bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fibrinogen levels and clot properties identify patients who benefit from catheter-directed thrombolysis after DVT
Authors: Iding Aaron F. J. , Alkarithi Ghadir , Cate Hugo ten , Ariëns Robert A. S. , ten Cate-Hoek Arina J. 
Published: March 2024

Abstract
Ultrasound-accelerated catheter–directed thrombolysis (UA-CDT) to improve patency after deep vein thrombosis (DVT) has not conclusively been shown to prevent postthrombotic syndrome (PTS) but might benefit patients who are unlikely to obtain patency with standard treatment. We hypothesized that these patients could be selected based on their fibrin clot properties. To study this, patients with acute iliofemoral DVT from the CAVA (Ultrasound-Accelerated Catheter-Directed Thrombolysis Versus Anticoagulation for the Prevention of Post-thrombotic Syndrome) trial had blood samples taken at inclusion. Fibrin clot properties in plasma were determined by turbidimetric clotting (lag time and maximal turbidity) and lysis assays (time to 50% lysis and lysis rate), permeation assay, and confocal microscopy (fiber density), as well as levels of fibrin clot modifiers fibrinogen and C-reactive protein (CRP). Patency was defined as &gt;90% iliofemoral vein compressibility at 12-month ultrasound. PTS was defined as ≥5 Villalta score at 6 or 12 months. In total, 91 of 152 patients were included, including 43 with additional UA-CDT and 48 with standard treatment. Patients with additional UA-CDT more often obtained patency (55.8 vs 27.1%) Patients who obtained patency had longer lag times and lower maximal turbidity, fibrinogen, and CRP; only maximal turbidity and fibrinogen remained associated when adjusting for treatment, thrombus load, and body mass index. Fibrinogen levels had an optimal cutoff at 4.85 g/L. Low fibrinogen levels best predicted patency. Additional UA-CDT decreased the risk of PTS only in patients with high fibrinogen. Therefore, additional UA-CDT might prevent PTS in selected patients based on routinely measured fibrinogen levels. This study was registered at www.ClinicalTrials.gov as #NCT00970619.
Polysomnographic airflow shapes and site of collapse during drug-induced sleep endoscopy
Authors: Op de Beeck Sara , Vena Daniel , Mann Dwayne , Azarbarzin Ali , Huyett Phillip , Van de Perck Eli , Gell Laura K. , Alex Raichel M. , Dieltjens Marijke , Willemen Marc , Verbraecken Johan , Wellman Andrew , Vanderveken Olivier M. , Sands Scott A. 
Published: March 2024

BackgroundDifferences in the pharyngeal site of collapse influence efficacy of non-continuous positive airway pressure therapies for obstructive sleep apnoea (OSA). Notably, complete concentric collapse at the level of the palate (CCCp) during drug-induced sleep endoscopy (DISE) is associated with reduced efficacy of hypoglossal nerve stimulation, but CCCp is currently not recognisable using polysomnography. Here we develop a means to estimate DISE-based site of collapse using overnight polysomnography.Methods182 OSA patients provided DISE and polysomnography data. Six polysomnographic flow shape characteristics (mean during hypopnoeas) were identified as candidate predictors of CCCp (primary outcome variable, n=44/182), including inspiratory skewness and inspiratory scoopiness. Multivariable logistic regression combined the six characteristics to predict clear presence (n=22)versusabsence (n=128) of CCCp (partial collapse and concurrent tongue base collapse excluded). Odds ratios for actual CCCp between predicted subgroups were quantified after cross-validation. Secondary analyses examined complete lateral wall, tongue base or epiglottis collapse. External validation was performed on a separate dataset (ntotal=466).ResultsCCCp was characterised by greater scoopiness (β=1.5±0.6 per 2sd, multivariable estimate±se) and skewness (β=11.4±2.4) compared with non-CCCp. The odds ratio for CCCp in predicted positiveversusnegative subgroups was 5.0 (95% CI 1.9–13.1). The same characteristics provided significant cross-validated prediction of lateral wall (OR 6.3, 95% CI 2.4–16.5), tongue base (OR 3.2, 95% CI 1.4–7.3) and epiglottis (OR 4.4, 95% CI 1.5–12.4) collapse. CCCp and lateral wall collapse shared similar characteristics (skewed, scoopy), diametrically opposed to tongue base and epiglottis collapse characteristics. External validation confirmed model prediction.ConclusionsThe current study provides a means to recognise patients with likely CCCp or other DISE-based site of collapse categories using routine polysomnography. Since site of collapse influences therapeutic responses, polysomnographic airflow shape analysis could facilitate precision site-specific OSA interventions.
Physical capacity and inactivity in obstructive airway diseases: a “can do, do do” analysis
Authors: Urroz Guerrero Paola D. , Lewthwaite Hayley , Gibson Peter G. , Clark Vanessa L. , Cordova-Rivera Laura , McDonald Vanessa M. 
Published: March 2024

