bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of viral communities and the host–pathogen interactions with ecological factors in bat caves
Authors: Li xiaolin , Li Aoqiang , Li Zhongle , Leng Haixia , Jin Longru , Xiao Yanhong , Sun Keping , Feng Jiang 
Published: July 2023

Abstract
Background
Bats (Chiroptera) are major sources of epidemics. To understand the dynamics of diseases, it is crucial to study the dynamics of microorganisms in the environment and the relationship between microorganisms and bats. In this study, we investigated the soil virus communities in bat caves using viral metagenomic sequencing technology. We further explored host–pathogen interactions with regard to the effects of the environment by combining analyses of microorganisms (viruses and bacteria) and immune genes (major histocompatibility complex, MHC) of the main resident species (Rhinolophus ferrumequinum) in the bat caves.
Results
A total of 31 families of viruses were identified. Significant differences were observed in alpha diversity, beta diversity, and the relative abundances of soil virus families, indicating their habitat specificity in bat caves. Zoonotic risk viruses were also found, and the composition of viruses in bat caves was similar to the distribution of virus families of R. ferrumequinum in a previous study. Second, the alpha diversity of both viruses and bacteria was significantly negatively correlated with precipitation of the wettest month. The relative abundances of viral and bacterial families were correlated with MHC allele frequencies. Moreover, a structural equation model further revealed that the precipitation of the coldest quarter significantly negatively affected virus diversity, which in turn significantly negatively affected the MHC allele frequencies in R. ferrumequinum. The MHC allele frequencies were negatively affected by bacterial alpha diversity.
Conclusions
The results of the present study suggest that the polymorphism of the MHC class I gene of R. ferrumequinum is driven by environmental pathogen selection pressure and that environmental climate affects the host immune genes by regulating the diversity of microorganisms. This study is the first to demonstrate the diversity of virus communities in bat caves, and thus has significance for protecting bat habitats from human disturbance and in preventing zoonotic diseases.
Quercetin improves epithelial regeneration from airway basal cells of COPD patients
Authors: McCluskey Elizabeth S. , Liu Nathan , Pandey Abhimaneu , Marchetti Nathaniel , Sajjan Umadevi 
Published: July 2023

Abstract
Background
Airway basal cells from patients with chronic obstructive pulmonary disease (COPD) regenerate abnormal airway epithelium and this was associated with reduced expression of several genes involved in epithelial repair. Quercetin reduces goblet cell metaplasia and the expression of pro-inflammatory cytokines in COPD models. This study assessed whether quercetin improves epithelial regeneration from COPD airway basal cells.
Methods
COPD airway basal cells were treated with DMSO or 1 µM quercetin for three days. The cells were then cultured at air/liquid interface (ALI) for up to 4 weeks. Basal cells from healthy donors cultured at air/liquid interface were used as controls. Polarization of cells was determined at 8 days of ALI. The cell types and IL-8 expression in differentiated cell cultures were quantified by flow cytometry and ELISA. Microarray analysis was conducted on DMSO or quercetin-treated COPD basal cells to identify differentially regulated genes (DEG) and the enriched biological pathways. Bronchial brushings from COPD patients treated with either placebo or quercetin for 6 months were used to confirm the effects of quercetin on gene expression.
Results
Compared to DMSO, quercetin-treated COPD basal cells showed an increase in TER and regenerated the airway epithelium with more ciliated cells, and less goblet cells and IL-8. Comparison of DMSO- and quercetin-treated COPD basal cell transcriptomic profiles indicated that quercetin upregulated genes associated with tissue and epithelial development and differentiation. COPD patients treated with quercetin, but not placebo showed significantly increased expression of two developmental genes HOXB2 and ELF3, which were also increased in quercetin-treated COPD basal cells. Bronchial brushings from active smokers showed significantly increased mRNA expression of TGF-β and IL-8, and it was reduced after quercetin treatment.
Conclusions
These results indicate that quercetin may improve airway epithelial regeneration by increasing the expression of genes involved in epithelial development/differentiation in COPD.
Trial registration
This study was registered at ClinicalTrials.gov on 6-18-2019. The study number is NCT03989271.
Low Diagnostic Performance of Thick Blood Smears of 50 µL in Comparison with Blood Direct Examination of 10 µL and Leukoconcentration Techniques among Loiasis-Suspected Patients with Low Microfilaremia in Gabon, Central Africa, using the STARD-BCLM Guidelines
Authors: M’Bondoukwé Noé Patrick , Owono-Medang Matthieu , Moussavou-Boussougou Marie Noëlle , Akoue Yvan , Migueba Valentin , Bulaev Dmitry , Neven Anouk , James Aurtin Joel Luice , Ntsame-Ella Julie , Mboumba Denise Patricia Mawili , Atsame Julienne , Vaillant Michel , Bouyou-Akotet Marielle Karine 
Published: July 2023

