Estimation and partitioning of polygenic variation captured by common SNPs for Alzheimer's disease, multiple sclerosis and endometriosis

Common diseases such as endometriosis (ED), Alzheimer's disease (AD) and multiple sclerosis (MS) account for a significant proportion of the health care burden in many countries. Genome-wide association studies (GWASs) for these diseases have identified a number of individual genetic variants contributing to the risk of those diseases. However, the effect size for most variants is small and collectively the known variants explain only a small proportion of the estimated heritability. We used a linear mixed model to fit all single nucleotide polymorphisms (SNPs) simultaneously, and estimated genetic variances on the liability scale using SNPs from GWASs in unrelated individuals for these three diseases. For each of the three diseases, case and control samples were not all genotyped in the same laboratory. We demonstrate that a careful analysis can obtain robust estimates, but also that insufficient quality control (QC) of SNPs can lead to spurious results and that too stringent QC is likely to remove real genetic signals. Our estimates show that common SNPs on commercially available genotyping chips capture significant variation contributing to liability for all three diseases. The estimated proportion of total variation tagged by all SNPs was 0.26 (SE 0.04) for ED, 0.24 (SE 0.03) for AD and 0.30 (SE 0.03) for MS. Further, we partitioned the genetic variance explained into five categories by a minor allele frequency (MAF), by chromosomes and gene annotation. We provide strong evidence that a substantial proportion of variation in liability is explained by common SNPs, and thereby give insights into the genetic architecture of the diseases.

Soil carbon stock in the tropical rangelands of Australia: Effects of soil type and grazing pressure, and determination of sampling requirement.

On-going, high-profile public debate about climate change has focussed attention on how to monitor the soil organic carbon stock (C(s)) of rangelands (savannas). Unfortunately, optimal sampling of the rangelands for baseline C(s) - the critical first step towards efficient monitoring - has received relatively little attention to date. Moreover, in the rangelands of tropical Australia relatively little is known about how C(s) is influenced by the practice of cattle grazing. To address these issues we used linear mixed models to: (i) unravel how grazing pressure (over a 12-year period) and soil type have affected C(s) and the stable carbon isotope ratio of soil organic carbon (delta(13)C) (a measure of the relative contributions of C(3) and C(4) vegetation to C(s)); (ii) examine the spatial covariation of C(s) and delta(13)C; and, (iii) explore the amount of soil sampling required to adequately determine baseline C(s). Modelling was done in the context of the material coordinate system for the soil profile, therefore the depths reported, while conventional, are only nominal. Linear mixed models revealed that soil type and grazing pressure interacted to influence C(s) to a depth of 0.3 m in the profile. At a depth of 0.5 m there was no effect of grazing on C(s), but the soil type effect on C(s) was significant. Soil type influenced delta(13)C to a soil depth of 0.5 m but there was no effect of grazing at any depth examined. The linear mixed model also revealed the strong negative correlation of C(s) with delta(13)C, particularly to a depth of 0.1 m in the soil profile. This suggested that increased C(s) at the study site was associated with increased input of C from C(3) trees and shrubs relative to the C(4) perennial grasses; as the latter form the bulk of the cattle diet, we contend that C sequestration may be negatively correlated with forage production. Our baseline C(s) sampling recommendation for cattle-grazing properties of the tropical rangelands of Australia is to: (i) divide the property into units of apparently uniform soil type and grazing management; (ii) use stratified simple random sampling to spread at least 25 soil sampling locations about each unit, with at least two samples collected per stratum. This will be adequate to accurately estimate baseline mean C(s) to within 20% of the true mean, to a nominal depth of 0.3 m in the profile.

Predicting Additive and Non-additive Genetic Effects from Trials Where Traits Are Affected by Interplot Competition

There are two key types of selection in a plant breeding program, namely selection of hybrids for potential commercial use and the selection of parents for use in future breeding. Oakey et al. (in Theoretical and Applied Genetics 113, 809-819, 2006) showed how both of these aims could be achieved using pedigree information in a mixed model analysis in order to partition genetic effects into additive and non-additive effects. Their approach was developed for field trial data subject to spatial variation. In this paper we extend the approach for data from trials subject to interplot competition. We show how the approach may be used to obtain predictions of pure stand additive and non-additive effects. We develop the methodology in the context of a single field trial using an example from an Australian sorghum breeding program.

