The effects of dominance, regular inbreeding and sampling design on Q(ST), an estimator of population differentiation for quantitative traits.

To test whether quantitative traits are under directional or homogenizing selection, it is common practice to compare population differentiation estimates at molecular markers (F(ST)) and quantitative traits (Q(ST)). If the trait is neutral and its determinism is additive, then theory predicts that Q(ST) = F(ST), while Q(ST) > F(ST) is predicted under directional selection for different local optima, and Q(ST) < F(ST) is predicted under homogenizing selection. However, nonadditive effects can alter these predictions. Here, we investigate the influence of dominance on the relation between Q(ST) and F(ST) for neutral traits. Using analytical results and computer simulations, we show that dominance generally deflates Q(ST) relative to F(ST). Under inbreeding, the effect of dominance vanishes, and we show that for selfing species, a better estimate of Q(ST) is obtained from selfed families than from half-sib families. We also compare several sampling designs and find that it is always best to sample many populations (>20) with few families (five) rather than few populations with many families. Provided that estimates of Q(ST) are derived from individuals originating from many populations, we conclude that the pattern Q(ST) > F(ST), and hence the inference of directional selection for different local optima, is robust to the effect of nonadditive gene actions.

Postglacial recolonization at a snail's pace (Trochulus villosus): confronting competing refugia hypotheses using model selection.

The localization of Last Glacial Maximum (LGM) refugia is crucial information to understand a species' history and predict its reaction to future climate changes. However, many phylogeographical studies often lack sampling designs intensive enough to precisely localize these refugia. The hairy land snail Trochulus villosus has a small range centred on Switzerland, which could be intensively covered by sampling 455 individuals from 52 populations. Based on mitochondrial DNA sequences (COI and 16S), we identified two divergent lineages with distinct geographical distributions. Bayesian skyline plots suggested that both lineages expanded at the end of the LGM. To find where the origin populations were located, we applied the principles of ancestral character reconstruction and identified a candidate refugium for each mtDNA lineage: the French Jura and Central Switzerland, both ice-free during the LGM. Additional refugia, however, could not be excluded, as suggested by the microsatellite analysis of a population subset. Modelling the LGM niche of T. villosus, we showed that suitable climatic conditions were expected in the inferred refugia, but potentially also in the nunataks of the alpine ice shield. In a model selection approach, we compared several alternative recolonization scenarios by estimating the Akaike information criterion for their respective maximum-likelihood migration rates. The 'two refugia' scenario received by far the best support given the distribution of genetic diversity in T. villosus populations. Provided that fine-scale sampling designs and various analytical approaches are combined, it is possible to refine our necessary understanding of species responses to environmental changes.

State of genomics and epigenomics research in the perspective of HIV cure.

PURPOSE OF REVIEW: One of the seven key scientific priorities identified in the road map on HIV cure research is to 'determine the host mechanisms that control HIV replication in the absence of therapy'. This review summarizes the recent work in genomics and in epigenetic control of viral replication that is relevant for this mission. RECENT FINDINGS: New technologies allow the joint analysis of host and viral transcripts. They identify the patterns of antisense transcription of the viral genome and its role in gene regulation. High-throughput studies facilitate the assessment of integration at the genome scale. Integration site, orientation and host genomic context modulate the transcription and should also be assessed at the level of single cells. The various models of latency in primary cells can be followed using dynamic study designs to acquire transcriptome and proteome data of the process of entry, maintenance and reactivation of latency. Dynamic studies can be applied to the study of transcription factors and chromatin modifications in latency and upon reactivation. SUMMARY: The convergence of primary cell models of latency, new high-throughput quantitative technologies applied to the study of time series and the identification of compounds that reactivate viral transcription bring unprecedented precision to the study of viral latency.

Spatially and genetically distinct control of seed germination by phytochromes A and B.

Phytochromes phyB and phyA mediate a remarkable developmental switch whereby, early upon seed imbibition, canopy light prevents phyB-dependent germination, whereas later on, it stimulates phyA-dependent germination. Using a seed coat bedding assay where the growth of dissected embryos is monitored under the influence of dissected endosperm, allowing combinatorial use of mutant embryos and endosperm, we show that canopy light specifically inactivates phyB activity in the endosperm to override phyA-dependent signaling in the embryo. This interference involves abscisic acid (ABA) release from the endosperm and distinct spatial activities of phytochrome signaling components. Under the canopy, endospermic ABA opposes phyA signaling through the transcription factor (TF) ABI5, which shares with the TF PIF1 several target genes that negatively regulate germination in the embryo. ABI5 enhances the expression of phytochrome signaling genes PIF1, SOMNUS, GAI, and RGA, but also of ABA and gibberellic acid (GA) metabolic genes. Over time, weaker ABA-dependent responses eventually enable phyA-dependent germination, a distinct type of germination driven solely by embryonic growth.

