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Analysis matrix data collection

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https://www.readbyqxmd.com/read/29137857/matricellular-proteins-and-survival-in-patients-with-pancreatic-cancer-a-systematic-review
#1
REVIEW
Sirio Fiorino, Maria Letizia Bacchi-Reggiani, Chiara Birtolo, Giorgia Acquaviva, Michela Visani, Adele Fornelli, Michele Masetti, Andrea Tura, Stefano Sbrignadello, Fabio Grizzi, Federica Patrinicola, Matteo Zanello, Laura Mastrangelo, Raffaele Lombardi, Claudia Benini, Luca Di Tommaso, Arrigo Bondi, Francesco Monetti, Elena Siopis, Paolo Emilio Orlandi, Michele Imbriani, Carlo Fabbri, Silvia Giovanelli, Andrea Domanico, Esterita Accogli, Salomone Di Saverio, Daniela Grifoni, Vincenzo Cennamo, Paolo Leandri, Elio Jovine, Dario de Biase
Extracellular matrix (ECM) plays a fundamental role in tissue architecture and homeostasis and modulates cell functions through a complex interaction between cell surface receptors, hormones, several bioeffector molecules, and structural proteins like collagen. These components are secreted into ECM and all together contribute to regulate several cellular activities including differentiation, apoptosis, proliferation, and migration. The so-called "matricellular" proteins (MPs) have recently emerged as important regulators of ECM functions...
November 4, 2017: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
https://www.readbyqxmd.com/read/29132619/a-statistical-analysis-based-recommender-model-for-heart-disease-patients
#2
Anam Mustaqeem, Syed Muhammad Anwar, Abdul Rashid Khan, Muhammad Majid
OBJECTIVES: An intelligent information technology based system could have a positive impact on the life-style of patients suffering from chronic diseases by providing useful health recommendations. In this paper, we have proposed a hybrid model that provides disease prediction and medical recommendations to cardiac patients. The first part aims at implementing a prediction model, that can identify the disease of a patient and classify it into one of the four output classes i.e., non-cardiac chest pain, silent ischemia, angina, and myocardial infarction...
December 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29130678/-expression-of-lox-in-colorectal-cancer-tissues-and-its-relationship-with-progress-and-prognosis
#3
Xiao-Ming Shi, Wei Zhao, Yong-Bin Yang, Bo-Nan Lü
OBJECTIVE: To analyze the expression of lysyl oxidase (LOX) in colorectal cancer and its relationship with clinicopathological characteristics, prognosis, and its progress. METHODS: 82 cases of colorectal tumor paraffin-embedded specimens and paired tumor-adjacent tissues were collected, and data of clinicopathological characteristics and prognosis of these patients were also recorded from 2009.1 to 2010.5. Expressions of LOX, hypoxia inducible factor-1α (HIF-1α), matrix metalloproteinase (MMP)-2, MMP-7 were determined by immunohistochemistry...
July 2017: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
https://www.readbyqxmd.com/read/29129223/infectious-pancreatic-necrosis-virus-infection-of-fish-cell-lines-preliminary-analysis-of-gene-expressions-related-to-extracellular-matrix-remodeling-and-immunity
#4
Melina Villalba, Valeria Pérez, Laura Herrera, Cristopher Stepke, Nicolas Maldonado, Fernanda Fredericksen, Alejandro Yáñez, Víctor H Olavarría
The pathogenic infectious pancreatic necrosis virus (IPNV) causes high economic losses in fish farming. This virus can modulate several cellular processes during infection, but little is known about the infection mechanism. To investigate gene activation in response to IPNV, CHSE/F and SHK-1 cell line were infected with a cytopathic Sp field isolate of IPNV, and the expression profiles of proinflammatory, antiviral cytokine, and extracellular matrix markers were analyzed. IPNV induced the production of perlecan, fibulin-1, matrix metalloproteinase-2, 14-3-3β, interleukin-1β, Mx1, and interferon regulatory factors-1, -3, and -9...
