bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of respiratory protection during exercising tasks between different wearing methods of replaceable particulate respirators and powered air-purifying respirators
Authors: Baba Hiroka , Ando Hajime , Ikegami Kazunori , Sekoguchi Shingo , Shirasaka Taiki , Ogami Akira 
Published: May 2021

AbstractBackgroundThis study evaluated the differences in respiratory protection between replaceable particulate respirators (RPRs) and powered air-purifying respirators (PAPRs), with different wearing methods, during exercising tasks.MethodsTen participants wore either RPR or PAPR according to the recommended method, with a knit cover placed between the facepiece cushion and the face, or with the headband on a helmet. We measured the number of particles inside and outside the respiratory protective equipment (RPE) during exercising tasks for each wearing variation. The exercise state was set to exercise with an ergometer set at 80W load. While exercising tasks, the participants performed five actions adopted from JIS T8150 in 2018 (1. Normal breathing, 2. Deep breathing, 3. Turning head side to side, 4. Moving head up and down, 5. Talking). Each action was performed for 1 min. For measurements of exercise state, after 10 minutes of exercise tasks, we measured while the exercise was continued. The fit factor was calculated by dividing the concentration within the RPE by the concentration outside of it. Data were analyzed after they were log-transformed with a linear mixed model, with fit factor as the dependent variable.ResultsWe compared the results with experimental data of resting state reported in our previous studies. Fit factor of RPRs in the exercise state was significantly lower (p<0.001) than that in the resting state, indicating inadequate respiratory protection. In contrast, the fit factor of PAPRs during exercising tasks was significantly lower (p<0.001) than that at rest; however, respiratory protection was maintained. PAPR did not show a significant decrease (p=1.000) in fit factor owing to the wearing variations during exercising tasks.ConclusionsPAPRs were found to be superior to RPRs in terms of respiratory protection. PAPRs are better than RPRs for workers who have to wear RPE inappropriately due to health problems.
Persistence of functional memory B cells recognizing SARS-CoV-2 variants despite loss of specific IgG
Authors: Winklmeier Stephan , Eisenhut Katharina , Taskin Damla , Rübsamen Heike , Schneider Celine , Eichhorn Peter , Keppler Oliver T. , Klein Matthias , Mader Simone , Kümpfel Tania , Meinl Edgar 
Published: May 2021

SummaryWhile some COVID-19 patients maintain SARS-CoV-2-specific serum IgGs for more than 6 months post-infection, others, especially mild cases, eventually lose IgG levels. We aimed to assess the persistence of SARS-CoV-2-specific B cells in patients who have lost specific IgGs and analyzed the reactivity of the immunoglobulins produced by these B cells. Circulating IgG memory B cells specific for SARS-CoV-2 were detected in all 16 patients 1–8 months post-infection, and 11 participants had specific IgA B cells. Four patients lost specific serum IgG after 5–8 months but had SARS-CoV-2-specific-B-cell levels comparable to those of seropositive donors. Immunoglobulins produced after in vitro differentiation blocked receptor-binding domain (RBD) binding to the cellular receptor ACE-2, indicating neutralizing activity. Memory-B-cell-derived IgGs recognized the RBD of B.1.1.7 similarly to the wild-type, while reactivity to B.1.351 and P.1. decreased by 30% and 50%, respectively. Memory-B-cell differentiation into antibody-producing cells is a more sensitive method for detecting previous infection than measuring serum antibodies. Circulating SARS-CoV-2 IgG memory B cells persist, even in the absence of specific serum IgG; produce neutralizing antibodies; and show differential cross-reactivity to emerging variants of concern. These features of SARS-CoV-2-specific memory B cells will help to understand and promote long-term protection.
Systematic Review and Meta-analysis on COVID-19 Vaccine Hesitancy
Authors: Fathalla Aboelsaad Iman Ahmed , Hafez Dina Mohamed , Almaghraby Abdallah , Abdulmoneim Shaimaa Abdulaziz , El-ganainy Samar Ossama , Hamdy Noha Alaa , Deghidy Ehsan Akram , El-Deen Ahmed El-Sayed Nour , Adel Elrewany Ehab Mohamed , Taha Khalil Alaa Hamdy , Salem Karem Mohamed , kabeel Samar Galal , Mohammed Elhadi Yasir Ahmed , Shaaban Ramy , Alnagar Amr , Fadel Elsherbeny Eman Ahmad , Elfeshawy Nagwa Ibrahim , Tahoun Mohamed Moustafa , Ghazy Ramy Mohamed 
Published: May 2021

