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https://www.readbyqxmd.com/read/28823056/exploiting-non-canonical-translation-to-identify-new-targets-for-t-cell-based-cancer-immunotherapy
#1
REVIEW
Céline M Laumont, Claude Perreault
Cryptic MHC I-associated peptides (MAPs) are produced via two mechanisms: translation of protein-coding genes in non-canonical reading frames and translation of allegedly non-coding sequences. In general, cryptic MAPs are coded by relatively short open reading frames whose translation can be regulated at the level of initiation, elongation or termination. In contrast to conventional MAPs, the processing of cryptic MAPs is frequently proteasome independent. The existence of cryptic MAPs derived from allegedly non-coding regions enlarges the scope of CD8 T cell immunosurveillance from a mere ~2% to as much as ~75% of the human genome...
August 19, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28822918/screening-for-frailty-in-community-dwelling-elderly-subjects-predictive-validity-of-the-modified-sega-instrument
#2
N Oubaya, M Dramé, J-L Novella, E Quignard, C Cunin, D Jolly, R Mahmoudi
AIMS: To study the capacity of the SEGAm instrument to predict loss of independence among elderly community-dwelling subjects. METHODS: The study was performed in four French departments (Ardennes, Marne, Meurthe-et-Moselle, Meuse). Subjects aged 65 years or more, living at home, who could read and understand French, with a degree of autonomy corresponding to groups 5 or 6 in the AGGIR autonomy evaluation scale were included. Assessment included demographic characteristics, comprehensive geriatric assessment, and the SEGAm instrument at baseline...
August 4, 2017: Archives of Gerontology and Geriatrics
https://www.readbyqxmd.com/read/28822884/with-directed-study-before-a-4-day-operating-room-management-course-trust-in-the-content-did-not-change-progressively-during-the-classroom-time
#3
Franklin Dexter, Richard H Epstein, Brenda G Fahy, Lyn M Van Swol
STUDY OBJECTIVE: A 4-day course in operating room (OR) management is sufficient to provide anesthesiologists with the knowledge and problem solving skills needed to participate in projects of the systems-based-practice competency. Anesthesiologists may need to learn fewer topics when the objective is, instead, limited to comprehension of decision-making on the day of surgery, We tested the hypothesis that trust in course content would not increase further after completion of topics related to OR decision-making on the day of surgery...
August 17, 2017: Journal of Clinical Anesthesia
https://www.readbyqxmd.com/read/28822858/comparison-of-genome-engineering-using-the-crispr-cas9-system-in-c-glabrata-wild-type-and-lig4-strains
#4
Yuke Cen, Bea Timmermans, Ben Souffriau, Johan M Thevelein, Patrick Van Dijck
Candida glabrata is reported as the second most prevalent human opportunistic fungal pathogen in North America and is threatening patients all over the world. Its incidence is rising, while it has developed resistance to the most widely used antifungal drugs, necessitating new approaches based on better insight into the biology of the organism. Despite its close phylogenetic relationship with Saccharomyces cerevisiae, generating precise genomic alterations in this species is problematic. Previously we have shown that deletion of LIG4, which encodes an enzyme involved in Non-Homologous End Joining (NHEJ), strongly enhances the probability of obtaining correctly modified transformants...
August 16, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28822821/what-makes-journal-club-effective-a-survey-of-orthopaedic-residents-and-faculty
#5
Sean T Campbell, Jason R Kang, Julius A Bishop
BACKGROUND: Journal clubs play an important role in the education of orthopaedic surgery residents; however, there are sparse data available on the characteristics that make journal clubs effective. OBJECTIVE: The primary goal of this study was to determine the characteristics of effective journal clubs as identified by orthopaedic residents and faculty. We sought to compare the opinions of residents and faculty in order to identify areas that may benefit from future research and discussion...
August 16, 2017: Journal of Surgical Education
https://www.readbyqxmd.com/read/28822795/strategies-for-analyzing-bisulfite-sequencing-data
#6
Katarzyna Wreczycka, Alexander Gosdschan, Dilmurat Yusuf, Björn Grüning, Yassen Assenov, Altuna Akalin
DNA methylation is one of the main epigenetic modifications in the eukaryotic genome; it has been shown to play a role in cell-type specific regulation of gene expression, and therefore cell-type identity. Bisulfite sequencing is the gold-standard for measuring methylation over the genomes of interest. Here, we review several techniques used for the analysis of high-throughput bisulfite sequencing. We introduce specialized short-read alignment techniques as well as pre/post-alignment quality check methods to ensure data quality...
