keyword
MENU ▼
Read by QxMD icon Read
search

python

keyword
https://www.readbyqxmd.com/read/29142808/analyzing-microtomography-data-with-python-and-the-scikit-image-library
#1
Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
The exploration and processing of images is a vital aspect of the scientific workflows of many X-ray imaging modalities. Users require tools that combine interactivity, versatility, and performance. scikit-image is an open-source image processing toolkit for the Python language that supports a large variety of file formats and is compatible with 2D and 3D images. The toolkit exposes a simple programming interface, with thematic modules grouping functions according to their purpose, such as image restoration, segmentation, and measurements...
2017: Advanced Structural and Chemical Imaging
https://www.readbyqxmd.com/read/29141489/non-linear-conversion-of-hx4-uptake-for-automatic-segmentation-of-hypoxic-volumes-and-dose-prescription
#2
Ana Ureba, Emely Lindblom, Alexandru Dasu, Johan Uhrdin, Aniek J G Even, Wouter van Elmpt, Philippe Lambin, Peter Wersäll, Iuliana Toma-Dasu
BACKGROUND: Tumour hypoxia is associated with increased radioresistance and poor response to radiotherapy. Pre-treatment assessment of tumour oxygenation could therefore give the possibility to tailor the treatment by calculating the required boost dose needed to overcome the increased radioresistance in hypoxic tumours. This study concerned the derivation of a non-linear conversion function between the uptake of the hypoxia-PET tracer (18)F-HX4 and oxygen partial pressure (pO2). MATERIAL AND METHODS: Building on previous experience with FMISO including experimental data on tracer uptake and pO2, tracer-specific model parameters were derived for converting the normalised HX4-uptake at the optimal imaging time point to pO2...
November 16, 2017: Acta Oncologica
https://www.readbyqxmd.com/read/29141013/indcaps-a-tool-for-designing-screening-primers-for-crispr-cas9-mutagenesis-events
#3
Charles Hodgens, Zachary L Nimchuk, Joseph J Kieber
Genetic manipulation of organisms using CRISPR/Cas9 technology generally produces small insertions/deletions (indels) that can be difficult to detect. Here, we describe a technique to easily and rapidly identify such indels. Sequence-identified mutations that alter a restriction enzyme recognition site can be readily distinguished from wild-type alleles using a cleaved amplified polymorphic sequence (CAPS) technique. If a restriction site is created or altered by the mutation such that only one allele contains the restriction site, a polymerase chain reaction (PCR) followed by a restriction digest can be used to distinguish the two alleles...
2017: PloS One
https://www.readbyqxmd.com/read/29140977/low-cost-and-open-source-multi-fluorescence-imaging-system-for-teaching-and-research-in-biology-and-bioengineering
#4
Isaac Nuñez, Tamara Matute, Roberto Herrera, Juan Keymer, Timothy Marzullo, Timothy Rudge, Fernán Federici
The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates...
2017: PloS One
https://www.readbyqxmd.com/read/29135037/analytical-hessian-fitting-schemes-for-efficient-determination-of-force-constant-parameters-in-molecular-mechanics
#5
Ruixing Wang, Mikhail Ozhgibesov, Hajime Hirao
Building upon our recently developed partial Hessian fitting (PHF) method (Wang et al., J. Comput. Chem. 2016, 37, 2349), we formulated and implemented two other rapid force-field parameterization schemes called full Hessian fitting (FHF) and internal Hessian fitting (IHF), and comparisons were made among these three parameterization schemes to assess their performance. FHF minimizes deviation between the Hessian matrices in Cartesian coordinates computed by quantum mechanics (QM) and molecular mechanics (MM), to determine the best possible MM force-constant parameters...
November 14, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29132360/neoanalysis-a-python-based-toolbox-for-quick-electrophysiological-data-processing-and-analysis
#6
Bo Zhang, Ji Dai, Tao Zhang
BACKGROUND: In a typical electrophysiological experiment, especially one that includes studying animal behavior, the data collected normally contain spikes, local field potentials, behavioral responses and other associated data. In order to obtain informative results, the data must be analyzed simultaneously with the experimental settings. However, most open-source toolboxes currently available for data analysis were developed to handle only a portion of the data and did not take into account the sorting of experimental conditions...
