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1.  Evolution of dominance mechanisms at a butterfly mimicry supergene 
Nature Communications  2014;5:5644.
Genetic dominance in polymorphic loci may respond to selection; however, the evolution of dominance in complex traits remains a puzzle. We analyse dominance at a wing-patterning supergene controlling local mimicry polymorphism in the butterfly Heliconius numata. Supergene alleles are associated with chromosomal inversion polymorphism, defining ancestral versus derived alleles. Using controlled crosses and the new procedure, Colour Pattern Modelling, allowing whole-wing pattern comparisons, we estimate dominance coefficients between alleles. Here we show strict dominance in sympatry favouring mimicry and inconsistent dominance throughout the wing between alleles from distant populations. Furthermore, dominance among derived alleles is uncoordinated across wing-pattern elements, producing mosaic heterozygous patterns determined by a hierarchy in colour expression. By contrast, heterozygotes with an ancestral allele show complete, coordinated dominance of the derived allele, independently of colours. Therefore, distinct dominance mechanisms have evolved in association with supergene inversions, in response to strong selection on mimicry polymorphism.
The evolution of genetic dominance in polymorphic traits remains poorly understood. Here, the authors show that distinct dominance mechanisms have evolved in association with supergene inversions controlling wing pattern in Heliconius butterflies, in response to strong selection favouring mimicry.
PMCID: PMC4263167  PMID: 25429605
3.  ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software 
PLoS ONE  2014;9(6):e98679.
Gephi is a network visualization software used in various disciplines (social network analysis, biology, genomics…). One of its key features is the ability to display the spatialization process, aiming at transforming the network into a map, and ForceAtlas2 is its default layout algorithm. The latter is developed by the Gephi team as an all-around solution to Gephi users’ typical networks (scale-free, 10 to 10,000 nodes). We present here for the first time its functioning and settings. ForceAtlas2 is a force-directed layout close to other algorithms used for network spatialization. We do not claim a theoretical advance but an attempt to integrate different techniques such as the Barnes Hut simulation, degree-dependent repulsive force, and local and global adaptive temperatures. It is designed for the Gephi user experience (it is a continuous algorithm), and we explain which constraints it implies. The algorithm benefits from much feedback and is developed in order to provide many possibilities through its settings. We lay out its complete functioning for the users who need a precise understanding of its behaviour, from the formulas to graphic illustration of the result. We propose a benchmark for our compromise between performance and quality. We also explain why we integrated its various features and discuss our design choices.
PMCID: PMC4051631  PMID: 24914678
4.  Classifying leukemia types with chromatin conformation data 
Genome Biology  2014;15(4):R60.
Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed.
Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data.
Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes.
PMCID: PMC4038739  PMID: 24995990
5.  Hox in motion: tracking HoxA cluster conformation during differentiation 
Nucleic Acids Research  2013;42(3):1524-1540.
Three-dimensional genome organization is an important higher order transcription regulation mechanism that can be studied with the chromosome conformation capture techniques. Here, we combined chromatin organization analysis by chromosome conformation capture-carbon copy, computational modeling and epigenomics to achieve the first integrated view, through time, of a connection between chromatin state and its architecture. We used this approach to examine the chromatin dynamics of the HoxA cluster in a human myeloid leukemia cell line at various stages of differentiation. We found that cellular differentiation involves a transient activation of the 5′-end HoxA genes coinciding with a loss of contacts throughout the cluster, and by specific silencing at the 3′-end with H3K27 methylation. The 3D modeling of the data revealed an extensive reorganization of the cluster between the two previously reported topologically associated domains in differentiated cells. Our results support a model whereby silencing by polycomb group proteins and reconfiguration of CTCF interactions at a topologically associated domain boundary participate in changing the HoxA cluster topology, which compartmentalizes the genes following differentiation.
PMCID: PMC3919592  PMID: 24174538
6.  Cholera in Pregnancy: Outcomes from a Specialized Cholera Treatment Unit for Pregnant Women in Léogâne, Haiti 
The association between cholera in pregnancy and negative fetal outcome has been described since the 19th century. However, there is limited published literature on the subject. We describe pregnancy outcomes from a specialized multidisciplinary hospital unit at the onset of a large cholera outbreak in Haiti in 2010 and 2011.
