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https://www.readbyqxmd.com/read/29793031/cloning-overexpression-and-purification-of-a-gene-of-unknown-function-of-prophage-loci-from-candidatus-liberibacter-asiaticus-the-destructive-bacterial-pathogen-of-huanglongbing-disease-in-citrus-plants
#1
Duangtip Sudhan, Thamrongjet Puttamuk, Supachai Vuttipongchaikij, Pitak Chuawong
Citrus Huanglongbing (HLB) or citrus greening is one of the most destructive diseases affecting citrus industry worldwide. The causal agent in Asia is a phloem-limited, Gram-negative bacterium, 'Candidatus Liberibacter asiaticus' (CLas). Within the genome of CLas lies prophage regions, classified as Type-A, B, C, and D. In particular, Type-D has been indicated to correlate with the blotchy-mottle symptoms of citrus trees. Here we reported the cloning, overexpression, and purification of the ORF1, an open reading frame from the partial Type-D region of CLas obtained from an infected lime tree (Citrus aurantifolia Swingle)...
May 21, 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/29792936/efficient-detection-of-copy-number-mutations-in-pms2-exons-with-close-homologs-detection-of-copy-number-variants-in-3-pms2-exons
#2
Daniel S Herman, Christina Smith, Chang Liu, Cecily P Vaughn, Selvi Palaniappan, Colin C Pritchard, Brian H Shirts
Detection of 3' PMS2 copy number mutations that cause Lynch syndrome is difficult, because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequence reads using PMS2 targets, maps sequences randomly amongst regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ranges...
May 21, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29792928/translation-of-dipeptide-repeat-proteins-from-the-c9orf72-expanded-repeat-is-associated-with-cellular-stress
#3
Yoshifumi Sonobe, Ghanashyam Ghadge, Katsuhisa Masaki, Ataman Sendoel, Elaine Fuchs, Raymond P Roos
Expansion of a hexanucleotide repeat (HRE), GGGGCC, in the C9ORF72 gene is recognized as the most common cause of familial amyotrophic lateral sclerosis (FALS), frontotemporal dementia (FTD) and ALS-FTD, as well as 5-10% of sporadic ALS. Despite the location of the HRE in the non-coding region (with respect to the main C9ORF72 gene product), dipeptide repeat proteins (DPRs) that are thought to be toxic are translated from the HRE in all three reading frames from both the sense and antisense transcript. Here, we identified a CUG translation initiation codon that has a good Kozak consensus sequence as the translation initiation codon...
May 21, 2018: Neurobiology of Disease
https://www.readbyqxmd.com/read/29792747/interpretation-time-using-a-concurrent-read-computer-aided-detection-system-for-automated-breast-ultrasound-in-breast-cancer-screening-of-women-with-dense-breast-tissue
#4
Yulei Jiang, Marc F Inciardi, Alexandra V Edwards, John Papaioannou
OBJECTIVE: The purpose of this study was to compare diagnostic accuracy and interpretation time of screening automated breast ultrasound (ABUS) for women with dense breast tissue without and with use of a recently U.S. Food and Drug Administration-approved computer-aided detection (CAD) system for concurrent read. MATERIALS AND METHODS: In a retrospective observer performance study, 18 radiologists interpreted a cancer-enriched set (i.e., cancer prevalence higher than in the original screening cohort) of 185 screening ABUS studies (52 with and 133 without breast cancer)...
May 24, 2018: AJR. American Journal of Roentgenology
https://www.readbyqxmd.com/read/29792713/gan-nanowire-arrays-for-efficient-optical-read-out-and-optoelectronic-control-of-nv-centers-in-diamond
#5
Martin Hetzl, Jakob Wierzbowski, Theresa Hoffmann, Max Kraut, Verena Zuerbig, Christoph E Nebel, Kai Müller, Jonathan J Finley, Martin Stutzmann
Solid state quantum emitters embedded in a semiconductor crystal environment are potentially scalable platforms for quantum optical networks operated at room temperature. Prominent representatives are nitrogen-vacancy (NV) centers in diamond showing coherent entanglement and interference with each other. However, these emitters suffer from inefficient optical outcoupling from the diamond and from fluctuations of their charge state. Here, we demonstrate the implementation of regular n-type gallium nitride nanowire arrays on diamond as photonic waveguides to tailor the emission direction of surface-near NV centers and to electrically control their charge state in a p-i-n nano-diode...
