Inférence robuste à la présence des valeurs aberrantes dans les enquêtes

Cette thèse comporte trois articles dont un est publié et deux en préparation. Le sujet central de la thèse porte sur le traitement des valeurs aberrantes représentatives dans deux aspects importants des enquêtes que sont : l’estimation des petits domaines et l’imputation en présence de non-réponse partielle. En ce qui concerne les petits domaines, les estimateurs robustes dans le cadre des modèles au niveau des unités ont été étudiés. Sinha & Rao (2009) proposent une version robuste du meilleur prédicteur linéaire sans biais empirique pour la moyenne des petits domaines. Leur estimateur robuste est de type «plugin», et à la lumière des travaux de Chambers (1986), cet estimateur peut être biaisé dans certaines situations. Chambers et al. (2014) proposent un estimateur corrigé du biais. En outre, un estimateur de l’erreur quadratique moyenne a été associé à ces estimateurs ponctuels. Sinha & Rao (2009) proposent une procédure bootstrap paramétrique pour estimer l’erreur quadratique moyenne. Des méthodes analytiques sont proposées dans Chambers et al. (2014). Cependant, leur validité théorique n’a pas été établie et leurs performances empiriques ne sont pas pleinement satisfaisantes. Ici, nous examinons deux nouvelles approches pour obtenir une version robuste du meilleur prédicteur linéaire sans biais empirique : la première est fondée sur les travaux de Chambers (1986), et la deuxième est basée sur le concept de biais conditionnel comme mesure de l’influence d’une unité de la population. Ces deux classes d’estimateurs robustes des petits domaines incluent également un terme de correction pour le biais. Cependant, ils utilisent tous les deux l’information disponible dans tous les domaines contrairement à celui de Chambers et al. (2014) qui utilise uniquement l’information disponible dans le domaine d’intérêt. Dans certaines situations, un biais non négligeable est possible pour l’estimateur de Sinha & Rao (2009), alors que les estimateurs proposés exhibent un faible biais pour un choix approprié de la fonction d’influence et de la constante de robustesse. Les simulations Monte Carlo sont effectuées, et les comparaisons sont faites entre les estimateurs proposés et ceux de Sinha & Rao (2009) et de Chambers et al. (2014). Les résultats montrent que les estimateurs de Sinha & Rao (2009) et de Chambers et al. (2014) peuvent avoir un biais important, alors que les estimateurs proposés ont une meilleure performance en termes de biais et d’erreur quadratique moyenne. En outre, nous proposons une nouvelle procédure bootstrap pour l’estimation de l’erreur quadratique moyenne des estimateurs robustes des petits domaines. Contrairement aux procédures existantes, nous montrons formellement la validité asymptotique de la méthode bootstrap proposée. Par ailleurs, la méthode proposée est semi-paramétrique, c’est-à-dire, elle n’est pas assujettie à une hypothèse sur les distributions des erreurs ou des effets aléatoires. Ainsi, elle est particulièrement attrayante et plus largement applicable. Nous examinons les performances de notre procédure bootstrap avec les simulations Monte Carlo. Les résultats montrent que notre procédure performe bien et surtout performe mieux que tous les compétiteurs étudiés. Une application de la méthode proposée est illustrée en analysant les données réelles contenant des valeurs aberrantes de Battese, Harter & Fuller (1988). S’agissant de l’imputation en présence de non-réponse partielle, certaines formes d’imputation simple ont été étudiées. L’imputation par la régression déterministe entre les classes, qui inclut l’imputation par le ratio et l’imputation par la moyenne sont souvent utilisées dans les enquêtes. Ces méthodes d’imputation peuvent conduire à des estimateurs imputés biaisés si le modèle d’imputation ou le modèle de non-réponse n’est pas correctement spécifié. Des estimateurs doublement robustes ont été développés dans les années récentes. Ces estimateurs sont sans biais si l’un au moins des modèles d’imputation ou de non-réponse est bien spécifié. Cependant, en présence des valeurs aberrantes, les estimateurs imputés doublement robustes peuvent être très instables. En utilisant le concept de biais conditionnel, nous proposons une version robuste aux valeurs aberrantes de l’estimateur doublement robuste. Les résultats des études par simulations montrent que l’estimateur proposé performe bien pour un choix approprié de la constante de robustesse.

