bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Experience With Methylprednisolone on SARS-CoV-2 Infection in the African American Population, a Retrospective Analysis
Authors: Saggi Subodh J , Nath Sridesh , Culas Roshni , Chittalae Seema , Burza Aaliya , Srinivasan Maya , Abdul Rishard , Silver Benjamin , Lora Alnardo , Ibtida Ishmam , Chokshi Tanuj , Capric Violeta , Mohamed Ammar , Worah Samrat , OuYang Jie , Geraghty Patrick , Gruessner Angelika , Salifu Moro O 
Published: December 2020

Background: Coronavirus disease-19 (COVID-19) is associated with acute kidney injury (AKI) and acute respiratory distress syndrome (ARDS) with high mortality rates. In African American (AA) populations, COVID-19 presentations and outcomes are more severe. NIH and Interim WHO guidelines had suggested against the use of corticosteroids unless in clinical trials until the recent publication of the RECOVERY trial. Here, we analyzed the treatment effect of methylprednisolone on patients with AKI and ARDS during the initial 2 months of COVID-19 and detail the learning effect within our institution. Methods: Between March 1 and April 30, 2020, 75 AA patients met our inclusion criteria for ARDS and AKI, of which 37 had received corticosteroids. Twenty-eight-day mortality, improvement in PaO2/FiO2 ratio, and renal function were analyzed. The impact of methylprednisolone treatment was assessed with multivariable methods. Results: Survival in the methylprednisolone group reached 51% at 21 days compared to 29% in the non-corticosteroid group ( P < .001). Methylprednisolone improved the likelihood of renal function improvement. PaO2/FiO2 ratio in the methylprednisolone group improved by 73% compared to 45% in the non-corticosteroid group ( P = .01). Age, gender, BMI, preexisting conditions, and other treatment factors did not show any impact on renal or PaO2/FiO2 ratio improvement. The use of anticoagulants, the month of treatment, and AKI during hospitalization also influenced outcomes. Conclusion: In AA COVID-19 positive patients with ARDS and AKI, IV methylprednisolone lowered the incidence of mortality and improved the likelihood of renal and lung function recovery. Further investigation with a randomized control trial of corticosteroids is warranted.
Impact of contrast-induced acute kidney injury on the association between renin-angiotensin system inhibitors and long-term mortality in heart failure patients
Authors: Lei Li , Huang Yulu , Guo Zhaodong , Song Feier , He Yibo , Liu Jin , Sun Guoli , Liu Bowen , Chen Pengyuan , Zhao Jianbin , Wu Dengxuan , Xue Yan , Yan Wenhe , Lin Zefeng , Huang Xiuqiong , Chen Guanzhong , Chen Shiqun , Liu Yong , Chen Jiyan 
Published: December 2020

Introduction: Renin-angiotensin system inhibitors (RASi) reduce mortality among heart failure (HF) patients, but their effect among those complicating contrast-induced acute kidney injury (CI-AKI) remains unexplored. We aimed to investigate whether the relationship between RASi prescription at discharge and mortality differs between HF patients with or without CI-AKI following coronary angiography (CAG). Methods: About 596 HF patients from an observational cohort were divided into a CI-AKI group ( n = 104) and a non-CI-AKI group ( n = 492) based on whether they had CI-AKI following CAG. The endpoint was all-cause mortality. Multivariable Cox regression was performed in each group to explore the associations between RASi at discharge and mortality. Results: During the median follow-up time of 2.26 (1.70; 3.24) years, higher mortality rate was observed in the CI-AKI group compared to the non-CI-AKI group (18.3% vs 8.9%, p = 0.002). Among HF patients with CI-AKI, after adjusting for confounding factors, the association was not significant between RASi prescription at discharge and mortality (HR: 0.39, 95%CI: 0.12–1.31, p = 0.128), while it was among those without CI-AKI (HR: 0.39, 95%CI: 0.18–0.84, p = 0.016). Conclusion: RASi prescription at discharge for HF patients complicating CI-AKI tended to be ineffective, while it benefited those without CI-AKI. Further randomized evidence is needed to confirm this trend.
White Matter Integrity Predicts Electrical Stimulation (tDCS) and Language Therapy Effects in Primary Progressive Aphasia
Authors: Zhao Yi , Ficek Bronte , Webster Kimberly , Frangakis Constantine , Caffo Brian , Hillis Argye E. , Faria Andreia , Tsapkini Kyrana 
Published: December 2020