AbstractBackground:The presented meta-analysis was developed in response to the publication of several studies addressing COVID-19 vaccines hesitancy. We aimed to identify the proportion of vaccine acceptance and rejection, and factors affecting vaccine hesitancy worldwide especially with the fast emergency approval of vaccines.Methods:Online database search was performed, and relevant studies were included with no language restriction. A meta-analysis was conducted using R software to obtain the random effect model of the pooled prevalence of vaccine acceptance and rejection. Egger’s regression test was performed to assess publication bias. Quality assessment was assessed using Newcastle-Ottawa Scale quality assessment tool.Results:Thirty-nine out of 12246 articles met the predefined inclusion criteria. All studies were cross-sectional designs. The pooled proportion of COVID-19 vaccine hesitancy was 17% (95% CI: 14-20) while the pooled proportion of COVID-19 vaccine acceptance was 75% (95% CI: 71-79). The vaccine hesitancy and the vaccine acceptance showed high heterogeneity (I2=100%). Case fatality ratio and the number of reported cases had significant effect on the vaccine acceptance as the pooled proportion of vaccine acceptance increased by 39.95% (95% CI: 20.1-59.8) for each 1% increase in case fatality (P<0.0001) and decreased by 0.1% (95% CI: -0.2-0.01) for each 1000 reported case of COVID-19, P= 0.0183).Conclusion:Transparency in reporting the number of newly diagnosed COVID-19 cases and deaths is mandatory as these factors are the main determinants of COVID-19 vaccine acceptance.
Two-phase sample selection strategies for design and analysis in post-genome wide association fine-mapping studies
Authors: Espin-Garcia Osvaldo , Craiu Radu V. , Bull Shelley B. 
Published: May 2021

AbstractPost-GWAS analysis, in many cases, focuses on fine-mapping targeted genetic regions discovered at GWAS-stage; that is, the aim is to pinpoint potential causal variants and susceptibility genes for complex traits and disease outcomes using next-generation sequencing (NGS) technologies. Large-scale GWAS cohorts are necessary to identify target regions given the typically modest genetic effect sizes. In this context, two-phase sampling design and analysis is a cost-reduction technique that utilizes data collected during phase 1 GWAS to select an informative subsample for phase 2 sequencing. The main goal is to make inference for genetic variants measured via NGS by efficiently combining data from phases 1 and 2. We propose two approaches for selecting a phase 2 design under a budget constraint. The first method identifies sampling fractions that select a phase 2 design yielding an asymptotic variance covariance matrix with certain optimal characteristics, e.g. smallest trace, via Lagrange multipliers (LM). The second relies on a genetic algorithm (GA) with a defined fitness function to identify exactly a phase 2 subsample. We perform comprehensive simulation studies to evaluate the empirical properties of the proposed designs for a genetic association study of a quantitative trait. We compare our methods against two ranked designs: residual-dependent sampling and a recently identified optimal design. Our findings demonstrate that the proposed designs, GA in particular, can render competitive power in combined phase 1 and 2 analysis compared to alternative designs while preserving type 1 error control. These results are especially apparent under the more practical scenario where design values need to be defineda prioriand are subject to mispecification. We illustrate the proposed methods in a study of triglyceride levels in the North Finland Birth Cohort of 1966. R code to reproduce our results is available atgithub.com/egosv/TwoPhase_postGWAS.
Clinical Burkholderia pseudomallei isolates from Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains
Authors: Burnard Delaney , Bauer Michelle J , Falconer Caitlin , Gassiep Ian , Norton Robert E , Paterson David L , Harris Patrick N A 
Published: May 2021

