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Rapid sequence

Kate Bunton, Brad H Story
OBJECTIVE: The goal of the Arizona Child Acoustic Database project was to obtain a large set of acoustic recordings, primarily vowels, collected from a cohort of children over a critical period of growth and development. METHOD: Data was recorded longitudinally from 63 children between the ages of 2;0 and 7;0 at 3-month intervals. The protocol included individual American English vowels and diphthongs, nonsense multi-vowel transitions, word level multi-vowel sequences (e...
October 27, 2016: Folia Phoniatrica et Logopaedica
Michael Worobey, Thomas D Watts, Richard A McKay, Marc A Suchard, Timothy Granade, Dirk E Teuwen, Beryl A Koblin, Walid Heneine, Philippe Lemey, Harold W Jaffe
The emergence of HIV-1 group M subtype B in North American men who have sex with men was a key turning point in the HIV/AIDS pandemic. Phylogenetic studies have suggested cryptic subtype B circulation in the United States (US) throughout the 1970s and an even older presence in the Caribbean. However, these temporal and geographical inferences, based upon partial HIV-1 genomes that postdate the recognition of AIDS in 1981, remain contentious and the earliest movements of the virus within the US are unknown. We serologically screened >2,000 1970s serum samples and developed a highly sensitive approach for recovering viral RNA from degraded archival samples...
October 26, 2016: Nature
V Shapaval, T Møretrø, A Wold Åsli, H P Suso, J Schmitt, D Lillehaug, A Kohler
Microbiological source tracking (MST) for food industry is a rapid growing area of research and technology development. In the paper at hand, a new library-independent approach for microbial source tracking is presented. It is based on a high-throughput liquid micro-cultivation and FTIR spectroscopy. In the approach, FTIR spectra obtained from microorganisms isolated along the production line and a product are compared to each other. We tested and evaluated the new source tracking approach by simulating a source tracking situation...
October 26, 2016: Letters in Applied Microbiology
Rohit Randhawa, Ajay Duseja, Harish Changotra
Various case-control studies have shown association of single nucleotide polymorphism rs12303764(G/T) in ULK1 with crohn's disease. The techniques used in these studies were time consuming, complicated and require sophisticated/expensive instruments. Therefore, in order to overcome these problems, we have developed a new, rapid and cost effective Tetra-primer ARMS-PCR assay to genotype single nucleotide polymorphism rs12303764(G/T) of ULK1 gene. We manually designed allele specific primers. DNA fragment amplified using outer primers was sequenced to obtain samples with known genotypes (GG, GT and TT) for further use in the development of T-ARMS-PCR assay...
October 25, 2016: Molecular Biology Reports
Thilini Piushani Keerthirathne, Dhammika Nayoma Magana-Arachchi, Dushantha Madegedara, Suneth Sithumini Sooriyapathirana
BACKGROUND: Mycobacteria have a spectrum of virulence and different susceptibilities to antibiotics. Distinguishing mycobacterial species is vital as patients with non-tuberculous mycobacterial (NTM) infections present clinical features that are similar to those of patients with tuberculosis. Thus, rapid differentiation of Mycobacterium tuberculosis complex from NTM is critical to administer appropriate treatment. Hence the aim of the study was to rapid identification of mycobacterial species present in bronchial washings using multiplex real time Polymerase Chain Reaction (PCR) and to determine the drug susceptibility in identified mycobacterial species...
October 26, 2016: BMC Infectious Diseases
M Migalska, A Sebastian, M Konczal, P Kotlík, J Radwan
The major histocompatibility complex (MHC) plays a central role in the adaptive immune response and is the most polymorphic gene family in vertebrates. Although high-throughput sequencing has increasingly been used for genotyping families of co-amplifying MHC genes, its potential to facilitate early steps in the characterisation of MHC variation in nonmodel organism has not been fully explored. In this study we evaluated the usefulness of de novo transcriptome assembly in characterisation of MHC sequence diversity...
October 26, 2016: Heredity
Kateryna S Pantiukh, Nikolay N Chekanov, Igor V Zaigrin, Alexei M Zotov, Alexander M Mazur, Egor B Prokhortchouk
Concerns of traditional prenatal aneuploidy testing methods, such as low accuracy of noninvasive and health risks associated with invasive procedures, were overcome with the introduction of novel noninvasive methods based on genetics (NIPT). These were rapidly adopted into clinical practice in many countries after a series of successful trials of various independent submethods. Here we present results of own NIPT trial carried out in Moscow, Russia. 1012 samples were subjected to the method aimed at measuring chromosome coverage by massive parallel sequencing...
