bluuebunny/crossref_metadata_2025_split huggingface dataset:
Supraclinoid Internal Carotid Artery Aneurysm Clipping Complicated by Aneurysm Dome Origin of the Anterior Choroidal Artery: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F 
Published: March 2020

Abstract
Supraclinoid internal carotid artery (ICA) aneurysms most commonly arise at the origin of the posterior communicating or anterior choroidal artery. The unique angioarchitecture presented in this case involved the anterior choroidal artery (AChA) originating from the dome of a supraclinoid ICA aneurysm. Treatment is associated with high morbidity because of the eloquent parenchyma perfused by the AChA. Therefore, the preservation of flow within the AChA during clipping is paramount. Anterior choroidal syndrome, comprising hemiplegia, hemianesthesia, and hemianopsia, conveys a significant morbidity. This syndrome is observed in the setting of AChA sacrifice and can be observed in a delayed manner after clipping. Anterior choroidal syndrome is of uncertain etiology but is associated with AChA infarction. This patient presented with tinnitus and was found to have an incidental supraclinoid ICA aneurysm with AChA originating from the aneurysmal dome. A right orbitozygomatic craniotomy was performed for a transsylvian approach to the aneurysm. A fenestrated clip was applied to occlude the aneurysmal portion of the ICA up to the point of AChA origin. A curved clip was then used to occlude the AChA segment of the aneurysm, providing patency to the AChA takeoff along the ICA. Patency of the AChA and ICA was confirmed with intraoperative angiography, and the patient had a favorable clinical outcome. This case exemplified an excellent surgical clipping of a challenging supraclinoid ICA aneurysm involving the need to preserve a vessel off the aneurysm dome. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Large Cervical Ependymoma: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F 
Published: March 2020

Abstract
Spinal ependymomas compose approximately 60% of spinal gliomas, the predominance occurring within adults. These tumors are generally benign, and maximal surgical resection with neurological preservation is the surgical goal. This patient had a large upper cervical ependymoma, which was approached through a cervical laminotomy. The surgical resection of this lesion demonstrates the principles of pial venous plexus preservation during posterior midline raphe identification and dissection. Gross total surgical resection was achieved with the preservation of the patient's baseline neurological function. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Trajectory analysis combining pain and physical function in individuals with knee and hip osteoarthritis: results from the French KHOALA cohort
Authors: Wieczorek Maud , Rotonda Christine , Coste Joël , Pouchot Jacques , Saraux Alain , Guillemin Francis , Rat Anne-Christine 
Published: March 2020

Abstract

Objectives
The aims of this study were to identify homogeneous subgroups of knee and/or hip OA patients with distinct trajectories of the combination of pain and physical function (PF) over time and to determine the baseline factors associated with these trajectories.

Methods
We used data from the Knee and Hip Osteoarthritis Long-term Assessment (KHOALA) cohort, a French population-based cohort of 878 patients with symptomatic knee and/or hip OA. Pain and PF were measured annually over 5 years with the Medical Outcomes Study Short Form 36 questionnaire. First, trajectory models were estimated with varying numbers of groups for each of the outcomes separately then fitted into a multi-trajectory model. We used multinomial logistic regression to determine the baseline characteristics associated with each trajectory.

Results
Univariate four-class models were identified as most appropriate for pain and PF. Comparison of separate trajectories showed that 41% of patients included in the severe functional limitations trajectory did not belong to the more severe pain trajectory (Cramér’s V statistic = 0.45). Group-based multi-trajectory modelling revealed four distinct trajectories of pain and PF. On multivariate analyses, female sex, older age, high Kellgren grade, low physical activity intensity, low psychosocial distress score (high distress) and low vitality score were associated with the more severe symptoms trajectory.

Conclusion
Over 5 years, we identified four distinct trajectories combining pain and PF. Management of weight, fatigue and psychosocial distress and the practice of physical activity seem important to maintain function and limit pain in patients with lower-limb OA.
White blood cell subtypes as predictors of adverse cardiac events
Authors: Kristono Gisela A. , Holley Ana S. , Harding Scott A. , Larsen Peter D. 
Published: March 2020

Background
White blood cell (WBC) subtypes have been associated with major adverse cardiovascular events (MACEs) in acute myocardial infarction (AMI). More recently, combining neutrophil and lymphocyte counts or lymphocyte and monocyte counts into a ratio has found to be promising for predicting MACE. This study aimed to confirm the association between MACE and the following WBC subtypes: neutrophils, lymphocytes, monocytes, neutrophil–lymphocyte ratio (NLR) and lymphocyte–monocyte ratio (LMR).

