From high throughput 454 GS FLX data analysis process of 16S RNA gene sequences using barcoding to bacterial community exploration

From high throughput 454 GS FLX data analysis process of 16S RNA gene sequences using barcoding to bacterial community exploratio

ModuleOrganizer: detecting modules in families of transposable elements

<p>Abstract</p> <p>Background</p> <p>Most known eukaryotic genomes contain mobile copied elements called transposable elements. In some species, these elements account for the majority of the genome sequence. They have been subject to many mutations and other genomic events (copies, deletions, captures) during transposition. The identification of these transformations remains a difficult issue. The study of families of transposable elements is generally founded on a multiple alignment of their sequences, a critical step that is adapted to transposons containing mostly localized nucleotide mutations. Many transposons that have lost their protein-coding capacity have undergone more complex rearrangements, needing the development of more complex methods in order to characterize the architecture of sequence variations.</p> <p>Results</p> <p>In this study, we introduce the concept of a <it>transposable element module</it>, a flexible motif present in at least two sequences of a family of transposable elements and built on a succession of maximal repeats. The paper proposes an assembly method working on a set of exact maximal repeats of a set of sequences to create such modules. It results in a graphical view of sequences segmented into modules, a representation that allows a flexible analysis of the transformations that have occurred between them. We have chosen as a demonstration data set in depth analysis of the transposable element Foldback in <it>Drosophila melanogaster</it>. Comparison with multiple alignment methods shows that our method is more sensitive for highly variable sequences. The study of this family and the two other families AtREP21 and SIDER2 reveals new copies of very different sizes and various combinations of modules which show the potential of our method.</p> <p>Conclusions</p> <p>ModuleOrganizer is available on the Genouest bioinformatics center at <url>http://moduleorganizer.genouest.org</url></p

Vivre avec un statut « dangereux » : l’expérience pénale d’hommes déclarés « délinquants dangereux » ou « délinquants à contrôler »

Cette recherche qualitative a comme objectif de comprendre et d’analyser l’expérience pénale d’individus ayant été déclarés « délinquants dangereux » ou « délinquants à contrôler », en vertu des dispositions légales prévues à la Partie XXIV (articles 752 et suivantes) du Code criminel canadien. Plus spécifiquement, nous avons voulu mettre en lumière comment se vit l’apposition de ce statut « dangereux » au plan personnel et social au moment des procédures judiciaires, lors de l’exécution de leur peine d’incarcération et dans le cadre de leur liberté surveillée, le cas échéant. Pour ce faire, nous avons rencontré dix-neuf hommes visés par ces dispositions légales afin de restituer en profondeur leur expérience pénale par rapport à ce « statut » légalement imposé, et ce, à partir de leur point de vue. Il en ressort que les individus faisant l’objet d’une déclaration spéciale traversent un grand bouleversement émotif, d’une part, en lien avec les délits qu’ils ont commis et d’autre part, relativement à la peine leur ayant été imposée. Ces sentiments complexes semblent se positionner en paradoxe entre un sentiment de culpabilité pour les gestes commis et l’impression d’avoir été traités injustement. Les hommes rencontrés partagent également un parcours pénal difficile marqué par de l’exclusion, du rejet ainsi que des mauvais traitements physiques ou psychologiques. Ils rapportent beaucoup d’impuissance à pouvoir faire évoluer leur situation, soit de se défaire de leur statut « dangereux ». Enfin, l’analyse des propos rapportés montre que l’imposition d’une déclaration spéciale ne constitue pas une « simple » peine puisqu’elle induit un processus de stigmatisation immédiat, discréditant et permanent qui a des implications importantes au niveau social et personnel. Ces implications ont de fait, engendré une transformation à l’égard de la perception qu’ils ont d’eux-mêmes ainsi que dans leurs façons de se comporter socialement.This thesis aims to understand and analyze the penal experiences of people who have been designated as “dangerous offenders” or “long-term offenders”; in virtue of Part XXIV (article 752 and following) of the Canadian Criminal Code. Nineteen men were interviewed as part of this study to get a deeper understanding of their experiences during their legal proceedings, while executing their prison sentence and in some cases during their long term supervision order. An important finding has shown that these individuals go through emotional turmoil; in part due to the crimes they have committed and in part due to the sentence that has been imposed on them. Additionally, some of the men felt that they had a difficult prison life marked by exclusion, rejection, and physical or psychological abuse. Over time they are left with the feeling that they are powerless in trying to improve their situation and in the end convince themselves that their situation is permanent. Labelling someone as “dangerous” appears to be much more than just a “regular” sentence. It immediately discredits them which in the end alters how they view themselves and impacts the way they interact with others

