Immune complexes containing modified lipoproteins are related to the progression of internal carotid intima-media thickness in patients with type 1 diabetes

Modified lipoproteins induce autoimmune responses including the synthesis of autoantibodies with pro-inflammatory characteristics. Circulating modified lipoprotein autoantibodies combine with circulating antigens and form immune complexes (IC). We now report the results of a study investigating the role of circulating IC containing modified lipoproteins in the progression of carotid intima-media thickness (IMT) in patients enrolled in the Epidemiology of Diabetes Interventions and Complications (EDIC) Trial, a follow-up study of the Diabetes Control and Complications Trial (DCCT). This cohort includes 1229 patients with type 1 diabetes in whom B-mode ultrasonography of internal and common carotid arteries was performed in 1994-1996 and in 1998-2000. Conventional CHD risk factors, antibodies against modified forms of LDL and modified lipoprotein IC were determined in 1050 of these patients from blood collected in 1996-1998. Cholesterol and apolipoprotein B content of IC (surrogate markers of modified ApoB-rich lipoproteins) were significantly higher in patients who showed progression of the internal carotid IMT than in those showing no progression, regression or mild progression. Multivariate linear and logistic regression modeling using conventional and non-conventional risk factors showed that the cholesterol content of IC was a significant positive predictor of internal carotid IMT progression. In conclusion these data demonstrate that increased levels of modified ApoB-rich IC are associated with increased progression of internal carotid IMT in the DCCT/EDIC cohort of type 1 diabetes.

Toward Quantitative Electrochemical Measurements on the Nanoscale by Scanning Probe Microscopy: Environmental and Current Spreading Effects

The application of electric bias across tip–surface junctions in scanning probe microscopy can readily induce surface and bulk electrochemical processes that can be further detected though changes in surface topography, Faradaic or conductive currents, or electromechanical strain responses. However, the basic factors controlling tip-induced electrochemical processes, including the relationship between applied tip bias and the thermodynamics of local processes, remains largely unexplored. Using the model Li-ion reduction reaction on the surface in Li-ion conducting glass ceramic, we explore the factors controlling Li-metal formation and find surprisingly strong effects of atmosphere and back electrode composition on the process. We find that reaction processes are highly dependent on the nature of the counter electrode and environmental conditions. Using a nondepleting Li counter electrode, Li particles could grow significantly larger and faster than a depleting counter electrode. Significant Li ion depletion leads to the inability for further Li reduction. Time studies suggest that Li diffusion replenishes the vacant sites after 12 h. These studies suggest the feasibility of SPM-based quantitative electrochemical studies under proper environmental controls, extending the concepts of ultramicroelectrodes to the single-digit nanometer scale.

Oxidized LDL and AGE-LDL in circulating immune complexes strongly predict progression of carotid artery IMT in type 1 diabetes

Over 90% of modified LDL in circulation is associated to specific antibodies circulating as part of immune complexes (IC); however, few studies have examined their relationship with cardiovascular disease.

Immune complex formation in human diabetic retina enhances toxicity of oxidized LDL towards retinal capillary pericytes

Recently it has been shown that levels of circulating oxidized LDL immune complexes (ox-LDL-IC) predict the development of diabetic retinopathy (DR). This study aimed to investigate whether ox-LDL-IC are actually present in the diabetic retina, and to define their effects on human retinal pericytes vs. ox-LDL. In retinal sections from people with type 2 diabetes, co-staining for ox-LDL and IgG was present, proportionate to DR severity, and detectable even in the absence of clinical DR. In contrast, no such staining was observed in retinas from non-diabetic subjects. In vitro, human retinal pericytes were treated with native (N-) LDL, ox-LDL, and ox-LDL-IC (0-200 mg protein/l), and measures of viability, receptor expression, apoptosis, ER and oxidative stresses, and cytokine secretion were evaluated. Ox-LDL-IC exhibited greater cytotoxicity than ox-LDL towards retinal pericytes. Acting through the scavenger (CD36) and IgG (CD64) receptors, low concentrations of ox-LDL-IC triggered apoptosis mediated by oxidative and ER stresses, and enhanced inflammatory cytokine secretion. The data suggest that IC formation in the diabetic retina enhances the injurious effects of ox-LDL. These findings offer new insights into pathogenic mechanisms of DR, and may lead to new preventive measures and treatments.

Age related differences in mental health scale scores and depression diagnosis: Adult responses to the CIDI-SF and MHI-5.

