bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 resistance mutations and genetic diversity among children failing antiretroviral treatment in five healthcare facilities in Benin, West Africa
Authors: Dagba Gbessin Edwige Hermione , Tchiakpe Edmond , Keke René Kpemahouton , Vidal Nicole , Gomgnimbou Michel Kiréopori , Sina Haziz , Adjou Euloge Senan , Afangnihoun Aldric , Bachabi Moussa , Yessoufou Akadiri , Ouedraogo Abdoul-Salam , Baba-Moussa Lamine 
Published: January 2025

Background
Antiretroviral treatment increases the risk of accumulation of resistance mutations that negatively impact the possibilities of future treatment. This study aimed to present the frequency of HIV-1 antiretroviral resistance mutations and the genetic diversity among children with virological failure in five pediatric care facilities in Benin.

Methods
A cross-sectional study was carried out from November 20, 2020, to November 30, 2022, in children under 15 years of age who failed ongoing antiretroviral treatment at five facilities care in Benin (VL > 3log10 on two consecutive realizations three months apart). Viral loads were measured using the m2000 RealTime Abbott platform. Genotyping was carried out with the commercial Viroseq kit. Sequences were read on the ABI 3500 sequencer and then edited with ViroSeqHIVv3.0 software. The HIV drug resistance database at Stanford University was used to identify mutations and viral subtypes were assigned by phylogenetic analyses.

Results
The HIV-1 pol gene was sequenced in 47 participants with virological failure of antiretroviral treatment. The median age was 120 [Interquartile Range 90–144] months. The prevalent treatment was EFV base regimen (22/47; 46.8%). Median viral load was 4.39 log10 [IQR 3.81–4.86 log10] respectively. Resistance testing was successful among (37/47; 78.72%) children, resistance mutations were detected in (32/37; 86.48%) children, and (29/32; 90.62%) had at least one surveillance drug resistance mutation. Respectively (25/32; 78.12%), (28/32; 87.5%), (4/32; 12.90%), (22/32; 68.75%) had at least one resistance mutation associated with NRTIs, NNRTIs, PIs and NNRTIs+NRTIs. (12/32; 37.5%) of children carried mutations related to TAMs. the most frequently NRTIs identified were M184V (21/62; 33.9%) followed by TAMs (20/62; 32.2%) and T69G/D (2/62; 3.2%)s. Among mutations associated with NNRTIs K103N represented (18/64; 28.1%) followed by P225H (7/64; 10.9%). The I54V (3/6; 50%) mutation is the major PI observed.
Genetic diversity is characterized by a preponderance of CRF02_AG (72%, 23/32), followed by unique recombinant forms (URFs) (25%, 8/32) and one subtype G.

Conclusion
A high rate of mutations has been observed in children. These data underline the importance of implementing routine genotypic testing in the biological monitoring of infected children to anticipate the accumulation of resistance mutations and thus compromise the treatment options available in Benin.
Nurses’ knowledge and its determinants in surgical site infection prevention: A comprehensive systematic review and meta-analysis
Authors: Habtie Tesfaye Engdaw , Feleke Sefineh Fenta , Terefe Aregash Birhan , Alamaw Addis Wondmagegn , Abate Melsew Dagne 
Published: January 2025

Objective
The objective of this systematic review and meta-analysis is to assess and synthesize the global evidence on the level of nurses’ knowledge and its determinants regarding the prevention of surgical site infections.

Methods
This systematic review and meta-analysis were conducted following strict methodological guidelines to ensure accuracy and reliability. Adhering to the 2020 PRISMA checklist, a systematic review and meta-analysis sought to establish the pooled proportion of nurse’s knowledge and its determinants regarding surgical site infection prevention globally. MeSH terms and keywords were included in the search. Data extraction, quality assessment, and analysis followed established protocols. Heterogeneity and publication bias was assessed using STATA version 17.0.

Results
A total of seventeen observational studies, with sample sizes ranging from 30 to 515 participants, were included in the final analysis in a global context. In this systematic review and meta-analysis, the pooled proportion of nurses with good knowledge of surgical site infection prevention is 62% (95% CI: 50–74%) when assessed using a dichotomous scale. However, when knowledge is measured using a three-point Likert scale, the pooled proportion of those with good knowledge drops to 46% (95% CI: 21–72%), with an additional 27% (95% CI: 16–38%) demonstrating fair or moderate knowledge.

