bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the prognostic gene signatures for the improvement of risk stratification in cancers by using deep learning algorithm coupled with wavelet transform
Authors: Zhao Yiru , Zhou Yifan , Liu Yuan , Hao Yinyi , Li Menglong , Pu Xuemei , Li Chuan , Wen Zhining 
Published: May 2020

Abstract
Background
The aim of gene expression-based clinical modelling in tumorigenesis is not only to accurately predict the clinical endpoints, but also to reveal the genome characteristics for downstream analysis for the purpose of understanding the mechanisms of cancers. Most of the conventional machine learning methods involved a gene filtering step, in which tens of thousands of genes were firstly filtered based on the gene expression levels by a statistical method with an arbitrary cutoff. Although gene filtering procedure helps to reduce the feature dimension and avoid overfitting, there is a risk that some pathogenic genes important to the disease will be ignored.

Results
In this study, we proposed a novel deep learning approach by combining a convolutional neural network with stationary wavelet transform (SWT-CNN) for stratifying cancer patients and predicting their clinical outcomes without gene filtering based on tumor genomic profiles. The proposed SWT-CNN overperformed the state-of-art algorithms, including support vector machine (SVM) and logistic regression (LR), and produced comparable prediction performance to random forest (RF). Furthermore, for all the cancer types, we firstly proposed a method to weight the genes with the scores, which took advantage of the representative features in the hidden layer of convolutional neural network, and then selected the prognostic genes for the Cox proportional-hazards regression. The results showed that risk stratifications can be effectively improved by using the identified prognostic genes as feature, indicating that the representative features generated by SWT-CNN can well correlate the genes with prognostic risk in cancers and be helpful for selecting the prognostic gene signatures.

Conclusions
Our results indicated that gene expression-based SWT-CNN model can be an excellent tool for stratifying the prognostic risk for cancer patients. In addition, the representative features of SWT-CNN were validated to be useful for evaluating the importance of the genes in the risk stratification and can be further used to identify the prognostic gene signatures.
Direct comparison shows that mRNA-based diagnostics incorporate information which cannot be learned directly from genomic mutations
Authors: Ravkin Hersh D. , Givton Ofer , Geffen David B. , Rubin Eitan 
Published: May 2020

Abstract
Background
Compared to the many uses of DNA-level testing in clinical oncology, development of RNA-based diagnostics has been more limited. An exception to this trend is the growing use of mRNA-based methods in early-stage breast cancer. Although DNA and mRNA are used together in breast cancer research, the distinct contribution of mRNA beyond that of DNA in clinical challenges has not yet been directly assessed. We hypothesize that mRNA harbors prognostically useful information independently of genomic variation. To validate this, we use both genomic mutations and gene expression to predict five-year breast cancer recurrence in an integrated test model. This is accomplished first by comparing the feature importance of DNA and mRNA features in a model trained on both, and second, by evaluating the difference in performance of models trained on DNA and mRNA data separately.

Results
We find that models trained on DNA and mRNA data give more weight to mRNA features than to DNA features, and models trained only on mRNA outperform models trained on DNA alone.

Conclusions
The evaluation process presented here may serve as a framework for the interpretation of the relative contribution of individual molecular markers. It also suggests that mRNA has a distinct contribution in a diagnostic setting, beyond and independently of DNA mutation data.
Transposable element persistence via potential genome-level ecosystem engineering
Authors: Kremer Stefan C. , Linquist Stefan , Saylor Brent , Elliott Tyler A. , Gregory T. Ryan , Cottenie Karl 
Published: May 2020

Abstract
Background
The nuclear genomes of eukaryotes vary enormously in size, with much of this variability attributable to differential accumulation of transposable elements (TEs). To date, the precise evolutionary and ecological conditions influencing TE accumulation remain poorly understood. Most previous attempts to identify these conditions have focused on evolutionary processes occurring at the host organism level, whereas we explore a TE ecology explanation.

