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https://www.readbyqxmd.com/read/29054825/integrative-mrna-mirna-interaction-analysis-associate-with-immune-response-of-sea-cucumber-apostichopus-japonicus-based-on-transcriptome-database
#1
Xiaoxu Zhou, Yaqing Chang, Yaoyao Zhan, Xiuli Wang, Kai Lin
MicroRNAs (miRNAs) constitute a family of endogenous non-coding small RNAs that have been demonstrated to be the key effectors in mediating host-pathogen interactions. Additionally, high-throughput sequencing provides unexampled opportunities to identify the pathogenic mechanism underlying miRNAs. In the present study, the target genes of immune-related miRNAs (miR-31, miR-2008, miR-92a, miR-210 and miR-7) and specific miRNAs (miR-2004) in Echinodermata were predicted in silico and validated. Gene ontology (GO) analysis of the target genes of these six miRNAs were conducted to further understand the regulatory function in thehost immunity of Apostichopus japonicus (A...
October 17, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29054765/characterization-of-germline-mutations-in-familial-lung-cancer-from-the-chinese-population
#2
Madiha Kanwal, Xiao-Jie Ding, Zhans-Han Ma, Lian-Wei Li, Ping Wang, Ying Chen, Yun-Chao Huang, Yi Cao
Compared with numerous studies of somatic mutations using sporadic lung cancer, the research into germline mutations using familial lung cancer (FLC) is limited. In the present study, we used FLC samples obtained from the Chinese population in highly air-polluted regions to screen for novel germline mutations in lung cancer. Through a whole genome sequencing (WGS) analysis of the nine subjects (four lung cancer patients and five normal family members of FLC), we obtained a whole genome dataset of DNA alterations in FLC samples...
October 17, 2017: Gene
https://www.readbyqxmd.com/read/29054701/intra-and-inter-laboratory-reproducibility-and-predictivity-of-the-hacasens-assay-a-skin-sensitization-test-using-human-keratinocytes-hacat
#3
Hyewon Chung, Hailian Quan, Daun Jung, Gautam Ravi, Ahrang Cho, Mijeong Kang, Eunju Kim, Jeonghwan Che, Eung-Seok Lee, Taecheon Jeong, Yong Heo, Seung Hyeok Seok
Due to considerable constraints in using animals for risk assessment, much effort has been directed at developing non-animal test methods. Developing assays for skin sensitization, the leading cause of contact dermatitis, is particularly important, but there are currently no in vitro skin sensitization tests that completely replace animal tests. HaCaSens, a simple skin sensitization test using non-transformed HaCaT cells, predicts keratinocyte activation by skin sensitizers with 75% sensitivity, 83% specificity and 77% accuracy in a previous study using 22 coded substances...
October 17, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/29054598/phlebotomus-papatasi-yellow-related-and-apyrase-salivary-proteins-are-candidates-for-vaccination-against-human-cutaneous-leishmaniasis
#4
Aymen Tlili, Soumaya Marzouki, Emna Chabaane, Maha Abdeladhim, Wafa Kammoun-Rebai, Rahma Sakkouhi, Nabil Belhadj Hmida, Fabiano Oliveira, Shaden Kamhawi, Hechmi Louzir, Jesus G Valenzuela, Melika Ben Ahmed
Nowadays, there is no available vaccine for human leishmaniasis. Animal experiments demonstrate that pre-exposure to sand fly saliva confers protection against leishmaniasis. Our preceding work in humans indicates that Phlebotomus (P) papatasi saliva, induce the production of IL-10 by CD8+ T lymphocytes. The neutralization of IL-10 enhanced the activation of a T cells CD4+ population producing IFN-γ. Herein, we used a biochemical and functional genomics approach to identify the sand fly salivary components that are responsible for the activation of the Th1 immune response in humans therefore constituting potential vaccine candidates against leishmaniasis...
