bluuebunny/crossref_metadata_2025_split huggingface dataset:
Piloting an automated query and scoring system to facilitate APDS patient identification from health systems
Authors: FitzPatrick Amy M. , Chin Aaron T. , Nirenberg Sharon , Cunningham-Rundles Charlotte , Sacco Keith , Perlmutter Jesse , Dasso Joseph F. , Tsalatsanis Athanasios , Maru Jay , Creech Jessica , Walter Jolan E. , Hartog Nicholas , Izadi Neema , Palmucci Mandy , Butte Manish J. , Loewy Klaus , Relan Anurag , Rider Nicholas L. 
Published: January 2025

IntroductionPatients with activated PI3Kδ syndrome (APDS) may elude diagnoses for nearly a decade. Methods to hasten the identification of these patients, and other patients with inborn errors of immunity (IEIs), are needed. We sought to demonstrate that querying electronic health record (EHR) systems by aggregating disparate signs into a risk score can identify these patients.MethodsWe developed a structured query language (SQL) script using literature-validated APDS-associated clinical concepts mapped to ICD-10-CM codes. We ran the query across EHRs from 7 large, US-based medical centers encompassing approximately 17 million patients. The query calculated an “APDS Score,” which stratified risk for APDS for all individuals in these systems. Scores for all known patients with APDS (n=46) were compared.ResultsThe query identified all but one known patient with APDS (98%; 45/46) as well as patients with other complex disease. Median score for all patients with APDS was 9 (IQR = 5.75; range 1-25). Sensitivity analysis suggested an optimal cutoff score of 7 (sensitivity = 0.70).ConclusionDisease-specific queries are a relatively simple method to foster patient identification across the rare-disease spectrum. Such methods are even more important for disorders such as APDS where an approved, pathway-specific treatment is available in the US.
Novel pyroptosis-immune-related lncRNA signature exhibits a distinct immune cell infiltration landscape in breast cancer
Authors: Kong Dedi , Cheng Hongju , Wang Meihong 
Published: January 2025

IntroductionThis study investigated pyroptosis- and immunity-related long non-coding RNAs (lncRNAs) to identify promising therapeutic targets for breast cancer (BC), and constructed lncRNA signatures to determine the prognosis and immunotherapy responses of BC patients.MethodsPearson’s correlation coefficient was used to identify pyroptosis- and immune-related differentially expressed lncRNAs (DE-pyrolncRNAs and DE-ImmlncRNAs, respectively). The Cancer Genome Atlas dataset was allocated to training and testing subsets. Prognostic lncRNA signatures were derived based on the training subset using univariate Cox regression analysis and Least Absolute Shrinkage and Selection Operator methods. Stepwise Cox regression was used to refine these signatures and to select the optimal lncRNA signature. The median risk score of the training subset was applied as a threshold to divide patients into high-risk (HR) and low-risk (LR) groups. The Wilcoxon test was used to reveal differences in immune scores, cell types, functions, and checkpoint genes between these groups. Single-cell sequencing data from GSE176078 were used to validate the immune cell infiltration landscape of the identified lncRNA signatures.ResultsWe identified a six-lncRNA pyroptosis-immune signature comprising MAPT.AS1, CTA.384, D8.34, RP11.561, I11.3, HID1.AS1, AC097713.3, and USP2.AS1. Patients in the HR group demonstrated inferior prognoses in the training, testing, and full datasets (P=3.622e-07, P=3.736e-03, and P=1.151e-08, respectively). Immune scores were significantly enhanced in the LR group, whereas tumor purity was elevated in the HR group. Fifty-eight immune scores showed significant differences between the groups (P&lt;0.05). Immune function (APC coinhibition, CCR, and checkpoints) more significantly impaired in the HR group. Expression levels of 38 immune checkpoint genes, including KIR2DS4, KIR3DL2, CD40LG, KIR3DL1, and PDCD1, were significantly higher in the LR group. Conversely, the TDO2, PVR, and CD276 levels were elevated in the HR group. Single-cell sequencing data from GSE176078 showed sparse T cell, B cell, myeloid, and plasmablast clusters in the HR group, whereas the LR group displayed significant clustering of B cells, myeloids, and plasmablasts.ConclusionThe six-lncRNA pyroptosis-immune signature effectively predicted BC prognosis and highlighted distinct immune cell infiltration patterns. This holds promise for evaluating immunotherapy responses and guiding therapeutic target identification in BC.
Prevalence and predictors of small intestinal bacterial overgrowth in inflammatory bowel disease: a meta-analysis
Authors: Feng Xin , Hu Jie , Zhang Xin 
Published: January 2025

