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https://www.readbyqxmd.com/read/28732215/a-method-for-next-generation-sequencing-of-paired-diagnostic-and-remission-samples-to-detect-mitochondrial-dna-mutations-associated-with-leukemia
#1
Ilaria S Pagani, Chung H Kok, Verity A Saunders, Mark B Van der Hoek, Susan L Heatley, Anthony P Schwarer, Christopher N Hahn, Timothy P Hughes, Deborah L White, David M Ross
Somatic mitochondrial DNA (mtDNA) mutations have been identified in many human cancers, including leukemia. To identify somatic mutations, it is necessary to have a control tissue from the same individual for comparison. When patients with leukemia achieve remission, the remission peripheral blood may be a suitable and easily accessible control tissue, but this approach has not previously been applied to the study of mtDNA mutations. We have developed and validated a next-generation sequencing approach for the identification of leukemia-associated mtDNA mutations in 26 chronic myeloid leukemia patients at diagnosis using either nonhematopoietic or remission blood samples as the control...
July 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28732156/fixed-bed-modeling-of-nonsteroidal-anti-inflammatory-drug-removal-by-ion-exchange-in-synthetic-urine-mass-removal-or-toxicity-reduction
#2
Kelly Ann Landry, Treavor H Boyer
Ion-exchange removal of nonsteroidal anti-inflammatory drugs (NSAIDs) in synthetic urine can selectively remove pharmaceuticals with minimal co-removal of nutrients to enhance nutrient recovery efforts. However, the effect of endogenous metabolites in urine on ion-exchange removal, and the corresponding reduction in ecotoxicity potential of pharmaceuticals in treated urine entering the environment, is unknown. To assess treatment efficacy, this work paired predicted breakthrough curves determined by the homogenous surface diffusion model to an in vitro bioassay to evaluate COX-1 inhibition...
July 21, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28730541/increased-sequencing-depth-does-not-increase-captured-diversity-of-arbuscular-mycorrhizal-fungi
#3
Martti Vasar, Reidar Andreson, John Davison, Teele Jairus, Mari Moora, Maido Remm, J P W Young, Martin Zobel, Maarja Öpik
The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing...
July 20, 2017: Mycorrhiza
https://www.readbyqxmd.com/read/28728601/transabdominal-laparoscopic-retroperitoneal-neurectomy-for-chronic-pain-after-inguinal-hernia-repair-and-appendicectomy-a-matched-pair-study
#4
Ioannis Karampinis, Johannes Weiss, Lothar Pilz, Stefan Post, Florian Herrle
BACKGROUND: Chronic debilitating pain is a rare but significant cause of postoperative morbidity after inguinal surgery. Such pain is usually of neuropathic origin and frequently caused by intraoperative nerve damage. In this retrospective matched-pair study we analysed results of a minimal-invasive approach to neurectomy on quality of life and pain relief. METHODS: From March 2010 to January 2012, 9 patients developing chronic neuropathic pain after inguinal hernia repair (8 patients) or open appendicectomy (one patient) were operated using a laparoscopic transabdominal approach in our department...
July 20, 2017: BMC Surgery
https://www.readbyqxmd.com/read/28708548/predicting-locations-of-high-risk-plaques-in-coronary-arteries-in-patients-receiving-statin-therapy
#5
Ling Zhang, Andreas Wahle, Zhi Chen, John J Lopez, Tomas Kovarnik, Milan Sonka
Features of high-risk coronary artery plaques prone to major adverse cardiac events (MACE) were identified by intravascular ultrasound (IVUS) virtual histology (VH). These plaque features are: Thin-cap fibroatheroma (TCFA), plaque burden PB≥70%, or minimal luminal area MLA≤4mm². Identification of arterial locations likely to later develop such high-risk plaques may help prevent MACE. We report a machine learning method for prediction of future high-risk coronary plaque locations and types in patients under statin therapy...