Methods
In a cohort of 860 AMI patients, we collected levels of WBC subtypes from the earliest blood tests recorded prior to angiography. Data on baseline demographics and one-year outcomes were also collected.

Results
At one year, 130 patients (15.1%) developed MACE. NLR and LMR were significantly associated with MACE on univariate analysis (P = 0.006 and 0.005, respectively). However, when combined into a multivariate model with age, hypertension, prior myocardial infarction and Type 2 diabetes, neither NLR nor LMR had significant associations (odds ratio = 1.058 and 0.966, P = 0.069 and 0.612, respectively).

Conclusion
As NLR and LMR were correlated with MACE only on univariate analysis, we do not believe that they are predictive enough to be used alone in a clinical setting. Further studies are required to assess the prognostic ability of these ratios in combination with other inflammatory markers.
Evolution of the gut microbiome in infancy within an ecological context
Authors: Donovan Sharon M. 
Published: March 2020

Purpose of review
Humans and their commensal microbiota coexist in a complex ecosystem molded by evolutionary and ecological factors. Ecological opportunity is the prospective, lineage-specific characteristic of an environment that contains both niche availability leading to persistence coupled with niche discordance that drives selection within that lineage. The newborn gut ecosystem presents vast ecological opportunity. Herein, factors affecting perinatal infant microbiome composition are discussed.

Recent findings
Establishing a healthy microbiota in early life is required for immunological programming and prevention of both short-term and long-term health outcomes. The holobiont theory infers that host genetics contributes to microbiome composition. However, in most human studies, environmental factors are predominantly responsible for microbiome composition and function. Key perinatal elements are route of delivery, diet and the environment in which that infant resides. Vaginal delivery seeds an initial microbiome, and breastfeeding refines the community by providing additional microbes, human milk oligosaccharides and immunological proteins.

Summary
Early life represents an opportunity to implement clinical practices that promote the optimal seeding and feeding of the gut microbial ecosystem. These include reducing nonemergent cesarean deliveries, avoiding the use of antibiotics, and promoting exclusive breastfeeding.
Fusional Single Vision with Prism-induced Vergence Has More Influence than Diplopia on Postural Stability
Authors: Kim Sang-Yeob , Cho Hyun Gug , Moon Byeong-Yeon , Yu Dong-Sik 
Published: March 2020

SIGNIFICANCEPrism-induced convergence and vertical vergence for maintaining binocular fusion induced postural instability to a greater extent than diplopic conditions. This finding has important implication in relation to postural control of patients with large exophoria or vertical phoria in optometric clinic.PURPOSEThe purpose of this study was to examine whether binocular single vision with prism-induced horizontal and vertical vergence and diplopia might affect the static postural stability.METHODSForty-two subjects with a mean ± standard deviation age of 23.79 ± 2.81 years were enrolled in this study. To simulate convergence and divergence, base-in and base-out (BO) prisms of 4 and 8 Δ were added, respectively. To simulate vertical vergence, vertical prism of 2 Δ was added in a trial frame that corrected for the subject's refractive error during far distance (6 m) gaze. The prism power necessary to break fusion in each subject was detected and applied to induce diplopia in horizontal and vertical directions. Indices of general instability and sway power were measured under visual conditions using Tetrax and compared with normal viewing without the prism. Correlations between general instability indices and the ranges of break point in convergence and divergence were analyzed.RESULTSPostural instability was increased significantly when convergence induced by BO 4 and 8 Δ and vertical vergence induced by 2 Δ were stimulated. The correlation coefficient between ranges of BO break point and indices of general instability was −0.308 in the BO 4 Δ and −0.306 in the BO 8 Δ condition.CONCLUSIONSAlthough binocular input is recognized as an important factor in postural stability, binocular input with excessively stimulated convergence and vertical vergence during a far distance gaze is a latent factor affecting postural stability. On the other hand, diplopia did not influence postural stability.
Caregiver Characteristics Associated With Quality of Cardiac Compressions on an Adult Mannequin With Real-Time Visual Feedback
Authors: Kessler David O. , Lemke Daniel S. , Jani Priti , Dewan Maya L. , Moore-Clingenpeel Melissa , Chang Todd P. , Pirie Jonathan , Lovett Marlina E. , Harwayne-Gidansky Ilana , Wolfe Heather A. 
Published: March 2020

