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https://www.readbyqxmd.com/read/28214992/data-mining-in-hiv-aids-surveillance-system-application-to-portuguese-data
#1
Alexandra Oliveira, Brígida Mónica Faria, A Rita Gaio, Luís Paulo Reis
The Human Immunodeficiency Virus (HIV) is an infectious agent that attacks the immune system cells. Without a strong immune system, the body becomes very susceptible to serious life threatening opportunistic diseases. In spite of the great progresses on medication and prevention over the last years, HIV infection continues to be a major global public health issue, having claimed more than 36 million lives over the last 35 years since the recognition of the disease. Monitoring, through registries, of HIV-AIDS cases is vital to assess general health care needs and to support long-term health-policy control planning...
April 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28212879/flow-cytometric-based-protocols-for-assessing-anti-mt-2-igg1-reactivity-high-dimensional-data-handling-to-define-predictors-for-clinical-follow-up-of-human-t-cell-leukemia-virus-type-1-infection
#2
Jordana Grazziela Coelho-Dos-Reis, Vanessa Peruhype-Magalhães, Marcelo Antônio Pascoal-Xavier, Matheus de Souza Gomes, Laurence Rodrigues do Amaral, Ludmila Melo Cardoso, Juan Jonathan-Gonçalves, Ágata Lopes Ribeiro, Ana Lúcia Borges Starling, João Gabriel Ribas, Denise Utsch Gonçalves, Anna Bárbara de Freitas Carneiro-Proietti, Andréa Teixeira-Carvalho, Olindo Assis Martins-Filho
The present work provides an innovative methodological approach to assess the anti-HTLV-1 IgG1 reactivity with practical application in clinical laboratory. Serum from non-infected healthy controls (NI) and HTLV-1-infected patients, categorized as asymptomatic (AS), putatively progressing to HTLV-1 associated myelopathy/tropical spastic paraparesis - HAM/TSP (pHAM) or with clinical diagnosis of HAM/TSP (HT) were assayed in two-parallel flow cytometry platforms, referred as: Fix and Fix&Perm protocols. Operating-characteristics analysis indicated that a single pair of attributes ("serum dilution/cut-off") for Fix and Fix&Perm protocols presented excellent performance for the diagnosis of HTLV-1 infection...
February 14, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28212290/defining-clinical-response-criteria-and-early-response-criteria-for-precision-oncology-current-state-of-the-art-and-future-perspectives
#3
Vivek Subbiah, Hubert H Chuang, Dhiraj Gambhire, Kalevi Kairemo
In this era of precision oncology, there has been an exponential growth in the armamentarium of genomically targeted therapies and immunotherapies. Evaluating early responses to precision therapy is essential for "go" versus "no go" decisions for these molecularly targeted drugs and agents that arm the immune system. Many different response assessment criteria exist for use in solid tumors and lymphomas. We reviewed the literature using the Medline/PubMed database for keywords "response assessment" and various known response assessment criteria published up to 2016...
February 15, 2017: Diagnostics
https://www.readbyqxmd.com/read/28211014/comprehensive-peptide-ion-structure-studies-using-ion-mobility-techniques-part-1-an-advanced-protocol-for-molecular-dynamics-simulations-and-collision-cross-section-calculation
#4
Samaneh Ghassabi Kondalaji, Mahdiar Khakinejad, Amirmahdi Tafreshian, Stephen J Valentine
Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics...
February 16, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28210983/multi-view-ensemble-classification-of-brain-connectivity-images-for-neurodegeneration-type-discrimination
#5
Michele Fratello, Giuseppina Caiazzo, Francesca Trojsi, Antonio Russo, Gioacchino Tedeschi, Roberto Tagliaferri, Fabrizio Esposito
Brain connectivity analyses using voxels as features are not robust enough for single-patient classification because of the inter-subject anatomical and functional variability. To construct more robust features, voxels can be aggregated into clusters that are maximally coherent across subjects. Moreover, combining multi-modal neuroimaging and multi-view data integration techniques allows generating multiple independent connectivity features for the same patient. Structural and functional connectivity features were extracted from multi-modal MRI images with a clustering technique, and used for the multi-view classification of different phenotypes of neurodegeneration by an ensemble learning method (random forest)...
