Within-family outliers: Segregating alleles or environmental effects? A linkage analysis of height from 5815 sibling pairs

Most information in linkage analysis for quantitative traits comes from pairs of relatives that are phenotypically most discordant or concordant. Confounding this, within-family outliers from non-genetic causes may create false positives and negatives. We investigated the influence of within-family outliers empirically, using one of the largest genome-wide linkage scans for height. The subjects were drawn from Australian twin cohorts consisting of 8447 individuals in 2861 families, providing a total of 5815 possible pairs of siblings in sibships. A variance component linkage analysis was performed, either including or excluding the within-family outliers. Using the entire dataset, the largest LOD scores were on chromosome 15q (LOD 2.3) and 11q (1.5). Excluding within-family outliers increased the LOD score for most regions, but the LOD score on chromosome 15 decreased from 2.3 to 1.2, suggesting that the outliers may create false negatives and false positives, although rare alleles of large effect may also be an explanation. Several regions suggestive of linkage to height were found after removing the outliers, including 1q23.1 (2.0), 3q22.1 (1.9) and 5q32 (2.3). We conclude that the investigation of the effect of within-family outliers, which is usually neglected, should be a standard quality control measure in linkage analysis for complex traits and may reduce the noise for the search of common variants of modest effect size as well as help identify rare variants of large effect and clinical significance. We suggest that the effect of within-family outliers deserves further investigation via theoretical and simulation studies.

Personality, health and lifestyle in a questionnaire family study: A comparison between highly cooperative and less cooperative families

The effect of nonresponse on health and lifestyle measures has received extensive study, showing at most relatively modest effects. Nonresponse bias with respect to personality has been less thoroughly investigated. The present study uses data from responding individuals as a proxy for the missing data of their nonresponding family members to examine the presence of nonresponse bias for personality traits and disorders as well as health and lifestyle traits. We looked at the Big Five personality traits, borderline personality disorder (BPD) features, attention-deficit/hyperactivity disorder, Anger, and several measures of health (Body Mass Index, migraine) and lifestyle (smoking, alcohol use). In general, outcomes tend to be slightly more favorable for individuals from highly cooperative families compared to individuals from less cooperative families. The only significant difference was found for BPD features (p = .001). However, the absolute difference in mean scores is very small, less than 1 point for a scale ranging from 0 to 72. In conclusion, survey data on personality, health and lifestyle are relatively unbiased with respect to nonresponse.

The effect of temperature on height growth of Scots pine in northern Finland

The effect of temperature on height growth of Scots pine in the northern boreal zone in Lapland was studied in two different time scales. Intra-annual growth was monitored in four stands in up to four growing seasons using an approximately biweekly measurement interval. Inter-annual growth was studied using growth records representing seven stands and five geographical locations. All the stands were growing on a dry to semi-dry heath that is a typical site type for pine stands in Finland. The applied methodology is based on applied time-series analysis and multilevel modelling. Intra-annual elongation of the leader shoot correlated with temperature sum accumulation. Height growth ceased when, on average, 41% of the relative temperature sum of the site was achieved (observed minimum and maximum were 38% and 43%). The relative temperature sum was calculated by dividing the actual temperature sum by the long-term mean of the total annual temperature sum for the site. Our results suggest that annual height growth ceases when a location-specific temperature sum threshold is attained. The positive effect of the mean July temperature of the previous year on annual height increment proved to be very strong at high latitudes. The mean November temperature of the year before the previous had a statistically significantly effect on height increment in the three northernmost stands. The effect of mean monthly precipitation on annual height growth was statistically insignificant. There was a non-linear dependence between length and needle density of annual shoots. Exceptionally low height growth results in high needle-density, but the effect is weaker in years of average or good height growth. Radial growth and next year s height growth are both largely controlled by current July temperature. Nevertheless, their growth variation in terms of minimum and maximum is not necessarily strongly correlated. This is partly because height growth is more sensitive to changes in temperature. In addition, the actual effective temperature period is not exactly the same for these two growth components. Yet, there is a long-term balance that was also statistically distinguishable; radial growth correlated significantly with height growth with a lag of 2 years. Temperature periods shorter than a month are more effective variables than mean monthly values, but the improvement is on the scale of modest to good when applying Julian days or growing-degree-days as pointers.