IntroductionPhysical capacity is an important determinant of physical activity in people with obstructive airway disease (OAD). This study aimed to extend the “can do, do do” concept in people with OAD, to identify if people categorised into quadrants based on physical capacity and activity differ by clinical and movement behaviour characteristics.MethodsA total of 281 participants (bronchiectasis n=60, severe asthma n=93, COPD n=70 and control n=58) completed assessments to characterise physical capacity as “can do”versus“can't do” (6-min walk distance < or ≥70% pred) and physical activity as “do do”versus“don't do” (accelerometer-derived moderate to vigorous intensity physical activity (MVPA) < or ≥150 min·week−1).ResultsThe control group had a greater proportion of people in the “can do, do do” quadrant compared with the OAD groups (76%versus10–33%). People with OAD in the “can't do, don‘t do” quadrant had worse clinical characteristics (airflow limitation, comorbidities, quality of life and functional dyspnoea) and spent less time doing light-intensity physical activity (LPA) and more time being sedentary compared with the “can do, do do” quadrant.DiscussionThis study highlights that many people with OAD may be inactive because they do not have the physical capacity to participate in MVPA, which is further impacted by greater disease severity. It is important to consider the potential benefits of addressing LPA and sedentary behaviour due to suboptimal levels of these movement behaviours across different quadrants. Future research is needed to investigate if tailoring intervention approaches based on quadrant allocation is effective in people with OAD.
Modified blood cell GAP model as a prognostic biomarker in idiopathic pulmonary fibrosis
Authors: Kreuter Michael , Lee Joyce S. , Tzouvelekis Argyrios , Oldham Justin M. , Molyneaux Philip L. , Weycker Derek , Atwood Mark , Samara Katerina , Kirchgässler Klaus-Uwe , Maher Toby M. 
Published: March 2024

BackgroundThe Gender, Age and Physiology (GAP) model is a simple mortality prediction tool in patients with idiopathic pulmonary fibrosis that uses demographic and physiological variables available at initial evaluation. White blood cell variables may have associations with idiopathic pulmonary fibrosis outcomes. We evaluated whether incorporating blood cell counts in modified GAP (cGAP) models would improve outcome prediction in patients with idiopathic pulmonary fibrosis.Patients and methodsThis retrospective analysis included pooled data from phase 3 randomised trials of pirfenidone in idiopathic pulmonary fibrosis (ASCEND, CAPACITY 004, CAPACITY 006). Study outcomes (disease progression, all-cause mortality, all-cause hospitalisation, respiratory-related hospitalisation) were evaluated during the initial 1-year period. Shared frailty models were used to evaluate associations between continuous and categorical baseline white and red blood cell parameters and study outcomes in a bivariate context, and to evaluate the impact of adding continuous monocyte count (cGAP1) or white and red blood cell parameters (cGAP2) to traditional GAP variables in a multivariable context based on C-statistics changes.ResultsData were pooled from 1247 patients (pirfenidone, n=623; placebo, n=624). Significant associations (bivariate analyses) were idiopathic pulmonary fibrosis progression with neutrophil and eosinophil counts; all-cause mortality with monocyte and neutrophil counts; all-cause hospitalisation with monocyte count, neutrophil count and haemoglobin level; and respiratory-related hospitalisation with monocyte count, neutrophil count and haemoglobin level. In multivariate analyses, C-statistics were highest for the cGAP2 model for each of the outcomes.ConclusionModified GAP models incorporating monocyte counts alone or plus other white and red blood cell variables may be useful to improve prediction of outcomes in patients with idiopathic pulmonary fibrosis.
Long-term impact of COVID-19 hospitalisation among individuals with pre-existing airway diseases in the UK: a multicentre, longitudinal cohort study – PHOSP-COVID
Authors: Elneima Omer , Hurst John R. , Echevarria Carlos , Quint Jennifer K. , Walker Samantha , Siddiqui Salman , Novotny Petr , Pfeffer Paul E. , Brown Jeremy S. , Shankar-Hari Manu , McAuley Hamish J.C. , Leavy Olivia C. , Shikotra Aarti , Singapuri Amisha , Sereno Marco , Richardson Matthew , Saunders Ruth M. , Harris Victoria C. , Houchen-Wolloff Linzy , Greening Neil J. , Harrison Ewen M. , Docherty Annemarie B. , Lone Nazir I. , Chalmers James D. , Ho Ling-Pei , Horsley Alex , Marks Michael , Poinasamy Krisnah , Raman Betty , Evans Rachael A. , Wain Louise V. , Sheikh Aziz , Brightling Chris E. , De Soyza Anthony , Heaney Liam G. 
Published: March 2024

