Equid herpesvirus (EHV) is a contagious viral disease affecting horses, causing illness character... more Equid herpesvirus (EHV) is a contagious viral disease affecting horses, causing illness characterized by respiratory symptoms, abortion and neurological disorders. It is common worldwide and causes severe economic losses to the equine industry. The present study was aimed at investigating the incidence of EHVs, the genetic characterization of Tunisian isolates and a spatiotemporal study, using 298 collected samples from diseased and clinically healthy horses. The global incidence of EHV infection was found to be about 71.81%. EHV2 and EHV5 were detected in 146 (48.99%) and 159 (53.35%) sampled horses, respectively. EHV1 was detected in 11 samples (3.69%); EHV4 was not detected. Co-infections with EHV1-EHV2, EHV1-EHV5 and EHV2-EHV5 were observed in 0.33%, 1.34% and 31.54% of tested horses, respectively. Phylogenetic analyses showed that gB of EHV2 and EHV5 displays high genetic diversity with a nucleotide sequence identity ranging from 88 to 100% for EHV2 and 97.5 to 100% for EHV5. P...
Artificial Neural Network (ANN) algorithms have been widely used to analyse genomic data. Single ... more Artificial Neural Network (ANN) algorithms have been widely used to analyse genomic data. Single Nucleotide Polymorphisms(SNPs) represent the genetic variations, the most common in the human genome, it has been shown that they are involved in many genetic diseases, and can be used to predict their development. Developing ANN to handle this type of data can be considered as a great success in the medical world. However, the high dimensionality of genomic data and the availability of a limited number of samples can make the learning task very complicated. In this work, we propose a New Neural Network classification method based on input perturbation. The idea is first to use SVD to reduce the dimensionality of the input data and to train a classification network, which prediction errors are then reduced by perturbing the SVD projection matrix. The proposed method has been evaluated on data from individuals with different ancestral origins, the experimental results have shown the effectiveness of the proposed method. Achieving up to 96.23% of classification accuracy, this approach surpasses previous Deep learning approaches evaluated on the same dataset.
Background: Despite rising incidence and mortality rates in Africa, cancer has been given low pri... more Background: Despite rising incidence and mortality rates in Africa, cancer has been given low priority in the research field and in healthcare services. Indeed, 57% of all new cancer cases around the world occur in low income countries exacerbated by lack of awareness, lack of preventive strategies, and increased life expectancies. Despite recent efforts devoted to cancer epidemiology, statistics on cancer rates in Africa are often dispersed across different registries. In this study our goal included identifying the most promising prevention and treatment approaches available in Africa. To do this, we collated and analyzed the incidence and fatality rates for the 10 most common and fatal cancers in 56 African countries grouped into 5 different regions (North, West, East, Central and South) over 16-years (2002-2018). We examined temporal and regional trends by investigating the most important risk factors associated to each cancer type. Data were analyzed by cancer type, African region, gender, measures of socioeconomic status and the availability of medical devices.
Leishmaniases are a group of diseases with different clinical manifestations. Macrophage-Leishman... more Leishmaniases are a group of diseases with different clinical manifestations. Macrophage-Leishmania interactions are central to the course of the infection. The outcome of the disease depends not only on the pathogenicity and virulence of the parasite, but also on the activation state, the genetic background, and the underlying complex interaction networks operative in the host macrophages. Mouse models, with mice strains having contrasting behavior in response to parasite infection, have been very helpful in exploring the mechanisms underlying differences in disease progression. We here analyzed previously generated dynamic transcriptome data obtained from Leishmania major (L. major) infected bone marrow derived macrophages (BMdMs) from resistant and susceptible mouse. We first identified differentially expressed genes (DEGs) between the M-CSF differentiated macrophages derived from the two hosts, and found a differential basal transcriptome profile independent of Leishmania infect...
Supplemental material, Supplementary_table_S3_xyz4733678337073 for Genomic Characteristics of Inv... more Supplemental material, Supplementary_table_S3_xyz4733678337073 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Supplemental material, Figure_S3_xyz47336f6d25d57 for Genomic Characteristics of Invasive Strepto... more Supplemental material, Figure_S3_xyz47336f6d25d57 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Supplemental material, Figure_S1_xyz47336f1c18c53 for Genomic Characteristics of Invasive Strepto... more Supplemental material, Figure_S1_xyz47336f1c18c53 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Supplemental material, Supplementary_table_S4_xyz47336c16c8561 for Genomic Characteristics of Inv... more Supplemental material, Supplementary_table_S4_xyz47336c16c8561 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Supplemental material, Supplementary_table_S2_xyz47336b4575fa2 for Genomic Characteristics of Inv... more Supplemental material, Supplementary_table_S2_xyz47336b4575fa2 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Supplemental material, Figure_S2_xyz47336f726fde2 for Genomic Characteristics of Invasive Strepto... more Supplemental material, Figure_S2_xyz47336f726fde2 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Additional file 2: Table S2. The Blastp output results between R.A73 protein sequences and BACTIB... more Additional file 2: Table S2. The Blastp output results between R.A73 protein sequences and BACTIBASE (a database dedicated to bacteriocins) protein sequences.
Additional file 1: Table S1. The DDH probabilities to distinguish between R.A73 strain and refere... more Additional file 1: Table S1. The DDH probabilities to distinguish between R.A73 strain and reference strains that belonged to the similar Enterococcus genus.
