bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence and Predictors of Mortality Among Preterm Neonates Admitted to Neonatal Intensive Care Units in Comprehensive Specialized Hospitals in Northeast Ethiopia: A Multi-Center Prospective Follow-Up Study
Authors: Birhanu Tarikua Afework , Tarekegn Setegn Mihret , Endeshaw Yaregal Semanew , Wondifraw Endalik Birrie , Getaneh Fekadeselassie Belege , Yitayew Yibeltal Asmamaw , Belete Melaku Ashagrie , Wudu Muluken Amare 
Published: August 2024

Abstract

Background
Despite numerous efforts, preterm mortality remains a significant public health burden in Ethiopia. Therefore, this study aimed to assess the incidence and predictors of preterm mortality among preterm neonates admitted to Comprehensive Specialized Hospitals in Northeast Ethiopia in 2024.
Methods
A multi-center prospective follow-up study conducted at the institutional level involved 356 preterm neonates, selected through consecutive sampling. A Weibull proportional hazards model was fitted to identify predictors of preterm neonatal mortality.
Result
The preterm neonatal mortality rate was 72 per 1,000 person-days of observation. The median time to death was 10 days (IQR = 7–20 days). Predictors of preterm neonatal mortality included young maternal age (15–19 years) [AHR 2.73 (95% CI: 1.3–5.9)], extremely low birth weight [AHR 2.4 (95% CI: 1.24–4.6)], respiratory distress syndrome [AHR 2.3 (95% CI: 1.34–3.8)], early preterm birth [AHR 1.8 (95% CI: 1.1–3)], lack of kangaroo mother care [AHR 2.2 (95% CI: 1.54–3.21)], multiple pregnancy [AHR 2.1 (95% CI: 1.1–4.3)], necrotizing enterocolitis [AHR 1.53 (95% CI: 1.1–2.22)], suboptimal continuous positive airway pressure therapy [AHR 1.43 (95% CI: 1.02–2.02)], and congenital anomalies [AHR 2.3 (95% CI: 1.32–3.9)].
Conclusion
The current study revealed that preterm neonatal mortality significantly exceeds the national average and is unacceptably high, necessitating immediate intervention. This underscores the urgency to improve optimal childbearing age, optimize continuous positive airway pressure therapy, improve kangaroo mother care practices, and enhance the management of necrotizing enterocolitis and respiratory distress syndrome.
Region-based analysis with functional annotation identifies genes associated with cognitive function in South Asians from India
Authors: Abu-Amara Hasan , Zhao Wei , Li Zheng , Leung Yuk Yee , Schellenberg Gerard D. , Wang Li-San , Moorjani Priya , Dey A. B. , Dey Sharmistha , Zhou Xiang , Gross Alden L. , Lee Jinkook , Kardia Sharon L.R. , Smith Jennifer A. 
Published: August 2024

Abstract

The prevalence of dementia among South Asians across India is approximately 7.4% in those 60 years and older, yet little is known about genetic risk factors for dementia in this population. Most known risk loci for Alzheimer’s disease (AD) have been identified from studies conducted in European Ancestry (EA) but are unknown in South Asians. Using whole-genome sequence data from 2680 participants from the Diagnostic Assessment of Dementia for the Longitudinal Aging Study of India (LASI-DAD), we performed a gene-based analysis of 84 genes previously associated with AD in EA. We investigated associations with the Hindi Mental State Examination (HMSE) score and factor scores for general cognitive function and five cognitive domains. For each gene, we examined missense/loss-of-function (LoF) variants and brain-specific promoter/enhancer variants, separately, both with and without incorporating additional annotation weights (e.g., deleteriousness, conservation scores) using the variant-Set Test for Association using Annotation infoRmation (STAAR). In the missense/LoF analysis without annotation weights and controlling for age, sex, state/territory, and genetic ancestry, three genes had an association with at least one measure of cognitive function (FDR q<0.1). APOE was associated with four measures of cognitive function, PICALM was associated with HMSE score, and TSPOAP1 was associated with executive function. The most strongly associated variants in each gene were rs429358 (APOE ε4), rs779406084 (PICALM), and rs9913145 (TSPOAP1). rs779406084 is a rare missense mutation that is more prevalent in LASI-DAD than in EA (minor allele frequency=0.075% vs. 0.0015%); the other two are common variants. No genes in the brain-specific promoter/enhancer analysis met criteria for significance. Results with and without annotation weights were similar. Missense/LoF variants in some genes previously associated with AD in EA are associated with measures of cognitive function in South Asians from India. Analyzing genome sequence data allows identification of potential novel causal variants enriched in South Asians.
3D Ultrasound Volume Quantification for Pediatric Urinary Tract Dilation: A Semi-Automated Segmentation Software Inter-Rater Analysis
Authors: Morales-Tisnés Tatiana , Sultan Laith , Rouet Laurence , Jago James , Morgan Trudy A , Lerebo Wondwossen , Elsingergy Mohamed M , Sriniva Arun , Sridha Anush , Otero Hansel J , Darge Kassa , Back Susan J 
Published: August 2024

