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https://www.readbyqxmd.com/read/29141011/nucleotide-patterns-aiding-in-prediction-of-eukaryotic-promoters
#1
Martin Triska, Victor Solovyev, Ancha Baranova, Alexander Kel, Tatiana V Tatarinova
Computational analysis of promoters is hindered by the complexity of their architecture. In less studied genomes with complex organization, false positive promoter predictions are common. Accurate identification of transcription start sites and core promoter regions remains an unsolved problem. In this paper, we present a comprehensive analysis of genomic features associated with promoters and show that probabilistic integrative algorithms-driven models allow accurate classification of DNA sequence into "promoters" and "non-promoters" even in absence of the full-length cDNA sequences...
2017: PloS One
https://www.readbyqxmd.com/read/29140876/evidence-based-guidance-to-assist-volunteers-working-with-at-risk-children-in-a-school-context
#2
Emmy De Buck, Philippe Vandekerckhove, Karin Hannes
AIM: One of the activities of the Belgian Red Cross is the 'Bridging the Gap' project, in collaboration with local schools. In this project, volunteers join the teaching staff to improve personal development goals in at-risk children with poor performance. The aim of this study was to develop evidence-based guidance for the volunteers to help them choose the right didactical approach for supporting these children. METHOD: Systematic literature searches were performed in three bibliographic databases (the Campbell Library, MEDLINE and ERIC) to find the effectiveness of 16 different didactical activities...
November 14, 2017: International Journal of Evidence-based Healthcare
https://www.readbyqxmd.com/read/29140785/ci-thermometer-visualizing-confidence-intervals-in-correlation-analysis
#3
Agnieszka Wnuk, Konrad J Debski, Marcin Kozak
Correlation analysis is one of the most popular statistical methods. Despite that, the way research reports correlation is often misleading. The difficulty increases with the amount of information that must be read and interpreted. The proposed CI thermometer makes correlation matrices much easier to read and provides information that would be difficult to interpret when presented in another way.
November 2017: IEEE Computer Graphics and Applications
https://www.readbyqxmd.com/read/29140688/an-rna-chemical-proteomics-approach-reveals-the-n6-methyladenosine-m6a-regulated-protein-rna-interactome
#4
A Emilia Arguello, Amanda N DeLiberto, Ralph Kleiner
Epitranscriptomic RNA modifications can regulate mRNA function; however, there is a major gap in our understanding of the biochemical mechanisms mediating their effects. Here, we develop a chemical proteomics approach relying upon photo-crosslinking with synthetic diazirine-containing RNA probes and quantitative proteomics to profile RNA-protein interactions regulated by N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic RNA. In addition to identifying YTH domain-containing proteins and ALKBH5, known interactors of this modification, we find that FMR1 and LRPPRC, two proteins associated with human disease, 'read' this modification...
November 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29140644/evaluation-of-low-cost-hydrogen-sulfide-monitors-for-use-in-livestock-production
#5
Jessica M Beswick-Honn, Thomas M Peters, T Renée Anthony
Direct-reading gas monitors warn workers of the risk of potentially fatal hydrogen sulfide (H2S) exposures that may arise during manure handling. Low-cost, low-maintenance H2S monitors are available from many manufacturers, but differences in their features and performance make selection challenging for farmers. Moreover, little information is available on the practical maintenance and performance of these devices in agricultural environments. The objective of this study was to provide information to agricultural workers to aid in the selection, maintenance, and use of low-cost H2S monitors...
