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https://www.readbyqxmd.com/read/28443105/identification-of-microrna-targets-of-capsicum-spp-using-mirtrans-a-trans-omics-approach
#1
Lu Zhang, Cheng Qin, Junpu Mei, Xiaocui Chen, Zhiming Wu, Xirong Luo, Jiaowen Cheng, Xiangqun Tang, Kailin Hu, Shuai C Li
The microRNA (miRNA) can regulate the transcripts that are involved in eukaryotic cell proliferation, differentiation, and metabolism. Especially for plants, our understanding of miRNA targets, is still limited. Early attempts of prediction on sequence alignments have been plagued by enormous false positives. It is helpful to improve target prediction specificity by incorporating the other data sources such as the dependency between miRNA and transcript expression or even cleaved transcripts by miRNA regulations, which are referred to as trans-omics data...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28442458/circulating-micrornas-in-delayed-cerebral-infarction-after-aneurysmal-subarachnoid-hemorrhage
#2
Gang Lu, Man Sze Wong, Mark Zhi Qiang Xiong, Chi Kwan Leung, Xian Wei Su, Jing Ye Zhou, Wai Sang Poon, Vera Zhi Yuan Zheng, Wai Yee Chan, George Kwok Chu Wong
BACKGROUND: Delayed cerebral infarction (DCI) is a major cause of morbidities after aneurysmal subarachnoid hemorrhage (SAH) and typically starts at day 4 to 7 after initial hemorrhage. MicroRNAs (miRNAs) play an important role in posttranscriptional gene expression control, and distinctive patterns of circulating miRNA changes have been identified for some diseases. We aimed to investigate miRNAs that characterize SAH patients with DCI compared with those without DCI. METHODS AND RESULTS: Circulating miRNAs were collected on day 7 after SAH in healthy, SAH-free controls (n=20), SAH patients with DCI (n=20), and SAH patients without DCI (n=20)...
April 25, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28438294/a-model-using-concomitant-markers-for-predicting-outcome-in-human-papillomavirus-positive-oropharyngeal-cancer
#3
Cinzia Bersani, Michael Mints, Nikolaos Tertipis, Linnea Haeggblom, Lars Sivars, Andreas Ährlund-Richter, Andrea Vlastos, Cecilia Smedberg, Nathalie Grün, Eva Munck-Wikland, Anders Näsman, Torbjörn Ramqvist, Tina Dalianis
OBJECTIVE: Head-neck cancer therapy has become intensified. With radiotherapy alone, 3-year disease-free survival (DFS) is 80% for HPV-positive TSCC/BOTSCC and better for patients with favorable characteristics, suggesting therapy could be tapered for some, decreasing side-effects. Therefore, we built a model to predict progression-free survival for patients with HPV-positive TSCC and BOTSCC. MATERIAL AND METHODS: TSCC/BOTSCC patients treated curatively between 2000 and 2011, with HPV16 DNA/E7 mRNA positive tumors examined for CD8(+) TILs, HPV16 mRNA and HLA class I expression were included...
May 2017: Oral Oncology
https://www.readbyqxmd.com/read/28435825/assessment-of-the-efficiency-of-hospitals-before-and-after-the-implementation-of-health-sector-evolution-plan-in-iran-based-on-pabon-lasso-model
#4
Ghobad Moradi, Bakhtiar Piroozi, Hossein Safari, Nader Esmail Nasab, Amjad Mohamadi Bolbanabad, Arezoo Yari
BACKGROUND: Pabon Lasso model was applied to assess the relative performance of hospitals affiliated to Kurdistan University of Medical Sciences (KUMS) before and after the implementation of Health Sector Evolution Plan (HSEP) in Iran. METHODS: This cross-sectional study was carried out in 11 public hospitals affiliated to KUMS in 2015. Twelve months before and after the implementation of the first phase of HSEP, a checklist was used to collect data from computerized databases within the hospitals' admission and discharge units...