Pregnant women with cholera were hospitalized in a specialized unit within the MSF hospital compound in Léogâne and treated using standard cholera treatment guidelines but with earlier, more intense fluid replacement. All women had intravenous access established at admission regardless of their hydration status, and all received antibiotic treatment. Data were collected on patient demographics, pregnancy and cholera status, and pregnancy outcome. In this analysis we calculated risk ratios for fetal death and performed logistic regression analysis to control for confounding factors.
263 pregnant women with cholera were hospitalized between December 2010 and July 2011. None died during hospitalization, 226 (86%) were discharged with a preserved pregnancy and 16 (6%) had live fullterm singleton births, of whom 2 died within the first 5 days postpartum. The remaining 21 pregnancies (8%) resulted in intrauterine fetal death. The risk of fetal death was associated with factors reflecting severity of the cholera episode: after adjusting for confounding factors, the strongest risk factor for fetal death was severe maternal dehydration (adjusted risk ratio for severe vs. mild dehydration was 9.4, 95% CI 2.5–35.3, p = 0.005), followed by severe vomiting (adjusted risk ratio 5.1, 95% 1.1–23.8, p = 0.041).
This is the largest cohort of pregnant women with cholera described to date. The main risk factor identified for fetal death was severity of dehydration. Our experience suggests that establishing specialized multidisciplinary units which facilitate close follow-up of both pregnancy and dehydration status due to cholera could be beneficial for patients, especially in large epidemics.
Author Summary
Cholera in pregnancy has been long associated with high rates of stillbirths and abortions, but there is very limited published literature describing this association or possible mechanisms. During the major cholera epidemic that hit Haiti in October 2010, we set-up a specialized cholera treatment unit for pregnant women inside the Médecins sans Frontières hospital in Léogâne, allowing for intensive follow-up of cholera-associated dehydration and of pregnancy, and facilitating access to high-quality obstetric and neonatal services in case of complications. To describe the pregnancy outcomes and risk factors for fetal death, we analyzed routinely collected data from patient files. Of 263 women hospitalized, 21 (8%) lost their pregnancy during hospitalization for cholera; an additional 16 (6%) delivered a live baby at the hospital, and the remaining 226 women (86%) were discharged with preserved pregnancy. The risk factor most strongly associated with fetal demise was severity of dehydration at admission. In large epidemics, multidisciplinary units can help prevent negative maternal, fetal and neonatal outcomes.
PMCID: PMC3744413  PMID: 23967361
7.  Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2 
Nucleic Acids Research  2013;41(14):6881-6891.
The RNA polymerase II (RNAP II)-associated protein (RPAP) 2 has been discovered through its association with various subunits of RNAP II in affinity purification coupled with mass spectrometry experiments. Here, we show that RPAP2 is a mainly cytoplasmic protein that shuttles between the cytoplasm and the nucleus. RPAP2 shuttling is tightly coupled with nuclear import of RNAP II, as RPAP2 silencing provokes abnormal accumulation of RNAP II in the cytoplasmic space. Most notably, RPAP4/GPN1 silencing provokes the retention of RPAP2 in the nucleus. Our results support a model in which RPAP2 enters the nucleus in association with RNAP II and returns to the cytoplasm in association with the GTPase GPN1/RPAP4. Although binding of RNAP II to RPAP2 is mediated by an N-terminal domain (amino acids 1–170) that contains a nuclear retention domain, and binding of RPAP4/GPN1 to RPAP2 occurs through a C-terminal domain (amino acids 156–612) that has a dominant cytoplasmic localization domain. In conjunction with previously published data, our results have important implications, as they indicate that RPAP2 controls gene expression by two distinct mechanisms, one that targets RNAP II activity during transcription and the other that controls availability of RNAP II in the nucleus.
PMCID: PMC3737550  PMID: 23723243
8.  A Newly Uncovered Group of Distantly Related Lysine Methyltransferases Preferentially Interact with Molecular Chaperones to Regulate Their Activity 
PLoS Genetics  2013;9(1):e1003210.
