bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond
Authors: Waldstein Kody A. , Yi Jirong , Cho Michael Myung , Mudumbai Raghu , Wu Xiaodong , Varga Steven M. , Xu Weiyu 
Published: August 2021

AbstractThe rapid spread of SARS-CoV-2 has placed a significant burden on public health systems to provide rapid and accurate diagnostic testing highlighting the critical need for innovative testing approaches for future pandemics. In this study, we present a novel sample pooling procedure based on compressed sensing theory to accurately identify virally infected patients at high prevalence rates utilizing an innovative viral RNA extraction process to minimize sample dilution. At prevalence rates ranging from 0-14.3%, the number of tests required to identify the infection status of all patients was reduced by 75.6% as compared to conventional testing in primary human SARS-CoV-2 nasopharyngeal swabs and a coronavirus model system. Additionally, our modified pooling and RNA extraction process minimized sample dilution which remained constant as pool sizes increased. Our use of compressed sensing can be adapted to a wide variety of diagnostic testing applications to increase throughput for routine laboratory testing as well as a means to increase testing throughput to combat future pandemics.Graphical Abstract
Genomic analysis of SARS-CoV-2 variants of concern identified from the ChAdOx1 nCoV-19 immunized patients from Southwest part of Bangladesh
Authors: Al-Emran Hassan M. , Hasan Md. Shazid , Setu Md. Ali Ahsan , Rahman Md. Shaminur , Alam ASM Rubayet Ul , Sarkar Shovon Lal , Islam Md. Tanvir , Islam Mir Raihanul , Rahman Mohammad Mahfuzur , Islam Ovinu Kibria , Jahid Iqbal Kabir , Hossain M. Anwar 
Published: August 2021

ABSTRACTIntroductionBangladesh introduced ChAdOx1 nCoV-19 since February, 2021 and in six months, only a small population (3.5%) received their first dose of vaccination like other low-income countries. The remaining populations are struggling with increased rate of infection due to beta and delta variants. Although this uncontrolled COVID-19 pandemic did not leave even the immunized group because of immune escaping capacity of those new variants.MethodsA total of 4718 nasopharygeal samples were collected from 1stMarch until 15thApril, 2021, of which, 834 (18%) were SARS-CoV-2 positive. Randomly generated 135 positive cases were selected for telephone interview and 108 were available and provided consent. The prevalence of SARS-CoV-2 variants and disease severity among both immunized and unimmunized group was measured. A total of 63 spike protein sequence and 14 whole genome sequences were performed from both groups and phylogenetic reconstruction and mutation analysis were compared.ResultsA total of 40 respondents (37%, N=108) received single-dose and 2 (2%) received both doses of ChAdOx1 nCoV-19 vaccine which significantly reduce dry cough, loss of appetite and difficulties in breathing compared to none. There was no significant difference in hospitalization, duration of hospitalization or reduction of other symptoms like running nose, muscle pain, shortness of breathing or generalized weakness between immunized and unimmunized group. Spike protein sequence assumed 21 (87.5%) B.1.351, one B.1.526 and two 20B variants in immunized group compared to 27 (69%) B.1.351, 5 (13%) B.1.1.7, 4 (10%) 20B, 2 B.1.526 and one B.1.427 variant in unimmunized group. Those variants were further confirmed by 14 whole genome sequence analysis. Complete genome analysis included seven B.1.351 Beta V2, three B.1.1.7 Alpha V1, one B.1.526 Eta and rest three 20B variant.ConclusionSingle dose of ChAdOx1 couldn’t prevent the new infection or disease severity by the COVID-19 variants of concern, B.1.351, in Bangladesh.
When does contacting more people lessen the transmission of infectious diseases?
Authors: Mello Bernardo A. 
Published: August 2021

