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https://www.readbyqxmd.com/read/28300375/photon-optimizer-po-prevails-over-progressive-resolution-optimizer-pro-for-vmat-planning-with-or-without-knowledge-based-solution
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28100961/auxin-extraction-and-purification-based-on-recombinant-aux-iaa-proteins
#12
Yi Su, Weigui Luo, Xiaofei Chen, Huizhen Liu, Yueqing Hu, Wanhuang Lin, Langtao Xiao
BACKGROUND: Indole-3-acetic acid (IAA) extraction and purification are of great importance in auxin research, which is a hot topic in the plant growth and development field. Solid-phase extraction (SPE) is frequently used for IAA extraction and purification. However, no IAA-specific SPE columns are commercially available at the moment. Therefore, the development of IAA-specific recognition materials and IAA extraction and purification methods will help researchers meet the need for more precise analytical methods for research on phytohormones...
2017: Biological Procedures Online
https://www.readbyqxmd.com/read/28092680/utilizing-somatic-mutation-data-from-numerous-studies-for-cancer-research-proof-of-concept-and-applications
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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...
February 2017: Pathology
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