March 2017: Iranian Journal of Public Health
https://www.readbyqxmd.com/read/28426817/evaluation-of-machine-learning-algorithms-and-structural-features-for-optimal-mri-based-diagnostic-prediction-in-psychosis
#5
Raymond Salvador, Joaquim Radua, Erick J Canales-Rodríguez, Aleix Solanes, Salvador Sarró, José M Goikolea, Alicia Valiente, Gemma C Monté, María Del Carmen Natividad, Amalia Guerrero-Pedraza, Noemí Moro, Paloma Fernández-Corcuera, Benedikt L Amann, Teresa Maristany, Eduard Vieta, Peter J McKenna, Edith Pomarol-Clotet
A relatively large number of studies have investigated the power of structural magnetic resonance imaging (sMRI) data to discriminate patients with schizophrenia from healthy controls. However, very few of them have also included patients with bipolar disorder, allowing the clinically relevant discrimination between both psychotic diagnostics. To assess the efficacy of sMRI data for diagnostic prediction in psychosis we objectively evaluated the discriminative power of a wide range of commonly used machine learning algorithms (ridge, lasso, elastic net and L0 norm regularized logistic regressions, a support vector classifier, regularized discriminant analysis, random forests and a Gaussian process classifier) on main sMRI features including grey and white matter voxel-based morphometry (VBM), vertex-based cortical thickness and volume, region of interest volumetric measures and wavelet-based morphometry (WBM) maps...
2017: PloS One
https://www.readbyqxmd.com/read/28425082/discriminating-between-positional-and-non-positional-obstructive-sleep-apnea-using-some-clinical-characteristics
#6
Abderrahim Oulhaj, Sharina Al Dhaheri, Brenda Bin Su, Mohammed Al-Houqani
PURPOSE: The primary objective of this paper was to identify significant factors associated with positional Obstructive Sleep Apnea (POSA) and to provide a clinical tool for discriminating non positional from POSA. Secondary objectives were about estimating the prevalence of POSA, comparing the polysomnographic variables across POSA and non-POSA patients. METHODS: This was a cross sectional study on 278 patients who completed an overnight sleep study for OSA assessment...
April 19, 2017: Sleep & Breathing, Schlaf & Atmung
https://www.readbyqxmd.com/read/28424602/assessing-the-driver-s-current-level-of-working-memory-load-with-high-density-functional-near-infrared-spectroscopy-a-realistic-driving-simulator-study
#7
Anirudh Unni, Klas Ihme, Meike Jipp, Jochem W Rieger
Cognitive overload or underload results in a decrease in human performance which may result in fatal incidents while driving. We envision that driver assistive systems which adapt their functionality to the driver's cognitive state could be a promising approach to reduce road accidents due to human errors. This research attempts to predict variations of cognitive working memory load levels in a natural driving scenario with multiple parallel tasks and to reveal predictive brain areas. We used a modified version of the n-back task to induce five different working memory load levels (from 0-back up to 4-back) forcing the participants to continuously update, memorize, and recall the previous 'n' speed sequences and adjust their speed accordingly while they drove for approximately 60 min on a highway with concurrent traffic in a virtual reality driving simulator...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28424482/logistic-bayesian-lasso-for-genetic-association-analysis-of-data-from-complex-sampling-designs
#8
Yuan Zhang, Jonathan N Hofmann, Mark P Purdue, Shili Lin, Swati Biswas
Detecting gene-environment interactions with rare variants is critical in dissecting the etiology of common diseases. Interactions with rare haplotype variants (rHTVs) are of particular interest. At the same time, complex sampling designs, such as stratified random sampling, are becoming increasingly popular for designing case-control studies, especially for recruiting controls. The US Kidney Cancer Study (KCS) is an example, wherein all available cases were included while the controls at each site were randomly selected from the population by frequency matching with cases based on age, sex and race...
April 20, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28422149/monitoring-seasonal-influenza-epidemics-by-using-internet-search-data-with-an-ensemble-penalized-regression-model
#9
Pi Guo, Jianjun Zhang, Li Wang, Shaoyi Yang, Ganfeng Luo, Changyu Deng, Ye Wen, Qingying Zhang
Seasonal influenza epidemics cause serious public health problems in China. Search queries-based surveillance was recently proposed to complement traditional monitoring approaches of influenza epidemics. However, developing robust techniques of search query selection and enhancing predictability for influenza epidemics remains a challenge. This study aimed to develop a novel ensemble framework to improve penalized regression models for detecting influenza epidemics by using Baidu search engine query data from China...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28401970/integrating-multiple-omics-data-for-the-discovery-of-potential-beclin-1-interactions-in-breast-cancer
#10
Yi Chen, Xuan Wang, Guan Wang, Zhaozhi Li, Jinjin Wang, Lingyu Huang, Ziyi Qin, Xiang Yuan, Zhong Cheng, Shu Zhang, Yiqiong Yin, Jun He
Breast cancer has been reported as one of the most frequently diagnosed malignant diseases and the leading cause of cancer death in women all around the world. Furthermore, this complicated cancer is divided into multiple subtypes which present different clinical symptoms and need correspondingly directed therapy. We took BECN1, a core gene in autophagy performing a tumor inhibitory effect, as a starting point. The study in this paper aims to identify genes related to breast cancer and its multiple subtypes by integrating multiple omics data using the least absolute shrinkage and selection operator (LASSO), which is a statistical method that can integrate more than two types of omics data...
