Making neurophysiological data analysis reproducible. Why and how?

Manuscript submitted to "The Journal of Physiology (Paris)". Second version.Reproducible data analysis is an approach aiming at complementing classical printed scientific articles with everything required to independently reproduce the results they present. ''Everything'' covers here: the data, the computer codes and a precise description of how the code was applied to the data. A brief history of this approach is presented first, starting with what economists have been calling replication since the early eighties to end with what is now called reproducible research in computational data analysis oriented fields like statistics and signal processing. Since efficient tools are instrumental for a routine implementation of these approaches, a description of some of the available ones is presented next. A toy example demonstrates then the use of two open source software for reproducible data analysis: the ''Sweave family'' and the org-mode of emacs. The former is bound to R while the latter can be used with R, Matlab, Python and many more ''generalist'' data processing software. Both solutions can be used with Unix-like, Windows and Mac families of operating systems. It is argued that neuroscientists could communicate much more efficiently their results by adopting the reproducible research paradigm from their lab books all the way to their articles, thesis and books

Encyclopedic Memory: Long-Term Memory Capacity for Knowledge Vocabulary in Middle School

This article is a synthesis of unpublished and published experiments showing that elementary memory scores (words and pictures immediate recall; delayed recall, recognition), which are very sensitive to aging and in pharmacological protocols, have little or no correlation with school achievement. The alternative assumption developed is that school achievement strongly depends on the long-term memory of scholastic knowledge (history, literature, sciences, maths, etc), called encyclopedic memory.A longitudinal study from the grade 6 to the grade 9 of a cohort of eight classes of a French college, was undertaken in order to observe the implication of the encyclopedic vocabulary (i.e. Julius Caesar, Manhattan, Shangaï, Uranus, vector) in school performance. An inventory in the school textbooks gives approximately 6000 encyclopedic words in grade 6, to 24000 in grade 9. The encyclopedic storage capacity was estimated at the end of each year by a multiple-choice questionnaire with random samples of words (800 items; 8 subject subjects). The results show an estimation of 2500 words acquired at the end of grade 6, to 17000 at the end of the grade 9. The correlations are from .61 to .72 between the score of encyclopedic memory and the average school grades

Comment sécuriser en cabinet de montagne la prise en charge des blessés de sport d'hiver ? (proposition d'une check-list)

La sécurité du patient est primordiale et l'utilisation de check-lists dans le domaine médical se développe. L'objectif de ce travail est de proposer une liste de critères à vérifier lors de la prise en charge en cabinet de montagne des patients traumatisés. Le but n'est pas de dicter une conduite à tenir aux professionnels mais de proposer un outil d'aide à la pratique permettant de constater un oubli et de le corriger avant qu'il ne devienne problématique. Nous avons d'abord réalisé une enquête de pratique permettant d'établir une pré-liste de critères. Une validation de chaque critère était ensuite nécessaire pour l'inclusion finale : soit par transposition de recommandations de domaines proches de la médecine de montagne, soit par avis d'experts. On obtient ainsi une liste de vingt-trois points essentiels de la prise en charge d'un patient traumatisé sans considérer une zone douloureuse en particulier. Il revient à chaque médecin de décliner cette check-list générale en check-list spécifique d'un type de traumatisme, selon les données actualisées de la science. Pour ne pas rendre chronophage la vérification, nous proposons d'intégrer la plupart des critères dans le logiciel médical. Cette check-list permet une amélioration des pratiques en évitant les oublis les plus fréquents. Elle vise à améliorer la sécurité des patients, avec des soins de qualité fondés sur des preuves. La principale limite à son utilisation est sa réactualisation nécessaire. C'est un premier travail sur le sujet qui introduit l'intérêt de l'utilisation de check-lists dans ce domaine particulier qu'est la médecine de montagne. Une validation secondaire est nécessaire.Patients' safety is paramount and to contribute to this the use of check-lists is currently developing in the medical field. The purpose of this work is to propose a list of criteria which need to be checked in mountain practices during the medical care of injured patients. The objective is not to dictate a procedure to professionals but to offer an aid to practice enabling to spot an oversight and correct it before it becomes an issue. We first realized a practice survey which enabled us to establish a pre-list of criteria. A validation of each of them has then been necessary before their final integration to the list: validation came either from transposition of recommendations acknowledged in medical fields close to mountain medicine or from expert opinion. Thanks to this process we obtain a list of twenty-three essential points for the medical care of injured patients without considering a specific painful area. lt is up to every physician to adapt this general check-list and create a specific one tailored to a given trauma according to state-of-the-art scientific knowledge. To avoid making the checking task time-consuming we propose to integrate most of the criteria into the medical software. This check-list enables to improve practices by preventing the most frequent oversights from happening. The check-list aims at improving patients' safety thanks to proof-based quality care. The main limit to its use is the need for regular updates. This work is a first step on this topic. lt shows the interest of using check-lists in the specific field of mountain medicine. A secondary validation is necessary.GRENOBLE1-BU Médecine pharm. (385162101) / SudocSudocFranceF