BackgroundSmall intestinal bacterial overgrowth (SIBO) has been reported to be very common among individuals with inflammatory bowel disease (IBD), and the prevalence of SIBO is highly variable. We conducted this study to calculate the prevalence and identify predictors of SIBO in IBD.MethodsPubMed, Cochrane Library, and EMBASE from inception to March 2024 were searched for studies evaluating the prevalence of SIBO in IBD. We calculated the pooled prevalence of SIBO among IBD patients and the odds ratio (OR) of SIBO in IBD compared with healthy controls. Besides, we also evaluated predictors of SIBO in IBD patients.ResultsTwenty-nine studies (3,250 IBD, 708 controls) were included in our study. The pooled prevalence of SIBO in IBD was 31.0% (95% CI 25.2–37.1), and the prevalence of SIBO was higher in IBD compared with healthy controls (OR 5.25, 95% CI 2.96–9.32). The pooled prevalence of SIBO was higher among CD patients (32.2, 95% CI 25.9–38.8) compared with UC patients (27.8, 95% CI 18.5–38.1). The odds of lower BMI (mean difference = −1.04; 95% CI −1.86 to −0.23), bloating (OR = 3.02, 95% CI 1.22–7.5), flatulence (OR = 4.70, 95% CI 1.44–15.35), history of abdominal surgery (OR = 2.05, 95% CI 1.35–3.11), and stricturing/penetrating disease behavior (OR = 3.51, 95% CI 1.67–7.40) increased significantly in IBD patients with SIBO compared to those without SIBO. Antibiotic treatment may be effective for SIBO in IBD patients.ConclusionNearly one-third of IBD patients present with SIBO positive, and the odds of SIBO in IBD was increased by 5.25-fold compared with healthy controls. Lower BMI, bloating, flatulence, history of abdominal surgery, and stricturing/penetrating disease behavior were predictors of SIBO in IBD patients.
Association between weight-adjusted waist index and cognitive impairment in Chinese older men: a 7-year longitudinal study
Authors: Lin Jie , Shen Hongchen , Yang Wenjuan , Zhang Guojun , Sun Jie , Shen Wenqin , Huang Li , Chen Huajian 
Published: January 2025

BackgroundObesity, through mechanisms such as insulin resistance and systemic low-grade inflammation, can damage the central nervous system and impair cognitive function. Weight-adjusted waist index (WWI) is a novel measure of obesity that may offer more precise assessments of muscle and fat mass. This study aims to investigate the association between WWI and cognitive function in older Chinese men.MethodsData from the 2011–2018 China Longitudinal Health and Longevity Survey (CLHLS) were used in this study. WWI and cognitive function were examined in both linear and non-linear situations using Kaplan–Meier survival curves, multivariate Cox regression models, and restricted cubic spline (RCS) regression.ResultsThis study included 1,392 older Chinese men aged 65 years and over for whom complete data were available. After controlling for all potential confounding variables, our analysis showed a statistically significant positive association between WWI and cognitive decline. Specifically, for every 1 cm/√kg increase in WWI, the risk of cognitive impairment increased by 17% (HR = 1.17, 95% CI: 1.02–1.35). Using 11.52 cm/√kg as the cutoff point for WWI, we found that High WWI was associated with a 44% increased risk of cognitive impairment compared with Low WWI (HR = 1.44, 95% CI: 1.07–1.96). RCS regression analysis confirmed a linear positive correlation between WWI and cognitive impairment.ConclusionHigher WWI is linked to worse cognitive performance in older Chinese men.
Enhancing ALS disease management: exploring integrated user value through online communities evidence
Authors: Hruška Jan , Bachmann Pavel , Odei Samuel Amponsah 
Published: January 2025