AbstractA primary concern in epidemics is to minimize the probability of contagion, often resorting to reducing the number of contacted people. However, the success of that strategy depends on the shape of the dose-response curve, which relates the response of the exposed person to the pathogen dose received from surrounding infected people. If the reduction is achieved by spending more time with each contacted person, the pathogen charge received from each infected individual will be larger. The extended time spent close to each person may worsen the expected response if the dose-response curve is concave for small doses. This is the case when the expected response is negligible below a certain dose threshold and rises sharply above it. This paper proposes a mathematical model to calculate the expected response and uses it to identify the conditions when it would be advisable to reduce the contact time with each individual even at the cost of increasing the number of contacted people.
Ignoring spatial heterogeneity in drivers of SARS-CoV-2 transmission in the US will impede sustained elimination
Authors: Susswein Zachary , Valdano Eugenio , Brett Tobias , Rohani Pejman , Colizza Vittoria , Bansal Shweta 
Published: August 2021

AbstractTo dissect the transmission dynamics of SARS-CoV-2 in the United States, we integrate parallel streams of high-resolution data on contact, mobility, seasonality, vaccination and seroprevalence within a metapopulation network. We find the COVID-19 pandemic in the US is characterized by a geographically localized mosaic of transmission along an urban-rural gradient, with many outbreaks sustained by between-county transmission. We detect a dynamic tension between the spatial scale of public health interventions and population susceptibility as pre-pandemic contact is resumed. Further, we identify regions rendered particularly at risk from invasion by variants of concern due to spatial connectivity. These findings emphasize the public health importance of accounting for the hierarchy of spatial scales in transmission and the heterogeneous impacts of mobility on the landscape of contagion risk.
Predictive Analysis of COVID-19 Spread in Sri Lanka using an Adaptive Compartmental Model: Susceptible-Exposed-Infected-Recovered-Dead (SEIRD) Model
Authors: Rajapaksha R. M. Nayani Umesha , Wijesinghe Millawage Supun Dilara , Thomas Toms K. , Jayasooriya Sujith P. , Gunawardana B. M. W. Indika , Weerasinghe W. M. Prasad Chathuranga , Bhakta Shalini , Assefa Yibeltal 
Published: August 2021

AbstractNovel Corona Virus (COVID-19) is still spreading throughout the world despite various degrees of movement restrictions and the availability of multiple safe and effective vaccines. Modelling in predicting the spread of an epidemic is important for health planning and policies. This study aimed to apply a dynamic Susceptible-Exposed-Infected-Recovered-Deaths (SEIRD) model and simulated it under a range of epidemic conditions using python programme language. The predictions were based on different scenarios from without any preventive measures to several different preventive measures under R0 of 4. The model shows that more weight to personal protection can halt the spread of transmission followed by the closure of public places and interprovincial movement restriction. Results after simulating various scenarios indicate that disregarding personal protective measures can have devastating effects on the local population. Strict adherence, maintaining and monitoring of self-preventive measures are vital towards minimizing the death toll from COVID-19.
Global prediction of candidate R-loop binding and R-loop regulatory proteins
Authors: Fournier Louis-Alexandre , Kumar Arun , Smith Theodore , Su Edmund , Moksa Michelle , Hirst Martin , Stirling Peter C. 
Published: August 2021

ABSTRACTIn the past decade there has been a growing appreciation for R-loop structures as important regulators of the epigenome, telomere maintenance, DNA repair and replication. Given these numerous functions, dozens, or potentially hundreds, of proteins could serve as direct or indirect regulators of R-loop writing, reading, and erasing. In order to understand common properties shared amongst potential R-loop binding proteins (RLBPs) we mined published proteomic studies and distilled 10 features that were enriched in RLBPs compared to the rest of the proteome. We used these RLBP-specific features along with their amino acid composition to create a random forest classifier which predicts the likelihood of a protein to bind to R-loops. In parallel, we employed a whole-genome CRISPR screen coupled with flow-cytometry using the S9.6 monoclonal antibody to sort guide RNAs associated with induction of high S9.6 staining. Known R-loop regulating pathways such as splicing and DNA damage repair are highly enriched in our datasets, and we validate two new R-loop modulating proteins. Together these resources provide a reference to pursue analyses of novel R-loop regulatory proteins.
Immediate Impact of Yogic Breathing on Pulsatile Cerebrospinal Fluid Dynamics
Authors: Yildiz Selda , Grinstead John , Hildebrand Andrea , Oshinski John , Rooney William D. , Lim Miranda M. , Oken Barry 
Published: August 2021