The compensatory potential of increased immigration following intensive American mink population control is diluted by male-biased dispersal

Attempts to mitigate the impact of invasive species on native ecosystems increasingly target large land masses where control, rather than eradication, is the management objective. Depressing numbers of invasive species to a level where their impact on native biodiversity is tolerable requires overcoming the impact of compensatory immigration from non-controlled portions of the landscape. Because of the expected scale-dependency of dispersal, the overall size of invasive species management areas relative to the dispersal ability of the controlled species will determine the size of any effectively conserved core area unaffected by immigration from surrounding areas. However, when dispersal is male-biased, as in many mammalian invasive carnivores, males may be overrepresented amongst immigrants, reducing the potential growth rate of invasive species populations in re-invaded areas. Using data collected from a project that gradually imposed spatially comprehensive control on invasive American mink (Neovison vison) over a 10,000 km2 area of NE Scotland, we show that mink captures were reduced to almost zero in 3 years, whilst there was a threefold increase in the proportion of male immigrants. Dispersal was often long distance and linking adjacent river catchments, asymptoting at 38 and 31 km for males and females respectively. Breeding and dispersal were spatially heterogeneous, with 40 % of river sections accounting for most captures of juvenile (85 %), adult female (65 %) and immigrant (57 %) mink. Concentrating control effort on such areas, so as to turn them into “attractive dispersal sinks” could make a disproportionate contribution to the management of recurrent re-invasion of mainland invasive species management areas

Rural populations of the red fox Vulpes vulpes show little evidence of reproductive senescence

International audienceThe ageing theory predicts fast and early senescence for fast-living species. We investigated whether the pattern of senescence of a medium-sized, fast-living and heavily-culled mammal, the red fox (Vulpes vulpes), fits this theoretical prediction. We used cross-sectional data from a large-scale culling experiment of red fox conducted over six years in five study sites located in two regions of France to explore the age-related variation in reproductive output. We used both placental scars and embryos counts from 755 vixens’ carcasses aged by the tooth cementum method (age range : 1-10) , as proxies for litter size. Mean litter size per vixen was 4.7 ± 1.4. Results from Generalized Additive Mixed Models revealed a significant variation of litter size with age. Litter size peaked at age 4 with 5. 0 ± 0.2 placental scars and decreased there after by 0.5 cubs per year. Interestingly, we found a different age-specific variation when counting embryos which reached a plateau at age 5-6 (5.5 ± 0.2)and decreased slower than placent al scars across older ages, pointing out embryo resorption as a potential physiological mechanism of reproductive senescence in the red fox. Contrary to our expectation, reproductive senescence is weak, occurs late in life and takes place at an age reached by less than 11.7% of the population such that very few females exhibit senescence in these heavily culled populations

Spatially explicit poisoning risk affects survival rates of an obligate scavenger

Obligate scavengers such as vultures provide critical ecosystem services and their populations have undergone severe declines in Asia and Africa. Intentional poisoning is a major threat to vultures in Africa, yet the impact on vulture populations of where poisoned carcasses are positioned is not known. We used re-sightings of 183 African white-backed vultures captured and tagged in two regions of South Africa, some 200 km apart, to estimate spatial differences in relative survival rates across life stages. Juvenile survival rates were similar in the two regions, whilst subadult and adult survival rates differed significantly. Using agent-based modelling, we show that this pattern of relative survival rates is consistent between regions that differ in intensity of poisoning, despite the proximity of the two regions. This may have important consequences for vulture conservation and the targeting of conservation efforts, particularly with regard to the efficacy of “vulture safe zones” around vulture breeding populations

