bluuebunny/crossref_metadata_2025_split huggingface dataset:
CT imaging changes of corona virus disease 2019(COVID-19): a multi-center study in Southwest China
Authors: Li Xiaoming , Zeng Wenbing , Li Xiang , Chen Haonan , Shi Linping , Li Xinghui , Xiang Hongnian , Cao Yang , Chen Hui , Liu Chen , Wang Jian 
Published: April 2020

Abstract
Background
Since the first case of a coronavirus disease 2019 (COVID-19) infection pneumonia was detected in Wuhan, China, a series of confirmed cases of the COVID-19 were found in Southwest China. The aim of this study was to describe the imaging manifestations of hospitalized patients with confirmed COVID-19 infection in southwest China.

Methods
In this retrospective study, data were collected from 131 patients with confirmed coronavirus disease 2019 (COVID-19) from 3 Chinese hospitals. Their common clinical manifestations, as well as characteristics and evolvement features of chest CT images, were analyzed.

Results
A total of 100 (76%) patients had a history of close contact with people living in Wuhan, Hubei. The clinical manifestations of COVID-19 included cough, fever. Most of the lesions identified in chest CT images were multiple lesions of bilateral lungs, lesions were more localized in the peripheral lung, 109 (83%) patients had more than two lobes involved, 20 (15%) patients presented with patchy ground glass opacities, patchy ground glass opacities and consolidation of lesions co-existing in 61 (47%) cases. Complications such as pleural thickening, hydrothorax, pericardial effusion, and enlarged mediastinal lymph nodes were detected but only in rare cases. For the follow-up chest CT examinations (91 cases), We found 66 (73%) cases changed very quickly, with an average of 3.5 days, 25 cases (27%) presented absorbed lesions, progression was observed in 41 cases (46%), 25 (27%) cases showed no significant changes.

Conclusion
Chest CT plays an important role in diagnosing COVID-19. The imaging pattern of multifocal peripheral ground glass or mixed consolidation is highly suspicious of COVID-19, that can quickly change over a short period of time.
Preparation of uniformly labelled 13C- and 15N-plants using customised growth chambers
Authors: Ćeranić Asja , Doppler Maria , Büschl Christoph , Parich Alexandra , Xu Kangkang , Koutnik Andrea , Bürstmayr Hermann , Lemmens Marc , Schuhmacher Rainer 
Published: April 2020

AbstractBackgroundStable isotopically labelled organisms have found wide application in life science research including plant physiology, plant stress and defense as well as metabolism related sciences. Therefore, the reproducible production of plant material enriched with stable isotopes such as13C and15N is of considerable interest. A high degree of enrichment (> 96 atom %) with a uniformly distributed isotope (global labelling) is accomplished by a continuous substrate supply during plant growth/cultivation. In the case of plants,13C-labelling can be achieved by growth in13CO2(g)atmosphere while global15N-labelling needs15N- containing salts in the watering/nutrient solution. Here, we present a method for the preparation of13C and15N-labelled plants by the use of closed growth chambers and hydroponic nutrient supply. The method is exemplified with durum wheat.ResultsIn total, 330 g of globally13C- and 295 g of15N-labelledTriticum durumwheat was produced during 87 cultivation days. For this, a total of 3.88 mol of13CO2(g)and 58 mmol of15N were consumed. The degree of enrichment was determined by LC-HRMS and ranged between 96 and 98 atom % for13C and 95–99 atom % for15N, respectively. Additionally, the isotopically labelled plant extracts were successfully used for metabolome-wide internal standardisation of nativeT.durumplants. Application of an isotope-assisted LC-HRMS workflow enabled the detection of 652 truly wheat-derived metabolites out of which 143 contain N.ConclusionA reproducible cultivation which makes use of climate chambers and hydroponics was successfully adapted to produce highly enriched, uniformly13C- and15N-labelled wheat. The obtained plant material is suitable to be used in all kinds of isotope-assisted research. The described technical equipment and protocol can easily be applied to other plants to produce13C-enriched biological samples when the necessary specific adaptations e.g. temperature and light regime, as well as nutrient supply are considered. Additionally, the15N-labelling method can also be carried out under regular glasshouse conditions without the need for customised atmosphere.
Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins
Authors: Van Nostrand Eric L. , Pratt Gabriel A. , Yee Brian A. , Wheeler Emily C. , Blue Steven M. , Mueller Jasmine , Park Samuel S. , Garcia Keri E. , Gelboin-Burkhart Chelsea , Nguyen Thai B. , Rabano Ines , Stanton Rebecca , Sundararaman Balaji , Wang Ruth , Fu Xiang-Dong , Graveley Brenton R. , Yeo Gene W. 
Published: April 2020