November 13, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/29131856/examination-of-sarcocystis-spp-of-giant-snakes-from-australia-and-southeast-asia-confirms-presence-of-a-known-pathogen-sarcocystis-nesbitti
#7
Marion Wassermann, Lisa Raisch, Jessica Ann Lyons, Daniel James Deans Natusch, Sarah Richter, Mareike Wirth, Piyarat Preeprem, Yuvaluk Khoprasert, Sulaiman Ginting, Ute Mackenstedt, Thomas Jäkel
We examined Sarcocystis spp. in giant snakes from the Indo-Australian Archipelago and Australia using a combination of morphological (size of sporocyst) and molecular analyses. We amplified by PCR nuclear 18S rDNA from single sporocysts in order to detect mixed infections and unequivocally assign the retrieved sequences to the corresponding parasite stage. Sarcocystis infection was generally high across the study area, with 78 (68%) of 115 examined pythons being infected by one or more Sarcocystis spp. Among 18 randomly chosen, sporocyst-positive samples (11 from Southeast Asia, 7 from Northern Australia) the only Sarcocystis species detected in Southeast Asian snakes was S...
2017: PloS One
https://www.readbyqxmd.com/read/29126132/cost-effective-and-accurate-method-of-measuring-fetal-fraction-using-snp-imputation
#8
Minjeong Kim, Jai-Hoon Kim, Kangseok Kim, Sunshin Kim
Motivation: With the discovery of cell-free fetal DNA in maternal blood, the demand for non-invasive prenatal testing (NIPT) has been increasing. To obtain reliable NIPT results, it is important to accurately estimate the fetal fraction. In this study, we propose an accurate and cost-effective method for measuring fetal fractions using single-nucleotide polymorphisms (SNPs). Results: A total of 84 samples were sequenced via semiconductor sequencing using a 0.3x sequencing coverage...
November 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29126124/predicting-drug-safety-and-communicating-risk-benefits-of-a-bayesian-approach
#9
Stanley E Lazic, Nicholas Edmunds, Christopher E Pollard
Drug toxicity is a major source of attrition in drug discovery and development. Pharmaceutical companies routinely use preclinical data to predict clinical outcomes and continue to invest in new assays to improve predictions. However, there are many open questions about how to make the best use of available data, combine diverse data, quantify risk, and communicate risk and uncertainty to enable good decisions. The costs of suboptimal decisions are clear: resources are wasted and patients may be put at risk...
November 6, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29121484/erp-evidence-of-distinct-processes-underlying-semantic-facilitation-and-interference-in-word-production
#10
Grégoire Python, Raphaël Fargier, Marina Laganaro
In everyday conversations, we take advantage of lexical-semantic contexts to facilitate speech production, but at the same time, we also have to reduce interference and inhibit semantic competitors. The blocked cyclic naming paradigm (BCNP) has been used to investigate such context effects. Typical results on production latencies showed semantic facilitation (or no effect) during the first presentation cycle, and interference emerging in subsequent cycles. Even if semantic contexts might be just as facilitative as interfering, previous BCNP studies focused on interference, which was interpreted as reflecting lemma selection and self-monitoring processes...
October 3, 2017: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/29121165/perf-an-exhaustive-algorithm-for-ultra-fast-and-efficient-identification-of-microsatellites-from-large-dna-sequences
#11
Akshay Kumar Avvaru, Divya Tej Sowpati, Rakesh Kumar Mishra
Motivation: Microsatellites or Simple Sequence Repeats (SSRs) are short tandem repeats of DNA motifs present in all genomes. They have long been used for a variety of purposes in the areas of population genetics, genotyping, marker-assisted selection, and forensics. Numerous studies have highlighted their functional roles in genome organization and gene regulation. Though several tools are currently available to identify SSRs from genomic sequences, they have significant limitations. Results: We present a novel algorithm called PERF for extremely fast and comprehensive identification of microsatellites from DNA sequences of any size...
November 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29121073/diffslc-a-graph-centrality-method-to-detect-essential-proteins-of-a-protein-protein-interaction-network
#12
Divya Mistry, Roger P Wise, Julie A Dickerson
Identification of central genes and proteins in biomolecular networks provides credible candidates for pathway analysis, functional analysis, and essentiality prediction. The DiffSLC centrality measure predicts central and essential genes and proteins using a protein-protein interaction network. Network centrality measures prioritize nodes and edges based on their importance to the network topology. These measures helped identify critical genes and proteins in biomolecular networks. The proposed centrality measure, DiffSLC, combines the number of interactions of a protein and the gene coexpression values of genes from which those proteins were translated, as a weighting factor to bias the identification of essential proteins in a protein interaction network...
