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https://www.readbyqxmd.com/read/28099995/technical-note-fast-respiratory-motion-estimation-using-sorted-singles-without-unlist-processing-a-feasibility-study
#1
Jaewon Yang, Mehdi Khalighi, Thomas A Hope, Karen Ordovas, Youngho Seo
PURPOSE: The study aims to demonstrate the feasibility of fast respiratory motion estimation using singles data available as a sorted format in list-mode files acquired in an integrated PET/MRI system for a proof-of-concept. METHODS: The derivation of SDRM is enabled by singles recorded and binned by second for each detector crystal in PET list-mode data acquired in a SIGNA PET/MR. The proposed method is to derive a SDRM trace by summing up all singles from all detectors through the PET data acquisition...
January 18, 2017: Medical Physics
https://www.readbyqxmd.com/read/28089412/whaddaya-know-a-guide-to-uncertainty-and-subjectivity-in-structural-biology
#2
REVIEW
Joel P Mackay, Michael J Landsberg, Andrew E Whitten, Charles S Bond
The methods of structural biology, while powerful, are technically complex. Although the Protein Data Bank (PDB) provides a repository that allows anyone to download any structure, many users would not appreciate the caveats that should be considered when examining a structure. Here, we describe several key uncertainties associated with the application of X-ray crystallography, NMR spectroscopy, single-particle electron microscopy (SPEM), and small-angle scattering (SAS) to biological macromolecules. The take-home message is that structures are not absolute truths - they are models that fit the experimental data and therefore have uncertainty and subjectivity associated with them...
January 11, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28071766/an-optimistic-protein-assembly-from-sequence-reads-salvaged-an-uncharacterized-segment-of-mouse-picobirnavirus
#3
Gabriel Gonzalez, Michihito Sasaki, Lucy Burkitt-Gray, Tomonori Kamiya, Noriko M Tsuji, Hirofumi Sawa, Kimihito Ito
Advances in Next Generation Sequencing technologies have enabled the generation of millions of sequences from microorganisms. However, distinguishing the sequence of a novel species from sequencing errors remains a technical challenge when the novel species is highly divergent from the closest known species. To solve such a problem, we developed a new method called Optimistic Protein Assembly from Reads (OPAR). This method is based on the assumption that protein sequences could be more conserved than the nucleotide sequences encoding them...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28051104/sequence-specific-sorting-of-dna-molecules-with-facs-using-3dpcr
#4
David J Sukovich, Shea T Lance, Adam R Abate
Genetic heterogeneity is an important feature of many biological systems, but introduces technical challenges to their characterization. Even with the best modern instruments, only a small fraction of DNA molecules present in a sample can be read, and they are recovered in the form of short, hundred-base reads. In this paper, we introduce 3dPCR, a method to sort DNA molecules with sequence specificity. 3dPCR allows heterogeneous populations of DNA to be sorted to recover long targets for deep sequencing. It is valuable whenever a target sequence is rare in a mixed population, such as for characterizing mutations in heterogeneous cancer cell populations or identifying cells containing a specific genetic sequence or infected with a target virus...
January 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28049418/chimpipe-accurate-detection-of-fusion-genes-and-transcription-induced-chimeras-from-rna-seq-data
#5
Bernardo Rodríguez-Martín, Emilio Palumbo, Santiago Marco-Sola, Thasso Griebel, Paolo Ribeca, Graciela Alonso, Alberto Rastrojo, Begoña Aguado, Roderic Guigó, Sarah Djebali
BACKGROUND: Chimeric transcripts are commonly defined as transcripts linking two or more different genes in the genome, and can be explained by various biological mechanisms such as genomic rearrangement, read-through or trans-splicing, but also by technical or biological artefacts. Several studies have shown their importance in cancer, cell pluripotency and motility. Many programs have recently been developed to identify chimeras from Illumina RNA-seq data (mostly fusion genes in cancer)...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28045081/batch-effects-and-the-effective-design-of-single-cell-gene-expression-studies
#6
Po-Yuan Tung, John D Blischak, Chiaowen Joyce Hsiao, David A Knowles, Jonathan E Burnett, Jonathan K Pritchard, Yoav Gilad
Single-cell RNA sequencing (scRNA-seq) can be used to characterize variation in gene expression levels at high resolution. However, the sources of experimental noise in scRNA-seq are not yet well understood. We investigated the technical variation associated with sample processing using the single-cell Fluidigm C1 platform. To do so, we processed three C1 replicates from three human induced pluripotent stem cell (iPSC) lines. We added unique molecular identifiers (UMIs) to all samples, to account for amplification bias...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27997030/experimental-investigation-on-the-accuracy-of-plastic-scintillators-and-of-the-spectrum-discrimination-method-in-small-photon-fields
#7
Pavlos Papaconstadopoulos, Louis Archambault, Jan Seuntjens
PURPOSE: To investigate the accuracy of output factor measurements using a commercial (Exradin W1, SI) and a prototype, "in-house" developed, plastic scintillation dosimeter (PSD) in small photon fields. METHODS: Repetitive detector-specific output factor OFdet measurements were performed in water (parallel to the CAX) using two W1 PSDs (SI), a PTW microLion, a PTW microDiamond and an unshielded diode D1V (SI) to which Monte Carlo calculated corrections factors were applied...
December 20, 2016: Medical Physics
https://www.readbyqxmd.com/read/27981917/an-observational-study-to-assess-if-automated-diabetic-retinopathy-image-assessment-software-can-replace-one-or-more-steps-of-manual-imaging-grading-and-to-determine-their-cost-effectiveness
#8
Adnan Tufail, Venediktos V Kapetanakis, Sebastian Salas-Vega, Catherine Egan, Caroline Rudisill, Christopher G Owen, Aaron Lee, Vern Louw, John Anderson, Gerald Liew, Louis Bolter, Clare Bailey, SriniVas Sadda, Paul Taylor, Alicja R Rudnicka
BACKGROUND: Diabetic retinopathy screening in England involves labour-intensive manual grading of retinal images. Automated retinal image analysis systems (ARIASs) may offer an alternative to manual grading. OBJECTIVES: To determine the screening performance and cost-effectiveness of ARIASs to replace level 1 human graders or pre-screen with ARIASs in the NHS diabetic eye screening programme (DESP). To examine technical issues associated with implementation. DESIGN: Observational retrospective measurement comparison study with a real-time evaluation of technical issues and a decision-analytic model to evaluate cost-effectiveness...
December 2016: Health Technology Assessment: HTA
https://www.readbyqxmd.com/read/27980100/synthetic-spike-in-standards-for-high-throughput-16s-rrna-gene-amplicon-sequencing
#9
Dieter M Tourlousse, Satowa Yoshiike, Akiko Ohashi, Satoko Matsukura, Naohiro Noda, Yuji Sekiguchi
High-throughput sequencing of 16S rRNA gene amplicons (16S-seq) has become a widely deployed method for profiling complex microbial communities but technical pitfalls related to data reliability and quantification remain to be fully addressed. In this work, we have developed and implemented a set of synthetic 16S rRNA genes to serve as universal spike-in standards for 16S-seq experiments. The spike-ins represent full-length 16S rRNA genes containing artificial variable regions with negligible identity to known nucleotide sequences, permitting unambiguous identification of spike-in sequences in 16S-seq read data from any microbiome sample...
December 15, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27933213/molecular-pathology-of-cancer-how-to-communicate-with-disease
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
Changhoon Kim
The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies...
December 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
#19
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
#20
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
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