bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computable Phenotype of a Crohn’s Disease Natural History Model
Authors: Kurowski Jacob A. , Achkar Jean-Paul , Sugano David , Milinovich Alex , Ji Xinge , Bauman Janine , Griffin Keyonna R. , Kattan Michael W. 
Published: June 2022

Background Analytic tools to study important clinical issues in complex, chronic diseases such as Crohn’s disease (CD) include randomized trials, claims database studies, or small longitudinal epidemiologic cohorts. Using natural language processing (NLP), we sought to define the computable phenotype health state of pediatric and adult CD and develop patient-level longitudinal histories for health outcomes. Methods We defined 6 health states for CD using a subjective symptom-based assessment (symptomatic/asymptomatic) and an objective disease state assessment (active/inactive/no testing). Gold standard for the 6 health states was derived using an iterative process during review by our CD experts. We calculated the transition probabilities to estimate the time to transitions between the various health states using nonparametric Kaplan-Meier estimation and a Markov model. Finally, we determined a standard utility measure from clinical patients assigned to different health states. Results The NLP computable phenotype health state model correctly ascertained the objective test results and symptoms 96% and 85% of the time, respectively, based on a blinded chart evaluation. In our model, >25% of patients who begin as asymptomatic/active transition to symptomatic/active over the following year. For both adult and pediatric CD health states, the utility assessments of a symptomatic/inactive health state closely resembled a symptomatic/active health state. Conclusions Our methodology for a computable phenotype health state demonstrates the application of real-world data to define progression and optimal management of a chronic disease such as CD. The application of the model has the potential to lead to a better understanding of the true impact of a therapeutic intervention and can provide long-term cost-effectiveness analyses for a new therapy. Highlights Using natural language processing, we defined the computable phenotype health state of Crohn’s disease and developed patient-level longitudinal histories for health outcomes. Our methodology demonstrates the application of real-world data to define the progression of a chronic disease. The application of the model has the potential to provide better understanding of the true impact of a new therapy.
Closure of the Quadriceps Tendon Autograft Harvest Site for Anterior Cruciate Ligament Reconstruction: A Systematic Review
Authors: Cole Wendell W. , Saraf Shreya M. , Stamm Michaela , Mulcahey Mary K. 
Published: June 2022

Background: The quadriceps tendon (QT) autograft is a commonly used and effective graft option for anterior cruciate ligament reconstruction (ACLR). Surgical techniques vary, and there is no current standard of care for management of the QT autograft harvest site. Purpose: To examine the literature on patient-reported outcomes and complications after ACLR with a QT autograft and to further clarify the frequency with which the harvest site is closed and potential biomechanical implications. Study Design: Systematic review; Level of evidence, 4. Methods: A systematic review according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines was performed using multiple medical databases. Level 1 to 4 studies on patients undergoing ACLR with a QT autograft were included. There were 2 independent reviewers who analyzed all studies. Study quality was analyzed using the methodological index for non-randomized studies checklist. Results: Overall, 13 studies with a total of 650 patients were included. The mean patient age for all studies was 31 years (range, 14-59 years) with a mean follow-up of 21.2 months (range, 6-84 months). Of the 13 studies, 12 studies (92%) documented patient sex, comprising 331 female patients (55%) and 274 male patients (45%). There were 8 studies (62%) that reported the use of a bony QT autograft in 273 patients, and 5 studies (38%) reported the use of a soft tissue QT autograft in 377 patients. The graft length harvested was most commonly 7 to 8 cm, while the tendon width harvested was 10 mm. Moreover, 5 studies (38%) did not discuss closure of the harvest site, while 2 studies (15%) only closed the harvest site if a capsular rent was present. The surgical technique for harvest-site closure varied when reported in 7 studies (54%). Good to excellent clinical outcomes were reported in 80% of patients when the harvest site was closed. Conclusion: Based on the results of this study, there is no consensus on whether the QT defect should be closed after harvesting the graft for ACLR. It has been reported that closure of the harvest site is performed if there is a capsular rent present. Several techniques are utilized to close the QT autograft harvest site; however, it is unclear if there is a difference in outcomes based on the technique used. Future studies should further clarify whether there are any biomechanical and clinical advantages to closing the QT autograft harvest site.
Stressors and Pain across the Late-Life Span: Findings from Two Parent Longitudinal Studies of Aging and Health
Authors: Brennan Penny L. 
Published: June 2022

