bluuebunny/crossref_metadata_2025_split huggingface dataset:
Driver gene alterations in lung adenocarcinoma: Demographic features of 2544 Chinese cases
Authors: Hu Mingming , Zhang Tongmei , Yang Yuan , Che Nanying , Li Jie , Liu Zichen , Li Baolan 
Published: October 2020

Background: To understand the association between driver gene variations and age and gender in patients with lung adenocarcinoma, we investigated mutations of the three most important driver genes—epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK) fusion genes and c-ros oncogene 1 (ROS1)—in this retrospective cohort study. Methods: Patients newly diagnosed with lung adenocarcinoma who received EGFR and ALK/ROS1 gene tests at our hospital from September 2014 to May 2019 were enrolled. EGFR mutations and ROS1 fusions were examined by ARMS-PCR and ALK fusions by Ventana-D5F3 IHC assay and ARMS-PCR. Results: Of 2544 eligible subjects, 2539 accomplished EGFR mutation tests. The prevalence of EGFR mutations was 62.1% in females, higher than that of 45.1% in males. In females, the EGFR mutation rate remained relatively stable at 60%–65% across the six age groups. Females showed an increased distribution of EGFR L858R and a decreased distribution of exon 19 deletion (19Del) by age. The incidence of ALK/ROS-1 rearrangements decreased significantly with age. Conclusions: EGFR 19Del mutation is more prevalent in younger males and females, while L858R mutation is prevalent in older females. Both ALK and ROS1 rearrangements are more common in younger lung adenocarcinoma. The young lung adenocarcinoma population is a distinct group rich in targetable genomic alterations, and more research is needed to understand the mechanism.
Continuous Glucose Monitoring in Critically Ill Patients With COVID-19: Results of an Emergent Pilot Study
Authors: Sadhu Archana R. , Serrano Ivan Alexander , Xu Jiaqiong , Nisar Tariq , Lucier Jessica , Pandya Anjani R. , Patham Bhargavi 
Published: October 2020

Background: Amidst the coronavirus disease 2019 (COVID-19) pandemic, continuous glucose monitoring (CGM) has emerged as an alternative for inpatient point-of-care blood glucose (POC-BG) monitoring. We performed a feasibility pilot study using CGM in critically ill patients with COVID-19 in the intensive care unit (ICU). Methods: Single-center, retrospective study of glucose monitoring in critically ill patients with COVID-19 on insulin therapy using Medtronic Guardian Connect and Dexcom G6 CGM systems. Primary outcomes were feasibility and accuracy for trending POC-BG. Secondary outcomes included reliability and nurse acceptance. Sensor glucose (SG) was used for trends between POC-BG with nursing guidance to reduce POC-BG frequency from one to two hours to four hours when the SG was in the target range. Mean absolute relative difference (MARD), Clarke error grids analysis (EGA), and Bland-Altman (B&A) plots were calculated for accuracy of paired SG and POC-BG measurements. Results: CGM devices were placed on 11 patients: Medtronic ( n = 6) and Dexcom G6 ( n = 5). Both systems were feasible and reliable with good nurse acceptance. To determine accuracy, 437 paired SG and POC-BG readings were analyzed. For Medtronic, the MARD was 13.1% with 100% of readings in zones A and B on Clarke EGA. For Dexcom, MARD was 11.1% with 98% of readings in zones A and B. B&A plots had a mean bias of −17.76 mg/dL (Medtronic) and −1.94 mg/dL (Dexcom), with wide 95% limits of agreement. Conclusions: During the COVID-19 pandemic, CGM is feasible in critically ill patients and has acceptable accuracy to identify trends and guide intermittent blood glucose monitoring with insulin therapy.
The feasibility of assessing cognitive and motor function in multiple sclerosis patients using robotics
Authors: Simmatis Leif ER , Jin Albert Y , Taylor Sean W , Bisson Etienne J , Scott Stephen H , Baharnoori Moogeh 
Published: October 2020

