bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical characteristics associated with small airways disease in systemic sclerosis
Authors: Varma Sanskriti , Yun Jae Hee , Kim John S , Podolanczuk Anna J , Patel Nina M , Bernstein Elana J 
Published: March 2022

Objective: Pulmonary manifestations of systemic sclerosis are a major cause of morbidity and mortality. Small airways disease can cause dyspnea and pulmonary function test abnormalities. We aimed to determine the prevalence of small airways disease and describe the characteristics associated with small airways disease in a cohort of systemic sclerosis patients. Methods: We performed a retrospective cohort study of adults with systemic sclerosis who met American College of Rheumatology/European League Against Rheumatism 2013 classification criteria and were evaluated at our institution between November 2000 and November 2015. Patients with prior lung transplantation were excluded. Small airways disease was defined as the presence of one or more of the following: airway-centered fibrosis on surgical lung biopsy, forced expiratory volume at 25–75% ⩽ 50% on pulmonary function tests, and/or high-resolution computed tomography scan of the chest with bronchiolitis, mosaic attenuation, or air trapping on expiratory views. The primary outcome was small airways disease diagnosis. We performed multivariable logistic regression to determine the association of clinical variables with small airways disease. Results: One-hundred thirty-six systemic sclerosis patients were included; 55 (40%) had small airways disease. Compared to those without small airways disease, a significantly greater proportion of those with small airways disease had interstitial lung disease, chronic obstructive pulmonary disease, pulmonary hypertension, and gastroesophageal reflux disease. On multivariable analysis, pulmonary hypertension (odds ratio = 2.91, 95% confidence interval = 1.11–7.65, p-value = 0.03), gastroesophageal reflux disease (odds ratio = 2.70, 95% confidence interval = 1.08–6.79, p-value = 0.034), and anti-topoisomerase I (anti-Scl-70) antibody positivity (odds ratio = 0.42, 95% confidence interval = 0.19–0.93, p-value = 0.033) were associated with diagnosis of small airways disease. Conclusion: Small airways disease is prevalent among systemic sclerosis patients; those with pulmonary hypertension or gastroesophageal reflux disease may have a higher risk of small airways disease.
Lightweight ProteinUnet2 network for protein secondary structure prediction: a step towards proper evaluation
Authors: Stapor Katarzyna , Kotowski Krzysztof , Smolarczyk Tomasz , Roterman Irena 
Published: March 2022

AbstractBackgroundThe prediction of protein secondary structures is a crucial and significant step for ab initio tertiary structure prediction which delivers the information about proteins activity and functions. As the experimental methods are expensive and sometimes impossible, many SS predictors, mainly based on different machine learning methods have been proposed for many years. Currently, most of the top methods use evolutionary-based input features produced by PSSM and HHblits software, although quite recently the embeddings—the new description of protein sequences generated by language models (LM) have appeared that could be leveraged as input features. Apart from input features calculation, the top models usually need extensive computational resources for training and prediction and are barely possible to run on a regular PC. SS prediction as the imbalanced classification problem should not be judged by the commonly used Q3/Q8 metrics. Moreover, as the benchmark datasets are not random samples, the classical statistical null hypothesis testing based on the Neyman–Pearson approach is not appropriate.ResultsWe present a lightweight deep network ProteinUnet2 for SS prediction which is based on U-Net convolutional architecture and evolutionary-based input features (from PSSM and HHblits) as well as SPOT-Contact features. Through an extensive evaluation study, we report the performance of ProteinUnet2 in comparison with top SS prediction methods based on evolutionary information (SAINT and SPOT-1D). We also propose a new statistical methodology for prediction performance assessment based on the significance from Fisher–Pitman permutation tests accompanied by practical significance measured by Cohen’s effect size.ConclusionsOur results suggest that ProteinUnet2 architecture has much shorter training and inference times while maintaining results similar to SAINT and SPOT-1D predictors. Taking into account the relatively long times of calculating evolutionary-based features (from PSSM in particular), it would be worth conducting the predictive ability tests on embeddings as input features in the future. We strongly believe that our proposed here statistical methodology for the evaluation of SS prediction results will be adopted and used (and even expanded) by the research community.
High morphological disparity in a bizarre Paleocene fauna of predatory freshwater reptiles
Authors: Brownstein Chase Doran 
Published: March 2022

