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https://www.readbyqxmd.com/read/28093409/deuterater-a-tool-for-quantifying-peptide-isotope-precision-and-kinetic-proteomics
#1
Bradley C Naylor, Michael T Porter, Elise Wilson, Adam Herring, Spencer Lofthouse, Austin Hannemann, Stephen R Piccolo, Alan L Rockwood, John C Price
MOTIVATION: Using mass spectrometry to measure the concentration and turnover of the individual proteins in a proteome, enables the calculation of individual synthesis and degradation rates for each protein. Software to analyze concentration is readily available, but software to analyze turnover is lacking. Data analysis workflows typically don't access the full breadth of information about instrument precision and accuracy that is present in each peptide isotopic envelope measurement...
January 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28080919/restrictive-cardiomyopathy-and-secondary-congestive-heart-failure-in-a-mcdowell-s-carpet-python-morelia-spilota-mcdowelli
#2
Lionel Schilliger, Valérie Chetboul, Cécile Damoiseaux, Alexandra Nicolier
Echocardiography is an established and noninvasive diagnostic tool used in herpetologic cardiology. Various cardiac lesions have been previously described in reptiles with the exception of restrictive cardiomyopathy. In this case report, restrictive cardiomyopathy and congestive heart failure associated with left atrial and sinus venosus dilation were diagnosed in a 2-yr-old captive lethargic McDowell's carpet python ( Morelia spilota mcdowelli), based on echocardiographic, Doppler, and histopathologic examinations...
December 2016: Journal of Zoo and Wildlife Medicine: Official Publication of the American Association of Zoo Veterinarians
https://www.readbyqxmd.com/read/28076851/pse-analysis-a-python-package-for-dna-rna-and-protein-peptide-sequence-analysis-based-on-pseudo-components-and-kernel-methods
#3
Bin Liu, Hao Wu, Deyuan Zhang, Xiaolong Wang, Kuo-Chen Chou
To expedite the pace in conducting genome/proteome analysis, we have developed a Python package called Pse-Analysis. The powerful package can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3) model training, (4) cross validation, and (5) evaluating prediction quality. All the work a user needs to do is to input a benchmark dataset along with the query biological sequences concerned. Based on the benchmark dataset, Pse-Analysis will automatically construct an ideal predictor, followed by yielding the predicted results for the submitted query samples...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28076801/msmbuilder-statistical-models-for-biomolecular-dynamics
#4
Matthew P Harrigan, Mohammad M Sultan, Carlos X Hernández, Brooke E Husic, Peter Eastman, Christian R Schwantes, Kyle A Beauchamp, Robert T McGibbon, Vijay S Pande
MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov state models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models and time-structure based independent component analysis...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28065903/caspo-a-toolbox-for-automated-reasoning-on-the-response-of-logical-signaling-networks-families
#5
Santiago Videla, Julio Saez-Rodriguez, Carito Guziolowski, Anne Siegel
: We introduce the caspo toolbox, a python package implementing a workflow for reasoning on logical networks families. Our software allows researchers to (i) LEARN: a family of logical networks derived from a given topology and explaining the experimental response to various perturbations; (ii) CLASSIFY: all logical networks in a given family by their input-output behaviors; (iii) PREDICT: the response of the system to every possible perturbation based on the ensemble of predictions; (iv) DESIGN: new experimental perturbations to discriminate among a family of logical networks; and (v) CONTROL: a family of logical networks by finding all interventions strategies forcing a set of targets into a desired steady state...
January 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28062450/the-structural-bioinformatics-library-modeling-in-biomolecular-science-and-beyond
#6
Frédéric Cazals, Tom Dreyfus
MOTIVATION: Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library (SBL, http://sbl.inria.fr), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28061810/pyviko-an-automated-python-tool-to-design-gene-knockouts-in-complex-viruses-with-overlapping-genes
#7
Louis J Taylor, Klaus Strebel
BACKGROUND: Gene knockouts are a common tool used to study gene function in various organisms. However, designing gene knockouts is complicated in viruses, which frequently contain sequences that code for multiple overlapping genes. Designing mutants that can be traced by the creation of new or elimination of existing restriction sites further compounds the difficulty in experimental design of knockouts of overlapping genes. While software is available to rapidly identify restriction sites in a given nucleotide sequence, no existing software addresses experimental design of mutations involving multiple overlapping amino acid sequences in generating gene knockouts...
