bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-exome sequencing as the first-tier test for patients in neonatal intensive care unit: a Chinese single-center study
Authors: Zhang Ruiping , Cui Xiaoyu , Zhang Yan , Ma Huiqing , Gao Jing , Zhang Ying , Shu Jianbo , Cai Chunquan , Liu Yang 
Published: May 2024

Abstract
Background
Genetic disorders significantly affect patients in neonatal intensive care units, where establishing a diagnosis can be challenging through routine tests and supplementary examinations. Whole-exome sequencing offers a molecular-based approach for diagnosing genetic disorders. This study aimed to assess the importance of whole-exome sequencing for neonates in intensive care through a retrospective observational study within a Chinese cohort.

Methods
We gathered data from neonatal patients at Tianjin Children’s Hospital between January 2018 and April 2021. These patients presented with acute illnesses and were suspected of having genetic disorders, which were investigated using whole-exome sequencing. Our retrospective analysis covered clinical data, genetic findings, and the correlation between phenotypes and genetic variations.

Results
The study included 121 neonates. Disorders affected multiple organs or systems, predominantly the metabolic, neurological, and endocrine systems. The detection rate for whole-exome sequencing was 52.9% (64 out of 121 patients), identifying 84 pathogenic or likely pathogenic genetic variants in 64 neonates. These included 13 copy number variations and 71 single-nucleotide variants. The most frequent inheritance pattern was autosomal recessive (57.8%, 37 out of 64), followed by autosomal dominant (29.7%, 19 out of 64). In total, 40 diseases were identified through whole-exome sequencing.

Conclusion
This study underscores the value and clinical utility of whole-exome sequencing as a primary diagnostic tool for neonates in intensive care units with suspected genetic disorders. Whole-exome sequencing not only aids in diagnosis but also offers significant benefits to patients and their families by providing clarity in uncertain diagnostic situations.
Examining determinants of stunting in Urban and Rural Indonesian: a multilevel analysis using the population-based Indonesian family life survey (IFLS)
Authors: Siramaneerat Issara , Astutik Erni , Agushybana Farid , Bhumkittipich Pimnapat , Lamprom Wanjai 
Published: May 2024

Abstract
Background
In Indonesia, chronic malnutrition leading to stunted growth in children represents a significant issue within the public health domain. The prevalence of stunting varies between urban and rural areas, reflecting disparities in access to nutrition, healthcare, and other socioeconomic factors. Understanding these disparities is crucial for developing targeted interventions to address the issue.

Methods
The study used data from the fifth wave of the Indonesian Family Life Survey (IFLS), which is a national cross-sectional population-based survey conducted across approximately 13 provinces in Indonesia in 2014–2015. Multivariate and Multilevel logistic regression models were utilized in the analysis to determine the factors associated with the prevalence of stunting in Indonesian children.

Results
The multivariate logistic regression analysis indicated that among children aged 24–59 months in Indonesia, stunting was associated with the age of the child, birth weight, maternal nutritional status, and residence. Subsequently, the multilevel logistic regression analysis revealed that in rural areas, the age of the child and birth weight exhibited significant associations with stunting. Conversely, in urban areas, stunted children were influenced by 7 factors, including the child’s age (months), age of weaning, birth weight (kg), mother and father’s age, place of birth, and maternal nutritional status.

Conclusions
Variations in childhood stunting between urban and rural regions in Indonesia were observed, indicating a differential prevalence. The study’s findings suggests the importance of age-appropriate nutritional support, healthcare interventions, and growth monitoring. Focused interventions are vital, potentially encompassing initiatives such as improving access to maternal and child healthcare services, promoting adequate nutrition during pregnancy and infancy, and facilitate greater parental engagement in childcare responsibilities.
Clinical characteristics and molecular mechanisms underlying bladder cancer in individuals with spinal cord injury: a systematic review
Authors: Wang Xin-Lei , Wang Yi-Xuan , Chen Jun-Zhi , Liu Xin-Yu , Liu Xing , Zhong Qi-Kai , Zhao Zi-Lin , Shi Zhen-Duo , Han Cong-Hui 
Published: May 2024

Abstract
Background
Patients with spinal cord injury have a relatively high risk for bladder cancer and often complicated with bladder cancer in advanced stages, and the degree of aggressiveness of malignancy is high. Most of the literature is based on disease clinical features while, our study reviews the clinical characteristics and molecular mechanisms of spinal cord injury patients with bladder cancer, so that it might help clinicians better recognize and manage these patients.

