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https://www.readbyqxmd.com/read/28092680/utilizing-somatic-mutation-data-from-numerous-studies-for-cancer-research-proof-of-concept-and-applications
#1
D Amar, S Izraeli, R Shamir
Large cancer projects measure somatic mutations in thousands of samples, gradually assembling a catalog of recurring mutations in cancer. Many methods analyze these data jointly with auxiliary information with the aim of identifying subtype-specific results. Here, we show that somatic gene mutations alone can reliably and specifically predict cancer subtypes. Interpretation of the classifiers provides useful insights for several biomedical applications. We analyze the COSMIC database, which collects somatic mutations from The Cancer Genome Atlas (TCGA) as well as from many smaller scale studies...
January 16, 2017: Oncogene
https://www.readbyqxmd.com/read/28090600/learning-based-3t-brain-mri-segmentation-with-guidance-from-7t-mri-labeling
#2
Renping Yu, Minghui Deng, Pew-Thian Yap, Zhihui Wei, Li Wang, Dinggang Shen
Brain magnetic resonance image segmentation is one of the most important tasks in medical image analysis and has considerable importance to the effective use of medical imagery in clinical and surgical setting. In particular, the tissue segmentation of white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) is crucial for brain measurement and disease diagnosis. A variety of studies have shown that the learning-based techniques are efficient and effective in brain tissue segmentation. However, the learning-based segmentation methods depend largely on the availability of good training labels...
October 2016: Machine Learning in Medical Imaging
https://www.readbyqxmd.com/read/28058947/the-learning-curve-for-veterinary-surgery-residents-performing-hemilaminectomy-surgeries-in-dogs
#3
Owen T Fink, Raymond C Boston, Tracy Wu, Dorothy Cimino Brown, Jeffrey J Runge
OBJECTIVE To describe the learning curve for veterinary surgery residents performing hemilaminectomy surgeries in dogs. DESIGN Retrospective case review and learning curve evaluation. SAMPLE 13 individuals who completed a 3-year surgery residency program at a university teaching hospital and who had no prior experience performing hemilaminectomies. PROCEDURES The 13 residents performed hemilaminectomies on 399 dogs between July 2006 and July 2013. Medical records were reviewed, and operative time was recorded...
January 15, 2017: Journal of the American Veterinary Medical Association
https://www.readbyqxmd.com/read/28057790/novel-risk-markers-and-risk-assessments-for-cardiovascular-disease
#4
REVIEW
Mark R Thomas, Gregory Y H Lip
The use of risk markers has transformed cardiovascular medicine, exemplified by the routine assessment of troponin, for both diagnosis and assessment of prognosis in patients with chest pain. Clinical risk factors form the basis for risk assessment of cardiovascular disease and the addition of biochemical, cellular, and imaging parameters offers further refinement. Identifying novel risk factors may allow greater risk stratification and a steady, but gradual progression toward precision medicine. Indeed, the generation of data in this area of research is explosive and when combined with new technologies and techniques provides the potential for more refined, targeted approaches to cardiovascular medicine...
January 6, 2017: Circulation Research
https://www.readbyqxmd.com/read/28050574/a-validation-study-of-a-novel-3-dimensional-mri-modeling-technique-to-identify-the-anatomic-insertions-of-the-anterior-cruciate-ligament
#5
Catherine Hui, Yeli Pi, Vimarsha Swami, Myles Mabee, Jacob L Jaremko
BACKGROUND: Anatomic single bundle anterior cruciate ligament (ACL) reconstruction is the current gold standard in ACL reconstructive surgery. However, placement of femoral and tibial tunnels at the anatomic center of the ACL insertion sites can be difficult intraoperatively. We developed a "virtual arthroscopy" program that allows users to identify ACL insertions on preoperative knee magnetic resonance images (MRIs) and generates a 3-dimensional (3D) bone model that matches the arthroscopic view to help guide intraoperative tunnel placement...
