bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute respiratory failure due to pulmonary exacerbation in children with cystic fibrosis admitted in a pediatric intensive care unit: outcomes and factors associated with mortality
Authors: Drummond David , Roy Charlotte , Cornet Matthieu , Bucher Julie , Boussaud Véronique , Pimpec-Barthes Françoise Le , Pontailler Margaux , Raisky Olivier , Lopez Vanessa , Barbanti Claudio , Guillemain Romain , Renolleau Sylvain , Grimaud Marion , Oualha Mehdi , de Saint Blanquat Laure , Sermet-Gaudelus Isabelle 
Published: April 2024

Abstract
Background
Children with advanced pulmonary disease due to cystic fibrosis (CF) are at risk of acute respiratory failure due to pulmonary exacerbations leading to their admission to pediatric intensive care units (PICU). The objectives of this study were to determine short and medium-term outcomes of children with CF admitted to PICU for acute respiratory failure due to pulmonary exacerbation and to identify prognosis factors.

Methods
This retrospective monocentric study included patients less than 18 years old admitted to the PICU of a French university hospital between 2000 and 2020. Cox proportional hazard regression methods were used to determine prognosis factors of mortality or lung transplant.

Results
Prior to PICU admission, the 29 patients included (median age 13.5 years) had a severe lung disease (median Forced Expiratory Volume in 1 s percentage predicted at 29%). Mortality rates were respectively 17%, 31%, 34%, 41% at discharge and at 3, 12 and 36 months post-discharge. Survival rates free of lung transplant were 34%, 32%, 24% and 17% respectively. Risk factors associated with mortality or lung transplant using the univariate analysis were female sex and higher pCO2 and chloride levels at PICU admission, and following pre admission characteristics: home respiratory and nutritional support, registration on lung transplant list and Stenotrophomonas Maltophilia bronchial colonization.

Conclusion
Children with CF admitted to PICU for acute respiratory failure secondary to pulmonary exacerbations are at high risk of death, both in the short and medium terms. Lung transplant is their main chance of survival and should be considered early.
Whole-genome sequencing of clinical isolates of Citrobacter Europaeus in China carrying blaOXA−48 and blaNDM−1
Authors: Ma Jie , Xu Ranran , Li Wanxiang , Liu Mi , Ding Xiaomei 
Published: April 2024

Abstract
Objective
To analyze the clinical infection characteristics and genetic environments of resistance genes in carbapenem-resistant Citrobacter europaeus using whole-genome sequencing.

Methods
The susceptibility of two clinical isolates of C. europaeus (WF0003 and WF1643) to 24 antimicrobial agents was assessed using the BD Phoenix™ M50 System and Kirby-Bauer (K-B) disk-diffusion method. Whole-genome sequencing was performed on the Illumina and Nanopore platforms, and ABRicate software was used to predict resistance and virulence genes of carbapenem-resistant C. europaeus. The characteristics of plasmids carrying carbapenem-resistance genes and their genetic environments were analyzed. Single nucleotide polymorphisms were used to construct a phylogenetic tree to analyze the homology of these two C. europaeus strains with ten strains of C. europaeus in the NCBI database.

Results
The two strains of carbapenem-resistant C. europaeus are resistant to various antimicrobial agents, particularly carbapenems and β-lactams. WF0003 carries blaNDM− 1, which is located on an IncX3 plasmid that has high homology to the pNDM-HN380 plasmid. blaNDM− 1 is located on a truncated Tn125. It differs from Tn125 by the insertion of IS5 in the upstream ISAba125 and the deletion of the downstream ISAba125, which is replaced by IS26. WF1643 carries blaOXA− 48 in a Tn1999 transposon on the IncL/M plasmid, carrying only that single drug resistance gene. Homology analysis of these two strains of C. europaeus with ten C. europaeus strains in the NCBI database revealed that the 12 strains can be classified into three clades, with both WF0003 and WF1643 in the B clade.

Conclusion
To the best of our knowledge, this is the first study to report an IncX3 plasmid carrying blaNDM− 1 in C. europaeus in China. C. europaeus strains harboring carbapenem-resistance genes are concerning in relation to the spread of antimicrobial resistance, and the presence of carbapenem-resistance genes in C. europaeus should be continuously monitored.
Dietary inflammatory impact on NAFLD development in obese vs. lean individuals: an analysis based on NHANES 2003–2018
Authors: Li Lurao , Shu Xiawen , Yi Yun , Wang Chun , Li Jianghui , Ding Yang , Li Jin , Chang Ying 
Published: April 2024

Abstract
Background
Non-alcoholic fatty liver disease (NAFLD), often linked with obesity, can also affect individuals with normal weight, a condition known as “lean NAFLD”, imposing comparable burdens and adverse effects. However, the impact of diet on lean NAFLD remains underexplored. The objective of this study is to investigate the correlation between the Dietary Inflammatory Index (DII) and NAFLD among Americans, stratified by waist-to-height ratio (WHtR) and body mass index (BMI).

