bluuebunny/crossref_metadata_2025_split huggingface dataset:
The potential impact of human visceral leishmaniasis vaccines on population incidence
Authors: le Rutte Epke A , Coffeng Luc E , Malvolti Stefano , Kaye Paul M. , de Vlas Sake J 
Published: May 2020

AbstractBackgroundHuman visceral leishmaniasis (VL) vaccines are currently under development and there is a need to understand their potential impact on population wide VL incidence.Methodology / Principal FindingsWe implement four characteristics from different human VL vaccine candidates into two published VL transmission model variants to estimate the potential impact of these vaccine characteristics on population-wide anthroponotic VL incidence on the Indian subcontinent (ISC). The vaccines that are simulated in this study 1) reduce the infectiousness of infected individuals towards sand flies, 2) reduce risk of developing symptoms after infection, 3) reduce the risk of developing post-kala-azar dermal leishmaniasis (PKDL), or 4) lead to the development of transient immunity. We also compare and combine a vaccine strategy with current interventions to identify their potential role in elimination of VL as public health problem. We show that the first two simulated vaccine characteristics can greatly reduce VL incidence. For these vaccines, an approximate 60% vaccine efficacy would lead to achieving the ISC elimination target (<1 VL case per 10,000 population per year) within 10 years’ time in a moderately endemic setting when vaccinating 100% of the population. Vaccinating VL cases to prevent the development of PKDL is a promising tool to sustain the low incidence elimination target after regular interventions are halted. Vaccines triggering the development of transient immunity protecting against infection lead to the biggest reduction in VL incidence, but booster doses are required to achieve perduring impact.Conclusions / SignificanceEven though vaccines are not yet available for implementation, their development should be pursued as their potential impact on transmission can be substantial, both in decreasing incidence at the population level as well as in sustaining the ISC elimination target when other interventions are halted.Author summaryVaccines for human visceral leishmaniasis (VL) are currently under development. In this study, we simulate VL transmission dynamics using mathematical models to explore the potential impact of vaccines on population-wide incidence. We show that some vaccines have high potential to reduce VL incidence, namely those that reduce the infectiousness of infected individuals to sand flies and those that reduce the chance of developing symptoms once infected. The effect of vaccines that lead to protection from infection is potentially the greatest, but depending on the duration of immunity, individuals would require booster doses to guarantee lifelong impact. Vaccines that prevent the development of post-kala-azar dermal leishmaniasis are a promising tool to sustain low VL incidence and prevent recrudescence of infection when regular interventions are halted. Our results strongly support the continued development of VL vaccines, as their potential impact on population incidence can be substantial.
Assessing the intrinsic and extrinsic drivers and targeting the observed resilience of malaria in northwestern and southern Tanzania: A protocol for a cross-sectional exploratory study
Authors: Chiduo Mercy G. , Mandara Celine I. , Rumisha Susan F. , Chaky Frank , Francis Filbert T. , Mmbando Bruno P. , Seth Misago D. , Challe Daniel P. , Ndekuka Leah , Massawe Isolide S. , Liheluka Edwin , Makunde Williams H. , Mhina Athanas D. , Baraka Vito , Segeja Method D. , Derua Yahya A. , Batengana Berndard M. , Hayuma Paul M. , Nkya Gineson , Madebe Rashid A. , Malimi Masunga C. , Mandike Renata , Mkude Sigsbert , Molteni Fabrizio , Njau Ritha , Mohamed Ally , Ishengoma Deus S. 
Published: May 2020

ABSTRACTBackgroundDespite high coverage and successes in malaria control strategies, some areas of Tanzania have indicated stagnantion or revesal of malaria burden. In malaria research, most studies are designed to assess drivers of malaria transmission focusing only on one dimension, single location while very few studies assess multiple components and their interactions at once. This article describes the protocol used to assess intrinsic and extrinsic drivers of persistent malaria transmission (hotsposts) in four regions from northwestern (Geita and Kigoma) and southern (Ruvuma and Mtwara) Tanzania.MethodsThis cross-sectional study was conducted between July and November 2017 in eight districts (two from each region). Based on the health facilities records, two villages were selected from each district. The study assessed five components individually and their linkages: socio-economic and malaria risk factors, parasitological, entomological, socio-anthropological and health system factors. Households (HHs) and household members were enumerated, socio-economic status and risk factors associated with malaria transmission were assessed. A total of 120 HHs were sampled from each village where malaria testing using rapid test and microscopy were done and blood spots on filter papers for genetic studies were collected. Heads of HHs were interviewed to capture information on knowledge, attitude, practice and beliefs towards malaria and its control. Assessment of adult mosquitoes in 25 HHs in each village and complimented with assessment of immature mosquitoes through larvae was conducted. The performance of the health system was assessed with respect to Information on availability, accessibility, affordability and quality of malaria prevention and case management services were collected from these health facilities.DiscussionThe proposed analysis plan and results from this study are expected to determine factors potentially responsible for persistence of malaria (hotspots) in the study areas. Rather than the traditional methodology of focusing on one metric, the approach proposed here triangulates observations from all five components, highlighting understanding of potential drivers while studying their complex interactions and map spatial heterogeneity. This study will provide an important framework and data which will guide future studies and malaria surveillance in Tanzania and other malaria endemic countries.
COVID-19 Scenarios: an interactive tool to explore the spread and associated morbidity and mortality of SARS-CoV-2
Authors: Noll Nicholas B , Aksamentov Ivan , Druelle Valentin , Badenhorst Abrie , Ronzani Bruno , Jefferies Gavin , Albert Jan , Neher Richard A 
Published: May 2020

