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Refinement technique validation

Christina Backes, Tobias Fehlmann, Fabian Kern, Tim Kehl, Hans-Peter Lenhof, Eckart Meese, Andreas Keller
The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014...
September 25, 2017: Nucleic Acids Research
S Abou-El-Karam, J Ratel, N Kondjoyan, C Truan, E Engel
Starting with an experiment to authenticate walnut oils based on GC-MS analysis of the volatolome, this paper aims to demonstrate the relevance of a two-step alignment-based strategy for the systematic research of VOC markers. The first step of the treatment consists of roughly reducing the time shifts with efficient, known warping techniques like COW (Correlation Optimized Warping). The second step relies on an accurate peak apex alignment in order to refine residual local misalignments and to enable further systematic marker research through univariate or multivariate data treatments...
October 23, 2017: Analytica Chimica Acta
Begonya Garcia-Zapirain, Ahmed Shalaby, Ayman El-Baz, Adel Elmaghraby
Ulcer tissue segmentation is of immense importance in helping medical personnel to assess wounds. This paper introduces a new computational framework employing state-of-the-art image processing techniques to segment pressure ulcer tissue structures from color images. The framework integrates a visual appearance model of an observed input image with prior color information from an available database of previously stored color RGB images. The following four processing steps are performed. First, to minimize the execution time and enhance the segmentation accuracy, a region-of-interest (ROI) of the whole ulcer area is automatically identified based on contrast changes...
September 22, 2017: Computers in Biology and Medicine
Geoffrey R Browning, Anthony H Le, Jennifer J Warnock, Ravi Balasubramanian
PURPOSE: The state-of-the-art tendon transfer surgery for high median-ulnar nerve palsy involves directly suturing four finger flexor tendons to one wrist extensor muscle. This couples finger flexion limiting the patient's ability to grasp objects. Therefore, we propose a new approach to attach a novel passive implant to the extensor digitorum longus tendon in order to create a differential mechanism in situ. The implant is expected to enable the fingers to adapt to an object's shape during grasping...
October 3, 2017: Journal of Investigative Surgery: the Official Journal of the Academy of Surgical Research
Stanley Njuangang, Champika Liyanage, Akintola Akintoye
Purpose The purpose of this paper is to examine the research design, issues and considerations in the application of the Delphi technique to identify, refine and rate the critical success factors and performance measures in maintenance-associated infections. Design/methodology/approach In-depth literature review through the application of open and axial coding were applied to formulate the interview and research questions. These were used to conduct an exploratory case study of two healthcare maintenance managers, randomly selected from two National Health Service Foundation Trusts in England...
October 9, 2017: International Journal of Health Care Quality Assurance
Félix Gendre, Denis Ricot, Guillaume Fritz, Pierre Sagaut
This study focuses on grid refinement techniques for the direct simulation of aeroacoustics, when using weakly compressible lattice Boltzmann models, such as the D3Q19 athermal velocity set. When it comes to direct noise computation, very small errors on the density or pressure field may have great negative consequences. Even strong acoustic density fluctuations have indeed a clearly lower amplitude than the hydrodynamic ones. This work deals with such very weak spurious fluctuations that emerge when a vortical structure crosses a refinement interface, which may contaminate the resulting aeroacoustic field...
August 2017: Physical Review. E
Zhu Liu, Zhou Gong, Yong Cao, Yue-He Ding, Meng-Qiu Dong, Yun-Bi Lu, Wei-Ping Zhang, Chun Tang
A protein dynamically samples multiple conformations, and the conformational dynamics enables protein function. Most biophysical measurements are ensemble-based, with the observables averaged over all members of the ensemble. Though attainable, the decomposition of the observables to the constituent conformational states can be computationally expensive and ambiguous. Here we show that the incorporation of single-molecule fluorescence resonance energy transfer (smFRET) data resolves the ambiguity and affords protein ensemble structures that are more precise and accurate...
October 2, 2017: Biochemistry
Tianyu Hu, Qiufeng Xu, Wei Lv, Qian Liu
Neuronal soma segmentation is essential for morphology quantification analysis. Rapid advances in light microscope imaging techniques have generated such massive amounts of data that time-consuming manual methods cannot meet requirements for high throughput. However, touching soma segmentation is still a challenge for automatic segmentation methods. In this paper, we propose a soma segmentation method that combines the Rayburst sampling algorithm and ellipsoid fitting. The improved Rayburst sampling algorithm is used to detect the soma surface; the ellipsoid fitting method then refines jagged sampled soma surface to generate smooth ellipsoidal shapes for efficient analysis...
