bluuebunny/crossref_metadata_2025_split huggingface dataset:
tRNA functional signatures classify plastids as late-branching cyanobacteria
Authors: Lawrence Travis J , Amrine Katherine CH , Swingley Wesley D , Ardell David H 
Published: December 2019

Abstract
Background
Eukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data.

Results
Using Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies (“phyloclassifies”) cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data.

Conclusions
Phylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies.
Transcriptome and microbiome of coconut rhinoceros beetle (Oryctes rhinoceros) larvae
Authors: Shelomi Matan , Lin Shih-Shun , Liu Li-Yu 
Published: December 2019

AbstractBackgroundThe coconut rhinoceros beetle,Oryctes rhinoceros, is a major pest of palm crops in tropical Asia and the Pacific Islands. Little molecular data exists for this pest, impeding our ability to develop effective countermeasures and deal with the species’ growing resistance to viral biocontrols. We present the first molecular biology analyses of this species, including a metagenomic assay to understand the microbiome of different sections of its digestive tract, and a transcriptomics assay to complement the microbiome data and to shed light on genes of interest like plant cell wall degrading enzymes and immunity and xenobiotic resistance genes.ResultsThe gut microbiota ofOryctes rhinoceroslarvae is quite similar to that of the termite gut, as both species feed on decaying wood. We found the first evidence for endogenous beta-1,4-endoglucanase in the beetle, plus evidence for microbial cellobiase, suggesting the beetle can degrade cellulose together with its gut microfauna. A number of antimicrobial peptides are expressed, particularly by the fat body but also by the midgut and hindgut.ConclusionsThis transcriptome provides a wealth of data about the species’ defense against chemical and biological threats, has uncovered several potentially new species of microbial symbionts, and significantly expands our knowledge about this pest.
DEBATE-statistical analysis plans for observational studies
Authors: Hiemstra Bart , Keus Frederik , Wetterslev Jørn , Gluud Christian , van der Horst Iwan C. C. 
Published: December 2019

AbstractBackgroundAll clinical research benefits from transparency and validity. Transparency and validity of studies may increase by prospective registration of protocols and by publication of statistical analysis plans (SAPs) before data have been accessed to discern data-driven analyses from pre-planned analyses.Main messageLike clinical trials, recommendations for SAPs for observational studies increase the transparency and validity of findings. We appraised the applicability of recently developed guidelines for the content of SAPs for clinical trials to SAPs for observational studies. Of the 32 items recommended for a SAP for a clinical trial, 30 items (94%) were identically applicable to a SAP for our observational study. Power estimations and adjustments for multiplicity are equally important in observational studies and clinical trials as both types of studies usually address multiple hypotheses. Only two clinical trial items (6%) regarding issues of randomisation and definition of adherence to the intervention did not seem applicable to observational studies. We suggest to include one new item specifically applicable to observational studies to be addressed in a SAP, describing how adjustment for possible confounders will be handled in the analyses.ConclusionWith only few amendments, the guidelines for SAP of a clinical trial can be applied to a SAP for an observational study. We suggest SAPs should be equally required for observational studies and clinical trials to increase their transparency and validity.
Associated factors in distinguishing patients with brucellosis from suspected cases
Authors: Luo Jingjing , Yang Huixin , Hu Fangfang , Zhang Siwen , Wang Taijun , Zhao Qian , Wang Ruize , Zhen Qing 
Published: December 2019

Abstract
Background
To investigate the risk factors for brucellosis in suspected cases of the disease.

Methods
A self-designed questionnaire was developed to collect data from 3557 people whose initial visit site was the Songyuan Center for Disease Control and Prevention (CDC) from January 1st, 2009 to December 31st, 2012. After collecting blood samples, a plate agglutination test (PAT) and serum agglutination test (SAT) were used to distinguish the patients with brucellosis from the suspected cases.

Results
Sex, occupation (farmers and herdsmen), contact with abortion products, and contact with feces were the main risk factors for brucellosis in the suspected cases (all P < 0.05). No difference existed between the confirmed cases and suspected cases in the demographic characteristics, contact with animals (except swine), contact with substances, or clinical symptoms (except fever). However, the confirmed cases showed significant differences from people without brucellosis in demographic characteristics, contact with animals (except cattle and swine), contact with substances, and clinical symptoms. Suspected cases exhibited significant differences from people without brucellosis in the demographic characteristics (except education), contact with animals (except swine), contact with substances (except dust), and clinical symptoms (except chills and acratia). Brucella was cultured from the blood samples of three of 30 suspected cases with fever. Using AMOS-PCR and agarose electrophoresis, the detailed species of Brucella strain was identified as Brucella melitensis.

