Showing papers by "Queensland University of Technology published in 2017"

10 Years of GWAS Discovery: Biology, Function, and Translation

Abstract: Application of the experimental design of genome-wide association studies (GWASs) is now 10 years old (young), and here we review the remarkable range of discoveries it has facilitated in population and complex-trait genetics, the biology of diseases, and translation toward new therapeutics. We predict the likely discoveries in the next 10 years, when GWASs will be based on millions of samples with array data imputed to a large fully sequenced reference panel and on hundreds of thousands of samples with whole-genome sequencing data.

The effect of multiple adverse childhood experiences on health: a systematic review and meta-analysis

Abstract: Summary Background A growing body of research identifies the harmful effects that adverse childhood experiences (ACEs; occurring during childhood or adolescence; eg, child maltreatment or exposure to domestic violence) have on health throughout life. Studies have quantified such effects for individual ACEs. However, ACEs frequently co-occur and no synthesis of findings from studies measuring the effect of multiple ACE types has been done. Methods In this systematic review and meta-analysis, we searched five electronic databases for cross-sectional, case-control, or cohort studies published up to May 6, 2016, reporting risks of health outcomes, consisting of substance use, sexual health, mental health, weight and physical exercise, violence, and physical health status and conditions, associated with multiple ACEs. We selected articles that presented risk estimates for individuals with at least four ACEs compared with those with none for outcomes with sufficient data for meta-analysis (at least four populations). Included studies also focused on adults aged at least 18 years with a sample size of at least 100. We excluded studies based on high-risk or clinical populations. We extracted data from published reports. We calculated pooled odds ratios (ORs) using a random-effects model. Findings Of 11 621 references identified by the search, 37 included studies provided risk estimates for 23 outcomes, with a total of 253 719 participants. Individuals with at least four ACEs were at increased risk of all health outcomes compared with individuals with no ACEs. Associations were weak or modest for physical inactivity, overweight or obesity, and diabetes (ORs of less than two); moderate for smoking, heavy alcohol use, poor self-rated health, cancer, heart disease, and respiratory disease (ORs of two to three), strong for sexual risk taking, mental ill health, and problematic alcohol use (ORs of more than three to six), and strongest for problematic drug use and interpersonal and self-directed violence (ORs of more than seven). We identified considerable heterogeneity ( I 2 of >75%) between estimates for almost half of the outcomes. Interpretation To have multiple ACEs is a major risk factor for many health conditions. The outcomes most strongly associated with multiple ACEs represent ACE risks for the next generation (eg, violence, mental illness, and substance use). To sustain improvements in public health requires a shift in focus to include prevention of ACEs, resilience building, and ACE-informed service provision. The Sustainable Development Goals provide a global platform to reduce ACEs and their life-course effect on health. Funding Public Health Wales.

Simple online and realtime tracking with a deep association metric

Abstract: Simple Online and Realtime Tracking (SORT) is a pragmatic approach to multiple object tracking with a focus on simple, effective algorithms. In this paper, we integrate appearance information to improve the performance of SORT. Due to this extension we are able to track objects through longer periods of occlusions, effectively reducing the number of identity switches. In spirit of the original framework we place much of the computational complexity into an offline pre-training stage where we learn a deep association metric on a largescale person re-identification dataset. During online application, we establish measurement-to-track associations using nearest neighbor queries in visual appearance space. Experimental evaluation shows that our extensions reduce the number of identity switches by 45%, achieving overall competitive performance at high frame rates.

Ti3C2 MXene co-catalyst on metal sulfide photo-absorbers for enhanced visible-light photocatalytic hydrogen production.

