High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H

Spike density in barley is under the control of several major genes, as documented previously by genetic analysis of a number of morphological mutants. One such class of mutants affects the rachis internode length leading to dense or compact spikes and the underlying genes were designated dense spike (dsp). We previously delimited two introgressed genomic segments on chromosome 3H (21 SNP loci, 35.5 cM) and 7H (17 SNP loci, 20.34 cM) in BW265, a BC7F3 nearly isogenic line (NIL) of cv. Bowman as potentially containing the dense spike mutant locus dsp.ar, by genotyping 1,536 single nucleotide polymorphism (SNP) markers in both BW265 and its recurrent parent. Here, the gene was allocated by high-resolution bi-parental mapping to a 0.37 cM interval between markers SC57808 (Hv_SPL14)-CAPSK06413 residing on the short and long arm at the genetic centromere of chromosome 7H, respectively. This region putatively contains more than 800 genes as deduced by comparison with the collinear regions of barley, rice, sorghum and Brachypodium, Classical map-based isolation of the gene dsp.ar thus will be complicated due to the infavorable relationship of genetic to physical distances at the target locus.

Micro-breaks matter: A diary study on the effects of energy management strategies on occupational well-being

Organizational researchers and practitioners are increasingly interested in self-regulatory strategies employees can use at work to sustain or improve their occupational well-being. A recent cross-sectional study on energy management strategies suggested that many work-related strategies (e.g., setting a new goal) are positively related to occupational well-being, whereas many micro-breaks (e.g., listening to music) are negatively related to occupational well-being. We used a diary study design to take a closer look at the effects of these energy management strategies on fatigue and vitality. Based on conservation of resources theory, we hypothesized that both types of energy management strategies negatively predict fatigue and positively predict vitality. Employees (N = 124) responded to a baseline survey and to hourly surveys across one work day (6.7 times on average). Consistent with previous research, between-person differences in the use of work-related strategies were positively associated with between-person differences in vitality. However, results of multilevel analyses of the hourly diary data showed that only micro-breaks negatively predicted fatigue and positively predicted vitality. These findings suggest that taking micro-breaks during the work day may have short-term effects on occupational well-being, whereas using work-related strategies may have long-term effects.

Metal ions in molecular association of porphyrins

Molecular association of porphyrins and their metal derivatives has been recognized as one of the important properties for many of their biological functions. The association is classified into (i) self-aggregation, (ii) intermolecular association and (iii) intramolecular association. The presence of metal ions in the porphyrin cavity is shown to alter the magnitudes of binding constants and thermodynamic parameters of complexation. The interaction between the porphyrin unit and the acceptor is described in terms of π-π interaction. The manifestation of charge transfer states both in the ground and excited states of these complexes is shown to influence the rates of excited state electron transfer reactions. Owing to paucity of crystal structure data, the time-averaged geometries of many of these complexes have been derived from magnetic resonance data.

Postharvest manual answers many questions

Many authors have noted that consumer confidence in buying fresh flowers is strongly related to their perceived value in that quality and vase life must be high and consistent over time for consumers to repeat buy. Growers, wholesalers, exporters and retailers seek practical information about recommended handling and treatments at the harvest and postharvest stages, including that relating to flowers native to Australia and South Africa ("wildflowers"). This information is essential for products to be of high quality with an acceptable vase life for the end consumer, especially if exported. Published postharvest manuals generally focus on traditional flower crops and so rarely include many, or any, wildflowers. A manual entitled Postharvest Handling of Australian flowers from Native Plants and Related Species was published in 2002 and addressed this gap, but required updating. This situation presented an opportunity to provide in-depth information to compliment the Australian wildflower quality specifications (see accompanying paper in the same volume), and to assemble the latest knowledge on wildflower quality and postharvest issues. The resultant manual contains extensive information about harvesting, quality issues and recommended postharvest care focussed on wildflowers. Much of the information is documented for the first time, being based on the most up to date research and development (R&D) as well as practical experience of the floral supply chain, researchers and other technical experts. The manual provides practical and detailed information on postharvest treatment of fresh wildflowers for growers, florists, wholesalers and exporters to use on a daily basis. It discusses the many unique features of wildflowers that must be understood and managed in order to maximise their quality and vase life after marketing and export. The manual also includes postharvest advice for 16 flower- and foliage lines for which quality specifications were not produced. This advice is presented according to the same template as the specifications.