AbstractBurkholderia pseudomallei is an environmental gram-negative bacterium that causes the disease melioidosis and is endemic in many countries of the Asia-Pacific region. In Australia, the mortality rate remains high at approximately 10%. The bacterium is almost exclusively found in the endemic region, which spans the Northern Territory, Western Australia and North Queensland. However, Queensland infections remain understudied compared to those of the Northern Territory. This pilot study aimed to assess the prevalence of central nervous system disease associated variant bimABm, identify circulating antimicrobial resistance mutations and genetically distinct strains from Queensland, via comparative genomics. From 76 clinical isolates, we identified the bimABm variant in 20 (26.3%) isolates and in 9 (45%) of the isolates with documented central nervous system infection (n=18). Explorative analysis suggests a significant association between isolates carrying the bimABm variant and central nervous system disease (OR 2.8, 95% CI 1.3-6.0, P=0.009) compared with isolates carrying the wildtype bimABp, with the possibility of additional driving factors. Furthermore, 50% of isolates were identified as novel multi-locus sequence types (STs), while the bimABm variant was more commonly identified in isolates with novel sequence STs, compared to those of previously described STs. Additionally, mutations associated with acquired antimicrobial resistance were only identified in 14.5% of all genomes. The findings of this research have provided clinically relevant genomic data of B. pseudomallei in Queensland and suggest that the bimABm variant may enable risk stratification for the development CNS complications and be a potential therapeutic target.
A multimodal biomarker predicts dissemination of bronchial carcinoid
Authors: Reuling E.M.B.P. , Naves D.D. , Thunnissen E. , Kortman P.C. , Broeckaert M.A.M.B. , Plaisier P.W. , Dickhoff C. , Daniels J.M.A. , Radonic T. 
Published: May 2021

AbstractIntroductionThe extensive loss of lung parenchyma is a drawback of anatomical resection in bronchial carcinoids. Endobronchial therapy (EBT) has emerged as a safe and effective minimally invasive tissue sparing alternative for small intraluminal tumors. Currently, therapeutic decision making in patients with bronchial carcinoid is mainly based on tumor morphology and patient characteristics. The availability of more accurate biomarkers might help clinicians in selecting low-risk tumors for EBT. Therefore, we investigated radiological (tumor diameter), morphometric (mitotic index) and immunohistochemical (OTP, CD44, Ki-67, Rb and P16) markers as predictors of dissemination.Material and methodsPatients referred to Amsterdam University Medical Centers with available histology were included. Clinical and morphological characteristics relevant for classification such as tumor diameter, mitotic count (MAI) and prognostic immunohistochemical markers as Ki-67, P16, Rb, Orthopedia homebox (OTP) and CD44 were analyzed.ResultsIn a cohort of 171 patients, the vast majority were curatively treated with either EBT (n=61, 36%) or surgery (n=103, 60%). Seven (4%) patients presented with distant metastases at diagnosis. TC was diagnosed in 112 (65%) and AC in 59 (35%) patients. Nine (15%) patients treated with EBT had a local recurrence of disease during follow up and none developed lymph node or distant metastasis. Of all surgically treated patients, 13 (13%) had level 1 or 2 lymph node metastases. Additional 13 (13%) patients developed distant metastases, 11 (85%) were AC and 2 (15%) TC. Patients with tumor stage IA (tumor diameter ≤1cm) irrespective of tumor classification or immunohistochemical results did not develop distant metastases. Patients with typical carcinoid (<2 mitoses per 2 mm2) stage ≥IB with Ki67 <5% and positive CD44 did not develop distant metastases either. All patients with atypical carcinoid (≥2 mitoses 2 mm2), Ki-67 of ≥5% (p=<0.000) and loss of CD44 (p=<0.0001) developed distant metastases. Tumors with stage ≥IB and either ≥2 mitoses, Ki-67 >5% or loss of CD44 metastasized occasionally (11%).ConclusionAdding tumor diameter, CD44 and Ki-67 to the widely used TC/AC classification, provides a multimodal biomarker that better stratifies patients in prognostically favorable and unfavorable categories than current standards. These findings enable risk stratification allowing a tailored treatment approach for patients with bronchial carcinoid.
Comparative and systems analyses of Leishmania spp. non-coding RNAs through developmental stages
Authors: Martinez-Hernandez J. Eduardo , Aliaga-Tobar Victor , González Carolina , Monte-Neto Rubens , Martin Alberto J. M. , Maracaja-Coutinho Vinicius 
Published: May 2021