July 11, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28690049/initial-validation-of-blubber-cortisol-and-progesterone-as-indicators-of-stress-response-and-maturity-in-an-otariid-the-california-sea-lion-zalophus-californianus
#6
Nicole E Beaulieu-McCoy, Kathryn K Sherman, Marisa L Trego, Daniel E Crocker, Nicholas M Kellar
Chronic stress can have detrimental effects on an individual's health and reproductive success. The use of cortisol quantification as an indicator of stress in free-ranging cetaceans and phocids is increasing but no studies have applied this technique on blubber in otariids. We measured cortisol concentrations in blubber samples obtained from California sea lions, Zalophus californianus, stranded in San Diego County and those incidentally killed in the California drift gillnet fishery. We also measured progesterone concentrations to assess female reproductive status and, in males, as a potential secondary measure of adrenal steroid production...
July 6, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28666879/correction-of-metal-induced-susceptibility-artifacts-for-functional-mri-during-deep-brain-stimulation
#7
Myung-Ho In, Shinho Cho, Yunhong Shu, Hoon-Ki Min, Matt A Bernstein, Oliver Speck, Kendall H Lee, Hang Joon Jo
Functional magnetic resonance imaging (fMRI) is an emerging tool for investigating brain activation associated with, or modulated by, deep brain stimulation (DBS). However, DBS-fMRI generally suffers from severe susceptibility to artifacts in regions near the metallic stimulation electrodes, as well as near tissue/air boundaries of the brain. These result in strong intensity and geometric distortions along the phase-encoding (PE) (i.e., blipped) direction in gradient-echo echo-planar imaging (GE-EPI). Distortion presents a major challenge to conducting reliable data analysis and in interpreting the findings...
June 27, 2017: NeuroImage
https://www.readbyqxmd.com/read/28649186/a-sas-macro-for-covariate-constrained-randomization-of-general-cluster-randomized-and-unstratified-designs
#8
Erich J Greene
Ivers et al. (2012) have recently stressed the importance to both statistical power and face validity of balancing allocations to study arms on relevant covariates. While several techniques exist (e.g., minimization, pair-matching, stratification), the covariate-constrained randomization (CCR) approach proposed by Moulton (2004) is favored when clusters can be recruited prior to randomization. CCRA V1.0, a macro published by Chaudhary and Moulton (2006), provides a SAS implementation of CCR for a particular subset of possible designs (those with two arms, small numbers of strata and clusters, an equal number of clusters within each stratum, and constraints that can be expressed as absolute mean differences between arms)...
April 2017: Journal of Statistical Software
https://www.readbyqxmd.com/read/28634149/a-non-invasive-restraining-system-for-awake-mouse-imaging
#9
Dan Madularu, Axel P Mathieu, Chathura Kumaragamage, Lauren M Reynolds, Jamie Near, Cecilia Flores, M Natasha Rajah
BACKGROUND: Preclinical neuroimaging allows for the assessment of brain anatomy, connectivity and function in laboratory animals, such as mice and rats. Most of these studies are performed under anesthesia to avoid movement during the scanning sessions. METHOD: Due to the limitations associated with anesthetized imaging, recent efforts have been made to conduct rodent imaging studies in awake animals, habituated to the restraint systems used in these instances. As of now, only one such system is commercially available for mouse scanning (Animal Imaging Research, Boston, MA, USA) integrating the radiofrequency coil electronics with the restraining element, an approach which, although effective in reducing head motion during awake imaging, has some limitations...
June 17, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28633695/how-should-discordance-between-molecular-and-growth-based-assays-for-rifampicin-resistance-be-investigated
#10
S Hofmann-Thiel, H Hoffmann, D Hillemann, L Rigouts, A Van Deun, K Kranzer
Molecular tests to detect the presence of Mycobacterium tuberculosis and genetic polymorphisms in the rpoB gene conferring resistance to rifampicin (RMP) have become integral parts of tuberculosis diagnostics worldwide. These assays are often performed sequentially or in parallel to phenotypic drug susceptibility testing. Discordances between molecular and phenotypic tests invariably occur. Root causes range from pre-, post- and analytic errors to co-existence of non-tuberculous mycobacteria, silent mutations, mutations outside the 81 base-pair RMP resistance-determining region, non-canonical mutations conferring increased minimal inhibitory concentrations below the critical concentration in some phenotypic drug susceptibility tests, and heteroresistance...