BackgroundThe long-term outcomes of COVID-19 hospitalisation in individuals with pre-existing airway diseases are unknown.MethodsAdult participants hospitalised for confirmed or clinically suspected COVID-19 and discharged between 5 March 2020 and 31 March 2021 were recruited to the Post-hospitalisation COVID-19 (PHOSP-COVID) study. Participants attended research visits at 5 months and 1 year post discharge. Clinical characteristics, perceived recovery, burden of symptoms and health-related quality of life (HRQoL) of individuals with pre-existing airway disease (i.e., asthma, COPD or bronchiectasis) were compared to the non-airways group.ResultsA total of 615 out of 2697 (22.8%) participants had a history of pre-existing airway diseases (72.0% diagnosed with asthma, 22.9% COPD and 5.1% bronchiectasis). At 1 year, the airways group participants were less likely to feel fully recovered (20.4%versus33.2%, p<0.001), had higher burden of anxiety (29.1%versus22.0%, p=0.002), depression (31.2%versus24.7%, p=0.006), higher percentage of impaired mobility using short physical performance battery ≤10 (57.4%versus45.2%, p<0.001) and 27% had a new disability (assessed by the Washington Group Short Set on Functioning)versus16.6%, p=0.014. HRQoL assessed using EQ-5D-5L Utility Index was lower in the airways group (mean±SD 0.64±0.27versus0.73±0.25, p<0.001). Burden of breathlessness, fatigue and cough measured using a study-specific tool was higher in the airways group.ConclusionIndividuals with pre-existing airway diseases hospitalised due to COVID-19 were less likely to feel fully recovered, had lower physiological performance measurements, more burden of symptoms and reduced HRQoL up to 1 year post-hospital discharge.
Comparison of structural variant callers for massive whole-genome sequence data
Authors: Joe Soobok , Park Jong-Lyul , Kim Jun , Kim Sangok , Park Ji-Hwan , Yeo Min-Kyung , Lee Dongyoon , Yang Jin Ok , Kim Seon-Young 
Published: March 2024

Abstract
Background
Detecting structural variations (SVs) at the population level using next-generation sequencing (NGS) requires substantial computational resources and processing time. Here, we compared the performances of 11 SV callers: Delly, Manta, GridSS, Wham, Sniffles, Lumpy, SvABA, Canvas, CNVnator, MELT, and INSurVeyor. These SV callers have been recently published and have been widely employed for processing massive whole-genome sequencing datasets. We evaluated the accuracy, sequence depth, running time, and memory usage of the SV callers.

Results
Notably, several callers exhibited better calling performance for deletions than for duplications, inversions, and insertions. Among the SV callers, Manta identified deletion SVs with better performance and efficient computing resources, and both Manta and MELT demonstrated relatively good precision regarding calling insertions. We confirmed that the copy number variation callers, Canvas and CNVnator, exhibited better performance in identifying long duplications as they employ the read-depth approach. Finally, we also verified the genotypes inferred from each SV caller using a phased long-read assembly dataset, and Manta showed the highest concordance in terms of the deletions and insertions.

Conclusions
Our findings provide a comprehensive understanding of the accuracy and computational efficiency of SV callers, thereby facilitating integrative analysis of SV profiles in diverse large-scale genomic datasets.
Metabolomics analysis reveals the metabolite profiles of Rheum tanguticum grown under different altitudinal gradients
Authors: Wang Lingling , Zhao Shuo , Li Jianan , Zhou Guoying 
Published: March 2024

Abstract
Background
Plant growth and quality are often affected by environmental factors, including geographical location, climate, and soil. In this study, we describe the effect of altitudinal differences on the growth and active ingredients in Rheum tanguticum Maxim. ex Balf. (R. tanguticum), a traditional Chinese medicinal herb known for its laxative properties.