Abstract
Background
The consequences of the K-Pg mass extinction are reflected across present biodiversity, but many faunas that appeared immediately after the extinction event were very different from current ones. Choristodera is a clade of reptiles of uncertain phylogenetic placement that have an extremely poor fossil record throughout their 150-million-year history. Yet, choristoderes survived the K-Pg event and persisted until the Miocene.

Results
I describe the skulls and skeletons of two new choristoderes from a single Paleocene ecosystem in western North America that reveal the hidden Cenozoic diversity of this reptile clade. Despite their similar size, the new species deviate dramatically in morphology. Kosmodraco magnicornis gen. et sp. nov. possesses an extremely short snout and extensive cranial ornamentation. The sacrum of K. magnicornis bears enlarged muscle attachment sites and other modifications reminiscent of some giant crocodylians. In contrast, Champsosaurus norelli sp. nov. is a longirostrine species with an uninflated and ventrally divergent postorbital skull. Together with a North American choristodere previously classified in the European genus Simoedosaurus, K. magnicornis substantiates a new clade of giant, short-snouted taxa endemic to the Americas. C. norelli is found to be an early-diverging member of the genus Champsosaurus from the Cretaceous-Paleogene of the northern hemisphere. This suggests the presence of several ghost lineages of champsosaurid that crossed the K-Pg boundary.

Conclusions
The new taxa greatly increase Cenozoic choristodere richness and strengthen the evidence for the existence of distinctive freshwater faunas in Paleogene Eurasia and North America, where this clade diversified to exploit newly available macropredatory niches in the aftermath of the asteroid impact. The new choristoderes also reveal the distinct ecological context in which extant freshwater predators of the Americas like alligatoroids and gars have their origins: Paleocene fluviolacustrine ecosystems in North America displayed high large predator diversity and morphological disparity relative to modern ones.
Comparative plastome analysis of Musaceae and new insights into phylogenetic relationships
Authors: Fu Ning , Ji Meiyuan , Rouard Mathieu , Yan Hai-Fei , Ge Xue-Jun 
Published: March 2022

Abstract
Background
Musaceae is an economically important family consisting of 70-80 species. Elucidation of the interspecific relationships of this family is essential for a more efficient conservation and utilization of genetic resources for banana improvement. However, the scarcity of herbarium specimens and quality molecular markers have limited our understanding of the phylogenetic relationships in wild species of Musaceae. Aiming at improving the phylogenetic resolution of Musaceae, we analyzed a comprehensive set of 49 plastomes for 48 species/subspecies representing all three genera of this family.

Results
Musaceae plastomes have a relatively well-conserved genomic size and gene content, with a full length ranging from 166,782 bp to 172,514 bp. Variations in the IR borders were found to show phylogenetic signals to a certain extent in Musa. Codon usage bias analysis showed different preferences for the same codon between species and three genera and a common preference for A/T-ending codons. Among the two genes detected under positive selection (dN/dS > 1), ycf2 was indicated under an intensive positive selection. The divergent hotspot analysis allowed the identification of four regions (ndhF-trnL, ndhF, matK-rps16, and accD) as specific DNA barcodes for Musaceae species.
Bayesian and maximum likelihood phylogenetic analyses using full plastome resulted in nearly identical tree topologies with highly supported relationships between species. The monospecies genus Musella is sister to Ensete, and the genus Musa was divided into two large clades, which corresponded well to the basic number of n = x = 11 and n = x =10/9/7, respectively. Four subclades were divided within the genus Musa. A dating analysis covering the whole Zingiberales indicated that the divergence of Musaceae family originated in the Palaeocene (59.19 Ma), and the genus Musa diverged into two clades in the Eocene (50.70 Ma) and then started to diversify from the late Oligocene (29.92 Ma) to the late Miocene. Two lineages (Rhodochlamys and Australimusa) radiated recently in the Pliocene /Pleistocene periods.

