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Refinement technique validation

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https://www.readbyqxmd.com/read/28427537/metabolomics-nutrition-and-potential-biomarkers-of-food-quality-intake-and-health-status
#1
Jean-Louis Sébédio
Diet, dietary patterns, and other environmental factors such as exposure to toxins are playing an important role in the prevention/development of many diseases, like obesity, type 2 diabetes, and consequently on the health status of individuals. A major challenge nowadays is to identify novel biomarkers to detect as early as possible metabolic dysfunction and to predict evolution of health status in order to refine nutritional advices to specific population groups. Omics technologies such as genomics, transcriptomics, proteomics, and metabolomics coupled with statistical and bioinformatics tools have already shown great potential in this research field even if so far only few biomarkers have been validated...
2017: Advances in Food and Nutrition Research
https://www.readbyqxmd.com/read/28425923/connectivity-restoration-in-wireless-sensor-networks-via-space-network-coding
#2
Alfred Uwitonze, Jiaqing Huang, Yuanqing Ye, Wenqing Cheng
The problem of finding the number and optimal positions of relay nodes for restoring the network connectivity in partitioned Wireless Sensor Networks (WSNs) is Non-deterministic Polynomial-time hard (NP-hard) and thus heuristic methods are preferred to solve it. This paper proposes a novel polynomial time heuristic algorithm, namely, Relay Placement using Space Network Coding (RPSNC), to solve this problem, where Space Network Coding, also called Space Information Flow (SIF), is a new research paradigm that studies network coding in Euclidean space, in which extra relay nodes can be introduced to reduce the cost of communication...
April 20, 2017: Sensors
https://www.readbyqxmd.com/read/28425345/surrogate-marker-analysis-in-cancer-clinical-trials-through-time-to-event-mediation-techniques
#3
Sjouke Vandenberghe, Luc Duchateau, Leen Slaets, Jan Bogaerts, Stijn Vansteelandt
The meta-analytic approach is the gold standard for validation of surrogate markers, but has the drawback of requiring data from several trials. We refine modern mediation analysis techniques for time-to-event endpoints and apply them to investigate whether pathological complete response can be used as a surrogate marker for disease-free survival in the EORTC 10994/BIG 1-00 randomised phase 3 trial in which locally advanced breast cancer patients were randomised to either taxane or anthracycline based neoadjuvant chemotherapy...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28422350/electronic-g-tensors-in-u-v-complexes-a-computational-study
#4
Helen Moylan, Joseph McDouall
The theory and computation of EPR parameters from first principles has seen a great deal of development over the past two decades. In particular, various techniques for the computation of the electronic g tensor have been implemented in many quantum chemistry packages. These methods have been successfully applied to paramagnetic organic species and transition metal systems. The situation is less well-understood and established in the case of actinide containing molecules and there is a dearth of experimental data available for validation of computations...
April 19, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28420133/using-dimensionality-reduction-techniques-for-refining-passive-indoor-positioning-systems-based-on-radio-fingerprinting
#5
Pedro E Lopez-de-Teruel, Oscar Canovas, Felix J Garcia
Indoor positioning methods based on fingerprinting and radio signals rely on the quality of the radio map. For example, for room-level classification purposes, it is required that the signal observations related to each room exhibit significant differences in their RSSI values. However, it is difficult to verify and visualize that separability since radio maps are constituted by multi-dimensional observations whose dimension is directly related to the number of access points or monitors being employed for localization purposes...
April 15, 2017: Sensors
https://www.readbyqxmd.com/read/28402873/saxs-oriented-ensemble-refinement-of-flexible-biomolecules
#6
Peng Cheng, Junhui Peng, Zhiyong Zhang
The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation. In this article, we present a tool written in Python, which iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics, and an ensemble optimization method to drive the biomolecule toward an ensemble that fits the SAXS data well...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28375653/an-innovative-method-of-ocular-prosthesis-fabrication-by-bio-cad-and-rapid-3-d-printing-technology-a-pilot-study
#7
Shahid Alam, M Sugavaneswaran, G Arumaikkannu, Bipasha Mukherjee
Ocular prosthesis is either a readymade stock shell or custom made prosthesis (CMP). Presently, there is no other technology available, which is either superior or even comparable to the conventional CMP. The present study was designed to fabricate ocular prosthesis using computer aided design (CAD) and rapid manufacturing (RM) technology and to compare it with custom made prosthesis (CMP). The ocular prosthesis prepared by CAD was compared with conventional CMP in terms of time taken for fabrication, weight, cosmesis, comfort, and motility...