Background Transcranial direct current stimulation (tDCS), in conjunction with language therapy, improves language therapy outcomes in primary progressive aphasia (PPA). However, no studies show whether white matter integrity predicts language therapy or tDCS effects in PPA. Objective We aimed to determine whether white matter integrity, measured by diffusion tensor imaging (DTI), predicts written naming/spelling language therapy effects (letter accuracy on trained and untrained words) with and without tDCS over the left inferior frontal gyrus (IFG) in PPA. Methods Thirty-nine participants with PPA were randomly assigned to tDCS or sham condition, coupled with language therapy for 15 daily sessions. White matter integrity was measured by mean diffusivity (MD) and fractional anisotropy (FA) in DTI scans before therapy. Written naming outcomes were evaluated before, immediately after, 2 weeks, and 2 months posttherapy. To assess tDCS treatment effect, we used a mixed-effects model with treatment evaluation and time interaction. We considered a forward model selection approach to identify brain regions/fasciculi of which white matter integrity can predict improvement in performance of word naming. Results Both sham and tDCS groups significantly improved in trained items immediately after and at 2 months posttherapy. Improvement in the tDCS group was greater and generalized to untrained words. White matter integrity of ventral language pathways predicted tDCS effects in trained items whereas white matter integrity of dorsal language pathways predicted tDCS effects in untrained items. Conclusions White matter integrity influences both language therapy and tDCS effects. Thus, it holds promise as a biomarker for deciding which patients will benefit from language therapy and tDCS.
Can Injuries Have a Lasting Effect on the Perception of Pain in Young, Healthy Women and Men?
Authors: Maciejewska-Skrendo Agnieszka , Pawlak Maciej , Leońska-Duniec Agata , Jurewicz Alina , Kaczmarczyk Mariusz , Cięszczyk Paweł , Leźnicka Katarzyna 
Published: December 2020

Background: Pain is a characteristic, unpleasant sensory and emotional experience associated with actual or potential tissue damage. Pain is a subjective sensation, modulated by many factors such as age, sex, emotional state, national origin, or physical activity. Moreover, it is closely associated with intense physical activity, injuries, and traumas, which can significantly modulate pain tolerance. Hypothesis: We postulate that there are correlations between past injuries, physical activity, and intensity of pain perception (pain threshold and pain tolerance) in a population of healthy men and women. Study Design: Retrospective cohort study. Level of Evidence: Level 4. Methods: A total of 302 participants aged 18 to 32 years were included. The participants were divided into 2 groups (active and inactive individuals), in accordance with the scope of physical activity they had indicated. The test of pressure pain threshold and pressure pain tolerance was performed using an algometer. Results: Active women achieved significantly higher pain threshold and pain tolerance values in all measurements on the upper limb (except for the pain threshold on the left hand) compared with inactive women. In mediation analysis, the effect of injury remained significant only for the pressure pain tolerance in the dominant arm and the left hand in the female group. In the case of men, there were no significant differences in all measurements in view of the threshold and tolerance for pain between the groups of active and inactive and between men with injuries and without injuries. Conclusion: Intense, regular physical activity is a factor modulating the perception of pain. This was demonstrated as lowered sensitivity to pain stimuli in a population of healthy women. Clinical Relevance: Injuries should be treated as an important factor modulating the perception of pain. We recommend detailed monitoring of injuries during treatment and control of pain sensation.
Glucocorticoids in Graves’ orbitopathy: mechanisms of action and clinical application
Authors: Längericht Jan , Krämer Irene , Kahaly George J. 
Published: December 2020