Abstract

Background
The aim of the study was to determine performance indicators of the Thick Blood Smear of 50 µL (TBS-50), following Standards for the Reporting of Diagnostic Accuracy Studies-Bayesian Latent Class Analysis (STARD-BLCA) guidelines. TBS-50 was compared to two common parasitological techniques – the blood direct examination of 10 µL and the leukoconcentration of 5 mL.
Methods
The study population was recruited among the patients of the Department of Parasitology-Mycology-Tropical Medicine of the Faculty of Medicine of the Université des Sciences de la Santé between July 2018 and July 2019. Age, sex, symptoms and eosinophilia variables were recorded from laboratory registers and medical files. The blood direct examination of 10 µL, TBS-50 and the leukoconcentration technique of 5 mL were performed for each patient. The Classica formula and BLCA were used to determine the diagnostic accuracies of the three techniques as well as the prevalence. Three models were built within the framework of BCLA: main model I and alternative models II and III for sensitivity analysis considering the leukoconcentration technique as the gold standard.
Results
In total, 191 patients consented to be included. The prevalence of Loa loa microfilaremia was 9.4% [95% CI: 5.7–14.5] (n = 18/191) with direct blood examination/TBS-50 and 12.6% [8.2–18.1] (n = 24/191) for leukoconcentration. The mean microfilaremia levels were comparable between blood direct examination (1005 [200-15000] mf/mL) and TBS-50 (815 [100-16720] mf/mL) (p = 0.97). Comparing TBS-50/direct blood examination with the leukoconcentration method, the sensitivity was 75.0% [53.3–90.2], the specificity was 100.0% [97.8–100.0], the positive predictive value was 100.0% [81.5–100.0], and the negative predictive value was 96.5% [92.6–98.7]. The prevalence estimates of microfilaremic loiasis were 9.7% [6.2–13.7], 10.2% [6.3–14.4] and 11.2% [6.7–16.4], respectively, in ascending order of the models. The outputs of main model I showed a sensitivity of 78.9% [65.3–90.3], a specificity of 100.0% [99.3–100.0], a positive predictive value of 99.1% [87.2–100.0] and a negative predictive value of 93.0% [87.3–97.7] for direct blood examination/TBS-50.
Conclusions
TBS-50/blood direct examination has a low sensitivity. In one in five cases, the result will be falsely declared negative using these two methods.
Comparing Approximated Heat Stress Measures ﻿Across the United States
Authors: Ahn Yoonjung , Tuholske Cascade , Parks Robbie M. 
Published: July 2023

Abstract
Extreme heat is a great threat to human health, and a growing public health concern, with recent higher intensity and duration of heat days coupled with increasing population exposure to hot environments. Utilizing accurate weather information and measures that reflect what people experience is a key component to understanding extreme heat impacts on human health. Numerous studies have suggested various heat metrics Heat Index (HI) and Wet Bulb Globe Temperature (WBGT) have been widely used in heat exposure guidelines. However, there are few systematic comparisons of daily heat measures and weather variables such as daily relative humidity, wind speed, and solar radiation which are highly related to human body thermoregulation and physiologic impact of heat. We compared three relevant heat measures (HImax, WBGTBernard, and WBGTLiljegren), derived from three widely-used gridded weather datasets (ERA5, PRISM, and Daymet) with ground-based weather observations. The heat measures calculated from gridded weather data and station data showed fairly strong agreement (R2 0.82–0.96, Root Mean Square Error (RMSE) 1.69–5.37°C). However, the discrepancies varied according to Köppen-Geiger climates (e.g., Adjusted R2 HImax (0.61–0.96), WBGTBernard (0.64–0.94), and WBGTLiljegren (0.34–0.94)). Gridded weather datasets offer a fairly reliable approach to assessing heat exposure of meteorological variables and heat measures. However, further research and establishing local ground station networks are necessary to reduce exposure measurement error and improve accuracy to ultimately better and more robustly understand the links between humid heat and health outcomes.
On-chip hybrid erbium-doped tellurium oxide-silicon nitride distributed Bragg reflector lasers
Authors: Frare Bruno L. Segat , Ahmadi Pooya Torab , Hashemi Batoul , Bonneville Dawson B. , Mbonde Hamidu M. , Frankis Henry C. , Knights Andrew P. , Mascher Peter , Bradley Jonathan D. B. 
Published: July 2023

