bluuebunny/crossref_metadata_2025_split huggingface dataset:
Redeployment and training of healthcare professionals to Intensive Care during COVID-19: a systematic review
Authors: Vera San Juan Norha , Camilleri Matthew , Jeans John Paul , Monkhouse Alexandra , Chisnall Georgia , Vindrola-Padros Cecilia 
Published: January 2021

AbstractBackgroundA rapid influx of patients to intensive care and infection control measures during the COVID-19 pandemic required the rapid development of innovative redeployment and training strategies.MethodsWe conducted a systematic search of 9 databases including key terms related to intensive care AND training AND redeployment AND healthcare workers. Analysis consisted of a narrative synthesis of quantitative study outputs, and a framework-based thematic analysis of qualitative study outputs and grey literature. These results were then combined applying an interpretative synthesis.ResultsTwenty papers were analysed. These took place primarily in the UK (N=8, 40%) and USA (N=5, 25%). Themes included in the results are Redeployment: Implementation strategies and learnings; Redeployed staff experience and strategies to address their needs; Redeployed staff learning needs; Training formats offered and training evaluations; and Future redeployment and training concerns. Some of the redeployment implementation and training strategies documented in this review are: Skills-based redeployment, buddy support systems, and agreeing on locally-specific principles, rather than strict procedures.ConclusionThe COVID-19 pandemic presented unique challenges to deliver training promptly while following infection control recommendations and develop flexible redeployment strategies. This study synthesises original approaches to tackle these challenges which are relevant to inform the development of targeted and adaptative training and redeployment plans.
Potential contribution of climate conditions on COVID-19 pandemic transmission over West and North African countries
Authors: Diouf Ibrahima , Sy Souleymane , Senghor Habib , Fall Papa , Diouf Diarra , Diakhaté Moussa , Thiaw Wassila M. , Gaye Amadou T. 
Published: January 2021

AbstractThe COVID-19 disease, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is a very contagious disease that has killed many people around the world. According to the World Health Organization (WHO) data, the spread of the disease appears to be slower in Africa. Although a number of studies have been published on the relationship between meteorological parameters and COVID-19 transmission, the effects of climate conditions on COVID-19 remain largely unexplored and without consensus following the main research finding over Africa (often based on a single country or city). Here, using available epidemiological data over 275 days (i.e., from March 1 to November 30, 2020) taken from the European Center for Disease Prevention and Control of the European Union database and daily data of surface air temperature and humidity from the National Center for Environmental Prediction (NCEP), this paper investigates the potential contributions of climate conditions on COVID-19 transmission over 16 countries selected from three bioclimatic regions of Africa (i.e., Sahel, Maghreb and Gulf of Guinea). On average, our main findings highlight statistically significant inverse correlations between COVID-19 cases and temperature over the Maghreb and the Gulf of Guinea regions, whereas positive correlations are found in the Sahel, especially over the central part including Niger and Mali. Correlations with specific humidity and water vapor parameters display significant and positive values over the Sahelian and the Gulf of Guinean countries and negative values over the Maghreb countries. In other word, results imply that the COVID-19 pandemic transmission is influenced differently across the three bioclimatic regions: i) cold and dry environmental conditions over the Maghreb; ii) warm and humid conditions over the Sahel iii) cold and humid conditions over the Gulf of Guinea. These findings could be useful for decision-makers who plan public health and control measures in affected African countries and would have substantial implications for directing respiratory disease surveillance activities.
Agent-Based Simulation of Covid-19 Vaccination Policies in CovidSIMVL
Authors: Chang Ernie , Moselle Kenneth A. 
Published: January 2021

