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https://www.readbyqxmd.com/read/28100494/quantification-of-bk-virus-standards-by-quantitative-real-time-pcr-and-droplet-digital-pcr-is-confounded-by-multiple-virus-populations-in-the-who-bkv-international-standard
#1
Allen C Bateman, Alexander L Greninger, Ederlyn E Atienza, Ajit P Limaye, Keith R Jerome, Linda Cook
BACKGROUND: The WHO recently released a BK virus (BKV) international standard. This study evaluated the WHO international standard and commercially available BKV standards by quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR). METHODS: WHO, Exact Diagnostics, Acrometrix, and Zeptometrix BKV standards were tested by qPCR and ddPCR. Two preparations of NIST BKV clones were also tested. Nucleic acid was extracted with the Roche MP96 and MPLC, followed by quantification in duplicate...
January 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28089353/cerebrospinal-fluid-mitochondrial-dna-in-the-alzheimer-s-disease-continuum
#2
Laura Cervera-Carles, Daniel Alcolea, Ainara Estanga, Mirian Ecay-Torres, Andrea Izagirre, Montserrat Clerigué, Maite García-Sebastián, Jorge Villanúa, Clàudia Escalas, Rafael Blesa, Pablo Martínez-Lage, Alberto Lleó, Juan Fortea, Jordi Clarimón
Low levels of cell-free mitochondrial DNA (mtDNA) in the cerebrospinal fluid (CSF) of Alzheimer's disease (AD) patients have been identified and proposed as a novel biomarker for the disease. The lack of validation studies of previous results prompted us to replicate this finding in a comprehensive series of patients and controls. We applied droplet digital polymerase chain reaction in CSF specimens from 124 patients representing the AD spectrum and 140 neurologically healthy controls. The following preanalytical and analytical parameters were evaluated: the effect of freeze-thaw cycles on mtDNA, the linearity of mtDNA load across serial dilutions, and the mtDNA levels in the diagnostic groups...
December 22, 2016: Neurobiology of Aging
https://www.readbyqxmd.com/read/28077562/sensitive-and-inexpensive-digital-dna-analysis-by-microfluidic-enrichment-of-rolling-circle-amplified-single-molecules
#3
Malte Kühnemund, Iván Hernández-Neuta, Mohd Istiaq Sharif, Matteo Cornaglia, Martin A M Gijs, Mats Nilsson
Single molecule quantification assays provide the ultimate sensitivity and precision for molecular analysis. However, most digital analysis techniques, i.e. droplet PCR, require sophisticated and expensive instrumentation for molecule compartmentalization, amplification and analysis. Rolling circle amplification (RCA) provides a simpler means for digital analysis. Nevertheless, the sensitivity of RCA assays has until now been limited by inefficient detection methods. We have developed a simple microfluidic strategy for enrichment of RCA products into a single field of view of a low magnification fluorescent sensor, enabling ultra-sensitive digital quantification of nucleic acids over a dynamic range from 1...
January 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28061740/prevalence-and-determinants-of-bullying-among-health-care-workers-in-portugal
#4
Pedro Norton, Viviana Costa, Joel Teixeira, Ana Azevedo, António Roma-Torres, Joana Amaro, Liliana Cunha
Bullying is defined as systematic exposure to humiliation as well as hostile and violent behaviors against one or more individuals. These behaviors are a serious, growing problem, which affects a significant proportion of health care professionals. To support the hospital's risk management policy, a cross-sectional study was undertaken to determine the prevalence of bullying in this institution and identify the determinants of bullying. Bullying was measured using the Negative Acts Questionnaire-Revised, Portuguese version (NAQ-R), a self-administered tool...
January 1, 2017: Workplace Health & Safety
https://www.readbyqxmd.com/read/28060259/measurement-of-differentially-methylated-ins-dna-species-in-human-serum-samples-as-a-biomarker-of-islet-%C3%AE-cell-death
#5
Sarah A Tersey, Jennifer B Nelson, Marisa M Fisher, Raghavendra G Mirmira
The death of islet β cells is thought to underlie the pathogenesis of virtually all forms of diabetes and to precede the development of frank hyperglycemia, especially in type 1 diabetes. The development of sensitive and reliable biomarkers of β cell death may allow for early therapeutic intervention to prevent or delay the development of diabetes. Recently, several groups including our own have reported that cell-free, differentially methylated DNA encoding preproinsulin (INS) in the circulation is correlated to β cell death in pre-type 1 diabetes and new-onset type 1 diabetes...
