Showing papers by "Research Triangle Park published in 2012"

Preexposure Prophylaxis for HIV Infection among African Women

Abstract: Background Preexposure prophylaxis with antiretroviral drugs has been effective in the prevention of human immunodeficiency virus (HIV) infection in some trials but not in others. Methods In this randomized, double-blind, placebo-controlled trial, we assigned 2120 HIV-negative women in Kenya, South Africa, and Tanzania to receive either a combination of tenofovir disoproxil fumarate and emtricitabine (TDF–FTC) or placebo once daily. The primary objective was to assess the effectiveness of TDF–FTC in preventing HIV acquisition and to evaluate safety. Results HIV infections occurred in 33 women in the TDF–FTC group (incidence rate, 4.7 per 100 person-years) and in 35 in the placebo group (incidence rate, 5.0 per 100 person-years), for an estimated hazard ratio in the TDF-FTC group of 0.94 (95% confidence interval, 0.59 to 1.52; P=0.81). The proportions of women with nausea, vomiting, or elevated alanine aminotransferase levels were significantly higher in the TDF–FTC group (P=0.04, P<0.001, and P=0.03, resp...

An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

Abstract: Rare genetic variants contribute to complex disease risk; however, the abundance of rare variants in human populations remains unknown. We explored this spectrum of variation by sequencing 202 genes encoding drug targets in 14,002 individuals. We find rare variants are abundant (1 every 17 bases) and geographically localized, so that even with large sample sizes, rare variant catalogs will be largely incomplete. We used the observed patterns of variation to estimate population growth parameters, the proportion of variants in a given frequency class that are putatively deleterious, and mutation rates for each gene. We conclude that because of rapid population growth and weak purifying selection, human populations harbor an abundance of rare variants, many of which are deleterious and have relevance to understanding disease risk.

Persistent systemic inflammation is associated with poor clinical outcomes in COPD: a novel phenotype.

Abstract: Background: Because chronic obstructive pulmonary disease (COPD) is a heterogeneous condition, the identification of specific clinical phenotypes is key to developing more effective therapies. To explore if the persistence of systemic inflammation is associated with poor clinical outcomes in COPD we assessed patients recruited to the well-characterized ECLIPSE cohort (NCT00292552). Methods and Findings: Six inflammatory biomarkers in peripheral blood (white blood cells (WBC) count and CRP, IL-6, IL-8, fibrinogen and TNF-a levels) were quantified in 1,755 COPD patients, 297 smokers with normal spirometry and 202 nonsmoker controls that were followed-up for three years. We found that, at baseline, 30% of COPD patients did not show evidence of systemic inflammation whereas 16% had persistent systemic inflammation. Even though pulmonary abnormalities were similar in these two groups, persistently inflamed patients during follow-up had significantly increased all-cause mortality (13% vs. 2%, p,0.001) and exacerbation frequency (1.5 (1.5) vs. 0.9 (1.1) per year, p,0.001) compared to non-inflamed ones. As a descriptive study our results show associations but do not prove causality. Besides this, the inflammatory response is complex and we studied only a limited panel of biomarkers, albeit they are those investigated by the majority of previous studies and are often and easily measured in clinical practice. Conclusions: Overall, these results identify a novel systemic inflammatory COPD phenotype that may be the target of specific research and treatment.

An 18-kDa Translocator Protein (TSPO) polymorphism explains differences in binding affinity of the PET radioligand PBR28

Abstract: [11C]PBR28 binds the 18-kDa Translocator Protein (TSPO) and is used in positron emission tomography (PET) to detect microglial activation. However, quantitative interpretations of signal are confounded by large interindividual variability in binding affinity, which displays a trimodal distribution compatible with a codominant genetic trait. Here, we tested directly for an underlying genetic mechanism to explain this. Binding affinity of PBR28 was measured in platelets isolated from 41 human subjects and tested for association with polymorphisms in TSPO and genes encoding other proteins in the TSPO complex. Complete agreement was observed between the TSPO Ala147Thr genotype and PBR28 binding affinity phenotype (P value=3.1 × 10−13). The TSPO Ala147Thr polymorphism predicts PBR28 binding affinity in human platelets. As all second-generation TSPO PET radioligands tested hitherto display a trimodal distribution in binding affinity analogous to PBR28, testing for this polymorphism may allow quantitative interpretation of TSPO PET studies with these radioligands.