January 7, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28057747/complete-genome-sequence-of-akkermansia-glycaniphila-strain-pytt-a-mucin-degrading-specialist-of-the-reticulated-python-gut
#8
Janneke P Ouwerkerk, Jasper J Koehorst, Peter J Schaap, Jarmo Ritari, Lars Paulin, Clara Belzer, Willem M de Vos
Akkermansia glycaniphila is a novel Akkermansia species that was isolated from the intestine of the reticulated python and shares the capacity to degrade mucin with the human strain Akkermansia muciniphila Muc(T) Here, we report the complete genome sequence of strain Pyt(T) of 3,074,121 bp. The genomic analysis reveals genes for mucin degradation and aerobic respiration.
January 5, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28052923/primerize-2d-automated-primer-design-for-rna-multidimensional-chemical-mapping
#9
Siqi Tian, Rhiju Das
Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allows synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors...
January 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28048855/th-d-brb-01-scripting-fundamentals-killing-cancer-with-code
#10
R Popple
: Scripting capabilities and application programming interfaces (APIs) are becoming commonly available in modern treatment planning systems. These links to the treatment planning system (TPS) allow users to read data from the TPS, and in some cases use TPS functionality and write data back to the TPS. Such tools are powerful extensions, allowing automation of routine clinical tasks and supporting research, particularly research involving repetitive tasks on large patient populations. The data and functionality exposed by scripting/API capabilities is vendor dependent, as are the languages used by script/API engines, such as the Microsoft ...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048754/su-f-j-204-carbon-digitally-reconstructed-radiography-cdrr-a-gpu-based-tool-for-fast-and-versatile-carbonimaging-simulation
#11
M F Dias, J Seco, G Baroni, M Riboldi
PURPOSE: Research in carbon imaging has been growing over the past years, as a way to increase treatment accuracy and patient positioning in carbon therapy. The purpose of this tool is to allow a fast and flexible way to generate CDRR data without the need to use Monte Carlo (MC) simulations. It can also be used to predict future clinically measured data. METHODS: A python interface has been developed, which uses information from CT or 4DCT and thetreatment calibration curve to compute the Water Equivalent Path Length (WEPL) of carbon ions...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048312/su-g-brb-02-an-open-source-software-analysis-library-for-linear-accelerator-quality-assurance
#12
J Kerns, D Yaldo
PURPOSE: Routine linac quality assurance (QA) tests have become complex enough to require automation of most test analyses. A new data analysis software library was built that allows physicists to automate routine linear accelerator quality assurance tests. The package is open source, code tested, and benchmarked. METHODS: Images and data were generated on a TrueBeam linac for the following routine QA tests: VMAT, starshot, CBCT, machine logs, Winston Lutz, and picket fence...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048235/su-g-tep4-09-development-of-a-plan-data-aggregator-for-time-efficient-physics-second-checks-of-machine-parameters-for-external-beam-treatment-plans
#13
M Belley, M Schmidt, N Knutson, M Price
PURPOSE: Physics second-checks for external beam radiation therapy are performed, in-part, to verify that the machine parameters in the Record-and-Verify (R&V) system that will ultimately be sent to the LINAC exactly match the values initially calculated by the Treatment Planning System (TPS). While performing the second-check, a large portion of the physicists' time is spent navigating and arranging display windows to locate and compare the relevant numerical values (MLC position, collimator rotation, field size, MU, etc...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048205/th-d-brb-02-eclipse-scripting-fundamentals-in-net
#14
R Cardan
: Scripting capabilities and application programming interfaces (APIs) are becoming commonly available in modern treatment planning systems. These links to the treatment planning system (TPS) allow users to read data from the TPS, and in some cases use TPS functionality and write data back to the TPS. Such tools are powerful extensions, allowing automation of routine clinical tasks and supporting research, particularly research involving repetitive tasks on large patient populations. The data and functionality exposed by scripting/API capabilities is vendor dependent, as are the languages used by script/API engines, such as the Microsoft ...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048177/th-d-brb-04-pinnacle-scripting-improving-efficiency-while-maintaining-safety