Inconsistencies surrounding the prevalence levels of depression in later life suggest that the measurement of depression in older people may be problematic. The current study aimed to map responses to a depressive symptom scale, the Mental Health Index-5 (MHI-5) which is part of the Short form 36 (SF-36, Ware et al., 1993) against the diagnostic screening items of the Composite International Diagnostic Instrument-Short Form (CIDI-SF, Kessler et al., 1998) to examine disagreement rates across age groups. The study examined data from a national random sample of 10,641 participants living in Ireland, 58.8% were female and 19% were over 65 (SLÁN, 2007). CIDI-SF depression screening endorsement was lower in older groups, whereas mean MHI-5 depressive symptoms showed less change across age groups. Results showed that the odds of MHI-5 endorsers aged 18–44 endorsing CIDI-SF screening questions were 5 times and 4.5 times (dysphoria and anhedonia, respectively) greater than the odds of people aged 75 or more endorsing these items. Findings suggest that although the risk of depressive disorder may decrease with age, complex diagnostic screening questions may exaggerate lower rates of depression among older people.

Large-scale association analysis identifies new risk loci for coronary artery disease

Coronary artery disease (CAD) is the commonest cause of death. Here, we report an association analysis in 63,746 CAD cases and 130,681 controls identifying 15 loci reaching genome-wide significance, taking the number of susceptibility loci for CAD to 46, and a further 104 independent variants (r(2)

A conserved spider silk domain acts as a molecular switch that controls fibre assembly

A huge variety of proteins are able to form fibrillar structures(1), especially at high protein concentrations. Hence, it is surprising that spider silk proteins can be stored in a soluble form at high concentrations and transformed into extremely stable fibres on demand(2,3). Silk proteins are reminiscent of amphiphilic block copolymers containing stretches of polyalanine and glycine-rich polar elements forming a repetitive core flanked by highly conserved non-repetitive amino-terminal(4,5) and carboxy-terminal(6) domains. The N-terminal domain comprises a secretion signal, but further functions remain unassigned. The C-terminal domain was implicated in the control of solubility and fibre formation(7) initiated by changes in ionic composition(8,9) and mechanical stimuli known to align the repetitive sequence elements and promote beta-sheet formation(10-14). However, despite recent structural data(15), little is known about this remarkable behaviour in molecular detail. Here we present the solution structure of the C-terminal domain of a spider dragline silk protein and provide evidence that the structural state of this domain is essential for controlled switching between the storage and assembly forms of silk proteins. In addition, the C-terminal domain also has a role in the alignment of secondary structural features formed by the repetitive elements in the backbone of spider silk proteins, which is known to be important for the mechanical properties of the fibre.

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.

Enhancing design space exploration by extending CPU/GPU specifications onto FPGAs

The design cycle for complex special-purpose computing systems is extremely costly and time-consuming. It involves a multiparametric design space exploration for optimization, followed by design verification. Designers of special purpose VLSI implementations often need to explore parameters, such as optimal bitwidth and data representation, through time-consuming Monte Carlo simulations. A prominent example of this simulation-based exploration process is the design of decoders for error correcting systems, such as the Low-Density Parity-Check (LDPC) codes adopted by modern communication standards, which involves thousands of Monte Carlo runs for each design point. Currently, high-performance computing offers a wide set of acceleration options that range from multicore CPUs to Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs). The exploitation of diverse target architectures is typically associated with developing multiple code versions, often using distinct programming paradigms. In this context, we evaluate the concept of retargeting a single OpenCL program to multiple platforms, thereby significantly reducing design time. A single OpenCL-based parallel kernel is used without modifications or code tuning on multicore CPUs, GPUs, and FPGAs. We use SOpenCL (Silicon to OpenCL), a tool that automatically converts OpenCL kernels to RTL in order to introduce FPGAs as a potential platform to efficiently execute simulations coded in OpenCL. We use LDPC decoding simulations as a case study. Experimental results were obtained by testing a variety of regular and irregular LDPC codes that range from short/medium (e.g., 8,000 bit) to long length (e.g., 64,800 bit) DVB-S2 codes. We observe that, depending on the design parameters to be simulated, on the dimension and phase of the design, the GPU or FPGA may suit different purposes more conveniently, thus providing different acceleration factors over conventional multicore CPUs.

Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment

Background: Interindividual epigenetic variation that occurs systemically must be established prior to gastrulation in the very early embryo and, because it is systemic, can be assessed in easily biopsiable tissues. We employ two independent genome-wide approaches to search for such variants.