Conclusions
The plastome sequences performed well in resolving the phylogenetic relationships of Musaceae and generated new insights into its evolution. Plastome sequences provided valuable resources for population genetics and phylogenetics at lower taxon.
Assessment of radial artery atherosclerosis in acute coronary syndrome patients: an in vivo study using optical coherence tomography
Authors: Li Zixuan , Tang Zhe , Wang Yujie , Liu Zijing , Wang Guozhong , Zhang Libin , Wu Yongxia , Guo Jincheng 
Published: March 2022

Abstract
Background
Radial artery (RA) atherosclerosis in acute coronary syndrome (ACS) patients has not been systematically observed in vivo. The study aims to characterize plaque morphology and intimal hyperplasia of the RA in patients with ACS, using optical coherence tomography (OCT).

Methods
In this retrospective study involving 239 ACS patients underwent RA OCT without guidewire shadow, 3 groups were divided according to the following criteria: radial artery plaque (RAP) group included patients with fibrous, lipid or calcified plaque; patients without RAP were further classified into radial intimal hyperplasia (RIH) group (intima media thickness ratio [IMR] ≥ 1) or normal group (IMR < 1). The presence and characteristics of RAP and its related risk factors were identified.

Results
The RAP, RIH and normal groups included 76 (31.8%), 69 (28.9%) and 94 (39.3%) patients, respectively. Patients in RAP group were the oldest, compared with those in the RIH and normal groups (p < 0.001), and more frequently had triple vessel disease (p = 0.004). The percentage of plaque rupture (72.4% vs. 56.4%, p = 0.018) and calcification (42.1% vs. 27.6%, p = 0.026) at culprit lesion were significantly higher in patients with RAP than those without RAP. A total of 148 RAP were revealed by OCT, including fibrous (72, 48.6%), lipid (50, 33.8%) and calcified plaques (26, 17.6%). The microvessels were also frequently observed in the RAP group than that in RIH and normal groups (59.2% vs. 8.7% vs. 9.6%, p < 0.001). Multivariate logistic regression analysis showed that age, diabetes, and smoking history (all p < 0.05) were independent risk factors for RAP.

Conclusions
In terms of insights gained from OCT, RA atherosclerosis is not uncommon in ACS patients by OCT, sharing several morphological characters with early coronary atherosclerosis. Aging, diabetes, and smoking are risk factors for RAP.
Research monitoring practices in critical care research: a survey of current state and attitudes
Authors: Le Marsney Renate , Williams Tara , Johnson Kerry , George Shane , Gibbons Kristen S. 
Published: March 2022

Abstract
Background/Aims
In 2016, international standards governing clinical research recommended that the approach to monitoring a research project should be undertaken based on risk, however it is unknown whether this approach has been adopted in Australia and New Zealand (ANZ) throughout critical care research. The aims of the project were to: 1) Gain an understanding of current research monitoring practices in academic-led clinical trials in the field of critical care research, 2) Describe the perceived barriers and enablers to undertaking research monitoring.

Methods
Electronic survey distributed to investigators, research co-ordinators and other research staff currently undertaking and supporting academic-led clinical trials in the field of critical care in ANZ.

Results
Of the 118 respondents, 70 were involved in the co-ordination of academic trials; the remaining results pertain to this sub-sample. Fifty-eight (83%) were working in research units associated with hospitals, 29 (41%) were experienced Research Coordinators and 19 (27%) Principal Investigators; 31 (44%) were primarily associated with paediatric research. Fifty-six (80%) develop monitoring plans with 33 (59%) of these undertaking a risk assessment; the most common barrier reported was lack of expertise. Nineteen (27%) indicated that centralised monitoring was used, noting that technology to support centralised monitoring (45/51; 88%) along with support from data managers and statisticians (45/52; 87%) were key enablers. Coronavirus disease-19 (COVID-19) impacted monitoring for 82% (45/55) by increasing remote (25/45; 56%) and reducing onsite (29/45; 64%) monitoring.

