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https://www.readbyqxmd.com/read/27933213/molecular-pathology-of-cancer-how-to-communicate-with-disease
#1
REVIEW
Peter Birner, Gerald Prager, Berthold Streubel
: Recent technical advances have brought insights into the biology of cancer in human, establishing it as a disease driven by genetic mutations. Beside inherited family tumour syndromes caused by germline mutations, somatic genetic alterations occur early in tumourigenesis, which accumulate during the progression of the disease and its treatment. Based on these observations, medical oncology has started to enter an era of stratified medicine, where treatment selection is becoming tailored to drugable molecular pathways...
2016: ESMO Open
https://www.readbyqxmd.com/read/27905880/the-lair-a-resource-for-exploratory-analysis-of-published-rna-seq-data
#2
Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted, Lior Pachter
Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is difficult to use in practice. We introduce a series of tools for processing and analyzing RNA-Seq data in the Sequence Read Archive, that together have allowed us to build an easily extendable resource for analysis of data underlying published papers. Our system makes the exploration of data easily accessible and usable without technical expertise...
December 1, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27897007/production-of-a-preliminary-quality-control-pipeline-for-single-nuclei-rna-seq-and-its-application-in-the-analysis-of-cell-type-diversity-of-post-mortem-human-brain-neocortex
#3
Brian Aevermann, Jamison McCorrison, Pratap Venepally, Rebecca Hodge, Trygve Bakken, Jeremy Miller, Mark Novotny, Danny N Tran, Francisco Diezfuertes, Lena Christiansen, Fan Zhang, Frank Steemers, Roger S Lasken, E D Lein, Nicholas Schork, Richard H Scheuermann
Next generation sequencing of the RNA content of single cells or single nuclei (sc/nRNA-seq) has become a powerful approach to understand the cellular complexity and diversity of multicellular organisms and environmental ecosystems. However, the fact that the procedure begins with a relatively small amount of starting material, thereby pushing the limits of the laboratory procedures required, dictates that careful approaches for sample quality control (QC) are essential to reduce the impact of technical noise and sample bias in downstream analysis applications...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896680/what-does-a-shoulder-mri-cost-the-consumer
#4
Robert W Westermann, Cameron Schick, Christopher M Graves, Kyle R Duchman, Stuart L Weinstein
BACKGROUND: More than 100 MRIs per 1000 inhabitants are performed in the United States annually, more than almost every other country. Little is known regarding the cost of obtaining an MRI and factors associated with differences in cost. QUESTIONS/PURPOSES: By surveying all hospital-owned and independent imaging centers in Iowa, we wished to determine (1) the cost to the consumer of obtaining a noncontrast shoulder MRI, (2) the frequency and magnitude of discounts provided, and (3) factors associated with differences in cost including location (hospital-owned or independent) and Centers for Medicare & Medicaid Services designation (rural, urban, and critical access)...
