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https://www.readbyqxmd.com/read/29145430/de-novo-sequencing-and-analysis-of-the-transcriptome-during-the-browning-of-fresh-cut-luffa-cylindrica-fusi-3-fruits
#1
Haisheng Zhu, Jianting Liu, Qingfang Wen, Mindong Chen, Bin Wang, Qianrong Zhang, Zhuzheng Xue
Fresh-cut luffa (Luffa cylindrica) fruits commonly undergo browning. However, little is known about the molecular mechanisms regulating this process. We used the RNA-seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut fruits from luffa cultivar 'Fusi-3'. Over 90 million high-quality reads were assembled into 58,073 Unigenes, and 60.86% of these were annotated based on sequences in four public databases. We detected 35,282 Unigenes with significant hits to sequences in the NCBInr database, and 24,427 Unigenes encoded proteins with sequences that were similar to those of known proteins in the Swiss-Prot database...
2017: PloS One
https://www.readbyqxmd.com/read/29140531/an-update-on-sorfs-org-a-repository-of-small-orfs-identified-by-ribosome-profiling
#2
Volodimir Olexiouk, Wim Van Criekinge, Gerben Menschaert
sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138948/correction-to-s-1-and-irinotecan-plus-bevacizumab-as-second-line-chemotherapy-for-patients-with-oxaliplatin-refractory-metastatic-colorectal-cancer-a-multicenter-phase-ii-study-in-japan-kscc1102
#3
Yuji Miyamoto, Akihito Tsuji, Hiroaki Tanioka, Soichiro Maekawa, Hirofumi Kawanaka, Masaki Kitazono, Eiji Oki, Yasunori Emi, Hidetsugu Murakami, Yutaka Ogata, Hiroshi Saeki, Mototsugu Shimokawa, Shoji Natsugoe, Yoshito Akagi, Hideo Baba, Yoshihiko Maehara
In the original publication, in Abstract, the sentence that reads as, "Oral S-1 at a dose of 80 mg/m(2) was…………. drug-free interval" should read as, "Oral S-1 at a dose of 40 mg/m(2) was administered twice daily for 2 weeks, followed by a 1-week drug-free interval.
November 14, 2017: International Journal of Clinical Oncology
https://www.readbyqxmd.com/read/29134700/comparative-analysis-of-ovarian-transcriptomes-between-prolific-and-non-prolific-goat-breeds-via-high-throughput-sequencing
#4
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/29134483/evaluating-the-impact-of-dyslexia-laws-on-the-identification-of-specific-learning-disability-and-dyslexia
#5
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/29130143/incorporating-social-media-into-your-support-tool-box-points-to-consider-from-genetics-based-communities
#6
Heather Mae Rocha, Juliann M Savatt, Erin Rooney Riggs, Jennifer K Wagner, W Andrew Faucett, Christa Lese Martin
Patients with newly-described or rare genetic findings are turning to social media to find and connect with others. Blogs, Facebook groups, and Twitter have all been reported as tools for patients to connect with one another. However, the preferences for social media use and privacy among patients, their families, and these communities have not been well characterized. To explore preferences about privacy and membership guidelines, an online survey was administered to two web-based patient registries, Simons Variation in Individuals Project ( www...
November 13, 2017: Journal of Genetic Counseling
https://www.readbyqxmd.com/read/29127589/correction-to-exercise-following-breast-cancer-exploratory-survival-analyses-of-two-randomised-controlled-trials
#7
S C Hayes, M L Steele, R R Spence, L Gordon, D Battistutta, J Bashford, C Pyke, C Saunders, E Eakin
In the original publication of the article, under the heading Discussion, 1st paragraph, the sentence that reads as, "Nonetheless, our observed improvements of over 50% for OS and over 30% for DFS (HRs: 0.45 and 0.66, respectively) are consistent with results from other available studies" should read as "Nonetheless, our observed improvements of over 50% for OS and DFS (HRs: 0.45 and 0.66, respectively) are consistent with results from other available studies." Under the heading Discussion, 3rd paragraph, the sentence that reads as "We cannot discount the possibility …such as education, income and access to care [1, 7]" should read as "We cannot discount the possibility…such as education, income and access to care, which ultimately have on survival outcomes [1, 7]...
