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https://www.readbyqxmd.com/read/28108660/from-benchmarking-hits-clip-peak-detection-programs-to-a-new-method-for-identification-of-mirna-binding-sites-from-ago2-clip-data
#1
Silvia Bottini, Nedra Hamouda-Tekaya, Bogdan Tanasa, Laure-Emmanuelle Zaragosi, Valerie Grandjean, Emanuela Repetto, Michele Trabucchi
Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonical and non-canonical miRNA-binding sites from peaks identified by Ago2 Cross-Linked ImmunoPrecipitation associated to high-throughput sequencing (CLIP-seq). Since the quality of peaks is of pivotal importance for the final output of the proposed method, we provide a comprehensive benchmarking of four peak detection programs, namely CIMS, PIPE-CLIP, Piranha and Pyicoclip, on four publicly available Ago2-HITS-CLIP datasets and one unpublished in-house Ago2-dataset in stem cells...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108657/risearch2-suffix-array-based-large-scale-prediction-of-rna-rna-interactions-and-sirna-off-targets
#2
Ferhat Alkan, Anne Wenzel, Oana Palasca, Peter Kerpedjiev, Anders Frost Rudebeck, Peter F Stadler, Ivo L Hofacker, Jan Gorodkin
Intermolecular interactions of ncRNAs are at the core of gene regulation events, and identifying the full map of these interactions bears crucial importance for ncRNA functional studies. It is known that RNA-RNA interactions are built up by complementary base pairings between interacting RNAs and high level of complementarity between two RNA sequences is a powerful predictor of such interactions. Here, we present RIsearch2, a large-scale RNA-RNA interaction prediction tool that enables quick localization of potential near-complementary RNA-RNA interactions between given query and target sequences...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108500/ophthalmic-artery-occlusion-after-pipeline-embolization-device-placement-with-reconstitution-of-flow-via-an-endoleak-a-report-of-two-cases
#3
Michael L Adix, Ian A Kaminsky, In Sup Choi
The Pipeline Embolization Device (PED) is a flow diverting stent used in the treatment of a wide variety of intracranial aneurysms. The device differs from traditional stents used in stent-assisted coil embolization in that it has a tighter lattice structure with smaller cell sizes designed specifically to disrupt blood flow into aneurysms rather than only to retain coils within aneurysms. While the PED has been shown to be safe and effective, it has a unique risk profile that includes side branch and perforator vessel occlusion...
January 20, 2017: Journal of Neurointerventional Surgery
https://www.readbyqxmd.com/read/28108477/quantitative-microscopy-uncovers-ploidy-changes-during-mitosis-in-live-drosophila-embryos-and-their-effect-on-nuclear-size
#4
Wee Choo Puah, Rambabu Chinta, Martin Wasser
Time-lapse microscopy is a powerful tool to investigate cellular and developmental dynamics. In Drosophila melanogaster, it can be used to study division cycles in embryogenesis. To obtain quantitative information from 3D time-lapse data and track proliferating nuclei from the syncytial stage until gastrulation, we developed an image analysis pipeline consisting of nuclear segmentation, tracking, annotation and quantification. Image analysis of maternal-haploid (mh) embryos revealed that a fraction of haploid syncytial nuclei fused to give rise to nuclei of higher ploidy (2n, 3n, 4n)...
January 20, 2017: Biology Open
https://www.readbyqxmd.com/read/28108448/arnapipe-a-balanced-efficient-and-distributed-pipeline-for-processing-rna-seq-data-in-high-performance-computing-environments
#5
Arnald Alonso, Brittany N Lasseigne, Kelly Williams, Josh Nielsen, Ryne C Ramaker, Andrew A Hardigan, Bobbi Johnston, Brian S Roberts, Sara J Cooper, Sara Marsal, Richard M Myers
The wide range of RNA-seq applications and their high computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing, and sequence variant calling...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108447/mirmine-a-database-of-human-mirna-expression-profiles
#6
Bharat Panwar, Gilbert S Omenn, Yuanfang Guan
MOTIVATION: MicroRNAs (miRNAs) are small non-coding RNAs that are involved in post-transcriptional regulation of gene expression. In this high-throughput sequencing era, a tremendous amount of RNA-seq data is accumulating, and full utilization of publicly available miRNA data is an important challenge. These data are useful to determine expression values for each miRNA, but quantification pipelines are in a primitive stage and still evolving; there are many factors that affect expression values significantly...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28107998/multiplex-and-accurate-quantification-of-acute-kidney-injury-biomarker-candidates-in-urine-using-protein-standard-absolute-quantification-psaq-and-targeted-proteomics
#7
Benoît Gilquin, Mathilde Louwagie, Michel Jaquinod, Alexandre Cez, Guillaume Picard, Leila El Kholy, Brigitte Surin, Jérôme Garin, Myriam Ferro, Thomas Kofman, Caroline Barau, Emmanuelle Plaisier, Pierre Ronco, Virginie Brun
There is a need for multiplex, specific and quantitative methods to speed-up the development of acute kidney injury biomarkers and allow a more specific diagnosis. Targeted proteomic analysis combined with stable isotope dilution has recently emerged as a powerful option for the parallelized evaluation of candidate biomarkers. This article presents the development of a targeted proteomic assay to quantify 4 acute kidney injury biomarker candidates in urine samples. The proteins included in the assessed panel consisted of myo-inositol oxygenase (MIOX), phosphoenolpyruvate carboxykinase 1 (PCK1), neutrophil gelatinase-associated lipocalin (NGAL) and liver fatty acid-binding protein (L-FABP)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107812/tissue-resolved-gene-structure-refined-equine-transcriptome
#8
T A Mansour, E Y Scott, C J Finno, R R Bellone, M J Mienaltowski, M C Penedo, P J Ross, S J Valberg, J D Murray, C T Brown
BACKGROUND: Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome...
