bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Resolution Rainfall Maps from Commercial Microwave Links for a Data-Scarce Region in West Africa
Authors: Djibo Moumouni , Chwala Christian , Graf Maximilian , Polz Julius , Kunstmann Harald , Zougmoré François 
Published: August 2023

Abstract
We present high-resolution rainfall maps from commercial microwave link (CML) data in the city of Ouagadougou, Burkina Faso. Rainfall was quantified based on data from 100 CMLs along unique paths and interpolated to achieve rainfall maps with a 5-min temporal and 0.55-km spatial resolution for the monsoon season of 2020. Established processing methods were combined with newly developed filtering methods, minimizing the loss of data availability. The rainfall maps were analyzed qualitatively both at a 5-min and aggregated daily scales. We observed high spatiotemporal variability on the 5-min scale that cannot be captured with any existing measurement infrastructure in West Africa. For the quantitative evaluation, only one rain gauge with a daily resolution was available. Comparing the gauge data with the corresponding CML rainfall map pixel showed a high agreement, with a Pearson correlation coefficient > 0.95 and an underestimation of the CML rainfall maps of ∼10%. Because the CMLs closest to the gauge have the largest influence on the map pixel at the gauge location, we thinned out the CML network around the rain gauge synthetically in several steps and repeated the interpolation. The performance of these rainfall maps dropped only when a radius of 5 km was reached and approximately one-half of all CMLs were removed. We further compared ERA5 and GPM IMERG data with the rain gauge and found that they had much lower correlation than data from the CML rainfall maps. This clearly highlights the large benefit that CML data can provide in the data-scarce but densely populated African cities.

Significance Statement
In this study, we investigate the possibility of deriving accurate high-resolution rainfall maps from commercial microwave link (CML) data in West Africa. The main challenges are the lack of reference data in this area and the adoption of existing processing tools without reference data. We show CML rainfall maps for Ouagadougou, Burkina Faso, with a resolution of 5 min and 0.55 km, which is unprecedented in this region. The comparison with the only available rain gauge, which provides data only at a daily resolution, yields a Pearson correlation of >0.95. An analysis of synthetically thinned-out networks shows that this accuracy is valid for the whole domain. Comparing reanalysis and satellite data with the rain gauge and CML data showed a poor performance of these gridded reference datasets. Also, a high coincidence of temporal dynamics between CML rainfall maps and satellite products was observed. Overall, these findings support the potential of CMLs for future hydrometeorological applications in West Africa.
The Prevalence and Association of Biofilms With Otitis Media With Effusion: A Systematic Review and Meta-Analysis
Authors: Elzayat Saad , El-Deeb Mohamed E. , El-Shirbeny Hussein A. , El-Shirbiny Hassan , Abdel-Maboud Mohamed , Nasr Khaled 
Published: August 2023

Purpose: We aimed to identify the role of bacterial biofilms in the chronicity of otitis media with effusion and its resistance to antibiotics. We illustrated this role by reviewing, analyzing, and correlating the findings with the results of the included studies to reach clear evidence. Methods: A comprehensive search of electronic databases (Scopus, PubMed, Web of Science, Cochrane, and GHL databases) was performed for all studies using the following strategy till April 2021 with the search terms: Biofilm and Middle ear effusion. We found 935 references, 421 were duplicates, and 514 were needed for further screening, and it was as follows: PubMed 215, Scopus 18, Cochrane 130, Web of Science 136, and GHL 15. Results: The pooled prevalence of culture-positive effusions was estimated to be 40% (95% CI [28%, 53%]) of the total OME population. Overall, the prevalence of PCR-positive effusions was estimated to be 97% (95% CI [95%, 99%]) of the total OME population. The pooled prevalence of EM-positive effusions was estimated to be 82% (95% CI [69%, 95%]) of the total OME population. Conclusion: The data presented in this study coincide with the significant role of bacterial biofilms in the pathogenesis of chronic otitis media with effusion. The involvement of bacterial biofilm as a component of the OME pathogenic process can help us to explain why antimicrobial therapy is not always effective in the eradication of the disease process and, also explain the recurrence of middle ear effusion after treatment with tympanostomy tubes either with or without adenoidectomy.
Enhancing involvement of people with multiple sclerosis in clinical trial design
Authors: Gray Emma , Amjad Anneesa , Robertson Jenny , Beveridge Judy , Scott Susan , Peryer Guy , Braisher Marie , Pugh Cheryl , Peres Sara , Marrie Ruth Ann , Sormani Maria Pia , Chataway Jeremy 
Published: August 2023

