Search results for "Array"
showing 10 items of 1264 documents
Detection of precancerous gastric lesions and gastric cancer through exhaled breath.
2015
Timely detection of gastric cancer (GC) and the related precancerous lesions could provide a tool for decreasing both cancer mortality and incidence.968 breath samples were collected from 484 patients (including 99 with GC) for two different analyses. The first sample was analysed by gas chromatography linked to mass spectrometry (GCMS) while applying t test with multiple corrections (p value0.017); the second by cross-reactive nanoarrays combined with pattern recognition. For the latter, 70% of the samples were randomly selected and used in the training set while the remaining 30% constituted the validation set. The operative link on gastric intestinal metaplasia (OLGIM) assessment staging…
Efficient FPGA Implementation of an Adaptive Noise Canceller
2006
A hardware implementation of an adaptive noise canceller (ANC) is presented. It has been synthesized within an FPGA, using a modified version of the least mean square (LMS) error algorithm. The results obtained so far show a significant decrease of the required gate count when compared with a standard LMS implementation, while increasing the ANC bandwidth and signal to noise (S/N) ratio. This novel adaptive noise canceller is then useful for enhancing the S/N ratio of data collected from sensors (or sensor arrays) working in noisy environment, or dealing with potentially weak signals.
CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification
2020
Abstract Background Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, including DNA sequence organization. Interestingly, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using DNA sequence as input data. Results In this work, we propose CORENup, a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel …
Transcriptome Analysis of PA Gain and Loss of Function Mutants
2017
Functional genomics has become a forefront methodology for plant science thanks to the widespread development of microarray technology. While technical difficulties associated with the process of obtaining raw expression data have been diminishing, allowing the appearance of tremendous amounts of transcriptome data in different databases, a common problem using "omic" technologies remains: the interpretation of these data and the inference of its biological meaning. In order to assist to this complex task, a wide variety of software tools have been developed. In this chapter we describe our current workflow of the application of some of these analyses. We have used it to compare the transcr…
Engineering a 2D protein-DNA crystal.
2005
(Figure Presented) Weaving with DNA: A DNA-binding protein was used to control the structure of a self-assembled 2D crystal. In the absence of protein, four oligonucleotides hybridize to form a Kagome lattice of interwoven double helices with p3 symmetry (see image). Addition of protein RuvA during assembly changes the symmetry and connectivity to give a DNA-protein crystal with an approximately square unit cell. © 2005 Wiley-VCH Verlag GmbH and Co. KGaA.
Variable phenotype in 17q12 microdeletions: Clinical and molecular characterization of a new case
2014
Microdeletions of 17q12 including the hepatocyte nuclear factor 1 beta (HNF1B) gene, as well as point mutations of this gene, are associated with the Renal Cysts and Diabetes syndrome (RCAD, OMIM 137920) and genitourinary alterations. Also, microdeletions encompassing HNF1B were identified as a cause of Mayer-Rokitansky-Kuster-Hauser Syndrome (MRKH, OMIM 277000) in females and, recently, were associated with intellectual disability, autistic features, cerebral anomaly and facial dysmorphisms. In this report, we describe a boy with a deletion in 17q12 region detected by SNP array, encompassing the HNF1B gene, that showed dysmorphic features, intellectual disability (ID), serious speech delay…
Microarray-Based Gene Expression Analysis of Hepatocellular Carcinoma
2009
Microarray studies have successfully shed light on various aspects of the molecular mechanisms behind the development of hepatocellular carcinoma (HCC), such as the identification of novel molecular subgroups and the genetic profiles associated with metastasis and venous invasion. These experiments, mainly comprising genome wide profiling, potentially represent the basis of novel targeted therapeutic strategies in HCC. In response, we summarize the multiple reported expression profiles in HCC associated with HCC development, novel subgroups, venous invasion and metastasis.
In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.
2007
Abstract Background The recent advances in human genetics have recently provided new insights into phenotypic variation and genome variability. Current forensic DNA techniques involve the search for genetic similarities and differences between biological samples. Consequently the selection of ideal genomic biomarkers for human identification is crucial in order to ensure the highest stability and reproducibility of results. Results In the present study, we selected and validated 24 SNPs which are useful in human identification in 1,040 unrelated samples originating from three different populations (Italian, Benin Gulf and Mongolian). A Rigorous in silico selection of these markers provided …
Lipid and apoprotein composition of HDL in partial or complete CETP deficiency
2012
Hyperalphalipoproteinemia, as observed in patients who are either homozygous or heterozygous for cholesteryl ester transfer protein (CETP) deficiency, has been shown to be associated with striking changes in apolipoprotein size distribution, namely, of high-density lipoprotein (HDL) and HDL-like particles. We compared the effect of varying degrees of CETP activity on the HDL apolipoprotein profile in Caucasian CETP-deficient subjects and following pharmacological decrease in CETP activity, using Size Exclusion Chromatography followed by Reverse Phase Protein Array (SEC RPA). The main HDL-associated apolipoproteins (Apo), i.e. ApoA-I, ApoA-II, ApoC-I, and ApoC-III, co-eluted with the HDL pea…
A simple timestamping data acquisition system for ToF-ERDA
2015
A new data acquisition system, ToF-DAQ, has been developed for a ToF-ERDA telescope and other ToF-E and ToF-ToF measurement systems. ToF-DAQ combines an analogue electronics front-end to asynchronous time stamped data acquisition by means of a FPGA device. Coincidences are sought solely in software based on the timestamps. Timestamping offers more options for data analysis as coincidence events can be built also in offline analysis. The system utilises a National Instruments R-series FPGA device and a Windows PC as a host computer. Both the FPGA code and the host software were developed using the National Instruments LabVIEW graphical programming environment. Up to eight NIM ADCs can be han…