December 2016: Orthopaedic Journal of Sports Medicine
https://www.readbyqxmd.com/read/28042769/discovery-of-an-unexplored-protein-structural-scaffold-of-serine-protease-from-big-blue-octopus-octopus-cyanea-a-new-prospective-lead-molecule
#6
Subhamay Panda, Leena Kumari
BACKGROUND: Serine proteases are a group of enzymes that hydrolyses the peptide bonds in proteins. In mammals, these enzymes help in the regulation of several major physiological functions such as digestion, blood clotting, responses of immune system, reproductive functions and the complement system. OBJECTIVE: Serine proteases obtained from the venom of Octopodidae family is a relatively unexplored area of research. In the present work, we tried to effectively utilize comparative composite molecular modeling technique...
January 2, 2017: Current Drug Discovery Technologies
https://www.readbyqxmd.com/read/28042172/a-newton-krylov-method-with-an-approximate-analytical-jacobian-for-implicit-solution-of-navier-stokes-equations-on-staggered-overset-curvilinear-grids-with-immersed-boundaries
#7
Hafez Asgharzadeh, Iman Borazjani
The explicit and semi-implicit schemes in flow simulations involving complex geometries and moving boundaries suffer from time-step size restriction and low convergence rates. Implicit schemes can be used to overcome these restrictions, but implementing them to solve the Navier-Stokes equations is not straightforward due to their non-linearity. Among the implicit schemes for nonlinear equations, Newton-based techniques are preferred over fixed-point techniques because of their high convergence rate but each Newton iteration is more expensive than a fixed-point iteration...
February 15, 2017: Journal of Computational Physics
https://www.readbyqxmd.com/read/28040199/molecular-classification-of-breast-cancer-what-the-pathologist-needs-to-know
#8
Emad A Rakha, Andrew R Green
Breast cancer is a heterogeneous disease featuring distinct histological, molecular and clinical phenotypes. Although traditional classification systems utilising clinicopathological and few molecular markers are well established and validated, they remain insufficient to reflect the diverse biological and clinical heterogeneity of breast cancer. Advancements in high-throughput molecular techniques and bioinformatics have contributed to the improved understanding of breast cancer biology, refinement of molecular taxonomies and the development of novel prognostic and predictive molecular assays...
December 28, 2016: Pathology
https://www.readbyqxmd.com/read/28017603/guideline-for-reporting-interventions-on-spinal-manipulative-therapy-consensus-on-interventions-reporting-criteria-list-for-spinal-manipulative-therapy-circle-smt
#9
Ruud Groeneweg, Sidney M Rubinstein, Rob A B Oostendorp, Raymond W J G Ostelo, Maurits W van Tulder
OBJECTIVE: The aim of the Consensus on Interventions Reporting Criteria List for Spinal Manipulative Therapy (CIRCLe SMT) study was to develop a criteria list for reporting spinal manipulative therapy (SMT). METHODS: A Delphi procedure was conducted from September 2011 to April 2013 and consisted of international experts in the field of SMT. The authors formed a steering committee and invited participants, selected initial items, structured the comments of the participants after each Delphi round, and formulated the feedback...
December 22, 2016: Journal of Manipulative and Physiological Therapeutics
https://www.readbyqxmd.com/read/27989662/immunoinformatics-analysis-and-in-silico-designing-of-a-novel-multi-epitope-peptide-vaccine-against-staphylococcus-aureus
#10
Nasim Hajighahramani, Navid Nezafat, Mahboobeh Eslami, Manica Negahdaripour, Seyyed Soheil Rahmatabadi, Younes Ghasemi
Staphylococcus aureus is a pathogen that causes a variety of infections in humans. Methicillin-resistant S. aureus, which is an antibiotic-resistant form, is responsible for nosocomial staphylococcal infections, whose frequency is increasing in healthy people. Thereby, the development of novel techniques is required to overcome this bacterial infection. In this context, the use of vaccines to control infections is an appropriate alternative. In this study, immunoinformatics analysis is used on three antigenic determinants as vaccine candidates, and a novel multi-epitope vaccine is designed to induce cellular, humoral, and innate immune responses against S...