ABSTRACTLeishmania spp. is the etiological agent of leishmaniases, neglected diseases that seek to be eradicated in the coming years. The life cycle of these parasites involve different host and stress environments. In recent years, many studies have shown that several protein coding genes are directly involved with the development and host interactions, however, little is still known about the role of ncRNAs in life cycle progression. In this study, we aimed to identify the genomic structure and function of ncRNAs from Leishmania spp. and to get insights into the RNAome of this protozoan genus. We studied 26 strains corresponding to 16 different species of Leishmania. Our RNAome analysis revealed the presence of several ncRNAs that are shared through different species, allowing us to differentiate between subgenus as well as species that are canonically related to visceral leishmaniasis. We also studied co-expression relationships between coding genes and ncRNAs which in the amastigote developmental stage for Leishmania braziliensis and L. donovani revealed the presence of miRNA-like co-expressed with several coding genes involved in starvation, survival and histone modification. This work constitutes the first effort to characterize the Leishmania RNAome, supporting further approaches to better understand the role of ncRNAs in the gene regulation, infective process and host-parasite interaction.
A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacteriumRhodothermus marinus
Authors: Kristjansdottir Thordis , Hreggvidsson Gudmundur O. , Stefansson Sigmar Karl , Gudmundsdottir Elisabet Eik , Bjornsdottir Snaedis H. , Fridjonsson Olafur H. , Karlsson Eva Nordberg , Vanhalst Justine , Reynisson Birkir , Gudmundsson Steinn 
Published: May 2021

AbstractThe thermophilic bacteriumRhodothermus marinushas mainly been studied for its thermostable enzymes. More recently, the potential of using the species as a cell factory and in biorefinery platforms has been explored, due to the elevated growth temperature, native production of compounds such as carotenoids and EPSs, the ability to grow on a wide range of carbon sources including polysaccharides, and available genetic tools. A comprehensive understanding of the metabolism of production organisms is crucial. Here, we report a genome-scale metabolic model ofR. marinusDSM 4252T. Moreover, the genome of the genetically amenableR. marinusISCaR-493 was sequenced and the analysis of the core genome indicated that the model could be used for both strains. Bioreactor growth data was obtained, used for constraining the model and the predicted and experimental growth rates were compared. The model correctly predicted the growth rates of both strains. During the reconstruction process, different aspects of theR. marinusmetabolism were reviewed and subsequently, both cell densities and carotenoid production were investigated for strain ISCaR-493 under different growth conditions. Additionally, thedxsgene, which was not found in theR. marinusgenomes, fromThermus thermophiluswas cloned on a shuttle vector into strain ISCaR-493 resulting in a higher yield of carotenoids.ImportanceA biorefinery converting biomass into fuels and value-added chemicals is a sustainable alternative to fossil fuel-based chemical synthesis.Rhodothermus marinusis a bacterium that is potentially well suited for biorefineries. It possesses various enzymes that degrade biomass, such as macroalgae and parts of plants (e.g. starch and xylan) and grows at high temperatures (55-77°C) which is beneficial in biorefinery processes. In this study, we reviewed the metabolism ofR. marinusand constructed a metabolic model. Such a model can be used to predict phenotypes, e.g. growth under different environmental and genetic conditions. We focused specifically on metabolic features that are of interest in biotechnology, including carotenoid pigments which are used in many different industries. We described cultivations ofR. marinusand the resulting carotenoid production in different growth conditions, which aids in understanding how carotenoid yields can be increased in the bacterium.
Defining dual-axis landscape gradients of human influence for studying ecological processes
Authors: Padilla Benjamin J. , Sutherland Chris 
Published: May 2021