The ongoing SARS-CoV-2 pandemic has caused large outbreaks around the world and every heavily affected community has experienced a substantial strain on the health care system and a high death toll. Communities therefore have to monitor the incidence of COVID-19 carefully and attempt to project the demand for health care. To enable such projections, we have developed an interactive web application that simulates an age-structured SEIR model with separate compartments for severely and critically ill patients. The tool allows the users to modify most parameters of the model, including age specific assumptions on severity. Infection control and mitigation measures that reduce transmission can be specified, as well as age-group specific isolation.The simulation of the model runs entirely on the client side in the browser; all parameter settings and results of the simulation can be exported for further downstream analysis. The tool is available at covid19-scenarios.org and the source code atgithub.com/neherlab/covid19_scenarios.
Evolution of COVID-19 pandemic: Power-law growth and saturation
Authors: Chatterjee Soumyadeep , Asad Ali , Shayak B. , Bhattacharya Shashwat , Alam Shadab , Verma Mahendra K. 
Published: May 2020

AbstractIn this paper, we analyze the real-time infection data of COVID-19 epidemic for 21 nations up to June 30, 2020. For most of these nations, the total number of infected individuals exhibits a succession of exponential growth and power-law growth before the flattening of the curve. In particular, we find a universal growth before they reach saturation. However, at present, India, which has I(t) ~ t2, and Russia and Brazil, which have I(t) ~ t, are yet to flatten their curves. Thus, the polynomials of the I(t) curves provide valuable information on the stage of the epidemic evolution, thus on the life cycle of COVID-19 pandemic. Besides these detailed analyses, we compare the predictions of an extended SEIR model and a delay differential equation-based model with the reported infection data and observed good agreement among them, including the behaviour. We argue that the power laws in the epidemic curves may be due to lockdowns.
Health seeking behaviors of patients with acute respiratory infections during the outbreak of novel coronavirus disease 2019 in Wuhan, China
Authors: Yang Juan , Gong Hui , Chen Xinhua , Chen Zhiyuan , Deng Xiaowei , Qian Mengcen , Hou Zhiyuan , Ajelli Marco , Viboud Cecile , Yu Hongjie 
Published: May 2020

AbstractWe conducted two surveys to evaluate the health-seeking behaviors of individuals with acute respiratory infections (ARI) during the COVID-19 outbreak in Wuhan, China. Among 351 participants reporting ARI (10.3%, 351/3,411), 36.5% sought medical assistance. Children were more likely to seek medical assistance than other age groups (66.1% vs. 28.0%-35.1%).
Acceptability of app-based contact tracing for COVID-19: Cross-country survey evidence
Authors: Altmann Samuel , Milsom Luke , Zillessen Hannah , Blasone Raffaele , Gerdon Frederic , Bach Ruben , Kreuter Frauke , Nosenzo Daniele , Toussaert Séverine , Abeler Johannes 
Published: May 2020

AbstractBackgroundThe COVID-19 pandemic is the greatest public health crisis of the last 100 years. Countries have responded with various levels of lockdown to save lives and stop health systems from being overwhelmed. At the same time, lockdowns entail large socio-economic costs. One exit strategy under consideration is a mobile phone app that traces close contacts of those infected with COVID-19. Recent research has demonstrated the theoretical effectiveness of this solution in different disease settings. However, concerns have been raised about such apps because of the potential privacy implications. This could limit the acceptability of app-based contact tracing among the general population. As the effectiveness of this approach increases strongly with app take-up, it is crucial to understand public support for this intervention.ObjectivesThe objective of this study is to investigate user acceptability of a contact-tracing app in five countries hit by the pandemic.MethodsWe conducted a multi-country, large-scale (N = 5995) study to measure public support for digital contact tracing of COVID-19 infections. We ran anonymous online surveys in France, Germany, Italy, the UK and the US. We measured intentions to use a contact-tracing app across different installation regimes (voluntary installation vs. automatic installation by mobile phone providers), and studied how these intentions vary across individuals and countries.ResultsWe found strong support for the app under both regimes, in all countries, across all sub-groups of the population, and irrespective of regional-level COVID-19 mortality rates. We investigated the main factors that may hinder or facilitate take-up and found that concerns about cyber security and privacy, together with lack of trust in government, are the main barriers to adoption.ConclusionsEpidemiological evidence shows that app-based contact-tracing can suppress the spread of COVID-19 if a high enough proportion of the population uses the app and that it can still reduce the number of infections if take-up is moderate. Our findings show that the willingness to install the app is very high. The available evidence suggests that app-based contact tracing may be a viable approach to control the diffusion of COVID-19.
Importance of Interaction Structure and Stochasticity for Epidemic Spreading: A COVID-19 Case Study
Authors: Großmann Gerrit , Backenköhler Michael , Wolf Verena 
Published: May 2020