Results
As an alternative (or additional) hypothesis, we propose that ecological mechanisms occurring within the host cell may contribute to patterns of TE accumulation. To test this idea, we conducted a series of experiments using a simulated asexual TE/host system. Each experiment tracked the accumulation rate for a given type of TE within a particular host genome. TEs in this system had a net deleterious effect on host fitness, which did not change over the course of experiments. As one might expect, in the majority of experiments TEs were either purged from the genome or drove the host population to extinction. However, in an intriguing handful of cases, TEs co-existed with hosts and accumulated to very large numbers. This tended to occur when TEs achieved a stable density relative to non-TE sequences in the genome (as opposed to reaching any particular absolute number). In our model, the only way to maintain a stable density was for TEs to generate new, inactive copies at a rate that balanced with the production of active (replicating) copies.

Conclusions
From a TE ecology perspective, we suggest this could be interpreted as a case of ecosystem engineering within the genome, where TEs persist by creating their own “habitat”.
Uncovering the role of Symbiodiniaceae assemblage composition and abundance in coral bleaching response by minimizing sampling and evolutionary biases
Authors: Swain Timothy D. , Lax Simon , Backman Vadim , Marcelino Luisa A. 
Published: May 2020

AbstractBackgroundBiodiversity and productivity of coral-reef ecosystems depend upon reef-building corals and their associations with endosymbiotic Symbiodiniaceae,which offer diverse functional capabilities to their hosts. The number of unique symbiotic partners (richness) and relative abundances (evenness) have been hypothesized to affect host response to climate change induced thermal stress. Symbiodiniaceae assemblages with many unique phylotypes may provide greater physiological flexibility or form less stable symbioses; assemblages with low abundance phylotypes may allow corals to retain thermotolerant symbionts or represent associations with less-suitable symbionts.ResultsHere we demonstrate that true richness of Symbiodiniaceae phylotype assemblages is generally not discoverable from direct enumeration of unique phylotypes in association records and that cross host-species comparisons are biased by sampling and evolutionary patterns among species. These biases can be minimized through rarefaction of richness (rarefied-richness) and evenness (Probability of Interspecific Encounter, PIE), and analyses that account for phylogenetic patterns. These standardized metrics were calculated for individual Symbiodiniaceae assemblages composed of 377 uniqueITS2phylotypes associated with 123 coral species. Rarefied-richness minimized correlations with sampling effort, while maintaining important underlying characteristics across host bathymetry and geography. Phylogenetic comparative methods reveal significant increases in coral bleaching and mortality associated with increasing Symbiodiniaceae assemblage richness and evenness at the level of host species.ConclusionsThese results indicate that the potential flexibility afforded by assemblages characterized by many phylotypes present at similar relative abundances does not result in decreased bleaching risk and point to the need to characterize the overall functional and genetic diversity of Symbiodiniaceae assemblages to quantify their effect on host fitness under climate change.
A novel gene expression system for Ralstonia eutropha based on the T7 promoter
Authors: Hu Muzi , Xiong Bin , Li Zhongkang , Liu Li , Li Siwei , Zhang Chunzhi , Zhang Xueli , Bi Changhao 
Published: May 2020

Abstract
Background
Ralstonia eutropha (syn. Cupriavidus necator) is a model microorganism for studying metabolism of polyhydroxyalkanoates (PHAs) and a potential chassis for protein expression due to various advantages. Although current plasmid systems of R. eutropha provide a basic platform for gene expression, the performance of the expression-inducing systems is still limited. In addition, the sizes of the cloned genes are limited due to the large sizes of the plasmid backbones.

Results
In this study, an R. eutropha T7 expression system was established by integrating a T7 RNA polymerase gene driven by the PBAD promoter into the genome of R. eutropha, as well as adding a T7 promoter into a pBBR1-derived plasmid for gene expression. In addition, the essential DNA sequence necessary for pBBR1 plasmid replication was identified, and the redundant parts were deleted reducing the expression plasmid size to 3392 bp, which improved the electroporation efficiency about 4 times. As a result, the highest expression level of RFP was enhanced, and the L-arabinose concentration for expression induction was decreased 20 times.

Conclusions
The R. eutropha T7 expression system provides an efficient platform for protein production and synthetic biology applications.
Viral metagenomic analysis of fecal samples reveals an enteric virome signature in irritable bowel syndrome
Authors: Ansari Mina Hojat , Ebrahimi Mehregan , Fattahi Mohammad Reza , Gardner Michael G. , Safarpour Ali Reza , Faghihi Mohammad Ali , Lankarani Kamran Bagheri 
Published: May 2020

Abstract
Background
Changes in the enteric microbiota have been suggested to contribute to gastrointestinal diseases, including irritable bowel syndrome. Most of the published work is on bacterial dysbiosis with meager data on the role of the virome in irritable bowel syndrome and other gastrointestinal diseases. In the current study, we therefore aimed to investigate the viral community composition of the gut and test for potential dysbiosis linked to irritable bowel syndrome.