Method
We searched PubMed, Web of Science and Embase, using retrieval type like (“Neurogenic Lower Urinary Tract Dysfunction” OR “Spinal cord injury” OR “Spinal Cord Trauma”) AND (“bladder cancer” OR “bladder neoplasm” OR “bladder carcinoma” OR “Urinary Bladder Neoplasms” OR “Bladder Tumor”). In Web of Science, the retrieval type was searched as “Topic”, and in PubMed and Embase, as “All Field”. The methodological quality of eligible studies and their risk of bias were assessed using the Newcastle-Ottawa scale. This article is registered in PROSPERO with the CBD number: CRD42024508514.

Result
In WOS, we searched 219 related papers, in PubMed, 122 and in Embase, 363. Thus, a total of 254 articles were included after passing the screening, within a time range between 1960 and 2023. A comprehensive analysis of the data showed that the mortality and incidence rates of bladder cancer in spinal cord injury patients were higher than that of the general population, and the most frequent pathological type was squamous cell carcinoma. In parallel to long-term urinary tract infection and indwelling catheterization, the role of molecules such as NO, MiR 1949 and Rb 1. was found to be crucial pathogenetically.

Conclusion
This review highlights the risk of bladder cancer in SCI patients, comprehensively addressing the clinical characteristics and related molecular mechanisms. However, given that there are few studies on the molecular mechanisms of bladder cancer in spinal cord injury, further research is needed to expand the understanding of the disease.
Preparedness for a first clinical placement in nursing: a descriptive qualitative study
Authors: Marriott Philippa H. M. , Weller-Newton Jennifer M. , Reid Katharine J. 
Published: May 2024

Abstract
Background
A first clinical placement for nursing students is a challenging period involving translation of theoretical knowledge and development of an identity within the healthcare setting; it is often a time of emotional vulnerability. It can be a pivotal moment for ambivalent nursing students to decide whether to continue their professional training. To date, student expectations prior to their first clinical placement have been explored in advance of the experience or gathered following the placement experience. However, there is a significant gap in understanding how nursing students’ perspectives about their first clinical placement might change or remain consistent following their placement experiences. Thus, the study aimed to explore first-year nursing students’ emotional responses towards and perceptions of their preparedness for their first clinical placement and to examine whether initial perceptions remain consistent or change during the placement experience.

Methods
The research utilised a pre-post qualitative descriptive design. Six focus groups were undertaken before the first clinical placement (with up to four participants in each group) and follow-up individual interviews (n = 10) were undertaken towards the end of the first clinical placement with first-year entry-to-practice postgraduate nursing students. Data were analysed thematically.

Results
Three main themes emerged: (1) adjusting and managing a raft of feelings, encapsulating participants’ feelings about learning in a new environment and progressing from academia to clinical practice; (2) sinking or swimming, comprising students’ expectations before their first clinical placement and how these perceptions are altered through their clinical placement experience; and (3) navigating placement, describing relationships between healthcare staff, patients, and peers.

Conclusions
This unique study of first-year postgraduate entry-to-practice nursing students’ perspectives of their first clinical placement adds to the extant knowledge. By examining student experience prior to and during their first clinical placement experience, it is possible to explore the consistency and change in students’ narratives over the course of an impactful experience. Researching the narratives of nursing students embarking on their first clinical placement provides tertiary education institutions with insights into preparing students for this critical experience.
Identification and validation of a novel risk model based on cuproptosis‑associated m6A for head and neck squamous cell carcinoma
Authors: Xing Zhongxu , Xu Yijun , Xu Xiaoyan , Yang Kaiwen , Qin Songbing , Jiao Yang , Wang Lili 
Published: May 2024

Abstract
Background
Head and neck squamous cell carcinoma (HNSCC) is a prevalent cancer with a poor survival rate due to anatomical limitations of the head and a lack of reliable biomarkers. Cuproptosis represents a novel cellular regulated death pathway, and N6-methyladenosine (m6A) is the most common internal RNA modification in mRNA. They are intricately connected to tumor formation, progression, and prognosis. This study aimed to construct a risk model for HNSCC using a set of mRNAs associated with m6A regulators and cuproptosis genes (mcrmRNA).