December 16, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27977044/li18-p6-n16-a-lithium-nitridophosphate-with-unprecedented-tricyclic-p6-n16-18-ions
#11
Eva-Maria Bertschler, Christian Dietrich, Jürgen Janek, Wolfgang Schnick
Li18 P6 N16 was synthesized by reaction of LiPN2 and Li7 PN4 at 5.5 GPa and 1273 K employing the multi-anvil technique. It is the first lithium nitridophosphate obtained by high-pressure synthesis. Moreover, it is the first example received by reaction of two ternary lithium nitrides. The combination of high-pressure conditions with a Li3 N flux enabled a complete structure determination using single-crystal X-ray diffraction. The hitherto unknown tricyclic [P6 N16 ](18-) anion is composed of six vertex-sharing PN4 tetrahedra forming one vierer- and two additional dreier-rings...
December 15, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27967135/grid-refinement-for-entropic-lattice-boltzmann-models
#12
B Dorschner, N Frapolli, S S Chikatamarla, I V Karlin
We propose a multidomain grid refinement technique with extensions to entropic incompressible, thermal, and compressible lattice Boltzmann models. Its validity and accuracy are assessed by comparison to available direct numerical simulation and experiment for the simulation of isothermal, thermal, and viscous supersonic flow. In particular, we investigate the advantages of grid refinement for the setups of turbulent channel flow, flow past a sphere, Rayleigh-Bénard convection, as well as the supersonic flow around an airfoil...
November 2016: Physical Review. E
https://www.readbyqxmd.com/read/27927609/data-analysis-protocol-for-the-development-and-evaluation-of-population-pharmacokinetic-models-for-incorporation-into-the-web-accessible-population-pharmacokinetic-service-hemophilia-wapps-hemo
#13
Alanna McEneny-King, Gary Foster, Alfonso Iorio, Andrea N Edginton
BACKGROUND: Hemophilia is an inherited bleeding disorder caused by a deficiency in a specific clotting factor. This results in spontaneous bleeding episodes and eventual arthropathy. The mainstay of hemophilia treatment is prophylactic replacement of the missing factor, but an optimal regimen remains to be determined. Rather, individualized prophylaxis has been suggested to improve both patient safety and resource utilization. However, uptake of this approach has been hampered by the demanding sampling schedules and complex calculations required to obtain individual estimates of pharmacokinetic (PK) parameters...
December 7, 2016: JMIR Research Protocols
https://www.readbyqxmd.com/read/27834115/long-term-functional-outcomes-after-radical-cystectomy-with-ileal-bladder-substitute-does-the-definition-of-continence-matter
#14
Fredrik Liedberg, Göran Ahlgren, Gediminas Baseckas, Sigurdur Gudjonsson, Ulf Håkansson, Sara Lindquist, Annica Löfgren, Oliver Patschan, Carina Siller, Gottfrid Sjödahl
OBJECTIVE: Functional outcomes after ileal bladder substitution reflect the expectations of future patients at a particular centre. The aim of this study was to use validated questionnaires and a pad-weighing test to investigate functional outcomes after neobladder reconstruction at long-term follow-up in patients at a single centre. MATERIALS AND METHODS: During 2005 - 2015, 75 patients received a Studer ileal bladder substitute at the Department of Urology, Malmö...
November 11, 2016: Scandinavian Journal of Urology
https://www.readbyqxmd.com/read/27823804/a-non-ionizing-technique-for-three-dimensional-measurement-of-the-lumbar-spine
#15
Terry K Koo, Wingchi Edmund Kwok
Comprehensive assessments of scoliotic deformity and spinal instability require repetitive three-dimensional (3D) measurements of motion segments at different functional postures. However, accurate 3D measurement of the spine is a challenging task. In this paper, we present a novel, non-invasive, non-ionizing technique to quantify 3D poses of lumbar motion segments in terms of clinically meaningful anatomical coordinates. The technique used ultra-short echo time (UTE) magnetic resonance (MR) images to construct subject-specific geometrical models of individual vertebrae and registered them with 3D ultrasound dataset acquired during pose measurements...