Objective: The objective is to determine associations between stressors and pain across the late-life span. Method: Multilevel linear modeling was applied separately to harmonized repeated measures data from the Longitudinal Late-Life Health study (LLLH; n = 342; 13-year interval) and the Health and Retirement Study (HRS; n = 2959; 8-year interval). Results: In both the LLLH and HRS samples, independent of age, gender, and race, participants with higher average stressor levels experienced more numerous painful conditions and higher pain severity over the study intervals. In the HRS sample, they also experienced higher levels of pain interference. In general, participants’ stressor levels did not influence rates of increase in their pain. Gender and race had few moderating effects on associations between stressors and pain. Discussion: Stressors and pain are associated across the late-life span. Future research should focus on the mediating mechanisms that account for this association and the moderating factors that affect its strength.
The effect of community-acquired pneumonia on myocardial injury in systemic lupus erythematosus: Insights from cardiac magnetic resonance
Authors: Cui Beibei , Pu Huaxia , Liu Jing , He Wenzhang , Zhou Yi , Xiaoyue Zhou  , Lin Hui , Peng Liqing 
Published: June 2022

Objectives Myocardial injury (MInj) in systemic lupus erythematosus (SLE) has been observed in several studies. However, clinical predictors of MInj remain unclear. We aim to explore the effects of community-acquired pneumonia (CAP) on MInj in SLE patients according to cardiac magnetic resonance (CMR) T1 mapping. Methods SLE patients with or without CAP and healthy controls underwent CMR screening. The CMR protocol included: cines, T1- and T2 mapping, and late gadolinium enhancement (LGE). Clinical characteristics, CMR findings, and T1 mapping measuremments were compared between subgroups. Clinical assessment was performed on the subjects. Results Thirty-eight SLE patients were screened, including 18 patients with CAP (CAP group) and 20 age- and gender-matched patients without CAP (non-CAP group) as well as 26 healthy controls. The platelet count of CAP group was higher than the non-CAP group ( p = 0.015). Compared with the health control group, native T1 was higher in the CAP group ( p < 0.001) and the non-CAP group ( p = 0.002). ECV was higher in the CAP group ( p < 0.001) and the non-CAP group ( p = 0.002). The LV ejection fraction ( p = 0.049) and RV ejection fraction ( p = 0.026) of the CAP group was lower than that of the healthy control group, whereas no significant difference was observed between non-CAP and healthy control groups. Conclusions This is the first study that assesses the effects of CAP on MInj of SLE patients by CMRI T1 mapping. We highlight SLE patients with CAP who are at increased risk of MInj, manifesting as myocardial inflammation, diffuse myocardial fibrosis, and decreased ventricular function.
Treatment of posterior circulation stroke: Acute management and secondary prevention
Authors: Markus Hugh S , Michel Patrik 
Published: June 2022