Abstract

Objective
We determined the reliability of a three-dimensional (3D) US segmentation software for evaluating hydronephrosis index (HI) and renal parenchymal and pelvicalyceal volume in children with UTD.
Material and methods
From 1/2019 to 9/2023, children clinically scheduled for a renal imaging exam to assess UTD at a single center were prospectively enrolled. They underwent a dedicated 2D and 3D US renal exam. A UTD score was assigned per kidney from the 2D images based on the 2014 consensus classification by an experienced pediatric radiologist. From the 3D dataset, the renal parenchyma and collecting system were independently segmented by three trained raters using a semi-automated software (Philips Health Technology Innovation, Paris, France). From this segmentation, the kidney parenchymal and pelvicalyceal volume, dimensions, and HI values, were analyzed using intraclass correlation coefficient, grading inter-rater reliability.
Results
Forty-eight studies from 47 patients were included (65% male; median age: 24 months; IQR: 61 months). From these, 46 right and 40 left kidneys were chosen based on image quality. Twenty-nine (33.7%) kidneys had no dilation, 10 (11.6%) had UTD P1, 23 (26.7%) UTD P2, and 24 (27.9%) UTD P3. Inter-rater reliability was almost perfect across all parameters, with estimates ranging from 0.85 to 0.95. In kidneys with UTD P2 and UTD P3, HI had the lowest inter-rater agreement (0.75 and 0.66, respectively).
Conclusions
We demonstrated that semi-automated 3D US segmentation for kidneys with UTD can reliably assess renal dimensions, parenchymal and collecting system volumes, and HI among raters.
A Cost-Utility Analysis of Screening and Cognitive Behavioral Therapy compared to usual care for Perinatal Depression
Authors: Wang Bohan , Shen Shuyuan , Smith Robert David 
Published: August 2024

Abstract

Background: Perinatal depression is common and the most prevalent cause of maternal mortality, implementing effective depression screening and therapy is a priority for public health internationally.
Objective: The aim of this study is to estimate the cost-effectiveness of implementing a strategy of perinatal depression screening with Cognitive Behavioral Therapy (CBT) compared with the current Treatment as Usual alone (TAU) for individuals with perinatal depression.
Methods: A decision tree model was constructed to estimate the potential cost and utility benefits for screening using the Whooley Questionnaire followed by referral to CBT compared to TAU alone in Hong Kong. The model used healthcare costs, in Hong Kong Dollars (HKD), and quality-adjusted life years (QALYs) to estimate economic and health utility outcomes. We used two states (remission, and depression) modeled over a single perinatal period, such as transfer probabilities, depression-specific quality of life, and cost data were retrieved from published studies. Deterministic and probabilistic sensitivity analyses were conducted to estimate the stability of the model.
Results: The baseline analysis suggested Whooley combined with CBT or TAU yielded an additional 0.02 QALY compared to TAU alone but added 900.26 HKD to the cost of treatment per patient. Our deterministic sensitivity analysis indicates several variables that have the greatest impact on the model. Our probabilistic sensitivity analysis shows that Whooley combined with CBT or TAU is approximately 84% more cost-effective than TAU alone at a willingness-to-pay (WTP) threshold of 194,780 HKD.
Conclusions: Whooley combined with CBT is estimated to be cost-effective in identifying and treating individuals with perinatal depression at an early stage compared to TAU alone. More research is required to assess the feasibility, cost-benefit, and clinical effectiveness of this strategy.
Scalable information extraction from free text electronic health records using large language models
Authors: Gu Bowen , Shao Vivian , Liao Ziqian , Carducci Valentina , Romero-Brufau Santiago , Yang Jie , Desai Rishi J 
Published: August 2024

