bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study
Authors: Abdi Mona , Aliyev Elbay , Trost Brett , Kohailan Muhammad , Aamer Waleed , Syed Najeeb , Shaath Rulan , Gandhi Geethanjali Devadoss , Engchuan Worrawat , Howe Jennifer , Thiruvahindrapuram Bhooma , Geng Melissa , Whitney Joe , Syed Amira , Lakshmi Jyothi , Hussein Sura , Albashir Najwa , Hussein Amal , Poggiolini Ilaria , Elhag Saba F. , Palaniswamy Sasirekha , Kambouris Marios , de Fatima Janjua Maria , Tahir Mohamed O. El , Nazeer Ahsan , Shahwar Durre , Azeem Muhammad Waqar , Mokrab Younes , Aati Nazim Abdel , Akil Ammira , Scherer Stephen W. , Kamal Madeeha , Fakhro Khalid A. 
Published: October 2023

Abstract
Background
Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social and communication skills, restricted interests, and repetitive behaviors. The prevalence of ASD among children in Qatar was recently estimated to be 1.1%, though the genetic architecture underlying ASD both in Qatar and the greater Middle East has been largely unexplored. Here, we describe the first genomic data release from the BARAKA-Qatar Study—a nationwide program building a broadly consented biorepository of individuals with ASD and their families available for sample and data sharing and multi-omics research.

Methods
In this first release, we present a comprehensive analysis of whole-genome sequencing (WGS) data of the first 100 families (372 individuals), investigating the genetic architecture, including single-nucleotide variants (SNVs), copy number variants (CNVs), tandem repeat expansions (TREs), as well as mitochondrial DNA variants (mtDNA) segregating with ASD in local families.

Results
Overall, we identify potentially pathogenic variants in known genes or regions in 27 out of 100 families (27%), of which 11 variants (40.7%) were classified as pathogenic or likely-pathogenic based on American College of Medical Genetics (ACMG) guidelines. Dominant variants, including de novo and inherited, contributed to 15 (55.6%) of these families, consisting of SNVs/indels (66.7%), CNVs (13.3%), TREs (13.3%), and mtDNA variants (6.7%). Moreover, homozygous variants were found in 7 families (25.9%), with a sixfold increase in homozygous burden in consanguineous versus non-consanguineous families (13.6% and 1.8%, respectively). Furthermore, 28 novel ASD candidate genes were identified in 20 families, 23 of which had recurrent hits in MSSNG and SSC cohorts.

Conclusions
This study illustrates the value of ASD studies in under-represented populations and the importance of WGS as a comprehensive tool for establishing a molecular diagnosis for families with ASD. Moreover, it uncovers a significant role for recessive variation in ASD architecture in consanguineous settings and provides a unique resource of Middle Eastern genomes for future research to the global ASD community.
Effects of iron homeostasis on epigenetic age acceleration: a two-sample Mendelian randomization study
Authors: Wang Zhihao , Liu Yi , Zhang Shuxin , Yuan Yunbo , Chen Siliang , Li Wenhao , Zuo Mingrong , Xiang Yufan , Li Tengfei , Yang Wanchun , Yang Yuan , Liu Yanhui 
Published: October 2023

Abstract
Background
Epigenetic clocks constructed from DNA methylation patterns have emerged as excellent predictors of aging and aging-related health outcomes. Iron, a crucial element, is meticulously regulated within organisms, a phenomenon referred as iron homeostasis. Previous researches have demonstrated the sophisticated connection between aging and iron homeostasis. However, their causal relationship remains relatively unexplored.

Results
Through two-sample Mendelian randomization (MR) utilizing the random effect inverse variance weighted (IVW) method, each standard deviation (SD) increase in serum iron was associated with increased GrimAge acceleration (GrimAA, BetaIVW = 0.27, P = 8.54E−03 in 2014 datasets; BetaIVW = 0.31, P = 1.25E−02 in 2021 datasets), HannumAge acceleration (HannumAA, BetaIVW = 0.32, P = 4.50E−03 in 2014 datasets; BetaIVW = 0.32, P = 8.03E−03 in 2021 datasets) and Intrinsic epigenetic age acceleration (IEAA, BetaIVW = 0.34, P = 5.33E−04 in 2014 datasets; BetaIVW = 0.49, P = 9.94E−04 in 2021 datasets). Similar results were also observed in transferrin saturation. While transferrin manifested a negative association with epigenetic age accelerations (EAAs) sensitivity analyses. Besides, lack of solid evidence to support a causal relationship from EAAs to iron-related biomarkers.

