bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Immunohistochemical Expression of Heparanase in Helicobacter pylori-Associated Chronic Gastritis
Authors: Ahmed Sheren Farrag Mahmoud , Abdelrahman Mona Mohammed , Mohammed Maisa Hashem 
Published: August 2023

Background: Chronic gastritis (CG) is a very common disease. More than half of the worldwide population suffers from symptoms of CG. This disease has received great attention since the discovery of H. pylori as the most important cause of CG. Symptoms experienced by patients with CG are attributed to H. pylori-induced inflammatory reactions. Heparanase (HPSE) is a mammalian β-endoglucoronidase. In inflammation; HPSE degrades and remodels the extracellular matrix’s heparan sulfate polysaccharide chains liberating heparan sulfate-bound cytokines and chemokines, HPSE also facilitates movement of inflammatory cells. Aims: This study aimed to detect the function of HPSE in CG by correlating levels of HPSE expression with histopathological features of CG, including H. pylori infection, acute and chronic inflammatory cells, mucosal atrophic and/or metaplastic features. Methods: Ninety-five upper endoscopic-guided gastric punch biopsies were enrolled in this study. From each specimen, formalin-fixed and paraffin-embedded tissue blocks were prepared. Tissue sections were stained by Hematoxylin and eosin, Giemsa, and anti-heparanase antibody. Results: HPSE expression was statistically associated with H. pylori infection ( P-value < .000), and intensity of chronic lymphocytic inflammatory infiltrate in the gastric mucosal tissues ( P = .004). High levels of HPSE expression were also related to the presence of neutrophils in the gastric surface epithelium and lamina propria ( P-value < .009). Conclusions: HPSE expression was upregulated in H. pylori-associated chronic gastritis. Thus, future therapeutic agents that could specifically inhibit HPSE enzyme activity, may aid in the reduction of sequelae of H. pylori infection.
Changes of migraine aura with advancing age of patients
Authors: Scutelnic Adrian , Drangova Hristina , Klein Antonia , Slavova Nedelina , Beyeler Morin , Lippert Julian , Silimon Norbert , Meinel Thomas R. , Arnold Marcel , Fischer Urs , Riederer Franz , Mattle Heinrich P. , Jung Simon , Schankin Christoph J. 
Published: August 2023

Abstract
Aim
Given the similar presentation of migraine aura and acute ischemic stroke, advancing patient age might change the characteristics of migraine with aura (MA) and be clinically important. Clinical data, however, are limited. Experimental studies indicate a decrease in the magnitude of cortical spreading depression (CSD), the pathophysiological correlate of migraine aura, with advancing age. Our study aimed to assess the influence of age on the clinical features of MA.

Methods
Three hundred and forty-three patients were interviewed using a structured questionnaire. The questions covered the headache characteristics and symptom types including the characteristics of the C-criterion, as defined by the International Classification of Headache Disorders 3rd Edition. The association of age with MA characteristics was assessed.

Results
The median age was 29 (IQR 28–52) and 235 of the 343 patients were women (69%). Individual symptoms of the C-criterion such as gradual aura spreading over longer than 5 min (P < 0.001), two or more aura symptoms occurring in succession (P = 0.005), duration of at least one MA symptom for longer than 60 min (P = 0.004), and associated headache (P = 0.01) were more frequent in younger patients. The number of symptoms (P = 0.003) including the C-characteristics decreased with increasing age (P < 0.027). Patients with sensory (P < 0.001), motor (P = 0.04) and speech disturbance (P = 0.02) were younger, and older patients with headache had less photophobia (P = 0.04) and phonophobia (P = 0.03). Sensitivity analyses yielded similar results.