Radiative Absorption Enhancements Due to the Mixing State of Atmospheric Black Carbon

Abstract: Atmospheric black carbon (BC) warms Earth’s climate, and its reduction has been targeted for near-term climate change mitigation. Models that include forcing by BC assume internal mixing with non-BC aerosol components that enhance BC absorption, often by a factor of ~2; such model estimates have yet to be clearly validated through atmospheric observations. Here, direct in situ measurements of BC absorption enhancements ( E abs ) and mixing state are reported for two California regions. The observed E abs is small—6% on average at 532 nm—and increases weakly with photochemical aging. The E abs is less than predicted from observationally constrained theoretical calculations, suggesting that many climate models may overestimate warming by BC. These ambient observations stand in contrast to laboratory measurements that show substantial E abs for BC are possible.

Influence of reported study design characteristics on intervention effect estimates from randomised controlled trials: combined analysis of meta-epidemiological studies

Abstract: The design of randomised controlled trials (RCTs) should incorporate characteristics (such as concealment of randomised allocation and blinding of participants and personnel) that avoid biases resulting from lack of comparability of the intervention and control groups. Empirical evidence suggests that the absence of such characteristics leads to biased intervention effect estimates, but the findings of different studies are not consistent.

Pollutant emissions and energy efficiency under controlled conditions for household biomass cookstoves and implications for metrics useful in setting international test standards.

Abstract: Realistic metrics and methods for testing household biomass cookstoves are required to develop standards needed by international policy makers, donors, and investors. Application of consistent test practices allows emissions and energy efficiency performance to be benchmarked and enables meaningful comparisons among traditional and advanced stove types. In this study, 22 cookstoves burning six fuel types (wood, charcoal, pellets, corn cobs, rice hulls, and plant oil) at two fuel moisture levels were examined under laboratory-controlled operating conditions as outlined in the Water Boiling Test (WBT) protocol, Version 4. Pollutant emissions (carbon dioxide, carbon monoxide, methane, total hydrocarbons, and ultrafine particles) were continuously monitored. Fine particle mass was measured gravimetrically for each WBT phase. Additional measurements included cookstove power, energy efficiency, and fuel use. Emission factors are given on the basis of fuel energy, cooking energy, fuel mass, time, and cooking tas...

Composition of air pollution particles and oxidative stress in cells, tissues, and living systems.

Abstract: Epidemiological studies demonstrated an association between increased levels of ambient air pollution particles and human morbidity and mortality. Production of oxidants, either directly by the air pollution particles or by the host response to the particles, appears to be fundamental in the biological effects seen after exposure to particulate matter (PM). However, the precise components and mechanisms responsible for oxidative stress following PM exposure are yet to be defined. Direct oxidant generation by air pollution particles is attributed to organic and metal components. Organic compounds generate an oxidative stress through redox cycling of quinone-based radicals, by complexing of metal resulting in electron transport, and by depletion of antioxidants by reactions between quinones and thiol-containing compounds. Metals directly support electron transport to generate oxidants and also diminish levels of antioxidants. In addition to direct generation of oxidants by organic and metal components, cellular responses contribute to oxidative stress after PM exposure. Reactive oxygen species (ROS) production occurs in the mitochondria, cell membranes, phagosomes, and the endoplasmic reticulum. Oxidative stress following PM exposure initiates a series of cellular reactions that includes activation of kinase cascades and transcription factors and release of inflammatory mediators, which ultimately lead to cell injury or apoptosis. Consequently, oxidative stress in cells and tissues is a central mechanism by which PM exposure leads to injury, disease, and mortality.

A simple method for quantifying functional selectivity and agonist bias.

