Surface reconstruction of wheat leaf morphology from three-dimensional scanned data

Realistic virtual models of leaf surfaces are important for a number of applications in the plant sciences, such as modelling agrichemical spray droplet movement and spreading on the surface. In this context, the virtual surfaces are required to be sufficiently smooth to facilitate the use of the mathematical equations that govern the motion of the droplet. While an effective approach is to apply discrete smoothing D2-spline algorithms to reconstruct the leaf surfaces from three-dimensional scanned data, difficulties arise when dealing with wheat leaves that tend to twist and bend. To overcome this topological difficulty, we develop a parameterisation technique that rotates and translates the original data, allowing the surface to be fitted using the discrete smoothing D2-spline methods in the new parameter space. Our algorithm uses finite element methods to represent the surface as a linear combination of compactly supported shape functions. Numerical results confirm that the parameterisation, along with the use of discrete smoothing D2-spline techniques, produces realistic virtual representations of wheat leaves.

Crime in rural Australia

As an academic who has spent a quarter of a century living, lecturing and researching in a rural community, I am often impressed by the discrepancies between the reality of rural life and its image in the public consciousness. At least two aspects of this are the most striking. First, there is often - especially, but not exclusively in English-speaking societies - the idea that rural communities represent the "real" or "true" aspects of a society's culture. For example, judging by the representations of rural Australia in the media, rural life is where we find the true Australian, the laconic, taciturn, but decent everyday man and woman, the "battlers", who are not corrupted by urban life. Such an attribution of genuineness to rurality is especially interesting given that the vast majority of contemporary Australians live in cities and that Australia is one of the most urbanised countries in the world. Second, and following from the first point, is the idea that rural areas remain somewhat behind the times, that somehow they are not quite part of the contemporary world. This is a mixed image as it combines both the negative idea of backwardness with the more positive one of a society that has not lost the virtues of stability and civility that we often feel is missing in the city. Both of these ideas combine in the popular image of rural communities as safe places in an increasingly dangerous world. In the popular mind it seems that there is an idea that whatever rural communities may lack in conveniences and sophistication, they remain places where you might walk down the street safely, leave your doors unlocked at night and raise your children confident that they will not be exposed to drugs, gangs and violence. Unfortunately, all of these ideas are fantasies. There is no reason to believe that the residents of rural communities are anymore the truer representations of Australian culture than the average suburbanite.

Cultural relativity as exchange : J.W. Lindt’s bush character and Aboriginal from The Grafton Album (circa 1872)

J.W.Lindt’s Colonial man and Aborigine image from the GRAFTON ALBUM: “On chemistry and optics all does not depend, art must with these in triple union blend” (text from J.W. Lindt’s photographic backing card)...

Néstor-Guillermo Progeria Syndrome: a biochemical insight into Barrier-to-Autointegration Factor 1, alanine 12 threonine mutation

Background Premature aging syndromes recapitulate many aspects of natural aging and provide an insight into this phenomenon at a molecular and cellular level. The progeria syndromes appear to cause rapid aging through disruption of normal nuclear structure. Recently, a coding mutation (c.34G > A [p.A12T]) in the Barrier to Autointegration Factor 1 (BANF1) gene was identified as the genetic basis of Néstor-Guillermo Progeria syndrome (NGPS). This mutation was described to cause instability in the BANF1 protein, causing a disruption of the nuclear envelope structure. Results Here we demonstrate that the BANF1 A12T protein is indeed correctly folded, stable and that the observed phenotype, is likely due to the disruption of the DNA binding surface of the A12T mutant. We demonstrate, using biochemical assays, that the BANF1 A12T protein is impaired in its ability to bind DNA while its interaction with nuclear envelope proteins is unperturbed. Consistent with this, we demonstrate that ectopic expression of the mutant protein induces the NGPS cellular phenotype, while the protein localizes normally to the nuclear envelope. Conclusions Our study clarifies the role of the A12T mutation in NGPS patients, which will be of importance for understanding the development of the disease.

Systematic constellations of neurons are activated in lateral amygdala following Pavlovian fear conditioning

How memory is organized within neural networks is a fundamental question in neuroscience. We used Pavlovian fear conditioning to study the discrete organization patterns of neurons activated in an associative memory paradigm. In Pavlovian fear conditioning a neutral stimulus, such as an auditory tone, is temporally paired with an aversive unconditioned stimulus (US), such as a foot shock...

