bluuebunny/crossref_metadata_2025_split huggingface dataset:
Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis
Authors: dos Santos Karen Cristine Gonçalves , Desgagné-Penix Isabel , Germain Hugo 
Published: January 2020

Abstract
Background
RNA sequencing allows the measuring of gene expression at a resolution unmet by expression arrays or RT-qPCR. It is however necessary to normalize sequencing data by library size, transcript size and composition, among other factors, before comparing expression levels. The use of internal control genes or spike-ins is advocated in the literature for scaling read counts, but the methods for choosing reference genes are mostly targeted at RT-qPCR studies and require a set of pre-selected candidate controls or pre-selected target genes.

Results
Here, we report an R-based pipeline to select internal control genes based solely on read counts and gene sizes. This novel method first normalizes the read counts to Transcripts per Million (TPM) and then excludes weakly expressed genes using the DAFS script to calculate the cut-off. It then selects as references the genes with lowest TPM coefficient of variation. We used this method to pick custom reference genes for the differential expression analysis of three transcriptome sets from transgenic Arabidopsis plants expressing heterologous fungal effector proteins tagged with GFP (using GFP alone as the control). The custom reference genes showed lower coefficient of variation and fold change as well as a broader range of expression levels than commonly used reference genes. When analyzed with NormFinder, both typical and custom reference genes were considered suitable internal controls, but the custom selected genes were more stably expressed. geNorm produced a similar result in which most custom selected genes ranked higher (i.e. were more stably expressed) than commonly used reference genes.

Conclusions
The proposed method is innovative, rapid and simple. Since it does not depend on genome annotation, it can be used with any organism, and does not require pre-selected reference candidates or target genes that are not always available.
The Prognostic Significance of Different Bleeding Classifications in off-pump coronary artery bypass grafting
Authors: Xi Ziwei , Gao Yanan , Yan Zhenxian , Zhou Yu-Jie , Liu Wei 
Published: January 2020

Abstract
Background
Perioperative bleeding during cardiac surgery are known to make patients susceptible to adverse outcomes and several bleeding classifications have been developed to stratify the severity of bleeding events. Further validation of different classifications was needed. The aim of present study was to validate and explore the prognostic value of different bleeding classifications in patients undergoing off-pump coronary artery bypass grafting (OPCAB).

Methods
Data on baseline and operative characteristics of 3988 patients who underwent OPCAB in Beijing Anzhen Hospital from February 2008 to December 2014 were available. The primary endpoint was a composite of in-hospital death and nonfatal postoperative myocardial infarction (MI). The secondary endpoint was postoperative acute kidney injury (AKI). We explored the association of major bleeding defined by the European registry of Coronary Artery Bypass Grafting (E-CABG), Universal Definition of Perioperative Bleeding (UDPB), Bleeding Academic Research Consortium (BARC) classification and Study of Platelet Inhibition and Patient Outcomes (PLATO) with primary endpoints by multivariable logistic regression analysis and investigated their significance of adverse event prediction using goodness-of-fit tests of − 2 log likelihood.

Results
In-hospital mortality was 1.23% (n = 49) and postoperative MI was observed in 4.76% (n = 190) of patients, AKI in 24.69% (n = 985). The incidence of the primary outcome was 5.99% (n = 239). Multivariable logistic regression analysis showed that BARC type 4 (OR = 2.64, 95% CI: 1.66–4.19, P < 0.001), UDPB class 4 (OR = 3.52, 95% CI: 2.05–6.02, P < 0.001) and E-CABG class 2–3 (class 2: OR = 2.24, 95% CI: 1.36–3.70, P = 0.001; class 3: OR = 12.65, 95% CI: 2.74–18.43, P = 0.002) bleeding but not PLATO bleeding were associated with an increased risk of in-hospital death and postoperative MI. Major bleeding defined by all the four classifications mentioned above was an independent risk factor of AKI after surgery. Inclusion of major bleeding defined by these four classifications improved the predictive performance of the multivariable model with baseline characteristics.