May 24, 2018: Nano Letters
https://www.readbyqxmd.com/read/29792677/ultra-low-power-smart-electronic-nose-system-based-on-three-dimensional-tin-oxide-nanotube-arrays
#6
Jiaqi Chen, Zhuo Chen, Farid Boussaid, Daquan Zhang, Xiaofang Pan, Huijuan Zhao, Amine Bermak, Chi-Ying Tsui, Xinran Wang, Zhiyong Fan
In this work, we present a high performance smart electronic nose (E-nose) system consisting of multiplexed tin dioxide (SnO2) nanotube sensor array, read-out circuit, wireless data transmission unit, mobile phone receiver and data processing application (App). Using the proposed nanotube sensor device structure in conjunction with multiple electrode materials, high sensitivity gas detection and discrimination have been achieved at room temperature, enabling a 1,000 times reduction of sensor's power consumption as compared to a conventional device using thin film SnO2...
May 24, 2018: ACS Nano
https://www.readbyqxmd.com/read/29792492/evaluation-of-second-step-on-early-elementary-students-academic-outcomes-a-randomized-controlled-trial
#7
Clayton R Cook, Sabina Low, Joanne Buntain-Ricklefs, Kelly Whitaker, Michael D Pullmann, Jaclyn Lally
Research has consistently linked social-emotional learning to important educational and life outcomes. Early elementary represents an opportune developmental period to proactively support children to acquire social-emotional skills that enable academic success. Using data from a large scale randomized controlled trial, the purpose of this study was to investigate the impact of the 4th edition of Second Step on early elementary students' academic-related outcomes. Participants were Kindergarten to 2nd grade students in 61 schools (310 teachers; 7,419 students) across six school districts in Washington State and Arizona...
May 24, 2018: School Psychology Quarterly
https://www.readbyqxmd.com/read/29792389/therapist-assisted-vision-therapy-improves-outcome-for-stroke-patients-with-homonymous-hemianopia-alone-or-combined-with-oculomotor-dysfunction
#8
Peter Smaakjær, Signe Tornøe Tødten, Rune Skovgaard Rasmussen
OBJECTIVE: To improve visual performance and perception in stroke patients suffering from visual impairments by the use of therapist-assisted vision therapy. METHODS: This study was an interventional efficacy open-label investigation. The vision therapy was designed to enhance binocular vision, and saccadic ability, and vergence ranges maximally, and for patients with hemianopia also to improve peripheral awareness. The vision training consisted of one lesson a week for 12 weeks carried out by an optometrist and a vision therapist...
May 24, 2018: Neurological Research
https://www.readbyqxmd.com/read/29792225/correction-to-lifetime-stress-accelerates-epigenetic-aging-in-an-urban-african-american-cohort-relevance-of-glucocorticoid-signaling
#9
Anthony S Zannas, Janine Arloth, Tania Carrillo-Roa, Stella Iurato, Simone Röh, Kerry J Ressler, Charles B Nemeroff, Alicia K Smith, Bekh Bradley, Christine Heim, Andreas Menke, Jennifer F Lange, Tanja Brückl, Marcus Ising, Naomi R Wray, Angelika Erhardt, Elisabeth B Binder, Divya Mehta
Upon publication of the original article [1] it was highlighted by the authors that a transposition error affected Additional file 1, causing the misplacement of several columns and rendering the table difficult to read. This transposition does not influence any of the results nor analyses presented in the paper and has since been formally noted in this correction article; the corrected file is available here as an Additional File. The publisher apologizes for this error.
