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Clément Niel, Christine Sinoquet, Christian Dina, Ghislain Rocheleau
Motivation: Large scale genome-wide association studies (GWAS) are tools of choice for discovering associations between genotypes and phenotypes. To date, many studies rely on univariate statistical tests for association between the phenotype and each assayed single nucleotide polymorphism (SNP). However, interaction between SNPs, namely epistasis, must be considered when tackling the complexity of underlying biological mechanisms. Epistasis analysis at large scale entails a prohibitive computational burden when addressing the detection of more than two interacting SNPs...
March 14, 2018: Bioinformatics
Alberto Perez, Florian Sittel, Gerhard Stock, Ken A Dill
The molecular actions of proteins occur along reaction coordinates. Current computer methods have limited ability to explore them. We describe a fast protocol called MELD-path that: (1) efficiently samples relevant conformational states via MELD, an accelerator of Molecular Dynamics (MD), (2) seeds multiple short MD trajectories from MELD states, then (3) constructs Markov State Models (MSM) that give the routes and kinetics. We tested the method against extensive (multi μs) MD simulations of the right-handed- to left-handed-helix transition of a 9-mer peptide of AIB, the symmetry of which allows us to establish convergence...
March 16, 2018: Journal of Chemical Theory and Computation
Ayori Mitsutake, Hiroshi Takano
Molecular dynamics simulation is a powerful method for investigating the structural stability, dynamics, and function of biopolymers at the atomic level. In recent years, it has become possible to perform simulations on time scales of the order of milliseconds using special hardware. However, it is necessary to derive the important factors contributing to structural change or function from the complicated movements of biopolymers obtained from long simulations. Although some analysis methods for protein systems have been developed using increasing simulation times, many of these methods are static in nature (i...
March 15, 2018: Biophysical Reviews
Edward W Gregg, Ji Lin, Barbara Bardenheier, Haiying Chen, W Jack Rejeski, Xiaohui Zhuo, Andrea L Hergenroeder, Stephen B Kritchevsky, Anne L Peters, Lynne E Wagenknecht, Edward H Ip, Mark A Espeland
OBJECTIVE: The impact of weight loss intervention on disability-free life expectancy in adults with diabetes is unknown. We examined the impact of a long-term weight loss intervention on years spent with and without physical disability. RESEARCH DESIGN AND METHODS: Overweight or obese adults with type 2 diabetes age 45-76 years ( n = 5,145) were randomly assigned to a 10-year intensive lifestyle intervention (ILI) or diabetes support and education (DSE). Physical function was assessed annually for 12 years using the SF-36...
March 15, 2018: Diabetes Care
Fur-Hsing Wen, Jen-Shi Chen, Wen-Chi Chou, Chia-Hsun Hsieh, Wen-Cheng Chang, Ming-Mo Hou, Siew Tzuh Tang
CONTEXT/OBJECTIVES: Our study addressed important knowledge gaps about trajectories of distinct conjoint symptom-functional states, i.e., patterns for different levels of combined symptom distress and functional impairment, over cancer patients' last year and their ability to predict survival. METHODS: We identified distinct symptom-functional states and explored their changes over 317 terminally ill cancer patients' last year by a transition model using hidden Markov modeling...
March 12, 2018: Journal of Pain and Symptom Management
Mathilde Wanneveich, Hélène Jacqmin-Gadda, Jean-François Dartigues, Pierre Joly
No abstract text is available yet for this article.
March 2018: Theoretical Population Biology
Robert I Cukier
Intrinsically disordered proteins (IDPs) sample a diverse conformational space. They are important to signaling and regulatory pathways in cells. An entropy penalty must be payed when an IDP becomes ordered upon interaction with another protein or a ligand. Thus, the degree of conformational disorder of an IDP is of interest. We create a dichotomic Markov model that can explore entropic features of an IDP. The Markov condition introduces local (neighbor residues in a protein sequence) rotamer dependences that arise from van der Waals and other chemical constraints...
