bluuebunny/crossref_metadata_2025_split huggingface dataset:
Difference in gait recovery rate of hemiparetic stroke patients according to paralyzed side
Authors: Kim Cheol-Hyun , Chu Hongmin , Kang Geon-Hui , Sung Kang-Keyng , Kang Dae Gill , Lee Ho Sub , Lee Sangkwan 
Published: November 2019

Abstract
In Donguibogam, a representative encyclopedic source of knowledge on traditional Korean medicine, left-sided hemiparesis due to stroke is called “Tan” as a sort of “Heyol-Byeong,” while right-sided hemiparesis due to stroke is called “Tan” as a sort of “Gi-Byeong.” According to the theory of Donguibogam, diseases on the left or right side of the human body must be treated differently. Clinically, the symptoms caused by left and right hemisphere lesions in stroke patients differ, as the functions of the left and right hemispheres differ. Considering these facts, when treating patients in clinical practice, it may be useful to distinguish between diseases on the left or right side according to Donguibogam. This study set out to confirm whether side-dependent gait rehabilitation could be used to treat hemiparetic stroke patients. Gait was selected for analysis, as it is the most important factor in returning stroke patients to daily life.
This study conducted a retrospective chart review of stroke patients who satisfied the following criteria: outpatient or inpatient at the Wonkwang University Korean Medicine Hospital in Gwangju (WKUGH) with hemiparesis due to stroke; aged between 19 and 85 years old; with a stroke onset within the past 6 months; having undergone gait analysis (GAITRite) more than twice between September 1, 2017 and June 30, 2018 at the WKUGH, with a minimum 2-week interval between the first and next gait analysis; right-handed stroke patient; able to walk unaided. The spatio-temporal parameters for analysis included the FAP, walking velocity, step length, stance time, and swing time as obtained with GAITRite.
In the initial gait analysis, there was no significant difference between the 2 groups in all spatio-temporal parameters. However, in the follow-up gait analysis, the left hemiparesis group showed a significantly higher FAP and faster walking velocity than the right hemiparesis group.
This study found a difference in the recovery rate between the left and right hemiparesis groups. Based on this, we suggest that a different treatment strategy for gait rehabilitation can be used according to the paralyzed side.
This study was approved by the Institutional Review Board (IRB) of the Wonkwang University Korean Medicine Hospital in Gwangju (WKUGH), Republic of Korea (WKIRB 2018 – 25, November 28, 2018). This trial was registered with the Clinical Research Information Service (CRIS) of the Korea National Institute of Health (NIH), Republic of Korea (KCT0002984).
Neutrophil to lymphocyte ratio (NLR) as a prognostic marker for in-hospital mortality of patients with sepsis
Authors: Ni Jie , Wang Hongye , Li Yue , Shu Yimei , Liu Yihai 
Published: November 2019

Abstract
Neutrophil-to-lymphocyte ratio (NLR) has been reported to serve as a prognostic marker in inflammatory diseases. The purpose of this study was to evaluate the association of NLR at admission with in-hospital mortality in patients with sepsis presenting to emergency department.
This was a secondary analysis based on a single-center, retrospective, cohort study. Patients with sepsis admitted to an academic emergency department between January 2010 and January 2015 were enrolled. NLR of patients was analyzed from the hospital's electronic health record (EHR) system. A total of 174 adult patients, of which 80 (46.0%) died in hospital. The primary outcome was in-hospital mortality. Secondary outcome was 28-day mortality.
Contrary to previous studies, a larger NLR was found to have less odds of in-hospital mortality, as well as the presence of bacteremia. Patients who has severe/shock or had a history of chronic heart failure (CHF) had larger odds of death during hospital. Multivariate logistic regression analysis indicated that low NLR was an independent predictor of in-hospital mortality (OR = –0.98; 95% CI –0.96 to –0.99; P = .022). However, no correlation was found between the NLR and 28-day hospital mortality in patients with sepsis (P = .988). As a predictor of in-hospital survival, the area under curve (AUC) of the NLR was 0.622 (95%CI 0.54–0.71; P = .006) and the cut-off value was 9.11 with 0.551 sensitivity and 0.707 specificity.
NLR at admission was an independent predictor of in-hospital mortality of sepsis patients.
Identification of breast cancer-related circRNAs by analysis of microarray and RNA-sequencing data
Authors: Zhao Chun-Hua , Qu Le , Zhang Hui , Qu Rui 
Published: November 2019

Abstract

Background:
An increasing number of studies indicate that circular RNAs (circRNAs) participate in tumorigenesis. The aim of this study was to elucidate the regulatory mechanisms of circRNAs in breast cancer based on the construction of the circRNA-related ceRNA network.

