bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mathematical modeling of the SARS-CoV-2 epidemic in Qatar and its impact on the national response to COVID-19
Authors: Ayoub Houssein H. , Chemaitelly Hiam , Seedat Shaheen , Makhoul Monia , Kanaani Zaina Al , Khal Abdullatif Al , Kuwari Einas Al , Butt Adeel A. , Coyle Peter , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Yassine Hadi M. , Al Kuwari Mohamed G. , Al Romaihi Hamad Eid , Al-Thani Mohamed H. , Bertollini Roberto , Abu Raddad Laith J. 
Published: November 2020

AbstractBackgroundMathematical modeling constitutes an important tool for planning robust responses to epidemics. This study was conducted to guide the Qatari national response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic. The study investigated the time course of the epidemic, forecasted healthcare needs, predicted the impact of social and physical distancing restrictions, and rationalized and justified easing of restrictions.MethodsAn age-structured deterministic model was constructed to describe SARS-CoV-2 transmission dynamics and disease progression throughout the population.ResultsThe enforced social and physical distancing interventions flattened the epidemic curve, reducing the peaks for incidence, prevalence, acute-care hospitalization, and intensive care unit (ICU) hospitalizations by 87%, 86%, 76%, and 78%, respectively. The daily number of new infections was predicted to peak at 12,750 on May 23, and active-infection prevalence was predicted to peak at 3.2% on May 25. Daily acute-care and ICU-care hospital admissions and occupancy were forecast accurately and precisely. By October 15, 2020, the basic reproduction numberR0had varied between 1.07-2.78, and 50.8% of the population were estimated to have been infected (1.43 million infections). The proportion of actual infections diagnosed was estimated at 11.6%. Applying the concept ofRttuning, gradual easing of restrictions was rationalized and justified to start on June 15, 2020, whenRtdeclined to 0.7, to buffer the increased interpersonal contact with easing of restrictions and to minimize the risk of a second wave. No second wave has materialized as of October 15, 2020, five months after the epidemic peak.ConclusionsUse of modeling and forecasting to guide the national response proved to be a successful strategy, reducing the toll of the epidemic to a manageable level for the healthcare system.
Continuously-Encoded Deep Recurrent Networks for Interpretable Knowledge Tracing in Speech-Language and Cognitive Therapy
Authors: Dadgar-Kiani Ehsan , Anantha Veera 
Published: November 2020

AbstractIntelligent Tutoring Systems (ITS), developed over the last few decades, have been especially important in delivering online education. These systems use Knowledge Tracing (KT) to model a student’s understanding of concepts as they perform exercises. Recently, there have been several advancements using Recurrent Neural Networks (RNNs) to develop Deep Knowledge Tracing (DKT) that eliminates the need for manually encoding the student knowledge space. In online education, these models are crucial for predicting student performance and designing personalized curricula (sequence of courses and exercises). In this paper we develop a novel Knowledge Tracing model, called Continuously-encoded Deep Knowledge Tracing (CE-DKT) to automatically encode the user’s knowledge space, when the user’s skill in a given task is continuous-valued instead of binary. We then apply Knowledge tracing, specifically CE-DKT, to the context of digital therapy. Specifically, patients suffering from various neurological disorders such as aphasia, traumatic brain injury, or dementia are often prescribed speech, language and cognitive therapy exercises to perform from a set of predefined workbooks that are not personalized for the patient. We use CE-DKT to automatically encode a patient’s skill level across different tasks, and predict how the patient will perform on unseen tasks. We use data from the digital therapy platform, Constant Therapy, to train a CE-DKT model and demonstrate its high degree of accuracy in predicting a patient’s performance in a digital therapy application. We also demonstrate how to extract interpretable confidence intervals from this model and how to trace predictions to previous tasks using time-step level feature importance. Finally, we describe how this model can be applied to significantly enhance future digital therapy platforms and online student learning systems.
Therapeutic use of convalescent plasma in COVID-19 patients with immunodeficiency
Authors: Senefeld Jonathon W. , Klassen Stephen A. , Ford Shane K. , Wiggins Chad C. , Bostrom Bruce C. , Thompson Michael A. , Baker Sarah E. , Nicholson Wayne T. , Johnson Patrick W. , Carter Rickey E. , Henderson Jeffrey P. , Hartman William R. , Pirofski Liise-anne , Wright R. Scott , Fairweather DeLisa , Bruno Katelyn A. , Paneth Nigel S. , Casadevall Arturo , Joyner Michael J. 
Published: November 2020