Background: Although often overlooked, patient and public involvement (PPI) is vital when considering the design and delivery of complex and adaptive clinical trial designs for chronic health conditions such as multiple sclerosis (MS). Methods: We conducted a rapid review to assess current status of PPI in the design and conduct of clinical trials in MS over the last 5 years. We provide a case study describing PPI in the development of a platform clinical trial in progressive MS. Results: We identified only eight unique clinical trials that described PPI as part of articles or protocols; nearly, all were linked with funders who encourage or mandate PPI in health research. The OCTOPUS trial was co-designed with people affected by MS. They were central to every aspect from forming part of a governance group shaping the direction and strategy, to the working groups for treatment selection, trial design and delivery. They led the PPI strategy which enabled a more accessible, acceptable and inclusive design. Conclusion: Active, meaningful PPI in clinical trial design increases the quality and relevance of studies and the likelihood of impact for the patient community. We offer recommendations for enhancing PPI in future MS clinical trials.
Does Running Increase the Risk of Hip and Knee Arthritis? A Survey of 3804 Marathon Runners
Authors: Hartwell Matthew J. , Tanenbaum Joseph E. , Chiampas George , Terry Michael A. , Tjong Vehniah K. 
Published: August 2023

Background: Long-distance running is a popular form of cardiovascular exercise with many well-described health benefits, from improving heart health to the management of obesity, diabetes, and mental illness. The impact of long-distance running on joint health in recreational runners, however, remains inconclusive. Hypothesis: The prevalence of osteoarthritis in runners is not associated with an athlete’s running-related history, including the number of marathons completed, cumulative years of running, average weekly mileage, and average running pace. Study Design: Prospective cohort study. Level of Evidence: Level 3. Methods: A survey was distributed to all participants registered for the 2019 or 2021 Chicago marathon (n = 37,917). Surveys collected runner demographics and assessed for hip/knee pain, osteoarthritis, family history, surgical history, and running-related history. Running history included the number of marathons run, number of years running, average running pace, and average weekly mileage. The overall prevalence of osteoarthritis was identified, and a multivariable logistic regression model was used to identify variables associated with the presence of hip and/or knee osteoarthritis. Results: Surveys were completed by 3804 participants (response rate of 10.0%). The mean age was 43.9 years (range, 18-83 years) and participants had completed on average 9.5 marathons (median, 5 marathons; range, 1-664 marathons). The prevalence of hip and/or knee arthritis was 7.3%. A history of hip/knee injuries or surgery, advancing age, family history, and body mass index (BMI) were risk factors for arthritis. Cumulative number of years running, number of marathons completed, weekly mileage, and mean running pace were not significant predictors for arthritis. The majority (94.2%) of runners planned to run another marathon, despite 24.2% of all participants being told by a physician to do otherwise. Conclusion: From this largest surveyed group of marathon runners, the most significant risk factors for developing hip or knee arthritis were age, BMI, previous injury or surgery, and family history. There was no identified association between cumulative running history and the risk for arthritis.
Fit for Purpose? The Suitability of Oral Health Outcome Measures to Inform Policy
Authors: Nguyen T.M. , Rogers H. , Taylor G.D. , Tonmukayakul U. , Lin C. , Hall M. , Calache H. , Vernazza C. 
Published: August 2023