Évaluation des besoins d’informations des intervenants en protection de la jeunesse

Domaine en plein développement, le transfert des connaissances (TC) se définit, comme l’ensemble des activités, des mécanismes et des processus favorisant l’utilisation de connaissances pertinentes (tacites et empiriques) par un public cible tel que les intervenants psychosociaux. Cette recherche vise à améliorer l’efficacité des méthodes linéaires écrites de TC en identifiant mieux les besoins d’information des intervenants en protection de la jeunesse. Notons que les méthodes linéaires écrites de TC désignent des outils d’information écrits unidirectionnels tels que les revues, les publications, les sites Internet, etc. Le premier objectif est de déterminer les catégories de besoins exprimés par les intervenants, c’est-à-dire déterminer si les besoins rapportés par des intervenants se regroupent en types ou sortes de besoins. Le deuxième objectif est d’établir l’importance relative de chacune de ces catégories. Enfin, cette étude vise à déterminer si ces besoins diffèrent selon les caractéristiques des intervenants ou de l’environnement. Deux facteurs sont étudiés, l’expérience de l’intervenant et la direction pour laquelle celui-ci travaille (Direction des services milieu à l’enfance ou Direction des services milieu à l’adolescence et ressources). Un devis mixte séquentiel exploratoire a été développé. Lors de la première étape, une analyse thématique a été effectuée à partir des réponses à une question ouverte posée aux membres de trois équipes et à partir d’un document résumant les requêtes effectuées auprès de l’équipe de la bibliothèque du Centre jeunesse de Montréal. Les résultats permettent de répondre au premier objectif de ce mémoire. En effet, les analyses ont permis de créer un arbre thématique comprenant 42 éléments classés hiérarchiquement. Les besoins se regroupent en deux thèmes généraux, soit les besoins qui concernent les « opérations » (c’est-à-dire l’action de l’intervenant) et les besoins concernant les « systèmes » (c’est-à-dire les éléments sur lesquels peuvent porter l’intervention). Cette dernière catégorie se subdivise entre l’usager, ses environnements et le contexte culturel et sociétal. Lors de la deuxième étape, une analyse de la variance (ANOVA) et une analyse de variance multivariée (MANOVA) ont été effectuées à partir des réponses de 82 intervenants à un questionnaire en ligne structuré selon les catégories de besoins d’informations déterminées à l’étape qualitative précédente. Les résultats permettent de répondre au deuxième objectif de ce mémoire et de mesurer le degré de force ou d’importance de chacune des catégories de besoins, identifiées lors de la première étape, selon les intervenants eux-mêmes. Les besoins ont ainsi pu être classés par ordre décroissant d’importance. Il a été possible de définir un groupe de neuf besoins prioritaires (portant sur l’animation, les caractéristiques personnelles des usagers, les caractéristiques des parents et leurs relations avec l’enfant, ainsi que l’intervention interculturelle et les problématiques sociales) et un autre groupe de sept besoins moins élevés (portant sur les autres « opérations » et les services professionnels dont a bénéficié l’usager). L’interprétation de ces résultats indique que les besoins en TC des intervenants se limitent aux informations qui concernent directement leur mandat, leur pratique ou les problématiques rencontrées. Les résultats de cette étape ont également permis de répondre au troisième objectif de ce mémoire. En effet, les résultats indiquent que l’importance ressentie des besoins (sur une échelle de 1 à 7) ne diffère pas significativement selon la direction pour laquelle travaille l’intervenant, mais elle diffère significativement selon l’expérience de ce dernier (moins de 10 ans ou plus de 10 ans). Cette différence est discutée et plusieurs hypothèses explicatives sont envisagées telles que l’accumulation de connaissances liée à l’expérience ou les changements cognitifs liés à l’expertise. Enfin, dans la discussion, les résultats sont mis en contexte parmi les autres types de besoins existants et les autres caractéristiques des connaissances qui doivent être prises en considération. Cela permet de formuler des recommandations pour améliorer la production de documents écrits ainsi que pour poursuivre la recherche dans le domaine de l’évaluation des besoins de TC. Bien que présentant certaines limites méthodologiques, cette recherche ouvre la voie au développement de meilleurs outils d’évaluation des besoins et à l’amélioration des techniques de transfert linéaires écrites.