Conclusions
Contrary to Good Clinical Practice guidance, risk assessments to inform monitoring plans are not being consistently performed due to lack of experience and guidance. There is an urgent need to enhance risk assessment methodologies and develop technological solutions for centralised statistical monitoring.
Developing a tool to assess the skills to perform a health technology assessment
Authors: Bidonde Julia , Meneses-Echavez Jose Francisco , Asare Brian , Chola Lumbwe , Gad Mohamed , Heupink Lieke Fleur , Peacocke Elizabeth Fleur ,   iDSI Ghana HTA collaboration Group, Ackon Angela , Dolphyne Akuba , Ruiz Francis , Sæterdal Ingvil , Espeland Anne Lien , Skjønsberg Eia Elena , Johansen Marit 
Published: March 2022

Abstract
Background
Health technology assessment (HTA) brings together evidence from various disciplines while using explicit methods to assess the value of health technologies. In resource-constrained settings, there is a growing demand to measure and develop specialist skills, including those for HTA, to aid the implementation of Universal Healthcare Coverage. The purpose of this study was twofold: a) to find validated tools for the assessment of the technical capacity to conduct a HTA, and if none were found, to develop a tool, and b) to describe experiences of its pilot.

Methods
First, a mapping review identified tools to assess the skills to conduct a HTA. A medical librarian conducted a comprehensive search in four databases (MEDLINE, Embase, Web of Science, ERIC). Then, incorporating results from the mapping and following an iterative process involving stakeholders and experts, we developed a HTA skills assessment tool. Finally, using an online platform to gather and analyse responses, in collaboration with our institutional partner, we piloted the tool in Ghana, and sought feedback on their experiences.

Results
The database search yielded 3871 records; fifteen those were selected based on a priori criteria. These records were published between 2003 and 2018, but none covered all technical skills to conduct a HTA. In the absence of an instrument meeting our needs, we developed a HTA skill assessment tool containing four sections (general information, core and soft skills, and future needs). The tool was designed to be administered to a broad range of individuals who would potentially contribute to the planning, delivery and evaluation of HTA. The tool was piloted with twenty-three individuals who completed the skills assessment and shared their initial impressions of the tool.

Conclusions
To our knowledge, this is the first comprehensive tool enabling the assessment of technical skills to conduct a HTA. This tool allows teams to understand where their individual strengths and weakness lie. The tool is in the early validation phases and further testing is needed.

Trial registration
Not applicable.
Functional principal component analysis for identifying the child growth pattern using longitudinal birth cohort data
Authors: Karuppusami Reka , Antonisamy Belavendra , Premkumar Prasanna S. 
Published: March 2022

AbstractBackgroundLongitudinal studies are important to understand patterns of growth in children and limited in India. It is important to identify an approach for characterising growth trajectories to distinguish between children who have healthy growth and those growth is poor. Many statistical approaches are available to assess the longitudinal growth data and which are difficult to recognize the pattern. In this research study, we employed functional principal component analysis (FPCA) as a statistical method to find the pattern of growth data. The purpose of this study is to describe the longitudinal child growth trajectory pattern under 3 years of age using functional principal component method.MethodsChildren born between March 2002 and August 2003 (n = 290) were followed until their third birthday in three neighbouring slums in Vellore, South India. Field workers visited homes to collect details of morbidity twice a week. Height and weight were measured monthly from 1 month of age in a study-run clinic. Longitudinal child growth trajectory pattern were extracted using Functional Principal Component analysis using B-spline basis functions with smoothing parameters. Functional linear model was used to assess the factors association with the growth functions.ResultsWe have obtained four FPCs explained by 86.5, 3.9, 3.1 and 2.2% of the variation respectively for the height functions. For height, 38% of the children’s had poor growth trajectories. Similarly, three FPCs explained 76.2, 8.8, and 4.7% respectively for the weight functions and 44% of the children’s had poor growth in their weight trajectories. Results show that gender, socio-economic status, parent’s education, breast feeding, and gravida are associated and, influence the growth pattern in children.ConclusionsThe FPC approach deals with subjects’ dynamics of growth and not with specific values at given times. FPC could be a better alternate approach for both dimension reduction and pattern detection. FPC may be used to offer greater insight for classification.
The association between community-level socioeconomic status and cognitive function among Chinese middle-aged and older adults: a study based on the China Health and Retirement Longitudinal Study (CHARLS)
Authors: Liu Yan , Liu Zhaorui , Liang Richard , Luo Yanan 
Published: March 2022

