bluuebunny/crossref_metadata_2025_split huggingface dataset:
Women's representation in clinical trials of patients with chronic kidney disease
Authors: Pinho-Gomes Ana-Catarina , Carcel Cheryl , Woodward Mark , Hockham Carinna 
Published: February 2023

ABSTRACT

Background
Sex and gender differences in chronic kidney disease (CKD), including epidemiology and response to treatment, remain poorly understood. This study aimed to investigate how women are represented in CKD clinical trials and whether sex- and gender-disaggregated outcomes were reported.

Methods
Clinical trials on CKD were identified from ClinicalTrials.gov. Randomised, phase 3/4 trials with ≥100 participants were selected to quantify women's representation among participants by computing the participation:prevalence ratio (PPR) and investigating whether sex-disaggregated analyses had been performed.

Results
In total, 192 CKD trials registered on ClinicalTrials.gov and published between 1995 and 2022 were included. Overall, women accounted for 66 875 (45%) of the 147 136 participants. Women's participation in clinical trials was lower than their representation in the underlying CKD population globally (55%). The PPR was 0.75 (95% confidence interval 0.72–0.78), with no significant variation irrespective of mean age, CKD stage, dialysis, location, type of intervention or funding agency. A total of 39 (20%) trials reported sex-disaggregated efficacy outcomes and none reported sex-disaggregated safety outcomes.

Conclusion
Women's participation in CKD clinical trials was lower than their representation in the underlying CKD population. Sex-disaggregated efficacy and safety outcomes were rarely reported. Improving women's enrolment into clinical trials is crucial to enable sex- and gender-disaggregated analysis and thus identify potential differences in treatment response between women and men.
Automatic Extraction of Medication Mentions from Tweets—Overview of the BioCreative VII Shared Task 3 Competition
Authors: Weissenbacher Davy , O’Connor Karen , Rawal Siddharth , Zhang Yu , Tsai Richard Tzong-Han , Miller Timothy , Xu Dongfang , Anderson Carol , Liu Bo , Han Qing , Zhang Jinfeng , Kulev Igor , Köprü Berkay , Rodriguez-Esteban Raul , Ozkirimli Elif , Ayach Ammer , Roller Roland , Piccolo Stephen , Han Peijin , Vydiswaran V G Vinod , Tekumalla Ramya , Banda Juan M , Bagherzadeh Parsa , Bergler Sabine , Silva João F , Almeida Tiago , Martinez Paloma , Rivera-Zavala Renzo , Wang Chen-Kai , Dai Hong-Jie , Alberto Robles Hernandez Luis , Gonzalez-Hernandez Graciela 
Published: February 2023

Abstract
This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user’s publicly available tweets (the user’s ‘timeline’). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user’s timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user’s timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.
Machine learning identifies pathophysiologically and prognostically informative phenotypes among patients with mitral regurgitation undergoing transcatheter edge-to-edge repair
Authors: Trenkwalder Teresa , Lachmann Mark , Stolz Lukas , Fortmeier Vera , Covarrubias Héctor Alfonso Alvarez , Rippen Elena , Schürmann Friederike , Presch Antonia , von Scheidt Moritz , Ruff Celine , Hesse Amelie , Gerçek Muhammed , Mayr N Patrick , Ott Ilka , Schuster Tibor , Harmsen Gerhard , Yuasa Shinsuke , Kufner Sebastian , Hoppmann Petra , Kupatt Christian , Schunkert Heribert , Kastrati Adnan , Laugwitz Karl-Ludwig , Rudolph Volker , Joner Michael , Hausleiter Jörg , Xhepa Erion 
Published: February 2023

Abstract

Aims
Patients with mitral regurgitation (MR) present with considerable heterogeneity in cardiac damage depending on underlying aetiology, disease progression, and comorbidities. This study aims to capture their cardiopulmonary complexity by employing a machine-learning (ML)-based phenotyping approach.