Methods:
The expression profiles of circRNAs, miRNAs, and mRNAs were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. A ceRNA network was constructed by Cytoscape. The interactions among proteins were analyzed using the STRING database, and hub genes were extracted using the cytoHubba application. The functions of the differentially expressed mRNAs (DEmRNAs) were analyzed by the Kyoto Encyclopedia of Gene and Genomes (KEGG) and the Gene Ontology (GO) database.

Results:
In total, 7 differentially expressed circRNAs (DEcircRNAs), 27 differentially expressed miRNAs (DEmiRNAs), and 102 DEmRNAs were selected for the construction of the ceRNA network of breast cancer. We established a protein–protein interaction network and identified 6 hub genes. Then, a circRNA-miRNA-hub gene regulatory module was established based on 2 DEcircRNAs, 2 DEmiRNAs, and 2 DEmRNAs. GO and KEGG pathway analyses indicated the possible association of DEmRNAs with breast cancer onset and progression.

Conclusions:
The circRNA hsa_circ_0000519 is likely critical in the pathogenesis of breast cancer and may serve as a future therapeutic biomarker.
Moral Distress of Clinicians in Canadian Pediatric and Neonatal ICUs*
Authors: Dryden-Palmer Karen , Moore Gregory , McNeil Clare , Larson Charles Philip , Tomlinson George , Roumeliotis Nadia , Janvier Annie , Parshuram Christopher S. ,   on behalf of the Program of Wellbeing, Ethical practice and Resilience (POWER) Investigators
Published: November 2019

Objective:
To quantify moral distress in neonatal ICU and PICU clinicians and to identify associated factors.

Design:
A national cross-sectional survey of clinicians working in an neonatal ICU or PICU. Moral distress was assessed with the Moral Distress Scale-Revised and by self-rating. Depersonalization was assessed on the subscale of the Maslach Burnout Inventory. Respondents reported their attendance at each of six hospital supports that may serve to mitigate moral distress in frontline staff. Analyses compared outcomes across respondent characteristics and hierarchical linear regression evaluated individual, ICU, hospital, and regional effects.

Setting:
Eligible ICUs were PICUs and level-3 neonatal ICUs in Canada.

Subjects:
Eligible participants had worked in the participating ICU for more than 3 months.

Interventions:
None.

Measurements and Main Results:
We identified 54 eligible ICUs from 31 hospitals. Forty-nine Canadian neonatal ICUs and PICUs (91%) contributed 2,852 complete responses for a 45.2% response rate. Most respondents were nurses (64.9%) or from a neonatal ICU (66.5%). The median and interquartile range Moral Distress Scale-Revised were 79 (52–113); 997 respondents (34.2%) had Moral Distress Scale-Revised scores greater than or equal to 100, and 234 respondents (8.3%) strongly agreed that work caused them significant moral distress. Nurses had a median (interquartile range) Moral Distress Scale-Revised score of 85 (57–121), 19 points higher than physicians and 8 points higher than respiratory therapists (p < 0.0001). Moral Distress Scale-Revised scores increased from 53 (35–79) for those working in ICU less than 1 year to 83 (54–120) in those working in ICU more than 30 years (p < 0.0001); 22.5% reported high degrees of depersonalization, which was associated with moral distress (p < 0.0001). Variability in Moral Distress Scale-Revised scores was explained by individual-level (92%), hospital-level (5%), and ICU-level effects (1%). Frequency of participation in potentially mitigating hospital supports had small effects (< 10 points) on mean Moral Distress Scale-Revised scores.

Conclusions:
Moral distress is common in clinicians working in ICUs for children. Addressing moral distress will require interventions tailored to individuals in higher-risk groups.
The Comparison of Pierre Robin Sequence and Non-Syndromic Cleft Palate
Authors: Kocaaslan Fatma Nihal Durmus , Sendur Samet , Koçak Ismail , Çelebiler Özhan 
Published: November 2019

Introduction:
The aim of this study was to evaluate pre-operative nutritional status, associated syndromes and abnormalities, and post-operative outcomes of patients with Pierre Robin Sequence (PRS) versus those with non-syndromic isolated cleft palate (CIP).