A generic method of engagement to elicit regional coastal management options

Stakeholder engagement is important for successful management of natural resources, both to make effective decisions and to obtain support. However, in the context of coastal management, questions remain unanswered on how to effectively link decisions made at the catchment level with objectives for marine biodiversity and fisheries productivity. Moreover, there is much uncertainty on how to best elicit community input in a rigorous manner that supports management decisions. A decision support process is described that uses the adaptive management loop as its basis to elicit management objectives, priorities and management options using two case studies in the Great Barrier Reef, Australia. The approach described is then generalised for international interest. A hierarchical engagement model of local stakeholders, regional and senior managers is used. The result is a semi-quantitative generic elicitation framework that ultimately provides a prioritised list of management options in the context of clearly articulated management objectives that has widespread application for coastal communities worldwide. The case studies show that demand for local input and regional management is high, but local influences affect the relative success of both engagement processes and uptake by managers. Differences between case study outcomes highlight the importance of discussing objectives prior to suggesting management actions, and avoiding or minimising conflicts at the early stages of the process. Strong contributors to success are a) the provision of local information to the community group, and b) the early inclusion of senior managers and influencers in the group to ensure the intellectual and time investment is not compromised at the final stages of the process. The project has uncovered a conundrum in the significant gap between the way managers perceive their management actions and outcomes, and community's perception of the effectiveness (and wisdom) of these same management actions.

Short and long term mortality rates after a lower limb amputation

Objective To determine mortality rates after a first lower limb amputation and explore the rates for different subpopulations. Methods Retrospective cohort study of all people who underwent a first amputation at or proximal to transtibial level, in an area of 1.7 million people. Analysis with Kaplan-Meier curves and Log Rank tests for univariate associations of psycho-social and health variables. Logistic regression for odds of death at 30-days, 1-year and 5-years. Results 299 people were included. Median time to death was 20.3 months (95%CI: 13.1; 27.5). 30-day mortality = 22%; odds of death 2.3 times higher in people with history of cerebrovascular disease (95%CI: 1.2; 4.7, P = 0.016). 1 year mortality = 44%; odds of death 3.5 times higher for people with renal disease (95%CI: 1.8; 7.0, P < 0.001). 5-years mortality = 77%; odds of death 5.4 times higher for people with renal disease (95%CI: 1.8; 16.0,P = 0.003). Variation in mortality rates was most apparent in different age groups; people 75–84 years having better short term outcomes than those younger and older. Conclusions Mortality rates demonstrated the frailty of this population, with almost one quarter of people dying within 30-days, and almost half at 1 year. People with cerebrovascular had higher odds of death at 30 days, and those with renal disease and 1 and 5 years, respectively.

Optimal adaptive sequential spatial sampling of soil using pair-copulas

A spatial sampling design that uses pair-copulas is presented that aims to reduce prediction uncertainty by selecting additional sampling locations based on both the spatial configuration of existing locations and the values of the observations at those locations. The novelty of the approach arises in the use of pair-copulas to estimate uncertainty at unsampled locations. Spatial pair-copulas are able to more accurately capture spatial dependence compared to other types of spatial copula models. Additionally, unlike traditional kriging variance, uncertainty estimates from the pair-copula account for influence from measurement values and not just the configuration of observations. This feature is beneficial, for example, for more accurate identification of soil contamination zones where high contamination measurements are located near measurements of varying contamination. The proposed design methodology is applied to a soil contamination example from the Swiss Jura region. A partial redesign of the original sampling configuration demonstrates the potential of the proposed methodology.