November 28, 2016: Clinical Orthopaedics and related Research
https://www.readbyqxmd.com/read/27895807/cpas-based-sequencing-on-the-bgiseq-500-to-explore-small-non-coding-rnas
#5
Tobias Fehlmann, Stefanie Reinheimer, Chunyu Geng, Xiaoshan Su, Snezana Drmanac, Andrei Alexeev, Chunyan Zhang, Christina Backes, Nicole Ludwig, Martin Hart, Dan An, Zhenzhen Zhu, Chongjun Xu, Ao Chen, Ming Ni, Jian Liu, Yuxiang Li, Matthew Poulter, Yongping Li, Cord Stähler, Radoje Drmanac, Xun Xu, Eckart Meese, Andreas Keller
BACKGROUND: We present the first sequencing data using the combinatorial probe-anchor synthesis (cPAS)-based BGISEQ-500 sequencer. Applying cPAS, we investigated the repertoire of human small non-coding RNAs and compared it to other techniques. RESULTS: Starting with repeated measurements of different specimens including solid tissues (brain and heart) and blood, we generated a median of 30.1 million reads per sample. 24.1 million mapped to the human genome and 23...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27895722/deciphering-fact-from-artifact-when-using-reporter-assays-to-investigate-the-roles-of-host-factors-on-l1-retrotransposition
#6
Pamela R Cook, G Travis Tabor
BACKGROUND: The Long INterspersed Element-1 (L1, LINE-1) is the only autonomous mobile DNA element in humans and has generated as much as half of the genome. Due to increasing clinical interest in the roles of L1 in cancer, embryogenesis and neuronal development, it has become a priority to understand L1-host interactions and identify host factors required for its activity. Apropos to this, we recently reported that L1 retrotransposition in HeLa cells requires phosphorylation of the L1 protein ORF1p at motifs targeted by host cell proline-directed protein kinases (PDPKs), which include the family of mitogen-activated protein kinases (MAPKs)...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27887717/the-continued-existence-of-significant-disparities-in-the-technical-practices-of-sperm-morphology-assessment-and-the-clinical-implications-results-of-a-french-questionnaire
#7
Nicolas Gatimel, Lucile Mansoux, Jessika Moreau, Jean Parinaud, Roger D Léandri
OBJECTIVE: To investigate current practices for sperm morphology assessment. DESIGN: E-mail survey questionnaire. SETTING: Diagnostic and clinical institutions/laboratories. PATIENT(S): French biologists and clinicians (n = 225). INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Answers to 24 questions. RESULT(S): The survey shows that even now in France there is great inconsistency in the use of sperm morphology assessments...
November 22, 2016: Fertility and Sterility
https://www.readbyqxmd.com/read/27887629/the-oxford-nanopore-minion-delivery-of-nanopore-sequencing-to-the-genomics-community
#8
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
November 25, 2016: Genome Biology
https://www.readbyqxmd.com/read/27881215/birth-of-an-asian-cool-reference-genome-ak1
#9
Changhoon Kim
The human reference genome, maintained by Genome Reference Consortium, is conceivably the most complete genome assembly ever since its first construction. It has been improved continually by incorporating corrections made to the previous assemblies thanks to various technological advances. Based on this reference genome, many population sequencing projects are ongoing to better represent human diversity, increasing hope for medical usage of genomic information, with recent maturation of the high-throughput sequencing technologies...
November 24, 2016: BMB Reports
https://www.readbyqxmd.com/read/27879606/improving-outcomes-in-tendon-repair-a-critical-look-at-the-evidence-for-flexor-tendon-repair-and-rehabilitation
#10
Wee S Khor, Martin F Langer, Richard Wong, Rui Zhou, Fiona Peck, Jason K F Wong
LEARNING OBJECTIVES: After reading this article, the participant should be able to: 1. Appreciate the variation and evolution of flexor tendon management 2. Know how to assess the patient who presents with a flexor tendon laceration. 3. Understand the biology of repairing flexor tendon lacerations. 4. Appreciate the technical challenges in flexor tendon repair relating to different zones. 5. Understand the rationale of postoperative hand therapy. 6. Have an overview of the types of secondary tendon surgery...
December 2016: Plastic and Reconstructive Surgery
https://www.readbyqxmd.com/read/27864325/a-technical-consideration-when-using-flow-diversion-for-recurrent-aneurysms-following-stent-assisted-coiling
#11
Justin R Mascitelli, Daniel Wei, Thomas J Oxley, Christopher P Kellner, Hazem Shoirah, Reade A De Leacy, J Mocco, Johanna T Fifi
Flow diversion (FD) is a treatment option for recurrent aneurysms including following stent-assisted coiling (SAC), although this approach is both 'off-label' and unproven. A technical challenge of FD placement may involve the microwire catching on the tines of the previously placed stent or potentially going 'in-out-in' from the central axis of the stent. We report a case and technique that assures the wire has safely remained within the central axis of the stent. The procedure was performed in standard fashion except that the intermediate catheter was passed completely through the previously placed stent after the microwire/microcatheter had crossed...