Methods:
Between January 1995 and December 2013, patients with a cleft palate Veau I-II according to the Veau classification with and without PRS who underwent primary repair were retrospectively analyzed. The nutrition status, age at the time of palatoplasty, additional anomalies, gestational complications, and post-operative speech abnormalities and outcomes were evaluated.

Results:
A total of 59 patients with PRS (PRS group) and 132 patients without PRS (non-PRS group) were included in the study. Of all patients, 92 were males and 99 were females with a mean age of 14 ± 4.18 (range, 6 to 26) years. The rate of gestational complications, enteral nutrition, complete cleft, additional anomalies, and velopharyngeal insufficiency was significantly higher in the PRS group (P < 0.05). However, the incidence of fistulas and age at the time of palatoplasty did not significantly differ between the groups.

Conclusion:
Based on our study results, enteral nutrition, respiratory problems, pregnancy complications, velopharyngeal insufficiency, and additional anomalies, but not post-operative palatal fistulas, are more frequently seen in patients with PRS. Although pre-operative care and treatment and rehabilitation in patients with PRS are more complicated than those with the CIP, our experience demonstrates that meticulous repair and follow-up can minimize complications, such as fistulas.
Automated Lesion Segmentation and Quantitative Analysis of Nevus in Whole-Face Images
Authors: Chen Wei , Chai Yuanhao , Chai Gang , Hu Yong , Chen Mingang , Xu Haisong , Zhang Yan 
Published: November 2019

Background:
Nevus is very common; however, melanoma is slightly related to the deterioration of nevus because of its vulnerability to solarization, friction, aging, heredity, and other factors. Early diagnosis is essential for melanoma treatment, since patients have a high survival rate with early detection and treatment. Computer-aided diagnosis has been applied in the differential diagnosis of melanoma and benign nevi and achieved high accuracy, but it does not suit the screening of nevi because most studies are based on dermoscopy with a narrow field of vision and performed by professional doctors. Therefore, this study aimed to present the accuracy and effectiveness of our algorithm.

Methods:
Based on whole-face images of patients, the authors used logistic regression and the Newton method to detect the nevus region. Then, Python and OpenCV were employed to detect the lesion edge and compute the area of the regions. A multicenter clinical trial with a sample size of 600 was then conducted to evaluate the effectiveness of the algorithm.

Results:
The algorithm detected 2672 nevi from 600 patients, in which there were 195 patients of missed diagnosis and 310 patients of misdiagnosis. The Kappa value between 2 groups was 0.860 (>0.8). Paired t-test showed no significant difference between 2 groups’ area results (P = 0.265, P > 0.05).

Conclusion:
Within the limitations of this study, the authors demonstrated a high agreement between algorithm's detection and doctor's diagnosis. Our new algorithm has great effectiveness in nevus detection, edge segmentation, and area measurement.
Mindfulness-based programs and practices for people with intellectual and developmental disability
Authors: Singh Nirbhay N. , Hwang Yoon-Suk 
Published: November 2019

Purpose of reviewPeople with intellectual and developmental disability (IDD) commonly exhibit behaviors that present challenges to their parents, caregivers, and teachers. Mindfulness-based practices and programs have emerged as a viable alternative to current interventions for such behaviors and the stress faced by their caregivers. This review addresses publications between 2018 and 2019 that examined the effectiveness of mindfulness-based practices and programs for people living with IDD.Recent findingsIndividuals with IDD can learn mindfulness practices to self-manage their aggressive and destructive behaviors. Individual practices and group-based programs continue to show that mindfulness approaches are effective for this population. Randomized controlled trials indicate that comprehensive mindfulness-based programs (e.g., mindfulness-based stress reduction, MYmind, and mindfulness-based positive behavior support) are effective for enhancing the quality of life of people living with IDD.SummaryResearch supports the use of informal mindfulness practices for challenging behaviors of people with IDD. Formal mindfulness-based programs continue to be evaluated for their effectiveness across different populations, cultures, levels of IDD, components of the program, and length of training. The research literature on mindfulness is still in the early stages of development and much work remains.
Revealing acquired resistance mechanisms of kinase-targeted drugs using an on-the-fly, function-site interaction fingerprint approach
Authors: Zhao Zheng , Bourne Philip E. 
Published: November 2019