Multi-site time-trend analysis of soil fertility management effects on crop production in sub-Saharan West Africa

Soil fertility constraints to crop production have been recognized widely as a major obstacle to food security and agro-ecosystem sustainability in sub-Saharan West Africa. As such, they have led to a multitude of research projects and policy debates on how best they should be overcome. Conclusions, based on long-term multi-site experiments, are lacking with respect to a regional assessment of phosphorus and nitrogen fertilizer effects, surface mulched crop residues, and legume rotations on total dry matter of cereals in this region. A mixed model time-trend analysis was used to investigate the effects of four nitrogen and phosphorus rates, annually applied crop residue dry matter at 500 and 2000 kg ha^-1, and cereal-legume rotation versus continuous cereal cropping on the total dry matter of cereals and legumes. The multi-factorial experiment was conducted over four years at eight locations, with annual rainfall ranging from 510 to 1300 mm, in Niger, Burkina Faso, and Togo. With the exception of phosphorus, treatment effects on legume growth were marginal. At most locations, except for typical Sudanian sites with very low base saturation and high rainfall, phosphorus effects on cereal total dry matter were much lower with rock phosphate than with soluble phosphorus, unless the rock phosphate was combined with an annual seed-placement of 4 kg ha^-1 phosphorus. Across all other treatments, nitrogen effects were negligible at 500 mm annual rainfall but at 900 mm, the highest nitrogen rate led to total dry matter increases of up to 77% and, at 1300 mm, to 183%. Mulch-induced increases in cereal total dry matter were larger with lower base saturation, reaching 45% on typical acid sandy Sahelian soils. Legume rotation effects tended to increase over time but were strongly species-dependent.

Cambios observados en las variables clínicas y paraclínicas en las primeras 48 horas de hospitalización en la Unidad de Cuidados Intensivos de pacientes con neumonía severa adquirida en la comunidad y su relación con la mortalidad

El pronóstico de la Neumonía Adquirida en la Comunidad Severa (NAC-S) depende de decisiones terapéuticas instauradas tempranamente. Los cambios fisiológicos ocurridos en las primeras horas pueden ser difíciles de detectar. No existe ningún modelo para la determinación temprana del éxito de la terapia instaurada en NAC-S. Metodología: Descripción de la totalidad de los pacientes con NAC-S hospitalizados en la Unidad de Cuidado Intensivo de la Fundación Cardioinfantil entre los años 2008 y 2012 haciendo comparaciones entre grupos (muertos vs. supervivientes) y entre momentos (0, 24 y 48 horas desde el ingreso a la UCI) y realizando regresión logística binaria. Resultados: Entre los pacientes que fallecieron la necesidad de soporte vasoactivo fue mayor en todos los momentos evaluados (sig=0.001), en la línea de base tuvieron mayores requerimientos de la Fracción Inspirada de O2 (mediana 0.55% vs. 0.50%, sig=0.011), a las 24 horas tuvieron pH (mediana 7.345 vs.7.370, sig=0.025) y tensión arterial diastólica (mediana 58.5mmHg vs.61.0mmHg, sig =0.049) menores, y a las 48 horas glicemia (mediana 157mg/dL vs.142mg/dL, sig =0.026) creatinina (mediana 1.1mg/dL vs.0.7mg/dL, sig =0.062) y nitrógeno ureico (mediana 35mg/dL vs. 22mg/dL, sig =0.003) mayores comparados con los pacientes que sobrevivieron. Entre los pacientes supervivientes hubo una disminución de la frecuencia cardiaca entre las 0 y 24 horas (mediana 97lpm vs. 86lpm, sig =0.000) y entre las 0 y las 48 horas (mediana 97lpm vs. 81lpm, sig=0.000) y una disminución de los neutrófilos entre las 0 y las 48 horas (mediana 9838 vs. 8617, sig=0.062). Conclusiones: Nuestros hallazgos sugieren la existencia de una secuencia de fenómenos fisiopatológicos que al ser reconocida temprana y claramente permitiría establecer un plan de reanimación más especifico y eficaz. Estas diferencias se pueden plantear en el contexto de un modelo mixto predictivo