Risk factors associated with corneal nerve alteration in type 1 diabetes in the absence of neuropathy: A longitudinal in vivo corneal confocal microscopy study

Purpose The aim of this study was to determine alterations to the corneal subbasal nerve plexus (SNP) over four years using in vivo corneal confocal microscopy (IVCM) in participants with type 1 diabetes and to identify significant risk factors associated with these alterations. Methods A cohort of 108 individuals with type 1 diabetes and no evidence of peripheral neuropathy at enrollment underwent laser-scanning IVCM, ocular screening, and health and metabolic assessment at baseline and the examinations continued for four subsequent annual visits. At each annual visit, eight central corneal images of the SNP were selected and analyzed to quantify corneal nerve fiber density (CNFD), branch density (CNBD) and fiber length (CNFL). Linear mixed model approaches were fitted to examine the relationship between risk factors and corneal nerve parameters. Results A total of 96 participants completed the final visit and 91 participants completed all visits. No significant relationships were found between corneal nerve parameters and time, sex, duration of diabetes, smoking, alcohol consumption, blood pressure or BMI. However, CNFD was negatively associated with HbA1c (β=-0.76, P<0.01) and age (β=-0.13, P<0.01) and positively related to high density lipids (HDL) (β=2.01, P=0.03). Higher HbA1c (β=-1.58, P=0.04) and age (β=-0.23, P<0.01) also negatively impacted CNBD. CNFL was only affected by higher age (β=-0.06, P<0.01). Conclusions Glycemic control, HDL and age have significant effects on SNP structure. These findings highlight the importance of diabetic management to prevent corneal nerve damage as well as the capability of IVCM for monitoring subclinical alterations in the corneal SNP in diabetes.

Resistance to Fusarium oxysporum f. sp fragariae and Predicted Breeding Values in Strawberry

Fusarium wilt of strawberry, incited by Fusarium oxysporum f. sp. fragariae (Fof), is a major disease of the cultivated strawberry (Fragaria xananassa) worldwide. An increase in disease outbreaks of the pathogen in Western Australia and Queensland plus the search for alternative disease management strategies place emphasis on the development of resistant cultivars. In response, a partial incomplete diallel cross involving four parents was performed for use in glasshouse resistance screenings. The resulting progeny were evaluated for their susceptibility to Fof. Best-performing progeny and suitability of progenies as parents were determined using data from disease severity ratings and analyzed using a linear mixed model incorporating a pedigree to produce best linear unbiased predictions of breeding values. Variation in disease response, ranging from highly susceptible to resistant, indicates a quantitative effect. The estimate of the narrow-sense heritability was 0.49 +/- 0.04 (SE), suggesting the population should be responsive to phenotypic recurrent selection. Several progeny genotypes have predicted breeding values higher than any of the parents. Knowledge of Fof resistance derived from this study can help select best parents for future crosses for the development of new strawberry cultivars with Fof resistance.

A retrospective study of vase life determinants for cut Acacia holosericea foliage

Short and variable vase life of cut Acacia holosericea foliage stems limits its commercial potential. Retrospective evaluation of factors affecting the vase life of this cut foliage line was assessed using primary data collected from 30 individual experiments. These data had been collected by four different researchers over 17 months, from late Summer to mid Winter across two consecutive years. Vase life data of cut A. holosericea stems held in deionised water (DIW) was analysed for general vase life variation and to define the most influential factor affecting vase life of the cut stems. Meanwhile, vase life of cut stems exposed to various chemical and physical postharvest treatments was analysed using meta-analysis to evaluate their efficacy in prolonging vase life of the stems. The overall mean vase life (±standard deviation) of cut A. holosericea stems was 6.4 ± 1.2 days (n = 30 trials). Longer vase life of ≥7 days was obtained from cut stems harvested at vegetative and flowering stage, which was between Summer and Autumn. Cut stems harvested at fruiting stage, between Winter and Spring displayed shorter vase life of ≤5.5 days. Mixed model analysis indicated that vase life variation of the cut stems was mostly determined by season (P < 0.001). In averaged, postharvest treatments increased vase life 1.4-fold compared to stems in DIW, with 68.32% had a large positive treatment effect size (d). Among the treatments, nano silver (NS) and copper (Cu2+) were the most beneficial to vase life. Retrospective analysis was found to be beneficial for identifying conditions and targeting practices to maximise the vase life of cut A. holosericea and, potentially for other species.