Abstract
We demonstrate integrated on-chip erbium-doped tellurite (TeO2:Er3+) waveguide lasers fabricated on a wafer-scale silicon nitride platform. A 0.352-µm-thick TeO2:Er3+ coating was deposited as an active medium on 0.2-µm-thick, 1.2- and 1.6-µm-wide, and 22-mm-long silicon nitride waveguides with sidewall-patterned asymmetrical distributed Bragg reflector cavities. The lasers yield efficiencies between 0.06 and 0.36%, lasing threshold ranging from 13 to 26 mW, and emission within the C-band (1530–1565 nm). These results establish new opportunities for this hybrid tellurite glass-silicon nitride platform, such as the co-integration of passive components and light sources in the telecom window, and provide the foundation for the development of efficient, compact, and high-output-power on-chip erbium-doped tellurite waveguide lasers.
Prediction of histopathologic grades of bladder cancer with radiomics based on MRI: comparison with traditional MRI
Authors: Li Longchao , Zhang Jing , Zhe Xia , Tang Min , Zhang Li , Lei Xiaoyan , Zhang Xiaoling 
Published: July 2023

Abstract
Purpose
To compare Magnetic resonance imaging (MRI) radiomics signatures and traditional MRI model for the preoperative prediction of bladder cancer (BCa) grade.
Methods
This retrospective study included 255 consecutive patients with pathologically confirmed 113 low-grade and 142 high-grade BCa who underwent preoperative MRI, including T2-weighted imaging (T2WI) and apparent diffusion coefficient (ADC). The traditional MRI nomogram model was developed using univariate and multivariate logistic regression by the mean apparent diffusion coefficient (mADC), vesical imaging reporting and data system (VI-RADS) scoring, tumor size and number of tumors. Volumes of interest were manually drawn on T2WI and ADC maps by two radiologists. Using ANOVA, correlation and LASSO methods to select features. Then, a logistic regression (LR) classifier was used to develop the radiomics signatures in the training set and assessed in the validation set. Receiver operating characteristic (ROC) analysis was used to compare the diagnostic abilities of the radiomics and traditional MRI models by the DeLong test. Finally, decision curve analysis (DCA) was performed by estimating the clinical usefulness of the two models in both the training and validation sets.
Results
The areas under the ROC curves (AUCs) of the traditional MRI model were 0.841 in the training cohort and 0.806 in the validation cohort. The AUCs of the three groups of radiomics model [ADC, T2WI, bi-parametric-MRI(bp-MRI, ADC and T2WI)]-based logistic regression analysis algorithms were 0.888, 0.875 and 0.899 in the training cohort and 0.863, 0.805 and 0.867 in the validation cohort, respectively. The combined radiomics model achieved higher AUCs than the traditional MRI model and was compared using the DeLong test (P = 0.026 and 0.023 in the training and validation cohorts, respectively). DCA indicated that the radiomics model had higher net benefits than the traditional MRI model.
Conclusions
The MRI radiomics model can be helpful for preoperatively predicting low-grade or high-grade BCa and outperformed the traditional MRI model.
Meta-analysis of root-associated microbial communities of widely distributed native and invasive Poaceae plants in Antarctic.
Authors: Wang Xumin , Qu Ying , Teng Xindong , Xu Li , Jin Liming , Xue Hao , Xun Zhuoran , Zhang Qingzheng , Wang Chenghong , Wang Lijun , Liu Xiumei , Wang Shuang , Zheng Li , Yu Yong , Qu Jiangyong , Xing Zhikai 
Published: July 2023