Methods and results
Data were obtained from 1426 patients undergoing mitral valve transcatheter edge-to-edge repair (MV TEER) for MR. The ML model was developed using 609 patients (derivation cohort) and validated on 817 patients from two external institutions. Phenotyping was based on echocardiographic data, and ML-derived phenotypes were correlated with 5-year outcomes. Unsupervised agglomerative clustering revealed four phenotypes among the derivation cohort: Cluster 1 showed preserved left ventricular ejection fraction (LVEF; 56.5 ± 7.79%) and regular left ventricular end-systolic diameter (LVESD; 35.2 ± 7.52 mm); 5-year survival in Cluster 1, hereinafter serving as a reference, was 60.9%. Cluster 2 presented with preserved LVEF (55.7 ± 7.82%) but showed the largest mitral valve effective regurgitant orifice area (0.623 ± 0.360 cm2) and highest systolic pulmonary artery pressures (68.4 ± 16.2 mmHg); 5-year survival ranged at 43.7% (P-value: 0.032). Cluster 3 was characterized by impaired LVEF (31.0 ± 10.4%) and enlarged LVESD (53.2 ± 10.9 mm); 5-year survival was reduced to 38.3% (P-value: &lt;0.001). The poorest 5-year survival (23.8%; P-value: &lt;0.001) was observed in Cluster 4 with biatrial dilatation (left atrial volume: 312 ± 113 mL; right atrial area: 46.0 ± 8.83 cm2) although LVEF was only slightly reduced (51.5 ± 11.0%). Importantly, the prognostic significance of ML-derived phenotypes was externally confirmed.

Conclusion
ML-enabled phenotyping captures the complexity of extra-mitral valve cardiac damage, which does not necessarily occur in a sequential fashion. This novel phenotyping approach can refine risk stratification in patients undergoing MV TEER in the future.
Premature atrial and ventricular contractions detected on wearable-format electrocardiograms and prediction of cardiovascular events
Authors: Orini Michele , van Duijvenboden Stefan , Young William J , Ramírez Julia , Jones Aled R , Tinker Andrew , Munroe Patricia B , Lambiase Pier D 
Published: February 2023

AbstractAimsWearable devices are transforming the electrocardiogram (ECG) into a ubiquitous medical test. This study assesses the association between premature ventricular and atrial contractions (PVCs and PACs) detected on wearable-format ECGs (15 s single lead) and cardiovascular outcomes in individuals without cardiovascular disease (CVD).Methods and resultsPremature atrial contractions and PVCs were identified in 15 s single-lead ECGs from N = 54 016 UK Biobank participants (median age, interquartile range, age 58, 50–63 years, 54% female). Cox regression models adjusted for traditional risk factors were used to determine associations with atrial fibrillation (AF), heart failure (HF), myocardial infarction (MI), stroke, life-threatening ventricular arrhythmias (LTVAs), and mortality over a period of 11.5 (11.4–11.7) years. The strongest associations were found between PVCs (prevalence 2.2%) and HF (hazard ratio, HR, 95% confidence interval = 2.09, 1.58–2.78) and between PACs (prevalence 1.9%) and AF (HR = 2.52, 2.11–3.01), with shorter prematurity further increasing risk. Premature ventricular contractions and PACs were also associated with LTVA (P &lt; 0.05). Associations with MI, stroke, and mortality were significant only in unadjusted models. In a separate UK Biobank sub-study sample [UKB-2, N = 29,324, age 64, 58–60 years, 54% female, follow-up 3.5 (2.6–4.8) years] used for independent validation, after adjusting for risk factors, PACs were associated with AF (HR = 1.80, 1.12–2.89) and PVCs with HF (HR = 2.32, 1.28–4.22).ConclusionIn middle-aged individuals without CVD, premature contractions identified in 15 s single-lead ECGs are strongly associated with an increased risk of AF and HF. These data warrant further investigation to assess the role of wearable ECGs for early cardiovascular risk stratification.
Real-world clinical outcomes with a next-generation left atrial appendage closure device: the FLXibility Post-Approval Study
Authors: Betts Tim R , Grygier Marek , Nielsen Kudsk Jens Erik , Schmitz Thomas , Sandri Marcus , Casu Gavino , Bergmann Martin , Hildick-Smith David , Christen Thomas , Allocco Dominic J ,   For the FLXibility investigators
Published: February 2023