Background Multiple sclerosis (MS) causes pervasive motor, sensory and cognitive dysfunction. The Expanded Disability Status Scale (EDSS) is the gold standard for assessing MS disability. The EDSS is biased towards mobility and may not accurately measure MS-related disabilities in the upper limb or in cognitive functions (e.g. executive function). Objective Our objectives were to determine the feasibility of using the Kinarm robotic system to quantify neurological deficits related to arm function and cognition in MS patients, and examine relationships between traditional clinical assessments and Kinarm variables. Methods Individuals with MS performed 8 robotic tasks assessing motor, cognitive, and sensory ability. We additionally collected traditional clinical assessments and compared these to the results of the robotic assessment. Results Forty-three people with MS were assessed. Most participants could complete the robotic assessment. Twenty-six (60%) were impaired on at least one cognitive task and twenty-six (60%) were impaired on at least one upper-limb motor task. Cognitive domain task performance correlated most strongly with the EDSS. Conclusions Kinarm robotic assessment of people with MS is feasible, can identify a broad range of upper-limb motor and sensory, as well as cognitive, impairments, and complements current clinical rating scales in the assessment of MS-related disability.
A Nomogram for Predicting 30-day Mortality in Elderly Patients Undergoing Hemiarthroplasty for Femoral Neck Fractures
Authors: Crawford Zachary Thomas , Southam Brendan , Matar Robert , Avilucea Frank R. , Bowers Katherine , Altaye Mekibib , Archdeacon Michael T. 
Published: October 2020

Introduction: Femoral neck fractures in the elderly are increasingly common as a result of a growing geriatric population with 1-year mortality rates approaching 35%. While preoperative medical optimization and early time to surgery have reduced morbidity and mortality, patients with numerous medical comorbidities remain high risk for death in the perioperative period. Identifying those with greatest risk with a scoring system or nomogram may assist multidisciplinary teams in reducing mortality following hemiarthroplasty. Purpose: Identify predictors of 30-day mortality in elderly patients who underwent hemiarthroplasty for a femoral neck fracture to generate a predictive nomogram to determine the probability of post-operative mortality. Methods: Retrospective evaluation using data from the ACS-NSQIP database from 2005 to 2014 with CPT code 27125 for hip hemiarthroplasty. Multiple factors including demographics and comorbidities were compared in patients who experienced 30-day mortality and those who did not. T-test and chi-square tests were used to analyze data and a multivariate model was generated using logistic regression. Results: Advanced age (odds ratio (OR) 1.04), underweight BMI (OR 1.55), male sex (OR 1.80), reduced functional status (OR 2.04), heart failure within 30 days prior to surgery (OR 2.22), American Society of Anesthesiologists grade > 2 (OR > 2.50), disseminated cancer (OR 3.43) were all found to have statistically significant odds ratios for 30-day mortality following hemiarthroplasty. Conclusion: A tool based on easily identifiable risk factors, demographics, and comorbidities was developed that can help predict elderly patients who will experience mortality within 30 days of following hemiarthroplasty. In addition to identifying high risk patients, the nomogram can serve as a counseling tool for physicians to use with patients and their families to assist with better understanding of perioperative mortality risk.
LDkit: a parallel computing toolkit for linkage disequilibrium analysis
Authors: Tang You , Li Zhuo , Wang Chao , Liu Yuxin , Yu Helong , Wang Aoxue , Zhou Yao 
Published: October 2020

Abstract
Background
Linkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, such as diseases. There are some tools for linkage disequilibrium analysis either in a local or online way; however, there has been no such tool supporting both graphical user interface (GUI) and parallel computing.

Results
We developed a GUI software called LDkit for LD analysis, which supports parallel computing. The LDkit supports both variant call format (VCF) and PLINK ‘ped + map’ format. At the same time, users could also just analyze a subset of individuals from the whole population. The LDkit reads the data by block and then paralleled the computation process by monitoring the usage of processes. Assessment on the Human 1000 genome data showed that when paralleled with 32 threads, the running time was reduced to less than 6 minutes from ~77 minutes using the chromosome 22 dataset with 1,103,547 SNPs and 2504 individuals.

Conclusions
The software LDkit can be effectively used to calculate and plot LD decay, LD block, and linkage disequilibrium analysis between a site and a given region. Most importantly, both graphical user interface (GUI) and stand-alone packages are available for users’ convenience. LDkit was written in JAVA language under cross-platform support.
The skill of tracheal intubation with rigid scopes – a randomised controlled trial comparing learning curves in 740 intubations
Authors: Theiler Lorenz , Greif Robert , Bütikofer Lukas , Arheart Kristopher , Kleine-Brueggeney Maren 
Published: October 2020

Abstract
Background
Rigid scopes are successfully used for management of difficult airways, but learning curves have not been established.