November 20, 2017: Journal of Agricultural Safety and Health
https://www.readbyqxmd.com/read/29137852/dysarthria-in-pallidal-deep-brain-stimulation-in-dystonia-depends-on-the-posterior-location-of-active-electrode-contacts-a-pilot-study
#6
K A M Pauls, P J Bröckelmann, S Hammesfahr, J Becker, A Hellerbach, V Visser-Vandewalle, T A Dembek, I G Meister, L Timmermann
BACKGROUND: Pallidal Deep Brain Stimulation (GPi-DBS) is an efficient treatment for primary dystonia. We investigated stimulation-induced dysarthria, which is the most frequent side-effect of GPi-DBS. METHODS: Speech was recorded while reading a standard text, and performing rapid syllable repetitions ON and OFF DBS in ten dystonia patients (6 men; 3 cervical, 4 segmental, 3 generalized, unselected for DBS-related speech impairments). Speech and articulation rate, pauses, and syllable repetition rates were extracted via acoustic analysis...
November 7, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/29137057/readability-of-internet-sourced-patient-education-material-related-to-labour-analgesia
#7
Nilay Boztas, Dilek Omur, Sule Ozbılgın, Gözde Altuntas, Ersan Piskin, Sevda Ozkardesler, Volkan Hanci
We evaluated the readability of Internet-sourced patient education materials (PEMs) related to "labour analgesia." In addition to assessing the readability of websites, we aimed to compare commercial, personal, and academic websites.We used the most popular search engine (http://www.google.com) in our study. The first 100 websites in English that resulted from a search for the key words "labour analgesia" were scanned. Websites that were not in English, graphs, pictures, videos, tables, figures and list formats in the text, all punctuation, the number of words in the text is less than 100 words, feedback forms not related to education, (Uniform Resource Locator) URL websites, author information, references, legal disclaimers, and addresses and telephone numbers were excluded...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29136615/videokymographic-visualization-of-phonasthenia-a-nonorganic-voice-disorder
#8
Mariam Salah Shadi, Mona A Hegazi, Jilan F Nassar, Samia Bassiouny, Sally Sarwat, Marwa M Saleh
BACKGROUND: Phonasthenia is a voice disorder where the larynx looks essentially normal and dysphonia is not heard but felt by the patient. This study aims to use videokymography (VKG) to detect any abnormalities in the vibratory pattern in phonasthenia and to find out whether or not these abnormalities change after vocal loading. METHODS: Thirty-seven phonasthenic patients and 31 normal subjects participated in a detailed protocol, including analysis of subjective complaints and videokymographic quasi-objective parameters (baseline) followed by loading their voices through prolonged loud reading for 45 min...
November 14, 2017: Folia Phoniatrica et Logopaedica
https://www.readbyqxmd.com/read/29136002/the-role-of-character-positional-frequency-on-chinese-word-learning-during-natural-reading
#9
Feifei Liang, Hazel I Blythe, Xuejun Bai, Guoli Yan, Xin Li, Chuanli Zang, Simon P Liversedge
Readers' eye movements were recorded to examine the role of character positional frequency on Chinese lexical acquisition during reading and its possible modulation by word spacing. In Experiment 1, three types of pseudowords were constructed based on each character's positional frequency, providing congruent, incongruent, and no positional word segmentation information. Each pseudoword was embedded into two sets of sentences, for the learning and the test phases. In the learning phase, half the participants read sentences in word-spaced format, and half in unspaced format...
2017: PloS One
https://www.readbyqxmd.com/read/29135584/concomitant-medication-polypharmacy-interactions-and-imperfect-adherence-are-common-in-australian-adults-on-suppressive-art
#10
Krista J Siefried, Limin Mao, Lucette A Cysique, John Rule, Michelle L Giles, Don E Smith, James Mcmahon, Tim R Read, Catriona Ooi, Ban K Tee, Mark Bloch, John de Wit, Andrew Carr
OBJECTIVES: We quantified concomitant medication (CM) polypharmacy, pharmacokinetic (PK) and pharmacodynamic (PD) interactions, adverse effects and adherence in Australian adults on effective ART. DESIGN: Cross-sectional. METHODS: Patients recruited into a nation-wide cohort and assessed for prevalence and type of CM (including polypharmacy, defined as ≥5 CMs), PK or PD interactions, potential CM adverse effects and CM adherence. Factors associated with CM polypharmacy and with imperfect adherence were identified using multivariable logistic regression...