Results
A metagenomics analysis on fecal samples of 50 individuals — 30 of whom met the Rome IV criteria for IBS and 20 healthy controls— was conducted. There was a noticeable alteration in viral taxa observed in association with irritable bowel syndrome when compared to healthy individuals — where some eukaryotic viral taxa noticeably prevail over others. We observed a significant decrease in the diversity and abundance of enteric virome particularly in eukaryotic viruses of Megavirales in patients with irritable bowel syndrome.

Conclusions
These findings shed light on a new hypothesis that the alteration of the viral taxa contributes to the pathogenesis of irritable bowel syndrome and related symptoms, and therefore, pave the way for developing a new diagnostic biomarker or anti-viral drugs for the treatment of irritable bowel syndrome.
Troponin I as a mortality marker after lung resection surgery – a prospective cohort study
Authors: Uchoa Ricardo B. , Caramelli Bruno 
Published: May 2020

Abstract
Background
Cardiovascular complications associated with thoracic surgery increase morbidity, mortality, and treatment costs. Elevated cardiac troponin level represents a predictor of complications after non-cardiac surgeries, but its role after thoracic surgeries remains undetermined. The objective of this study was to analyze the relationship between troponin I elevation and morbidity and mortality after one year in patients undergoing lung resection surgery.

Methods
This prospective cohort study evaluated 151 consecutive patients subjected to elective lung resection procedures using conventional and video-assisted thoracoscopic techniques at a University Hospital in Brazil, from July 2012 to November 2015. Preoperative risk stratification was performed using the scores obtained by the American College of Physicians (ACP) and the Society of Cardiology of the state of São Paulo (EMAPO) scoring systems. Troponin I levels were measured in the immediate postoperative period (POi) and on the first and second postoperative days.

Results
Most patients had a low risk for complications according to the ACP (96.7%) and EMAPO (82.8%) scores. Approximately 49% of the patients exhibited increased troponin I (≥0.16 ng/ml), at least once, and 22 (14.6%) died in one year. Multivariate analysis showed that the elevation of troponin I, on the first postoperative day, correlated with a 12-fold increase in mortality risk within one year (HR 12.02, 95% CI: 1.82–79.5; p = 0.01).

Conclusions
In patients undergoing lung resection surgery, with a low risk of complications according to the preoperative evaluation scores, an increase in troponin I levels above 0.16 ng/ml in the first postoperative period correlated with an increase in mortality within one year.
Pharmacological management of modifiable cardiovascular risk factors (blood pressure and lipids) following diagnosis of myocardial infarction, stroke and diabetes: comparison between population-based studies in Russia and Norway
Authors: Cook Sarah , Hopstock Laila A. , Eggen Anne Elise , Bates Katie , Iakunchykova Olena , Kontsevaya Anna , McKee Martin , Schirmer Henrik , Voevoda Michael , Kudryavtsev Alexander V. , Malyutina Sofia , Leon David A. 
Published: May 2020

Abstract
Background
Cardiovascular disease (CVD) mortality is substantially higher in Russia than in neighbouring Norway. We aimed to compare blood pressure- and lipid-lowering medication use and proportion meeting treatment targets between general population samples in the two countries in those with CVD and diabetes.

Methods
The study population was adults aged 40–69 years reporting a diagnosis of myocardial infarction (MI), stroke and/or diabetes participating in cross-sectional population-based studies in Russia (Know Your Heart (KYH) 2015–18 N = 626) and Norway (The Tromsø Study 2015–16 (Tromsø 7) N = 1353). Reported medications were coded according to the 2016 WHO Anatomical Therapeutic Chemical Classification system. Treatment targets were defined using the Joint European Societies guidelines for CVD prevention in clinical practice (2016).