Methods
Five thousand one hundred fifty-two participants from the National Health and Nutrition Examination Survey (NHANES) 2003–2018 were comprised in the final analysis. NAFLD and advanced liver fibrosis were diagnosed by serological markers. Lean and abdominal lean individuals were identified using BMI and WHtR, separately. DII was determined by assigning scores to 28 distinct food parameters based on their inflammatory potential, obtained from the NAHNES website. Differences across DII quartiles were evaluated using the Kruskal-Wallis H Test, Chi-Square Test along with One-Way ANOVA. The correlation between DII and NAFLD was determined by multiple regression models and subgroup analyses.

Results
Among the 5152 subjects, 2503 were diagnosed with NAFLD, including 86 cases of lean NAFLD and 8 cases of abdominal lean NAFLD. DII was positively linked with NAFLD (Odds Ratio (OR) = 1.81 [1.48–2.21], P < 0.001) and advanced liver fibrosis (OR = 1.46 [1.02–2.07], P = 0.037). Further analysis revealed that this association was primarily observed in obese or abdominal obese participants (In BMI ≥ 25.00 kg/m^2, OR = 1.56 [1.23–1.98], P < 0.001. In WHtR> 0.50, OR = 1.48 [1.23–1.79], P < 0.001.), rather than their lean counterparts. Subgroup analyses indicated that female individuals, without a diagnosis of hypertension or diabetes appeared to be more sensitive to the rise in DII.

Conclusions
Our data demonstrated a significant positive correlation between DII and NAFLD in the general population. However, the impact of a pro-inflammatory diet was less prominent in lean individuals compared to obese ones.
Association between the atherogenic index of plasma and hearing loss based on a nationwide cross-sectional study
Authors: Wu Zhiyuan , Wang Shu , Huang Xiaowu , Xie Mengyao , Han Zhijin , Li Chen , Wang Shuyi , Tang Qi , Yang Hua 
Published: April 2024

Abstract
Background
Hearing loss (HL) is a worldwide public health issue for which the role of dyslipidemia has not been fully elucidated. This study aimed to use the atherogenic index of plasma (AIP), a well-established serum lipid marker, to investigate the association of dyslipidemia with HL among the general population.

Methods
Participants (n = 3267) from the National Health and Nutrition Examination Survey database (2005–2012, 2015–2018) were included in the present study. The AIP was calculated based on the following formula: log10 (triglycerides/high-density lipoprotein cholesterol). HL was defined as a pure-tone average of at least 20 dBHL in the better ear. Weighted multivariable logistic regression, subgroup analysis, generalized additive model, and threshold analysis were adopted to reveal the association between the AIP and HL.

Results
In this study of US adults, a positive association was found between the AIP and high-frequency HL. However, the association between the AIP and low-frequency HL was not as strong. In addition, a reverse L-shaped curve with an inflection point located at -0.27 was detected between the AIP and high-frequency HL, followed by a significant positive association after the inflection point.

Conclusions
The potential of the AIP as a bioindicator for high-frequency HL is noteworthy, and maintaining an AIP value below a certain threshold might provide beneficial outcomes in the management of high-frequency HL.
Faculty members as academic knowledge brokers in Iran's health sector: a social network analysis study
Authors: Shabankareh Khadijeh , Hamidi Ali , Soleymani Mohammad Reza , Sajadi Haniye Sadat , Alavi Mousa 
Published: April 2024

Abstract
Background
Interaction between researchers and policymakers is an essential factor to facilitate the evidence-informed policymaking. One of the effective ways to establish this relationship and promote evidence-informed policymaking is to employ people or organizations that can play the role of knowledge brokers. This study aims to analyze the communication network and interactions between researchers and policymakers in Iran's health sector and identify key people serving as academic knowledge brokers.

Methods
This study was a survey research. Using a census approach, we administered a sociometric survey to faculty members in the health field in top ten Iranian medical universities to construct academic-policymaker network using social network analysis method. Network maps were generated using UCINET and NetDraw software. We used Indegree Centrality, Outdegree Centrality, and Betweenness Centrality indicators to determine knowledge brokers in the network.

