bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors associated with severe pneumonia among children <5 years, Kasese District, Uganda: a case-control study, January–April 2023
Authors: Wanyana Mercy Wendy , Migisha Richard , King Patrick , Muhesi Abraham Kibaba , Kwesiga Benon , Kadobera Daniel , Bulage Lilian , Ario Alex Riolexus 
Published: July 2024

Abstract
Background
Pneumonia is one of the leading causes of infant mortality globally, particularly in sub-Saharan Africa. In Uganda, pneumonia was the fourth leading cause of death in children <5 years in 2018. Analysis of 2013–2022 data for children <5 years from the District Health Information System indicated a high incidence of severe pneumonia in Kasese District, Uganda. We investigated to identify factors associated with severe pneumonia among children <5 years in Kasese District to inform prevention and control strategies.

Methods
We conducted a 1:1 hospital-based case-control study among children aged 2–59 months presenting with pneumonia at five high-volume facilities in Kasese District from January to April 2023. A case was defined as pneumonia with ≥1 of the following danger signs: low oxygen saturation, central cyanosis, severe respiratory distress, feeding difficulties, altered consciousness, and convulsions. Controls were outpatient children aged 2–59 months with a diagnosis of non-severe pneumonia. We reviewed medical records at facilities and used an interviewer-administered questionnaire with caregivers to obtain information on socio-demographic and clinical characteristics. Logistic regression was used to identify factors associated with severe pneumonia.

Results
We enrolled 199 cases and 174 controls. The odds of severe pneumonia were higher among children with diarrhoea only (adjusted odds ratio [aOR] = 2.9, 95%CI: 1.7–4.9), or malaria and diarrhoea (aOR = 3.4, 95%CI: 2.0-5.9), than those without a co-existing illness at the time of pneumonia diagnosis. Not being exclusively breastfed for ≥ 6 months (aOR = 2.0, 95%CI: 1.1–3.3) and exposure to indoor air pollution from cooking combustion sources (aOR = 2.9, 95%CI: 1.8–4.7) increased odds of severe pneumonia.

Conclusion
The findings highlight the significance of comorbidities, lack of exclusive breastfeeding, and exposure to indoor air pollution in the development of severe pneumonia. Promoting exclusive breastfeeding for ≥ 6 months and advocating for the use of clean energy sources, could mitigate morbidity attributable to severe pneumonia in the region.
Endovascular thrombectomy in patients with anterior circulation stroke: an emulated real-world comparison
Authors: Sembill Jochen A. , Sprügel Maximilian I. , Haupenthal David , Kremer Svenja , Knott Michael , Mühlen Iris , Kallmünzer Bernd , Kuramatsu Joji B. 
Published: July 2024

Abstract
Background
Endovascular thrombectomy (EVT) has been proven effective in anterior circulation stroke due to large vessel occlusion (LVO). However, translation from randomized clinical trials (RCTs) with highly selected patients to real-world requires confirmation, particularly to identify associations outside of strict selection criteria.

Aims
This study aims to compare functional outcomes after EVT in real-world with those reported in RCTs, and to identify associations with functional outcome after EVT outside RCT-criteria.

Methods
This study analyzed longitudinal German real-world data from the Stroke Research Consortium in Northern Bavaria (STAMINA) cohort from January, 2015 to June, 2019. We conducted a trial emulation, comparing patients with anterior circulation stroke and LVO meeting selection criteria for RCTs investigating EVT (1) predominantly within 6 hours with those from HERMES meta-analysis, and (2) within 6-24 hours with those from AURORA meta-analysis. We (3) analyzed treatment effects of EVT and association with functional outcome in patients treated outside RCT criteria.

