bluuebunny/crossref_metadata_2025_split huggingface dataset:
Doppler Lidar and Mobile Radiosonde Observation-Based Evaluation of Warn-on-Forecast System Predicted Near-Supercell Environments during TORUS 2019
Authors: Laser Jordan J. , Coniglio Michael C. , Skinner Patrick S. , Smith Elizabeth N. 
Published: July 2022

Abstract
Observational data collection is extremely hazardous in supercell storm environments, which makes for a scarcity of data used for evaluating the storm-scale guidance from convection allowing models (CAMs) like the National Oceanic and Atmospheric Administration (NOAA) Warn-on-Forecast System (WoFS). The Targeted Observations with UAS and Radar of Supercells (TORUS) 2019 field mission provided a rare opportunity to not only collect these observations, but to do so with advanced technology: vertically pointing Doppler lidar. One standing question for WoFS is how the system forecasts the feedback between supercells and their near-storm environment. The lidar can observe vertical profiles of wind over time, creating unique datasets to compare to WoFS kinematic predictions in rapidly evolving severe weather environments. Mobile radiosonde data are also presented to provide a thermodynamic comparison. The five lidar deployments (three of which observed tornadic supercells) analyzed show WoFS accurately predicted general kinematic trends in the inflow environment; however, the predicted feedback between the supercell and its environment, which resulted in enhanced inflow and larger storm-relative helicity (SRH), were muted relative to observations. The radiosonde observations reveal an overprediction of CAPE in WoFS forecasts, both in the near and far field, with an inverse relationship between the CAPE errors and distance from the storm.

Significance Statement
It is difficult to evaluate the accuracy of weather prediction model forecasts of severe thunderstorms because observations are rarely available near the storms. However, the TORUS 2019 field experiment collected multiple specialized observations in the near-storm environment of supercells, which are compared to the same near-storm environments predicted by the National Oceanic and Atmospheric Administration (NOAA) Warn-on-Forecast System (WoFS) to gauge its performance. Unique to this study is the use of mobile Doppler lidar observations in the evaluation; lidar can retrieve the horizontal winds in the few kilometers above ground on time scales of a few minutes. Using lidar and radiosonde observations in the near-storm environment of three tornadic supercells, we find that WoFS generally predicts the expected trends in the evolution of the near-storm wind profile, but the response is muted compared to observations. We also find an inverse relationship of errors in instability to distance from the storm. These results can aid model developers in refining model physics to better predict severe storms.
Prediction of intensive care unit admission (>24h) after surgery in elective noncardiac surgical patients using machine learning algorithms
Authors: Lan Lan , Chen Fangwei , Luo Jiawei , Li Mengjiao , Hao Xuechao , Hu Yao , Yin Jin , Zhu Tao , Zhou Xiaobo 
Published: July 2022

Background To develop a highly discriminative machine learning model for the prediction of intensive care unit admission (>24h) using the easily available preoperative information from electronic health records. An accurate prediction model for ICU admission after surgery is of great importance for surgical risk assessment and appropriate utilization of ICU resources. Method Data were collected retrospectively from a large hospital, comprising 135,442 adult patients who underwent surgery except for cardiac surgery between 1 January 2014, and 31 July 2018 in China. Multiple existing predictive machine learning algorithms were explored to construct the prediction model, including logistic regression, random forest, adaptive boosting, and gradient boosting machine. Four secondary analyses were conducted to improve the interpretability of the results. Results A total of 2702 (2.0%) patients were admitted to the intensive care unit postoperatively. The gradient boosting machine model attained the highest area under the receiver operating characteristic curve of 0.90. The machine learning models predicted intensive care unit admission better than the American Society of Anesthesiologists Physical Status (area under the receiver operating characteristic curve: 0.68). The gradient boosting machine recognized several features as highly significant predictors for postoperatively intensive care unit admission. By applying subgroup analysis and secondary analysis, we found that patients with operations on the digestive, respiratory, and vascular systems had higher probabilities for intensive care unit admission. Conclusion Compared with conventional American Society of Anesthesiologists Physical Status and logistic regression model, the gradient boosting machine could improve the performance in the prediction of intensive care unit admission. Machine learning models could be used to improve the discrimination and identify the need for intensive care unit admission after surgery in elective noncardiac surgical patients, which could help manage the surgical risk.
Avapritinib for advanced systemic mastocytosis
Authors: Gotlib Jason , Reiter Andreas , DeAngelo Daniel J. 
Published: July 2022