Methylation is a post-translational modification that can affect numerous features of proteins, notably cellular localization, turnover, activity, and molecular interactions. Recent genome-wide analyses have considerably extended the list of human genes encoding putative methyltransferases. Studies on protein methyltransferases have revealed that the regulatory function of methylation is not limited to epigenetics, with many non-histone substrates now being discovered. We present here our findings on a novel family of distantly related putative methyltransferases. Affinity purification coupled to mass spectrometry shows a marked preference for these proteins to associate with various chaperones. Based on the spectral data, we were able to identify methylation sites in substrates, notably trimethylation of K135 of KIN/Kin17, K561 of HSPA8/Hsc70 as well as corresponding lysine residues in other Hsp70 isoforms, and K315 of VCP/p97. All modification sites were subsequently confirmed in vitro. In the case of VCP, methylation by METTL21D was stimulated by the addition of the UBX cofactor ASPSCR1, which we show directly interacts with the methyltransferase. This stimulatory effect was lost when we used VCP mutants (R155H, R159G, and R191Q) known to cause Inclusion Body Myopathy with Paget's disease of bone and Fronto-temporal Dementia (IBMPFD) and/or familial Amyotrophic Lateral Sclerosis (ALS). Lysine 315 falls in proximity to the Walker B motif of VCP's first ATPase/D1 domain. Our results indicate that methylation of this site negatively impacts its ATPase activity. Overall, this report uncovers a new role for protein methylation as a regulatory pathway for molecular chaperones and defines a novel regulatory mechanism for the chaperone VCP, whose deregulation is causative of degenerative neuromuscular diseases.
Author Summary
Methylation, or transfer of a single or multiple methyl groups (CH3), is one of many post-translational modifications that occur on proteins. Such modifications can, in turn, affect numerous aspects of a protein, notably cellular localization, turnover, activity, and molecular interactions. In addition to post-translational modifications, the structural organization of a protein or protein complex can also have a significant impact on its function and stability. A group of factors known as “molecular chaperones” aid newly synthesized proteins in reaching their native conformation or alternating between physiologically relevant states. We present here a new family of factors that promote methylation of chaperones and show that, at least in one case, this modification translates into a modulation in the activity of the substrate chaperone. Our results not only characterize the function of previously unknown gene products, uncover a new role for protein methylation as a regulatory pathway for chaperones, and define a novel regulatory mechanism for the chaperone VCP, whose deregulation is causative of neuromuscular diseases, but also suggest the existence of a post-translational modification code that regulates molecular chaperones. Further decrypting this “chaperone code” will help understanding how the functional organization of the proteome is orchestrated.
PMCID: PMC3547847  PMID: 23349634
9.  Relation of mitral valve morphology and motion to mitral regurgitation severity in patients with mitral valve prolapse 
Mitral valve thickness is used as a criterion to distinguish the classical from the non-classical form of mitral valve prolapse (MVP). Classical form of MVP has been associated with higher risk of mitral regurgitation (MR) and concomitant complications. We sought to determine the relation of mitral valve morphology and motion to mitral regurgitation severity in patients with MVP.
We prospectively analyzed transthoracic echocardiograms of 38 consecutive patients with MVP and various degrees of MR. In the parasternal long-axis view, leaflets length, diastolic leaflet thickness, prolapsing depth, billowing area and non-coaptation distance between both leaflets were measured.
Twenty patients (53%) and 18 patients (47%) were identified as having moderate to severe and mild MR respectively (ERO = 45 ± 27 mm2 vs. 5 ± 7 mm2, p < 0.001). Diastolic leaflet thickness was similar in both groups (5.5 ± 0.9 mm vs. 5.3 ± 1 mm, p = 0.57). On multivariate analysis, the non-coaptation distance (OR 7.9 per 1 mm increase; 95% CI 1.72-37.2) was associated with significant MR. Thick mitral valve leaflet as traditionally reported (≥ 5 mm) was not associated with significant MR (OR 0.9; 95% CI 0.2-3.4).
In patients with MVP, thick mitral leaflet is not associated with significant MR. Leaflet thickness is probably not as important in risk stratification as previously reported in patients with MVP. Other anatomical and geometrical features of the mitral valve apparatus area appear to be much more closely related to MR severity.
PMCID: PMC3296553  PMID: 22284298
mitral regurgitation; mitral valve; echocardiography; mitral valve prolapse
10.  Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling 
BMC Bioinformatics  2011;12:414.
Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mechanism of gene expression regulation. Chromosome Conformation Capture Carbon Copy (5C) and its variant Hi-C are techniques used to measure the interaction frequency (IF) between specific regions of the genome. Our goal is to use the IF data generated by these experiments to computationally model and analyze three-dimensional chromatin organization.
