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Magdalena Anna Mozolewska, Pawel Krupa, Bartlomiej Zaborowski, Adam Liwo, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
Recently, we developed a new approach to protein-structure prediction, which combines template-based modeling with the physics-based coarse-grained UNited RESidue (UNRES) force field. In this approach, restrained multiplexed replica exchange molecular dynamics (MREMD) simulations with UNRES, with the C(α)-distance and virtual-bond-dihedral-angle restraints derived from knowledge-based models are carried out. In this work, we report a test of this approach in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11), in which we used the template-based models from early-stage predictions by the LEE group CASP11 server (group 038, called 'nns'), and further improvement of the method...
October 17, 2016: Journal of Chemical Information and Modeling
Rajkishor Mishra, Himanshu Kumar Sanju, Prawin Kumar
Introduction "Diabetes mellitus is a group of metabolic disorders characterized by elevated blood sugar and abnormalities in insulin secretion and action" (American Diabetes Association). Previous literature has reported connection between diabetes mellitus and hearing impairment. There is a dearth of literature on auditory temporal resolution ability in individuals with diabetes mellitus type 2. Objective The main objective of the present study was to assess auditory temporal resolution ability through GDT (Gap Detection Threshold) in individuals with diabetes mellitus type 2 with high frequency hearing loss...
October 2016: International Archives of Otorhinolaryngology
Chelsea Blankenship, Fawen Zhang, Robert Keith
BACKGROUND: Although most cochlear implant (CI) users achieve improvements in speech perception, there is still a wide variability in speech perception outcomes. There is a growing body of literature that supports the relationship between individual differences in temporal processing and speech perception performance in CI users. Previous psychophysical studies have emphasized the importance of temporal acuity for overall speech perception performance. Measurement of gap detection thresholds (GDTs) is the most common measure currently used to assess temporal resolution...
October 2016: Journal of the American Academy of Audiology
Poonam Malhotra Kapoor, Rohan Magoon, Rajinder Rawat, Yatin Mehta
Goal-directed therapy (GDT) encompasses guidance of intravenous (IV) fluid and vasopressor/inotropic therapy by cardiac output or similar parameters to help in early recognition and management of high-risk cardiac surgical patients. With the aim of establishing the utility of perioperative GDT using robust clinical and biochemical outcomes, we conducted the present study. This multicenter randomized controlled study included 130 patients of either sex, with European system for cardiac operative risk evaluation ≥3 undergoing coronary artery bypass grafting on cardiopulmonary bypass...
October 2016: Annals of Cardiac Anaesthesia
Anya Pedersen, Robert Göder, Samuel Tomczyk, Patricia Ohrmann
BACKGROUND AND OBJECTIVES: Patients with schizophrenia reveal impaired decision-making strategies causing social, financial and health care problems. The extent to which deficits in decision-making reflect intentional risky choices in schizophrenia is still under debate. Based on previous studies we expected patients with schizophrenia to reveal a riskier performance on the GDT and to make more disadvantageous decisions on the IGT. METHODS: In the present study, we investigated 38 patients with schizophrenia and 38 matched healthy control subjects with two competing paradigms regarding feedback: (1) The Game of Dice Task (GDT), in which the probabilities of winning or losing are stable and explicitly disclosed to the subject, to assess decision-making under risk and (2) the Iowa Gambling Task (IGT), which requires subjects to infer the probabilities of winning or losing from feedback, to investigate decision-making under ambiguity...
August 7, 2016: Journal of Behavior Therapy and Experimental Psychiatry
Bernardo Bollen Pinto, Glen Atlas, Bart F Geerts, Karim Bendjelid
The oesophageal Doppler (OD) is a minimally invasive haemodynamic monitor used in the surgical theatre and the ICU. Using the OD, goal-directed therapy (GDT) has been shown to reduce perioperative complications in high-risk surgical patients. However, most GDT protocols currently in use are limited to stroke volume optimisation. In the present manuscript, we examine the conceptual models behind new OD-based measurements. These would provide the clinician with a comprehensive view of haemodynamic pathophysiology; including pre-load, contractility, and afterload...
August 27, 2016: Journal of Clinical Monitoring and Computing
A Toner, N Jenkins, G L Ackland
BACKGROUND: Baroreflex dysfunction is a common feature of established cardiometabolic diseases that are most frequently associated with the development of critical illness. Laboratory models show that baroreflex dysfunction impairs cardiac contractility and cardiovascular performance, thereby increasing the risk of morbidity after trauma and sepsis. We hypothesized that baroreflex dysfunction contributes to excess postoperative morbidity after major surgery as a consequence of the inability to achieve adequate perioperative tissue oxygen delivery...