November 18, 2016: Journal of Neurointerventional Surgery
https://www.readbyqxmd.com/read/27861231/wavelet-based-angiographic-reconstruction-of-computed-tomography-perfusion-data-diagnostic-value-in-cerebral-venous-sinus-thrombosis
#12
Wolfgang G Kunz, Felix Schuler, Wieland H Sommer, Matthias P Fabritius, Lukas Havla, Felix G Meinel, Maximilian F Reiser, Birgit Ertl-Wagner, Kolja M Thierfelder
OBJECTIVE: The aim of this study was to test the diagnostic value of wavelet-based angiographic reconstruction of CT perfusion data (waveletCTA) to detect cerebral venous sinus thrombosis (CVST) in patients who underwent whole-brain CT perfusion imaging (WB-CTP). MATERIALS AND METHODS: Datasets were retrospectively selected from an initial cohort of 2863 consecutive patients who had undergone multiparametric CT including WB-CTP. WaveletCTA was reconstructed from WB-CTP: the angiographic signal was generated by voxel-based wavelet transform of time attenuation curves (TACs) from WB-CTP raw data...
November 17, 2016: Investigative Radiology
https://www.readbyqxmd.com/read/27852655/a-technical-consideration-when-using-flow-diversion-for-recurrent-aneurysms-following-stent-assisted-coiling
#13
Justin R Mascitelli, Daniel Wei, Thomas J Oxley, Christopher P Kellner, Hazem Shoirah, Reade A De Leacy, J Mocco, Johanna T Fifi
Flow diversion (FD) is a treatment option for recurrent aneurysms including following stent-assisted coiling (SAC), although this approach is both 'off-label' and unproven. A technical challenge of FD placement may involve the microwire catching on the tines of the previously placed stent or potentially going 'in-out-in' from the central axis of the stent. We report a case and technique that assures the wire has safely remained within the central axis of the stent. The procedure was performed in standard fashion except that the intermediate catheter was passed completely through the previously placed stent after the microwire/microcatheter had crossed...
November 15, 2016: BMJ Case Reports
https://www.readbyqxmd.com/read/27830281/a-family-information-brochure-and-dedicated-website-to-improve-the-icu-experience-for-patients-relatives-an-italian-multicenter-before-and-after-study
#14
Giovanni Mistraletti, Michele Umbrello, Elena Silvia Mantovani, Benedetta Moroni, Paolo Formenti, Paolo Spanu, Stefania Anania, Elisa Andrighi, Alessandra Di Carlo, Federica Martinetti, Irene Vecchi, Alessandra Palo, Cristina Pinna, Riccarda Russo, Silvia Francesconi, Federico Valdambrini, Enrica Ferretti, Giulio Radeschi, Edda Bosco, Paolo Malacarne, Gaetano Iapichino
PURPOSE: Good communication between ICU staff and patients' relatives may reduce the occurrence of post-traumatic stress disorder, anxiety or depression, and dissatisfaction with clinicians. An information brochure and website to meet relatives' needs were designed to explain in technical yet simple terms what happens during and after an ICU stay, to legitimize emotions such as fear, apprehension, and suffering, and to improve cooperation with relatives without increasing staff workload...
November 9, 2016: Intensive Care Medicine
https://www.readbyqxmd.com/read/27822312/on-the-evaluation-of-the-fidelity-of-supervised-classifiers-in-the-prediction-of-chimeric-rnas
#15
Sacha Beaumeunier, Jérôme Audoux, Anthony Boureux, Florence Ruffle, Thérèse Commes, Nicolas Philippe, Ronnie Alves
BACKGROUND: High-throughput sequencing technology and bioinformatics have identified chimeric RNAs (chRNAs), raising the possibility of chRNAs expressing particularly in diseases can be used as potential biomarkers in both diagnosis and prognosis. RESULTS: The task of discriminating true chRNAs from the false ones poses an interesting Machine Learning (ML) challenge. First of all, the sequencing data may contain false reads due to technical artifacts and during the analysis process, bioinformatics tools may generate false positives due to methodological biases...