November 10, 2017: AIDS
https://www.readbyqxmd.com/read/29135456/probiotics-and-their-use-in-inflammatory-bowel-disease
#11
Muhammad Amer, Muhammad Nadeem, Saeed Ur Rashid Nazir, Maira Fakhar, Fatima Abid, Qurat-Ul Ain, Elliyah Asif
Context • Crohn's disease and ulcerative colitis result in similar gastrointestinal (GI) symptoms, including pain, diarrhea, stools with mucus or blood, and ulceration or tissue damage within the alimentary canal. Gut microbiota play a crucial role in triggering, maintaining, and exacerbating inflammatory bowel disease (IBD). Probiotics might help to rebalance the gut flora in a positive way, shifting from pro- to anti-inflammatory. Objectives • The study intended to investigate the safety and use of probiotics and the biological effects of probiotic bacteria on IBD...
November 14, 2017: Alternative Therapies in Health and Medicine
https://www.readbyqxmd.com/read/29134790/soybean-mosaic-virus-a-successful-potyvirus-with-a-wide-distribution-but-restricted-natural-host-range
#12
M R Hajimorad, L L Domier, S A Tolin, S A Whitham, M A Saghai Maroof
Taxonomy. Soybean mosaic virus (SMV) is a species within the genus Potyvirus, family Potyviridae that includes almost a quarter of all known plant RNA viruses affecting agriculturally important plants. The Potyvirus genus is the largest of all genera of plant RNA viruses with 160 species. Particle. The filamentous particles of SMV, typical of potyviruses, are about 7,500 Å long and 120 Å in diameter with a central hole of about 15 Å in diameter. Coat protein residues are arranged in helice of about 34 Å pitch having slightly less than 9 subunits per turn...
November 14, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29134700/comparative-analysis-of-ovarian-transcriptomes-between-prolific-and-non-prolific-goat-breeds-via-high-throughput-sequencing
#13
X-D Zi, J-Y Lu, H Zhou, L Ma, W Xia, X-R Xiong, D-L Lan, X-H Wu
To increase the current understanding of the gene expression in the pre-ovulatory ovary and identify the key genes involved in the regulation of ovulation rate, we compared the transcriptomes of ovaries from the prolific Jintang black goat (JTG) and the non-prolific Tibetan goat (TBG) during the follicular phase using the Illumina RNA-Seq method. Three ovarian libraries were constructed for each breed. On average, we obtained approximately 49.2 and 45.9 million reads for each individual ovary of TBGs and JTGs, respectively, of which 79...
November 14, 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/29134591/sequencing-assembling-and-finishing-complete-bacteriophage-genomes
#14
Daniel A Russell
Next-generation DNA sequencing (NGS) technologies have made generating genomic sequence for organisms of interest affordable and commonplace. However, NGS platforms and analysis software are generally tuned to be used on large and complex genomes or metagenomic samples. Determining the complete genome sequence of a single bacteriophage requires a somewhat different perspective, workflow, and sensitivity to the nature of phages. Because phage genomes consist of mostly coding regions (see Pope/Jacobs-Sera chapter), a very high standard should be adopted when completing these genomes so that the subsequent steps of annotation and analysis are not sabotaged by sequencing errors...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134483/evaluating-the-impact-of-dyslexia-laws-on-the-identification-of-specific-learning-disability-and-dyslexia
#15
B Anne Barber Phillips, Timothy N Odegard
Dyslexia is a specific learning disability that impacts word reading accuracy and/or reading fluency. Over half of the states in the USA have passed legislation intended to promote better identification of individuals with dyslexia. To date, no study has been conducted to investigate the potential impact of state laws on the identification of specific learning disability (SLD), and limited data has been presented on the rate at which students in public school settings are identified with dyslexia. The first aim of the current study was to determine if any detectable changes in the identification rates of SLD have occurred in states implementing dyslexia laws because most states do not report number of students identified as dyslexic but rather those students identified with an SLD...
