Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data

Background: The identification of biologically interesting genes in a temporal expression profiling dataset is challenging and complicated by high levels of experimental noise. Most statistical methods used in the literature do not fully exploit the temporal ordering in the dataset and are not suited to the case where temporal profiles are measured for a number of different biological conditions. We present a statistical test that makes explicit use of the temporal order in the data by fitting polynomial functions to the temporal profile of each gene and for each biological condition. A Hotelling T2-statistic is derived to detect the genes for which the parameters of these polynomials are significantly different from each other. Results: We validate the temporal Hotelling T2-test on muscular gene expression data from four mouse strains which were profiled at different ages: dystrophin-, beta-sarcoglycan and gammasarcoglycan deficient mice, and wild-type mice. The first three are animal models for different muscular dystrophies. Extensive biological validation shows that the method is capable of finding genes with temporal profiles significantly different across the four strains, as well as identifying potential biomarkers for each form of the disease. The added value of the temporal test compared to an identical test which does not make use of temporal ordering is demonstrated via a simulation study, and through confirmation of the expression profiles from selected genes by quantitative PCR experiments. The proposed method maximises the detection of the biologically interesting genes, whilst minimising false detections. Conclusion: The temporal Hotelling T2-test is capable of finding relatively small and robust sets of genes that display different temporal profiles between the conditions of interest. The test is simple, it can be used on gene expression data generated from any experimental design and for any number of conditions, and it allows fast interpretation of the temporal behaviour of genes. The R code is available from V.V. The microarray data have been submitted to GEO under series GSE1574 and GSE3523

Ex Post Assessment of European Competition Policy: Buyer Power in Concentration Cases

acceptedVersio

Recovery: What does this mean to patients with low back pain?

Copyright © 2009, American College of Rheumatology. This article is freely available through the publisher’s link below.Objective - To explore patients' perceptions of recovery from low back pain, about which little is known. Methods - A qualitative study was conducted in which 36 participants, either recovered or unrecovered from low back pain, participated in focus groups. Interviews were audiorecorded and transcribed verbatim. Framework analysis was used to identify emergent themes and domains of recovery. Results - Patients' views of recovery encompassed a range of factors that can be broadly classified into the domains of symptom attenuation, improved capacity to perform a broad scope of self-defined functional activities, and achievement of an acceptable quality of life. An interactive model is proposed to describe the relationships between these domains, cognitive appraisal of the pain experience, and self-rated recovery. Pain attenuation alone was not a reliable indicator of recovery. Conclusion - The construct of recovery for typical back pain patients seeking primary care is more complex than previously recognized and is a highly individual construct, determined by appraisal of the impact of symptoms on daily functional activities as well as quality of life factors. These findings will be valuable for reassessing how to optimize measures of recovery from low back pain by addressing the spectrum of factors patients consider meaningful

Biological evaluation and molecular modelling of didanosine derivatives

Five carbonate derivatives of 50-O-20,30-dideoxyinosine (DDI, 1) have been synthesized by combination with aliphatic alcohols, with their in vitro anti-HIV activity and cytotoxicity being evaluated afterward in human peripheral blood mononuclear cells (PBMCs). One particular compound, namely DDI-Penta, exhibited an outstanding performance because it was found to have both a higher inhibitory potency and a lower cytotoxicity than the lead compound, resulting in a 100 enhancement in its selectivity index. In order to further study this phenomenon, the ability of these derivatives to bind to the cytoplasmatic nucleotidase (ncN-II) was studied by in silico methods. Also, the higher calculated lipophilicity of the synthesized compounds was proposed to improve their permeability through the cell membrane since said lipophilicity would allow a higher concentration of the corresponding prodrug inside the infected cell. Overall, a combination of an optimal lipophilicity and the ability of DDI-Penta to bind to ncN-II is suggested due to the higher potency and lower cytotoxicity observed for this compound. Based on the reported findings, we believe that the combination of certain aliphatic alcohols and DDI through a carbonate linkage could significantly increase the performance of this class of therapeutic compounds; therefore, it merits further evaluations.Fil: Ravetti, Soledad. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Farmacia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: de Candia, Cristian Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; ArgentinaFil: Gualdesi, María Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Farmacia; ArgentinaFil: Pampuro, Sandra Esther. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; ArgentinaFil: Turk, Gabriela Julia Ana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; ArgentinaFil: Quevedo, Mario Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Farmacia; ArgentinaFil: Briñon, Margarita Cristina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Farmacia; Argentin

Non-universal Voronoi cell shapes in amorphous ellipsoid packings

In particulate systems with short-range interactions, such as granular matter or simple fluids, local structure plays a pivotal role in determining the macroscopic physical properties. Here, we analyse local structure metrics derived from the Voronoi diagram of configurations of oblate ellipsoids, for various aspect ratios $\alpha$ and global volume fractions $\phi_g$. We focus on jammed static configurations of frictional ellipsoids, obtained by tomographic imaging and by discrete element method simulations. In particular, we consider the local packing fraction $\phi_l$, defined as the particle's volume divided by its Voronoi cell volume. We find that the probability $P(\phi_l)$ for a Voronoi cell to have a given local packing fraction shows the same scaling behaviour as function of $\phi_g$ as observed for random sphere packs. Surprisingly, this scaling behaviour is further found to be independent of the particle aspect ratio. By contrast, the typical Voronoi cell shape, quantified by the Minkowski tensor anisotropy index $\beta=\beta_0^{2,0}$, points towards a significant difference between random packings of spheres and those of oblate ellipsoids. While the average cell shape $\beta$ of all cells with a given value of $\phi_l$ is very similar in dense and loose jammed sphere packings, the structure of dense and loose ellipsoid packings differs substantially such that this does not hold true. This non-universality has implications for our understanding of jamming of aspherical particles.Comment: 6 pages, 5 figure