Abstract
Background
A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis across datasets. The development of enhanced CLIP (eCLIP) enabled the mapping of targets for 150 RBPs in K562 and HepG2, creating a unique resource of RBP interactomes profiled with a standardized methodology in the same cell types.

Results
Our analysis of 223 eCLIP datasets reveals a range of binding modalities, including highly resolved positioning around splicing signals and mRNA untranslated regions that associate with distinct RBP functions. Quantification of enrichment for repetitive and abundant multicopy elements reveals 70% of RBPs have enrichment for non-mRNA element classes, enables identification of novel ribosomal RNA processing factors and sites, and suggests that association with retrotransposable elements reflects multiple RBP mechanisms of action. Analysis of spliceosomal RBPs indicates that eCLIP resolves AQR association after intronic lariat formation, enabling identification of branch points with single-nucleotide resolution, and provides genome-wide validation for a branch point-based scanning model for 3′ splice site recognition. Finally, we show that eCLIP peak co-occurrences across RBPs enable the discovery of novel co-interacting RBPs.

Conclusions
This work reveals novel insights into RNA biology by integrated analysis of eCLIP profiling of 150 RBPs with distinct functions. Further, our quantification of both mRNA and other element association will enable further research to identify novel roles of RBPs in regulating RNA processing.
A simulation study comparing the power of nine tests of the treatment effect in randomized controlled trials with a time-to-event outcome
Authors: Royston Patrick , B. Parmar Mahesh K. 
Published: April 2020

Abstract
Background
The logrank test is routinely applied to design and analyse randomized controlled trials (RCTs) with time-to-event outcomes. Sample size and power calculations assume the treatment effect follows proportional hazards (PH). If the PH assumption is false, power is reduced and interpretation of the hazard ratio (HR) as the estimated treatment effect is compromised. Using statistical simulation, we investigated the type 1 error and power of the logrank (LR)test and eight alternatives. We aimed to identify test(s) that improve power with three types of non-proportional hazards (non-PH): early, late or near-PH treatment effects.

Methods
We investigated weighted logrank tests (early, LRE; late, LRL), the supremum logrank test (SupLR) and composite tests (joint, J; combined, C; weighted combined, WC; versatile and modified versatile weighted logrank, VWLR, VWLR2) with two or more components. Weighted logrank tests are intended to be sensitive to particular non-PH patterns. Composite tests attempt to improve power across a wider range of non-PH patterns. Using extensive simulations based on real trials, we studied test size and power under PH and under simple departures from PH comprising pointwise constant HRs with a single change point at various follow-up times. We systematically investigated the influence of high or low control-arm event rates on power.

Results
With no preconceived type of treatment effect, the preferred test is VWLR2. Expecting an early effect, tests with acceptable power are SupLR, C, VWLR2, J, LRE and WC. Expecting a late effect, acceptable tests are LRL, VWLR, VWLR2, WC and J. Under near-PH, acceptable tests are LR, LRE, VWLR, C, VWLR2 and SupLR. Type 1 error was well controlled for all tests, showing only minor deviations from the nominal 5%. The location of the HR change point relative to the cumulative proportion of control-arm events considerably affected power.

Conclusions
Assuming ignorance of the likely treatment effect, the best choice is VWLR2. Several non-standard tests performed well when the correct type of treatment effect was assumed. A low control-arm event rate reduced the power of weighted logrank tests targeting early effects. Test size was generally well controlled. Further investigation of test characteristics with different types of non-proportional hazards of the treatment effect is warranted.
Expression of interferon-regulated genes in juvenile dermatomyositis versus Mendelian autoinflammatory interferonopathies
Authors: Kim Hanna , Gunter-Rahman Fatima , McGrath John A. , Lee Esther , de Jesus Adriana A. , Targoff Ira N. , Huang Yan , O’Hanlon Terrance P. , Tsai Wanxia L. , Gadina Massimo , Miller Frederick W. , Goldbach-Mansky Raphaela , Rider Lisa G. 
Published: April 2020