Abstract: Activation of seven-transmembrane (7TM) receptors by agonists does not always lead to uniform activation of all signaling pathways mediated by a given receptor. Relative to other ligands, many agonists are “biased” toward producing subsets of receptor behaviors. A hallmark of such “functional selectivity” is cell type dependence; this poses a particular problem for the profiling of agonists in whole cell test systems removed from the therapeutic one(s). Such response-specific cell-based variability makes it difficult to guide medicinal chemistry efforts aimed at identifying and optimizing therapeutically meaningful agonist bias. For this reason, we present a scale, based on the Black and Leff operational model, that contains the key elements required to describe 7TM agonism, namely, affinity (KA–1) for the receptor and efficacy (τ) in activating a particular signaling pathway. Utilizing a “transduction coefficient” term, log(τ/KA), this scale can statistically evaluate selective agonist effects in a manne...

One-to-many propensity score matching in cohort studies

Abstract: Background Among the large number of cohort studies that employ propensity score matching, most match patients 1:1. Increasing the matching ratio is thought to improve precision but may come with a trade-off with respect to bias. Objective To evaluate several methods of propensity score matching in cohort studies through simulation and empirical analyses. Methods We simulated cohorts of 20 000 patients with exposure prevalence of 10%–50%. We simulated five dichotomous and five continuous confounders. We estimated propensity scores and matched using digit-based greedy (“greedy”), pairwise nearest neighbor within a caliper (“nearest neighbor”), and a nearest neighbor approach that sought to balance the scores of the comparison patient above and below that of the treated patient (“balanced nearest neighbor”). We matched at both fixed and variable matching ratios and also evaluated sequential and parallel schemes for the order of formation of 1:n match groups. We then applied this same approach to two cohorts of patients drawn from administrative claims data. Results Increasing the match ratio beyond 1:1 generally resulted in somewhat higher bias. It also resulted in lower variance with variable ratio matching but higher variance with fixed. The parallel approach generally resulted in higher mean squared error but lower bias than the sequential approach. Variable ratio, parallel, balanced nearest neighbor matching generally yielded the lowest bias and mean squared error. Conclusions 1:n matching can be used to increase precision in cohort studies. We recommend a variable ratio, parallel, balanced 1:n, nearest neighbor approach that increases precision over 1:1 matching at a small cost in bias. Copyright © 2012 John Wiley & Sons, Ltd.

Coordination of the transcriptome and metabolome by the circadian clock

Abstract: The circadian clock governs a large array of physiological functions through the transcriptional control of a significant fraction of the genome. Disruption of the clock leads to metabolic disorders, including obesity and diabetes. As food is a potent zeitgeber (ZT) for peripheral clocks, metabolites are implicated as cellular transducers of circadian time for tissues such as the liver. From a comprehensive dataset of over 500 metabolites identified by mass spectrometry, we reveal the coordinate clock-controlled oscillation of many metabolites, including those within the amino acid and carbohydrate metabolic pathways as well as the lipid, nucleotide, and xenobiotic metabolic pathways. Using computational modeling, we present evidence of synergistic nodes between the circadian transcriptome and specific metabolic pathways. Validation of these nodes reveals that diverse metabolic pathways, including the uracil salvage pathway, oscillate in a circadian fashion and in a CLOCK-dependent manner. This integrated map illustrates the coherence within the circadian metabolome, transcriptome, and proteome and how these are connected through specific nodes that operate in concert to achieve metabolic homeostasis.

Experiments and modeling of iron-particle-filled magnetorheological elastomers

Abstract: Magnetorheological elastomers (MREs) are ferromagnetic particle impregnated rubbers whose mechanical properties are altered by the application of external magnetic fields. Due to their coupled magnetoelastic response, MREs are finding an increasing number of engineering applications. In this work, we present a combined experimental and theoretical study of the macroscopic response of a particular MRE consisting of a rubber matrix phase with spherical carbonyl iron particles. The MRE specimens used in this work are cured in the presence of strong magnetic fields leading to the formation of particle chain structures and thus to an overall transversely isotropic composite. The MRE samples are tested experimentally under uniaxial stresses as well as under simple shear in the absence or in the presence of magnetic fields and for different initial orientations of their particle chains with respect to the mechanical and magnetic loading direction. Using the theoretical framework for finitely strained MREs introduced by Kankanala and Triantafyllidis (2004) , we propose a transversely isotropic energy density function that is able to reproduce the experimentally measured magnetization, magnetostriction and simple shear curves under different prestresses, initial particle chain orientations and magnetic fields. Microscopic mechanisms are also proposed to explain (i) the counterintuitive effect of dilation under zero or compressive applied mechanical loads for the magnetostriction experiments and (ii) the importance of a finite strain constitutive formulation even at small magnetostrictive strains. The model gives an excellent agreement with experiments for relatively moderate magnetic fields but has also been satisfactorily extended to include magnetic fields near saturation.