Methods
RNA-seq and clinical data of HNSCC patients from The Cancer Genome Atlas (TCGA) database were analyzed to develop a risk model through the least absolute shrinkage and selection operator (LASSO) analysis. Survival analysis and receiver operating characteristic (ROC) analysis were performed for the high- and low-risk groups. Additionally, the model was validated using the GSE41613 dataset from the Gene Expression Omnibus (GEO) database. GSEA and CIBERSORT were applied to investigate the immune microenvironment of HNSCC.

Results
A risk model consisting of 32 mcrmRNA was developed using the LASSO analysis. The risk score of patients was confirmed to be an independent prognostic indicator by multivariate Cox analysis. The high-risk group exhibited a higher tumor mutation burden. Additionally, CIBERSORT analysis indicated varying levels of immune cell infiltration between the two groups. Significant disparities in drug sensitivity to common medications were also observed. Enrichment analysis further unveiled significant differences in metabolic pathways and RNA processing between the two groups.

Conclusions
Our risk model can predict outcomes for HNSCC patients and offers valuable insights for personalized therapeutic approaches.
A new Zymomonas mobilis platform strain for the efficient production of chemicals
Authors: Frohwitter Jonas , Behrendt Gerrich , Klamt Steffen , Bettenbrock Katja 
Published: May 2024

Abstract
Background
Zymomonas mobilis is well known for its outstanding ability to produce ethanol with both high specific productivity and with high yield close to the theoretical maximum. The key enzyme in the ethanol production pathway is the pyruvate decarboxylase (PDC) which is converting pyruvate to acetaldehyde. Since it is widely considered that its gene pdc is essential, metabolic engineering strategies aiming to produce other compounds derived from pyruvate need to find ways to reduce PDC activity.

Results
Here, we present a new platform strain (sGB027) of Z. mobilis in which the native promoter of pdc was replaced with the IPTG-inducible PT7A1, allowing for a controllable expression of pdc. Expression of lactate dehydrogenase from E. coli in sGB027 allowed the production of D-lactate with, to the best of our knowledge, the highest reported specific productivity of any microbial lactate producer as well as with the highest reported lactate yield for Z. mobilis so far. Additionally, by expressing the L-alanine dehydrogenase of Geobacillus stearothermophilus in sGB027 we produced L-alanine, further demonstrating the potential of sGB027 as a base for the production of compounds other than ethanol.

Conclusion
We demonstrated that our new platform strain can be an excellent starting point for the efficient production of various compounds derived from pyruvate with Z. mobilis and can thus enhance the establishment of this organism as a workhorse for biotechnological production processes.
Can neonicotinoid and pyrrole insecticides manage malaria vector resistance in high pyrethroid resistance areas in Côte d'Ivoire?
Authors: Ekra Armand K. , Edi Constant A. V. , Gbalegba Guy Constant N. , Zahouli Julien Z. B. , Danho Mathias , Koudou Benjamin G. 
Published: May 2024

Abstract
Background
Anopheles mosquito resistance to insecticide remains a serious threat to malaria vector control affecting several sub-Sahara African countries, including Côte d’Ivoire, where high pyrethroid, carbamate and organophosphate resistance have been reported. Since 2017, new insecticides, namely neonicotinoids (e.g.; clothianidin) and pyrroles (e.g.; chlorfenapyr) have been pre-qualified by the World Health Organization (WHO) for use in public health to manage insecticide resistance for disease vector control.

Methods
Clothianidin and chlorfenapyr were tested against the field-collected Anopheles gambiae populations from Gagnoa, Daloa and Abengourou using the WHO standard insecticide susceptibility biossays. Anopheles gambiae larvae were collected from several larval habitats, pooled and reared to adulthood in each site in July 2020. Non-blood-fed adult female mosquitoes aged 2 to 5 days were exposed to diagnostic concentration deltamethrin, permethrin, alpha-cypermethrin, bendiocarb, and pirimiphos-methyl. Clothianidin 2% treated papers were locally made and tested using WHO tube bioassay while chlorfenapyr (100 µg/bottle) was evaluated using WHO bottle assays. Furthermore, subsamples of exposed mosquitoes were identified to species and genotyped for insecticide resistance markers including the knock-down resistance (kdr) west and east, and acetylcholinesterase (Ace-1) using molecular techniques.