Methods
This randomised controlled trial was performed at the University Hospital Bern in Switzerland to establish learning curves for the rigid scopes Bonfils and SensaScope and to assess their performance. Fifteen consultant anaesthetists and 15 anaesthesia registrars performed a total of 740 intubations (10 to 20 intubations with each device per physician) in adult patients without predictors of a difficult airway under general anaesthesia. According to randomisation, physicians intubated the patient’s trachea with either the Bonfils or the SensaScope. A maximum of three intubation attempts was allowed. Primary outcome was overall time to successful intubation. Secondary outcome parameters included first attempt success, first attempt success within 60 s, failures and adverse events.

Results
A clear learning effect was demonstrated: Over 20 trials, intubations became 2.5-times quicker and first attempt intubation success probability increased by 21–28 percentage points. Fourteen and 20 trials were needed with the Bonfils and the SensaScope, respectively, to reach a 90% first attempt success probability. Intubation times were 23% longer (geometric mean ratio 1.23, 95% confidence interval 1.12–1.36, p < 0.001) and first attempt success was less likely (odds ratio 0.64, 95% confidence interval 0.45–0.92, p = 0.016) with the SensaScope. Consultants showed a tendency for a better first attempt success compared to registrars. Overall, 23 intubations (10 Bonfils, 13 SensaScope) failed. Adverse events were rare and did not differ between devices.

Conclusions
A clear learning effect was demonstrated for both rigid scopes. Fourteen intubations with the Bonfils and 20 intubations with the SensaScope were required to reach a 90% first attempt success probability. Learning of the technique seemed more complex with the SensaScope compared to the Bonfils.

Trial registration
Current Controlled Trials, ISRCTN14429285. Registered 28 September 2011, retrospectively registered.
Determinants of referral of women with urinary incontinence to specialist services: a national cohort study using primary care data from the UK
Authors: Gurol-Urganci Ipek , Geary Rebecca S. , Mamza Jil B. , Iwagami Masao , El-Hamamsy Dina , Duckett Jonathan , Wilson Andrew , Tincello Douglas , van der Meulen Jan 
Published: October 2020

Abstract
Background
Female urinary incontinence is underdiagnosed and undertreated in primary care. There is little evidence on factors that determine whether women with urinary incontinence are referred to specialist services. This study aimed to investigate characteristics associated with referrals from primary to specialist secondary care for urinary incontinence.

Methods
We carried out a cohort study, using primary care data from over 600 general practices contributing to the Clinical Practice Research Datalink (CPRD) in the United Kingdom. We used multi-level logistic regression to estimate adjusted odds ratios (aOR) that reflect the impact of patient and GP practice-level characteristics on referrals to specialist services in secondary care within 30 days of a urinary incontinence diagnosis. All women aged ≥18 years newly diagnosed with urinary incontinence between 1 April 2004 and 31 March 2013 were included. One-year referral was estimated with death as competing event.

Results
Of the 104,466 included women (median age: 58 years), 28,476 (27.3%) were referred within 30 days. Referral rates decreased with age (aOR 0.34, 95% CI 0.31–0.37, comparing women aged ≥80 with those aged 40–49 years) and was lower among women who were severely obese (aOR 0.84, 95% CI 0.78–0.90), smokers (aOR 0.94, 95% CI 0.90–0.98), women from a minority-ethnic backgrounds (aOR 0.76, 95% CI 0.65–0.89 comparing Asian with white women), women with pelvic organ prolapse (aOR 0.77, 95% CI 0.68–0.87), and women in Scotland (aOR 0.60, 95% CI 0.46–0.78, comparing women in Scotland and England). One-year referral rate was 34.0% and the pattern of associations with patient characteristics was almost the same as for 30-day referrals.

Conclusions
About one in four women with urinary incontinence were referred to specialist secondary care services within one month after a UI diagnosis and one in three within one year. Referral rates decreased with age which confirms concerns that older women with UI are less likely to receive care according to existing clinical guidelines. Referral rates were also lower in women from minority-ethnic backgrounds. These finding may reflect clinicians’ beliefs about the appropriateness of referral, differences in women’s preferences for treatment, or other factors leading to inequities in referral for urinary incontinence.
Determinants of participation in a post-hospitalization physical exercise program for older adults
Authors: Urquiza Miriam , Echeverria Iñaki , Besga Ariadna , Amasene María , Labayen Idoia , Rodriguez-Larrad Ana , Barroso Julia , Aldamiz Mikel , Irazusta Jon 
Published: October 2020

Abstract
Background
Older patients often experience a decline in physical function and cognitive status after hospitalization. Although interventions involving physical exercise are effective in improving functional performance, participation in physical exercise interventions among older individuals is low. We aimed to identify factors that contribute to exercise refusal among post-hospitalized older patients.