0AbstractIn the absence of effective countermeasures, human convalescent plasma has been widely used to treat severe acute respiratory syndrome coronavirus 2 including among patients with innate or acquired immunodeficiency. However, the association between COVID-19-associated mortality in patients with immunodeficiency and therapeutic use of convalescent plasma is unknown. We review clinical features and treatment protocols of COVID-19 patients with immunodeficiency after treatment with human convalescent plasma. We also discuss the time course and clinical features of recovery. These insights provide evidence for the need to develop a clear treatment protocol for COVID-19 patients with immunodeficiency and support the efficacy of convalescent plasma in patients with primary or secondary immunodeficiency.
Spatial dynamics of SARS-Cov-2 and reduced risk of contagion: evidence from the second Italian epidemic wave*
Authors: Buonanno Paolo , Galletta Sergio , Puca Marcello 
Published: November 2020

AbstractWe highlight a negative association between the severity of the first-wave of SARS-Cov-2 and the spread of the virus during the second-wave. Analyzing data of a sample of municipalities from the Italian region of Lombardy, we find that a one standard deviation increase in excess of mortality during the first-wave is associated with a reduction of approximately 30% in the number of detected infected individuals in the initial phase of the second-wave. Our findings may reflect a behavioral response in more severely hit areas as well as a cross-protection between successive waves.JEL ClassificationI10; I18
cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters
Authors: Gilchrist Cameron L.M. , Booth Thomas J. , van Wersch Bram , van Grieken Liana , Medema Marnix H. , Chooi Yit-Heng 
Published: November 2020

AbstractGenes involved in coordinated biological pathways, including metabolism, drug resistance and virulence, are often collocalised as gene clusters. Identifying homologous gene clusters aids in the study of their function and evolution, however existing tools are limited to searching local sequence databases. Tools for remotely searching public databases are necessary to keep pace with the rapid growth of online genomic data. Here, we presentcblaster, a Python based tool to rapidly detect collocated genes in local and remote databases.cblasteris easy to use, offering both a command line and a user-friendly graphical user interface (GUI). It generates outputs that enable intuitive visualisations of large datasets, and can be readily incorporated into larger bioinformatic pipelines.cblasteris a significant update to the comparative genomics toolbox.cblastersource code and documentation is freely available from GitHub under the MIT license (github.com/gamcil/cblaster).
clinker & clustermap.js: Automatic generation of gene cluster comparison figures
Authors: Gilchrist Cameron L.M. , Chooi Yit-Heng 
Published: November 2020

AbstractSummaryGenes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and evolutionary history. However, comparison and visualisation of gene cluster homology is a tedious process, particularly when many clusters are being compared. Here, we presentclinker, a Python based tool, andclustermap.js, a companion JavaScript visualisation library, which used together can automatically generate accurate, interactive, publication-quality gene cluster comparison figures directly from sequence files.Availability and ImplementationSource code and documentation forclinkerandclustermap.jsis available on GitHub (github.com/gamcil/clinkerandgithub.com/gamcil/clustermap.js, respectively) under the MIT license.clinkercan be installed directly from the Python Package Index viapip.ContactE-mail:cameron.gilchrist@research.uwa.edu.au,yitheng.chooi@uwa.edu.au
Resistance of endothelial cells to SARS-CoV-2 infectionin vitro
Authors: Ahmetaj-Shala Blerina , Peacock Thomas P. , Baillon Laury , Swann Olivia C. , Gashaw Hime , Barclay Wendy S. , Mitchell Jane A. 
Published: November 2020

