Background: Septic shock patients exhibit an increased incidence of viral reactivation. Precise t... more Background: Septic shock patients exhibit an increased incidence of viral reactivation. Precise timing of such reactivation-as an early marker of immune suppression, or as a consequence of the later-is not known precisely. Here, using a fully designed nucleic acid extraction automated procedure together with tailored commercial PCR kits, we focused on the description of early reactivation within the first week of ICU admission of several herpes viruses and Torque Teno virus (TTV) in 98 septic shock patients. Results: Most of septic shock patients had at least one viremia event during the first week (88%). TTV and herpesviruses were detected in 56% and 53% of septic shock patient, respectively. The two most frequent herpesviruses detected within the first week were EBV (35%) and HSV1 (26%). Different kinetic were observed among herpesviruses, faster for EBV and HSV1 than for CMV and HHV6. Although no association was found between herpes viremia and secondary infections, patients with herpesviridae-related viremia were more severe, e.g., higher SOFA scores and plasma lactate levels. While reactivating only 1 virus was not associated with mortality, patients with multiple viremia events had higher ICU mortality. Surprisingly, EBV + TTV early reactivation seemed associated with a lower D28 mortality. No clear association was observed between viremia and immune biomarkers. Conclusion: Applying a semi-automated process of viral DNAemia determination to this cohort of 98 patients with septic shock, we observed that the number of patients with positive viremia increased during the first week in the ICU. Of note, there was no improvement in predicting the outcome when using viremia status. Nevertheless, this pilot study, introducing standardized procedures from extraction to detection, provides the basis for future standardized diagnostic criteria. A prospective longitudinal clinical study using these procedures will enable determination of whether such viremia is due to a lack of a latent virus control by the immune system or a true clinical viral infection.
Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, 2013
We propose the statistical RqPCRAnalysis tool for quantitative real-time PCR data analysis which ... more We propose the statistical RqPCRAnalysis tool for quantitative real-time PCR data analysis which includes the use of several normalization genes, biological as well as technical replicates and provides statistically validated results. This RqPCRAnalysis tool improved methods developed by Genorm and qBASE programs. The algorithm was developed in R language and is freely available. The main contributions of RqPCRAnalysis tool are: (1) determining the most stable reference genes (REF)-housekeeping genes-across biological replicates and technical replicates; (2) computing the normalization factor based on REF; (3) computing the normalized expression of the genes of interest (GOI), as well as rescaling the normalized expression across biological replicates; (4) comparing the level expression between samples across biological replicates via the test of statistical significance. In this paper we describe and demonstrate the available statistical functions for practical analysis of quantitative real-time PCR data. Our statistical RqPCRAnalysis tool is user-friendly and should help biologist with no prior formation in R programming to analyze their quantitative PCR data.
... les arbres pondérés de plus long préfixe Tran Trang, Nguyen Cam Chi, Hoang Ngoc Minh Centre I... more ... les arbres pondérés de plus long préfixe Tran Trang, Nguyen Cam Chi, Hoang Ngoc Minh Centre Intégré de Bio-informatique Université de Lille 2 1 Place Verdun, 59045 Lille Cedex, France {trang.tran,cnguyen,hoang}@univ-lille2.fr RÉSUMÉ. ...
Table S1. (A) Virus strain-reference panel and (B) viral PCR-reference panel used for determinati... more Table S1. (A) Virus strain-reference panel and (B) viral PCR-reference panel used for determination of the LOD in the automated process. Figure S1. Selection of the so-called "viral cohort", a subset of the MIP REA cohort. Figure S2. (A) Semi-automated procedure applied to detect DNA viremia in plasma. Internal controls are used all along the process to qualify each single step, namely extraction, amplification, detection. Figure S3. (A) Procedure applied to determine the LOD (B) Last performed dilution giving a positive count and selection (red) of the LOD (left), and amplification on blood extracts from healthy volunteers; a TTV LOD in plasma was derived from Kulifaj D. et al., 2018 ( https://doi.org/10.1016/j.jcv.2018.06.010 ). Table S2. Association between binary endpoints or markers and viremia presence. Clinical outcomes are mortality at D28 following ICU admission and HAI occurrence occurring during the hospitalization. Biomarkers, quantified by RT-PCR, consisted of...