The Electronic Structure of Graphite from Compton Profile Measurements

Compton profile data are used to investigate the ground state wavefunction of graphite. The results of two new $\gamma$-ray measurements are reported and compared with the results of earlier $\gamma$-ray and electron scattering measurements. A tight-binding calculation has been carried out and the results of earlier calculations based on a molecular model and a pseudo-potential wavefunction are considered. The analysis, in terms of the reciprocal form factor, shows that none of the calculations gives an adequate description of the data in the basal plane although the pseudo-potential calculation describes the anisotropy in the plane reasonably well. In the basal plane the zero-crossing theorem appears to be violated and this problem must be resolved before more accurate models can be derived. In the c-axis direction the molecular model and the tight binding calculation give better agreement with the experimental data than does the pseudopotential calculation.

Optical Barker sequences and self-orthogonal convolutional codes

The relation between optical Barker codes and self-orthogonal convolutional codes is pointed out. It is then used to update the results in earlier publication.

'Take away from the dry sixties style marking': Lecturer and student perceptions and experiences of audio feedback

Providing audio feedback to assessment is relatively uncommon in higher education. However, published research suggests that it is preferred over written feedback by students but lecturers were less convinced. The aim of this paper is to examine further these findings in the context of a third year business ethics unit. Data was collected from two sources. The first is a series of in-depth, semi-structured interviews conducted with three lecturers providing audio feeback for the first time in Semester One 2011. The second source of data was drawn from the university student evaluation system. A total of 363 responses were used providing 'before' and 'after' perspectives about the effectiveness of audio feedback versus written feedback. Between 2005 and 2009 the survey data provided information about student attitudes to written assessment feedback (n=261). From 2010 onwards the data relates to audio (mp3) feedback (n=102). The analysis of he interview data indicated that introducing audio feedback should be done with care. The perception of the participating lecturers was mixed, ranging from sceptism to outright enthusiasm, but over time the overall approach became positive. It was found that particular attention needs to be paid to small (but important) technical details, and lecturers need to be convinced of its effectieness, especially that it is not necessarily more time consuming than providing written feedback. For students, the analysis revealed a clear preference for audio feedback. It is concluded that there is cause for concern and reason for optimism. It is a cause for concern because there is a possibility that scepticism on the part of academic staff seems to be based on assumptions about what students prefer and a concern about using the technology. There is reason for optimism because the evidence points towards students preferring audio feedback and as academic staff become more familiar with the technology the scepticism tends to evaporate. While this study is limited in scope, questions are raised about tackling negative staff perceptions of audio feedback that are worthy of further research.

A Finite Variable Difference Relaxation Scheme for hyperbolic-parabolic equations

Using the framework of a new relaxation system, which converts a nonlinear viscous conservation law into a system of linear convection-diffusion equations with nonlinear source terms, a finite variable difference method is developed for nonlinear hyperbolic-parabolic equations. The basic idea is to formulate a finite volume method with an optimum spatial difference, using the Locally Exact Numerical Scheme (LENS), leading to a Finite Variable Difference Method as introduced by Sakai [Katsuhiro Sakai, A new finite variable difference method with application to locally exact numerical scheme, journal of Computational Physics, 124 (1996) pp. 301-308.], for the linear convection-diffusion equations obtained by using a relaxation system. Source terms are treated with the well-balanced scheme of Jin [Shi Jin, A steady-state capturing method for hyperbolic systems with geometrical source terms, Mathematical Modeling Numerical Analysis, 35 (4) (2001) pp. 631-645]. Bench-mark test problems for scalar and vector conservation laws in one and two dimensions are solved using this new algorithm and the results demonstrate the efficiency of the scheme in capturing the flow features accurately.

Polymorphic low penetrance genes and breast cancer : The role of genes involved in metabolism of xenobiotics, estrogens and reactive oxygen species