Results
Of 598 patients, 281 (47.0%) met RCT-criteria for treatment within 6 hours (hereinafter STAMINA-HERMES), 74 (12.4%) met RCT-criteria for treatment within 6–24 hours (STAMINA-AURORA), and 277 (46.3%) patients received EVT outside RCT-criteria. We observed no difference in rates of functional independence or mortality, comparing STAMINA-HERMES with HERMES meta-analysis (mRS 0-1: n=120/281 [43%] vs. 291/633 [46%], p=0.36; mortality: n=34/281 [12%] vs. 97/633 [15%], p=0.20), and STAMINA-AURORA with AURORA meta-analysis (mRS 0-1: n=26/74 [35%] vs. 122/266 [46%], p=0.10, mortality: n=10/74 [14%] vs. 45/266 [17%], p=0.48). Patients treated outside RCT-criteria had worse outcome (mRS 0-1: n=38/277 [14%], mortality: n=90/277 [32%], both p<0.001); possibly driven by pre-existing functional dependence (n=172/277 [62%]). Compared to matched controls, EVT outside of RCT-criteria was associated with lower mortality (absolute treatment effect: -14%, 95% Confidence Interval [CI] -23 to -5, p<0.01), but not with recovery to functional independence or premorbid functional status (treatment effect: 4%, CI -4 to 11, p=0.34), which was associated with lower NIHSS (Odds ratio [OR] 0.86, CI 0.80-0.92, p<0.001) and age (OR 0.95, CI 0.93-0.98, p=0.002).

Conclusions
Translation of EVT outcomes reported in RCTs into real-world is possible, however, almost half of patients did not meet trial criteria. Identification of patients who functionally benefit from frequently performed EVT outside RCT-criteria requires further investigation.

Trial registration
Clinicaltrials.gov, NCT04357899.
Identification of Novel DNA Methylation Prognostic Biomarkers for AML With Normal Cytogenetics
Authors: Cardoso Cândida , Pestana Daniel , Gokuladhas Sreemol , Marreiros Ana D. , O'Sullivan Justin M. , Binnie Alexandra , Fernandes Mónica Teotónio , Castelo-Branco Pedro 
Published: July 2024

PURPOSE
AML is a hematologic cancer that is clinically heterogeneous, with a wide range of clinical outcomes. DNA methylation changes are a hallmark of AML but are not routinely used as a criterion for risk stratification. The aim of this study was to explore DNA methylation markers that could risk stratify patients with cytogenetically normal AML (CN-AML), currently classified as intermediate-risk.

MATERIALS AND METHODS
DNA methylation profiles in whole blood samples from 77 patients with CN-AML in The Cancer Genome Atlas (LAML cohort) were analyzed. Individual 5’-cytosine-phosphate-guanine-3’ (CpG) sites were assessed for their ability to predict overall survival. The output was validated using DNA methylation profiles from bone marrow samples of 79 patients with CN-AML in a separate data set from the Gene Expression Omnibus.

RESULTS

In the training set, using DNA methylation data derived from the 450K array, we identified 2,549 CpG sites that could potentially distinguish patients with CN-AML with an adverse prognosis (
intermediate-poor
) from those with a more favorable prognosis (
intermediate-favorable
) independent of age. Of these, 25 CpGs showed consistent prognostic potential across both the 450K and 27K array platforms. In a separate validation data set, nine of these 25 CpGs exhibited statistically significant differences in 2-year survival. These nine validated CpGs formed the basis for a combined prognostic biomarker panel, which includes an 8-CpG Somatic Panel and the methylation status of cg23947872. This panel displayed strong predictive ability for 2-year survival, 2-year progression-free survival, and complete remission in the validation cohort.

CONCLUSION
This study highlights DNA methylation profiling as a promising approach to enhance risk stratification in patients with CN-AML, potentially offering a pathway to more personalized treatment strategies.
Biological resilience in health and disease
Authors: Weavers Helen 
Published: July 2024

ABSTRACT
All living organisms – from single-celled prokaryotes through to invertebrates and humans – are frequently exposed to numerous challenges during their lifetime, which could damage their molecular and cellular contents and threaten their survival. Nevertheless, these diverse organisms are, on the whole, remarkably resilient to potential threats. Recent years have seen rapid advances in our mechanistic understanding of this emerging phenomenon of biological resilience, which enables cells, tissues and whole organisms to bounce back from challenges or stress. In this At a Glance article, I discuss current knowledge on the diverse molecular mechanisms driving biological resilience across scales, with particular focus on its dynamic and adaptive nature. I highlight emerging evidence that loss of biological resilience could underly numerous pathologies, including age-related frailty and degenerative disease. Finally, I present the multi-disciplinary experimental approaches that are helping to unravel the causal mechanisms of resilience and how this emerging knowledge could be harnessed therapeutically in the clinic.
Fairness Regulation of Prices in Competitive Markets
Authors: Yang Zongsen , Fu Xingyu , Gao Pin , Chen Ying-Ju 
Published: July 2024