IntroductionChest compression (CC) quality directly impacts cardiac arrest outcomes. Provider body type can influence the quality of cardiopulmonary resuscitation (CPR); however, the magnitude of this impact while using visual feedback is not well described. The aim of the study was to determine the association between provider anthropometric variables on fatigue and CC adherence to 2015 American Heart Association CPR while receiving visual feedback.MethodsThis was a planned secondary analysis of healthcare professionals from multiple hospitals performing continuous CC for 2 minutes on an adult CPR mannequin with dynamic visual feedback. Main outcome measures include compression data (depth, rate, and lean) evaluated in 30-second epochs to explore performance fatigue. Multivariable models examined the relationship of provider anthropometrics to CC quality. Binomial mixed effects models were used to characterize fatigue by examining performance for 4 epochs.ResultsThree hundred seventy-seven 2-minute CC episodes were analyzed. Extreme (low and high) BMI and weight are associated with poorer CC. Larger size (height, weight, and BMI) is associated with better depth but worse lean compliance. Performance fatigued for all providers for 2 minutes, but shorter, lighter weight, female participants had the greatest decline. On multivariable analysis, rate compliance did not deteriorate regardless of provider anthropometrics.ConclusionsAnthropometrics impact provider CC quality. Despite visual feedback, variable effects are seen on compression depth, rate, recoil, and fatigue depending on the provider sex, weight, and BMI. The 2-minute interval for changing chest compressors should be reconsidered based on individual provider characteristics and risk of fatigue's impact on high-quality CPR.
Outcome reporting from protocols of clinical trials of Coronavirus Disease 2019 (COVID-19): a review
Authors: Qiu Ruijin , Wei Xuxu , Zhao Mengzhu , Zhong Changming , Zhao Chen , Hu Jiayuan , Li Min , Huang Ya , Han Songjie , He Tianmai , Chen Jing , Shang Hongcai 
Published: March 2020

ObjectivesTo examine heterogeneity of outcomes in protocols of clinical trials of Coronavirus Disease 2019 (COVID-19) and to identify outcomes for prioritization in developing a core outcome set (COS) in this field.DesignThis study is a review.Data sourcesDatabases of ICMJE-accepted clinical trial registry platform were searched on February 14, 2020.Eligibility CriteriaRandomized controlled trials (RCTs) and non-RCTs of COVID-19 were considered. Conditions of patients include common type, severe type or critical type. Interventions include traditional Chinese medicine (TCM) and Western medicine. We excluded trials that for discharged patients, psychological intervention and complications of COVID-19.Data extraction and synthesisThe general information and outcomes, outcome measurement instruments and measurement times were extracted. The results were analysed by descriptive analysis.Results19 registry platforms were searched. A total of 97 protocols were included from 160 protocols. For protocols of TCM clinical trials, 76 outcomes from 16 outcome domains were reported, and almost half (34/76, 44.74%) of outcomes were reported only once; the most frequently reported outcome was time of SARS-CoV-2 RNA turns to negative. 27 (27/76, 35.53%) outcomes were provided one or more outcome measurement instruments. 10 outcomes were provided one or more measurement time frame. For protocols of western medicine clinical trials, 126 outcomes from 17 outcome domains were reported; almost half (62/126, 49.21%) of outcomes were reported only once; the most frequently reported outcome was proportion of patients with negative SARS-CoV-2. 27 outcomes were provided one or more outcome measurement instruments. 40 (40/126, 31.75%) outcomes were provided one or more measurement time frame.ConclusionOutcome reporting in protocols of clinical trials of COVID-19 is inconsistent. Thus, developing a core outcome set is necessary.Strengths and limitations of this study1.This review is the first to describe variation in outcomes, outcome measurement instruments and outcome measurement time reporting in clinical trials for Coronavirus Disease 2019 (COVID-19).2.All the database of ICMJE-accepted clinical trial registry platform were searched, and randomized controlled trials and observational studies were considered.4.The aim of this review was to provide a list of outcomes for clinical trials of COVID-19, both interventions of Traditional Chinese Medicine and western medicine were considered.5.When the searching was conducted, no clinical trials were registered by countries out of China, so all of included protocols were from China.
pyrpipe: a python package for RNA-Seq workflows
Authors: Singh Urminder , Li Jing , Seetharam Arun , Wurtele Eve Syrkin 
Published: March 2020