Abstract

Background
A vast amount of potentially useful information such as description of patient symptoms, family, and social history is recorded as free-text notes in electronic health records (EHRs) but is difficult to reliably extract at scale, limiting their utility in research. This study aims to assess whether an “out of the box” implementation of open-source large language models (LLMs) without any fine-tuning can accurately extract social determinants of health (SDoH) data from free-text clinical notes.
Methods
We conducted a cross-sectional study using EHR data from the Mass General Brigham (MGB) system, analyzing free-text notes for SDoH information. We selected a random sample of 200 patients and manually labeled nine SDoH aspects. Eight advanced open-source LLMs were evaluated against a baseline pattern-matching model. Two human reviewers provided the manual labels, achieving 93% inter-annotator agreement. LLM performance was assessed using accuracy metrics for overall, mentioned, and non-mentioned SDoH, and macro F1 scores.
Results
LLMs outperformed the baseline pattern-matching approach, particularly for explicitly mentioned SDoH, achieving up to 40% higher Accuracymentioned. openchat_3.5 was the best-performing model, surpassing the baseline in overall accuracy across all nine SDoH aspects. The refined pipeline with prompt engineering reduced hallucinations and improved accuracy.
Conclusions
Open-source LLMs are effective and scalable tools for extracting SDoH from unstructured EHRs, surpassing traditional pattern-matching methods. Further refinement and domain-specific training could enhance their utility in clinical research and predictive analytics, improving healthcare outcomes and addressing health disparities.
Optimisation of low and ultra-low dose scanning protocols for ultra-extended field of view PET in a real-world clinical setting
Authors: Ingbritsen Johanna , Callahan Jason , Morgan Hugh , Munro Melissa , Ware Robert E. , Hicks Rodney J. 
Published: August 2024

Abstract

True total-body and extended axial field-of-view (AFOV) PET/CT with 1m or more of body coverage are now commercially available and dramatically increase system sensitivity over conventional AFOV PET/CT. The Siemens Biograph Vision Quadra (Quadra), with an AFOV of 106cm, potentially allows use of significantly lower administered radiopharmaceuticals as well as reduced scan times. The aim of this study was to optimise acquisition protocols for routine clinical imaging with FDG on the Quadra the prioritisation of reduced activity given physical infrastructure constraints in our facility. Low-dose (1 MBq/kg) and ultra-low dose (0.5 MBq/g) cohorts, each of 20 patients were scanned in a single bed position for 10 and 15 minutes respectively with list-mode data acquisition. These data were then reconstructed simulating progressively shorter acquisition times down to 30 seconds and 1 minute, respectively and then reviewed by 2 experienced PET readers who selected the shortest optimal and minimal acquisition durations based on personal preferences. Quantitative analysis was also performed of image noise to assess how this correlated with qualitative preferences. At the consensus minimum acquisition durations at both dosing levels, the coefficient of variance in the liver as a measure of image noise was 10% or less and there was minimal reduction in this measure between the optimal and longest acquisition durations. These data support the reduction in both administered activity and scan acquisition times for routine clinical FDG PET/CT on the Quadra providing efficient workflows and low radiation doses to staff and patients, while achieving high quality images.
Double-negative T cells with a distinct transcriptomic profile are abundant in the peripheral blood of patients with breast cancer
Authors: Zhu Huiru , Wei Yunbo , Guo Jiaqi , Liu Xiaofei 
Published: August 2024

Abstract

Background
Double-negative T (DNT) cells comprise a distinctive subset of T lymphocytes that play a significant role in the immune system. This study characterized peripheral DNT cells in individuals diagnosed with breast cancer (BC).
Methods
Peripheral blood DNT cells were collected from patients with BC and healthy controls by flow cytometry. The sorted DNT cells were analyzed by Smart-seq2 for single-cell full-length transcriptome profiling. Conducting bioinformatics analysis to pinpoint pivotal genes and investigate potential underlying mechanisms. RT -PCR was used to measure the relative expression of TMEM176B, EGR1, C1QB and C1QC.
Result
The percentage of DNT cells was higher in patients with BC than in healthy controls. In total, 289 differentially expressed genes (DEGs) were identified (|log2FC| > 2, P < 0.05). Gene enrichment analysis indicated that the DEGs were significantly associated with complement activation, and B cell receptor signaling. We identified 2 module-related and 10 hub genes, including IFIT1, IFI27, RSAD2, IFIT3, EGR1, IFI44L, C1QB, C1QC, TMEM176A, TMEM176B, NGFR, and VCAM1. The results of RT-qPCR showed significant differential expression of TMEM176B, EGR1, C1QB and C1QC between the DNT cells of BC patients and healthy controls (P < 0.05).
Conclusions
DNT cells are abundant in patients with BC, and they might exert anti-tumor immune responses by regulating genes such as TMEM176B and EGR1.
The impact of different surgical methods on the survival rate of patients with uterine sarcoma
Authors: Yang Qianni , Han Xiaodong 
Published: August 2024