Measuring outcomes for oral health is frequently undertaken using the decayed, missing, and filled teeth (DMFT) index. DMFT measures dental caries experience. As a condition-specific outcome, it is not relatable to consumers, nor does it capture the impact of dental caries on quality of life or outcomes that matter most to consumers. Efficient resource allocation should include patient values. It is crucial to use measurement instruments that record consumer values or preferences for oral health and oral diseases. These measures are often called patient-reported outcome measures and/or patient-reported experience measures. Outcome measures relevant to patients are recommended to influence and inform policy decision-making for oral health. Knowledge Transfer Statement: Oral health research and program evaluation should consider alternative outcome measures for population oral health other than the DMFT index.
High-intensity versus moderate-intensity statin treatment for patients with ischemic stroke: Nationwide cohort study
Authors: Bach Frederikke , Skajaa Nils , Esen Buket Öztürk , Fuglsang Cecilia Hvitfeldt , Horváth-Puhó Erzsébet , Sørensen Henrik Toft , Adelborg Kasper 
Published: August 2023

Purpose: Guidelines recommend high-intensity statin treatment after ischemic stroke, but evidence is sparse on the effectiveness and safety of different statin treatment intensities. We examined effectiveness and safety outcomes among patients initiating high-intensity versus moderate-intensity statins after ischemic stroke. Methods: In this population-based new-user active-comparator cohort study, we used the Danish Stroke Registry, covering all Danish hospitals, to identify patients with a first-time ischemic stroke during 2012–2021. Using multiple Danish registries, patients who redeemed a statin prescription within 21 days after stroke admission were classified as high-intensity statin initiators or moderate-intensity statin initiators. Propensity score inverse probability of treatment weighting was used to balance patient characteristics. We used competing risk methods to compute 5 year risk differences (RDs) and Cox proportional hazards regression to compute 5 year hazard ratios (HRs) of stroke recurrence, myocardial infarction, heart failure, venous thromboembolism, and all-cause mortality (effectiveness outcomes) and diabetes, liver disease, and kidney disease (safety outcomes). Results: High-intensity ( n = 13,032) and moderate-intensity ( n = 14,355) statin initiators were identified. Risks of most examined effectiveness outcomes were comparable between statin intensities. There was no clear association between statin intensity and stroke recurrence (RD: 0.8% [95% CI: 0.1, 1.4], HR: 1.08 [95% CI: 0.96, 1.22]). All-cause mortality was slightly reduced among high-intensity statin initiators (RD: −1.1% [95% CI: −0.1, −2.1], HR: 0.93 [95% CI: 0.85, 1.01]. Risks of most safety outcomes were comparable between statin intensities, but high-intensity statin use was associated with an increased risk of diabetes (RD: 1.2% [95% CI: 0.4, 1.9], HR: 1.10 [95% CI: 1.00, 1.21]). Discussion and conclusion: Compared with initiation of moderate-intensity statins, initiation of high-intensity statins after ischemic stroke was associated with similar risks of most effectiveness and safety outcomes. However, mortality risk was reduced, and diabetes risk was increased.
Fixed-intensity exercise tests to measure exertional dyspnoea in chronic heart and lung populations: a systematic review
Authors: Palmer Tanya , Obst Steven J. , Aitken Craig R. , Walsh James , Sabapathy Surendran , Adams Lewis , Morris Norman R. 
Published: August 2023