ABSTRACTThe availability of terabytes of RNA-Seq data and continuous emergence of new analysis tools, enable unprecedented biological insight. However, implementing RNA-Seq analysis pipelines in a reproducible, flexible manner is challenging as data gets bigger and more complex. Thus, there is a pressing requirement for frameworks that allows for fast, efficient, easy-to-manage, and reproducibile analysis. Simple scripting has many challenges and drawbacks. We have developed a python package, python RNA-Seq Pipeliner (pyrpipe) that enables straightforward development of flexible, reproducible and easy-to-debug computational pipelines purely in python, in an object-oriented manner.pyrpipeprovides access to popular RNA-Seq tools, within python, via easy-to-use high level APIs. Pipelines can be customized by integrating new python code, third-party programs, or python libraries. Users can create checkpoints in the pipeline or integratepyrpipeinto a workflow management system, thus allowing execution on multiple computing environments.pyrpipeproduces detailed analysis, and benchmark reports which can be shared or included in publications.pyrpipeis implemented in python and is compatible with python versions 3.6 and higher. To illustrate the rich functionality ofpyrpipe, we provide case studies using RNA-Seq data from GTEx, SARS-CoV-2-infected human cells, and Zea mays. All source code is freely available athttps://github.com/urmi-21/pyrpipe; the package can be installed from the source or from PyPI (https://pypi.org/project/pyrpipe). Documentation is available at (http://pyrpipe.rtfd.io).
Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism
Authors: Othman Houcemeddine , Bouslama Zied , Brandenburg Jean-Tristan , Rocha Jorge da , Hamdi Yosr , Ghedira Kais , Srairi-Abid Najet , Hazelhurst Scott 
Published: March 2020

AbstractThe spread of COVID-19 caused by the SARS-CoV-2 outbreak has been growing since its first identification in December 2019. The publishing of the first SARS-CoV-2 genome made a valuable source of data to study the details about its phylogeny, evolution, and interaction with the host. Protein-protein binding assays have confirmed that Angiotensin-converting enzyme 2 (ACE2) is more likely to be the cell receptor through which the virus invades the host cell. In the present work, we provide an insight into the interaction of the viral spike Receptor Binding Domain (RBD) from different coronavirus isolates with host ACE2 protein. By calculating the binding energy score between RBD and ACE2, we highlighted the putative jump in the affinity from a progenitor form of SARS-CoV-2 to the current virus responsible for COVID-19 outbreak. Our result was consistent with previously reported phylogenetic analysis and corroborates the opinion that the interface segment of the spike protein RBD might be acquired by SARS-CoV-2 via a complex evolutionary process rather than a progressive accumulation of mutations. We also highlighted the relevance of Q493 and P499 amino acid residues of SARS-CoV-2 RBD for binding to human ACE2 and maintaining the stability of the interface. Moreover, we show from the structural analysis that it is unlikely for the interface residues to be the result of genetic engineering. Finally, we studied the impact of eight different variants located at the interaction surface of ACE2, on the complex formation with SARS-CoV-2 RBD. We found that none of them is likely to disrupt the interaction with the viral RBD of SARS-CoV-2.
Cryo-electron microscopy structure of the SADS-CoV spike glycoprotein provides insights into an evolution of unique coronavirus spike proteins
Authors: Guan Hongxin , Wang Youwang , Saeed Abdullah F.U.H. , Li Jinyu , Jan Syed Sajid , Perčulija Vanja , Li Yu , Zhu Ping , Ouyang Songying 
Published: March 2020