AbstractCerebrospinal fluid (CSF), a clear fluid bathing the central nervous system (CNS), undergoes pulsatile movements, and plays a critical role for the removal of waste products from the brain including amyloid beta, a protein associated with Alzheimer’s disease. Regulation of CSF dynamics is critical for maintaining CNS health, and increased pulsatile CSF dynamics may alter brain’s waste clearance due to increased mixing and diffusion. As such, understanding the mechanisms driving CSF movement, and interventions that influence its resultant removal of wastes from the brain is of high scientific and clinical impact. Since pulsatile CSF dynamics is sensitive and synchronous to respiratory movements, we are interested in identifying potential integrative therapies such as yogic breathing to regulate and enhance CSF dynamics, which has not been reported before. Here, we investigated the pre-intervention baseline data from our ongoing randomized controlled trial, and examined whether yogic breathing immediately impacts pulsatile CSF dynamics compared to spontaneous breathing. We utilized our previously established non-invasive real-time phase contrast magnetic resonance imaging (RT-PCMRI) approach using a 3T MRI instrument, and computed and rigorously tested differences in CSF velocities (instantaneous, respiratory, cardiac 1st and 2nd harmonics) at the level of foramen magnum during spontaneous versus four yogic breathing patterns. In examinations of 18 healthy participants (eight females, ten males; mean age 34.9 ± 14 (SD) years; age range: 18-61 years), we discovered immediate increase in cranially-directed velocities of instantaneous-CSF 16% - 28% and respiratory-CSF 60% - 118% during yogic versus spontaneous breathing, with most statistically significant changes during deep abdominal breathing (28%, p=0.0008, and 118%, p=0.0001, respectively). Further, cardiac pulsation was the primary source of pulsatile CSF during all breathing conditions except during deep abdominal breathing, when there was a comparable contribution of respiratory and cardiac 1st harmonic power [0.59 ± 0.78], demonstrating respiration can be the primary regulator of CSF depending on individual differences in breath depth and location. Further work is needed to investigate the impact of sustained training yogic breathing on increased pulsatile CSF dynamics and brain waste clearance for CNS health.
Immune Cell Profiling Reveals MAIT and Effector Memory CD4+ T Cell Recovery Link to Control of Cytomegalovirus Reactivation after Stem Cell Transplant
Authors: Stern Lauren , McGuire Helen M. , Avdic Selmir , de St Groth Barbara Fazekas , Gottlieb David , Abendroth Allison , Blyth Emily , Slobedman Barry 
Published: August 2021

SummaryHuman cytomegalovirus (HCMV) reactivation is a major opportunistic infection after allogeneic haematopoietic stem cell transplantation and has a complex relationship with post-transplant immune reconstitution. Here, we used mass cytometry to comprehensively define global patterns of innate and adaptive immune cell reconstitution at key phases of HCMV reactivation (before detection, initial detection, peak and near resolution) in the first 100 days post-transplant. In addition to identifying patterns of immune reconstitution in those with or without HCMV reactivation, we found mucosal-associated invariant T (MAIT) cell levels at the initial detection of HCMV DNAemia distinguished patients who subsequently developed low-level versus high-level HCMV reactivation. In addition, early recovery of effector-memory CD4+T cells distinguished low-level and high-level reactivation. Our data describe distinct immune signatures that emerged with HCMV reactivation post-HSCT, and highlight MAIT cell levels at the initial detection of reactivation as a potential prognostic marker to guide clinical decisions regarding pre-emptive therapy.
The role of viscoelasticity in long-time cell rearrangement
Authors: Pajic-Lijakovic Ivana , Milivojevic Milan 
Published: August 2021