September 22, 2017: Neuroinformatics
Alexander Seiler, Nicholas P Blockley, Ralf Deichmann, Ulrike Nöth, Oliver C Singer, Michael A Chappell, Johannes C Klein, Marlies Wagner
Oxygenation-sensitive spin relaxation time T2' and relaxation rate R2' (1/T2') are presumed to be markers of the cerebral oxygen extraction fraction (OEF) in acute ischemic stroke. In this study, we investigate the relationship of T2'/R2' with dynamic susceptibility contrast-based relative cerebral blood flow (rCBF) in acute ischemic stroke to assess their plausibility as surrogate markers of the ischemic penumbra. Twenty-one consecutive patients with internal carotid artery and/or middle cerebral artery occlusion were studied at 3...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
Sarah N Bowe, Christopher J Hartnick
PURPOSE OF REVIEW: To summarize the pediatric Type I and Type II laryngeal cleft literature, paying special attention to recent trends, including evolution of surgical techniques, standardization of outcome assessments, and utilization of management algorithms. RECENT FINDINGS: There are a variety of options to choose from whenever considering Type I and Type II cleft repair, including endoscopic repair, transoral robotic surgery, and injection laryngoplasty. Conservative management including feeding therapy and treatment of comorbid medical conditions is recommended prior to repair...
September 12, 2017: Current Opinion in Otolaryngology & Head and Neck Surgery
Ki Mun Kang, Hoon Sik Choi, Bae Kwon Jeong, Jin Ho Song, In-Bong Ha, Yun Hee Lee, Chul Hang Kim, Hojin Jeong
An alternative pseudo CT generation method for magnetic resonance image (MRI)-based radiotherapy planning was investigated in the work. A pseudo CT was initially generated using the rigid image registration between the planning MRI and previously acquired diagnostic CT scan. The pseudo CT generated was then refined to have the same morphology with that of the referenced planning image scan by applying the outer body correction scheme. This method was applied to some sample of brain image data and the feasibility of the method was assessed by comparing dosimetry results with those from the current gold standard CT-based calculations...
August 15, 2017: Oncotarget
Christian Kreutzer, Guillermo Kreutzer
In spite of excellent long term survival the Fontan Kreutzer procedure commonly presents late failure due to end-organ damage. Several advances have been described to refine single ventricle management and surgical techniques. However, very little research has been dedicated to the lymphatic circulation in the precarious Fontan hemodynamic state. The lymphatic circulation is clearly affected since there is increased lymph production, which requires to be drained at a similar or higher pressure than it is produced, commonly resulting in chronic lymphedema...
September 2017: World Journal for Pediatric & Congenital Heart Surgery
April L McPherson, John D Berry, Nathanial A Bates, Timothy E Hewett
BACKGROUND: Previous investigations of single-camera 3D motion analysis camera systems validity have yielded mixed results for clinical applications. PURPOSE: The purpose of the current study was to determine the validity of a single-camera 3D motion analysis system for subject standing height, vertical jump height, and broad jump length. It was hypothesized that single-camera system values would demonstrate high correlation to the values obtained from accepted standard clinical measurements...
August 2017: International Journal of Sports Physical Therapy
J L Browne, A D Ventura, K Mosely, J Speight
AIMS: To develop and validate a self-report measure designed to assess perceived and experienced stigma for adults with Type 1 diabetes: the Type 1 Diabetes Stigma Assessment Scale. METHODS: A large item-pool (64 items) was drafted based on qualitative data from interviews with 27 adults with Type 1 diabetes. Eleven adults with Type 1 diabetes completed the draft questionnaire (responding to items using a five-point Likert scale), and participated in cognitive debriefing interviews...
September 11, 2017: Diabetic Medicine: a Journal of the British Diabetic Association
A Lago, J I Tembl, G Fortea, L Morales, C Nieves, M Campins, F Aparici
INTRODUCTION: Though uncommon, ischaemic stroke due to temporal arteritis carries serious difficulties for diagnosis and subsequent management and requires a high level of suspicion. METHODS: We analysed a series of 6 patients with biopsy-proven temporal arteritis presenting with ischaemic stroke. We discuss clinical characteristics, difficulties of assessment, short- and long-term progression, treatment, and the usefulness of new diagnostic techniques. RESULTS: Our sample of 6 patients had a mean age of 68...
August 28, 2017: Neurología: Publicación Oficial de la Sociedad Española de Neurología
Lorena A Maia, Ian Velloso, Jose G Abreu
Understanding embryogenesis currently relies largely on the control of gene expression via several signaling pathways. Many of the embryonic signaling pathways guiding embryological events are implicated in diseases that lack effective cure or treatment. Because of the large number and size of the eggs, the rapid development of the embryos and the fact they are amenable to pharmacological, surgical and genetic techniques, Xenopus laevis has been successfully used in searching for compounds that target embryonic signaling pathways...