August 16, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28822172/-safflower-s-origin-and-changes-of-producing-areas
#7
Chao-Xiang Ren, Yi-Yun Wu, Xiao-Hui Tang, Jing Hu, Jiang Chen, Qing-Hua Wu, Jin Pei
Human's application of safflower (Carthamus tinctorius) has a long history, but the origin remains unclear. Safflower was introduced into China for traditional Chinese medicine, and Sichuan was major producing area. However, in recent years, the main producing area is in Xinjiang province, in contrast Sichuan safflower is difficult to find. By reading relevant document literature and the production and marketing information of safflower, and having field investigation in the main producing areas, the origin of safflower and the reasons of producing areas' changes were explored...
June 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28821872/microbiota-in-the-coelomic-fluid-of-two-common-coastal-starfish-species-and-characterization-of-an-abundant-helicobacter-related-taxon
#8
Satoshi Nakagawa, Hikari Saito, Akihiro Tame, Miho Hirai, Hideyuki Yamaguchi, Takashi Sunata, Masanori Aida, Hisashi Muto, Shigeki Sawayama, Yoshihiro Takaki
Marine invertebrates associate with diverse microorganisms. Microorganisms even inhabit coelomic fluid (CF), namely, the fluid filling the main body cavity of echinoderms. The CF microbiota potentially impacts host health and disease. Here, we analysed the CF microbiota in two common coastal starfish species, Patiria pectinifera and Asterias amurensis. Although microbial community structures were highly variable among individual starfish, those of P. pectinifera were compositionally similar to those in the surrounding seawater...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821766/protein-composition-analysis-of-polyhedra-matrix-of-bombyx-mori-nucleopolyhedrovirus-bmnpv-showed-powerful-capacity-of-polyhedra-to-encapsulate-foreign-proteins
#9
Zhong-Jian Guo, Meng-Han Yu, Xian-Yun Dong, Wei-Li Wang, Ting Tian, Xian-Yin Yu, Xu-Dong Tang
Polyhedra can encapsulate other proteins and have potential applications as protein stabilizers. The extremely stable polyhedra matrix may provide a platform for future engineered micro-crystal devices. However, the protein composition of the polyhedra matrix remains largely unknown. In this study, the occlusion-derived virus (ODV)-removed BmNPV polyhedra matrix fraction was subjected to SDS-PAGE and then an LC-ESI-MS/MS analysis using a Thermo Scientific Q Exactive mass spectrometer. In total, 28 host and 91 viral proteins were identified...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821591/specifying-cell-fate-in-roots-requires-coordinative-lineage-instruction-and-positional-reprogramming
#10
Qiaozhi Yu, Pengxue Li, Nengsong Liang, Hong Wang, Meizhi Xu, Shuang Wu
Tissue organization and pattern formation within a multicellular organism relies on coordinated cell division and cell fate determination. In animals cell fates are mainly determined by a cell lineage dependent mechanism, whereas in plants positional information is thought to be the primary determinant of cell fates (Scheres, 2001; Kidner et al., 2000; Kim et al., 2005; Scheres et al., 2002). However, our understanding of cell fate regulation in plants mostly relies on the histological and anatomical studies on Arabidopsis roots which contain a single layer of each cell type in non-vascular tissues (Scheres et al...
August 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28821351/screening-for-atrial-fibrillation-in-patients-%C3%A2-65-years-using-an-automatic-blood-pressure-monitor-in-a-skilled-nursing-facility
#11
Joseph Wiesel, Thomas J Salomone
Early detection of asymptomatic atrial fibrillation (AF) provides an opportunity to treat patients to reduce their risk of stroke. Long-term residents of skilled nursing facilities frequently have multiple risk factors for strokes due to AF and may benefit from screening for AF. Patients in a skilled nursing facility 65 years and older, without a history of AF and without a pacemaker or defibrillator, were evaluated using a Microlife WatchBP Home A automatic blood pressure monitor that can detect AF when set to a triple reading mode...
July 24, 2017: American Journal of Cardiology
https://www.readbyqxmd.com/read/28821255/the-whole-genomic-analysis-of-orf-virus-strain-hn3-12-isolated-from-henan-province-central-china
#12
Huiqin Chen, Wei Li, Zhenzhan Kuang, Daxiang Chen, Xiaoqing Liao, Ming Li, Shuhong Luo, Wenbo Hao
BACKGROUND: The Orf virus (ORFV) is the causative agent of orf, a globally-occurring, acute, pustular, contagious disease affecting sheep, goats and humans with a worldwide distribution. Currently, the genomic analysis of four ORFV strains from the Fujian province in southern China and a NA1/11 strain isolated from the Jilin province in northeast China have been reported. However, little is known about the genomic information of ORFV strains from central China. RESULTS: From a recent outbreak in a sheep herd in the Henan province of central China, a novel ORFV strain (HN3/12) was isolated and cultured in ovine fetal turbinate (OFTu) cells...