Conclusion and recommendation
This systematic review and meta-analysis is the first to synthesize data on nurses’ knowledge of surgical site infection (SSI) prevention. The findings reveal poor knowledge levels, highlighting the need for targeted educational interventions globally. While the pooled odds ratio is not statistically significant, training, longer service years, and higher education improve SSI prevention knowledge by enhancing critical thinking, boosting confidence, and fostering adherence to evidence-based practices. Future research should focus on identifying factors influencing nurses’ knowledge, particularly through longitudinal and interventional studies. Policymakers should incorporate international guidelines such as those recommended by the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) into nursing curricula, supported by robust assessment tools and educator training, to improve knowledge transfer and implementation of best practices.
Comparison of observational methods to identify and characterize post-COVID syndrome in the Netherlands using electronic health records and questionnaires
Authors: Bos Isabelle , Bosman Lisa , van den Hoek Rinske , van Waarden Willemijn , Berends Matthijs S. , Homburg Maarten S. , Olde Hartman Tim , Muris Jean , Peters Lilian S. , Knottnerus Bart , Hek Karin S. , Verheij Robert A. 
Published: January 2025

Background
Some of those infected with SARS-CoV-2 suffer from post-COVID syndrome (PCS). However, an uniform definition of PCS is lacking, causing uncertainty about the prevalence and nature of this syndrome. We aimed to improve understanding of PCS by operationalizing different classifications and to explore clinical subtypes.

Methods
We used data from Nivel Primary Care database from 2019–2020 which consists of electronic health records (EHR) from general practices (GPs) combined with sociodemographic data for n = 10,313 individuals infected with the SARS-CoV-2. In addition, data from n = 276 individuals who had been infected with the SARS-CoV-2 in 2021, collected via a longitudinal survey, was used. In the GP-EHR data, we operationalized two classifications of PCS (based on symptoms and diagnosis recorded in GP-EHR data and healthcare utilization 3–12 months after acute infection) to calculate frequency and characteristics and compared this to the survey results. In a subgroup of the EHR data we conducted community detection analyses to explore clinical subtypes of PCS.

Results
The frequency of PCS was 15% with on average 4.6 symptoms for which the GP was consulted using the narrow definition and 32% with on average 6.8 symptoms for the broad definition. Across all methods and classifications, the mean age of individuals with PCS was around 53 years and they were more often female. There were small sex differences in the type of symptoms and overall symptoms were persistent for 6 months. The community detection analysis revealed three possible clinical subtypes.

Discussion
We showed that frequency rates of PCS differ between methods and data sources, but characteristics of the affected individuals are relatively stable. Overall, PCS is a heterogeneous syndrome affecting a substantial group of individuals who need adequate care. Future studies should focus on care trajectories and qualitative measures such as quality of life of individuals living with PCS.
Rural-urban disparity in uptaking skilled antenatal care visits by pregnant women in Bangladesh: Zero and One Inflated Poisson regression model
Authors: Tanvia Lubana , Haque M. Ershadul , Bari Wasimul 
Published: January 2025

Background
Utilization of maternal health care services, specifically, antenatal care services from skilled health providers have been given utmost priority in low- and middle-income countries over years with a view of mitigating complications during pregnancy as well as safeguarding the health and survival of both mother and newborn. However, there is a general tendency of pregnant mothers in Bangladesh of receiving skilled antenatal care (SANC) service once, or even never which refrains us to ensure World Health Organization (WHO) recommended eight plus SANC visits, additionally, to meet Sustainable Development Goal (SDG) number three.

Objectives
The study aims at assessing how the average number of SANC visits taken by the reproductive women in Bangladesh changes over the time in rural and urban areas together with finding out the potential demographic and socio-economic factors associated with SANC visits by addressing possible accumulation of zero and one counts in SANC visits.

Methods
In this study, data have been retrieved from last four waves of Bangladesh Demographic and Health Surveys ranging from 2011 to 2022 and later combined together to form a pooled dataset. Non-parametric Kruskal-Wallis test has been performed for exploring unadjusted association of covariates with the response and Mann-Whitney U test has been conducted for multiple comparison in case of significant association for a covariate having more than two categories. For checking the existence of concurrent inflation at zero and one in the pooled dataset, partial score test has been performed. Based on the results of score test, Zero and One Inflated Poisson regression model has been fitted to the pooled dataset, where an interaction term between area of residence and survey year has been considered for trend analysis.

Results
The study highlights that the rate of mean SANC visits is rapidly rising with time among pregnant women not only from the urban areas but also from the rural areas of Bangladesh. However, the rate of change in uptaking the SANC visits is higher in rural area compared to urban area. It was observed that for a given survey year, the rate of mean SANC visits was higher among women from urban areas compared to that among women from rural areas of Bangladesh. This study provides the evidence of 17.2% extra zero counts and 1.1% extra one counts in the pooled dataset.