AbstractIn the recent COVID-19 pandemic, computer simulations are used to predict the evolution of the virus propagation and to evaluate the prospective effectiveness of non-pharmaceutical interventions. As such, the corresponding mathematical models and their simulations are central tools to guide political decision-making. Typically, ODE-based models are considered, in which fractions of infected and healthy individuals change deterministically and continuously over time.In this work, we translate an ODE-based COVID-19 spreading model from literature to a stochastic multi-agent system and use a contact network to mimic complex interaction structures. We observe a large dependency of the epidemic’s dynamics on the structure of the underlying contact graph, which is not adequately captured by existing ODE-models. For instance, existence of super-spreaders leads to a higher infection peak but a lower death toll compared to interaction structures without super-spreaders. Overall, we observe that the interaction structure has a crucial impact on the spreading dynamics, which exceeds the effects of other parameters such as the basic reproduction numberR0.We conclude that deterministic models fitted to COVID-19 outbreak data have limited predictive power or may even lead to wrong conclusions while stochastic models taking interaction structure into account offer different and probably more realistic epidemiological insights.
Cooperative virus propagation in COVID-19 transmission
Authors: Dai Ziwei , Locasale Jason W. 
Published: May 2020

AbstractThe global pandemic due to the emergence of a novel coronavirus (COVID-19) is a threat to humanity. There remains an urgent need to understand its transmission characteristics and design effective interventions to mitigate its spread. In this study, we define a non-linear (known in biochemistry models as allosteric or cooperative) relationship between viral shedding, viral dose and COVID-19 infection propagation. We develop a mathematical model of the dynamics of COVID-19 to link quantitative features of viral shedding, human exposure and transmission in nine countries impacted by the ongoing COVID-19 pandemic, and state-wide transmission in the United States of America (USA). The model was then used to evaluate the efficacy of interventions against virus transmission. We found that cooperativity was important to capture country-specific transmission dynamics and leads to resistance to mitigating transmission in mild or moderate interventions. The behaviors of the model emphasize that strict interventions greatly limiting both virus shedding and human exposure are indispensable to achieving effective containment of COVID-19. Finally, in the USA we find that by the summer of 2021, a difference of about 1.5 million deaths may be observed depending on whether the interventions are to be maintained strictly or lifted in entirety.
Pervasive prophage recombination occurs during evolution of spore-formingBacilli
Authors: Dragoš Anna , B. Priyadarshini , Hasan Zahraa , Lenz-Strube Mikael , Kempen Paul J , Maróti Gergely , Kaspar Charlotte , Bose Baundauna , Burton Briana M. , Bischofs Ilka B , Kovács Ákos T. 
Published: May 2020

AbstractPhages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage ofBacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within theB. subtilispopulation. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis ofBacillussp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison ofBacillussp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.
Conserved Keratin Gene Clusters in Ancient Fish: an Evolutionary Seed for Terrestrial Adaptation
Authors: Kimura Yuki , Nikaido Masato 
Published: May 2020

AbstractType I and type II keratins are subgroups of intermediate filament proteins that provide toughness to the epidermis and protect it from water loss. In terrestrial vertebrates, the keratin genes form two major clusters, clusters 1 and 2, each of which is dominated by type I and II keratin genes. By contrast, such clusters are not observed in teleost fish. Although the diversification of keratins is believed to have made a substantial contribution to terrestrial adaptation, its evolutionary process has not been clarified. Here, we performed a comprehensive genomic survey of the keratin genes of a broad range of vertebrates. As a result, we found that ancient fish lineages such as elephant shark, reedfish, spotted gar, and coelacanth share both keratin gene clusters. We also discovered an expansion of keratin genes that form a novel subcluster in reedfish. Syntenic and phylogenetic analyses revealed that two pairs ofkrt18/krt8keratin genes were shared among all vertebrates, thus implying that they encode ancestral type I and II keratin protein sets. We further revealed that distinct keratin gene subclusters, which show specific expressions in the epidermis of adult amphibians, stemmed from canonical keratin genes in non-terrestrial ancestors. Molecular evolutionary analyses suggested that the selective constraints were relaxed in the adult epidermal subclusters of amphibians as well as the novel subcluster of reedfish. The results of the present study represent the process of diversification of keratins through a series of gene duplications that could have facilitated the terrestrial adaptation of vertebrates.HighlightsTwo major keratin clusters are conserved from sharks to terrestrial vertebrates.Adult epidermis-specific keratins in amphibians stem from the two major clusters.A novel keratin gene subcluster was found in reedfish.Ancestralkrt18/krt8gene sets were found in all vertebrates.Functional diversification signatures were found in reedfish and amphibian keratins.
AtPIG-S, a predicted Glycosylphosphatidylinositol Transamidase Subunit, is critical for pollen tube growth in Arabidopsis
Authors: Desnoyer Nick , Howard Greg , Jong Emma , Palanivelu Ravishankar 
Published: May 2020

