gael even - Academia.edu (original) (raw)

Papers by gael even

2022 IEEE International Conference on Image Processing (ICIP), Oct 16, 2022

In this article, we propose a new approach for the cow heat detection from endoscopic images. Our... more In this article, we propose a new approach for the cow heat detection from endoscopic images. Our approach permits to identify on the fly the cow heat state through two successive stages, namely cervix detection then heat classification. For this purpose, images are analyzed by a Transformer based detection model to localize the cervix, in which case they are analyzed by a CNN-based heat classification model. The proposed approach permits to assist the farmer during the insemination operation by localizing the cervix in an accurate way. Moreover, the confidence level of the final decision of the classification model is increased by focusing its analysis only on cervix images. The effectiveness of our method is demonstrated on our generated dataset and the obtained performance outperform the state of the art.

Microorganisms

Blastocystis sp. is a single-celled parasite estimated to colonize the digestive tract of 1 to 2 ... more Blastocystis sp. is a single-celled parasite estimated to colonize the digestive tract of 1 to 2 billion people worldwide. Although it represents the most frequent intestinal protozoa in human stools, it remains still under-investigated in countries with a high risk of infection due to poor sanitary and hygiene conditions, such as in Africa. Therefore, the present study was carried out to determine the prevalence and subtype (ST) distribution of Blastocystis sp. in the Guinean population. For this purpose, fecal samples were collected from 500 individuals presenting or not digestive disorders in two hospitals of Conakry. Search for the parasite in stools was performed by real-time PCR targeting the small subunit rDNA gene followed by sequencing of the PCR products for subtyping of the isolates. A total of 390 participants (78.0%) was positive for Blastocystis sp. Five STs were identified in the Guinean cohort (ST1, ST2, ST3, ST4 and ST14) with varying frequency, ST3 being predominan...

International Journal of Molecular Sciences

The basis of any animal experimentation begins with the housing of animals that should take into ... more The basis of any animal experimentation begins with the housing of animals that should take into account the need for splitting animals into similar groups. Even if it is generally recommended to use the minimum number of animals necessary to obtain reliable and statistically significant results (3Rs rule), the allocation of animals is currently mostly based on randomness. Since variability in gut microbiota is an important confounding factor in animal experiments, the main objective of this study was to develop a new approach based on 16S rRNA gene sequencing analysis of the gut microbiota of animals participating in an experiment, in order to correctly assign the animals across batches. For this purpose, a pilot study was performed on 20 mouse faecal samples with the aim of establishing two groups of 10 mice as similar as possible in terms of their faecal microbiota fingerprinting assuming that this approach limits future analytical bias and ensures reproducibility. The suggested ...

Frequency of Cryptosporidium infection in biopsies from patients with... more Frequency of Cryptosporidium infection in biopsies from patients with colonic intraepithelial neoplasia/adenocarcinoma compared to control groups.</p

Each box represents half of the data between upper and lower quartile, the black line be... more Each box represents half of the data between upper and lower quartile, the black line being the median.</p

(A) Cryptosporidium developmental stages were observed in the apical ... more (A) Cryptosporidium developmental stages were observed in the apical position (arrows) within the epithelial cells of the intestinal glands (hematoxylin and eosin). (B) A Cryptosporidium oocyst is shown (arrow) in the lumen of an intestinal gland after immunofluorescence (fluorescein isothiocyanate (FITC)-conjugated anti-Cryptosporidium spp. MAbs.) (C) Four sporozoites in the oocyst were observed (arrow) (staining with 4,6-diamidino 2-phenylindole dihydrochloride (DAPI)).</p

Multivariate binary logistic regression analysis of the association between Cry... more Multivariate binary logistic regression analysis of the association between Cryptosporidium infection and colonic neoplasia/cancer development, age, sex or affected organ.</p

Compressed file that contains the four home-made scripts used in the home-made bioinformatics pip... more Compressed file that contains the four home-made scripts used in the home-made bioinformatics pipeline: fasta_dealigner.py: Python script used in the first step of the home-made bioinformatics pipeline, that generates an unaligned FASTA file. rarefaction.R: R script (v2.14.1) used in the second step of the home-made bioinformatics pipeline, that generates intra-sample rarefaction curves. OTU_tables_format.pl: Perl script that generates OTU count tables at the end of the second step of the home-made bioinformatics pipeline. OTU_tables_merge.py: Python script that merges OTU count tables from all samples produced at the end of the second step of the home-made bioinformatics pipeline in order to produce a global OTU Table tsv file.

The normalized_global BIOM file was obtained at the end of the third analytical step of the home-... more The normalized_global BIOM file was obtained at the end of the third analytical step of the home-made bioinformatics pipeline, after using DESeq2 normalization and conversion into a full annotated and normalized global BIOM file.

