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https://www.readbyqxmd.com/read/28730153/assessment-of-isomir-discrimination-using-commercial-qpcr-methods
#1
Rogan Magee, Aristeidis G Telonis, Tess Cherlin, Isidore Rigoutsos, Eric Londin
We sought to determine whether commercial quantitative polymerase chain reaction (qPCR) methods are capable of distinguishing isomiRs: variants of mature microRNAs (miRNAs) with sequence endpoint differences. We used two commercially available miRNA qPCR methods to quantify miR-21-5p in both synthetic and real cell contexts. We find that although these miRNA qPCR methods possess high sensitivity for specific sequences, they also pick up background signals from closely related isomiRs, which influences the reliable quantification of individual isomiRs...
June 2017: Non-Coding RNA
https://www.readbyqxmd.com/read/28729854/microbiome-of-trichodesmium-colonies-from-the-north-pacific-subtropical-gyre
#2
Mary R Gradoville, Byron C Crump, Ricardo M Letelier, Matthew J Church, Angelicque E White
Filamentous diazotrophic Cyanobacteria of the genus Trichodesmium, often found in colonial form, provide an important source of new nitrogen to tropical and subtropical marine ecosystems. Colonies are composed of several clades of Trichodesmium in association with a diverse community of bacterial and eukaryotic epibionts. We used high-throughput 16S rRNA and nifH gene sequencing, carbon (C) and dinitrogen (N2) fixation assays, and metagenomics to describe the diversity and functional potential of the microbiome associated with Trichodesmium colonies collected from the North Pacific Subtropical Gyre (NPSG)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28729372/intraoperative-optical-coherence-tomography-compatible-surgical-instruments-for-real-time-image-guided-ophthalmic-surgery
#3
Justis P Ehlers, Atsuro Uchida, Sunil K Srivastava
Intraoperative optical coherence tomography (OCT) is a potentially transformational technology that is now commercially available to ophthalmic surgeons. Currently, the use of the technology is primarily limited to a 'stop and image' approach due to the lack of OCT compatibility with surgical instrumentation. In this report, we describe multiple OCT-compatible surgical instruments that were developed for various surgical needs, based on previous evaluation of potential surgical materials for optical features and physical properties...
July 20, 2017: British Journal of Ophthalmology
https://www.readbyqxmd.com/read/28729210/deficiency-of-quorum-sensing-system-inhibits-the-resistance-selection-of-pseudomonas-aeruginosa-to-ciprofloxacin-and-levofloxacin-in-vitro
#4
Yating Gao, Jinju Duan, Xin Geng, Zhiqi Zhang, Ruiqin Zhang, Xiaoxia Li, Shuyun Wang, Jianbang Kang, Donghong Yin, Yan Song
OBJECTIVES: The objective was to investigate how deficient of quorum sensing system (QS) affects minimal inhibitory concentrations (MICs) of Pseudomonas aeruginosa strains to ciprofloxacin (CIP) and levofloxacin (LEV) in vitro. METHODS: Collected the clinical Pseudomonas aeruginosa isolates. Screened the strains deficient of QS genes by the PCR agarose electrophoresis, and then randomly picked out normal strains with the same number of deficient ones. All strains incubated on the different CIP-concentration Mueller-Hinton agars for five days, the different concentrations of CIP respectively refered to 0...
July 17, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28728811/newborn-screening-for-lysosomal-storage-disorders-in-illinois-the-initial-15-month-experience
#5
Barbara K Burton, Joel Charrow, George E Hoganson, Darrell Waggoner, Brad Tinkle, Stephen R Braddock, Michael Schneider, Dorothy K Grange, Claudia Nash, Heather Shryock, Rebecca Barnett, Rong Shao, Khaja Basheeruddin, George Dizikes
OBJECTIVES: To assess the outcomes of newborn screening for 5 lysosomal storage disorders (LSDs) in the first cohort of infants tested in the state of Illinois. STUDY DESIGN: Tandem mass spectrometry was used to assay for the 5 LSD-associated enzymes in dried blood spot specimens obtained from 219 973 newborn samples sent to the Newborn Screening Laboratory of the Illinois Department of Public Health in Chicago. RESULTS: The total number of cases with a positive diagnosis and the incidence for each disorder were as follows: Fabry disease, n = 26 (1 in 8454, including the p...