December 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/29115927/transcriptomic-responses-to-wounding-meta-analysis-of-gene-expression-microarray-data
#5
Piotr Andrzej Sass, Michał Dąbrowski, Agata Charzyńska, Paweł Sachadyn
BACKGROUND: A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wounding in different organisms and tissues. This meta-analysis is the first study to compare gene expression profiles in response to wounding in as different tissues as heart, liver, skin, bones, and spinal cord, and species, including rat, mouse and human. RESULTS: We collected available microarray transcriptomic profiles obtained from different tissue injury experiments and selected the genes showing a minimum twofold change in expression in response to wounding in prevailing number of experiments for each of five wound healing stages we distinguished: haemostasis & early inflammation, inflammation, early repair, late repair and remodelling...
November 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29114638/how-to-manage-a-failed-cartilage-repair-a-systematic-literature-review
#6
REVIEW
Donato Rosa, Sigismondo Luca Di Donato, Giovanni Balato, Alessio D'Addona, Francesco Smeraglia, Gaetano Correra, Gianni Di Vico
Purpose  The aims of this paper are to report the rate and risk factors for the failure of the most common cartilage repair technique, and analyze the most important factors that could influence the choice of a specific surgical treatment to revise a failed cartilage repair. Methods  A review of the literature was performed focusing on failed cartilage repair and related treatments. Two of the authors independently screened articles. Conflicts about the inclusion of a paper was resolved by further evaluation by the senior author...
June 2017: Joints
https://www.readbyqxmd.com/read/29108696/metagenomics-for-the-study-of-viruses-in-urban-sewage-as-a-tool-for-public-health-surveillance
#7
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/29106758/transcriptomic-analysis-of-synovial-extracellular-rna-following-knee-trauma-a-pilot-study
#8
Anthony J Griswold, Jose Perez, Karen Nuytemans, Thomas Strong, Liyong Wang, Danica D Vance, Hayley Ennis, Marvin K Smith, Thomas M Best, Jeffery M Vance, Margaret A Pericak-Vance, Lee D Kaplan
Traumatic knee injuries often result in damage to articular cartilage and other joint structures. Such trauma is a strong risk factor for the future development and progression of osteoarthritis (OA). The molecular mechanisms and signaling pathways modulating response to knee joint trauma remain unclear. Moreover, investigations of biomarkers influencing responses have been targeted rather than broad, unbiased discovery studies. Herein we characterize the complete complement of extracellular RNA (exRNA) in the synovial fluid of 14 subjects following knee injury...
November 6, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/29078774/the-kessler-psychological-distress-scale-translation-and-validation-of-an-arabic-version
#9
Scott D Easton, Najwa S Safadi, Yihan Wang, Robert G Hasson
BACKGROUND: The Kessler Psychological Distress Scale has been widely used in assessing psychological distress among general and clinical populations from different cultural backgrounds. To our knowledge, however, researchers have not yet validated any translated versions in Arabic. The purpose of this study was to test the reliability and validity of Arabic translations of the ten item (K10) and six item (K6) versions among public sector employees in the Occupied Palestinian Territories...
October 27, 2017: Health and Quality of Life Outcomes
https://www.readbyqxmd.com/read/29063513/variability-in-c-reactive-protein-is-associated-with-cognitive-impairment-in-women-living-with-and-without-hiv-a-longitudinal-study
#10
Leah H Rubin, Lorie Benning, Sheila M Keating, Philip J Norris, Jane Burke-Miller, Antonia Savarese, Krithika N Kumanan, Saria Awadalla, Gayle Springer, Kathyrn Anastos, Mary Young, Joel Milam, Victor G Valcour, Kathleen M Weber, Pauline M Maki
Despite the availability of effective antiretroviral therapies, cognitive impairment (CI) remains prevalent in HIV-infected (HIV+) individuals. Evidence from primarily cross-sectional studies, in predominantly male samples, implicates monocyte- and macrophage-driven inflammatory processes linked to HIV-associated CI. Thus, peripheral systemic inflammatory markers may be clinically useful biomarkers in tracking HIV-associated CI. Given sex differences in immune function, we focused here on whether mean and intra-individual variability in inflammatory marker-predicted CI in HIV+ and HIV- women...
