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https://www.readbyqxmd.com/read/28636181/identification-of-biomarkers-for-early-diagnosis-of-acute-myocardial-infarction
#1
Wen-Han Ge, Yong Lin, Sen Li, Xuefeng Zong, Zhong-Chun Ge
Acute myocardial infarction (AMI) is a common disease with serious consequences in mortality and cost. Here we aim to screen the differentially expressed genes (DEGs) as biomarkers for early diagnosis of AMI. The microarray data of AMI was downloaded from Gene Expression Omnibus (GEO), including two independent types of research GSE66360 and GSE62646. The DEGs between control and processed samples were screened out by using limma package. Meanwhile, we performed functional analysis of GO terms and/or KEGG pathways to observe the enriched pathways of the DEGs...
June 21, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28635682/relationship-between-human-mutl-homolog-1-hmlh1-hypermethylation-and-colorectal-cancer-a-meta-analysis
#2
Hui-Feng Zhang, You-Wang Lu, Zhen-Rong Xie, Kun-Hua Wang
BACKGROUND Hypermethylation of CpG islands in gene promoter regions is an important mechanism of gene inactivation in cancers. Promoter hypermethylation of human mutL homolog 1 (hMLH1) has been implicated in a subset of colorectal cancers that show microsatellite instability (MSI), while the connection of the epigenetic inactivation of hMLH1 in colorectal cancers remains unknown. The aim of this study was to evaluate the relationship between the promoter hypermethylation of hMLH1 and colorectal cancers by performing a meta-analysis...
June 21, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28633423/rqt-an-r-package-for-gene-level-meta-analysis
#3
Ilya Y Zhbannikov, Konstantin G Arbeev, Anatoliy I Yashin
Motivation: Despite recent advances of modern GWAS methods, it is still remains an important problem of addressing calculation an effect size and corresponding p -value for the whole gene rather than for single variant. Results: We developed an R package rqt , which offers gene-level GWAS meta-analysis. The package can be easily included into bioinformatics pipeline or used stand-alone. We applied this tool to the analysis of Alzheimer's disease data from three datasets CHS, FHS, and LOADFS...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633391/kmerpyramid-an-interactive-visualization-tool-for-nucleobase-and-k-mer-frequencies
#4
Jochen Kruppa, Erhard van der Vries, Wendy K Jo, Alexander Postel, Paul Becher, Albert Osterhaus, Klaus Jung
Summary: Bioinformatics methods often incorporate the frequency distribution of nulecobases or k -mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k -mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633357/matter-an-r-package-for-rapid-prototyping-with-larger-than-memory-datasets-on-disk
#5
Kylie A Bemis, Olga Vitek
Summary: We introduce matter , an R package for direct interactions with larger-than-memory datasets, stored in an arbitrary number of files of any size. matter is primarily designed for datasets in new and rapidly evolving file formats, which may lack extensive software support. matter enables a wide variety of data exploration and manipulation steps, and is extensible to many bioinformatics applications. It supports reproducible research by minimizing the need of converting and storing data in multiple formats...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28632399/prokaryotic-contig-annotation-pipeline-server-web-application-for-a-prokaryotic-genome-annotation-pipeline-based-on-the-shiny-app-package
#6
Byeonghyeok Park, Min-Jeong Baek, Byoungnam Min, In-Geol Choi
Genome annotation is a primary step in genomic research. To establish a light and portable prokaryotic genome annotation pipeline for use in individual laboratories, we developed a Shiny app package designated as "P-CAPS" (Prokaryotic Contig Annotation Pipeline Server). The package is composed of R and Python scripts that integrate publicly available annotation programs into a server application. P-CAPS is not only a browser-based interactive application but also a distributable Shiny app package that can be installed on any personal computer...
June 20, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28630888/gillespy-a-python-package-for-stochastic-model-building-and-simulation
#7
John H Abel, Brian Drawert, Andreas Hellander, Linda R Petzold
GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms (SSA). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand, action-oriented programming interface. Here, we describe the components of this package and provide a detailed example relevant to the computational biology community...
September 2016: IEEE Life Sciences Letters
https://www.readbyqxmd.com/read/28629822/structure-based-designed-nano-dysferlin-significantly-improves-dysferlinopathy-in-bla-j-mice
#8
Telmo Llanga, Nadia Nagy, Laura Conatser, Catherine Dial, R Bryan Sutton, Matthew L Hirsch
Dysferlinopathy is an autosomal recessive muscular dystrophy characterized by the progressive loss of motility that is caused by mutations throughout the DYSF gene. There are currently no approved therapies that ameliorate or reverse dysferlinopathy. Gene delivery using adeno-associated vectors (AAVs) is a leading therapeutic strategy for genetic diseases; however, the large size of dysferlin cDNA (6.2 kB) precludes packaging into a single AAV capsid. Therefore, using 3D structural modeling and hypothesizing dysferlin C2 domain redundancy, a 30% smaller, dysferlin-like molecule amenable to single AAV vector packaging was engineered (termed Nano-Dysferlin)...