December 8, 2016: Journal of Biomechanics
https://www.readbyqxmd.com/read/27813346/validation-of-a-non-conforming-monolithic-fluid-structure-interaction-method-using-phase-contrast-mri
#16
A Hessenthaler, O Röhrle, D A Nordsletten
This paper details the validation of a non-conforming arbitrary Lagrangian-Eulerian fluid-structure interaction (FSI) technique using a recently developed experimental 3D FSI benchmark problem. Numerical experiments for steady and transient test cases of the benchmark were conducted employing an inf-sup stable and a general Galerkin scheme. The performance of both schemes is assessed. Spatial refinement with three mesh refinement levels and fluid domain truncation with two fluid domain lengths are studied as well as employing a sequence of increasing time step sizes for steady-state cases...
November 4, 2016: International Journal for Numerical Methods in Biomedical Engineering
https://www.readbyqxmd.com/read/27766412/reflectance-based-determination-of-age-and-species-of-blowfly-puparia
#17
Sasha C Voss, Paola Magni, Ian Dadour, Christian Nansen
Forensic entomology is primarily concerned with the estimation of time since death and involves determination of the age of immature insects colonising decomposing remains. Accurate age determination of puparia is usually accomplished by dissection, which means destructive sampling of evidence. As part of improving abilities to correctly identify species and developmental age, it is highly desirable to have available non-destructive methods. In this study, we acquired external hyperspectral imaging (HSI) data (77 spectral bands, 389-892 nm) from the dorsal and ventral sides of individual puparia of two species of blowfly (Diptera: Calliphoridae), Calliphora dubia Macquart 1855 and Chrysomya rufifacies Macquart 1842...
January 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/27754385/a-fast-superpixel-segmentation-algorithm-for-polsar-images-based-on-edge-refinement-and-revised-wishart-distance
#18
Yue Zhang, Huanxin Zou, Tiancheng Luo, Xianxiang Qin, Shilin Zhou, Kefeng Ji
The superpixel segmentation algorithm, as a preprocessing technique, should show good performance in fast segmentation speed, accurate boundary adherence and homogeneous regularity. A fast superpixel segmentation algorithm by iterative edge refinement (IER) works well on optical images. However, it may generate poor superpixels for Polarimetric synthetic aperture radar (PolSAR) images due to the influence of strong speckle noise and many small-sized or slim regions. To solve these problems, we utilized a fast revised Wishart distance instead of Euclidean distance in the local relabeling of unstable pixels, and initialized unstable pixels as all the pixels substituted for the initial grid edge pixels in the initialization step...
October 13, 2016: Sensors
https://www.readbyqxmd.com/read/27741494/micro-ct-based-finite-element-models-of-cancellous-bone-predict-accurately-displacement-once-the-boundary-condition-is-well-replicated-a-validation-study
#19
Yuan Chen, Enrico Dall Ara, Erika Sales, Krishnagoud Manda, Robert Wallace, Pankaj Pankaj, Marco Viceconti
Non-destructive 3D micro-computed tomography (microCT) based finite element (microFE) models are used to estimate bone mechanical properties at tissue level. However, their validation remains challenging. Recent improvements in the quantification of displacements in bone tissue biopsies subjected to staged compression, using refined Digital Volume Correlation (DVC) techniques, now provide a full field displacement information accurate enough to be used for microFE validation. In this study, three specimens (two humans and one bovine) were tested with two different experimental set-ups, and the resulting data processed with the same DVC algorithm...
January 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/27739434/multiparametric-mri-based-differentiation-of-who-grade-ii-iii-glioma-and-who-grade-iv-glioblastoma
#20
Benedikt Wiestler, Anne Kluge, Mathias Lukas, Jens Gempt, Florian Ringel, Jürgen Schlegel, Bernhard Meyer, Claus Zimmer, Stefan Förster, Thomas Pyka, Christine Preibisch
Non-invasive, imaging-based examination of glioma biology has received increasing attention in the past couple of years. To this end, the development and refinement of novel MRI techniques, reflecting underlying oncogenic processes such as hypoxia or angiogenesis, has greatly benefitted this research area. We have recently established a novel BOLD (blood oxygenation level dependent) based MRI method for the measurement of relative oxygen extraction fraction (rOEF) in glioma patients. In a set of 37 patients with newly diagnosed glioma, we assessed the performance of a machine learning model based on multiple MRI modalities including rOEF and perfusion imaging to predict WHO grade...
October 14, 2016: Scientific Reports
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