February 16, 2017: Neuroinformatics
https://www.readbyqxmd.com/read/28210891/aquatic-monitoring-programs-conducted-during-environmental-impact-assessments-in-canada-preliminary-assessment-before-and-after-weakened-environmental-regulation
#6
Brynn Roach, Tony R Walker
Aquatic monitoring programs are imperative for the functioning of the environmental impact assessment (EIA) process and a cornerstone for industrial compliance in Canada. However, in 2012, several leading pieces of federal environmental legislation (e.g., Canadian Environmental Assessment Act c.19, s. 52, 2012) were drastically altered, effectively weakening levels of environmental protection for aquatic ecosystems during project developments. This paper assesses the impact of CEAA 2012 on aquatic monitoring programs (and subsequent monitoring data reporting) across Canada for ten projects (five completed pre-CEAA 2012 and five completed post-CEAA 2012)...
March 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28210230/acute-mental-discomfort-associated-with-suicide-behavior-in-a-clinical-sample-of-patients-with-affective-disorders-ascertaining-critical-variables-using-artificial-intelligence-tools
#7
Susana Morales, Jorge Barros, Orietta Echávarri, Fabián García, Alex Osses, Claudia Moya, María Paz Maino, Ronit Fischman, Catalina Núñez, Tita Szmulewicz, Alemka Tomicic
AIM: In efforts to develop reliable methods to detect the likelihood of impending suicidal behaviors, we have proposed the following. OBJECTIVE: To gain a deeper understanding of the state of suicide risk by determining the combination of variables that distinguishes between groups with and without suicide risk. METHOD: A study involving 707 patients consulting for mental health issues in three health centers in Greater Santiago, Chile. Using 345 variables, an analysis was carried out with artificial intelligence tools, Cross Industry Standard Process for Data Mining processes, and decision tree techniques...
2017: Frontiers in Psychiatry
https://www.readbyqxmd.com/read/28209268/inorganic-mercury-prevents-the-differentiation-of-sh-sy5y-cells-amyloid-precursor-protein-microtubule-associated-proteins-and-ros-as-potential-targets
#8
Miguel Chin Chan, Elizabeth Bautista, Isabel Alvarado-Cruz, Betzabet Quintanilla-Vega, José Segovia
Exposure to mercury (Hg) occurs through different pathways and forms including methylmecury (MeHg) from seafood and rice, ethylmercury (EtHg), and elemental Hg (Hg(0)) from dental amalgams and artisanal gold mining. Once in the brain all these forms are transformed to inorganic Hg (I-Hg), where it bioaccumulates and remains for long periods. Hg is a well-known neurotoxicant, with its most damaging effects reported during brain development, when cellular key events, such as cell differentiation take place. A considerable number of studies report an impairment of neuronal differentiation due to MeHg exposure, however the effects of I-Hg, an important form of Hg found in brain, have received less attention...
February 6, 2017: Journal of Trace Elements in Medicine and Biology
https://www.readbyqxmd.com/read/28208223/conceptualization-of-karstic-aquifer-with-multiple-outlets-using-a-dual-porosity-model
#9
Seiyed Mossa Hosseini, Behzad Ataie-Ashtiani
In this study, two conceptual models, the classic reservoir (CR) model and exchange reservoirs model embedded by dual porosity approach (DPR) are developed for simulation of karst aquifer functioning drained by multiple outlets. The performances of two developed models are demonstrated at a less developed karstic aquifer with three spring outlets located in Zagros Mountain in the south-west of Iran using 22-years of daily data. During the surface recharge, a production function based on water mass balance is implemented for computing the time series of surface recharge to the karst formations...