June 16, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28629365/evaluation-and-improvement-of-the-regulatory-inference-for-large-co-expression-networks-with-limited-sample-size
#9
Wenbin Guo, Cristiane P G Calixto, Nikoleta Tzioutziou, Ping Lin, Robbie Waugh, John W S Brown, Runxuan Zhang
BACKGROUND: Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis methods mostly focus on networks of small or medium size of up to a few hundred nodes. For large networks, simulated expression data usually consist of hundreds or thousands of profiles with different perturbations or knock-outs, which is uncommon in real experiments due to their cost and the amount of work required...
June 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28627731/cell-migration-analysis-a-low-cost-laboratory-experiment-for-cell-and-developmental-biology-courses-using-keratocytes-from-fish-scales
#10
Daniel Prieto, Gonzalo Aparicio, Jose R Sotelo-Silveira
Cell and developmental processes are complex, and profoundly dependent on spatial relationships that change over time. Innovative educational or teaching strategies are always needed to foster deep comprehension of these processes and their dynamic features. However, laboratory exercises in cell and developmental biology at the undergraduate level do not often take into account the time dimension. In this article, we provide a laboratory exercise focused in cell migration, aiming to stimulate thinking in time and space dimensions through a simplification of more complex processes occurring in cell or developmental biology...
June 19, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28627688/danger-recognizing-proteins-%C3%AE-defensin-128-and-histatin-3-as-potential-biomarkers-of-recurrent-coronary-events
#11
Madankumar Ghatge, Ankit Sharma, Sangeeta Maity, Vijay V Kakkar, Rajani Kanth Vangala
Conventional risk factors have limited ability to predict recurrent events in subjects with first-time coronary artery disease (CAD). This aim of this study was to identify novel biomarkers using comparative global proteome analysis to improve the risk assessment for recurrent coronary events. We used samples from phase-I of the Indian Atherosclerosis Research Study (IARS), consisting of 2,332 subjects, of whom 772 were CAD-affected subjects, including 152 with recurrent events identified during a 5-year follow-up period...
June 19, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28627042/deciding-about-nursing-home-care-in-dementia-a-conjoint-analysis-of-how-older-people-balance-competing-goals
#12
Alison Fahey, Dearbhail Ní Chaoimh, Grainne R Mulkerrin, Eamon C Mulkerrin, Shaun T O'Keeffe
AIM: "Don't put me in a home" is a common preference of older people, but so too is "I don't want to be a burden on my family." These and other goals often conflict with each other when people have worsening dementia and the issue of possible nursing home admission arises. METHODS: Community-dwelling older hospital patients were asked to imagine that they lived alone, had dementia and were experiencing increasing practical difficulties, and were presented with 11 possible "outcome packages...
June 18, 2017: Geriatrics & Gerontology International
https://www.readbyqxmd.com/read/28624079/effect-of-the-state-of-water-and-relative-humidity-on-ageing-of-pla-films
#13
J R Rocca-Smith, N Chau, D Champion, C-H Brachais, E Marcuzzo, A Sensidoni, F Piasente, T Karbowiak, F Debeaufort
Various types of food are now commercialized in packaging materials based on poly(lactic acid) (PLA) due to its eco-friendly nature. However, one of the main limitations related to PLA is its reactivity with water. For food applications, it is of critical importance to better understand the hydrolysis of PLA driven by water molecules either in liquid or in vapour state. This work focuses on the modifications of PLA induced by water when simulating contact with semi-dry foods (aw≈0.5), high moisture foods (aw≈1) and liquid foods (aw≈1)...
December 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28623573/bisphenol-a-exposure-assessment-from-olive-oil-consumption
#14
Tarek F Abou Omar, Carol Sukhn, Souha A Fares, Mohamad G Abiad, Rima R Habib, Hassan R Dhaini
The use of bisphenol A (BPA) in packaging has grown over the past 50 years despite concerns of its migration into packaged food and beverages, resulting in human exposure. Many studies have reported tumorigenic effects and endocrine alterations associated with BPA in animal models. This study aims at assessing human exposure to BPA from olive oil. A total of 27 olive oil samples were collected from mills and local villagers in the Hasbaya District, a major olive oil harvesting region in Lebanon. Information on storage conditions was also collected...