Results: First, we screen for metastable epialleles by performing genomewide bisulfite sequencing in peripheral blood lymphocyte (PBL) and hair follicle DNA from two Caucasian adults. Second, we conduct a genomewide screen for genomic regions at which PBL DNA methylation is affected by season of conception in rural Gambia. Remarkably, both approaches identify the genomically imprinted VTRNA2-1 as a top environmentally responsive epiallele. We demonstrate systemic and stochastic interindividual variation in DNA methylation at the VTRNA2-1 differentially methylated region in healthy Caucasian and Asian adults and show, in rural Gambians, that periconceptional environment affects offspring VTRNA2-1 epigenotype, which is stable over at least 10 years. This unbiased screen also identifies over 100 additional candidate metastable epialleles, and shows that these are associated with cis genomic features including transposable elements.

Conclusions: The non-coding VTRNA2-1 transcript (also called nc886) is a putative tumor suppressor and modulator of innate immunity. Thus, these data indicating environmentally induced loss of imprinting at VTRNA2-1 constitute a plausible causal pathway linking early embryonic environment, epigenetic alteration, and human disease. More broadly, the list of candidate metastable epialleles provides a resource for future studies of epigenetic variation and human disease.

HpMC: An Energy- Aware Management System for Multi-Level Memory Architectures

DRAM technology faces density and power challenges to increase capacity because of limitations of physical cell design. To overcome these limitations, system designers are exploring alternative solutions that combine DRAM and emerging NVRAM technologies. Previous work on heterogeneous memories focuses, mainly, on two system designs: PCache, a hierarchical, inclusive memory system, and HRank, a flat, non-inclusive memory system. We demonstrate that neither of these designs can universally achieve high performance and energy efficiency across a suite of HPC workloads. In this work, we investigate the impact of a number of multilevel memory designs on the performance, power, and energy consumption of applications. To achieve this goal and overcome the limited number of available tools to study heterogeneous memories, we created HMsim, an infrastructure that enables n-level, heterogeneous memory studies by leveraging existing memory simulators. We, then, propose HpMC, a new memory controller design that combines the best aspects of existing management policies to improve performance and energy. Our energy-aware memory management system dynamically switches between PCache and HRank based on the temporal locality of applications. Our results show that HpMC reduces energy consumption from 13% to 45% compared to PCache and HRank, while providing the same bandwidth and higher capacity than a conventional DRAM system.

An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes

Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome sequencing data identified recessive mutations in PIBF1, also known as CEP90, and C21orf2, also known as LRRC76, as causes of the ciliopathies Joubert and Jeune syndromes. Biochemical approaches place C21orf2 within key ciliopathy-associated protein modules, offering an explanation for the skeletal and retinal involvement observed in individuals with C21orf2 variants. Our global, unbiased approaches provide insights into ciliogenesis complexity and identify roles for unanticipated pathways in human genetic disease.

On the performance of LDPC and turbo decoder architectures with unreliable memories

In this paper, we investigate the impact of faulty memory bit-cells on the performance of LDPC and Turbo channel decoders based on realistic memory failure models. Our study investigates the inherent error resilience of such codes to potential memory faults affecting the decoding process. We develop two mitigation mechanisms that reduce the impact of memory faults rather than correcting every single error. We show how protection of only few bit-cells is sufficient to deal with high defect rates. In addition, we show how the use of repair-iterations specifically helps mitigating the impact of faults that occur inside the decoder itself.

Identification of diagnostic biomarkers for infection in premature neonates

Infection is a leading cause of neonatal morbidity and mortality worldwide. Premature neonates are particularly susceptible to infection because of physiologic immaturity, comorbidity, and extraneous medical interventions. Additionally premature infants are at higher risk of progression to sepsis or severe sepsis, adverse outcomes, and antimicrobial toxicity. Currently initial diagnosis is based upon clinical suspicion accompanied by nonspecific clinical signs and is confirmed upon positive microbiologic culture results several days after institution of empiric therapy. There exists a significant need for rapid, objective, in vitro tests for diagnosis of infection in neonates who are experiencing clinical instability. We used immunoassays multiplexed on microarrays to identify differentially expressed serum proteins in clinically infected and non-infected neonates. Immunoassay arrays were effective for measurement of more than 100 cytokines in small volumes of serum available from neonates. Our analyses revealed significant alterations in levels of eight serum proteins in infected neonates that are associated with inflammation, coagulation, and fibrinolysis. Specifically P- and E-selectins, interleukin 2 soluble receptor alpha, interleukin 18, neutrophil elastase, urokinase plasminogen activator and its cognate receptor, and C-reactive protein were observed at statistically significant increased levels. Multivariate classifiers based on combinations of serum analytes exhibited better diagnostic specificity and sensitivity than single analytes. Multiplexed immunoassays of serum cytokines may have clinical utility as an adjunct for rapid diagnosis of infection and differentiation of etiologic agent in neonates with clinical decompensation.