One-fifth of strokes occur in the territory of the posterior circulation, but their management, particularly acute reperfusion therapy and neurointervention procedures for secondary prevention, has received much less attention than similar interventions for the anterior circulation. In this review, we overview the treatment of posterior circulation stroke, including both interventions in the acute setting and secondary prevention. We focus on areas in which the management of posterior circulation stroke differs from that of stroke in general and highlight recent advances. Effectiveness of acute revascularization of posterior circulation strokes remains in large parts unproven. Thrombolysis seems to have similar benefits and lower hemorrhage risks than in the anterior circulation. The recent ATTENTION and BAOCHE trials have demonstrated that thrombectomy benefits strokes with basilar artery occlusion, but its effect on other posterior occlusion sites remains uncertain. Ischemic and hemorrhagic space-occupying cerebellar strokes can benefit from decompressive craniectomy. Secondary prevention of posterior circulation strokes includes aggressive treatment of cerebrovascular risk factors with both drugs and lifestyle interventions and short-term dual anti-platelet therapy. Randomized controlled trial (RCT) data suggest basilar artery stenosis is better treated with medical therapy than stenting, which has a high peri-procedural risk. Limited data from RCTs in stenting for vertebral stenosis suggest that intracranial stenosis is currently best treated with medical therapy alone; the situation for extracranial stenosis is less clear where stenting for symptomatic stenosis is an option, particularly for recurrent symptoms; larger RCTs are required in this area.
A pulmonary rehabilitation shared decision-making intervention for patients living with COPD: PReSent: protocol for a feasibility study
Authors: Barradell Amy C. , Houchen-Wolloff Linzy , Robertson Noelle , Bekker Hilary L. , Singh Sally J. 
Published: June 2022

BackgroundDespite the variety of pulmonary rehabilitation programmes for patients living with COPD, uptake remains low. To improve this, it is recommended that health professionals engage patients in informed decisions about pulmonary rehabilitation. Shared decision-making (SDM) facilitates informed and value-based decision-making between patients and health professionals. This protocol describes the development and evaluation of a complex SDM intervention for patients living with COPD, who are referred for pulmonary rehabilitation, and their pulmonary rehabilitation health professional.Methods and analysisWe are developing a complex SDM intervention involving a patient decision aid (PtDA) and a decision coaching workshop. Prior to patient recruitment, pulmonary rehabilitation health professionals will attend the workshop. Upon referral to pulmonary rehabilitation, patients will receive the PtDA to support their decision-making prior to and during their pulmonary rehabilitation assessment with a health professional. The intervention will be evaluated in a one-arm exploratory study to investigate its feasibility and acceptability for patients and health professionals, with an integrated fidelity assessment. The primary outcome is recruitment feasibility, data collection feasibility and intervention fidelity. Secondary outcomes include routine pulmonary rehabilitation data, decisional conflict, patient activation, intervention attendance/attrition and patient and pulmonary rehabilitation health professional experience of the intervention. Quantitative outcomes will be evaluated using the most appropriate statistical test, dependent on the sample distribution. Qualitative outcomes will be evaluated using reflexive thematic analysis. Fidelity will be assessed using the Observer OPTION 5 scale.ConclusionThis intervention will provide structure for an informed and values-based decision-making consultation between a patient with COPD and a pulmonary rehabilitation health professional with the potential for optimising pulmonary rehabilitation decision-making.
Accurate reconstruction of viral genomes in human cells from short reads using iterative refinement
Authors: Lee Sau-Dan , Wu Man , Lo Kwok-Wai , Yip Kevin Y. 
Published: June 2022

Abstract
Background
After an infection, human cells may contain viral genomes in the form of episomes or integrated DNA. Comparing the genomic sequences of different strains of a virus in human cells can often provide useful insights into its behaviour, activity and pathology, and may help develop methods for disease prevention and treatment. To support such comparative analyses, the viral genomes need to be accurately reconstructed from a large number of samples. Previous efforts either rely on customized experimental protocols or require high similarity between the sequenced genomes and a reference, both of which limit the general applicability of these approaches. In this study, we propose a pipeline, named ASPIRE, for reconstructing viral genomes accurately from short reads data of human samples, which are increasingly available from genome projects and personal genomics. ASPIRE contains a basic part that involves de novo assembly, tiling and gap filling, and additional components for iterative refinement, sequence corrections and wrapping.

