ABCtoolbox: a versatile toolkit for approximate Bayesian computations.

BACKGROUND: The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. RESULTS: Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. CONCLUSION: ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results.

List of books by Iowa authors : collected by the Auxiliary Committee of the Iowa Commission, Louisiana Purchase Exposition, for the exhibit of books by Iowa authors in the Iowa State Building, St. Louis, 1904

This is a list of Iowa authors that grew out of the efforts of the auxiliary committee of the Iowa Commission of the Louisiana Purchase Exposition to bring together a collection of books by Iowa authors for the Iowa State building at the St. Louis Exposition.

Construcción de un índice de calidad ocupacional (ICO) para el análisis de la inserción profesional de los graduados universitarios = Building an employment quality index (EQI) to analyse graduates’ access to the labour market

En este trabajo se propone la construcción de un índice de calidad ocupacional (ICO) a partir de los datos de la Encuesta de Inserción Laboral de los Graduados de las Universidades Catalanas realizada por la Agencia para la Calidad del Sistema Universitario de Catalunya (AQU), que ha de permitir un mejor análisis de la información que proporciona la encuesta y facilitar su comparación con estudios similares. La encuesta se realiza tres años después de la graduación. En este artículo, se utiliza la segunda encuesta realizada el año 2005 entre 11.456 graduados (52,63%) de la promoción 2001 (AQU, 2005, Serra-Ramoneda, 2007). El índice se ha elaborado a partir de los indicadores objetivos ‘tipo y duración del contrato laboral’, ‘retribución económica’, ‘adecuación entre la formación universitaria y el empleo’ a los que se otorga una puntuación ponderada según las respuestas dadas por los graduados. La suma de las puntuaciones se matiza con un coeficiente derivado del indicador subjetivo ‘satisfacción con el trabajo en general’. A partir de la información proporcionada por el índice, se realiza un análisis comparativo del nivel de calidad ocupacional que han logrado los graduados de áreas de conocimiento, ámbitos de trabajo, ramas de actividad y ubicaciones territoriales del empleo diferentes. Los resultados obtenidos permiten observar que entre los graduados catalanes los siguientes hechos son buenos predictores de la calidad de la ocupación: haber estudiado una carrera que no sea de Humanidades, ser un hombre, haber desempeñado durante la carrera un trabajo relacionado con los estudios, estar ocupado en la construcción, en instituciones financieras o en servicios a empresas, haber tenido algún tipo de movilidad por motivos de trabajo, trabajar fuera de Cataluña y hacerlo en empresas grandes, especialmente con más de 500 trabajadores. Finalmente, se presentan algunas reflexiones y propuestas que pueden resultar de interés para la orientación de los estudiantes y la planificación universitaria

The temporoparietal fascia flap: a versatile tool in head and neck reconstruction.

PURPOSE OF REVIEW: The article reviews recent significant advances and current applications of the temporoparietal fascia flap (TPFF) in head and neck surgery. RECENT FINDINGS: The recent literature describes a wide span of new applications of the TPFF in many areas. Significant developments and refinements in the reconstruction of orbitomaxillary composite defects and orbital exenteration cavities are reported. The TPFF combined with alloplastic framework is gaining in importance in external ear reconstruction. Innovative prefabricated skin or soft-tissue grafts based on the TPFF are used to restore facial contour or in the reconstruction of complex facial defects. The free TPFF finds a role in laryngotracheal reconstruction as a vascular carrier to support cartilage grafts. SUMMARY: Owing to its reliability and unequalled structural properties, the TPFF still plays a central role in facial reconstruction. Future investigation will likely incorporate the free TPFF as a vascular carrier of bioengineered tissues, such as cartilage and mucosa, for various head and neck indications.

Building a Better Future.... Together, We Can: Iowa's Program and Budget Fiscal Years 2016-2017, January 2015

Governor Terry E. Branstad's FY2016-17 budget report.

Building the niche through time: using 13,000 years of data to predict the effects of climate change on three tree species in Europe

Aim Species distribution models (SDMs) based on current species ranges underestimate the potential distribution when projected in time and/or space. A multi-temporal model calibration approach has been suggested as an alternative, and we evaluate this using 13,000 years of data. Location Europe. Methods We used fossil-based records of presence for Picea abies, Abies alba and Fagus sylvatica and six climatic variables for the period 13,000 to 1000yr bp. To measure the contribution of each 1000-year time step to the total niche of each species (the niche measured by pooling all the data), we employed a principal components analysis (PCA) calibrated with data over the entire range of possible climates. Then we projected both the total niche and the partial niches from single time frames into the PCA space, and tested if the partial niches were more similar to the total niche than random. Using an ensemble forecasting approach, we calibrated SDMs for each time frame and for the pooled database. We projected each model to current climate and evaluated the results against current pollen data. We also projected all models into the future. Results Niche similarity between the partial and the total-SDMs was almost always statistically significant and increased through time. SDMs calibrated from single time frames gave different results when projected to current climate, providing evidence of a change in the species realized niches through time. Moreover, they predicted limited climate suitability when compared with the total-SDMs. The same results were obtained when projected to future climates. Main conclusions The realized climatic niche of species differed for current and future climates when SDMs were calibrated considering different past climates. Building the niche as an ensemble through time represents a way forward to a better understanding of a species' range and its ecology in a changing climate.