July 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28622336/a-knowledge-based-t2-statistic-to-perform-pathway-analysis-for-quantitative-proteomic-data
#15
En-Yu Lai, Yi-Hau Chen, Kun-Pin Wu
Approaches to identify significant pathways from high-throughput quantitative data have been developed in recent years. Still, the analysis of proteomic data stays difficult because of limited sample size. This limitation also leads to the practice of using a competitive null as common approach; which fundamentally implies genes or proteins as independent units. The independent assumption ignores the associations among biomolecules with similar functions or cellular localization, as well as the interactions among them manifested as changes in expression ratios...
June 16, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28621925/kpic2-an-effective-framework-for-mass-spectrometry-based-metabolomics-using-pure-ion-chromatograms
#16
Hongchao Ji, Fanjuan Zeng, Yamei Xu, Hongmei Lu, Zhimin Zhang
Distilling accurate quantitation information of metabolites from liquid chromatography coupled with mass spectrometry (LC-MS) datasets is crucial for further statistical analysis and biomarker identification. However, it is still challenging due to the complexity of biological systems. The concept of pure ion chromatograms (PIC) is an effective way for extracting meaningful ions, but few toolboxes provide full processing workflow for LC-MS datasets based on PIC. In this study, an integrated framework, KPIC2, has been developed for metabolomics studies, which can detect pure ions accurately, align PICs across samples, group PICs to identify isotope and potential adducts, fill missing peaks and do multivariate pattern recognition...
June 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28621274/evaluation-to-prevent-the-physical-changes-in-colored-elastomeric-modules-when-exposed-to-various-dietary-media
#17
S Dhivya Kanya, K Pradeep Babu, R Venkatesan, A Nanda Kumar
AIM AND OBJECTIVE: The aim of the study is to analyze and compare the variation of lumen size and thickness of the elastomeric colored modules when immersed in four selected dietary media. MATERIALS AND METHODS: Sample size of 40 modules on each color - such as red, blue, green, and black - was taken and immersed in four dietary media (artificial saliva, coke mixed with artificial saliva, turmeric mixed with artificial saliva, and coffee mixed with artificial saliva)...
June 1, 2017: Journal of Contemporary Dental Practice
https://www.readbyqxmd.com/read/28620455/haplor-an-r-package-for-querying-web-based-annotation-tools
#18
Ilya Y Zhbannikov, Konstantin Arbeev, Anatoliy I Yashin
There exists a set of web-based tools for integration and exploring information linked to annotated genetic variants. We developed haploR, an R-package for querying such web-based genome annotation tools (currently implementing on HaploReg and RegulomeDB) and gathering information in a format suitable for downstream bioinformatic analyses. This will facilitate post-genome wide association studies streamline analysis for rapid discovery and interpretation of genetic associations.
2017: F1000Research
https://www.readbyqxmd.com/read/28617170/adherence-of-heart-transplant-recipients-to-prescribed-medication-and-recommended-lifestyle-habits
#19
Y Brocks, A Zittermann, D Grisse, G Schmid-Ott, S Stock-Gießendanner, U Schulz, J Brakhage, A Benkler, J Gummert, Katharina Tigges-Limmer
INTRODUCTION: Nonadherence may cause severe health problems in heart transplant (HTx) recipients. RESEARCH QUESTIONS: The present study aimed to investigate adherence to prescribed medication and recommended lifestyle habits in post-HTx patients and to assess associations between adherence, quality of life (QOL), and psychological well-being. DESIGN: A questionnaire package was sent to all HTx patients from our clinic (n = 858) to answer questions anonymously on medication adherence, dietary recommendations (avoidance of raw animal products and ice cream), pet keeping (risk of zoonosis), anxiety and depression, QOL, and posttraumatic stress disorders...
June 2017: Progress in Transplantation
https://www.readbyqxmd.com/read/28612601/classification-of-bladder-cancer-patients-via-penalized-linear-discriminant-analysis
#20
Hadi Raeisi Shahraki, Peyman Bemani, Maryam Jalali
Objectives: In order to identify genes with the greatest contribution to bladder cancer, we proposed a sparse model making the best discrimination from other patients. Methods: In a cross-sectional study, 22 genes with a key role in most cancers were considered in 21 bladder cancer patients and 14 participants of the same age (± 3 years) without bladder cancer in Shiraz city, Southern Iran. Real time-PCR was carried out using SYBR Green and for each of the 22 target genes 2-Δct as a quantitative index of gene expression was reported...
May 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
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