Abstract: Scalable and sustainable solar hydrogen production through photocatalytic water splitting requires highly active and stable earth-abundant co-catalysts to replace expensive and rare platinum. Here we employ density functional theory calculations to direct atomic-level exploration, design and fabrication of a MXene material, Ti3C2 nanoparticles, as a highly efficient co-catalyst. Ti3C2 nanoparticles are rationally integrated with cadmium sulfide via a hydrothermal strategy to induce a super high visible-light photocatalytic hydrogen production activity of 14,342 μmol h−1 g−1 and an apparent quantum efficiency of 40.1% at 420 nm. This high performance arises from the favourable Fermi level position, electrical conductivity and hydrogen evolution capacity of Ti3C2 nanoparticles. Furthermore, Ti3C2 nanoparticles also serve as an efficient co-catalyst on ZnS or ZnxCd1−xS. This work demonstrates the potential of earth-abundant MXene family materials to construct numerous high performance and low-cost photocatalysts/photoelectrodes.

The burden of primary liver cancer and underlying etiologies from 1990 to 2015 at the global, regional, and national level : results from the Global Burden of Disease Study 2015

Abstract: Importance Liver cancer is among the leading causes of cancer deaths globally. The most common causes for liver cancer include hepatitis B virus (HBV) and hepatitis C virus (HCV) infection and alcohol use. Objective To report results of the Global Burden of Disease (GBD) 2015 study on primary liver cancer incidence, mortality, and disability-adjusted life-years (DALYs) for 195 countries or territories from 1990 to 2015, and present global, regional, and national estimates on the burden of liver cancer attributable to HBV, HCV, alcohol, and an “other” group that encompasses residual causes. Design, Settings, and Participants Mortality was estimated using vital registration and cancer registry data in an ensemble modeling approach. Single-cause mortality estimates were adjusted for all-cause mortality. Incidence was derived from mortality estimates and the mortality-to-incidence ratio. Through a systematic literature review, data on the proportions of liver cancer due to HBV, HCV, alcohol, and other causes were identified. Years of life lost were calculated by multiplying each death by a standard life expectancy. Prevalence was estimated using mortality-to-incidence ratio as surrogate for survival. Total prevalence was divided into 4 sequelae that were multiplied by disability weights to derive years lived with disability (YLDs). DALYs were the sum of years of life lost and YLDs. Main Outcomes and Measures Liver cancer mortality, incidence, YLDs, years of life lost, DALYs by etiology, age, sex, country, and year. Results There were 854 000 incident cases of liver cancer and 810 000 deaths globally in 2015, contributing to 20 578 000 DALYs. Cases of incident liver cancer increased by 75% between 1990 and 2015, of which 47% can be explained by changing population age structures, 35% by population growth, and −8% to changing age-specific incidence rates. The male-to-female ratio for age-standardized liver cancer mortality was 2.8. Globally, HBV accounted for 265 000 liver cancer deaths (33%), alcohol for 245 000 (30%), HCV for 167 000 (21%), and other causes for 133 000 (16%) deaths, with substantial variation between countries in the underlying etiologies. Conclusions and Relevance Liver cancer is among the leading causes of cancer deaths in many countries. Causes of liver cancer differ widely among populations. Our results show that most cases of liver cancer can be prevented through vaccination, antiviral treatment, safe blood transfusion and injection practices, as well as interventions to reduce excessive alcohol use. In line with the Sustainable Development Goals, the identification and elimination of risk factors for liver cancer will be required to achieve a sustained reduction in liver cancer burden. The GBD study can be used to guide these prevention efforts.

Simple Online and Realtime Tracking with a Deep Association Metric

Abstract: Simple Online and Realtime Tracking (SORT) is a pragmatic approach to multiple object tracking with a focus on simple, effective algorithms. In this paper, we integrate appearance information to improve the performance of SORT. Due to this extension we are able to track objects through longer periods of occlusions, effectively reducing the number of identity switches. In spirit of the original framework we place much of the computational complexity into an offline pre-training stage where we learn a deep association metric on a large-scale person re-identification dataset. During online application, we establish measurement-to-track associations using nearest neighbor queries in visual appearance space. Experimental evaluation shows that our extensions reduce the number of identity switches by 45%, achieving overall competitive performance at high frame rates.