ABSTRACTAn agent-based infectious disease modeling tool (CovidSIMVL) is employed in this paper to explore outcomes associated with MRNA two-dose vaccination regimens set out in Emergency Use Authorization (EUA) documents submitted by Pfizer and Moderna to the US Department of Health & Human Services. As well, the paper explores outcomes associated with a third “Hybrid” policy that reflects ranges of expected levels of protection according to Pfizer and Moderna EUA’s, but entails a 35 day separation between first and second dose, which exceeds the 21 days set out in Pfizer documentation or the 28 days in Moderna documentation.Four CovidSIMVL parameters are varied in the course of 75 simulated clinical trials. Two relate directly to the vaccines and their impacts (duration between doses; degree of expected protection conferred by different vaccines following first or second dose). Two relate to the simulation contexts to which the vaccines are applied (degree of infectivity; duration of infectivity). The simulated trials demonstrate expected effects for timing of second dose, and for degree of protection associated with first and second dose of Pfizer and Moderna vaccines, and the effects are consistent with an assumed value of 75% for degree of protection after first and second doses for the Hybrid vaccine. However, the simulated trials suggest a more complex interaction between expected level of protection following first dose, timing of second dose and degree of infectivity. These results suggest that policy options should not be considered independent of the transmission dynamics that are manifested in the contexts in which the policies could be applied.CovidSIMVL embodies stochasticity in the mechanisms that govern viral transmission, and it treats the basic reproduction number (R0)as an emergent characteristic of transmission dynamics, not as a pre-set value that determines those dynamics. As such, results reported in this paper reflect outcomes that could happen, but do not necessarily reflect what is more or less likely to happen, given different configurations of parameters. The discussion section goes into some measure of detail regarding next steps that could be pursued to enhance the potential for agent-based models such as CovidSIMVL to inform exploration of possible vaccination policies, and to project outcomes that are possible or likely in local contexts, where stochasticity and heterogeneity of transmission must be featured in models that are intended to reflect local realism.
Assessing the efficacy of interventions to control indoor SARS-Cov-2 transmission: an agent-based modeling approach
Authors: Farthing Trevor S. , Lanzas Cristina 
Published: January 2021

AbstractIntervention strategies for minimizing indoor SARS-CoV-2 transmission are often based on anecdotal evidence because there is little evidence-based research to support them. We developed a spatially-explicit agent-based model for simulating indoor respiratory pathogen transmission, and used it to compare effects of four interventions on reducing individual-level SARS-CoV-2 transmission risk by simulating a well-known case study. We found that imposing movement restrictions and efficacious mask usage appear to have the greatest effects on reducing infection risk, but multiple concurrent interventions are required to minimize the proportion of susceptible individuals infected. Social distancing had little effect on reducing transmission if individuals move during the gathering. Furthermore, our results suggest that there is potential for ventilation airflow to expose susceptible people to aerosolized pathogens even if they are relatively far from infectious individuals. Maximizing rates of aerosol removal is the key to successful transmission-risk reduction when using ventilation systems as intervention tools.Article Summary LineImposing mask usage requirements, group size restrictions, duration limits, and social distancing policies can have additive, and in some cases multiplicative protective effects on SARS-CoV-2 infection risk during indoor events.
Air passenger travel and international surveillance data predict spatiotemporal variation in measles importations to the United States
Authors: Poterek Marya L. , Kraemer Moritz U.G. , Watts Alexander , Khan Kamran , Perkins T. Alex 
Published: January 2021

AbstractMeasles incidence in the United States has grown dramatically, as vaccination rates are declining and transmission internationally is on the rise. Measles virus is highly infectious and can cause severe symptoms and even death. Because imported cases are necessary drivers of outbreaks in non-endemic settings, predicting measles outbreaks in the US depends on predicting imported cases. To assess the predictability of imported measles cases, we performed a regression of imported measles cases in the US against an inflow variable that combines air travel data with international measles surveillance data. To understand the contribution of each data type to these predictions, we repeated the regression analysis with alternative versions of the inflow variable that replaced each data type with averaged values and with versions of the inflow variable that used modeled inputs. We assessed the performance of these regression models using correlation, coverage probability, and area under the curve statistics, including with resampling and cross-validation. Our regression model had good predictive ability with respect to the presence or absence of imported cases in a given state in a given year (AUC = 0.78) and the magnitude of imported cases (Pearson correlation = 0.84). By comparing alternative versions of the inflow variable averaging over different inputs, we found that both air travel data and international surveillance data contribute to the model’s ability to predict numbers of imported cases, and individually contribute to its ability to predict the presence or absence of imported cases. Predicted sources of imported measles cases varied considerably across years and US states, depending on which countries had high measles activity in a given year. Our results emphasize the importance of the relationship between global connectedness and the spread of measles.
Personalized Virus Load Curves of SARS-CoV-2 Infection
Authors: Hillen Thomas , Contreras Carlos , Newby Jay M. 
Published: January 2021