AbstractAlthough kinase-targeted drugs have achieved significant clinical success, they are frequently subject to the limitations of drug resistance, which has become a primary vulnerability to targeted drug therapy. Therefore, deciphering resistance mechanisms is an important step in designing more efficacious, anti-resistant, drugs. Here we studied two FDA-approved kinase drugs: Crizotinib and Ceritinib, which are first- and second-generation anaplastic lymphoma kinase (ALK) targeted inhibitors, to unravel drug-resistance mechanisms. We used an on-the-fly, function-site interaction fingerprint (on-the-fly Fs-IFP) approach by combining binding free energy surface calculations with the Fs-IFPs. Establishing the potentials of mean force and monitoring the atomic-scale protein-ligand interactions, before and after the L1196M-induced drug resistance, revealed insights into drug-resistance/anti-resistant mechanisms. Crizotinib prefers to bind the wild type ALK kinase domain, whereas Ceritinib binds more favorably to the mutated ALK kinase domain, in agreement with experimental results. We determined that ALK kinase-drug interactions in the region of the front pocket are associated with drug resistance. Additionally, we find that the L1196M mutation does not simply alter the binding modes of inhibitors, but also affects the flexibility of the entire ALK kinase domain. Our work provides an understanding of the mechanisms of ALK drug resistance, confirms the usefulness of the on-the-fly Fs-IFP approach and provides a practical paradigm to study drug-resistance mechanisms in prospective drug discovery.
Chimpanzee fibroblasts exhibit greater adherence and migratory phenotypes than human fibroblasts
Authors: Zintel Trisha M. , Ducey Delaney , Babbitt Courtney C. 
Published: November 2019

ABSTRACTBackground and objectivesPrevious work has identified that gene expression differences in cell adhesion pathways exist between humans and chimpanzees. Here, we used a comparative cell biology approach to assay interspecies differences in cell adhesion phenotypes in order to better understand the basic biological differences between species’ epithelial cells that may underly the organism-level differences we see in wound healing and cancer.MethodologyWe used skin fibroblast cell lines from humans and chimpanzees to assay cell adhesion and migration. We then utilized published RNA-Seq data from the same cell lines exposed to a cancer / wound-healing mimic to determine what gene expression changes may be corresponding to altered cellular adhesion dynamics between species.ResultsThe functional adhesion and migration assays revealed that chimpanzee fibroblasts adhered sooner and remained adherent for significantly longer and move into a “wound” at faster rate than human fibroblasts. The gene expression data suggest that the enhanced adhesive properties of chimpanzee fibroblasts may be due to chimpanzee fibroblasts exhibiting significantly higher expression of cell and focal adhesion molecule genes than human cells, both during a wound healing assay and at rest.Conclusions and implicationsChimpanzee fibroblasts exhibit stronger adhesion and greater cell migration than human fibroblasts. This may be due to divergent gene expression of focal adhesion and cell adhesion molecules, such as integrins, laminins, and cadherins, as well as ECM proteins like collagens. This is one of few studies demonstrating that these divergences in gene expression between closely related species can manifest in fundamental differences in cell biology. Our results provide better insight into species-specific cell biology phenotypes and how they may influence more complex traits, such as cancer metastasis and wound healing.
GPCRmd uncovers the dynamics of the 3D-GPCRome
Authors: Rodríguez-Espigares Ismael , Torrens-Fontanals Mariona , Tiemann Johanna K.S. , Aranda-García David , Ramírez-Anguita Juan Manuel , Stepniewski Tomasz Maciej , Worp Nathalie , Varela-Rial Alejandro , Morales-Pastor Adrián , Lacruz Brian Medel , Pándy-Szekeres Gáspár , Mayol Eduardo , Giorgino Toni , Carlsson Jens , Deupi Xavier , Filipek Slawomir , Filizola Marta , Gómez-Tamayo José Carlos , Gonzalez Angel , Gutierrez-de-Teran Hugo , Jimenez Mireia , Jespers Willem , Kapla Jon , Khelashvili George , Kolb Peter , Latek Dorota , Marti-Solano Maria , Matricon Pierre , Matsoukas Minos-Timotheos , Miszta Przemyslaw , Olivella Mireia , Perez-Benito Laura , Provasi Davide , Ríos Santiago , Rodríguez-Torrecillas Iván , Sallander Jessica , Sztyler Agnieszka , Vaidehi Nagarajan , Vasile Silvana , Weinstein Harel , Zachariae Ulrich , Hildebrand Peter W. , Fabritiis Gianni De , Sanz Ferran , Gloriam David E. , Cordomi Arnau , Guixà-González Ramon , Selent Jana 
Published: November 2019

