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Shannon E Ellis, Leonardo Collado-Torres, Andrew Jaffe, Jeffrey T Leek
Publicly available genomic data are a valuable resource for studying normal human variation and disease, but these data are often not well labeled or annotated. The lack of phenotype information for public genomic data severely limits their utility for addressing targeted biological questions. We develop an in silico phenotyping approach for predicting critical missing annotation directly from genomic measurements using well-annotated genomic and phenotypic data produced by consortia like TCGA and GTEx as training data...
March 5, 2018: Nucleic Acids Research
Leanne Winter, Paul B Colditz, Matthew R Sanders, Roslyn N Boyd, Margo Pritchard, Peter H Gray, Koa Whittingham, Kylee Forrest, Rebecca Leeks, Lachlan Webb, Louise Marquart, Karen Taylor, Judith Macey
To determine the prevalence, associated factors, and relationships between symptoms of depression, symptoms of posttraumatic stress (PTS), and relationship distress in mothers and fathers of very preterm (VPT) infants (< 32 weeks). Mothers (n = 323) and fathers (n = 237) completed self-report measures on demographic and outcome variables at 38 days (SD = 23.1, range 9-116) postpartum while their infants were still hospitalised. Of mothers, 46.7% had a moderate to high likelihood of depression, 38...
March 3, 2018: Archives of Women's Mental Health
Ben Beck, Janet Bray, Peter Cameron, 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, Gavin D Perkins, Graham Nichol, Judith Finn
INTRODUCTION: The aim of this study was to investigate regional variation in the characteristics, incidence and outcomes of out-of-hospital cardiac arrest (OHCA) in Australia and New Zealand. METHODS: This was a population-based cohort study of OHCA using data from the Aus-ROC Australian and New Zealand OHCA Epistry over the period of 01 January 2015 to 31 December 2015. Seven ambulance services contributed data to the Epistry with a capture population of 19.8 million people...
February 27, 2018: Resuscitation
Víctor Cutillas, María Martínez Galera, Łukasz Rajski, Amadeo R Fernández-Alba
Supercritical fluid chromatography coupled to triple quadrupole mass spectrometry has been evaluated for pesticide residues in food. In order to check its advantages and limitations it was developed a method to identify and quantify 164 pesticides in three different matrices (tomato, orange and leek). A carbon dioxide gradient with methanol (containing 1 mM ammonium formate) was used allowing a flow rate of 1.5 mL/min that made the total run time of 12 min without any problem of overpressure. Addition of a post column flow 150 μL/min of Methanol with ammonium formate/formic acid was necessary to improve the ionization...
February 23, 2018: Journal of Chromatography. A
Shaun P Stice, Spencer D Stumpf, Ron D Gitaitis, Brian H Kvitko, Bhabesh Dutta
Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen with a broad host range. Although P. ananatis strains can be aggressive on onion causing foliar necrosis and onion center rot, previous genomic analysis has shown that P. ananatis lacks the primary virulence secretion systems associated with other plant pathogens. We assessed a collection of fifty P. ananatis strains collected from Georgia over three decades to determine genetic factors that correlated with onion pathogenic potential...
2018: Frontiers in Microbiology
Mehruba Anwar, Matthew Turner, Natalija Farrell, Wendy B Zomlefer, Owen M McDougal, Brent W Morgan
INTRODUCTION: Steroidal alkaloids are found in plants of the genus Veratrum. Their toxicity manifests as gastrointestinal symptoms followed by a Bezold-Jarisch reflex: hypopnea, hypotension, and bradycardia. Some Veratrum steroidal alkaloids are also teratogens interfering with the hedgehog-2 signaling pathway, which causes cyclopsia and holoprosencephaly. We present a case of accidental poisoning from Veratrum parviflorum mistaken for the edible Allium tricoccum (ramps, wild leek). CASE HISTORY: A 27-year-old man and his 25-year-old wife presented to the emergency department with nausea, vomiting, hypotension, and bradycardia after foraging and ingesting plants that they believed to be a local native species of wild leek...
February 28, 2018: Clinical Toxicology
Xiaomin Xu, Lingyun Li, Xiaodong Huang, Huan Lin, Guangyang Liu, Donghui Xu, Jianhui Jiang
The present study investigated the concentrations of residues of four groups of pesticides in the People's Republic of China: organophosphorus, carbamate, pyrethroid, and triazine pesticides. Twenty-six pesticides were examined using gas chromatography-tandem mass spectrometry and liquid chromatography-tandem mass spectrometry in 2,169 samples of 12 typical vegetables collected from 15 provinces in China. The results showed that 908 (41.9%) samples were positive, with 133 (6.1%) samples exceeding the limit legal in China...