In vitro dynamics of HIV-1 BF intersubtype recombinants genomic regions involved in the regulation of gene expression

HIV-1 intersubtype recombination is a very common phenomenon that has been shown to frequently affect different viral genomic regions. Vpr and Tat are viral proteins known to interact with viral promoter (LTR) during the replication cycle. This interaction is mainly involved in the regulation of viral gene expression, so, any structural changes in the LTR and/or these regulatory proteins may have an important impact on viral replication and spread. It has been reported that these genetic structures underwent recombination in BF variants widely spread in South America. To gain more insight of the consequences of the BF intersubtype recombination phenomenon on these different but functionally related genomic regions we designed and performed and in vitro study that allowed the detection and recovery of intersubtype recombinants sequences and its subsequent analysis. Our results indicate that recombination affects differentially these regions, showing evidence of a time-space relationship between the changes observed in the viral promoter and the ones observed in the Vpr/Tat coding region. This supports the idea of intersubtype recombination as a mechanism that promotes biological adaptation and compensates fitness variations

Viral replication is enhanced by an HIV-1 intersubtype recombination-derived Vpu protein

Background: Multiple HIV-1 intersubtype recombinants have been identified in human populations. Previous studies from our lab group have shown that the epidemic in Argentina is characterized by the high prevalence of a circulating recombinant form, CRF12_BF, and many related BF recombinant forms. In these genomic structures a recombination breakpoint frequently involved the vpu coding region. Due to the scarce knowledge of Vpu participation in the virion release process and its impact on pathogenesis and of the functional capacities of intersubtype recombinant Vpu proteins, the aim of this work was to perform a comparative analysis on virion release capacity and relative replication capacity among viral variants harboring either a BF recombinant Vpu or a subtype B Vpu. Results: Our results showed that BF recombinant Vpu was associated to an increased viral particles production when compared to WT B variant in tetherin-expressing cell lines. This observation was tested in the context of a competition assay between the above mentioned variants. The results showed that the replication of the BF Vpu-harboring variant was more efficient in cell cultures than subtype B, reaching a higher frequency in the viral population in a short period of time. Conclusion: This study showed that as a result of intersubtype recombination, a structurally re-organized HIV-1 Vpu has an improved in vitro capacity of enhancing viral replication, and provides evidence of the changes occurring in this protein function that could play an important role in the successful spread of intersubtype recombinant variants.Fil: de Candia, Cristian Ariel. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología. Centro Nacional de Referencia Para El Sida; ArgentinaFil: Espada, Constanza Eleonora. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología. Centro Nacional de Referencia Para El Sida; ArgentinaFil: Duette, Gabriel. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología. Centro Nacional de Referencia para el Sida; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ghiglione, Yanina Alexandra. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología. Centro Nacional de Referencia para el Sida; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Turk, Gabriela Julia Ana. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología. Centro Nacional de Referencia para el Sida; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Salomon, Horacio Eduardo. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología. Centro Nacional de Referencia para el Sida; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Carobene, Mauricio. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología. Centro Nacional de Referencia para el Sida; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Progressive refinement rendering of implicit surfaces

The visualisation of implicit surfaces can be an inefficient task when such surfaces are complex and highly detailed. Visualising a surface by first converting it to a polygon mesh may lead to an excessive polygon count. Visualising a surface by direct ray casting is often a slow procedure. In this paper we present a progressive refinement renderer for implicit surfaces that are Lipschitz continuous. The renderer first displays a low resolution estimate of what the final image is going to be and, as the computation progresses, increases the quality of this estimate at an interactive frame rate. This renderer provides a quick previewing facility that significantly reduces the design cycle of a new and complex implicit surface. The renderer is also capable of completing an image faster than a conventional implicit surface rendering algorithm based on ray casting

Simulating the Common Envelope Phase of a Red Giant Using SPH and Uniform Grid Codes

We use three-dimensional hydrodynamical simulations to study the rapid infall phase of the common envelope interaction of a red giant branch star of mass equal to 0.88 \msun and a companion star of mass ranging from 0.9 down to 0.1 \msun. We first compare the results obtained using two different numerical techniques with different resolutions, and find overall very good agreement. We then compare the outcomes of those simulations with observed systems thought to have gone through a common envelope. The simulations fail to reproduce those systems in the sense that most of the envelope of the donor remains bound at the end of the simulations and the final orbital separations between the donor's remnant and the companion, ranging from 26.8 down to 5.9 \rsun, are larger than the ones observed. We suggest that this discrepancy vouches for recombination playing an essential role in the ejection of the envelope and/or significant shrinkage of the orbit happening in the subsequent phase.Comment: 45 pages, 19 figures, accepted to Ap