiving antiretroviral therapy (ART).MethodsA cross-sectional study was conducted from October to December 2018 among 146 consenting participants enrolled in two health facilities of the East-Region of Cameroon. Socio-demographic data, basic clinical information and treatment history were collected; blood samples were collected by venipuncture for laboratory analysis (HIV-1 viral load, CD4-CD8 Tcells measurement and biochemical analysis) performed at the “Chantal Biya” International Reference Center”, Yaounde, Cameroon. Nutritional profile was evaluated using anthropometric and biochemical parameters. Data were analyzed using Excel 2016, Graph pad prism version 6 and R.version3.5.0; Spearman correlation was used; with p<0.05 considered statistically significant.ResultsMedian [IQR] age was 42 [33-51] years, 76.0% (111/146) were female and median [IQR] duration on ART was 54 [28-86] months. Of these participants, 11.6% (17/146) were underweight based on the body mass index and 4.7% (7/146) were at the stage of advanced weight loss. According to immunovirological responses, 44.5% (65/146) were immunocompromised (CD4<500 cell/µl) and 75.3% (110/146) had an undetectable viremia (<40 copies/mL). CD4 count inversely correlated with total protein concentration (r=-0.18, p=0.030) and viremia was inversely correlated with total cholesterol (r=-0.65; p=0.001), and positively correlated with total protein (r=0.28; p<0.001) and seemingly with triglycerides (r=0.27; p=0.070) concentrations.ConclusionIn this RLS with patients having about five years of ART-experience, half are immunocompromised while the majority have achieved good virological response. Interestingly, one out of eight patients might be experiencing malnutrition. Specifically, increasing CD4 may favour hypo-proteinemia while increasing viral load may prone hyper-proteinemia and hypo-cholesterolemia. Further studies are needed in RLS with high burden of HIV-infection.
Profile-likelihood Bayesian model averaging for two-sample summary data Mendelian randomization in the presence of horizontal pleiotropy
Authors: Shapland Chin Yang , Zhao Qingyuan , Bowden Jack 
Published: February 2020

AbstractTwo-sample summary data Mendelian randomisation is a popular method for assessing causality in epidemiology, by using genetic variants as instrumental variables. If genes exert pleiotropic effects on the outcome not entirely through the exposure of interest, this can lead to heterogeneous and (potentially) biased estimates of causal effect. We investigate the use of Bayesian model averaging to preferentially search the space of models with the highest posterior likelihood. We develop a Metropolis-Hasting algorithm to perform the search using the recently developed Robust Adjusted Profile Likelihood of Zhao et al as the basis for defining a posterior distribution that efficiently accounts for pleiotropic and weak instrument bias. We demonstrate how our general modelling approach can be extended from a standard one-parameter causal model to a two-parameter model, which allows a large proportion of SNPs to violate the Instrument Strength Independent of Direct Effect assumption. We use Monte Carlo simulations to illustrate our methods and compare it to several related approaches. We finish by applying our approach in practice to investigate the causal role of cholesterol on the development age-related macular degeneration.
Integrating multimodal data sets into a mathematical framework to describe and predict therapeutic resistance in cancer
Authors: Johnson Kaitlyn , Howard Grant R. , Morgan Daylin , Brenner Eric A. , Gardner Andrea L. , Durrett Russell E. , Mo William , Al’Khafaji Aziz , Sontag Eduardo D. , Jarrett Angela M. , Yankeelov Thomas E. , Brock Amy 
Published: February 2020

SummaryA significant challenge in the field of biomedicine is the development of methods to integrate the multitude of dispersed data sets into comprehensive frameworks to be used to generate optimal clinical decisions. Recent technological advances in single cell analysis allow for high-dimensional molecular characterization of cells and populations, but to date, few mathematical models have attempted to integrate measurements from the single cell scale with other data types. Here, we present a framework that actionizes static outputs from a machine learning model and leverages these as measurements of state variables in a dynamic mechanistic model of treatment response. We apply this framework to breast cancer cells to integrate single cell transcriptomic data with longitudinal population-size data. We demonstrate that the explicit inclusion of the transcriptomic information in the parameter estimation is critical for identification of the model parameters and enables accurate prediction of new treatment regimens. Inclusion of the transcriptomic data improves predictive accuracy in new treatment response dynamics with a concordance correlation coefficient (CCC) of 0.89 compared to a prediction accuracy of CCC = 0.79 without integration of the single cell RNA sequencing (scRNA-seq) data directly into the model calibration. To the best our knowledge, this is the first work that explicitly integrates single cell clonally-resolved transcriptome datasets with longitudinal treatment response data into a mechanistic mathematical model of drug resistance dynamics. We anticipate this approach to be a first step that demonstrates the feasibility of incorporating multimodal data sets into identifiable mathematical models to develop optimized treatment regimens from data.
How many bird and mammal extinctions has recent conservation action prevented?
Authors: Bolam Friederike C. , Mair Louise , Angelico Marco , Brooks Thomas M. , Burgman Mark , Hermes Claudia , Hoffmann Michael , Martin Rob W. , McGowan Philip J.K. , Rodrigues Ana S.L. , Rondinini Carlo , Wheatley Hannah , Bedolla-Guzmán Yuliana , Calzada Javier , Child Matthew F. , Cranswick Peter A. , Dickman Christopher R. , Fessl Birgit , Fisher Diana O. , Garnett Stephen T. , Groombridge Jim J. , Johnson Christopher N. , Kennerley Rosalind J. , King Sarah R.B. , Lamoreux John F. , Lees Alexander C. , Lens Luc , Mahood Simon P. , Mallon David P. , Meijaard Erik , Méndez-Sánchez Federico , Percequillo Alexandre Reis , Regan Tracey J. , Renjifo Luis Miguel , Rivers Malin C. , Roach Nicolette S. , Roxburgh Lizanne , Safford Roger J. , Salaman Paul , Squires Tom , Vázquez-Domínguez Ella , Visconti Piero , Westrip James R.S. , Woinarski John C.Z. , Young Richard P. , Butchart Stuart H.M. 
Published: February 2020

AbstractAichi Target 12 of the Convention on Biological Diversity (CBD) aims to ‘prevent extinctions of known threatened species’. To measure its success, we used a Delphi expert elicitation method to estimate the number of bird and mammal species whose extinctions were prevented by conservation action in 1993 - 2020 (the lifetime of the CBD) and 2010 - 2020 (the timing of Aichi Target 12). We found that conservation prevented 21–32 bird and 7–16 mammal extinctions since 1993, and 9–18 bird and 2–7 mammal extinctions since 2010. Many remain highly threatened, and may still become extinct in the near future. Nonetheless, given that ten bird and five mammal species did go extinct (or are strongly suspected to) since 1993, extinction rates would have been 2.9–4.2 times greater without conservation action. While policy commitments have fostered significant conservation achievements, future biodiversity action needs to be scaled up to avert additional extinctions.