bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive expanded carrier screening using next-generation sequencing in Southern Chinese couples
Authors: Guo Danhua , Zhou Nani , He Qianqian , Lin Na , He Shuqiong , He Deqin , Dai Yifang , Li Ying , Chen Xuemei , Huang Hailong , Jia Jia , Cao Hua , Xu Liangpu 
Published: July 2024

Abstract

Background
Carrier screening has been an effective way to prevent severe birth defects in many countries. However, it has not been widely performed in China. In order to identify the local carrier mutation spectrum of autosomal/X-linked recessive diseases in the southeast coastal region in China, a pilot study of mutation carrier screening analysis of a 332-genes panel has been performed on 440 samples from Fujian Province.
Methods
An NGS-based, expanded carrier screening (ECS) panel of 332 genes implicated in 343 AR/XLR diseases in 220 couples in the Fujian region has been developed. Multidimensional data analysis on the detected SNV/Indels and CNVs, including demographics, carrier frequencies and mutation burden of the corresponding diseases has been performed.
Results
511 mutations, including 43 (8.41%) CNVs, were identified in 440 samples, involving 133 genes and 123 diseases. The overall estimated incidence is 1/51. The average P/LP mutation burden per sample (MBP) was 1.16. The highest MBP was observed in Reproductive Assistance (RA)-group who had histories of second and third trimesters fetal loss/abnormalities or postnatal abnormalities. The rate of at-risk couples (ARCs) was 6.36% (n = 14), implicating seven diseases. No difference was observed in the ARCs rate between the Genetic Screening (GS)-group and RA-group. Totally 23 diseases were identified (28 genes) with accumulated carrier frequency ≥ 1/100. The recurrent mutations in GAA, GALT, CYP1B1, and MEFV showed a different mutation spectrum compared to hotspots previously reported in the Han Chinese.
Conclusions
Our study showed that NGS-based ECS has great potential to identify disease carrier burdens and at-risk couples in this Southeast China coastal region, Fujian province. Regional carrier screening disease priority list, instead of a general Chinese population screening gene list, should be carefully determined before the launch of an official public health decision to perform carrier screening at local hospitals in this region.
Prevalence and topography of bifid and trifid mandibular canal in Turkish Western Anatolia Population: Evaluation of the inferior alveolar canal with CBCT
Authors: Bulut Duygu Göller , alçın Gizem Kartal Y , Tanrıseven Zeynep , Aydın Banu , Taşkın Betül 
Published: July 2024

Abstract

Purpose Various anatomical variations of the inferior alveolar canal increase the incidence of surgical complications; Therefore, this study aimed to evaluate the frequency and configuration of bifid and trifid mandibular canals using cone beam computed tomography (CBCT) in the Turkish subpopulation.Methods The inferior alveolar canal was evaluated on 1014 hemi-mandibles in the CBCT (I-CAT 3D Imaging System) images of 513 patients. The frequency and configuration of the bifid and trifid mandibular canal (MC) were examined. The relationship between bifid MC configuration and dental status and age groups was analyzed. The distance of the accessory canal to the buccal and lingual walls and to the alveolar crest was measured. The diameter of the main canal and accessory canal was measured and its relationship with dental status and age groups was evaluated.Results Bifid mandibular canal was found in 266 hemi-mandibles (24.7%) and 212 (41.3%) of 513 patients. The most common type of bifid MC was the retromolar canal (87 sides), followed by the forward canal without confluence (41; 4%) and the dental canal (34; 3.4%). 10 of the dental canals were opening to the 1st molar, 14 of the 2nd molars, and 10 of the 3rd molars. The number of retromolar foramina was 1 on 56 sides, 2 on 15 sides, and 3 on 4 sides. Forward canal without confluence was more common in edentulous patients than in dentulous patients, while the dental canal was more common in dentulous patients. The main canal diameter was 3.53 ± 0.97 mm and bifid MC diameter was 1.82 ± 0.70 mm. Distance of the bifid MC to the lingual wall was higher in > 64 years group than in 18–39 years group (p = 0.022). Distance of the bifid MC to the alveolar crest was lower in the > 64 years group compared to 18–39 years group and 40–64 years group (p = 0.015). The main canal diameter was higher in 40–64 years group than in 18–39 years group (p = 0.012).Conclusion Bifid Mandibular canal has a high prevalence, occurring in almost one in two patients. Dental and retromolar types, which are close to the teeth, are more common, and this increases the possibility of complications. CBCT is the most accurate imaging technique used to detect and define these variations.
Predictive model and clinical application for lymph node metastasis in papillary thyroid microcarcinoma
Authors: Su Yuanhao , Sun Tingkai , Wu Yongke , Li Cheng , Li Yunhao , Jin Xing , Ji Yuanyuan , Wang Zhidong 
Published: July 2024