Towards a theory of the credit-risk balance sheet

This article designs what it calls a Credit-Risk Balance Sheet (the risk being that of default by customers), a tool which, in principle, can contribute to revealing, controlling and managing the bad debt risk arising from a company¿s commercial credit, whose amount can represent a significant proportion of both its current and total assets.To construct it, we start from the duality observed in any credit transaction of this nature, whose basic identity can be summed up as Credit = Risk. ¿Credit¿ is granted by a company to its customer, and can be ranked by quality (we suggest the credit scoring system) and ¿risk¿ can either be assumed (interiorised) by the company itself or transferred to third parties (exteriorised).What provides the approach that leads to us being able to talk with confidence of a real Credit-Risk Balance Sheet with its methodological robustness is that the dual vision of the credit transaction is not, as we demonstrate, merely a classificatory duality (a double risk-credit classification of reality) but rather a true causal relationship, that is, a risk-credit causal duality.Once said Credit-Risk Balance Sheet (which bears a certain structural similarity with the classic net asset balance sheet) has been built, and its methodological coherence demonstrated, its properties ¿static and dynamic¿ are studied.Analysis of the temporal evolution of the Credit-Risk Balance Sheet and of its applications will be the object of subsequent works.

Iowa Comprehensive Highway Safety Plan, September 2006

In Iowa, hundreds of people die and thousands more are injured on our public roadways each year despite decades of efforts to end this su�ffering. Past safety e�efforts have resulted in Iowans bene�fiting from one of the best state roadway systems in the nation. Due to multi-agency e�efforts, Iowa has achieved 90 percent compliance with the state’s mandatory front seat belt use law, earned the nation’s second-lowest percent of alcohol involvement in fatal crashes and made safety gains in system-wide roadway design and operational improvements. Despite these ongoing e�efforts, the state’s annual average of 445 deaths and thousands of life-changing injuries is a tragic toll and an unacceptable public health epidemic in our state. To save more lives on our roadways, Iowans must be challenged to think �differently about lifesaving measures addressing young drivers, safety belts, and motorcycle helmet use and accept innovative designs such as roundabouts. Iowa must apply evidence-based strategies and create a safety culture that motivates all citizens to travel more responsibly. They must demand a lower level of tolerance for Iowa’s roadway deaths and injuries. The Iowa Comprehensive Highway Safety Plan (CHSP) engages diverse safety stakeholders and charts the course for this state, bringing to bear sound science and the power of shared community values to change the culture and achieve a standard of safer travel for our citizens. How many roadway deaths and injuries are too many? Iowa’s highway safety stakeholders believe that, “One death is one too many” and e�effective culture-changing policy and program strategies must be implemented to help reduce this death toll from an annual average of 445 to 400 by the year 2015.

Growth, optical characterization, and laser operation of a stoichiometric crystal KYb(WO4)(2)

We present our recent achievements in the growing and optical characterization of KYb(WO4)2 (hereafter KYbW) crystals and demonstrate laser operation in this stoichiometric material. Single crystals of KYbW with optimal crystalline quality have been grown by the top-seeded-solution growth slow-cooling method. The optical anisotropy of this monoclinic crystal has been characterized, locating the tensor of the optical indicatrix and measuring the dispersion of the principal values of the refractive indices as well as the thermo-optic coefficients. Sellmeier equations have been constructed valid in the visible and near-IR spectral range. Raman scattering has been used to determine the phonon energies of KYbW and a simple physical model is applied for classification of the lattice vibration modes. Spectroscopic studies (absorption and emission measurements at room and low temperature) have been carried out in the spectral region near 1 µm characteristic for the ytterbium transition. Energy positions of the Stark sublevels of the ground and the excited state manifolds have been determined and the vibronic substructure has been identified. The intrinsic lifetime of the upper laser level has been measured taking care to suppress the effect of reabsorption and the intrinsic quantum efficiency has been estimated. Lasing has been demonstrated near 1074 nm with 41% slope efficiency at room temperature using a 0.5 mm thin plate of KYbW. This laser material holds great promise for diode pumped high-power lasers, thin disk and waveguide designs as well as for ultrashort (ps/fs) pulse laser systems.