May 23, 2018: Genome Biology
https://www.readbyqxmd.com/read/29792160/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data
#10
Li Fang, Jiang Hu, Depeng Wang, Kai Wang
BACKGROUND: Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is needed and how to optimally use the aligners and SV callers. RESULTS: In this study, we developed NextSV, a meta-caller to perform SV calling from low coverage long-read sequencing data...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29792081/efficacy-of-a-word-and-text-based-intervention-for-students-with-significant-reading-difficulties
#11
Sharon Vaughn, Garrett J Roberts, Jeremy Miciak, Pat Taylor, Jack M Fletcher
We examine the efficacy of an intervention to improve word reading and reading comprehension in fourth- and fifth-grade students with significant reading problems. Using a randomized control trial design, we compare the fourth- and fifth-grade reading outcomes of students with severe reading difficulties who were provided a researcher-developed treatment with reading outcomes of students in a business-as-usual (BAU) comparison condition. A total of 280 fourth- and fifth-grade students were randomly assigned within school in a 1:1 ratio to either the BAU comparison condition ( n = 139) or the treatment condition ( n = 141)...
May 1, 2018: Journal of Learning Disabilities
https://www.readbyqxmd.com/read/29791785/expressed-exome-capture-sequencing-eecseq-a-method-for-cost-effective-exome-sequencing-for-all-organisms
#12
Jonathan B Puritz, Katie E Lotterhos
Exome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require annotated genomic resources. Here, we present a method for creating cDNA probes from expressed mRNA, which are then used to enrich and capture genomic DNA for exon regions. This approach, called "EecSeq", eliminates the need for costly probe design and synthesis. We tested EecSeq in the eastern oyster, Crassostrea virginica, using a controlled exposure experiment. Four adult oysters were heat shocked at 36° C for 1 hour along with four control oysters kept at 14° C...
May 23, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29791750/tiled-array-based-sequencing-identifies-enrichment-of-loss-of-function-variants-in-the-highly-homologous-filaggrin-gene-in-african-american-children-with-severe-atopic-dermatitis
#13
Mary Elizabeth Mathyer, Ashley M Quiggle, X F Colin C Wong, Simon L I J Denil, Monique G Kumar, Heather M Ciliberto, Susan J Bayliss, John E Common, Cristina de Guzman Strong
Filaggrin (FLG) loss of function (LOF) variants are a major risk factor for the common inflammatory skin disease, atopic dermatitis (AD), and are often population-specific. African American (AA) children are disproportionately affected with AD, often later developing asthma and/or allergic rhinitis and comprise an atopy health disparity group for which the role of FLG LOF is not well known. Discovery of FLG LOF using exome sequencing is challenging given the known difficulties for accurate short-read alignment to FLG's high homology repeat variation...
May 23, 2018: Experimental Dermatology
https://www.readbyqxmd.com/read/29791686/extruded-upper-first-molar-intrusion-comparison-between-unilateral-and-bilateral-miniscrew-anchorage
#14
Mari Miura Sugii, Bruno de Castro Ferreira Barreto, Waldemir Francisco Vieira-Júnior, Katia Regina Izola Simone, Ataís Bacchi, Ricardo Armini Caldas
OBJECTIVE: The aim of his study was to evaluate the stress on tooth and alveolar bone caused by orthodontic intrusion forces in a supraerupted upper molar, by using a three-dimensional Finite Element Method (FEM). METHODS: A superior maxillary segment was modeled in the software SolidWorks 2010 (SolidWorks Corporation, Waltham, MA, USA) containing: cortical and cancellous bone, supraerupted first molar, periodontal tissue and orthodontic components. A finite element model has simulated intrusion forces of 4N onto a tooth, directed to different mini-screw locations...