AbstractThe current outbreak of Coronavirus Disease 2019 (COVID-19) by a novel betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has aroused great public health concern. Coronavirus has a history of causing epidemics in human and animals. In 2017 an outbreak in piglets by a novel coronavirus was emerged designated as swine acute diarrhea syndrome coronavirus (SADS-CoV) which is originated from the same genus of horseshoe bats (Rhinolophus) as Severe Acute Respiratory Syndrome CoV (SARS-CoV) having a broad species tropism. In addition to human cells, it can also infect cell lines from diverse species. Coronavirus host range is determined by its spike glycoprotein (S). Given the importance of S protein in viral entry to cells and host immune responses, here we report the cryo-EM structure of the SADS-CoV S in the prefusion conformation at a resolution of 3.55 Å. Our study reveals that SADS-CoV S structure takes an intra-subunit quaternary packing mode where the NTD and CTD from the same subunit pack together by facing each other. The comparison of NTD and CTD with that of the other four genera suggests the evolutionary process of the SADS-CoV S. Moreover, SADS-CoV S has several characteristic structural features, such as more compact architecture of S trimer, and masking of epitopes by glycan shielding, which may facilitate viral immune evasion. These data provide new insights into the evolutionary relationships of SADS-CoV S and would extend our understanding of structural and functional diversity, which will facilitate to vaccine development.
Genome-wide data inferring the evolution and population demography of the novel pneumonia coronavirus (SARS-CoV-2)
Authors: Fang Bin , Liu Linlin , Yu Xiao , Li Xiang , Ye Guojun , Xu Juan , Zhang Ling , Zhan Faxian , Liu Guiming , Pan Tao , Shu Yilin , Jiang Yongzhong 
Published: March 2020

AbstractAs the highly risk and infectious diseases, the outbreak of coronavirus disease 2019 (COVID-19) poses unprecedent challenges to global health. Up to March 3, 2020, SARS-CoV-2 has infected more than 89,000 people in China and other 66 countries across six continents. In this study, we used 10 new sequenced genomes of SARS-CoV-2 and combined 136 genomes from GISAID database to investigate the genetic variation and population demography through different analysis approaches (e.g. Network, EBSP, Mismatch, and neutrality tests). The results showed that 80 haplotypes had 183 substitution sites, including 27 parsimony-informative and 156 singletons. Sliding window analyses of genetic diversity suggested a certain mutations abundance in the genomes of SARS-CoV-2, which may be explaining the existing widespread. Phylogenetic analysis showed that, compared with the coronavirus carried by pangolins (Pangolin-CoV), the virus carried by bats (bat-RaTG13-CoV) has a closer relationship with SARS-CoV-2. The network results showed that SARS-CoV-2 had diverse haplotypes around the world by February 11. Additionally, 16 genomes, collected from Huanan seafood market assigned to 10 haplotypes, indicated a circulating infection within the market in a short term. The EBSP results showed that the first estimated expansion date of SARS-CoV-2 began from 7 December 2019.
Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis Mechanisms of SARS-Related Coronaviruses
Authors: Tan Yongjun , Schneider Theresa , Leong Matthew , Aravind L , Zhang Dapeng 
Published: March 2020

ABSTRACTA novel coronavirus (SARS-CoV-2) is the causative agent of an emergent severe respiratory disease (COVID-19) in humans that is threatening to result in a global health crisis. By using genomic, sequence, structural and evolutionary analysis, we show that Alpha- and Beta-CoVs possess several novel families of immunoglobulin (Ig) domain proteins, including ORF8 and ORF7a from SARS-related coronaviruses and two protein groups from certain Alpha-CoVs. Among them, ORF8 is distinguished in being rapidly evolving, possessing a unique insert and a hypervariable position among SARS-CoV-2 genomes in its predicted ligand-binding groove. We also uncover many Ig proteins from several metazoan viruses which are distinct in sequence and structure but share an architecture comparable to that of CoV Ig domain proteins. Hence, we propose that deployment of Ig domain proteins is a widely-used strategy by viruses, and SARS-CoV-2 ORF8 is a potential pathogenicity factor which evolves rapidly to counter the immune response and facilitate the transmission between hosts.