Conclusions
The results of present investigation unveiled the causality of iron overload on acceleration of epigenetic clocks. Researches are warranted to illuminate the underlying mechanisms and formulate strategies for potential interventions.
Primary hyperoxaluria: a case series
Authors: Rather Jawad Iqbal , Rasheed Rabiya , Wani Muzafar Maqsood , Bhat Mohammad Ashraf , Wani Imtiyaz Ahmad 
Published: October 2023

Abstract
Background
Primary hyperoxaluria (PH) is a rare genetic disorder characterized by the excessive production and accumulation of oxalate. We present five cases of PH, each exhibiting varying manifestations of the disorder including a case presenting as postpartum kidney failure. Notably, three of these cases involve a previously unreported mutation.

Case presentations
We evaluated five Indian patients who presented with varying manifestations of PH. The first case, a 30 year old woman, presented as post-partum kidney failure and was found to be having oxalate nephropathy precipitated by dietary oxalate overload in the setting of previously undiagnosed PH. Genetic analysis revealed a previously unreported mutation in the alanine-glyoxylate aminotransferase gene. The patient underwent simultaneous kidney liver transplant. The second and third cases, 26 and 28 year old women respectively, were asymptomatic siblings of the first patient, who were diagnosed through screening. The fourth case is a 12 year boy with PH type 1 presenting as nephrolithiasis and rapidly worsening kidney function requiring combined kidney liver kidney transplant. Case 5 is a 6 year old male child with type 2 PH presenting with nephrolithiasis, nephrocalcinosis and normal kidney function. All the patients were born to consanguineous parents.

Conclusions
Due to limited clinical suspicion and inadequate diagnostic resources in certain countries with limited resources, it is possible for PH to go undiagnosed. The manifestations of the disease can range from no noticeable symptoms to severe disease. Interestingly, in some individuals with primary hyperoxaluria, the disease may not exhibit any symptoms until it is triggered by a high intake of dietary oxalate.
Privacy and integrity-preserving data aggregation scheme for wireless sensor networks digital twins
Authors: Zhang Zhiming , Yang Wei , Wu Fuying , Li Ping 
Published: October 2023

AbstractThe security technology of digital twin is an important guarantee to ensure the security of digital twin operation, which mainly includes network security technology, data security technology and privacy protection technology. In wireless sensor networks, data aggregation technologies are known as a suitable solution to reduce energy consumption. In addition, due to wireless communications, wireless sensor networks are subject to many attacks. Therefore, it is very important to provide data security in the data aggregation process. In this paper, in order to protect data privacy and verify data integrity, moreover, balance the energy consumption and security during the data aggregation, we present a privacy and integrity–preserving data aggregation scheme for wireless sensor networks based on digital twins technology and homomorphic fingerprinting (HFPIDA). The HFPIDA adopts privacy function to protect data privacy and adopts homomorphic fingerprinting technology to verify the aggregation data integrity. Security analysis shows that the HFPIDA can effectively preserve data privacy and verify data integrity. Simulation results show that the HFPIDA requires less communication and energy overheads, and can achieve higher aggregation accuracy.
Lymphangiogenesis in gastric cancer: function and mechanism
Authors: Liu Pengpeng , Ding Ping’an , Sun Chenyu , Chen Shuya , Lowe Scott , Meng Lingjiao , Zhao Qun 
Published: October 2023

AbstractIncreased lymphangiogenesis and lymph node (LN) metastasis are thought to be important steps in cancer metastasis, and are associated with patient's poor prognosis. There is increasing evidence that the lymphatic system may play a crucial role in regulating tumor immune response and limiting tumor metastasis, since tumor lymphangiogenesis is more prominent in tumor metastasis and diffusion. Lymphangiogenesis takes place in embryonic development, wound healing, and a variety of pathological conditions, including tumors. Tumor cells and tumor microenvironment cells generate growth factors (such as lymphangiogenesis factor VEGF-C/D), which can promote lymphangiogenesis, thereby inducing the metastasis and diffusion of tumor cells. Nevertheless, the current research on lymphangiogenesis in gastric cancer is relatively scattered and lacks a comprehensive understanding. Therefore, in this review, we aim to provide a detailed perspective on molecules and signal transduction pathways that regulate gastric cancer lymphogenesis, which may provide new insights for the diagnosis and treatment of cancer.
Percutaneous closure of simple congenital heart diseases under echocardiographic guidance
Authors: Jiang Ying , Luo Fanyan , Bu Haisong 
Published: October 2023