Isoprene epoxydiols as precursors to secondary organic aerosol formation: acid-catalyzed reactive uptake studies with authentic compounds.

Abstract: Isoprene epoxydiols (IEPOX), formed from the photooxidation of isoprene under low-NOx conditions, have recently been proposed as precursors of secondary organic aerosol (SOA) on the basis of mass spectrometric evidence. In the present study, IEPOX isomers were synthesized in high purity (>99%) to investigate their potential to form SOA via reactive uptake in a series of controlled dark chamber studies followed by reaction product analyses. IEPOX-derived SOA was substantially observed only in the presence of acidic aerosols, with conservative lower-bound yields of 4.7–6.4% for β-IEPOX and 3.4–5.5% for δ-IEPOX, providing direct evidence for IEPOX isomers as precursors to isoprene SOA. These chamber studies demonstrate that IEPOX uptake explains the formation of known isoprene SOA tracers found in ambient aerosols, including 2-methyltetrols, C5-alkene triols, dimers, and IEPOX-derived organosulfates. Additionally, we show reactive uptake on the acidified sulfate aerosols supports a previously unreported acid...

Prevalence and Sociodemographic Correlates of Antinuclear Antibodies In the United States

Abstract: Autoantibodies to cellular constituents are the serologic hallmarks of autoimmunity and are frequently seen in systemic autoimmune diseases, including systemic lupus erythematosus (SLE), scleroderma, and polymyositis/dermatomyositis (1). They also are detected in patients with organ-specific autoimmune diseases, such as autoimmune thyroiditis and hepatitis (1), certain infections and neoplasms (2), and in some individuals without diagnosed disease (2, 3). The most common autoantibodies are antinuclear antibodies (ANA), which are traditionally assessed by indirect immunofluorescence and include antibodies to both nuclear and cytoplasmic components (4). The cellular staining patterns and specific autoantibodies detected in those with ANA are clinically useful as they are strongly associated with particular autoimmune diseases, such as the nucleolar staining patterns that are often seen in scleroderma and anti-Sm autoantibodies that are included in SLE classification criteria (1). A variety of methods have been used to estimate ANA prevalence in selected populations, including blood donors (5, 6), hospital workers (6, 7), healthy volunteers (3, 8), or residents in small areas (9, 10), leading to a wide range of prevalence estimates (from 1.1% to 20%), which are difficult to compare. Factors associated with ANA production are largely unknown with the exception of some reports suggesting higher prevalence of ANA in females (8, 10–13) and older individuals (12, 14–16). A proportion of the ANA-positive population is thought to represent the preclinical stage of autoimmune diseases based on observations that autoantibodies are usually produced prior to clinical manifestations of disease (17). Thus, defining the prevalence and types of ANA, as well as characterizing factors associated with their production, may provide insight into the etiology of autoimmune diseases, which are thought to be increasing in frequency but are more difficult to characterize and study than ANA at the population level (18). Therefore, we evaluated serum samples from the United States (U.S.) National Health and Nutrition Examination Survey (NHANES) from 1999–2004 to estimate ANA prevalence, cellular patterns and specific autoantibody reactivities, and to identify sociodemographic and biobehavioral factors associated with their production. We specifically assessed selected systemic autoimmune disease risk factors including smoking (19) and alcohol use (20). We also evaluated C-reactive protein (21) and obesity, the former being a marker and the latter an underlying cause of chronic inflammation (22) and a growing public health concern.

