bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drug Response Modeling across Cancers: Proteomics vs. Transcriptomics
Authors: Zheng Zetian , Huang Lei , Wang Fuzhou , Liu Linjing , Yu Jixiang , Xie Weidun , Chen Xingjian , Li Xiangtao , Wong Ka-Chun 
Published: December 2024

ABSTRACTCancer cell lines are the most commonin-vitromodels for the evaluation of anti-cancer drug sensitivities. Past studies have been conducted to decipher and characterize the pharmacogenomic feature of cell lines based on other omics data, such as genomic mutation data and whole-genome RNA sequencing (RNA-seq) profiles. In particular, proteomic data is also an essential component for the characterization of tumours. However, different from RNA-seq datasets rich in numerous transcriptome profiles of cancer cell lines and cell viability assay of drug responses, the pharmacogenomic protein quantifications are relatively scarce. With the availability of the recently enriched proteomic dataset ProCan-DepMapSanger, we systematically evaluated the interplays among genomic mutations, transcription, and protein expressions across cancer cell lines. In general, blood cancers have higher RNA-protein correlations than those in solid cancers. The differential expression analysis on protein data helped identify more expressional and functional impact of genomic mutations of cancer genes. We also integrated the proteomic map with drug molecular chemical features to construct a bi-modal machine learning model to infer the drug sensitivities of cancer cell lines. Our results demonstrated that protein quantifications can lead to better drug response prediction performance than the model trained on transcriptome profiles. In addition, integrating protein data with drug chemical features, represented as molecular graphs and learned by Graph Neural Network, outperformed the state-of-the-art model DeepOmicNet for drug response prediction in proteomics.
The evolution of pectate lyase-like genes across land plants, and their roles in haustorium formation in parasitic plants
Authors: Zhang Huiting , Wafula Eric , Kelly Elizabeth , Ko Itsuhiro , Yocca Alan , Gunathilake Pradeepa , Yang Zhenzhen , Yoder John , Honaas Loren , dePamphilis Claude 
Published: December 2024

AbstractParasitic plants in the Orobanchaceae family are noxious agricultural pests that severely impact crops worldwide. These plants acquire water and nutrients from their hosts through a specialized organ called the haustorium. A critical process in the formation and function of the haustorium involves cell wall modification. In this study, we identified and analyzed the evolutionary relationships ofpectate lyase-like(PLL) genes in parasitic plants and other major land plant lineages. One particularPLLgene, denoted asPLL1in parasitic Orobanchaceae, which our previous research identified as a potential key parasitism gene, belongs to the largest sub-clade of this gene family. To explore the role ofPLL1gene in parasitic Orobanchaceae further, we manipulated its transcript abundance during haustorium development inTriphysaria versicolor, a model species in parasitic Orobanchaceae, using both direct transformation of the parasite and host-induced-gene-silencing (HIGS). For HIGS, we generated transgenic hosts (Medicago truncatulaandArabidopsis thaliana) carrying hairpin RNAs targeting thePLLgene inT. versicolor. Our results demonstrated that both methods effectively reduced thePLL1expression in the haustorium ofT. versicolor, leading to an increase in poorly adhered parasites. These findings highlightPLL1’s crucial role in haustorium development in Orobanchaceae and may inform novel strategies towards parasitic weed management.
A randomized controlled trial comparing epinephrine and dexamethasone to placebo in the treatment of infants with bronchiolitis: the Bronchiolitis in Infants Placebo versus Epinephrine and Dexamethasone (BIPED) study protocol
Authors: Plint Amy C. , Heath Anna , Rowe Tremaine , Vogel Kristina I. , Wills-Ibarra Natasha , O’Brien Sharon , Borland Meredith L. , Johnson David W. , Zorc Joseph J. , Pechlivanoglou Petros , Schuh Suzanne , Rao Medhawani , Bonisch Megan , Craig Simon S. , Gouin Serge , Kochar Amit , Thompson Graham C. , Lash Chris , Dixon Andrew , Sawyer Scott , Joubert Gary , Oakley Ed , Offringa Martin , Klassen Terry P. , Dalziel Stuart R. 
Published: December 2024