Abstract

Purpose
Papillary thyroid microcarcinomas (PTMC), small tumors under 10 mm, represent a major part of the increase in papillary thyroid cancer cases. The treatment plans for PTMC patients with lymph node metastasi should be different from those without lymph node metastasis. Therefore, accurately identifying patients with cervical lymph node metastasis is of great clinical significance.
Methods
We analyzed data from 256 patients diagnosed with PTMC, using age, gender, tumor size, lesion count, and ACR score as predictors. Outcomes were based on cervical lymph node pathology. Four machine learning models—Random Forest, Multivariate Logistic Regression, Support Vector Machine, and Xgboost—were tested for their predictive accuracy and clinical utility. We then created an online website for direct prediction and designed online platforms that allow other researchers to upload their data for model building and prediction. The website and platform design is based on "shiny" package.
Results
The Random Forest model proved optimal, achieving an AUC of 0.92. It showed high sensitivity (0.83) and specificity (0.90) at the best threshold of 0.46. The link to the website we built based on this model is as follows: http://yucemoxing.online:8082. Additionally, the link to the online platforms that allows userss to upload their own data for model building and prediction is as follows: http://yucemoxing.online:8081,http://yucemoxing.site:8089,http://yucemoxing.online:8084,http://yucemoxing.online:8085,http://yucemoxing.online:8083,http://yucemoxing.online:8088, http://yucemoxing.online:8087, http://yucemoxing.online:8086
Conclusions
Machine learning tools can reliably predict cervical lymph node metastasis in PTMC patients. The developed websites offer valuable tools for clinical application, enhancing decision-making in treatment strategies.
Climate and Tectonic Aspects of the Quadrilátero Ferrífero (Central Brazil) From the Perspective of Pleistocene Alluvial Fans
Authors: Lopes Fabrício Antonio , Castro Paulo de Tarso Amorim , Carvalho Alex , Lana Cláudio Eduardo 
Published: July 2024

Abstract

This study presents data related to the unconsolidated alluvial fans of the Quadrilátero Ferrífero, a little-studied geomorphological and sedimentary feature located in southeastern Brazil. These alluvial fans were submitted to stratigraphic survey and dating by Optically Stimulated Luminescence (OSL). The description and interpretation of the sedimentary facies evidenced a lack of aggradational processes, which are inactive. About 40% of the identified facies are plastic (Gmm) and pseudoplastic (Gcm) debris flows interspersed with occasional channel-filling facies (Gt), hyper-concentrated (Sm) and mud (Fm) flows. The geochronological data elucidated the importance of the SAR protocol, where the quartz grains demonstrated high sensitivity and adequate dose-response curves, allowing better reflections and reliability of determined ages. The unconsolidated alluvial fans of the Quadrilátero Ferrífero had their genesis throughout the Pleistocene, mostly in a dry climate, with vegetation retraction and sedimentary filling of river valleys. The Cenozoic tectonics acted on the surface of the fans through the strong fluvial incision in the Holocene, caused by uplifts of the Brazilian continental shelf.
Integrated Virtual Screening and MD Simulation Study to Discover Potential Inhibitors of Mycobacterial Electron Transfer Flavoprotein-Oxidoreductase
Authors: Arshad Kaleem , Kanwal Nazia 
Published: July 2024