Equid herpesvirus (EHV) is a contagious viral disease affecting horses, causing illness character... more Equid herpesvirus (EHV) is a contagious viral disease affecting horses, causing illness characterized by respiratory symptoms, abortion and neurological disorders. It is common worldwide and causes severe economic losses to the equine industry. The present study was aimed at investigating the incidence of EHVs, the genetic characterization of Tunisian isolates and a spatiotemporal study, using 298 collected samples from diseased and clinically healthy horses. The global incidence of EHV infection was found to be about 71.81%. EHV2 and EHV5 were detected in 146 (48.99%) and 159 (53.35%) sampled horses, respectively. EHV1 was detected in 11 samples (3.69%); EHV4 was not detected. Co-infections with EHV1-EHV2, EHV1-EHV5 and EHV2-EHV5 were observed in 0.33%, 1.34% and 31.54% of tested horses, respectively. Phylogenetic analyses showed that gB of EHV2 and EHV5 displays high genetic diversity with a nucleotide sequence identity ranging from 88 to 100% for EHV2 and 97.5 to 100% for EHV5. P...
Artificial Neural Network (ANN) algorithms have been widely used to analyse genomic data. Single ... more Artificial Neural Network (ANN) algorithms have been widely used to analyse genomic data. Single Nucleotide Polymorphisms(SNPs) represent the genetic variations, the most common in the human genome, it has been shown that they are involved in many genetic diseases, and can be used to predict their development. Developing ANN to handle this type of data can be considered as a great success in the medical world. However, the high dimensionality of genomic data and the availability of a limited number of samples can make the learning task very complicated. In this work, we propose a New Neural Network classification method based on input perturbation. The idea is first to use SVD to reduce the dimensionality of the input data and to train a classification network, which prediction errors are then reduced by perturbing the SVD projection matrix. The proposed method has been evaluated on data from individuals with different ancestral origins, the experimental results have shown the effectiveness of the proposed method. Achieving up to 96.23% of classification accuracy, this approach surpasses previous Deep learning approaches evaluated on the same dataset.
Background: Despite rising incidence and mortality rates in Africa, cancer has been given low pri... more Background: Despite rising incidence and mortality rates in Africa, cancer has been given low priority in the research field and in healthcare services. Indeed, 57% of all new cancer cases around the world occur in low income countries exacerbated by lack of awareness, lack of preventive strategies, and increased life expectancies. Despite recent efforts devoted to cancer epidemiology, statistics on cancer rates in Africa are often dispersed across different registries. In this study our goal included identifying the most promising prevention and treatment approaches available in Africa. To do this, we collated and analyzed the incidence and fatality rates for the 10 most common and fatal cancers in 56 African countries grouped into 5 different regions (North, West, East, Central and South) over 16-years (2002-2018). We examined temporal and regional trends by investigating the most important risk factors associated to each cancer type. Data were analyzed by cancer type, African region, gender, measures of socioeconomic status and the availability of medical devices.
Leishmaniases are a group of diseases with different clinical manifestations. Macrophage-Leishman... more Leishmaniases are a group of diseases with different clinical manifestations. Macrophage-Leishmania interactions are central to the course of the infection. The outcome of the disease depends not only on the pathogenicity and virulence of the parasite, but also on the activation state, the genetic background, and the underlying complex interaction networks operative in the host macrophages. Mouse models, with mice strains having contrasting behavior in response to parasite infection, have been very helpful in exploring the mechanisms underlying differences in disease progression. We here analyzed previously generated dynamic transcriptome data obtained from Leishmania major (L. major) infected bone marrow derived macrophages (BMdMs) from resistant and susceptible mouse. We first identified differentially expressed genes (DEGs) between the M-CSF differentiated macrophages derived from the two hosts, and found a differential basal transcriptome profile independent of Leishmania infect...
Supplemental material, Supplementary_table_S3_xyz4733678337073 for Genomic Characteristics of Inv... more Supplemental material, Supplementary_table_S3_xyz4733678337073 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Supplemental material, Figure_S3_xyz47336f6d25d57 for Genomic Characteristics of Invasive Strepto... more Supplemental material, Figure_S3_xyz47336f6d25d57 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Supplemental material, Figure_S1_xyz47336f1c18c53 for Genomic Characteristics of Invasive Strepto... more Supplemental material, Figure_S1_xyz47336f1c18c53 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Supplemental material, Supplementary_table_S4_xyz47336c16c8561 for Genomic Characteristics of Inv... more Supplemental material, Supplementary_table_S4_xyz47336c16c8561 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Supplemental material, Supplementary_table_S2_xyz47336b4575fa2 for Genomic Characteristics of Inv... more Supplemental material, Supplementary_table_S2_xyz47336b4575fa2 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Supplemental material, Figure_S2_xyz47336f726fde2 for Genomic Characteristics of Invasive Strepto... more Supplemental material, Figure_S2_xyz47336f726fde2 for Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13 by Mariem Hanachi, Anmol Kiran, Jennifer Cornick, Emna Harigua-Souiai, Dean Everett, Alia Benkahla and Oussama Souiai in Bioinformatics and Biology Insights
Additional file 2: Table S2. The Blastp output results between R.A73 protein sequences and BACTIB... more Additional file 2: Table S2. The Blastp output results between R.A73 protein sequences and BACTIBASE (a database dedicated to bacteriocins) protein sequences.
Additional file 1: Table S1. The DDH probabilities to distinguish between R.A73 strain and refere... more Additional file 1: Table S1. The DDH probabilities to distinguish between R.A73 strain and reference strains that belonged to the similar Enterococcus genus.
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