Organotypic liver culture models: Meeting current challenges in toxicity testing

Abstract: Prediction of chemical-induced hepatotoxicity in humans from in vitro data continues to be a significant challenge for the pharmaceutical and chemical industries. Generally, conventional in vitro hepatic model systems (i.e. 2-D static monocultures of primary or immortalized hepatocytes) are limited by their inability to maintain histotypic and phenotypic characteristics over time in culture, including stable expression of clearance and bioactivation pathways, as well as complex adaptive responses to chemical exposure. These systems are less than ideal for longer-term toxicity evaluations and elucidation of key cellular and molecular events involved in primary and secondary adaptation to chemical exposure, or for identification of important mediators of inflammation, proliferation and apoptosis. Progress in implementing a more effective strategy for in vitro-in vivo extrapolation and human risk assessment depends on significant advances in tissue culture technology and increasing their level of biological complexity. This article describes the current and ongoing need for more relevant, organotypic in vitro surrogate systems of human liver and recent efforts to recreate the multicellular architecture and hemodynamic properties of the liver using novel culture platforms. As these systems become more widely used for chemical and drug toxicity testing, there will be a corresponding need to establish standardized testing conditions, endpoint analyses and acceptance criteria. In the future, a balanced approach between sample throughput and biological relevance should provide better in vitro tools that are complementary with animal testing and assist in conducting more predictive human risk assessment.

Roles of Reactive Oxygen Species and Antioxidants in Ovarian Toxicity

Abstract: Proper functioning of the ovary is critical to maintain fertility and overall health, and ovarian function depends on the maintenance and normal development of ovarian follicles. This review presents evidence about the potential impact of oxidative stress on the well-being of primordial, growing and preovulatory follicles, as well as oocytes and early embryos, examining cell types and molecular targets. Limited data from genetically modified mouse models suggest that several antioxidant enzymes that protect cells from reactive oxygen species (ROS) may play important roles in follicular development and/or survival. Exposures to agents known to cause oxidative stress, such as gamma irradiation, chemotherapeutic drugs, or polycyclic aromatic hydrocarbons, induce rapid primordial follicle loss; however, the mechanistic role of ROS has received limited attention. In contrast, ROS may play an important role in the initiation of apoptosis in antral follicles. Depletion of glutathione leads to atresia of antral follicles in vivo and apoptosis of granulosa cells in cultured antral follicles. Chemicals, such as cyclophosphamide, dimethylbenzanthracene, and methoxychlor, increase proapoptotic signals, preceded by increased ROS and signs of oxidative stress, and cotreatment with antioxidants is protective. In oocytes, glutathione levels change rapidly during progression of meiosis and early embryonic development, and high oocyte glutathione at the time of fertilization is required for male pronucleus formation and for embryonic development to the blastocyst stage. Because current evidence suggests that oxidative stress can have significant negative impacts on female fertility and gamete health, dietary or pharmacological intervention may prove to be effective strategies to protect female fertility.

Evaluation of the association between arsenic and diabetes: A National Toxicology Program workshop review

Abstract: Background: Diabetes affects an estimated 346 million persons globally, and total deaths from diabetes are projected to increase > 50% in the next decade. Understanding the role of environmental ch...

Cigarette smoking behaviors and time since quitting are associated with differential DNA methylation across the human genome

Abstract: The impact of cigarette smoking can persist for extended periods following smoking cessation and may involve epigenetic reprogramming. Changes in DNA methylation associated with smoking may help to identify molecular pathways that contribute to the latency between exposure and disease onset. Cross-sectional cohort data from subjects in the International COPD Genetics Network (n = 1085) and the Boston Early-Onset COPD study (n = 369) were analyzed as the discovery and replication cohorts, respectively. Genome-wide methylation data on 27 578 CpG sites in 14 475 genes were obtained on DNA from peripheral blood leukocytes using the Illumina HumanMethylation27K Beadchip in both cohorts. We identified 15 sites significantly associated with current smoking, 2 sites associated with cumulative smoke exposure, and, within the subset of former smokers, 3 sites associated with time since quitting cigarettes. Two loci, factor II receptor-like 3 (F2RL3) and G-protein-coupled receptor 15 (GPR15), were significantly associated in all three analyses and were validated by pyrosequencing. These findings (i) identify a novel locus (GPR15) associated with cigarette smoking and (ii) suggest the existence of dynamic, site-specific methylation changes in response to smoking which may contribute to the extended risks associated with cigarette smoking that persist after cessation.