Conclusions
Abortion products and feces are the main risk factors for brucellosis in suspected cases of the disease. Pyrexia in suspected cases with a history of contact with abortion products or feces should raise suspicion for the disease.
Evaluation of the relationship between IL-12, IL-13 and TNF-α gene polymorphisms with the susceptibility to brucellosis: a case control study
Authors: Kazemi Sima , Vaisi-Raygani Asad , Keramat Fariba , Saidijam Massoud , Soltanian Ali Reza , Alahgholi-Hajibehzad Mahdi , Hashemi Seyed Hamid , Alikhani Mohammad Yousef 
Published: December 2019

Abstract
Background
The cytokine gene polymorphism is important for the genetic susceptibility of infectious diseases. The aim of the present study was to investigate the relationship between TNF-α, IL-12, and IL-13 gene polymorphisms and predisposition to brucellosis.

Methods
In this study, 107 patients with brucellosis and 107 healthy individuals were evaluated. The SNPs of TNF-α)- 238 G/A) and IL-12 (+ 1188 A/C) were done by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and IL-13 genotyping at positions − 1512 (A/C) and − 1112 (C/T) were analysis by restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) methods. IL-12, IL-13 and TNF-α serum levels were measured by a sandwich enzyme-linked immunosorbent assay (ELISA).

Results
IL-13 (−1512A/C) was associated with Brucellosis risk in dominant model (OR (95% CI) = 2.17 (1.02–4.62)), P-value = 0.041. However, there was no difference in allele and genotype frequencies of TNF-α)- 238 G/A), IL-12 (+ 1188 A/C) and IL-13 [− 1512 (A/C) and − 1112 (C/T)] between patients and controls. Serum levels of IL-12 and TNF-α were significantly more frequent in the patients than in the control groups.

Conclusions
The IL-13 gene polymorphism can be used as a biomarker for detecting susceptibility to Brucella disease.
Transplant outcomes in positive complement-dependent cytotoxicity- versus flow cytometry-crossmatch kidney transplant recipients after successful desensitization: a retrospective study
Authors: Kim Deok Gie , Lee Juhan , Park Younhee , Kim Myoung Soo , Jeong Hyeon Joo , Kim Soon Il , Kim Yu Seun , Kim Beom Seok , Huh Kyu Ha 
Published: December 2019

Abstract
Background
Despite the obvious survival benefit compared to that among waitlist patients, outcomes of positive crossmatch kidney transplantation (KT) are generally inferior to those of human leukocyte antigen (HLA)-compatible KT. This study aimed to compare the outcomes of positive complement-dependent cytotoxicity (CDC) crossmatch (CDC + FC+) and positive flow cytometric crossmatch (CDC-FC+) with those of HLA-compatible KT (CDC-FC-) after successful desensitization.

Methods
We retrospectively analyzed 330 eligible patients who underwent KTs between June 2011 and August 2017: CDC-FC- (n = 274), CDC-FC+ (n = 39), and CDC + FC+ (n = 17). Desensitization protocol targeting donor-specific antibody (DSA) involved plasmapheresis, intravenous immunoglobulin (IVIG), and rituximab with/without bortezomib for positive-crossmatch KT.

Results
Death-censored graft survival and patient survival were not different among the three groups. The median estimated glomerular filtration rate was significantly lower in the CDC + FC+ group than in the compatible group at 6 months (P < 0.001) and 2 years (P = 0.020). Biopsy-proven rejection within 1 year of CDC-FC-, CDC-FC+, and CDC + FC+ were 15.3, 28.2, and 47.0%, respectively. Urinary tract infections (P < 0.001), Pneumocystis jirovecii pneumonia (P < 0.001), and cytomegalovirus viremia (P < 0.001) were more frequent in CDC-FC+ and CDC + FC+ than in CDC-FC-.

Conclusions
This study showed that similar graft and patient survival was achieved in CDC-FC+ and CDC + FC+ KT compared with CDC-FC- through DSA-targeted desensitization despite the higher incidence of rejection and infection than that in compatible KT.
Prevalence and profile of users and non-users of anabolic steroids among resistance training practitioners
Authors: PEREIRA Ericson , MOYSES Samuel Jorge , IGNÁCIO Sérgio Aparecido , MENDES Daniel Komarchewski , SILVA Diego Sgarbi D. A. , CARNEIRO Everdan , HARDY Ana Maria Trindade Grégio , ROSA Edvaldo Antônio Ribeiro , BETTEGA Patrícia Vida Cassi , JOHANN Aline Cristina Batista Rodrigues 
Published: December 2019