2016: F1000Research
Irena Maus, Yong Sung Kim, Daniel Wibberg, Yvonne Stolze, Sandra Off, Sebastian Antonczyk, Alfred Pühler, Paul Scherer, Andreas Schlüter
Process surveillance within agricultural biogas plants (BGPs) was concurrently studied by high-throughput 16S rRNA gene amplicon sequencing and an optimized quantitative microscopic fingerprinting technique (QMF). In contrast to 16S rRNA gene amplicons, digitalized microscopy is a rapid and cost effective method which facilitates enumeration and morphological differentiation of the most significant groups of methanogens regarding their shape and characteristic auto-fluorescent factor 420. Moreover, the fluorescence signal mirrors cell vitality...
October 25, 2016: Journal of Microbiology and Biotechnology
Felicia S L Ng, David Ruau, Lorenz Wernisch, Berthold Göttgens
Integrated analysis of multiple genome-wide transcription factor (TF)-binding profiles will be vital to advance our understanding of the global impact of TF binding. However, existing methods for measuring similarity in large numbers of chromatin immunoprecipitation assays with sequencing (ChIP-seq), such as correlation, mutual information or enrichment analysis, are limited in their ability to display functionally relevant TF relationships. In this study, we propose the use of graphical models to determine conditional independence between TFs and showed that network visualization provides a promising alternative to distinguish 'direct' versus 'indirect' TF interactions...
October 25, 2016: Briefings in Bioinformatics
José R Valverde, Sonia Gullón, Rafael Pérez Mellado
INTRODUCTION: Biological communities present in soil are essential to sustainable and productive agricultural practices; however, an accurate determination of the ecological status of agricultural soils remains to date an elusive task. An ideal indicator should be pervasive, play a relevant role in the ecosystem, show a rapid and proportional answer to external perturbations and be easily and economically measurable. Rhizobacteria play a major role in determining soil properties, becoming an attractive candidate for the detection of ecological indicators...
2016: PloS One
Jay N Lozier, Mark T Kloos, Elizabeth P Merricks, Nathaly Lemoine, Margaret H Whitford, Robin A Raymer, Dwight A Bellinger, Timothy C Nichols
Animals with hemophilia are models for gene therapy, factor replacement, and inhibitor development in humans. We have actively sought dogs with severe hemophilia A that have novel factor VIII mutations unlike the previously described factor VIII intron 22 inversion. A male Old English Sheepdog with recurrent soft-tissue hemorrhage and hemarthrosis was diagnosed with severe hemophilia A (factor VIII activity less than 1% of normal). We purified genomic DNA from this dog and ruled out the common intron 22 inversion; we then sequenced all 26 exons...
2016: Comparative Medicine
Megan Johnson, Kenji Inaba, Saskya Byerly, Erika Falsgraf, Lydia Lam, Elizabeth Benjamin, Aaron Strumwasser, Jean-Stephane David, Demetrios Demetriades
Intraosseous (IO) needle placement is an alternative for patients with difficult venous access. The purpose of this retrospective study was to examine indications and outcomes associated with IO use at a Level 1 trauma center (January 2008-May 2015). Data points included demographics, time to insertion, intravenous (IV) access points, indications, infusions, hospital and intensive care unit length of stay, and mortality. Of 68 patients with IO insertion analyzed (63.2% blunt trauma, 29.4% penetrating trauma, and 7...
October 2016: American Surgeon
Michael J Mitchell, Catherine Metzler-Guillemain, Toure Aminata, Charles Coutton, Christophe Arnoult, Pierre F Ray
Azoospermia, defined by the absence of sperm in the ejaculate, is estimated to affect up to 1% of men in the general population. Assisted reproductive technologies have revolutionized the treatment of infertility, and some azoospermic men, those with a post-meiotic defect, can conceive following the use of viable spermatoza recovered from testicular or epididymal biopsies. Although male infertility is a multifactorial disease, it is believed that genetic factors are predominant in the etiology of azoospermia and severe oligozoospermia...
October 25, 2016: Clinical Genetics
H Bayram, A Sayadi, J Goenaga, E Immonen, G Arnqvist
The seed beetle Callosobruchus maculatus is a significant agricultural pest and increasingly studied model of sexual conflict. Males possess genital spines that increase the transfer of seminal fluid proteins (SFPs) into the female body. As SFPs alter female behaviour and physiology, they are likely to modulate reproduction and sexual conflict in this species. Here, we identified SFPs using proteomics combined with a de novo transcriptome. A prior 2D-sodium dodecyl sulphate polyacrylamide gel electrophoresis analysis identified male accessory gland protein spots that were probably transferred to the female at mating...