IntroductionAssistive technologies (ATs) offer significant potential to improve the quality of life for individuals with Amyotrophic Lateral Sclerosis (ALS). This study explores the concept of integrated user value (IUV), focusing on five key aspects: quality, user experience, cost-effectiveness, safety, and accessibility. Understanding IUV is crucial for enhancing the development and deployment of ATs in ALS disease management.MethodsA systematic search approach was utilized to collect data from Facebook ALS support groups, comprising posts from individuals with ALS and their caregivers. Using a predefined set of keywords, 416 posts were analyzed. The posts were categorized based on the five aspects of IUV, and an in-depth content analysis was conducted to explore patterns, challenges, and experiences associated with AT usage.ResultsThe analysis revealed significant challenges across all aspects of IUV. Quality and user experience were interlinked, with users frequently citing inadequate designs and unmet customization needs. Cost-effectiveness was a key concern, with high costs and limited insurance coverage contributing to financial strain. Accessibility issues, including delays in acquiring devices and insufficient public facilities, further highlighted systemic challenges. Safety concerns emphasized the need for personalized and intuitive AT designs.DiscussionThe findings underscore the importance of a holistic approach to AT development, integrating all five aspects of IUV. Recommendations include enhancing product quality, ensuring affordability, prioritizing user-centered design, and addressing accessibility gaps. Collaboration between AT designers, healthcare providers, and policymakers is essential to optimize AT value and improve the quality of life for individuals with ALS and their caregivers.
Development and validation of a diagnostic model for migraine without aura in inpatients
Authors: Chen Zhu-Hong , Yang Guan , Zhang Chi , Su Dan , Li Yu-Ting , Shang Yu-Xuan , Zhang Wei , Wang Wen 
Published: January 2025

ObjectivesThis study aimed to develop and validate a robust predictive model for accurately identifying migraine without aura (MWoA) individuals from migraine patients.MethodsWe recruited 637 migraine patients, randomizing them into training and validation cohorts. Participant’s medical data were collected such as demographic data (age, gender, self-reported headache characteristics) and clinical details including symptoms, triggers, and comorbidities. The model stability, which was developed using multivariable logistic regression, was tested by the internal validation cohort. Model efficacy was evaluated using the area under the receiver operating characteristic curve (AUC), alongside with nomogram, calibration curve, and decision curve analysis (DCA).ResultsThe study included 477 females (average age 46.62 ± 15.64) and 160 males (average age 39.78 ± 19.53). A total of 397 individuals met the criteria for MWoA. Key predictors in the regression model included patent foramen ovale (PFO) (OR = 2.30, p = 0.01), blurred vision (OR = 0.40, p = 0.001), dizziness (OR = 0.16, p &lt; 0.01), and anxiety/depression (OR = 0.41, p = 0.02). Common symptoms like nausea (OR = 0.79, p = 0.43) and vomiting (OR = 0.64, p = 0.17) were not statistically significant predictors for MWoA. The AUC values were 79.1% and 82.8% in the training and validation cohorts, respectively, with good calibration in both.ConclusionThe predictive model developed and validated in this study demonstrates significant efficacy in identifying MWoA. Our findings highlight PFO as a potential key risk factor, underscoring its importance for early prevention, screening, and diagnosis of MWoA.
Textural analysis and artificial intelligence as decision support tools in the diagnosis of multiple sclerosis – a systematic review
Authors: Orzan Filip , Iancu Ştefania D. , Dioşan Laura , Bálint Zoltán 
Published: January 2025

IntroductionMagnetic resonance imaging (MRI) is conventionally used for the detection and diagnosis of multiple sclerosis (MS), often complemented by lumbar puncture—a highly invasive method—to validate the diagnosis. Additionally, MRI is periodically repeated to monitor disease progression and treatment efficacy. Recent research has focused on the application of artificial intelligence (AI) and radiomics in medical image processing, diagnosis, and treatment planning.MethodsA review of the current literature was conducted, analyzing the use of AI models and texture analysis for MS lesion segmentation and classification. The study emphasizes common models, including U-Net, Support Vector Machine, Random Forest, and K-Nearest Neighbors, alongside their evaluation metrics.ResultsThe analysis revealed a fragmented research landscape, with significant variation in model architectures and performance. Evaluation metrics such as Accuracy, Dice score, and Sensitivity are commonly employed, with some models demonstrating robustness across multi-center datasets. However, most studies lack validation in clinical scenarios.DiscussionThe absence of consensus on the optimal model for MS lesion segmentation highlights the need for standardized methodologies and clinical validation. Future research should prioritize clinical trials to establish the real-world applicability of AI-driven decision support tools. This review provides a comprehensive overview of contemporary advancements in AI and radiomics for analyzing and monitoring emerging MS lesions in MRI.
A multi-centre, randomised trial for diagnostic efficacy of the automatic breast volume scanner ultrasound for breast cancer screening in China
Authors: Xu Ying , Xu Yali , Shen Songjie , Mao Feng , Zhang Xiaohui , Zhang Yanna , Lin Yan , Zhou Yidong , Sun Qiang 
Published: January 2025