Whole blood transcriptional signatures distinguishing active tuberculosis patients from asymptoma... more Whole blood transcriptional signatures distinguishing active tuberculosis patients from asymptomatic latently infected individuals exist. Consensus has not been achieved regarding the optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases. Here we show a blood transcriptional signature of active tuberculosis using RNA-Seq, confirming microarray results, that discriminates active tuberculosis from latently infected and healthy individuals, validating this signature in an independent cohort. Using an advanced modular approach, we utilise the information from the entire transcriptome, which includes overabundance of type I interferon-inducible genes and underabundance of IFNG and TBX21, to develop a signature that discriminates active tuberculosis patients from latently infected individuals or those with acute viral and bacterial infections. We suggest that methods targeting gene selection across multiple discriminant modules can improve...
Methoxyfenozide and methoprene are two insecticides that mimic the action of the main hormones in... more Methoxyfenozide and methoprene are two insecticides that mimic the action of the main hormones involved in the control of insect growth and development, 20-hydroxyecdysone and juvenile hormone. We investigated their effect on the Spodoptera frugiperda Sf9 cell line. ...
... les arbres pondérés de plus long préfixe Tran Trang, Nguyen Cam Chi, Hoang Ngoc Minh Centre I... more ... les arbres pondérés de plus long préfixe Tran Trang, Nguyen Cam Chi, Hoang Ngoc Minh Centre Intégré de Bio-informatique Université de Lille 2 1 Place Verdun, 59045 Lille Cedex, France {trang.tran,cnguyen,hoang}@univ-lille2.fr RÉSUMÉ. ...
We investigate discrete structures and combinatoric modeling of weighted prefix trees for managin... more We investigate discrete structures and combinatoric modeling of weighted prefix trees for managing and analyzing DNA microarray data. We describe the algorithms to construct the weighted trees for these data. Using these weighted trees with our algorithms, we propose methods to compute the appearance probability of a DNA microarray, to compare the informational distances in the expression of genes between the DNA microarrays, to search the characteristic microarrays and the group of candidate genes suggestive of a pathology.
Background: Septic shock patients exhibit an increased incidence of viral reactivation. Precise t... more Background: Septic shock patients exhibit an increased incidence of viral reactivation. Precise timing of such reactivation-as an early marker of immune suppression, or as a consequence of the later-is not known precisely. Here, using a fully designed nucleic acid extraction automated procedure together with tailored commercial PCR kits, we focused on the description of early reactivation within the first week of ICU admission of several herpes viruses and Torque Teno virus (TTV) in 98 septic shock patients. Results: Most of septic shock patients had at least one viremia event during the first week (88%). TTV and herpesviruses were detected in 56% and 53% of septic shock patient, respectively. The two most frequent herpesviruses detected within the first week were EBV (35%) and HSV1 (26%). Different kinetic were observed among herpesviruses, faster for EBV and HSV1 than for CMV and HHV6. Although no association was found between herpes viremia and secondary infections, patients with herpesviridae-related viremia were more severe, e.g., higher SOFA scores and plasma lactate levels. While reactivating only 1 virus was not associated with mortality, patients with multiple viremia events had higher ICU mortality. Surprisingly, EBV + TTV early reactivation seemed associated with a lower D28 mortality. No clear association was observed between viremia and immune biomarkers. Conclusion: Applying a semi-automated process of viral DNAemia determination to this cohort of 98 patients with septic shock, we observed that the number of patients with positive viremia increased during the first week in the ICU. Of note, there was no improvement in predicting the outcome when using viremia status. Nevertheless, this pilot study, introducing standardized procedures from extraction to detection, provides the basis for future standardized diagnostic criteria. A prospective longitudinal clinical study using these procedures will enable determination of whether such viremia is due to a lack of a latent virus control by the immune system or a true clinical viral infection.
Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, 2013
We propose the statistical RqPCRAnalysis tool for quantitative real-time PCR data analysis which ... more We propose the statistical RqPCRAnalysis tool for quantitative real-time PCR data analysis which includes the use of several normalization genes, biological as well as technical replicates and provides statistically validated results. This RqPCRAnalysis tool improved methods developed by Genorm and qBASE programs. The algorithm was developed in R language and is freely available. The main contributions of RqPCRAnalysis tool are: (1) determining the most stable reference genes (REF)-housekeeping genes-across biological replicates and technical replicates; (2) computing the normalization factor based on REF; (3) computing the normalized expression of the genes of interest (GOI), as well as rescaling the normalized expression across biological replicates; (4) comparing the level expression between samples across biological replicates via the test of statistical significance. In this paper we describe and demonstrate the available statistical functions for practical analysis of quantitative real-time PCR data. Our statistical RqPCRAnalysis tool is user-friendly and should help biologist with no prior formation in R programming to analyze their quantitative PCR data.
... les arbres pondérés de plus long préfixe Tran Trang, Nguyen Cam Chi, Hoang Ngoc Minh Centre I... more ... les arbres pondérés de plus long préfixe Tran Trang, Nguyen Cam Chi, Hoang Ngoc Minh Centre Intégré de Bio-informatique Université de Lille 2 1 Place Verdun, 59045 Lille Cedex, France {trang.tran,cnguyen,hoang}@univ-lille2.fr RÉSUMÉ. ...
Table S1. (A) Virus strain-reference panel and (B) viral PCR-reference panel used for determinati... more Table S1. (A) Virus strain-reference panel and (B) viral PCR-reference panel used for determination of the LOD in the automated process. Figure S1. Selection of the so-called "viral cohort", a subset of the MIP REA cohort. Figure S2. (A) Semi-automated procedure applied to detect DNA viremia in plasma. Internal controls are used all along the process to qualify each single step, namely extraction, amplification, detection. Figure S3. (A) Procedure applied to determine the LOD (B) Last performed dilution giving a positive count and selection (red) of the LOD (left), and amplification on blood extracts from healthy volunteers; a TTV LOD in plasma was derived from Kulifaj D. et al., 2018 ( https://doi.org/10.1016/j.jcv.2018.06.010 ). Table S2. Association between binary endpoints or markers and viremia presence. Clinical outcomes are mortality at D28 following ICU admission and HAI occurrence occurring during the hospitalization. Biomarkers, quantified by RT-PCR, consisted of...
Whole blood transcriptional signatures distinguishing active tuberculosis patients from asymptoma... more Whole blood transcriptional signatures distinguishing active tuberculosis patients from asymptomatic latently infected individuals exist. Consensus has not been achieved regarding the optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases. Here we show a blood transcriptional signature of active tuberculosis using RNA-Seq, confirming microarray results, that discriminates active tuberculosis from latently infected and healthy individuals, validating this signature in an independent cohort. Using an advanced modular approach, we utilise the information from the entire transcriptome, which includes overabundance of type I interferon-inducible genes and underabundance of IFNG and TBX21, to develop a signature that discriminates active tuberculosis patients from latently infected individuals or those with acute viral and bacterial infections. We suggest that methods targeting gene selection across multiple discriminant modules can improve...
Methoxyfenozide and methoprene are two insecticides that mimic the action of the main hormones in... more Methoxyfenozide and methoprene are two insecticides that mimic the action of the main hormones involved in the control of insect growth and development, 20-hydroxyecdysone and juvenile hormone. We investigated their effect on the Spodoptera frugiperda Sf9 cell line. ...
... les arbres pondérés de plus long préfixe Tran Trang, Nguyen Cam Chi, Hoang Ngoc Minh Centre I... more ... les arbres pondérés de plus long préfixe Tran Trang, Nguyen Cam Chi, Hoang Ngoc Minh Centre Intégré de Bio-informatique Université de Lille 2 1 Place Verdun, 59045 Lille Cedex, France {trang.tran,cnguyen,hoang}@univ-lille2.fr RÉSUMÉ. ...
We investigate discrete structures and combinatoric modeling of weighted prefix trees for managin... more We investigate discrete structures and combinatoric modeling of weighted prefix trees for managing and analyzing DNA microarray data. We describe the algorithms to construct the weighted trees for these data. Using these weighted trees with our algorithms, we propose methods to compute the appearance probability of a DNA microarray, to compare the informational distances in the expression of genes between the DNA microarrays, to search the characteristic microarrays and the group of candidate genes suggestive of a pathology.
Uploads
Papers by Trang Tran