December 21, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28059149/volumetric-light-field-encryption-at-the-microscopic-scale
#6
Haoyu Li, Changliang Guo, Inbarasan Muniraj, Bryce C Schroeder, John T Sheridan, Shu Jia
We report a light-field based method that allows the optical encryption of three-dimensional (3D) volumetric information at the microscopic scale in a single 2D light-field image. The system consists of a microlens array and an array of random phase/amplitude masks. The method utilizes a wave optics model to account for the dominant diffraction effect at this new scale, and the system point-spread function (PSF) serves as the key for encryption and decryption. We successfully developed and demonstrated a deconvolution algorithm to retrieve both spatially multiplexed discrete data and continuous volumetric data from 2D light-field images...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28059126/an-exploratory-study-of-predisposing-genetic-factors-for-digeorge-velocardiofacial-syndrome
#7
Laia Vergés, Francesca Vidal, Esther Geán, Alexandra Alemany-Schmidt, Maria Oliver-Bonet, Joan Blanco
DiGeorge/velocardiofacial syndrome (DGS/VCFS) is a disorder caused by a 22q11.2 deletion mediated by non-allelic homologous recombination (NAHR) between low-copy repeats (LCRs). We have evaluated the role of LCR22 genomic architecture and PRDM9 variants as DGS/VCFS predisposing factors. We applied FISH using fosmid probes on chromatin fibers to analyze the number of tandem repeat blocks in LCR22 in two DGS/VCFS fathers-of-origin with proven 22q11.2 NAHR susceptibility. Results revealed copy number variations (CNVs) of L9 and K3 fosmids in these individuals compared to controls...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28058543/genomic-profiling-of-canine-mast-cell-tumors-identifies-dna-copy-number-aberrations-associated-with-kit-mutations-and-high-histological-grade
#8
Hiroyuki Mochizuki, Rachael Thomas, Scott Moroff, Matthew Breen
Mast cell tumor (MCT) is the most common skin malignancy of domestic dogs and presents with a widely variable clinical behavior. Although activating KIT mutations are present in approximately 20% of canine MCTs, molecular etiology is largely unknown for the majority of this cancer. Characterization of genomic alterations in canine MCTs may identify genomic regions and/or genes responsible for their development and progression, facilitating the discovery of new therapeutic targets and improved clinical management of this heterogeneous cancer...
January 5, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28052139/application-of-stochastic-labeling-with-random-sequence-barcodes-for-simultaneous-quantification-and-sequencing-of-environmental-16s-rrna-genes
#9
Tatsuhiko Hoshino, Fumio Inagaki
Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA...
2017: PloS One
https://www.readbyqxmd.com/read/28046094/analysis-of-genetic-variation-in-cyp450-genes-for-clinical-implementation
#10
Liuh Ling Goh, Chia Wei Lim, Wey Cheng Sim, Li Xian Toh, Khai Pang Leong
BACKGROUND: Genetic determinants of drug response remain stable throughout life and offer great promise to patient-tailored drug therapy. The adoption of pharmacogenetic (PGx) testing in patient care requires accurate, cost effective and rapid genotyping with clear guidance on the use of the results. Hence, we evaluated a 32 SNPs panel for implementing PGx testing in clinical laboratories. METHODS: We designed a 32-SNP panel for PGx testing in clinical laboratories...