April 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28396994/identifying-the-white-matter-impairments-among-art-na%C3%A3-ve-hiv-patients-a-multivariate-pattern-analysis-of-dti-data
#11
Zhenchao Tang, Zhenyu Liu, Ruili Li, Xin Yang, Xingwei Cui, Shuo Wang, Dongdong Yu, Hongjun Li, Enqing Dong, Jie Tian
OBJECTIVE: To identify the white matter (WM) impairments of the antiretroviral therapy (ART)-naïve HIV patients by conducting a multivariate pattern analysis (MVPA) of Diffusion Tensor Imaging (DTI) data METHODS: We enrolled 33 ART-naïve HIV patients and 32 Normal controls in the current study. Firstly, the DTI metrics in whole brain WM tracts were extracted for each subject and feed into the Least Absolute Shrinkage and Selection Operators procedure (LASSO)-Logistic regression model to identify the impaired WM tracts...
April 10, 2017: European Radiology
https://www.readbyqxmd.com/read/28389671/identification-of-a-six-lncrna-signature-associated-with-recurrence-of-ovarian-cancer
#12
Kai Yang, Yan Hou, Ang Li, Zhenzi Li, Wenjie Wang, Hongyu Xie, Zhiwei Rong, Ge Lou, Kang Li
Ovarian cancer (OvCa) is the leading cause of death among all gynecological malignancies, and recurrent OvCa is almost always incurable. In this study, we developed a signature based on long non-coding RNAs (lncRNAs) associated with OvCa recurrence to facilitate personalized OvCa therapy. lncRNA expression data were extracted from GSE9891 and GSE30161. LASSO (least absolute shrinkage and selection operator) penalized regression was used to identify an lncRNA-based signature using the GSE9891 training cohort...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28382466/using-a-system-of-differential-equations-that-models-cattle-growth-to-uncover-the-genetic-basis-of-complex-traits
#13
Mateus Castelani Freua, Miguel Henrique de Almeida Santana, Ricardo Vieira Ventura, Luis Orlindo Tedeschi, José Bento Sterman Ferraz
The interplay between dynamic models of biological systems and genomics is based on the assumption that genetic variation of the complex trait (i.e., outcome of model behavior) arises from component traits (i.e., model parameters) in lower hierarchical levels. In order to provide a proof of concept of this statement for a cattle growth model, we ask whether model parameters map genomic regions that harbor quantitative trait loci (QTLs) already described for the complex trait. We conducted a genome-wide association study (GWAS) with a Bayesian hierarchical LASSO method in two parameters of the Davis Growth Model, a system of three ordinary differential equations describing DNA accretion, protein synthesis and degradation, and fat synthesis...
April 5, 2017: Journal of Applied Genetics
https://www.readbyqxmd.com/read/28379528/a-reliable-grading-system-for-prediction-of-chronic-subdural-hematoma-recurrence-requiring-reoperation-after-initial-burr-hole-surgery
#14
Milo Stanišic, Are Hugo Pripp
BACKGROUND: There is no widely adopted grading system for the prediction of postoperative recurrence requiring reoperation (RrR) in patients with chronic subdural hematoma (CSDH). OBJECTIVE: We developed a CSDH grading system to predict RrR based on predictive characteristics that can be objectively assessed at the time of first presentation and initial surgery. METHODS: Prospectively collected data from 107 consecutive surgical patients with CSDH were reviewed...
March 30, 2017: Neurosurgery
https://www.readbyqxmd.com/read/28365450/a-microrna-expression-profile-for-vascular-invasion-can-predict-overall-survival-in-hepatocellular-carcinoma
#15
Zhuo Lin, Yi-Jing Cai, Rui-Cong Chen, Bi-Cheng Chen, Liang Zhao, Shi-Hao Xu, Xiao-Dong Wang, Mei Song, Jian-Min Wu, Yu-Qun Wang, Meng-Tao Zhou, Ke-Qing Shi
BACKGROUND: The presence of vascular invasion (VI) in pathology specimens is a well-known unfavorable prognostic factor of hepatocellular carcinoma (HCC) recurrence and overall survival (OS). We investigated the vascular invasion related microRNA (miRNA) expression profiles and potential of prognostic value in HCC. METHODS: MiRNA and mRNA expression data for HCC were accessed from The Cancer Genome Atlas (TCGA). LASSO logistic regression models were used to develop a miRNA-based classifier for predicting VI...