April 4, 2017: Orbit
https://www.readbyqxmd.com/read/28341584/development-of-videogrammetry-as-a-tool-for-gas-particle-fluidization-research
#8
S Anweiler
Many industries use fluidization of solid particles for energy efficiency or environmental friendly process development, and this paper introduces research techniques developed for investigating gas-particle systems At present there is plenty of room for refining gas-particle fluidization process. With the rapidly rising application of mathematical modelling, real time visualization of processes will be widely used for validation of those models in the near future. In presented research, photogrammetry, as a part of close range vision metrology, has been expanded to allow dynamic space and time analysis of the phase concentration distribution inside fluidization devices...
March 21, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28331530/kras-detection-on-archival-cytological-smears-by-the-novel-fully-automated-polymerase-chain-reaction-based-idylla-mutation-test
#9
Caterina De Luca, Elena Vigliar, Melania d'Anna, Pasquale Pisapia, Claudio Bellevicine, Umberto Malapelle, Giancarlo Troncone
BACKGROUND: Molecular techniques are relevant to modern cytopathology, but their implementation is difficult without molecular expertise and infrastructure. The assessment of KRAS mutational status on cytological preparations may be useful either to refine uncertain diagnoses on pancreatic aspirates or to yield predictive information to plan targeted treatment of metastatic colorectal cancer (mCRC). The novel test Idylla™ enables fully automated KRAS genotyping in approximately 2 h, even in less experienced hands...
2017: CytoJournal
https://www.readbyqxmd.com/read/28300375/photon-optimizer-po-prevails-over-progressive-resolution-optimizer-pro-for-vmat-planning-with-or-without-knowledge-based-solution
#10
Fan Jiang, Hao Wu, Haizhen Yue, Fei Jia, Yibao Zhang
The enhanced dosimetric performance of knowledge-based volumetric modulated arc therapy (VMAT) planning might be jointly contributed by the patient-specific optimization objectives, as estimated by the RapidPlan model, and by the potentially improved Photon Optimizer (PO) algorithm than the previous Progressive Resolution Optimizer (PRO) engine. As PO is mandatory for RapidPlan estimation but optional for conventional manual planning, appreciating the two optimizers may provide practical guidelines for the algorithm selection because knowledge-based planning may not replace the current method completely in a short run...
March 2017: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28296903/the-potential-distribution-of-cassava-mealybug-phenacoccus-manihoti-a-threat-to-food-security-for-the-poor
#11
Tania Yonow, Darren J Kriticos, Noboru Ota
The cassava mealybug is a clear and present threat to the food security and livelihoods of some of the world's most impoverished citizens. Niche models, such as CLIMEX, are useful tools to indicate where and when such threats may extend, and can assist with planning for biosecurity and the management of pest invasions. They can also contribute to bioeconomic analyses that underpin the allocation of resources to alleviate poverty. Because species can invade and establish in areas with climates that are different from those that are found in their native range, it is essential to define robust range-limiting mechanisms in niche models...
2017: PloS One
https://www.readbyqxmd.com/read/28272524/atomistic-structural-ensemble-refinement-reveals-non-native-structure-stabilizes-a-sub-millisecond-folding-intermediate-of-chey
#12
Jade Shi, R Paul Nobrega, Christian Schwantes, Sagar V Kathuria, Osman Bilsel, C Robert Matthews, T J Lane, Vijay S Pande
The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28268161/minimally-invasive-pancreatic-resections-cost-and-value-perspectives
#13
Kevin C Conlon, Thijs de Rooij, Jony van Hilst, Mohammad Abu Hidal, Julie Fleshman, Mark Talamonti, Tsafrir Vanounou, Richard Garfinkle, Vic Velanovich, David Kooby, Charles M Vollmer
BACKGROUND: The number of minimally invasive pancreatic resections (MIPR) performed for benign or malignant disease, have increased in recent years. However, there is limited information regarding cost/value implications. METHODS: An international conference evaluating MIPR was held during the 12th Bi-Annual International Hepato-Pancreato-Biliary Association (IHPBA) World Congress in Sao Paulo, Brazil, on April 20th, 2016. This manuscript summarizes the presentations that reviewed current topics in cost and value as they pertain to MIPR...