IntroductionThe US plays a crucial role in screening Asian women for breast disease. ABUS offers several advantages over traditional HHUS, including quicker examination, objectivity, and the ability to store and reconstruct images. This study marks the first large-scale opportunistic screening of ABUS in the population.MethodsBetween January 1, 2016, and December 31, 2019, 10,537 women aged 35–75 years from nine districts were randomly assigned to either HHUS or ABUS groups. Diagnostic methods were quantified, and comparisons were made using the Chi-square test.ResultsThe screening groups consisted of 5,445 participants for HHUS and 4,936 for ABUS. The HHUS and ABUS groups identified 90 carcinomas and 292 benign lesions or 71 carcinomas and 178 benign lesions, respectively. SE), SP, AC, PPV, and NPV for HHUS were 51.11%, 93.84%, 93.13%, 12.23%, and 99.13%, respectively, while for ABUS, they were 66.20%, 93.77%, 93.38%, 13.43%, and 98.98%. The area under the curve (AUC) values for HHUS and ABUS were 0.72 (95% CI: 0.67–0.78) and 0.86 (95% CI: 0.82–0.91), respectively, indicating superior diagnostic performance of ABUS over HHUS (Delong test p &lt; 0.05).DiscussionABUS is user-friendly, requires minimal training, reduces reliance on examiner experience, and demonstrates potential for superior sensitivity compared to HHUS in breast cancer screening.
Clinical characteristics and outcomes of surgical resection for brain metastases from lung adenocarcinoma
Authors: Li Ming , Li Zhiying , Zhang Hang , Wakimoto Hiroaki , Sun Linlin , Wang Tiantian , Zhou Shengli , Zhou Liyun 
Published: January 2025

ObjectiveThe purpose of this study was to explore the clinical characteristics, survival time and prognostic factors of patients undergoing craniotomy for brain metastases (BM) from lung adenocarcinoma (LUAD).MethodsA total of 208 patients with BM from LUAD who underwent craniotomy at the Zhengzhou University People’s Hospital, Henan province, China from March 2005 to October 2022 were included in this retrospective study. All patients were confirmed as BM of LUAD by histopathology. The clinical data included patient gender, age, occupation, family history of tumor, smoking history, alcohol drinking history, neurological symptoms, history of lung cancer treatment, tumor location, tumor number, tumor size, gene status, expression of S-100, CEA, Ki67, and PD-L1 by immunohistochemistry, KPS after craniotomy, whether tumor therapy was continued after craniotomy, and survival time. Univariate and multivariate Cox regression was used to analyze the prognostic factors of patients undergoing craniotomy for LUAD BM.ResultsA total of 208 patients met the inclusion and exclusion criteria, including 110 males (52.9%) and 98 females (47.1%), with an average age of 61.4 years. 203 patients (97.6%) had neurological symptoms. 84 patients (40.4%) had smoking history, 89 patients (42.8%) had alcohol drinking history, and 31 patients (14.9%) had the family history of tumor. Only 5 patients (2.4%) had received lung cancer treatment before craniotomy. The intracranial location of BM was mostly in the frontal lobe (54, 26.0%) and the metastatic sites were mostly single (117, 56.3%); the metastatic tumor size was mostly between 2-5 cm (141, 67.8%). Genetically, 43.3% patients (90 cases) had EGFR mutations, and immunohistochemical analysis showed that most patients were PD-L1 positive (160, 76.9%) and Ki67 &gt; 30% (137, 65.9%). Most patients (145, 69.7%) had KPS score under 80 after craniotomy. Only 72 patients (34.7%) received continued tumor therapy after craniotomy. 190 patients (91.3%) were successfully followed up. The median survival time was 11.5 months, and the 3-year survival rate was 15.7%. Multivariate analysis revealed that smoking history, Ki67 percentage, KPS after craniotomy, and molecular targeted therapy after craniotomy were independent factors affecting the survival time of patients.ConclusionsAlthough survival remains poor, patients who had no-smoking history, Ki67 percentage ≤30%, KPS≥80 after craniotomy, and molecular targeted therapy after craniotomy can improve the prognosis and prolong the survival time.
Clinical and genetic analysis of epilepsy with myoclonic-atonic seizures caused by SLC6A1 gene variant
Authors: Li Zhen , Han Changming , Zhao Hongwei 
Published: January 2025