Results
The results showed that plants grown at lower altitudes had better growth performances than those in higher altitude areas. The yield varied by 2.45–23.68 times with altitude, reaching a maximum of 102.01 t/ha. In addition, total anthraquinone and total sennoside contents decreased with increasing altitude, whereas total tannins increased with increasing altitude. The total anthraquinone content of the indicator compound reached 5.15% at five experimental sites, which exceeded the Chinese Pharmacopoeia standard by 70.87%. The content of the other two categories of active ingredients reached a maximum value of 0.94% (total sennosides) and 2.65% (total tannins). Redundancy analysis revealed that annual rainfall, annual average temperature, annual sunshine hours, and pH significantly affected growth and active ingredients. Moreover, key metabolites, such as flavonoids, amino acids and their derivatives, phenolic acids, lipids, and terpenes, were differentially expressed between samples from low- and high-altitude cultivation areas. These metabolites were enriched in the flavonoid and flavonol biosynthetic pathway and the monoterpene biosynthetic pathway.

Conclusions
These results suggest that high anthraquinone content was observed in the lowest-latitude cultivation area due to low rainfall and alkaline soil pH. Key metabolites were significantly upregulated in high-latitude cultivation areas. These results provide a scientific basis for quality control and the systematic cultivation of R. tanguticum.
The impact of preoperative biliary drainage on postoperative healthcare-associated infections and clinical outcomes following pancreaticoduodenectomy: a ten-year retrospective analysis
Authors: Yu Zheng-Hao , Du Ming-Mei , Zhang Xuan , Suo Ji-Jiang , Zeng Tao , Xie Xiao-Lian , Xiao Wei , Lu Qing-Bin , Liu Yun-Xi , Yao Hong-Wu 
Published: March 2024

Abstract
Background
Pancreaticoduodenectomy (PD) is a complex procedure and easily accompanied by healthcare-associated infections (HAIs). This study aimed to assess the impact of PBD on postoperative infections and clinical outcomes in PD patients.

Methods
The retrospective cohort study were conducted in a tertiary hospital from January 2013 to December 2022. Clinical and epidemiological data were collected from HAIs surveillance system and analyzed.

Results
Among 2842 patients who underwent PD, 247 (8.7%) were diagnosed with HAIs, with surgical site infection being the most frequent type (n = 177, 71.7%). A total of 369 pathogenic strains were detected, with Klebsiella pneumoniae having the highest proportion, followed by Enterococcu and Escherichia coli. Although no significant association were observed generally between PBD and postoperative HAIs, subgroup analysis revealed that PBD was associated with postoperative HAIs in patients undergoing robotic PD (aRR = 2.174; 95% CI:1.011–4.674; P = 0.047). Prolonging the interval between PBD and PD could reduce postoperative HAIs in patients with cholangiocarcinoma (≥4 week: aRR = 0.292, 95% CI 0.100–0.853; P = 0.024) and robotic PD (≤2 week: aRR = 3.058, 95% CI 1.178–7.940; P = 0.022). PBD was also found to increase transfer of patients to ICU (aRR = 1.351; 95% CI 1.119–1.632; P = 0.002), extended length of stay (P < 0.001) and postoperative length of stay (P = 0.004).

Conclusion
PBD does not exhibit a significant association with postoperative HAIs or other outcomes. However, the implementation of robotic PD, along with a suitable extension of the interval between PBD and PD, appear to confer advantages concerning patients’ physiological recuperation. These observations suggest potential strategies that may contribute to enhanced patient outcomes.
Absorbent hygiene products disposal behaviour in informal settlements: identifying determinants and underlying mechanisms in Durban, South Africa
Authors: Slekiene Jurgita , Swan Nick , Kalina Marc 
Published: March 2024

Abstract
Background
Within South Africa, many low-income communities lack reliable waste management services. Within these contexts, absorbent hygiene product (AHP) waste, including nappies (diapers), are not recycled, and are often dumped, ending up in watercourses and polluting the local environment. The structural barriers to collection which have been well explored, however the behavioural determinants of safe disposal for AHPs remains poorly understood. The purpose of this study is to determine the psycho-social factors driving AHP disposal behaviour for caregivers, while identifying potential underlying mechanisms (such as mental health), which may be influencing disposal behaviour, with the intention of informing a future, contextually appropriate and sustainable, collection system.