February 8, 2018: Journal of Food Protection
Qiurui Liu, Mingdi Jiang, Zeliang Ju, Xuguang Qiao, Zhixiang Xu
A direct competitive biomimetic immunosorbent assay method based on molecularly imprinted polymer was developed for the determination of trichlorfon. A CdSe/ZnS quantum dot label was used as the marker. The hydrophilic imprinted film was synthesized directly on the surface of a 96-well plate, and characterized by Fourier-transform infrared spectroscopy and thermo-gravimetric analyses. The method exhibited high stability, selectivity, and sensitivity. Under optimal conditions, the limits of detection and sensitivity of the biomimetic immunosorbent assay method were 9...
June 1, 2018: Food Chemistry
Daniel E Shearer, Michelle R Molis, Keri O Bennett, Marjorie R Leek
Individuals with hearing loss are thought to be less sensitive to the often subtle variations of acoustic information that support auditory stream segregation. Perceptual segregation can be influenced by differences in both the spectral and temporal characteristics of interleaved stimuli. The purpose of this study was to determine what stimulus characteristics support sequential stream segregation by normal-hearing and hearing-impaired listeners. Iterated rippled noises (IRNs) were used to assess the effects of tonality, spectral resolvability, and hearing loss on the perception of auditory streams in two pitch regions, corresponding to 250 and 1000 Hz...
January 2018: Journal of the Acoustical Society of America
Jianhui Fu, Qiang Xu, Guifang Han, Bo Wu, Cheng Hon Alfred Huan, Meng Lee Leek, Tze Chien Sum
The original version of this Article omitted an affiliation of Cheng Hon Alfred Huan: 'Institute of Materials Research and Engineering (IMRE), A*STAR, 2 Fusionopolis Way, Innovis #08-03 138634, Singapore'.This has now been corrected in both the PDF and HTML versions of the article.
January 11, 2018: Nature Communications
Yongqiang Li, Anning Jia, Yan Qiao, Jun Xiang, Yongjiang Zhang, Wenhe Wang
Lily plants exhibiting virus-like symptoms of leaf yellowing, twisting and brownish necrotic spots were collected, and next-generation sequencing of small RNAs was conducted to identify the associated viruses. Cucumber mosaic virus, lily symptomless virus and a hitherto unrecorded potyvirus, tentatively named "lily yellow mosaic virus" (LYMV), were detected. The genomic RNA of LYMV was 9811 nt in length, encoding a large polyprotein of 3,124 amino acids with a predicted Mr of 353.3 kDa. BLAST analysis showed that LYMV shared a high degree of amino acid sequence identity with Thunberg fritillary mosaic virus (55%), bean yellow mosaic virus (52%), clover yellow vein virus (51%), leek yellow stripe virus (51%), and lily mottle virus (52%), and these viruses clustered together in a phylogenetic tree...
December 26, 2017: Archives of Virology
Sean L Hammond, Ashley N Leek, Evan H Richman, Ronald B Tjalkens
The non-pathogenic parvovirus, adeno-associated virus (AAV), is an efficient vector for transgene expression in vivo and shows promise for treatment of brain disorders in clinical trials. Currently, there are more than 100 AAV serotypes identified that differ in the binding capacity of capsid proteins to specific cell surface receptors that can transduce different cell types and brain regions in the CNS. In the current study, multiple AAV serotypes expressing a GFP reporter (AAV1, AAV2/1, AAVDJ, AAV8, AAVDJ8, AAV9, AAVDJ9) were screened for their infectivity in both primary murine astrocyte and neuronal cell cultures...
2017: PloS One
Aaron P Van der Leek, Yarden Yanishevsky, Anita L Kozyrskyj
In the past few decades, the indoleamine 2,3 dioxygenase (IDO) subset of the kynurenine (KYN) pathway of tryptophan (TRP) metabolism has been the subject of much research in the area of immune tolerance. In this review, we aim to incorporate new findings on this pathway in relation to allergy and the gut microbiome, while providing a comprehensive overview of the pathway itself. Stimulated by interferon gamma, IDO acts as a tolerogenic, immunosuppressive enzyme to attenuate allergic responses by the induction of the KYN-IDO pathway, resultant depletion of TRP, and elevation in KYN metabolites...