Fertility and schooling : how this relation changed between 1995 and 2005 in Colombia

En este trabajo se pretende evaluar la existencia de cambios en la relación entre fecundidad y escolaridad en Colombia para mujeres de 30 a 40 años de edad entre 1995 y 2005. Para tal efecto se utilizan modelos de Poisson sobre la Encuesta Nacional de Demografía y Salud 1995 y 2005. Se encuentra una reducción en la fecundidad durante el periodo y su relación inversa con la escolaridad, que puede ser explicada por el efecto de la educación sobre otras variables como el incremento en el conocimiento sobre los programas de control natal. Se encuentra además que el efecto de culminar un nivel educativo sobre la fecundidad es mayor en 2005 que en 1995. De otro lado, se encuentra que las diferencias entre zonas urbanas y rurales son significativas en la explicación de la fecundidad en Colombia durante la última década.

Breast cancer incidence and overdiagnosis in Catalonia (Spain)

Early detection of breast cancer (BC) with mammography may cause overdiagnosis and overtreatment, detecting tumors which would remain undiagnosed during a lifetime. The aims of this study were: first, to model invasive BC incidence trends in Catalonia (Spain) taking into account reproductive and screening data; and second, to quantify the extent of BC overdiagnosis. We modeled the incidence of invasive BC using a Poisson regression model. Explanatory variables were: age at diagnosis and cohort characteristics (completed fertility rate, percentage of women that use mammography at age 50, and year of birth). This model also was used to estimate the background incidence in the absence of screening. We used a probabilistic model to estimate the expected BC incidence if women in the population used mammography as reported in health surveys. The difference between the observed and expected cumulative incidences provided an estimate of overdiagnosis.Incidence of invasive BC increased, especially in cohorts born from 1940 to 1955. The biggest increase was observed in these cohorts between the ages of 50 to 65 years, where the final BC incidence rates more than doubled the initial ones. Dissemination of mammography was significantly associated with BC incidence and overdiagnosis. Our estimates of overdiagnosis ranged from 0.4% to 46.6%, for women born around 1935 and 1950, respectively.Our results support the existence of overdiagnosis in Catalonia attributed to mammography usage, and the limited malignant potential of some tumors may play an important role. Women should be better informed about this risk. Research should be oriented towards personalized screening and risk assessment tools

Use of Large Clear-Cuts by Wilson’s Warbler in an Eastern Canadian Boreal Forest

Wilson’s Warbler (Cardellina pusilla; WIWA) has been declining for several decades, possibly because of habitat loss. We compared occupancy of territorial males in two habitat types of Québec’s boreal forest, alder (Alnus spp.) scrubland and recent clear-cuts. Singing males occurred in clusters, their occupancy was similar in both habitats, but increased with the amount of alder or clear-cut within 400 m of point-count stations. A despotic distribution of males between habitats appeared unlikely, because there were no differences in morphology between males captured in clear-cuts vs. alder. Those results contrast with the prevailing view, mostly based on western populations, that WIWA are wetland or riparian specialists, and provide the first evidence for a preference for large tracts of habitat in this species. Clear-cuts in the boreal forest may benefit WIWA by supplying alternative nesting habitat. However, the role of clear-cuts as source or sink habitats needs to be addressed with data on reproduction.