Fen ecosystem carbon gas dynamics in changing hydrological conditions

Northern peatlands are thought to store one third of all soil carbon (C). Besides the C sink function, peatlands are one of the largest natural sources of methane (CH4) to the atmosphere. Climate change may affect the C gas dynamics as well as the labile C pool. Because the peatland C sequestration and CH4 emissions are governed by high water levels, changes in hydrology are seen as the driving factor in peatland ecosystem change. This study aimed to quantify the carbon dioxide (CO2) and CH4 dynamics of a fen ecosystem at different spatial scales: plant community components scale, plant community scale and ecosystem scale, under hydrologically normal and water level drawdown conditions. C gas exchange was measured in two fens in southern Finland applying static chamber and eddy covariance techniques. During hydrologically normal conditions, the ecosystem was a CO2 sink and CH4 source to the atmosphere. Sphagnum mosses and sedges were the most important contributors to the community photosynthesis. The presence of sedges had a major positive impact on CH4 emissions while dwarf shrubs had a slightly attenuating impact. C fluxes varied considerably between the plant communities. Therefore, their proportions determined the ecosystem scale fluxes. An experimental water level drawdown markedly reduced the photosynthesis and respiration of sedges and Sphagnum mosses and benefited shrubs. Consequently, changes were smaller at the ecosystem scale than at the plant group scale. The decrease in photosynthesis and the increase in respiration, mostly peat respiration, made the fen a smaller CO2 sink. CH4 fluxes were significantly lowered, close to zero. The impact of natural droughts was similar to, although more modest than, the impact of the experimental water level drawdown. The results are applicable to the short term impacts of the water level drawdown and to climatic conditions in which droughts become more frequent.

Skogsbränslets elementära sammansättning med tanke på förbränningsprocessen och för näringsämnesförluster i ekosystemet

There are several reasons for increasing the usage of forest biomass for energy in Finland. Apart from the fact that forest biomass is a CO2 -neutral energy source, it is also a domestic resource distributed throughout the country. Usage of forest biomass in the form of logging residues decreases Finland’s dependence of energy import and increases both incomes and employment. Wood chips are mainly made from logging residues, which constitute 64 % of the raw material. A large-scale use of forest biomass requires heed also to the potential negative aspects. Forest bioenergy is used extensively, but its impacts on the forests soil nutrition and carbon balance has not been studied much. Nor have there been many studies on the heavy metal or chlorine content of logging residues. The goal of this study was to examine the content of carbon, macronutrients, heavy metals and other for the combustion harmful substances in Scots pine and Norway spruce wood chips, and to estimate the effect of harvesting of logging residues on the forests carbon and nutrient balance. Another goal was to examine the energy content of the clear cut remains. The Wood chips for this study were gathered from pine and spruce dominated clear cut sites in southern Finland, in the costal forests between Hankoo and Siuntio. The number of sample locations were 29, and the average area was 3,15 ha and the average timber volume 212,6 m3 ha -1. The average logged timber volume was for Scots pine timber 70 m3 ha -1 and for Norway spruce timber 124 m3 ha -1 and for deciduous timber (birch and alder) 18,5 m3 ha -1. The proportion of spruce in the logging residues and the stand-volume were relevant for how much nutrients were taken from the forest ecosystem when harvesting logging residues. In this study it was noted that the nutrient content of the logging residues clearly increased when the percentage of spruce in the timber volume increased. The S, K, Na and Cl -contents in the logging residues in this study increased with an increasing percentage of spruce, which is probably due to the fact that the spruce is an effective collector of atmospheric dry-deposition. The amounts of nutrients that were lost when harvesting logging residues were less than those referred to in the literature. Within a circulation period (100 years), the forest soil gets substantially more nutrients from atmospheric deposition, litter fall and weathering than is lost through harvesting of logging residues after a clear cut. Harvesting of the logging residues makes for a relatively modest increase of the quantity of carbon that is removed from the forest compared to traditional forestry. Due to the fact that the clear cut remains in my study showed a high content of chlorine, there is a risk of corrosion in connection to the incineration of the logging residues in power plants especially at coastal areas/forests. The risk of sulphur -related corrosion is probably rather small, because S concentrations are relatively low in woodchips. The clear cut remains showed rather high heavy metal contents. If the heavy metal contents in this study are representative for the clear cut remains in the coastal forests generally, there might be reason to exert some caution when using the ash for forest fertilizing purposes.

