Search results for "Profiling"

Transcriptome profiling of citrus fruit response to huanglongbing disease.

2010

Huanglongbing (HLB) or "citrus greening" is the most destructive citrus disease worldwide. In this work, we studied host responses of citrus to infection with Candidatus Liberibacter asiaticus (CaLas) using next-generation sequencing technologies. A deep mRNA profile was obtained from peel of healthy and HLB- affected fruit. It was followed by pathway and protein-protein network analysis and quantitative real time PCR analysis of highly regulated genes. We identified differentially regulated pathways and constructed networks that provide a deep insight into the metabolism of affected fruit. Data mining revealed that HLB enhanced transcription of genes involved in the light reactions of phot…

New Insights of Profile Oriented Marketing and Adaption Management for a Future-Oriented City Development

2017

The world is changing fast, and cities are facing complex transitions in economic, social and environmental areas. Therefore, the design of city systems will play an essential role in shaping a sustainable, innovative and livable future. Adaptive urban profiling was recently presented as a useful tool for municipals to enhance sustainable city development. It builds upon profile oriented marketing while including elements of adaption management. Thus, city managers can increase their cities attractiveness by providing it with a clear profile that is recognized around the world on the one hand, while flexibly adapting to change if necessary. Only an integrated approach that puts people first…

Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

2015

AbstractBackgroundLife history traits like developmental time, age and size at maturity are directly related to fitness in all organisms and play a major role in adaptive evolution and speciation processes. Comparative genomic or transcriptomic approaches to identify positively selected genes involved in species divergence can help to generate hypotheses on the driving forces behind speciation. Here we use a bottom-up approach to investigate this hypothesis by comparative analysis of orthologous transcripts of four closely related EuropeanRadixspecies.ResultsSnails of the genusRadixoccupy species specific distribution ranges with distinct climatic niches, indicating a potential for natural …

SMART: Unique splitting-while-merging framework for gene clustering

2014

© 2014 Fa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Successful clustering algorithms are highly dependent on parameter settings. The clustering performance degrades significantly unless parameters are properly set, and yet, it is difficult to set these parameters a priori. To address this issue, in this paper, we propose a unique splitting-while-merging clustering framework, named "splitting merging awareness tactics" (SMART), which does not require any a priori knowledge of either the number …

GenClust: A genetic algorithm for clustering gene expression data

2005

Abstract Background Clustering is a key step in the analysis of gene expression data, and in fact, many classical clustering algorithms are used, or more innovative ones have been designed and validated for the task. Despite the widespread use of artificial intelligence techniques in bioinformatics and, more generally, data analysis, there are very few clustering algorithms based on the genetic paradigm, yet that paradigm has great potential in finding good heuristic solutions to a difficult optimization problem such as clustering. Results GenClust is a new genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, …

Comprehensive analysis of forty yeast microarray datasets reveals a novel subset of genes (APha-RiB) consistently negatively associated with ribosome…

2014

Background The scale and complexity of genomic data lend themselves to analysis using sophisticated mathematical techniques to yield information that can generate new hypotheses and so guide further experimental investigations. An ensemble clustering method has the ability to perform consensus clustering over the same set of genes from different microarray datasets by combining results from different clustering methods into a single consensus result. Results In this paper we have performed comprehensive analysis of forty yeast microarray datasets. One recently described Bi-CoPaM method can analyse expressions of the same set of genes from various microarray datasets while using different cl…

A variant of Smurf2 protects mice against colitis-associated colon cancer by inducing transforming growth factor β signaling.

2011

Background & Aims Transforming growth factor (TGF)-β signaling, which is down-regulated by the E3 ubiquitin ligase Smad ubiquitin regulating factor 2 (Smurf2), promotes development of cancer. We identified a splice variant of Smurf2 (ΔE2Smurf2) and investigated its role in colon carcinogenesis in mice. Methods Colitis-associated colon cancer was induced in mice by administration of azoxymethane, followed by 3 cycles of oral administration of dextran sodium sulfate. Messenger RNA levels of Smurf2 in colon tumors and control tissue were measured by quantitative polymerase chain reaction; lymphocyte and cytokine levels were measured in tumor and tissue samples. Results Tumor-infiltrating CD4 +…

Prototype proposal for profiling and identification of tv viewers using watching patterns

2020

Algorithms, Artificial Intelligence and Automated Decisions about Workers and the Risks of Discrimination: The Necessary Collective Governance of Dat…

2018

Big data, algorithms and artificial intelligence currently allow entrepreneurs to process information about their employees in a far more efficient manner and at a much lower cost than has been the case until now. This makes it possible to profile workers automatically and even allows technology itself to replace human resources supervisors and managers and to make decisions that have legal effects on the employees (recruitment, promotion, dismissals, etc.). This entails great risks of discrimination by the technology in command, as well as the defencelessness of the worker, who is unaware of the reasons underlying such a decision. This study analyses the guarantees established in the exist…

A population genetic study of the endangered plant speciesLimonium dufourii(Plumbaginaceae) based on amplified fragment length polymorphism (AFLP)

1999

Limonium dufourii (Plumbaginaceae) is a triploid species with obligate apomictic reproduction and is endemic to the East Mediterranean coast of Spain, where it is present in only six populations, most of which have a very low number of individuals. Genetic variation and population structure in this species was studied using amplified fragment length polymorphisms (AFLPs) as markers, using the same individuals as in a previous study with random amplified polymorphic DNA (RAPD). Three different primers provided 252 bands of which 51 were polymorphic among the 152 individuals analysed. Those polymorphic bands were able to define 65 different phenotypes, of which all but two were present in onl…