Ecological and life-history traits predict bee species responses to environmental disturbances

The ability to predict the responses of ecological communities and individual species to human-induced environmental change remains a key issue for ecologists and conservation managers alike. Responses are often variable among species within groups making general predictions difficult. One option is to include ecological trait information that might help to disentangle patterns of response and also provide greater understanding of how particular traits link whole clades to their environment. Although this ‘‘trait-guild” approach has been used for single disturbances, the importance of particular traits on general responses to multiple disturbances has not been explored. We used a mixed model analysis of 19 data sets from throughout the world to test the effect of ecological and life-history traits on the responses of bee species to different types of anthropogenic environmental change. These changes included habitat loss, fragmentation, agricultural intensification, pesticides and fire. Individual traits significantly affected bee species responses to different disturbances and several traits were broadly predictive among multiple disturbances. The location of nests – above vs. below ground – significantly affected response to habitat loss, agricultural intensification, tillage regime (within agriculture) and fire. Species that nested above ground were on average more negatively affected by isolation from natural habitat and intensive agricultural land use than were species nesting below ground. In contrast below-ground-nesting species were more negatively affected by tilling than were above-ground nesters. The response of different nesting guilds to fire depended on the time since the burn. Social bee species were more strongly affected by isolation from natural habitat and pesticides than were solitary bee species. Surprisingly, body size did not consistently affect species responses, despite its importance in determining many aspects of individuals’ interaction with their environment. Although synergistic interactions among traits remain to be explored, individual traits can be useful in predicting and understanding responses of related species to global change.

Meta-analysis: a unifying meta-likelihood approach framing unobserved heterogeneity, study covariates, publication bias, and study quality

OBJECTIVES: This contribution provides a unifying concept for meta-analysis integrating the handling of unobserved heterogeneity, study covariates, publication bias and study quality. It is important to consider these issues simultaneously to avoid the occurrence of artifacts, and a method for doing so is suggested here. METHODS: The approach is based upon the meta-likelihood in combination with a general linear nonparametric mixed model, which lays the ground for all inferential conclusions suggested here. RESULTS: The concept is illustrated at hand of a meta-analysis investigating the relationship of hormone replacement therapy and breast cancer. The phenomenon of interest has been investigated in many studies for a considerable time and different results were reported. In 1992 a meta-analysis by Sillero-Arenas et al. concluded a small, but significant overall effect of 1.06 on the relative risk scale. Using the meta-likelihood approach it is demonstrated here that this meta-analysis is due to considerable unobserved heterogeneity. Furthermore, it is shown that new methods are available to model this heterogeneity successfully. It is argued further to include available study covariates to explain this heterogeneity in the meta-analysis at hand. CONCLUSIONS: The topic of HRT and breast cancer has again very recently become an issue of public debate, when results of a large trial investigating the health effects of hormone replacement therapy were published indicating an increased risk for breast cancer (risk ratio of 1.26). Using an adequate regression model in the previously published meta-analysis an adjusted estimate of effect of 1.14 can be given which is considerably higher than the one published in the meta-analysis of Sillero-Arenas et al. In summary, it is hoped that the method suggested here contributes further to a good meta-analytic practice in public health and clinical disciplines.

