Search

Background. Because of its high metastatic potential, inflammatory breast cancer (IBC) is the most lethal and aggressive form of breast cancer. We previously demonstrated that Myristoylated Alanine-Rich C Kinase Substrate (MARCKS) protein overexpression was associated with shorter metastasis-free survival (MFS) in IBC patients, but not in non-IBC (nIBC) patients. However, the mechanism of action of MARCKS and its particular association to poorer outcome in IBC compared to nIBC are poorly understood. Methods. We evaluated in vitro the inhibitory effect of MPS (MARCKS phosphorylation site domain), a peptide targeting MARCKS phosphorylation site domain (PSD) in single and in combination with paclitaxel treatment, on cell proliferation and cell motility in two cell lines of different phenotype (SUM149 for IBC and MDA-MB-231 for nIBC), as well as its distinct molecular mechanisms of action. We also assessed the clinical relevance of the protein expression of MARCKS and phosphatase and tensin homolog (PTEN) in a large series of IBC vs. nIBC patients. Results. In vitro, the treatment with MPS peptide impaired cell proliferation, migration, and invasion in SUM149 compared to MDA-MB-231 cells. More important, MARCKS inhibition increased paclitaxel sensitivity when using combination therapy in SUM149 cells compared to MDA-MB-231 cells. Interestingly, we could partially explain this specific inhibitory effect in IBC cells using western blot: MARCKS inhibition in single and in combination induced up and downregulation of the PTEN/AKT signaling pathway respectively in IBC compared to nIBC cells. Importantly, a negative correlation of MARCKS and PTEN was only found in the clinical IBC samples (180 patients) compared to nIBC samples (355 patients). More importantly, the group of patients with negative MARCKS and positive PTEN protein expression was associated to better 5-year MFS only in IBC patients. Conclusion. These results indicate two major findings: first, the important prognostic value of the negative correlation of MARCKS and PTEN expression in IBC patients, and second the specific role of MARCKS in regulating different downstream pathways and increasing the paclitaxel response in combination treatment in IBC compared to non-IBC. They suggest a potential IBC-specific targetable biomarker, the inhibition of which might impair disease aggressiveness and perhaps enhance patients’ survival. Citation Format: Maroua Manai, Ines Bini, Pascal Finetti, Haifa Bichiou, Carolina Reduzzi, Naziha Ben Hamida, Marc Lopez, Khaled Rahal, Karima Mrad, Mohamed Manai, Massimo Cristofanilli, Hamouda Boussen, Raoudha Doghri, Maher Kharrat, François Bertucci. Targeting MARCKS in inflammatory breast cancer increased paclitaxel sensitivity [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-10-15.

This paper focuses on the Fault-Tolerant Tracking Control (FTTC) design for a PV pumping system using an Induction Motor (IM) drive. This control strategy offsets the effect of the sensor faults an...

Helitrons, eukaryotic transposable elements (TEs) transposed by rolling-circle mechanism, have been found in various species with highly variable copy numbers and sometimes with a large portion of their genomes. The impact of helitrons sequences in the genome is to frequently capture host genes during their transposition. Since their discovery, 18 years ago, by computational analysis of whole genome sequences of Arabidopsis thaliana plant and Caenorhabditis elegans (C. elegans) nematode, the identification and classification of these mobile genetic elements remain a challenge due to the fact that the wide majority of their families are non-autonomous. In C. elegans genome, DNA helitrons sequences possess great variability in terms of length that varies between 11 and 8965 base pairs (bps) from one sequence to another. In this work, we develop a new method to predict helitrons DNA-sequences, which is particularly based on Frequency Chaos Game Representation (FCGR) DNA-images. Thus, we introduce an automatic system in order to classify helitrons families in C. elegans genome, based on a combination between machine learning approaches and features extracted from DNA-sequences. Consequently, the new set of helitrons features (the FCGR images and K-mers) are extracted from DNA sequences. These helitrons features consist of the frequency apparition number of K nucleotides pairs (Tandem Repeat) in the DNA sequences. Indeed, three different classifiers are used for the classification of all existing helitrons families. The results have shown potential global score equal to 72.7% due to FCGR images which constitute helitrons features and the pre-trained neural network as a classifier. The two other classifiers demonstrate that their efficiency reaches 68.7% for Support Vector Machine (SVM) and 91.45% for Random Forest (RF) algorithms using the K-mers features corresponding to the genomic sequences.

Coronaviruses are a type of frequent RNA virus. They are responsible for digestive and respiratory infections in animal and human genomes. A coronavirus renamed COVID-19 appeared and spread in the world which makes it declared in March 2020 a pandemic by the World Health Organization. SARS-CoV-2 genome, responsible for COVID-19 virus, has a size equal to 29,903 nucleotides, and its genetic makeup is composed of 11 functional open reading frames (ORFs). This paper proposes comparison algorithms to find SARS-Cov2 origin using digital genomic signatures. As a result, the five closest genomes related to SARS-CoV-2 are RaTG13, Pangolin-cov-PCoV_GX-P2V, Pangolin CoV MP789, bat-SL-CoVZC45 and bat-SL-CoVZXC21.