A Heterostructure Coupling of Exfoliated Ni–Fe Hydroxide Nanosheet and Defective Graphene as a Bifunctional Electrocatalyst for Overall Water Splitting

Abstract: Herein, the authors demonstrate a heterostructured NiFe LDH-NS@DG10 hybrid catalyst by coupling of exfoliated Ni-Fe layered double hydroxide (LDH) nanosheet (NS) and defective graphene (DG). The catalyst has exhibited extremely high electrocatalytic activity for oxygen evolution reaction (OER) in an alkaline solution with an overpotential of 0.21 V at a current density of 10 mA cm-2, which is comparable to the current record (≈0.20 V in Fe-Co-Ni metal-oxide-film system) and superior to all other non-noble metal catalysts. Also, it possesses outstanding kinetics (Tafel slope of 52 mV dec-1) for the reaction. Interestingly, the NiFe LDH-NS@DG10 hybrid has also exhibited the high hydrogen evolution reaction (HER) performance in an alkaline solution (with an overpotential of 115 mV by 2 mg cm-2 loading at a current density of 20 mA cm-2) in contrast to barely HER activity for NiFe LDH-NS itself. As a result, the bifunctional catalyst the authors developed can achieve a current density of 20 mA cm-2 by a voltage of only 1.5 V, which is also a record for the overall water splitting. Density functional theory calculation reveals that the synergetic effects of highly exposed 3d transition metal atoms and carbon defects are essential for the bifunctional activity for OER and HER

Cortical abnormalities in adults and adolescents with major depression based on brain scans from 20 cohorts worldwide in the ENIGMA Major Depressive Disorder Working Group.

Abstract: The neuro-anatomical substrates of major depressive disorder (MDD) are still not well understood, despite many neuroimaging studies over the past few decades. Here we present the largest ever worldwide study by the ENIGMA (Enhancing Neuro Imaging Genetics through Meta-Analysis) Major Depressive Disorder Working Group on cortical structural alterations in MDD. Structural T1-weighted brain magnetic resonance imaging (MRI) scans from 2148 MDD patients and 7957 healthy controls were analysed with harmonized protocols at 20 sites around the world. To detect consistent effects of MDD and its modulators on cortical thickness and surface area estimates derived from MRI, statistical effects from sites were meta-analysed separately for adults and adolescents. Adults with MDD had thinner cortical gray matter than controls in the orbitofrontal cortex (OFC), anterior and posterior cingulate, insula and temporal lobes (Cohen's d effect sizes: -0.10 to -0.14). These effects were most pronounced in first episode and adult-onset patients (>21 years). Compared to matched controls, adolescents with MDD had lower total surface area (but no differences in cortical thickness) and regional reductions in frontal regions (medial OFC and superior frontal gyrus) and primary and higher-order visual, somatosensory and motor areas (d: -0.26 to -0.57). The strongest effects were found in recurrent adolescent patients. This highly powered global effort to identify consistent brain abnormalities showed widespread cortical alterations in MDD patients as compared to controls and suggests that MDD may impact brain structure in a highly dynamic way, with different patterns of alterations at different stages of life.

2D MXenes: A New Family of Promising Catalysts for the Hydrogen Evolution Reaction

Abstract: Developing highly conductive, stable, and active nonprecious hydrogen evolution reaction (HER) catalysts is a key step for the proposed hydrogen economy. However, few catalysts, except for noble metals, meet all the requirements. By using state-of-the-art density functional calculations, herein we demonstrate that 2D MXenes, like Ti2C, V2C, and Ti3C2, are terminated by a mixture of oxygen atoms and hydroxyl, while Nb2C and Nb4C3O2 are fully terminated by oxygen atoms under standard conditions [pH 0, p(H2) = 1 bar, U = 0 V vs standard hydrogen electrode], findings in good agreement with experimental observation. Furthermore, all these MXenes are conductive under standard conditions, thus allowing high charge transfer kinetics during the HER. Remarkably, the Gibbs free energy for the adsorption of atomic hydrogen (ΔGH*0) on the terminated O atoms (e.g., Ti2CO2) is close to the ideal value (0 eV). Our results demonstrate terminated oxygens as catalytic active sites for the HER at these materials and highligh...