March 30, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28357879/a-comparative-investigation-of-the-combined-effects-of-pre-processing-wavelength-selection-and-regression-methods-on-near-infrared-calibration-model-performance
#16
Jian Wan, Yi-Chieh Chen, A Julian Morris, Suresh N Thennadil
Near-infrared (NIR) spectroscopy is being widely used in various fields ranging from pharmaceutics to the food industry for analyzing chemical and physical properties of the substances concerned. Its advantages over other analytical techniques include available physical interpretation of spectral data, nondestructive nature and high speed of measurements, and little or no need for sample preparation. The successful application of NIR spectroscopy relies on three main aspects: pre-processing of spectral data to eliminate nonlinear variations due to temperature, light scattering effects and many others, selection of those wavelengths that contribute useful information, and identification of suitable calibration models using linear/nonlinear regression ...
January 1, 2017: Applied Spectroscopy
https://www.readbyqxmd.com/read/28349554/regularized-regression-analysis-of-digitized-molecular-structures-in-organic-reactions-for-quantification-of-steric-effects
#17
Shigeru Yamaguchi, Takahiro Nishimura, Yuta Hibe, Masaki Nagai, Hirofumi Sato, Ian Johnston
In organic chemistry, Comparative Molecular Field Analysis (CoMFA) can be defined as a regression analysis between reaction outcomes and molecular fields, wherein we can extract and visualize important structural information from the coefficients of the constructed regression models. In CoMFA, partial least-squares (PLS) regression, which determines all coefficients in the model, is used for fitting the regression models. However, in organic reactions, steric effects are observed only near the reactive site, indicating that a large number of regression coefficients in the CoMFA of organic reactions should be assigned as 0...
March 27, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28344431/control-engineering-methods-for-the-design-of-robust-behavioral-treatments
#18
Korkut Bekiroglu, Constantino Lagoa, Suzan A Murphy, Stephanie T Lanza
In this paper, a robust control approach is used to address the problem of adaptive behavioral treatment design. Human behavior (e.g., smoking and exercise) and reactions to treatment are complex and depend on many unmeasurable external stimuli, some of which are unknown. Thus, it is crucial to model human behavior over many subject responses. We propose a simple (low order) uncertain affine model subject to uncertainties whose response covers the most probable behavioral responses. The proposed model contains two different types of uncertainties: uncertainty of the dynamics and external perturbations that patients face in their daily life...
May 2017: IEEE Transactions on Control Systems Technology: a Publication of the IEEE Control Systems Society
https://www.readbyqxmd.com/read/28343409/development-of-a-prediction-model-for-post-concussive-symptoms-following-mild-traumatic-brain-injury-a-track-tbi-pilot-study
#19
Maryse C Cnossen, Ethan A Winkler, John K Yue, David O Okonkwo, Alex Valadka, Ewout W Steyerberg, Hester Lingsma, Geoffrey T Manley
Post-concussive symptoms occur frequently after mild traumatic brain injury (mTBI) and may be categorized as cognitive, somatic, or emotional. We aimed to: 1) assess whether patient demographics and clinical variables predict development of each of these three symptom categories, and 2) develop a prediction model for six-month post-concussive symptoms. MTBI patients (Glasgow Coma Scale score 13-15) from the prospective multicenter Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Pilot study (2010-2012) who completed the Rivermead Post-Concussion Symptoms Questionnaire (RPQ) at six-months post-injury were included...
March 27, 2017: Journal of Neurotrauma
https://www.readbyqxmd.com/read/28342127/robotic-single-site-plus-one-port-distal-pancreatectomy
#20
Sung Hyun Kim, Chang Moo Kang, Woo Jung Lee
Laparoscopic distal pancreatectomy is regarded as safe and effective surgical approach in benign and low-grade malignant tumor of the pancreas. With the advances of laparoscopic techniques and instruments, many efforts to reduce the number of the trocar site has been made. There are a few available surgical techniques of laparoscopic single-site (single port or reduced port) distal pancreatectomy, suggesting its safety and feasibility. However, it is true that laparoscopic single-site distal pancreatectomy is difficult and technically quite demanding...
March 24, 2017: Surgical Endoscopy
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