bluuebunny/crossref_metadata_2025_split huggingface dataset:
Syringe service program-based telemedicine linkage to opioid use disorder treatment: the randomized mixed method STAMINA trial
Authors: Watson Dennis P. , Franceschini Dana , Swartz James A. , Dewey Jodie , Mackesy-Amiti Mary Ellen , Taylor Lisa , Staton Monte , Zhao Peipei , Messmer Sarah , Jimenez Antonio D. , Gastala Nicole 
Published: October 2024

Abstract

Background
The opioid overdose crisis necessitates expanded access to medications for opioid use disorder (MOUD). Treatment programs often struggle to engage individuals at the highest overdose risk. This study, STAMINA, aimed to engage participants at a syringe service program (SSP) and connect them to treatment through a telemedicine platform.
Methods
In a pragmatic mixed methods trial, participants were randomized to either telemedicine (n = 138) or standard referral (n = 136). Baseline and 90-day structured interviews, urine testing, and administrative data from MOUD providers were collected. Additionally, a subset of participants (n = 36) completed semi-structured qualitative interviews. The study took place at two SSP sites in Chicago, IL, involving 274 individuals (78% male, 61% African American, 78% non-Latino, mean age = 48) interested in starting MOUD treatment. Interventions included an immediate telemedicine appointment with transportation to the first in-person MOUD appointment versus standard referral. Participants could choose from methadone, buprenorphine, or extended-release naltrexone.
Results
The primary outcome was measured by attendance at the first in-person appointment, indicating successful treatment linkage. Secondary outcomes included MOUD engagement, retention, and non-MOUD opioid use, assessed through self-report and urinalysis. The key determinant of linkage success was scheduling an in-person appointment within 48 hours of study enrollment (aOR = 3.20, p < .01). Methadone treatment posed significant requirements but showed greater success compared to buprenorphine. Participants reported various reasons for continued illicit opioid use.
Conclusions
Telemedicine alone is insufficient to overcome MOUD access barriers. Differences in MOUD requirements should inform the design of linkage interventions. Additional supports may be necessary to enhance the success of flexible treatments like buprenorphine.
Trial registration
ClinicalTrials.gov (NCT04575324).
Photoinduced Modulation of the Oxidation State
of Dibenzothiophene S-Oxide Molecules
on an Insulating Substrate
Authors: Nony Laurent , Hankache Mélissa , Magné Valentin , Geagea Elie , Marqués Pablo Simón , Clair Sylvain , Giovanelli Luca , Loppacher Christian , Mallet-Ladeira Sonia , Maerten Eddy , Kammerer Claire , Madec David 
Published: October 2024

Abstract

On-surface chemistry aims to overcome the limitations of conventional in-solution synthesis by taking advantage of the confinement in two dimensions to master highly ordered covalent structures with tailored properties. So far, most of the reported work was conducted on metal substrates and relied on unconventional mechanisms, thereby precluding a direct transposition of well-established organic reactions from solutions to surfaces. In addition, the intrinsic properties and reactivity of metal substrates often limit the activation methods available to trigger on-surface reactions, and photoinduced processes are especially difficult to handle due to quenching of the adsorbed precursor molecules. Herein, the photoinduced deoxygenation of dibenzothiophene S-oxide (DBTO) derivatives was transposed from solutions to insulating alkali halide surfaces in ultra-high vacuum. By combining in-solution and on-surface investigations by means of scanning tunneling microscopy, non-contact atomic force microscopy, as well as Bias spectroscopy measurements, we provide evidence of the successful on-surface deoxygenation of individual DBTO derivatives under UV irradiation. The photoinduced deoxygenation is conducted at low temperature (< 25 K) on a NaCl thin film formed on a Au(111) substrate to yield the reduced dibenzothiophene (DBT) product with excellent chemoselectivity. This work thus opens the way to in-situ photocontrolled charge state manipulation in purely organic compounds.
First-year growth trajectories of preterm infants receiving kangaroo mother care, their early life predictors and association with one-year malnutrition
Authors: Nel Sanja , Feucht Ute , Botha Tanita , Arashi Mohammad , Wenhold Friedeburg 
Published: October 2024

