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Heewon Park, Atsushi Niida, Seiya Imoto, Satoru Miyano
Driver gene selection is crucial to understand the heterogeneous system of cancer. To identity cancer driver genes, various statistical strategies have been proposed, especially the L1-type regularization methods have drawn a large amount of attention. However, the statistical approaches have been developed purely from algorithmic and statistical point, and the existing studies have applied the statistical approaches to genomic data analysis without consideration of biological knowledge. We consider a statistical strategy incorporating biological knowledge to identify cancer driver gene...
October 19, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Johanna Freese, Mihaela Pricop-Jeckstadt, Thorsten Heuer, Matthias Clemens, Heiner Boeing, Sven Knüppel, Ute Nöthlings
Next to the information on frequency of food consumption, information on consumption-day amounts is important to estimate usual dietary intake in epidemiological studies. Our objective was to identify determinants of consumption-day amounts to derive person-specific standard consumption-day amounts applicable for the estimation of usual dietary intake using separate sources to assesss information on consumption probability and amount consumed. 24-h Dietary recall data from the German National Nutrition Survey II (n = 8522; aged 20-80 years) conducted between 2005 and 2007 were analysed for determinants of consumption-day amounts of thirty-eight food and beverage groups using LASSO variable selection for linear mixed-effects models...
2016: Journal of Nutritional Science
Shaozhou Zhu, Christopher D Fage, Julian D Hegemann, Andreas Mielcarek, Dushan Yan, Uwe Linne, Mohamed A Marahiel
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with a unique lariat knot-like fold that endows them with extraordinary stability and biologically relevant activity. However, the biosynthetic mechanism of these fascinating molecules remains largely speculative. Generally, two enzymes (B for processing and C for cyclization) are required to assemble the unusual knot-like structure. Several subsets of lasso peptide gene clusters feature a "split" B protein on separate open reading frames (B1 and B2), suggesting distinct functions for the B protein in lasso peptide biosynthesis...
October 18, 2016: Scientific Reports
Luisa Matos Do Canto, Catalin Marian, Rency S Varghese, Jaeil Ahn, Patricia A Da Cunha, Shawna Willey, Mary Sidawy, Janice D Rone, Amrita K Cheema, George Luta, Mohammad R Nezami Ranjbar, Habtom W Ressom, Bassem R Haddad
Identification of new biomarkers for breast cancer remains critical in order to enhance early detection of the disease and improve its prognosis. Towards this end, we performed an untargeted metabolomic analysis of breast ductal fluid using an ultra-performance liquid chromatography coupled with a quadrupole time-of-light (UPLC-QTOF) mass spectrometer. We investigated the metabolomic profiles of breast tumors using ductal fluid samples collected by ductal lavage (DL). We studied fluid from both the affected breasts and the unaffected contralateral breasts (as controls) from 43 women with confirmed unilateral breast cancer...
October 13, 2016: International Journal of Oncology
Cao Xiao, Jesse Bledsoe, Shouyi Wang, Wanpracha Art Chaovalitwongse, Sonya Mehta, Margaret Semrud-Clikeman, Thomas Grabowski
Today, diagnosis of attention deficit hyperactivity disorder (ADHD) still primarily relies on a series of subjective evaluations that highly rely on a doctor's experiences and intuitions from diagnostic interviews and observed behavior measures. An accurate and objective diagnosis of ADHD is still a challenge and leaves much to be desired. Many children and adults are inappropriately labeled with ADHD conditions, whereas many are left undiagnosed and untreated. Recent advances in neuroimaging studies have enabled us to search for both structural (e...
September 2016: Brain Informatics
Steffi Kopprasch, Srirangan Dheban, Kai Schuhmann, Aimin Xu, Klaus-Martin Schulte, Charmaine J Simeonovic, Peter E H Schwarz, Stefan R Bornstein, Andrej Shevchenko, Juergen Graessler
OBJECTIVE: Glucolipotoxicity is a major pathophysiological mechanism in the development of insulin resistance and type 2 diabetes mellitus (T2D). We aimed to detect subtle changes in the circulating lipid profile by shotgun lipidomics analyses and to associate them with four different insulin sensitivity indices. METHODS: The cross-sectional study comprised 90 men with a broad range of insulin sensitivity including normal glucose tolerance (NGT, n = 33), impaired glucose tolerance (IGT, n = 32) and newly detected T2D (n = 25)...