Background: Graves’ orbitopathy (GO) is the most frequent extrathyroidal manifestation of the autoimmune Graves’ disease. GO significantly impacts quality of life and has a psycho-social morbidity. Inflammation and swelling of the orbital tissue often leads to proptosis, diplopia, and decrease of visual acuity. Due to the inflammatory background of the disease, glucocorticoids (GC) have been used as a first-line treatment for decades. Methods: PubMed and MeSH database were searched for original articles, clinical trials, reviews, and meta-analyses published between 1 January 2000 and 31 March 2020 and pertaining to both the mechanism of action and immunological effects of GC as well as to the treatment of GO by GC. The publications were evaluated according to their setting and study design. Results: GC act through genomic (trans-activation and trans-repression) and rapid non-genomic mechanisms. GC in general, and the intravenous (IV) administration of GC in particular, markedly decrease the activity and number of the most potent antigen-presenting dendritic cells. According to the internationally acknowledged European Thyroid Association Guidelines for the management of GO, weekly IVGC application over 12 weeks is recommended as first-line treatment for patients with active and severe GO. The daily and cumulative dose should be tailored according to clinical severity, for example, 4.5 g of IV methylprednisolone for the inflammatory component versus 7.5 g in the presence of diplopia and severe proptosis. Fast and significant improvements in orbital symptoms and signs are noted in 65–70% of patients. Long-term experience over decades, and worldwide availability at low cost, underline the clinical and therapeutic relevance of GC. Adverse events are rarely severe, dose-dependent, and usually reversible, hence easy to handle by medical investigators. Oral GC application on a daily basis is characterized by high bioavailability but reduced efficacy and increased toxicity. Conclusion: IVGC still represents the standard of care in active/severe GO. Innovative biologicals, like monoclonal antibodies targeting the thyrotropin/Insulin-like growth factor-1 receptors or pro-inflammatory cytokines (e.g., Interleukin-6) should be compared with standard GC treatment with respect to short- and long-term efficacy, safety, costs, and global availability.
FiberWire vs FiberTape: Comparison of Bacterial Adherence in a Murine Air Pouch Wound Model
Authors: Blumenthal Allison M. , Bou-akl Therese , Rossi Mario D. , Wu Bin , Ren Wei-Ping , Markel David C. 
Published: December 2020

Background: For high–tensile strength sutures, past research has largely focused on mechanical properties or bacterial adherence across various manufacturers. Purpose: This study investigated high-tensile strength sutures with different shapes but otherwise identical composition. The purpose was to evaluate the differences between high–tensile strength suture wire and suture tape relative to bacterial adherence and bacterial retention after washout. Study Design: Controlled laboratory study. Methods: Sutures were implanted in dorsal air pouches of 72 BALB/cJ mice. Experimental pouches were inoculated with Staphylococcus aureus; no bacteria were used in the control conditions. The mice were randomized into 3 groups: group 1 underwent suture extraction 7 days after implantation; group 2 underwent an irrigation procedure, followed by immediate suture extraction on day 7; and group 3 underwent an irrigation procedure on day 7, with delayed suture extraction on day 14 after implantation. The sutures were evaluated using confocal microscopy; electron microscopy; and spectrophotometry, through which optical density, as measured by the amount of scattered light, is directly correlated with the number of bacteria. Histological assessment was performed on the pouches. Results: Optical density (mean ± SD) was significantly higher for FiberTape sutures than for FiberWire sutures, respectively, at the 2-hour time point for all groups (group 1, 0.0550 ± 0.0081 vs 0.0162 ± 0.006 [ P = .0054]; group 2, 0.0225 ± 0.0049 vs 0.0056 ± 0.0006 [ P = .0045]; group 3, 0.055 ± 0.0222 vs 0.0043 ± 0.0005 [ P = .0103]). Additionally, groups 2 and 3 showed statistically significant results at the 4-hour time points (group 2, 0.0384 ± 0.0087 vs 0.0145 ± 0.0042 [ P = .0280]; group 3, 0.0532 ± 0.0159 vs 0.0101 ± 0.0025 [ P = .0058]). The wash fluid also demonstrated significantly greater optical density for the FiberTape than the FiberWire sutures, respectively, at the 2-hour time point for all groups (group 1, 0.1657 ± 0.0319 vs 0.0317 ± 0.008 [ P = .0063]; group 2, 0.0522 ± 0.0156 vs 0.0127 ± 0.0022 [ P = .0219]; group 3, 0.1707 ± 0.0205 vs 0.0191 ± 0.0053 [ P < .0001]). No bacterial growth occurred in the control conditions. Histological assessment revealed only mild inflammation in the control groups as compared with more severe responses in the experimental groups at all time points. Conclusion: FiberTape was associated with increased bacterial adhesion as well as retention as compared with FiberWire in an in vivo murine wound model. Clinical Relevance: This study demonstrates that suture design influences the occurrence of and ability to clear surgical infection and must be considered when selecting high-tensile strength sutures in a clinical setting.
Male recombination map of the autosomal genome in German Holstein
Authors: Qanbari Saber , Wittenburg Dörte 
Published: December 2020