Abstract

Background
Longitudinal growth of South African preterm infants is inadequately described. This study characterises first-year growth trajectories in a historical preterm infant cohort, and investigates associations with early-life predictors and one-year anthropometry.
Methods
Clinic records of 322 preterm infants followed up for one year post-discharge from a South African tertiary hospital’s kangaroo mother care unit were analysed. Latent class trajectory modelling identified characteristic trajectories of weight-for-age (WAZ), length-for-age (LAZ), weight-for-length (WLZ), and head circumference-for-age (HCZ) z-scores, calculated using Fenton Growth Chart and WHO Growth Standards (age-corrected). Ordinal regression analysis determined odds ratios (ORs) for early life predictors (maternal/infant factors, birth weight, early WAZ gain) of growth trajectories. One-year underweight (WAZ<-2), stunting (LAZ<-2), wasting (WLZ<-2) and overweight (BMI-for-age z-score > + 2) were compared using Chi-squared/Fisher’s Exact tests.
Results
Best-fit models identified three WAZ and LAZ trajectories (faltering, gradual gain, catch-up), two WLZ trajectories (faltering, gain) and two HCZ trajectories (maintenance, gain). Lower birth weight z-score (BWZ) predicted LAZ catch-up (OR:8.33(3.13-20.00)), WLZ faltering (OR:1.69(1.11–2.70)) and HCZ gain (OR:1.92 (1.23–3.13)), but lowered odds of gradual WAZ gain (OR:0.36(0.19–0.68)) and WAZ faltering (OR:0.56(0.34–0.92)). Smaller early WAZ gain predicted gradual WAZ gain (OR:2.27(1.56–3.33)), WAZ faltering (OR:1.47(1.11,1.96)), LAZ catch-up (OR:1.85(1.25–2.70)), LAZ faltering (OR:1.39(1.09–1.75)). WAZ and WLZ faltering respectively resulted in more underweight (49.1%, 22.4%), stunting (45.5%, 23.5%) and wasting (21.8%, 10.3%), while gradual LAZ gain resulted in least underweight (2.0%), stunting (2.1%) and wasting (2.1%, all p < 0.001).
Conclusions
Preterm infants display various first-year growth trajectories. Lower BWZ predicted catch-up growth, while poor early WAZ growth predicted growth faltering.
Impact of Advanced Practice Nurses on Blood Pressure Control in Hypertension Management: A Scoping Review
Authors: VAY-DEMOUY Juliette , LELONG Hélène , BLACHER Jacques 
Published: October 2024

Abstract

Background: Hypertension is a major public health problem, with serious consequences in terms of morbidity and mortality. Its high prevalence makes it the leading chronic pathology in the world. Since the 1960s, advanced practice nurses have gradually emerged worldwide. With their wide range of skills, they play an increasingly important role in the management of hypertension. This scoping review aimed to map the literature about the impact of an advanced practice nurse intervention on blood pressure control in hypertension management and to identify research gaps.
Methods: A scoping review was carried out using Pubmed, CINHAL, Cairn, Embase, Cochrane and Google scholar databases. The major inclusion criterion was advanced practice nurse interventions including the ability to prescribe antihypertensive treatment (renewal +/- initiation).
Results: A total of 8 studies were included according to our eligibility criteria. All agreed on the significant benefits of an advanced practice nurse intervention on blood pressure control in hypertension management versus usual care or physician care only. The lack of literature and the poor quality of available data were deplored.
Conclusion: All references supported the hypothesis that advanced practice nurses can be a considerable lever to optimize blood pressure control in the overall hypertension management. Nevertheless, research of good methodological quality remains needed to draw any conclusion.
Investigation of the Female Genital Tract Microbiome and its Association with Hydrosalpinx in Women Undergoing Salpingectomy
Authors: Yagel Yael , Motro Yair , Green Stefan , Klapper-Goldstein Hadar , Pardo Ella , Moran-Gilad Jacob , Weintraub Adi Y. 
Published: October 2024