AbstractRationaleThe secondary thrombotic/vascular clinical syndrome of COVID-19 suggests that SARS-CoV-2 infects not only respiratory epithelium but also the endothelium activating thrombotic pathways, disrupting barrier function and allowing access of the virus to other organs of the body. However, a direct test of susceptibility to SARS-CoV-2 of authentic endothelial cell lines has not been performed.ObjectiveTo determine infectibility of primary endothelial cell lines with live SARS-CoV-2 and pseudoviruses expressing SARS-CoV-2 spike protein.Methods and ResultsExpression of ACE2 and BSG pathways genes was determined in three types of endothelial cells; blood outgrowth, lung microvascular and aortic endothelial cells. For comparison nasal epithelial cells, Vero E6 cells (primate kidney fibroblast cell line) and HEK 293T cells (human embryonic kidney cells) transfected with either ACE2 or BSG were used as controls. Endothelial and Vero E6 cells were treated with live SARS-CoV-2 virus for 1 hour and imaged at 24 and 72 hours post infection. Pseudoviruses containing SARS-CoV-2, Ebola and Vesicular Stomatis Virus glycoproteins were generated and added to endothelial cells and HEK 239Ts for 2 hours and infection measured using luminescence at 48 hours post infection. Compared to nasal epithelial cells, endothelial cells expressed low or undetectable levels of ACE2 and TMPRSS2 but comparable levels of BSG, PPIA and PPIB. Endothelial cells showed no susceptibility to live SARS-CoV-2 or SARS-CoV-2 pseudovirus (but showed susceptibility to Ebola and Vesicular Stomatitis Virus). Overexpression of ACE2 but not BSG in HEK 239T cells conferred SARS-CoV-2 pseudovirus entry. Endothelial cells primed with IL-1ß remained resistant to SARS-CoV-2.ConclusionEndothelial cells are resistant to infection with SARS-CoV-2 virus, in line with relatively low levels of ACE2 and TMPRSS2, suggesting that the vascular dysfunction and thrombosis seen in severe COVID-19 is a result of factors released by adjacent infected cells (e.g. epithelial cells) and/or circulating, systemic inflammatory mediators.
Revision of Indian Bipaliid species with description of a new species,Bipalium bengalensisfrom West Bengal, India (Platyhelminthes: Tricladida: Terricola)
Authors: Bhakat Somnath 
Published: November 2020

AbstractA new species of Bipaliid land planarian,Bipalium bengalensisis described from Suri, West Bengal, India. The species is jet black in colour without any band or line but with a thin indistinct mid-dorsal groove. Semilunar head margin is pinkish in live condition with numerous eyes on its margin. Body length (BL) ranged from 19.00 to 45.00mm and width varied from 9.59 to 13.16% BL. Position of mouth and gonopore from anterior end ranged from 51.47 to 60.00% BL and 67.40 to 75.00 % BL respectively. Comparisons were made with its Indian as well as Bengal congeners.Salient features, distribution and biometric data of all the 29 species of Indian Bipaliid land planarians are revised thoroughly. Genus controversy in Bipaliid taxonomy is critically discussed and a proposal of only two generaBipaliumandHumbertiumis suggested.
Beta and theta oscillations correlate with subjective time during musical improvisation in ecological and controlled settings: a single subject study
Authors: Farrugia Nicolas , Lamouroux Alix , Rocher Christophe , Bouvet Jules , Lioi Giulia 
Published: November 2020