February 16, 2017: Ground Water
https://www.readbyqxmd.com/read/28207410/data-mining-for-age-related-tsh-reference-intervals-in-adulthood
#10
Christopher-John L Farrell, Lan Nguyen, Andrew C Carter
No abstract text is available yet for this article.
February 16, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28204975/surface-and-exoproteomes-of-gram-positive-pathogens-for-vaccine-discovery
#11
Massimiliano Biagini, Fabio Bagnoli, Nathalie Norais
Reverse vaccinology has been very successful in the discovery of vaccine candidates against many pathogenic bacteria by integrating genome and proteome mining. This great achievement was facilitated by the complementarity of the in silico prediction of antigens and the empirical data on protein localization, expression, and immunogenicity obtained through different techniques based on electrophoresis, immunoblotting and mass spectrometry. An iterative process between information provided by DNA sequence analysis and proteomic data has been established leading to precise antigen identification...
February 16, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28203233/exo-mirexplorer-a-comprehensive-resource-for-exploring-and-comparatively-analyzing-exogenous-micrornas
#12
Ling-Ling Zheng, Kai-Wen Deng, An-Cheng Deng, Jie Wu, Jian-Hua Yang, Zhao-Rong Lun, Liang-Hu Qu
MicroRNAs (miRNAs) are small regulatory RNAs that play important roles in animals, plants, and viruses. Deep-sequencing technology has been widely adopted in miRNA investigations. However, it is still a big mysterious why nearly all sequencing data contain miRNA sequences from exogenous species, called exo-miRNAs. In this study, we developed a novel platform, exo-miRExplorer, for mining and identifying exo-miRNAs from high-throughput small RNA sequencing experiments which originated from tissues and cell lines of multiple organisms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28203090/exploring-targeted-therapy-of-osteosarcoma-using-proteomics-data
#13
Parunya Chaiyawat, Jongkolnee Settakorn, Apiruk Sangsin, Pimpisa Teeyakasem, Jeerawan Klangjorhor, Aungsumalee Soongkhaw, Dumnoensun Pruksakorn
Despite multimodal therapeutic treatments of osteosarcoma (OS), some patients develop resistance to currently available regimens and eventually end up with recurrent or metastatic outcomes. Many attempts have been made to discover effective drugs for improving outcome; however, due to the heterogeneity of the disease, new therapeutic options have not yet been identified. This study aims to explore potential targeted therapy related to protein profiles of OS. In this review of proteomics studies, we extracted data on differentially expressed proteins (DEPs) from archived literature in PubMed and our in-house repository...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28202203/female-specific-effect-of-the-bdnf-gene-on-alzheimer-s-disease
#14
Guo-Dong Li, Rui Bi, Deng-Feng Zhang, Min Xu, Rongcan Luo, Dong Wang, Yiru Fang, Tao Li, Chen Zhang, Yong-Gang Yao
Alzheimer's disease (AD) is the most common neurodegenerative disease influenced by genetic and environmental factors. Brain-derived neurotrophic factor (BDNF) plays an important role in the progression of AD, but the genetic association between BDNF and AD remains controversial. In this study, we aimed to explore the potential association between genetic variants in BDNF and AD in Han Chinese and to investigate whether the association is affected by gender. A 3-stage study was conducted to evaluate the genetic association between BDNF and AD...
January 24, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28198667/pan-cancer-analysis-of-frequent-dna-co-methylation-patterns-reveals-consistent-epigenetic-landscape-changes-in-multiple-cancers
#15
Jie Zhang, Kun Huang
BACKGROUND: DNA methylation is the major form of epigenetic modifications through which the cell regulates the gene expression and silencing. There have been extensive studies on the roles of DNA methylation in cancers, and several cancer drugs were developed targeting this process. However, DNA co-methylation cluster has not been examined in depth, and co-methylation in multiple cancer types has never been studied previously. RESULTS: In this study, we applied newly developed lmQCM algorithm to mine co-methylation clusters using methylome data from 11 cancer types in TCGA database, and found frequent co-methylated gene clusters exist in these cancer types...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28195566/rgs2-expression-predicts-amyloid-%C3%AE-sensitivity-mci-and-alzheimer-s-disease-genome-wide-transcriptomic-profiling-and-bioinformatics-data-mining
#16
A Hadar, E Milanesi, A Squassina, P Niola, C Chillotti, M Pasmanik-Chor, O Yaron, P Martásek, M Rehavi, D Weissglas-Volkov, N Shomron, I Gozes, D Gurwitz
No abstract text is available yet for this article.