October 23, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/29060415/muscle-synergy-analysis-in-dart-throwing
#11
Bao Nguyen Tran, Shiro Yano, Toshiyuki Kondo
This study aims to analyze muscle synergies in darts throwing movement to clarify how the central nervous system (CNS) controls muscle activation to produce complicated motion. Activities of 10 different muscles on upper limb were recorded through surface electromyography (EMG) electrodes from four participants with less experience of dart throwing. Subsequently, non-negative matrix factorization (NNMF) was applied to the collected EMG signals for muscle synergy analysis. Results showed that three muscle synergies could explain sufficiently the observed EMG data, with determination coefficient r(2) = 0...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/29029874/sperm-subpopulations-in-ejaculated-sperm-and-spermatozoa-recovered-from-ovine-epididymides-up-to-48h-after-death
#12
Tácia Gomes Bergstein-Galan, Romildo Romualdo Weiss, Luiz Ernandes Kozicki, Sony Dimas Bicudo
The objectives of this study were threefold: to identify subpopulations of sperm based on the kinetics of frozen/thawed sheep epididymal spermatozoa or semen collected with an artificial vagina; to evaluate the effects on sperm subpopulations in the thawed samples of post mortem storage at room temperature and the addition of 20% of seminal plasma to the freezing extender and to correlate the percentage of subpopulations with gestation rate following artificial intrauterine insemination. The categorization of the subpopulations was based on sperm kinetic data from Computer Assisted Sperm Analysis (CASA)...
October 5, 2017: Animal Reproduction Science
https://www.readbyqxmd.com/read/29028685/use-of-genetic-algorithm-combinational-single-nucleotide-polymorphisms-could-modify-the-association-of-blood-lead-levels-and-bone-matrix-density
#13
Chien-Juan Chen, Hsueh-Wei Chang, Cheng-Hong Yang, Hung-Yi Chuang, Hsin-Su Yu
BACKGROUND: Previous studies have not explored the relationship between a single gene and a single disease. Our study aims to investigate the association of multiple genotypes with blood lead levels and bone matrix density (BMD) by using genetic algorithms. METHODS: Our research focused on 506 employees (245 males and 261 females) of a lead battery factory in Taiwan. We collected data on their BMD, blood lead level, and 6 SNPs (ACE, alpha-adducin, Bsm, Tag, Apa, and ALAD); these factors were analyzed using discrete binary particle swarm optimization (DBPSO) and logistic regression analysis...
October 2017: Epidemiology
https://www.readbyqxmd.com/read/28987921/tka-patients-with-unsatisfying-knee-function-show-changes-in-neuromotor-synergy-pattern-but-not-joint-biomechanics
#14
Marzieh M Ardestani, Philip Malloy, Denis Nam, Aaron G Rosenberg, Markus A Wimmer
Nearly 20% of patients who have undergone total knee arthroplasty (TKA) report persistent poor knee function. This study explores the idea that, despite similar knee joint biomechanics, the neuro-motor synergies may be different between high-functional and low-functional TKA patients. We hypothesized that (1) high-functional TKA recruit a more complex neuro-motor synergy pattern compared to low-functional TKA and (2) high-functional TKA patients demonstrate more stride-to-stride variability (flexibility) in their synergies...
September 28, 2017: Journal of Electromyography and Kinesiology
https://www.readbyqxmd.com/read/28986766/comprehensive-risk-assessment-and-source-identification-of-selected-heavy-metals-cu-cd-pb-zn-hg-as-in-tidal-saltmarsh-sediments-of-shuangtai-estuary-china
#15
Chang-Fa Liu, Bing Li, Yi-Ting Wang, Yuan Liu, Heng-Jiang Cai, Hai-Feng Wei, Jia-Wen Wu, Jin Li
Heavy metals do not degrade and can remain in the environment for a long time. In this study, we analyzed the effects of Cu, Cd, Pb, Zn, Hg, and As, on environmental quality, pollutant enrichment, ecological hazard, and source identification of elements in sediments using data collected from samples taken from Shuangtai tidal wetland. The comprehensive pollution indices were used to assess environmental quality; fuzzy similarity analysis and geoaccumulation index were used to analyze pollution accumulation; correlation matrix, principal component analysis, and clustering analysis were used to analyze pollution source; environmental risk index and ecological risk index were used to assess ecological risk...