AbstractWe introduce an explicit function that describes virus-load curves on a patient-specific level. This function is based on simple and intuitive model parameters. It allows virus load analysis without solving a full virus load dynamic model. We validate our model on data from influenza A as well as SARS-CoV-2 infection data for Macaque monkeys and humans. Further, we compare the virus load function to an established target model of virus dynamics, which shows an excellent fit. Our virus-load function offers a new way to analyse patient virus load data, and it can be used as input to higher level models for the physiological effects of a virus infection, for models of tissue damage, and to estimate patient risks.
Do Pandemics Obey the Elliott Wave Principle of Financial Markets?
Authors: Dogra Prashant , Koay Eugene J. , Wang Zhihui , Vahidy Farhaan S. , Ferrari Mauro , Pasqualini Renata , Arap Wadih , Boom Marc L. , Sostman H. Dirk , Cristini Vittorio 
Published: January 2021

AbstractThe Elliott Wave principle is a time-honored, oft-used method for predicting variations in the financial markets. It is based on the notion that human emotions drive financial decisions. In the fight against COVID-19, human emotions are similarly decisive, for instance in that they determine one’s willingness to be vaccinated, and/or to follow preventive measures including the wearing of masks, the application of social distancing protocols, and frequent handwashing. On this basis, we postulated that the Elliott Wave Principle may similarly be used to predict the future evolution of the COVID-19 pandemic. We demonstrated that this method reproduces the data pattern especially well for USA (daily new cases). Potential scenarios were then extrapolated, from the best-case corresponding to a rapid, full vaccination of the population, to the utterly disastrous case of slow vaccination, and poor adherence to preventive protocols.
Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions
Authors: Salavati Mazdak , Woolley Shernae A. , Araya Yennifer Cortés , Halstead Michelle M. , Stenhouse Claire , Johnsson Martin , Ashworth Cheryl J. , Archibald Alan L. , Donadeu Francesc X. , Hassan Musa A. , Clark Emily L. 
Published: January 2021

AbstractThere is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programmes. In order to address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We have optimised the ‘Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)’ to profile regions of open chromatin in flash frozen pig muscle tissue samples. This protocol has allowed us to identify putative regulatory regions in semitendinosus muscle from 24 male piglets. We collected samples from the smallest, average, and largest sized male piglets from each litter through five developmental time points. The ATAC-Seq data were mapped to Sscrofa11.1 using Bowtie2 and Genrich was used for post-alignment peak-calling. Of the 4,661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with down regulation of genes involved in muscle development that were present in small sized foetal piglets but absent in large foetal piglets at day 90 of gestation. The dataset that we have generated provides: i) a resource for studies of genome regulation in pigs, and ii) contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programmes.
HLA-G gene editing: a novel therapeutic alternative in cancer immunotherapy
Authors: Palma María Belén , Roux Diana Tronik-Le , Amín Guadalupe , Castañeda Sheila , Möbbs Alan M. , Scarafia María Agustina , La Greca Alejandro , Daouya Marina , Poras Isabelle , Inda Ana María , Moro Lucía N. , Carosella Edgardo D. , García Marcela N. , Miriuka Santiago G. 
Published: January 2021

AbstractCancer immunotherapies based mainly on the blockade of immune-checkpoint (IC) molecules by anti-IC antibodies offer new alternatives for treatment in oncological diseases. However, a considerable proportion of patients remain unresponsive to them. Hence, the development of novel clinical immunotherapeutic approaches and/or targets are crucial. In this context, targeting the immune-checkpoint HLA-G/ILT2/ILT4 has caused great interest since it is abnormally expressed in several malignancies generating a tolerogenic microenvironment. Here, we used CRISPR/Cas9 gene editing to block the HLA-G expression in two tumor cell lines expressing HLA-G, including a renal cell carcinoma (RCC7) and a choriocarcinoma (JEG-3). Different sgRNA/Cas9 plasmids targetingHLA-Gexon 1 and 2 were transfected in both cell lines. Downregulation of HLA-G was reached to different degrees, including complete silencing. Most importantly, HLA-G – cells triggered a higherin vitroresponse of immune cells with respect to HLA-G + wild type cells. Altogether, we demonstrated for the first time the HLA-G downregulation through gene editing. We propose this approach as a first step to develop novel clinical immunotherapeutic approaches in cancer.
A chromosomal inversion drives evolution of multiple adaptive traits in deer mice
Authors: Hager Emily R. , Harringmeyer Olivia S. , Wooldridge T. Brock , Theingi Shunn , Gable Jacob T. , McFadden Sade , Neugeboren Beverly , Turner Kyle M. , Hoekstra Hopi E. 
Published: January 2021