Problem definition: The loyalty penalty refers to a pricing strategy where companies charge higher prices to loyal customers for exploitation while offering lower prices to nonloyal customers for attraction. To address this unfair business practice, various regulatory agencies, such as the Competition and Markets Authority and the Financial Conduct Authority in the United Kingdom, have proposed or implemented regulations aimed at promoting fairness in pricing. In this study, we analyze the impact of such regulations on both firms and consumers. Methodology/results: We develop a stylized model to investigate duopoly competition in two symmetric markets, where consumers exhibit loyalty to different firms in each market. The regulatory intervention mandates that the price difference between the two markets, set by each firm, must not exceed a certain threshold. Our analysis reveals an intriguing interaction between market competition and price fairness regulation. When competition is intense, fairness regulation can alleviate cutthroat competition between firms, resulting in Pareto improvements compared with a scenario with no regulation. On the other hand, when competition is weak, fairness regulation can further enhance firms’ existing monopoly power, potentially leading to collusive high prices that are detrimental to consumers and society. We also consider several extensions to enrich our findings, including fairness regulation on relative price discounts, asymmetric markets, and a two-pronged policy regulating the price gap and price cap. Managerial implications: Our study reveals the economic consequences of price fairness regulations; firms can benefit by pricing fairly, but well-intended fairness requirements may have adverse effects on consumers. Funding: P. Gao is supported by the National Natural Science Foundation of China [Grants 72201234 and 72192805], the Hong Kong Research Grants Council (the Collaborative Research Fund) [Grant C6032-21G], and the Guangdong Provincial Key Laboratory of Mathematical Foundations for Artificial Intelligence [Grant 2023B1212010001]. Y.-J. Chen acknowledges financial support from the Hong Kong Research Grants Council [Grants CRF HKUST C6020-21GF, GRF 16500821, and GRF 16501722]. Supplemental Material: The online appendix is available at https://doi.org/10.1287/msom.2022.0552 .
Performance study of an optical modulator based on a funnel-shaped waveguide with tip-plasma effect
Authors: Li Jiabin , Fan Zenghui 
Published: July 2024

Electro-optical modulators play a crucial role in the field of optical communications; high modulation depth and low loss are used to qualify optical modulators. In this study, the tip-plasmon effect was utilized to improve the optical mode confinement and achieve a significant enhancement of the optical-graphene coupling. The evaluated modulator demonstrates robust performance characteristics, exhibiting a modulation depth of up to 8.5 dB/µm while sustaining a transmission loss of 2.3 dB/µm. Furthermore, the modulator operates with an energy efficiency of 4.36 fJ/bit and achieves a modulation bandwidth of 293 GHz, assuming a modulation length of 20 µm.
Facilitators and barriers to contraception access and use for Hispanic American adolescent women: An integrative literature review
Authors: Batek Lindsay M. , Leblanc Natalie M. , Alio Amina P. , Stein Karen F. , McMahon James M. 
Published: July 2024

Statement of the problem
Hispanic American adolescents experience high rates of pregnancy with profound consequences. Compared with White teens, Hispanic teens use contraception less frequently and often choose less effective forms of contraception. Access to contraception is a primary barrier to use which contributes to relatively high and disparate rates of pregnancy in Hispanic teens. This integrative review identifies facilitators and barriers of contraception access and use for Hispanic women, 13–17 years of age, living in the U.S.

Methodology
Following the Whittemore and Knafl (2005) methodology and PRISMA guidelines, peer reviewed studies were retrieved from PUBMED, CINAHL and EMBASE. The Mixed Methods Appraisal Tool was used to assess the study quality and thematic analysis was used to categorize barriers and facilitators.

