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Ian B Mertes, Marjorie R Leek
Contralateral suppression of otoacoustic emissions (OAEs) is frequently used to assess the medial olivocochlear (MOC) efferent system, and may have clinical utility. However, OAEs are weak or absent in hearing-impaired ears, so little is known about MOC function in the presence of hearing loss. A potential alternative measure is contralateral suppression of the auditory steady-state response (ASSR) because ASSRs are measurable in many hearing-impaired ears. This study compared contralateral suppression of both transient-evoked otoacoustic emissions (TEOAEs) and ASSRs in a group of ten primarily older adults with either normal hearing or mild sensorineural hearing loss...
September 2016: Journal of the Acoustical Society of America
Fatemeh Atarzadeh, Babak Daneshfard, Ladan Dastgheib, Amir-Mohammad Jaladat, Gholamreza Amin
Pemphigus is an autoimmune blistering skin disease that is strongly associated with different environmental factors. Among these, nutritional factors are considered to trigger pemphigus; however, their role may be underestimated. Investigated more recently in conventional medicine, this causative bond between dietary factors and blistering skin diseases was mentioned by Persian scholars such as Avicenna a thousand years ago. Avicenna, a well-known Persian physician and philosopher, who could be considered a pioneer in dermatology, discussed skin diseases in a chapter in The Canon of Medicine...
2016: Skinmed
Yuh Chwen G Lee, Courtney Leek, Mia T Levine
Telomeres are nucleoprotein complexes at the ends of linear chromosomes. These specialized structures ensure genome integrity and faithful chromosome inheritance. Recurrent addition of repetitive, telomere-specific DNA elements to chromosome ends combats end-attrition, while specialized telomere-associated proteins protect naked, double-stranded chromosome ends from promiscuous repair into end-to-end fusions. Although telomere length homeostasis and end-protection are ubiquitous across eukaryotes, there is sporadic but building evidence that the molecular machinery supporting these essential processes evolves rapidly...
November 11, 2016: Molecular Biology and Evolution
Alexander Castro Grijalba, Estefanía M Martinis, Rodolfo G Wuilloud
A highly sensitive vortex assisted liquid-liquid microextraction (VA-LLME) method was developed for inorganic Se [Se(IV) and Se(VI)] speciation analysis in Allium and Brassica vegetables. Trihexyl(tetradecyl)phosphonium decanoate phosphonium ionic liquid (IL) was applied for the extraction of Se(IV)-ammonium pyrrolidine dithiocarbamate (APDC) complex followed by Se determination with electrothermal atomic absorption spectrometry. A complete optimization of the graphite furnace temperature program was developed for accurate determination of Se in the IL-enriched extracts and multivariate statistical optimization was performed to define the conditions for the highest extraction efficiency...
March 15, 2017: Food Chemistry
Ben Beck, Janet E Bray, Karen Smith, Tony Walker, Hugh Grantham, Cindy Hein, Melanie Thorrowgood, Anthony Smith, Madoka Inoue, Tony Smith, Bridget Dicker, Andy Swain, Emma Bosley, Katherine Pemberton, Michael McKay, Malcolm Johnston-Leek, Peter Cameron, Gavin D Perkins, Judith Finn
OBJECTIVE: The present study aimed to describe and examine similarities and differences in the current service provision and resuscitation protocols of the ambulance services participating in the Aus-ROC Australian and New Zealand out-of-hospital cardiac arrest (OHCA) Epistry. Understanding these similarities and differences is important in identifying ambulance service factors that might explain regional variation in survival of OHCA in the Aus-ROC Epistry. METHODS: A structured questionnaire was completed by each of the ambulance services participating in the Aus-ROC Epistry...
December 2016: Emergency Medicine Australasia: EMA
Ali Pourzand, Aynaz Tajaddini, Saeed Pirouzpanah, Mohammad Asghari-Jafarabadi, Nasser Samadi, Ali-Reza Ostadrahimi, Zohre Sanaat
PURPOSE: The protective effect of Allium vegetables against carcinogenesis has been reported in experimental studies particularly focusing on the gut. Therefore, we conducted a hospital-based matched case-control study to explore the association between dietary Allium consumption and risk of breast cancer among Iranian women in northwest Iran. METHODS: A validated, quantitative, food frequency questionnaire was completed in 285 women (aged 25-65 years old) newly diagnosed with histopathologically confirmed breast cancer (grade II, III or clinical stage II, III) in Tabriz, northwest Iran, and the completed questionnaires were included in an age- and regional-matched hospital based-control study...