The innate immune sensor NLRC3 attenuates Toll-like receptor signaling via modification of the signaling adaptor TRAF6 and transcription factor NF-κB

Abstract: Several members of the NLR family of sensors activate innate immunity. In contrast, we found here that NLRC3 inhibited Toll-like receptor (TLR)-dependent activation of the transcription factor NF-κB by interacting with the TLR signaling adaptor TRAF6 to attenuate Lys63 (K63)-linked ubiquitination of TRAF6 and activation of NF-κB. We used bioinformatics to predict interactions between NLR and TRAF proteins, including interactions of TRAF with NLRC3. In vivo, macrophage expression of Nlrc3 mRNA was diminished by the administration of lipopolysaccharide (LPS) but was restored when cellular activation subsided. To assess biologic relevance, we generated Nlrc3(-/-) mice. LPS-treated Nlrc3(-/-) macrophages had more K63-ubiquitinated TRAF6, nuclear NF-κB and proinflammatory cytokines. Finally, LPS-treated Nlrc3(-/-) mice had more signs of inflammation. Thus, signaling via NLRC3 and TLR constitutes a negative feedback loop. Furthermore, prevalent NLR-TRAF interactions suggest the formation of a 'TRAFasome' complex.

Once daily dolutegravir (S/GSK1349572) in combination therapy in antiretroviral-naive adults with HIV: planned interim 48 week results from SPRING-1, a dose-ranging, randomised, phase 2b trial

Abstract: Summary Background Dolutegravir (S/GSK1349572) is a new HIV-1 integrase inhibitor that has antiviral activity with once daily, unboosted dosing. SPRING-1 is an ongoing study designed to select a dose for phase 3 assessment. We present data from preplanned primary and interim analyses. Methods In a phase 2b, multicentre, dose-ranging study, treatment-naive adults were randomly assigned (1:1:1:1) to receive 10 mg, 25 mg, or 50 mg dolutegravir or 600 mg efavirenz. Dose but not drug allocation was masked. Randomisation was by a central integrated voice-response system according to a computer-generated code. Study drugs were given with either tenofovir plus emtricitabine or abacavir plus lamivudine. Our study was done at 34 sites in France, Germany, Italy, Russia, Spain, and the USA beginning on July 9, 2009. Eligible participants were seropositive for HIV-1, aged 18 years or older, and had plasma HIV RNA viral loads of at least 1000 copies per mL and CD4 counts of at least 200 cells per μL. Our primary endpoint was the proportion of participants with viral load of less than 50 copies per mL at week 16 and we present data to week 48. Analyses were done on the basis of allocation group and included all participants who received at least one dose of study drug. This study is registered with ClinicalTrials.gov, number NCT00951015. Findings 205 patients were randomly allocated and received at least one dose of study drug: 53, 51, and 51 to receive 10 mg, 25 mg, and 50 mg dolutegravir, respectively, and 50 to receive efavirenz. Week 16 response rates to viral loads of at most 50 copies per mL were 93% (144 of 155 participants) for all doses of dolutegravir (with little difference between dose groups) and 60% (30 of 50) for efavirenz; week 48 response rates were 87% (139 of 155) for all doses of dolutegravir and 82% (41 of 50) for efavirenz. Response rates between nucleoside reverse transcriptase inhibitor subgroups were similar. We identified three virological failures in the dolutegravir groups and one in the efavirenz group—we did not identify any integrase inhibitor mutations. We did not identify any dose-related clinical or laboratory toxic effects, with more drug-related adverse events of moderate-or-higher intensity in the efavirenz group (20%) than the dolutegravir group (8%). We did not judge that any serious adverse events were related to dolutegravir. Interpretation Dolutegravir was effective when given once daily without a pharmacokinetic booster and was well tolerated at all assessed doses. Our findings support the assessment of once daily 50 mg dolutegravir in phase 3 trials. Funding Shionogi-GlaxoSmithKline Pharmaceuticals, LLC, now Shionogi-ViiV Healthcare, LLC.