ObjectiveThis research intends to examine the clinical characteristics and genetic diversity of a child experiencing epilepsy with myoclonic-atonic seizures (EMAS) attributed to a variant in the SLC6A1 gene.MethodsA male child diagnosed with EMAS underwent clinical and electroencephalographic evaluation. Peripheral blood samples were collected for DNA extraction and subsequent whole-exon gene sequencing. For previously identified patients, high-throughput sequencing was utilized, whereas Sanger sequencing was employed for the parents to determine the site of the gene mutation and examine the connection between genotype and phenotype.ResultsThe male child showed delays in intellectual and language development before the disease began. At 1 year and 2 months, he had a febrile seizures, which was succeeded by seizures at 2 years and 9 months; these seizures presented as generalized tonic-clonic, myoclonic, and myoclonic-atonic seizures, along with symptoms showing inattention and hyperactivity. After receiving treatment with levetiracetam (50 mg·kg·d−1), the child has been free of seizures for the last 8 months. Genetic analysis indicated a heterozygous missense variant of c.263T &gt; C (p.L88P) in the SLC6A1 gene in the child, recognized as a spontaneous mutation that has not been previously documented in the literature.ConclusionThe variant in the SLC6A1 gene is implicated as one of the etiological factors contributing to EMAS coupled with neurodevelopmental abnormalities. The identification of this novel mutation enriches the spectrum of known SLC6A1 gene variants.
Traditional Chinese medicine manual therapy for adolescent idiopathic scoliosis: a case report
Authors: Zhu Bowen , Li Miaoxiu , Ren Jun , He Tianxiang , Zhou Xin , Wang Shoujian , Kong Lingjun , Fang Min 
Published: January 2025

ObjectivesThis case demonstrates the efficacy and safety of Traditional Chinese Medicine manual therapy (TCMMT) for the treatment of mild to moderate AIS.MethodsAn 10-year-old girl who suffered from low back pain (LBP) with marked shoulder inequality and razorback postural abnormalities, with a clinical diagnosis of idiopathic scoliosis, and the Cobb angle of 20° and angle of trunk rotation (ATR) of the thoracic vertebral segment at 7°, and ATR of the lumbar vertebral segment at 8°, was treated with TCMMT. The patient initially recovered from centralized LBP with repeated TCMMT twice per week for 1 month. Subsequently, the frequency of TCMMT treatment was changed to 1–2 sessions weekly for 6 months. Before treatment, after the first TCMMT, 1 month and 7 months of treatment, and 18 months of follow-up, we used ATR or Cobb angle and health-related quality of life (HRQOL) for assessment. The HRQOL was assessed using the visual analog scale (VAS) scores and the Scoliosis Research Society-22 (SRS-22) patient questionnaire. The minimum clinically important difference (MCID) was used to assess the effectiveness of clinical measures based on a “responder analysis”.Results(a) The patient's VAS score was 40/100 before treatment, 25/100 after the first treatment, 15/100 after 1 month of treatment, 12/100 after 7 months of treatment, and 15/100 at follow-up to 18 months. (b) The patient's SRS-22 score was 54/110 before treatment, 61/110 after the first treatment, 79/110 after 1 month of treatment, 106/110 after 7 months of treatment, and 104/110 at follow-up to 18 months. (c) Before treatment, the patient's thoracic ATR angle was 7° and the lumbar ATR angle was 8°, there was no change in the ATR angles of the thoracic and lumbar spine after the first treatment. The thoracic ATR angle was 6° and the lumbar ATR angle was 5° after 1 month of treatment. The thoracic ATR angle was 1.5° and the lumbar ATR angle was 3.5° after 7 months of treatment. The thoracic ATR angle was 2° and the lumbar ATR angle was 4° at the follow up till 18 months. (d) The patient's Cobb angle was 20° before treatment, 7° after the 7 month of treatment, and 8° at follow-up to 18 months. No adverse events during treatment.ConclusionsTCMMT is a conservative treatment option worthy of consideration when considering a conservative treatment strategy for AIS.