bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ontology-based tool for modeling and documenting events in neurosurgery
Authors: Romao Patricia , Neuenschwander Stefanie , Zbinden Chantal , Seidel Kathleen , Sariyar Murat 
Published: July 2024

Abstract
Background
Intraoperative neurophysiological monitoring (IOM) plays a pivotal role in enhancing patient safety during neurosurgical procedures. This vital technique involves the continuous measurement of evoked potentials to provide early warnings and ensure the preservation of critical neural structures. One of the primary challenges has been the effective documentation of IOM events with semantically enriched characterizations. This study aimed to address this challenge by developing an ontology-based tool.

Methods
We structured the development of the IOM Documentation Ontology (IOMDO) and the associated tool into three distinct phases. The initial phase focused on the ontology’s creation, drawing from the OBO (Open Biological and Biomedical Ontology) principles. The subsequent phase involved agile software development, a flexible approach to encapsulate the diverse requirements and swiftly produce a prototype. The last phase entailed practical evaluation within real-world documentation settings. This crucial stage enabled us to gather firsthand insights, assessing the tool’s functionality and efficacy. The observations made during this phase formed the basis for essential adjustments to ensure the tool’s productive utilization.

Results
The core entities of the ontology revolve around central aspects of IOM, including measurements characterized by timestamp, type, values, and location. Concepts and terms of several ontologies were integrated into IOMDO, e.g., the Foundation Model of Anatomy (FMA), the Human Phenotype Ontology (HPO) and the ontology for surgical process models (OntoSPM) related to general surgical terms. The software tool developed for extending the ontology and the associated knowledge base was built with JavaFX for the user-friendly frontend and Apache Jena for the robust backend. The tool’s evaluation involved test users who unanimously found the interface accessible and usable, even for those without extensive technical expertise.

Conclusions
Through the establishment of a structured and standardized framework for characterizing IOM events, our ontology-based tool holds the potential to enhance the quality of documentation, benefiting patient care by improving the foundation for informed decision-making. Furthermore, researchers can leverage the semantically enriched data to identify trends, patterns, and areas for surgical practice enhancement. To optimize documentation through ontology-based approaches, it’s crucial to address potential modeling issues that are associated with the Ontology of Adverse Events.
Antifibrotics and mortality in idiopathic pulmonary fibrosis: external validity and avoidance of immortal time bias
Authors: Hozumi Hironao , Miyashita Koichi , Nakatani Eiji , Inoue Yusuke , Yasui Hideki , Suzuki Yuzo , Karayama Masato , Furuhashi Kazuki , Enomoto Noriyuki , Fujisawa Tomoyuki , Inui Naoki , Suda Takafumi 
Published: July 2024

Abstract
Background and objective
Pooled analyses of previous randomized controlled trials reported that antifibrotics improved survival in patients with idiopathic pulmonary fibrosis (IPF), but the results were only based on short-term outcome data from selected patients who met strict criteria. Observational studies/meta-analyses also suggested that antifibrotics improve survival, but these studies failed to control for immortal time bias that considerably exaggerates drug effects. Therefore, whether antifibrotics truly improve long-term survival in patients with IPF in the real world remains undetermined and requires external validity.

Methods
We used data from the Japanese National Claims Database to estimate the intention-to-treat effect of antifibrotics on mortality. To address immortal time bias, we employed models treating antifibrotic initiation as a time-dependent covariate and target trial emulation (TTE), both incorporating new-user designs for antifibrotics and treating lung transplantation as a competing event.

Results
Of 30,154 patients with IPF, 14,525 received antifibrotics. Multivariate Fine–Gray models with antifibrotic initiation as a time-dependent covariate revealed that compared with no treatment, nintedanib (adjusted hazard ratio [aHR], 0.85; 95% confidence interval [CI], 0.81–0.89) and pirfenidone (aHR, 0.89; 95% CI, 0.86–0.93) were associated with reduced mortality. The TTE model also replicated the associations of nintedanib (aHR, 0.69; 95% CI, 0.65–0.74) and pirfenidone (aHR, 0.81; 95% CI, 0.78–0.85) with reduced mortality. Subgroup analyses confirmed this association regardless of age, sex, and comorbidities, excluding certain subpopulations.