January 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28107396/mixfit-methodology-for-computing-ancestry-related-genetic-scores-at-the-individual-level-and-its-application-to-the-estonian-and-finnish-population-studies
#9
Toomas Haller, Liis Leitsalu, Krista Fischer, Marja-Liisa Nuotio, Tõnu Esko, Dorothea Irene Boomsma, Kirsten Ohm Kyvik, Tim D Spector, Markus Perola, Andres Metspalu
Ancestry information at the individual level can be a valuable resource for personalized medicine, medical, demographical and history research, as well as for tracing back personal history. We report a new method for quantitatively determining personal genetic ancestry based on genome-wide data. Numerical ancestry component scores are assigned to individuals based on comparisons with reference populations. These comparisons are conducted with an existing analytical pipeline making use of genotype phasing, similarity matrix computation and our addition-multidimensional best fitting by MixFit...
2017: PloS One
https://www.readbyqxmd.com/read/28106794/a-thoroughly-validated-virtual-screening-strategy-for-discovery-of-novel-hdac3-inhibitors
#10
Huabin Hu, Jie Xia, Dongmei Wang, Xiang Simon Wang, Song Wu
Histone deacetylase 3 (HDAC3) has been recently identified as a potential target for the treatment of cancer and other diseases, such as chronic inflammation, neurodegenerative diseases, and diabetes. Virtual screening (VS) is currently a routine technique for hit identification, but its success depends on rational development of VS strategies. To facilitate this process, we applied our previously released benchmarking dataset, i.e., MUBD-HDAC3 to the evaluation of structure-based VS (SBVS) and ligand-based VS (LBVS) combinatorial approaches...
January 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28105916/gpcrs-from-fusarium-graminearum-detection-modeling-and-virtual-screening-the-search-for-new-routes-to-control-head-blight-disease
#11
Emmanuel Bresso, Roberto Togawa, Kim Hammond-Kosack, Martin Urban, Bernard Maigret, Natalia Florencio Martins
BACKGOUND: Fusarium graminearum (FG) is one of the major cereal infecting pathogens causing high economic losses worldwide and resulting in adverse effects on human and animal health. Therefore, the development of new fungicides against FG is an important issue to reduce cereal infection and economic impact. In the strategy for developing new fungicides, a critical step is the identification of new targets against which innovative chemicals weapons can be designed. As several G-protein coupled receptors (GPCRs) are implicated in signaling pathways critical for the fungi development and survival, such proteins could be valuable efficient targets to reduce Fusarium growth and therefore to prevent food contamination...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105152/evaluation-by-quantitative-image-analysis-of-anticancer-drug-activity-on-multicellular-spheroids-grown-in-3d-matrices
#12
Aurélie Gomes, Adrien Russo, Guillaume Vidal, Elise Demange, Pauline Pannetier, Zied Souguir, Jean-Michel Lagarde, Bernard Ducommun, Valérie Lobjois
Pharmacological evaluation of anticancer drugs using 3D in vitro models provides invaluable information for predicting in vivo activity. Artificial matrices are currently available that scale up and increase the power of such 3D models. The aim of the present study was to propose an efficient and robust imaging and analysis pipeline to assess with quantitative parameters the efficacy of a particular cytotoxic drug. HCT116 colorectal adenocarcinoma tumor cell multispheres were grown in a 3D physiological hyaluronic acid matrix...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28103917/a-fast-and-robust-protocol-for-metataxonomic-analysis-using-rnaseq-data
#13
Jeremy W Cox, Richard A Ballweg, Diana H Taft, Prakash Velayutham, David B Haslam, Aleksey Porollo
BACKGROUND: Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, primarily from 16S rRNA gene sequencing and DNAseq, to identify microorganisms and viruses within a complex mixture. With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make metatranscriptomic data sufficient for metataxonomics, new analytical workflows are needed to deal with sparse and taxonomically less informative sequencing data...
January 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28103801/parasite-infection-of-public-databases-a-data-mining-approach-to-identify-apicomplexan-contaminations-in-animal-genome-and-transcriptome-assemblies
#14
Janus Borner, Thorsten Burmester
BACKGROUND: Contaminations from various exogenous sources are a common problem in next-generation sequencing. Another possible source of contaminating DNA are endogenous parasites. On the one hand, undiscovered contaminations of animal sequence assemblies may lead to erroneous interpretation of data; on the other hand, when identified, parasite-derived sequences may provide a valuable source of information. RESULTS: Here we show that sequences deriving from apicomplexan parasites can be found in many animal genome and transcriptome projects, which in most cases derived from an infection of the sequenced host specimen...