AbstractBackgroundRecombination is a process by which chromosomes are broken and recombine to generate new combinations of alleles, therefore playing a major role in shaping genome variation. Recombination frequencies ($$\theta$$θ) between markers are used to construct genetic maps, which have important implications in genomic studies. Here, we report a recombination map for 44,696 autosomal single nucleotide polymorphisms (SNPs) according to the coordinates of the most recent bovine reference assembly. The recombination frequencies were estimated across 876 half-sib families with a minimum number of 39 and maximum number of 4236 progeny, comprising over 367 K genotyped German Holstein animals.ResultsGenome-wide, over 8.9 million paternal recombination events were identified by investigating adjacent markers. The recombination map spans 24.43 Morgan (M) for a chromosomal length of 2486 Mbp and an average of ~ 0.98 cM/Mbp, which concords with the available pedigree-based linkage maps. Furthermore, we identified 971 putative recombination hotspot intervals (defined as$$\theta$$θ > 2.5 standard deviations greater than the mean). The hotspot regions were non-uniformly distributed as sharp and narrow peaks, corresponding to ~ 5.8% of the recombination that has taken place in only ~ 2.4% of the genome. We verified genetic map length by applying a likelihood-based approach for the estimation of recombination rate between all intra-chromosomal marker pairs. This resulted in a longer autosomal genetic length for male cattle (25.35 cM) and in the localization of 51 putatively misplaced SNPs in the genome assembly.ConclusionsGiven the fact that this map is built on the coordinates of the ARS-UCD1.2 assembly, our results provide the most updated genetic map yet available for the cattle genome.
Analysis of readability and structural accuracy in SNOMED CT
Authors: Abad-Navarro Francisco , Quesada-Martínez Manuel , Duque-Ramos Astrid , Fernández-Breis Jesualdo Tomás 
Published: December 2020

AbstractBackgroundThe increasing adoption of ontologies in biomedical research and the growing number of ontologies available have made it necessary to assure the quality of these resources. Most of the well-established ontologies, such as the Gene Ontology or SNOMED CT, have their own quality assurance processes. These have demonstrated their usefulness for the maintenance of the resources but are unable to detect all of the modelling flaws in the ontologies. Consequently, the development of efficient and effective quality assurance methods is needed.MethodsHere, we propose a series of quantitative metrics based on the processing of the lexical regularities existing in the content of the ontology, to analyse readability and structural accuracy. The readability metrics account for the ratio of labels, descriptions, and synonyms associated with the ontology entities. The structural accuracy metrics evaluate how two ontology modelling best practices are followed: (1) lexically suggest locally define (LSLD), that is, if what is expressed in natural language for humans is available as logical axioms for machines; and (2) systematic naming, which accounts for the amount of label content of the classes in a given taxonomy shared.ResultsWe applied the metrics to different versions of SNOMED CT. Both readability and structural accuracy metrics remained stable in time but could capture some changes in the modelling decisions in SNOMED CT. The value of the LSLD metric increased from 0.27 to 0.31, and the value of the systematic naming metric was around 0.17. We analysed the readability and structural accuracy in the SNOMED CT July 2019 release. The results showed that the fulfilment of the structural accuracy criteria varied among the SNOMED CT hierarchies. The value of the metrics for the hierarchies was in the range of 0–0.92 (LSLD) and 0.08–1 (systematic naming). We also identified the cases that did not meet the best practices.ConclusionsWe generated useful information about the engineering of the ontology, making the following contributions: (1) a set of readability metrics, (2) the use of lexical regularities to define structural accuracy metrics, and (3) the generation of quality assurance information for SNOMED CT.
Modeling clinical activities based on multi-perspective declarative process mining with openEHR’s characteristic
Authors: Xu Haifeng , Pang Jianfei , Yang Xi , Yu Jinghui , Li Xuemeng , Zhao Dongsheng 
Published: December 2020

