Detecting epistasis with restricted response patterns in pairs of biallelic loci.

Well-established examples of genetic epistasis between a pair of loci typically show characteristic patterns of phenotypic distributions in joint genotype tables. However, inferring epistasis given such data is difficult due to the lack of power in commonly used approaches, which decompose the epistatic patterns into main plus interaction effects followed by testing the interaction term. Testing additive-only or all terms may have more power, but they are sensitive to nonepistatic patterns. Alternatively, the epistatic patterns of interest can be enumerated and the best matching one is found by searching through the possibilities. Although this approach requires multiple testing correction over possible patterns, each pattern can be fitted with a regression model with just one degree of freedom and thus the overall power can still be high, if the number of possible patterns is limited. Here we compare the power of the linear decomposition and pattern search methods, by applying them to simulated data generated under several patterns of joint genotype effects with simple biological interpretations. Interaction-only tests are the least powerful; while pattern search approach is the most powerful if the range of possibilities is restricted, but still includes the true pattern.

The multipoint Morisita index for the analysis of spatial patterns

In many fields, the spatial clustering of sampled data points has many consequences. Therefore, several indices have been proposed to assess the level of clustering affecting datasets (e.g. the Morisita index, Ripley's Kfunction and Rényi's generalized entropy). The classical Morisita index measures how many times it is more likely to select two measurement points from the same quadrats (the data set is covered by a regular grid of changing size) than it would be in the case of a random distribution generated from a Poisson process. The multipoint version (k-Morisita) takes into account k points with k >= 2. The present research deals with a new development of the k-Morisita index for (1) monitoring network characterization and for (2) detection of patterns in monitored phenomena. From a theoretical perspective, a connection between the k-Morisita index and multifractality has also been found and highlighted on a mathematical multifractal set.

Head motion detection using FID navigators.

This work explores a concept for motion detection in brain MR examinations using high channel-count RF coil arrays. It applies ultrashort (<100 μsec) free induction decay signals, making use of the knowledge that motion induces variations in these signals when compared to a reference free induction decay signal. As a proof-of-concept, the method was implemented in a standard structural MRI sequence. The stability of the free induction decay-signal was verified in phantom experiments. Human experiments demonstrated that the observed variations in the navigator data provide a sensitive measure for detection of relevant and common subject motion patterns. The proposed methodology provides a means to monitor subject motion throughout a MRI scan while causing little or no impact on the sequence timing and image contrast. It could hence complement available motion detection and correction methods, thus further reducing motion sensitivity in MR applications.

Potassium channel alterations mediate peripheral nerve hyperexcitability in a mouse model of type 2 diabetes mellitus

Diabetes mellitus (DM) is a major cause of peripheral neuropathy. More than 220 million people worldwide suffer from type 2 DM, which will, in approximately half of them, lead to the development of diabetic peripheral neuropathy. While of significant medical importance, the pathophysiological changes present in DPN are still poorly understood. To get more insight into DPN associated with type 2 DM, we decided to use the rodent model of this form of diabetes, the db/db mice. During the in-vivo conduction velocity studies on these animals, we observed the presence of multiple spiking followed by a single stimulation. This prompted us to evaluate the excitability properties of db/db peripheral nerves. Ex-vivo electrophysiological evaluation revealed a significant increase in the excitability of db/db sciatic nerves. While the shape and kinetics of the compound action potential of db/db nerves were the same as for control nerves, we observed an increase in the after-hyperpolarization phase (AHP) under diabetic conditions. Using pharmacological inhibitors we demonstrated that both the peripheral nerve hyperexcitability (PNH) and the increased AHP were mostly mediated by the decreased activity of Kv1-channels. Importantly, we corroborated these data at the molecular level. We observed a strong reduction of Kv1.2 channel presence in the juxtaparanodal regions of teased fibers in db/db mice as compared to control mice. Quantification of the amount of both Kv1.2 isoforms in DRG neurons and in the endoneurial compartment of peripheral nerve by Western blotting revealed that less mature Kv1.2 was integrated into the axonal membranes at the juxtaparanodes. Our observation that peripheral nerve hyperexcitability present in db/db mice is at least in part a consequence of changes in potassium channel distribution suggests that the same mechanism also mediates PNH in diabetic patients. ∗Current address: Department of Physiology, UCSF, San Francisco, CA, USA.

