bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Plaque Size, Thermal Stability, and Replication Rate among SARS-CoV-2 Variants of Concern
Authors: Jeong Gi Uk , Yoon Gun Young , Moon Hyun Woo , Lee Wooseong , Hwang Insu , Kim Hae Soo , Kim Kyun-Do , Kim Chonsaeng , Ahn Dae-Gyun , Kim Bum-Tae , Kim Seong-Jun , Kwon Young-Chan 
Published: October 2021

ABSTRACTSARS-CoV-2, like other RNA viruses, has a propensity for genetic evolution owing to the low fidelity of its viral polymerase. This evolution results in the emergence of novel variants with different characteristics than their ancestral strain. Several recent reports have described a series of novel SARS-CoV-2 variants. Some of these have been identified as variants of concern (VOCs), including alpha (B.1.1.7, Clade GRY), beta (B.1.351, Clade GH), gamma (P.1, Clade GR), and delta (B.1.617.2, Clade G). VOCs are likely to have some effect on transmissibility, antibody evasion, and changes in therapeutic or vaccine effectiveness. However, the physiological and virological understanding of these variants remains poor. We demonstrated that these four VOCs exhibited differences in plaque size, thermal stability at physiological temperature, and replication rates. The mean plaque size of beta was the largest, followed by those of gamma, delta, and alpha. Thermal stability, evaluated by measuring infectivity and half-life after prolonged incubation at physiological temperature, was correlated with plaque size in all variants except alpha. However, despite its relatively high thermal stability, alpha’s small plaque size resulted in lower replication rates and fewer progeny viruses. Our findings may inform further virological studies of SARS-CoV-2 variant characteristics, VOCs, and variants of interest. These studies are important for the effective management of the COVID-19 pandemic.IMPORTANCEThe global pandemic caused by SARS-CoV-2 continues to persist, due in part to mutations that have resulted in the emergence of different variants. Many of these variants have become more virulent and infectious than their ancestral strain, resulting in an ever-increasing spread. However, our virological understanding of these variants remains poor. Here, we directly compared the plaque size, stability, and replication kinetics of four SARS-CoV-2 variants of concern following prolonged incubation at physiological temperatures. Our observations may help to characterize each variant in terms of their interactions with host factors and responses to environmental conditions. We also believe that our evaluations will improve understanding of the emergence of new variants and contribute to controlling their spread.
Stress response inEntamoeba histolyticais associated with robust processing of tRNA to tRNA-halves
Authors: Sharma Manu , Zhang Hanbang , Ehrenkaufer Gretchen , Singh Upinder 
Published: October 2021

AbstracttRNA-derived fragments have been reported in many different organisms and have diverse cellular roles such as regulating gene expression, inhibiting protein translation, silencing transposable elements and modulating cell proliferation. In particular tRNA halves, a class of tRNA fragments produced by the cleavage of tRNAs in the anti-codon loop, have been widely reported to accumulate under stress and regulate translation in cells. Here we report the presence of tRNA-derived fragments inEntamoebawith tRNA halves being the most abundant. We further established that tRNA halves accumulate in the parasites upon different stress stimuli such as oxidative stress, heat shock, and serum starvation. We also observed differential expression of tRNA halves during developmental changes of trophozoite to cyst conversion with various tRNA halves accumulating during early encystation. In contrast to other systems, the stress response does not appear to be mediated by a few specific tRNA halves as multiple tRNAs appear to be processed during the various stresses. Furthermore, we identified some tRNA-derived fragments are associated withEntamoebaArgonaute proteins,EhAgo2-2, andEhAgo2-3, which have a preference for different tRNA-derived fragment species. Finally, we show that tRNA halves are packaged inside extracellular vesicles secreted by amoeba. The ubiquitous presence of tRNA-derived fragments, their association with the Argonaute proteins, and the accumulation of tRNA halves during multiple different stresses including encystation suggest a nuanced level of gene expression regulation mediated by different tRNA-derived fragments inEntamoeba.ImportancetRNA-derived fragments are small RNAs formed by the cleavage of tRNAs at specific positions. These have been reported in many organisms to modulate gene expression and thus regulate various cell functions. In the present study, we report for the first time the presence of tRNA-derived fragments inEntamoeba. tRNA-derived fragments were identified by bioinformatics analyses of small RNA sequencing datasets from the parasites and also confirmed experimentally. We found that tRNA halves accumulated in parasites exposed to environmental stress or during developmental process of encystation. We also found that shorter tRNA-derived fragments are bound toEntamoebaArgonaute proteins, indicating that they may have a potential role in the Argonaute-mediated RNA-interference pathway which mediates robust gene silencing inEntamoeba. Our results suggest that tRNA-derived fragments inEntamoebahave a possible role in regulating gene expression during environmental stress.
Identification of candidate genes for developmental colour agnosia in a single unique family
Authors: Nijboer Tanja C. , Hessel Ellen V.S. , van Haaften Gijs W. , van Zandvoort Martine J. , van der Spek Peter J. , Troelstra Christine , Kovel Carolien de , Koeleman Bobby P.C. , van der Zwaag Bert , Brilstra Eva H. , Burbach J. Peter H. 
Published: October 2021