Quality of life in patients with locked-in syndrome: Evolution over a 6-year period

International audienceBackground: Improved knowledge of the quality of life (QoL) of locked-in syndrome (LIS) patients have implications for managing their care, and assists clinicians in choosing the most appropriate interventions. We performed a survey of a population of LIS patients to describe the course of the QoL of LIS patients over a 6-year period and to determine the potential predictive factors of QoL changes over time. Method: This is a study performed over a 6-year period in patients with a LIS diagnosis. Questionnaires were sent in 2007 and 2013. The following data were recorded: i) sociodemographic data; ii) clinical data related to LIS, physical/handicap status, psychological status; iii) self-reported QoL: Anamnestic Comparative Self-Assessment (ACSA); iv) Integration in life: French Reintegration to Normal Living Index (RNLI). Results: Among the 67 patients included in 2007, 39 (58 %) patients returned their questionnaire in 2013. The LIS etiology was stroke in 51 individuals. The QoL of the patients was relatively satisfactory compared to populations in other severe conditions. Twenty-one (70 %) individuals reported a stable/improved QoL between 2007 and 2013. The physical/handicap statuses in 2007 and 2013 were not related to the QoL 6 years later, with the exception of one communication parameter: the individuals who used yes-no code reported significantly lower QoL levels than those who did not in 2013. Discussion: In opposition to a widespread opinion, LIS persons report a relatively satisfactory QoL level that stays stable over time, suggesting that life with LIS is worth living. Preservation of autonomy and communication may help them to live as normal life as possible

Wages for Housework—The Canadian Context

This evening session focused on the global campaign Wages for Housework. This transversal movement highlighted the capitalist appropriation of unpaid domestic labour, and demanded its remuneration by the state. The event highlights Wages for Housework’s actions in and around Toronto and Montreal in the 1970s and 1980s, which included the Women’s Liberation Bookmobile, the paper “The Autonomy of Black Lesbian Women,” by Wilmette Brown of Black Women for Wages for Housework, and the manifesto “Fucking is Work,” by Wages Due Lesbians. These activities aimed to meet the intersecting needs of lesbian feminists, migrant workers, domestic labourers, and Black and working class women. Following the format of the Feminist Duration Reading Group in London, which Helena Reckitt initiated in 2015 to bring to light feminisms from outside the Anglo-American canon, this session will centre on an out-loud reading activity. The meeting aims to open up discussions on how feminism operates transnationally, the politics of undervalued care work and what it means to “take care.” No pre-reading or preparation is required

Up the leash: Exploring canine handlers’ perceptions of volunteering in canine-assisted interventions

To date, research on university and college based canine-assisted interventions for post-secondary students have focused on identifying the effects of spending time with therapy dogs on the well-being of participants and, to a lesser extent, exploring the effects of canine-assisted interventions on therapy dogs as a means of safeguarding canine welfare. Little empirical attention has focused on understanding the experience of volunteer canine handlers – agents at the heart of the success of canine-assisted interventions. The aim of this exploratory research was to first capture the voice of these key stakeholders to better understand their experience as canine handler volunteers and second to provide preliminary insights into their well-being. Sixty volunteer handlers with varying volunteer experience with a canine therapy program at a mid-size Canadian university responded to a series of open-ended prompts related to their volunteer work and completed a battery of well-being measures. Qualitative findings revealed that most participants identified social benefits to volunteering for themselves (64%) and for their dog (55%). The perceived impact on students (33%) and the ability to help university students (36%) were the most rewarding aspects of volunteering. Though enticed to volunteer by qualities of the CAI program (36%), participant motivations to continue volunteering were predominantly associated with personal benefits of volunteering (44%). Most handlers reported no challenges associated with volunteering (73%) and described their dog as happy after sessions (71%). Participants commonly described good therapy dogs as relaxed, calm, and respectful (66%) and strong handlers as having good awareness of their dog (48%). Quantitative findings revealed volunteer handlers reported elevated levels of positive affect (p = < 0.001, d = 1.19), greater satisfaction with life (p = < 0.001, d = 0.85) and lower levels of avoidant attachment to their therapy dog (p = < 0.001, d = -1.16) when compared to normative samples. Implications for the governing of university and college based programs and handler well-being are discussed