A review of: "Wrong-Doing, Truth-Telling: The Function of Avowal in Justice. By Michel Foucault. Edited by Fabienne Brion and Bernard E. Harcourt. Translated by Stephen W. Sawyer"

Wrong-Doing, Truth-Telling: The Function of Avowal in Justice is a collection of seven lectures delivered by French philosopher and historian Michel Foucault at the Catholic University of Louvain in 1981. Compiled from audiovisual recordings and Foucault’s original manuscripts, these lectures explore the notion of avowal and its place within criminal justice processes. Accompanied by three contemporaneous interviews given by Foucault (only one of which has previously been available in English), and a preface and concluding essay by the editors contextualizing these lectures in Foucault’s oeuvre, this volume contributes much to Foucaultian scholarship, particularly when considered alongside the recently published volumes of Foucault’s lecture courses at the Collège de France. However, while the book promises to offer some insights of relevance to criminology, it is important to remember that this is not its key purpose, and criminologists should read it with this caveat in mind...

Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis

Variation in body iron is associated with or causes diseases, including anaemia and iron overload. Here, we analyse genetic association data on biochemical markers of iron status from 11 European-population studies, with replication in eight additional cohorts (total up to 48,972 subjects). We find 11 genome-wide-significant (P<5 × 10−8) loci, some including known iron-related genes (​HFE, ​SLC40A1, ​TF, ​TFR2, ​TFRC, ​TMPRSS6) and others novel (​ABO, ​ARNTL, ​FADS2, ​NAT2, ​TEX14). SNPs at ​ARNTL, ​TF, and ​TFR2 affect iron markers in ​HFE C282Y homozygotes at risk for hemochromatosis. There is substantial overlap between our iron loci and loci affecting erythrocyte and lipid phenotypes. These results will facilitate investigation of the roles of iron in disease.

Market structure of international construction professional services: Evidences from top design firms

Construction professional service (CPS) in the international arena has been very competitive despite that the industry is proliferating at a high rate. To excel in international business, CPS firms have the importance of building overseas competition strategies on a proper understanding of the international CPS (I-CPS) market. However, subject to borderless trade, information technology–based networking, global outsourcing, and changing forms of procurement, the I-CPS market structure has become more covert, intricate, and unstraightforward than before. Through examining business competition among top international design firms, this study aims to identify the attributes of the I-CPS market structure from two perspectives—concentration and turnover. Data from Engineering News-Record over the period 2001–2011 were collected to calculate market concentration ratios and turnover indices. The results show that I-CPS competition is characterized by atomism, much turbulence with a steady increase in competition intensity, and the predominant role of new entrants and exiting firms in market turnovers. The combination of concentration and turnover is found useful to address the attributes of the I-CPS market structure, which favors I-CPS firms to formulate international competition strategies in due ways.

Global, regional, and national disability-adjusted life years (DALYs) for 306 diseases and injuries and healthy life expectancy (HALE) for 188 countries, 1990–2013: Quantifying the epidemiological transition

Background The Global Burden of Disease Study 2013 (GBD 2013) aims to bring together all available epidemiological data using a coherent measurement framework, standardised estimation methods, and transparent data sources to enable comparisons of health loss over time and across causes, age–sex groups, and countries. The GBD can be used to generate summary measures such as disability-adjusted life-years (DALYs) and healthy life expectancy (HALE) that make possible comparative assessments of broad epidemiological patterns across countries and time. These summary measures can also be used to quantify the component of variation in epidemiology that is related to sociodemographic development. Methods We used the published GBD 2013 data for age-specific mortality, years of life lost due to premature mortality (YLLs), and years lived with disability (YLDs) to calculate DALYs and HALE for 1990, 1995, 2000, 2005, 2010, and 2013 for 188 countries. We calculated HALE using the Sullivan method; 95% uncertainty intervals (UIs) represent uncertainty in age-specific death rates and YLDs per person for each country, age, sex, and year. We estimated DALYs for 306 causes for each country as the sum of YLLs and YLDs; 95% UIs represent uncertainty in YLL and YLD rates. We quantified patterns of the epidemiological transition with a composite indicator of sociodemographic status, which we constructed from income per person, average years of schooling after age 15 years, and the total fertility rate and mean age of the population. We applied hierarchical regression to DALY rates by cause across countries to decompose variance related to the sociodemographic status variable, country, and time. Findings Worldwide, from 1990 to 2013, life expectancy at birth rose by 6·2 years (95% UI 5·6–6·6), from 65·3 years (65·0–65·6) in 1990 to 71·5 years (71·0–71·9) in 2013, HALE at birth rose by 5·4 years (4·9–5·8), from 56·9 years (54·5–59·1) to 62·3 years (59·7–64·8), total DALYs fell by 3·6% (0·3–7·4), and age-standardised DALY rates per 100 000 people fell by 26·7% (24·6–29·1). For communicable, maternal, neonatal, and nutritional disorders, global DALY numbers, crude rates, and age-standardised rates have all declined between 1990 and 2013, whereas for non–communicable diseases, global DALYs have been increasing, DALY rates have remained nearly constant, and age-standardised DALY rates declined during the same period. From 2005 to 2013, the number of DALYs increased for most specific non-communicable diseases, including cardiovascular diseases and neoplasms, in addition to dengue, food-borne trematodes, and leishmaniasis; DALYs decreased for nearly all other causes. By 2013, the five leading causes of DALYs were ischaemic heart disease, lower respiratory infections, cerebrovascular disease, low back and neck pain, and road injuries. Sociodemographic status explained more than 50% of the variance between countries and over time for diarrhoea, lower respiratory infections, and other common infectious diseases; maternal disorders; neonatal disorders; nutritional deficiencies; other communicable, maternal, neonatal, and nutritional diseases; musculoskeletal disorders; and other non-communicable diseases. However, sociodemographic status explained less than 10% of the variance in DALY rates for cardiovascular diseases; chronic respiratory diseases; cirrhosis; diabetes, urogenital, blood, and endocrine diseases; unintentional injuries; and self-harm and interpersonal violence. Predictably, increased sociodemographic status was associated with a shift in burden from YLLs to YLDs, driven by declines in YLLs and increases in YLDs from musculoskeletal disorders, neurological disorders, and mental and substance use disorders. In most country-specific estimates, the increase in life expectancy was greater than that in HALE. Leading causes of DALYs are highly variable across countries. Interpretation Global health is improving. Population growth and ageing have driven up numbers of DALYs, but crude rates have remained relatively constant, showing that progress in health does not mean fewer demands on health systems. The notion of an epidemiological transition—in which increasing sociodemographic status brings structured change in disease burden—is useful, but there is tremendous variation in burden of disease that is not associated with sociodemographic status. This further underscores the need for country-specific assessments of DALYs and HALE to appropriately inform health policy decisions and attendant actions.

Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks in 188 countries, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013

Background The Global Burden of Disease, Injuries, and Risk Factor study 2013 (GBD 2013) is the first of a series of annual updates of the GBD. Risk factor quantification, particularly of modifiable risk factors, can help to identify emerging threats to population health and opportunities for prevention. The GBD 2013 provides a timely opportunity to update the comparative risk assessment with new data for exposure, relative risks, and evidence on the appropriate counterfactual risk distribution. Methods Attributable deaths, years of life lost, years lived with disability, and disability-adjusted life-years (DALYs) have been estimated for 79 risks or clusters of risks using the GBD 2010 methods. Risk–outcome pairs meeting explicit evidence criteria were assessed for 188 countries for the period 1990–2013 by age and sex using three inputs: risk exposure, relative risks, and the theoretical minimum risk exposure level (TMREL). Risks are organised into a hierarchy with blocks of behavioural, environmental and occupational, and metabolic risks at the first level of the hierarchy. The next level in the hierarchy includes nine clusters of related risks and two individual risks, with more detail provided at levels 3 and 4 of the hierarchy. Compared with GBD 2010, six new risk factors have been added: handwashing practices, occupational exposure to trichloroethylene, childhood wasting, childhood stunting, unsafe sex, and low glomerular filtration rate. For most risks, data for exposure were synthesised with a Bayesian meta-regression method, DisMod-MR 2.0, or spatial-temporal Gaussian process regression. Relative risks were based on meta-regressions of published cohort and intervention studies. Attributable burden for clusters of risks and all risks combined took into account evidence on the mediation of some risks such as high body-mass index (BMI) through other risks such as high systolic blood pressure and high cholesterol. Findings All risks combined account for 57·2% (95% uncertainty interval [UI] 55·8–58·5) of deaths and 41·6% (40·1–43·0) of DALYs. Risks quantified account for 87·9% (86·5–89·3) of cardiovascular disease DALYs, ranging to a low of 0% for neonatal disorders and neglected tropical diseases and malaria. In terms of global DALYs in 2013, six risks or clusters of risks each caused more than 5% of DALYs: dietary risks accounting for 11·3 million deaths and 241·4 million DALYs, high systolic blood pressure for 10·4 million deaths and 208·1 million DALYs, child and maternal malnutrition for 1·7 million deaths and 176·9 million DALYs, tobacco smoke for 6·1 million deaths and 143·5 million DALYs, air pollution for 5·5 million deaths and 141·5 million DALYs, and high BMI for 4·4 million deaths and 134·0 million DALYs. Risk factor patterns vary across regions and countries and with time. In sub-Saharan Africa, the leading risk factors are child and maternal malnutrition, unsafe sex, and unsafe water, sanitation, and handwashing. In women, in nearly all countries in the Americas, north Africa, and the Middle East, and in many other high-income countries, high BMI is the leading risk factor, with high systolic blood pressure as the leading risk in most of Central and Eastern Europe and south and east Asia. For men, high systolic blood pressure or tobacco use are the leading risks in nearly all high-income countries, in north Africa and the Middle East, Europe, and Asia. For men and women, unsafe sex is the leading risk in a corridor from Kenya to South Africa. Interpretation Behavioural, environmental and occupational, and metabolic risks can explain half of global mortality and more than one-third of global DALYs providing many opportunities for prevention. Of the larger risks, the attributable burden of high BMI has increased in the past 23 years. In view of the prominence of behavioural risk factors, behavioural and social science research on interventions for these risks should be strengthened. Many prevention and primary care policy options are available now to act on key risks.