#15
J Moore
: Scripting capabilities and application programming interfaces (APIs) are becoming commonly available in modern treatment planning systems. These links to the treatment planning system (TPS) allow users to read data from the TPS, and in some cases use TPS functionality and write data back to the TPS. Such tools are powerful extensions, allowing automation of routine clinical tasks and supporting research, particularly research involving repetitive tasks on large patient populations. The data and functionality exposed by scripting/API capabilities is vendor dependent, as are the languages used by script/API engines, such as the Microsoft ...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048030/tu-ab-brc-12-optimized-parallel-montecarlo-dose-calculations-for-secondary-mu-checks
#16
S French, M Bellor, D Nazareth
PURPOSE: Secondary MU checks are an important tool used during a physics review of a treatment plan. Commercial software packages offer varying degrees of theoretical dose calculation accuracy, depending on the modality involved. Dose calculations of VMAT plans are especially prone to error due to the large approximations involved. Monte Carlo (MC) methods are not commonly used due to their long run times. We investigated two methods to increase the computational efficiency of MC dose simulations with the BEAMnrc code...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047834/su-c-bra-04-automated-segmentation-of-head-and-neck-ct-images-for-radiotherapy-treatment-planning-via-multi-atlas-machine-learning-maml
#17
X Ren, G Sharp, H Gao
PURPOSE: Accurate image segmentation is a crucial step during image guided radiation therapy. This work proposes multi-atlas machine learning (MAML) algorithm for automated segmentation of head-and-neck CT images. METHODS: As the first step, the algorithm utilizes normalized mutual information as similarity metric, affine registration combined with multiresolution B-Spline registration, and then fuses together using the label fusion strategy via Plastimatch. As the second step, the following feature selection strategy is proposed to extract five feature components from reference or atlas images: intensity (I), distance map (D), box (B), center of gravity (C) and stable point (S)...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047809/su-c-brc-07-parametrized-gpu-accelerated-electron-monte-carlo-second-check
#18
J Haywood
PURPOSE: I am presenting a parameterized 3D GPU accelerated electron Monte Carlo second check program. METHOD: I wrote the 3D grid dose calculation algorithm in CUDA and utilized an NVIDIA GeForce GTX 780 Ti to run all of the calculations. The electron path beyond the distal end of the cone is governed by four parameters: the amplitude of scattering (AMP), the mean and width of a Gaussian energy distribution (E and α), and the percentage of photons. In my code, I adjusted all parameters until the calculated PDD and profile fit the measured 10×10 open beam data within 1%/1mm...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047670/su-f-p-20-predicting-waiting-times-in-radiation-oncology-using-machine-learning
#19
A Joseph, D Herrera, T Hijal, L Hendren, A Leung, J Wainberg, M Sawaf, M Gorshkov, R Maglieri, M Keshavarz, J Kildea
PURPOSE: Waiting times remain one of the most vexing patient satisfaction challenges facing healthcare. Waiting time uncertainty can cause patients, who are already sick or in pain, to worry about when they will receive the care they need. These waiting periods are often difficult for staff to predict and only rough estimates are typically provided based on personal experience. This level of uncertainty leaves most patients unable to plan their calendar, making the waiting experience uncomfortable, even painful...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047665/su-d-201-01-a-multi-institutional-study-quantifying-the-impact-of-simulated-linear-accelerator-vmat-errors-for-nasopharynx
#20
E Pogson, C Hansen, S Blake, S Arumugam, J Juresic, C Ochoa, J Yakobi, A Haman, A Trtovac, L Holloway, D Thwaites
PURPOSE: To quantify the impact of differing magnitudes of simulated linear accelerator errors on the dose to the target volume and organs at risk for nasopharynx VMAT. METHODS: Ten nasopharynx cancer patients were retrospectively replanned twice with one full arc VMAT by two institutions. Treatment uncertainties (gantry angle and collimator in degrees, MLC field size and MLC shifts in mm) were introduced into these plans at increments of 5,2,1,-1,-2 and -5. This was completed using an in-house Python script within Pinnacle3 and analysed using 3DVH and MatLab...
June 2016: Medical Physics
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