Abstract

Objective: This article plans to retrospectively analyze patients with uterine sarcoma in our hospital to determine whether expanding the surgical resection range can improve patient prognosis, increase survival rate, and prolong survival.
Methods: A retrospective analysis was conducted on 153 patients with uterine sarcoma who underwent surgical treatment in our hospital, and factors affecting their prognosis were determined through survival analysis.
Results: The Kaplan Meier survival analysis revealed that pathological grading, staging, and surgical approach were the main factors significantly affecting the 5-year survival rate of patients (p<0.05), and postoperative radiotherapy can improve the overall 5-year survival rate. Multivariate COX regression survival analysis: postoperative adjuvant radiotherapy: HR=1.277, p=0.485，95%CI= 0.643- 2.536 . Staging: HR=0.647, p=0.176，95%CI= 0.344-1.216.Surgical methods: HR=2.249, p=0.007，95%CI=1.252- 4.038.Pathological grading: HR=0.503, p=0.026 95%CI= 0.275-0.923.
Conclusion: The use of extensive hysterectomy with double adnexectomy compared to simple hysterectomy with double adnexectomy can significantly improve the overall 5-year survival rate of patients, and is an independent prognostic factor for this type of patient. Postoperative radiotherapy may prolong patient survival and improve 5-year survival rate.
Spinal Muscular Atrophy Carrier Screening Program: Awareness and Attitude of Healthcare Professionals in Turkey
Authors: CELIK Kubra Muge , KOSE Canan CEYLAN , KAYA Derya , TEKIN Koray , SILAN Fatma 
Published: August 2024

Abstract

Spinal Muscular Atrophy (SMA) is an autosomal recessive disease caused by mutations in the SMN1 gene, leading to progressive muscle weakness. The global incidence of SMA is approximately 1–3 per 10,000 live births, and the carrier frequency of SMN1 gene mutations is estimated to be about 1 in 50 individuals. In response to increasing carrier rates, especially due to consanguineous marriages, Turkey launched the SMA Carrier Screening Program in 2021. Considering that recent SMA cases have emerged among healthcare workers, we aimed to evaluate their awareness of this program. After receiving ethics approval, 1,322 healthcare professionals completed a 15-item survey based on the SMA Carrier Screening Guidelines. Of these, 5.8% were unaware of SMA, and 26% lacked information about the national screening program. Awareness of the screening program was significantly lower among secondary and tertiary healthcare professionals compared to primary healthcare professionals (p < 0.0001), and among non-physician healthcare professionals compared to physician (p < 0.0001). Additionally, a serious lack of information was observed concerning the parts of the screening covering the pregnancy period. Although there is generally high awareness of the SMA Carrier Screening Program among healthcare professionals, significant knowledge gaps exist. These findings highlight the need for increased efforts to more effectively deliver screening programs and continue the education of healthcare professionals. Education and awareness campaigns can enhance program awareness and effectiveness, reach wider audiences, and contribute to preventive measures for the health of future generations.
Co-altered vaginal Lactobacillus, metabolome and host gene expression associate with the grade of cervical intraepithelial neoplasia in Chinese women
Authors: Dai Wenkui , Guo Chunlei , Jiang Xin , Liu Yu , Wang Yinan , Zhou Qian , Xu Ruinan , Hou Jun , Wu Di , Yang Qing , Yang Qin , Li Changzhong , Li Shuai Cheng , Du Hui , Wu Ruifang 
Published: August 2024

