High-Throughput最新文献_第7页

Genomics and Epigenetics of Malignant Mesothelioma. 恶性间皮瘤的基因组学和表观遗传学。

High-Throughput Pub Date : 2018-07-27 DOI: 10.3390/ht7030020

Adam P Sage, Victor D Martinez, Brenda C Minatel, Michelle E Pewarchuk, Erin A Marshall, Gavin M MacAulay, Roland Hubaux, Dustin D Pearson, Aaron A Goodarzi, Graham Dellaire, Wan L Lam

{"title":"Genomics and Epigenetics of Malignant Mesothelioma.","authors":"Adam P Sage, Victor D Martinez, Brenda C Minatel, Michelle E Pewarchuk, Erin A Marshall, Gavin M MacAulay, Roland Hubaux, Dustin D Pearson, Aaron A Goodarzi, Graham Dellaire, Wan L Lam","doi":"10.3390/ht7030020","DOIUrl":"10.3390/ht7030020","url":null,"abstract":"Malignant mesothelioma is an aggressive and lethal asbestos-related disease. Diagnosis of malignant mesothelioma is particularly challenging and is further complicated by the lack of disease subtype-specific markers. As a result, it is especially difficult to distinguish malignant mesothelioma from benign reactive mesothelial proliferations or reactive fibrosis. Additionally, mesothelioma diagnoses can be confounded by other anatomically related tumors that can invade the pleural or peritoneal cavities, collectively resulting in delayed diagnoses and greatly affecting patient management. High-throughput analyses have uncovered key genomic and epigenomic alterations driving malignant mesothelioma. These molecular features have the potential to better our understanding of malignant mesothelioma biology as well as to improve disease diagnosis and patient prognosis. Genomic approaches have been instrumental in identifying molecular events frequently occurring in mesothelioma. As such, we review the discoveries made using high-throughput technologies, including novel insights obtained from the analysis of the non-coding transcriptome, and the clinical potential of these genetic and epigenetic findings in mesothelioma. Furthermore, we aim to highlight the potential of these technologies in the future clinical applications of the novel molecular features in malignant mesothelioma.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht7030020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36357647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 29

Venomics: A Mini-Review. Venomics：小型综述。

High-Throughput Pub Date : 2018-07-23 DOI: 10.3390/ht7030019

David Wilson, Norelle L Daly

引用次数: 0

Microfluidic Devices for Drug Assays. 药物检测用微流体装置。

High-Throughput Pub Date : 2018-06-20 DOI: 10.3390/ht7020018

Clément Regnault, Dharmendra S Dheeman, Axel Hochstetter

引用次数: 42

A Parallel Software Pipeline for DMET Microarray Genotyping Data Analysis. DMET微阵列基因分型数据分析的并行软件流水线。

High-Throughput Pub Date : 2018-06-14 DOI: 10.3390/ht7020017

Giuseppe Agapito, Pietro Hiram Guzzi, Mario Cannataro

{"title":"A Parallel Software Pipeline for DMET Microarray Genotyping Data Analysis.","authors":"Giuseppe Agapito, Pietro Hiram Guzzi, Mario Cannataro","doi":"10.3390/ht7020017","DOIUrl":"https://doi.org/10.3390/ht7020017","url":null,"abstract":"Personalized medicine is an aspect of the P4 medicine (predictive, preventive, personalized and participatory) based precisely on the customization of all medical characters of each subject. In personalized medicine, the development of medical treatments and drugs is tailored to the individual characteristics and needs of each subject, according to the study of diseases at different scales from genotype to phenotype scale. To make concrete the goal of personalized medicine, it is necessary to employ high-throughput methodologies such as Next Generation Sequencing (NGS), Genome-Wide Association Studies (GWAS), Mass Spectrometry or Microarrays, that are able to investigate a single disease from a broader perspective. A side effect of high-throughput methodologies is the massive amount of data produced for each single experiment, that poses several challenges (e.g., high execution time and required memory) to bioinformatic software. Thus a main requirement of modern bioinformatic softwares, is the use of good software engineering methods and efficient programming techniques, able to face those challenges, that include the use of parallel programming and efficient and compact data structures. This paper presents the design and the experimentation of a comprehensive software pipeline, named microPipe, for the preprocessing, annotation and analysis of microarray-based Single Nucleotide Polymorphism (SNP) genotyping data. A use case in pharmacogenomics is presented. The main advantages of using microPipe are: the reduction of errors that may happen when trying to make data compatible among different tools; the possibility to analyze in parallel huge datasets; the easy annotation and integration of data. microPipe is available under Creative Commons license, and is freely downloadable for academic and not-for-profit institutions.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht7020017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36223425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Handling Complexity in Animal and Plant Science Research-From Single to Functional Traits: Are We There Yet? 处理动植物科学研究中的复杂性——从单一性状到功能性状:我们做到了吗?