Diseño de líneas mixtas en un entorno Lean. Aplicación a un caso mediante Excel

[ES]Este trabajo tiene como objetivo analizar las soluciones existentes para el diseño de las líneas mixtas. Se trata de un tipo de líneas bastante complejas de diseñar y que por lo general han sido poco estudiadas por la sociedad académica, a pesar de las numerosas ventajas que ofrece en comparación a las líneas simples, mucho más investigadas. Para facilitar la comprensión de su diseño, y antes de su estudio, se realiza un análisis de las características de las líneas mixtas. Posteriormente se introduce una metodología desarrollada por Lluis Cuatrecasas (Presidente del Instituto Lean Management de España), que permite salvar la brecha que existe a su juicio entre los estudios sobre los diseños de este tipo de líneas y su aplicación a la empresa. Finalmente, se ilustra dicha metodología mediante un caso práctico y se evalúan sus fortalezas y debilidades.

Impacto solvencia II en un seguro de vida

La actividad aseguradora supone la transferencia de riesgos del asegurado al asegurador. El asegurador se compromete al pago de una prestación si el riesgo se realiza. Se produce un cambio en el ciclo productivo. El asegurador vende una cobertura sin conocer el momento y el coste exacto de dicha cobertura. Esta particularidad de la actividad aseguradora explica la necesidad para una entidad aseguradora de ser solvente en cada momento y ante cualquier imprevisto. Por ello, la solvencia de las entidades aseguradoras es un aspecto que se ha ido recogiendo en las distintas normativas que han regulado la actividad aseguradora y al que se ha ido dando cada vez más importancia. Actualmente la legislación vigente en materia de solvencia de las aseguradoras esta regulada por la directiva europea Solvencia I. Esta directiva establece dos conceptos para garantizar la solvencia: las provisiones técnicas y el margen de solvencia. Las provisiones técnicas son las calculadas para garantizar la solvencia estática de la compañía, es decir aquella que hace frente, en un instante temporal determinado, a los compromisos asumidos por la entidad. El margen de solvencia se destina a cubrir la solvencia dinámica, aquella que hace referencia a eventos futuros que puedan afectar la capacidad del asegurador. Sin embargo en una corriente de gestión global del riesgo en la que el sector bancario ya se había adelantado al sector asegurador con la normativa Basilea II, se decidió iniciar un proyecto europeo de reforma de Solvencia I y en noviembre del 2009 se adoptó la directiva 2009/138/CE del parlamento europeo y del consejo, sobre el seguro de vida, el acceso a la actividad de seguro y de reaseguro y su ejercicio mas conocida como Solvencia II. Esta directiva supone un profundo cambio en las reglas actuales de solvencia para las entidades aseguradoras. Este cambio persigue el objetivo de establecer un marco regulador común a nivel europeo que sea más adaptado al perfil de riesgo de cada entidad aseguradora. Esta nueva directiva define dos niveles distintos de capital: el SCR (requerimiento estándar de capital de solvencia) y el MCR (requerimiento mínimo de capital). Para el calculo del SCR se ha establecido que el asegurador tendrá la libertad de elegir entre dos modelos. Un modelo estándar propuesto por la Autoridad Europea de Seguros y Pensiones de Jubilación (EIOPA por sus siglas en inglés), que permitirá un calculo simple, y un modelo interno desarrollado por la propia entidad que deberá ser aprobado por las autoridades competentes. También se contempla la posibilidad de utilizar un modelo mixto que combine ambos, el estándar y el interno. Para el desarrollo del modelo estándar se han realizado una serie de estudios de impacto cuantitativos (QIS). El último estudio (QIS 5) ha sido el que ha planteado de forma más precisa el cálculo del SCR. Plantea unos shocks que se deberán de aplicar al balance de la entidad con el objetivo de estresarlo, y en base a los resultados obtenidos constituir el SCR. El objetivo de este trabajo es realizar una síntesis de las especificaciones técnicas del QIS5 para los seguros de vida y realizar una aplicación práctica para un seguro de vida mixto puro. En la aplicación práctica se determinarán los flujos de caja asociados a este producto para calcular su mejor estimación (Best estimate). Posteriormente se determinará el SCR aplicando los shocks para los riesgos de mortalidad, rescates y gastos. Por último, calcularemos el margen de riesgo asociado al SCR. Terminaremos el presente TFG con unas conclusiones, la bibliografía empleada así como un anexo con las tablas empleadas.