Abstract

Tuberculosis (TB) remains a global health crisis, contributing significantly to both morbidity and mortality. The escalating resistance to existing drugs exacerbates the urgency for innovative therapeutic strategies. This study focuses on repurposing drugs against the crucial mycobacterial protein, electron transfer flavoprotein oxidoreductase (EtfD), integral to utilizing fatty acids and cholesterol as a carbon source during infection. The research adopted an integrative approach, beginning with virtual screening of approved drugs against EtfD, followed by molecular docking, and concluding with molecular dynamics (MD) simulations. Virtual screening and molecular docking against a database of approved drugs identified diacerein, levonadifloxacin, and gatifloxacin as promising candidates for repurposing against TB. The MD simulations revealed stable binding of these compounds to EtfD, supported by hydrogen bonding and hydrophobic interactions. Binding free energy calculations and ADMET analyses further confirmed their potential efficacy and safety for TB treatment. Diacerein and levonadifloxacin, previously unexplored in anti-tuberculous therapy, alongside gatifloxacin, known for its efficacy in drug-resistant TB, emerged as promising candidates. Their broad-spectrum antimicrobial properties and favorable pharmacokinetic profiles suggest potential as alternatives to current TB treatments, especially against resistant strains. This study underscores the efficacy of computational drug repurposing, highlighting bacterial energy metabolism and lipid catabolism as fruitful targets. Further research is necessary to validate the clinical suitability and efficacy of diacerein, levonadifloxacin, and gatifloxacin, potentially enhancing the arsenal against global TB.
Vaccine refusal and hesitancy in Spain: an online cross-sectional questionnaire
Authors: Huguet-Feixa Agnes , Artigues-Barberà Eva , Sol Joaquim , Gomez-Arbones Xavier , Godoy Pere , Bravo Marta Ortega 
Published: July 2024

Abstract

Blackground Vaccine refusal and hesitancy pose a critical challenge to public health, leading to delays in vaccination and compromising herd immunity. Method To address this issue, we conducted a comprehensive observational study on the adult Spanish population in 2021. Through an online questionnaire, we explored the sociodemographic and sociocultural factors, beliefs, and opinions of those refusing or holding hesitancy about vaccines, and their vaccination behaviours by vaccine type and sex. Results There were 1,312 respondents: 74.5% were female, 73.7% were between 31 and 59 years old, and 71.0% had university studies. Our findings revealed that vaccine refusal rates were relatively low (16.8%), and mainly associated with influenza vaccination (10.3%). Greater refusal of vaccination was observed in over 60 years old, in those expressing hesitancy due to vaccine components and opposing free and compulsory vaccination, unaware that vaccination protects the community and being against consuming cow’s milk and the use of infant formulas for breastfeeding. Vaccine hesitancy was greatest in individuals under 31 years old, women, parents of children under 15 years old, against compulsory vaccination, unaware that vaccination protects the community, with hesitancy due to vaccine costs, and in favour of alternative and complementary treatments. Conclusions These insights underscore the need for strategies to improve education about vaccination and dispel misconceptions are crucial for effectively reducing vaccine refusal and hesitancy across the population.
guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel.
Authors: Schwaiger Michaela , Mohn Fabio , Bühler Marc , Kaaij Lucas 
Published: July 2024

Abstract

Since the introduction of next generation sequencing technologies, the field of epigenomics has evolved rapidly. However, most commonly used assays are enrichment-based methods and thus only semi-quantitative. Nucleosome occupancy and methylome sequencing (NOMe-seq) allows for quantitative inference of chromatin states with single locus resolution, but this requires high sequencing depth and is therefore prohibitively expensive to routinely apply to organisms with large genomes. To overcome this limitation, we introduce guidedNOMe-seq, where we combine NOMe profiling with large scale sgRNA synthesis and Cas9-mediated region-of-interest (ROI) liberation. To facilitate quantitative comparisons between multiple samples, we additionally develop an R package to standardize differential analysis of any type of NOMe-seq data. We extensively benchmark guidedNOMe-seq in a proof-of-concept study, dissecting the interplay of ChAHP and CTCF on chromatin. In summary we present a cost-effective, scalable, and customizable target enrichment extension to the existing NOMe-seq protocol allowing genome-scale quantification of nucleosome occupancy and transcription factor binding at single allele resolution.
Effect of Oregano and Cinnamon Essential Oils in Salmon Trout Fish Diets on Growth Performance and Meat Traits 1
Authors: Hasan Yazen Wisam , Yılmaz Erdal , Konca Yusuf 
Published: July 2024