AbstractBackgroundBronchiolitis exerts a significant burden of illness on infants worldwide predominantly due to need for hospitalization. Currently only supportive care is advised by national guidelines for infants with bronchiolitis. There is evidence that treating infants with bronchiolitis with a combination of inhaled epinephrine and dexamethasone may reduce hospital admissions. Synergy between beta-agonists and corticosteroids is recognized in asthma management and basic science literature demonstrates that co-administration of these medications enhances each other’s effectiveness.ObjectiveTo determine if infants with bronchiolitis treated with inhaled epinephrine (delivered by metered dose inhaler with spacer or nebulizer) in the emergency department and a 2-day course of oral dexamethasone have fewer hospitalizations (due to bronchiolitis) over 7 days compared to infants treated with placebo.DesignThe BIPED study (Bronchiolitis in Infants Epinephrine versus Dexamethasone and Placebo) is a randomized, placebo-controlled, observer, investigator, clinician, and patient blinded superiority clinical trial being conducted in 12 emergency departments across three countries (Canada, New Zealand, and Australia). We will recruit 864 infants between 60 days and 12 months of age with bronchiolitis to receive either (1) two inhaled epinephrine treatments (3 mg via nebulizer or 625 mcg via metered dose inhaler with spacer) 30 minutes apart and a simultaneous dose of oral dexamethasone (0.6 mg/kg, maximum 10 mg) in the emergency department with the dexamethasone repeated at 24 hours or (2) inhaled placebo and oral placebo. The primary outcome is hospital admission for bronchiolitis within 7 days (168 hours) of enrolment. Secondary outcomes include hospital admission during enrolment, and all cause hospital admissions and healthcare provider visits within 21 days of enrolment. We will use a Bayesian approach for data analysis and inference.DiscussionGiven the healthcare burden of bronchiolitis, there is urgent need for a trial to confirm if combination therapy with epinephrine and dexamethasone is effective.Trial registrationClinicalTrials.gov:NCT03567473. Registered on 2018-06-13.Protocol versionCTO 1423, dated 20 January 2023Sponsor-InvestigatorDr. Amy C Plint, Children’s Hospital of Eastern Ontario, Ottawa, Ontario, CanadaSecondary SponsorChildren’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
Transparency in epidemiological analyses of cohort data A case study of the Norwegian Mother, Father, and Child cohort study (MoBa)
Authors: Roettger Timo , Askelund Adrian Dahl , Birkenæs Viktoria , Bjørndal Ludvig Daae , Bochynska Agata , Glaser Bernt Damian , Kalandadze Tamara , Korbmacher Max , Malovic Ivana , Mayor Julien , Parekh Pravesh , Quintana Daniel S. , Hannigan Laurie J. 
Published: December 2024

AbstractBackgroundEpidemiological research is central to our understanding of health and disease. Secondary analysis of cohort data is an important tool in epidemiological research, but is vulnerable to practices that can reduce the validity and robustness of results. As such, adopting measures to increase the transparency and reproducibility of secondary data analysis is paramount to ensuring the robustness and usefulness of findings. The uptake of such practices has not yet been systematically assessed.MethodsUsing the Norwegian Mother, Father and Child Cohort study (MoBa; Magnus et al., 2006, 2016) as a case study, we assessed the prevalence of the following reproducible practices in publications between 2007-2023: preregistering secondary analyses, sharing of synthetic data, additional materials, and analysis scripts, conducting robustness checks, directly replicating previously published studies, declaring conflicts of interest and publishing publicly available versions of the paper.ResultsPreregistering secondary data analysis was only found in 0.4% of articles. No articles used synthetic data sets. Sharing practices of additional data (2.3%), additional materials (3.4%) and analysis scripts (4.2%) were rare. Several practices, including data and analysis sharing, preregistration and robustness checks became more frequent over time. Based on these assessments, we present a practical example for how researchers might improve transparency and reproducibility of their research.ConclusionsThe present assessment demonstrates that some reproducible practices are more common than others, with some practices being virtually absent. In line with a broader shift towards open science, we observed an increasing use of reproducible research practices in recent years. Nonetheless, the large amount of analytical flexibility offered by cohorts such as MoBa places additional responsibility on researchers to adopt such practices with urgency, to both ensure the robustness of their findings and earn the confidence of those using them. A particular focus in future efforts should be put on practices that help mitigating bias due to researcher degrees of freedom – namely, preregistration, transparent sharing of analysis scripts, and robustness checks. We demonstrate by example that challenges in implementing reproducible research practices in analysis of secondary cohort data - even including those associated with data sharing - can be meaningfully overcome.
Virtual Care and Medical Cannabis Access: A Geospatial Study of Telemedicine’s Role in Reducing Socioeconomic Disparities
Authors: Doucette Mitchell L. , Fisher Emily , Hemraj Dipak , Kasabuski Mark , Chin Junella 
Published: December 2024