Abstract
Background
Juvenile dermatomyositis (JDM) is a systemic autoimmune disease with a prominent interferon (IFN) signature, but the pathogenesis of JDM and the etiology of its IFN signature remain unknown. The Mendelian autoinflammatory interferonopathies, Chronic Atypical Neutrophilic Dermatosis with Lipodystrophy and Elevated temperature (CANDLE) and STING-Associated Vasculopathy with onset in Infancy (SAVI), are caused by genetic mutations and have extremely elevated IFN signatures thought to drive pathology. The phenotypic overlap of some clinical features of CANDLE and SAVI with JDM led to the comparison of a standardized interferon-regulated gene score (IRG-S) in JDM and myositis-specific autoantibody (MSA) JDM subgroups, with CANDLE and SAVI.

Methods
A peripheral 28-component IRG-S assessed by NanoString™ in 57 JDM patients subtyped by MSA was compared with IRG-S in healthy controls (HC) and CANDLE/SAVI patients. Principal component analysis (PCA) was performed, and individual genes were evaluated for their contribution to the score. IRG-S were correlated with disease assessments and patient characteristics.

Results
IRG-S in JDM patients were significantly higher than in HC but lower than in CANDLE or SAVI. JDM IRG-S overlapped more with SAVI than CANDLE by PCA. Among MSA groups, anti-MDA5 autoantibody-positive patients’ IRG-S overlapped most with SAVI. The IFI27 proportion was significantly higher in SAVI and CANDLE than JDM, but IFIT1 contributed more to IRG-S in JDM. Overall, the contribution of individual interferon-regulated genes (IRG) in JDM was more similar to SAVI. IRG-S correlated moderately with JDM disease activity measures (rs = 0.33–0.47) and more strongly with skin activity (rs = 0.58–0.79) in anti-TIF1 autoantibody-positive patients. Weakness and joint disease activity (multinomial OR 0.91 and 3.3) were the best predictors of high IRG-S.

Conclusions
Our findings demonstrate peripheral IRG expression in JDM overlaps with monogenic interferonopathies, particularly SAVI, and correlates with disease activity. Anti-MDA5 autoantibody-positive JDM IRG-S were notably more similar to SAVI. This may reflect both a shared IFN signature, which is driven by IFN-β and STING pathways in SAVI, as well as the shared phenotype of vasculopathy in SAVI and JDM, particularly in anti-MDA5 autoantibody-positive JDM, and indicate potential therapeutic targets for JDM.
Methotrexate and relative risk of dementia amongst patients with rheumatoid arthritis: a multi-national multi-database case-control study
Authors: Newby Danielle , Prieto-Alhambra Daniel , Duarte-Salles Talita , Ansell David , Pedersen Lars , van der Lei Johan , Mosseveld Mees , Rijnbeek Peter , James Glen , Alexander Myriam , Egger Peter , Podhorna Jana , Stewart Robert , Perera Gayan , Avillach Paul , Grosdidier Solène , Lovestone Simon , Nevado-Holgado Alejo J. 
Published: April 2020

Abstract
Background
Inflammatory processes have been shown to play a role in dementia. To understand this role, we selected two anti-inflammatory drugs (methotrexate and sulfasalazine) to study their association with dementia risk.

Methods
A retrospective matched case-control study of patients over 50 with rheumatoid arthritis (486 dementia cases and 641 controls) who were identified from electronic health records in the UK, Spain, Denmark and the Netherlands. Conditional logistic regression models were fitted to estimate the risk of dementia.

Results
Prior methotrexate use was associated with a lower risk of dementia (OR 0.71, 95% CI 0.52–0.98). Furthermore, methotrexate use with therapy longer than 4 years had the lowest risk of dementia (odds ratio 0.37, 95% CI 0.17–0.79). Sulfasalazine use was not associated with dementia (odds ratio 0.88, 95% CI 0.57–1.37).