September 2016: British Journal of Anaesthesia
S Bayard, E Joly, P Ghisletta, A Rossignol, Y Herades, C Geny, M-C Gély-Nargeot, L Rochat
BACKGROUND: Poor impulse control is a common feature in patients with Parkinson's disease (PD). However, before testing whether patients with PD and controls differ in impulsivity, one must assess whether impulsivity measures are invariant across groups. Consequently, we examined (a) the measurement and structural invariance of a scale assessing changes in four dimensions of impulsivity (urgency, lack of premeditation, lack of perseverance and sensation seeking) among patients with PD and controls; and (b) whether the four impulsivity traits relate differentially to risky decisions by patients...
October 2016: Psychological Medicine
Thomas Kratz, Christina Simon, Volker Fendrich, Ralph Schneider, Hinnerk Wulf, Caroline Kratz, Turgay Efe, Karl F Schüttler, Martin Zoremba
BACKGROUND: Goal directed fluid management in major abdominal surgery has shown to reduce perioperative complications. The approach aims to optimize the intravascular fluid volume by use of minimally invasive devices which calculate flow-directed variables such as stroke volume (SV) and stroke volume variation (SVV). OBJECTIVE: We aimed to show the feasibility of routinely implementing this type of hemodynamic monitoring during pancreatic surgery, and to evaluate its effects in terms of perioperative fluid management and postoperative outcomes...
July 8, 2016: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
Woo Kyung Lee, Ha Yeon Kim, Jinae Lee, Shin Ok Koh, Jeong Min Kim, Sungwon Na
PURPOSE: Owing to the recommendations of the Surviving Sepsis Campaign guidelines, protocol-based resuscitation or goal-directed therapy (GDT) is broadly advocated for the treatment of septic shock. However, the most recently published trials showed no survival benefit from protocol-based resuscitation in septic shock patients. Hence, we aimed to assess the effect of GDT on clinical outcomes in such patients. MATERIALS AND METHODS: We performed a systematic review that included a meta-analysis...
September 2016: Yonsei Medical Journal
Tsutomu Nakazawa, Mitsutoshi Nakamura, Ryosuke Matsuda, Fumihiko Nishimura, Young Soo Park, Yasushi Motoyama, Yasuo Hironaka, Ichiro Nakagawa, Hiroshi Yokota, Shuichi Yamada, Kentaro Tamura, Yasuhiro Takeshima, Kouji Omoto, Yoshitaka Tanaka, Yukiteru Ouji, Masahide Yoshikawa, Takahiro Tsujimura, Hiroyuki Nakase
Nitrogen-containing bisphosphonates (N-BPs), which prevent bone resorption, exert direct and γδT cell (GDT)-mediated antitumor effects against several tumor cell types, including glioblastoma (GBM). However, limited information is available regarding the antitumor effects of N-BPs in GBM. Specifically, the antitumor effects of minodronate (MDA), a third-generation N-BP, in GBM are yet unclear. This study aimed to investigate the antitumor effects of MDA in GBM in vitro and in vivo. We performed growth inhibition and apoptosis detection assays using the GBM cell lines U87MG and U138MG...
September 2016: Journal of Neuro-oncology
Belinda Pletzer, Tuulia M Ortner
Personality assessment has been challenged by the fact that different assessment methods (implicit measures, behavioral measures and explicit rating scales) show little or no convergence in behavioral studies. In this neuroimaging study we address for the first time, whether different assessment methods rely on separate or overlapping neuronal systems. Fifty nine healthy adult participants completed two objective personality tests of risk propensity: the more implicit Balloon Analogue Risk Task (BART) and the more explicit Game of Dice Task (GDT)...
September 2016: Biological Psychology
Peter J Huwe, Qifang Xu, Maxim V Shapovalov, Vivek Modi, Mark D Andrake, Roland L Dunbrack
In CASP11, the organizers sought to bring the biological inferences from predicted structures to the fore. To accomplish this, we assessed the models for their ability to perform quantifiable tasks related to biological function. First, for 10 targets that were probable homodimers, we measured the accuracy of docking the models into homodimers as a function of GDT-TS of the monomers, which produced characteristic L-shaped plots. At low GDT-TS, none of the models could be docked correctly as homodimers. Above GDT-TS of ∼60%, some models formed correct homodimers in one of the largest docked clusters, while many other models at the same values of GDT-TS did not...