Results
Evaluated by the alignment quality of sequencing reads to the reconstructed genomes, these additional components improve the assembly quality in general, and in some particular samples quite substantially, especially when the sequenced genome is significantly different from the reference. We use ASPIRE to reconstruct the genomes of Epstein Barr Virus (EBV) from the whole-genome sequencing data of 61 nasopharyngeal carcinoma (NPC) samples and provide these sequences as a resource for EBV research.

Conclusions
ASPIRE improves the quality of the reconstructed EBV genomes in published studies and outperforms TRACESPipe in some samples considered.
Non-invasive quantification of pressure–volume loops in patients with Fontan circulation
Authors: Sjöberg Pia , Liuba Petru , Arheden Håkan , Heiberg Einar , Carlsson Marcus 
Published: June 2022

Abstract
Background
Pressure–volume (PV) loops provide comprehensive information of cardiac function, but commonly implies an invasive procedure under general anesthesia. A novel technique has made it possible to non-invasively estimate PV loops with cardiac magnetic resonance (CMR) and brachial pressure which would enable good volume estimation of often anatomically complex ventricles without the need of anesthesia in most cases. In this study we aimed to compare how hemodynamic parameters derived from PV loops in patients with Fontan circulation differ to controls.

Methods
Patients with Fontan circulation (n = 17, median age 12 years, IQR 6–15) and healthy controls (n = 17, 14 years, IQR 13–22) were examined with CMR. Short axis balanced steady-state free-precession cine images covering the entire heart were acquired. PV loops were derived from left ventricular volumes in all timeframes and brachial blood pressure from cuff sphygmomanometry.

Results
Fontan patients had lower stroke work, ventricular mechanical efficiency and external power compared to controls. Fontan patients with dominant right ventricle had higher potential energy indexed to body surface area but lower contractility (Ees) compared to controls. Fontan patients had higher arterial elastance (Ea) and Ea/Ees ratio than controls. Contractility showed no correlation with ejection fraction (EF) in Fontan patients irrespective of ventricular morphology. No difference was seen in energy per ejected volume between Fontan patients and controls.

Conclusions
This non-invasive PV-loop method could be used in future studies to show the potential prognostic value of these measures and if changes in ventricular function over time can be detected earlier by this method compared to changes in ventricular volumes and EF. In contrast to patients with acquired heart failure, Fontan patients had similar energy per ejected volume as controls which suggests similar ventricular oxygen consumption to deliver the same volume in Fontan patients as in controls.
Comprehensive assessment of holding urine as a behavioral risk factor for UTI in women and reasons for delayed voiding
Authors: Jagtap S. , Harikumar S. , Vinayagamoorthy V. , Mukhopadhyay S. , Dongre A. 
Published: June 2022

Abstract
Background
Women of reproductive age group have greater predilection to urinary tract infections (UTI). Various risk factors increase the prevalence in women. Emergence of multidrug resistant uropathogens make clinical management of UTI challenging. Here we assess holding of urine as risk factor of UTI in women and reasons for delayed voiding. We also investigate the relationship between frequency of UTIs and overall behavioural features, menstrual hygiene and attitude of women towards their own health issues.

Methods
A questionnaire based cross-sectional study was performed with 816 hostel residents with written consent. Self-reported data was statistically analysed using SPSS software. Urinalysis and urine culture were done for 50 women by random sampling to obtain the information on leading causative agents of UTI in the study population and their antimicrobial resistance profile.

Results
The prevalence of UTI among the participants without risk factors was found to be 27.5 (95% CI: 24.4–30.7). Attitude of women towards their own personal health issues and use of public toilets showed a correlation with prevalence of infection. Delay in urination on habitual basis was found to be associated with UTI. Uropathogens isolated by random sampling were resistant to multiple drugs that are generally used to treat UTI.