We formulate a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC) approach called MCMC5C to generate a representative sample from the posterior distribution over structures from IF data. Structures produced from parallel MCMC runs on the same dataset demonstrate that our MCMC method mixes quickly and is able to sample from the posterior distribution of structures and find subclasses of structures. Structural properties (base looping, condensation, and local density) were defined and their distribution measured across the ensembles of structures generated. We applied these methods to a biological model of human myelomonocyte cellular differentiation and identified distinct chromatin conformation signatures (CCSs) corresponding to each of the cellular states. We also demonstrate the ability of our method to run on Hi-C data and produce a model of human chromosome 14 at 1Mb resolution that is consistent with previously observed structural properties as measured by 3D-FISH.
We believe that tools like MCMC5C are essential for the reliable analysis of data from the 3C-derived techniques such as 5C and Hi-C. By integrating complex, high-dimensional and noisy datasets into an easy to interpret ensemble of three-dimensional conformations, MCMC5C allows researchers to reliably interpret the result of their assay and contrast conformations under different conditions.
PMCID: PMC3245522  PMID: 22026390
11.  ALG: Automated Genotype Calling of Luminex Assays 
PLoS ONE  2011;6(5):e19368.
Single nucleotide polymorphisms (SNPs) are the most commonly used polymorphic markers in genetics studies. Among the different platforms for SNP genotyping, Luminex is one of the less exploited mainly due to the lack of a robust (semi-automated and replicable) freely available genotype calling software. Here we describe a clustering algorithm that provides automated SNP calls for Luminex genotyping assays. We genotyped 3 SNPs in a cohort of 330 childhood leukemia patients, 200 parents of patient and 325 healthy individuals and used the Automated Luminex Genotyping (ALG) algorithm for SNP calling. ALG genotypes were called twice to test for reproducibility and were compared to sequencing data to test for accuracy. Globally, this analysis demonstrates the accuracy (99.6%) of the method, its reproducibility (99.8%) and the low level of no genotyping calls (3.4%). The high efficiency of the method proves that ALG is a suitable alternative to the current commercial software. ALG is semi-automated, and provides numerical measures of confidence for each SNP called, as well as an effective graphical plot. Moreover ALG can be used either through a graphical user interface, requiring no specific informatics knowledge, or through command line with access to the open source code. The ALG software has been implemented in R and is freely available for non-commercial use either at or by request to
PMCID: PMC3089621  PMID: 21573116
12.  Burden of Malaria during Pregnancy at the Time of IPTp/SP Implementation in Gabon 
The new recommendations to prevent malaria in pregnant women have recently been implemented in Gabon. There is little information on the pregnancy indicators that are useful for their evaluation. A cross-sectional study for the assessment of the prevalence of peripheral, placental, and cord malaria and anemia among delivering women was performed at the largest public hospital of Gabon. Malaria prevalence was 34.4%, 53.6%, and 18.2% for maternal peripheral, placental, and cord blood respectively, with no difference between primigravidae and multigravidae. Submicroscopic infections were frequent and concerned all the positive cord samples. Maternal peripheral, late placental, and cord infections were all associated with a reduced mean birth weight in primigravidae (P = 0.02). Anemia prevalence was 53%, low birth rate was 13%, and prematurity was 25%. The use of intermittent preventive treatment with sulfadoxine-pyrimethamine (greater than or equal to one dose) combined with bed net was associated with a reduction in infection only in multigravidae and with a reduced risk of maternal anemia.
PMCID: PMC2813157  PMID: 20133992
13.  The Protein Interaction Network of the Human Transcription Machinery Reveals a Role for the Conserved GTPase RPAP4/GPN1 and Microtubule Assembly in Nuclear Import and Biogenesis of RNA Polymerase II* 
RNA polymerase II (RNAPII), the 12-subunit enzyme that synthesizes all mRNAs and several non-coding RNAs in eukaryotes, plays a central role in cell function. Although multiple proteins are known to regulate the activity of RNAPII during transcription, little is known about the machinery that controls the fate of the enzyme before or after transcription. We used systematic protein affinity purification coupled to mass spectrometry (AP-MS) to characterize the high resolution network of protein interactions of RNAPII in the soluble fraction of human cell extracts. Our analysis revealed that many components of this network participate in RNAPII biogenesis. We show here that RNAPII-associated protein 4 (RPAP4/GPN1) shuttles between the nucleus and the cytoplasm and regulates nuclear import of POLR2A/RPB1 and POLR2B/RPB2, the two largest subunits of RNAPII. RPAP4/GPN1 is a member of a newly discovered GTPase family that contains a unique and highly conserved GPN loop motif that we show is essential, in conjunction with its GTP-binding motifs, for nuclear localization of POLR2A/RPB1 in a process that also requires microtubule assembly. A model for RNAPII biogenesis is presented.