Conclusions
Bleeding assessed by BARC, E-CABG and UDPB classifications were significantly associated with poorer immediate outcomes. These classifications seemed to be valuable tool in the assessment of prognostic effect of perioperative bleeding.
Reliability and validity of a sedentary behavior questionnaire for South American pediatric population: SAYCARE study
Authors: De Moraes Augusto César Ferreira , Nascimento-Ferreira Marcus Vinícius , Forjaz Claudia Lucia de Moraes , Aristizabal Juan Carlos , Azzaretti Leticia , Nascimento Junior Walter Viana , Miguel-Berges Maria L. , Skapino Estela , Delgado Carlos , Moreno Luis A. , Carvalho Heráclito Barbosa 
Published: January 2020

Abstract
Background
Multicenter studies from Europe and the United States have developed specifically standardized questionnaires for assessing and comparing sedentary behavior, but they cannot be directly applied for South American countries. The aim of this study was to assess the reliability and validity of the South American Youth Cardiovascular and Environmental (SAYCARE) sedentary behavior questionnaire.

Methods
Children and adolescents from seven South American cities were involved in the test-retest reliability (children: n = 55; adolescents: n = 106) and concurrent validity (children: n = 93; adolescents: n = 94) studies. The SAYCARE sedentary behavior questionnaire was administered twice with two-week interval and the behaviors were parent-reported for children and self-reported for adolescents. Questions included time spent watching television, using a computer, playing console games, passive playing (only in children) and studying (only in adolescents) over the past week. Accelerometer was used for at least 3 days, including at least one weekend day. We compared values of sedentary time, using accelerometers, by quartiles of reported sedentary behavior time and their sum.

Results
The reliability of sedentary behavior time was moderate for children (rho ≥0.45 and k ≥ 0.40) and adolescents (rho ≥0.30). Comparisons between the questionnaire and accelerometer showed a low overall agreement, with the questionnaire systematically underreporting sedentary time in children (at least, − 332.6 ± 138.5 min/day) and adolescents (at least, − 399.7 ± 105.0 min/day).

Conclusion
The SAYCARE sedentary behavior questionnaire has acceptable reliability in children and adolescents. However, the findings of current study indicate that SAYCARE questionnaire is not surrogate of total sedentary time.
Assessing and reducing PET radiotracer infiltration rates: a single center experience in injection quality monitoring methods and quality improvement
Authors: Osborne Dustin R. , Acuff Shelley N. , Fang Michael , Weaver Melissa D. , Fu Yitong 
Published: January 2020

Abstract
Background
Successful injection of radiolabeled compounds is critical for positron emission tomography (PET) imaging. A poor quality injection limits the tracer availability in the body and can impact diagnostic results. In this study, we attempt to quantify our infiltration rates, develop an actionable quality improvement plan to reduce potentially compromised injections, and compare injection scoring to PET/CT imaging results.

Methods
A commercially available system that uses external radiation detectors was used to monitor and score injection quality. This system compares the time activity curves of the bolus relative to a control reading in order to provide a score related to the quality of the injection. These injection scores were used to assess infiltration rates at our facility in order to develop and implement a quality improvement plan for our PET imaging center. Injection scores and PET imaging results were reviewed to determine correlations between image-based assessments of infiltration, such as liver SUVs, and injection scoring, as well as to gather infiltration reporting statistics by physicians.

Results
A total of 1033 injections were monitored at our center. The phase 1 infiltration rate was 2.1%. In decision tree analysis, patients < 132.5lbs were associated with infiltrations. Additional analyses suggested patients > 127.5 lbs. with non-antecubital injections were associated with lower quality injections. Our phase 2 infiltration rate was 1.9%. Comparison of injection score to SUV showed no significant correlation and indicated that only 63% of suspected infiltrations were visible on PET/CT imaging.