Abstract
Deschampsia antarctica Desv. and Poa annua L. are two Poaceae plants with enough endurance to successfully establish populations in the Antarctic region. Their adaptation to the Antarctic environment is closely linked to root-associated microbial communities. In this study, we obtained 16S rRNA sequencing data of the root-associated microbial communities of these two Poaceae plants from NCBI. Meta-analysis was used to investigate the similarities and differences between the root-endosphere and rhizosphere-dwelling microbial communities in these two Poaceae plants. Here we report that two Poaceae-Poaceae plants’ rhizospheric communities were found to be more species diversity than endospheric communities. The species diversity of P. annua was higher than that of D. antarctica in both endosphere and rhizosphere communities. Seven bacterial families form a core microbiome of two Antarctic Poaceae plants’ root endosphere, in which Microbacteriaceae appears to be obligatory root endophytes of the two Antarctic Poaceae plants. The core microbiome of the two Poaceae plants' rhizosphere has six bacterial families. Chitinophagaceae, Burkholderiaceae, and Flavobacteriaceae are most likely to play a crucial role in Poaceae plants' adaptation to cold Antarctic conditions. Sphingobacteriaceae, Caulobacteraceae, Gemmatimonadaceae, and Flavobacteriaceae have a great influence on two Antarctic Poaceae plants.
Mosquito (Diptera: Culicidae) communities in contrasting areas from the Western regions of Burkina Faso: species diversity, abundance and implication in pathogen transmission
Authors: KABORE Patindé Didier Alexandre , Soma Dieudonné Diloma , Gil Patricia , Kientega Mahamadi , Sawadogo Simon P. , Ouédraogo Georges Anicet , Perre Philippe , Baldet Thierry , Gutierrez Serafin , Dabiré Roch K. 
Published: July 2023

Abstract
Background: Mosquitoes (Diptera : Culicidae) are the arthropods that have the greatest negative impact on human health. The transformation of natural environments changing into urban and agricultural areas and population growing are phenomena that affect mosquito communities, thus influencing the risk of emerging or re-emerging vector-borne diseases. Here, we describe the diversity and abundance of adult mosquitoes in four environments with different anthropization levels (rural, urban, rice fields and forest) in a West African savannah zone.
Methods: Mosquitoes were collected from two region (Hauts-Bassins and Sud-Ouest) of Burkina Faso during five periods between August 2019 and June 2021. Sampling sites were grouped according to anthropized environments. Mosquitoes were collected using BG sentinel traps and Prokopack aspirator. Analyses were performed using R software version 4.1.2. Logistic regression by generalized mixed linear models were used to test the effect of environment on mosquito abundance and diversity. Alpha diversity analysis was also performed using Vegan package.
Results: A total of 10,625 adult mosquitoes were collected, belonging to 33 species, 5 genera: Culex, Aedes, Anopheles, Mansonia, and Ficalbia. The most dominant species were Cx. quinquefasciatus, An. gambiae s.l. and Ae. aegypti. Alpha diversity was similar across the regions. Habitat had a significant effect on mosquito species richness, Shannon index and Simpson index. The rural environment had the highest species richness (n = 28) followed by the forest environment (n= 24). The highest number (4,977/10,625) of mosquitoes was collected in urban environment.
Conclusions: The composition of mosquito communities depended on the type of environment, with fewer species in highly anthropized environments such as urban and rice fields areas. Diversity and abundance of mosquito vectors could expose human populations from each environment to a potential risk of mosquito-borne diseases.
Analytical Fitting of gamma-ray Photopeaks in Germanium Cross Strip Detectors
Authors: Boggs Steven E. , Pike Sean N. 
Published: July 2023