Methods
A cross-sectional study of recruitment data from a randomized controlled trial was conducted involving 495 hospitalized people ≥70 years old. Sociodemographic and clinical data were obtained from the Basque Public Health System database. We determined physical function with the Short Physical Performance Battery (SPPB), nutritional status with the Mini-Nutritional Assessment, frailty according to the Fried phenotype criteria, and cognitive function with the Short Portable Mental Status Questionnaire (SPMSQ). Student’s t, Mann-Whitney U, or chi-squared tests were applied for bivariate analysis. Parameters significantly associated with participation were introduced in a logistic multivariate regression model.

Results
Among the analyzed patients, 88.8% declined participation in the physical exercise program. Multivariate regression revealed that older age (OR: 1.13; 95% CI: 1.07–1.19), poor nutritional status (OR: 0.81; 95% CI: 0.69–0.95), and reduced home accessibility (OR: 0.27; 95% CI: 0.08–0.94) were predictors of participation refusal. Moreover, patients who declined participation had worse performance on the SPPB (P < 0.05) and its tests of balance, leg strength, and walking speed (P < 0.05). No differences were found between groups in other variables.

Conclusions
This study confirms low participation of older adults in a post-hospitalization physical exercise program. Non-participation was associated with increased age, poor nutritional status, and reduced home accessibility. Our findings support the need for intervention design that accounts for these factors to increase older patient participation in beneficial exercise programs.

Trial registration
Australian New Zealand Clinical Trials Registry, ACTRN12619000093189, (date: January 22, 2019, retrospectively registered).
Differential diagnosis of atypical encephalopathy in critical care: a case report
Authors: Li Chung , Peng Ming-Yieh , Chang Chia-Hui , Hsu Yuan-Yu , Hsieh Min-Shiau , Lin Shinn-Kuang , Lee Yi-Hsin , Yang Mei-Chen 
Published: October 2020

Abstract
Background
A lower level of consciousness is a common presentation in critical care, with many different causes and contributory factors, of which more than one may be present concurrently.

Case presentation
We described a woman with poorly controlled diabetes and steroid-dependent asthma who presented in a deep coma. She was found to have Streptococcus intermedius bacteremia and pyogenic ventriculitis that originated from right middle lobe pneumonia. Also, multiple small parenchymal lesions were observed on brain magnetic resonance imaging and increased protein concentration was noted in cerebral spinal fluid. Initially, her coma was thought to be due to diabetic ketoacidosis and septic encephalopathy. However, her lowered level of consciousness was disproportionate to either diabetic ketoacidosis or septic encephalopathy, and her clinical course was not as expected for these two conditions. Treatment with antibiotic, corticosteroid and antihelminthic drugs was administered resulting in improving consciousness. The Streptococcus intermedius pneumonia progressed to form a large cavity that needed an early surgical lobectomy and resulted in the unexpected diagnosis of chronic cavitary pulmonary aspergillosus.

Conclusions
In critical care, a lowered level of consciousness may have many etiologies, and critical care clinicians should be familiar with the signs and symptoms of all possible causes to enable prompt diagnosis and appropriate treatment.
Role of circulating free DNA in evaluating clinical tumor burden and predicting survival in Chinese metastatic colorectal cancer patients
Authors: Xu Xiaojing , Yu Yiyi , Shen Minna , Liu Mengling , Wu Shengchao , Liang Li , Huang Fei , Zhang Chenlu , Guo Wei , Liu Tianshu 
Published: October 2020

Abstract
Background
The aim of this study was to explore the utility of circulating free DNA (cfDNA) in the evaluation of clinical tumor burden and survival in Chinese patients with metastatic colorectal cancer (mCRC) and to preliminarily summarize some metastatic characteristics associated with mutational status.