Spectrally-normalized margin bounds for neural networks

Abstract: This paper presents a margin-based multiclass generalization bound for neural networks that scales with their margin-normalized "spectral complexity": their Lipschitz constant, meaning the product of the spectral norms of the weight matrices, times a certain correction factor. This bound is empirically investigated for a standard AlexNet network trained with SGD on the MNIST and CIFAR10 datasets, with both original and random labels; the bound, the Lipschitz constants, and the excess risks are all in direct correlation, suggesting both that SGD selects predictors whose complexity scales with the difficulty of the learning task, and secondly that the presented bound is sensitive to this complexity.

Whole-genome landscape of pancreatic neuroendocrine tumours

Abstract: The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the mutational signatures they harbour, including a deficiency in G:C > T:A base excision repair due to inactivation of MUTYH, which encodes a DNA glycosylase. Clinically sporadic PanNETs contain a larger-than-expected proportion of germline mutations, including previously unreported mutations in the DNA repair genes MUTYH, CHEK2 and BRCA2. Together with mutations in MEN1 and VHL, these mutations occur in 17% of patients. Somatic mutations, including point mutations and gene fusions, were commonly found in genes involved in four main pathways: chromatin remodelling, DNA damage repair, activation of mTOR signalling (including previously undescribed EWSR1 gene fusions), and telomere maintenance. In addition, our gene expression analyses identified a subgroup of tumours associated with hypoxia and HIF signalling.

A liquid metal reaction environment for the room-temperature synthesis of atomically thin metal oxides.

Abstract: Two-dimensional (2D) oxides have a wide variety of applications in electronics and other technologies. However, many oxides are not easy to synthesize as 2D materials through conventional methods. We used nontoxic eutectic gallium-based alloys as a reaction solvent and co-alloyed desired metals into the melt. On the basis of thermodynamic considerations, we predicted the composition of the self-limiting interfacial oxide. We isolated the surface oxide as a 2D layer, either on substrates or in suspension. This enabled us to produce extremely thin subnanometer layers of HfO2, Al2O3, and Gd2O3. The liquid metal–based reaction route can be used to create 2D materials that were previously inaccessible with preexisting methods. The work introduces room-temperature liquid metals as a reaction environment for the synthesis of oxide nanomaterials with low dimensionality.

Revisiting the Holy Grail: using plant functional traits to understand ecological processes

Abstract: One of ecology's grand challenges is developing general rules to explain and predict highly complex systems. Understanding and predicting ecological processes from species' traits has been considered a 'Holy Grail' in ecology. Plant functional traits are increasingly being used to develop mechanistic models that can predict how ecological communities will respond to abiotic and biotic perturbations and how species will affect ecosystem function and services in a rapidly changing world; however, significant challenges remain. In this review, we highlight recent work and outstanding questions in three areas: (i) selecting relevant traits; (ii) describing intraspecific trait variation and incorporating this variation into models; and (iii) scaling trait data to community- and ecosystem-level processes. Over the past decade, there have been significant advances in the characterization of plant strategies based on traits and trait relationships, and the integration of traits into multivariate indices and models of community and ecosystem function. However, the utility of trait-based approaches in ecology will benefit from efforts that demonstrate how these traits and indices influence organismal, community, and ecosystem processes across vegetation types, which may be achieved through meta-analysis and enhancement of trait databases. Additionally, intraspecific trait variation and species interactions need to be incorporated into predictive models using tools such as Bayesian hierarchical modelling. Finally, existing models linking traits to community and ecosystem processes need to be empirically tested for their applicability to be realized.