Conclusions
The results of this large-scale real-world analysis support the generalizability of the association between antifibrotics and improved survival in various IPF populations.
Socioeconomic inequality in child health outcomes in India: analyzing trends between 1993 and 2021
Authors: Jain Anoop , Kim Rockli , Swaminathan Soumya , Subramanian SV 
Published: July 2024

Abstract
Background
The health of India’s children has improved over the past thirty years. Rates of morbidity and anthropometric failure have decreased. What remains unknown, however, is how those patterns have changed when examined by socioeconomic status. We examine changes in 11 indicators of child health by household wealth and maternal education between 1993 and 2021 to fill this critical gap in knowledge. Doing so could lead to policies that better target the most vulnerable children.

Methods
We used data from five rounds of India’s National Family Health Survey conducted in 1993, 1999, 2006, 2016, and 2021 for this repeated cross-sectional analysis. We studied mother-reported cases of acute respiratory illness and diarrhea, hemoglobin measurements for anemia, and height and weight measurements for anthropometric failure. We examined how the prevalence rates of each outcome changed between 1993 and 2021 by household wealth and maternal education. We repeated this analysis for urban and rural communities.

Results
The socioeconomic gradient in 11 indicators of child health flattened between 1993 and 2021. This was in large part due to large reductions in the prevalence among children in the lowest socioeconomic groups. For most outcomes, the largest reductions occurred before 2016. Yet as of 2021, except for mild anemia, outcome prevalence remained the highest among children in the lowest socioeconomic groups. Furthermore, we show that increases in the prevalence of stunting and wasting between 2016 and 2021 are largely driven by increases in the severe forms of these outcomes among children in the highest socioeconomic groups. This finding underscores the importance of examining child health outcomes by severity.

Conclusions
Despite substantial reductions in the socioeconomic gradient in 11 indicators of child health between 1993 and 2021, outcome prevalence remained the highest among children in the lowest socioeconomic groups in most cases. Thus, our findings emphasize the need for a continued focus on India’s most vulnerable children.
Cytoreductive surgery without intra-peritoneal chemotherapy for metachronous colorectal peritoneal metastases
Authors: Ota Emi , Fukunaga Yosuke , Mukai Toshiki , Hiyoshi Yukiharu , Yamaguchi Tomohiro , Nagasaki Toshiya , Akiyoshi Takashi 
Published: July 2024

Abstract
Background
Cytoreductive surgery and chemotherapy reportedly improve the prognosis of patients with metachronous peritoneal metastases. However, the types of peritoneal metastases indicated for cytoreductive surgery remains unclear. Therefore, we aimed to clarify the category of cases for which cytoreductive surgery would be effective and report the prognosis associated with cytoreductive surgery for metachronous peritoneal metastases.

Methods
This study included 52 consecutive patients who underwent cytoreductive surgery for metachronous peritoneal metastases caused by colorectal cancer between January 2005 and December 2018 and fulfilled the selection criteria. The median follow-up period was 54.9 months. Relapse-free survival was calculated as the time from cytoreductive surgery of metachronous peritoneal metastases to recurrence. Overall survival was defined as the time from cytoreductive surgery of metachronous peritoneal metastases to death or the end of the follow-up period.

Results
The 5-year relapse-free survival rate was 30.0% and the 5-year overall survival rate was 72.3%. None of the patients underwent hyperthermic intraperitoneal chemotherapy. The analysis indicated no potential risk factors for 5-year relapse-free survival. However, for 5-year overall survival, the multivariate analysis revealed that time to diagnosis of metachronous peritoneal metastases of < 2 years after primary surgery (hazard ratio = 4.1, 95% confidence interval = 2.0–8.6, p = 0.0002) and number of metachronous peritoneal metastases ≥ 3 (hazard ratio = 9.8, 95% confidence interval = 2.3–42.3, p = 0.002) as independent factors associated with a poor prognosis.