AbstractAimsThe FLXibility Post-Approval Study collected data on unselected patients implanted with a WATCHMAN FLX in a commercial clinical setting.Methods and resultsPatients were implanted with a WATCHMAN FLX per local standard of care, with a subsequent first follow-up visit from 45 to 120 days post-implant and a final follow-up at 1-year post-procedure. A Clinical Event Committee adjudicated all major adverse events and TEE/CT imaging results were adjudicated by a core laboratory. Among 300 patients enrolled at 17 centres in Europe, the mean age was 74.6 ± 8.0 years, mean CHA2DS2-VASc score was 4.3 ± 1.6, and 62.1% were male. The device was successfully implanted in 99.0% (297/300) of patients. The post-implant medication regimen was DAPT for 87.3% (262/300). At first follow-up, core-lab adjudicated complete seal was 88.2% (149/169), 9.5% (16/169) had leak &lt;3 mm, 2.4 (4/169) had leak ≥3 mm to ≤5 mm, and 0% had &gt;5 mm leak. At 1 year, 93.3% (280/300) had final follow-up; 60.5% of patients were on a single antiplatelet medication, 21.4% were on DAPT, 5.6% were on direct oral anticoagulation, and 12.1% were not taking any antiplatelet/anticoagulation medication. Adverse event rates through 1 year were: all-cause death 10.8% (32/295); CV/unexplained death 5.1% (15/295); disabling and non-disabling stroke each 1.0% (3/295, all non-fatal); pericardial effusion requiring surgery or pericardiocentesis 1.0% (3/295); and device-related thrombus 2.4% (7/295).ConclusionThe WATCHMAN FLX device had excellent procedural success rates, high LAA seal rates, and low rates of thromboembolic events in everyday clinical practice.
Performance Based on Measurements from Individual-Tree Progeny Tests Strongly Predicts Early Stand Yield in Loblolly Pine
Authors: Shalizi Mohammad Nasir , Walker Trevor D , Heine Austin J , Payn Kitt G , Isik Fikret , Bullock Bronson P , McKeand Steven E 
Published: February 2023

AbstractTo facilitate the utility of genetic improvement in loblolly pine, individual-tree volume (productivity) scores estimated from single-tree plot or row-plot progeny test designs were compared with stand-level volume per unit area from block plots. A large number of families representing a wide range of progeny test scores for volume were established in growth and yield trials to generalize the results to families created by the breeding program. Individual-tree volume scores from progeny tests strongly corresponded with stand-level volume from block plots, especially after accounting for site quality and the risk of fusiform rust disease. A ten-point increase in the volume score from progeny test data was estimated to increase stand-level volume by 3.9 m3 ha-1 at age 6 years. A prediction model is presented that includes a new statistic, rust risk index, which is the expected rust incidence for a family at a new site when the hazard of rust for a checklot can be estimated from historical data. The study results through age 6 years corroborate the Performance Rating System as effective in guiding family deployment decisions. The models presented are based on pre-crown closure data at 6 years and will be updated with older measurements as the study matures.Study Implications: The Performance Rating System (PRS™) has been a successful tool for presenting genetic merit of improved loblolly pine families for landowners and forest managers in a more coherent and standardized manner. This system can be easily applied in other forest tree improvement programs, because it makes genetic improvement user-friendly for silviculturists and forest managers. Landowners can use this system to make decisions for selecting improved families suited to their specific forest management objectives. Seed orchard and nursery managers also depend on the PRS to choose the families to produce and as a third-party verification to market their genetic merit to customers. This study demonstrates that higher stand-level volume per unit area can be achieved when forest managers plant fast growing families with low fusiform rust disease risk on productive sites. The combined effect of genetic improvement for productivity and fusiform rust disease resistance is significant on stand-level volume per unit area.
Organizational and Resident Characteristics of Nursing Homes Associated With Partial and Complete Implementation of the Preferences for Everyday Living Inventory
Authors: Madrigal Caroline , Moore Reese , Kunkel Miranda C , Bowblis John R , Straker Jane , Van Haitsma Kimberly , Abbott Katherine M 
Published: February 2023