Conclusion
The frequency of typical characteristics of migraine aura and migraine headache including photophobia and phonophobia decreases with advancing patient age. This might have potentially difficult implications for the diagnosis of MA in the elderly.
VariantscanR: an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals
Authors: Boeykens Fréderique , Bhatti Sofie F. M. , Peelman Luc , Broeckx Bart J. G. 
Published: August 2023

Abstract
Background
Since the introduction of next-generation sequencing (NGS) techniques, whole-exome sequencing (WES) and whole-genome sequencing (WGS) have not only revolutionized research, but also diagnostics. The gradual switch from single gene testing to WES and WGS required a different set of skills, given the amount and type of data generated, while the demand for standardization remained. However, most of the tools currently available are solely applicable for human analysis because they require access to specific databases and/or simply do not support other species. Additionally, a complicating factor in clinical genetics in animals is that genetic diversity is often dangerously low due to the breeding history. Combined, there is a clear need for an easy-to-use, flexible tool that allows standardized data processing and preferably, monitoring of genetic diversity as well. To fill these gaps, we developed the R-package variantscanR that allows an easy and straightforward identification and prioritization of known phenotype-associated variants identified in dogs and other domestic animals.

Results
The R-package variantscanR enables the filtering of variant call format (VCF) files for the presence of known phenotype-associated variants and allows for the estimation of genetic diversity using multi-sample VCF files. Next to this, additional functions are available for the quality control and processing of user-defined input files to make the workflow as easy and straightforward as possible. This user-friendly approach enables the standardisation of complex data analysis in clinical settings.

Conclusion
We developed an R-package for the identification of known phenotype-associated variants and calculation of genetic diversity.
Drivers of plateau adaptability in cashmere goats revealed by genomic and transcriptomic analyses
Authors: Wu Cuiling , Ma Shengchao , Zhao Bingru , Qin Chongkai , Wu Yujiang , Di Jiang , Suo Langda , Fu Xuefeng 
Published: August 2023

Abstract
Background
The adaptive evolution of plateau indigenous animals is a current research focus. However, phenotypic adaptation is complex and may involve the interactions between multiple genes or pathways, many of which remain unclear. As a kind of livestock with important economic value, cashmere goat has a high ability of plateau adaptation, which provides us with good materials for studying the molecular regulation mechanism of animal plateau adaptation.

Results
In this study, 32 Jiangnan (J) and 32 Tibetan (T) cashmere goats were sequenced at an average of 10. Phylogenetic, population structure, and linkage disequilibrium analyses showed that natural selection or domestication has resulted in obvious differences in genome structure between the two breeds. Subsequently, 553 J vs. T and 608 T vs. J potential selected genes (PSGs) were screened. These PSGs showed potential relationships with various phenotypes, including myocardial development and activity (LOC106502520, ATP2A2, LOC102181869, LOC106502520, MYL2, ISL1, and LOC102181869 genes), pigmentation (MITF and KITLG genes), hair follicles/hair growth (YAP1, POGLUT1, AAK1, HES1, WNT1, PRKAA1, TNKS, WNT5A, VAX2, RSPO4, CSNK1G1, PHLPP2, CHRM2, PDGFRB, PRKAA1, MAP2K1, IRS1, LPAR1, PTEN, PRLR, IBSP, CCNE2, CHAD, ITGB7, TEK, JAK2, and FGF21 genes), and carcinogenesis (UBE2R2, PIGU, DIABLO, NOL4L, STK3, MAP4, ADGRG1, CDC25A, DSG3, LEPR, PRKAA1, IKBKB, and ABCG2 genes). Phenotypic analysis showed that Tibetan cashmere goats has finer cashmere than Jiangnan cashmere goats, which may allow cashmere goats to better adapt to the cold environment in the Tibetan plateau. Meanwhile, KRTs and KAPs expression in Jiangnan cashmere goat skin was significantly lower than in Tibetan cashmere goat.