AbstractAlthough collective cell migration (CCM) is a highly coordinated and ordered migratory mode, perturbations in the form of mechanical waves appear even in 2D. These perturbations caused by the viscoelastic nature of cell rearrangement are involved in various biological processes, such as embryogenesis, wound healing and cancer invasion. The mechanical waves, as a product of the active turbulence occurred at low Reynolds number, represent an oscillatory change in cell velocity and the relevant rheological parameters. The velocity oscillations, in the form of forward and backward flows, are driven by: viscoelastic force, surface tension force, and traction force. The viscoelastic force represents a consequence of inhomogeneous distribution of cell residual stress accumulated during CCM. This cause-consequence relation is considered on a model system such as the cell monolayer free expansion. The collision of forward and backward flows causes an increase in cell packing density which has a feedback impact on the tissue viscoelasticity and on that base influences the tissue stiffness. The evidence of how the tissue stiffness is changed near the cell jamming is conflicting. To fill this gap, we discussed the density driven change in the tissue viscoelasticity by accounting for the cell pseudo-phase transition from active (contractile) to passive (non-contractile) state appeared near cell jamming in the rheological modeling consideration.
Genetic diversity of wild and cultivatedCoffeacanephora in northeastern DR Congo and the implications for conservation
Authors: Abeele Samuel Vanden , Janssens Steven B. , Anio Justin Asimonyio , Bawin Yves , Depecker Jonas , Kambale Bienfait , Mwanga Ithé Mwanga , Ebele Tshimi , Ntore Salvator , Stoffelen Piet , Vandelook Filip 
Published: August 2021

AbstractPremiseMany cultivated coffee varieties descend fromCoffea canephora, commonly known as Robusta coffee. The Congo Basin has a century long history of Robusta coffee cultivation and breeding, and is hypothesized to be the region of origin of many of the cultivated Robusta varieties. Since little is known about the genetic composition ofC. canephorain this region, we assessed the genetic diversity of wild and cultivatedC. canephorashrubs in the Democratic Republic of the Congo.MethodsUsing 18 microsatellite markers, we studied the genetic composition of wild and backyard-grownC. canephorashrubs in the Tshopo and Ituri provinces, and from the INERA Yangambi Coffee Collection. We assessed genetic clustering patterns, genetic diversity, and genetic differentiation between populations.Key resultsGenetic differentiation was relatively strong between wild and cultivatedC. canephorashrubs, and both gene pools harbored multiple unique alleles. Strong genetic differentiation was also observed between wild populations. The level of genetic diversity in wild populations was similar to that of the INERA Yangambi Coffee Collection, but local wild genotypes were mostly missing from that collection. Shrubs grown in the backyards were genetically similar to the breeding material from INERA Yangambi.ConclusionsMostC. canephorathat is grown in local backyards originated from INERA breeding programs, while a few shrubs were obtained directly from surrounding forests. The INERA Yangambi Coffee Collection could benefit from an enrichment with local wild genotypes, to increase the genetic resources available for breeding purposes, as well as to support ex situ conservation.
Bisphosphonate drugs have actions outside the skeleton and inhibit the mevalonate pathway in alveolar macrophages
Authors: Munoz Marcia A. , Fletcher Emma K. , Skinner Oliver P. , Jurczyluk Julie , Kristianto Esther , Hodson Mark P. , Sun Shuting , Ebetino Frank H. , Croucher David R. , Hansbro Philip M. , Center Jacqueline R. , Rogers Michael J. 
Published: August 2021