AbstractBackground and ObjectivesPerson-centered care practices are essential to providing high-quality care for nursing home (NH) residents. A key component of implementing person-centered care is the assessment and fulfillment of residents’ preferences. However, few NHs consistently assess and implement residents’ preferences into care. From 2015 to 2019, the Ohio Department of Medicaid added the Preference for Everyday Living Inventory (PELI), a scientifically validated tool to assess residents’ preferences, as a quality indicator to improve the person centeredness of Ohio’s NHs. In this study, we sought to identify the associations between resident and organizational characteristics and PELI implementation in Ohio NHs.Research Design and MethodsWe constructed an NH-level database that merged data from the Ohio Biennial Survey of Long-Term Care Facilities, Ohio Medicaid Cost Reports, the Certification and Survey Provider Enhanced Reports data, the WWAMI Rural Health Research Center, and the Minimum Data Set. Freestanding NHs were included if they were owned by a for-profit or not-for-profit organization, and had data collected in 1 of 2 years (n = 1,320; year 2015, n = 814; year 2017, n = 506). Descriptive statistics and multiple logistic regression were used to understand the relationships between resident demographics, NH organizational characteristics, and partial versus complete PELI implementation.ResultsMost NHs (71.2%) reported complete implementation of the PELI over 2 years with implementation increasing over time. There was a relationship between complete PELI implementation and for-profit status, higher number of beds, higher Medicare funding, higher certified nursing assistants and activity staff hours, and urban location.Discussion and ImplicationsThis work has important implications for the implementation of person-centered care interventions in NHs and our understanding of what NH characteristics are related to successful implementation. The next steps should include a continued, detailed assessment of PELI implementation and an exploration of the potential impact of PELI implementation on residents, staff, and organizational outcomes.
Biopsy-detected myocardial fibrosis predicts adverse cardiac events after pulmonary valve replacement in patients with repaired tetralogy of Fallot
Authors: Yuan Jianhui , Su Zhanhao , Wang Guanxi , Yang Keming , Zhang Benqing , Ma Kai , Zhang Sen , Yang Yang , Feng Zicong , Mao Fengqun , He Qiyu , Dou Zheng , Li Shoujun 
Published: February 2023

AbstractOBJECTIVESRisk factors associated with adverse cardiac events (cardiac AEs) after pulmonary valve replacement (PVR) in patients with repaired tetralogy of Fallot are incompletely understood. In this study, we aimed to determine the relationship between histological myocardial fibrosis and cardiac AEs after PVR in patients with rTOF.METHODSWe consecutively collected clinical, cardiac magnetic resonance, echocardiography and electrocardiogram data of 51 patients with rTOF who underwent surgical PVR. The right ventricular outflow tract tissue was collected during the PVR and the degree of histological myocardial fibrosis was determined by a tailor-made automated image analysis method of picrosirius red staining.RESULTSThe median follow-up time was 4.9 years, and 14 patients had cardiac AEs (a composite of heart failure admission and arrhythmia) during follow-up. The total analysis area of myocardial samples was 5782.18 mm2, and the median percentage of myocardial fibrosis was 20.6% (interquartile range 16.7–27.0%), which were significantly elevated in patients with cardiac AEs compared with patients without cardiac AEs (24.1% vs 19.7%, P = 0.007). Right ventricular ejection fraction and left ventricular end-systolic volume index were significantly associated with myocardial fibrosis in multivariable stepwise linear regression analysis (R2 = 0.238). Cox proportional hazards regression identified degree of myocardial fibrosis [hazard ratio 1.127; 95% confidence interval (CI) 1.047–1.213; P = 0.001] and age at PVR (hazard ratio 1.062; 95% CI 1.010–1.116; P = 0.019) were associated with increased risk of cardiac AEs. The incidence of adverse cardiac events was significantly increased when myocardial fibrosis &gt;20.1% and age at PVR &gt;18.2 years.CONCLUSIONSHistological myocardial fibrosis was associated with biventricular systolic functions in rTOF. Higher myocardial fibrosis and older age at PVR are independent risk factors for the adverse cardiac events after PVR in patients with rTOF.
Research recruitment through the patient portal: perspectives of community focus groups in Seattle and Atlanta
Authors: Porter Kathryn M , Kraft Stephanie A , Speight Candace D , Duenas Devan M , Niyibizi Nyiramugisha K , Mitchell Andrea , O’Connor M Rebecca , Gregor Charles , Liljenquist Kendra , Shah Seema K , Wilfond Benjamin S , Dickert Neal W 
Published: February 2023