Conclusions
Long intervals of more than 2 years after primary surgery and 2 or less metachronous peritoneal metastases were good selection criteria for cytoreductive surgery for metachronous peritoneal metastases from colorectal cancer.
“They don't have the luxury of time”: interviews exploring the determinants of public health research activity that contextualise embedded researcher roles in local government
Authors: Edwards Rachael C. , Kneale Dylan , Stansfield Claire , Lester Sarah 
Published: July 2024

Abstract
Background
Embedded researchers are a novel intervention to improve the translation of research evidence into policy and practice settings, including public health. These roles are being implemented with increasing popularity, but they often lack clear evaluative frameworks. Understanding initial levels of research activity, including associated barriers and opportunities, is essential to developing theories of change and thus shaping the roles and defining expectations. We aimed to identify the principal determinants of research activity in public health that contextualise embedded researcher roles, including attributes of the embedded researcher themselves.

Methods
We undertook seventeen semi-structured interviews with embedded researchers in diverse public health settings in English local government. Interviews were analysed using thematic analysis.

Results
We identified thirteen interlinked determinants of research activity within local government public health settings. Research and interpersonal skills, as well as pre-existing connections and knowledge within local government, were highly valued individual attributes for embedded researchers. Resource deficiencies (funding, time, and infrastructure) were primary barriers to research activity, whereas a strong local appetite for evidence informed decision making presented a valuable opportunity. However, there was inconsistencies across public health teams relating to perceptions of what constituted “research” and the resources that would be required.

Conclusions
Our results suggest that successful embedded researchers will have equally strong research and communication skills and should be offered mentorship and clear career progression pathways. Perceptions of research within local government are closely linked to resource deficiencies and senior endorsement. Embedded researchers could benefit from taking the time to develop locally contextualised knowledge of this research culture. Theories of change for embedded researchers should conceptualise the interconnections across individual, interpersonal, and organisational barriers and opportunities underlying local government research activity. Further research is needed to identify methods for exploring the influence of embedded researchers as well as to unpack the stages of research activity within local government and the associated behaviours.
Female legislators decrease epidemic deaths
Authors: Saito Takaharu 
Published: July 2024

AbstractRecent discourse has lauded the efficacy of female leadership in national governments, particularly during the COVID-19 pandemic. This study employs two-way fixed effect (TWFE) and instrumental variable (IV) regression methodologies to reveal a more pronounced association between the proportion of female legislators and reduced epidemic-related mortality, rather than a direct correlation with female executive leadership. Further analysis elucidates that the effectiveness of female legislative representation is amplified through its interaction with the deliberative processes in governance. This suggests that policy diversity and inclusive decision-making mechanisms are instrumental in enhancing epidemic response efficacy.
Effect of patellofemoral joint overstuffing following total knee arthroplasty without patella resurfacing on clinical efficacy and related factors analysis
Authors: Wang Feida , Zhang Guohao , Wei Xiaochun 
Published: July 2024

Abstract
Objective
To analyze the influencing factors for patellofemoral joint (PFJ) overstuffing following total knee arthroplasty (TKA) without patella resurfacing, and explore the effect of PFJ overstuffing on clinical efficacy.

Methods
A retrospective analysis was conducted on 168 patients with end-stage knee osteoarthritis who underwent TKA without patella resurfacing at our hospital between Match 2019 and September 2021. The clinical data of these patients were retrospectively analyzed. In this study, PFJ overstuffing was defined as a postoperative PFJ distance greater than 1 mm compared to the preoperative measurement. The occurrence of postoperative PFJ overstuffing was counted. The patients were divided into the overstuffing group (n = 109) and the non-overstuffing group (n = 59) to count the patellar thickness and thickness of femoral anterior condyle in all patients before and after surgery, and analyze the influencing factors for postoperative PFJ overstuffing in such patients. Patients were followed up for 2 years to compare the recovery time of postoperative pain, score of visual analogue scale (VAS) and flexion activity between the two groups.