August 18, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28821237/evaluation-of-the-impact-of-illumina-error-correction-tools-on-de-novo-genome-assembly
#13
Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier
BACKGROUND: Recently, many standalone applications have been proposed to correct sequencing errors in Illumina data. The key idea is that downstream analysis tools such as de novo genome assemblers benefit from a reduced error rate in the input data. Surprisingly, a systematic validation of this assumption using state-of-the-art assembly methods is lacking, even for recently published methods. RESULTS: For twelve recent Illumina error correction tools (EC tools) we evaluated both their ability to correct sequencing errors and their ability to improve de novo genome assembly in terms of contig size and accuracy...
August 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28821228/sg-adviser-mtdna-a-web-server-for-mitochondrial-dna-annotation-with-data-from-200-samples-of-a-healthy-aging-cohort
#14
Manuel Rueda, Ali Torkamani
BACKGROUND: Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appropriately. As a consequence, any researcher desiring to add mtDNA variant analysis to their investigations is forced to explore the literature for mtDNA pipelines, evaluate them, and implement their own instance of the desired tool. This task is far from trivial, and can be prohibitive for non-bioinformaticians...
August 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28821183/improvement-of-the-threespine-stickleback-genome-using-a-hi-c-based-proximity-guided-assembly
#15
Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, Michael A White
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28821018/a-cross-language-study-of-acoustic-predictors-of-speech-intelligibility-in-individuals-with-parkinson-s-disease
#16
Yunjung Kim, Yaelin Choi
Purpose: The present study aimed to compare acoustic models of speech intelligibility in individuals with the same disease (Parkinson's disease [PD]) and presumably similar underlying neuropathologies but with different native languages (American English [AE] and Korean). Method: A total of 48 speakers from the 4 speaker groups (AE speakers with PD, Korean speakers with PD, healthy English speakers, and healthy Korean speakers) were asked to read a paragraph in their native languages...
August 18, 2017: Journal of Speech, Language, and Hearing Research: JSLHR
https://www.readbyqxmd.com/read/28820934/supramolecular-sensors-for-opiates-and-their-metabolites
#17
Elena G Shcherbakova, Ben Zhang, Samer Gozem, Tsuyoshi Minami, Peter Y Zavalij, Mariia Pushina, Lyle Isaacs, Pavel Anzenbacher
The present work develops a sensing approach for opiates using acyclic cucurbituril (aCBs) sensors comprising four glycouril units terminated on both ends with naphthalene fluorophore walls. The connectivity between the glycourils and the naphthalene rings largely defines the opening size of the cucurbituril cavity and its diameter. The large hydrophobic binding cavity is flexible and is able to adapt to guests of various size and topology. The recognition event between the aCBs and guests results in modification of the fluorescence of the terminal walls, a fluorescence response that can be used to sense the drugs of abuse morphine, heroin and oxycodone as well as their metabolites...
August 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28820919/a-preliminary-comparison-of-reading-subtypes-in-a-clinical-sample-of-children-with-specific-language-impairment
#18
Krystal L Werfel, Hannah Krimm
Purpose: The purpose of this preliminary study was to (a) compare the pattern of reading subtypes among a clinical sample of children with specific language impairment (SLI) and children with typical language and (b) evaluate phonological and nonphonological language deficits within each reading impairment subtype. Method: Participants were 32 children with SLI and 39 children with typical language in Grades 2 through 4. Each child was classified as demonstrating 1 of 4 reading subtypes on the basis of word-level and text-level skills: typical reading, dyslexia, specific reading comprehension impairment, or garden variety reading impairment...
August 18, 2017: Journal of Speech, Language, and Hearing Research: JSLHR
https://www.readbyqxmd.com/read/28820665/size-matters-penis-size-and-sexual-position-in-gay-porn-profiles
#19
Joseph Brennan
This article combines qualitative and quantitative textual approaches to the representation of penis size and sexual position of performers in ten of the most visited gay pornography websites currently in operation. Specifically, in excess of 6,900 performer profiles sourced from ten commercial websites are analysed. Textual analysis of the profile descriptions is combined with a quantitative representation of disclosed penis size and sexual position, which is presented visually by two figures. The figures confirm that these sites generally market themselves as featuring penises that are extraordinarily large, and finds a sample-wide correlation between smaller penis sizes (5-6...
August 18, 2017: Journal of Homosexuality
https://www.readbyqxmd.com/read/28820632/media-presentation-of-breastfeeding-beliefs-in-newspapers
#20
Rose Hitt, Jie Zhuang, Jennifer Anderson
Despite numerous health benefits for babies and mothers, many women do not either initiate or continue breastfeeding for the recommended duration, and increasing breastfeeding is a national priority. It is important to understand media messages on the topic, given that breastfeeding is influenced by many environmental factors and that perceived norms, social support, and perceptions of difficulties predict breastfeeding. The current study analyzes how media covers (1) breastfeeding in general, (2) public breastfeeding, and (3) extended breastfeeding (past 1 year)...
August 18, 2017: Health Communication
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