September 2016: Proteins
Jilong Li, Jianlin Cheng
Generating tertiary structural models for a target protein from the known structure of its homologous template proteins and their pairwise sequence alignment is a key step in protein comparative modeling. Here, we developed a new stochastic point cloud sampling method, called MTMG, for multi-template protein model generation. The method first superposes the backbones of template structures, and the Cα atoms of the superposed templates form a point cloud for each position of a target protein, which are represented by a three-dimensional multivariate normal distribution...
2016: Scientific Reports
Wenlin Li, R Dustin Schaeffer, Zbyszek Otwinowski, Nick V Grishin
The Critical Assessment of techniques for protein Structure Prediction (or CASP) is a community-wide blind test experiment to reveal the best accomplishments of structure modeling. Assessors have been using the Global Distance Test (GDT_TS) measure to quantify prediction performance since CASP3 in 1998. However, identifying significant score differences between close models is difficult because of the lack of uncertainty estimations for this measure. Here, we utilized the atomic fluctuations caused by structure flexibility to estimate the uncertainty of GDT_TS scores...
2016: PloS One
Anders Winther Voldby, Birgitte Brandstrup
BACKGROUND: Perioperative hypovolemia and fluid overload have effects on both complications following surgery and on patient survival. Therefore, the administration of intravenous fluids before, during, and after surgery at the right time and in the right amounts is of great importance. This review aims to analyze the literature concerning perioperative fluid therapy in abdominal surgery and to provide evidence-based recommendations for clinical practice. RESULTS: Preoperative oral or intravenous administration of carbohydrate containing fluids has been shown to improve postoperative well-being and muscular strength and to reduce insulin resistance...
2016: Journal of Intensive Care
Vivek Modi, Qifang Xu, Sam Adhikari, Roland L Dunbrack
We present the assessment of predictions submitted in the template-based modeling (TBM) category of CASP11 (Critical Assessment of Protein Structure Prediction). Model quality was judged on the basis of global and local measures of accuracy on all atoms including side chains. The top groups on 39 human-server targets based on model 1 predictions were LEER, Zhang, LEE, MULTICOM, and Zhang-Server. The top groups on 81 targets by server groups based on model 1 predictions were Zhang-Server, nns, BAKER-ROSETTASERVER, QUARK, and myprotein-me...
September 2016: Proteins
Mariateresa Giglio, Fabio Manca, Lidia Dalfino, Nicola Brienza
BACKGROUND: Recent data found that perioperative goal directed therapy (GDT) was effective only in higher control mortality rate (>20%) with a relatively high heterogeneity that limited the strength of evidence. The aim of the present meta- analysis was to clearly understand which high risk patients may benefit of GDT. METHODS: Systematic review of randomised controlled trials with meta-analyses, including a meta regression technique. MEDLINE, EMBASE, and The Cochrane Library databases were searched (1980-January 2015)...
April 13, 2016: Minerva Anestesiologica
Axel W Fischer, Sten Heinze, Daniel K Putnam, Bian Li, James C Pino, Yan Xia, Carlos F Lopez, Jens Meiler
In silico prediction of a protein's tertiary structure remains an unsolved problem. The community-wide Critical Assessment of Protein Structure Prediction (CASP) experiment provides a double-blind study to evaluate improvements in protein structure prediction algorithms. We developed a protein structure prediction pipeline employing a three-stage approach, consisting of low-resolution topology search, high-resolution refinement, and molecular dynamics simulation to predict the tertiary structure of proteins from the primary structure alone or including distance restraints either from predicted residue-residue contacts, nuclear magnetic resonance (NMR) nuclear overhauser effect (NOE) experiments, or mass spectroscopy (MS) cross-linking (XL) data...
2016: PloS One
Renzhi Cao, Jianlin Cheng
Protein quality assessment (QA) has played an important role in protein structure prediction. We developed a novel single-model quality assessment method-Qprob. Qprob calculates the absolute error for each protein feature value against the true quality scores (i.e. GDT-TS scores) of protein structural models, and uses them to estimate its probability density distribution for quality assessment. Qprob has been blindly tested on the 11th Critical Assessment of Techniques for Protein Structure Prediction (CASP11) as MULTICOM-NOVEL server...
2016: Scientific Reports
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