July 17, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28727806/genocore-a-simple-and-fast-algorithm-for-core-subset-selection-from-large-genotype-datasets
#6
Seongmun Jeong, Jae-Yoon Kim, Soon-Chun Jeong, Sung-Taeg Kang, Jung-Kyung Moon, Namshin Kim
Selecting core subsets from plant genotype datasets is important for enhancing cost-effectiveness and to shorten the time required for analyses of genome-wide association studies (GWAS), and genomics-assisted breeding of crop species, etc. Recently, a large number of genetic markers (>100,000 single nucleotide polymorphisms) have been identified from high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. However, there is no software available for picking out the efficient and consistent core subset from such a huge dataset...
2017: PloS One
https://www.readbyqxmd.com/read/28727731/pregnancy-incidence-and-intention-after-hiv-diagnosis-among-women-living-with-hiv-in-canada
#7
Kate Salters, Mona Loutfy, Alexandra de Pokomandy, Deborah Money, Neora Pick, Lu Wang, Shahab Jabbari, Allison Carter, Kath Webster, Tracey Conway, Daniele Dubuc, Nadia O'Brien, Karene Proulx-Boucher, Angela Kaida
BACKGROUND: Pregnancy incidence rates among women living with HIV (WLWH) have increased over time due to longer life expectancy, improved health status, and improved access to and HIV prevention benefits of combination antiretroviral therapy (cART). However, it is unclear whether intended or unintended pregnancies are contributing to observed increases. METHODS: We analyzed retrospective data from the Canadian HIV Women's Sexual and Reproductive Health Cohort Study (CHIWOS)...
2017: PloS One
https://www.readbyqxmd.com/read/28726404/predicting-optimal-deer-label-positions-to-study-protein-conformational-heterogeneity
#8
Shriyaa Mittal, Diwakar Shukla
Double electron-electron resonance (DEER) spectroscopy is a powerful experimental technique for understanding the conformational heterogeneity of proteins. It involves attaching nitroxide spin labels to two residues in the protein to obtain a distance distribution between them. However, the choice of residue pairs to label in the protein, requires cautious thought and experimentalists are required to pick label positions from a large set of all possible residue pair combinations in the protein. In this paper, we address the problem of the choice of DEER spin label positions in a protein...
July 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28724913/time-averaged-disease-activity-fits-better-joint-destruction-in-rheumatoid-arthritis
#9
Hideaki Tsuji, Koichiro Yano, Moritoshi Furu, Noriyuki Yamakawa, Katsunori Ikari, Motomu Hashimoto, Hiromu Ito, Takao Fujii, Wataru Yamamoto, Koichiro Ohmura, Atsuo Taniguchi, Shigeki Momohara, Fumihiko Matsuda, Cornelia F Allaart, Hisashi Yamanaka, Tsuneyo Mimori, Chikashi Terao
Disease activity of rheumatoid arthritis (RA), evaluated as Disease Activity Score (DAS), is associated with joint destruction. Since joint destruction reflects the history of disease activities, we hypothesized that time-averaged disease activity would better correlate with joint destruction than one-time disease activity. We recruited RA patients in IORRA (n = 557) and KURAMA (n = 204) cohorts, and calculated time-averaged DAS28 to model a modified Sharp/van der Heijde score (SHS). We evaluated the fitting of the model using time-averaged DAS28 among 1000 models in which we randomly picked up one-time DAS28...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724888/crosscheck-an-open-source-web-tool-for-high-throughput-screen-data-analysis
#10
Jamil Najafov, Ayaz Najafov
Modern high-throughput screening methods allow researchers to generate large datasets that potentially contain important biological information. However, oftentimes, picking relevant hits from such screens and generating testable hypotheses requires training in bioinformatics and the skills to efficiently perform database mining. There are currently no tools available to general public that allow users to cross-reference their screen datasets with published screen datasets. To this end, we developed CrossCheck, an online platform for high-throughput screen data analysis...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724562/the-role-of-macrophages-in-interstitial-lung-diseases-number-3-in-the-series-pathology-for-the-clinician-edited-by-peter-dorfm%C3%A3-ller-and-alberto-cavazza
#11
Giulio Rossi, Alberto Cavazza, Paolo Spagnolo, Salvatore Bellafiore, Elisabetta Kuhn, Pierpaolo Carassai, Laura Caramanico, Gloria Montanari, Gaia Cappiello, Alessandro Andreani, Francesca Bono, Nazarena Nannini
The finding of collections of macrophages/histiocytes in lung biopsy and bronchoalveolar lavage is relatively common in routine practice. This morphological feature in itself is pathological, but the exact clinical significance and underlying disease should be evaluated together with clinical data, functional respiratory and laboratory tests and imaging studies.Morphological characteristics of macrophages and their distribution along the different pulmonary structures should be examined carefully by pathologists...