Conclusions
Developing a quality improvement plan and monitoring PET injections can lead to reduced infiltration rates. No significant correlation between reference SUVs and injection score provides evidence that determination of infiltration based on PET images alone may be limited. Results also indicate that the number of infiltrated PET injections is under-reported.
Uveitis–glaucoma–hyphema syndrome with sclera-fixed posterior-chamber two-haptic intraocular lens in a highly myopic eye: a case report
Authors: Du Yu , Zhu Xiangjia , Yang Jin , Zhang Yinglei , Cai Lei , Lu Yi 
Published: January 2020

Abstract
Background
We report a case of uveitis–glaucoma–hyphema (UGH) syndrome in a highly myopic pseudophakic eye with seemingly normal positioning of a two-haptic intraocular lens (IOL).

Case presentation
The patient was a 61-year-old woman suffering recurrent episodes of blurred vision, floaters, redness, elevated intraocular pressure (IOP), and pain in the right eye following implantation of a sclera-fixed IOL. The symptoms were alleviated by the systemic and topical administration of IOP-lowering and anti-inflammatory medications. A slit-lamp examination revealed depigmentation and atrophy of the iris, and a quiet anterior chamber in the right eye. Endophthalmitis caused by hypovirulent bacteria and UGH syndrome were both considered. Ultrasound biomicroscopy (UBM) and gonioscopy provided direct evidence of malpositioned IOL haptics, which pushed the root of the iris forward, resulting in persistent mechanical chaffing, the probable cause of UGH syndrome. IOL explantation resolved her symptoms. Negative bacterial culture results for the IOL excluded the possibility of endophthalmitis.

Conclusions
Heightened awareness of underlying UGH syndrome and prompt UBM are important when doctors encounter a patient with a sclera-fixed IOL suffering from recurrent anterior segment inflammation and elevated IOP.
Adult low-risk drinkers and abstainers are not the same
Authors: Mugavin Janette , MacLean Sarah , Room Robin , Callinan Sarah 
Published: January 2020

Abstract
Background
Alcohol consumption, even at low-levels, can not be guaranteed as safe or risk free. Specifically, the 2009 Australian National Health and Medical Research Council drinking guidelines recommend that adults should not drink more than two standard drinks on any day on average, and no more than four drinks on a single occasion. Nearly 40% of Australians aged 12 years and older drink alcohol but don’t exceed these recommended limits, yet adult low-risk drinkers have been largely overlooked in Australian alcohol survey research, where they are usually grouped with abstainers. This paper examines the socio-demographic profile of low-risk drinking adults (18+ years old), compared to those who abstain.

Methods
Data from the 2013 National Drug Strategy Household Survey were used. In the past 12 months, 4796 Australians had not consumed alcohol and 8734 had consumed alcohol at low-risk levels, accounting for both average volume and episodic drinking (hereafter low-risk).

Results
Multivariate logistic regression results indicated that low-risk drinkers were more likely to be older, married, Australian-born, and reside in a less disadvantaged neighbourhood compared with abstainers. There was no significant difference by sex between low-risk drinkers and abstainers.

Conclusions
The socio-demographic profile of low-risk drinkers differed from that of abstainers. Combining low-risk drinkers and abstainers into a single group, which is often the practice in survey research, may mask important differences. The study may support improved targeting of health promotion initiatives that encourage low-risk drinkers not to increase consumption or, in view of increasing evidence that low-risk drinking is not risk free, to move towards abstinence.
Knowledge of heart attack and stroke symptoms among US Native American Adults: a cross-sectional population-based study analyzing a multi-year BRFSS database
Authors: Van Hooser Jared C. , Rouse Krista L. , Meyer Mandy L. , Siegler Amanda M. , Fruehauf Beth M. , Ballance Elliot H. , Solberg Sarah M. , Dibble Michael J. , Lutfiyya M. Nawal 
Published: January 2020

Abstract
Background
Heart disease and stroke are among the leading causes of death in Native Americans. Knowledge of heart attack and stroke symptomology are essential for prompt identification of symptoms and for appropriate action in seeking care. Knowledge of heart attack and stroke symptoms among US Native American adults was this study’s focus.

