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https://www.readbyqxmd.com/read/28817597/a-unified-censored-normal-regression-model-for-qpcr-differential-gene-expression-analysis
#1
Peter Pipelers, Lieven Clement, Matthijs Vynck, Jan Hellemans, Jo Vandesompele, Olivier Thas
Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is considered as the gold standard for accurate, sensitive, and fast measurement of gene expression. Prior to downstream statistical analysis, RT-qPCR fluorescence amplification curves are summarized into one single value, the quantification cycle (Cq). When RT-qPCR does not reach the limit of detection, the Cq is labeled as "undetermined". Current state of the art qPCR data analysis pipelines acknowledge the importance of normalization for removing non-biological sample to sample variation in the Cq values...
2017: PloS One
https://www.readbyqxmd.com/read/28817486/overcoming-clopidogrel-resistance-three-promising-novel-antiplatelet-drugs-developed-in-china
#2
Hong-Guang Xie, Yu-Meng Jia, Ting Tai, Jin-Zi Ji
Clopidogrel is one of the most frequently prescribed drugs worldwide; however, the presence of clopidogrel resistance and high susceptibility to genetic variations and drug interactions are facilitating the development of other antiplatelet drugs. To overcome clopidogrel resistance, several promising clopidogrel analogues have been developed in China, such as vicagrel (and its deuterated analogues), PLD-301, and W1. These novel chemical analogues are all characterized by much faster and more efficient bioconversion to clopidogrel thiolactone (or 2-oxo-clopidogrel, the precursor of clopidogrel active metabolite) in the intestine than clopidogrel through bypassing the first-step P450-mediated oxidation of clopidogrel in the liver...
August 4, 2017: Journal of Cardiovascular Pharmacology
https://www.readbyqxmd.com/read/28817304/medical-education-and-leadership-in-breastfeeding-medicine
#3
Julie Scott Taylor, Esther Bell
Physicians' experience with high quality training in breastfeeding during their medical education is historically varied. The process of becoming a board-certified physician entails more than 20 years of education, and although medical school and residency training timelines and courses are relatively standardized across the United States and even internationally, breastfeeding education varies greatly across schools and programs. The Academy of Breastfeeding Medicine (ABM) exists, in part, because historically, physicians have received too little clinical training in breastfeeding and infant nutrition...
August 17, 2017: Breastfeeding Medicine: the Official Journal of the Academy of Breastfeeding Medicine
https://www.readbyqxmd.com/read/28816435/fiber-based-double-sided-reduced-graphene-oxide-films-for-efficient-solar-vapor-generation
#4
Ankang Guo, Xin Ming, Yang Fu, Gang Wang, Xianbao Wang
Solar vapor generation is a promising and whole new branch of photothermal conversion for harvesting solar energy. Various materials and devices for solar thermal conversion were successively produced and reported for higher solar energy utilization in the past few years. Herein, a compact device of reduced graphene oxides (rGO) and paper fibers was designed and assembled for efficient solar steam generation under light illumination, and it consists of water supply pipelines (WSP), a thermal insulator (TI) and a double-sided absorbing film (DSF)...
August 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28815141/identifying-metastases-related-information-from-pathology-reports-of-lung-cancer-patients
#5
Ergin Soysal, Jeremy L Warner, Joshua C Denny, Hua Xu
Metastatic patterns of spread at the time of cancer recurrence are one of the most important prognostic factors in estimation of clinical course and survival of the patient. This information is not easily accessible since it's rarely recorded in a structured format. This paper describes a system for categorization of pathology reports by specimen site and the detection of metastatic status within the report. A clinical NLP pipeline was developed using sentence boundary detection, tokenization, section identification, part-of-speech tagger, and chunker with some rule based methods to extract metastasis site and status in combination with five types of information related to tumor metastases: histological type, grade, specimen site, metastatic status indicators and the procedure...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28813925/stereo-3d-tracking-of-infants-in-natural-play-conditions
#6
Shreyas S Shivakumar, Helen Loeb, Daniel K Bogen, Frances Shofer, Phillip Bryant, Laura Prosser, Michelle J Johnson
This paper describes the design and implementation of a multiple view stereoscopic 3D vision system and a supporting infant tracker pipeline to track limb movement in natural play environments and identify potential metrics to quantify movement behavior. So far, human pose estimation and tracking with 3D cameras has been focused primarily on adults and cannot be directly extended to infants because of differences in visual features such as shapes, sizes and appearance. With rehabilitation in mind, we propose a portable, compact, markerless, low cost and high resolution 3D vision system and a tracking algorithm that exploits infant appearance attributes and depth information...
