Comparative analysis of meta-analysis methods: when to use which?

Background: Several meta-analysis methods can be used to quantitatively combine the results of a group of experiments, including the weighted mean difference, statistical vote counting, the parametric response ratio and the non-parametric response ratio. The software engineering community has focused on the weighted mean difference method. However, other meta-analysis methods have distinct strengths, such as being able to be used when variances are not reported. There are as yet no guidelines to indicate which method is best for use in each case. Aim: Compile a set of rules that SE researchers can use to ascertain which aggregation method is best for use in the synthesis phase of a systematic review. Method: Monte Carlo simulation varying the number of experiments in the meta analyses, the number of subjects that they include, their variance and effect size. We empirically calculated the reliability and statistical power in each case Results: WMD is generally reliable if the variance is low, whereas its power depends on the effect size and number of subjects per meta-analysis; the reliability of RR is generally unaffected by changes in variance, but it does require more subjects than WMD to be powerful; NPRR is the most reliable method, but it is not very powerful; SVC behaves well when the effect size is moderate, but is less reliable with other effect sizes. Detailed tables of results are annexed. Conclusions: Before undertaking statistical aggregation in software engineering, it is worthwhile checking whether there is any appreciable difference in the reliability and power of the methods. If there is, software engineers should select the method that optimizes both parameters.

Estudios de eficiencia en el uso de la luz y estimaciones de biomasa en cultivos energéticos de Salix sp. en Central New York, USA

La productividad es un factor importante que influye en la viabilidad económica de un cultivo energético de sauce y maximizarla se convierte en un tema primordial. Esta investigación está directamente relacionada con dicha característica. La productividad varía según los clones cultivados, que pueden ser mejorados y seleccionados genéticamente. Los programas genéticos requieren de una información previa (productividad media en función del porte y número de los tallos, características de las hojas, resistencia a las plagas, etc.) que ayudará a obtener clones más productivos y resistentes. Por ello, nuestra investigación consta de dos estudios: (1) Evaluación de la eficiencia del uso de la luz o LUE (Light Use Efficiency). El incremento de biomasa y la eficiencia del uso de la luz (LUE) fue estudiado en 15 clones del genero Salix durante los meses de junio a septiembre de 2011 en Belleville (Central New York, USA). Los objetivos de este estudio fueron: (1) Evaluar la eficiencia del uso de la luz en la explicación a la variación en la producción de biomasa y (2) Determinar si existen diferencias significativas entre clones evaluando el índice de área foliar (LAI) y algunos componentes de las hojas (N, P, K,…). Se concluye que la variación de biomasa está relacionada con la cantidad de luz interceptada y con la eficiencia de su uso. Dicha información debe de ser transferida para ayudar a mejorar genéticamente los futuros clones a comercializar, con el fin de maximizar la productividad y aumentar la resistencia a plagas. (2) Estimación de biomasa a través de modelos de regresión. Los estudios de investigación relacionados con la productividad requieren estimaciones no destructivas de la biomasa aérea. Sin embargo, el nivel de precisión requerido y la inversión de tiempo son excesivos para operaciones comerciales con grandes extensiones (plantaciones de 10.000 ha). Por esta razón, se estudia el nivel de especificidad (específico, intermedio y general) en la toma de datos de campo sobre los mismos 15 clones (12 de ellos se pueden agrupar en 5 grupos según su genotipo origen) del genero Salix, empleados en el estudio anterior. Para todos los niveles estudiados se observaron diferencias significativas. Pero desde nuestro punto de vista, las diferencias obtenidas no son relevantes. Para validar los modelos finalmente seleccionados se calcularon los porcentajes de error entre la biomasa estimada por los modelos de regresión calculados y la biomasa real obtenida tras los pesajes de biomasa, todo ello se realizó para cada clon según nivel de especificidad. ABSTRACT Productivity is an important factor in the economic viability of a willow crop´s, therefore, maximize it becomes a major factor. This study is directly related to this feature. Productivity, among other factors, may vary depending on different clones, which can be improved and selected genetically. Genetic programs require prior information (average productivity, size and number of stems, leaf characteristics, resistance to pests, etc.) to help you get more productive clones resistant to local pests. Our research consists of two studies: (1) Evaluation of the efficiency of use of light (LUE, Light Use Efficiency). The increase of biomass and light use efficiency (LUE) was tested on 15 clones of the genus Salix during June and September 2011 in Belleville (Central New York, USA). The objectives of this study were: (1) evaluate the light use efficiency and its relationship with the variation in biomass production and (2) determine whether there are significant differences between clones evaluating the leaf area index (LAI) and some traits of the leaves (N, P, K). We studied the correlation with the light use efficiency. It is concluded that the variation of biomass was related to the amount of light intercepted and its efficiency. Such information must be transferred to help improve future genetically clones to market in order to maximize productivity and increase resistance to pests. (2) Estimation of biomass through regression models. Research studies related to productivity estimates require precision and non destructive biomass. However, the level of accuracy required and the investment of time are excessive for large commercial operations with extensions (plantations of 10,000 ha). Precisely for this reason, we study the level of specificity (specific, intermediate and general) in making field data on the same 15 clones (12 of them can be grouped into five groups according to their genotype origin) of the genus Salix, employees in the previous study. For all levels studied some significant differences were observed. But from our practical standpoint, the differences are not relevant. Finally, to validate the selected models, we calculated the percent of bias between estimated biomass (by the regression models) and real biomass obtained after the weighing of biomass, all this process was done for each clone by level of specificity.