AbstractBackgroundTo verify the prevalence and profile of users and non-users of anabolic steroid (AS) among resistance training practitioners.MethodsAn observational, cross-sectional survey was performed in 100 gyms in Curitiba city, involving 5773 individuals and self-administered questionnaires. The chi-square and z-tests of proportions were used for comparison between the groups (p < 0.05).Results83.2% did not use, 9.1% formerly used, 3.4% currently used, and 4.3% intended used AS. The prevalence of former or current AS users was 16.9 and 6.5% among men and women, respectively. The prevalence ratios were as follows: 1) 2.6 male users for each woman; 2) 3.3 individuals aged 30–44 years and 2.8 individuals aged 18–29 years for each individual aged over 45 years. Beginners were not interested in using AS, but individuals who had trained longer had higher prevalence of AS use.ConclusionsThe gym environment encouraged the use of AS owing to aesthetic appeal. Thus, suggesting the need for actions to prevent abusive use of AS considering the practitioners profile (practitioners were young, university and single).
Misconceptions about traumatic brain injury among nursing students in India: implications for nursing care and curriculum
Authors: Gurusamy Jothimani , Gandhi Sailaxmi , Amudhan Senthil , Veerabhadraiah Kathyayani B. , Narayanasamy Padmavathi , Sreenivasan Sunitha T. , Palaniappan Marimuthu 
Published: December 2019

Abstract
Background
Despite the devastating consequences of Traumatic brain injuries (TBIs), TBI misconceptions are common among healthcare professionals. As an essential member of multi-professional team providing TBI care, it is important that nurses have correct information and adequate skills to achieve the best possible outcomes for TBI. For example, some common misconceptions about TBIs are that a second blow to the head can improve memory functioning and wearing seatbelts can cause as many brain injuries as it prevents. In India, perhaps such misconceptions towards TBI among nursing professionals were not yet documented. As nursing students form the future health workforce, understanding TBI misconceptions among nursing students in resource-limited settings like India will provide useful information for strengthening the nursing curricula for improved care and rehabilitation of TBIs.

Methods
We used a cross-sectional survey to study the TBI misconceptions among nursing students in India. A Common Misconceptions about Traumatic Brain Injury (CM-TBI) questionnaire was administered to 154 nursing students from a nursing college of a tertiary care neuro-centre in India. The mean percentage of misconceptions were calculated for 7-domains of CM-TBI. T-test for independent samples and ANOVA were used to study the association of misconception with socio-demographic variables using total score for each respondent.

Results
Of the 143 nursing students who completed the survey, majority of them were female (97%) and in the 19-20 year age-group (95.1%). Domain on brain damage (81.1%) had highest rate, while amnesia domain (42.0%) had lowest rate of misconception. The overall mean-score was 22.73 (Standard Deviation: 4.69) which was significantly higher than the median score of 19.5. The study did not show significant differences on overall misconceptions about TBI for any of the socio-demographic characteristics.

Conclusions
Misconceptions about TBIs were common among nursing students and it was pervasive irrespective of age, gender, place of residence and year of education. A need to strengthen nursing curriculum in the area of TBIs has been emphasized for improved care and management of TBIs. The study findings also suggest the need for understanding such misconceptions among other healthcare professionals involved in TBI care.
Training and well-equipped facility increases the odds of skills of health professionals on helping babies breathe in public hospitals of Southern Ethiopia: cross-sectional study
Authors: Mersha Abera , Shibiru Shitaye , Gultie Teklemariam , Degefa Nega , Bante Agegnehu 
Published: December 2019

Abstract
Background
Health professionals equipped with the adequate skills of helping baby breath remain the backbone in the health system in improving neonatal outcomes. However, there is a great controversy between studies to show the proximate factors of the skills of health care providers in helping babies breathe. In Ethiopia, there is a paucity of evidence on the current status of health care provider’s skills of helping babies breathe despite the improvement in neonatal health care services. Therefore, this study intends to fill those gaps in assessing the skills of helping babies breathe and its associated factors among health professionals in public hospitals in Southern Ethiopia.

Methods
A facility-based cross-sectional study was conducted among 441 health professionals from March 10 to 30, 2019. A simple random sampling method was used to select the study participants. The data were collected through pre-tested interviewer-administered questionnaire and observational checklist. A binary logistic regression model was used to identify significant factors for the skills of helping babies breathe by using SPSS version 25. The P-value < 0.05 used to declare statistical significance.

Results
Overall, 71.1% (95%CI: 66.2, 75.4%) of health professionals had good skills in helping babies breathe. Age group from 25 to 34 (AOR = 2.24; 95%CI: 1.04, 4.81), training on helping babies breathe (AOR = 2.69; 95%CI: 1.49, 4.87), well-equipped facility (AOR = 2.15; 95%CI: 1.09, 4.25), and adequate knowledge on helping babies breathe (AOR = 2.21; 95%CI: 1.25, 3.89) were significantly associated with a health professionals good skill on helping babies breathe.