Various endogenous and exogenous factors have been reported to increase the risk of breast cancer. Many of those are related to prolonged lifetime exposure to estrogens. Furthermore, a positive family history of breast cancer and certain benign breast diseases are known to increase the risk of breast cancer. The role of lifestyle factors, such as use of alcohol and smoking has been an area of intensive study. Alcohol has been found to increase the risk of breast cancer, whereas the role of smoking has remained obscure. A multitude of enzymes are involved in the metabolism of estrogens and xenobiotics including the carcinogens found in tobacco smoke. Many of the metabolic enzymes exhibit genetic polymorphisms that can lead to inter-individual differences in their abilities to modify hazardous substrates. Therefore, in presence of a given chemical exposure, one subgroup of women may be more susceptible to breast carcinogenesis, since they carry unfavourable forms of the polymorphic genes involved in the metabolism of the chemical. In this work, polymorphic genes encoding for cytochrome P450 (CYP) 1A1 and 1B1, N-acetyl transferase 2 (NAT2), sulfotransferase 1A1 (SULT1A1), manganese superoxide dismutase (MnSOD) and vitamin D receptor (VDR) were investigated in relation to breast cancer susceptibility in a Finnish population. CYP1A1, CYP1B1 and SULT1A1 are involved in the metabolism of both estrogens and xenobiotics, whereas NAT2 is involved only in the latter. MnSOD is an antioxidant enzyme protecting cells from oxidative damage. VDR, in turn, mediates the effects of the active form of vitamin D (1,25(OH)2D3, calcitriol) on maintenance of calcium homeostasis and it has anti-proliferative effects in many cancer cells. A 1.3-fold (95% CIs 1.01-1.73) increased risk of breast cancer was seen among women who carried the NAT2 slow acetylator genotype and a 1.5-fold (95% CI 1.1-2.0) risk was found in women with a MnSOD variant A allele containing genotypes compared to women with the NAT2 rapid acetylator genotype or to those with the MnSOD VV genotype, respectively. Instead, women with the VDR a allele containing genotypes were found to be at a decreased risk for breast cancer (OR 0.73; 95% CI 0.54-0.98) compared to women with the AA genotype. No significant overall associations were found between SULT1A1 or CYP genotypes and breast cancer risk, whereas a combination of the CYP1B1 432Val allele containing genotypes with the NAT2 slow acetylator genotypes posed a 1.5-fold (95% CI 1.03-2.24) increased risk. Moreover, NAT2 slow acetylator genotype was found to be confined to women with an advanced stage of breast cancer (stages III and IV). Further evidence for the association of xenobiotic metabolising genes with breast cancer risk was found when active smoking was taken into account. Women who smoked less than 10 cigarettes/day and carried at least one CYP1B1 432Val variant allele, were at 3.1-fold (95% CI 1.32-7.12) risk of breast cancer compared to women who smoked the same amount but did not carry the variant allele. Furthermore, the risk was significantly increased with increasing number of the CYP1B1 432Val alleles (p for trend 0.005). In addition, women who smoked less than 5 pack-years and carried the NAT2 slow acetylator genotype were at a 2.6-fold (95% CI 1.01-6.48) increased risk of breast cancer compared to women who smoked the same amount but carried the NAT2 rapid acetylator genotype. Furthermore, the combination of the CYP1B1 432Val allele and the NAT2 slow acetylator genotype increased the risk of breast cancer by 2.5-fold (95% CI 1.11-5.45) among ever smokers. Instead, the MnSOD A allele was found to be a risk factor among postmenopausal long-term smokers (>15 years of smoking) (OR 5.1; 95% CI 1.4-18.4) or among postmenopausal women who had smoked more than 10 cigarettes/day (OR 5.5; 95% CI 1.3-23.4) compared to women who had similar smoking habits but carried the MnSOD V/V genotype. Similarly, within subgroups of postmenopausal women who were using oral contraceptives, hormone replacement therapy or alcohol, women carrying the MnSOD A allele genotypes seemed to be at increased risk of breast cancer compared to women with the MnSOD V/V genotype. A positive family history of breast cancer and high parity were shown to be inversely associated with breast cancer risk among women carrying the VDR ApaI a allele or among premenopausal women carrying the SULT1A1*2 allele, respectively.