Towards a theory of the credit-risk balance sheet

This article designs what it calls a Credit-Risk Balance Sheet (the risk being that of default by customers), a tool which, in principle, can contribute to revealing, controlling and managing the bad debt risk arising from a company¿s commercial credit, whose amount can represent a significant proportion of both its current and total assets.To construct it, we start from the duality observed in any credit transaction of this nature, whose basic identity can be summed up as Credit = Risk. ¿Credit¿ is granted by a company to its customer, and can be ranked by quality (we suggest the credit scoring system) and ¿risk¿ can either be assumed (interiorised) by the company itself or transferred to third parties (exteriorised).What provides the approach that leads to us being able to talk with confidence of a real Credit-Risk Balance Sheet with its methodological robustness is that the dual vision of the credit transaction is not, as we demonstrate, merely a classificatory duality (a double risk-credit classification of reality) but rather a true causal relationship, that is, a risk-credit causal duality.Once said Credit-Risk Balance Sheet (which bears a certain structural similarity with the classic net asset balance sheet) has been built, and its methodological coherence demonstrated, its properties ¿static and dynamic¿ are studied.Analysis of the temporal evolution of the Credit-Risk Balance Sheet and of its applications will be the object of subsequent works.

Personality and Culture Cross-Cultural Psychology at the Next Crossroads

A review of nearly three decades of cross-cultural research shows that this domain still has to address several issues regarding the biases of data collection and sampling methods, the lack of clear and consensual definitions of constructs and variables, and measurement invariance issues that seriously limit the comparability of results across cultures. Indeed, a large majority of the existing studies are still based on the anthropological model, which compares two cultures and mainly uses convenience samples of university students. This paper stresses the need to incorporate a larger variety of regions and cultures in the research designs, the necessity to theorize and identify a larger set of variables in order to describe a human environment, and the importance of overcoming methodological weaknesses to improve the comparability of measurement results. Cross-cultural psychology is at the next crossroads in it's development, and researchers can certainly make major contributions to this domain if they can address these weaknesses and challenges.

Uso de la estadística en la oncología y la hematología

En este artículo abordamos el uso y la importancia de las herramientas estadísticas que se utilizan principalmente en los estudios médicos del ámbito de la oncología y la hematología, pero aplicables a muchos otros campos tanto médicos como experimentales o industriales. El objetivo del presente trabajo es presentar de una manera clara y precisa la metodología estadística necesaria para analizar los datos obtenidos en los estudios rigurosa y concisamente en cuanto a las hipótesis de trabajo planteadas por los investigadores. La medida de la respuesta al tratamiento elegidas en al tipo de estudio elegido determinarán los métodos estadísticos que se utilizarán durante el análisis de los datos del estudio y también el tamaño de muestra. Mediante la correcta aplicación del análisis estadístico y de una adecuada planificación se puede determinar si la relación encontrada entre la exposición a un tratamiento y un resultado es casual o por el contrario, está sujeto a una relación no aleatoria que podría establecer una relación de causalidad. Hemos estudiado los principales tipos de diseño de los estudios médicos más utilizados, tales como ensayos clínicos y estudios observacionales (cohortes, casos y controles, estudios de prevalencia y estudios ecológicos). También se presenta una sección sobre el cálculo del tamaño muestral de los estudios y cómo calcularlo, ¿Qué prueba estadística debe utilizarse?, los aspectos sobre fuerza del efecto ¿odds ratio¿ (OR) y riesgo relativo (RR), el análisis de supervivencia. Se presentan ejemplos en la mayoría de secciones del artículo y bibliografía más relevante.

Measurement of Pavement Surface Variations, July 1974

The measurement of pavement roughness has been the concern of highway engineers for more than 70 years. This roughness is referred to as "riding quality" by the traveling public. Pavement roughness evaluating devices have attempted to place either a graphical or numerical value on the public's riding comfort or discomfort. Early graphical roughness recorders had many different designs. In 1900 an instrument called the "Viagraph" was developed by an Irish engineer.' The "Viagraph" consisted of a twelve foot board with graphical recorder drawn over the pavement. The "Profilometer" built in Illinois in 1922 was much more impressive. ' The instrument's recorder was mounted on a frame supported by 32 bicycle wheels mounted in tandem. Many other variations of profilometers with recorders were built but most were difficult to handle and could not secure uniformly reproducible results. The Bureau of Public Roads (BPR) Road Roughness Indicator b u i l t in 1941 is the most widely used numerical roughness recorder.' The BPR Road Roughness Indicator consists of a trailer unit with carefully selected springs, means of dampening, and balanced wheel.

