bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of mosaic and population-level structural variants with Sniffles2
Authors: Smolka Moritz , Paulin Luis F. , Grochowski Christopher M. , Horner Dominic W. , Mahmoud Medhat , Behera Sairam , Kalef-Ezra Ester , Gandhi Mira , Hong Karl , Pehlivan Davut , Scholz Sonja W. , Carvalho Claudia M. B. , Proukakis Christos , Sedlazeck Fritz J. 
Published: January 2024

AbstractCalling structural variations (SVs) is technically challenging, but using long reads remains the most accurate way to identify complex genomic alterations. Here we present Sniffles2, which improves over current methods by implementing a repeat aware clustering coupled with a fast consensus sequence and coverage-adaptive filtering. Sniffles2 is 11.8 times faster and 29% more accurate than state-of-the-art SV callers across different coverages (5–50×), sequencing technologies (ONT and HiFi) and SV types. Furthermore, Sniffles2 solves the problem of family-level to population-level SV calling to produce fully genotyped VCF files. Across 11 probands, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. As a result, we identified multiple mosaic SVs in brain tissue from a patient with multiple system atrophy. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements.
A comprehensive dataset of U.S. federal laws (1789–2022)
Authors: Libgober Brian 
Published: January 2024

AbstractU.S. federal laws figure importantly in many research projects in political science, law, sociology, economics, and other disciplines. Despite their prominence, there is no authoritative, current, and comprehensive dataset of U.S. federal laws. In part, this is because such laws have been enacted over hundreds of years, resulting in a complicated patchwork of documents published in numerous and inconsistent formats. As a simplification, many scholars have relied upon selective lists of major legislative enactments or complete lists of relatively recent enactments. Here, I report on an effort to transparently and reproducibly assemble a complete database of US laws and their revision histories by combining data from HeinOnline, the Governmental Printing Office, and the National Archives and Records Administration. The result is a database of 49,746 laws spanning 1789 to 2022.
Transcriptomic datasets of Verticillium wilt resistant and non-resistant Gossypium barbadense varieties during pathogen inoculation
Authors: Xiong Xianpeng , Sun Cong , Chen Bin , Sun Jie , Fei Cong , Xue Fei 
Published: January 2024

AbstractCotton is a significant cash crop and the primary source of natural fiber globally. Among the numerous diseases encountered in cotton production, Verticillium wilt is one of the most serious, caused by the pathogen Verticillium dahliae (V. dahliae). Unfortunately, there are no effective targeted methods to combat this disease. Genomic resources for Verticillium wilt resistance primarily exist in Gossypium barbadense (G. barbadense). Regrettably, there have been limited transcriptomic comparisons between V. dahliae-resistant and -susceptible varieties of G. barbadense due to the scarcity of susceptible resources. In this study, we conducted a transcriptome analysis on both V. dahliae-resistant and -susceptible varieties of G. barbadense at the 0, 12, 24 and 48 hours after V. dahliae inoculation. This comparative transcriptome analysis yielded high-quality data and offered new insights into the molecular mechanisms underlying cotton’s resistance against this destructive pathogen.
HSV1 microRNAs in glioblastoma development: an in silico study
Authors: Abdoli Shadbad Mahdi , Hemmat Nima , Abdoli Shadbad Mahla , Brunetti Oronzo , Silvestris Nicola , Baradaran Behzad 
Published: January 2024

AbstractGlioblastoma multiforme (GBM) is a highly aggressive primary brain tumor. Recent findings highlighted the significance of viral microRNAs (miRs) in regulating post-transcriptional mRNA expression in various human conditions. Although HSV1 encodes viral miRs and affects the central nervous system, no study investigated the roles of HSV1-encoding miRs in GBM development. This study applied in silico approaches to investigate whether HSV1-encoding miRs are involved in GBM development and, if so, how they regulate tumor-suppressive/oncogenes expression in GBM. This study leveraged bioinformatics approaches to identify the potential effect of HSV1 miRs in GBM development. The GSE158284, GSE153679, and GSE182109 datasets were analyzed to identify differentially expressed genes in GBM tissues and cell lines using the limma package in the R software. The GSE182109 dataset was analyzed to determine gene expression at the single-cell levels using the Seurat package in the R software. The TCGA-GTEX, GDSC, CTRP, immunogenetic, and enrichment analyses were performed to study the impact of identified viral HSV1 miRs targets in GBM development. hsv1-miR-H6-3p is upregulated in GBM and can be responsible for EPB41L1 and SH3PXD2A downregulation in GBM tissues. Also, hsv1-miR-H1-5p is upregulated in GBM and can decrease the expression of MELK, FZD2, NOVA1, TMEM97, PTPRZ1, and PDGFC in GBM development. The single-cell RNA sequencing analyses have demonstrated that MELK, FZD2, NOVA1, TMEM97, PTPRZ1, and PDGFC are expressed in astrocytes residing in the GBM microenvironment. This study provides novel insights into the potential roles of HSV1 miRs in GBM pathogenesis and offers a reference for further studies on the significance of HSV1 miRs in GBM development.
Wintertime investigation of PM10 concentrations, sources, and relationship with different meteorological parameters
Authors: Zeb Bahadar , Ditta Allah , Alam Khan , Sorooshian Armin , Din Badshah Ud , Iqbal Rashid , Habib ur Rahman Muhammed , Raza Ahsan , Alwahibi Mona S. , Elshikh Mohamed S. 
Published: January 2024

