keyword
MENU ▼
Read by QxMD icon Read
search

reading technics

keyword
https://www.readbyqxmd.com/read/28230889/quantification-of-the-borderline-range-and-implications-for-evaluating-non-animal-testing-methods-precision
#1
Maria Leontaridou, Daniel Urbisch, Susanne N Kolle, Katharina Ott, Denis S Mulliner, Silke Gabbert, Robert Landsiedel
Testing methods to assess the skin sensitisation potential of a substance usually use threshold criteria to dichotomise continuous experimental read-outs into yes/no conclusions. The threshold criteria are prescribed in the respective OECD test guidelines and the conclusion is used for regulatory hazard assessment, i.e. classification and labelling of the substance. We can identify a borderline range (BR) around the classification threshold within which test results are non-conclusive due to a testing method's biological and technical variability...
February 23, 2017: ALTEX
https://www.readbyqxmd.com/read/28227673/colorimetric-determinations-of-lithium-levels-in-drop-volumes-of-human-plasma-for-monitoring-patients-with-bipolar-mood-disorder
#2
M Qassem, M Hickey, P A Kyriacou, M Qassem, M Hickey, P A Kyriacou, M Qassem, M Hickey, P A Kyriacou
Lithium preparations are considered the most reliable form of mood stabilizing medication for patients with Bipolar disorder. Nevertheless, lithium is a toxic element and its therapeutic range is extremely narrow, with levels of 0.61.0 mEq considered normal, whereas levels above 1.5 mEq are toxic. Thus unfortunately, many patients reach toxic levels that lead to unnecessary complications. It is believed that personal monitoring of blood lithium levels would benefit patients taking lithium medication. Therefore, our aim is to develop a personal lithium blood level analyzer for patients with bipolar mood disorder, and we report here our initial results of a colorimetric-based method used to test drop-volumes of human plasma that had been spiked with lithium...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28159771/improving-and-correcting-the-contiguity-of-long-read-genome-assemblies-of-three-plant-species-using-optical-mapping-and-chromosome-conformation-capture-data
#3
Wen-Biao Jiao, Gonzalo Garcia Accinelli, Benjamin Hartwig, Christiane Kiefer, David Baker, Edouard Severing, Eva-Maria Willing, Mathieu Piednoel, Stefan Woetzel, Eva Madrid-Herrero, Bruno Huettel, Ulrike Hümann, Richard Reinhard, Marcus A Koch, Daniel Swan, Bernardo Clavijo, George Coupland, Korbinian Schneeberger
Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes, however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated PacBio long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding...
February 3, 2017: Genome Research
https://www.readbyqxmd.com/read/28148242/exome-qtl-seq-maps-monogenic-locus-and-qtls-in-barley
#4
Hiroshi Hisano, Kazuki Sakamoto, Hiroki Takagi, Ryohei Terauchi, Kazuhiro Sato
BACKGROUND: QTL-seq, in combination with bulked segregant analysis and next-generation sequencing (NGS), is used to identify loci in small plant genomes, but is technically challenging to perform in species with large genomes, such as barley. A combination of exome sequencing and QTL-seq (exome QTL-seq) was used to map the mono-factorial Mendelian locus black lemma and pericarp (Blp) and QTLs for resistance to net blotch disease, a common disease of barley caused by the fungus Pyrenophora teres, which segregated in a population of 100 doubled haploid barley lines...
February 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28134443/challenges-and-opportunities-for-whole-genome-sequencing-based-surveillance-of-antibiotic-resistance
#5
Anita C Schürch, Willem van Schaik
Infections caused by drug-resistant bacteria are increasingly reported across the planet, and drug-resistant bacteria are recognized to be a major threat to public health and modern medicine. In this review, we discuss how whole-genome sequencing (WGS)-based approaches can contribute to the surveillance of the emergence and spread of antibiotic resistance. We outline the characteristics of sequencing technologies that are currently most used for WGS (Illumina short-read technologies and the long-read sequencing platforms developed by Pacific Biosciences and Oxford Nanopore)...
January 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28130155/ms-read-quantitative-measurement-of-amino-acid-incorporation
#6
Kyle Mohler, Hans-Rudolph Aerni, Brandon Gassaway, Jiqiang Ling, Michael Ibba, Jesse Rinehart
Ribosomal protein synthesis results in the genetically programmed incorporation of amino acids into a growing polypeptide chain. Faithful amino acid incorporation that accurately reflects the genetic code is critical to the structure and function of proteins as well as overall proteome integrity. Errors in protein synthesis are generally detrimental to cellular processes yet emerging evidence suggest that proteome diversity generated through mistranslation may be beneficial under certain conditions. Cumulative translational error rates have been determined at the organismal level, however codon specific error rates and the spectrum of misincorporation errors from system to system remain largely unexplored...
January 24, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28123711/gaseous-nitric-oxide-for-the-local-treatment-of-bacterial-keratitis-in-mice
#7
Mona Deichelbohrer, Ming-Feng Wu, Berthold Seitz, Stefan Wagenpfeil, Carola Meier, Markus Bischoff, Thomas Tschernig
The successful treatment of severe bacterial keratitis continues to be a challenge in animals and humans. In the present study the aim was to assess gaseous therapy using gaseous nitric oxide (gNO) in a murine model of Pseudomonas aeruginosa keratitis. The cornea of anesthetized mice was mechanically scratched and covered with a bacterial suspension of P. aeruginosa. One day later, the infected eyes were exposed to 200 ppm NO for 30 min. Three to seven days later the mice were sacrificed and the bulbi were obtained and processed for light microscopy...
January 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28121723/design-of-interrogation-protocols-for-radiation-dose-measurements-using-optically-stimulated-luminescent-dosimeters
#8
Sara A Abraham, Kimberlee J Kearfott, Ali H Jawad, Andrew J Boria, Tobias J Buth, Alexander S Dawson, Sheldon C Eng, Samuel J Frank, Crystal A Green, Mitchell L Jacobs, Kevin Liu, Joseph A Miklos, Hien Nguyen, Muhammad Rafique, Blake D Rucinski, Travis Smith, Yanliang Tan
Optically-stimulated luminescent dosimeters are capable of being interrogated multiple times post-irradiation. Each interrogation removes a fraction of the signal stored within the optically-stimulated luminescent dosimeter. This signal loss must be corrected to avoid systematic errors in estimating the average signal of a series of optically-stimulated luminescent dosimeter interrogations and requires a minimum number of consecutive readings to determine an average signal that is within a desired accuracy of the true signal with a desired statistical confidence...
March 2017: Health Physics
https://www.readbyqxmd.com/read/28116567/-point-of-care-tests-for-the-rapid-diagnosis-of-shigellosis
#9
C Haddar, E Begaud, J Maslin, Y Germani
Worldwide, it is estimated that 140 million people suffer from shigellosis annually. The traditional identification of Shigella spp. by culture lacks sensitivity. Rapid diagnosis of shigellosis is important because it allows to engage appropriate antimicrobial treatment that shortens the duration and severity of the illness and reduces microbial carriage, thus the spread of infection in the community. Onestep immunochromatographic dipstick tests have been successfully developed at Institut Pasteur for Shigella spp...
January 23, 2017: Bulletin de la Société de Pathologie Exotique
https://www.readbyqxmd.com/read/28099995/technical-note-fast-respiratory-motion-estimation-using-sorted-singles-without-unlist-processing-a-feasibility-study
#10
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
#11
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...
February 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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
93757
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"