July 2017: IEEE ... International Conference on Rehabilitation Robotics: [proceedings]
https://www.readbyqxmd.com/read/28812996/reliable-detection-of-herpes-simplex-virus-sequence-variation-by-high-throughput-resequencing
#7
Alison M Morse, Kaitlyn R Calabro, Justin M Fear, David C Bloom, Lauren M McIntyre
High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines...
August 16, 2017: Viruses
https://www.readbyqxmd.com/read/28811031/bayesian-approach-to-peak-deconvolution-and-library-search-for-high-resolution-gas-chromatography-mass-spectrometry
#8
A Barcaru, H G J Mol, M Tienstra, G Vivó-Truyols
A novel probabilistic Bayesian strategy is proposed to resolve highly coeluting peaks in high-resolution GC-MS (Orbitrap) data. Opposed to a deterministic approach, we propose to solve the problem probabilistically, using a complete pipeline. First, the retention time(s) for a (probabilistic) number of compounds for each mass channel are estimated. The statistical dependency between m/z channels was implied by including penalties in the model objective function. Second, Bayesian Information Criterion (BIC) is used as Occam's razor for the probabilistic assessment of the number of components...
August 29, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28810710/testing-convergent-evolution-in-auditory-processing-genes-between-echolocating-mammals-and-the-aye-aye-a-percussive-foraging-primate
#9
Richard J Bankoff, Michael Jerjos, Baily Hohman, M Elise Lauterbur, Logan Kistler, George H Perry
Several taxonomically distinct mammalian groups-certain microbats and cetaceans (e.g., dolphins)-share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes (Daubentonia madagascariensis) are nocturnal lemurs with a specialized auditory processing system. Aye-ayes tap rapidly along the surfaces of trees, listening to reverberations to identify the mines of wood-boring insect larvae; this behavior has been hypothesized to functionally mimic echolocation...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28810611/three-dimensional-spiral-ct-measurement-of-atlantal-pedicle-and-its-clinical-application
#10
Wengui Xie, Pengfei Gao, Lixin Ji
The study aimed to establish the safe placement area and corresponding entry angle of atlantal pedicle screw using axial computed tomography (CT) measurement of atlas, in order to guide the clinical operation. Spiral thin-slice CT scan of atlas and three-dimensional reconstruction of 38 patients were randomly selected. Screw placement space was defined as the distance between the tangent lines of entry channel on the atlantal cross section and inner edge of transverse foramen and outer edge of spinal canal...
August 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28809825/analysis-of-histone-antibody-specificity-with-peptide-microarrays
#11
Evan M Cornett, Bradley M Dickson, Scott B Rothbart
Post-translational modifications (PTMs) on histone proteins are widely studied for their roles in regulating chromatin structure and gene expression. The mass production and distribution of antibodies specific to histone PTMs has greatly facilitated research on these marks. As histone PTM antibodies are key reagents for many chromatin biochemistry applications, rigorous analysis of antibody specificity is necessary for accurate data interpretation and continued progress in the field. This protocol describes an integrated pipeline for the design, fabrication and use of peptide microarrays for profiling the specificity of histone antibodies...
August 1, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28809689/natural-environment-illumination-coherent-interactive-augmented-reality-for-mobile-and-non-mobile-devices
#12
Kai Rohmer, Johannes Jendersie, Thorsten Grosch
Augmented Reality offers many applications today, especially on mobile devices. Due to the lack of mobile hardware for illumination measurements, photorealistic rendering with consistent appearance of virtual objects is still an area of active research. In this paper, we present a full two-stage pipeline for environment acquisition and augmentation of live camera images using a mobile device with a depth sensor. We show how to directly work on a recorded 3D point cloud of the real environment containing high dynamic range color values...