Abstract

Background
Vaginal Lactobacillus has been implicated in modulating the risk of cervical intraepithelial neoplasia (CIN) progression. However, there remains a gap in population-based studies elucidating the underlying mechanisms that link Lactobacillus with CIN progression and carcinogenesis.
Methods
To address this knowledge gap, we conducted an in-depth analysis of vaginal microbiota (VM), metabolome, and host transcriptome profiles in a cohort of 75 Chinese women, stratified into two groups based on their CIN status: low-grade CIN1 (n = 38) and high-grade CIN2+ (n = 37).
Results
Our findings revealed that samples dominated by Lactobacillus were more prevalent in the CIN1 cohort. Furthermore, the vaginal metabolome displayed a significant interplay with the microbiota, with Lactobacillus emerging as a key influencer. Among the 100 metabolites that distinguished the CIN1 and CIN2 + cohorts, 26 were inversely correlated with Lactobacillus levels, including L-Carnitine and UDP-D-glucose. Conversely, five metabolites, such as Succinic anhydride, exhibited a positive correlation with Lactobacillus abundance. Differential gene expression analysis revealed 176 genes upregulated in the CIN1 cohort compared to the CIN2 + cohort, primarily related to immune responses and negative regulation of cell migration. Notably, COL4A2 and CCBE1, both negatively correlated with L-Carnitine, were among the upregulated genes. Conversely, 82 genes were downregulated in the CIN1 cohort, including TP63 and FOXD1, which positively correlated with UDP-D-glucose. Further mediation analysis suggested that L-Carnitine plays a crucial role in mediating the positive association between Lactobacillus and COL4A2 expression, both of which are enriched in the CIN1 cohort. Similarly, UDP-D-glucose emerged as a mediator in the negative association between Lactobacillus and FOXD1, a gene depleted in the CIN1 cohort.
Conclusions
These findings provide insights into the complex interplay between vaginal Lactobacillus, the metabolome, and host gene expression patterns associated with CIN progression. The identified Lactobacillus:L-Carnitine:COL4A2 and Lactobacillus:UDP-D-glucose:FOXD1 regulatory axes underscore the potential significance of these pathways in modulating CIN risk. These population-based discoveries hold promise for future research aimed at developing targeted interventions to prevent or delay CIN progression.
The crossroads of the hypercoagulability and patient outcomes in osteoarthritis: interactions and connections
Authors: zhou Qiao , liu jian , Zhu Yan , Wang Guizhen , Guo Jinchen 
Published: August 2024

Abstract

Background
Our study aimed to probe whether coagulation indices are linked to patient-reported outcomes (PROs) in OA.
Methods
A thorough review of the literature on OA and coagulation indices was conducted using bibliometric approaches. Clinical data were retrospectively analyzed in OA patients (7,068) and healthy controls (HC, 795). Coagulation indices—prothrombin time (PT), fibrinogen (FIB), activated partial thromboplastin time (APTT), thrombin time (TT), D-dimer, and platelet count (PLT)—as well as immune-inflammatory indices, PROs (visual analogue scale and Short Form 36), were analyzed for correlations.
Results
Co-cited literature revealed that research related to OA and coagulation indices focused on inflammation, pain, and clinical utility. The levels of PLT, TT, FIB, and D-dimer were elevated in the OA group compared to the HC group. Hypercoagulable states are present in the OA. The results of the ROC demonstrate that they can differentiate between OA and healthy individuals. Coagulation indices were strongly linked to immune-inflammatory indicators and PROs. Logistic regression analysis indicated that PLT, D-dimer, and C-reactive protein (CRP) were all predictive of disease activity. However, PLT and D-dimer combined with CRP had a superior predictive effect than CRP alone.
Conclusion
PLT and D-dimer may serve as appropriate biomarkers to correlate with OA disease activity.
Neurobiological insights into Persistent Genital Arousal Disorder (PGAD): A resting-state functional MRI analysis
Authors: Dalkeranidis Eleni , Sinke Christopher , Krüger Tillmann H.C. , Kümpers Franziska M. L. M. 
Published: August 2024

Abstract

Persistent genital arousal disorder (PGAD) is a rare disease causing high emotional distress eminently impacting the individual’s quality of life. Experts in this field assume that the disease is caused by a multifaceted interplay of different etiologies which may share a common neurobiological basis. However, only few functional neuroimaging investigations exists, and a more in-depth comprehension of the neurobiological foundation is required. Therefore, this study aims to provide new insights into how the functional integration of brain regions may relate to PGAD. By using the functional magnetic resonance imaging (fMRI) technique, functional connectivity at rest (rs-FC) was compared between patients suffering PGAD (n = 26) and healthy controls (n = 26) within the sensorimotor, salience, emotional-arousal and brain-bladder control networks. As hypothesized, patients with PGAD showed altered rs-FC within these four networks when compared to healthy controls. The brain regions exhibiting significant group differences in resting-state activity showed no correlation with clinical and behavioral measures. The study offers valuable insights into the anatomical, psychological and somatic dimensions of PGAD shedding light on its characteristics and underlying neural mechanisms. While the study examines exploratory hypotheses, future research is encouraged to validate these ideas, aiming to enhance the understanding of the central mechanisms of PGAD further.