Background Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in the protection against COVID-19. Sequences of the main antigenic proteins in the investigated vaccines and SARS-CoV-2 proteins were compared to identify similar patterns. The immunogenic effect of identified segments was, then, assessed using a combination of structural and antigenicity prediction tools. Results A total of 14 highly similar segments were identified in the investigated vaccines. Structural and antigenicity prediction analysis showed that, among the identified patterns, three segments in Hepatitis B, Tetanus, and Measles proteins presented antigenic properties that can induce putative protective effect against COVID-19. Conclusions Our results suggest a possible protective effect of HBV, Tetanus and Measles vaccines against COVID-19, which may explain the variation of the disease severity among regions.

DNA hypomethylation of long interspersed repetitive DNA retrotransposon (LINE-1) and Alu repeats elements of short interspersed elements family (SINEs) is an early event in carcinogenesis that causes transcriptional activation and leads to chromosomal instability. In the current study, DNA methylation levels of LINE-1 and Alu repeats were analyzed in tumoral tissues of invasive breast cancer in a Tunisian cohort and its association with the clinicopathological features of patients was defined. DNA methylation of LINE-1 and Alu repeats were analyzed using pyrosequencing in 61 invasive breast cancers. Median values observed for DNA methylation of LINE-1 and Alu repeats were considered as the cut-off (59.81 and 18.49%, respectively). The results of the current study demonstrated a positive correlation between DNA methylation levels of LINE-1 and Alu repeats (rho=0.284; P

Nephropathic cystinosis is an autosomal recessive disease caused by a mutation in the CTNS gene which encodes cystinosin, a lysosomal cystine transporter. The spectrum of mutations in the CTNS gene is not well defined in the North African population. Here, we investigated twelve patients with nephropathic cystinosis belonging to eight Tunisian families in order to analyze the clinical and genetic characteristics of Tunisian children with infantile nephropathic cystinosis.Clinical data were collected retrospectively. Molecular analysis of the CTNS gene was performed by Sanger sequencing.We describe a new splicing mutation c.971-1G C in the homozygous state in 6/12 patients which seems to be a founder mutation. The reported deletion of 23nt c.771_793 Del (p.Gly258Serfs*30) was detected in a homozygous state in one patient and in a heterozygous compound state with the c.971-1G C mutation in 3/12 patients. Two of 12 patients have a deletion of exons 4 and 5 of the CTNS gene. None of our patients had the most common 57-kb deletion.The mutational spectrum in the Tunisian population is different from previously described populations. Thus, a molecular diagnostic strategy must be implemented in Tunisia, by targeting as a priority the common mutations described in this country. Such a strategy will allow a cost-effective diagnosis confirmation as well as early administration of treatment with oral cysteamine. A higher resolution version of the Graphical abstract is available as Supplementary information.

Since the beginning of the Coronavirus disease-2019 pandemic, there has been a growing interest in exploring SARS-CoV-2 genetic variation to understand the origin and spread of the pandemic, improve diagnostic methods and develop the appropriate vaccines. The objective of this study was to identify the SARS-CoV-2s lineages circulating in Tunisia and to explore their amino acid signature in order to follow their genome dynamics. Whole genome sequencing and genetic analyses of fifty-eight SARS-CoV-2 samples collected during one-year between March 2020 and March 2021 from the National Influenza Center were performed using three sampling strategies.. Multiple lineage introductions were noted during the initial phase of the pandemic, including B.4, B.1.1, B.1.428.2, B.1.540 and B.1.1.189. Subsequently, lineages B1.160 (24.2%) and B1.177 (22.4%) were dominant throughout the year. The Alpha variant (B.1.1.7 lineage) was identified in February 2021 and firstly observed in the center of our country. In addition, A clear diversity of lineages was observed in the North of the country. A total of 335 mutations including 10 deletions were found. The SARS-CoV-2 proteins ORF1ab, Spike, ORF3a, and Nucleocapsid were observed as mutation hotspots with a mutation frequency exceeding 20%. The 2 most frequent mutations, D614G in S protein and P314L in Nsp12 appeared simultaneously and are often associated with increased viral infectivity. Interestingly, deletions in coding regions causing consequent deletions of amino acids and frame shifts were identified in NSP3, NSP6, S, E, ORF7a, ORF8 and N proteins. These findings contribute to define the COVID-19 outbreak in Tunisia. Despite the country's limited resources, surveillance of SARS-CoV-2 genomic variation should be continued to control the occurrence of new variants.

Warburg Micro syndrome (WARBM) is a rare autosomal recessive genetic disease characterized by ocular, neurologic, and endocrine anomalies. WARBM is a phenotypically and genetically heterogeneous syndrome caused by mutations inWe applied whole-exome sequencing (WES) to two affected young males presenting a WARBM-compatible phenotype.We reveal a new variation inWES analysis of a consanguineous Tunisian family with WARBM revealed a novel variation in

In this paper, we deal with a Fault Tolerant Control (FTC) design for an Induction Motor (IM). In spite of the sensor fault and rotor speed variation, this control strategy is able to compensate the fault effect while ensuring the tracking of the desired trajectory, delivered by a Takagi Sugeno (TS) fuzzy reference model. The physical model of the IM is expressed first by a TS fuzzy model and then a TS descriptor observer is developed so that the estimation of the system states and the sensor fault is reached simultaneously. The developed control strategy depends on the Lyapunov theory and H∞ approach, to minimize the disturbances effect. Based on Linear Matrix Inequality (LMI), the controller and the descriptor observer gains are calculated in one phase. At last, simulations have been carried out to show the tracking performance of the designed control strategy.