AbstractCongenital heart disease (CHD), birth defect with the highest incidence rates worldwide, and is mainly characterized by the abnormal internal structure of the heart or/and the anatomical structure of great vessels. In the past few decades, CHD repair surgery through standard median sternotomy incision combined with cardiopulmonary bypass (CPB) technology has been considered the gold standard for surgical correction of heart and great vessels. With the promotion and clinical application of interventional catheterization technology, transcatheter closure of CHD under radioactive radiation has gradually been recognized and applied. However, its radiation exposure and potential complications related to arteriovenous vessels still face challenges. In recent years, an increasing number of surgeons have explored new surgical procedures, for the safe and effective treatment of CHD, as far as possible to reduce surgical trauma, avoid radiation exposure, and improve the cosmetic effect. Therefore, on the premise of satisfactory exposure or guidance, how to integrate ultrasound and percutaneous interventional technology remained the focus of the exploration. This mini-review highlights and summarizes the signs of progress of ultrasound intervention in the last decade that have proven the effectiveness and operability of a well-established procedure for percutaneous closure of congenital heart diseases under echocardiographic guidance only. We discuss potential diseases that will benefit from this emerging procedure based on this progress. Owing to the crucial advantages played by this strategy in the treatment of CHD, better understanding and promotion of this less exploited field may contribute to the development of therapeutics targeting CHD, improve medical utilization rate, promote the optimization of medical resources, and ultimately achieve precise and efficient medical treatment.
The biological functions and metabolic pathways of valine in swine
Authors: Wang Chuni , Peng Yao , Zhang Yiru , Xu Juan , Jiang Sheng , Wang Leli , Yin Yulong 
Published: October 2023

AbstractValine is an essential amino acid and a type of branched-chain amino acid. Due to the involvement of branched-chain amino acids in various metabolic pathways, there has been a surge of interests in valine nutrition and its role in animal physiology. In pigs, the interactions between valine and other branched-chain amino acids or aromatic amino acids are complex. In this review, we delve into the interaction mechanism, metabolic pathways, and biological functions of valine. Appropriate valine supplementation not only enhances growth and reproductive performances, but also modulates gut microbiota and immune functions. Based on past observations and interpretations, we provide recommended feed levels of valine for weaned piglets, growing pigs, gilts, lactating sows, barrows and entire males. The summarized valine nutrient requirements for pigs at different stages offer valuable insights for future research and practical applications in animal husbandry.
Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs
Authors: Zong Wencheng , Wang Jinbu , Zhao Runze , Niu Naiqi , Su Yanfang , Hu Ziping , Liu Xin , Hou Xinhua , Wang Ligang , Wang Lixian , Zhang Longchao 
Published: October 2023

Abstract
Background
During approximately 10,000 years of domestication and selection, a large number of structural variations (SVs) have emerged in the genome of pig breeds, profoundly influencing their phenotypes and the ability to adapt to the local environment. SVs (≥ 50 bp) are widely distributed in the genome, mainly in the form of insertion (INS), mobile element insertion (MEI), deletion (DEL), duplication (DUP), inversion (INV), and translocation (TRA). While studies have investigated the SVs in pig genomes, genome-wide association studies (GWAS)-based on SVs have been rarely conducted.

Results
Here, we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools, with 53.95% of the SVs being reported for the first time. These high-quality SVs were used to recover the population genetic structure, confirming the accuracy of genotyping. Potential functional SV loci were then identified based on positional effects and breed stratification. Finally, GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions. We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7, with FKBP5 containing the most significant SV locus for almost all traits. In addition, we found several significant loci in intramuscular fat, abdominal circumference, heart weight, and liver weight, etc.

Conclusions
We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits, 7 skeletal traits, and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.
Factors associated with recommendation behaviors of four non-National Immunization Program vaccines: a cross-sectional survey among public health workers in China
Authors: Lyu Yun , Lai Xiaozhen , Ma Yidi , Fang Hai 
Published: October 2023

Abstract
Background
Immunization is a crucial preventive measure to safeguard children under five years old against a range of diseases. In China, the coverage rate of non-National Immunization Program (non-NIP) vaccines can be improved by leveraging the recommendation from public health workers. Hence, understanding the influencing factors of recommendation behaviors assume paramount importance. This study aims to investigate influencing factors of public health workers' recommendation behaviors towards non-NIP vaccines, with a particular emphasis on financial incentives.

Methods
A cross-sectional survey was conducted using a multi-stage sampling method in 2019 from August to October. 627 public health workers were recruited from 148 community healthcare centers in ten provincial-level administrative divisions in China. An anonymous questionnaire was used to collect demographic information, attitudes towards vaccination, and recommendation behaviors towards non-NIP vaccines, including Haemophilus influenzae type b (Hib) vaccine, pneumococcal conjugate vaccine, varicella vaccine, and rotavirus vaccine. Descriptive analysis and multivariate logistic regression analysis were adopted in this study.