Iowa's Living Roadway Plant Profiler, August 21, 2003

This publication is a guide to understanding the Iowa Department of Transportation’s roadside management programs. It offers descriptions of various landscape designs or planting styles used within or adjacent to Iowa’s highway rights-of-way, as well as various plant profiles. In addition, this guide will help you learn more about the value of plants and their contribution to our environment and society. This publication is written for persons having little or no formal training in botany, and technical terminology has been kept to the minimum necessary to maintain standards of accuracy and conciseness in the descriptions. Plants are known by common names and botanical names. Most people prefer to use common names because they are easier to spell and say. Both have been used in this publication. Botanical names are taken from Latin, Greek or “Latinized” words of other languages. Each plant species has a unique botanical name, consisting of the genus, followed by the species. Some botanical names contain additional words after the species name to designate cultivars or subspecies. Plant species are grouped into families by flower structure. Family names are Latin, so the associated common family names are included in parenthesis. Sources of information for this publication are not cited within the text to save space, avoid repetition and make it more readable. However, all references used are included in the bibliography at the end of this publication.

Five (or so) challenges for species distribution modelling

Species distribution modelling is central to both fundamental and applied research in biogeography. Despite widespread use of models, there are still important conceptual ambiguities as well as biotic and algorithmic uncertainties that need to be investigated in order to increase confidence in model results. We identify and discuss five areas of enquiry that are of high importance for species distribution modelling: (1) clarification of the niche concept; (2) improved designs for sampling data for building models; (3) improved parameterization; (4) improved model selection and predictor contribution; and (5) improved model evaluation. The challenges discussed in this essay do not preclude the need for developments of other areas of research in this field. However, they are critical for allowing the science of species distribution modelling to move forward.

The immune space: a concept and template for rationalizing vaccine development.

Abstract Empirical testing of candidate vaccines has led to the successful development of a number of lifesaving vaccines. The advent of new tools to manipulate antigens and new methods and vectors for vaccine delivery has led to a veritable explosion of potential vaccine designs. As a result, selection of candidate vaccines suitable for large-scale efficacy testing has become more challenging. This is especially true for diseases such as dengue, HIV, and tuberculosis where there is no validated animal model or correlate of immune protection. Establishing guidelines for the selection of vaccine candidates for advanced testing has become a necessity. A number of factors could be considered in making these decisions, including, for example, safety in animal and human studies, immune profile, protection in animal studies, production processes with product quality and stability, availability of resources, and estimated cost of goods. The "immune space template" proposed here provides a standardized approach by which the quality, level, and durability of immune responses elicited in early human trials by a candidate vaccine can be described. The immune response profile will demonstrate if and how the candidate is unique relative to other candidates, especially those that have preceded it into efficacy testing and, thus, what new information concerning potential immune correlates could be learned from an efficacy trial. A thorough characterization of immune responses should also provide insight into a developer's rationale for the vaccine's proposed mechanism of action. HIV vaccine researchers plan to include this general approach in up-selecting candidates for the next large efficacy trial. This "immune space" approach may also be applicable to other vaccine development endeavors where correlates of vaccine-induced immune protection remain unknown.

Evaluation of Bridge Replacement Alternatives for the County Bridge System, HR-365 August 1994

Recent reports have indicated that 23.5 percent of the nation's highway bridges are structurally deficient and 17.7 percent are functionally obsolete. A significant number of these bridges are on the Iowa county road system. The objective of the investigation described in this report was to identify, review and evaluate replacement bridges currently being used by various counties in Iowa and surrounding states. Iowa county engineers, county engineers in neighboring states as well as private manufacturers of bridge components, and regional precad prestressed concrete manufacturers were contacted to determine the most common replacement bridge types being used. Depending upon the findings of the review, possible improvements and/or new replacement bridge systems were to be proposed. A questionnaire was developed and sent to county engineers in Iowa and several counties in surrounding states. The results of the questionnaire showed that the most common replacement bridges in Iowa are the continuous concrete slab and prestressed concrete bridges. The primary reason these types are used is because of the availability of standard designs and because of their ease of maintenance. Counties seldom construct these types of bridges using their own labor forces, but instead contract the work. However, county forces are used to construct steel stringer, precast reinforced concrete and timber bridges. In general, 69 percent of the counties indicate an ability and willingness to use their own forces to design and construct relatively short span bridges (i.e., 40 A or less) provided the construction procedures are relatively simple. Several unique replacement bridge types used in Iowa that are constructed by county forces are documented and presented in this report. Sufficient details are provided to allow county engineers to determine if some of these bridges could be used to resolve some of their own replacement bridge problems. Where possible, cost information has also been provided. Each of these bridge types were evaluated for various criteria (e.g., cost effectiveness, conformance to AASI-ITO standards, range of sizes, etc.) by a panel of four Iowa county engineers; a summary of this critique is included. After evaluating the questionnaire responses from the counties and evaluating the various bridge replacement concepts currently in use, one new bridge replacement concept and one modification of a current Iowa county bridge replacement concept were developed. Both of these concepts would utilize county labor forces.