January 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28103739/newer-medical-therapies-for-metastatic-soft-tissue-sarcoma
#15
Akash Tiwari, Vineet Govinda Gupta, Sameer Bakhshi
Metastatic/advanced soft tissue sarcoma has a poor prognosis and conventionally, treatment options have been limited. In recent years, this area has been a rich ground for research with many new drugs being approved and several more in the pipeline. With multiple new treatment options available, it is vital to keep up pace with this rapidly changing field. Areas covered: Recent data regarding use of novel agents in advanced soft tissue sarcoma is reviewed with a focus on clinical applicability. The goal is to guide the clinician into choosing appropriate lines of therapy for the individual patient in light of recent availability of multiple new treatment options...
January 20, 2017: Expert Review of Anticancer Therapy
https://www.readbyqxmd.com/read/28103193/comprehensive-use-of-curvature-for-robust-and-accurate-online-surface-reconstruction
#16
Damien Lefloch, Markus Kluge, Hamed Sarbolandi, Tim Weyrich, Andreas Kolb
Interactive real-time scene acquisition from hand-held depth cameras has recently developed much momentum, enabling applications in ad-hoc object acquisition, augmented reality and other fields. A key challenge to online reconstruction remains error accumulation in the reconstructed camera trajectory, due to drift-inducing instabilities in the range scan alignments of the underlying iterative-closest-point (ICP) algorithm. Various strategies have been proposed to mitigate that drift, including SIFT-based pre-alignment, color-based weighting of ICP pairs, stronger weighting of edge features, and so on...
January 5, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28102960/nine-degrees-of-freedom-flexmap-for-a-cone-beam-computed-tomography-imaging-device-with-independently-movable-source-and-detector
#17
Peter Keuschnigg, Daniel Kellner, Karl Fritscher, Andrea Zechner, Ulrich Mayer, Philipp Huber, Felix Sedlmayer, Heinz Deutschmann, Philipp Steininger
PURPOSE: Couch-mounted cone-beam computed tomography (CBCT) imaging devices with independently rotatable x-ray source and flat-panel detector arms for acquisitions of arbitrary regions of interest (ROI) have recently been introduced in image-guided radiotherapy (IGRT). This work analyzes mechanical limitations and gravity-induced effects influencing the geometric accuracy of images acquired with arbitrary angular constellations of source and detector in nonisocentric trajectories, which is considered essential for IGRT...
January 2017: Medical Physics
https://www.readbyqxmd.com/read/28101263/team-based-learning-in-a-pipeline-course-in-medical-microbiology-for-under-represented-student-populations-in-medicine-improves-learning-of-microbiology-concepts
#18
K C Behling, M M Murphy, J Mitchell-Williams, H Rogers-McQuade, O J Lopez
As part of an undergraduate pipeline program at our institution for students from underrepresented minorities in medicine backgrounds, we created an intensive four-week medical microbiology course. Team-based learning (TBL) was implemented in this course to enhance student learning of course content. Three different student cohorts participated in the study, and there were no significant differences in their prior academic achievement based on their undergraduate grade point average (GPA) and pre-course examination scores...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28100649/incidence-of-delivery-wire-recapture-failure-with-the-pipeline-flex-device
#19
Michael A Mooney, Karam Moon, Bradley A Gross, Andrew F Ducruet, Felipe C Albuquerque
BACKGROUND: The Pipeline Flex embolization device has several advantages over the first-generation Pipeline embolization device (Covidien, Dublin, Republic of Ireland). Despite these advantages, we have observed frequent difficulty in recapturing the device's delivery wire. OBJECTIVE: To prospectively document the incidence of failure to recapture the delivery wire. METHODS: We tracked our experience in patients undergoing endovascular treatment with a flow-diverting stent for cerebral aneurysms between 1 May and 30 September 2016...
January 18, 2017: Journal of Neurointerventional Surgery
https://www.readbyqxmd.com/read/28100566/loss-of-axin1-drives-acquired-resistance-to-wnt-pathway-blockade-in-colorectal-cancer-cells-carrying-rspo3-fusions
#20
Gabriele Picco, Consalvo Petti, Alessia Centonze, Erica Torchiaro, Giovanni Crisafulli, Luca Novara, Andrea Acquaviva, Alberto Bardelli, Enzo Medico
In colorectal cancer (CRC), WNT pathway activation by genetic rearrangements of RSPO3 is emerging as a promising target. However, its low prevalence severely limits availability of preclinical models for in-depth characterization. Using a pipeline designed to suppress stroma-derived signal, we find that RSPO3 "outlier" expression in CRC samples highlights translocation and fusion transcript expression. Outlier search in 151 CRC cell lines identified VACO6 and SNU1411 cells as carriers of, respectively, a canonical PTPRK(e1)-RSPO3(e2) fusion and a novel PTPRK(e13)-RSPO3(e2) fusion...
January 18, 2017: EMBO Molecular Medicine
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