Methods
The cross-sectional study was conducted within three low-income communities located within eThekwini Municipality (Durban), South Africa. The study included a pre-study and a quantitative survey of 452 caregivers, utilising the RANAS approach of behaviour change. The quantitative questionnaire was based on the RANAS model to measure psycho-social factors underlying sanitary disposal of AHPs. Mental health was assessed using the Self-Reporting Questionnaire (SRQ-20). Statistical analysis involved regressing psycho-social factors onto disposal behaviour and exploring their interaction with mental health through a moderation model.

Results
Our findings suggest that one third of caregivers do not dispose of nappies sanitarily, despite intent (86.9%). Regression analysis revealed ten psycho-social factors which significantly predict the desired behavioural outcome, the sanitary disposal of AHPs. Caregivers with poor mental health were less likely to dispose of AHP sanitarily, which reflects previous research linking poor mental health and the impairment of health-related daily activities, particularly within vulnerable groups. Specifically, several psycho-social factors underlying were moderated by poor mental health, the prevalence of sanitary disposal of AHPs depended on mental condition of caregiver.

Conclusions
Our findings confirmed the link between poor mental health and unsanitary AHPs disposal. This is especially relevant because poor mental health is common within South Africa. Addressing mental health problems within these communities is an essential step to providing sustainable waste management services. The findings informed an intervention strategy to implement a future collection system for these communities, and similar low-income or informal contexts within South Africa.
Chronic diseases and determinants of community health services utilization among adult residents in southern China: a community-based cross-sectional study
Authors: Gu Junwang , Wang Qi , Qiu Wei , Wu Chunmei , Qiu Xiaoqiang 
Published: March 2024

AbstractBackgroundThe burden of chronic diseases has become a major public health concern, and high-efficiency use of community health services is essential in combating chronic diseases. This study described the status of chronic diseases in southern China and explored the determinants of health service utilization among adult residents.MethodsData were obtained from one part of community survey data from four counties in Ganzhou City, southern China. A multistage, stratified random sampling method was used to conduct a cross-sectional survey between 2018 and 2020. Overall, 7430 valid questionnaires were collected. A lasso-linear regression analysis was performed to explore the determinants of community health service utilization.ResultsAccording to the study, most participants (44.6%) reported having relatively good health, while 42.1% reported having moderate health. Chronic diseases were reported by 66.9% of the respondents. The three most prevalent self-reported chronic diseases were hypertension (22.6%), hyperlipidemia (5.9%), and diabetes (5.9%). Among residents with chronic diseases, 72.1% had one chronic disease, while the rest had multiple. Only 13.9% of residents frequently utilized community health services, while 18.9% never used them. Additionally, among residents who reported having chronic diseases, 14.1% had never attended community health services. Four categories of factors were the key determinants of community health service utilization: (1) personal characteristics, age, and sex; (2) health-related factors, such as family history, self-reported health conditions, and the number of chronic diseases; (3) community health service characteristics, such as satisfaction with and accessibility to community health services; and (4) knowledge of chronic diseases. Specifically, women tend to utilize healthcare services more frequently than men. Additionally, residents who are advanced in age, have a family history of chronic diseases, suffer from multiple chronic conditions, rate their self-reported health condition as poor, have a better knowledge about chronic diseases, have better accessibility to community health services, and have higher the satisfaction with community health services, tend to utilize them more frequently.ConclusionsGiven the limited healthcare resources, the government should promote the effective utilization of community health facilities as a critical community-based strategy to combat the growing threat of chronic diseases in southern China. The priority measures involve enhancing residents’ access to and satisfaction with community health services and raising awareness of chronic illnesses among older individuals with poor health status.
A novel generative adversarial networks modelling for the class imbalance problem in high dimensional omics data
Authors: Cusworth Samuel , Gkoutos Georgios V. , Acharjee Animesh 
Published: March 2024

AbstractClass imbalance remains a large problem in high-throughput omics analyses, causing bias towards the over-represented class when training machine learning-based classifiers. Oversampling is a common method used to balance classes, allowing for better generalization of the training data. More naive approaches can introduce other biases into the data, being especially sensitive to inaccuracies in the training data, a problem considering the characteristically noisy data obtained in healthcare. This is especially a problem with high-dimensional data. A generative adversarial network-based method is proposed for creating synthetic samples from small, high-dimensional data, to improve upon other more naive generative approaches. The method was compared with ‘synthetic minority over-sampling technique’ (SMOTE) and ‘random oversampling’ (RO). Generative methods were validated by training classifiers on the balanced data.