Results
There was no significant difference in patellar thickness between preoperative and postoperative measurements of the patients (P > 0.05). However, the thickness of the femoral anterior condyle and the PFJ distance after surgery increased significantly compared with those before surgery (P < 0.05). Among the 168 patients, 109 cases (64.88%) experienced PFJ overstuffing. The risk of PFJ overstuffing was higher in female patients than in male (P < 0.05). The preoperative thickness of the femoral anterior condyle in the overstuffing group was significantly smaller compared to the non-overstuffing group (P < 0.001). Compared with the non-overstuffing group, the overstuffing group had longer recovery time of postoperative pain (P < 0.05), and had lower flexion activity at 2 years after surgery (P < 0.001). However, no significant difference was found in VAS score between the overstuffing group and the non-overstuffing group at 2 years after surgery (P > 0.05). Spearman rank correlation analysis indicated females tend to have a lower preoperative thickness of the femoral anterior condyle (r=-0.424, P < 0.001), as well as a positive postoperative PFJ overstuffing (r = 0.237, P < 0.05). Furthermore, there was a negative correlation between preoperative thickness of the femoral anterior condyle and postoperative PFJ overstuffing (r=-0.540, P < 0.001).

Conclusion
Following TKA without patella resurfacing, there is a high risk of PFJ overstuffing, particularly among female patients and those with a small thickness of the femoral anterior condyle. Therefore, special attention should be given to these high-risk groups during clinical treatment.
Rare disease clinical trials in the European Union: navigating regulatory and clinical challenges
Authors: Mishra Sangita , Venkatesh MP 
Published: July 2024

Abstract
Background
Clinical development for orphan drugs presents significant difficulties and challenges. There is no unique or standard design, conduct, and outcome assessment methodology and it is sometimes impractical to fit design models of rare disease trials in any practiced and well-known framework. In the European Union (EU) these challenges encompass a broad array of subjects, including trial design, study outcomes, patient recruitment, trial conduct ethics, trial cost, and chances of success. This literature-based review study aims to provide a thorough overview of the critical aspects of rare disease trials in the EU by analyzing the current landscape of rare disease trials, highlighting key challenges, delving into regulatory and research initiatives and innovation in trial designs, and proposing multi-faceted solutions to implement effective rare disease clinical trials in the region.

Discussion
Traditional clinical trial designs, validation, and evaluation methodologies used for nonorphan drugs often prove unsuitable for orphan drugs, given the small patient populations, sometimes fewer than 1000 cases. There is an increasing need for accessible therapies and both regulators as well as industry are trying to develop affordable and effective drugs to address this need. Despite several steps that have been taken, the timely development of drugs remains a challenge. One of the reasons behind the long development timeline is the recruitment, retention, and conduct of rare disease trials. To optimize the development timelines of orphan drugs in the EU, it is important to ensure that the safety and efficacy of the product is not compromised. Industry and regulatory agencies must implement innovative trial designs, devise flexible policies, and incorporate real-world data for assessing clinical outcomes.

Conclusion
Collaboration among academic institutions, pharmaceutical companies (both small and major), patient groups, and health authorities is crucial in overcoming obstacles related to clinical trials and providing assistance and creative ideas. The ultimate objective of granting rare disease patients timely and affordable access to medications with a positive balance between benefits and risks is to be met.
A randomized clinical trial testing a health literacy intervention to reduce disparities in access to care among Justice-Impacted Adults (JIA)
Authors: Ojeda Victoria D. , Groneman Arthur , Hiller-Venegas Sarah , Moreno Melissa , Schuler Briana , Barksdale Jerrica , Berliant Emily , Romero Natalie , Edwards Todd M. , Lister Zephon , Gilmer Todd , Gaines Tommi , Bazzi Angela 
Published: July 2024

Abstract
Background
Low health literacy is costly and observed among justice-impacted adults (JIA), a group that often faces numerous barriers in accessing healthcare and a disproportionate burden of illness. Health literacy interventions for JIA are critically needed to improve healthcare access and related outcomes.