The raw_global BIOM file was obtained in the third analytical step of the home-made bioinformatic... more The raw_global BIOM file was obtained in the third analytical step of the home-made bioinformatics pipeline. All the annotated OTU tables were merged into a global OTU table based on each OTU's taxonomic annotation, in which each column of this table represents a sample, and each line represents a taxon (identified by its OTU identifier in the first column, and the taxonomic annotation in the last column). Finally, this annotated OTU table was converted into a global BIOM file to obtain the raw_global BIOM file.

This compressed file contains the OTU_count_tables tsv file that is the output of the second anal... more This compressed file contains the OTU_count_tables tsv file that is the output of the second analytical step (clustering analysis and OTU classification) of the home-made bioinformatics pipeline. It contains, for each sample, four columns: the first column is the consensus read name associated to the OTU, the second column is the OTU raw counts, the third column is the consensus read name (same as first column) and the fourth column is the associated taxon.

Copyright information:Taken from "The Genopolis Microarray Database"... more Copyright information:Taken from "The Genopolis Microarray Database"http://www.biomedcentral.com/1471-2105/8/S1/S21BMC Bioinformatics 2007;8(Suppl 1):S21-S21.Published online 8 Mar 2007PMCID:PMC1885851.tabase. We represent data by means of a business objects layer. The representation is consistent with the MIAME recommendations and is similar to MAGE-OM. Respect to this two main simplifications have been introduced. First, we ignore chips manufacturing, since we make use of only one standard platform already described by Affymetrix. Second, we model the experiment design as a tree structure. Although this is not general (for instance, the same stimulus could be applied to two samples) it is a good compromise between flexibility and easy of use. We use controlled vocabulary and protocol classes to manage non free text fields.

Applied Intelligence, 2021

International audienceIn cattle farming, the artificial insemination technique is a biotechnology... more International audienceIn cattle farming, the artificial insemination technique is a biotechnology that brings to farmers a wide range of benefits namely health security, genetic gain and economic costs. The main condition for the success of artificial insemination within cattle is the heat (or estrus) detection. In this context, several cow heat detection systems have been recently proposed in the literature to assist the farmer in this task. Nevertheless, they are mainly based on the analysis of the physical behavior of the cow which may be affected by several factors related to its health and its environment. In this paper, we present a new vision system for cow heat detection which is based on the analysis of the genital tract of the cow. The main core of our system is a CNN model that has been designed and tailored for analyzing endoscopic images collected using an innovative insemination technology named Eye breed. The conducted experiments on two datasets namely our own dataset and a public dataset show the high accuracy of our CNN model (more than 97% for both datasets) outperforming 19 methods from the state of the art. Moreover, we propose an optimized version of our model for an Android deployment by exploiting several techniques namely quantization, GPU acceleration and video downsampling. The conducted tests on a smart-phone shows that our heat detection system has a response time of a few seconds

Genome biology, Jan 19, 2017

The increase in available sequence data has advanced the field of microbiology; however, making s... more The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples. MICRA is fast, producing few false-positive annotations and variant calls compared to current methods, making it a tool of great interest for fully exploiting sequencing data.

Scientific Data, 2017

In the past decade, metagenomics studies have become widespread due to the arrival of second-gene... more In the past decade, metagenomics studies have become widespread due to the arrival of second-generation sequencing platforms characterized by low costs, high throughput and short read lengths. Today, although benchtop sequencers are considered to be accurate platforms to deliver data for targeted metagenomics studies, the limiting factor has become the analysis of these data. In a previous paper, we performed an Ion Torrent PGM 16S rDNA gene sequencing of faecal DNAs from 48 Blastocystis-colonized patients and 48 Blastocystis-negative subjects, in order to decipher the impact of this widespread protist on gut microbiota composition and diversity. We report here on the Ion Torrent targeted metagenomic sequencing and analysis of these 96 human faecal samples, and the complete datasets from raw to analysed data. We also provide the key steps of the bioinformatic analyses, from library preparation to data filtering and OTUs tables generation. This data represents a valuable resource for...

Genetics and molecular biology, Jan 22, 2017

Genotypic and phenotypic data of 1,562 animals were analyzed to find genomic regions that potenti... more Genotypic and phenotypic data of 1,562 animals were analyzed to find genomic regions that potentially influence the birth weight (BW), weaning weight at seven months of age (WW) and yearling weight (YW) of Colombian Brahman cattle, with genotyping conducted using Illumina Bead chip array with 74,669 SNPs. A Single Step Genomic BLUP (ssGBLP), approach was used to estimate the proportion of variance explained by each marker. Multiple regions scattered across the genome were found to influence weights at different ages, also dependent on the trait component (direct or maternal). The most interesting regions were connected to previously identified QTLs and genes, such as ADAMTSL3, CAPN2, CAPN2, FABP6, ZEB2 influencing growth and weight traits. The identified regions will contribute to the development and refinement of genomic selection programs for Zebu Brahman cattle in Colombia.

Journal of Animal Science, 2016