August 10, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28809016/application-of-a-cage-method-to-an-avian-development-study
#13
Ruslan Deviatiiarov, Marina Lizio, Oleg Gusev
Cap analysis of gene expression (CAGE) is a convenient approach for genome-wide identification of promoter regions at single base-pair resolution level and accurate expression estimation of the corresponding transcripts. Depending on the initial biomaterial amount and sequencing technology, different computational pipelines for data processing are available, as well as variations of the CAGE protocol that improve sensitivity and accuracy. Therefore, this chapter elucidates the key steps of sample preparation, sequencing, and data analysis via an example of a promoter expression estimation study in chicken development...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28809015/systems-biology-analyses-in-chicken-workflow-for-transcriptome-and-chip-seq-analyses-using-the-chicken-skin-paradigm
#14
Yung-Chih Lai, Randall B Widelitz, Cheng-Ming Chuong
With advances in molecular biology, various biological phenomena can now be explored at higher resolution using mRNA sequencing (RNA-Seq) and chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), two powerful high-throughput next-generation sequencing (NGS) technologies. While methods are used widely in mouse, human, etc., less information is available in other animals, such as the chicken. Here we assemble a workflow of the RNA-Seq and ChIP-Seq analyses for the chicken studies using chicken skin appendage tissue as an example...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808954/heavy-metal-pollutants-in-selected-organs-of-african-giant-rats-from-three-agro-ecological-zones-of-nigeria-evidence-for-their-role-as-an-environmental-specimen-bank
#15
Ifukibot Levi Usende, Benjamin O Emikpe, James Olukayode Olopade
An assessment of the concentration of heavy metals in the liver, brain, kidney, bone, and lungs of African giant rats (AGRs) from three agro-ecological zones of Nigeria having different industrial activities was carried out using atomic absorption spectrophotometer. Twenty adult AGRs from cities in mangrove/freshwater swamp, rainforest, and woodland/tall grass savanna agro-ecological zones of Nigeria were used for this study. AGRs were euthanized, carefully dissected, and the brains, liver, lungs, bone, and kidneys were harvested, digested, and analyzed for concentrations of vanadium (V), lead (Pb), cadmium (Cd), zinc (Zn), selenium (Se), copper (Cu), and iron (Fe)...
August 14, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28807046/a-comprehensive-evaluation-of-the-sl1p-pipeline-for-16s-rrna-gene-sequencing-analysis
#16
Fiona J Whelan, Michael G Surette
BACKGROUND: Advances in next-generation sequencing technologies have allowed for detailed, molecular-based studies of microbial communities such as the human gut, soil, and ocean waters. Sequencing of the 16S rRNA gene, specific to prokaryotes, using universal PCR primers has become a common approach to studying the composition of these microbiota. However, the bioinformatic processing of the resulting millions of DNA sequences can be challenging, and a standardized protocol would aid in reproducible analyses...
August 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28807044/metameta-integrating-metagenome-analysis-tools-to-improve-taxonomic-profiling
#17
Vitor C Piro, Marcel Matschkowski, Bernhard Y Renard
BACKGROUND: Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations...
August 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28806759/peculiar-genes-selection-a-new-features-selection-method-to-improve-classification-performances-in-imbalanced-data-sets
#18
Federica Martina, Marco Beccuti, Gianfranco Balbo, Francesca Cordero
High-Throughput technologies provide genomic and trascriptomic data that are suitable for biomarker detection for classification purposes. However, the high dimension of the output of such technologies and the characteristics of the data sets analysed represent an issue for the classification task. Here we present a new feature selection method based on three steps to detect class-specific biomarkers in case of high-dimensional data sets. The first step detects the differentially expressed genes according to the experimental conditions tested in the experimental design, the second step filters out the features with low discriminative power and the third step detects the class-specific features and defines the final biomarker as the union of the class-specific features...
2017: PloS One
https://www.readbyqxmd.com/read/28805666/multiple-cracks-detection-in-pipeline-using-damage-index-matrix-based-on-piezoceramic-transducer-enabled-stress-wave-propagation
#19
Guofeng Du, Qingzhao Kong, Hua Zhou, Haichang Gu
Cracks in oil and gas pipelines cause leakage which results in property damage, environmental pollution, and even personal injury or loss of lives. In this paper, an active-sensing approach was conducted to identify the crack damage in pipeline structure using a stress wave propagation approach with piezoceramic transducers. A pipeline segment instrumented with five distributed piezoceramic transducers was used as the testing specimen in this research. Four cracks were artificially cut on the specimen, and each crack had six damage cases corresponding to different crack depths...
August 12, 2017: Sensors
https://www.readbyqxmd.com/read/28803971/otp-an-automatized-system-for-managing-and-processing-ngs-data
#20
Eva Reisinger, Lena Genthner, Jules Kerssemakers, Philip Kensche, Stefan Borufka, Alke Jugold, Andreas Kling, Manuel Prinz, Ingrid Scholz, Gideon Zipprich, Roland Eils, Christian Lawerenz, Jürgen Eils
The One Touch Pipeline (OTP) is an automation platform managing Next-Generation Sequencing (NGS) data and calling bioinformatic pipelines for processing these data. OTP handles the complete digital process from import of raw sequence data via alignment of sequencing reads to identify genomic events in an automated and scalable way. Three major goals are pursued: firstly, reduction of human resources required for data management by introducing automated processes. Secondly, reduction of time until the sequences can be analyzed by bioinformatic experts, by executing all operations more reliably and quickly...
August 10, 2017: Journal of Biotechnology
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