January 2018: Dental Press Journal of Orthodontics
https://www.readbyqxmd.com/read/29791619/temporal-ordering-and-reading-competence-of-words-and-pseudowords-a-preliminary-study
#15
Cintia Alves de Souza, Andrezza Gonzalez Escarce, Stela Maris Aguiar Lemos
Purpose Analyze the association of simple and complex auditory temporal ordering skills with reading competence tasks in students. Methods Pilot phase of a cross-sectional study conducted with a non-probabilistic sample of 22 schoolchildren aged eight to ten years. Instruments for evaluation of reading competence tasks and simple and complex auditory temporal ordering abilities were used. Results Most participants obtained adequate results in the tests of simple auditory temporal ordering (SATO) and reading competence (RC), but inadequate results in the test of complex auditory temporal ordering (CATO)...
2018: CoDAS
https://www.readbyqxmd.com/read/29791613/speech-language-pathology-program-for-reading-comprehension-and-orthography-effects-on-the-spelling-of-dyslexic-individuals
#16
Débora Manzano Nogueira, Maria Silvia Cárnio
Purpose Prepare a Speech-language Pathology Program for Reading Comprehension and Orthography and verify its effects on the reading comprehension and spelling of students with Developmental Dyslexia. Methods The study sample was composed of eleven individuals (eight males), diagnosed with Developmental Dyslexia, aged 09-11 years. All participants underwent a Speech-language Pathology Program in Reading Comprehension and Orthography comprising 16 individual weekly sessions. In each session, tasks of reading comprehension of texts and orthography were developed...
2018: CoDAS
https://www.readbyqxmd.com/read/29791271/language-skills-but-not-frequency-discrimination-predict-reading-skills-in-children-at-risk-of-dyslexia
#17
Margaret J Snowling, Debbie Gooch, Genevieve McArthur, Charles Hulme
This study evaluated the claim that auditory processing deficits are a cause of reading and language difficulties. We report a longitudinal study of 245 children at family risk of dyslexia, children with preschool language impairments, and control children. Children with language impairments had poorer frequency-discrimination thresholds than controls at 5.5 years, but children at family risk of dyslexia did not. A model assessing longitudinal relationships among frequency discrimination, reading, language, and executive function skills showed that frequency discrimination was predicted by executive skills but was not a longitudinal predictor of reading or language skills...
May 1, 2018: Psychological Science
https://www.readbyqxmd.com/read/29791032/social-egg-freezing-better-early-than-never
#18
Gabriel Levin, Amihai Rottenstreich
We read the commentary by Jones et al. with great interest (1). The authors describe the utilization of an elective oocyte cryopreservation as an opportunity to postpone motherhood. Although the authors delineate a comprehensive overview of the subject, several important issues need further consideration regarding the aforementioned commentary. This article is protected by copyright. All rights reserved.
May 23, 2018: Acta Obstetricia et Gynecologica Scandinavica
https://www.readbyqxmd.com/read/29790906/bcseq-an-r-package-for-fast-sequence-mapping-in-high-throughput-shrna-and-crispr-screens
#19
Jiaxing Lin, Jeremy Gresham, Tongrong Wang, So Young Kim, James Alvarez, Jeffrey S Damrauer, Scott Floyd, Joshua Granek, Andrew Allen, Cliburn Chan, Jichun Xie, Kouros Owzar
Summary: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we present bcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790902/combining-probabilistic-alignments-with-read-pair-information-improves-accuracy-of-split-alignments
#20
Anish M S Shrestha, Naruki Yoshikawa, Kiyoshi Asai
Motivation: Split-alignments provide base-pair-resolution evidence of genomic rearrangements. In practice, they are found by first computing high-scoring local alignments, parts of which are then combined into a split-alignment. This approach is challenging when aligning a short read to a large and repetitive reference, as it tends to produce many spurious local alignments leading to ambiguities in identifying the correct split-alignment. This problem is further exacerbated by the fact that rearrangements tend to occur in repeat-rich regions...
May 18, 2018: Bioinformatics
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