AbstractEcological processes are strongly shaped by human landscape modification, and understanding the reciprocal relationship between ecosystems and modified landscapes is critical for informed conservation. Single axis measures of spatial heterogeneity proliferate in the contemporary gradient ecology literature, though they are unlikely to capture the complexity of ecological responses. Here, we develop a standardized approach for defining multi-dimensional gradients of human influence in heterogeneous landscapes and demonstrate this approach to analyze landscape characteristics of ten ecologically distinct US cities. Using occupancy data of a common human-adaptive songbird collected in each of the cities, we then use our dual-axis gradients to evaluate the utility of our approach. Spatial analysis of landscapes surrounding ten US cities revealed two important axes of variation that are intuitively consistent with the characteristics of multi-use landscapes, but are often confounded in single axis gradients. These were, a hard-to-soft gradient, representing transition from developed areas to non-structural soft areas; and brown-to-green, differentiating between two dominant types of soft landscapes: agriculture (brown) and natural areas (green). Analysis of songbird data demonstrated that occupancy responds to both hard-to-soft (decreasing with development intensity) and brown-to-green gradient (increasing with more natural area). Overall, our results reveal striking consistency in the dominant sources of variation across ten geographically distinct cities and suggests that our approach advances how we relate variation in ecological responses to human influence. Our case study demonstrates this: robins show a remarkably consistent response to a gradient differentiating agricultural and natural areas, but city-specific responses to the more traditional gradient of development intensity, which would be overlooked with a single gradient approach. Managing ecological communities in human dominated landscapes is extremely challenging due to a lack of standardized approaches and a general understanding of how socio-ecological systems function, and our approach offers promising solutions.
Transcriptome-wide identification and expression profiling of the ERF gene family suggest roles as transcriptional activators and repressors of fruit ripening in durian
Authors: Khaksar Gholamreza , Sirikantaramas Supaart 
Published: May 2021

AbstractThe involvement of the phytohormone ethylene as the main trigger of climacteric fruit ripening is well documented. However, our knowledge regarding the role of ethylene response factor (ERF) transcription factor in the transcriptional regulation of ethylene biosynthesis during fruit ripening remains limited. Here, comprehensive transcriptome analysis and expression profiling revealed 63 ERFs in durian pulps, termed DzERF1–DzERF63, of which 34 exhibited ripening-associated expression patterns at three stages (unripe, midripe, and ripe) during fruit ripening. Hierarchical clustering analysis classified 34 ripening-associated DzERFs into three distinct clades, among which, clade I consisted of downregulated DzERFs and clade III included those upregulated during ripening. Phylogenetic analysis predicted the functions of some DzERFs based on orthologs of previously characterized ERFs. Among downregulated DzERFs, DzERF6 functional prediction revealed its role as a negative regulator of ripening via ethylene biosynthetic gene repression, whereas among upregulated genes, DzERF9 was predicted to positively regulate ethylene biosynthesis. Correlation network analysis of 34 ripening-associated DzERFs with potential target genes revealed a strong negative correlation between DzERF6 and ethylene biosynthetic genes and a strong positive correlation between DzERF9 and ethylene biosynthesis. DzERF6 and DzERF9 showed differential expression patterns in association with different ripening treatments (natural, ethylene-induced, and 1-methylcyclopropene-delayed ripening). DzERF6 was downregulated, whereas DzERF9 was upregulated, during ripening and after ethylene treatment. The auxin-repressed and auxin-induced expression of DzERF6 and DzERF9, respectively, confirmed its dose-dependent responsiveness to exogenous auxin. We suggest ethylene- and auxin-mediated roles of DzERF6 and DzERF9 during fruit ripening, possibly through transcriptional regulation of ethylene biosynthetic genes.
Trend, Population Structure and Trait Mapping from 15 Years of National Varietal Trials of UK Winter Wheat
Authors: Shorinola Oluwaseyi , Simmonds James , Wingen Luzie U. , Gardner Keith , Uauy Cristobal 
Published: May 2021

ABSTRACTThere are now a rich variety of genomic and genotypic resources available to wheat researchers and breeders. However, the generation of high-quality and field-relevant phenotyping data which is required to capture the complexities of gene x environment interactions remains a major bottleneck. Historical datasets from national variety performance trials (NVPT) provide sufficient dimensions, in terms of numbers of years and locations, to examine phenotypic trends and study gene x environment interactions. Using NVPT for winter wheat varieties grown in the UK between 2002 – 2017, we examined temporal trends for eight traits related to yield, adaptation, and grain quality performance. We show a non-stationary linear trend for yield, grain protein content, HFN and days to ripening. Our data also show high environmental stability for yield, grain protein content and specific weight in UK winter wheat varieties and high environmental sensitivity for Hagberg Falling Number. Using the historical NVPT data in a genome-wide association analysis, we uncovered a significant marker-trait association peak on wheat chromosome 6A spanning the NAM-A1 gene that have been previously associated with early senescence. Together our results show the value of utilizing the data routinely collected during variety evaluation process for examining breeding progress and the genetic architecture of important traits.