ABSTRACTBisphosphonates drugs target the skeleton and are used globally for the treatment of common bone disorders. Nitrogen-containing bisphosphonates act by inhibiting the mevalonate pathway in bone-resorbing osteoclasts but, surprisingly, also appear to reduce the risk of death from pneumonia. We overturn the long-held belief that these drugs act only in the skeleton and show that a fluorescently-labelled bisphosphonate is internalised by alveolar macrophages and peritoneal macrophages in vivo. Furthermore, a single dose of a nitrogen-containing bisphosphonate (zoledronic acid) in mice was sufficient to inhibit the mevalonate pathway in tissue-resident macrophages, causing the build-up of a mevalonate metabolite and preventing protein prenylation. Importantly, one dose of bisphosphonate enhanced the immune response to bacterial endotoxin in the lung and increased the level of cytokines and chemokines in bronchoalveolar fluid. These studies suggest that bisphosphonates, as well as preventing bone loss, may boost immune responses to infection in the lung and provide a mechanistic basis to fully examine the potential of bisphosphonates to help combat respiratory infections that cause pneumonia.
Reprogramming of the intestinal epithelial-immune cell interactome during SARS-CoV-2 infection
Authors: Poletti Martina , Treveil Agatha , Csabai Luca , Gul Leila , Modos Dezso , Madgwick Matthew , Olbei Marton , Bohar Balazs , Valdeolivas Alberto , Turei Denes , Verstockt Bram , Triana Sergio , Alexandrov Theodore , Saez-Rodriguez Julio , Stanifer Megan L. , Boulant Steeve , Korcsmaros Tamas 
Published: August 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents an unprecedented worldwide health problem. Although the primary site of infection is the lung, growing evidence points towards a crucial role of the intestinal epithelium. Yet, the exact effects of viral infection and the role of intestinal epithelial-immune cell interactions in mediating the inflammatory response are not known. In this work, we apply network biology approaches to single-cell RNA-seq data from SARS-CoV-2 infected human ileal and colonic organoids to investigate how altered intracellular pathways upon infection in intestinal enterocytes leads to modified epithelial-immune crosstalk. We point out specific epithelial-immune interactions which could help SARS-CoV-2 evade the immune response. By integrating our data with existing experimental data, we provide a set of epithelial ligands likely to drive the inflammatory response upon infection. Our integrated analysis of intra- and inter-cellular molecular networks contribute to finding potential drug targets, and suggest using existing anti-inflammatory therapies in the gut as promising drug repurposing strategies against COVID-19.
Atmospheric particulate matter aggravates CNS demyelination via TLR-4/NF-κB-mediated microglia pathogenic activities
Authors: Han Bing , Li Xing , Deng Si-Ying , Ye Ze-Qing , Ai Ruo-Song , Deng Xin , Ma Wen , Xiao Shun , Wang Jing-Zhi , Wang Li-Mei , Xie Chong , Zhang Yan , Xu Yan , Zhang Yuan 
Published: August 2021

AbstractAtmospheric Particulate Matter (PM) is one of the leading environmental risk factors for the global burden of disease. Increasing epidemiological studies demonstrated that PM plays a significant role in CNS demyelinating disorders; however, there is no direct testimony of this, and yet the molecular mechanism by which the occurrence remains unclear. Using multiple in vivo and in vitro strategies, in the present study we demonstrate that PM exposure aggravates neuroinflammation, myelin injury, and dysfunction of movement coordination ability via boosting microglial pro-inflammatory activities, in both the pathological demyelination and physiological myelinogenesis animal models. Indeed, pharmacological disturbance combined with RNA-seq and ChIP-seq suggests that TLR-4/NF-κB signaling mediated a core network of genes that control PM-triggered microglia pathogenicity. In summary, our study defines a novel atmospheric environmental mechanism that mediates PM-aggravated microglia pathogenic activities, and establishes a systematic approach for the investigation of the effects of environmental exposure in neurologic disorders.SignificanceAn atmospheric trigger, the respirable particulate matter boost microglia pathogenic activities in the context of CNS demyelination by activating TLR-4/NF-κB signaling axis in animal models of immune- and toxicity-induced demyelination, as well as myelinogenesis during postnatal development.
Preferential associations of soil fungal taxa under mixed compositions of eastern American tree species
Authors: Kutos Steve , Barnes Elle M. , Bhutada Arnav , Lewis J.D. 
Published: August 2021

ABSTRACTSoil fungi are vital to forest ecosystem functions, in part through their role mediating tree responses to environmental factors, as well as directly through effects on resource cycling. While the distribution of these key taxa may vary with a suite of abiotic and biotic factors, the relative role of host species identity on soil fungal community composition and function remains unresolved. In this study, we used a combination of amplicon sequencing and enzymatic assays to assess soil fungal composition and associated function under three tree species,Quercus rubra, Betula nigra, andAcer rubrum, planted individually and in all combinations in a greenhouse, with added fungal inoculum collected below mature field trees. Across treatments, fungal communities were dominated by the phylum Ascomycota, followed by Basidiomycota and Mortierellomycota. Nonetheless, fungal communities differed between each of the solo planted treatments, suggesting at least some taxa may associate preferentially with these tree species. Additionally, fungal community composition under mixed sapling treatments broadly differed from solo saplings. The data also suggests that there were larger enzymatic activities in the solo treatments as compared with all mixed treatments. This difference may be due to the greater relative abundance of saprobic taxa found in the solo treatments. This study provides evidence of the importance of tree identity on soil microbial communities and functional changes to forest soils.