AbstractBackgroundIt is significant to model clinical activities for process mining, which assists in improving medical service quality. However, current process mining studies in healthcare pay more attention to the control flow of events, while the data properties and the time perspective are generally ignored. Moreover, classifying event attributes from the view of computers usually are difficult for medical experts. There are also problems of model sharing and reusing after it is generated.MethodsIn this paper, we presented a constraint-based method using multi-perspective declarative process mining, supporting healthcare personnel to model clinical processes by themselves. Inspired by openEHR, we classified event attributes into seven types, and each relationship between these types is represented in a Constrained Relationship Matrix. Finally, a conformance checking algorithm is designed.ResultsThe method was verified in a retrospective observational case study, which consists of Electronic Medical Record (EMR) of 358 patients from a large general hospital in China. We take the ischemic stroke treatment process as an example to check compliance with clinical guidelines. Conformance checking results are analyzed and confirmed by medical experts.ConclusionsThis representation approach was applicable with the characteristic of easily understandable and expandable for modeling clinical activities, supporting to share the models created across different medical facilities.
A partial encryption algorithm for medical images based on quick response code and reversible data hiding technology
Authors: Li Jian , Zhang Zelin , Li Shengyu , Benton Ryan , Huang Yulong , Kasukurthi Mohan Vamsi , Li Dongqi , Lin Jingwei , Borchert Glen M. , Tan Shaobo , Li Gang , Ma Bin , Yang Meihong , Huang Jingshan 
Published: December 2020

Abstract
Background
Medical image data, like most patient information, have a strong requirement for privacy and confidentiality. This makes transmitting medical image data, within an open network, problematic, due to the aforementioned issues, along with the dangers of data/information leakage. Possible solutions in the past have included the utilization of information-hiding and image-encryption technologies; however, these methods can cause difficulties when attempting to recover the original images.

Methods
In this work, we developed an algorithm for protecting medical image key regions. Coefficient of variation is first employed to identify key regions, a.k.a. image lesion areas; then additional areas are processed as blocks and texture complexity is analyzed. Next, our novel reversible data-hiding algorithm embeds lesion area contents into a high-texture area, after which an Arnold transformation is utilized to protect the original lesion information. After this, we use image basic information ciphertext and decryption parameters to generate a quick response (QR) code used in place of original key regions.

Results
The approach presented here allows for the storage (and sending) of medical image data within open network environments, while ensuring only authorized personnel are able to recover sensitive patient information (both image and meta-data) without information loss.

Discussion
Peak signal to noise ratio and the Structural Similarity Index measures show that the algorithm presented in this work can encrypt and restore original images without information loss. Moreover, by adjusting the threshold and the Mean Squared Error, we can control the overall quality of the image: the higher the threshold, the better the quality and vice versa. This allows the encryptor to control the amount of degradation as, at appropriate amounts, degradation aids in the protection of the image.

Conclusions
As shown in the experimental results, the proposed method allows for (a) the safe transmission and storage of medical image data, (b) the full recovery (no information loss) of sensitive regions within the medical image following encryption, and (c) meta-data about the patient and image to be stored within and recovered from the public image.
Quality assurance and enrichment of biological and biomedical ontologies and terminologies
Authors: Agrawal Ankur , Cui Licong 
Published: December 2020

AbstractBiological and biomedical ontologies and terminologies are used to organize and store various domain-specific knowledge to provide standardization of terminology usage and to improve interoperability. The growing number of such ontologies and terminologies and their increasing adoption in clinical, research and healthcare settings call for effective and efficient quality assurance and semantic enrichment techniques of these ontologies and terminologies. In this editorial, we provide an introductory summary of nine articles included in this supplement issue for quality assurance and enrichment of biological and biomedical ontologies and terminologies. The articles cover a range of standards including SNOMED CT, National Cancer Institute Thesaurus, Unified Medical Language System, North American Association of Central Cancer Registries and OBO Foundry Ontologies.