October 17, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29054261/development-and-validation-of-various-phenotyping-algorithms-for-diabetes-mellitus-using-data-from-electronic-health-records
#5
Santiago Esteban, Manuel Rodríguez Tablado, Francisco E Peper, Yamila S Mahumud, Ricardo I Ricci, Karin S Kopitowski, Sergio A Terrasa
BACKGROUND AND OBJECTIVE: Recent progression towards precision medicine has encouraged the use of electronic health records (EHRs) as a source for large amounts of data, which is required for studying the effect of treatments or risk factors in more specific subpopulations. Phenotyping algorithms allow to automatically classify patients according to their particular electronic phenotype thus facilitating the setup of retrospective cohorts. Our objective is to compare the performance of different classification strategies (only using standardized problems, rule-based algorithms, statistical learning algorithms (six learners) and stacked generalization (five versions)), for the categorization of patients according to their diabetic status (diabetics, not diabetics and inconclusive; Diabetes of any type) using information extracted from EHRs...
December 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29053596/elucidating-the-role-of-host-long-non-coding-rna-during-viral-infection-challenges-and-paths-forward
#6
REVIEW
David J Lemler, Hayden N Brochu, Fang Yang, Erin A Harrell, Xinxia Peng
Research over the past decade has clearly shown that long non-coding RNAs (lncRNAs) are functional. Many lncRNAs can be related to immunity and the host response to viral infection, but their specific functions remain largely elusive. The vast majority of lncRNAs are annotated with extremely limited knowledge and tend to be expressed at low levels, making ad hoc experimentation difficult. Changes to lncRNA expression during infection can be systematically profiled using deep sequencing; however, this often produces an intractable number of candidate lncRNAs, leaving no clear path forward...
October 20, 2017: Vaccines
https://www.readbyqxmd.com/read/29050775/differential-expression-of-long-non-coding-rnas-in-patients-with-tuberculosis-infection
#7
Jianan He, Qingye Ou, Chunxiao Liu, Lei Shi, Chunzhong Zhao, Yunqing Xu, Siu Kai Kong, Jacky Fong Chuen Loo, Boan Li, Dayong Gu
Tuberculosis (TB) remains a major worldwide health problem and has caused millions of deaths in the past few years. Current diagnostic methods, such as sputum smear microscopy and sputum culture, are time-consuming and cannot prevent the rapid spreading of TB during the diagnostic period. In this connection, detecting biomarkers specific to TB at molecular level in plasma of patients will provide a rapid means for diagnosis. In this study, we first evaluated the differential expression of the long non-coding RNAs (lncRNAs) in the plasma from patients with TB (TB positive), community acquired pneumonia (CAP) and healthy individuals (CG) using lncRNA microarray scanning...
December 2017: Tuberculosis
https://www.readbyqxmd.com/read/29050269/long-non-coding-rna-carlo-5-promotes-tumor-progression-in-hepatocellular-carcinoma-via-suppressing-mir-200b-expression
#8
Chunqing Dou, Liyuan Sun, Xin Jin, Mingming Han, Bao Zhang, Xian Jiang, Jinyong Lv, Tao Li
Long non-coding RNAs (lncRNAs) play key roles in cancer initiation and progression. The aim was to investigate the biological functions and clinical significance of long non-coding RNA CARLo-5 in hepatocellular carcinoma (HCC). QRT-PCR was performed to investigate CARLo-5 expression in HCC tissues and cells. Kaplan-Meier curve and multivariate analysis validated the association between CARLo-5 expression and overall survival (OS) in HCC patients. Cell proliferation and invasion was performed by CCK8 cell proliferation, cell colony formation and transwell invasion assays...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049020/comparison-of-methods-for-estimating-prevalence-of-chronic-diseases-and-health-behaviors-for-small-geographic-areas-boston-validation-study-2013
#9
Yan Wang, James B Holt, Xingyou Zhang, Hua Lu, Snehal N Shah, Daniel P Dooley, Kevin A Matthews, Janet B Croft
INTRODUCTION: Local health authorities need small-area estimates for prevalence of chronic diseases and health behaviors for multiple purposes. We generated city-level and census-tract-level prevalence estimates of 27 measures for the 500 largest US cities. METHODS: To validate the methodology, we constructed multilevel logistic regressions to predict 10 selected health indicators among adults aged 18 years or older by using 2013 Behavioral Risk Factor Surveillance System (BRFSS) data; we applied their predicted probabilities to census population data to generate city-level, neighborhood-level, and zip-code-level estimates for the city of Boston, Massachusetts...