QTL for root angle and number in a population developed from bread wheats (Triticum aestivum) with contrasting adaptation to water-limited environments

Root architecture traits in wheat are important in deep soil moisture acquisition and may be used to improve adaptation to water-limited environments. The genetic architecture of two root traits, seminal root angle and seminal root number, were investigated using a doubled haploid population derived from SeriM82 and Hartog. Multiple novel quantitative trait loci (QTL) were identified, each one having a modest effect. For seminal root angle, four QTL (-log10(P) >3) were identified on 2A, 3D, 6A and 6B, and two suggestive QTL (-log10(P) >2) on 5D and 6B. For root number, two QTL were identified on 4A and 6A with four suggestive QTL on 1B, 3A, 3B and 4A. QTL for root angle and root number did not co-locate. Transgressive segregation was found for both traits. Known major height and phenology loci appear to have little effect on root angle and number. Presence or absence of the T1BL.1RS translocation did not significantly influence root angle. Broad sense heritability (h 2) was estimated as 50 % for root angle and 31 % for root number. Root angle QTL were found to be segregating between wheat cultivars adapted to the target production region indicating potential to select for root angle in breeding programs. © 2013 Springer-Verlag Berlin Heidelberg.

An exploratory study to assess the activity of the acarine growth inhibitor, fluazuron, against Sarcoptes scabei infestation in pigs

Background: The most common treatments for scabies in human and veterinary settings are topical 5% permethrin or systemic treatment with ivermectin. However, these treatments have very little activity against arthropod eggs, and therefore repeated treatment is frequently required. In-vitro, biochemical and molecular studies have demonstrated that human mites are becoming increasingly resistant to both acaricides. To identify alternate acaricides, we undertook a pilot study of the in vivo activity of the benzoylphenyl urea inhibitor of chitin synthesis, fluazuron, in pigs with sarcoptic mange. Findings: Pigs (n = 5) were infested with S. scabei var suis, and randomised to treatment at the start of peak infestation with fluazuron at a dose of 10 mg/kg/day per os for 7 days (n = 3) or no treatment (n = 2). Clinical scores, skin scrapings for mite counts and blood sampling for pharmacokinetic analysis were undertaken. Fluazuron was well absorbed in treated pigs with measureable blood levels up to 4 weeks post treatment. No adverse effects were observed. Modest acaricidal activity of the compound was observed, with a reduction in severity of skin lesions in treated pigs, as well as a reduction in number of scabies mite's early life stages. Conclusions: The moderate efficacy of fluazuron against scabies mites indicates a lead to the development of alternate treatments for scabies, such as combination therapies that maybe applicable for human use in the future.