Abstract

This study was conducted to determine the effects of oregano and cinnamon essential oil supplementation in the trout diet (Oncorhynchus mykiss) on growth performance and meat quality. The experiment placed 96 trout fry fish in 12 controlled laboratory ponds. The water temperature was adjusted to 14 to 15°C, oxygen was 12.2 mg/liter, and water circulated continuously with the circulation system for 24 hours/day. Each aquarium included eight fish, which were fed twice daily. The experimental groups are as follows: 1: Control diet (basal diet, no supplementation), 2: addition of 100 mg/kg oregano essential oil (OEO), and 3: addition of 100 mg/kg cinnamon essential oil (CEO) in feeds. Performance traits, survival, activity in tanks, meat quality, blood components, meat fatty acid composition, and antioxidant activity were determined. The result of cinnamon and oregano essential oils did not have a significant effect on body weight, weight gain, and feed intake. The feed conversion ratio had a significant dissimilarity between the groups. There was no statistically significant effect among the groups regarding fish activity in the tank or interest in feeding. The best survival rate was in the CEO-supplemented group. The addition of OEO and CEO did not affect the carcass characteristics and fish meat's chemical composition (dry matter, crude protein, fat, ash, and fatty acid composition). No significant difference was observed in fish meat colors (L*: lightness, a*: redness, b*: yellowness), pH, cooking, and thawing losses. No significant effect was recorded in the blood lipid profile, glucose, AST, and ALT. Still, in the EO-supplemented groups, the serum lipid total protein ratio was lower than that of the control group. In conclusion, essential oils from oregano and cinnamon can be used without negatively affecting performance and carcass quality traits. However, they can increase the livability of fry trout fish.
Elastic Properties of TiS 2 Material at High Pressure, Using Pseudo-Potentials Technique
Authors: Guesmi Ibtissam , Malki Siham , Darhi Zakariae , Bouammali Mohammed Amine , Challioui Allal , Farh Larbi El 
Published: July 2024

Abstract

Our study investigates the effect of pressure within the range of 0 to 20 GPa on elastic properties of titanium disulfide (TiS2) using density-functional theory (DFT), plane waves (PW), and pseudopotentials (PP) techniques within the framework of the Generalized Gradient Approximation (GGA). Our primary objective is to unveil the anisotropic nature of TiS2's elastic properties by scrutinizing the spatial variations in key parameters, including shear modulus (G), bulk modulus (B), Young's modulus (E), hardness (H), and Debye temperature (ƟD), under variable pressure conditions. The elastic properties of TiS2 exhibit a significant degree of anisotropy due to its hexagonal crystal structure, where the arrangement of atoms results in variable mechanical responses along the crystallographic axes. However, this anisotropy tends to decrease progressively with increasing pressure. These results not only deepen our understanding of TiS2's mechanical behavior but also open avenues for potential applications in diverse technological domains such as flexible electronics, optoelectronics and the energy industry.
Nonlinear vibration isolation performance enhancement using elastic constraint and linkage mechanism
Authors: Dai Wei , Xu Weiye , Wang Lin , Yang Jian , Li Tianyun , Zhu Xiang 
Published: July 2024

Abstract

This research presents nonlinear vibration isolators with elastic constraint included in linkage mechanism with geometry nonlinearity. The vibration attenuation enhancement of integrating nonlinear elements to a single-stage isolation system and an isolation system with flexible foundation considering the applications in marine engineering or aerospace engineering is investigated. The harmonic balance method (HBM) with the Alternating Frequency/Time (AFT) scheme and a time-marching method are employed to calculate responses. The vibration transmissibilities and power transmission indices are taken as measures of isolation performance. The results show that the nonlinear isolator dramatically decreases power flow and vibration transmissibility to the base in a broad frequency range. The use of the elastic constraint enables wider ranges of parameters of spring-linkage in design and the proposed isolator can provide improved vibration attenuation capabilities in low frequencies. By a collaborative design using the elastic constraint and linkage mechanism, the peaks in curves force transmission and power flow to the flexible foundation can be significantly suppressed and shifted towards lower frequencies. The study demonstrates that the proposed isolator designs can be further applied in the isolation platform of mechanical systems on board.
Utilising pupillometry as a biomarker for diagnosing ADHD
Authors: Bhatt Pranjal , Maroju Dheeraj 
Published: July 2024