Background: Coronavirus Disease 19 (COVID-19) is a viral pandemic disease that induces severe pneumonia in human. Until now, no effective therapeutic interventions or specific vaccines have been developed. In this paper, we attempt to investigate the putative implication of 12 vaccines, including BCG, OPV and MMR in the protection against COVID-19. First, we compared sequences of the main antigenic proteins in the investigated vaccines and SARS-CoV-2 proteins. Then, we investigated identified segments using a combination of structural and antigenicity prediction tools to predict their immunogenic effect.Results: A total of 14 highly similar segments were identified in investigated vaccines. After mapping on S and N proteins and analysis of the antigenicity prediction, three segments, in Hepatitis B, Tetanus and Measles proteins showed structural and antigenic properties that can induce possible putative protective effect.Conclusions: HBV, Tetanus and Measles vaccines should constitute a good candidate for a clinical trial to evaluate their real protective effect against COVID-19.

Androgens are critical for male sex differentiation. Their actions are mediated by the androgen receptor (AR). Mutations disrupting AR function result in the androgen insensitivity syndrome (AIS). In this study, we identified in a patient with complete AIS, a novel AR mutation p.R856L. To investigate the functional properties of p.R856L, we performed functional studies. In comparison, we have characterized two already described mutations: p.R856H and p.R856C. We used a model composed of two different promoters fused to a reporter gene, two cell lines, and showed that all mutations were able to transactivate the (ARE)2-TATA promoter expressed in CHO cells more highly. Moreover, we confirmed the pathogenicity of the p.R856L and p.R856C mutations, and their associations with complete AIS. In contrast, the p.R856H mutation, which is associated with a spectrum of AIS phenotypes, showed less severe transcriptional constraints. Altogether, our studies allowed us to better characterize arginine residue at p.R856 position.

Coronaviruses are responsible on respiratory diseases in animal and human. The combination of numerical encoding techniques and digital signal processing methods are becoming increasingly important in handling large genomic data. In this paper, we propose to analyze the SARS-CoV-2 genomic signature using the combination of different nucleotide representations and signal processing tools in the aim to identify its genetic origin. The sequence of SARS-CoV-2 was compared with 21 relevant sequences including bat, yak and pangolin coronavirus sequences. In addition, we developed a new algorithm to locate the nucleotide modifications. The results show that the Bat and Pangolin coronaviruses were the most related to SARS-CoV-2 with 96% and 86% of identity all along the genome. Within the S gene sequence, the Pangolin sequence presents local highest nucleotide identity. Those findings suggest genesis of SARS-Cov-2 through evolution from bat and pangolin strains. This study offers new ways to automatically characterize viruses., Highlights • We propose to analyze the SARS-CoV-2 genomic signature using the combination of different nucleotide representations in the aim to identify its genetic origin. • The sequence of SARS-CoV-2 was compared with 21 relevant sequences including bat, yak and pangolin coronavirus sequences. • the Bat and Pangolin coronaviruses were the most related to SARS-CoV-2 • Within the S gene sequence, the Pangolin sequence presents local highest nucleotide identity. • This study suggests genesis of SARS-Cov-2 through evolution from bat and pangolin strains.

Journal of Cybersecurity and Information Management (JCIM) Vol. 3, No. 1, PP. 5-13, 2020 &nbsp

In humans, mutations of Desert Hedgehog gene (DHH) have been described in patients with 46,XY gonadal dysgenesis (GD), associated or not with polyneuropathy. In this study, we describe two patients diagnosed with GD, both harboring novel DHH compound heterozygous mutations p.[Tyr176*];[Asn337Lysfs*24] and p.[Tyr176*];[Glu212Lys]. To investigate the functional consequences of p.(Asn337Lysfs*24) and p.(Glu212Lys) mutations, located within the C-terminal part of DHh on auto-processing, we performed in vitro cleavage assays of these proteins in comparison with Drosophila melanogaster Hedgehog (Hh). We found that p.(Glu212Lys) mutation retained 50% of its activity and led to a partially abolished DHh auto-processing. In contrast, p.(Asn337Lysfs*24) mutation resulted in a complete absence of auto-proteolysis. Furthermore, we found a different auto-processing profile between Drosophila Hh and human DHh, which suggests differences in the processing mechanism between the two species. Review of the literature shows that proven polyneuropathy and GD is associated with complete disruption of DHh-N, whereas disruption of the DHh auto-processing is only described with GD. We propose a model that may explain the differences between Schwann and Leydig cell development by autocrine versus paracrine DHh signaling. To our knowledge, this is the first study investigating the effect of DHH mutations on DHh in vitro auto-processing.