November 13, 2017: Annals of Dyslexia
https://www.readbyqxmd.com/read/29134393/metatranscriptomics-reveals-the-hydrolytic-potential-of-peat-inhabiting-planctomycetes
#16
Anastasia A Ivanova, Carl-Eric Wegner, Yongkyu Kim, Werner Liesack, Svetlana N Dedysh
Members of the phylum Planctomycetes are common inhabitants of northern Sphagnum-dominated wetlands. Evidence is accumulating that, in these environments, some planctomycetes may be involved in degrading polymeric organic matter. The experimental data, however, remain scarce due to the low number of characterized representatives of this phylum. In a previous study, we used metatranscriptomics to assess the activity response of peat-inhabiting microorganisms to biopolymers abundantly present in native peat. The community responses to cellulose, xylan, pectin, and chitin availability were analysed relative to unamended controls...
November 13, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29134141/metabarcoding-analysis-of-the-stomach-contents-of-the-antarctic-toothfish-dissostichus-mawsoni-collected-in-the-antarctic-ocean
#17
Tae-Ho Yoon, Hye-Eun Kang, Soo Rin Lee, Jae-Bong Lee, Gun Wook Baeck, Hyun Park, Hyun-Woo Kim
Stomach contents of the Antarctic toothfish, Dissostichus mawsoni, collected from subareas 58.4 and 88.3, were analyzed using next generation sequencing (NGS) technology. After processing the raw reads generated by the MiSeq platform, a total of 131,233 contigs (130 operational taxonomic units [OTUs]) were obtained from 163 individuals in subarea 58.4, and 75,961 contigs (105 OTUs) from 164 fish in subarea 88.3. At 98% sequence identity, species names were assigned to most OTUs in this study, indicating the quality of the DNA barcode database for the Antarctic Ocean was sufficient for molecular analysis, especially for fish species...
2017: PeerJ
https://www.readbyqxmd.com/read/29133907/a-primacy-code-for-odor-identity
#18
Christopher D Wilson, Gabriela O Serrano, Alexei A Koulakov, Dmitry Rinberg
Humans can identify visual objects independently of view angle and lighting, words independently of volume and pitch, and smells independently of concentration. The computational principles underlying invariant object recognition remain mostly unknown. Here we propose that, in olfaction, a small and relatively stable set comprised of the earliest activated receptors forms a code for concentration-invariant odor identity. One prediction of this "primacy coding" scheme is that decisions based on odor identity can be made solely using early odor-evoked neural activity...
November 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133900/100-articles-every-ecologist-should-read
#19
Franck Courchamp, Corey J A Bradshaw
Reading scientific articles is a valuable and major part of the activity of scientists. Yet, with the upsurge of currently available articles and the increasing specialization of scientists, it becomes difficult to identify, let alone read, important papers covering topics not directly related to one's own specific field of research, or that are older than a few years. Our objective was to propose a list of seminal papers deemed to be of major importance in ecology, thus providing a general 'must-read' list for any new ecologist, regardless of particular topic or expertise...
November 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29133211/beta-lactam-resistance-among-enterobacteriaceae-in-cambodia-the-four-year-itch
#20
REVIEW
Yannick Caron, Rattanak Chheang, Puthea Nop, Soda Meng, Sébastien Boyer, Arnaud Tarantola, Alexandra Kerléguer
Although antibiotics are too often used inappropriately in Cambodia, few data have been published on antimicrobial resistance in this country. Epidemic dissemination and the transfer of resistance genes to other bacterial species put the population at risk. The aim of this study was to evaluate the frequency and characteristics of extended-spectrum beta-lactamase (ESBL) enterobacteriaceae (ESBL-E) isolated in consecutive samples tested at Institut Pasteur du Cambodge (IPC) over a four-year period (2012-2015)...
November 10, 2017: International Journal of Infectious Diseases: IJID
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