AbstractColour agnosia is a disorder that impairs colour knowledge (naming, recognition) despite intact colour perception. Previously, we have identified the first and only-known family with hereditary developmental colour agnosia. The aim of the current study was to explore genomic regions and candidate genes that potentially cause this trait in this family. For three family members with developmental colour agnosia and three unaffected family members CGH-array analysis and exome sequencing was performed, and linkage analysis was carried out using DominantMapper, resulting in the identification of 19 cosegregating chromosomal regions. Whole exome sequencing resulted in 11 rare coding variants present in all affected family members with developmental colour agnosia and absent in unaffected members. These variants affected genes that have been implicated in neural processes and functions (CACNA2D4, DDX25, GRINA, MYO15A), that have a indirect link to brain function or development (MAML2, STAU1, TMED3), and a remaining group lacking brain expression or involved in non-neural traits (DEPDC7, OR1J1, OR8D4, RABEPK). Although this is an explorative study, the small set of candidate genes that could serve as a starting point for unravelling mechanisms of higher level cognitive functions and cortical specialization, and disorders therein such as developmental colour agnosia.
COVID-19 Pandemic Response in a Migrant Farmworker Community: Excess Mortality, Testing Access and Contact Tracing in Immokalee, Florida
Authors: Limaye Neha , Ninesling Brennan , Marcelin Frantzso , Nolan Cody , Sobba Walter , Hing Matthew , Ptaszek Emily , Léandre Fernet , Palazuelos Daniel 
Published: October 2021

AbstractIntroductionWe aim to estimate the impact of COVID-19 in Immokalee, FL and assess community experiences with workplace conditions, access to testing, sources of information, and contact tracing to inform and strengthen local public health sector efforts in reaching and providing high-quality care to the community.MethodsWe conducted a descriptive analysis of data on COVID-19 deaths for Collier County from May-August 2020. We surveyed a cross-sectional, randomized representative sample of 318 adults living in Immokalee from March-November 2020 to assess socio-demographics, sources of information, ability to follow guidelines, and experiences with local programs. Results were compared across language groups.ResultsAverage excess mortality in Collier County was 108%. The majority surveyed in Immokalee had socio-demographic factors associated with higher COVID risk. Non-English speakers had higher workplace risk due to less ability to work from home. Haitian Creole speakers were less likely to be tested, though all participants were willing to get symptomatic testing and quarantine. Those participants who tested positive or had COVID-19 exposures had low engagement with the contact tracing program, and Spanish-speakers reported lower quality of contact tracing than English speakers.ConclusionsThe community of Immokalee, FL is a vulnerable population that suffered disproportionate deaths from COVID-19. This study reveals language inequities in COVID testing and contact tracing should be targeted in future pandemic response in Immokalee and other migrant farmworker communities.
Research output is low, but increasing, and focuses on public health at new universities in southern Ethiopia
Authors: Lindtjørn Bernt , Massebo Fekadu , Gari Taye , Tesfaye Solomon Hailemariam 
Published: October 2021