PMCID: PMC3002788  PMID: 20855544
14.  The three-dimensional architecture of Hox cluster silencing 
Nucleic Acids Research  2010;38(21):7472-7484.
Spatial chromatin organization is emerging as an important mechanism to regulate the expression of genes. However, very little is known about genome architecture at high-resolution in vivo. Here, we mapped the three-dimensional organization of the human Hox clusters with chromosome conformation capture (3C) technology. We show that computational modeling of 3C data sets can identify candidate regulatory proteins of chromatin architecture and gene expression. Hox genes encode evolutionarily conserved master regulators of development which strict control has fascinated biologists for over 25 years. Proper transcriptional silencing is key to Hox function since premature expression can lead to developmental defects or human disease. We now show that the HoxA cluster is organized into multiple chromatin loops that are dependent on transcription activity. Long-range contacts were found in all four silent clusters but looping patterns were specific to each cluster. In contrast to the Drosophila homeotic bithorax complex (BX-C), we found that Polycomb proteins are only modestly required for human cluster looping and silencing. However, computational three-dimensional Hox cluster modeling identified the insulator-binding protein CTCF as a likely candidate mediating DNA loops in all clusters. Our data suggest that Hox cluster looping may represent an evolutionarily conserved structural mechanism of transcription regulation.
PMCID: PMC2995065  PMID: 20660483
15.  Chromatin conformation signatures of cellular differentiation 
Genome Biology  2009;10(4):R37.
A suite of computer programs to identify genome-wide chromatin conformation signatures with 5C technology is reported.
One of the major genomics challenges is to better understand how correct gene expression is orchestrated. Recent studies have shown how spatial chromatin organization is critical in the regulation of gene expression. Here, we developed a suite of computer programs to identify chromatin conformation signatures with 5C technology . We identified dynamic HoxA cluster chromatin conformation signatures associated with cellular differentiation. Genome-wide chromatin conformation signature identification might uniquely identify disease-associated states and represent an entirely novel class of human disease biomarkers.
PMCID: PMC2688928  PMID: 19374771
16.  Changes in the endurance shuttle walk test in COPD patients with chronic respiratory failure after pulmonary rehabilitation: the minimal important difference obtained with anchor- and distribution-based method 
Respiratory Research  2015;16(1):27.
Although the endurance shuttle walk test (ESWT) has proven to be responsive to change in exercise capacity after pulmonary rehabilitation (PR) for COPD, the minimally important difference (MID) has not yet been established. We aimed to establish the MID of the ESWT in patients with severe COPD and chronic hypercapnic respiratory failure following PR.
Data were derived from a randomized controlled trial, investigating the value of noninvasive positive pressure ventilation added to PR. Fifty-five patients with stable COPD, GOLD stage IV, with chronic respiratory failure were included (mean (SD) FEV1 31.1 (12.0) % pred, age 62 (9) y). MID estimates of the ESWT in seconds, percentage and meters change were calculated with anchor based and distribution based methods. Six minute walking distance (6MWD), peak work rate on bicycle ergometry (Wpeak) and Chronic Respiratory Questionnaire (CRQ) were used as anchors and Cohen’s effect size was used as distribution based method.
The estimated MID of the ESWT with the different anchors ranged from 186–199 s, 76–82% and 154–164 m. Using the distribution based method the MID was 144 s, 61% and 137 m.
Estimates of the MID for the ESWT after PR showed only small differences using different anchors in patients with COPD and chronic respiratory failure. Therefore we recommend using a range of 186–199 s, 76–82% or 154–164 m as MID of the ESWT in COPD patients with chronic respiratory failure. Further research in larger populations should elucidate whether this cut-off value is also valid in other COPD populations and with other interventions.
Trial registration
ClinicalTrials.Gov (ID NCT00135538).
Electronic supplementary material
The online version of this article (doi:10.1186/s12931-015-0182-x) contains supplementary material, which is available to authorized users.
PMCID: PMC4336738
Endurance shuttle walk test; Minimally important difference; COPD; Respiratory failure
17.  Types of skin afferent fibers and spinal opioid receptors that contribute to touch-induced inhibition of heart rate changes evoked by noxious cutaneous heat stimulation 
Molecular Pain  2015;11:4.