July 1, 2017: International Journal of Tuberculosis and Lung Disease
https://www.readbyqxmd.com/read/28606893/young-people-adult-worries-randomized-controlled-trial-and-feasibility-study-of-the-internet-based-self-support-method-feel-the-vibe-for-adolescents-and-young-adults-exposed-to-family-violence
#11
Karin van Rosmalen-Nooijens, Sylvie Lo Fo Wong, Judith Prins, Toine Lagro-Janssen
BACKGROUND: Adolescents and young adults (AYAs) are of special interest in a group of children exposed to family violence (FV). Past-year prevalence of exposure to FV is known to be highest in AYAs and has severe consequences. Peer support is an effective approach to behavior change and the Internet is considered suitable as a mode of delivery. OBJECTIVE: The study aimed to evaluate both effectiveness and feasibility of a randomized controlled trial (RCT) and feasibility study of the Internet-based self-support method "Feel the ViBe" (FtV) using mixed-methods approach to fully understand the strengths and weaknesses of a new intervention...
June 12, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28604610/an-nfc-on-two-coil-wpt-link-for-implantable-biomedical-sensors-under-ultra-weak-coupling
#12
Chen Gong, Dake Liu, Zhidong Miao, Wei Wang, Min Li
The inductive link is widely used in implantable biomedical sensor systems to achieve near-field communication (NFC) and wireless power transfer (WPT). However, it is tough to achieve reliable NFC on an inductive WPT link when the coupling coefficient is ultra-low (0.01 typically), since the NFC signal (especially for the uplink from the in-body part to the out-body part) could be too weak to be detected. Traditional load shift keying (LSK) requires strong coupling to pass the load modulation information to the power source...
June 11, 2017: Sensors
https://www.readbyqxmd.com/read/28600436/accurate-quantification-of-chromosomal-lesions-via-short-tandem-repeat-analysis-using-minimal-amounts-of-dna
#13
Johann-Christoph Jann, Daniel Nowak, Florian Nolte, Stephanie Fey, Verena Nowak, Julia Obländer, Jovita Pressler, Iris Palme, Christina Xanthopoulos, Alice Fabarius, Uwe Platzbecker, Aristoteles Giagounidis, Katharina Götze, Anne Letsch, Detlef Haase, Richard Schlenk, Gesine Bug, Michael Lübbert, Arnold Ganser, Ulrich Germing, Claudia Haferlach, Wolf-Karsten Hofmann, Maximilian Mossner
BACKGROUND: Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings...
June 9, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28595649/data-driven-prediction-of-adverse-drug-reactions-induced-by-drug-drug-interactions
#14
Ruifeng Liu, Mohamed Diwan M AbdulHameed, Kamal Kumar, Xueping Yu, Anders Wallqvist, Jaques Reifman
BACKGROUND: The expanded use of multiple drugs has increased the occurrence of adverse drug reactions (ADRs) induced by drug-drug interactions (DDIs). However, such reactions are typically not observed in clinical drug-development studies because most of them focus on single-drug therapies. ADR reporting systems collect information on adverse health effects caused by both single drugs and DDIs. A major challenge is to unambiguously identify the effects caused by DDIs and to attribute them to specific drug interactions...
June 8, 2017: BMC Pharmacology & Toxicology
https://www.readbyqxmd.com/read/28587598/methodologic-considerations-in-the-design-and-analysis-of-nested-case-control-studies-association-between-cytokines-and-postoperative-delirium
#15
Long H Ngo, Sharon K Inouye, Richard N Jones, Thomas G Travison, Towia A Libermann, Simon T Dillon, George A Kuchel, Sarinnapha M Vasunilashorn, David C Alsop, Edward R Marcantonio
BACKGROUND: The nested case-control study (NCC) design within a prospective cohort study is used when outcome data are available for all subjects, but the exposure of interest has not been collected, and is difficult or prohibitively expensive to obtain for all subjects. A NCC analysis with good matching procedures yields estimates that are as efficient and unbiased as estimates from the full cohort study. We present methodological considerations in a matched NCC design and analysis, which include the choice of match algorithms, analysis methods to evaluate the association of exposures of interest with outcomes, and consideration of overmatching...