Effectiveness of commercial harvesting in controlling feral-pig populations

Context. The feral pig (Sus scrofa) is a widespread pest species in Australia and its populations are commonly controlled to reduce damage to agriculture and the environment. Feral pigs are also a resource and harvested for commercial export as game meat. Although many other control techniques are used, commercial harvesting of feral pigs is often encouraged by land managers, because it carries little or no cost and is widely perceived to control populations. Aims. To use feral-pig harvesting records, density data and simple harvest models to examine the effectiveness of commercial harvesting to reduce feral-pig populations. Methods. The present study examined commercial harvest off-take on six sites (246-657 km2) in southern Queensland, and 20 large blocks (~2-6000 km2) throughout Queensland. The harvest off-take for each site was divided by monthly or average annual population size, determined by aerial survey, to calculate monthly and annual harvest rates.Asimple harvest model assuming logistic population growth was used to determine the likely effectiveness of harvesting. Key results. Commercial harvest rates were generally low (<~20%) and are likely to provide only modest reductions in population size. Additionally, harvest rates capable of substantial reductions (>50%) in long-term population size were isolated occurrences and not maintained across sites and years. High harvest rates were observed only at low densities. Although these harvest rates may be sufficiently high to hold populations at low densities, the population is likely to escape this entrapment following a flush in food supply or a reduction in harvest effort. Implications. Our results demonstrated that, at current harvest rates, commercial harvesting is ineffective for the landscape-scale control of feral-pig populations. Unless harvest rates can be significantly increased, commercial harvesting should be used as a supplement to, rather than as a substitute for, other damage-control techniques.

The cost-effectiveness of exercise referral schemes

Background Exercise referral schemes (ERS) aim to identify inactive adults in the primary care setting. The primary care professional refers the patient to a third party service, with this service taking responsibility for prescribing and monitoring an exercise programme tailored to the needs of the patient. This paper examines the cost-effectiveness of ERS in promoting physical activity compared with usual care in primary care setting. Methods A decision analytic model was developed to estimate the cost-effectiveness of ERS from a UK NHS perspective. The costs and outcomes of ERS were modelled over the patient's lifetime. Data were derived from a systematic review of the literature on the clinical and cost-effectiveness of ERS, and on parameter inputs in the modelling framework. Outcomes were expressed as incremental cost per quality-adjusted life-year (QALY). Deterministic and probabilistic sensitivity analyses investigated the impact of varying ERS cost and effectiveness assumptions. Sub-group analyses explored the cost-effectiveness of ERS in sedentary people with an underlying condition. Results Compared with usual care, the mean incremental lifetime cost per patient for ERS was £169 and the mean incremental QALY was 0.008, generating a base-case incremental cost-effectiveness ratio (ICER) for ERS at £20,876 per QALY in sedentary individuals without a diagnosed medical condition. There was a 51% probability that ERS was cost-effective at £20,000 per QALY and 88% probability that ERS was cost-effective at £30,000 per QALY. In sub-group analyses, cost per QALY for ERS in sedentary obese individuals was £14,618, and in sedentary hypertensives and sedentary individuals with depression the estimated cost per QALY was £12,834 and £8,414 respectively. Incremental lifetime costs and benefits associated with ERS were small, reflecting the preventative public health context of the intervention, with this resulting in estimates of cost-effectiveness that are sensitive to variations in the relative risk of becoming physically active and cost of ERS. Conclusions ERS is associated with modest increase in lifetime costs and benefits. The cost-effectiveness of ERS is highly sensitive to small changes in the effectiveness and cost of ERS and is subject to some significant uncertainty mainly due to limitations in the clinical effectiveness evidence base.

Liikennepolttoaineeksi tarkoitettu ohraetanoli, Suomen ohramarkkinat ja ilmastonmuutos