2017: PloS One
https://www.readbyqxmd.com/read/28042001/relationship-between-ccr5-wt-%C3%AE-32-heterozygosity-and-hiv-1-reservoir-size-in-adolescents-and-young-adults-with-perinatally-acquired-hiv-1-infection
#11
Marta Martínez-Bonet, A González-Serna, Maria Isabel Clemente, Sara Morón-López, Laura Díaz, Marisa Navarro, Maria C Puertas, Manuel Leal, Ezequiel Ruiz-Mateos, Javier Martinez-Picado, Maria Angeles Muñoz Fernández
BACKGROUND: Several host factors contribute to HIV disease progression in the absence of combination antiretroviral therapy (cART). Among them, the CC-chemokine receptor 5 (CCR5) is known to be the main coreceptor used by HIV-1 to enter target cells during the early stages of an HIV-1 infection. OBJECTIVE: We evaluated the association of CCR5((WT/Δ32)) heterozygosity with HIV-1 reservoir size, lymphocyte differentiation, activation and immunosenescence in adolescents and young adults with perinatally acquired HIV-infection receiving cART...
December 29, 2016: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28039535/use-of-droplet-digital-pcr-for-quantitative-and-automatic-analysis-of-the-her2-status-in-breast-cancer-patients
#12
Kazutaka Otsuji, Takeshi Sasaki, Atsushi Tanaka, Akiko Kunita, Masako Ikemura, Keisuke Matsusaka, Keiichiro Tada, Masashi Fukayama, Yasuyuki Seto
PURPOSE: Digital polymerase chain reaction (dPCR) has been used to yield an absolute measure of nucleic acid concentrations. Recently, a new method referred to as droplet digital PCR (ddPCR) has gained attention as a more precise and less subjective assay to quantify DNA amplification. We demonstrated the usefulness of ddPCR to determine HER2 gene amplification of breast cancer. METHODS: In this study, we used ddPCR to measure the HER2 gene copy number in clinical formalin-fixed paraffin-embedded samples of 41 primary breast cancer patients...
December 30, 2016: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28035386/microduplication-of-7q36-3-encompassing-the-shh-long%C3%A2-range-regulator-zrs-in-a-patient-with-triphalangeal-thumb%C3%A2-polysyndactyly-syndrome-and-congenital-heart-disease
#13
Zhenghua Liu, Ni Yin, Lianghui Gong, Zhiping Tan, Bangliang Yin, Yifeng Yang, Cheng Luo
Triphalangeal thumb‑polysyndactyly syndrome (TPT‑PS) is an autosomal dominant disorder with complete penetrance and a variable expression consisting of opposable triphalangeal thumbs, duplication of the distal thumb phalanx, pre‑axial polydactyly and duplication of the big toes (hallux). The causative gene of TPT‑PS has been mapped to 7q36.3. Sonic hedgehog (SHH) expressed in the zone of polarizing activity (ZPA) has an important role in defining the anterior‑posterior axis and numbers of digits in limb bud development...
February 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28024776/comparison-of-reconstructed-rapid-prototyping-models-produced-by-3-dimensional-printing-and-conventional-stone-models-with-different-degrees-of-crowding
#14
Wan Nurazreena Wan Hassan, Yusnilawati Yusoff, Noor Azizi Mardi
INTRODUCTION: Rapid prototyping models can be reconstructed from stereolithographic digital study model data to produce hard-copy casts. In this study, we aimed to compare agreement and accuracy of measurements made with rapid prototyping and stone models for different degrees of crowding. METHODS: The Z Printer 450 (3D Systems, Rock Hill, SC) reprinted 10 sets of models for each category of crowding (mild, moderate, and severe) scanned using a structured-light scanner (Maestro 3D, AGE Solutions, Pisa, Italy)...
January 2017: American Journal of Orthodontics and Dentofacial Orthopedics
https://www.readbyqxmd.com/read/28018200/a-cultural-evolution-approach-to-digital-media
#15
REVIEW
Alberto Acerbi
Digital media have today an enormous diffusion, and their influence on the behavior of a vast part of the human population can hardly be underestimated. In this review I propose that cultural evolution theory, including both a sophisticated view of human behavior and a methodological attitude to modeling and quantitative analysis, provides a useful framework to study the effects and the developments of media in the digital age. I will first give a general presentation of the cultural evolution framework, and I will then introduce this more specific research program with two illustrative topics...