Conclusions
The mutations in these PSGs maybe closely related to the plateau adaptation ability of cashmere goats. In addition, the expression differences of KRTs and KAPs may directly determine phenotypic differences in cashmere fineness between the two breeds. In conclusion, this study provide a reference for further studying plateau adaptive mechanism in animals and goat breeding.
Analytical method for detecting outlier evaluators
Authors: Wu Yujie , Curhan Sharon , Rosner Bernard , Curhan Gary , Wang Molin 
Published: August 2023

AbstractBackgroundEpidemiologic and medical studies often rely on evaluators to obtain measurements of exposures or outcomes for study participants, and valid estimates of associations depends on the quality of data. Even though statistical methods have been proposed to adjust for measurement errors, they often rely on unverifiable assumptions and could lead to biased estimates if those assumptions are violated. Therefore, methods for detecting potential ‘outlier’ evaluators are needed to improve data quality during data collection stage.MethodsIn this paper, we propose a two-stage algorithm to detect ‘outlier’ evaluators whose evaluation results tend to be higher or lower than their counterparts. In the first stage, evaluators’ effects are obtained by fitting a regression model. In the second stage, hypothesis tests are performed to detect ‘outlier’ evaluators, where we consider both the power of each hypothesis test and the false discovery rate (FDR) among all tests. We conduct an extensive simulation study to evaluate the proposed method, and illustrate the method by detecting potential ‘outlier’ audiologists in the data collection stage for the Audiology Assessment Arm of the Conservation of Hearing Study, an epidemiologic study for examining risk factors of hearing loss in the Nurses’ Health Study II.ResultsOur simulation study shows that our method not only can detect true ‘outlier’ evaluators, but also is less likely to falsely reject true ‘normal’ evaluators.ConclusionsOur two-stage ‘outlier’ detection algorithm is a flexible approach that can effectively detect ‘outlier’ evaluators, and thus data quality can be improved during data collection stage.
Key outcomes for reporting in studies of pregnant women with multiple long-term conditions: a qualitative study
Authors: Lee Siang Ing , Hanley Stephanie , Vowles Zoe , Plachcinski Rachel , Azcoaga-Lorenzo Amaya , Taylor Beck , Nelson-Piercy Catherine , McCowan Colin , O’Reilly Dermot , Hope Holly , Abel Kathryn M. , Eastwood Kelly-Ann , Locock Louise , Singh Megha , Moss Ngawai , Brophy Sinead , Nirantharakumar Krishnarajah , Thangaratinam Shakila , Black Mairead 
Published: August 2023

Abstract
Background
Maternal multiple long-term conditions are associated with adverse outcomes for mother and child. We conducted a qualitative study to inform a core outcome set for studies of pregnant women with multiple long-term conditions.

Methods
Women with two or more pre-existing long-term physical or mental health conditions, who had been pregnant in the last five years or planning a pregnancy, their partners and health care professionals were eligible. Recruitment was through social media, patients and health care professionals’ organisations and personal contacts. Participants who contacted the study team were purposively sampled for maximum variation. Three virtual focus groups were conducted from December 2021 to March 2022 in the United Kingdom: (i) health care professionals (n = 8), (ii) women with multiple long-term conditions (n = 6), and (iii) women with multiple long-term conditions (n = 6) and partners (n = 2). There was representation from women with 20 different physical health conditions and four mental health conditions; health care professionals from obstetrics, obstetric/maternal medicine, midwifery, neonatology, perinatal psychiatry, and general practice. Participants were asked what outcomes should be reported in all studies of pregnant women with multiple long-term conditions. Inductive thematic analysis was conducted. Outcomes identified in the focus groups were mapped to those identified in a systematic literature search in the core outcome set development.

Results
The focus groups identified 63 outcomes, including maternal (n = 43), children’s (n = 16) and health care utilisation (n = 4) outcomes. Twenty-eight outcomes were new when mapped to the systematic literature search. Outcomes considered important were generally similar across stakeholder groups. Women emphasised outcomes related to care processes, such as information sharing when transitioning between health care teams and stages of pregnancy (continuity of care). Both women and partners wanted to be involved in care decisions and to feel informed of the risks to the pregnancy and baby. Health care professionals additionally prioritised non-clinical outcomes, including quality of life and financial implications for the women; and longer-term outcomes, such as children’s developmental outcomes.