Progesterone down-regulates the open probability of the amiloride-sensitive epithelial sodium channel via a Nedd4-2-dependent mechanism.

Activation of the mitogen-activated protein (MAP) kinase cascade by progesterone in Xenopus oocytes leads to a marked down-regulation of activity of the amiloride-sensitive epithelial sodium channel (ENaC). Here we have studied the signaling pathways involved in progesterone effect on ENaC activity. We demonstrate that: (i) the truncation of the C termini of the alphabetagammaENaC subunits results in the loss of the progesterone effect on ENaC; (ii) the effect of progesterone was also suppressed by mutating conserved tyrosine residues in the Pro-X-X-Tyr (PY) motif of the C termini of the beta and gamma ENaC subunits (beta(Y618A) and gamma(Y628A)); (iii) the down-regulation of ENaC activity by progesterone was also suppressed by co-expression ENaC subunits with a catalytically inactive mutant of Nedd4-2, a ubiquitin ligase that has been previously demonstrated to decrease ENaC cell-surface expression via a ubiquitin-dependent internalization/degradation mechanism; (iv) the effect of progesterone was significantly reduced by suppression of consensus sites (beta(T613A) and gamma(T623A)) for ENaC phosphorylation by the extracellular-regulated kinase (ERK), a MAP kinase previously shown to facilitate the binding of Nedd4 ubiquitin ligases to ENaC; (v) the quantification of cell-surface-expressed ENaC subunits revealed that progesterone decreases ENaC open probability (whole cell P(o), wcP(o)) and not its cell-surface expression. Collectively, these results demonstrate that the binding of active Nedd4-2 to ENaC is a crucial step in the mechanism of ENaC inhibition by progesterone. Upon activation of ERK, the effect of Nedd4-2 on ENaC open probability can become more important than its effect on ENaC cell-surface expression.

Inadequate and infrequent are not alike : ERPs to deviant prosodic patterns in spoken sentence comprehension

The current study on German investigates Event-Related brain Potentials (ERPs) for the perception of sentences with intonations which are infrequent (i.e. vocatives) or inadequate in daily conversation. These ERPs are compared to the processing correlates for sentences in which the syntax-to-prosody relations are congruent and used frequently during communication. Results show that perceiving an adequate but infrequent prosodic structure does not result in the same brain responses as encountering an inadequate prosodic pattern. While an early negative-going ERP followed by an N400 were observed for both the infrequent and the inadequate syntax-to-prosody association, only the inadequate intonation also elicits a P600.

Méthodes de visualisation en analyse criminelle: approche générale de conception des schémas relationnels et développement d'un catalogue de patterns