Results
The drawn network had a total of 188 nodes consisting of 94 university faculty members and 94 policymakers at three national, provincial, and university levels. The network comprised a total of 177 links, with 125 connecting to policymakers and 52 to peers. Of 56 faculty members, we identified four knowledge brokers. Six policymakers were identified as key policymakers in the network, too.

Conclusions
It seems that the flow of knowledge produced by research in the health field in Iran is not accomplished well from the producers of research evidence to the users of knowledge. Therefore, it seems necessary to consider incentive and support mechanisms to strengthen the interaction between researchers and policymakers in Iran's health sector.
Relationship between vaginal and oral microbiome in patients of human papillomavirus (HPV) infection and cervical cancer
Authors: Zhang Wei , Yin Yanfei , Jiang Yisha , Yang Yangyang , Wang Wentao , Wang Xiaoya , Ge Yan , Liu Bin , Yao Lihe 
Published: April 2024

Abstract
Background
The aim of this study was to assess the microbial variations and biomarkers in the vaginal and oral environments of patients with human papillomavirus (HPV) and cervical cancer (CC) and to develop novel prediction models.

Materials and methods
This study included 164 samples collected from both the vaginal tract and oral subgingival plaque of 82 women. The participants were divided into four distinct groups based on their vaginal and oral samples: the control group (Z/KZ, n = 22), abortion group (AB/KAB, n = 17), HPV-infected group (HP/KHP, n = 21), and cervical cancer group (CC/KCC, n = 22). Microbiota analysis was conducted using full-length 16S rDNA gene sequencing with the PacBio platform.

Results
The vaginal bacterial community in the Z and AB groups exhibited a relatively simple structure predominantly dominated by Lactobacillus. However, CC group shows high abundances of anaerobic bacteria and alpha diversity. Biomarkers such as Bacteroides, Mycoplasma, Bacillus, Dialister, Porphyromonas, Anaerococcus, and Prevotella were identified as indicators of CC. Correlations were established between elevated blood C-reactive protein (CRP) levels and local/systemic inflammation, pregnancy, childbirth, and abortion, which contribute to unevenness in the vaginal microenvironment. The altered microbial diversity in the CC group was confirmed by amino acid metabolism. Oral microbial diversity exhibited an inverse pattern to that of the vaginal microbiome, indicating a unique relationship. The microbial diversity of the KCC group was significantly lower than that of the KZ group, indicating a link between oral health and cancer development. Several microbes, including Fusobacterium, Campylobacter, Capnocytophaga, Veillonella, Streptococcus, Lachnoanaerobaculum, Propionibacterium, Prevotella, Lactobacillus, and Neisseria, were identified as CC biomarkers. Moreover, periodontal pathogens were associated with blood CRP levels and oral hygiene conditions. Elevated oral microbial amino acid metabolism in the CC group was closely linked to the presence of pathogens. Positive correlations indicated a synergistic relationship between vaginal and oral bacteria.

Conclusion
HPV infection and CC impact both the vaginal and oral microenvironments, affecting systemic metabolism and the synergy between bacteria. This suggests that the use of oral flora markers is a potential screening tool for the diagnosis of CC.
NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model
Authors: Liu Yushu , Edrisi Mohammadamin , Yan Zhi , A Ogilvie Huw , Nakhleh Luay 
Published: April 2024

AbstractCopy number aberrations (CNAs) are ubiquitous in many types of cancer. Inferring CNAs from cancer genomic data could help shed light on the initiation, progression, and potential treatment of cancer. While such data have traditionally been available via “bulk sequencing,” the more recently introduced techniques for single-cell DNA sequencing (scDNAseq) provide the type of data that makes CNA inference possible at the single-cell resolution. We introduce a new birth-death evolutionary model of CNAs and a Bayesian method, NestedBD, for the inference of evolutionary trees (topologies and branch lengths with relative mutation rates) from single-cell data. We evaluated NestedBD’s performance using simulated data sets, benchmarking its accuracy against traditional phylogenetic tools as well as state-of-the-art methods. The results show that NestedBD infers more accurate topologies and branch lengths, and that the birth-death model can improve the accuracy of copy number estimation. And when applied to biological data sets, NestedBD infers plausible evolutionary histories of two colorectal cancer samples. NestedBD is available at https://github.com/Androstane/NestedBD.
Efficacy of PE-PLIF with a novel ULBD approach for lumbar degeneration diseases: a large-channel endoscopic retrospective study
Authors: Zhou Yichi , Zhou Chuankun , Li Qingbo , Cai Lei , Kou Bowen , Fang Weizhi , Yao Zhi , Wei Mengcheng , Zhang Shishuang , Liu Weijun 
Published: April 2024

Abstract
Purpose
This study aims to assess the effectiveness of Percutaneous Endoscopic Posterior Lumbar Interbody Fusion (PE-PLIF) combined with a novel Unilateral Laminotomy for Bilateral Decompression (ULBD) approach using a large-channel endoscope in treating Lumbar Degenerative Diseases (LDD).