Conclusions
Further studies are still required to clarify the relationship between prior methotrexate use and duration as well as biological treatments with dementia risk.
Geolocation of covert communication entity on the Internet for post-steganalysis
Authors: Zhang Fan , Liu Fenlin , Luo Xiangyang 
Published: April 2020

AbstractGeolocation of covert communication entity is significantly important for the forensics of the crime but has significant challenges when the steganalyst locks the guilty actor IP and wants to know the physical location of the actor. This kind of post-steganalysis involves not only the stegos transmitted on the Internet but the IP package head and content. This paper presents a geolocation method for the location of the covert communication entity based on hop-hot path coding. The method estimates the location of the covert communication entity by combining the path and delay between probes and the covert communication entity IP, which improves the deficiency that similar delays do not necessarily mean close geographical locations of the IPs. Moreover, the similarity between the IPs’ paths can be measured by coding the paths between IPs and probes. The results of a series of experiments show that the median error of the proposed method is within 6.16 km using different thresholds.
A class of new derivative-free gradient type methods for large-scale nonlinear systems of monotone equations
Authors: Fang Xiaowei 
Published: April 2020

AbstractIn this paper, we present a class of new derivative-free gradient type methods for large-scale nonlinear systems of monotone equations. The methods combine the RMIL conjugate gradient method, the strategy of hyperplane projection and the derivative-free line search technique. Under some appropriate assumptions, the global convergence of the given methods is established. Numerical experiments indicate that the proposed methods are effective.
A novel method to predict essential proteins based on tensor and HITS algorithm
Authors: Zhang Zhihong , Luo Yingchun , Hu Sai , Li Xueyong , Wang Lei , Zhao Bihai 
Published: April 2020

Abstract
Background
Essential proteins are an important part of the cell and closely related to the life activities of the cell. Hitherto, Protein-Protein Interaction (PPI) networks have been adopted by many computational methods to predict essential proteins. Most of the current approaches focus mainly on the topological structure of PPI networks. However, those methods relying solely on the PPI network have low detection accuracy for essential proteins. Therefore, it is necessary to integrate the PPI network with other biological information to identify essential proteins.

Results
In this paper, we proposed a novel random walk method for identifying essential proteins, called HEPT. A three-dimensional tensor is constructed first by combining the PPI network of Saccharomyces cerevisiae with multiple biological data such as gene ontology annotations and protein domains. Then, based on the newly constructed tensor, we extended the Hyperlink-Induced Topic Search (HITS) algorithm from a two-dimensional to a three-dimensional tensor model that can be utilized to infer essential proteins. Different from existing state-of-the-art methods, the importance of proteins and the types of interactions will both contribute to the essential protein prediction. To evaluate the performance of our newly proposed HEPT method, proteins are ranked in the descending order based on their ranking scores computed by our method and other competitive methods. After that, a certain number of the ranked proteins are selected as candidates for essential proteins. According to the list of known essential proteins, the number of true essential proteins is used to judge the performance of each method. Experimental results show that our method can achieve better prediction performance in comparison with other nine state-of-the-art methods in identifying essential proteins.

Conclusions
Through analysis and experimental results, it is obvious that HEPT can be used to effectively improve the prediction accuracy of essential proteins by the use of HITS algorithm and the combination of network topology with gene ontology annotations and protein domains, which provides a new insight into multi-data source fusion.
Current state of open educational resources in the Arab region: an investigation in 22 countries
Authors: Tlili Ahmed , Jemni Mohamed , Khribi Mohamed Koutheair , Huang Ronghuai , Chang Ting-Wen , Liu Dejian 
Published: April 2020

AbstractWhile several studies were conducted to investigate the current state of Open Educational Resources (OER) in several regions (e.g., Europe, America, Middle East and MENA), to the best of our knowledge, no study was conducted to cover the entire Arab region, specifically the twenty-two Arab countries. Therefore, to identify the OER gap in this region and then provide recommendations to facilitate OER adoption, this study investigates the current state of OER in the Arab region, specifically in twenty-two Arab countries. The obtained results showed that the OER progress is unbalanced within the Arab countries. Interestingly, several Arab countries are still lack behind when it comes to the application of OER in universities and schools. Finally, several recommendations are identified to several stakeholders, including policy makers and educators, to achieve social justice and facilitate the adoption and use of OER in the Arab region.
Prerequisites for artificial intelligence in further education: identification of drivers, barriers, and business models of educational technology companies
Authors: Renz André , Hilbig Romy 
Published: April 2020