In anesthetized rats and conscious humans, a gentle touch using a soft disc covered with microcones (with a texture similar to that of a finger), but not with a flat disc, inhibits nociceptive somatocardiac reflexes. Such an inhibitory effect is most reliably evoked when touch is applied to the skin ipsilateral and closest to nociceptive inputs. However, the mechanism of this inhibition is not completely elucidated. We aimed to clarify the types of cutaneous afferent fibers and spinal opioid receptors that contribute to antinociceptive effects of microcone touch.
The present study comprised two experiments with urethane-anesthetized rats. In the first experiment, unitary activity of skin afferent fibers was recorded from the saphenous nerve, and responses to a 10-min touch using a microcone disc and a flat disc (control) were compared. Greater discharge rate during microcone touch was observed in low-threshold mechanoreceptive Aδ and C afferent units, whereas many Aβ afferents responded similarly to the two types of touch. In the second experiment, the effect of an intrathecal injection of opioid receptor antagonists on the inhibitory effects of microcone touch on heart rate responses to noxious heat stimulation was examined. The magnitude of the heart rate response was significantly reduced by microcone touch in rats that received saline or naltrindole (δ-opioid receptor antagonist) injections. However, such an inhibition was not observed in rats that received naloxone (non-selective opioid receptor antagonist) or Phe-Cys-Tyr-Trp-Orn-Thr-Pen-Thr-NH2 (CTOP; μ-opioid receptor antagonist) injections.
Microcone touch induced greater responses of low-threshold mechanoreceptive Aδ and C afferent units than control touch. The antinociceptive effect of microcone touch was abolished by intrathecal injection of μ-opioid receptor antagonist. These results suggest that excitation of low-threshold mechanoreceptive Aδ and C afferents produces the release of endogenous μ-opioid ligands in the spinal cord, resulting in the inhibition of nociceptive transmission that contributes to somatocardiac reflexes.
PMCID: PMC4335417
Touch; Skin; Low-threshold mechanoreceptors; Noxious stimulation; Cardiovascular system; Spinal cord; μ-opioid receptor
18.  An Innovative Lab-Based Training Program to Help Patient Groups Understand Their Disease and the Research Process 
PLoS Biology  2015;13(2):e1002067.
Genuine partnership between patient groups and medical experts is important but challenging. Our training program meets this challenge by organizing hands-on, lab-based training sessions for members of patient groups. These sessions allow “trainees” to better understand their disease and the biomedical research process, and strengthen links between patients and local researchers. Over the past decade, we and our partner institutes have received more than 900 French patients, with the participation of over 60 researchers and clinicians.
Lab-based mini-research projects allow members of patient groups to understand the scientific method and how research works in practice, thereby fostering genuine partnership between patient groups and medical experts.
PMCID: PMC4323103  PMID: 25668201
19.  Transient improvement of poststroke apathy with zolpidem: a single-case, placebo-controlled double-blind study 
BMJ Case Reports  2013;2013:bcr2012007816.
We report the case of a 44-year-old patient with severe and disabling apathy nearly 2 years after a right hemisphere haemorrhagic stroke. The effect of a single dose of zolpidem was tested over a 2-week period, in alternation with either no treatment or a placebo in a double-blind randomised trial. Zolpidem was associated with a dramatic improvement in apathy, as assessed with the Apathy Inventory and the Behavioral Dysexecutive Syndrome Inventory. No adverse effect occurred during the trial.
PMCID: PMC3604023  PMID: 23396925
20.  How Many Have Died from Undiagnosed Human Immunodeficiency Virus–Associated Histoplasmosis, A Treatable Disease? Time to Act 
Human immunodeficiency virus (HIV)–associated disseminated Histoplasma capsulatum capsulatum infection often mimics tuberculosis. This disease is well know in the United States but is dramatically underdiagnosed in Central and South America. In the Amazon region, given the available incidence data and the regional HIV prevalence, it is expected that, every year, 1,500 cases of histoplasmosis affect HIV patients in that region alone. Given the mortality in undiagnosed patients, at least 600 patients would be expected to die from an undiagnosed but treatable disease. The lack of a simple diagnostic tool and the lack of awareness by clinicians spiral in a vicious cycle and made a major problem invisible for 30 years. The HIV/acquired immunodeficiency syndrome community should tackle this problem now to prevent numerous avoidable deaths from HIV-associated histoplasmosis in the region and elsewhere.