The aim of the thesis was to analyze the use of barley as an input for bioethanol production and the impacts the use has on the Finnish barley markets. Two main research questions were formulated. First, privately and socially optimal bioethanol production levels were examined. In the social optimum, the climate benefits of bioethanol production were considered. It was calculated that the production and use of bioethanol created smaller CO2 -emissions when compared with the production and use of gasoline. Second, the impacts of bioethanol production on farmland allocation and agricultural production were analyzed. In more detail, the second aim was to analyze the farmland allocation between wheat and barley cultivation and green set aside in the private and social optimum. An analytical model was produced to analyze the barley markets in Finland. To provide an empirical counterpart to this model, existing research data on bioethanol production and barley cultivation was used. The aim of the model was to analyze the supply and the demand as well as market equilibrium of barley. Furthermore, the model provided a framework for analyzing the differences between the private optimum and social optimum of bioethanol production in Finland. The demand for barley consists of animal feed demand and bioethanol demand. On the supply side, a heterogeneous model of farmland quality was used. With this framework, it is possible to analyze farmland allocation between barley and wheat cultivation and green set aside and how the climate benefits of bioethanol production affects the allocation. Moreover, the relative changes in barley price between the private and social optimum were analyzed. Based on the empirical analysis, the private optimum for barley based bioethanol production is 58 691 metric tons. However, the social optimum for barley based bioethanol production is 72 736 metric tons. The portion of farmland that is allocated to barley cultivation is increased if the climate benefits of bioethanol production are considered. In the private optimum, 1/19 of the total farmland is allocated to barley cultivation whereas in social optimum the share increases to 7/19. Furthermore, the increase in barley price between private and social optimum is rather modest. Total increase in price is only about 1,8 percent.

Structural Veneer Based Composite Products from Hardwood Thinning - Part I: Background and Manufacturing

In Australia, plantation forests have increased in area by around 50% in the last 10 years. While this expansion has seen a modest 8% increase for softwoods, hardwood plantations have dramatically increased by over 150%. Hardwood plantations grown for high quality sawn timber are slow to mature, with a crop rotation time potentially reaching 35 years. With this long lead-time, each year the risk from fire, pests and adverse weather events dramatically increases, while not translating into substantially higher financial returns to the grower. To justify continued expansion of Australia's current hardwood plantation estate, it is becoming necessary to develop higher value end-uses for both pulpwood and smaller 'sawlog' resources. The use of the low commercial value stems currently culled during thinning appears to be a necessary option to improve the industry profitability and win new markets. This paper provides background information on Australian forests and plantations and gives an overview of potential uses of Australian hardwood plantation thinning logs, as their mechanical properties. More specifically, this paper reports on the development of structural Veneer Based Composite (VBC) products from hardwood plantation thinning logs, taking advantage of a recent technology developed to optimise the processing of this resource. The process used to manufacture a range of hollow-form veneer laminated structural products is presented and the mechanical characteristics of these products are investigated in the companion paper. The market applications and future opportunities for the proposed products are also discussed, as potential benefits to the timber industry. © RILEM 2014.

Modelling the effect of plant water use traits on yield and stay-green expression in sorghum

Post-rainy sorghum (Sorghum bicolor (L.) Moench) production underpins the livelihood of millions in the semiarid tropics, where the crop is affected by drought. Drought scenarios have been classified and quantified using crop simulation. In this report, variation in traits that hypothetically contribute to drought adaptation (plant growth dynamics, canopy and root water conducting capacity, drought stress responses) were virtually introgressed into the most common post-rainy sorghum genotype, and the influence of these traits on plant growth, development, and grain and stover yield were simulated across different scenarios. Limited transpiration rates under high vapour pressure deficit had the highest positive effect on production, especially combined with enhanced water extraction capacity at the root level. Variability in leaf development (smaller canopy size, later plant vigour or increased leaf appearance rate) also increased grain yield under severe drought, although it caused a stover yield trade-off under milder stress. Although the leaf development response to soil drying varied, this trait had only a modest benefit on crop production across all stress scenarios. Closer dissection of the model outputs showed that under water limitation, grain yield was largely determined by the amount of water availability after anthesis, and this relationship became closer with stress severity. All traits investigated increased water availability after anthesis and caused a delay in leaf senescence and led to a ‘stay-green’ phenotype. In conclusion, we showed that breeding success remained highly probabilistic; maximum resilience and economic benefits depended on drought frequency. Maximum potential could be explored by specific combinations of traits.