2016: PloS One
Sachia J Traving, Mikkel Bentzon-Tilia, Helle Knudsen-Leerbeck, Mustafa Mantikci, Jørgen L S Hansen, Colin A Stedmon, Helle Sørensen, Stiig Markager, Lasse Riemann
Bacterioplankton play a key role in marine waters facilitating processes important for carbon cycling. However, the influence of specific bacterial populations and environmental conditions on bacterioplankton community performance remains unclear. The aim of the present study was to identify drivers of bacterioplankton community functions, taking into account the variability in community composition and environmental conditions over seasons, in two contrasting coastal systems. A Least Absolute Shrinkage and Selection Operator (LASSO) analysis of the biological and chemical data obtained from surface waters over a full year indicated that specific bacterial populations were linked to measured functions...
2016: Frontiers in Microbiology
Ye Wen, Fu-Hua Pi, Pi Guo, Wen-Ya Dong, Yu-Qing Xie, Xiang-Yu Wang, Fang-Fang Xia, Shao-Jie Pang, Yan-Chun Wu, Yuan-Yuan Wang, Qing-Ying Zhang
Sleep habits are associated with stroke in western populations, but this relation has been rarely investigated in China. Moreover, the differences among stroke subtypes remain unclear. This study aimed to explore the associations of total stroke, including ischemic and hemorrhagic type, with sleep habits of a population in southern China. We performed a case-control study in patients admitted to the hospital with first stroke and community control subjects. A total of 333 patients (n = 223, 67.0%, with ischemic stroke; n = 110, 23...
October 4, 2016: Scientific Reports
Mark Schiffman, Kai Yu, Rosemary Zuna, S Terence Dunn, Han Zhang, Joan Walker, Michael Gold, Noorie Hyun, Greg Rydzak, Hormuzd A Katki, Nicolas Wentzensen
A challenge in implementation of sensitive HPV-based screening is limiting unnecessary referrals to colposcopic biopsy. We combined two commonly recommended triage methods: partial HPV typing and "reflex" cytology, evaluating the possibility of automated cytology. This investigation was based on 1,178 exfoliated cervical specimens collected during the enrollment phase of The Study to Understand Cervical Cancer Early Endpoints and Determinants (SUCCEED, Oklahoma City, OK). We chose a colposcopy clinic population to maximize number of outcomes, for this proof-of-principle cross-sectional study...
October 1, 2016: International Journal of Cancer. Journal International du Cancer
Loic Yengo, Abdelilah Arredouani, Michel Marre, Ronan Roussel, Martine Vaxillaire, Mario Falchi, Abdelali Haoudi, Jean Tichet, Beverley Balkau, Amélie Bonnefond, Philippe Froguel
OBJECTIVE: Characterizing specific metabolites in sub-clinical phases preceding the onset of type 2 diabetes to enable efficient preventive and personalized interventions. RESEARCH DESIGN AND METHODS: We developed predictive models of type 2 diabetes using two strategies. One strategy focused on the probability of incidence only and was based on logistic regression (MRS1); the other strategy accounted for the age at diagnosis of diabetes and was based on Cox regression (MRS2)...
October 2016: Molecular Metabolism
Joshua S Niedzielski, Jinzhong Yang, Zhongxing Liao, Daniel R Gomez, Francesco Stingo, Radhe Mohan, Mary K Martel, Tina M Briere, Laurence E Court
PURPOSE: We sought to investigate the ability of mid-treatment (18)F-fluorodeoxyglucose positron emission tomography (PET) studies to objectively and spatially quantify esophageal injury in vivo from radiation therapy for non-small cell lung cancer. METHODS AND MATERIALS: This retrospective study was approved by the local institutional review board, with written informed consent obtained before enrollment. We normalized (18)F-fluorodeoxyglucose PET uptake to each patient's low-irradiated region (<5 Gy) of the esophagus, as a radiation response measure...
November 1, 2016: International Journal of Radiation Oncology, Biology, Physics
Yaohui Zeng, Patrick Breheny
Discovering important genes that account for the phenotype of interest has long been a challenge in genome-wide expression analysis. Analyses such as gene set enrichment analysis (GSEA) that incorporate pathway information have become widespread in hypothesis testing, but pathway-based approaches have been largely absent from regression methods due to the challenges of dealing with overlapping pathways and the resulting lack of available software. The R package grpreg is widely used to fit group lasso and other group-penalized regression models; in this study, we develop an extension, grpregOverlap, to allow for overlapping group structure using a latent variable approach...