November 10, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29126224/dbtss-dbkero-for-integrated-analysis-of-transcriptional-regulation
#8
Ayako Suzuki, Shin Kawano, Toutai Mitsuyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki
DBTSS (Database of Transcriptional Start Sites)/DBKERO (Database of Kashiwa Encyclopedia for human genome mutations in Regulatory regions and their Omics contexts) is the database originally initiated with the information of transcriptional start sites and their upstream transcriptional regulatory regions. In recent years, we updated the database to assist users to elucidate biological relevance of the human genome variations or somatic mutations in cancers which may affect the transcriptional regulation. In this update, we facilitate interpretations of disease associated genomic variation, using the Japanese population as a model case...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29126106/airvf-a-filtering-toolbox-for-precise-variant-calling-in-ion-torrent-sequencing
#9
Sunguk Shin, Hanna Lee, Hyeonju Son, Soonmyung Paik, Sangwoo Kim
Summary: Ion Torrent sequencing is one of the most frequently used platforms in healthcare research and industry. Despite many advantages, platform-specific artifacts complicate efficient separation of true variants from errors, especially in variants with lower allele frequencies (<15%). Here, we developed a multi-step filtering toolbox AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-house commercial solution, with a minimal loss of sensitivity...
November 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29121825/the-impact-of-staff-training-on-special-educational-needs-professionals-attitudes-toward-and-understanding-of-applied-behavior-analysis
#10
Sinéad Smyth, Benjamin E Reading, Claire McDowell
BACKGROUND: Research-based evidence points to the efficacy and value of applied behavior analysis (ABA) in meeting the needs of individuals with learning disabilities and autism. Nonetheless, public, government, and professional perception of ABA can be negative. The current study was designed to measure the impact of a short intervention on professionals' attitudes toward, and knowledge of, ABA. METHOD: Teachers and classroom assistants from two separate schools for children with severe learning difficulties completed a self-report survey on knowledge of and attitudes toward ABA...
January 1, 2017: Journal of Intellectual Disabilities: JOID
https://www.readbyqxmd.com/read/29120459/informative-priors-on-fetal-fraction-increase-power-of-the-noninvasive-prenatal-screen
#11
Hanli Xu, Shaowei Wang, Lin-Lin Ma, Shuai Huang, Lin Liang, Qian Liu, Yang-Yang Liu, Ke-Di Liu, Ze-Min Tan, Hao Ban, Yongtao Guan, Zuhong Lu
PurposeNoninvasive prenatal screening (NIPS) sequences a mixture of the maternal and fetal cell-free DNA. Fetal trisomy can be detected by examining chromosomal dosages estimated from sequencing reads. The traditional method uses the Z-test, which compares a subject against a set of euploid controls, where the information of fetal fraction is not fully utilized. Here we present a Bayesian method that leverages informative priors on the fetal fraction.MethodOur Bayesian method combines the Z-test likelihood and informative priors of the fetal fraction, which are learned from the sex chromosomes, to compute Bayes factors...
November 9, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29116028/prenacel-a-mhealth-messaging-system-to-complement-antenatal-care-a-cluster-randomized-trial
#12
Lívia Oliveira-Ciabati, Carolina Sales Vieira, Ana Carolina Arruda Franzon, Domingos Alves, Fabiani Spessoto Zaratini, Giordana Campos Braga, Jazmin Andrea Cifuentes Sanchez, Lívia Pimenta Bonifácio, Magna Santos Andrade, Mariana Fernandes, Silvana Maria Quintana, Suzi Volpato Fabio, Vicky Nogueira Pileggi, Elisabeth Meloni Vieira, João Paulo Souza
BACKGROUND: The aim of this study was to determine whether PRENACEL (a bi-directional, mobile-phone based, short text message service (SMS)) increases the coverage of recommended antenatal care (ANC) practices. METHODS: A parallel, cluster-randomized trial in which 20 public primary Health Care Units (PHCUs) were randomly allocated to the intervention (10 PHCUs) or control (10 PHCUs) group. The study population included pregnant women aged 18 or above with a gestational age of 20 weeks or less...
November 7, 2017: Reproductive Health
https://www.readbyqxmd.com/read/29114401/aligner-optimization-increases-accuracy-and-decreases-compute-times-in-multi-species-sequence-data
#13
Kelly M Robinson, Aziah S Hawkins, Ivette Santana-Cruz, Ricky S Adkins, Amol C Shetty, Sushma Nagaraj, Lisa Sadzewicz, Luke J Tallon, David A Rasko, Claire M Fraser, Anup Mahurkar, Joana C Silva, Julie C Dunning Hotopp
As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows-Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority member (i...