Graphical abstract, Highlights • We converted X and Y chromosomes genomic sequences to numerical representation: DNA images. • We developed a new algorithm in the goal to localize the repetitive patterns in the DNA images corresponding to the repetitive sequences. • Based on Convolutional neural network (CNN), we developed a classification system to predict the repetitive DNA classes. • Furthermore, to the best of our knowledge, our work provides the first deep learning methods applied to DNA images classification task., Repetitive DNA sequences occupy the major proportion of DNA in the human genome and even in the other species’ genomes. The importance of each repetitive DNA type depends on many factors: structural and functional roles, positions, lengths and numbers of these repetitions are clear examples. Conserving such DNA sequences or not in different locations in the chromosome remains a challenge for researchers in biology. Detecting their location despite their great variability and finding novel repetitive sequences remains a challenging task. To side-step this problem, we developed a new method based on signal and image processing tools. In fact, using this method we could find repetitive patterns in DNA images regardless of the repetition length. This new technique seems to be more efficient in detecting new repetitive sequences than bioinformatics tools. In fact, the classical tools present limited performances especially in case of mutations (insertion or deletion). However, modifying one or a few numbers of pixels in the image doesn’t affect the global form of the repetitive pattern. As a consequence, we generated a new repetitive patterns database which contains tandem and dispersed repeated sequences. The highly repetitive sequences, we have identified in X and Y chromosomes, are shown to be located in other human chromosomes or in other genomes. The data we have generated is then taken as input to a Convolutional neural network classifier in order to classify them. The system we have constructed is efficient and gives an average of 94.4% as recognition score.

Two techniques for the control of a grid side converter in a wind energy conversion system. The system is composed of a fixed pitch angle wind turbine followed by a permanent magnet synchronous generator and power electronic converters AC-DC-AC. The main interest is in how to control the inverter in order to ensure the stability of the DC link voltage. Two control methods based on the fuzzy approach are applied and compared. First, a direct Mamdani fuzzy logic controller is presented. Then, a T-S fuzzy controller is elaborated based on a T-S fuzzy model. The Lyapunov theorem and H-infinity performance are exploited for stability analysis. Besides, the feedback controller gains are determined using linear matrix inequality tools. Simulation results are derived in order to prove the robustness of the proposed control algorithms and to compare their performances.

Breast cancer is a genetic disease but the known genes explain a minority of cases. To elucidate the molecular basis of breast cancer in the Tunisian population, we performed exome sequencing on six BRCA1/BRCA2 mutation-negative patients with familial breast cancer and identified a novel frameshift mutation in RCC1, encoding the Regulator of Chromosome Condensation 1. Subsequent genotyping detected the 19-bp deletion in additional 5 out of 153 (3%) breast cancer patients but in none of 400 female controls (p = 0.0015). The deletion was enriched in patients with a positive family history (5%, p = 0.0009) and co-segregated with breast cancer in the initial pedigree. The mutant allele was lost in 4/6 breast tumors from mutation carriers which may be consistent with the hypothesis that RCC1 dysfunction provides a selective disadvantage at the stage of tumor progression. In summary, we propose RCC1 as a likely breast cancer susceptibility gene in the Tunisian population.

Complete gonadal dysgenesis (CGD) is characterized by an incomplete differentiation of the genital organs in a patient with a 46,XY karyotype. It is induced by mutations in the sex-determining region Y (SRY) gene which plays a key role in testis-determining pathways. The aim of this study was to investigate the possible pathogenic nature of a novel SRY mutation (p.Y127H) identified in a 46,XY female patient. To determine the effect of this mutation on SRY function, we studied its impact on DNA interaction by electrophoretic mobility shift assays. Since tyrosine 127 is close to the C-terminal nuclear localization signal of SRY, we conducted HA-SRY protein expression to observe the impact of the mutation on the nuclear import function in transfected cells. Our results showed that the Y127H mutation nearly abolishes the DNA-binding capacity of SRY and strongly impairs the nuclear localization of the mutated protein. Together with a previously described mutation analyzed in parallel in this paper (p.Y127C), our results highlight this tyrosine residue as a crucial structural determinant of the high mobility group box domain. This is the first report to explain the molecular mechanism of the Y127H mutation causing sex reversal and gives new insights for clinical practice to benefit patients with disorders of sex development.

Germline mutations in the BRCA tumor suppressor genes account for a substantial proportion of hereditary breast/ovarian cancer. However, this contribution is lower than expected. This underestimation can partly be explained by the BRCA alterations missed by using Sanger sequencing methods. Thus, large genomic rearrangements (LGRs) in BRCA1 and BRCA2 are responsible for 4-28% of all inherited BRCA mutations. In this study, Multiplex ligation-dependent probe amplification (MLPA) assay was used for detection of large rearrangements of BRCA1 and BRCA2 genes in 36 unrelated high-risk breast/ovarian cancer patients negative for BRCA1/2 point mutations. MLPA assay for all exons of both genes and for 1100delC variant of CHEK2 gene were performed. Positive MLPA results were confirmed by real-time quantitative PCR (qPCR). Two different rearrangements in the BRCA1 gene were identified consisting of exon 5 deletion and exon 20 duplication. MLPA analysis did not reveal any large genomic rearrangements in BRCA2 gene. Overall BRCA1/2 LGRs prevalence among high-risk Tunisian patients was 5.5%. Quantitative real-time PCR confirmed MPLA findings. Our results suggest the usefulness of screening for LGRs in BRCA genes in the Tunisian population. To avoid false-negative results, we suggest that MLPA should be used in genetic testing programs. These results are important for guidance counseling and clinical management of Tunisian high-risk patients.