October 6, 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28985334/simultaneous-quantitation-of-methamphetamine-ketamine-opiates-and-their-metabolites-in-urine-by-spe-and-lc-ms-ms
#16
Chu-An Yang, Hsiu-Chuan Liu, Dong-Liang Lin, Ray H Liu, You-Zung Hsieh, Shu-Pao Wu
Heroin, methamphetamine and ketamine have been the most commonly abused drugs in Taiwan. The presence of these drugs and their metabolites in postmortem specimens has been routinely monitored in our laboratory mostly by gas chromatographic-mass spectrometric methods. This study aimed to evaluate a more effective approach to simultaneously quantify these analytes (i.e., amphetamine, methamphetamine, 3,4-methylenedioxyamphetamine, 3,4-methylenedioxymethamphetamine (MDMA), morphine, codeine, 6-acetylmorphine, 6-acetylcodeine, ketamine and norketamine) in postmortem urine and blood specimens by liquid chromatography-tandem mass spectrometry (LC-MS-MS)...
July 18, 2017: Journal of Analytical Toxicology
https://www.readbyqxmd.com/read/28979891/at1-expression-in-human-urethral-stricture-tissue
#17
Safendra Siregar, Aga Parardya, Jupiter Sibarani, Tjahjodjati Romdan, Kuncoro Adi, Bethy S Hernowo, Anglita Yantisetiasti
BACKGROUND: Urethral stricture has a high recurrence rate. There is a common doctrine stating that "once a stricture, always a stricture". This fibrotic disease pathophysiology, pathologically characterized by excessive production, deposition and contraction of extracellular matrix is unknown. Angiotensin II type 1 (AT1) receptor primarily induces angiogenesis, cellular proliferation and inflammatory responses. AT1 receptors are also expressed in the fibroblasts of hypertrophic scars, whereas angiotensin II (AngII) regulates DNA synthesis in hypertrophic scar fibroblasts through a negative cross talk between AT1 and angiotensin II type 2 (AT2) receptors, which might contribute to the formation and maturation of human hypertrophic scars...
2017: Research and Reports in Urology
https://www.readbyqxmd.com/read/28976646/untangling-cell-tracks-quantifying-cell-migration-by-time-lapse-image-data-analysis
#18
REVIEW
Carl-Magnus Svensson, Anna Medyukhina, Ivan Belyaev, Naim Al-Zaben, Marc Thilo Figge
Automated microscopy has given researchers access to great amounts of live cell imaging data from in vitro and in vivo experiments. Much focus has been put on extracting cell tracks from such data using a plethora of segmentation and tracking algorithms, but further analysis is normally required to draw biologically relevant conclusions. Such relevant conclusions may be whether the migration is directed or not, whether the population has homogeneous or heterogeneous migration patterns. This review focuses on the analysis of cell migration data that are extracted from time lapse images...
October 4, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28972992/a-landscape-genetic-analysis-of-important-agricultural-pest-species-in-tunisia-the-whitefly-bemisia-tabaci
#19
Ahmed Ben Abdelkrim, Tarek Hattab, Hatem Fakhfakh, Mohamed Sadok Belkadhi, Faten Gorsane
Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status...
2017: PloS One
https://www.readbyqxmd.com/read/28957322/shared-genetic-regulatory-networks-for-cardiovascular-disease-and-type-2-diabetes-in-multiple-populations-of-diverse-ethnicities-in-the-united-states
#20
Le Shu, Kei Hang K Chan, Guanglin Zhang, Tianxiao Huan, Zeyneb Kurt, Yuqi Zhao, Veronica Codoni, David-Alexandre Trégouët, Jun Yang, James G Wilson, Xi Luo, Daniel Levy, Aldons J Lusis, Simin Liu, Xia Yang
Cardiovascular diseases (CVD) and type 2 diabetes (T2D) are closely interrelated complex diseases likely sharing overlapping pathogenesis driven by aberrant activities in gene networks. However, the molecular circuitries underlying the pathogenic commonalities remain poorly understood. We sought to identify the shared gene networks and their key intervening drivers for both CVD and T2D by conducting a comprehensive integrative analysis driven by five multi-ethnic genome-wide association studies (GWAS) for CVD and T2D, expression quantitative trait loci (eQTLs), ENCODE, and tissue-specific gene network models (both co-expression and graphical models) from CVD and T2D relevant tissues...
September 2017: PLoS Genetics
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