AbstractA long-standing question in evolutionary biology is how differences in multiple traits can evolve quickly and be maintained together during local adaptation. Using forest and prairie ecotypes in deer mice, which differ in both tail length and coat color, we discovered a 41 Mb chromosomal inversion that is strongly linked to variation in both traits. The inversion maintains highly divergent loci in strong linkage disequilibrium and likely originated ~170 kya, long before the forest-prairie divergence ~10 kya. Consistent with a role in local adaptation, inversion frequency is associated with phenotype and habitat across both a local transect and the species range. Still, although eastern and western forest subspecies share similar phenotypes, the inversion is absent in eastern North America. This work highlights the significance of inversion polymorphisms for the establishment and maintenance of multiple locally adaptive traits in mammals, and demonstrates that, even within a species, parallel phenotypes may evolve through nonparallel genetic mechanisms.
Connectome: computation and visualization of cell-cell signaling topologies in single-cell systems data
Authors: Raredon Micha Sam Brickman , Yang Junchen , Garritano James , Wang Meng , Kushnir Dan , Schupp Jonas Christian , Adams Taylor S. , Greaney Allison M. , Leiby Katherine L. , Kaminski Naftali , Kluger Yuval , Levchenko Andre , Niklason Laura E. 
Published: January 2021

AbstractSingle-cell RNA-sequencing data can revolutionize our understanding of the patterns of cell-cell and ligand-receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns are major computational and epistemological challenges. Here, we presentConnectome, a software package for R which facilitates rapid calculation, and interactive exploration, of cell-cell signaling network topologies contained in single-cell RNA-sequencing data.Connectomecan be used with any reference set of known ligand-receptor mechanisms. It has built-in functionality to facilitate differential and comparative connectomics, in which complete mechanistic networks are quantitatively compared between systems.Connectomeincludes computational and graphical tools designed to analyze and explore cell-cell connectivity patterns across disparate single-cell datasets. We present approaches to quantify these topologies and discuss some of the biologic theory leading to their design.
Matriptase generates a tissue damage response via promoting Gq signalling, leading to RSK and DUOX activation
Authors: Jiajia MA , Scott Claire A. , Ying Na HO , Mahabaleshwar Harsha , Marsay Katherine S. , Zhang Changqing , Teow Christopher K. J. , Ser Sue NG , Zhang Weibin , Tergaonkar Vinay , Partridge Lynda J. , Roy Sudipto , Amaya Enrique , Carney Tom J. 
Published: January 2021

AbstractTissues respond to damage by increasing inflammation and epithelial cell motility. How damage detection and responses are orchestrated is unclear. Overexpression of the membrane bound protease, Matriptase, or mutation of its inhibitor, Hai1, results in inflamed epithelia, in which cells have increased motility and are prone to carcinoma. How Matriptase leads to these cellular outcomes is unknown. We demonstrate that zebrafishhai1amutants show increased H2O2, NfκB signalling, and IP3R-mediated calcium flashes, and that these promote inflammation, but do not generate epithelial cell motility. In contrast, inhibition of the Gq subunit rescues both thehai1ainflammation and epithelial phenotypes, with the latter recapitulated by the DAG analogue, PMA. We demonstrate thathai1ahas elevated pERK, inhibition of which rescues the epidermal defects. Finally, we identify RSK kinases as pERK targets disrupting adherens junctions inhai1amutants. Our work maps novel signalling cascades mediating the potent effects of Matriptase on epithelia, with implications for tissue damage response and carcinoma progression.
Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin
Authors: Manomohan Vandana , Saravanan Ramasamy , Pichler Rudolf , Murali Nagarajan , Sivakumar Karuppusamy , Sudhakar Krovvidi , Nachiappan Raja K , Periasamy Kathiravan 
Published: January 2021

ABSTRACTThe present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately higher. A significantly strong negative correlation coefficient of −0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The phylogeny and genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.