Methods
A panel covering a total of 197 hotspot mutations of KRAS, NRAS, BRAF and PIK3CA was used to evaluate the mutational status in plasma by next-generation sequencing (NGS) technology in 126 patients with mCRC. An amplification-refractory mutation system (ARMS) was used to analyze genomic DNA from matched tissue samples. Clinical markers including carcinoembryonic antigen (CEA), carbohydrate antigen 199 (CA199), carbohydrate antigen 125 (CA125), neuron-specific enolase (NSE) and lactate dehydrogenase (LDH) in serum and the sum of all tumor diameters on CT or PET/CT were collected to indicate clinical tumor burden. The correlations between cfDNA and clinical tumor burden were analyzed using Pearson correlation and linear regression models. The median progression-free survival (PFS) and 1-year overall survival (OS) rates were calculated by Kaplan-Meier (K-M) survival analysis.

Results
Of the 126 enrolled patients, patients who were tested positive for mutations in plasma accounted for 45.2% (57/126). Mutations in KRAS, NRAS, BRAF and PIK3CA were detected in 37.3% (47/126), 1.6% (2/126), 3.2% (4/126) and 13.5% (17/126) of patients, respectively. The overall concordance rate of mutational status between plasma and matched tissues was 78.6% (99/126). Sixteen patients had mutations in plasma that were not detected in tissue, including some rare hotspot mutations. The cfDNA concentration was significantly correlated with the levels of clinical markers, especially CEA (P < 0.0001, Pearson r = 0.81), LDH (P < 0.0001, Pearson r = 0.84) and the sum of tumor diameters (P < 0.0001, Pearson r = 0.80). Patients with a high cfDNA concentration (> 17.91 ng/ml) had shorter median progression-free survival (6.6 versus 11.7 months, P < 0.0001) and lower 1-year overall survival rate (56% versus 94%, P < 0.0001) than those with a low cfDNA concentration (≤17.91 ng/ml). The most common metastatic site was the liver (77.8%), followed by the lymph nodes (62.7%), lung (40.5%), peritoneum (14.3%) and bone (10.3%), in all patients. There was no significant difference in metastasis between different mutational statuses.

Conclusion
Analyzing mutations in plasma could provide a more comprehensive overview of the mutational landscape than analyzing mutations in tissue. The cfDNA concentration could be a quantitative biomarker of tumor burden and could predict survival in Chinese patients with mCRC.
Factors associated with cyber-victimization among immigrants and non-immigrants in Canada: a cross-sectional nationally-representative study
Authors: Kenny Kathleen S. , Merry Lisa , Brownbridge Douglas A. , Urquia Marcelo L. 
Published: October 2020

AbstractObjectivesThere is a paucity of research on patterns of cyber-victimization in minority groups, including immigrants. This study aimed to identify individual, interpersonal and contextual characteristics associated with cyber-victimization among immigrants and non-immigrants.MethodsWe drew on nationally representative data from adolescents and adults in the Canadian General Social Survey on victimization (2014). We used multivariable logistic regression to identify potential factors associated with cyber-victimization in the last 12 months, stratified by immigrant status and sex.ResultsAmong 27,425 survey respondents, the weighted prevalence of cyber-victimization in the last 12 months was 2.1% among immigrants and 2.3% among non-immigrants. Cyber-victimization rates differed significantly by sex among immigrants (2.8% for males vs. 1.4% for females), but not among non-immigrants (2.1% for males vs. 2.4% for females). While most other factors associated with cyber-victimization were similar for immigrants and non-immigrants, there were pronounced associations of past child maltreatment (adjusted prevalence odds ratio [aPOR] 4.85, 95% confidence interval [CI] 2.76, 8.52) and residence in an unwelcoming neighbourhood (aPOR 5.08, 95% CI 2.44, 10.55) with cyber-victimization among immigrants that were diminished or absent among non-immigrants. Additionally, sex-stratified analyses among immigrants showed cyber-victimization to be strongly associated with having a mental health condition (aPOR 3.50, 95% CI 1.36, 8.97) among immigrant males only, and with perceived discrimination (aPOR 4.08, 95% CI 1.65, 10.08), as well as being under 24 years old (aPOR 3.24, 95% CI 1.09, 9.60) among immigrant females.ConclusionsImmigration status and sex were differentially associated with cyber-victimization. Findings support the salience of a social-ecological perspective and gender-stratified analyses to better elucidate complex pathways linking cyber-victimization to potential gender-based health inequities among immigrants.