Computational problems in perfect phylogeny haplotyping: Typing without calling the allele

A haplotype is an m-long binary vector. The XOR-genotype of two haplotypes is the m-vector of their coordinate-wise XOR. We study the following problem: Given a set of XOR-genotypes, reconstruct their haplotypes so that the set of resulting haplotypes can be mapped onto a perfect phylogeny (PP) tree. The question is motivated by studying population evolution in human genetics and is a variant of the PP haplotyping problem that has received intensive attention recently. Unlike the latter problem, in which the input is '' full '' genotypes, here, we assume less informative input and so may be more economical to obtain experimentally. Building on ideas of Gusfield, we show how to solve the problem in polynomial time by a reduction to the graph realization problem. The actual haplotypes are not uniquely determined by the tree they map onto and the tree itself may or may not be unique. We show that tree uniqueness implies uniquely determined haplotypes, up to inherent degrees of freedom, and give a sufficient condition for the uniqueness. To actually determine the haplotypes given the tree, additional information is necessary. We show that two or three full genotypes suffice to reconstruct all the haplotypes and present a linear algorithm for identifying those genotypes.

Typologie des sols sur gypse et végétation associée en Suisse

Soils on gypsum are well known in dry climates, but were very little described in temperate climate, and never in Switzerland. This study aims to describe soils affected by gypsum in temperate climate and to understand their pedogenesis using standard laboratory analyzes performed on ten Swiss soils located on gypsum outcrops. In parallel, phytosociological relevés described the vegetation encountered in gypsiferous grounds. Gypsification process (secondary gypsum enrichment by precipitation) was observed in all soils. It was particularly important in regions where potential evapotranspiration exceed strongly precipitations in summer (central Valais, Chablais under influence of warm wind). Gypsum contents were regularly measured above 20% in deep horizons, and exceeded locally 70%, building a white, indurate horizon. However, the absence of such a gypsic horizon in the top soil hindered the use of gypsosol (according to the Référentiel pédologique, BAIZE & GIRARD 2009), the typical name of soils affected by gypsum, but restricted to dry regions. As all soils had a high content of magnesium carbonates, they were logically classified in the group of DOLOMITOSOLS. However, according to the World Reference Base for Soil Resources (IUSS 2014), five soils can be classified among the Gypsisols, criteria being here less restricting. These soils are characterized by a coarse texture and a particulate brittle structure making a filtering substrate. They allow water to flow easily taking nutrients. They are not retained by clay, which does generally not exceed 1% of the fine material. The saturation of calcium blocks the breakdown of organic matter. Moreover, these soils are often rejuvenated by erosion caused by the rough relief due to gypsum (landslides, sinkholes, cliffs and slopes). Hence, the vegetation is mainly characterized by calcareous and drought tolerant species, with mostly xerothermophilic beech (Cephalanthero-Fagenion) and pine forests (Erico-Pinion sylvestris) in lowlands, or subalpine heathlands (Ericion) and dry calcareous grasslands (Caricion firmae) in higher elevations.

Building Iowa's Future, Board of Regents Annual Report, 2012

This report is the annual report for the Board of Regents.

Filamin depletion blocks endoplasmic spreading and destabilizes force-bearing adhesions

Cell motility is an essential process that depends on a coherent, cross-linked actin cytoskeleton that physically coordinates the actions of numerous structural and signaling molecules. The actin cross-linking protein, filamin (Fln), has been implicated in the support of three-dimensional cortical actin networks capable of both maintaining cellular integrity and withstanding large forces. Although numerous studies have examined cells lacking one of the multiple Fln isoforms, compensatory mechanisms can mask novel phenotypes only observable by further Fln depletion. Indeed, shRNA-mediated knockdown of FlnA in FlnB¿/¿ mouse embryonic fibroblasts (MEFs) causes a novel endoplasmic spreading deficiency as detected by endoplasmic reticulum markers. Microtubule (MT) extension rates are also decreased but not by peripheral actin flow, because this is also decreased in the Fln-depleted system. Additionally, Fln-depleted MEFs exhibit decreased adhesion stability that appears in increased ruffling of the cell edge, reduced adhesion size, transient traction forces, and decreased stress fibers. FlnA¿/¿ MEFs, but not FlnB¿/¿ MEFs, also show a moderate defect in endoplasm spreading, characterized by initial extension followed by abrupt retractions and stress fiber fracture. FlnA localizes to actin linkages surrounding the endoplasm, adhesions, and stress fibers. Thus we suggest that Flns have a major role in the maintenance of actin-based mechanical linkages that enable endoplasmic spreading and MT extension as well as sustained traction forces and mature focal adhesions.

Targeting vascular NADPH oxidase 1 blocks tumor angiogenesis through a PPARα mediated mechanism.

Reactive oxygen species, ROS, are regulators of endothelial cell migration, proliferation and survival, events critically involved in angiogenesis. Different isoforms of ROS-generating NOX enzymes are expressed in the vasculature and provide distinct signaling cues through differential localization and activation. We show that mice deficient in NOX1, but not NOX2 or NOX4, have impaired angiogenesis. NOX1 expression and activity is increased in primary mouse and human endothelial cells upon angiogenic stimulation. NOX1 silencing decreases endothelial cell migration and tube-like structure formation, through the inhibition of PPARα, a regulator of NF-κB. Administration of a novel NOX-specific inhibitor reduced angiogenesis and tumor growth in vivo in a PPARα dependent manner. In conclusion, vascular NOX1 is a critical mediator of angiogenesis and an attractive target for anti-angiogenic therapies.