Determinación de la distribución de tamaño y número de partículas provenientes de motores diesel operando en trafico real con equipos embarcados

El presente trabajo se propone determinar la distribución de tamaño y número de partículas nanométricas provenientes de motores diésel con equipos embarcados en tráfico extraurbano. Para ello, se utilizaron equipos de medición de última generación en condiciones promedio de conducción en tráfico extraurbano por más de 800 km a lo largo del trayecto Madrid-Badajoz-Madrid mediante un vehículo característico del parque automotor español y se implementaron métodos novedosos y pioneros en el registro de este tipo de emisiones. Todo ello abre el camino para líneas de investigación y desarrollo que contribuirán a entender, dimensionar y cualificar el comportamiento de las partículas, así como su impacto en la calidad de vida de la población. El estudio hace dos grandes aportes al campo. Primero, permite registrar las emisiones en condiciones transitorias propias del tráfico real. Segundo, permite mantener controladas las condiciones de medición y evita la formación aleatoria de partículas provenientes de material volátil, gracias al sistema de adecuación de la muestra de gases de escape incorporado. Como resultado, se obtuvo una muestra abundante y confiable que permitió construir modelos matemáticos para calcular la emisión de partículas nanométricas, ultrafinas, finas y totales sobre las bases volumétrica, espacial y temporal en función de la pendiente del perfil orográfico de la carretera, siempre y cuando esté dentro del intervalo ±5.0%. Estos modelos de cálculo de emisiones reducen tanto los costos de experimentación como la complejidad de los equipos necesarios, y fundamentaron el desarrollo de la primera versión de una aplicación informática que calcula las partículas emitidas por un motor diésel en condiciones de tráfico extraurbano ("Partículas Emitidas por Motores Diésel, PEMDI). ABSTRACT The purpose of this research is to determine the distribution of size and number of nanometric particles that come from diesel engines by means of on-board equipment in extra-urban traffic. In order to do this, cutting-edge measuring equipment was used under average driving conditions in extra-urban traffic for more than 800 km along the Madrid-Badajoz-Madrid route using a typical vehicle from Spain's automotive population and innovative, groundbreaking registering methods for this type of emissions were used. All this paves the way for lines of research and development which should help understand, measure and characterize the behavior of such particles, as well as their impact in the quality of life of the general population. The study makes two important contributions to the field. First, it makes it possible to register emissions under transient conditions, which are characteristic to real traffic. Secondly, it provides a means to keep the measuring conditions under control and prevents the random formation of particles of volatile origin through the built-in adjustment system of the exhaust gas sample. As a result, an abundant and reliable sample was gathered, which enabled the building of mathematical models to estimate the emission of nanometric, ultrafine, fine and total particles on volumetric, spatial and temporal bases as a function of the orographic outline of the road within a ±5.0% range. These emission estimating models lower both the experimentation costs and the required equipment's complexity, and they provided the basis for the development of a first software application version that estimates the particles emitted from diesel engines under extra-urban traffic conditions (Partículas Emitidas por Motores Diésel, PEMDI).