High-Throughput Pub Date : 2018-05-28 DOI: 10.3390/ht7020016

Jessica Roberts, Aoife Power, Shaneel Chandra, James Chapman, Daniel Cozzolino

{"title":"Handling Complexity in Animal and Plant Science Research-From Single to Functional Traits: Are We There Yet?","authors":"Jessica Roberts, Aoife Power, Shaneel Chandra, James Chapman, Daniel Cozzolino","doi":"10.3390/ht7020016","DOIUrl":"https://doi.org/10.3390/ht7020016","url":null,"abstract":"The current knowledge of the main factors governing livestock, crop and plant quality as well as yield in different species is incomplete. For example, this can be evidenced by the persistence of benchmark crop varieties for many decades in spite of the gains achieved over the same period. In recent years, it has been demonstrated that molecular breeding based on DNA markers has led to advances in breeding (animal and crops). However, these advances are not in the way that it was anticipated initially by the researcher in the field. According to several scientists, one of the main reasons for this was related to the evidence that complex target traits such as grain yield, composition or nutritional quality depend on multiple factors in addition to genetics. Therefore, some questions need to be asked: are the current approaches in molecular genetics the most appropriate to deal with complex traits such as yield or quality? Are the current tools for phenotyping complex traits enough to differentiate among genotypes? Do we need to change the way that data is collected and analysed?","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht7020016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36173390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia. 豆科植物与固氮根瘤菌共生关系的功能基因组学研究。

High-Throughput Pub Date : 2018-05-18 DOI: 10.3390/ht7020015

Martina Lardi, Gabriella Pessi

引用次数: 12

Computational Convolution of SELDI Data for the Diagnosis of Alzheimer's Disease. 用于阿尔茨海默病诊断的SELDI数据的计算卷积。

High-Throughput Pub Date : 2018-05-17 DOI: 10.3390/ht7020014

Destiny E O Anyaiwe, Gautam B Singh, George D Wilson, Timothy J Geddes

引用次数: 1

Comparison of Cell Arrays and Multi-Well Plates in Microscopy-Based Screening. 细胞阵列和多孔板在显微镜筛选中的比较。

High-Throughput Pub Date : 2018-05-15 DOI: 10.3390/ht7020013

Ann-Kristin Becker, Holger Erfle, Manuel Gunkel, Nina Beil, Lars Kaderali, Vytaute Starkuviene

{"title":"Comparison of Cell Arrays and Multi-Well Plates in Microscopy-Based Screening.","authors":"Ann-Kristin Becker, Holger Erfle, Manuel Gunkel, Nina Beil, Lars Kaderali, Vytaute Starkuviene","doi":"10.3390/ht7020013","DOIUrl":"https://doi.org/10.3390/ht7020013","url":null,"abstract":"Multi-well plates and cell arrays enable microscopy-based screening assays in which many samples can be analysed in parallel. Each of the formats possesses its own strengths and weaknesses, but reference comparisons between these platforms and their application rationale is lacking. We aim to fill this gap by comparing two RNA interference (RNAi)-mediated fluorescence microscopy-based assays, namely epidermal growth factor (EGF) internalization and cell cycle progression, on both platforms. Quantitative analysis revealed that both platforms enabled the generation of data with the appearance of the expected phenotypes significantly distinct from the negative controls. The measurements of cell cycle progression were less variable in multi-well plates. The result can largely be attributed to higher cell numbers resulting in less data variability when dealing with the assay generating phenotypic cell subpopulations. The EGF internalization assay with a uniform phenotype over nearly the whole cell population performed better on cell arrays than in multi-well plates. The result was achieved by scoring five times less cells on cell arrays than in multi-well plates, indicating the efficiency of the cell array format. Our data indicate that the choice of the screening platform primarily depends on the type of the cellular assay to achieve a maximum data quality and screen efficiency.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht7020013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40527087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Reactive Chemicals and Electrophilic Stress in Cancer: A Minireview. 癌症中的反应化学和亲电应激:综述。