March 14, 2018: Journal of Chemical Physics
Dragana Mijac, Irena Vukovic-Petrovic, Vera Mijac, Vladimir Perovic, Natasa Milic, Srdjan Djuranovic, Daniela Bojic, Dragan Popovic, Djordje Culafic, Miodrag Krstic, Goran Jankovic, Vera Pravica, Milos Markovic
BACKGROUND: Inflammatory bowel disease (IBD) is a chronic disease of unknown etiology in which genetic factors contribute to development of disease. Single nucleotide polymorphisms (SNPs) in multidrug resistance 1 (MDR1) gene encoding transporter P-glycoprotein have been associated with IBD, but their role in disease susceptibility remains unclear. Therefore, the aim of this study was to investigate the association of three MDR1 polymorphisms, C1236T (rs1128503), G2677T/A (rs2032582) and C3435T (rs1045642), with Serbian IBD patients...
2018: PloS One
Maxime Markov, Jelena Sjakste, Giuliana Barbarino, Giorgia Fugallo, Lorenzo Paulatto, Michele Lazzeri, Francesco Mauri, Nathalie Vast
Bismuth is one of the rare materials in which second sound has been experimentally observed. Our exact calculations of thermal transport with the Boltzmann equation predict the occurrence of this Poiseuille phonon flow between ≈1.5 and ≈3.5  K, in a sample size of 3.86 and 9.06 mm, consistent with the experimental observations. Hydrodynamic heat flow characteristics are given for any temperature: heat wave propagation length, drift velocity, and Knudsen number. We discuss a gedanken experiment allowing us to assess the presence of a hydrodynamic regime in any bulk material...
February 16, 2018: Physical Review Letters
Xiao Wu, Ajay Malhotra, Bertie Geng, Vivek B Kalra, Khalid Abbed, Howard P Forman, Pina Sanelli
Importance: Magnetic resonance imaging (MRI) continues to be performed for cervical clearance of obtunded blunt trauma, despite poor evidence regarding its utility after a normal computed tomographic (CT) finding. Objective: To evaluate the utility and cost-effectiveness of MRI vs no follow-up after a normal cervical CT finding in patients with obtunded blunt trauma. Design, Setting and Participants: This cost-effectiveness analysis evaluated an average patient aged 40 years with blunt trauma from an institutional practice...
March 14, 2018: JAMA Surgery
Antoneicka L Harris, Samantha E Lee, Louis K Dawson, Laura A Marlow, Brandy H Edenfield, William F Durham, Thomas J Flotte, Michael Thompson, Daniel L Small, Aidan J Synnott, Svetomir N Markovic, John A Copland
Patient-derived tumor xenograft (PDTX) mouse models were used to discover new therapies for naïve and drug resistant BRAF V600E -mutant melanoma. Tumor histology, oncogenic protein expression, and antitumor activity were comparable between patient and PDTX-matched models thereby validating PDTXs as predictive preclinical models of therapeutic response in patients. PDTX models responsive and non-responsive to BRAF/MEK standard of care (SOC) therapy were used to identify efficacious combination therapies. One such combination includes a CDK4/6 inhibitor that blocks cell cycle progression...
February 16, 2018: Oncotarget
(no author information available yet)
Background: Type 1 diabetes is a condition in which the pancreas produces little or no insulin. People with type 1 diabetes must manage their blood glucose levels by monitoring the amount of glucose in their blood and administering appropriate amounts of insulin via injection or an insulin pump. Continuous glucose monitoring may be beneficial compared to self-monitoring of blood glucose using a blood glucose meter. It provides insight into a person's blood glucose levels on a continuous basis, and can identify whether blood glucose levels are trending up or down...
2018: Ontario Health Technology Assessment Series
Yulun Liu, Stacia M DeSantis, Yong Chen
Many randomized controlled trials (RCTs) report more than one primary outcome. As a result, multivariate meta-analytic methods for the assimilation of treatment effects in systematic reviews of RCTs have received increasing attention in the literature. These methods show promise with respect to bias reduction and efficiency gain compared to univariate meta-analysis. However, most methods for multivariate meta-analysis have focused on pairwise treatment comparisons (i.e., when the number of treatments is two)...
January 2018: Journal of the Royal Statistical Society. Series C, Applied Statistics
Asghar M Razavi, George Khelashvili, Harel Weinstein
BACKGROUND: Much of the structure-based mechanistic understandings of the function of SLC6A neurotransmitter transporters emerged from the study of their bacterial LeuT-fold homologs. It has become evident, however, that structural differences such as the long N- and C-termini of the eukaryotic neurotransmitter transporters are involved in an expanded set of functional properties to the eukaryotic transporters. These functional properties are not shared by the bacterial homologs, which lack the structural elements that appeared later in evolution...