A Polymer Model for the Structural Organization of Chromatin Loops and Minibands in Interphase Chromosomes

A quantitative model of interphase chromosome higher-order structure is presented based on the isochore model of the genome and results obtained in the field of copolymer research. G1 chromosomes are approximated in the model as multiblock copolymers of the 30-nm chromatin fiber, which alternately contain two types of 0.5- to 1-Mbp blocks (R and G minibands) differing in GC content and DNA-bound proteins. A G1 chromosome forms a single-chain string of loop clusters (micelles), with each loop ∼1–2 Mbp in size. The number of ∼20 loops per micelle was estimated from the dependence of geometrical versus genomic distances between two points on a G1 chromosome. The greater degree of chromatin extension in R versus G minibands and a difference in the replication time for these minibands (early S phase for R versus late S phase for G) are explained in this model as a result of the location of R minibands at micelle cores and G minibands at loop apices. The estimated number of micelles per nucleus is close to the observed number of replication clusters at the onset of S phase. A relationship between chromosomal and nuclear sizes for several types of higher eukaryotic cells (insects, plants, and mammals) is well described through the micelle structure of interphase chromosomes. For yeast cells, this relationship is described by a linear coil configuration of chromosomes.

Identification of a nuclear domain with deacetylase activity

Here, we describe the identification and characterization of a nuclear body (matrix-associated deacetylase body) whose formation and integrity depend on deacetylase activity. Typically, there are 20–40 0.5-μM bodies per nucleus, although the size and number can vary substantially. The structure appears to contain both class I and the recently described class II histone deacetylases (HDAC)5 and 7 along with the nuclear receptor corepressors SMRT (silencing mediator for retinoid and thyroid receptor) and N-CoR (nuclear receptor corepressor). Addition of the deacetylase inhibitors trichostatin A and sodium butyrate completely disrupt these nuclear bodies, providing a demonstration that the integrity of a nuclear body is enzyme dependent. We demonstrate that HDAC5 and 7 can associate with at least 12 distinct proteins, including several members of the NuRD and Sin3A repression complexes, and appear to define a new but related complex.

Pre-mRNA splicing in plants: characterization of Ser/Arg splicing factors.

The fact that animal introns are not spliced out in plants suggests that recognition of pre-mRNA splice sites differs between the two kingdoms. In plants, little is known about proteins required for splicing, as no plant in vitro splicing system is available. Several essential splicing factors from animals, such as SF2/ASF and SC-35, belong to a family of highly conserved proteins consisting of one or two RNA binding domain(s) (RRM) and a C-terminal Ser/Arg-rich (SR or RS) domain. These animal SR proteins are required for splice site recognition and spliceosome assembly. We have screened for similar proteins in plants by using monoclonal antibodies specific for a phosphoserine epitope of the SR proteins (mAb1O4) or for SF2/ASF. These experiments demonstrate that plants do possess SR proteins, including SF2/ASF-like proteins. Similar to the animal SR proteins, this group of proteins can be isolated by two salt precipitations. However, compared to the animal SR proteins, which are highly conserved in size and number, SR proteins from Arabidopsis, carrot, and tobacco exhibit a complex pattern of intra- and interspecific variants. These plant SR proteins are able to complement inactive HeLa cell cytoplasmic S1OO extracts that are deficient in SR proteins, yielding functional splicing extracts. In addition, plant SR proteins were active in a heterologous alternative splicing assay. Thus, these plant SR proteins are authentic plant splicing factors.

Avaliação do comportamento mecânico de corpos de prova de misturas asfálticas a quente resultantes de diferentes métodos de compactação.