2017: PloS One
https://www.readbyqxmd.com/read/29114125/prevalence-of-amblyomma-gervaisi-ticks-on-captive-snakes-in-tamil-nadu
#13
B R Catherine, M G Jayathangaraj, C Soundararajan, C Bala Guru, D Yogaraj
Ticks are the important ectoparasites that occur on snakes and transmit rickettsiosis, anaplasmosis and ehrlichiosis. A total of 62 snakes (Reticulated python, Indian Rock Python, Rat snakes and Spectacled cobra) were examined for tick infestation at Chennai Snake Park Trust (Guindy), Arignar Anna Zoological Park (Vandalur) and Rescue centre (Velachery) in Tamil Nadu from September, 2015 to June, 2016. Ticks from infested snakes were collected and were identified as Amblyomma gervaisi (previously known as Aponomma gervaisi)...
December 2017: Journal of Parasitic Diseases: Official Organ of the Indian Society for Parasitology
https://www.readbyqxmd.com/read/29106469/dfast-a-flexible-prokaryotic-genome-annotation-pipeline-for-faster-genome-publication
#14
Yasuhiro Tanizawa, Takatomo Fujisawa, Yasukazu Nakamura
Summary: We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes...
November 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29106441/orchid-a-novel-management-annotation-and-machine-learning-framework-for-analyzing-cancer-mutations
#15
Clinton L Cario, John S Witte
Motivation: As whole-genome tumor sequence and biological annotation datasets grow in size, number, and content, there is an increasing basic science and clinical need for efficient and accurate data management and analysis software. With the emergence of increasingly sophisticated data stores, execution environments, and machine learning algorithms, there is also a need for the integration of functionality across frameworks. Results: We present orchid, a python based software package for the management, annotation, and machine learning of cancer mutations...
November 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29104852/a-streaming-multi-gpu-implementation-of-image-simulation-algorithms-for-scanning-transmission-electron-microscopy
#16
Alan Pryor, Colin Ophus, Jianwei Miao
Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods...
2017: Advanced Structural and Chemical Imaging
https://www.readbyqxmd.com/read/29104445/development-of-a-microbial-dose-response-visualization-and-modelling-application-for-qmra-modelers-and-educators
#17
Mark H Weir, Jade Mitchell, William Flynn, Joanna M Pope
Microbial dose response modelling is vital to a well-characterized microbial risk estimate. Dose response modelling is an inherently multidisciplinary field, which collates knowledge and data from disparate scientific fields. This multidisciplinary nature presents a key challenge to the expansion of microbial dose response modelling into new groups of researchers and modelers. This research employs a dose response optimization R code used in 18 peer-reviewed research studies to develop a multi-functional dose response software...
February 2017: Environmental Modelling & Software: with Environment Data News
https://www.readbyqxmd.com/read/29104018/the-influence-of-midazolam-on-heart-rate-arises-from-cardiac-autonomic-tones-alterations-in-burmese-pythons-python-molurus
#18
Ivã Guidini Lopes, Vinicius Araújo Armelin, Victor Hugo da Silva Braga, Luiz Henrique Florindo
The GABAA receptor agonist midazolam is a compound widely used as a tranquilizer and sedative in mammals and reptiles. It is already known that this benzodiazepine produces small to intermediate heart rate (HR) alterations in mammals, however, its influence on reptiles' HR remains unexplored. Thus, the present study sought to verify the effects of midazolam on HR and cardiac modulation in the snake Python molurus. To do so, the snakes' HR, cardiac autonomic tones, and HR variability were evaluated during four different experimental stages...
October 28, 2017: Autonomic Neuroscience: Basic & Clinical
https://www.readbyqxmd.com/read/29095974/beam-web-server-a-tool-for-structural-rna-motif-discovery
#19
Marco Pietrosanto, Marta Adinolfi, Riccardo Casula, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich
Motivation: RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. Results: The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance...
October 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29095557/developmental-genetic-and-genomic-insights-into-the-evolutionary-loss-of-limbs-in-snakes
#20
REVIEW
Francisca Leal, Martin J Cohn
The evolution of snakes involved dramatic modifications to the ancestral lizard body plan. Limb loss and elongation of the trunk are hallmarks of snakes, although convergent evolution of limb-reduced and trunk-elongated forms occurred multiple times in snake-like lizards. Advanced snakes are completely limbless, but intermediate and basal snakes have retained rudiments of hindlimbs and pelvic girdles. Moreover, the snake fossil record indicates that complete legs were re-acquired at least once, suggesting that the potential for limb development was retained in some limb-reduced taxa...
November 2, 2017: Genesis: the Journal of Genetics and Development
keyword
keyword
29490
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"