Abstract

Objective: To describe the microbiome of the vagina and fallopian tubes, and its relation with hydrosalpinx.
Methods: Case-control study was conducted in women who underwent salpingectomy for hydrosalpinx (case) or other indications (controls). Samples were obtained during surgery and were subjected to 16S rRNA amplicon sequencing, and analyses of alpha diversity and beta diversity measures were compared between sites and groups. Differential abundances of bacteria associated with vaginal dysbiosis was compared between cases and controls.
Results: Nine women with hydrosalipnx, and 23 women without hydrosalpinx were included in the study. The mean age of studied women was 41 (range: 29-54), and most (89%) were premenopausal. After in silico decontamination, only 30% of control fallopian tubes samples, and 10% of case fallopian tubes samples, had evidence of bacterial presence. The vaginal microbiota of control patients showed greater abundance of lactobacilli whereas the vaginal microbiome of case patients contained relatively more bacterial vaginosis associated bacteria such as Prevotella, Gardenrella and Atopobium. A significant difference was found in alpha and beta diversity between the vaginal and FT microbiomes in control patients, as fallopian tubes samples were more diverse. We found that women with hydrosalpinx had a more “dysbiotic” vaginal microbiome, and in women without hydrosalpinx, microbial composition within the vagina and FT differed, possibly representing two distinct ecological environments.
Conclusion: women undergoing salpingectomy for various reasons harbored bacteria within their FT, women with hydrosalpinx generally did not. This suggests that even though infection may be an underlying cause of hydrosalpinx, bacteria may not be present by the time patients require surgery.
Multiomics-based Analysis Reveals Differences in intratumoral microbiota and Prognostic in Gastric Cancer Patients with Different BMI
Authors: Liu Kang , Jiang Zhengchen , Ma Yubo , Xia Ruihong , Zheng Yingsong , Yin Kailai , Pang Chuhong , Yuan Li , Cheng Xiangdong , Liu Zhuo , Zhang Bo , Wang Shi 
Published: October 2024

Abstract

Body mass index (BMI) is considered a significant prognostic factor for tumor outcomes;however, the role of BMI in gastric cancer (GC) remains controversial. Currently, there is a lack of research investigating the impact of BMI on GC from the perspective of intratumoral microbiota. This study aimed to compare and analyze the differences in and functions of intratumoral microbiota among GC patients with varying BMIs, aiming to ascertain whether specific microbial features are associated with prognosis in low-BMI gastric cancer patients.A retrospective analysis of the clinicopathological features and prognosis of 5567 patients with different BMIs were performed between January 2010 and December 2019. Tumor tissues from 189 GC patients were collected for 16S rRNA sequencing, 64 samples were selected for transcriptome sequencing, and 57 samples were selected for untargeted metabolomic analysis.Clinical cohort analysis revealed that GC patients with a low BMI(LBMI) presented poorer clinical and pathological characteristics than those with a nonlow- BMI༈NLBMI༉. LBMI has as a significant independent risk factor for adverse prognosis, potentially exerting immunosuppressive effects on postoperative adjuvant chemotherapy. 16S rRNA sequencing revealed no significant differences in the alpha and beta diversity of the intratumoral microbiota between the two groups of GC patients. However, LEfSe analysis revealed 32 differential intratumoral microbiota between the LBMI and NLBMI groups. Notably, g_Abiotrophia was significantly enriched in the LBMI group. In GC patients with LBMI, g_Abiotrophia was negatively correlated with the eosinophil, P2RY12, and SCN4B genes but positively correlated with LGR6. Metabolomic analysis further revealed a positive correlation between g_Abiotrophia and the purine metabolism products guanine and idp.LBMI is an independent risk factor for poor prognosis in patients with gastric cancer and may have inhibitory effects on postoperative adjuvant chemotherapy. There are differences in intratumoral microbiota between GC patients with different BMIs, along with distinct immune cell infiltration and metabolic characteristics.g_Abiotrophia may promote the occurrence and development of GC by regulating eosinophils and purine metabolism pathways, providing new solutions for precision treatment of GC.
Clinicopathological manifestations of biopsy-proven renal sarcoidosis: A retrospective cohort study
Authors: Liu Aichun , Wang Yina , Yan Yu , Dong Bao , Cai Meishun , Zuo Li 
Published: October 2024

Abstract

Background
While many studies have reported renal involvement in sarcoidosis, there is limited description of the pathological manifestations of renal sarcoidosis. The relationship between clinical presentation, renal pathology, and prognosis remains unclear. The aim of this study is to examine the clinical, laboratory, and histological characteristics, as well as the prognosis of patients with renal sarcoidosis (RS).
Methods
We conducted a retrospective, single-center study of RS in renal biopsy cases treated in our department between January 2019 and December 2023.
Results
We identified 5 patients (4 men, 1 woman; median age 52 years, IQR 36–61 years). All patients had renal insufficiency with a median creatine level of 456 µmol/L (IQR 430.5-942.5µmol/L) and a median proteinuria of 0.5 g/24 h (IQR 0.2–0.73 g/24 h). Three (60%) of the five patients presented with both hypercalcemia and hypercalciuria. Histologically, two of the three patients who with hypercalcemia presented with renal calcinosis and tubulointerstitial nephritis (TIN) without granuloma. The other patient with hypercalcemia presented with renal calcinosis and acute tubular necrosis (ATN). The other two (40%) patients who with normal serum calcium presented with noncaseating granulomas interstitial nephritis (GTIN). For light microscopy, the interstitial inflammatory infiltrate also contains lymphocytes, monocytes cells, and sometimes eosinophils. By immunohistochemical stain, the infiltrating lymphocytes were CD4 + T cells that formed nodular granulomas, surrounded by CD8 + T cells. Chronic lesions such as interstitial fibrosis was mild in all five patients. A favorable response to steroid therapy was noted in all cases, and only one (case 4) had biopsy-proven recurrence of sarcoidosis granulomatous interstitial nephritis.
Conclusions
RS is extremely rare among kidney biopsy cases. Early and accurately diagnosis depends on renal pathology. The hallmark histological manifestation of RS is noncaseating GTIN, with CD4 + T cells primarily located in the center and CD8 + T cells primarily located in the periphery. Early diagnosis and prompt treatment with corticosteroids can improve the prognosis.
Human epididymis protein 4: a novel predictor of acute non-ST segment myocardial infarction
Authors: Tang Yi , Liu Zhibin , Hu ZhengQi , Liu Tiancheng , Peng Jianqiang , Pan Hongwei , He Jin 
Published: October 2024