Le travail policier et l'enquête judiciaire nécessitent de prendre de nombreuses décisions : choisir quelle trace analyser, mettre sous surveillance ou en détention un suspect, sont autant de décisions qui sont prises quotidiennement par les acteurs du système judiciaire. Ces décisions font l'objet de pesées d'intérêts qui se fondent sur l'analyse de l'information accessible. C'est le rôle de l'analyse criminelle de mettre en perspective l'information colligée pour la rendre intelligible aux décideurs compétents. L'usage de représentations graphiques est notamment recommandé pour soutenir l'analyse et la communication de ces informations.Des techniques de visualisation relationnelle sont notamment exploitées dans les enquêtes judiciaires afin de faciliter le traitement d'affaires d'envergure. Les éléments pertinents de l'enquête sont représentés sous la forme de schémas décrivant les relations entre les événements et les entités d'intérêts (tel que des personnes, des objets et des traces). Les exploitations classiques de ces techniques qui s'apparentent à des graphes, sont par exemple : la représentation de réseaux criminels, de trafics de marchandises, de chronologies d'événements, ainsi que la visualisation de relations téléphoniques et financières. Dans ce contexte, la visualisation soutient un nombre importants d'objectifs, tels qu'analyser les traces et les informations collectées, évaluer a posteriori une investigation, aider à qualifier les infractions, faciliter l'appréhension d'un dossier, voire soutenir une argumentation lors du procès.La pratique intègre des outils logiciels simples qui produisent des graphiques élégants et souvent percutants. Leur utilisation semble néanmoins soulever des difficultés. Cette recherche tend à montrer qu'il existe des disparités étonnantes lors de l'exploitation de ces techniques. Des biais de raisonnement et de perception peuvent être induits, allant jusqu'à provoquer des décisions aux conséquences parfois désastreuses. Ce constat révèle la nécessité de consolider les méthodes pratiquées.Pour mettre en évidence ces difficultés, des évaluations ont été effectuées avec des praticiens et des étudiants. Elles ont permis d'établir une image empirique de l'étendue des variations de conception et d'interprétation des représentations, ainsi que de leurs impacts sur la prise de décision. La nature et la diversité des concepts à représenter, l'absence d'un consensus émergeant sur la manière de représenter les données, la diversité des solutions visuelles envisageables, les contraintes imposées par les outils exploités et l'absence d'une formalisation claire du langage, sont autant de causes supposées des difficultés.Au cours des vingt dernières années, plusieurs axes de développement ont été proposés pour traiter les difficultés observées, tels que l'amélioration des automatismes facilitant la conception d'une représentation, l'exploitation des techniques de réseaux sociaux, l'automatisation de l'identification et de l'extraction des entités dans du texte non-structuré et la définition de langages formels. Cette recherche propose une approche parallèle fondée sur une exploitation adaptée de structures de graphe et de propriétés visuelles pour optimiser la représentation en fonction des objectifs définis et de la nature des informations à représenter.Des solutions ont été recherchées selon plusieurs axes. Des recommandations générales, issues de diverses communautés de recherche liées à la visualisation, ont été recherchées afin de proposer une démarche générale de conception des schémas relationnels. Par ailleurs, le développement d'un catalogue de bonnes pratiques formalisées sous la forme de patterns de visualisation a été amorcé. Chaque pattern décrit une solution particulière pour un problème d'analyse récurrent, tel que l'analyse d'une série de cambriolages. Finalement, l'impact sur les outils de la méthodologie proposée est discuté en regard des limites qu'ils imposent. Un prototype de visualisation multidimensionnel a été élaboré.Cette recherche met en évidence les difficultés rencontrées lors de l'exploitation de représentations graphiques pour soutenir le processus de l'enquête judiciaire et propose des éléments de méthode et des innovations techniques utiles tant pour l'enseignement de la discipline que pour sa pratique.

Regulation of the voltage-gated sodium channel Nav1.7 by ubiquitin ligase Nedd4-2

Background and aim: Neuropathic pain (NP) is a frequent and disabling disorder occurring as a consequence of a direct lesion of the nervous system and recurrently associated with a positive shift toward nervous system excitability. Peripheral nerve activity is mainly carried by voltage-gated sodium channels (VGSC), with Nav1.7 isoform being an important candidate since loss of function mutations of its gene is associated with congenital inability to experience pain. Interestingly, ubiquitin ligases from the Nedd4 family are well known proteins that regulate the turnover of many membrane proteins such as VGSC and we showed Nedd2-2 is downregualted in experimental models of chronic pain. The aim of this study was to investigate the importance of Nedd4-2 in the modulation of Nav1.7 at the membrane. Methods: In vitro: whole cell patch clamp on HEK293 cell line stably expressing Nav1.7 was used to record sodium currents (INa), where the peak current of INa reflects the quantity of functional Nav1.7 expressed at the membrane. The possibility that Nedd4-2 modulates the currents was assessed by investigating the effect of its cotransfection on INa. Biotinylation of cell surface was used to isolate membrane-targeted Nav1.7. Furthermore, as the interaction between Nedd4-2 and Nav isoforms was previously reported to rely on an xPPxYx sequence (PY-motif), we mutated this latter to study its impact in the specific interaction between Nav1.7 and Nedd4-2. GST-fusion proteins composed of the Nav1.7 c terminal 66 amino acids (wild-type or PY mutated) and GST were used to pull-down Nedd4-2 from lysates. Results: Co-transfection of Nav1.7 with Nedd4-2 reduced the Nav1.7 current amplitude by ~80% (n = 36, p <0.001), without modifying the biophysical properties of INa. In addition, we show that the quantity of Nav1.7 at the membrane was decreased when Nedd4-2 was present. This effect was dependent on the PY-motif since mutations in this sequence abolished the down-regulatory effect of Nedd4-2. The importance of this motif was further confirmed by pull down experiments since the PY mutant completely eliminate the interaction with Nedd4-2. Perspectives: Altogether, these results point to the importance of Nedd4-2 as a Nav1.7 regulator through cell surface modulation of this sodium channel. Further experiments in freshly dissociated neurons from wild type and Scn1bflox/Nedd4-2Cre mice are needed to confirm in vivo these preliminary data.