Rights and duties in parenting practices

[EN] Parenting Practices (PP) studies is a way to inquire about the exercise of rights and duties within the home, where members operate in complex networks of interactive relations in (un) dynamic equilibrium with the context. The PC transcend into the public domain by registering variability in the socialization of children. The aim of this presentation is to transmit the results for the PC in the exercise of rights and duties of three non-standard research (qualitative) with interviews to mothers (2009-2013). The privileged were directed to the omission of the Duties of the child as happens in the title of the Rights of the Child were found. In fact, PP denote an external locus of control mothers regarding schooling for children older than 10 years who were absent from school until the abandonment. Also, respected internal locus of control of children who avoided collaborate on housework. However, mothers and children agreed long exposure to television, early departures and shaping couples. The PP avoided guide children towards external locus of control demanded by the exercise of duties by children and frustration tolerance (postponement of pleasure) as in the case of school requirements and collaboration in household activities. The study of the rankings in the PC to consider timely interventions in programs and projects is recommended.[ES] El objetivo de esta presentación es exponer los resultados de tres investigaciones cualitativas sobre el ejercicio de los derechos y deberes en las PC, realizadas en Buenos Aires, Argentina. Ellas incluyeron entrevistas a madres de niños con Necesidades Básicas Insatisfechas concretadas entre los años 2009 y 2013. Su análisis, reveló que en este conjunto de hogares se llevaban a cabo tres tipos de PC: imposición, guía y libre albedrío, siendo esta última la más utilizada. Como parte de esta práctica, los niños administraban sus horarios de sueño, vigilia y tiempo libre, sin intervención de sus padres. Se observó, por ejemplo, que los niños mayores de 10 años decidían sobre aspectos relativos a su escolaridad, ausentándose de manera progresiva a la escuela, hasta el abandono. Estas prácticas eran respetadas por sus padres. Por defecto, no se ejercitó la postergación del placer (tolerancia a la frustración), debido a que se dejaba hacer a los niños a voluntad. También se advirtió una tendencia al embarazo adolescente y a la formación de parejas de niños entre 14 a 16 años, con consentimiento de sus padres. En este sentido, aun cuando los niños residían en un hogar en contacto con sus padres, con una oferta de alimentos y escolar, el ejercicio indiscriminado del libre albedrío de los niños ponía en riesgo la propia salud y el desarrollo pleno, cercenando sus propios derechos. Se recomienda profundizar este tipo de estudios para promover intervenciones oportunas en programas y proyectos destinados a orientar a los padres en aspectos relacionados con la constitución de los niños como sujetos de Derechos y DeberesSolans, AP.; Rotstein De Gueller, B.; Caggianelli, A. (2015). Configuración de derechos y deberes en las prácticas de crianza. Revista sobre la infancia y la adolescencia. (9):60-73. doi:10.4995/reinad.2015.3881.SWORD60739Ander-Egg, E. (2009). Diccionario de Pedagogía. Buenos Aires: Magisterio Río de la Plata.Becker, H. (2009). Trucos del oficio. Buenos Aires: Siglo XXI.Código Civil de la República Argentina y Legislación Complementaria. (2003). Buenos Aires: Euros EditoresGarrido Genovés, V. (2005). Qué es la psicología criminológica. Madrid: Biblioteca Nueva.González Tornaría, M. L., Vandemeulebroecke, L. y Colpin, H. (2001). Pedagogía Familiar. Aportes desde la teoría y la investigación. Montevideo: Trilce.Harrington, C. y Boardman, S. (1997). Path to Success. U.S.A.: HarvardLieury, A., y Fenouille, F. (2006). Motivación y éxito escolar. Buenos Aires: Fondo de Cultura Económica.Prada, M.A., Actis, W. y Pereda, C. (1989). Infancia Moderna y Designación Social. Madrid: Mostoles.Quintero Velásquez, A. M. (2007). Diccionario especializado en Familia y Género. Buenos Aires: Lumen-HumanitasRotstein de Gueller B., Soláns, A.P. (2013). Prácticas de Crianza. Necesidades Básicas Insatisfechas y Problemas Escolares. Berlín: Editorial Académica Espa-ol

Positive demographic effects of nest surveillance campaigns to counter illegal harvest of the Bonelli's eagle in Sicily (Italy)

Illegal trade in wildlife has been identified as one of the main challenges to wildlife conservation. In 2010, an illegal trade-ring trafficking in birds of prey was uncovered in Sicily (southern Italy). This illegal trade targeted the three most endangered species in Italy: Bonelli's eagle Aquila fasciata, Lanner falcon Falco biarmicus and Egyptian vulture Neophron percnopterus, all of them long-lived territorial raptors threatened with extinction across their European distribution. Illegal harvest primarily involved young birds and eggs taken from nests. After the discovery of these activities, surveillance camps and camera traps connected to the mobile Global System for Mobile communications network were established in nine Bonelli's eagle breeding sites in which illegal harvest was reported. Surveillance activities resulted in a sharp reduction in illegal harvest that has contributed to the recent increase in population size and number of breeding pairs of Bonelli's eagle in the island. This population represents 95% of the entire Italian population and is catalogued as Critically Endangered in this country. Importantly, our results highlight the impact of illegal harvest on the population dynamics of endangered species as demonstrated by a population viability analysis. This is particularly important in the case of insular species for which demographic recovery due to immigration from other geographic areas is unlikely. Systematic patrols by forestry police authorities, a resolute application of Convention on International Trade in Endangered Species legislation via legal punishment, and the requirement of including all live captive specimens used for falconry in an obligatory DNA data bank would contribute to reducing the risk of extinction for small populations of endangered species of birds of prey