Hypertrophic cardiomyopathy (HCM) is characterized by thickening of the ventricular muscle without dilation and is often associated with dominant pathogenic variants in cardiac sarcomeric protein genes. Here, we report a family with two infants diagnosed with infantile-onset HCM and mitral valve dysplasia that led to death before one year of age. Using exome sequencing, we discovered that one of the affected children had a homozygous frameshift variant in Myosin light chain 2 (MYL2:NM_000432.3:c.431_432delCT: p.Pro144Argfs*57;MYL2-fs), which alters the last 20 amino acids of the protein and is predicted to impact the most C-terminal of the three EF-hand domains in MYL2. The parents are unaffected heterozygous carriers of the variant and the variant is absent in control cohorts from gnomAD. The absence of the phenotype in carriers and the infantile presentation of severe HCM is in contrast to HCM associated with dominant MYL2 variants. Immunohistochemical analysis of the ventricular muscle of the deceased patient with the MYL2-fs variant showed a marked reduction of MYL2 expression compared to an unaffected control. In vitro overexpression studies further indicate that the MYL2-fs variant is actively degraded. In contrast, an HCM-associated missense variant (MYL2:p.Gly162Arg) and three other MYL2 stop-gain variants (p.E22*, p.K62*, p.E97*) that result in loss of the EF domains are stably expressed but show impaired localization. The degradation of the MYL2-fs can be rescued by inhibiting the cell’s proteasome function supporting a post-translational effect of the variant. In vivo rescue experiments with a Drosophila MYL2-homolog (Mlc2) knockdown model indicate that neither the MYL2-fs nor the MYL2:p.Gly162Arg variant supports normal cardiac function. The tools that we have generated provide a rapid screening platform for functional assessment of variants of unknown significance in MYL2. Our study supports an autosomal recessive model of inheritance for MYL2 loss-of-function variants in infantile HCM and highlights the variant-specific molecular differences found in MYL2-associated cardiomyopathy., Author summary We report a novel frameshift variant in MYL2 that is associated with a severe form of infantile-onset hypertrophic cardiomyopathy. The impact of the variant is only observed in the recessive form of the disease found in the proband and not in the parents who are carriers of the variant. This contrasts with other dominant variants in MYL2 that are associated with cardiomyopathies. We compared the stability of this variant to that of other cardiomyopathy associated MYL2 variants and found molecular differences that correlated with disease pathology. We also show different protein domain requirements for stability and localization of MYL2 in cardiomyocytes. Furthermore, we used a fly model to demonstrate functional deficits due to the variant in the developing heart. Overall, our study shows a molecular mechanism by which loss-of-function variants in MYL2 are recessive while missense variants are dominant. We highlight the use of exome sequencing and functional testing to assist in the diagnosis of rare forms of disease where pathogenicity of the variant is not obvious. The new tools we developed for in vitro functional study and the fly fluorescent reporter analysis will permit rapid analysis of MYL2 variants of unknown significance.

The Androgen insensitivity syndrome (AIS) in its complete form (CAIS) is a disorder in abnormal male development characterized by a complete female phenotype in a 46,XY individual. The most frequent cause of this disorder is a hemizygous mutation in androgen receptor (AR) gene located in X chromosome. The first aim of this study was to confirm the clinical diagnosis in a series of Tunisian patients with a typical phenotype of CAIS by molecular genetic analysis. The second aim was to determine the AR mutational profile in the local population. The entire coding region and the exon-intron junctions of the AR gene were sequenced in a series of ten patients. AR defects were found in nine patients. Despite the small number of cases, two of the nine identified mutations were novel. The first novel mutation was an 8-bp deletion in exon 1 (c.862_869del) resulting in a frameshift (p.A288Qfs*14). The second was a splice site mutation c.1885 + 1G > T (IVS3 + 1G > T). In this study, genetic testing has confirmed the diagnosis of most CAIS patients and has revealed two novel mechanisms responsible for the pathogenesis of AIS, as well as seven other reported mutations.

This paper traits the modeling of a PV pumping system composed of an induction motor (IM) connected to a centrifugal pump and subject to variable solar irradiations. A Maximum Power Point Tracker based on Perturb and Observe (P&O) algorithm is applied for the objective of ameliorating the performance of the pumping system. A Takagi-Sugeno (TS) fuzzy controller, based on a reference tracking TS model, is implemented to the IM. First, A mathematical model in the synchronous d-q frame rotating is developed, that is later converted to a TS model with field-oriented control strategy. After that, basing on the $\mathrm{H}^{\infty}$ performance, a fuzzy state feedback controller is established to insure the reference trajectory tracking, provided by the TS reference model. The fuzzy observer is applied to estimate the rotor flux which is inaccessible. The control law developed is based on the minimization of the disturbances effect on the tracking error according to the $\mathrm{H}^{\infty}$ criterion. The control strategy is based on the Lyapunov theorem to guarantee the trajectory tracking performance. Thus, stability conditions, the controller and observer gains are formulated as linear matrix inequalities (LMI). At last, simulation is done to illustrate the tracking performance of the developed T-S tracking controller.