Abstract

The prognostic value of human epididymis protein 4 (HE4) in patients with acute non-ST-segment elevation myocardial infarction (NSTEMI) remains unclear. From August 2021 to October 2023, patients diagnosed with NSTEMI at Hunan Provincial People's Hospital were prospectively enrolled. The HE4 levels of enrolled patients were measured using the chemiluminescent microparticle immunoassay.The endpoint events of the study included hospitalization for unstable angina, readmission for heart failure, nonfatal myocardial infarction, and cardiovascular death.A total of 240 NSTEMI patients were finally included, among whom 53 experienced endpoint events. The serum HE4 levels in patients who experienced events were significantly higher than those in patients without events [154.50 (96.25-324.45) pmol/L vs. 72.5 (50.60,125.65) pmol/L, P < 0.001]. Multivariate Cox regression analysis shows that HE4 [HR = 1.001 (1.000-1.002), P < 0.004] and The Global Registry of Acute Coronary Events (GRACE) risk score [HR = 1.017 (1.003–1.030), P < 0.014] are independent predictors of endpoint events. The receiver operating characteristic (ROC) curve analysis show that the area under the curve (AUC) of HE4 is the largest, with an AUC value of 0.712. In the Kaplan-Meier curve, the survival rate of patients with HE4 > 100.25 pmol/L is lower than that of patients with HE4 ≤ 100.25 pmol/L (P < 0.001).These findings show that HE4 can independently predict the occurrence of endpoint events in patients with NSTEMI.
Ecological Dynamics and Human Impact Assessment of a Small Mangrove Forest in the Northern Persian Gulf: A Multidimensional Approach Using Satellite-derived, Drone- based, and Field-measured Data
Authors: Kabiri Keivan , Abedi Ehsan 
Published: October 2024

Abstract

The ecological dynamics of Mangroves of Dayyer City (MDC) in the northern Persian Gulf were assessed. This study employs satellite-based data, drone-based photography, and field measurements/observations to assess changes in mangrove areas, investigate human-made structures affecting the MDC. Satellite imagery from Google Earth, spanning from 2011 to 2022, reveals fluctuations in the MDC area, with notable afforestation efforts until 2018, followed by rapid degradation. The mangrove forest, initially covering ~ 2.2 ha in 2011, expanded to 3.2 ha by 2015 due to mangrove planting efforts. However, subsequent years witnessed a decline, with the area diminishing to 1.7 ha by June 2022. Human-made structures, specifically a nonstandard road and its relevant bridge construction in 2018, are identified as the main potential cause of mangrove degradation by obstructing freshwater flow from upper areas. Drone-based observations conducted on March 2023, provided a detailed map revealing that ~ 44% of healthy mangroves are damaged. However, field measurements performed on November 2023, revealed higher salinity levels at MDC stations than at other adjacent mangrove areas (Nayband and Melgonzeh). The principal component analysis (PCA) showed that the first two principal components explained a significant portion (99.7%) of the variability in the environmental data. Specifically, the first principal component represented variations in water temperature, accounting for 93.2% of the observed environmental variability. On the other hand, the second principal component was associated with salinity and dissolved oxygen concentrations, explaining 6.5% of the observed variability. This multidimensional approach enhances our understanding of the complex interactions influencing mangrove ecosystems.
A network-based systems genetics framework identifies pathobiology and drug repurposing in Parkinson’s disease
Authors: Cheng Feixiong , Dou Lijun , Xu Zhenxin , Xu Jielin , Su Chang , Pieper Andrew , Zhu Xiongwei , Leverenz James , Wang Fei , Cummings Jeffrey 
Published: October 2024