AbstractBackgroundAlthough numerous studies focused on the relationship between area socioeconomic status (SES) and health, only a few of them investigated how community-level SES was linked to late-life cognitive function as well as the potential pathways underlying this association, and very few of them focused on the context of China. This study examined how community-level SES was linked to cognitive function and the potential pathways underlying this association among middle-aged and older adults in China.MethodsData was drawn from the waves 1–4 of China Health and Retirement Longitudinal Study. We measured cognitive function with the components of the Telephone Interview of Cognitive Status battery. Community-level SES was derived from a sum of z scores of the percentage of the illiterate and the per-capita net income status within communities. We adopted two-level hierarchical linear regression models to explore the associations between community-level SES and cognitive function. A multilevel mediation analysis with structural equation modeling was undertaken to disaggregate the direct and indirect pathways of the associations.ResultsHigher community-level SES was associated with better cognitive function (β = 0.562, 95% CI = 0.390, 0.734), and this significant association was only present in rural participants, not in urban participants. Furthermore, we discovered the mediating effects of outdoor exercise facilities within communities (β = 0.023, 95% CI = 0.000, 0.056) and individual-level SES (β = 0.108, 95% CI = 0.057, 0.156) to explain the relationship between community SES and cognitive function.ConclusionsThese findings highlight the importance of community environmental interventions in maintaining individuals’ cognitive health in China, especially for older adults. Our results provided solid empirical evidence for reducing mental health inequalities in China, and suggested that developing an aging-friendly environment and properly distributing community resources are important to improve cognitive function of older adults.
Associations between dietary patterns and stages of chronic kidney disease
Authors: Lin Hsin-I. , Chen Hui-Ming , Hsu Chien-Chin , Lin Hung-Jung , Wang Jhi-Joung , Weng Shih-Feng , Kao Yuan , Huang Chien-Cheng 
Published: March 2022

Abstract
Background
Studies have revealed that patients with chronic kidney disease (CKD) have dietary patterns different from those of the general population. However, no studies have compared the dietary patterns of between patients with early-stages (stages 1–3a) and late-stages (stages 3b–5) of CKD. Our objective was to investigate the associations between dietary patterns in early and late-stage CKD.

Methods
We analyzed 4480 participants with CKD at various stages based on the data recorded between 2007 and 2016 from the database of the American National Health and Nutrition Examination Survey.

Results
In total, 3683 and 797 participants had early and late-stage CKD, respectively. Through principal components analysis, the dietary intake dimension was reduced from 63 variables to 3 dietary patterns. We adopted logistic regression for analysis. The three dietary patterns are as follows: (1) saturated fatty acids and mono-unsaturated fatty acids (MUFA); (2) vitamins and minerals; and (3) cholesterols and polyunsaturated fatty acids (PUFA). These 3 patterns explained > 50% of dietary nutrient intake. Results indicated that among participants with dietary patterns 2 (vitamins and minerals) and 3 (cholesterols and PUFA), those with low intakes were more likely to have late-stage CKD. The odds ratios for patterns 2 and 3 were 1.74 (95% CI: 1.21–2.50) and 1.66 (95% CI: 1.13–2.43), respectively.

Conclusions
This study revealed that intakes of vitamins and minerals and cholesterols and PUFA were associated with the stages of CKD.