Evaluation of milk urea nitrogen as a diagnostic of protein feeding

An evaluation of milk urea nitrogen (MUN) as a diagnostic of protein feeding in dairy cows was performed using mean treatment data (n = 306) from 50 production trials conducted in Finland (n = 48) and Sweden (n = 2). Data were used to assess the effects of diet composition and certain animal characteristics on MUN and to derive relationships between MUN and the efficiency of N utilization for milk production and urinary N excretion. Relationships were developed using regression analysis based on either models of fixed factors or using mixed models that account for between-experiment variations. Dietary crude protein (CP) content was the best single predictor of MUN and accounted for proportionately 0.778 of total variance [ MUN (mg/dL) = -14.2 + 0.17 x dietary CP content (g/kg dry matter)]. The proportion of variation explained by this relationship increased to 0.952 when a mixed model including the random effects of study was used, but both the intercept and slope remained unchanged. Use of rumen degradable CP concentration in excess of predicted requirements, or the ratio of dietary CP to metabolizable energy as single predictors, did not explain more of the variation in MUN (R-2 = 0.767 or 0.778, respectively) than dietary CP content. Inclusion of other dietary factors with dietary CP content in bivariate models resulted in only marginally better predictions of MUN (R-2 = 0.785 to 0.804). Closer relationships existed between MUN and dietary factors when nutrients (CP to metabolizable energy) were expressed as concentrations in the diet, rather than absolute intakes. Furthermore, both MUN and MUN secretion (g/d) provided more accurate predictions of urinary N excretion (R-2 = 0.787 and 0.835, respectively) than measurements of the efficiency of N utilization for milk production (R-2 = 0.769). It is concluded that dietary CP content is the most important nutritional factor influencing MUN, and that measurements of MUN can be utilized as a diagnostic of protein feeding in the dairy cow and used to predict urinary N excretion.

Crossbred cow adoption and milk market participation in a multivariate count data framework

Cross-bred cow adoption is an important and potent policy variable precipitating subsistence household entry into emerging milk markets. This paper focuses on the problem of designing policies that encourage and sustain milkmarket expansion among a sample of subsistence households in the Ethiopian highlands. In this context it is desirable to measure households’ ‘proximity’ to market in terms of the level of deficiency of essential inputs. This problem is compounded by four factors. One is the existence of cross-bred cow numbers (count data) as an important, endogenous decision by the household; second is the lack of a multivariate generalization of the Poisson regression model; third is the censored nature of the milk sales data (sales from non-participating households are, essentially, censored at zero); and fourth is an important simultaneity that exists between the decision to adopt a cross-bred cow, the decision about how much milk to produce, the decision about how much milk to consume and the decision to market that milk which is produced but not consumed internally by the household. Routine application of Gibbs sampling and data augmentation overcome these problems in a relatively straightforward manner. We model the count data from two sites close to Addis Ababa in a latent, categorical-variable setting with known bin boundaries. The single-equation model is then extended to a multivariate system that accommodates the covariance between crossbred-cow adoption, milk-output, and milk-sales equations. The latent-variable procedure proves tractable in extension to the multivariate setting and provides important information for policy formation in emerging-market settings

The detection of atmospheric rivers in atmospheric reanalyses and their links to British winter floods and the large-scale climatic circulation

Atmospheric Rivers (ARs), narrow plumes of enhanced moisture transport in the lower troposphere, are a key synoptic feature behind winter flooding in midlatitude regions. This article develops an algorithm which uses the spatial and temporal extent of the vertically integrated horizontal water vapor transport for the detection of persistent ARs (lasting 18 h or longer) in five atmospheric reanalysis products. Applying the algorithm to the different reanalyses in the vicinity of Great Britain during the winter half-years of 1980–2010 (31 years) demonstrates generally good agreement of AR occurrence between the products. The relationship between persistent AR occurrences and winter floods is demonstrated using winter peaks-over-threshold (POT) floods (with on average one flood peak per winter). In the nine study basins, the number of winter POT-1 floods associated with persistent ARs ranged from approximately 40 to 80%. A Poisson regression model was used to describe the relationship between the number of ARs in the winter half-years and the large-scale climate variability. A significant negative dependence was found between AR totals and the Scandinavian Pattern (SCP), with a greater frequency of ARs associated with lower SCP values.