Effect of biochar amendment on yield and photosynthesis of peanut on two types of soils

Abstract Biochar has significant potential to improve crop performance. This study examined the effect of biochar application on the photosynthesis and yield of peanut crop grown on two soil types. The commercial peanut cultivar Middleton was grown on red ferrosol and redoxi-hydrosol (Queensland, Australia) amended with a peanut shell biochar gradient (0, 0.375, 0.750, 1.50, 3.00 and 6.00 %, w/w, equivalent up to 85 t ha−1) in a glasshouse pot experiment. Biomass and pod yield, photosynthesis-[CO2] response parameters, leaf characteristics and soil properties (carbon, nitrogen (N) and nutrients) were quantified. Biochar significantly improved peanut biomass and pod yield up to 2- and 3-folds respectively in red ferrosol and redoxi-hydrosol. A modest (but significant) biochar-induced improvement of the maximumelectron transport rate and saturating photosynthetic rate was observed for red ferrosol. This response was correlated to increased leaf N and accompanied with improved soil available N and biological N fixation. Biochar application also improved the availability of other soil nutrients, which appeared critical in improving peanut performance, especially on infertile redoxihydrosol. Our study suggests that application of peanut shell derived biochar has strong potential to improve peanut yield on red ferrosol and redoxi-hydrosol. Biochar soil amendment can affect leaf N status and photosynthesis, but the effect varied with soil type.

Dependence Logic: Investigations into Higher-Order Semantics Defined on Teams

This thesis is a study of a rather new logic called dependence logic and its closure under classical negation, team logic. In this thesis, dependence logic is investigated from several aspects. Some rules are presented for quantifier swapping in dependence logic and team logic. Such rules are among the basic tools one must be familiar with in order to gain the required intuition for using the logic for practical purposes. The thesis compares Ehrenfeucht-Fraïssé (EF) games of first order logic and dependence logic and defines a third EF game that characterises a mixed case where first order formulas are measured in the formula rank of dependence logic. The thesis contains detailed proofs of several translations between dependence logic, team logic, second order logic and its existential fragment. Translations are useful for showing relationships between the expressive powers of logics. Also, by inspecting the form of the translated formulas, one can see how an aspect of one logic can be expressed in the other logic. The thesis makes preliminary investigations into proof theory of dependence logic. Attempts focus on finding a complete proof system for a modest yet nontrivial fragment of dependence logic. A key problem is identified and addressed in adapting a known proof system of classical propositional logic to become a proof system for the fragment, namely that the rule of contraction is needed but is unsound in its unrestricted form. A proof system is suggested for the fragment and its completeness conjectured. Finally, the thesis investigates the very foundation of dependence logic. An alternative semantics called 1-semantics is suggested for the syntax of dependence logic. There are several key differences between 1-semantics and other semantics of dependence logic. 1-semantics is derived from first order semantics by a natural type shift. Therefore 1-semantics reflects an established semantics in a coherent manner. Negation in 1-semantics is a semantic operation and satisfies the law of excluded middle. A translation is provided from unrestricted formulas of existential second order logic into 1-semantics. Also game theoretic semantics are considerd in the light of 1-semantics.

Fertilising for yield and quality in sown grass pastures and forage crops

Sown pasture rundown and declining soil fertility for forage crops are too serious to ignore with losses in beef production of up to 50% across Queensland. The feasibility of using strategic applications of nitrogen (N) fertiliser to address these losses was assessed by analysing a series of scenarios using data drawn from published studies, local fertiliser trials and expert opinion. While N fertilser can dramatically increase productivity (growth, feed quality and beef production gains of over 200% in some scenarios), the estimated economic benefits, derived from paddock level enterprise budgets for a fattening operation, were much more modest. In the best-performing sown grass scenarios, average gross margins were doubled or tripled at the assumed fertiliser response rates, and internal rates of return of up to 11% were achieved. Using fertiliser on forage sorghum or oats was a much less attractive option and, under the paddock level analysis and assumptions used, forages struggled to be profitable even on fertile sites with no fertiliser input. The economics of nitrogen fertilising on grass pasture were sensitive to the assumed response rates in both pasture growth and liveweight gain. Consequently, targeted research is proposed to re-assess the responses used in this analysis, which are largely based on research 25-40 years ago when soils were generally more fertile and pastures less rundown.