Conclusions
Even though a significant number of care providers had good skills in helping babies breathe, yet there is a need to further improve the skills of the provider in helping babies breathe. Hence, health facilities should be equipped with adequate materials and facilitate frequent training to the provider.
Descriptive epidemiology of physical activity energy expenditure in UK adults (The Fenland study)
Authors: Lindsay Tim , Westgate Kate , Wijndaele Katrien , Hollidge Stefanie , Kerrison Nicola , Forouhi Nita , Griffin Simon , Wareham Nick , Brage Søren 
Published: December 2019

Abstract
Background
Physical activity (PA) plays a role in the prevention of a range of diseases including obesity and cardiometabolic disorders. Large population-based descriptive studies of PA, incorporating precise measurement, are needed to understand the relative burden of insufficient PA levels and to inform the tailoring of interventions. Combined heart and movement sensing enables the study of physical activity energy expenditure (PAEE) and intensity distribution. We aimed to describe the sociodemographic correlates of PAEE and moderate-to-vigorous physical activity (MVPA) in UK adults.

Methods
The Fenland study is a population-based cohort study of 12,435 adults aged 29–64 years-old in Cambridgeshire, UK. Following individual calibration (treadmill), participants wore a combined heart rate and movement sensor continuously for 6 days in free-living, from which we derived PAEE (kJ•day− 1•kg− 1) and time in MVPA (> 3 & > 4 METs) in bouts greater than 1 min and 10 min. Socio-demographic information was self-reported. Stratum-specific summary statistics and multivariable analyses were performed.

Results
Women accumulated a mean (sd) 50(20) kJ•day− 1•kg− 1 of PAEE, and 83(67) and 33(39) minutes•day− 1 of 1-min bouted and 10-min bouted MVPA respectively. By contrast, men recorded 59(23) kJ•day− 1•kg− 1, 124(84) and 60(58) minutes•day− 1. Age and BMI were also important correlates of PA. Association with age was inverse in both sexes, more strongly so for PAEE than MVPA. Obese individuals accumulated less PA than their normal-weight counterparts, whether considering PAEE or allometrically-scaled PAEE (− 10 kJ•day− 1•kg− 1 or − 15 kJ•day− 1•kg-2/3 in men). Higher income and manual work were associated with higher PA; manual workers recorded 13–16 kJ•kg− 1•day− 1 more PAEE than sedentary counterparts. Overall, 86% of women and 96% of men accumulated a daily average of MVPA (> 3 METs) corresponding to 150 min per week. These values were 49 and 74% if only considering bouts > 10 min (15 and 31% for > 4 METs).

Conclusions
PA varied by age, sex and BMI, and was higher in manual workers and those with higher incomes. Light physical activity was the main driver of PAEE; a component of PA that is currently not quantified as a target in UK guidelines.
Plasma sTNFR1 and IL8 for prognostic enrichment in sepsis trials: a prospective cohort study
Authors: Anderson Brian J. , Calfee Carolyn S. , Liu Kathleen D. , Reilly John P. , Kangelaris Kirsten N. , Shashaty Michael G. S. , Lazaar Aili L. , Bayliffe Andrew I. , Gallop Robert J. , Miano Todd A. , Dunn Thomas G. , Johansson Erik , Abbott Jason , Jauregui Alejandra , Deiss Thomas , Vessel Kathryn , Belzer Annika , Zhuo Hanjing , Matthay Michael A. , Meyer Nuala J. , Christie Jason D. 
Published: December 2019

Abstract
Background
Enrichment strategies improve therapeutic targeting and trial efficiency, but enrichment factors for sepsis trials are lacking. We determined whether concentrations of soluble tumor necrosis factor receptor-1 (sTNFR1), interleukin-8 (IL8), and angiopoietin-2 (Ang2) could identify sepsis patients at higher mortality risk and serve as prognostic enrichment factors.

Methods
In a multicenter prospective cohort study of 400 critically ill septic patients, we derived and validated thresholds for each marker and expressed prognostic enrichment using risk differences (RD) of 30-day mortality as predictive values. We then used decision curve analysis to simulate the prognostic enrichment of each marker and compare different prognostic enrichment strategies.

Measurements and main results
An admission sTNFR1 concentration > 8861 pg/ml identified patients with increased mortality in both the derivation (RD 21.6%) and validation (RD 17.8%) populations. Among immunocompetent patients, an IL8 concentration > 94 pg/ml identified patients with increased mortality in both the derivation (RD 17.7%) and validation (RD 27.0%) populations. An Ang2 level > 9761 pg/ml identified patients at 21.3% and 12.3% increased risk of mortality in the derivation and validation populations, respectively. Using sTNFR1 or IL8 to select high-risk patients improved clinical trial power and efficiency compared to selecting patients with septic shock. Ang2 did not outperform septic shock as an enrichment factor.

Conclusions
Thresholds for sTNFR1 and IL8 consistently identified sepsis patients with higher mortality risk and may have utility for prognostic enrichment in sepsis trials.