IntroductionExertional dyspnoea is the primary diagnostic symptom for chronic cardiopulmonary disease populations. Whilst a number of exercise tests are used, there remains no gold standard clinical measure of exertional dyspnoea. The aim of this review was to comprehensively describe and evaluate all types of fixed-intensity exercise tests used to assess exertional dyspnoea in chronic cardiopulmonary populations and, where possible, report the reliability and responsiveness of the tests.MethodsA systematic search of five electronic databases identified papers that examined 1) fixed-intensity exercise tests and measured exertional dyspnoea, 2) chronic cardiopulmonary populations, 3) exertional dyspnoea reported at isotime or upon completion of fixed-duration exercise tests, and 4) published in English.ResultsSearches identified 8785 papers. 123 papers were included, covering exercise tests using a variety of fixed-intensity protocols. Three modes were identified, as follows: 1) cycling (n=87), 2) walking (n=31) and 3) other (step test (n=8) and arm exercise (n=2)). Most studies (98%) were performed on chronic respiratory disease patients. Nearly all studies (88%) used an incremental exercise test. 34% of studies used a fixed duration for the exercise test, with the remaining 66% using an exhaustion protocol recording exertional dyspnoea at isotime. Exertional dyspnoea was measured using the Borg scale (89%). 7% of studies reported reliability. Most studies (72%) examined the change in exertional dyspnoea in response to different interventions.ConclusionConsiderable methodological variety of fixed-intensity exercise tests exists to assess exertional dyspnoea and most test protocols require incremental exercise tests. There does not appear to be a simple, universal test for measuring exertional dyspnoea in the clinical setting.
Post-COVID-19 dyspnoea and pulmonary imaging: a systematic review and meta-analysis
Authors: Guinto Elizabeth , Gerayeli Firoozeh V. , Eddy Rachel L. , Lee Hyun , Milne Stephen , Sin Don D. 
Published: August 2023

BackgroundA proportion of coronavirus disease 2019 (COVID-19) survivors experience persistent dyspnoea without measurable impairments in lung function. We performed a systematic review and meta-analysis to determine relationships between dyspnoea and imaging abnormalities over time in post-COVID-19 patients.MethodsUsing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we analysed studies published prior to 15 September 2022 and indexed by Google Scholar, PubMed and LitCOVID which assessed chest imaging in adults ≥3 months after COVID-19. Demographic, chest imaging, spirometric and post-COVID-19 symptom data were extracted. The relationships between imaging abnormalities and dyspnoea, sex and age were determined using a random effects model and meta-regression.Results47 studies were included in the meta-analysis (n=3557). The most prevalent computed tomography (CT) imaging abnormality was ground-glass opacities (GGOs) (44.9% (95% CI 37.0–52.9%) at any follow-up time-point). Occurrence of reticulations significantly decreased between early and late follow-up (p=0.01). The prevalence of imaging abnormalities was related to the proportion of patients with dyspnoea (p=0.012). The proportion of females was negatively correlated with the presence of reticulations (p=0.001), bronchiectasis (p=0.001) and consolidations (p=0.025). Age was positively correlated with imaging abnormalities across all modalities (p=0.002) and imaging abnormalities present only on CT (p=0.001) (GGOs (p=0.004) and reticulations (p=0.001)). Spirometric values improved during follow-up but remained within the normal range at all time-points.ConclusionsImaging abnormalities were common 3 months after COVID-19 and their occurrence was significantly related to the presence of dyspnoea. This suggests that CT imaging is a sensitive tool for detecting pulmonary abnormalities in patients with dyspnoea, even in the presence of normal spirometric measurements.
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
Authors: Song Yabing , Wang Jianbin 
Published: August 2023

AbstractBackgroundVisualizing genome coverage is of vital importance to inspect and interpret various next-generation sequencing (NGS) data. Besides genome coverage, genome annotations are also crucial in the visualization. While different NGS data require different annotations, how to visualize genome coverage and add the annotations appropriately and conveniently is challenging. Many tools have been developed to address this issue. However, existing tools are often inflexible, complicated, lack necessary preprocessing steps and annotations, and the figures generated support limited customization.ResultsHere, we introduceggcoverage, an R package to visualize and annotate genome coverage of multi-groups and multi-omics. The input files forggcoveragecan be in BAM, BigWig, BedGraph and TSV formats. For better usability,ggcoverageprovides reliable and efficient ways to perform read normalization, consensus peaks generation and track data loading with state-of-the-art tools.ggcoverageprovides various available annotations to adapt to different NGS data (e.g. WGS/WES, RNA-seq, ChIP-seq) and all the available annotations can be easily superimposed with ‘ + ’.ggcoveragecan generate publication-quality plots and users can customize the plots withggplot2. In addition,ggcoveragesupports the visualization and annotation of protein coverage.Conclusionsggcoverageprovides a flexible, programmable, efficient and user-friendly way to visualize and annotate genome coverage of multi-groups and multi-omics. Theggcoveragepackage is available athttps://github.com/showteeth/ggcoverageunder the MIT license, and the vignettes are available athttps://showteeth.github.io/ggcoverage/.
CapsNetYY1: identifying YY1-mediated chromatin loops based on a capsule network architecture
Authors: Zhang Zhimin , Li Fenglin , Zhao Jianping , Zheng Chunhou 
Published: August 2023