Findings
Of 131 studies retrieved, 16 met inclusion criteria. Individual, interpersonal and healthcare provider factors were identified as primary categories of barriers and facilitators with structural issues comprising an additional barrier category. Individual level barriers were disproportionately represented and further categorized into themes: beliefs/misconceptions, dislike of contraception, pregnancy risk perception, lack of knowledge, and lack of control. Barriers related to cultural and religious influences were identified in individual, interpersonal and structural levels. The most frequently reported facilitators were perceived parent comfort discussing sexual health and past experience of pregnancy.

Discussion
Limitations in this review may stem from heterogeneity in the acculturation and geography of participants and analysis by a single reviewer. Implications include considering the range of information sources and the influence they have on risk perception and risk mitigation for this population.

Conclusion & significance
Adolescents describe many modifiable influences on contraception access and use. Misperceptions related to contraception, stemming from beliefs and perceptions, can be corrected through increased access to reliable sources of sex education, parental support, and direct access to nurses and healthcare providers. Awareness of these influences can inform further research and intervention development to address these health disparities.
Clinical characteristics of enteric fever and performance of TUBEX TF IgM test in Indonesian hospitals
Authors: Nurmawati Syndi , Alam Anggraini , Djauhari Hofiya , Merati Tuti P. , Sudarmono Pratiwi , Setiawaty Vivi , Arlinda Dona , Sugiyono Retna Indah , Arief Mansyur , Hadi Usman , Aman Abu Tholib , Lokida Dewi , Gasem M. Hussein , Tjitra Emiliana , Liang C. Jason , Neal Aaron , Kosasih Herman , Karyana Muhammad , Lau Chuen-Yen , Alisjahbana Bachti 
Published: July 2024

Background
Accurate diagnosis of enteric fever is challenging, particularly in low- and middle-income countries, due to the overlap of clinical and laboratory features with other pathogens. To better understand the difficulties in enteric fever diagnosis, we evaluated the characteristics of patients clinically diagnosed with enteric fever and the real-world performance of TUBEX TF, one of the most used tests in Indonesia.

Methodology/Principal findings
Patients were recruited through the AFIRE (Etiology of Acute Febrile Illness Requiring Hospitalization) study at eight Indonesian hospitals. Blood culture was performed for all patients, and TUBEX TF was performed for suspected enteric cases. Salmonella PCR and ELISA tests were performed at a reference lab. Sensitivity and specificity of TUBEX TF and IgM and IgG anti-S. Typhi ELISA were determined. Of 301 patients clinically diagnosed with enteric fever, 50 (16.6%) were confirmed by blood culture and/or PCR. Confirmed cases were mostly school-aged children presenting with fever, anorexia, dizziness and/or abdominal pain with normal leukocyte count or leukopenia. TUBEX TF demonstrated a sensitivity of 97.6% to 70.7% and specificity of 38.3% to 67.2% at cutoffs of 4 and 6, respectively. Acute IgG demonstrated the best sensitivity and specificity, at 90.7% and 82.7%, respectively, and the best ROC characteristics.

Conclusions/Significance
A substantial proportion of enteric fever was misdiagnosed at all study hospitals, likely due to the overlap of clinical characteristics and lab parameters with those of other common pathogens. The TUBEX TF rapid serological assay demonstrated suboptimal performance in our setting and tended to over-diagnose enteric fever. The role of IgG from acute specimens for identification of enteric fever cases merits additional consideration.
Pangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia
Authors: Chekesa Basha , Singh Harinder , Gonzalez-Juarbe Norberto , Vashee Sanjay , Wiscovitch-Russo Rosana , Dupont Christopher L. , Girma Musse , Kerro Oudessa , Gumi Balako , Ameni Gobena 
Published: July 2024

Background
The lineage 4 (L4) of Mycobacterium tuberculosis (MTB) is not only globally prevalent but also locally dominant, surpassing other lineages, with lineage 2 (L2) following in prevalence. Despite its widespread occurrence, factors influencing the expansion of L4 and its sub-lineages remain poorly understood both at local and global levels. Therefore, this study aimed to conduct a pan-genome and identify genomic signatures linked to the elevated prevalence of L4 sublineages among extrapulmonary TB (EPTB) patients in western Ethiopia.