Conclusion
The study results depict that inequity in SANC services based on area of residence prevails in Bangladesh. However, the gap in the rate of mean SANC visits in rural areas compared to urban areas has gradually reduced over time. Based on the results, the study comes up with some recommendations to facilitate the policy makers in improvising strategies and ensuring sustainable rise in SANC counts as well as WHO recommended positive pregnancy experience in the country to meet SDGs.
A systematic review on the influence of coagulopathy and immune activation on New Onset Atrial Fibrillation in patients with sepsis
Authors: Johnston Brian W. , Downes Michael , Hall Angela , Thomas Zachary , Welters Ingeborg D. 
Published: January 2025

Introduction
New Onset Atrial Fibrillation (NOAF) is the most common arrhythmia in intensive care. Complications of NOAF include thromboembolic events such as myocardial infarction and stroke, which contribute to a greater risk of mortality. Inflammatory and coagulation biomarkers in sepsis are thought to be associated with NOAF development. The aim of this systematic review and narrative synthesis is to identify inflammatory and coagulation biomarkers as predisposing risk factors for NOAF in sepsis.

Methods
Three databases (Medline, Cochrane Library, and Scopus) were searched using a predefined search strategy. Inclusion / exclusion criteria were applied, and quality assessments were performed using the Newcastle Ottawa Scale (NOS).

Results
We identified 1776 articles; and 12 articles were included in this review. 8 articles were retrospective observational studies and 4 were prospective observational studies. There was considerable heterogeneity between studies regarding outcomes, methodological design, quality, definitions and reported biomarkers of interest. There is evidence that C-reactive protein (CRP) is associated with NOAF, with hazard ratios 3.33 (3.32–3.35) p = 0.001 and odds ratios of 1.011 (1.008–1.014) p<0.001. International Normalised Ratio (INR) and fibrinogen may be associated with NOAF with odds ratios reported as 1.837 (1.270–2.656) p = 0.001 and 1.535(1.232–1.914) p<0.001 respectively.

Conclusion
Further research is required to confirm the association between inflammatory and coagulation biomarkers and the development of NOAF in sepsis. A broader evidence base will guide treatment strategies, improving the standard of care for patients who develop NOAF in sepsis. Furthermore, given the heterogeneity between studies consideration should be given to inclusion of immune biomarkers in future core outcome sets for trials investigating NOAF.
Trajectory of the arterial-alveolar oxygen gradient in COPD for a decade
Authors: Nagata Kazuma , Sato Susumu , Uemasu Kiyoshi , Tanabe Naoya , Sato Atsuyasu , Muro Shigeo , Hirai Toyohiro 
Published: January 2025

Background
Chronic respiratory failure (CRF) is a critical complication in patients with chronic obstructive pulmonary disease (COPD) and is characterized by an increase in the arterial-alveolar oxygen gradient (A-aDO2). The long-term trajectory and prognostic significance remain unclear. This study aimed to assess the prognostic impact of A-aDO2 and elucidate its trajectory over ten years.

Methods
We enrolled 170 outpatients with COPD from a prospective cohort study. Arterial blood gas (ABG) analyses were conducted annually for ten years while monitoring the development of CRF.

Results
157 patients completed the observation period, of whom 21 developed CRF (CRF group) and 136 did not (non-CRF group). In the CRF group, there was a gradual increase in A-aDO2 along with decreases in partial pressure of oxygen (PaO2) and partial pressure of carbon dioxide (PaCO2) over ten years, although there were no changes in the non-CRF group. The CRF group had higher baseline A-aDO2 and higher ΔA-aDO2 in the first year than the non-CRF group (3.76 vs. 0.42 Torr/year, p = 0.030). Kaplan-Meier analyses, and multivariate Cox proportional hazards analysis revealed that both baseline A-aDO2 and ΔA-aDO2 were significantly associated with the development of CRF. Retrospective tracking from the initiation of long-term oxygen therapy (LTOT) revealed significant increases in A-aDO2 from 5 years prior to LTOT initiation in the CRF group when compared to the non-CRF group.