AbstractObjectiveThe aim of this work is to describe the developments in research publication at three new universities in southern Ethiopia.DesignBibliometric analysis.MethodsWe retrieved references from 1998 to July 2021 from the Web of Science database using the authors’ affiliation. English language publications and peer-reviewed journals were included. The bibliometric analyses were conducted by using Web of Science and the bibliometrix package (version 3.1) under R version 4.0.5.ResultsWe reviewed 1019 scientific papers, and there was a substantial increase in the number of publications over the years, especially since 2016. The publications were in 304 different journals with 2606 authors; the number of documents per author was 0·39. Most of the studies were descriptive, 17 (1·7%) were clinical trials, 60 (5·9%) were case-control studies, and 83 (8·1%) were cohort studies. Topics related to public health were the most often studied. The average citations per publication was 9·1. The most frequently cited papers occurred with international collaboration. A total of 886 (84%) publications were “All Open Access” and only 5% of the papers were published in Ethiopian journals. We identified ten groups that maintained scientific production for 8 years or more, mainly in research on malaria and vector borne diseases, nutrition, microbiology, and various public health issues. One of seven papers were published with support from external funding, and with collaborative links with the United States, Europe, and New Zealand.ConclusionsThere has been a remarkable increase in health research at the three universities. The institutions should enhance the research culture, strengthening their health research capacity by encouraging good research practice and ensuring connections between health research and implementation.
HPV vaccination of girls in the German model region Saarland: Insurance data-based analysis and identification of starting points for improving vaccination rates
Authors: Marthaler Anna , Berkó-Göttel Barbara , Rissland Jürgen , Schöpe Jakob , Taurian Emeline , Müller Hanna , Weber Gero , Lohse Stefan , Lamberty Thomas , Holleczek Bernd , Stoffel Harry , Hauptmann Gunter , Giesen Martin , Firk Christiane , Schanzenbach Alexandra , Brandt Florian , Hohmann Heike , Werthner Quirin , Selzer Dominik , Lehr Thorsten , Wagenpfeil Stefan , Smola Sigrun 
Published: October 2021

AbstractIn Germany, the incidence of cervical cancer, a disease caused by human papillomaviruses (HPV), is higher than in neighboring European countries. HPV vaccination has been recommended for girls since 2007. However, it continues to be significantly less well received than other childhood vaccines, so its potential for cancer prevention is not fully realized.To find new starting points for improving vaccination rates, we analyzed pseudonymized routine billing data from statutory health insurers in the PRÄZIS study in the federal state Saarland serving as a model region. We show that lowering the HPV vaccination age to 9 years led to more completed HPV vaccinations already in 2015. Since then, HPV vaccination rates and the proportion of 9-to 11-year-old girls among HPV-vaccinated females have steadily increased. However, HPV vaccination rates among 15-year-old girls in Saarland remained well below 50% in 2019. Pediatricians vaccinated the most girls overall, with a particularly high proportion at the recommended vaccination age of 9-14 years, while gynecologists provided more HPV catch-up vaccinations among 15-17-year-old girls, and general practitioners compensated for HPV vaccination in Saarland communities with fewer pediatricians or gynecologists. We also provide evidence for a significant association between attendance at the U11 or J1 medical check-ups and HPV vaccination. In particular, participation in HPV vaccination is high on the day of U11. However, obstacles are that U11 is currently not funded by all statutory health insurers and there is a lack of invitation procedures for both U11 and J1, resulting in significantly lower participation rates than for the earlier U8 or U9 screenings, which are conducted exclusively with invitations and reminders.Based on our data, we propose to restructure U11 and J1 screening in Germany, with mandatory funding for U11 and organized invitations for HPV vaccination at U11 or J1 for both boys and girls.
Model-based Bayesian inference of the ventilation distribution in patients with Cystic Fibrosis from multiple breath washout, with comparison to ventilation MRI
Authors: Whitfield Carl A. , Horsley Alexander , Jensen Oliver E. , Horn Felix C. , Collier Guilhem J. , Smith Laurie J. , Wild Jim M. 
Published: October 2021