October 24, 2016: Insect Molecular Biology
Xiaole Wang, Fang He, Fei Yin, Chao Chen, Liwen Wu, Lifen Yang, Jing Peng
Leukoencephalopathies are diseases with high clinical heterogeneity. In clinical work, it's difficult for doctors to make a definite etiological diagnosis. Here, we designed a custom probe library which contains the known pathogenic genes reported to be associated with Leukoencephalopathies, and performed targeted gene capture and massively parallel sequencing (MPS) among 49 Chinese patients who has white matter damage as the main imaging changes, and made the validation by Sanger sequencing for the probands' parents...
October 25, 2016: Scientific Reports
J D Thiessen, E Shams, G Stortz, G Schellenberg, D Bishop, M S Khan, P Kozlowski, F Retière, V Sossi, C J Thompson, A L Goertzen
A full-ring PET insert consisting of 16 PET detector modules was designed and constructed to fit within the 114 mm diameter gradient bore of a Bruker 7 T MRI. The individual detector modules contain two silicon photomultiplier (SiPM) arrays, dual-layer offset LYSO crystal arrays, and high-definition multimedia interface (HDMI) cables for both signal and power transmission. Several different RF shielding configurations were assessed prior to construction of a fully assembled PET insert using a combination of carbon fibre and copper foil for RF shielding...
November 21, 2016: Physics in Medicine and Biology
Emna Farhat, Mourad Zouari, Ines Ben Abdelaziz, Cyrine Drissi, Rahma Beyrouti, Mohamed Ben Hammouda, Fayçal Hentati
BACKGROUND: Cerebellar ataxia represents a rare and severe complication of Sjӧgren syndrome (SS), especially with a progressive onset and cerebellar atrophy on imaging. CASE PRESENTATION: We report the case of a 30-year-old woman, with a past history of dry eyes and mouth, who presented a severe cerebellar ataxia worsening over 4 years associated with tremor of the limbs and the head. Brain MRI showed bilateral hyperintensities on T2 and FLAIR sequences, affecting periventricular white matter, with marked cerebellar atrophy...
2016: Cerebellum & Ataxias
Donna M Bond, Nick W Albert, Robyn H Lee, Gareth B Gillard, Chris M Brown, Roger P Hellens, Richard C Macknight
BACKGROUND: Transcription factors (TFs) coordinate precise gene expression patterns that give rise to distinct phenotypic outputs. The identification of genes and transcriptional networks regulated by a TF often requires stable transformation and expression changes in plant cells. However, the production of stable transformants can be slow and laborious with no guarantee of success. Furthermore, transgenic plants overexpressing a TF of interest can present pleiotropic phenotypes and/or result in a high number of indirect gene expression changes...
2016: Plant Methods
James A Bashford, Fahmida A Chowdhury, Chris E Shaw
The clinical diagnosis of Brown-Vialetto-Van Laere syndrome in this woman with rapidly progressive pontobulbar palsy led to empirical high-dose oral riboflavin (1200 mg/day) therapy. This resulted in a dramatic improvement in her motor function from being anarthric, dysphagic, tetraparetic and in ventilatory failure to living independently with mild dysarthria and distal limb weakness. DNA sequencing of the SLC52A3 gene found compound heterozygous C-terminus mutations, V413A1/D461Y, consistent with recent reports of mutations within the riboflavin transporter genes (SLC52A2 and SLC52A3) in this condition...
October 24, 2016: Practical Neurology
Rosiane Yamasaki, Arlindo Montagnoli, Emi Z Murano, Eloisa Gebrim, Adriana Hachiya, Jorge Vicente Lopes da Silva, Mara Behlau, Domingos Tsuji
OBJECTIVE: To determine the impact of jitter and shimmer on the degree of naturalness perception of synthesized vowels produced by acoustical simulation with glottal pulses (GP) and with solid model of the vocal tract (SMVT). STUDY DESIGN: Prospective study. METHODS: Synthesized vowels were produced in three steps: 1. Eighty GP were developed (20 with jitter, 20 with shimmer, 20 with jitter+shimmer, 20 without perturbation); 2. A SMVT was produced based on magnetic resonance imaging (MRI) from a woman during phonation-/ε/ and using rapid prototyping technology; 3...
October 21, 2016: Journal of Voice: Official Journal of the Voice Foundation
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