2016: Cancer Informatics
Maggie Haitian Wang, Ka Chun Chong, Malina Storer, John W Pickering, Zoltan H Endre, Steven Yf Lau, Chloe Kwok, Maria Lai, Hau Yin Chung, Benny Chung Ying Zee
Selected ion flow tube-mass spectrometry (SIFT-MS) provides rapid, non-invasive measurements of a full-mass scan of volatile compounds in exhaled breath. Although various studies have suggested that breath metabolites may be indicators of human disease status, many of these studies have included few breath samples and large numbers of compounds, limiting their power to detect significant metabolites. This study employed a least absolute shrinkage and selective operator (LASSO) approach to SIFT-MS data of breath samples to preliminarily evaluate the ability of exhaled breath findings to monitor the efficacy of dialysis in hemodialysis patients...
2016: Journal of Breath Research
Xiao-Fei Zhang, Le Ou-Yang, Xing-Ming Zhao, Hong Yan
Understanding how the structure of gene dependency network changes between two patient-specific groups is an important task for genomic research. Although many computational approaches have been proposed to undertake this task, most of them estimate correlation networks from group-specific gene expression data independently without considering the common structure shared between different groups. In addition, with the development of high-throughput technologies, we can collect gene expression profiles of same patients from multiple platforms...
September 28, 2016: Scientific Reports
H Brastianos, T Vaughan, M Westerland, A Lasso, J Gooding, G Fichtinger, C B Falkson
No abstract text is available yet for this article.
October 1, 2016: International Journal of Radiation Oncology, Biology, Physics
Kevin Lamote, Matthijs Vynck, Joris Van Cleemput, Olivier Thas, Kristiaan Nackaerts, Jan P van Meerbeeck
Malignant pleural mesothelioma (MPM) is predominantly caused by previous asbestos exposure. Diagnosis often happens in advanced stages restricting any therapeutic perspectives. Early stage detection via breath analysis was explored using multicapillary column/ion mobility spectrometry (MCC/IMS) to detect volatile organic compounds (VOCs) in the exhaled breath of MPM patients in comparison to former occupational asbestos-exposed and non-exposed controls. Breath and background samples of 23 MPM patients, 22 asymptomatic former asbestos (AEx) workers and 21 healthy non-asbestos exposed persons were taken for analysis...
2016: Journal of Breath Research
An-Min Tang, Xingqiu Zhao, Nian-Sheng Tang
This paper presents a novel semiparametric joint model for multivariate longitudinal and survival data (SJMLS) by relaxing the normality assumption of the longitudinal outcomes, leaving the baseline hazard functions unspecified and allowing the history of the longitudinal response having an effect on the risk of dropout. Using Bayesian penalized splines to approximate the unspecified baseline hazard function and combining the Gibbs sampler and the Metropolis-Hastings algorithm, we propose a Bayesian Lasso (BLasso) method to simultaneously estimate unknown parameters and select important covariates in SJMLS...
September 26, 2016: Biometrical Journal. Biometrische Zeitschrift
Milos Jovanovic, Sandro Radovanovic, Milan Vukicevic, Sven Van Poucke, Boris Delibasic
OBJECTIVES: Quantification and early identification of unplanned readmission risk have the potential to improve the quality of care during hospitalization and after discharge. However, high dimensionality, sparsity, and class imbalance of electronic health data and the complexity of risk quantification, challenge the development of accurate predictive models. Predictive models require a certain level of interpretability in order to be applicable in real settings and create actionable insights...
September 2016: Artificial Intelligence in Medicine
Chuyang Ye, Jerry L Prince
Diffusion magnetic resonance imaging (dMRI) can be used for noninvasive imaging of white matter tracts. Using fiber tracking, which propagates fiber streamlines according to fiber orientations (FOs) computed from dMRI, white matter tracts can be reconstructed for investigation of brain diseases and the brain connectome. Because of image noise, probabilistic tractography has been proposed to characterize uncertainties in FO estimation. Bootstrap provides a nonparametric approach to the estimation of FO uncertainties and residual bootstrap has been used for developing probabilistic tractography...
September 16, 2016: Medical Image Analysis
Yi Dong, Chang-Jie Zhang, Jie Shi, Jinggui Deng, Chun-Na Lan
This study was aimed to identify and evaluate the International Classification of Functioning (ICF) key codes for dysphagia in stroke patients. Thirty patients with dysphagia after stroke were enrolled in our study. To evaluate the ICF dysphagia scale, 6 scales were used as comparisons, namely the Barthel Index (BI), Repetitive Saliva Swallowing Test (RSST), Kubota Water Swallowing Test (KWST), Frenchay Dysarthria Assessment, Mini-Mental State Examination (MMSE), and the Montreal Cognitive Assessment (MoCA)...
September 2016: Medicine (Baltimore)
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