2017: Frontiers in Immunology
Ian B Mertes, Erin C Wilbanks, Marjorie R Leek
OBJECTIVES: The medial olivocochlear (MOC) efferent system can modify cochlear function to improve sound detection in noise, but its role in speech perception in noise is unclear. The purpose of this study was to determine the association between MOC efferent activity and performance on two speech-in-noise tasks at two signal-to-noise ratios (SNRs). It was hypothesized that efferent activity would be more strongly correlated with performance at the more challenging SNR, relative to performance at the less challenging SNR...
November 9, 2017: Ear and Hearing
Waziha Farha, A M Abd El-Aty, Md Musfiqur Rahman, Ji Hoon Jeong, Ho-Chul Shin, Jing Wang, Sung Shik Shin, Jae-Han Shim
The category of 'leafy vegetables' comprises a wide range of plants, including cabbage, lettuce, leeks, spinach, Swiss chard and kale, and it forms a significant component of the human diet. Typically, leafy vegetables are low in calories and fat, are great sources of vitamins, protein, dietary fibre and minerals (including iron, calcium, and nitrates), and are rich in phytochemicals. To counter the impact of pests on vegetables, a broad variety of pesticides are used. Because of their large surface areas, leafy vegetables are expected to have high residual pesticide levels...
January 2018: Biomedical Chromatography: BMC
V L van Stokkom, A E Blok, O van Kooten, C de Graaf, M Stieger
It has been shown that the identification of many foods including vegetables based on flavour cues is often difficult. The effect of providing texture cues in addition to flavour cues on the identification of foods and the effect of providing taste cues only on the identification of foods have not been studied. The aim of this study was to assess the role of smell, taste, flavour and texture cues in the identification of ten vegetables commonly consumed in The Netherlands (broccoli, cauliflower, French bean, leek, bell pepper, carrot, cucumber, iceberg lettuce, onion and tomato)...
February 1, 2018: Appetite
Jianhui Fu, Qiang Xu, Guifang Han, Bo Wu, Cheng Hon Alfred Huan, Meng Lee Leek, Tze Chien Sum
Halide perovskites exhibit unique slow hot-carrier cooling properties capable of unlocking disruptive perovskite photon-electron conversion technologies (e.g., high-efficiency hot-carrier photovoltaics, photo-catalysis, and photodetectors). Presently, the origins and mechanisms of this retardation remain highly contentious (e.g., large polarons, hot-phonon bottleneck, acoustical-optical phonon upconversion etc.). Here, we investigate the fluence-dependent hot-carrier dynamics in methylammonium lead triiodide using transient absorption spectroscopy, and correlate with theoretical modeling and first-principles calculations...
November 3, 2017: Nature Communications
Diego Comparini, Hieu Th Nguyen, Kota Ueda, Kyoshi Moritaka, Toshihiko Kihara, Tomonori Kawano
BACKGROUND: In the present study high-brightness light-emitting diodes were used to investigate the influence of different light spectra on garlic discoloration at different humidity levels and temperature. Many processes involved in the discoloration process of garlic/leek during storage under different conditions remain unanswered. For this reason in this study the ability of specific light spectra to enhance the production of desirable pigments has been evaluated in elephant garlic...
October 24, 2017: Journal of the Science of Food and Agriculture
Matthias Mergenthaler, Junjie Liu, Jennifer J Le Roy, Natalia Ares, Amber L Thompson, Lapo Bogani, Fernando Luis, Stephen J Blundell, Tom Lancaster, Arzhang Ardavan, G Andrew D Briggs, Peter J Leek, Edward A Laird
Coupling between a crystal of di(phenyl)-(2,4,6-trinitrophenyl)iminoazanium radicals and a superconducting microwave resonator is investigated in a circuit quantum electrodynamics (circuit QED) architecture. The crystal exhibits paramagnetic behavior above 4 K, with antiferromagnetic correlations appearing below this temperature, and we demonstrate strong coupling at base temperature. The magnetic resonance acquires a field angle dependence as the crystal is cooled down, indicating anisotropy of the exchange interactions...
October 6, 2017: Physical Review Letters
Riccardo Manenti, Anton F Kockum, Andrew Patterson, Tanja Behrle, Joseph Rahamim, Giovanna Tancredi, Franco Nori, Peter J Leek
The experimental investigation of quantum devices incorporating mechanical resonators has opened up new frontiers in the study of quantum mechanics at a macroscopic level. It has recently been shown that surface acoustic waves (SAWs) can be piezoelectrically coupled to superconducting qubits, and confined in high-quality Fabry-Perot cavities in the quantum regime. Here we present measurements of a device in which a superconducting qubit is coupled to a SAW cavity, realising a surface acoustic version of cavity quantum electrodynamics...
October 17, 2017: Nature Communications
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