AbstractBackgroundIndices of ventilation heterogeneity (VH) from multiple breath washout (MBW) have been shown to correlate well with VH indices derived from hyperpolarised gas ventilation MRI. Here we report the prediction of ventilation distributions from MBW data using a mathematical model, and the comparison of these predictions with imaging data.MethodsWe developed computer simulations of the ventilation distribution in the lungs to model MBW measurement with 3 parameters: σV, determining the extent of VH; V0, the lung volume; and VD, the dead-space volume. These were inferred for each individual from supine MBW data recorded from 25 patients with cystic fibrosis (CF) using approximate Bayesian computation. The fitted models were used to predict the distribution of gas imaged by 3He ventilation MRI measurements collected from the same visit.ResultsThe MRI indices measured (I1/3, the fraction of pixels below one-third of the mean intensity and ICV, the coefficient of variation of pixel intensity) correlated strongly with those predicted by the MBW model fits (r = 0.93, 0.88 respectively). There was also good agreement between predicted and measured MRI indices (mean bias ± limits of agreement: I1/3 : − 0.003 ± 0.118 and ICV: − 0.004 ± 0.298). Fitted model parameters were robust to truncation of MBW data.ConclusionWe have shown that the ventilation distribution in the lung can be inferred from an MBW signal, and verified this using ventilation MRI. The Bayesian method employed extracts this information with fewer breath cycles than required for LCI, reducing acquisition time required, and gives uncertainty bounds, which are important for clinical decision making.
Reduced amplification efficiency of the RNA-dependent-RNA-polymerase (RdRp) target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests
Authors: Valley-Omar Ziyaad , Marais Gert , Iranzadeh Arash , Naidoo Michelle , Korsman Stephen , Maponga Tongai , Hussey Hannah , Davies Mary-Ann , Boulle Andrew , Doolabh Deelan , Laubscher Mariska , Deetlefs JD , Maritz Jean , Scott Lesley , Msomi Nokukhanya , Tegally Houriiyah , de Oliveira Tulio , Bhiman Jinal , Williamson Carolyn , Preiser Wolfgang , Hardie Diana , Hsiao Nei-yuan 
Published: October 2021

AbstractRoutine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced PCR amplification efficiency of the RdRp gene target of the Seegene, Allplex 2019-nCoV diagnostic assay when detecting the Delta variant. We propose that this can be used as a surrogate for variant detection.
Mental Health and Time Management Behavior among Students During COVID-19 Pandemic: Towards Persuasive Technology Design
Authors: Alhasani Mona , Alkhawaji Ali , Orji Rita 
Published: October 2021

ABSTRACTThe study explored the impact of the COVID-19 pandemic on students’ mental health in higher education while capturing their perceptions and attitudes towards time management. The aim was to examine relationships between stress, anxiety, and specific time management related factors. Considering possible differences between genders and degree levels, we developed five structural equation models (SEMs) to delineate these relationships. Results of a large-scale study of 502 participants show that students suffered from stress and two types of COVID-19-related anxiety: disease and consequences. Students’ preference for organization was the only factor that significantly promoted their perceived control over time, which contributes to reducing stress, hence, anxiety. However, female students reported higher stress and anxiety levels than male students. Graduate students reported higher anxiety levels related to the consequences of the pandemic compared to undergrads. To promote students’ preference for organization, we map the three categories of organization to corresponding persuasive strategies which could be used in the design of persuasive interventions. This creates an opportunity for developing technological interventions to improve students’ perceived control over time, thus, reduce stress and anxiety.
JIA patient T cells differentiate into Th1, Th17 and Th1.17 effector cells under Th1 polarizing conditions
Authors: Patrick Anna E. , Esmond Tashawna , Shoaff Kayla , Patrick David M. , Flaherty David K. , Graham T. Brent , Crooke Philip S. , Thompson Susan , Aune Thomas M. 
Published: October 2021