Application of a roughness-length representation to parameterize energy loss in 3-D numerical simulations of large rivers

Recent technological advances in remote sensing have enabled investigation of the morphodynamics and hydrodynamics of large rivers. However, measuring topography and flow in these very large rivers is time consuming and thus often constrains the spatial resolution and reach-length scales that can be monitored. Similar constraints exist for computational fluid dynamics (CFD) studies of large rivers, requiring maximization of mesh-or grid-cell dimensions and implying a reduction in the representation of bedform-roughness elements that are of the order of a model grid cell or less, even if they are represented in available topographic data. These ``subgrid'' elements must be parameterized, and this paper applies and considers the impact of roughness-length treatments that include the effect of bed roughness due to ``unmeasured'' topography. CFD predictions were found to be sensitive to the roughness-length specification. Model optimization was based on acoustic Doppler current profiler measurements and estimates of the water surface slope for a variety of roughness lengths. This proved difficult as the metrics used to assess optimal model performance diverged due to the effects of large bedforms that are not well parameterized in roughness-length treatments. However, the general spatial flow patterns are effectively predicted by the model. Changes in roughness length were shown to have a major impact upon flow routing at the channel scale. The results also indicate an absence of secondary flow circulation cells in the reached studied, and suggest simpler two-dimensional models may have great utility in the investigation of flow within large rivers. Citation: Sandbach, S. D. et al. (2012), Application of a roughness-length representation to parameterize energy loss in 3-D numerical simulations of large rivers, Water Resour. Res., 48, W12501, doi: 10.1029/2011WR011284.

The fou2 mutation in the major vacuolar cation channel TPC1 confers tolerance to inhibitory luminal calcium.

The SV channel encoded by the TPC1 gene represents a Ca(2+)- and voltage-dependent vacuolar cation channel. Point mutation D454N within TPC1, named fou2 for fatty acid oxygenation upregulated 2, results in increased synthesis of the stress hormone jasmonate. As wounding causes Ca2+ signals and cytosolic Ca2+ is required for SV channel function, we here studied the Ca(2+)-dependent properties of this major vacuolar cation channel with Arabidopsis thaliana mesophyll vacuoles. In patch clamp measurements, wild-type and fou2 SV channels did not exhibit differences in cytosolic Ca2+ sensitivity and Ca2+ impermeability. K+ fluxes through wild-type TPC1 were reduced or even completely faded away when vacuolar Ca2+ reached the 0.1-mm level. The fou2 protein under these conditions, however, remained active. Thus, D454N seems to be part of a luminal Ca2+ recognition site. Thereby the SV channel mutant gains tolerance towards elevated luminal Ca2+. A three-fold higher vacuolar Ca/K ratio in the fou2 mutant relative to wild-type plants seems to indicate that fou2 can accumulate higher levels of vacuolar Ca(2+) before SV channel activity vanishes and K(+) homeostasis is impaired. In response to wounding fou2 plants might thus elicit strong vacuole-derived cytosolic Ca2+ signals resulting in overproduction of jasmonate.

Cell surface expression of the epithelial Na channel and a mutant causing Liddle syndrome: a quantitative approach.