Conclusions
The findings will inform the design of a core outcome set. Participants’ experiences provided useful insights of how maternity care for pregnant women with multiple long-term conditions can be improved.
Rational application of EGFR-TKI adjuvant therapy in patients with completely resected stage IB-IIIA EGFR-mutant NSCLC: a systematic review and meta-analysis of 11 randomized controlled trials
Authors: Zhang Shu-Ling , Yi Xiao-Fang , Huang Le-Tian , Sun Li , Ma Jie-Tao , Han Cheng-Bo 
Published: August 2023

Abstract
Purpose
To determine the role and rational application of epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) adjuvant therapy in patients with completely resected stage IB-IIIA EGFR-mutant non-small-cell lung cancer (NSCLC).

Method
Randomized controlled trials (RCTs) that compared the survival outcomes between adjuvant EGFR-TKIs and adjuvant chemotherapy or a placebo, or between different EGFR-TKI treatment durations for resected NSCLC, were eligible for inclusion. Disease-free survival (DFS) and overall survival (OS) with hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated as effective measures using random-effect or fixed-effect models. Subgroup analysis was also performed.

Results
Eleven RCTs involving 2102 EGFR-mutant NSCLC patients with or without EGFR-TKI adjuvant therapy were included. For all stage IB-IIIA NSCLC patients, EGFR-TKIs adjuvant therapy could not only significantly improve DFS (HR 0.43, 95% CI 0.30–0.63, P < 0.001) and 2- and 3-year DFS rates, but also improve OS (HR 0.72, 95% CI, 0.54–0.96, P = 0.024), compared with chemotherapy or the placebo. Further subgroup analyses indicated prolonged OS from first-generation EGFR-TKI adjuvant therapy in stage III patients, compared with chemotherapy or the placebo (HR for OS, 0.34; 95% CI, 0.18–0.63; P = 0.001). Of note, osimertinib adjuvant therapy led to the OS benefit expanding from stage III to stage II-III patients, with significantly improved DFS and a lower risk of brain recurrence, compared with the placebo. A 2-year treatment duration with EGFR-TKI adjuvant therapy showed a significantly lower recurrence risk than a ≤ 1-year duration.

Conclusion
The DFS advantage from first-generation EGFR-TKI adjuvant therapy can translate into an OS benefit in stage III NSCLC patients. Osimertinib might be more suitable for adjuvant therapy than first-generation EGFR-TKIs, because of the lower recurrence rate and the potential OS benefit even in early-stage patients. The optimal treatment duration for EGFR-TKIs at different stages of disease needs to be validated.
Prevalence and correlates of alcohol use and risky drinking among undergraduate students in Johannesburg, South Africa: a cross-sectional study
Authors: Chen Cassandra , Mpinganjira Mafuno G , Motilal Asha , Matukane Sandile , Letsoalo Relebohile , McKee Tyler , Ntombela Zakithi , Mbulaheni Limuwani , Hargovan Taveer , Francis Joel M 
Published: August 2023

Abstract
Background
Alcohol use and risky drinking are significant public health problem globally. Young people, including university students, are among the most affected populations. We conducted the study to determine the prevalence and correlates of alcohol use and risky drinking among undergraduate students in the Faculty of Health Sciences at the University of the Witwatersrand, South Africa.

Methods
We conducted a cross-sectional study using an anonymous, self-administered online survey in REDCap. The survey questionnaire consisted of socio demographic, and alcohol use questions using the risky drinking identification screening tool (AUDIT-C). We performed descriptive statistics, bivariate and multivariable logistic regression to determine factors associated with alcohol use and risky drinking. The p-value of < 0.05 was considered statistically significant.

Results
The response rate was 15.7%. Most participants were female (69.6%) and majority of the participants were White (38.1%). The prevalence of lifetime use of alcohol was 79.1%, and among the lifetime users; 70.2% reported alcohol use in the last 12-months, 37.1% reported alcohol use in the last 30 days. The prevalence of risky drinking was 54.8% among lifetime drinkers. Factors significantly associated with current alcohol use were siblings alcohol use (aOR = 1.79, 95% CI: 1.02–3.15) and parents alcohol use (aOR = 2.58, 95% CI: 1.39–4.80), white race (aOR = 5.70, 95% CI: 3.12–10.41), and always or daily exposure to alcohol marketing in the media (aOR = 3.31, 95% CI: 1.07–10.24). Factors associated with risky drinking were: Indian/Asian race (aOR = 2.82, 95% CI: 1.09–7.31), White race (aOR = 2.15, 95% CI: 1.14–4.04), and exposure to alcohol marketing in the media as follows, most of the time (aOR = 3.42, 95% CI: 1.29–9.04) and Always/daily exposure (aOR = 3.31, 95% CI: 1.07–10.24).