Methods
A cross-sectional study was conducted at an institutional level involving confirmed cases of extrapulmonary tuberculosis (EPTB) patients from August 5, 2018, to December 30, 2019. A total of 75 MTB genomes, classified under lineage 4 (L4), were used for conducting pan-genome and genome-wide association study (GWAS) analyses. After a quality check, variants were identified using MTBseq, and genomes were de novo assembled using SPAdes. Gene prediction and annotation were performed using Prokka. The pan-genome was constructed using GET_HOMOLOGUES, and its functional analysis was carried out with the Bacterial Pan-Genome Analysis tool (BPGA). For GWAS analysis, Scoary was employed with Benjamini-Hochberg correction, with a significance threshold set at p-value ≤ 0.05.

Results
The analysis revealed a total of 3,270 core genes, predominantly associated with orthologous groups (COG) functions, notably in the categories of ‘[R] General function prediction only’ and ‘[I] Lipid transport and metabolism’. Conversely, functions related to ‘[N] Cell motility’ and ‘[Q] Secondary metabolites biosynthesis, transport, and catabolism’ were primarily linked to unique and accessory genes. The pan-genome of MTB L4 was found to be open. Furthermore, the GWAS study identified genomic signatures linked to the prevalence of sublineages L4.6.3 and L4.2.2.2.

Conclusions
Apart from host and environmental factors, the sublineage of L4 employs distinct virulence factors for successful dissemination in western Ethiopia. Given that the functions of these newly identified genes are not well understood, it is advisable to experimentally validate their roles, particularly in the successful transmission of specific L4 sublineages over others.
Quality of primary health care for chronic diseases in low-resource settings: Evidence from a comprehensive study in rural China
Authors: Li Mingyue , Zhang Xiaotian , Tang Haoqing , Zheng Huixian , Long Ren , Cheng Xiaoran , Cheng Haozhe , Dong Jiajia , Wang Xiaohui , Zhang Xiaoyan , Geldsetzer Pascal , Liu Xiaoyun 
Published: July 2024

Background
There is a paucity of evidence regarding the definition of the quality of primary health care (PHC) in China. This study aims to evaluate the PHC quality for chronic diseases in rural areas based on a modified conceptual framework tailored to the context of rural China.

Methods
This comprehensive study, involving a patient survey, a provider survey and chart abstraction, and second-hand registered data, was set in three low-resource counties in rural China from 2021 to 2022. Rural patients with hypertension or type 2 diabetes, and health care workers providing care on hypertension or diabetes were involved. The modified PHC quality framework encompasses three core domains: a competent PHC system (comprehensiveness, accessibility, continuity, and coordination), effective clinical care (assessment, diagnosis, treatment, disease management, and provider competence), and positive user experience (information sharing, shared decision-making, respect for patient’s preferences, and family-centeredness). Standardized PHC quality score was generated by arithmetic means or Rasch models of Item Response Theory.

Results
This study included 1355 patients, 333 health care providers and 2203 medical records. Ranging from 0 (the worst) to 1 (the best), the average quality score for the PHC system was 0.718, with 0.887 for comprehensiveness, 0.781 for accessibility, 0.489 for continuity, and 0.714 for coordination. For clinical care, average quality was 0.773 for disease assessment, 0.768 for diagnosis, 0.677 for treatment, 0.777 for disease management, and 0.314 for provider competence. The average quality for user experience was 0.727, with 0.933 for information sharing, 0.657 for shared decision-making, 0.936 for respect for patients’ preferences, and 0.382 for family-centeredness. The differences in quality among population subgroups, although statistically significant, were small.

Conclusion
The PHC quality in rural China has shown strengths and limitations. We identified large gaps in continuity of care, treatment, provider competence, family-centeredness, and shared decision-making. Policymakers should invest more effort in addressing these gaps to improve PHC quality.