AbstractIntroductionTelemedicine has the potential to improve healthcare access and reduce disparities. We examined whether the incidence rate of medical cannabis patients (MC) was associated with concentrated disadvantage in Pennsylvania in 2022, accounting for a population of patients approved through telemedicine.MethodsThis zip code-level analysis examined associations between the Concentrated Disadvantage Index (CDI) and two outcomes: (1) the number of telemedicine-approved MC patients, as obtained from a specific telemedicine provider, and (2) the number of all other MC patients, calculated by subtracting the number of telemedicine-approved patients from the total number of MC patients at the zip code-level. Total counts of MC patients and in-office MC providers for Pennsylvania were sourced from the Pennsylvania Department of Health, while CDI data were derived from the 2022 American Community Survey. We used multivariate negative binomial regression models with population offsets and robust standard errors, adjusting for spatial autocorrelation through spatial lag adjustments.ResultsThe CDI was not associated with the incidence rate of telemedicine-approved MC patients (IRR = 0.962;p= 0.355), but it was significantly negatively associated with the incidence rate of all other MC patients (IRR = 0.904;p= 0.000). The density of in-office MC providers was significantly associated with the incidence rate of all other MC patients but not with telemedicine-approved patients. Spatial factors, including autocorrelation, significantly influenced the distribution of both groups of patients.DiscussionThese findings suggest that telemedicine plays a crucial role in improving access to MC for socioeconomically disadvantaged areas. The lack of a significant association between the CDI and telemedicine-approved MC patients highlights the ability of telemedicine to bypass barriers such as provider scarcity and transportation challenges. By facilitating remote consultations and approvals, telemedicine ensures access for patients who might otherwise face difficulties obtaining MC.
Carbapenem Stewardship Program in a Cardiovascular Hospital in Tehran, Iran and Literature Review
Authors: Nazari Elham , Roumi Azin , Kamali Monireh , Sabooteh Toomaj 
Published: December 2024

ABSTRACTIntroductionHealthcare-associated infections (HAIs) and antimicrobial resistance (AMR) are critical global challenges. Antimicrobial Stewardship Programs (ASPs) aim to optimize antibiotic use and reduce resistance. This study evaluates carbapenem stewardship compliance in open-heart surgery patients at Shaheed Rajaie Cardiovascular Medical and Research Center, Tehran, emphasizing improved infection control and antibiotic management.MethodologyThis descriptive, cross-sectional study assessed carbapenem antibiotic use compliance with national guidelines in open-heart surgery patients at Shaheed Rajaie Cardiovascular Medical Center, Tehran. Seventy patients were selected, and data on demographics, clinical factors, microbiology, and antibiotic use were analyzed using SPSS 26 to evaluate compliance rates and prescribing factors.ResultsThis study analyzed data from 70 patients undergoing open-heart surgery at a cardiovascular hospital in Tehran. The cohort had an equal gender distribution and a mean age of 59.15 years (SD: 12.0). Of the procedures, 51.43% were elective, while 48.57% were emergencies. The most common surgeries included CABG (45.71%) and valvular procedures (30%). Meropenem was the most prescribed antibiotic (92.9%), with prophylactic use noted in 78.57% intraoperatively. Positive cultures identified Candida albicans (32.7%), Klebsiella pneumoniae (29.8%), and Staphylococcus aureus (22.6%) as predominant pathogens. Serum creatinine levels exceeded the normal range in 55.7% of patients, necessitating dosage adjustments. Antibiotic side effects led to treatment discontinuation in 15.7% of cases.ConclusionThis study highlights a high level of rational carbapenem use in a specialized cardiac surgery ICU, with prescribing guided by infectious disease consultations and adherence to guidelines. Implementing antibiotic stewardship programs can further optimize carbapenem use, reduce antibiotic resistance, and improve treatment outcomes, emphasizing the importance of individualized infection management and monitoring in cardiac surgery patients.
Increased risk of asthma in female night shift workers
Authors: Maidstone Robert J. , Ray David W. , Liu Junxi , Bowden Jack , Rutter Martin K. , Durrington Hannah J. 
Published: December 2024