Abstract
Avapritinib, a highly selective inhibitor of KIT D816V, was approved by the Food and Drug Administration in 2021 for treatment of advanced systemic mastocytosis (AdvSM) and by the European Medicines Agency in 2022 for AdvSM after prior systemic therapy. The phase 1 EXPLORER and phase 2 PATHFINDER trials demonstrated that avapritinib can elicit complete and durable clinical responses and molecular remission of KIT D816V. Key management challenges relate to the complex mutational landscape of AdvSM, often found with an associated hematologic neoplasm.
Developing disruptive mobility scenarios for rural areas. Participatory mobility scenario building in a Belgian village for the year 2050
Authors: Tori Sara , Pappers Jesse , Keserü Imre 
Published: July 2022

Abstract
Background
Historically, quantitative forecasting methods have been used in transport planning. As forecasts can be unreliable to plan for the medium- and long-term, scenario building has recently been increasingly used. However, scenario building methods often fail to take disruptions and wild cards into account, i.e., low probability but high impact events. When unaccounted for, wild card events, like the COVID-19 pandemic, lower the efficacy of scenario building in policy making, as these events may completely disturb the developed scenarios of the future.

Methods
In this paper, we develop and apply a creative and participatory methodology to develop visions and disrupted scenarios for rural mobility. Our research was carried out in the Belgian village of Oetingen, where inhabitants developed more resilient views of the future by creating disrupted mobility scenarios and a preferred mobility vision for their village for the year 2050 in a participatory scenario building exercise. Wild cards related to mobility were collected from mobility experts and inhabitants in three workshops. Inhabitants were engaged to define their mobility vision on a postcard that was distributed to all houses in the village as well as on a project website. Respondents were invited for a follow-up interview in which their preferred mobility vision was subjected to the wild cards, and participants described how these wild cards would change their preferred vision. As children tend to have more creative ideas, they were engaged via workshops at school.

Results
This process resulted in mobility scenarios for the village for the year 2050 based on the different wild cards, as well as an overall desired vision. We found that the use of wild cards did not significantly change the scenarios when compared to the vision, although it did make the interviewees step outside of their comfort zones. We also found that the citizens did not have more original and less path-dependent ideas in developing wild cards when compared to experts. Lastly, we found that children have many outside-of-the-box suggestions when it comes to the future. Although some of their ideas can be judged as impractical by today’s standards, many ideas had an indirect implication for mobility in the village and gave insights into children’s priorities, as potential future residents of the village.
SparkGC: Spark based genome compression for large collections of genomes
Authors: Yao Haichang , Hu Guangyong , Liu Shangdong , Fang Houzhi , Ji Yimu 
Published: July 2022

AbstractSince the completion of the Human Genome Project at the turn of the century, there has been an unprecedented proliferation of sequencing data. One of the consequences is that it becomes extremely difficult to store, backup, and migrate enormous amount of genomic datasets, not to mention they continue to expand as the cost of sequencing decreases. Herein, a much more efficient and scalable program to perform genome compression is required urgently. In this manuscript, we propose a new Apache Spark based Genome Compression method called SparkGC that can run efficiently and cost-effectively on a scalable computational cluster to compress large collections of genomes. SparkGC uses Spark’s in-memory computation capabilities to reduce compression time by keeping data active in memory between the first-order and second-order compression. The evaluation shows that the compression ratio of SparkGC is better than the best state-of-the-art methods, at least better by 30%. The compression speed is also at least 3.8 times that of the best state-of-the-art methods on only one worker node and scales quite well with the number of nodes. SparkGC is of significant benefit to genomic data storage and transmission. The source code of SparkGC is publicly available athttps://github.com/haichangyao/SparkGC.
Genome-wide characterization of Salmonella Typhimurium genes required for the fitness under iron restriction
Authors: Karash Sardar , Jiang Tieshan , Kwon Young Min 
Published: July 2022

Abstract
Background
Iron is a crucial element for bacterial survival and virulence. During Salmonella infection, the host utilizes a variety of mechanisms to starve the pathogen from iron. However, Salmonella activates distinctive defense mechanisms to acquire iron and survive in iron-restricted host environments. Yet, the comprehensive set of the conditionally essential genes that underpin Salmonella survival under iron-restricted niches has not been fully explored.

Results
Here, we employed transposon sequencing (Tn-seq) method for high-resolution elucidation of the genes in Salmonella Typhimurium (S. Typhimurium) 14028S strain required for the growth under the in vitro conditions with four different levels of iron restriction achieved by iron chelator 2,2′-dipyridyl (Dip): mild (100 and 150 μM), moderate (250 μM) and severe iron restriction (400 μM). We found that the fitness of the mutants reduced significantly for 28 genes, suggesting the importance of these genes for the growth under iron restriction. These genes include sufABCDSE, iron transport fepD, siderophore tonB, sigma factor E ropE, phosphate transport pstAB, and zinc exporter zntA. The siderophore gene tonB was required in mild and moderate iron-restricted conditions, but it became dispensable in severe iron-restricted conditions. Remarkably, rpoE was required in moderate and severe iron restrictions, leading to complete attenuation of the mutant under these conditions. We also identified 30 genes for which the deletion of the genes resulted in increased fitness under iron-restricted conditions.