March 14, 2018: BMC Biology
HaYeon Kim, John A Vargo, Sushil Beriwal, David A Clump, James P Ohr, Robert L Ferris, Dwight E Heron, M Saiful Huq, Kenneth J Smith
BACKGROUND: The purpose of this study was to present our evaluation of the cost-effectiveness of salvage therapies for patients with recurrent head and neck cancer. METHODS: A Markov model was developed with 5 salvage treatment strategies: (1) platinum-based chemotherapy alone; (2) chemotherapy plus cetuximab; (3) stereotactic body radiotherapy (SBRT) alone; (4) SBRT plus cetuximab; and (5) intensity-modulated radiotherapy (IMRT) plus chemotherapy. Clinical parameters were obtained from comprehensive literature review and 2016 Medicare reimbursement...
March 14, 2018: Head & Neck
Verica Radojicic, Milica Keckarevic Markovic, Feđa Puac, Miljana Kecmanovic, Dusan Keckarevic
Casings represent common evidence in a forensic laboratory, due to high frequency of firearms usage during perpetration of criminal offenses. Possible DNA evidence from casings is compromised by degradation, inhibition, and initial low-quantity deposition of biological material. For that reason, in the last 15 years, scientists have been trying to optimize procedures for recovery and amplification of DNA possibly present on its surface. In this study, we share our 12-year experience done on a total of 698 casework casings, comparing two DNA recovery methods commonly used-soaking and swabbing, as well as efficacy of two commercially available DNA amplification kits (AmpFLSTR® Identifiler® and AmpFLSTR® Identifiler® Plus kits)...
March 13, 2018: International Journal of Legal Medicine
Shuang Huang, Chengcheng Hu, Melanie L Bell, Dean Billheimer, Stefano Guerra, Denise Roe, Monica M Vasquez, Edward J Bedrick
Continuous-time Markov models are commonly used to analyze longitudinal transitions between multiple disease states in panel data, where participants' disease states are only observed at multiple time points, and the exact state paths between observations are unknown. However, when covariate effects are incorporated and allowed to vary for different transitions, the number of potential parameters to estimate can become large even when the number of covariates is moderate, and traditional maximum likelihood estimation and subset model selection procedures can easily become unstable due to overfitting...
March 13, 2018: Biometrics
Marta Trapero-Bertran, Celia Muñoz, Kathryn Coyle, Doug Coyle, Adam Lester-George, Reiner Leidl, Bertalan Németh, Kei-Long Cheung, Subhash Pokhrel, Ángel Lopez-Nicolás
AIMS: To assess the cost-effectiveness of alternative smoking cessation scenarios from the perspective of the Spanish National Health Service (NHS). DESIGN: We used the European study on Quantifying Utility of Investment in Protection from Tobacco model (EQUIPTMOD), a Markov-based state transition economic model, to estimate the return on investment (ROI) of: (a) the current provision of smoking cessation services (brief physician advice and printed self-helped material + smoking ban and tobacco duty at current levels); and (b) four alternative scenarios to complement the current provision: coverage of proactive telephone calls; nicotine replacement therapy (mono and combo) [prescription nicotine replacement therapy (Rx NRT)]; varenicline (standard duration); or bupropion...
March 13, 2018: Addiction
Lauren E Markovic, Brian A Scansen
BACKGROUND: Different methods to perform reference calibration of an angiographic image exist; however, a prospective comparison of calibration methods has yet to be investigated in veterinary medicine. OBJECTIVE: To compare angiographic measurements using two commonly employed reference calibration methods, an esophageal pigtail marker catheter (EC) versus a radiopaque table ruler (TR). ANIMALS: Thirty-five client-owned dogs undergoing transcatheter intervention...
March 12, 2018: Journal of Veterinary Internal Medicine
Ariela Gordon-Shaag, David P Piñero, Cyril Kahloun, David Markov, Tzadok Parnes, Liat Gantz, Einat Shneor
BACKGROUND: The VX120 (Visionix Luneau, France) is a novel multi-diagnostic platform that combines Hartmann-Shack based autorefraction, Placido-disk based corneal-topography and anterior segment measurements made with a stationary-Scheimpflug camera. We investigate the agreement between different parameters measured by the VX120 with accepted or gold-standard techniques to test if they are interchangeable, as well as to evaluate the repeatability and reproducibility. METHODS: The right-eyes of healthy subjects were included in the study...
March 8, 2018: Journal of Optometry
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