Macrophage Phenotypes Regulate Scar Formation and Chronic Wound Healing.

Abstract: Macrophages and inflammation play a beneficial role during wound repair with macrophages regulating a wide range of processes, such as removal of dead cells, debris and pathogens, through to extracellular matrix deposition re-vascularisation and wound re-epithelialisation. To perform this range of functions, these cells develop distinct phenotypes over the course of wound healing. They can present with a pro-inflammatory M1 phenotype, more often found in the early stages of repair, through to anti-inflammatory M2 phenotypes that are pro-repair in the latter stages of wound healing. There is a continuum of phenotypes between these ranges with some cells sharing phenotypes of both M1 and M2 macrophages. One of the less pleasant consequences of quick closure, namely the replacement with scar tissue, is also regulated by macrophages, through their promotion of fibroblast proliferation, myofibroblast differentiation and collagen deposition. Alterations in macrophage number and phenotype disrupt this process and can dictate the level of scar formation. It is also clear that dysregulated inflammation and altered macrophage phenotypes are responsible for hindering closure of chronic wounds. The review will discuss our current knowledge of macrophage phenotype on the repair process and how alterations in the phenotypes might alter wound closure and the final repair quality.

Prevalence and trends of metabolic syndrome among adults in the asia-pacific region: a systematic review.

Abstract: The Asia-Pacific region is home to nearly half of the world’s population. The region has seen a recent rapid increase in the prevalence of obesity, type-2 diabetes and cardiovascular disease. The present systematic review summarizes the recent prevalence and trends of Metabolic Syndrome (MetS) among adults in countries of the Asia-Pacific Region. Data on MetS in Asia-Pacific countries were obtained using a stepwise process by searching the online Medline database using MeSH terms ‘Metabolic Syndrome X’ and ‘Epidemiology/EP’. For the purpose of describing prevalence data for the individual countries, studies that were most recent, nationally representative or with the largest sample size were included. When evaluating secular trends in prevalence in a country we only considered studies that evaluated the temporal change in prevalence between similar populations, prospective studies based on the same population or National surveys conducted during different time periods. This literature search yielded a total of 757 articles, and five additional article were identified by screening of reference lists. From this total, 18 studies were eligible to be included in the final analysis. Of the 51 Asia-Pacific countries (WHO) we only located data for 15. There was wide between country variation in prevalence of MetS. A national survey from Philippines conducted in 2003 revealed the lowest reported prevalence of 11.9% according to NCEP ATP III criteria. In contrast, the highest recorded prevalence in the region (49.0%) came from a study conducted in urban Pakistan (Karachchi, 2004). Most studies reported a higher prevalence of MetS in females and urban residents. Data on secular trends were available for China, South Korea and Taiwan. An increase in the prevalence of MetS was observed in all three countries. Despite differences in methodology, diagnostic criteria and age of subjects studied, the Asia-Pacific region is facing a significant epidemic of MetS. In most countries nearly 1/5th of the adult population or more were affected by MetS with a secular increase in prevalence. Strategies aimed at primary prevention are required to ameliorate a further increase in the epidemic and for the reduction of the morbidity and mortality associated with MetS.

Predictive Business Process Monitoring with LSTM Neural Networks

Abstract: Predictive business process monitoring methods exploit logs of completed cases of a process in order to make predictions about running cases thereof. Existing methods in this space are tailor-made for specific prediction tasks. Moreover, their relative accuracy is highly sensitive to the dataset at hand, thus requiring users to engage in trial-and-error and tuning when applying them in a specific setting. This paper investigates Long Short-Term Memory (LSTM) neural networks as an approach to build consistently accurate models for a wide range of predictive process monitoring tasks. First, we show that LSTMs outperform existing techniques to predict the next event of a running case and its timestamp. Next, we show how to use models for predicting the next task in order to predict the full continuation of a running case. Finally, we apply the same approach to predict the remaining time, and show that this approach outperforms existing tailor-made methods.