The significance of many BRCA unclassified variants (UVs) has not been evaluated. Classification of these variations as neutral or pathogenic presents a significant challenge and has important implications for breast and ovarian cancer genetic counseling. Here we report a combined molecular and computational approach to classify BRCA UVs missense variations. By using the LOH (Loss of heterozygosity) analysis at the BRCA1/BRCA2 loci, five bioinformatics approaches namely fathmm, PhD-SNP, SNAP, MutationTaster and Human Splicing Finder and the association with the clinico-pathological characteristics related to BRCA tumors, we were able to classify the R2787H (in BRCA2 gene) variant as pathogenic. Then, to investigate the functional role of the R2787H variation in altering BRCA2 structure, the homology model of this variant was constructed using the Rattus norvegicus BRCA2 (PDB ID: 1IYJ) as a template. The predicted model was then assessed for stereochemical quality and side chain environment. Furthermore, docking and binding free energy simulations were performed to investigate the ssDNA-BRCA2 complex interaction. Binding energy value calculation proves that this substitution affects the complex stability. Moreover, this alteration was not found in one hundred healthy controls. These findings suggest that R2787H variant could have potential functional impact. Our approach might be useful for evaluation of BRCA unclassified variants. However additional functional analyzes may provide appropriate assessment to classify such variants.

Helitrons, eukaryotic transposable elements (TEs), were discovered 18 years ago in various genomes. In the Cænorhabditis elegans (C.elegans) genome, helitron sequences have high variability in terms of size by base pairs (bp) varied from 11 to 8965 bp from one sequence to another. These TEs are not uniformly dispersed sequences, and they have the ability to mobilize within a genome by a rolling-circle mechanism. This ability to move and reproduce in genomes enables these elements to play a major role in genomic evolution. In order to follow the evolution, we predicted helitron families (10 classes) in the C.elegans genome using the combination of the features extracted from signals corresponding to DNA sequences and the Support Vector Machine (SVM) classifier. In our classification system, the features extracted from the signals were shown to be efficient to automatically predict helitronic sequences. As a result, the Gaussian radial kernel over 100-fold cross-validation gave the best accuracy rates, ranging from 68% to 97%, with an overall mean score of 83.7%, and we successfully identified the Helitron Y1A class for a specific value of c and gamma, reaching an accuracy rate of 100%. In addition, other notable helitrons (NDNAX2, NDNAX3 Helitron_Y2) were predicted with interesting accuracy rates. Keywords: Helitrons classification, Signal, FCGS coding technique, Machine learning, SVM

Clopidogrel (clopi) is a prodrug widely prescribed in the management of coronary artery disease and requires the intervention of hepatic cytochrome P450 2C19 (CYP2C19) for its activation. However, there is interindividual variability in response to clopi despite the use of recommended doses. Thus, the studies have highlighted the effect of the CYP2C19 gene polymorphism or Cyp2C19 gene on the response to clopi and particularly Cyp2C19 * 2 which may be associated with an increased risk of major cardiovascular events or MACE.To evaluate the effect of Cyp2C19 * 2 polymorphism on MACE occurrence and hemorrhagic complications in patients treated with clopi.We carried out a descriptive longitudinal study including 71 patients placed under clopi for a minimum duration of one month. Genotyping of the Cyp2C19 allele was performed by conventional polymerase chain reaction (PCR). After a follow-up period of 495 ± 183 days, we performed a statistical analysis to evaluate the association between the Cyp2C19 * 2 polymorphism and the occurrence of MACE or hemorrhagic complications.Among our patients, 51% had an angioplasty, 42% medical treatment and 7% a coronary artery bypass surgery. In our study population, 52% were heterozygous (HTZ), 28% homozygous (HMZ) healthy * 1 / * 1 and 20% HMZ had the loss of function allele * 2 / * 2. The allelic frequency of Cyp2C19 * 2 was 46%. Follow-up mean duration was of 495 ± 183 days. During this period, the prevalence of MACE was 11% and that of hemorrhagic complications was 13%. In our study, we did not observe a significant association between the occurrence of MACE or hemorrhagic complications with the genotype carrying the Cyp2C19 * 2 allele.Among patients treated with clopi, wearing a Cyp2C19 * 2 function loss allele didn't seem to be associated with a significantly higher risk of MACE, nor a significantly lower risk of hemorragic complications. This suggests the necessity of larger studies.

Breast cancer is a genetic disease but the known genes explain a minority of cases. To elucidate the molecular basis of breast cancer in the Tunisian population, we performed exome sequencing on six BRCA1/BRCA2 mutation-negative patients with familial breast cancer and identified a novel frameshift mutation in RCC1, encoding the Regulator of Chromosome Condensation 1. Subsequent genotyping detected the 19-bp deletion in additional 5 out of 153 (3%) breast cancer patients but in none of 400 female controls (p = 0.0015). The deletion was enriched in patients with a positive family history (5%, p = 0.0009) and co-segregated with breast cancer in the initial pedigree. The mutant allele was lost in 4/6 breast tumors from mutation carriers which may be consistent with the hypothesis that RCC1 dysfunction provides a selective disadvantage at the stage of tumor progression. In summary, we propose RCC1 as a likely breast cancer susceptibility gene in the Tunisian population.

An augmented TS fuzzy plant model has been proposed to model the nonlinear plant subject to large parameter uncertainties, sensor faults and actuator faults. Based on this augmented TS fuzzy plant model, three different methods to design the fuzzy FTC have been proposed to tackle this nonlinear system. A design procedure of fuzzy fault tolerant controllers has been developed. The stability and robustness of the fuzzy FTC systems have been investigated based on the results of Chapters 11.2 and 11.3. An application example on stabilizing a WES with sensor faults, actuator faults and parameter uncertainties has been given to illustrate the design procedure and merits of the proposed fuzzy fault tolerant controller.