October 19, 2017: Preventing Chronic Disease
https://www.readbyqxmd.com/read/29048466/pybel-a-computational-framework-for-biological-expression-language
#10
Charles Tapley Hoyt, Andrej Konotopez, Christian Ebeling
Summary: Biological Expression Language (BEL) assembles knowledge networks from biological relations across multiple modes and scales. Here, we present PyBEL; a software package for parsing, validating, converting, storing, querying, and visualizing networks encoded in BEL. Availability: PyBEL is implemented in platform-independent, universal Python code. Its source is distributed under the Apache 2.0 License at https://github.com/pybel. Contact: charles...
October 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29047791/optimal-defocus-selection-based-on-normed-fourier-transform-for-digital-fringe-pattern-profilometry
#11
Abel Kamagara, Xiangzhao Wang, Sikun Li
Owing to gamma-effect robustness and high-speed imaging capabilities, projector defocusing of binary-coded fringe patterns is by far the most widely used and effective technique in generating sinusoidal fringe patterns for three-dimensional optical topography measurement with digital fringe projection techniques. However, this technique is not trouble-free. It is borne with uncertainty and challenges mainly because it remains somewhat difficult to quantify and ascertain the level of defocus required for desired fidelity in sinuousness of the projected fringe pattern...
October 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/29047586/beam-steering-efficiency-optimization-method-based-on-a-rapid-search-algorithm-for-liquid-crystal-optical-phased-array
#12
Feng Xiao, Lingjiang Kong, Jian Chen
A rapid-search algorithm to improve the beam-steering efficiency for a liquid crystal optical phased array was proposed and experimentally demonstrated in this paper. This proposed algorithm, in which the value of steering efficiency is taken as the objective function and the controlling voltage codes are considered as the optimization variables, consisted of a detection stage and a construction stage. It optimized the steering efficiency in the detection stage and adjusted its search direction adaptively in the construction stage to avoid getting caught in a wrong search space...
June 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/29047500/step-by-step-guide-to-reduce-spatial-coherence-of-laser-light-using-a-rotating-ground-glass-diffuser
#13
Tim Stangner, Hanqing Zhang, Tobias Dahlberg, Krister Wiklund, Magnus Andersson
Wide field-of-view imaging of fast processes in a microscope requires high light intensities motivating the use of lasers as light sources. However, due to their long spatial coherence length, lasers are inappropriate for such applications, as they produce coherent noise and parasitic reflections, such as speckle, degrading image quality. Therefore, we provide a step-by-step guide for constructing a speckle-free and high-contrast laser illumination setup using a rotating ground glass diffuser driven by a stepper motor...
July 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/29047334/a-support-vector-machine-based-method-to-distinguish-long-non-coding-rnas-from-protein-coding-transcripts
#14
Hugo W Schneider, Taina Raiol, Marcelo M Brigido, Maria Emilia M T Walter, Peter F Stadler
BACKGROUND: In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed when analyzing this data is distinguishing between long non-coding RNAs (lncRNAs) and protein coding transcripts (PCTs). Thus, we present a Support Vector Machine (SVM) based method to distinguish lncRNAs from PCTs, using features based on frequencies of nucleotide patterns and ORF lengths, in transcripts...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29047232/knockdown-of-long-non-coding-rna-neat1-inhibits-proliferation-and-invasion-and-induces-apoptosis-of-osteosarcoma-by-inhibiting-mir-194-expression
#15
Heping Wang, Yanzhang Yu, Shuxin Fan, Leifeng Luo
PURPOSE: Long non-coding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1) has been implicated as an oncogene in the development and progression of osteosarcoma. This study aims to explore the mechanism of NEAT1 in osteosarcoma. MATERIALS AND METHODS: Expressions of NEAT1 and miR-194 in osteosarcoma tissues and cells were detected by quantitative real-time PCR. The effects of NEAT1 knockdown or miR-194 overexpression on cell proliferation, invasion, and apoptosis were determined by 3-[4, 5-dimethylthiazol-2-yl]-2, 5 diphenyl tetrazolium bromide (MTT) assay, transwell invasive assay, and flow cytometry analysis, respectively...