The epithelial amiloride-sensitive sodium channel (ENaC) controls transepithelial Na+ movement in Na(+)-transporting epithelia and is associated with Liddle syndrome, an autosomal dominant form of salt-sensitive hypertension. Detailed analysis of ENaC channel properties and the functional consequences of mutations causing Liddle syndrome has been, so far, limited by lack of a method allowing specific and quantitative detection of cell-surface-expressed ENaC. We have developed a quantitative assay based on the binding of 125I-labeled M2 anti-FLAG monoclonal antibody (M2Ab*) directed against a FLAG reporter epitope introduced in the extracellular loop of each of the alpha, beta, and gamma ENaC subunits. Insertion of the FLAG epitope into ENaC sequences did not change its functional and pharmacological properties. The binding specificity and affinity (Kd = 3 nM) allowed us to correlate in individual Xenopus oocytes the macroscopic amiloride-sensitive sodium current (INa) with the number of ENaC wild-type and mutant subunits expressed at the cell surface. These experiments demonstrate that: (i) only heteromultimeric channels made of alpha, beta, and gamma ENaC subunits are maximally and efficiently expressed at the cell surface; (ii) the overall ENaC open probability is one order of magnitude lower than previously observed in single-channel recordings; (iii) the mutation causing Liddle syndrome (beta R564stop) enhances channel activity by two mechanisms, i.e., by increasing ENaC cell surface expression and by changing channel open probability. This quantitative approach provides new insights on the molecular mechanisms underlying one form of salt-sensitive hypertension.

Variability of gait patterns during unconstrained walking assessed by satellite positioning (GPS).

It is established that the ratio between step length (SL) and step frequency (SF) is constant over a large range of walking speed. However, few data are available about the spontaneous variability of this ratio during unconstrained outdoor walking, in particular over a sufficient number of steps. The purpose of the present study was to assess the inter- and intra-subject variability of spatio-temporal gait characteristics [SL, SF and walk ratio (WR=SL/SF)] while walking at different freely selected speeds. Twelve healthy subjects walked three times along a 100-m athletic track at: (1). a slower than preferred speed, (2). preferred speed and (3). a faster than preferred speed. Two professional GPS receivers providing 3D positions assessed the walking speed and SF with high precision (less than 0.5% error). Intra-subject variability was calculated as the variation among eight consecutive 5-s samples. WR was found to be constant at preferred and fast speeds [0.41 (0.04) m.s and 0.41 (0.05) m.s respectively] but was higher at slow speeds [0.44 (0.05) m.s]. In other words, between slow and preferred speed, the speed increase was mediated more by a change in SF than SL. The intra-subject variability of WR was low under preferred [CV, coefficient of variation = 1.9 (0.6)%] and fast [CV=1.8 (0.5)%] speed conditions, but higher under low speed condition [CV=4.1 (1.5)%]. On the other hand, the inter-subject variability of WR was 11%, 10% and 12% at slow, preferred and fast walking speeds respectively. It is concluded that the GPS method is able to capture basic gait parameters over a short period of time (5 s). A specific gait pattern for slow walking was observed. Furthermore, it seems that the walking patterns in free-living conditions exhibit low intra-individual variability, but that there is substantial variability between subjects.

Concurrent and simultaneous polydrug use among young Swiss males: use patterns and associations of number of substances used with health issues.

Background: Simultaneous polydrug use (SPU) may represent a greater incremental risk factor for human health than concurrent polydrug use (CPU). However, few studies have examined these patterns of use in relation to health issues, particularly with regard to the number of drugs used. Methods: In the present study, we have analyzed data from a representative sample of 5734 young Swiss males from the Cohort Study on Substance Use Risk Factors. Exposure to drugs (i.e., alcohol, tobacco, cannabis, and 15 other illicit drugs), as well as mental, social and physical factors, were studied through regression analysis. Results: We found that individuals engaging in CPU and SPU followed the known stages of drug use, involving initial experiences with licit drugs (e.g., alcohol and tobacco), followed by use of cannabis and then other illicit drugs. In this regard, two classes of illicit drugs were identified, including first uppers, hallucinogens and sniffed drugs; and then "harder" drugs (ketamine, heroin, and crystal meth), which were only consumed by polydrug users who were already taking numerous drugs. Moreover, we observed an association between the number of drugs used simultaneously and social issues (i.e., social consequences and aggressiveness). In fact, the more often the participants simultaneously used substances, the more likely they were to experience social problems. In contrast, we did not find any relationship between SPU and depression, anxiety, health consequences, or health. Conclusions: We identified some associations with SPU that were independent of CPU. Moreover, we found that the number of concurrently used drugs can be a strong factor associated with mental and physical health, although their simultaneous use may not significantly contribute to this association. Finally, the negative effects related to the use of one substance might be counteracted by the use of an additional substance.