September 30, 2017: European Respiratory Review: An Official Journal of the European Respiratory Society
https://www.readbyqxmd.com/read/28721745/pesticide-genotoxicity-in-cotton-picking-women-in-pakistan-evaluated-using-comet-assay
#12
Tayyaba Ali, Muhammad Ismail, Farkhanda Asad, Asma Ashraf, Usman Waheed, Qaiser M Khan
To control agricultural pests and meet the increasing food demands, pesticides use has been increased substantially over time. Although pesticides are relatively specific to their targets, they can affect non-target organisms and are hazardous for the population around the application areas particularly to the individuals engaged in different types of agricultural activities. This situation is worse in developing and under-developed countries where personal protective equipment is merely used and regulatory guidelines are hardly practiced...
July 19, 2017: Drug and Chemical Toxicology
https://www.readbyqxmd.com/read/28721407/3d-printed-reversible-shape-changing-soft-actuators-assisted-by-liquid-crystal-elastomers
#13
Chao Yuan, Devin J Roach, Conner K Dunn, Quanyi Mu, Xiao Kuang, Christopher M Yakacki, T J Wang, Kai Yu, H Jerry Qi
In this work, we advance printed active composites by combining 3D printing, printed electronics, and liquid crystal elastomers (LCEs) to achieve soft actuators with free-standing two-way shape changing behaviors. Incorporated LCE strips are activated by Joule heating produced by printed conductive wires, while uniaxial deformation of the LCE strip is utilized as a driving force to achieve bending in the printed composite. The bending behavior of laminated hinges is first characterized in order to obtain a precise control of actuation, which is then exploited to actuate four demonstrative designs: a morphing airplane, a miura-ori structure, a cubic box, and a soft crawler...
July 19, 2017: Soft Matter
https://www.readbyqxmd.com/read/28717646/genetic-variation-and-its-reflection-on-posttranslational-modifications-in-frequency-clock-and-mating-type-a-1-proteins-in-sordaria-fimicola
#14
Rabia Arif, Faiza Akram, Tazeen Jamil, Hamid Mukhtar, Siu Fai Lee, Muhammad Saleem
Posttranslational modifications (PTMs) occur in all essential proteins taking command of their functions. There are many domains inside proteins where modifications take place on side-chains of amino acids through various enzymes to generate different species of proteins. In this manuscript we have, for the first time, predicted posttranslational modifications of frequency clock and mating type a-1 proteins in Sordaria fimicola collected from different sites to see the effect of environment on proteins or various amino acids pickings and their ultimate impact on consensus sequences present in mating type proteins using bioinformatics tools...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28715377/creation-of-cardiac-tissue-exhibiting-mechanical-integration-of-spheroids-using-3d-bioprinting
#15
Chin Siang Ong, Takuma Fukunishi, Andrew Nashed, Adriana Blazeski, Huaitao Zhang, Samantha Hardy, Deborah DiSilvestre, Luca Vricella, John Conte, Leslie Tung, Gordon Tomaselli, Narutoshi Hibino
This protocol describes 3D bioprinting of cardiac tissue without the use of biomaterials, using only cells. Cardiomyocytes, endothelial cells and fibroblasts are first isolated, counted and mixed at desired cell ratios. They are co-cultured in individual wells in ultra-low attachment 96-well plates. Within 3 days, beating spheroids form. These spheroids are then picked up by a nozzle using vacuum suction and assembled on a needle array using a 3D bioprinter. The spheroids are then allowed to fuse on the needle array...