AbstractIn this paper, we describe the results of a single subject study attempting at a better understanding of the subjective state during musical improvisation. In a first experiment, we setup an ecological paradigm measuring EEG on a musician in free improvised concerts with an audience, followed by retrospective rating of the mental state of the improviser. We introduce Subjective Temporal Resolution (STR), a retrospective rating assessing the instantaneous quantization of subjective timing of the improviser. We identified high and low STR states using Hidden Markov Models in two performances, and were able to decode those states using supervised learning on instantaneous EEG power spectrum, showing increases in theta and alpha power with high STR values. In a second experiment, we found an increase of theta and beta power when experimentally manipulating STR in a musical improvisation imagery experiment. These results are interpreted with respect to previous research on flow state in creativity, as well as with the temporal processing literature. We suggest that a component of the subjective state of musical improvisation may be reflected in an underlying mechanism related to the subjective quantization of time. We also demonstrate the feasibility of single case studies of musical improvisation using brain activity measurements and retrospective reports, by obtaining consistent results across multiple sessions.
Retardation of folding rates of substrate proteins in the nanocage of GroEL
Authors: Koculi Eda , Thirumalai D. 
Published: November 2020

AbstractTheE. Coli. ATP-consuming chaperonin machinery, a complex between GroEL and GroES, has evolved to facilitate folding of substrate proteins (SPs) that cannot do so spontaneously. A series of kinetic experiments show that the SPs are encapsulated in the GroEL/ES nano cage for a short duration. If confining the SPs in the predominantly polar cage of GroEL in order to help folding, the assisted folding rate, relative to the bulk value, shouldalwaysbe enhanced. Here, we show that this is not the case for the folding of rhodanese in the presence of the full machinery of GroEL/ES and ATP. The assisted folding rate of rhodanese decreases. Based on our finding and those reported in other studies, we suggest that the ATP-consuming chaperonin machinery has evolved to optimize the product of the folding rate and the yield of the folded SPs on the biological time scale. Neither the rate nor the yield is separately maximized.
Evolution of the complex transcription network controlling biofilm formation inCandidaspecies
Authors: Mancera Eugenio , Nocedal Isabel , Hammel Stephen , Gulati Megha , Mitchell Kaitlin F. , Andes David R. , Nobile Clarissa J. , Butler Geraldine , Johnson Alexander D. 
Published: November 2020

ABSTRACTWe examine how a complex transcription network composed of seven “master” regulators and hundreds of target genes evolved over a span of approximately 70 million years. The network controls biofilm formation in severalCandidaspecies, a group of fungi that are present in humans both as constituents of the microbiota and as opportunistic pathogens. The ability to form biofilms is crucial for microbial colonization of different host niches, particularly when an implanted medical device is present. We examined and compared the network underlying biofilm formation across fourCandidaspecies (C. albicans, C. dubliniensis, C. tropicalis, and C. parapsilosis), all of which form biofilms composed of multiple cell types. To describe the salient features of the network across different species, we employed four approaches: (1) we phenotypically characterized the biofilms formed by these species using a variety of methods; (2) we knocked out — one by one — the master regulators identified inC. albicansin the four species and monitored their effect on biofilm formation; (3) we identified the target genes of 18 master regulator orthologs across the four species by performing ChIP-seq experiments; and (4) we carried out transcriptional profiling across each species during biofilm formation. Additional network information was obtained by analyzing an interspecies hybrid formed between the two most closely related species,C. albicansandC. dubliniensis. We observed two major types of changes that have occurred in the biofilm circuit since the four species last shared a common ancestor. Master regulator “substitutions” occurred over relatively long evolutionary times, resulting in different species having overlapping, but different sets of master regulators of biofilm formation. Second, massive changes in the connections between the master regulators and their target genes occurred over much shorter timescales. Both types of change are crucial to account for the structures of the biofilm networks in extant species. We believe this analysis is the first detailed, empirical description of how a complex transcription network has evolved.
Impact network analysis and the INA R package: Decision support for regional management interventions
Authors: Garrett K. A. 
Published: November 2020