AbstractMeteorological factors play a crucial role in affecting air quality in the urban environment. Peshawar is the capital city of the Khyber Pakhtunkhwa province in Pakistan and is a pollution hotspot. Sources of PM10 and the influence of meteorological factors on PM10 in this megacity have yet to be studied. The current study aims to investigate PM10 mass concentration levels and composition, identify PM10 sources, and quantify links between PM10 and various meteorological parameters like temperature, relative humidity (RH), wind speed (WS), and rainfall (RF) during the winter months from December 2017 to February 2018. PM10 mass concentrations vary from 180 – 1071 µg m−3, with a mean value of 586 ± 217 µg m−3. The highest concentration is observed in December, followed by January and February. The average values of the mass concentration of carbonaceous species (i.e., total carbon, organic carbon, and elemental carbon) are 102.41, 91.56, and 6.72 μgm−3, respectively. Water-soluble ions adhere to the following concentration order: Ca2+  > Na+  > K+  > NH4+  > Mg2+. Twenty-four elements (Al, Si, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Co, Zn, Ga, Ge, As, Se, Kr, Ag, Pb, Cu, and Cd) are detected in the current study by PIXE analysis. Five sources based on Positive Matrix Factorization (PMF) modeling include industrial emissions, soil and re-suspended dust, household combustion, metallurgic industries, and vehicular emission. A positive relationship of PM10 with temperature and relative humidity is observed (r = 0.46 and r = 0.56, respectively). A negative correlation of PM10 is recorded with WS (r =  − 0.27) and RF (r =  − 0.46). This study’s results motivate routine air quality monitoring owing to the high levels of pollution in this region. For this purpose, the establishment of air monitoring stations is highly suggested for both PM and meteorology. Air quality standards and legislation need to be revised and implemented. Moreover, the development of effective control strategies for air pollution is highly suggested.
Stable composition of gut microbiome in the Asian ladybeetle Coccinella septempunctata reared on natural and artificial diets
Authors: Lu Qiu-Cheng , Yu Jia-Min , Liu Hong-Ling , Wu Xing-Long , Wei Shu-Jun , Lei Min , Cai Peng , He Heng-Guo , Pu De-Qiang 
Published: January 2024

AbstractThe Asian ladybeetle, Coccinella septempunctata, is an important insect of predatory natural enemy, which has a strong control effect and application prospects for aphids, whiteflies, mealybugs, and other small-sized pests of agriculture and forestry crops. Gut microbiota composition posed impacts on development of insects. In order to clarify the effect of artificial feed feeding on the intestinal microbial species and structure of C. septempunctata, we compared the intestinal microbial flora of C. septempunctata reared on bean aphids and artificial food for 15 days. Results show that Proteobacteria was the dominant component in all groups at phylum level, Rhodobacter, Methylovigula, Burkholderia, and Bradyrhizobium were the dominant bacteria among all groups at genus level. As to the differences in bacterial community structure and diversity, there is no significant difference between Shannon index and Simpson index, the principal components analysis of the bacterial communities, and the samples were roughly distributed in different regions. After 15 days of feeding, artificial diet did not significantly reduce the microbial diversity of the gut of C. septempunctata compared to the aphid group, and there was no significant effect on the abundance of dominant flora in the gut of C. septempunctata, C. septempunctata gut has a similar core microbiota. This study clarifies the effects in intestinal microbial diversity and composition structure of the C. septempunctata with artificial diet, and provides a theoretical basis for understanding the intestinal microorganisms and optimizating the artificial diet of C. septempunctata.
Lateral distal femoral condyle has more uniform cartilage wear in varus knee osteoarthritis
Authors: Wei Maozheng , Hao Kuo , Kang Huijun , Kong Lingce , Wang Fei 
Published: January 2024