AbstractG protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new 3D molecular structures of GPCRs (3D-GPCRome) during the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. While experimentally-resolved structures undoubtedly provide valuable snapshots of specific GPCR conformational states, they give only limited information on their flexibility and dynamics associated with function. Molecular dynamics (MD) simulations have become a widely established technique to explore the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations requires efficient storage resources and specialized software, hence limiting the dissemination of these data to specialists in the field. Here we present the GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyse and share GPCR MD data. GPCRmd originates from a community-driven effort to create the first open, interactive, and standardized database of GPCR MD simulations. We demonstrate the power of this resource by performing comparative analyses of multiple GPCR simulations on two mechanisms critical to receptor function: internal water networks and sodium ion interaction.
When polymorphism and monomorphism meet: discordant genomic and phenotypic clines across a lizard contact zone
Authors: Dong Caroline M. , McLean Claire A. , Elliott Adam , Moussalli Adnan , Stuart-Fox Devi 
Published: November 2019

AbstractColour polymorphism can promote rapid evolution and speciation, particularly when populations differ in the number or composition of morphs. The contact zone betweenCtenophorus modestus(swift dragon) andC. decresii(tawny dragon) is a compelling study system in which to examine evolutionary processes and outcomes when polymorphic and monomorphic populations meet.Ctenophorus modestusis polymorphic for male throat coloration and lacks ultraviolet (UV) reflectance whileC. decresiiis monomorphic with UV-blue throats. We characterised genomic and phenotypic clines across the contact zone based on single nucleotide polymorphisms, the mitochondrial ND4 gene, and male colour traits, and concurrently assessed the phenotype of captive-bred F1 hybrids. Our results indicate that genomic introgression is asymmetric, with high frequencies of backcrossing toC. modestusbut notC. decresii, accompanied by the prevalence of theC. modestusmtDNA haplotype in hybrids. The clines for throat phenotype are abrupt and displaced towards the range ofC. decresii, relative to the genetic and dorsolateral phenotype clines. By contrast, both throat and dorsolateral phenotypes in captive-bred F1 hybrids are intermediate. Our results are consistent with the hypothesis that throat coloration, a polymorphic sexual signal inC. modestus, is the target of selection during incipient speciation and provide insight into the microevolutionary processes that may link polymorphism and speciation.
CRISPR screening of porcine sgRNA library identified host factors essential for Japanese encephalitis virus replication
Authors: Zhao Changzhi , Liu Hailong , Xiao Tianhe , Wang Zichang , Nie Xiongwei , Li Xinyun , Qian Ping , Qin Liuxing , Han Xiaosong , Zhang Jinfu , Ruan Jinxue , Zhu Mengjin , Miao Yiliang , Zuo Bo , Yang Kui , Xie Shengsong , Zhao Shuhong 
Published: November 2019

ABSTRACTJapanese encephalitis virus (JEV) is a mosquito-borne zoonotic flavivirus that causes encephalitis and reproductive disorders in mammalian species. However, key host genes involved in the JEV life cycle and cell death are poorly understood. Here, we designed 85,674 single guide RNAs (sgRNAs) targeting 17,743 protein-coding genes, 11,053 long ncRNAs (lncRNAs), and 551 microRNAs (miRNAs) in the porcine genome, and subsequently developed a porcine sgRNA library and genome-scale CRISPR/Cas9 knockout (PigGeCKO) system. These sgRNAs were delivered into porcine kidney-15 (PK-15) cells that constitutively express Cas9, positive selection screening of the resulting PigGeCKO cell collection for resistance to JEV-induced cell death led to the identification of several previously unreported genes required for JEV infection. We conducted follow-up studies to verify the dependency of JEV on these genes, and identified functional contributions for six of the many candidate JEV-related host genes, including an endoplasmic reticulum membrane protein complex subunit 3 (EMC3) and calreticulin (CALR). Additionally, we identified that four genes associated with heparan sulfate proteoglycans (HSPGs) metabolism, specifically those responsible for HSPG sulfurylation, facilitated JEV entry into PK-15 cells. Thus, beyond our development of the largest CRISPR-based functional genomic screening platform for pig research to date, this work deepens our basic understanding of flavivirus infection and identifies multiple potentially vulnerable targets for the development of medical and breeding technologies to prevent and treat diseases caused by Japanese encephalitis virus.