2016: BioData Mining
https://www.readbyqxmd.com/read/27812680/critical-analysis-of-the-quality-readability-and-technical-aspects-of-online-information-provided-for-neck-lifts
#16
Hani Rayess, Giancarlo F Zuliani, Amar Gupta, Peter F Svider, Adam J Folbe, Jean Anderson Eloy, Michael A Carron
Importance: The number of patients using the internet to obtain health information is growing. This material is unregulated and heterogeneous and can influence patient decisions. Objective: To compare the quality, readability, and technical aspects of online information about neck-lifts provided by private practice websites vs academic medical centers and reference sources. Design, Setting, and Participants: In this cross-sectional analysis conducted between November 2015 and January 2016, a Google search of the term neck-lift was performed, and the first 45 websites were evaluated...
November 3, 2016: JAMA Facial Plastic Surgery
https://www.readbyqxmd.com/read/27806082/metagenomic-investigation-of-plasma-in-individuals-with-me-cfs-highlights-the-importance-of-technical-controls-to-elucidate-contamination-and-batch-effects
#17
Ruth R Miller, Miguel Uyaguari-Diaz, Mark N McCabe, Vincent Montoya, Jennifer L Gardy, Shoshana Parker, Theodore Steiner, William Hsiao, Matthew J Nesbitt, Patrick Tang, David M Patrick
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating disease causing indefinite fatigue. ME/CFS has long been hypothesised to have an infectious cause; however, no specific infectious agent has been identified. We used metagenomics to analyse the RNA from plasma samples from 25 individuals with ME/CFS and compare their microbial content to technical controls as well as three control groups: individuals with alternatively diagnosed chronic Lyme syndrome (N = 13), systemic lupus erythematosus (N = 11), and healthy controls (N = 25)...
2016: PloS One
https://www.readbyqxmd.com/read/27798637/the-technical-and-biological-reproducibility-of-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-maldi-tof-ms-based-typing-employment-of-bioinformatics-in-a-multicenter-study
#18
Michael Oberle, Nadia Wohlwend, Daniel Jonas, Florian P Maurer, Geraldine Jost, Sarah Tschudin-Sutter, Katleen Vranckx, Adrian Egli
BACKGROUND: The technical, biological, and inter-center reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) typing data has not yet been explored. The aim of this study is to compare typing data from multiple centers employing bioinformatics using bacterial strains from two past outbreaks and non-related strains. MATERIAL/METHODS: Participants received twelve extended spectrum betalactamase-producing E. coli isolates and followed the same standard operating procedure (SOP) including a full-protein extraction protocol...
2016: PloS One
https://www.readbyqxmd.com/read/27793585/methodologies-for-probing-the-metatranscriptome-of-grassland-soil
#19
Aaron Garoutte, Erick Cardenas, James Tiedje, Adina Howe
Metatranscriptomics provides an opportunity to identify active microbes and expressed genes in complex soil communities in response to particular conditions. Currently, there are a limited number of soil metatranscriptome studies to provide guidance for using this approach in this challenging matrix. Hence, we evaluated the technical challenges of applying soil metatranscriptomics to a highly diverse, low activity natural system. We used a non-targeted rRNA removal approach, duplex nuclease specific (DSN) normalization, to generate a metatranscriptomic library from field collected soil supporting a perennial grass, Miscanthus x giganteus (a biofuel crop), and evaluated its ability to provide insight into its active community members and their expressed protein-coding genes...
October 25, 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27790830/strategies-for-complete-plastid-genome-sequencing
#20
Alex D Twyford, Rob W Ness
Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low-cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly...
October 28, 2016: Molecular Ecology Resources
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