June 6, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/28578266/next-generation-sequencing-based-multigene-panel-for-high-throughput-detection-of-food-borne-pathogens
#16
Chiara Ferrario, Gabriele Andrea Lugli, Maria Cristina Ossiprandi, Francesca Turroni, Christian Milani, Sabrina Duranti, Leonardo Mancabelli, Marta Mangifesta, Giulia Alessandri, Douwe van Sinderen, Marco Ventura
Contamination of food by chemicals or pathogenic bacteria may cause particular illnesses that are linked to food consumption, commonly referred to as foodborne diseases. Bacteria are present in/on various foods products, such as fruits, vegetables and ready-to-eat products. Bacteria that cause foodborne diseases are known as foodborne pathogens (FBPs). Accurate detection methods that are able to reveal the presence of FBPs in food matrices are in constant demand, in order to ensure safe foods with a minimal risk of causing foodborne diseases...
May 3, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28552265/synergistic-target-combination-prediction-from-curated-signaling-networks-machine-learning-meets-systems-biology-and-pharmacology
#17
Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg
Given a signaling network, the target combination prediction problem aims to predict efficacious and safe target combinations for combination therapy. State-of-the-art in silico methods use Monte Carlo simulated annealing (mcsa) to modify a candidate solution stochastically, and use the Metropolis criterion to accept or reject the proposed modifications. However, such stochastic modifications ignore the impact of the choice of targets and their activities on the combination's therapeutic effect and off-target effects, which directly affect the solution quality...
May 24, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28551764/autofluorescence-spectroscopy-for-nerve-sparing-laser-surgery-of-the-head-and-neck-the-influence-of-laser-tissue-interaction
#18
Florian Stelzle, Maximilian Rohde, Max Riemann, Nicolai Oetter, Werner Adler, Katja Tangermann-Gerk, Michael Schmidt, Christian Knipfer
The use of remote optical feedback systems represents a promising approach for minimally invasive, nerve-sparing laser surgery. Autofluorescence properties can be exploited for a fast, robust identification of nervous tissue. With regard to the crucial step towards clinical application, the impact of laser ablation on optical properties in the vicinity of structures of the head and neck has not been investigated up to now. We acquired 24,298 autofluorescence spectra from 135 tissue samples (nine ex vivo tissue types from 15 bisected pig heads) both before and after ER:YAG laser ablation...
May 27, 2017: Lasers in Medical Science
https://www.readbyqxmd.com/read/28545042/hierarchical-ordering-with-partial-pairwise-hierarchical-relationships-on-the-macaque-brain-data-sets
#19
Woosang Lim, Jungsoo Lee, Yongsub Lim, Doo-Hwan Bae, Haesun Park, Dae-Shik Kim, Kyomin Jung
Hierarchical organizations of information processing in the brain networks have been known to exist and widely studied. To find proper hierarchical structures in the macaque brain, the traditional methods need the entire pairwise hierarchical relationships between cortical areas. In this paper, we present a new method that discovers hierarchical structures of macaque brain networks by using partial information of pairwise hierarchical relationships. Our method uses a graph-based manifold learning to exploit inherent relationship, and computes pseudo distances of hierarchical levels for every pair of cortical areas...
2017: PloS One
https://www.readbyqxmd.com/read/28541404/m2align-parallel-multiple-sequence-alignment-with-a-multi-objective-metaheuristic
#20
Cristian Zambrano-Vega, Antonio J Nebro, José García-Nieto, José F Aldana Montes
Motivation: Multiple Sequence Alignment (MSA) is an NP-complete optimization problem found in computational biology, where the time complexity of finding an optimal alignment raises exponentially along with the number of sequences and their lengths. Additionally, to assess the quality of a MSA, a number of objectives can be taken into account, such as maximizing the sum-of-pairs, maximizing the totally conserved columns, minimizing the number of gaps, or maximizing structural information based scores such as STRIKE...
May 24, 2017: Bioinformatics
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