Droplet spatial distribution in a spray under evaporating and reacting conditions

In order to study spray combustion, an experimental test rig was developed at ONERA to partially characterize the flow conditions inside the combustion chamber of a gas turbine. Experimental campaigns using laser-based diagnostics were performed to provide an experimental database under reacting and non-reacting conditions. The paper first describes the Mie scattering image-processing to detect the droplets in the spray, and to calculate 2D maps of droplet number density and mean inter-droplet distance. The method is subsequently used to investigate the spray behavior under both reacting and non-reacting conditions according to global-averaging and phase-averaging methods. Experimental findings on the spatial droplet distribution in the spray are compared to the simple regular grid distribution and the Hertz-Chandrasekhar distribution. Results show that, under both conditions, there is an affine relationship between the inverse square root of the mean droplet number density and the nearest-neighbor inter-droplet distance. Moreover, observations suggest that the droplet spatial distribution fits more closely to a Hertz-Chandrasekhar distribution than a simple regular grid distribution, which may bring new insight for spray modeling

Influence of droplet spatial distribution on spray evaporation

In aero-engines, fuel is injected as a liquid which involves two-phase flow combustion. Consequently, different phenomena such as atomization, droplet dispersion by turbulence or spray evaporation impact combustion processes. In order to study spray combustion, an experimental test rig has been developed at ONERA to partially feature the flow conditions inside the combustion chamber of a turbo-reactor. Experimental campaigns have been conducted in non-reactive and reactive conditions to obtain an experimental database. The present paper focuses on the correlation between droplet density and the nearest-neighbour droplet distance obtained from the analysis of Mie scattering images under non-reactive conditions. Results show that the nearest-neighbour droplet distance varies linearly with the inverse square-root of mean spray density. Findings are compared with the theoretical law of Hertz-Chandrasekhar and the regular arrangement law

Impact of exposure to diesel exhaust during pregnancy on mammary gland development and milk composition in the rabbit

Exposure to fine-particulate air pollution is a major global health concern because it is associated with reduced birth weight and an increased risk of cardiovascular disease. Here we have investigated the potential for exposure to diesel exhaust during pregnancy to influence mammary gland development and milk composition. Female rabbits were therefore exposed by nose-only inhalation to either diluted diesel exhaust fumes (1 mg/m3) or clean air for 2h/day, 5 days/week, from the 3rd to the 27th days of pregnancy. On Day 28 of pregnancy, mammary glands were collected from twelve females (six controls and six diesel-exposed) and assessed for morphological and functional alterations. Milk samples were collected from eighteen dams (nine controls and nine diesel-exposed) during early (days 2 to 4) and established (days 13 to 16) lactation to verify the composition of fatty acids and major proteins and leptin levels. The mammary alveolar lumina contained numerous fat globules, and stearoyl CoA reductase expression was higher in mammary epithelia from diesel exhaust-exposed rabbits, which together suggested increased mammary lipid biosynthesis. Gas chromatography analysis of the composition of milk fatty acids revealed a sharp rise in the total fatty acid content, mainly due to monounsaturated fatty acids. Liquid chromatography-mass spectrometry analysis of milk samples enabled identification and quantification of the main rabbit milk proteins and their main phosphorylated isoforms, and revealed important changes to individual casein and whey protein contents and to their most phosphorylated isoforms during early lactation. Taken together, these findings suggest that repeated daily exposure to diesel exhaust fumes during pregnancy at urban pollution levels can influence lipid metabolism in the mammary gland and the lipid and protein composition of milk. As milk may contribute to metabolic programming, such alterations affecting milk composition should be taken into account from a public health perspective