Patterns of Impact Resulting from a 'Sit Less, Move More' Web-Based Program in Sedentary Office Employees

Purpose Encouraging office workers to 'sit less and move more' encompasses two public health priorities. However, there is little evidence on the effectiveness of workplace interventions for reducing sitting, even less about the longer term effects of such interventions and still less on dual-focused interventions. This study assessed the short and mid-term impacts of a workplace web-based intervention (Walk@WorkSpain, W@WS; 2010-11) on self-reported sitting time, step counts and physical risk factors (waist circumference, BMI, blood pressure) for chronic disease. Methods Employees at six Spanish university campuses (n=264; 42 +/- 10 years; 171 female) were randomly assigned by worksite and campus to an Intervention (used W@WS; n=129; 87 female) or a Comparison group (maintained normal behavior; n=135; 84 female). This phased, 19-week program aimed to decrease occupational sitting time through increased incidental movement and short walks. A linear mixed model assessed changes in outcome measures between the baseline, ramping (8 weeks), maintenance (11 weeks) and follow-up (two months) phases for Intervention versus Comparison groups. Results A significant 2 (group) x 2 (program phases) interaction was found for self-reported occupational sitting (F[3]=7.97, p=0.046), daily step counts (F[3]=15.68, p=0.0013) and waist circumference (F[3]=11.67, p=0.0086). The Intervention group decreased minutes of daily occupational sitting while also increasing step counts from baseline (446 +/- 126; 8,862 +/- 2,475) through ramping (+425 +/- 120; 9,345 +/- 2,435), maintenance (+422 +/- 123; 9,638 +/- 3,131) and follow-up (+414 +/- 129; 9,786 +/- 3,205). In the Comparison group, compared to baseline (404 +/- 106), sitting time remained unchanged through ramping and maintenance, but decreased at follow-up (-388 +/- 120), while step counts diminished across all phases. The Intervention group significantly reduced waist circumference by 2.1cms from baseline to follow-up while the Comparison group reduced waist circumference by 1.3cms over the same period. Conclusions W@WSis a feasible and effective evidence-based intervention that can be successfully deployed with sedentary employees to elicit sustained changes on "sitting less and moving more".

Perspectives from agriculture: advances in livestock breeding - implications for aquaculture genetics

In this paper we present livestock breeding developments that could be taken into consideration in the genetic improvement of farmed aquaculture species, especially in freshwater fish. Firstly, the current breeding objective in aquatic species has focused almost exclusively on the improvement of body weight at harvest or on growth related traits. This is unlikely to be sufficient to meet the future needs of the aquaculture industry. To meet future demands breeding programs will most likely have to include additional traits, such as fitness related ones (survival, disease resistance), feed efficiency, or flesh quality, rather than only growth performance. In order to select for a multi-trait breeding objective, genetic variation in traits of interest and the genetic relationships among them need to be estimated. In addition, economic values for these traits will be required. Generally, there is a paucity of data on variable and fixed production costs in aquaculture, and this could be a major constraint in the further expansion of the breeding objectives. Secondly, genetic evaluation systems using the restricted maximum likelihood method (REML) and best linear unbiased prediction (BLUP) in a framework of mixed model methodology could be widely adopted to replace the more commonly used method of mass selection based on phenotypic performance. The BLUP method increases the accuracy of selection and also allows the management of inbreeding and estimation of genetic trends. BLUP is an improvement over the classic selection index approach, which was used in the success story of the genetically improved farmed tilapia (GIFT) in the Philippines, with genetic gains from 10 to 20 per cent per generation of selection. In parallel with BLUP, optimal genetic contribution theory can be applied to maximize genetic gain while constraining inbreeding in the long run in selection programs. Thirdly, by using advanced statistical methods, genetic selection can be carried out not only at the nucleus level but also in lower tiers of the pyramid breeding structure. Large scale across population genetic evaluation through genetic connectedness using cryopreserved sperm enables the comparison and ranking of genetic merit of all animals across populations, countries or years, and thus the genetically superior brood stock can be identified and widely used and exchanged to increase the rate of genetic progress in the population as a whole. It is concluded that sound genetic programs need to be established for aquaculture species. In addition to being very effective, fully pedigreed breeding programs would also enable the exploration of possibilities of integrating molecular markers (e.g., genetic tagging using DNA fingerprinting, marker (gene) assisted selection) and reproductive technologies such as in-vitro fertilization using cryopreserved spermatozoa.