Rare Variants in APP, PSEN1 and PSEN2 Increase Risk for AD in Late-Onset Alzheimer's Disease Families

Abstract: Pathogenic mutations in APP, PSEN1, PSEN2, MAPT and GRN have previously been linked to familial early onset forms of dementia. Mutation screening in these genes has been performed in either very small series or in single families with late onset AD (LOAD). Similarly, studies in single families have reported mutations in MAPT and GRN associated with clinical AD but no systematic screen of a large dataset has been performed to determine how frequently this occurs. We report sequence data for 439 probands from late-onset AD families with a history of four or more affected individuals. Sixty sequenced individuals (13.7%) carried a novel or pathogenic mutation. Eight pathogenic variants, (one each in APP and MAPT, two in PSEN1 and four in GRN) three of which are novel, were found in 14 samples. Thirteen additional variants, present in 23 families, did not segregate with disease, but the frequency of these variants is higher in AD cases than controls, indicating that these variants may also modify risk for disease. The frequency of rare variants in these genes in this series is significantly higher than in the 1,000 genome project (p = 5.09 × 10⁻⁵; OR = 2.21; 95%CI = 1.49-3.28) or an unselected population of 12,481 samples (p = 6.82 × 10⁻⁵; OR = 2.19; 95%CI = 1.347-3.26). Rare coding variants in APP, PSEN1 and PSEN2, increase risk for or cause late onset AD. The presence of variants in these genes in LOAD and early-onset AD demonstrates that factors other than the mutation can impact the age at onset and penetrance of at least some variants associated with AD. MAPT and GRN mutations can be found in clinical series of AD most likely due to misdiagnosis. This study clearly demonstrates that rare variants in these genes could explain an important proportion of genetic heritability of AD, which is not detected by GWAS.

Unlocking the potential of metagenomics through replicated experimental design

Abstract: Metagenomics holds enormous promise for discovering novel enzymes and organisms that are biomarkers or drivers of processes relevant to disease, industry and the environment. In the past two years, we have seen a paradigm shift in metagenomics to the application of cross-sectional and longitudinal studies enabled by advances in DNA sequencing and high-performance computing. These technologies now make it possible to broadly assess microbial diversity and function, allowing systematic investigation of the largely unexplored frontier of microbial life. To achieve this aim, the global scientific community must collaborate and agree upon common objectives and data standards to enable comparative research across the Earth's microbiome. Improvements in comparability of data will facilitate the study of biotechnologically relevant processes, such as bioprospecting for new glycoside hydrolases or identifying novel energy sources.

Science and Engineering Beyond Moore's Law

Abstract: In this paper, the historical effects and benefits of Moore's law for semiconductor technologies are reviewed, and it is offered that the rapid learning curve obtained to the benefit of society by feature size scaling might be continued in several different ways. The problem is that as features approach the range of a few nanometers, electron-based devices depart radically from the ideal switch and, in fact, become very leaky in the off state. It is argued that there are some short-term solutions involving more highly parallel manufacturing, increased design efficiency, and lower cost packaging technologies that could continue the steep learning curve for cost reductions that have historically been achieved via Moore's Law scaling. Another alternative might be to increase chip functionality by integrating devices that offer broadened chip functionality including, e.g., sensors, energy sources, oscillators, etc. A third alternative would be to invent an entirely new information processing state variable based on different physics, using electron spin, magnetic dipoles, photons, etc., to improve the performance and reduce switching energy for devices whose smallest features are on the order of a few nanometers. Each of these alternatives is being actively explored and an overview of each strategy and progress to date is given in the paper. A final alternative offered in the paper is to learn from information processing examples in nature, specifically in living systems. An E.coli cell of about one cubic micrometer volume is shown to be an incredibly powerful and energy-efficient information processor relative to the performance of an end-of-scaling silicon processor of the same volume. The paper concludes by pointing out some of the crucial differences between E.coli information processing and conventional approaches with the hope technologies can be invented using the hints offered by biosystems.