Abstract

Neurodivergent conditions, notably Attention-deficit Hyperactivity Disorder (ADHD) and Autism Spectrum Disorder (ASD), pose considerable challenges in unraveling their pathophysiology due to intricate genetic underpinnings and diverse symptom presentations. The locus coeruleus-norepinephrine (LC-NE) system, central to noradrenergic signaling crucial for cognitive processes like sustained attention, has emerged as a focal point for understanding these conditions. However, the LC's small size and deep brainstem location pose significant hurdles to its cellular, molecular, and physiological investigation. Given these challenges, this study explores pupillometry as a non-invasive, objective measure of cognitive load reflecting LC-NE activity. The aim is to establish pupillometry as a novel biomarker and potentially an endophenotype for ADHD. Leveraging an elastic-net logistic model alongside meticulous five-fold cross-validation and hyperparameter tuning, our research yields promising evidence for future research, achieving an Area under the Curve (AUC) score of 0.969, accompanied by a precision of 100% and a recall of 86%. These findings underscore the efficacy of pupillometry in discerning dysfunction within the LC-NE system, thereby enabling accurate diagnosis of ADHD in pediatric populations.
Anomaly Detection in Cloud Computing Workloads based on Re- source Usage
Authors: Jahani Arezoo , Amirkhizi Paria Jourabchi 
Published: July 2024

Abstract

In recent years, the widespread adoption of cloud computing for data storage and processing has underscored the critical importance of security within cloud computing servers. Adherence to cloud service regulations mandates that all aspects, from resource procurement to data backup and security, are the responsibility of the service provider. Consequently, providers are actively seeking methods to detect and mitigate attacks promptly to safeguard their interests and users. However, the effectiveness of existing attack detection methods varies depending on the attack type, with known attacks being more easily identified and prevented through artificial intelligence-based techniques. Yet, even minor alterations in attack characteristics pose challenges to detection, highlighting an ongoing challenge in the field. Additionally , prior methods often rely on a fixed number of features during both learning and operational phases, limiting their adaptability.To address these challenges, this research proposes Pattern-AD, a novel anomaly detection method that models attacks as anomalies against the system’s normal states. Unlike traditional approaches, Pattern-AD extracts frequent patterns using the Apriori data mining algorithm, offering flexibility regardless of pattern length. Comparative analysis against established anomaly detection methods demonstrates Pattern-AD’s superior accuracy and reduced error rates, showcasing its potential as a reliable security solution for cloud computing environments.
The Mediating Role of IDL Particles in the Relationship between Primary Hypertension and Cardiovascular Diseases: Insights from Mendelian Randomization and Multi-Omics Analysis
Authors: Liu Yingmei , Wu Haiyang , Lv Hanlu , Zhou Youtao 
Published: July 2024

Abstract

Background
Primary hypertension is a major risk factor for various cardiovascular diseases. Although low-density lipoprotein and high-density lipoprotein are known to influence cardiovascular diseases, the role of intermediate-density lipoprotein remains unclear.
Objective
This study investigated the mediating role of intermediate-density lipoprotein particle concentration in primary hypertension in four major cardiovascular diseases (coronary heart disease, peripheral atherosclerosis, stroke, and deep vein thrombosis) using multiomics data and Mendelian randomization methods.
Methods
This study was conducted in three phases: confirming the relationship between hypertension and cardiovascular outcomes via two-step Mendelian randomization, identifying common risk genes through colocalization analysis, and analyzing key genes in lipid metabolism pathways via differential expression and GSEA, with further validation via PheWas analysis.
Results
Primary hypertension significantly increased the risk of four cardiovascular diseases. Intermediate-density lipoprotein particle concentration mediates the risk of hypertension on coronary heart disease and peripheral atherosclerosis, reducing the risk by 22% and 13%, respectively. Colocalization analysis identified 119 common risk genes, with CYP21A2 and HSD17B8 involved in lipid metabolism pathways. GSEA highlighted the importance of the glycerophospholipid metabolism pathway.
Conclusion
This study revealed the mediating role of intermediate-density lipoprotein particle concentration in hypertension and cardiovascular diseases, emphasizing the critical role of lipid metabolism pathways. These findings offer new perspectives and potential therapeutic targets for hypertension-related cardiovascular diseases.