Abstract
Background
Previous studies have identified that chromosome structure plays a very important role in gene control. The transcription factor Yin Yang 1 (YY1), a multifunctional DNA binding protein, could form a dimer to mediate chromatin loops and active enhancer-promoter interactions. The deletion of YY1 or point mutations at the YY1 binding sites significantly inhibit the enhancer-promoter interactions and affect gene expression. To date, only a few computational methods are available for identifying YY1-mediated chromatin loops.

Results
We proposed a novel model named CapsNetYY1, which was based on capsule network architecture to identify whether a pair of YY1 motifs can form a chromatin loop. Firstly, we encode the DNA sequence using one-hot encoding method. Secondly, multi-scale convolution layer is used to extract local features of the sequence, and bidirectional gated recurrent unit is used to learn the features across time steps. Finally, capsule networks (convolution capsule layer and digital capsule layer) used to extract higher level features and recognize YY1-mediated chromatin loops. Compared with DeepYY1, the only prediction for YY1-mediated chromatin loops, our model CapsNetYY1 achieved the better performance on the independent datasets (AUC $$> 0.99$$

>
0.99

).

Conclusion
The results indicate that CapsNetYY1 is an excellent method for identifying YY1-mediated chromatin loops. We believe that the CapsNetYY1 method will be used for predictive classification of other DNA sequences.
Population size as a major determinant of mating system and population genetic differentiation in a narrow endemic chasmophyte
Authors: Surina Boštjan , Balant Manica , Glasnović Peter , Radosavljević Ivan , Fišer Živa , Fujs Nataša , Castro Sílvia 
Published: August 2023

Abstract
Background
Mating system is one of the major determinants of intra- and interspecific genetic structure, but may vary within and between plant populations. Our study model included all known populations of Moehringia tommasinii (Caryophyllaceae), a narrow endemic plant inhabiting rock crevices in the northwestern Adriatic, and some populations of co-occurring and widespread M. muscosa, an ecologically divergent relative with an overlapping flowering period. We performed reciprocal crosses within and between taxa and used molecular markers to assess the extent of gene flow within and between populations and taxa. Using coefficient of inbreeding, population size, seed weight, pollen-to-ovule ratio, and flower display size, we also looked for evidence of a selfing syndrome.

Results
A surprisingly high variation in mating systems was observed among populations of M. tommasinii. These populations exhibited genetic structuring, with their size positively correlated with both seed weight and pollen production. Although a selfing syndrome could not be confirmed as the majority of selfing resulted from allogamous treatments, the occurrence of selfing was notable. In the presence of M. muscosa, at a site where both species coexist closely, a distinct pattern of fruit production was observed in M. tommasinii following various pollination treatments. Molecular and morphometric data provided evidence of hybridization followed by local extinction at this site.

Conclusions
Population size proved to be the most important factor affecting the mating system in genetically structured populations of M. tommasinii. Lighter seeds and lower pollen production observed in populations with pronounced selfing do not provide enough evidence for the selfing syndrome. Detected gene flow between M. tommasinii and the sympatric M. muscosa suggested weak reproductive barriers between the taxa, which could pose a conservation problems for the former species. Hybridization leading to local extinction may also resulted in floral polymorphism and disruption of mating patterns of M. tommasinii.