Methods
Multivariate techniques were used to analyze national surveillance data. Native American adults comprised the study population. Low heart attack and stroke knowledge score was the dependent variable.

Results
Logistic regression analysis yielded that Native American adults with low heart attack and stroke composite knowledge scores were more likely to be: older, less educated, poorer, uninsured, a rural resident, male, without a primary health care provider, and lacking a recent medical checkup.

Conclusions
The identified characteristics of Native American adults with heart attack and stroke knowledge deficits or disparities should guide educational initiatives by health care providers focusing on improving such knowledge.
SALaMA study protocol: a mixed methods study to explore mental health and psychosocial support for conflict-affected youth in Detroit, Michigan
Authors: Stark Lindsay , Robinson Mackenzie V. , Seff Ilana , Hassan Wafa , Allaf Carine 
Published: January 2020

AbstractBackgroundFamilies resettling to the U.S. from conflict-affected countries in the Middle East and North Africa (MENA) face countless challenges. These families must cope with experiences of armed conflict and forced migration while also assimilating to a new society. According to the ‘immigrant paradox,’ time spent in a new country can compound the effects of migration and assimilation challenges and lead to deteriorated mental health. This study aims to assess the psychosocial wellbeing of MENA-born or first-generation adolescents attending school in the Detroit metropolitan area (DMA) to understand how schools, families, and communities play a role in supporting these adolescents’ wellbeing.MethodsThe quantitative component of this mixed methods study will involve a self-administered survey with a sample of students whose responses will be linked to academic records and behavioral assessments. The survey will utilize validated instruments to measure depressive and anxiety symptoms (Hopkins Symptom Checklist-37A), hope (Children’s Hope Scale), resilience (Child and Youth Resilience Measure-12), externalizing and prosocial behavior (Hopkins Symptom Checklist-37A, Strengths and Difficulties Questionnaire), school belonging (Psychological Sense of School Membership), and peer relationships (Multidimensional Scale of Perceived Social Support). Differences in outcomes will be analyzed across two strata: students born in the MENA region and first-generation students whose parents immigrated to the US from the MENA region. The qualitative component will involve semi-structured key informant interviews with parents, school administrators, educators, and mental health providers, and focus group discussions (FGDs) with a purposive sample of adolescents born – or whose parents were born - in the MENA region. The FGDs will include a participatory ranking activity where participants will be asked to free-list and rank ideas about how schools can better support students like them. Thematic content analysis will be conducted to identify common themes.DiscussionThis study will contribute evidence about the wellbeing of adolescents who come from – or whose parents come from - conflict-affected countries currently living in the U.S. Findings can be used to inform program and policy development to enable schools and their community partners to serve this population more effectively.
Age-specific incidence of allergic and non-allergic asthma
Authors: Pakkasela Johanna , Ilmarinen Pinja , Honkamäki Jasmin , Tuomisto Leena E. , Andersén Heidi , Piirilä Päivi , Hisinger-Mölkänen Hanna , Sovijärvi Anssi , Backman Helena , Lundbäck Bo , Rönmark Eva , Kankaanranta Hannu , Lehtimäki Lauri 
Published: January 2020