July 2, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28714100/why-is-it-so-hard-to-reach-agreement-on-terminology-the-case-of-developmental-language-disorder-dld
#16
Dorothy V M Bishop
A recent project entitled CATALISE used the Delphi method to reach a consensus on terminology for unexplained language problems in children. 'Developmental language disorder' (DLD) was the term agreed by a panel of 57 experts. Here I reflect on points of difficulty that arose when attempting to reach a consensus, using qualitative information from comments made by panel members to illustrate the kinds of argument used. One issue of debate was the use of labels, in particular the term 'disorder', which was seen as having both pros and cons...
July 17, 2017: International Journal of Language & Communication Disorders
https://www.readbyqxmd.com/read/28712896/prospective-evaluation-of-the-non-invasive-headsense-icp-monitor-in-tbi-patients-undergoing-invasive-icp-monitoring
#17
Martin W Herklots, Walid Moudrous, Annemarie Oldenbeuving, Gerwin Roks, Stylianos Mourtzoukos, Guus G Schoonman, Oliver Ganslandt
BACKGROUND: Currently intracranial pressure (ICP) is measured by invasive methods with a significant risk of infectious and hemorrhagic complications. Because of these high risks, there is need for a noninvasive ICP (nICP) monitor with an accuracy similar to that of an invasive ICP monitor. OBJECTIVE: To assess prospectively the accuracy and precision of a nICP monitor compared with invasive intracranial pressure (iICP) measurement in severe TBI patients. METHODS: Participants were ICP-monitored patients who had sustained TBI...
July 13, 2017: World Neurosurgery
https://www.readbyqxmd.com/read/28712168/justification-for-re-look-cystoscopy-after-posterior-urethral-valve-fulguration
#18
Gul Nawaz, Ijaz Hussain, Shujah Muhammad, Muhammad Imran Jamil, Asad Ur Rehman, Nadeem Iqbal, Saeed Akhter
BACKGROUND: Posterior urethral valve (PUV) is life-threatening congenital anomaly of the urinary tract that results in vesicoureteric reflux, recurrent UTI, voiding dysfunction and renal insufficiency if not treat timely. Endoscopic ablation of posterior urethral valves using cold knife or laser is the current gold standard therapy. Many urologists go for repeat cystoscopy to see residual valve or stricture while others repeat VCUG to measure the posterior to anterior urethral ratio for residual obstruction...
January 2017: Journal of Ayub Medical College, Abbottabad: JAMC
https://www.readbyqxmd.com/read/28710748/longitudinal-changes-in-white-matter-fractional-anisotropy-in-adult-onset-niemann-pick-disease-type-c-patients-treated-with-miglustat
#19
Elizabeth A Bowman, Dennis Velakoulis, Patricia Desmond, Mark Walterfang
Niemann-Pick disease type C (NPC) is a rare neurometabolic disorder resulting in impaired intracellular lipid trafficking. The only disease-modifying treatment currently available is miglustat, an iminosugar that inhibits the accumulation of lipid metabolites in neurons and other cells. This longitudinal diffusion tensor imaging (DTI) study examined how the rate of white matter change differed between treated and non-treated adult-onset NPC patient groups. Nine adult-onset NPC patients (seven undergoing treatment with miglustat, two not treated) underwent DTI neuroimaging...
July 15, 2017: JIMD Reports
https://www.readbyqxmd.com/read/28709281/how-the-fittest-compete-for-leadership-a-tale-of-tails
#20
J M Luck, A Mehta
We investigate how leaders emerge as a consequence of the competitive dynamics between coupled papers in a model citation network. Every paper is allocated an initial fitness depending on its intrinsic quality. Its fitness then involves dynamically as a consequence of the competition between itself and all the other papers in the field. It picks up citations as a result of this adaptive dynamics, becoming a leader if it has the highest citation count at a given time. Extensive analytical and numerical investigations of this model suggest the existence of a universal phase diagram, divided into regions of weak and strong coupling...
June 2017: Physical Review. E
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