AbstractBone resection is highly valued in total knee arthroplasty (TKA), but how to determine the amount of distal femur resection is still controversial. The purpose of this study was to explore how to use lateral condyle as a reference for distal femoral osteotomy in TKA. Magnetic resonance imaging (MRI) and Radiographic images from 118 nonarthritic subjects and 123 osteoarthritis (OA) subjects were used to assess the cartilage wear pattern of the distal femur in varus knees. Measurements were performed on three-dimensional reconstruction after virtual bone cutting. The difference between the resection amount of distal (0°) and posterior (90°) was calculated when the medial condyle was used as a reference in OA patients. The osteotomy amount on lateral was calculated in nonarthritic subjects when the medial condylar osteotomy was consistent with the thickness of the implants. In 43% of OA patients, there was > 1 mm difference between the 0° and 90° in medial condyle cartilage, and no difference was observed in lateral. When using medial condyle as a reference for osteotomy, there was a difference of 1.3 ± 0.56 mm between the resection amount of 0° and 90°, and the difference was 0.24 ± 0.27 mm when using lateral condyle. Statistical analysis showed that there was a linear correlation between the resection amount of lateral condyle and mechanical lateral distal femoral angle (mLDFA) in nonarthritic subjects (r = 0.845, p < 0.001). Lateral distal femoral condyle has more uniform cartilage wear in varus knee osteoarthritis. Using the lateral condyle as the reference for distal femoral osteotomy is more suitable for the cartilage wear pattern of the varus knee. The position of cutting guide can be adjusted by preoperative measurements of mLDFA.
Water vapor transport properties of bio-based multilayer materials determined by original and complementary methods
Authors: Guivier Manon , Chevigny Chloé , Domenek Sandra , Casalinho Joel , Perré Patrick , Almeida Giana 
Published: January 2024

AbstractTo enhance PLA gas barrier properties, multilayer designs with highly polar barrier layers, such as nanocelluloses, have shown promising results. However, the properties of these polar layers change with humidity. As a result, we investigated water transport phenomena in PLA films coated with nanometric layers of chitosan and nanocelluloses, utilizing a combination of techniques including dynamic vapor sorption (DVS) and long-term water vapor adsorption–diffusion experiments (back-face measurements) to understand the influence of each layer on the behavior of multilayer films. Surprisingly, nanometric coatings impacted PLA water vapor transport. Chitosan/nanocelluloses layers, representing less than 1 wt.% of the multilayer film, increased the water vapor uptake of the film by 14.6%. The nanometric chitosan coating appeared to have localized effects on PLA structure. Moreover, nanocelluloses coatings displayed varying impacts on sample properties depending on their interactions (hydrogen, ionic bonds) with chitosan. The negatively charged CNF TEMPO coating formed a dense network that demonstrated higher resistance to water sorption and diffusion compared to CNF and CNC coatings. This work also highlights the limitations of conventional water vapor permeability measurements, especially when dealing with materials containing ultrathin nanocelluloses layers. It shows the necessity of considering the synergistic effects between layers to accurately evaluate the transport properties.
The impact of intersectional racial and gender biases on minority female leadership over two centuries
Authors: Pogrebna Ganna , Angelopoulos Spyros , Motsi-Omoijiade Immaculate , Kharlamov Alexander , Tkachenko Nataliya 
Published: January 2024

AbstractThis study scrutinizes the enduring effects of racial and gender biases that contribute to the consistent underrepresentation of minority women in leadership roles within American private, public, and third sector organizations. We adopt a behavioural data science approach, merging psychological schema theory with sociological intersectionality theory, to evaluate the enduring implications of these biases on female leadership development using mixed methods including machine learning and econometric analysis. Our examination is concentrated on Black female leaders, employing an extensive analysis of leadership rhetoric data spanning 200 years across the aforementioned sectors. We shed light on the continued scarcity of minority female representation in leadership roles, highlighting the role of intersectionality dynamics. Despite Black female leaders frequently embracing higher risks to counter intersectional invisibility compared to their White counterparts, their aspirations are not realized and problems not solved generation after generation, forcing Black female leaders to concentrate on the same issues for dozens and, sometimes, hundreds of years. Our findings suggest that the compound influence of racial and gender biases hinders the advancement of minority female leadership by perpetuating stereotypical behavioral schemas, leading to persistent discriminatory outcomes. We argue for the necessity of organizations to initiate a cultural transformation that fosters positive experiences for future generations of female leaders, recommending a shift in focus from improving outcomes for specific groups to creating an inclusive leadership culture.
High-dose benzodiazepine use and QTc interval prolongation, a latent class analysis study
Authors: Zamboni Lorenzo , Portoghese Igor , Casari Rebecca , Fusina Francesca , Santin Laura , Lecca Luigi Isaia , Campagnari Simone , Carli Silvia , Zandonai Thomas , Lugoboni Fabio 
Published: January 2024