J.W.Lindt’s Colonial man and Aborigine image from the GRAFTON ALBUM : “On chemistry and optics all does not depend, art must with these in triple union blend”

J.W.Lindt’s Colonial man and Aborigine image from the GRAFTON ALBUM: “On chemistry and optics all does not depend, art must with these in triple union blend” (text from J.W. Lindt’s photographic backing card) In this paper, I follow an argument that Lindt held a position in his particular colonial environment where he was simultaneously both an insider and an outsider and that such a position may be considered prerequisite in stimulating exchange. A study of the transition of J.W. Lindt in Grafton, N.S.W. in the 1860s from a traveller to a migrant and subsequently to a professional photographer, as well as Lindt’s photographic career, which evolved through strategic action and technical approaches to photography, bears witness to his cultural relativity. One untitled photograph from this period of work constructs a unique commentary of Australian colonial life that illustrates a non-hegemonic position, particularly as it was included in one of the first albums of photographs of Aborigines that Lindt gifted to an illustrious person (in this case the Mayor of Grafton). As in his other studio constructions, props and backdrops were arranged and sitters were positioned with care, but this photograph is the only one in the album that includes a non-Aborigine in a relationship to an Aborigine. An analysis of the props, technical details of the album and the image suggests a reconciliatory aspect that thwarts the predominant attitudes towards Aborigines in the area at that time.

New genetic loci link adipose and insulin biology to body fat distribution

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10−8). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

Fine mapping of variants associated with endometriosis in the WNT4 region on chromosome 1p36

Genome-wide association studies show strong evidence of association with endometriosis for markers on chromosome 1p36 spanning the potential candidate genes WNT4, CDC42 and LINC00339. WNT4 is involved in development of the uterus, and the expression of CDC42 and LINC00339 are altered in women with endometriosis. We conducted fine mapping to examine the role of coding variants in WNT4 and CDC42 and determine the key SNPs with strongest evidence of association in this region. We identified rare coding variants in WNT4 and CDC42 present only in endometriosis cases. The frequencies were low and cannot account for the common signal associated with increased risk of endometriosis. Genotypes for five common SNPs in the region of chromosome 1p36 show stronger association signals when compared with rs7521902 reported in published genome scans. Of these, three SNPs rs12404660, rs3820282, and rs55938609 were located in DNA sequences with potential functional roles including overlap with transcription factor binding sites for FOXA1, FOXA2, ESR1, and ESR2. Functional studies will be required to identify the gene or genes implicated in endometriosis risk.

FTO genotype is associated with phenotypic variability of body mass index

There is evidence across several species for genetic control of phenotypic variation of complex traits1, 2, 3, 4, such that the variance among phenotypes is genotype dependent. Understanding genetic control of variability is important in evolutionary biology, agricultural selection programmes and human medicine, yet for complex traits, no individual genetic variants associated with variance, as opposed to the mean, have been identified. Here we perform a meta-analysis of genome-wide association studies of phenotypic variation using ~170,000 samples on height and body mass index (BMI) in human populations. We report evidence that the single nucleotide polymorphism (SNP) rs7202116 at the FTO gene locus, which is known to be associated with obesity (as measured by mean BMI for each rs7202116 genotype)5, 6, 7, is also associated with phenotypic variability. We show that the results are not due to scale effects or other artefacts, and find no other experiment-wise significant evidence for effects on variability, either at loci other than FTO for BMI or at any locus for height. The difference in variance for BMI among individuals with opposite homozygous genotypes at the FTO locus is approximately 7%, corresponding to a difference of ~0.5 kilograms in the standard deviation of weight. Our results indicate that genetic variants can be discovered that are associated with variability, and that between-person variability in obesity can partly be explained by the genotype at the FTO locus. The results are consistent with reported FTO by environment interactions for BMI8, possibly mediated by DNA methylation9, 10. Our BMI results for other SNPs and our height results for all SNPs suggest that most genetic variants, including those that influence mean height or mean BMI, are not associated with phenotypic variance, or that their effects on variability are too small to detect even with samples sizes greater than 100,000.