September 2016: Journal of Breast Cancer
Leonardo Collado-Torres, Abhinav Nellore, Alyssa C Frazee, Christopher Wilks, Michael I Love, Ben Langmead, Rafael A Irizarry, Jeffrey T Leek, Andrew E Jaffe
Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. We previously introduced an intermediate statistical approach called differentially expressed region (DER) finder that seeks to identify contiguous regions of the genome showing differential expression signal at single base resolution without relying on existing annotation or potentially inaccurate transcript assembly.We present the derfinder software that improves our annotation-agnostic approach to RNA-seq analysis by: (i) implementing a computationally efficient bump-hunting approach to identify DERs that permits genome-scale analyses in a large number of samples, (ii) introducing a flexible statistical modeling framework, including multi-group and time-course analyses and (iii) introducing a new set of data visualizations for expressed region analysis...
September 29, 2016: Nucleic Acids Research
Hanna Leek, Linda Thunberg, Anna C Jonson, Kristina Öhlén, Magnus Klarqvist
A strategy for large-scale chiral resolution is illustrated by the isolation of pure enantiomer from a 5kg batch. Results from supercritical fluid chromatography will be presented and compared with normal phase liquid chromatography. Solubility of the compound in the supercritical mobile phase was shown to be the limiting factor. To circumvent this, extraction injection was used but shown not to be efficient for this compound. Finally, a method for chiral resolution by crystallization was developed and applied to give diastereomeric salt with an enantiomeric excess of 99% at a 91% yield...
September 28, 2016: Drug Discovery Today
Dorota Tchórzewska, Kamil Deryło, Krystyna Winiarczyk
Using a live-cell-imaging approach and autofluorescence-spectral imaging, we showed quantitative/qualitative fluctuations of chemical compounds within the meiocyte callose wall, providing insight into the molecular basis of male sterility in plants from the genus Allium. Allium sativum (garlic) is one of the plant species exhibiting male sterility, and the molecular background of this phenomenon has never been thoroughly described. This study presents comparative analyses of meiotically dividing cells, which revealed inhibition at the different microsporogenesis stages in male-sterile A...
September 29, 2016: Planta
Richard M Tolman, Erin A Casey, Christopher T Allen, Juliana Carlson, Cliff Leek, Heather L Storer
Organizations addressing gender-based violence (GBV) increasingly include men as partners in prevention efforts. However, little is known about men who get involved in those efforts and what specific actions they take. We present analyses of data from an international sample of men involved in gender-based prevention work that aimed to describe (a) the nature of participants' involvement in prevention efforts, in both formal programming and in their daily lives; (b) characteristics of engaged men, including gender and bystander-related attitudes and beliefs, and social networks; and (c) factors that sustain men's involvement in GBV movements over time...
September 26, 2016: Journal of Interpersonal Violence
David A C Manning, Joana Baptista, Mallely Sanchez Limon, Kirsten Brandt
The availability of K, essential for plant growth, from syenite (a silicate rock in which potassium feldspar is the dominant mineral; >90wt%), and phlogopite mica has been demonstrated using carefully designed plant growth pot experiments in which the only added source of K was the mineral of interest, with no loss of nutrients through drainage. Using pure quartz sand as a soil, both growth (increase in diameter) of leek plants and K-content of the plant material showed a dose-dependent positive response to the application (114-43000mgK/pot) of milled syenite with increases in plant diameter of 0...
September 16, 2016: Science of the Total Environment
Emelie Glenne, Hanna Leek, Magnus Klarqvist, Jörgen Samuelsson, Torgny Fornstedt
In supercritical fluid chromatography (SFC) the mobile phase comprises of carbon dioxide (CO2) as main solvent and smaller amounts of an organic polar solvent (often an alcohol) as co-solvent. The co-solvent is considered to function by changing the overall polarity of the eluent, i.e. by acting as a "modifier". However, recent studies indicate that the co-solvent methanol can also adsorb to some common SFC stationary phases. Hence, the co-solvent should also be able to function as an "adsorbing additive", i...
October 14, 2016: Journal of Chromatography. A
Abhinav Nellore, Leonardo Collado-Torres, Andrew E Jaffe, José Alquicira-Hernández, Christopher Wilks, Jacob Pritt, James Morton, Jeffrey T Leek, Ben Langmead
MOTIVATION: RNA sequencing (RNA-seq) experiments now span hundreds to thousands of samples. Current spliced alignment software is designed to analyze each sample separately. Consequently, no information is gained from analyzing multiple samples together, and it requires extra work to obtain analysis products that incorporate data from across samples. RESULTS: We describe Rail-RNA, a cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added...