The role of glycodelin as an immune-modulating agent at the feto-maternal interface

Glycodelin A is a progesterone-induced endometrial glycoprotein which has been amply documented to play a role in down-modulation of the maternal immune response to fetal allo-antigens and to be indispensable for the maintenance and progression of pregnancy. Earlier studies from our laboratory have focused on the effect of glycodelin on T cells, key regulators of both the antibody and cell-mediated arms of the acquired immune system. Glycodelin-induced apoptosis inactivated T cells occurs through a caspase-dependant intrinsic mitochondrial pathway. Interestingly, glycodelin inhibited the proliferation of B cells but did not induce apoptosis. More recently, we have studied the effect of glycodelin on the cells of the innate immune system, namely monocytes and NK cells. We have found that glycodelin induced apoptosis in monocytic cells before their differentiation to macrophages, via the mitochondrial pathway, but did not affect their phagocytic capacity after differentiation. Glycodelin induced apoptosis in NK cells but this activity was independent of caspases. In conclusion, glycodelin is observed to affect many cells of the immune system, although the nature of the effect and signaling mechanisms involved in each cell type may be distinct.

Preoperative visual acuity of cataract patients. Repeatability of visual acuity and refractive error measurements in clinical settings

Visual acuities at the time of referral and on the day before surgery were compared in 124 patients operated on for cataract in Vaasa Central Hospital, Finland. Preoperative visual acuity and the occurrence of ocular and general disease were compared in samples of consecutive cataract extractions performed in 1982, 1985, 1990, 1995 and 2000 in two hospitals in the Vaasa region in Finland. The repeatability and standard deviation of random measurement error in visual acuity and refractive error determination in a clinical environment in cataractous, pseudophakic and healthy eyes were estimated by re-examining visual acuity and refractive error of patients referred to cataract surgery or consultation by ophthalmic professionals. Altogether 99 eyes of 99 persons (41 cataractous, 36 pseudophakic and 22 healthy eyes) with a visual acuity range of Snellen 0.3 to 1.3 (0.52 to -0.11 logMAR) were examined. During an average waiting time of 13 months, visual acuity in the study eye decreased from 0.68 logMAR to 0.96 logMAR (from 0.2 to 0.1 in Snellen decimal values). The average decrease in vision was 0.27 logMAR per year. In the fastest quartile, visual acuity change per year was 0.75 logMAR, and in the second fastest 0.29 logMAR, the third and fourth quartiles were virtually unaffected. From 1982 to 2000, the incidence of cataract surgery increased from 1.0 to 7.2 operations per 1000 inhabitants per year in the Vaasa region. The average preoperative visual acuity in the operated eye increased by 0.85 logMAR (in decimal values from 0.03to 0.2) and in the better eye 0.27 logMAR (in decimal values from 0.23 to 0.43) over this period. The proportion of patients profoundly visually handicapped (VA in the better eye <0.1) before the operation fell from 15% to 4%, and that of patients less profoundly visually handicapped (VA in the better eye 0.1 to <0.3) from 47% to 15%. The repeatability visual acuity measurement estimated as a coefficient of repeatability for all 99 eyes was ±0.18 logMAR, and the standard deviation of measurement error was 0.06 logMAR. Eyes with the lowest visual acuity (0.3-0.45) had the largest variability, the coefficient of repeatability values being ±0.24 logMAR and eyes with a visual acuity of 0.7 or better had the smallest, ±0.12 logMAR. The repeatability of refractive error measurement was studied in the same patient material as the repeatability of visual acuity. Differences between measurements 1 and 2 were calculated as three-dimensional vector values and spherical equivalents and expressed by coefficients of repeatability. Coefficients of repeatability for all eyes for vertical, torsional and horisontal vectors were ±0.74D, ±0.34D and ±0.93D, respectively, and for spherical equivalent for all eyes ±0.74D. Eyes with lower visual acuity (0.3-0.45) had larger variability in vector and spherical equivalent values (±1.14), but the difference between visual acuity groups was not statistically significant. The difference in the mean defocus equivalent between measurements 1 and 2 was, however, significantly greater in the lower visual acuity group. If a change of ±0.5D (measured in defocus equivalents) is accepted as a basis for change of spectacles for eyes with good vision, the basis for eyes in the visual acuity range of 0.3 - 0.65 would be ±1D. Differences in repeated visual acuity measurements are partly explained by errors in refractive error measurements.

Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5

Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 angstrom resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alpha beta alpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.