Methods
This retrospective analysis evaluates 41 LDD patients treated with PE-PLIF and ULBD from January 2021 to June 2023. A novel ULBD approach, called ‘Non-touch Over-Top’ technique, was utilized in this study. We compared preoperative and postoperative metrics such as demographic data, Visual Analogue Scale (VAS) for pain, Oswestry Disability Index (ODI), Japanese Orthopedic Association (JOA) score, surgical details, and radiographic changes.

Results
The average follow-up duration was 14.41 ± 2.86 months. Notable improvements were observed postoperatively in VAS scores for back and leg pain (from 5.56 ± 0.20 and 6.95 ± 0.24 to 0.20 ± 0.06 and 0.12 ± 0.05), ODI (from 58.68 ± 0.80% to 8.10 ± 0.49%), and JOA scores (from 9.37 ± 0.37 to 25.07 ± 0.38). Radiographic measurements showed significant improvements in lumbar and segmental lordosis angles, disc height, and spinal canal area. A high fusion rate (97.56% at 6 months, 100% at 12 months) and a low cage subsidence rate (2.44%) were noted.

Conclusions
PE-PLIF combined with the novel ULBD technique via a large-channel endoscope offers significant short-term benefits for LDD management. The procedure effectively expands spinal canal volume, decompresses nerve structures, improves lumbar alignment, and stabilizes the spine. Notably, it improves patients' quality of life and minimizes complications, highlighting its potential as a promising LDD treatment option.
L-DOPA regulates neuroinflammation and Aβ pathology through NEP and ADAM17 in a mouse model of AD
Authors: Lee Hyun-ju , Nam JinHan , Hwang Jeong-Woo , Park Jin-Hee , Jeong Yoo Joo , Jang Ji-Yeong , Kim Su-Jeong , Jo A-Ran , Hoe Hyang-Sook 
Published: April 2024

AbstractDopamine plays important roles in cognitive function and inflammation and therefore is involved in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease (AD). Drugs that increase or maintain dopamine levels in the brain could be a therapeutic strategy for AD. However, the effects of dopamine and its precursor levodopa (L-DOPA) on Aβ/tau pathology in vivo and the underlying molecular mechanisms have not been studied in detail. Here, we investigated whether L-DOPA treatment alters neuroinflammation, Aβ pathology, and tau phosphorylation in 5xFAD mice, a model of AD. We found that L-DOPA administration significantly reduced microgliosis and astrogliosis in 5xFAD mice. In addition, L-DOPA treatment significantly decreased Aβ plaque number by upregulating NEP and ADAM17 levels in 5xFAD mice. However, L-DOPA-treated 5xFAD mice did not exhibit changes in tau hyperphosphorylation or tau kinase levels. These data suggest that L-DOPA alleviates neuroinflammatory responses and Aβ pathology but not tau pathology in this mouse model of AD.
A novel defined programmed cell death related gene signature for predicting the prognosis of serous ovarian cancer
Authors: Zhan Feng , Guo Yina , He Lidan 
Published: April 2024

Abstract
Purpose
This study aims to explore the contribution of differentially expressed programmed cell death genes (DEPCDGs) to the heterogeneity of serous ovarian cancer (SOC) through single-cell RNA sequencing (scRNA-seq) and assess their potential as predictors for clinical prognosis.

Methods
SOC scRNA-seq data were extracted from the Gene Expression Omnibus database, and the principal component analysis was used for cell clustering. Bulk RNA-seq data were employed to analyze SOC-associated immune cell subsets key genes. CIBERSORT and single-sample gene set enrichment analysis (ssGSEA) were utilized to calculate immune cell scores. Prognostic models and nomograms were developed through univariate and multivariate Cox analyses.

Results
Our analysis revealed that 48 DEPCDGs are significantly correlated with apoptotic signaling and oxidative stress pathways and identified seven key DEPCDGs (CASP3, GADD45B, GNA15, GZMB, IL1B, ISG20, and RHOB) through survival analysis. Furthermore, eight distinct cell subtypes were characterized using scRNA-seq. It was found that G protein subunit alpha 15 (GNA15) exhibited low expression across these subtypes and a strong association with immune cells. Based on the DEGs identified by the GNA15 high- and low-expression groups, a prognostic model comprising eight genes with significant prognostic value was constructed, effectively predicting patient overall survival. Additionally, a nomogram incorporating the RS signature, age, grade, and stage was developed and validated using two large SOC datasets.