PMCID: PMC3919218  PMID: 24277783
21.  Tuberculosis and Histoplasmosis among Human Immunodeficiency Virus–Infected Patients: A Comparative Study 
In disease-endemic areas, histoplasmosis is the main differential diagnosis for tuberculosis among human immunodeficiency virus (HIV)–infected patients. However, no study has compared the two diseases. Thus, the objective of this study was to compare tuberculosis and histoplasmosis in HIV-infected patients. A population of 205 HIV-infected patients (99 with tuberculosis and 106 with histoplasmosis) hospitalized in Cayenne, French Guiana during January 1, 1997–December 31, 2008 were selected retrospectively from the French Hospital Database on HIV. Multivariate analysis showed that tuberculosis was associated with cough (adjusted odds ratio [AOR] = 0.20, 95% confidence interval [CI] = 0.05–0.73) and a C-reactive protein level > 70 mg/L (AOR = 0.98, 95% CI = 0.97–0.99). Variables associated with disseminated histoplasmosis were a γ-glutamyl transferase level > 72 IU/L (AOR = 4.99, 95% CI = 1.31–18.99), origin from French Guiana (AOR = 5.20, 95% CI = 1.30–20.73), disseminated localization (AOR = 6.40, 95% CI = 1.44–28.45), a concomitant opportunistic infection (AOR = 6.71, 95% CI = 1.50–29.96), a neutrophil count < 2,750 cells/mm3 (AOR = 10.54, 95% CI = 2.83–39.24), a CD4 cell count < 60 cells/mm3 (AOR = 11.62, 95% CI = 2.30–58.63), and a platelet count < 150,000/mm3 (AOR = 19.20, 95% CI = 3.35–110.14). Tuberculosis and histoplasmosis have similarities, but some factors show a greater association with one of these diseases. Thus, adapted therapeutic choices can be made by using simple clinical and paraclinical criteria.
PMCID: PMC3919221  PMID: 24394475
22.  Phosphatidylinositol 3-Kinase–Independent Signaling Pathways Contribute to ICOS-Mediated T Cell Costimulation in Acute Graft-Versus-Host Disease in Mice 
We and others have previously shown that ICOS plays an important role in inducing acute graft-versus-host disease (GVHD) in murine models of allogeneic bone marrow transplantation. ICOS potentiates TCR-mediated PI3K activation and intracellular calcium mobilization. However, ICOS signal transduction pathways involved in GVHD remain unknown. In this study, we examined the contribution of ICOS-PI3K signaling in the pathogenic potential of T cells using a knock-in mouse strain, ICOS-YF, which selectively lost the ability to activate PI3K. We found that when total T cells were used as alloreactive T cells, ICOS-YF T cells caused less severe GVHD compared with ICOS wild-type T cells, but they induced much more aggressive disease than ICOS knockout T cells. This intermediate level of pathogenic capacity of ICOS-YF T cells was correlated with similar levels of IFN-g–producing CD8 T cells that developed in the recipients of ICOS-WT or ICOS-YF T cells. We further evaluated the role of ICOS-PI3K signaling in CD4 versus CD8 T cell compartment using GVHD models that are exclusively driven by CD4 or CD8 T cells. Remarkably, ICOS-YF CD8 T cells caused disease similar to ICOS wild-type CD8 T cells, whereas ICOS-YF CD4 T cells behaved very similarly to their ICOS knockout counterparts. Consistent with their in vivo pathogenic potential, CD8 T cells responded to ICOS ligation in vitro by PI3K-independent calcium flux, T cell activation, and proliferation. Thus, in acute GVHD in mice, CD4 T cells heavily rely on ICOS-PI3K signaling pathways; in contrast, CD8 T cells can use PI3K-independent ICOS signaling pathways, possibly through calcium.
PMCID: PMC4318500  PMID: 23729441
23.  A Simple Echocardiographic Method To Estimate Pulmonary Vascular Resistance 
The American journal of cardiology  2013;112(6):873-882.