AbstractThe success of intervention projects in ecological systems depends not only on the quality of management technologies, but also patterns of adoption among land managers. Impact network analysis (INA) is a new framework for evaluating the likely success of regional interventions before, during, and after projects, for project implementers, policy makers, and funders. INA integrates across three key system components in a multilayer network analysis: (a) the quality of a management technology and the quality of research supporting it, (b) the socioeconomic networks through which managers learn about management technologies and decide whether to use them, and (c) the linked biophysical network for target species success or failure in the management landscape that results from managers’ decisions.The specific objectives of this paper are (1) to introduce the INA framework and INA R package, (2) to illustrate identification of key nodes for smart surveillance, for networks where the likelihood of invasive species entry into the biophysical network at a given node may be based on information available to the corresponding node in the socioeconomic network, (3) to illustrate application of the INA framework for evaluating the likely degree of success of a project in intervention ecology, before, during and after an intervention, and (4) to illustrate the use of INA for evaluating adaptation strategies under global change scenarios with pulse and press stressors, introducing ‘adaptation functions’ for sustainability and resilience.Examples of use of the INA package show one of the key outcomes of analyses: identifying when systems may be non-responsive to the system components that are readily changed through management decisions, to explore what additional adaptations may be necessary for intervention success.The broader goal for the development of impact network analysis and the INA package is to provide a common framework that integrates across intervention ecology, to enhance opportunities for lessons learned across systems and scientific disciplines, to support the development of a community of practice, and to create a general platform for analysis of sustainability, resilience, and economic viability in intervention ecology applications.
Virucidal efficacy of different formulations for hand and surface disinfection targeting SARS CoV-2
Authors: Steinhauer Katrin , Meister Toni Luise , Todt Daniel , Krawczyk Adalbert , Paßvogel Lars , Becker Britta , Paulmann Dajana , Bischoff Birte , Eggers Maren , Pfaender Stephanie , Brill Florian H H , Steinmann Eike 
Published: November 2020

AbstractIn the ongoing SARS CoV-2 pandemic effective measures are needed, and guidance based on the methodological framework of the European committee for standardization (CEN) can help to choose effective disinfectants on an immediate basis. This study demonstrates that two commercially available formulations for surface disinfection and one formulation for hand disinfection claiming“virucidal activity against enveloped viruses”are effectively inactivating SARS-CoV-2. This study emphasizes that chemical disinfectants claiming“virucidal activity against enveloped viruses”are an effective choice to target enveloped SARS-CoV-2 as a preventive measure.
Critical appraisal of the European Union Scientific Committee on Health, Environmental and Emerging Risks (SCHEER) Preliminary Opinion on electronic cigarettes
Authors: O’Leary R. , Polosa R. , Li Volti G. 
Published: November 2020

AbstractBackgroundIn preparation for the 2021 revision of the European Union Tobacco Products Directive, the Scientific Committee on Health, Environmental and Emerging Risks (SCHEER) has posted its Preliminary Opinion on Electronic Cigarettes. They conclude that e-cigarettes only achieve a sub-optimal level of protection of human health. In this paper we provide evidence that Opinion’s conclusions are not adequately backed up by scientific evidence and totally disregard the potential health benefits of using alternative combustion-free nicotine containing products as substitute for tobacco cigarettes.MethodSearches for articles were conducted in PubMed and by citation chasing in Google Scholar. Articles were also retrieved with a review of references in major publications. Primary data from World Health Organization surveys, the conclusions of reviews, and peer-reviewed non-industry studies were cited to address errors and omissions identified in the Opinion.ResultsThe Opinion omitted reporting on the individual and population health benefits of the substitution of e-cigarettes (ENDS) for cigarette smoking. Alternative hypotheses to the gateway theory were not evaluated. Its assessment of cardiovascular risk is contradicted by numerous reviews. It exhibits biases in its statements from the measurements selected on the frequency of use. It did not report non-nicotine use. It misrepresented trends in ENDS prevalence. It over-emphasized the role of flavours in youth ENDS initiation. It did not discuss cessation in sufficient length.ConclusionsFor the delivery of a robust and comprehensive final report, the members of the Working Group of the Scientific Committee on Health, Environmental and Emerging Risks will need to consider (1) the potential health benefits of ENDS substitution for cigarette smoking, (2) alternative hypotheses and contradictory studies on the gateway effect, (3) its assessment of cardiovascular risk, (4) biases arising from the measurements of frequency of use, (5) non-nicotine use, (6) the role of flavours, and (7) a fulsome discussion of cessation.