Conclusions
The findings broaden our knowledge of how S. Typhimurium survives in iron-deficient environments, which could be utilized for the development of new therapeutic strategies targeting the pathways vital for iron metabolism, trafficking, and scavenging.
Sample size recalculation based on the prevalence in a randomized test-treatment study
Authors: Hot Amra , Benda Norbert , Bossuyt Patrick M. , Gerke Oke , Vach Werner , Zapf Antonia 
Published: July 2022

Abstract
Background
Randomized test-treatment studies aim to evaluate the clinical utility of diagnostic tests by providing evidence on their impact on patient health. However, the sample size calculation is affected by several factors involved in the test-treatment pathway, including the prevalence of the disease. Sample size planning is exposed to strong uncertainties in terms of the necessary assumptions, which have to be compensated for accordingly by adjusting prospectively determined study parameters during the course of the study.

Method
An adaptive design with a blinded sample size recalculation in a randomized test-treatment study based on the prevalence is proposed and evaluated by a simulation study. The results of the adaptive design are compared to those of the fixed design.

Results
The adaptive design achieves the desired theoretical power, under the assumption that all other nuisance parameters have been specified correctly, while wrong assumptions regarding the prevalence may lead to an over- or underpowered study in the fixed design. The empirical type I error rate is sufficiently controlled in the adaptive design as well as in the fixed design.

Conclusion
The consideration of a blinded recalculation of the sample size already during the planning of the study may be advisable in order to increase the possibility of success as well as an enhanced process of the study. However, the application of the method is subject to a number of limitations associated with the study design in terms of feasibility, sample sizes needed to be achieved, and fulfillment of necessary prerequisites.
Comparison of risk scoring systems for upper gastrointestinal bleeding in patients after renal transplantation: a retrospective observational study in Hunan, China
Authors: Wang Rui , Wang Qiang 
Published: July 2022

Abstract
Background
Upper gastrointestinal bleeding (UGIB) is a common complication in renal transplant recipients. However, the risk stratification value of bleeding scoring systems in these patients is unclear, and data regarding risk factors are limited.

Methods
Clinical data of renal transplant recipients in The Third Xiangya hospital were collected. The predictive ability of Glasgow Blatchford score (GBS), pre-endoscopy Rockall score (pRS), and AIMS65 score were assessed by the area under the receiver operating characteristic curve (AUROC). Risk factors of UGIB were analyzed using binary logistic regression analysis.

Results
A total of 220 patients were enrolled, of which 55 with UGIB. Endoscopy improved the overall survival rate of patients. Glasgow Blatchford score (AUROC 0.868) performed best at predicting UGIB patients who need intervention or death, with a threshold of 10, sensitivity and specificity were 82.4% and 70%, respectively. In terms of predicting mortality, the GBS score was comparable with AIMS65 score (p = 0.30) and pRS score (p = 0.42). Viral hepatitis, intravenous hormone usage, low platelet count, and low albumin level were significant factors associated with UGIB.

Conclusions
The Glasgow Blatchford score (AUROC 0.868) was best at predicting the need for intervention or death. However, their ability to predict mortality was limited, with AUROC less than 0.8. Our study also identified four independent risk factors for renal transplant recipients with UGIB.
Exploring the difference between men and women in physical functioning: How do sociodemographic, lifestyle- and health-related determinants contribute?
Authors: Sialino Lena Dirkje , Picavet H. Susan J. , Wijnhoven Hanneke A. H. , Loyen Anne , Verschuren W. M. Monique , Visser Marjolein , Schaap Laura S. , van Oostrom Sandra H. 
Published: July 2022

AbstractBackgroundTo explore whether differences between men and women in the sensitivity to (strength of the association) and/or in the exposure to determinants (prevalence) contribute to the difference in physical functioning, with women reporting more limitations.MethodsData of the Doetinchem Cohort Study was used (n = 5856, initial ages 26–70 years), with follow-up measurements every 5 years (up to 20). Physical functioning (subscale SF-36, range:0–100), sex (men or women) and a number of socio-demographic, lifestyle- and health-related determinants were assessed. Mixed-model multivariable analysis was used to investigate differences between men and women in sensitivity (interaction term with sex) and in exposure (change of the sex difference when adjusting) to determinants of physical functioning.ResultsThe physical functioning score among women was 6.55 (95%CI:5.48,7.61) points lower than among men. In general, men and women had similar determinants, but pain was more strongly associated with physical functioning (higher sensitivity), and also more prevalent among women (higher exposure). The higher exposure to low educational level and not having a paid job also contributed to the lower physical functioning score among women. In contrast, current smoking, mental health problems and a low educational level were more strongly associated with a lower physical functioning score among men and lower physical activity and higher BMI were more prevalent among men.ConclusionsAlthough important for physical functioning among both men and women, our findings provide no indications for reducing the difference in physical functioning by promoting a healthy lifestyle but stress the importance of differences in pain, work and education.
Amphotericin B plus fluorocytosine combined with voriconazole for the treatment of non-HIV and non-transplant-associated cryptococcal meningitis: a retrospective study
Authors: Liu Junyu , Liu Jia , Su Xiaohong , Yang Lu , Wang Yijie , Wang Anni , Xu Xiaofeng , Li Min , Jiang Ying , Peng Fuhua 
Published: July 2022