Abstract

Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorder. However, current treatments are directed at symptoms and lack ability to slow or prevent disease progression. Large-scale genome-wide association studies (GWAS) have identified numerous genomic loci associated with PD, which may guide the development of disease-modifying treatments. We presented a systems genetics approach to identify potential risk genes and repurposable drugs for PD. First, we leveraged non-coding GWAS loci effects on multiple human brain-specific quantitative trait loci (xQTLs) under the protein-protein interactome (PPI) network. We then prioritized a set of PD likely risk genes (pdRGs) by integrating five types of molecular xQTLs: expression (eQTLs), protein (pQTLs), splicing (sQTLs), methylation (meQTLs), and histone acetylation (haQTLs). We also integrated network proximity-based drug repurposing and patient electronic health record (EHR) data observations to propose potential drug candidates for PD treatments. We identified 175 pdRGs from QTL-regulated GWAS findings, such as SNCA, CTSB, LRRK2, DGKQ, CD38 and CD44. Multi-omics data validation revealed that the identified pdRGs are likely to be druggable targets, differentially expressed in multiple cell types and impact both the parkin ubiquitin-proteasome and alpha-synuclein (a-syn) pathways. Based on the network proximity-based drug repurposing followed by EHR data validation, we identified usage of simvastatin as being significantly associated with reduced incidence of PD (fall outcome: hazard ratio (HR) = 0.91, 95% confidence interval (CI): 0.87–0.94; for dementia outcome: HR = 0.88, 95% CI: 0.86-0.89), after adjusting for 267 covariates. Our network-based systems genetics framework identifies potential risk genes and repurposable drugs for PD and other neurodegenerative diseases if broadly applied.
Comparative evaluation of large-language models and purpose-built software for medical record de-identification
Authors: Kuo Rachel , Soltan Andrew , O’Hanlon Ciaran , Hasanic Alan , Clifton David , Collins Gary , Furniss Dominic , Eyre David 
Published: October 2024

Abstract

Background:

Robust de-identification is necessary to preserve patient confidentiality and maintain public acceptability for electronic health record (EHR) research. Manual redaction of personally identifiable information (PII) is time-consuming and expensive, limiting the scale of data-sharing. Automated de-identification could alleviate this burden, but the best strategy is not clear. Advances in natural language processing (NLP) and the emergence of foundational large language models (LLMs) show promise in performing clinical NLP tasks with no, or limited training.

Methods:

We evaluated two task-specific (Microsoft Azure de-identification service, AnonCAT) and five general LLMs (Gemma-7b-IT, Llama-3-8B-Instruct, Phi-3-mini-128k-instruct, GPT3.5-turbo-base, GPT-4-0125) in de-identifying 3650 medical records from a UK hospital group, split into general and specialised datasets. Records were dual-annotated by clinicians for PII. Inter-annotator reliability was used to benchmark performance. The primary outcome was F1, precision (positive predictive value) and recall (sensitivity) for each comparator in classifying words as PII vs. non-PII. The secondary outcomes were performance per-PII-subtype, per-dataset, and the presence of LLM hallucinations. We report outcomes at zero- and few-shot learning for LLMs, and with/without fine-tuning for AnonCAT.

Results:

17496/479760 (3.65%) words were PII. Inter-annotator F1 for word-level PII/non-PII was 0.977 (95%CI 0.957-0.991), precision 0.967 (0.923-0.993), and recall 0.986 (0.971-0.997). The best performing redaction tool was the Microsoft Azure de-identification service: F1 0.933 (0.928-0.938), precision 0.916 (0.930-0.922), recall 0.950 (0.942-0.957). The next-best were fine-tuned-AnonCAT: F1 0.873 (0.864-0.882), precision 0.981 (0.977-0.985), recall 0.787 (0.773-0.800), and GPT-4-0125 (ten-shots): F1 0.898 (0.876-0.915), precision 0.924 (0.914-0.933), recall 0.874 (0.834-0.905). There was hallucinatory output in Phi-3-mini-128k-instruct and Llama-3-8B-Instruct at zero-, one-, and five-shots, and universally for Gemma-7b-IT. Names/dates were consistently redacted by all comparators; there was variable performance for other categories. Fine-tuned-AnonCAT demonstrated the least performance shift across datasets.

Conclusion:

Automated EHR de-identification could facilitate large-scale, domain-agnostic record sharing for medical research, alongside other safeguards to prevent patient reidentification.