Extending the Lincoln–Petersen estimator for multiple identifications in one source

The Lincoln–Petersen estimator is one of the most popular estimators used in capture–recapture studies. It was developed for a sampling situation in which two sources independently identify members of a target population. For each of the two sources, it is determined if a unit of the target population is identified or not. This leads to a 2 × 2 table with frequencies f11, f10, f01, f00 indicating the number of units identified by both sources, by the first but not the second source, by the second but not the first source and not identified by any of the two sources, respectively. However, f00 is unobserved so that the 2 × 2 table is incomplete and the Lincoln–Petersen estimator provides an estimate for f00. In this paper, we consider a generalization of this situation for which one source provides not only a binary identification outcome but also a count outcome of how many times a unit has been identified. Using a truncated Poisson count model, truncating multiple identifications larger than two, we propose a maximum likelihood estimator of the Poisson parameter and, ultimately, of the population size. This estimator shows benefits, in comparison with Lincoln–Petersen’s, in terms of bias and efficiency. It is possible to test the homogeneity assumption that is not testable in the Lincoln–Petersen framework. The approach is applied to surveillance data on syphilis from Izmir, Turkey.

Meta-analysis of relationships between enteric methane yield and milk fatty acid profile in dairy cattle

Various studies have indicated a relationship between enteric methane (CH4) production and milk fatty acid (FA) profiles of dairy cattle. However, the number of studies investigating such a relationship is limited and the direct relationships reported are mainly obtained by variation in CH4 production and milk FA concentration induced by dietary lipid supplements. The aim of this study was to perform a meta-analysis to quantify relationships between CH4 yield (per unit of feed and unit of milk) and milk FA profile in dairy cattle and to develop equations to predict CH4 yield based on milk FA profile of cows fed a wide variety of diets. Data from 8 experiments encompassing 30 different dietary treatments and 146 observations were included. Yield of CH4 measured in these experiments was 21.5 ± 2.46 g/kg of dry matter intake (DMI) and 13.9 ± 2.30 g/ kg of fat- and protein-corrected milk (FPCM). Correlation coefficients were chosen as effect size of the relationship between CH4 yield and individual milk FA concentration (g/100 g of FA). Average true correlation coefficients were estimated by a random-effects model. Milk FA concentrations of C6:0, C8:0, C10:0, C16:0, and C16:0-iso were significantly or tended to be positively related to CH4 yield per unit of feed. Concentrations of trans-6+7+8+9 C18:1, trans-10+11 C18:1, cis- 11 C18:1, cis-12 C18:1, cis-13 C18:1, trans-16+cis-14 C18:1, and cis-9,12 C18:2 in milk fat were significantly or tended to be negatively related to CH4 yield per unit of feed. Milk FA concentrations of C10:0, C12:0, C14:0-iso, C14:0, cis-9 C14:1, C15:0, and C16:0 were significantly or tended to be positively related to CH4 yield per unit of milk. Concentrations of C4:0, C18:0, trans-10+11 C18:1, cis-9 C18:1, cis-11 C18:1, and cis- 9,12 C18:2 in milk fat were significantly or tended to be negatively related to CH4 yield per unit of milk. Mixed model multiple regression and a stepwise selection procedure of milk FA based on the Bayesian information criterion to predict CH4 yield with milk FA as input (g/100 g of FA) resulted in the following prediction equations: CH4 (g/kg of DMI) = 23.39 + 9.74 × C16:0- iso – 1.06 × trans-10+11 C18:1 – 1.75 × cis-9,12 C18:2 (R2 = 0.54), and CH4 (g/kg of FPCM) = 21.13 – 1.38 × C4:0 + 8.53 × C16:0-iso – 0.22 × cis-9 C18:1 – 0.59 × trans-10+11 C18:1 (R2 = 0.47). This indicated that milk FA profile has a moderate potential for predicting CH4 yield per unit of feed and a slightly lower potential for predicting CH4 yield per unit of milk. Key words: methane , milk fatty acid profile , metaanalysis , dairy cattle

Detecting regular sound changes in linguistics as events of concerted evolution

Background: Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family. Results: Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular sound change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations. Conclusions: We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group.