混流汽车总装配线上的零部件优化配送方案研究

配送车每次配送的利用率大小是提高配送效率的主要因素,因此设计一种启发式算法使配送车一次装载的标准塑料周转箱尽可能多,提高配送车空间利用率。最后的仿真实验验证了上述配送方法的实用性,提出的零部件配送管理方法,只需使用较少的配送工人,同时降低了线旁库存,能为企业节省人力,降低生产成本。

汽车混流总装线投产排序优化研究

汽车混流总装线上交替装配不同型号的汽车产品,不同型号的汽车在同一装配工位上装配的零部件可能不同,如果不对车型的投产顺序加以优化排序,连续投入一种相同的车型,会使同一个工位的零部件消耗率严重不均衡。为了使各装配工位的零部件消耗率达到均匀化和平准化,本文采用模拟退火优化算法,对车型上线序列进行优化,最后的实例验证表明算法是可行的。

基于RFID的混流装配汽车生产线物料动态配送研究

针对混流装配的汽车自动化生产线提出了基于RFID的车辆追踪和基于条码的无线物料库存管理实现方法。在此基础上,设计了装配生产线的物料动态配送调度业务流程,给出了物料动态配送的规划依据,并进行了实例计算。

混流汽车装配线物料配送优化策略研究

随着世界经济的迅速发展和科学技术的不断进步，物流对经济贸易活动的影响与日俱增，受到越来越多人们的关注。在中国，越来越多的人们已经意识到物流对企业发展的重要性，因为物流业的发展必然降低物流成本在GDP中的比重；加快企业流动资金周转速度；还必然带动固定资产投资，降低企业的物流成本，提高市场竞争力。汽车生产物流系统是制造业界公认的最复杂，组织难度最大，物流管理任务最繁重的系统，对企业内部来说，生产的全过程更多的转化为生产物料的配送与装配，而不是过去的原材料的加工生产。据统计在装配线的实际运行过程中，由于物料配送不及时或错误导致输送链停止的情况占有很大的比例，优化装配线上的物料配送管理系统就显得非常重要。 本文结合当地某汽车总装厂的生产物流现状，研究设计一种高效的物流配送管理系统。汽车混流装配线上多种型号的汽车共线生产，一个好的物料配送系统应保证将正确数量的合格零部件在准确的时间配送到需要的工位旁边。在分析混流装配线上物料流的基础上，我们提出了针对系统的几个优化目标，首先以使各工位的零部件使用速率均衡化为目标，采用模拟退火算法，来得到车身上线的最优投产排序序列，在此基础上，我们设计物流配送系统的体系结构，包括库房条形码管理系统和线上物料配送管理系统，然后根据配送管理系统中存在的一系列问题，文中研究提出了一种插入启发式优化算法，来实现零部件从库房到生产线旁的动态配送，最后我们采用数字化工厂仿真软件Em-plant建立一套物流配送管理系统的仿真模型，仿真结果验证了该系统的高效性，并对汽车制造业的企业管理者作决策起到一定的参考意义。

Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.)

Sk?t, L., Humphreys, J., Humphreys, M. O., Thorogood, D., Gallagher, J. A., Sanderson, R., Armstead, I. P., Thomas, I. D. (2007). Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics, 177 (1), 535-547. Sponsorship: BBSRC RAE2008