Results
Of the 610 public health workers with complete survey data, 53.8%, 57.4%, 84.1%, and 54.1% often recommended Hib vaccine, pneumococcal pneumonia vaccine (PCV), varicella vaccine, and rotavirus vaccine, respectively. Logistic regression revealed that gender (Hib vaccine: OR = 0.4, 95% CI: 0.2–0.8; PCV: OR = 0.4, 95% CI: 0.2–0.8; rotavirus vaccine: OR = 0.3, 95% CI: 0.2–0.6), financial incentives for non-NIP vaccination (Hib vaccine: OR = 1.9, 95% CI: 1.1–3.6; PCV: OR = 2.1, 95% CI: 1.1–3.9; rotavirus vaccine: OR = 2.0, 95% CI: 1.1–3.8) and perception of vaccine safety (Hib vaccine: OR = 2.7, 95% CI: 1.1–7.0; PCV: OR = 3.2, 95% CI: 1.2–8.0; rotavirus vaccine: OR = 3.0, 95% CI: 1.2–7.7) were associated with public health workers’ recommendation towards Hib vaccine, PCV and rotavirus vaccine.

Conclusions
The findings highlighted public health workers’ recommendation behaviors of non-NIP vaccines in China and revealed strong association between vaccine recommendation and financial incentives. This highlights the importance of financial incentives in public health workers’ recommendation toward non-NIP vaccines in China. Proper incentives are recommended for public health workers to encourage effective health promotion in immunization practices.

Graphical Abstract
The predicting role of EFL teachers’ immediacy behaviors in students’ willingness to communicate and academic engagement
Authors: Hu Li , Wang Yongliang 
Published: October 2023

Abstract
Background
Teacher-student interactions and proximity have been shown influential in second/foreign (L2) education. However, the role of L2 teachers’ immediacy behaviors on students’ willingness to communicate (WTC) and academic engagement remains relatively unexamined in the context of English as a foreign language (EFL).

Purpose
This study intended to examine the association among EFL teachers’ immediacy behaviors and students’ WTC and engagement.

Methods
In this quantitative study, three online questionnaires were completed by 400 Chinese EFL students in different universities out of which 364 were valid.

Results
The results of statistical analysis and structural equation modeling (SEM) indicated that teachers’ immediacy behaviors (verbal, nonverbal) had a highly significant influence on EFL students’ WTC (ß=0.89, p = .000) and academic engagement (ß=0.71, p = .000). It was also revealed that teachers’ immediacy could predict 89% and 71% of variances in students’ WTC academic engagement, respectively.

Conclusions
Based on the results, I could be concluded that EFL teachers’ interpersonal communication abilities (e.g., immediacy) foster the establishment and growth of other positive outcomes among learners.

Implications
The study presents some conclusions and practical implications for EFL teachers, materials developers, and trainers to integrate the nonverbal cues of L2 communication into their practices. Such practices have the potential to enhance students’ willingness to communicate (WTC) and improve academic engagement.
Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste
Authors: Kracmarova-Farren Martina , Papik Jakub , Uhlik Ondrej , Freeman John , Foster Andrea , Leewis Mary-Cathrine , Creamer Courtney 
Published: October 2023

AbstractFinding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.
Molecular identification of the brown marmorated stink bug’s egg parasitoids by species-specific PCR collected from Beijing, China
Authors: Ali Muhammad Yasir , Liu Yu-Di , Li Feng-Qi , Hou Mao-Lin , Zhang Jin-Ping , Zhang Feng 
Published: October 2023

AbstractBrown marmorated stink bug (BMSB), Halyomorpha halys (Stål) (Hemiptera: Penta-tomidae), is a highly polyphagous and invasive insect pest with more than 300 plant species as hosts, including a wide range of economic crops. To date, several egg parasitoid species are reported to attack BMSB. In this study, two species of Trissolcus (Hymenoptera: Platygastridae) and one Anastatus (Hymenoptera: Eupelmidae) were recovered from field exposed BMSB sentinel eggs in Beijing, China. The wasps’ small size of only 1.5 mm and 4 mm in length make them difficult to identify morphologically and required taxonomist for identification of specific species. In addition, these parasitoids have morphology sibling species and have been misidentified several times in China. To overcome these problems, a molecular method with species-specific primers designed for the COI gene has been developed to identify Trissolcus, Anastatus and their host samples from field collected samples. After successful morphological confirmation with experts, DNA extractions were carried out from these samples. PCR amplification using published primers for T. japonicus, A. japonicus and BMSB specimens confirmed the species. As for T. cultratus, species specific primers TCYF and TCYR were developed which produce 340-bp PCR products length while no positive amplifications found in other wasps and host. Sensitivity analysis of markers revealed that TCYF and TCYR primers could detect as low a DNA template concentration as 0.00025 ng/μL. This indicates that PCR with these primers specifically and sensitively differentiates T. cultratus specimens from other similar wasp species. All the primers tested in this study could discriminate between parasitized and non-parasitized BMSB eggs. This molecular identification method shows promise for conveniently identifying Trissolcus and Anastatus species in host-parasitoid associations and accurately evaluating parasitism rates in the field.