AbstractObjectiveT helper cells develop into discrete Th1, Th2 or Th17 lineages that selectively express IFNγ, IL-4/IL-5/IL-13, or IL-17, respectively and actively silence signature cytokines expressed by opposing lineages. Our objective was to compare Th1, Th2 and Th17 polarization in cell culture models using JIA patient samples.MethodsPeripheral blood mononuclear cells were isolated from JIA or healthy prepubescent children. T cell naïve and memory phenotypes were assessed by flow cytometry. T cell proliferation was measured using a fluorescence-based assay. Th cell cultures were generated in vitro and IFNγ, IL-17, and TNFα measured by ELISA and flow cytometry.ResultsJIA Th1 cells produced increased IFNγ and inappropriately produced IL-17. JIA Th17 cells produced increased IL-17. JIA Th1 cell cultures develop dual producers of IFNγ and IL-17, which are Th1.17 cells. JIA Th1 cultures expressed elevated levels of both T-bet and RORγT. RNA sequencing confirmed activation of immune responses and inappropriate activation of IL-17 signaling pathways in Th1 cultures. A subset of JIA patient samples was disproportionally responsible for the enhanced IFNγ and IL-17 phenotype and Th1.17 phenotype.ConclusionsThis study reveals that JIA patient uncommitted T cell precursors, but not healthy children, inappropriately develop into inflammatory effector Th1.17 and Th17 cells under Th1 polarizing conditions.Rheumatology key messagesTh1 differentiation of JIA PBMCs generates high IFNγ, IL-17, and dual IFNγ-IL-17 producing cells.JIA Th1 differentiation increases master transcription factor expression for Tbet and RORγT.Enhanced JIA Th1 IFNγ and IL-17 production occurs in a subset of JIA patients.
Localization free super-resolution microbubble velocimetry using a long short-term memory neural network
Authors: Chen Xi , Lowerison Matthew R. , Dong Zhijie , Chandra Sekaran Nathiya Vaithiyalingam , Huang Chengwu , Chen Shigao , Fan Timothy M. , Llano Daniel A. , Song Pengfei 
Published: October 2021

AbstractUltrasound localization microscopy is a super-resolution imaging technique that exploits the unique characteristics of contrast microbubbles to side-step the fundamental trade-off between imaging resolution and penetration depth. However, the conventional reconstruction technique is confined to low microbubble concentrations to avoid localization and tracking errors. Several research groups have introduced sparsity- and deep learning-based approaches to overcome this constraint to extract useful vascular structural information from overlapping microbubble signals, but these solutions have not been demonstrated to produce blood flow velocity maps of the microcirculation. Here, we introduce Deep-SMV, a localization free super-resolution microbubble velocimetry technique, based on a long short-term memory neural network, that provides high imaging speed and robustness to high microbubble concentrations, and directly outputs blood velocity measurements at a super-resolution. Deep-SMV is trained efficiently using microbubble flow simulation on real in vivo vascular data and demonstrates real-time velocity map reconstruction suitable for functional vascular imaging and pulsatility mapping at super-resolution. The technique is successfully applied to a wide variety of imaging scenarios, include flow channel phantoms, chicken embryo chorioallantoic membranes, and mouse kidney, tumor, and brain imaging.
Natural and designed proteins inspired by extremotolerant organisms can form condensates and attenuate apoptosis in human cells
Authors: Veling Mike T. , Nguyen Dan T. , Thadani Nicole N. , Oster Michela E. , Rollins Nathan J. , Brock Kelly P. , Bethel Neville P. , Lim Samuel , Baker David , Way Jeffrey C. , Marks Debora S. , Chang Roger L. , Silver Pamela A. 
Published: October 2021

ABSTRACTMany organisms can survive extreme conditions and successfully recover to normal life. This extremotolerant behavior has been attributed in part to repetitive, amphipathic, and intrinsically disordered proteins that are upregulated in the protected state. Here, we assemble a library of approximately 300 naturally-occurring and designed extremotolerance-associated proteins to assess their ability to protect human cells from chemically-induced apoptosis. We show that several proteins from tardigrades, nematodes, and the Chinese giant salamander are apoptosis protective. Notably, we identify a region of the human ApoE protein with similarity to extremotolerance-associated proteins that also protects against apoptosis. This region mirrors the phase separation behavior seen with such proteins, like the tardigrade protein CAHS2. Moreover, we identify a synthetic protein, DHR81, that shares this combination of elevated phase separation propensity and apoptosis protection. Finally, we demonstrate that driving protective proteins into the condensate state increases apoptosis protection, and highlight the ability for DHR81 condensates to sequester caspase-7. Taken together, this work draws a link between extremotolerance-associated proteins, condensate formation, and designing human cellular protection.