High-Throughput Pub Date : 2018-04-27 DOI: 10.3390/ht7020012

Vehary Sakanyan

{"title":"Reactive Chemicals and Electrophilic Stress in Cancer: A Minireview.","authors":"Vehary Sakanyan","doi":"10.3390/ht7020012","DOIUrl":"https://doi.org/10.3390/ht7020012","url":null,"abstract":"Exogenous reactive chemicals can impair cellular homeostasis and are often associated with the development of cancer. Significant progress has been achieved by studying the macromolecular interactions of chemicals that possess various electron-withdrawing groups and the elucidation of the protective responses of cells to chemical interventions. However, the formation of electrophilic species inside the cell and the relationship between oxydative and electrophilic stress remain largely unclear. Derivatives of nitro-benzoxadiazole (also referred as nitro-benzofurazan) are potent producers of hydrogen peroxide and have been used as a model to study the generation of reactive species in cancer cells. This survey highlights the pivotal role of Cu/Zn superoxide dismutase 1 (SOD1) in the production of reactive oxygen and electrophilic species in cells exposed to cell-permeable chemicals. Lipophilic electrophiles rapidly bind to SOD1 and induce stable and functionally active dimers, which produce excess hydrogen peroxide leading to aberrant cell signalling. Moreover, reactive oxygen species and reactive electrophilic species, simultaneously generated by redox reactions, behave as independent entities that attack a variety of proteins. It is postulated that the binding of the electrophilic moiety to multiple proteins leading to impairing different cellular functions may explain unpredictable side effects in patients undergoing chemotherapy with reactive oxygen species (ROS)-inducing drugs. The identification of proteins susceptible to electrophiles at early steps of oxidative and electrophilic stress is a promising way to offer rational strategies for dealing with stress-related malignant tumors.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht7020012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36049708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 16

Fast-GPU-PCC: A GPU-Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Time Series Data-fMRI Study. 快速GPU PCC：一种基于GPU的技术，用于计算时间序列数据fMRI研究的成对Pearson相关系数。

High-Throughput Pub Date : 2018-04-20 DOI: 10.3390/ht7020011

Taban Eslami, Fahad Saeed

{"title":"Fast-GPU-PCC: A GPU-Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Time Series Data-fMRI Study.","authors":"Taban Eslami, Fahad Saeed","doi":"10.3390/ht7020011","DOIUrl":"10.3390/ht7020011","url":null,"abstract":"Functional magnetic resonance imaging (fMRI) is a non-invasive brain imaging technique, which has been regularly used for studying brain’s functional activities in the past few years. A very well-used measure for capturing functional associations in brain is Pearson’s correlation coefficient. Pearson’s correlation is widely used for constructing functional network and studying dynamic functional connectivity of the brain. These are useful measures for understanding the effects of brain disorders on connectivities among brain regions. The fMRI scanners produce huge number of voxels and using traditional central processing unit (CPU)-based techniques for computing pairwise correlations is very time consuming especially when large number of subjects are being studied. In this paper, we propose a graphics processing unit (GPU)-based algorithm called Fast-GPU-PCC for computing pairwise Pearson’s correlation coefficient. Based on the symmetric property of Pearson’s correlation, this approach returns N ( N − 1 ) / 2 correlation coefficients located at strictly upper triangle part of the correlation matrix. Storing correlations in a one-dimensional array with the order as proposed in this paper is useful for further usage. Our experiments on real and synthetic fMRI data for different number of voxels and varying length of time series show that the proposed approach outperformed state of the art GPU-based techniques as well as the sequential CPU-based versions. We show that Fast-GPU-PCC runs 62 times faster than CPU-based version and about 2 to 3 times faster than two other state of the art GPU-based methods.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht7020011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36027679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 22