2016: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28003065/easy-detection-of-multiple-alexandrium-species-using-dna-chromatography-chip
#16
Satoshi Nagai, Shigehiko Miyamoto, Keita Ino, Seisuke Tajimi, Hiromi Nishi, Jun Tomono
In this study, the Kaneka DNA chromatography chip (KDCC) for the Alexandrium species was successfully developed for simultaneous detection of five Alexandrium species. This method utilizes a DNA-DNA hybridization technology. In the PCR process, specifically designed tagged-primers are used, i.e. a forward primer consisting of a tag domain, which can conjugate with gold nanocolloids on the chip, and a primer domain, which can anneal/amplify the target sequence. However, the reverse primer consists of a tag domain, which can hybridize to the solid-phased capture probe on the chip, and a primer domain, which can anneal/amplify the target sequence...
January 2016: Harmful Algae
https://www.readbyqxmd.com/read/28000274/digital-technology-in-fixed-implant-prosthodontics
#17
REVIEW
Tim Joda, Marco Ferrari, German O Gallucci, Julia-Gabriela Wittneben, Urs Brägger
Digital protocols are increasingly influencing prosthodontic treatment concepts. Implant-supported single-unit and short-span reconstructions will benefit mostly from the present digital trends. In these protocols, monolithic implant crowns connected to prefabricated titanium abutments, which are created based on data obtained from an intraoral scan followed by virtual design and production, without the need of a physical master cast, have to be considered in lieu of conventional manufacturing techniques for posterior implant restorations...
February 2017: Periodontology 2000
https://www.readbyqxmd.com/read/27999770/digital-recording-and-documentation-of-endoscopic-procedures-do-patients-and-doctors-think-alike
#18
Nadav Willner, Maya Peled-Raz, Dan Shteinberg, Michal Shteinberg, Dean Keren, Tova Rainis
Aims and Methods. Conducting a survey study of a large number of patients and gastroenterologists aimed at identifying relevant predictors of interest in digital recording and documentation (DRD) of endoscopic procedures. Outpatients presenting to the endoscopy unit at our institution for an endoscopy examination were anonymously surveyed, regarding their views and opinions of a possible recording of the procedure. A parallel survey for gastroenterologists was conducted. Results. 417 patients and 62 gastroenterologists participated in two parallel surveys regarding DRD of endoscopic procedures...
2016: Canadian Journal of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/27997533/exploratory-analysis-of-tp53-mutations-in-circulating-tumour-dna-as-biomarkers-of-treatment-response-for-patients-with-relapsed-high-grade-serous-ovarian-carcinoma-a-retrospective-study
#19
Christine A Parkinson, Davina Gale, Anna M Piskorz, Heather Biggs, Charlotte Hodgkin, Helen Addley, Sue Freeman, Penelope Moyle, Evis Sala, Karen Sayal, Karen Hosking, Ioannis Gounaris, Mercedes Jimenez-Linan, Helena M Earl, Wendi Qian, Nitzan Rosenfeld, James D Brenton
BACKGROUND: Circulating tumour DNA (ctDNA) carrying tumour-specific sequence alterations may provide a minimally invasive means to dynamically assess tumour burden and response to treatment in cancer patients. Somatic TP53 mutations are a defining feature of high-grade serous ovarian carcinoma (HGSOC). We tested whether these mutations could be used as personalised markers to monitor tumour burden and early changes as a predictor of response and time to progression (TTP). METHODS AND FINDINGS: We performed a retrospective analysis of serial plasma samples collected during routine clinical visits from 40 patients with HGSOC undergoing heterogeneous standard of care treatment...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27993152/copy-number-variability-of-expression-plasmids-determined-by-cell-sorting-and-droplet-digital-pcr
#20
Michael Jahn, Carsten Vorpahl, Thomas Hübschmann, Hauke Harms, Susann Müller
BACKGROUND: Plasmids are widely used for molecular cloning or production of proteins in laboratory and industrial settings. Constant modification has brought forth countless plasmid vectors whose characteristics in terms of average plasmid copy number (PCN) and stability are rarely known. The crucial factor determining the PCN is the replication system; most replication systems in use today belong to a small number of different classes and are available through repositories like the Standard European Vector Architecture (SEVA)...
December 19, 2016: Microbial Cell Factories
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