September 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29114259/identification-of-splicing-quantitative-trait-loci-sqtl-in-drosophila-melanogaster-with-developmental-lead-pb-2-exposure
#14
Wen Qu, Katherine Gurdziel, Roger Pique-Regi, Douglas M Ruden
Lead (Pb) poisoning has been a major public health issue globally and the recent Flint water crisis has drawn nation-wide attention to its effects. To better understand how lead plays a role as a neurotoxin, we utilized the Drosophila melanogaster model to study the genetic effects of lead exposure during development and identified lead-responsive genes. In our previous studies, we have successfully identified hundreds of lead-responsive expression QTLs (eQTLs) by using RNA-seq analysis on heads collected from the Drosophila Synthetic Population Resource...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29113561/metagenome-sequence-clustering-with-hash-based-canopies
#15
Mohammad Arifur Rahman, Nathan LaPierre, Huzefa Rangwala, Daniel Barbara
Metagenomics is the collective sequencing of co-existing microbial communities which are ubiquitous across various clinical and ecological environments. Due to the large volume and random short sequences (reads) obtained from community sequences, analysis of diversity, abundance and functions of different organisms within these communities are challenging tasks. We present a fast and scalable clustering algorithm for analyzing large-scale metagenome sequence data. Our approach achieves efficiency by partitioning the large number of sequence reads into groups (called canopies) using hashing...
October 9, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29110707/correction-to-effects-of-a-multi-level-intervention-on-the-pattern-of-physical-activity-among-in-school-adolescents-in-oyo-state-nigeria-a-cluster-randomised-trial
#16
Mojisola Morenike Oluwasanu, Oladimeji Oladepo
After publication of the article [1], it has been brought to our attention that there is an error in figure 1. The number of excluded secondary schools should read "50" and not "72". The rest of the data in the figure is accurate.
November 6, 2017: BMC Public Health
https://www.readbyqxmd.com/read/29108696/metagenomics-for-the-study-of-viruses-in-urban-sewage-as-a-tool-for-public-health-surveillance
#17
X Fernandez-Cassi, N Timoneda, S Martínez-Puchol, M Rusiñol, J Rodriguez-Manzano, N Figuerola, S Bofill-Mas, J F Abril, R Girones
The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS data processing. One important step towards this goal is finding methods that can efficiently concentrate viruses from sewage samples. Here the application of a virus concentration method based on skimmed milk organic flocculation (SMF) using 10L of sewage collected in different seasons enabled the detection of many viruses...
November 3, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29108068/rapid-communication-16s-ribosomal-ribonucleic-acid-characterization-of-liver-abscesses-in-feedlot-cattle-from-three-states-in-the-united-states
#18
M D Weinroth, C R Carlson, J N Martin, J L Metcalf, P S Morley, K E Belk
Liver abscesses are a major economic burden to beef producers. Although a few causative organisms have been cultured from purulent material, the full polymicrobial diversity of liver abscesses has not been reported. The objective of this study was to characterize purulent material collected from liver abscess in beef cattle produced in different production systems in 3 cattle producing states in the United States using 16S rRNA gene sequencing. Differences between purulent material microbial communities among geographic region of feeding and application of a common antimicrobial were also investigated...
October 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/29106613/3div-a-3d-genome-interaction-viewer-and-database
#19
Dongchan Yang, Insu Jang, Jinhyuk Choi, Min-Seo Kim, Andrew J Lee, Hyunwoong Kim, Junghyun Eom, Dongsup Kim, Inkyung Jung, Byungwook Lee
Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide investigation of 3D chromatin structure. However, broad application of Hi-C data have been hindered by the level of complexity in processing Hi-C data and the large size of raw sequencing data. In order to overcome these limitations, we constructed a database named 3DIV (a 3D-genome Interaction Viewer and database) that provides a list of long-range chromatin interaction partners for the queried locus with genomic and epigenomic annotations...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29102999/prospective-cohort-study-to-investigate-the-burden-and-transmission-of-acute-gastroenteritis-in-care-homes-a-study-protocol
#20
Thomas Inns, Anna Pulawska-Czub, John P Harris, Roberto Vivancos, Jonathan M Read, Nicholas J Beeching, David J Allen, Miren Iturriza-Gomara, Sarah J O'Brien
INTRODUCTION: Noroviruses are the leading cause of acute gastroenteritis in all age groups, but illness is more severe and causes excess mortality in the elderly, particularly those in long-term care. The total burden of norovirus disease in the elderly in the UK is poorly defined; no current surveillance programmes systematically or accurately quantify norovirus infection in those living in care homes. The aim of this study is to evaluate an enhanced surveillance system for acute gastroenteritis among the elderly in care homes...
November 3, 2017: BMJ Open
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