Conclusions
An increasing trend in A-aDO2 may be a significant sign for the future development of CRF. A transition of the annual change of A-aDO2 from a stable state to a deterioration phase can serve as a prognostic factor for developing CRF within 5 years.
Association of Gastric Sarcina With Malignant Pyloric Stenosis
Authors: Duggal Shivangini , Garrison Keith , Meza-Rodriguez Samantha , Williams Ben , Konstantinidis Ioannis , Zuckerman Marc J. , Elhanafi Sherif E. 
Published: January 2025

ABSTRACT

Sarcina ventriculi (SV) is a Gram-positive cocci that thrives in the acidic stomach environment and may cause gastrointestinal symptoms. A 65-year-old woman with a history of Helicobacter pylori gastritis and diabetes presented with abdominal pain, vomiting, diarrhea, and weight loss. Initial esophagogastroduodenoscopy revealed pyloric stenosis with thickened prepyloric gastric folds, and endoscopic biopsy revealed SV without malignancy. Owing to persistent symptoms, endoscopic ultrasound was done with repeat biopsies and was nondiagnostic. Subsequently, a robotic gastrojejunostomy was done due to persistent gastric outlet obstruction symptoms. Surgical specimens revealed signet ring cell carcinoma. This case highlights the importance of suspecting underlying malignancy in patients with SV and the necessity of comprehensive diagnostic evaluation when endoscopic findings are inconclusive.
A Severe Case of Disseminated Herpes Zoster in a Patient With Crohn's Disease on Upadacitinib Who Completed the Recombinant Zoster Vaccine Series
Authors: Lue Nicole , Burdine Lauren , Kahan Tamara , Reddy Kirthan , Nelson Ryan , Lopez Corina , Lee Matthew , Wolf Jacqueline 
Published: January 2025

ABSTRACT
Herpes zoster (HZ) is caused by the reactivation of the varicella zoster virus and presents with painful vesicular lesions in a dermatomal distribution. Disseminated HZ occurs when skin lesions erupt in numerous dermatomes. Upadacitinib is the first oral medication approved to treat moderate-severe Crohn's disease and has been associated with nonsevere cases of HZ. We present a case of a 60-year-old woman with refractory Crohn's disease who failed multiple immunosuppressive therapies, completed the recombinant zoster vaccines, and developed disseminated HZ on high-dose upadacitinib. She was treated with intravenous acyclovir, upadacitinib was discontinued, and was discharged on suppressive valacyclovir.
Pencemaran Tanah oleh Logam Berat di Kotagede, Yogyakarta
Authors: Nabila Hana Riska , Budianta Wawan 
Published: January 2025

Keberadaan industri kerajinan perak di Kotagede, Yogyakarta yang sudah berlangsung lama, menghasilkan limbah cair yang diduga telah mencemari tanah di lokasi industri dan sekitarnya. Penelitian ini dilakukan untuk menginvestigasi kandungan logam berat dalam tanah, yaitu Cu dan Pb, serta faktor penyebarannya di lokasi kerajinan perak dan sekitarnya di Kotagede, Yogyakarta. Sampel tanah diambil di lokasi penelitian, yang merupakan daerah kerajinan perak dan sekitarnya. Sebanyak 35 titik sampling diambil pada kedalaman 5 cm, 15 cm, dan 25 cm. Analisis ukuran butir, pH, kandungan organik, kandungan Cu dan Pb, dilakukan pada 105 sampel yang telah diambil serta dihitung pula untuk nilai indeks geoakumulasi. Analisis dilakukan dengan menyajikan dalam peta sebaran kandungan Cu dan Pb yang dilakukan secara spasial, maupun secara vertikal menurut kedalaman sampel, yang bertujuan untuk menganalisis penyebaran secara lateral dan vertikal. Hasil penelitian menunjukkan kandungan Cu dan Pb di dalam sampel tanah yang diambil, telah melebihi nilai latar belakang (background) namun masih berada di bawah baku mutu rujukan. Penyebaran Cu dan Pb pada tanah di lokasi penelitian dipengaruhi oleh dua faktor, yaitu faktor alamiah yaitu ukuran butir, pH serta kandungan organik dalam tanah. Sedangkan faktor manusia yang diduga berpengaruh adalah faktor kegiatan industri kerajinan perak yang menghasilkan limbah cair. Untuk faktor lainnya seperti arah aliran air permukaan dan morfologi, diduga kurang berpengaruh terhadap penyebaran Cu dan Pb pada tanah di lokasi penelitian.
Pemantauan Konsentrasi Radionuklida Cs-137, Co-60, I-131 Serta Kualitas Air Daerah Aliran Sungai Bekasi
Authors: Sukandar Dede , Amri Ghulam Fathul , Dasumiati Dasumiati , Fauzih Dewi 
Published: January 2025