Conclusion
The reported alcohol use and risky drinking were common amongst undergraduate students at Wits university. There is an urgent need to design, pilot and adapt targeted interventions for this population group.
Self-rated health and quality of life in female sex workers with substance use disorders in Tehran, Iran
Authors: Khoei Effat Merghati , Rezaei Zahed , Parvari Arash , Korte Jeffrey E. 
Published: August 2023

Abstract
Background
While self-rated health (SRH) and quality of life (QoL) has been associated with substance use disorders (SUDs) in sex-working populations, little is known about this association in Iran. This study aimed to assess QoL and SRH in Iranian female sex workers (FSWs) in Tehran.

Method
FSWs were recruited using convenience sampling methods from substance abuse treatment centers in Tehran that exclusively provided services for women. Participants completed an interviewer-administered demographic questionnaire in Persian and the Iranian version of the Short Form Health Survey (SF-36). Descriptive analyses, means and standard deviations; frequency and percentages, t-test and one-way ANOVA, and Chi-square tests were utilized to analyze the data.

Results
The mean age among 161 participants clinically diagnosed with SUD was 34.09 years (SD 7.97; range: 18–57). The total mean QoL score was 41.03 (SD: 12.92). The highest and lowest mean scores were observed in the physical functioning (52.23) and role emotional (26.64) dimensions, respectively. Significant differences (p < 0.05) in QoL were observed according to education and marital status, and the average QoL score was lower in women who reported permanent marriages and women who were illiterate. The average score of QoL was significantly higher in employed women. Overall, 51.6% of the women rated their health as sub-optimal, with divorced participants and women who were illiterate more likely to rate their health as sub-optimal (p < 0.05).

Conclusion
Results emphasize the need for mental, physical, and sexual health screening and gender-specific interventions to improve QoL in this population. Further investigation may elucidate the consequences of poor SRH and QoL on SUD treatment adherence, sexual risk behavior, and morbidity and mortality in FSWs.
Design and evaluation of a Mobile-Based decision support system to enhance lung transplant candidate assessment and management: knowledge translation integrated with clinical workflow
Authors: Abtahi Hamidreza , Shahmoradi Leila , Amini Shahideh , Gholamzadeh Marsa 
Published: August 2023

Abstract
Background
Accurate and timely decision-making in lung transplantation (LTx) programs is critical. The main objective of this study was to develop a mobile-based evidence-based clinical decision support system (CDSS) to enhance the management of lung transplant candidates.

Method
An iterative participatory software development process was employed to develop the ImamLTx CDSS. This study was accomplished in three phases. First, required data and standard clinical workflow were identified according to the literature review and expert consensus. Second, a rule-based knowledge-based CDSS application was developed. In the third phase, this CDSS was evaluated. The evaluation was done using the standard Post-Study System Usability Questionnaire (PSSUQ 18.3) and ten usability heuristics factors for user interface design.

Results
According to expert consensus, fifty-five data items were identified as essential data sets using the Content Validity Ratio (CVR) formula. By integrating information flow in clinical practices with clinical protocols, more than 450 rules and 500 knowledge statements were extracted. This CDSS provides clinical decision support on an Android platform regarding inclusion and exclusion referral criteria, optimum transplant time based on the type of lung disease, findings of initial assessment, and the overall evaluation of lung transplant candidates. Evaluation results showed high usability ratings due to the fact provided accuracy and sensitivity of this lung transplant CDSS with the information quality domain receiving the highest score (6.305 from 7).

Conclusion
Through a stepwise approach, the ImamLTx CDSS was developed to provide LTx programs with timely patient data access via a mobile platform. Our results suggest integration with existing workflow to support clinical decision-making and provide patient-specific recommendations.