AbstractBackgroundOnset of allergic asthma has a strong association with childhood but only a few studies have analyzed incidence of asthma from childhood to late adulthood in relation to allergy. The purpose of the study was to assess age-specific incidence of allergic and non-allergic asthma.MethodsQuestionnaires were sent to 8000 randomly selected recipients aged 20–69 years in Finland in 2016. The response rate was 52.3% (n = 4173). The questionnaire included questions on e.g. atopic status, asthma and age at asthma diagnosis. Asthma was classified allergic if also a physician-diagnosed allergic rhinitis was reported.ResultsThe prevalence of physician-diagnosed asthma and allergic rhinitis were 11.2 and 17.8%, respectively. Of the 445 responders with physician-diagnosed asthma, 52% were classified as allergic and 48% as non-allergic. Median ages at diagnosis of allergic and non-allergic asthma were 19 and 35 years, respectively. Among subjects with asthma diagnosis at ages 0–9, 10–19, 20–29, 30–39, 40–49, 50–59 and 60–69 years, 70, 62, 58, 53, 38, 19 and 33%, respectively, were allergic. For non-allergic asthma, the incidence rate was lowest in children and young adults (0.7/1000/year). It increased after middle age and was highest in older age groups (2.4/1000/year in 50–59 years old).ConclusionsThe incidence of allergic asthma is highest in early childhood and steadily decreases with advancing age, while the incidence of non-allergic asthma is low until it peaks in late adulthood. After approximately 40 years of age, most of the new cases of asthma are non-allergic.
Madurella mycetomatis infection of the foot: a case report of a neglected tropical disease in a non-endemic region
Authors: Karrakchou Basma , Boubnane Ibtissam , Senouci Karima , Hassam Badreddine 
Published: January 2020

Abstract
Background
Mycetoma is an uncommon chronic granulomatous infection of cutaneous and subcutaneous tissues that can be caused by filamentous bacteria (actinomycetoma) or fungi (eumycetoma). It is the prerogative of young men between the third and fourth decade and is transmitted through any trauma causing an inoculating point. The classic clinical triad associates a painless hard and swelling subcutaneous mass, multiple fistulas, and the pathognomonic discharge of grains. Although endemic in many tropical and subtropical countries, mycetoma can also be found in non-endemic areas as in Morocco, and causes then diagnosis problems leading to long lasting complications. Therefore, we should raise awareness of this neglected disease for an earlier management. Under medical treatment however, mycetoma has a slow healing and surgery is often needed, and relapses are possible.

Case presentation
Herein we report a case of a 64 years old patient, with a history of eumycetoma occurring ten years ago treated with oral terbinafine coupled with surgery. A complete remission was seen after 2 years. He presented a relapse on the previous scar 6 months ago. There wasn’t any bone involvement in the magnetic resonance imaging (MRI). The patient was put under oral terbinafine with a slow but positive outcome.

Conclusion
Through this case report, we perform a literature review and highlight the importance of increase awareness of mycetoma in clinical practice especially in non-endemic regions.
Reduced risk of clinically important deteriorations by ICS in COPD is eosinophil dependent: a pooled post-hoc analysis
Authors: Bafadhel Mona , Singh Dave , Jenkins Christine , Peterson Stefan , Bengtsson Thomas , Wessman Peter , Fagerås Malin 
Published: January 2020

Abstract
Background
Clinically Important Deterioration (CID) is a novel composite measure to assess treatment effect in chronic obstructive pulmonary disease (COPD). We examined the performance and utility of CID in assessing the effect of inhaled corticosteroids (ICS) in COPD.

Methods
This post-hoc analysis of four budesonide/formoterol (BUD/FORM) studies comprised 3576 symptomatic moderate-to-very-severe COPD patients with a history of exacerbation. Analysis of time to first CID event (exacerbation, deterioration in forced expiratory volume in 1 second [FEV1] or worsening St George’s Respiratory Questionnaire [SGRQ] score) was completed using Cox proportional hazards models.

Results
The proportion of patients with ≥1 CID in the four studies ranged between 63 and 77% and 69–84% with BUD/FORM and FORM, respectively, with an average 25% reduced risk of CID with BUD/FORM. All components contributed to the CID event rate. Experiencing a CID during the first 3 months was associated with poorer outcomes (lung function, quality of life, symptoms and reliever use) and increased risk of later CID events. The effect of BUD/FORM versus FORM in reducing CID risk was positively associated with the blood eosinophil count.

Conclusions
Our findings suggest that BUD/FORM offers protective effects for CID events compared with FORM alone, with the magnitude of the effect dependent on patients’ eosinophil levels. CID may be an important tool for evaluation of treatment effect in a complex, multifaceted, and progressive disease like COPD, and a valuable tool to allow for shorter and smaller future outcome predictive trials in early drug development.