Pulmonary hypertension is comprised of heterogeneous diagnoses with distinct hemodynamic pathophysiology. Identifying elevated pulmonary vascular resistance (PVR) is critical for appropriate treatment. We reviewed data for patients seen at referral PH clinics who underwent echocardiography and right heart catheterization within 1 year. We derived equations to estimate PVR based on the ratio of estimated pulmonary artery (PA) systolic pressure (PASPDoppler) to RVOT VTI. We validated these equations in a separate sample and compared them to a published model based on the ratio of transtricuspid flow velocity to RVOT VTI (Model 1, Abbas et al 2003). The derived models were: (Model 2)PVR=1.2×PASPRVOT VTI (Model 3)PVR=PASPRVOT VTI+3if notch present
The cohort included 217 patients with mean PA pressure=45.3±11.9mmHg, PVR=7.3±5.0WU and PA wedge pressure=14.8±8.1mmHg; just over 1/3rd had PA wedge pressure >15mmHg (35.5%) and 82.0% had PVR>3WU. Model 1 systematically underestimated PVR, especially with high PVR. The derived models demonstrated no systematic bias. Model 3 correlated best with PVR (r=0.80 vs. 0.73 and 0.77 for Models 1 and 2 respectively). Model 3 had superior discriminatory power for PVR>3WU (AUC=0.946) and PVR>5WU (AUC=0.924), though all models discriminated well. Model 3 estimated PVR>3 was 98.3% sensitive and 61.1% specific for PVR>3WU (PPV=93%; NPV=88%). In conclusion, we present an equation to estimate PVR, using the ratio of PASPDoppler to RVOT VTI and a constant designating presence of RVOT VTI mid-systolic notching, which provides superior agreement with PVR across a wide range of values.
PMCID: PMC4317360  PMID: 23735649
pulmonary hypertension; hemodynamics; echocardiography
24.  Family Violence Among Older Adult Patients Consulting in Primary Care Clinics: Results From the ESA (Enquête sur la santé des aînés) Services Study on Mental Health and Aging 
To document the reliability and construct validity of the Family Violence Scale (FVS) in the older adult population aged 65 years and older.
Data came from a cross-sectional survey, the Enquête sur la santé des aînés et l’utilisation des services de santé (ESA Services Study), conducted in 2011–2013 using a probabilistic sample of older adults waiting for medical services in primary care clinics (n = 1765). Family violence was defined as a latent variable, coming from a spouse and from children.
A model with 2 indicators of violence; that is, psychological and financial violence, and physical violence, adequately fitted the observed data. The reliability of the FVS was 0.95. According to our results, 16% of older adults reported experiencing some form of family violence in the past 12 months of their interview, and 3% reported a high level of family violence (FVS > 0.36). Our results showed that the victim’s sex was not associated with the degree of violence (β = 0.02). However, the victim’s age was associated with family violence (β = −0.12). Older adults, aged 75 years and older, reported less violence than those aged between 65 and 74 years.
Our results lead us to conclude that family violence against older adults is common and warrants greater public health and political attention. General practitioners could play an active role in the detection of violence among older adults.
PMCID: PMC4143299  PMID: 25161067
family violence; older adults; populational study
25.  Corticokinematic coherence mainly reflects movement-induced proprioceptive feedback 
Neuroimage  2015;106:382-390.
Corticokinematic coherence (CKC) reflects coupling between magnetoencephalographic (MEG) signals and hand kinematics, mainly occurring at hand movement frequency (F0) and its first harmonic (F1). Since CKC can be obtained for both active and passive movements, it has been suggested to mainly reflect proprioceptive feedback to the primary sensorimotor (SM1) cortex. However, the directionality of the brain–kinematics coupling has not been previously assessed and was thus quantified in the present study by means of renormalized partial directed coherence (rPDC).
MEG data were obtained from 15 subjects who performed right index-finger movements and whose finger was, in another session, passively moved, with or without tactile input. Four additional subjects underwent the same task with slowly varying movement pace, spanning the 1–5 Hz frequency range. The coupling between SM1 activity recorded with MEG and finger kinematics was assessed with coherence and rPDC.
In all conditions, the afferent rPDC spectrum, which resembled the coherence spectrum, displayed higher values than the efferent rPDC spectrum. The afferent rPDC was 37% higher when tactile input was present, and it was at highest at F1 of the passive conditions; the efferent rPDC level did not differ between conditions. The apparent latency for the afferent input, estimated within the framework of the rPDC analysis, was 50–100 ms.
The higher directional coupling between hand kinematics and SM1 activity in afferent than efferent direction strongly supports the view that CKC mainly reflects movement-related somatosensory proprioceptive afferent input to the contralateral SM1 cortex.
•Neural activity in primary sensorimotor cortex is coupled with hand kinematics.•The coupling is stronger in the afferent than in the efferent direction.•The afferent delay estimated with phase–frequency plots is 50–100 ms.•During movements, <5-Hz sensorimotor activity mainly reflects proprioceptive feedback.
PMCID: PMC4295920  PMID: 25463469
Kinematics; Human brain; Magnetoencephalography; Proprioception; Sensorimotor cortex; Partial directed coherence; Movement

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