September 4, 2016: Bioinformatics
James D Miller, Charles S Watson, Judy R Dubno, Marjorie R Leek
Following an overview of theoretical issues in speech-perception training and of previous efforts to enhance hearing aid use through training, a multisite study, designed to evaluate the efficacy of two types of computerized speech-perception training for adults who use hearing aids, is described. One training method focuses on the identification of 109 syllable constituents (45 onsets, 28 nuclei, and 36 codas) in quiet and in noise, and on the perception of words in sentences presented in various levels of noise...
November 2015: Seminars in Hearing
J Sharifi-Rad, D Mnayer, G Tabanelli, Z Z Stojanović-Radić, M Sharifi-Rad, Z Yousaf, L Vallone, W N Setzer, M Iriti
Plants belonging to the genus Allium are widely cultivated and used all over the world as food and medicinal plants. Since ancient times, these plants, particularly garlic (Allium sativum L.) and onion (Allium cepa L.), have represented important components of typical recipes and traditional healing systems. Not the least of which, their use as food biopreservatives is well documented, due to the relevant antibacterial activity of their extracts and essential oils. In addition to garlic and onion, this review article deals with the main members of the genus Allium, including A...
2016: Cellular and Molecular Biology
Mihaela Pertea, Daehwan Kim, Geo M Pertea, Jeffrey T Leek, Steven L Salzberg
High-throughput sequencing of mRNA (RNA-seq) has become the standard method for measuring and comparing the levels of gene expression in a wide variety of species and conditions. RNA-seq experiments generate very large, complex data sets that demand fast, accurate and flexible software to reduce the raw read data to comprehensible results. HISAT (hierarchical indexing for spliced alignment of transcripts), StringTie and Ballgown are free, open-source software tools for comprehensive analysis of RNA-seq experiments...
September 2016: Nature Protocols
Hans G J Mol, Marc Tienstra, Paul Zomer
Gas chromatography with electron ionization and full scan high resolution mass spectrometry with an Orbitrap mass analyzer (GC-EI-full scan Orbitrap HRMS) was evaluated for residue analysis. Pesticides in fruit and vegetables were taken as an example application. The relevant aspects for GC-MS based residue analysis, including the resolving power (15,000 to 120,000 FWHM at m/z 200), scan rate, dynamic range, selectivity, sensitivity, analyte identification, and utility of existing EI-libraries, are assessed and discussed in detail...
September 7, 2016: Analytica Chimica Acta
Solaiappan Manimaran, Heather Marie Selby, Kwame Okrah, Claire Ruberman, Jeffrey T Leek, John Quackenbush, Benjamin Haibe-Kains, Hector Corrada Bravo, W Evan Johnson
: Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. There are several existing batch adjustment tools for '-omics' data, but they do not indicate a priori whether adjustment needs to be conducted or how correction should be applied. We present a software pipeline, BatchQC, which addresses these issues using interactive visualizations and statistics that evaluate the impact of batch effects in a genomic dataset...
August 18, 2016: Bioinformatics
Viktorija Eisinaite, Rimante Vinauskiene, Pranas Viskelis, Daiva Leskauskaite
The aim of this study was to compare the chemical composition of freeze-dried vegetable powders: celery, celery juice, parsnip and leek. The effect of different freeze-dried vegetables onto the ripening process and the properties of dry fermented sausages was also evaluated. Vegetable products significantly (p < 0.05) differed in their chemical composition: celery products contained higher amounts of nitrates, total phenolic compounds and lower amounts of sucrose, parsnip had higher concentration of proteins, leek was rich in fat...
September 2016: Journal of Food Science
Vahideh Fatoorechi, Marjan Rismanchi, Javad Nasrollahzadeh
OBJECTIVE: Persian leek is one of the most widely used herbal foods among Iranians. In this study, effects of oral administration of Persian leek on plasma and liver lipids were examined in hamster. MATERIALS AND METHODS: Male Syrian hamsters were randomly divided into three groups: control (standard diet), high fat control (high-fat/high-cholesterol diet), Persian leek (high-fat/high-cholesterol diet + 1% per weight of diet from dried powdered Persian leek) for 14 weeks...
July 2016: Avicenna Journal of Phytomedicine
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