AbstractThe ongoing datafication of our social reality has resulted in the emergence of new data-based business models. This development is also reflected in the education market. An increasing number of educational technology (EdTech) companies are entering the traditional education market with data-based teaching and learning solutions, and they are permanently transforming the market. However, despite the current market dynamics, there are hardly any business models that implement the possibilities of Learning Analytics (LA) and Artificial Intelligence (AI) to create adaptive teaching and learning paths. This paper focuses on EdTech companies and the drivers and barriers that currently affect data-based teaching and learning paths. The results show that LA especially are integrated into the current business models of EdTech companies on three levels, which are as follows: basic Learning Analytics, Learning Analytics and algorithmic or human-based recommendations, and Learning Analytics and adaptive teaching and learning (AI based). The discourse analysis reveals a diametrical relationship between the traditional educational ideal and the futuristic idea of education and knowledge transfer. While the desire for flexibility and individualization drives the debate on AI-based learning systems, a lack of data sovereignty, uncertainty and a lack of understanding of data are holding back the development and implementation of appropriate solutions at the same time.
Prophylactic Cefazolin Dosing in Women With Body Mass Index >35 kg·m−2 Undergoing Cesarean Delivery: A Pharmacokinetic Study of Plasma and Interstitial Fluid
Authors: Eley Victoria A. , Christensen Rebecca , Ryan Rochelle , Jackson Dwane , Parker Suzanne L. , Smith Matthew , van Zundert Andre A. , Wallis Steven C. , Lipman Jeffrey , Roberts Jason A. 
Published: April 2020

BACKGROUND:
Obesity is a risk factor for surgical site infection after cesarean delivery. There is inadequate pharmacokinetic data available regarding prophylactic cefazolin dosing in obese pregnant women. We aimed to describe the plasma and interstitial fluid (ISF) pharmacokinetics of cefazolin in obese women undergoing elective cesarean delivery and use dosing simulations to predict optimal dosing regimens.

METHODS:
Eligible women were scheduled for elective cesarean delivery at term, with a body mass index (BMI) of >35 kg·m−2. Plasma and ISF samples were collected following 2 g of intravenous cefazolin. Concentrations were determined using liquid chromatography-mass spectrometry. Population pharmacokinetic modeling and Monte Carlo dosing simulations were performed using Pmetrics. Total and unbound cefazolin concentrations in plasma and ISF were compared with the minimum inhibitory concentration at which 90% of isolates are inhibited (MIC90) of cefazolin for Staphylococcus aureus, 2 mg·L−1. The fractional target attainment (FTA) of dosing regimens to achieve a pre-established target of 95% unbound ISF concentrations >2 mg·L−1 throughout a 3-hour duration of the surgery was calculated.

RESULTS:
The 12 women recruited had a median (interquartile range [IQR]) BMI of 41.5 (39.7–46.6) kg·m−2 and a median (IQR) gestation of 38.7 weeks (37.9–39.0). For each timepoint up to 180 minutes, the median across subjects of total and unbound plasma concentration of cefazolin remained above 2 mg·L−1. The minimum observed total plasma concentration was 31.7 mg·L−1 and plasma unbound concentration was 7.7 mg·L−1 (observed in the same participant). For each timepoint up to 150 minutes, the median across subjects of unbound ISF concentrations remained above 2 mg·L−1. The minimum observed unbound ISF concentration was 0.7 mg·L−1 (observed in 1 participant). In 2 participants, the ISF concentration of cefazolin was not maintained above 2 mg·L−1. The mean (± standard error [SE]) penetration of cefazolin (calculated as area under the concentration-time curve for the unbound fraction of drug [fAUC]tissue/fAUCplasma) into the ISF was 0.884 ± 1.11. Simulations demonstrated that FTA >95% was achieved in patients weighing 90–150 kg by an initial 2 g dose with redosing of 2 g at 2 hours. FTA was improved to >99% when an initial 3 g dose was repeated at 2 hours.

CONCLUSIONS:
To maintain adequate ISF antibiotic concentrations in obese pregnant women, our results suggest that redosing of cefazolin may be required. When wound closure has not occurred within 2 hours, redosing is suggested, following either a 2 or 3 g initial bolus. These preliminary results require validation in a larger population.