AbstractBackgroundGlycosylphosphatidylinositol (GPI) addition is one of the several post-translational modifications to proteins that increase their affinity for membranes. In eukaryotes, the GPI transamidase complex (GPI-T) catalyzes the attachment of pre-assembled GPI anchors to GPI-anchored proteins (GAPs) through a transamidation reaction. A mutation inAtGPI8(gpi8-2), the putative catalytic subunit of GPI-T in Arabidopsis, is transmitted normally through the female gametophyte (FG), indicating the FG tolerates loss of GPI transamidation. In contrast,gpi8-2almost completely abolishes male gametophyte (MG) function. Still, the unexpected finding thatgpi8-2FGs function normally requires further investigation. Additionally, specific developmental defects in the MG caused by loss of GPI transamidation remain poorly characterized.ResultsHere we investigated the effect of loss ofAtPIG-S,another GPI-T subunit, in both gametophytes. Likegpi8-2, we showed that a mutation inAtPIG-S(pigs-1) disrupted synergid localization of LORELEI (LRE), a putative GAP critical for pollen tube reception by the FG, yet is transmitted normally through the FG. Conversely,pigs-1severely impaired male gametophyte (MG) function during pollen tube emergence and growth in the pistil. ApPIGS:PIGS-GFPtransgene complemented these MG defects and enabled generation ofpigs-1/pigs-1seedlings, but seemingly failed to rescue the function of AtPIG-S in the sporophyte, aspigs-1/pigs-1, pPIGS:PIGS-GFPseedlings died soon after germination.ConclusionsCharacterization ofpigs-1provided further evidence that the FG tolerates loss of GPI transamidation more than the MG and that the MG compared to the FG may be a better haploid system to study the role of GPI-anchoring.pigs-1pollen develops normally and thus represent a tool in which GPI anchor biosynthesis and transamidation of GAPs have been uncoupled, offering a potential way to study free GPI in plant development. While previously reported male fertility defects of GPI biosynthesis mutants could have been due either to loss of GPI or GAPs lacking the GPI anchor, our results clarified that the loss of mature GAPs underlie male fertility defects of GPI-deficient pollen grains, aspigs-1is defective only in the downstream transamidation step. Our study also provided further evidence that GPI transamidation is essential in seedling development.
The Conquering influence of the Nano extracts of pomegranate peels and pistachio leaves in amelioration of acute liver failure
Authors: Hassan Sohair Aly , Hammam Olfat , Hussein Sahar Awdallah , Aziz Wessam Magdi 
Published: May 2020

AbstractObjectiveAcute liver failure (ALF) is a clinical condition with an unclear history of pathophysiology, making it a challenging task for scientists to reverse the disease in its initial phase and to help the liver re-function as usual: this study was proposed to estimate the hepatoprotective effects of Punicagranatum peel andPistaciaatlanticaleaves as a multi-rich antioxidants ingredients either in their normal and/or in their nano forms against thioacetamide induced acute liver failure in a rodent model.MethodSixty male Wistar rats were divided into six equal groups, the first group employed as a control; the second group was given a dose of thioacetamide (TAA)-350 mg/bwip., from the third to the sixth group received TAA □ 2ml of 100gm of aqueous extracts ofPunicagranatumLandPistaciaatlanticaeither in their normal and/or Nano forms consecutively along 2 weeks.Resultsrecorded significant elevation in liver enzymes, lipid profiles, LPO and NO with marked significant decrease in GSH and SOD accompanied by elevation in inflammatory cytokine (IL6,TNF-α and AFP) in addition to a noticeable increase in HSP70level & degradation in DNA respectively in TAA challenged group. However significant and subsequent amelioration of most of the impaired markers has been observed with ipnano treatment of both extracts.ConclusionThe current results highlighted the high performance of both plant nano extracts and their hepatoprotective impact and their possible therapeutic role in the amelioration of TAA induced acute liver failure in experimental animals.