AbstractBackgroundAsthma is more common in females and more common in night shift workers. Since increasing numbers of females are becoming shift workers it is important to determine if shift work-associated asthma risk is higher in females.Research QuestionIs increasing frequency of night shift work more strongly related to prevalent asthma in females than in males?Study Design and MethodsWe used cross-sectional data from >280,000 UK Biobank participants and logistic regression models adjusted for demographic and lifestyle factors to describe sex differences in prevalent asthma related to shift work frequency. To obtain mechanistic insights, we explored associations with chronotype, sex hormones and menopause.ResultsCompared to female day workers, female permanent night shift workers had higher covariate-adjusted odds of moderate-severe asthma (OR: 1.50 (95% CI 1.18 – 1.91)) but there was no corresponding relationship in males (OR 0.95 (95% CI 0.72 – 1.26); sex interaction p-value = 0.01). Similar relationships were observed for ‘all asthma’ and for ‘wheeze or whistling in the chest’ outcomes. Female shift work-related asthma was driven by relationships in postmenopausal women not using HRT (e.g., adjusted OR: 1.89 (1.24-2.87) for moderate-severe asthma; sex interaction p-value = 0.02 in permanent nightshift workers compared to dayworkers) but these relationships attenuated to the null in postmenopausal women using HRT.InterpretationOur finding that increasing shift work frequency is more strongly related to asthma in females than in males could have Public Health implications. Intervention studies should determine if modifying shift work schedules or HRT can reduce asthma risk in females.
The diagnostic value of hyperlipidemia and lipophagy-related genes, PLAUR, IVNS1ABP, and QKI, in acute myocardial infarction
Authors: Zou Jun-Hua , Wang Hua-Wei , Long Jia-Zhi , Yang Xiao-Na , Yang Li-Hong , Li Long-Jun , Chen Li-Xing , Dong Ling , Chen Jing , Meng Zhao-Hui , Wan Wen 
Published: December 2024

AbstractBackgroundHyperlipidemia (HLP) may intensify myocardial cell damage by disrupting lipophagy, a pivotal lipid metabolism pathway, thereby heightening the risk of acute myocardial infarction (AMI). This study aims to identify HLP- and lipophagy-associated biomarkers for AMI through a combined transcriptomic and mendelian randomization (MR) approach.MethodsThe mRNA expression data for AMI, along with HLP-related genes (HRGs) and lipophagy-related genes (LRGs), were sourced from public databases. Biomarkers were identified by conducting differential expression analysis, weighted gene co-expression network analysis (WGCNA), MR analysis, and receiver operating characteristic (ROC) analysis, complemented by two machine learning algorithms and expression validation. These biomarkers facilitated an investigation into the role of platelet activation-related genes (PARGs) in AMI, with enrichment analysis providing insights into their underlying mechanisms. Finally, reverse transcription quantitative polymerase chain reaction (RT-qPCR) was employed to validate biomarker expression in clinical samples.ResultsThree biomarkers exhibited a consistently significant upregulation trend in AMI samples, corroborated by RT-qPCR findings. Notably, PLAUR [Odds ratio (OR) = 1.115, 95% confidence interval (CI): 1.006–1.237,P= 0.038] and IVNS1ABP (OR = 1.047, 95% CI: 1.000–1.096,P= 0.048) emerged as AMI risk factors, while QKI (OR = 0.946, 95% CI: 0.903– 0.991,P= 0.020) was identified as a protective factor. Additionally, PLAUR, QKI, and IVNS1ABP demonstrated robust diagnostic efficacy with area under the curve (AUC) values of 0.773, 0.933, and 0.807, respectively; when integrated into a nomogram, the combined AUC reached 0.924. These genes were enriched in pathways linked to cardiovascular diseases, inflammatory responses, and cellular metabolic processes and appeared actively involved in platelet activation, as indicated by their strong associations with PARGs.ConclusionIn summary, the biomarkers PLAUR, QKI, and IVNS1ABP, connected to HLP and lipophagy, showed a causal relationship with AMI and marked diagnostic potential for predicting AMI risk, offering valuable support for clinical diagnostics and AMI research.
Occupational Exposures to Blood and other Body Fluids among Healthcare Workers in Cameroon: A Systematic Review and Meta-analysis
Authors: Cheuyem Fabrice Zobel Lekeumo , Mouangue Christian , Ajong Brian Ngongheh , Edzamba Michel Franck , Hamadama Dilane Christian Maidey , Achangwa Chabeja , Mohamadou Adama , Sonfack Pamela , Amani Adidja 
Published: December 2024