Results
Age- and sex-standardized prevalence of use of lipid-lowering medications was higher in Tromsø 7 for all three conditions with a disproportionately large difference in those reporting MI (+ 48% (95% CI 39, 57%)). Proportion meeting treatment targets for LDL cholesterol was poor in both studies (age- and sex-standardized prevalence of control KYH vs Tromsø 7: MI 5.1% vs 10.1%; stroke 11.6% vs 5.8%; diabetes 24.9% vs 23.3%). Use of antihypertensive medication was higher in KYH for stroke (+ 40% (95% CI 30, 50%)) and diabetes (+ 27% (95% CI 19, 34%)) groups but approximately equal for the MI group (− 1% (95% CI -1, 1%)). Proportion meeting blood pressure targets was lower in KYH vs Tromsø 7 (MI 51.8% vs 76.3%; stroke 49.5% vs 69.6%; diabetes 51.9% vs 63.9%).

Conclusions
We identified different patterns of medication use in people with CVD and diabetes. However despite higher use of lipid-lowering medication in the Norwegian study treatment to target for total cholesterol was poor in both Russian and Norwegian studies. In contrast we found higher levels of use of antihypertensive medications in the Russian study but also that less participants met treatment targets for blood pressure. Further work should investigate what factors are responsible for this seeming paradox and how management of modifiable risk factors for secondary prevention could be improved.
Burden and correlates of atrial fibrillation among hypertensive patients attending a tertiary hospital in Tanzania
Authors: Bhalia Smita , Pallangyo Pedro , Dalidali Abuu , Salum Saada , Kawajika Richard , Kajuna Edna , Kusiima Happiness , Kifai Engerasiya , Kisenge Peter , Waane Tatizo , Janabi Mohamed 
Published: May 2020

AbstractBackgroundAtrial fibrillation (AF) is the most common supra ventricular cardiac arrhythmia, which presents with variety of clinical symptoms. Hypertension increases risk of developing Atrial fibrillation by 1.5 fold. Together Atrial fibrillation and hypertension doubles the risk of morbidity and mortality. We aimed to determine the prevalence of AF and describe associated factors among hypertensive patients attending tertiary hospital in Tanzania.MethodsA cross-sectional hospital-based study, involving 391 hypertensive patients visiting the Jakaya Kikwete Cardiac Institute was conducted between October to December 2017. Categorical variables were analyzed using chi square while student t- test was used to analyze continuous variables. Multivariate logistic regression analysis was performed to determine factors associated with AF. All analysis was two sided and p- value of < 0.05 was used to be not significant.ResultsAF was detected in 40 (10.2%) patients. Atrial fibrillation was associated with BMI ≥ 25 (OR 4.4, 95% CI 1.1–7.7,p-value 0.02), ejection fraction < 50% (OR 3.0, 95%CI 1.1–8.2, p-value 0.03), Left Atrial diameter > 40 mm (OR 9.4,95%CI 2.1–43.2, p-value < 0.01) and eGFR< 60 (OR 2.9, 95%CI 1.1–7.8, p-value 0.04).ConclusionAtrial fibrillation is considerably prevalent among the hypertensive sub-population. Prompt diagnosis and timely management is vital to prevent complications and premature mortality.
Potential impacts of the 2017 American College of Cardiology/American Heart Association high blood pressure guideline on Chinese adults and how to address them
Authors: Jiao Yundi , Sun Zhaoqing , Xie Yanxia , Zheng Jia , Li Zhao , Guo Xiaofan , Dai Yue , Zheng Liqiang , Sun Yingxian 
Published: May 2020

Abstract
Background
The current analysis was performed to estimate the percentage and number of Chinese adults with hypertension and the percentage and number of Chinese adults recommended to receive pharmacological antihypertensive treatment according to the 2017 American College of Cardiology/American Heart Association (ACC/AHA) guideline compared with the same parameters according to the 2010 Chinese guideline.

Methods
We used 2011 data from the China Health and Nutrition Survey (CHNS). A total of 12,499 Chinese adults aged ≥18 years with complete blood pressure (BP) values were selected for the present analysis.

Results
The crude prevalence rates (95% CI) of hypertension according to the definitions from the 2017 ACC/AHA guideline and the 2010 Chinese guideline were 58.0% (57.2 to 58.9%) and 25.4% (24.7 to 26.2%), respectively. Moreover, the percentage of the participants recommended to take antihypertensive medications were 31.5 and 28.8%, respectively. Among adults who took antihypertensive medications, 88.8% had above-goal BP levels compared to 53.3%. Overall, 613.3 million Chinese adults (aged ≥18 years) met the criteria for hypertension according to the 2017 ACC/AHA guideline, and 267.7 million met the criteria according to 2010 Chinese guideline. An additional 28.4 million (2.7%) Chinese adults were recommended to take antihypertensive medication.