Conclusions
Holding urine for long time had proven to be an important risk factor and amongst different reasons of holding urine, holding due to poor sanitary condition of public toilets was the most common. Higher frequency of self-reported UTIs is related to holding of urine, behavioural features and attitude of women.
Ruptured peripheral superior cerebellar artery dissecting aneurysms associated with primitive trigeminal artery: a case report
Authors: Ito Sayaka , Higuchi Kazushi 
Published: June 2022

Abstract
Background
Persistent primitive trigeminal artery (PPTA) is a remnant of the carotid-vertebrobasilar anastomoses in the embryo. Although PPTAs are discovered incidentally in most cases, altered hemodynamics may lead to increased risk of stroke. To the best of our knowledge, no reports of PPTA associated with superior cerebellar artery (SCA) dissecting aneurysms have been published in the English language.
We describe the case of a patient who presented with subarachnoid hemorrhage (SAH) due to ruptured peripheral SCA dissecting aneurysms in association with PPTA. Additionally, we discuss the relationship between PPTA and peripheral SCA aneurysms and the treatment of peripheral SCA aneurysms.

Case presentation
A 43-year-old woman presented with acute onset of headache and nausea and admitted to our hospital. She was diagnosed with SAH due to ruptured left SCA dissecting aneurysm(s) and had undergone digital subtraction angiography. The left vertebral angiography showed aneurysmal dilatations of the left S2 segment (lateral pontomesencephalic segment) along with dissection through the segments of S2 and S3 (cerebellomesencephalic segment). It also showed ipsilateral PPTA. The left vertebral artery (VA) had normal caliber and the basilar artery segment proximal to the orifice of the left PPTA was not hypoplastic. The patient underwent proximal parent artery occlusion at the S2 segment via the left VA and was successfully treated with no neurological deficits having lasted 5 months.

Conclusions
The flow alteration with PPTA may have influenced the formation of SCA dissection in this patient. Further studies are needed to understand the etiology and treatment outcomes of peripheral SCA aneurysms better.
Characterization of the prevalence of excess weight in Brazil
Authors: Barancelli Marcia Domênica Cunico , Gazolla Marcio , Schneider Sergio 
Published: June 2022

Abstract
Introduction/Background
This work aims to analyse the prevalence of excess weight in Brazil to demonstrate the nutritional transition that is occurring. The data mobilized in the research are from the Food and Nutritional Surveillance System (FNSS).

Materials and methods
This study employed a quantitative approach from the FNSS online secondary data survey through reports of nutritional status in different phases of life (child, adolescent, adult, elderly and pregnant), in different macroregions of the country (South, Southeast, Midwest, Northeast and North) and with a 12-year historical series (2008 to 2019).

Results
In the adult life stage, there was a time trend of increasing excess weight in all regions of this historical series. The southern region of Brazil and the adult life stage had the highest national percentage of excess weight (69,1%) in 2019 and had the lowest percentage of eutrophy (29.3%) in the region in 2019. In the elderly life phase, in the South, Southeast and Midwest regions, excess weight was higher than the other outcomes in the time series, with the highest annual prevalence in the South region (58,6%) in 2019. In the adolescent life stage, there was a time trend of increasing excess weight in all regions, and excess weight had the highest prevalence in 2019 in the South (35,8%). The lowest prevalence rates of excess weight were in the following age groups: children aged 0 to <  2 years old and children aged 2 to <  5 years old. Additionally, it was in Group 5 to < 10 years old that the most critical prevalence of excess weight (35,07%) was found in 2018. However, malnutrition (low weight) persists, especially in the elderly and children. In the pregnancy life stage, there was a temporal trend of increase in excess weight in all regions, with higher percentages in 2019 in the South (53.5%) and Southeast (50.8%).

Conclusion
Excess weight has shown increasing time trends in the adolescent, adult, elderly and pregnant life stages in all regions of Brazil, suggesting that public FNS policymakers should be more assertive in the planning and management of programs and actions to reduce the percentages of diseases.