August 28, 2017: Expert Opinion on Drug Discovery
Antje Gumz, Karolin Neubauer, Julia Katharina Horstkotte, Michael Geyer, Bernd Löwe, Alexandra M Murray, Denise Kästner
OBJECTIVE: Knowing which specific verbal techniques "good" therapists use in their daily work is important for training and evaluation purposes. In order to systematize what is being practiced in the field, our aim was to empirically identify verbal techniques applied in psychodynamic sessions and to differentiate them according to their basic semantic features using a bottom-up, qualitative approach. METHOD: Mixed-Method-Design: In a comprehensive qualitative study, types of techniques were identified at the level of utterances based on transcribed psychodynamic therapy sessions using Qualitative Content Analysis (4211 utterances)...
2017: PloS One
Muriel Elhai, Christophe Meune, Marouane Boubaya, Jérôme Avouac, Eric Hachulla, Alexandra Balbir-Gurman, Gabriela Riemekasten, Paolo Airò, Beatriz Joven, Serena Vettori, Franco Cozzi, Susanne Ullman, László Czirják, Mohammed Tikly, Ulf Müller-Ladner, Paola Caramaschi, Oliver Distler, Florenzo Iannone, Lidia P Ananieva, Roger Hesselstrand, Radim Becvar, Armando Gabrielli, Nemanja Damjanov, Maria J Salvador, Valeria Riccieri, Carina Mihai, Gabriella Szücs, Ulrich A Walker, Nicolas Hunzelmann, Duska Martinovic, Vanessa Smith, Carolina de Souza Müller, Carlo Maurizio Montecucco, Daniela Opris, Francesca Ingegnoli, Panayiotis G Vlachoyiannopoulos, Bojana Stamenkovic, Edoardo Rosato, Stefan Heitmann, Jörg H W Distler, Thierry Zenone, Matthias Seidel, Alessandra Vacca, Ellen De Langhe, Srdan Novak, Maurizio Cutolo, Luc Mouthon, Jörg Henes, Carlo Chizzolini, Carlos Alberto von Mühlen, Kamal Solanki, Simona Rednic, Lisa Stamp, Branimir Anic, Vera Ortiz Santamaria, Maria De Santis, Sule Yavuz, Walter Alberto Sifuentes-Giraldo, Emmanuel Chatelus, Jiri Stork, Jacob van Laar, Esthela Loyo, Paloma García de la Peña Lefebvre, Kilian Eyerich, Vanesa Cosentino, Juan Jose Alegre-Sancho, Otylia Kowal-Bielecka, Grégoire Rey, Marco Matucci-Cerinic, Yannick Allanore
OBJECTIVES: To determine the causes of death and risk factors in systemic sclerosis (SSc). METHODS: Between 2000 and 2011, we examined the death certificates of all French patients with SSc to determine causes of death. Then we examined causes of death and developed a score associated with all-cause mortality from the international European Scleroderma Trials and Research (EUSTAR) database. Candidate prognostic factors were tested by Cox proportional hazards regression model by single variable analysis, followed by a multiple variable model stratified by centres...
August 23, 2017: Annals of the Rheumatic Diseases
Marawan Ahmed, Horia Jalily Hasani, Aravindhan Ganesan, Michael Houghton, Khaled Barakat
Abnormalities in the human Nav1.5 (hNav1.5) voltage-gated sodium ion channel (VGSC) are associated with a wide range of cardiac problems and diseases in humans. Current structural models of hNav1.5 are still far from complete and, consequently, their ability to study atomistic interactions of this channel is very limited. Here, we report a comprehensive atomistic model of the hNav1.5 ion channel, constructed using homology modeling technique and refined through long molecular dynamics simulations (680 ns) in the lipid membrane bilayer...
2017: Drug Design, Development and Therapy
Daniele Licari, Nicola Tasinato, Lorenzo Spada, Cristina Puzzarini, Vincenzo Barone
The Virtual Multifrequency Spectrometer (VMS) is a tool that aims at integrating a wide range of computational and experimental spectroscopic techniques with the final goal of disclosing the static and dynamic physical-chemical properties "hidden" in molecular spectra. VMS is composed of two parts, namely, VMS-Comp, which provides access to the latest developments in the field of computational spectroscopy, and VMS-Draw, which provides a powerful graphical user interface (GUI) for an intuitive interpretation of theoretical outcomes and a direct comparison to experiment...
September 12, 2017: Journal of Chemical Theory and Computation
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