Results
High pyrethroid resistance was recorded with diagnostic dose in Abengourou (1.1 to 3.4% mortality), in Daloa (15.5 to 33.8%) and in Gagnoa (10.3 to 41.6%). With bendiocarb, mortality rates ranged from 49.5 to 62.3%. Complete mortality (100% mortality) was recorded with clothianidin in Gagnoa, 94.9% in Daloa and 96.6% in Abengourou, while susceptibility (mortality > 98%) to chlorfenapyr 100 µg/bottle was recorded at all sites and to pirimiphos-methyl in Gagnoa and Abengourou. Kdr-west mutation was present at high frequency (0.58 to 0.73) in the three sites and Kdr-east mutation frequency was recorded at a very low frequency of 0.02 in both Abengourou and Daloa samples and absent in Gagnoa. The Ace-1 mutation was present at frequencies between 0.19 and 0.29 in these areas. Anopheles coluzzii represented 100% of mosquitoes collected in Daloa and Gagnoa, and 72% in Abengourou.

Conclusions
This study showed that clothianidin and chlorfenapyr insecticides induce high mortality in the natural and pyrethroid-resistant An. gambiae populations in Côte d’Ivoire. These results could support a resistance management plan by proposing an insecticide rotation strategy for vector control interventions.
A systematic review and meta-analysis of the association between e-cigarette use among non-tobacco users and initiating smoking of combustible cigarettes
Authors: Kim Mimi M. , Steffensen Isabella , Miguel Red Thaddeus D. , Babic Tanja , Carlone Julien 
Published: May 2024

Abstract
Introduction
The rapid increase in e-cigarette use over the past decade has triggered an important public health question on the potential association between e-cigarette use and combustible cigarette smoking. Following AMSTAR 2 and PRISMA guidelines, this evidence synthesis sought to identify and characterize any associations between e-cigarette use among individuals not smoking cigarettes and initiation of cigarette smoking.

Methods
The protocol was registered on September 24, 2018 (PROSPERO 2018 CRD42018108540). Three databases were queried from January 01, 2007 to April 26, 2023. Search results were screened using the PICOS review method.

Results
Among 55 included studies (40 “good” and 15 “fair”; evidence grade: “high”) that adjusted for gender, age, and race/ethnicity between groups, generally, there was a significant association between non-regular e-cigarette use and initiation of cigarette smoking, further supported by the meta-analytic results (AOR 3.71; 95% CI 2.86–4.81). However, smoking initiation was most often measured as ever/current cigarette smoking. Two studies (quality: 2 “good”) evaluated progression to regular cigarette smoking among individuals with regular use of e-cigarettes, and generally found no significant associations. One study (“good”) evaluated smoking initiation among individuals with regular use of e-cigarettes, finding an increasing probability of ever smoking cigarettes with increased e-cigarette use. Twelve studies (10 “good” and two “fair”) examining progression to regular smoking among individuals with non-regular use of e-cigarettes reported inconsistent findings.

Conclusions
Numerous methodological flaws in the body of literature limit the generalizability of these results to all individuals who are not smoking cigarettes with few studies measuring established/regular use/smoking of e-cigarettes and cigarettes. Further, studies did not control adequately for specific confounding variables representing common liabilities between e-cigarette use and cigarette smoking, nor did they account for sufficient follow-up durations. Collectively, these flaws limit the generalizability of findings to the question of an association between e-cigarette use and cigarette smoking initiation.
First report of molecular epidemiology and phylogenetic characteristics of feline herpesvirus (FHV-1) from naturally infected cats in Kunshan, China
Authors: Kim Semin , Cheng Yixi , Fang Zhenkun , Zhongqi Qiu , Weidong Yu , Yilmaz Aysun , Yilmaz Huseyin , Umar Sajid 
Published: May 2024

Abstract
Background
Feline herpesvirus type 1 (FHV-1) is a life threatening highly contagious virus in cats and typically causes upper respiratory tract infections as well as conjunctival and corneal ulcers. Genetic variability could alter the severity of diseases and clinical signs. Despite regular vaccine practices against FHV-1 in China, new FHV-1 cases still commonly occur. The genetic and phylogenetic characteristics of FHV-1 in Kunshan city of China has not been studied yet. Therefore, this study was planned to investigate the prevalence, molecular characteristics of circulating strains, and phylogenetic analyses of FHV-1. This is the first report of molecular epidemiology and phylogenetic characteristics of FHV-1 from naturally infected cats in Kunshan, China.