Methods
This manuscript describes the protocol for a longitudinal mixed-methods randomized clinical trial that assesses the effectiveness of a coach-guided health literacy intervention on JIA’s healthcare access. The intervention was previously piloted with justice impacted adults. We will recruit 300 JIA ages 18 + in San Diego, California. Participants will be randomized 1:1 to the Treatment Group (i.e., coach-guided intervention providing 12 sessions of individualized health coaching and service navigation over 6 months) or the Control Group (i.e., self-study of the health coaching program, and brief service navigation support). We will quantitatively assess JIA’s healthcare access defined as: use of healthcare, health insurance status, and regular source of care at 6-months as the primary outcomes. Participants will also be surveyed at 12-months. Statistical analyses will incorporate the intent-to-treat (ITT) principle and we will estimate mixed-effects logistic regression for the primary outcomes. We will also conduct qualitative interviews at 6 and 12-months with 40 purposively sampled participants, stratified by study arm, who reported healthcare access barriers at baseline. Interviews will explore participants’ satisfaction with the intervention, healthcare attitudes, self-efficacy for and barriers to healthcare access over time, perceived contribution of the intervention to health and well-being, and diffusion of intervention-related information within participants’ social networks. We will conduct deductive thematic analyses of qualitative data.

Discussion
Low health literacy among JIA is a foundational challenge requiring tailored intervention strategies. Findings from this trial may inform policies and the structure of service delivery models to build health literacy among JIA in institutional and community settings throughout the United States and elsewhere.

Trial registration
This study is registered with the United States’ ClinicalTrials.gov registry under protocol # 161,903.
Movement patterns of a small-bodied minnow suggest nomadism in a fragmented, desert river
Authors: Chavez Martinique J. , Budy Phaedra , Pennock Casey A. , Archdeacon Thomas P. , MacKinnon Peter D. 
Published: July 2024

Abstract
Background
Unfettered movement among habitats is crucial for fish to access patchily distributed resources and complete their life cycle, but many riverscapes in the American Southwest are fragmented by dams and dewatering. The endangered Rio Grande silvery minnow (Hybognathus amarus, RGSM) persists in a fragmented remnant of its former range (ca. 5%), and its movement ecology is understudied.

Methods
We tracked movements of hatchery-reared RGSM, tagged with passive integrated transponder tags, using stationary and mobile antennas from 2019 to 2022. We quantified probability of movement and total distance moved by RGSM released above and below a dam. We then assessed how well two prevailing riverine movement theories (i.e., restricted movement paradigm [RMP] and colonization cycle hypothesis [CCH]) explained RGSM movement patterns.

Results
We detected 36.8% of released RGSM (n = 37,215) making at least one movement. Movements were leptokurtic and substantially greater than expected based on the RMP for both stationary (1.7–5.9 m) and mobile (30.3–77.8 m) individuals. On average, RGSM were detected at large for 75 days and moved a total of 12.2 rkm within a year. The maximum total distance moved by RGSM was 103 rkm. Similarly, we observed a multimodal distribution of detected range sizes with a mean detected range of 2.4 rkm and a maximum detected range of 78.2 rkm. We found little support for an upstream movement bias, as expected under the CCH, and most movements (74%) were directed downstream.

Conclusions
Our data suggest RGSM are highly mobile, with the ability to make long-distance movements. Neither movement theory adequately described movement patterns of RGSM; instead, our findings support a nomadic movement pattern and an apparent drift paradox matching recent studies of other pelagic-broadcast spawning minnows where populations persist upstream despite experiencing downstream drift as larvae. Resolution of the drift paradox may be achieved through further, targeted studies into different aspects of the species’ life history. Quantification of RGSM movement provides crucial insights into the species’ movement ecology and may help define the appropriate scale of recovery efforts.