Radionuklida menjadi sesuatu yang krusial untuk diketahui penyebaran, intensitas radiasi, sumber dan proses yang mempengaruhinya di dalam air. Diantara radionuklida yang menarik perhatian adalah Cs-137, Co-60, I-131. Radionuklida Cs-137 adalah unsur radioaktif yang memiliki sifat mudah terdispersi dalam badan air, sedangkan Co-60 dan I-131 banyak digunakan untuk keperluan rumah sakit khususnya radioterapi. Penelitian ini bertujuan untuk mengetahui konsentrasi radionuklida Cs-137, Co-60, I-131 serta kualitas air di Sungai Bekasi. Analisis karakteristik sifat air dari Sungai Bekasi adalah suhu, pH, dan Total Dissolved Solids (TDS), dan pemekatan. Pengukuran konsentrasi radionuklida Cs-137, Co-60, dan I-131 menggunakan instrumen spektrometer gamma. Hasil penelitian diperoleh konsentrasi radionuklida Cs-137, Co-60, dan I-131 adalah masing-masing berturut-turut: 0,00642 - 0,00428 Bq/L, 0,00713 - 0,01272 Bq/L dan 0,00077 - 0,00584 Bq/L. Konsentrasi radionuklida Cs-137, Co-60, I-131 masih berada di bawah batas aman (Cs-137 1,2 x 102 Bq/L , Co-60 1,4 x 103 Bq/L, I-131 3,0 x 105 Bq/L) yang ditetapkan oleh Peraturan Kepala BAPETEN Nomor 7 Tahun 2013. Pada penentuan kualitas air berdasarkan parameter suhu, TDS, dan pH hasil yang didapatkan masih dibawah batas aman (suhu 25-310C, TDS 1000 mg/L , pH 6-9) dalam kategori kelas II yang ditetapkan oleh Peraturan Pemerintah No 22 Tahun 2021.
Comparative analysis of fruit quality parameters and volatile compounds in commercially grown citrus cultivars
Authors: Polat Yakup , Cimen Berken , Celik Ferit , Ekşi Esra , Koc Gokmen , Ercisli Sezai , Assouguem Amine , Aberkani Kamal , Iqbal Zafar , Mehta Chandra Mohan , Kafkas Nesibe Ebru 
Published: January 2025

Abstract
This study compared key fruit quality parameters among seven commercially grown citrus cultivars (kumquat, limequat, Moro blood, Alacalı calamondin, Lem-onquat, pink lemon, Indio mandarinquat) from different species. Total phenolic content ranged from 92.37 to 550.28 mg gallic acid equivalent/g, and total antioxidant capacity varied from 65.03 to 92.74%. Sucrose was identified as the predominant sugar across all cultivars, with the highest content (63.66 g/kg) found in “Moro blood.” Citric acid was the major organic acid present in all varieties, with “Pink lemon” exhibiting the highest level (58.91 g/kg). l-Ascorbic acid, valued for its vitamin and antioxidant properties, reached its peak (1.03 g/kg FW) in the Moro blood variety. Volatile compound analysis was conducted using gas chromatography/mass spectrometry with solid-phase micro extraction (SPME) fibres (blue, red, and grey) for both fruit peel and juice. Dl-Limonene was identified as the predominant volatile compound in both peel and juice extracts across all SPME fibres used.
A study of a stochastic model and extinction phenomenon of meningitis epidemic
Authors: Yaga Samaila Jackson , Saporu Funmilayo W.O. 
Published: January 2025

Abstract

Objectives
A stochastic version of the deterministic model for meningitis epidemic by Yaga and Saporu (A study of a deterministic model for meningitis epidemic. J Epidemiol Methods 2024;13:20230023) is developed.

Method
The stochastic mean system of equations for possible state of an individual in the model and the extinction probabilities for carrier and infective are derived. Comparison of the system of stochastic mean equations and its deterministic analogue of profiles for the various compartments and the case-carrier trajectories show similar pattern with a time shift difference.

Results
This indicates that there must be caution in using the deterministic analogue as an approximating system of the stochastic mean equations for inferential purpose. Simulation studies of the comparison of the compartmental profiles for the general case; model I, with the assumption that a proportion (φ≠0), of the infected susceptible can move directly to the infective stage and that of the special case, model II, when φ=0 is examined for various values of ϵ (odds in favour of a carrier transmitting infection)

≤
2

$\le 2$

. It is only when ϵ=2 that model II can approximate model I in all compartments except that of the carrier. Transmission rate, β, loss of carriership rate, σ and ϵ are identified as the most sensitive parameters of the extinction probabilities. Threshold results derived for carrier and infective extinction probabilities are distinct but bear some relation, transmission rate required for carrier extinction is square of that for infective.

Conclusion
It is concluded that carriership play a more prominent role in the transmission of meningitis epidemic and efforts aimed at control should be targeted at reducing the transmission rate and increasing the loss of carriership.