Methods
The occulo-nasal swabs were collected from diseased cats showing respiratory distress, conjunctivitis, and corneal ulcers at different veterinary clinics in Kunshan from 2022 to 2023. Clinical data and general information were recorded. Swab samples were processed for preliminary detection of FHV-1. Thymidine kinase (TK), glycoprotein B (gB) and glycoprotein D (gD) genes were sequenced and analyzed to investigate genetic diversity and evolution of FHV-1.

Results
The FHV-1 genome was detected in 43 (43/200, 21.5%) samples using RT-PCR targeting the TK gene. Statistical analysis showed a significant correlation between age, vaccination status and living environment (p < 0.05) with FHV-1 positivity, while a non-significant correlation was observed for FHV-1 positivity and sex of cats (p > 0.05). Additionally, eight FHV-1 positive cats were co-infected with feline calicivirus (8/43,18.6%). FHV-1 identified in the present study was confirmed as FHV-1 based on phylogenetic analyses. The sequence analyses revealed that 43 FHV-1 strains identified in the present study did not differ much with reference strains within China and worldwide. A nucleotide homology of 99-100% was determined among gB, TK and gD genes nucleotide sequences when compared with standard strain C-27 and vaccine strains. Amino acid analysis showed some amino acid substitutions in TK, gB and gD protein sequences. A potential N-linked glycosylation site was observed in all TK protein sequences. Phylogenetic analyses revealed minor variations and short evolutionary distance among FHV-1 strains detected in this study.

Conclusions
Our findings indicate that genomes of 43 FHV-1 strains are highly homogenous and antigenically similar, and the degree of variation in major envelope proteins between strains is low. This study demonstrated some useful data about prevalence, genetic characteristics, and evolution of FHV-1 in Kunshan, which may aid in future vaccine development.
Assessment of gene–disease associations and recommendations for genetic testing for somatic variants in vascular anomalies by VASCERN-VASCA
Authors: Revencu Nicole , Eijkelenboom Astrid , Bracquemart Claire , Alhopuro Pia , Armstrong Judith , Baselga Eulalia , Cesario Claudia , Dentici Maria Lisa , Eyries Melanie , Frisk Sofia , Karstensen Helena Gásdal , Gene-Olaciregui Nagore , Kivirikko Sirpa , Lavarino Cinzia , Mero Inger-Lise , Michiels Rodolphe , Pisaneschi Elisa , Schönewolf-Greulich Bitten , Wieland Ilse , Zenker Martin , Vikkula Miikka 
Published: May 2024

Abstract
Background
Vascular anomalies caused by somatic (postzygotic) variants are clinically and genetically heterogeneous diseases with overlapping or distinct entities. The genetic knowledge in this field is rapidly growing, and genetic testing is now part of the diagnostic workup alongside the clinical, radiological and histopathological data. Nonetheless, access to genetic testing is still limited, and there is significant heterogeneity across the approaches used by the diagnostic laboratories, with direct consequences on test sensitivity and accuracy. The clinical utility of genetic testing is expected to increase progressively with improved theragnostics, which will be based on information about the efficacy and safety of the emerging drugs and future molecules. The aim of this study was to make recommendations for optimising and guiding the diagnostic genetic testing for somatic variants in patients with vascular malformations.

Results
Physicians and lab specialists from 11 multidisciplinary European centres for vascular anomalies reviewed the genes identified to date as being involved in non-hereditary vascular malformations, evaluated gene–disease associations, and made recommendations about the technical aspects for identification of low-level mosaicism and variant interpretation. A core list of 24 genes were selected based on the current practices in the participating laboratories, the ISSVA classification and the literature. In total 45 gene–phenotype associations were evaluated: 16 were considered definitive, 16 strong, 3 moderate, 7 limited and 3 with no evidence.

Conclusions
This work provides a detailed evidence-based view of the gene–disease associations in the field of vascular malformations caused by somatic variants. Knowing both the gene–phenotype relationships and the strength of the associations greatly help laboratories in data interpretation and eventually in the clinical diagnosis. This study reflects the state of knowledge as of mid-2023 and will be regularly updated on the VASCERN-VASCA website (VASCERN-VASCA, https://vascern.eu/groupe/vascular-anomalies/).