Conclusions
The present analysis revealed that the 2017 ACC/AHA hypertension guideline will result in a substantial increase in the percentage and number of Chinese adults defined as having hypertension and a small increase in the percentage of adults who are recommended to take antihypertensive medications compared to the same parameters based on the 2010 Chinese guideline. More intensive management and antihypertensive medications use are suggested to improve the control rate of hypertension among Chinese adults.
Prevalence of self-reported coronary heart disease and its associated risk factors in Tabari cohort population
Authors: Ghaemian Ali , Nabati Maryam , Saeedi Majid , Kheradmand Motahareh , Moosazadeh Mahmood 
Published: May 2020

Abstract
Background
Prevalence of coronary heart disease (CHD) risk factors are increasing in developing countries. The present study aimed to assess the prevalence of self-reported CHD and evaluate the role of various risk factors on its prevalence in the Tabari cohort study (TCS) population.

Methods
The enrollment phase of TCS was performed between June 2015 and November 2017. In the current study, data were derived from information collecting from the enrollment phase of TCS. In the enrollment phase, 10,255 individuals aged 35–70 living in urban and mountainous areas of Sari (northern part of Iran) were entered into the study. Educational level, socioeconomic and marital status, history of smoking, opium and alcohol abuse/addiction, level of daily physical activity, indices of obesity, and traditional risk factors of the participants were determined.

Results
The prevalence of CHD was measured at 9.2%. Older individuals (P<0.001), people with a body mass index≥30kg/m2 (P<0.001), diabetics (P<0.001), and hypertensive (P<0.001) have been shown to have an increased risk for CHD compared with participants of without CHD. Furthermore, the CHD was more prevalent in individuals with higher waist circumference (P<0.001), higher low-density lipoprotein cholesterol (P<0.001), lower high-density lipoprotein cholesterol (P<0.001), and a higher waist to hip ratio (P<0.001). In addition, individuals with low socioeconomic status, illiterate people, and opium users had a higher prevalence of CHD (P<0.001). The results of the multivariable logistic regression analysis showed that the probability of CHD among individuals who had 8-10 risk factors was estimated at 8.41 (95% confidence interval: 5.75-12.31) times higher than those with less than 3 risk factors.

Conclusion
According to the results of the present study, it seems that the prevalence of CHD in the Iranian population is relatively high.
Frequently repeated measurements -our experience of collecting data with SMS
Authors: Axén I. , Jensen I. , Butler Forslund E. , Grahn B. , Jørgensen V. , Opava C. H. , Bodin L. 
Published: May 2020

Abstract
Background
As technology is advancing, so are the possibilities for new data collection methods in research, potentially improving data quality and validity of the results. In Sweden, a system using frequent repeated data collection using text messages, SMS Track, has been used in clinical research for more than a decade. In this paper, compliance with repeated text message questions was examined across five different studies, i.e. if compliance was
1: associated with study-specific factors (age or gender of the subjects, the condition, its’ severity or course, i.e. improvement, relapse or steady state) and/or.
2: associated with the methodology itself (the question being asked, the frequency and number of questions, duration of data collection, initial compliance or the management of the system).

Methods
Descriptive comparisons were done across five studies. Three studies were collecting weekly responses over at least 52 weeks (“Weekly studies”) and were used to investigate the effect of age, sex and pain severity on compliance, the effect of early compliance for late compliance, and finally the early occurrence of two successive weeks with non-compliance.

Result
Compliance was excellent across all five studies, and only influenced somewhat by age, sex and pain-level. The factor “study” remained significant in the final model thus the observed differences may be a result of the conditions studied but does not seem to be attributable to severity or development of these conditions. Number and frequency of questions did not influence compliance, nor did study duration.

Conclusions
Compliance was excellent in the included studies and was not affected by population factors. However, differences in compliance were observed that cannot be easily explained and warrant further investigation. In particular, the nature of the variables or the management of the study are potential areas for further investigations.