AbstractBackgroundOccupational exposure to blood and body fluids has become a serious public health problem for healthcare workers and is a major risk for the transmission of bloodborne infections such as human immune-deficiency, hepatitis B, and hepatitis C viruses. It has been identified as one of the most serious issues affecting the health and well-being of health workers in most health systems especially in developing countries. The present systematic review and meta-analysis was conducted to estimate the pooled prevalence of blood and other body fluids exposures among healthcare workers in Cameroon.MethodsOnline platform including PubMed, Google Scholar, Cochrane Library, and Science Direct were systematically searched to collect relevant research reports. Unpublished studies in a national library were also consulted. TheI2tests were used to assess the heterogeneity of the included studies. A fixed and random-effects meta-analysis model was used to estimate the lifetime and 12-month prevalence of occupational exposure to blood and other body fluids among healthcare workers in Cameroon.ResultsOf the 539 records identified through the database search, 15 study reports were included in the final analysis. The random-effects model showed that the estimated overall pooled prevalence of 12-month and lifetime exposure to blood and other body fluids among healthcare workers in Cameroon was 55.44% (95% Confidence Interval (CI): 41.20-69.68); (I2=97.5%;p<0.001) and 57.27% (95% CI: 42.43-72.10); (I2=97.7%;p<0.001) respectively. The highest 12-month pooled prevalence was observed in intermediate level health facilities (84.73%; 95% CI: 85.55-88.50), in Regions other than the Centre (70.87%; 95% CI: 37.26-95.13) and for studies conducted from 2017 to 2023 (65.63%; 95% CI: 45.73-83.06). The lifetime prevalence of blood and other body fluids exposures was the highest for Regions namely the North-west and South-west Regions (77.96%; 95% CI: 57.39-93.19).ConclusionHealthcare workers in Cameroon face a significant risk of occupational exposure to blood and body fluids (BBFs), with a high prevalence of exposure over their lifetime and in the past 12 months. This highlights the urgent need to enhance and implement effective occupational safety and health policies to protect healthcare workers in Cameroon.
School bullying and its association with psychological wellbeing: findings of the Fujian Adolescent Mental Wellness Study (FAMWeS)
Authors: Jiang Jian , Luo Zhijie , Chen Yuhang , Alias Haridah , Wong Li Ping , Lin Yulan , Hu Zhijian 
Published: December 2024

AbstractBackgroundSchool bullying is becoming a prevalent phenomenon in China, posing a growing threat to the psychological well-being of children and adolescents. This study aims to examine bullying victimization and bullying behavior using data from FAMWeS (the Fujian Adolescent Mental Wellness Study), and how they impact emotional state and psychological distress.MethodThe study conducted in entire Fujian Province, China, involved a cross-sectional questionnaire survey on adolescent students from secondary and high schools, employing multi-stage stratified cluster sampling methods from May to July 2023. Primary outcome measures were bullying victimization and bullying behavior. Emotional state was evaluated using the Depression, Anxiety, and Stress Scale for Youth (DASS-Y), and psychological distress was assessed using the General Health Questionnaire-12 (GHQ-12).ResultsAnalysis of 54,368 responses revealed that 19.3% of respondents reported being victims of bullying, 9.8% reported engaging in bullying behavior, and 8.1% reported experiencing both bullying victimization and engaging in bullying themselves. A minority were found to have depressive (19.1%), anxiety (22.0%), and stress (9.2%) symptoms. The presence of psychological distress was observed in 54.4% of the participants (GHQ score of 3-12). Significant associations were found between bullying victimization and the DASS-Y subscales of depression, anxiety, and stress. Odds ratios indicated a 1.75 times higher likelihood for depression (OR 1.75, 95% CI 1.55-1.99), 2.24 times higher for anxiety (OR 2.24, 95% CI 1.96-2.55), and 1.82 times higher for stress (OR 1.82, 95% CI 1.73-1.91). Similarly, psychological distress measured by the GHQ was significantly associated with bullying victimization (OR 1.82, 95% CI 1.73-1.91). Bullying behavior also showed significant associations with all DASS-Y subscales and psychological distress. Geographic disparities revealed varying rates across districts, while factors such as age, academic performance, and parental education emerged as significant influences on bullying victimization and behavior.ConclusionThe findings underscore a concerning prevalence of bullying victimization and behavior, highlighting the critical need for comprehensive anti-bullying strategies that address both victimization and perpetration dynamics. There is also a clear need for interventions targeting socio-economic disparities across various geographic regions.