The identification essentially of hMSH2 and/or hMLH1 alterations has clinical implications for recognition and prognosis of MSI phenotypes cases. In this study, we tried to identify instability by immunohistochemical expression pattern analysis, compared the results with molecular investigation and shown their usefulness as predictive factors for determination of Microsatellite Instability in patients with colorectal carcinomas in routinely.Forty seven colorectal cancers and their adjacent colonic mucosa were selected retrospectively for this study. We first studied the potential value of molecular investigation to identify microsatellite instability in which a NCI panel (or Bethesda panel) of five microsatellite was analyzed (Bat-25, Bat-26, D2S123, D5S346 and D17S250). Secondary, we evaluated the immunohistochemical assessment of hMLH1, hMSH2, hMSH6 and PMS2 proteins in tumor and adjacent normal colorectal mucosa tissues.Fourteen cases were scored as MSI and the remaining MSS. Moreover, we found loss of expression for hMLH1, hMSH2, hMSH6 and PMS2 respectively in 9, 10, 6 and 9 of cases. The MSI patients were less than 45 years old, have right localization and mucinous histological type. We found an association between MSH2, age (P=0.03) and staging (P=0.02). MLH1 is associated only with age (P=0.02) while MSH6 with tumor grade (P=0.01).We found an association between MSI molecular investigation and MMR immunohistochemical expression which may allow one to specifically identify MSI phenotype of patients with colorectal carcinomas. Furthermore, immunohistochemical analysis of MMR protein can be used in routinely for detection of microsatellite instability without occurs to molecular investigation.

This work deals with fault estimation and robust state feedback control design for T-S fuzzy uncertain systems against sensor failures and subject to external disturbance with unmeasurable premise variables. The simultaneous estimation of faulty signal and system states is based on the descriptor approach which introduce the faults in the system having the property of auxiliary state. An observer based control strategy is developed based on the state estimates to stabilize the resulting closed-loop system using the technique of performance. The robust stability conditions are derived in the form of linear matrix inequalities (LMIs). The performances of the proposed control approach are demonstrated through numerical example.

This paper deals with wind energy conversion system (WECS). The system includes essentially wind turbine, permanent magnetic synchronous generator and power converters. All these parts have been modeled. In addition a maximum power point tracking (MPPT) method is presented. We have been used a specific controller to maintain a constant level voltage at the DC bus. An LCL type filter has been used to obtain a perfect sinusoidal signal, after the inverter. Although, we have been present a control of active and reactive power. All the parts of system have been simulated on Matlab-Simulink software and the results are presented at the end of paper.

As the photovoltaic produced power is depending on weather conditions, Maximum Power Point Tracking (MPPT) controller are usually applied to extract the maximum amount of generated power. This work provides a review of MPPT controllers based on fuzzy logic concept. The studied system includes a PV panel, a DC-DC converter and a resistive load. The classical MPPT algorithms fail to track the maximum peak power point (MPP) accurately, so that fuzzy logic is introduced to reduce oscillations around the operating point as it can trace the maximum power for all the cases. Three fuzzy Logic Controllers (FLC) are developed using different types, Mamdani and Takagi-Sugeno (T-S), and different input and output signals. The proposed algorithms are tested under dissimilar atmospheric conditions and compared to a conventional MPPT technique, Perturb and Observe. FLCs provide quick reaction to the weather conditions variation and decreased fluctuations around the MPP.

This paper proposes a grid-connected Photovoltaic energy system through a three-phases DC-AC converter. For this purpose, the characterization of the PV system, integrating the maximum power point strategy (MPPT) based on Fractional Open-Circuit Voltage (FOV) and Fractional Short-Circuit Current (FSC) methods, is developed and treated under the software MATLAB / Simulink. Thereafter, the proposed design of three phases grid-connected inverter system has been simulated.

SummaryConsanguineous unions are a deeply rooted social practice among traditional societies. Despite their presumed social advantages, they can result in several health conditions. The aim of this study was: i) to compare consanguinity levels between Tunisian patients affected with autosomal recessive disorders (ARDs) and those with a chromosomal abnormality; and ii) to gain more insight into the mutational status of patients affected with ARDs. Data were collected from 290 files of patients affected by one of five ARDs confirmed by molecular analysis and 248 files of patients with confirmed Down syndrome. Information on the disease, mutation defining the disease, parents' relatedness and geographical origin was gathered. Consanguinity was found among 58% of the ARD patients and among 22% of Down syndrome patients, and a homozygous status was found in 90% of the patients born to related parents and in 70% of patients born to unrelated parents. Also, children from unrelated parents from the same geographical background were found to be more frequently affected by homozygous mutations than those from unrelated parents from different geographical backgrounds. The present study shows how marriage practices affect patterns of genetic variations and how they can lead to homogenization in the genetic pool.