AbstractBenzodiazepine (BDZ) addiction is a widespread and multifaceted phenomenon. For many patients, especially females, the concomitant use of other drugs also increases their risk of QTc prolongation, possibly leading to complications such as seizures and even sudden death. However, the relationship between BDZ use and QTc prolongation is currently unclear. The present study aims to examine patterns of polysubstance use among a sample of Italian adults with BDZ dependence in relation with their QTc prolongation risk. We used Latent Class Analysis (LCA) on data collected from 251 inpatients of the Addiction Medicine Unit in Verona to group patients into three classes according to their substance use and their QTc prolongation risk. Results showed no significant relationship between QTc prolongation and BDZ use in any of the classes considered. We conclude that BDZs, even if used long-term and at high dosages, can be considered safe in terms of cardiovascular complications for patients.
Genome-wide association studies for economically important traits in mink using copy number variation
Authors: Davoudi Pourya , Do Duy Ngoc , Colombo Stefanie , Rathgeber Bruce , Sargolzaei Mehdi , Plastow Graham , Wang Zhiquan , Hu Guoyu , Valipour Shafagh , Miar Younes 
Published: January 2024

AbstractCopy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.
Interaural and sex differences in the natural evolution of hearing levels in pre-symptomatic and symptomatic carriers of the p.Pro51Ser variant in the COCH gene
Authors: Moyaert Julie , Gilles Annick , Mertens Griet , Lammers Marc J. W. , Gommeren Hanne , Janssens de Varebeke Sebastien , Fransen Erik , Verhaert Nicolas , Denys Sam , van de Berg Raymond , Pennings Ronald , Vanderveken Olivier , Van Rompaey Vincent 
Published: January 2024

AbstractHearing impairment constitutes a significant health problem in developed countries. If hearing loss is slowly progressive, the first signs may not be noticed in time, or remain untreated until the moment the auditory dysfunction becomes more apparent. The present study will focus on DFNA9, an autosomal dominant disorder caused by pathogenic variants in the COCH gene. Although several cross-sectional studies on this topic have been conducted, a crucial need for longitudinal research has been reported by many authors. Longitudinal trajectories of individual hearing thresholds were established as function of age and superimposed lowess curves were generated for 101 female and male carriers of the p.Pro51Ser variant. The average number of times patients have been tested was 2.49 years with a minimum of 1 year and a maximum of 4 years. In addition, interaural and sex differences were studied, as they could modify the natural evolution of the hearing function. The current study demonstrates that, both in female carriers and male carriers, the first signs of hearing decline, i.e. hearing thresholds of 20 dB HL, become apparent as early as the 3rd decade in the highest frequencies. In addition, a rapid progression of SNHL occurs between 40 and 50 years of age. Differences between male and female carriers in the progression of hearing loss are most obvious between the age of 50 and 65 years. Furthermore, interaural discrepancies also manifest from the age of 50 years onwards. High-quality prospective data on the long-term natural evolution of hearing levels offer the opportunity to identify different disease stages in each cochlea and different types of evolution. This will provide more insights in the window of opportunity for future therapeutic intervention trials.
Viral and bacterial microorganisms in Vietnamese children with severe and non-severe pneumonia
Authors: Tran Xuan Duong , Hoang Van-Thuan , Goumballa Ndiaw , Vu Thi Nguyet , Tran Trong Kiem , Pham Thi Dung , Dao Thi-Loi , Vu Thi Thuy , Nguyen Duy Cuong , Nguyen Quoc Tien , Marty Pierre , Gautret Philippe 
Published: January 2024

AbstractTo investigate potential respiratory pathogens in children with community-acquired pneumonia (CAP) and risk factors for severe disease. This prospective study was conducted among 467 children at the Thai Binh Paediatric Hospital, Vietnam between 1 July 2020 and 30 June 2021. Clinical data and laboratory results were collected. Twenty-four respiratory microorganisms were tested from nasopharyngeal swabs using real-time PCR. Logistical regression was used to estimate a factor’s adjusted odd ratios of the severity of disease. Mean age of patients = 15.4 ± 13.3 months, 63.0% were male. Over 97% of patients had a positive PCR result. 87% of patients were positive for multiple (up to eight) microorganisms. Rhinovirus (46%), respiratory syncytial virus (RSV) (24%), enterovirus (17%), and parainfluenza viruses-3 (13%) were the most frequent viruses. H. influenzae (61%), S. pneumoniae (45%) and M. catarrhalis (30%) were the most common bacteria. 128 (27%) cases were classified as severe pneumonia. Presence of smokers at home (aOR 2.11, 95% CI 1.27–3.52, P value = 0.004), CRP level ≥ 50 mg/dL (aOR  6.11, 95% CI  3.86–9.68, P value < 0.0001), RSV (aOR  1.78, 95% CI  1.07–2.96, P value = 0.03) and H. influenzae (aOR  1.66, 95% CI  1.03–2.67, P value = 0.04) PCR detection associated with a higher risk of severe pneumonia; ,. Causative agents of pneumonia in children are complex. Children positive with RSV and H. influenzae need to be closely monitored to prevent severe pneumonia.