February 14, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28194977/a-spectral-counting-approach-to-measure-selectivity-of-high-resolution-lc-ms-methods-for-environmental-analysis
#17
Justin B Renaud, Lyne Sabourin, Edward Topp, Mark W Sumarah
Advances in high resolution mass spectrometers have allowed for the development of non-targeted screening methods, where datasets can be archived and retrospectively mined as new environmental contaminants are identified. We have developed a spectral counting approach to calculate the selectivities of LC-MS acquisition modes taking mass accuracy, sample matrix and the analyte properties into account. The selectivities of high resolution MS (HRMS) alone or in combination with all-ion-fragmentation (AIF), data-independent-acquisition (DIA) and data-dependent-acquisition (DDA) modes, performed on a Q-Exactive Orbitrap were compared by retrospectively screening surface water samples for 95 pharmaceuticals...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28194669/mir-143-targeting-tak1-attenuates-pancreatic-ductal-adenocarcinoma-progression-via-mapk-and-nf-%C3%AE%C2%BAb-pathway-in-vitro
#18
Feng-Ting Huang, Juan-Fei Peng, Wen-Jie Cheng, Yan-Yan Zhuang, Ling-Yun Wang, Chu-Qiang Li, Jian Tang, Wen-Ying Chen, Yuan-Hua Li, Shi-Neng Zhang
BACKGROUND: Transforming growth factor (TGF)-β-activated kinase 1 (TAK1) is one of the major regulators of inflammation-induced cancer cell growth and progression. MiR-143 dysregulation is a common event in a variety of human diseases including pancreatic ductal adenocarcinoma (PDA). AIMS: To identify the interaction between TAK1 and miR-143 in PDA. METHODS: Data mining of TAK1 expression in PDA patient gene profiling was conducted. QRT-PCR and western blot were performed to detect the expression of TAK1 in PDA tissues and cell lines...
February 13, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28194337/development-of-statistics-as-a-discipline-for-clinical-research-past-present-and-future
#19
REVIEW
Chitra Lele
This article traces the history and evolution of statistics in the era of evidence based medicine, and focuses on the Indian perspective of this growth of statistics as a discipline for clinical research. Statistics will assume a more inter disciplinary form. Use of software other than SAS likely to grow further. In India, innovative statistical methods will help propel the development of biosimilars. The future is exciting with statistics being used for real world evidence, development of biosimilars, mining of adverse event data and becoming a core function in medicinal product development and lifecycle maintenance...
January 2017: Perspectives in Clinical Research
https://www.readbyqxmd.com/read/28192214/immune-recognition-surface-construction-of-mycobacterium-tuberculosis-epitope-specific-antibody-responses-in-tuberculosis-patients-identified-by-peptide-microarrays
#20
REVIEW
Davide Valentini, Martin Rao, Giovanni Ferrara, Marc Perkins, Ernest Dodoo, Alimuddin Zumla, Markus Maeurer
BACKGROUND: Understanding of humoral immune responses in tuberculosis (TB) is gaining interest, since B cells and antibodies may be important in diagnosis as well as protective immune responses. High-content peptide microarrays (HCPM) are highly precise and reliable for gauging specific antibody responses to pathogens, as well as autoantigens. METHODS: We used a HCPM comprising epitopes spanning 154 proteins of Mycobacterium tuberculosis (M. tb) to gauge specific IgG antibody responses in sera of TB patients from Africa and South America...
February 9, 2017: International Journal of Infectious Diseases: IJID
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