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk

Abstract: The timing of puberty is a highly polygenic childhood trait that is epidemiologically associated with various adult diseases. Using 1000 Genomes Project-imputed genotype data in up to ∼370,000 women, we identify 389 independent signals (P < 5 × 10-8) for age at menarche, a milestone in female pubertal development. In Icelandic data, these signals explain ∼7.4% of the population variance in age at menarche, corresponding to ∼25% of the estimated heritability. We implicate ∼250 genes via coding variation or associated expression, demonstrating significant enrichment in neural tissues. Rare variants near the imprinted genes MKRN3 and DLK1 were identified, exhibiting large effects when paternally inherited. Mendelian randomization analyses suggest causal inverse associations, independent of body mass index (BMI), between puberty timing and risks for breast and endometrial cancers in women and prostate cancer in men. In aggregate, our findings highlight the complexity of the genetic regulation of puberty timing and support causal links with cancer susceptibility.

The Horizon of Materiobiology: A Perspective on Material-Guided Cell Behaviors and Tissue Engineering

Abstract: Although the biological functions of cell and tissue can be regulated by biochemical factors (e.g., growth factors, hormones), the biophysical effects of materials on the regulation of biological activity are receiving more attention. In this Review, we systematically summarize the recent progress on how biomaterials with controllable properties (e.g., compositional/degradable dynamics, mechanical properties, 2D topography, and 3D geometry) can regulate cell behaviors (e.g., cell adhesion, spreading, proliferation, cell alignment, and the differentiation or self-maintenance of stem cells) and tissue/organ functions. How the biophysical features of materials influence tissue/organ regeneration have been elucidated. Current challenges and a perspective on the development of novel materials that can modulate specific biological functions are discussed. The interdependent relationship between biomaterials and biology leads us to propose the concept of “materiobiology”, which is a scientific discipline that st...

Metallic Biomaterials: Current Challenges and Opportunities.

Abstract: Metallic biomaterials are engineered systems designed to provide internal support to biological tissues and they are being used largely in joint replacements, dental implants, orthopaedic fixations and stents. Higher biomaterial usage is associated with an increased incidence of implant-related complications due to poor implant integration, inflammation, mechanical instability, necrosis and infections, and associated prolonged patient care, pain and loss of function. In this review, we will briefly explore major representatives of metallic biomaterials along with the key existing and emerging strategies for surface and bulk modification used to improve biointegration, mechanical strength and flexibility of biometals, and discuss their compatibility with the concept of 3D printing.

Grassland management impacts on soil carbon stocks: a new synthesis.

Abstract: Grassland ecosystems cover a large portion of Earths’ surface and contain substantial amounts of soil organic carbon. Previous work has established that these soil carbon stocks are sensitive to management and land use changes: grazing, species composition, and mineral nutrient availability can lead to losses or gains of soil carbon. Because of the large annual carbon fluxes into and out of grassland systems, there has been growing interest in how changes in management might shift the net balance of these flows, stemming losses from degrading grasslands or managing systems to increase soil carbon stocks (i.e., carbon sequestration). A synthesis published in 2001 assembled data from hundreds of studies to document soil carbon responses to changes in management. Here we present a new synthesis that has integrated data from the hundreds of studies published after our previous work. These new data largely confirm our earlier conclusions: improved grazing management, fertilization, sowing legumes and improved grass species, irrigation, and conversion from cultivation all tend to lead to increased soil C, at rates ranging from 0.105 to more than 1 Mg C·ha−1·yr−1. The new data include assessment of three new management practices: fire, silvopastoralism, and reclamation, although these studies are limited in number. The main area in which the new data are contrary to our previous synthesis is in conversion from native vegetation to grassland, where we find that across the studies the average rate of soil carbon stock change is low and not significant. The data in this synthesis confirm that improving grassland management practices and conversion from cropland to grassland improve soil carbon stocks.