Abstract
Background
Our previous study explored Amphotericin B (AMB) plus 5-flucytosine (5-FC) combined with fluconazole (FLU) therapy in the induction period, which seemed to be better than the previous AMB + 5-FC antifungal therapy in non-HIV and non-transplant-associated CM. However, based on our clinical finding, the outcomes of some CM patients who received AMB plus 5-FC combined with FLU antifungal therapy were still poor. Therefore, we need to explore new antifungal methods in non-HIV and non-transplant-associated CM during the induction period.

Methods
Clinical data from 148 patients admitted to the Third Affiliated Hospital of Sun Yat Sen University from January 2011 to December 2020 were collected. These patients were stratified based on antifungal treatment methods in the induction period (group I with AMB + 5-FC + VOR, group II with AMB + 5-FC + FLU, group III with AMB + 5-FC).

Results
The first hospitalization time of Group I (median: 25 days, IQR: 20–34.5) was significantly shorter than that of Group II (median: 43 days, IQR: 29–62) (p < 0.001) and Group III (median: 50.5 days, IQR: 43–77.5) (p < 0.001). After 2 weeks of follow-up, Group I (26/49) had more patients reaching CSF clearance (p = 0.004) than Group II (18/71) and Group III (7/28). In multivariable analysis, Group II (OR: 3.35, 95%CI 1.43–7.82, p = 0.005) and Group III (OR: 3.8, 95%CI 1.23–11.81, p = 0.021) were associated with higher risk about CSF clearance failure at 2 weeks follow-up than Group I. After 10 weeks of follow-up, the incidence of hypokalemia in Group I was significantly lower than that in Group II (p = 0.003) and Group III (p = 0.004), and the incidence of gastrointestinal discomfort in Group I was significantly lower than that in Group II (p = 0.004).

Conclusion
AMB plus 5-FC combined with VOR may rapidly improve clinical manifestation, decrease CSF OP and clear the cryptococci in CSF during the early phase, substantially shorten the hospitalization time, and reduce the incidences of hypokalemia and gastrointestinal discomfort.
Reduced brain subcortical volumes in patients with glaucoma: a pilot neuroimaging study using the region-of-interest-based approach
Authors: Ha Yae Won , Jang Heeseon , Koh Sang-Baek , Noh Young , Lee Seung-Koo , Seo Sang Won , Cho Jaelim , Kim Changsoo 
Published: July 2022

AbstractBackgroundWhile numerous neuroimaging studies have demonstrated that glaucoma is associated with smaller volumes of the visual cortices in the brain, only a few studies have linked glaucoma with brain structures beyond the visual cortices. Therefore, the objective of this study was to compare brain imaging markers and neuropsychological performance between individuals with and without glaucoma.MethodsWe identified 64 individuals with glaucoma and randomly selected 128 age-, sex-, and education level-matched individuals without glaucoma from a community-based cohort. The study participants underwent 3 T brain magnetic resonance imaging and neuropsychological assessment battery. Regional cortical thickness and subcortical volume were estimated from the brain images of the participants. We used a linear mixed model after adjusting for potential confounding variables.ResultsCortical thickness in the occipital lobe was significantly smaller in individuals with glaucoma than in the matched individuals (β = − 0.04 mm,P = 0.014). This did not remain significant after adjusting for cardiovascular risk factors (β = − 0.02 mm,P = 0.67). Individuals with glaucoma had smaller volumes of the thalamus (β = − 212.8 mm3,P = 0.028), caudate (β = − 170.0 mm3,P = 0.029), putamen (β = − 151.4 mm3,P = 0.051), pallidum (β = − 103.6 mm3,P = 0.007), hippocampus (β = − 141.4 mm3,P = 0.026), and amygdala (β = − 87.9 mm3,P = 0.018) compared with those without glaucoma. Among neuropsychological battery tests, only the Stroop color reading test score was significantly lower in individuals with glaucoma compared with those without glaucoma (β = − 0.44,P = 0.038).ConclusionsWe found that glaucoma was associated with smaller volumes of the thalamus, caudate, putamen, pallidum, amygdala, and hippocampus.