Objective Estimating the total allele frequency of all pathogenic alleles of an autosomal recessive disease is not possible if only mutational data of a sample of affected individuals are available. However, if the affected individuals come from a population where consanguinity is not uncommon, this total allele frequency can be estimated by additionally using the positive individual inbreeding coefficients or an estimate of the population inbreeding coefficient. In this paper, we propose two estimators. Methods/results We propose to estimate the total allele frequency by a conditional maximum likelihood estimator if a part of the affected individuals in the sample comes from consanguineous marriages with known inbreeding coefficients. A simulation study shows that this estimator is unbiased and robust. We propose a second estimator which is based on an estimate of the population inbreeding coefficient. The method is applied to mutational data and individual inbreeding coefficients of Tunisian patients with congenital adrenal hyperplasia. Conclusion Additionally using individual inbreeding coefficients or an estimate of the population inbreeding coefficient makes it possible to estimate the total allele frequency. Since consanguinity is commonly practiced in many parts of the world, the estimators proposed in the paper are of practical importance.

Introduction: Bacterial meningitis is a medical emergency requiring a fast and reliable diagnosis. Molecular methods such as real-time PCR (rt-PCR) offer an attractive alternative. Thus, this study aims to establish multiplex rt-PCRs detecting N. meningitidis, S. pneumoniae and H. influenzae b from cerebrospinal fluid in Tunisian children beyond neonatal age. Methodology: Using bioinformatic tools and experimentation, we validated the specificity and optimal criteria of PCRs for primers and probes of plyA (S. pneumoniae), ctrA and sodC (N. meningitidis) and bexA genes (H. influenzae b). We performed one multiplex RT-PCR for detection of S. pneumoniae and N. meningitidis targeting plyA and ctrA, sodC genes respectively, simultaneously with a singleplex RT-PCR for H. influenzae b. The sensitivity and specificity of our methods were assessed. Then, we tested our methods for 122 CSF samples collected from suspected meningitis cases between 2014 and 2016 in Bechir Hamza Children’s Hospital of Tunis. Results: Our results have shown the sensitivity of the designed PCRs was up to 10-4 DNA dilution and the specificity was 100%. PCR evaluation has shown 51 positive samples: 38 of pneumococcal cases, 12 meningococcal cases, 1 case of H. influenzae b with 8.57% and 50% of supplementary positive cases rates respectively. Conclusions: Our assay proved to be very sensitive, specific and rapid for bacterial meningitis diagnosis. In the recent context of Hib vaccination, the possibility of detecting S. pneumoniae and N. meningitidis separately constitute an attractive opportunity. Nevertheless, simultaneous detection of Hib remains relevant in specific clinical context and for epidemiologic study.

Complete gonadal dysgenesis (CGD) is characterized by an incomplete differentiation of the genital organs in a patient with a 46,XY karyotype. It is induced by mutations in the sex-determining region Y (SRY) gene which plays a key role in testis-determining pathways. The aim of this study was to investigate the possible pathogenic nature of a novel SRY mutation (p.Y127H) identified in a 46,XY female patient. To determine the effect of this mutation on SRY function, we studied its impact on DNA interaction by electrophoretic mobility shift assays. Since tyrosine 127 is close to the C-terminal nuclear localization signal of SRY, we conducted HA-SRY protein expression to observe the impact of the mutation on the nuclear import function in transfected cells. Our results showed that the Y127H mutation nearly abolishes the DNA-binding capacity of SRY and strongly impairs the nuclear localization of the mutated protein. Together with a previously described mutation analyzed in parallel in this paper (p.Y127C), our results highlight this tyrosine residue as a crucial structural determinant of the high mobility group box domain. This is the first report to explain the molecular mechanism of the Y127H mutation causing sex reversal and gives new insights for clinical practice to benefit patients with disorders of sex development.

The contribution of BRCA1/BRCA2 mutations to hereditary breast cancer in the Tunisian population has not been accurately estimated. The purpose of our study was to estimate the incidence and spectrum of pathogenic mutations in BRCA1/2 genes in early onset and familial breast/ovarian cancer among Tunisian women. To identify predictive factors for BRCA1/2 mutations, we screened the entire coding sequences and intron/exon boundaries of BRCA1/BRCA2 genes in 48 patients by direct sequencing. Twelve pathogenic mutations were detected (25%); three in BRCA1 (c.211dupA in four families, c.5266dupC in three families and c.1504_1508delTTAAA in one family) and two novel mutations in BRCA2 (c.1313dupT in two families and c.7654dupT in two families). We also identified 23 different polymorphisms and unclassified variants. These results indicate that our population has a spectrum of recurrent BRCA mutations.

In this paper, an analysis for ill conditioning problem in subspace identification method is provided. The subspace identification technique presents a satisfactory robustness in the parameter estimation of process model which performs control. As a first step, the main geometric and mathematical tools used in subspace identification are briefly presented. In the second step, the problem of analyzing ill-conditioning matrices in the subspace identification method is considered. To illustrate this situation, a simulation study of an example is introduced to show the ill-conditioning in subspace identification. Algorithms numerical subspace state space system identification (N4SID) and multivariable output error state space model identification (MOESP) are considered to study, the parameters estimation while using the induction motor model, in simulation (Matlab environment). Finally, we show the inadequacy of the oblique projection and validate the effectiveness of the orthogonal projection approach which is needed in ill-conditioning; a real application dealing with induction motor parameters estimation has been experimented. The obtained results proved that the algorithm based on orthogonal projection MOESP, overcomes the situation of ill-conditioning in the Hankel's block, and thereby improving the estimation of parameters.