March 4, 2017: HPB: the Official Journal of the International Hepato Pancreato Biliary Association
https://www.readbyqxmd.com/read/28223945/toward-respiratory-assessment-using-depth-measurements-from-a-time-of-flight-sensor
#14
Charles Sharp, Vahid Soleimani, Sion Hannuna, Massimo Camplani, Dima Damen, Jason Viner, Majid Mirmehdi, James W Dodd
Introduction: There is increasing interest in technologies that may enable remote monitoring of respiratory disease. Traditional methods for assessing respiratory function such as spirometry can be expensive and require specialist training to perform and interpret. Remote, non-contact tracking of chest wall movement has been explored in the past using structured light, accelerometers and impedance pneumography, but these have often been costly and clinical utility remains to be defined. We present data from a 3-Dimensional time-of-flight camera (found in gaming consoles) used to estimate chest volume during routine spirometry maneuvres...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28218823/review-of-the-development-of-methods-for-characterization-of-microspheres-for-use-in-embolotherapy-translating-bench-to-cathlab
#15
REVIEW
Marcus Caine, Dario Carugo, Xunli Zhang, Martyn Hill, Matthew R Dreher, Andrew L Lewis
Therapeutic embolotherapy is the deliberate occlusion of a blood vessel within the body, which can be for the prevention of internal bleeding, stemming of flow through an arteriovenous malformation, or occlusion of blood vessels feeding a tumor. This is achieved using a wide selection of embolic devices such as balloons, coils, gels, glues, and particles. Particulate embolization is often favored for blocking smaller vessels, particularly within hypervascularized tumors, as they are available in calibrated sizes and can be delivered distally via microcatheters for precise occlusion with associated locoregional drug delivery...
February 20, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28208471/analysis-of-thermodiffusive-cellular-instabilities-in-continuum-combustion-fronts
#16
Hossein Azizi, Sebastian Gurevich, Nikolas Provatas
We explore numerically the morphological patterns of thermodiffusive instabilities in combustion fronts with a continuum fuel source, within a range of Lewis numbers and ignition temperatures, focusing on the cellular regime. For this purpose, we generalize the recent model of Brailovsky et al. to include distinct process kinetics and reactant heterogeneity. The generalized model is derived analytically and validated with other established models in the limit of infinite Lewis number for zero-order and first-order kinetics...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28177306/validation-and-extraction-of-molecular-geometry-information-from-small-molecule-databases
#17
Fei Long, Robert A Nicholls, Paul Emsley, Saulius Graǽulis, Andrius Merkys, Antanas Vaitkus, Garib N Murshudov
A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28160722/molecular-modeling-simulation-and-docking-study-of-ebola-virus-glycoprotein
#18
Nasir Ahmad, Aqsa Farman, Syed Lal Badshah, Ata Ur Rahman, Haroon Ur Rashid, Khalid Khan
Ebola virus (EBOV) is a filamentous, enveloped, non-segmented, negative-strand ribonucleic acid (RNA) virus which belongs to family Filoviridae. Ebola virus includes different glycoproteins each of which plays their roles in different aspects of viral life cycle. In this study secreted glycoprotein (Q7T9E0) of Ebola virus was acquired from Uniprot. The formation of alpha helix and beta sheets of secondary structures were predicted through online servers. Higher flexibility and disordered regions of proteins were determined through RONN, GLOBPLOT and DISSEMBLE...
March 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28148504/identification-of-dietary-patterns-associated-with-obesity-in-a-nationally-representative-survey-of-canadian-adults-application-of-a-priori-hybrid-and-simplified-dietary-pattern-techniques
#19
Mahsa Jessri, Russell D Wolfinger, Wendy Y Lou, Mary R L'Abbé
Background: Analyzing the effects of dietary patterns is an important approach for examining the complex role of nutrition in the etiology of obesity and chronic diseases.Objectives: The objectives of this study were to characterize the dietary patterns of Canadians with the use of a priori, hybrid, and simplified dietary pattern techniques, and to compare the associations of these patterns with obesity risk in individuals with and without chronic diseases (unhealthy and healthy obesity).Design: Dietary recalls from 11,748 participants (≥18 y of age) in the cross-sectional, nationally representative Canadian Community Health Survey 2...
March 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28105919/snoreport-2-0-new-features-and-a-refined-support-vector-machine-to-improve-snorna-identification
#20
João Victor de Araujo Oliveira, Fabrizio Costa, Rolf Backofen, Peter Florian Stadler, Maria Emília Machado Telles Walter, Jana Hertel
BACKGROUND: snoReport uses RNA secondary structure prediction combined with machine learning as the basis to identify the two main classes of small nucleolar RNAs, the box H/ACA snoRNAs and the box C/D snoRNAs. Here, we present snoReport 2.0, which substantially improves and extends in the original method by: extracting new features for both box C/D and H/ACA box snoRNAs; developing a more sophisticated technique in the SVM training phase with recent data from vertebrate organisms and a careful choice of the SVM parameters C and γ; and using updated versions of tools and databases used for the construction of the original version of snoReport...
December 15, 2016: BMC Bioinformatics
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