November 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/29045858/circulating-circular-rna-hsa_circ_0001785-acts-as-a-diagnostic-biomarker-for-breast-cancer-detection
#16
Wei-Bing Yin, Ming-Guang Yan, Xiao Fang, Jian-Jun Guo, Ruo-Peng Zhang, Wei Xiong
BACKGROUND: Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) and characterized by covalently closed loop without 5' and 3' end. Recently, the diagnostic value of circRNAs has received more and more attention. However, the in-depth study about circRNAs diagnosis in breast cancer is still rarely reported. In present study, we try to investigate the circRNAs expression profiles in breast cancer peripheral blood and discover valuable diagnostic biomarkers. METHODS: The expression profiles of circRNAs in plasma specimens were screened from five breast cancer and paired healthy volunteer s...
October 15, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29045632/patient-general-practitioner-and-oncologist-views-regarding-long-term-cancer-shared-care
#17
Heike Schütze, Melvin Chin, David Weller, Mark F Harris
Background: The rising incidence of cancer and increasing number of cancer survivors place competing demands on specialist oncology clinics. This has led to a need to consider collaborative care between primary and secondary care for the long-term post-treatment care of cancer survivors. Objective: To explore the views of breast and colorectal cancer survivors, their oncologist and GP about GPs taking a more active role in long-term cancer follow-up care. Methods: Semi-structured interviews using a thematic analysis framework...
October 14, 2017: Family Practice
https://www.readbyqxmd.com/read/29042817/accuracy-of-the-hypospadias-diagnoses-and-surgical-treatment-registrations-in-the-danish-national-patient-register
#18
Linn Håkonsen Arendt, Andreas Ernst, Morten Søndergaard Lindhard, Anne Aggerholm Jønsson, Tine Brink Henriksen, Jørn Olsen, Jorgen Thorup, L Henning Olsen, Cecilia Høst Ramlau-Hansen
PURPOSE: The Danish National Health registers provide a valuable data source that offers unique opportunities for observational research, including studies on the congenital anomaly hypospadias. The accuracy of the diagnosis and surgical treatment registration of hypospadias in the Danish National Patient Register (DNPR) remains unknown. PATIENTS AND METHODS: We randomly sampled 500 patients diagnosed with hypospadias in the DNPR from January 1, 1995 to December 31, 2012...
2017: Clinical Epidemiology
https://www.readbyqxmd.com/read/29042551/integrating-evolutionary-and-regulatory-information-with-a-multispecies-approach-implicates-genes-and-pathways-in-obsessive-compulsive-disorder
#19
Hyun Ji Noh, Ruqi Tang, Jason Flannick, Colm O'Dushlaine, Ross Swofford, Daniel Howrigan, Diane P Genereux, Jeremy Johnson, Gerard van Grootheest, Edna Grünblatt, Erik Andersson, Diana R Djurfeldt, Paresh D Patel, Michele Koltookian, Christina M Hultman, Michele T Pato, Carlos N Pato, Steven A Rasmussen, Michael A Jenike, Gregory L Hanna, S Evelyn Stewart, James A Knowles, Stephan Ruhrmann, Hans-Jörgen Grabe, Michael Wagner, Christian Rück, Carol A Mathews, Susanne Walitza, Daniëlle C Cath, Guoping Feng, Elinor K Karlsson, Kerstin Lindblad-Toh
Obsessive-compulsive disorder is a severe psychiatric disorder linked to abnormalities in glutamate signaling and the cortico-striatal circuit. We sequenced coding and regulatory elements for 608 genes potentially involved in obsessive-compulsive disorder in human, dog, and mouse. Using a new method that prioritizes likely functional variants, we compared 592 cases to 560 controls and found four strongly associated genes, validated in a larger cohort. NRXN1 and HTR2A are enriched for coding variants altering postsynaptic protein-binding domains...
October 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29042462/infrequent-provision-of-palliative-care-to-patients-with-dialysis-requiring-aki
#20
Kelly Chong, Samuel A Silver, Jin Long, Yuanchao Zheng, V Shane Pankratz, Mark L Unruh, Glenn M Chertow
BACKGROUND AND OBJECTIVES: The use of palliative care in AKI is not well described. We sought to better understand palliative care practice patterns for hospitalized patients with AKI requiring dialysis in the United States. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Using the 2012 National Inpatient Sample, we identified patients with AKI and palliative care encounters using validated International Classification of Diseases, Ninth Revision, Clinical Modification codes...
October 17, 2017: Clinical Journal of the American Society of Nephrology: CJASN
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