Abstract
In an ideal germanium detector, fully-absorbed monoenergetic gamma-rays will appear in the measured spectrum as a narrow peak, broadened into a Gaussian of width determined only by the statistical properties of charge cloud generation and the electronic noise of the readout electronics. Multielectrode detectors complicate this picture. Broadening of the charge clouds as they drift through the detector will lead to charge sharing between neighboring electrodes and, inevitably, low-energy tails on the photopeak spectra. We simulate charge sharing in our germanium cross strip detectors in order to reproduce the low-energy tails due to charge sharing. Our goal is to utilize these simulated spectra to develop an analytical fit (shape function) for the spectral lines that provides a robust and high-quality fit to the spectral profile, reliably reproduces the interaction energy, noise width, and the number of counts in both the true photopeak and the low-energy tail, and minimizes the number of additional parameters. Accurate modeling of the detailed line profiles is crucial for both calibration of the detectors as well as scientific interpretation of measured spectra.
Numerical method and Validation using ANN of Composite Steel-Concrete Beam for Optimized Geometry and Emplacement of Web Opening
Authors: Mastan Sheik , S Anandh , S Sindhu Nachiar 
Published: July 2023

Abstract
Composite steel-concrete beams are widely used in buildings and bridges due to their nature, ease of construction, low cost, and excellent structural performance. Ventilation ducts and pipes under beams in high-rise buildings restrict floor clearance. Composite steel-concrete beams with web openings can overcome the abovementioned impediments but have lower flexural strength and load-carrying capacity. This study has been conducted to optimize the geometry and emplacement of the opening for the enhancement of its structural behavior. Three geometries (circle, rectangle, and triangle) were considered in the composite steel-concrete beam and analyzed using ABAQUS v6.14. The optimized geometry is emplaced at varying positions between the end of the support and mid-the span. Based on stress concentration and the maximum stress resistance, the circular geometry placed at one-third of the span was effective from the numerical analysis. The load-carrying capacity of the beams was predicted using the Artificial Neural Network (ANN) model, and the results were validated by Multiple Determination Coefficients (R2) and Mean Square Error (MSE). The results of R2 and MSE for all the models were found to be greater than 0.94 and less than 0.09, respectively. This indicates that ANN provides a perfect fit for the numerical data.
Statistical Inference on the Inverse Weibull Model ParametersBased on Generalized Fuzzy Order Statistics
Authors: Maswadah M. 
Published: July 2023

Abstract

In statistical inference, the parameter estimations for lifetime distribution usually deal with precise information. However, in real world situations, experimental performance results cannot always be recorded or measured precisely, and each observable event may only be identified with a fuzzy subset of the sample space. The mean objective of this work is to apply Bayes estimation for the inverse Weibull distribution parameters based on generalized fuzzy order statistics when the available observations are described by means of fuzzy information. The Bayesian estimates are compared to the maximum likelihood estimates (MLEs) and the expectation maximization (EM) estimates, via Monte Carlo simulations, in terms of the mean square errors and mean percentage errors. The results are quite favorable to Bayes’ method, which provides better estimates and outperforms the maximum likelihood and the EM estimates for different sample sizes and several values for the true parameters. Finally, a numerical example is given to demonstrate the efficiency of the proposed method.
Illuminating T cell-dendritic cell interactions in vivo by FlAsHing antigens
Authors: Akkaya Munir , Souz Jafar Al , Williams Daniel , Kamdar Rahul , Kamenyeva Olena , Kabat Juraj , Shevach Ethan M. , Akkaya Billur 
Published: July 2023

Abstract

Delineating the complex network of interactions between antigen-specific T cells and antigen presenting cells (APCs) is crucial for effective precision therapies against cancer, chronic infections, and autoimmunity. However, the existing arsenal for examining antigen-specific T cell interactions is restricted to a select few antigen-T cell receptor pairs, with limited in situ utility. This lack of versatility is largely due to the disruptive effects of reagents on the immune synapse, which hinder real-time monitoring of antigen-specific interactions. To address this limitation, we have developed a novel and versatile immune monitoring strategy by adding a short cysteine-rich tag to antigenic peptides that emits fluorescence upon binding to thiol-reactive biarsenical hairpin compounds. Our findings demonstrate the specificity and durability of the novel antigen-targeting probes during dynamic immune monitoring in vitro and in vivo. This strategy opens new avenues for biological validation of T-cell receptors with newly identified epitopes by revealing the behavior of previously unrecognized antigen-receptor pairs, expanding our understanding of T cell responses.

The authors would like to note that Munir Akkaya and Jafar Al Souz contributed equally.