Os procedimentos de dosagem Marshall e Superpave definem os teores de ligante de projeto baseados em parâmetros volumétricos. Nessa situação, sistemáticas de dosagem com tipos de compactação diferentes podem conduzir a teores de ligante de projeto distintos que definirão a vida útil dos revestimentos asfálticos. O objetivo principal desse trabalho é avaliar o comportamento mecânico de misturas asfálticas moldadas por diferentes métodos de compactação de laboratório e analisar a relação com os resultados de amostras obtidas a partir de misturas compactadas por rolagem pneumática na mesa compactadora francesa. A fase experimental consistiu na dosagem de misturas pelos métodos Marshall e Superpave (este último com dois tamanhos de moldes), além da compactação na Prensa de Cisalhamento Giratória (PCG) e da moldagem de placas na mesa compactadora. Avaliou-se o efeito do tipo de compactação, do tamanho do molde e do número de giros do Compactador Giratório Superpave (CGS) no teor de projeto, nos parâmetros volumétricos, no comportamento mecânico e no desempenho quanto à fadiga e à resistência ao afundamento em trilha de roda. Adicionalmente, foi avaliada a eficiência do método Bailey de composição granulométrica quanto à resistência à deformação permanente em função do tipo de agregado. Constatou-se que o método Bailey, por si só, não garante resistência à deformação permanente, sendo essa dependente do tipo de agregado incluindo seus parâmetros de forma. O principal produto da pesquisa, com efeitos práticos no projeto de misturas asfálticas, traduz-se na recomendação do método Superpave com molde de 100 mm (para TMN <= 12,5 mm) para volume de tráfego médio a alto em detrimento ao método Superpave com 150 mm, tendo em vista que o primeiro apresenta densificação mais semelhante às amostras preparadas na compactação por rolagem (similar ao que ocorre em pista) o que resulta em comportamento mecânico também mais próximo da realidade de campo. A utilização dos moldes de 150 mm de diâmetro no CGS pode ser viabilizada desde que se adote um número de giros menor do aquele proposto para projeto pelo Asphalt Institute (2001). Por fim, é fundamental que os ensaios e os cálculos para obtenção dos parâmetros volumétricos e escolha do teor de projeto sigam ao normatizado pela ASTM, pelo Asphalt Institute (2001) e pela ABNT.

Drosophila melanogaster larvae make nutritional choices that minimize developmental time

Organisms from slime moulds to humans carefully regulate their macronutrient intake to optimize a wide range of life history characters including survival, stress resistance, and reproductive success. However, life history characters often differ in their response to nutrition, forcing organisms to make foraging decisions while balancing the trade-offs between these effects. To date, we have a limited understanding of how the nutritional environment shapes the relationship between life history characters and foraging decisions. To gain insight into the problem, we used a geometric framework for nutrition to assess how the protein and carbohydrate content of the larval diet affected key life history traits in the fruit fly, Drosophila melanogaster. In no-choice assays, survival from egg to pupae, female and male body size, and ovariole number - a proxy for female fecundity - were maximized at the highest protein to carbohydrate (P:C) ratio (1.5:1). In contrast, development time was minimized at intermediate P:C ratios, around 1:2. Next, we subjected larvae to two-choice tests to determine how they regulated their protein and carbohydrate intake in relation to these life history traits. Our results show that larvae targeted their consumption to P:C ratios that minimized development time. Finally, we examined whether adult females also chose to lay their eggs in the P:C ratios that minimized developmental time. Using a three-choice assay, we found that adult females preferentially laid their eggs in food P:C ratios that were suboptimal for all larval life history traits. Our results demonstrate that D. melanogaster larvae make foraging decisions that trade-off developmental time with body size, ovariole number, and survival. In addition, adult females make oviposition decisions that do not appear to benefit the larvae. We propose that these decisions may reflect the living nature of the larval nutritional environment in rotting fruit. These studies illustrate the interaction between the nutritional environment, life history traits, and foraging choices in D. melanogaster, and lend insight into the ecology of their foraging decisions.