Abstract

Objective
Research recruitment through patient portals (ie, patient-facing, web-based clinical interfaces) has the potential to be effective, efficient, and inclusive, but best practices remain undefined. We sought to better understand how patients view this recruitment approach.

Materials and Methods
We conducted 6 focus groups in Atlanta, GA and Seattle, WA with members of patient advisory committees and the general public. Discussions addressed acceptability of patient portal recruitment and communication preferences. Focus groups were audio-recorded, transcribed, and analyzed using deductive and inductive codes. Iterative team discussions identified major themes.

Results
Of 49 total participants, 20 were patient advisory committee members. Participants’ mean age was 49 (range 18–74); 59% identified as non-Hispanic White and 31% as Black/African American. Participants were supportive of patient portal recruitment and confident that messages were private and legitimate. Participants identified transparency and patient control over whether and how to participate as essential features. Concerns included the frequency of research messages and the ability to distinguish between research and clinical messages. Participants also discussed how patient portal recruitment might affect diversity and inclusion.

Discussion
Focus group participants generally found patient portal recruitment acceptable and perceived it as secure and trustworthy. Transparency, control, and attention to inclusiveness were identified as key considerations for developing best practices.

Conclusion
For institutions implementing patient portal recruitment programs, continued engagement with patient populations can help facilitate translation of these findings into best practices and ensure that implemented strategies accomplish intended goals.
Problem-oriented documentation: design and widespread adoption of a novel toolkit in a commercial electronic health record
Authors: Altman Richard L , Lin Chen-Tan , Earnest Mark 
Published: February 2023

Abstract

Background
Problem-oriented documentation is an accepted method of note construction which facilitates clinical thought processes. However, problem-oriented documentation is challenging to put into practice using commercially available electronic health record (EHR) systems.

Objective
Our goal was to create, iterate, and distribute a problem-oriented documentation toolkit within a commercial EHR that maximally supported clinicians’ thinking, was intuitive to use, and produced clear documentation.

Materials and Methods
We used an iterative design process that stressed visual simplicity, data integration, a predictable interface, data reuse, and clinician efficiency. Creation of the problem-oriented documentation toolkit required the use of EHR-provided tools and custom programming.

Results
We developed a problem-oriented documentation interface with a 3-column view showing (1) a list of visit diagnoses, (2) the current overview and assessment and plan for a selected diagnosis, and (3) a list of medications, labs, data, and orders relevant to that diagnosis. We also created a series of macros to bring information collected through the interface into clinicians’ notes. This toolkit was put into a live environment in February 2019. Over the first 9 months, the custom problem-oriented documentation toolkit was used in a total of 8385 discrete visits by 28 clinicians in 13 ambulatory departments. After 9 months, the go-live education and EHR optimization teams in our health system began promoting the toolkit to new and existing users of our EHR resulting in a significantly increased uptake by outpatient clinicians. In April 2022 alone, the toolkit was used in more than 92 000 ambulatory visits by 894 users in 271 departments across our health system.

Conclusions
As a health-system client of a commercial EHR, we developed and deployed a revised problem-oriented documentation toolkit that is used by clinicians more than 92 000 times a month. Key success elements include an emphasis on usability and an effective training effort.