Conclusion
GNA15 emerged as an independent and excellent prognostic marker for SOC patients. This study provides valuable insights into the prognostic potential of DEPCDGs in SOC, presenting new avenues for personalized treatment strategies.
Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes
Authors: Wieder Nechama , D’Souza Elston N. , Martin-Geary Alexandra C. , Lassen Frederik H. , Talbot-Martin Jonathan , Fernandes Maria , Chothani Sonia P. , Rackham Owen J. L. , Schafer Sebastian , Aspden Julie L. , MacArthur Daniel G. , Davies Robert W. , Whiffin Nicola 
Published: April 2024

Abstract
Background
Untranslated regions (UTRs) are important mediators of post-transcriptional regulation. The length of UTRs and the composition of regulatory elements within them are known to vary substantially across genes, but little is known about the reasons for this variation in humans. Here, we set out to determine whether this variation, specifically in 5’UTRs, correlates with gene dosage sensitivity.

Results
We investigate 5’UTR length, the number of alternative transcription start sites, the potential for alternative splicing, the number and type of upstream open reading frames (uORFs) and the propensity of 5’UTRs to form secondary structures. We explore how these elements vary by gene tolerance to loss-of-function (LoF; using the LOEUF metric), and in genes where changes in dosage are known to cause disease. We show that LOEUF correlates with 5’UTR length and complexity. Genes that are most intolerant to LoF have longer 5’UTRs, greater TSS diversity, and more upstream regulatory elements than their LoF tolerant counterparts. We show that these differences are evident in disease gene-sets, but not in recessive developmental disorder genes where LoF of a single allele is tolerated.

Conclusions
Our results confirm the importance of post-transcriptional regulation through 5'UTRs in tight regulation of mRNA and protein levels, particularly for genes where changes in dosage are deleterious and lead to disease. Finally, to support gene-based investigation we release a web-based browser tool, VuTR, that supports exploration of the composition of individual 5'UTRs and the impact of genetic variation within them.
Adherence and acceptability of multiple micronutrient supplementation during pregnancy: Study protocol for a cluster-randomized non-inferiority trial in Cambodia
Authors: Hoang Mai-Anh , Kroeun Hou , Klemm Rolf , Gupta Aman Sen , Rem Ngik , Meng Sokchea , Prak Sophonneary , Rattana Kim , Chea Mary , Karakochuk Crystal D. , Sauer Cassandra , Mishra Ashutosh , Mohan Diwakar , de-Graffenried Meredith Jackson 
Published: April 2024

Abstract
Background
Iron and folic acid (IFA) supplements are currently provided to Cambodian women during pregnancy. However, recent research has found benefits of a multiple micronutrient supplement (MMS) over just IFA alone on several outcomes of perinatal and infant health. The Ministry of Health in Cambodia has proposed a transition from IFA to MMS but to effectively guide this transition requires implementation research on the acceptability and adherence to MMS (over IFA).

Methods
This non-inferiority trial aims to assess the adherence and acceptability of IFA (60 mg elemental iron and 400 μg folic acid) compared to MMS (standard UNIMMAP formulation including 15 micronutrients) during antenatal care in Cambodia. A prospective cohort of 1545 pregnant women will be assigned to one of three trial arms: (1) IFA for 90 days [IFA-90]; (2) MMS for 180 days with two distributions of 90-count tablet bottles [MMS-90]; or (3) MMS for 180 days with one 180-count tablet bottle [MMS-180]. Each arm will enroll 515 women across 48 health centers (clusters) in Kampong Thom Province in Cambodia. The primary outcome is the non-inferiority of adherence rates of MMS-180 compared to IFA-90, as assessed by tablet counts. Mixed-effects logistic and linear regression models will be used to estimate the difference in the adherence rate between the two groups, with an ‘a priori’ determined non-inferiority margin of 15%. Acceptability of MMS and IFA will be measured using a quantitative survey conducted with enrolled pregnant women at 30-day, 90-day, and 180-day time-points.

Discussion
Findings from this study will guide an effective and feasible MMS scale-up strategy for Cambodia. Additionally, the findings will be shared globally with other stakeholders planning to scale up MMS in other countries.

Trial registration
NCT05867836 (ClinicalTrials.gov, registered May 18, 2023).