Showing papers by "University College Dublin published in 2010"

Biofuels from microalgae—A review of technologies for production, processing, and extractions of biofuels and co-products

Abstract: Sustainability is a key principle in natural resource management, and it involves operational efficiency, minimisation of environmental impact and socio-economic considerations; all of which are interdependent. It has become increasingly obvious that continued reliance on fossil fuel energy resources is unsustainable, owing to both depleting world reserves and the green house gas emissions associated with their use. Therefore, there are vigorous research initiatives aimed at developing alternative renewable and potentially carbon neutral solid, liquid and gaseous biofuels as alternative energy resources. However, alternate energy resources akin to first generation biofuels derived from terrestrial crops such as sugarcane, sugar beet, maize and rapeseed place an enormous strain on world food markets, contribute to water shortages and precipitate the destruction of the world's forests. Second generation biofuels derived from lignocellulosic agriculture and forest residues and from non-food crop feedstocks address some of the above problems; however there is concern over competing land use or required land use changes. Therefore, based on current knowledge and technology projections, third generation biofuels specifically derived from microalgae are considered to be a technically viable alternative energy resource that is devoid of the major drawbacks associated with first and second generation biofuels. Microalgae are photosynthetic microorganisms with simple growing requirements (light, sugars, CO 2 , N, P, and K) that can produce lipids, proteins and carbohydrates in large amounts over short periods of time. These products can be processed into both biofuels and valuable co-products. This study reviewed the technologies underpinning microalgae-to-biofuels systems, focusing on the biomass production, harvesting, conversion technologies, and the extraction of useful co-products. It also reviewed the synergistic coupling of microalgae propagation with carbon sequestration and wastewater treatment potential for mitigation of environmental impacts associated with energy conversion and utilisation. It was found that, whereas there are outstanding issues related to photosynthetic efficiencies and biomass output, microalgae-derived biofuels could progressively substitute a significant proportion of the fossil fuels required to meet the growing energy demand.

Source partitioning using stable isotopes: coping with too much variation.

Abstract: Background Stable isotope analysis is increasingly being utilised across broad areas of ecology and biology. Key to much of this work is the use of mixing models to estimate the proportion of sources contributing to a mixture such as in diet estimation. Methodology By accurately reflecting natural variation and uncertainty to generate robust probability estimates of source proportions, the application of Bayesian methods to stable isotope mixing models promises to enable researchers to address an array of new questions, and approach current questions with greater insight and honesty. Conclusions We outline a framework that builds on recently published Bayesian isotopic mixing models and present a new open source R package, SIAR. The formulation in R will allow for continued and rapid development of this core model into an all-encompassing single analysis suite for stable isotope research.

Clinical practice guidelines for the management of cryptococcal disease: 2010 update by the infectious diseases society of america.

Abstract: Cryptococcosis is a global invasive mycosis associated with significant morbidity and mortality. These guidelines for its management have been built on the previous Infectious Diseases Society of America guidelines from 2000 and include new sections. There is a discussion of the management of cryptococcal meningoencephalitis in 3 risk groups: (1) human immunodeficiency virus (HIV)-infected individuals, (2) organ transplant recipients, and (3) non-HIV-infected and nontransplant hosts. There are specific recommendations for other unique risk populations, such as children, pregnant women, persons in resource-limited environments, and those with Cryptococcus gattii infection. Recommendations for management also include other sites of infection, including strategies for pulmonary cryptococcosis. Emphasis has been placed on potential complications in management of cryptococcal infection, including increased intracranial pressure, immune reconstitution inflammatory syndrome (IRIS), drug resistance, and cryptococcomas. Three key management principles have been articulated: (1) induction therapy for meningoencephalitis using fungicidal regimens, such as a polyene and flucytosine, followed by suppressive regimens using fluconazole; (2) importance of early recognition and treatment of increased intracranial pressure and/or IRIS; and (3) the use of lipid formulations of amphotericin B regimens in patients with renal impairment. Cryptococcosis remains a challenging management issue, with little new drug development or recent definitive studies. However, if the diagnosis is made early, if clinicians adhere to the basic principles of these guidelines, and if the underlying disease is controlled, then cryptococcosis can be managed successfully in the vast majority of patients.

Functional impact of global rare copy number variation in autism spectrum disorders

Abstract: The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 x 10(-4)). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.

Testosterone therapy in men with androgen deficiency syndromes: an Endocrine Society clinical practice guideline.

Abstract: Objective: Our objective was to update the guidelines for the evaluation and treatment of androgen deficiency syndromes in adult men published previously in 2006. Participants: The Task Force was composed of a chair, selected by the Clinical Guidelines Subcommittee of The Endocrine Society, five additional experts, a methodologist, and a medical writer. The Task Force received no corporate funding or remuneration. Conclusions: We recommend making a diagnosis of androgen deficiency only in men with consistent symptoms and signs and unequivocally low serum testosterone levels. We suggest the measurement of morning total testosterone level by a reliable assay as the initial diagnostic test. We recommend confirmation of the diagnosis by repeating the measurement of morning total testosterone and, in some men in whom total testosterone is near the lower limit of normal or in whom SHBG abnormality is suspected by measurement of free or bioavailable testosterone level, using validated assays. We recommend testos...

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Abstract: Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

The Peregrine soliton in nonlinear fibre optics

Abstract: The Peregrine soliton — a wave localized in both space and time — is now observed experimentally for the first time by using femtosecond pulses in an optical fibre. The results give some insight into freak waves that can appear out of nowhere before simply disappearing.

Activation of the NLRP3 inflammasome by islet amyloid polypeptide provides a mechanism for enhanced IL-1β in type 2 diabetes

Abstract: Interleukin 1β (IL-1β) is an important inflammatory mediator of type 2 diabetes Here we show that oligomers of islet amyloid polypeptide (IAPP), a protein that forms amyloid deposits in the pancreas during type 2 diabetes, triggered the NLRP3 inflammasome and generated mature IL-1β One therapy for type 2 diabetes, glyburide, suppressed IAPP-mediated IL-1β production in vitro Processing of IL-1β initiated by IAPP first required priming, a process that involved glucose metabolism and was facilitated by minimally oxidized low-density lipoprotein Finally, mice transgenic for human IAPP had more IL-1β in pancreatic islets, which localized together with amyloid and macrophages Our findings identify previously unknown mechanisms in the pathogenesis of type 2 diabetes and treatment of pathology caused by IAPP

What the Cell “Sees” in Bionanoscience

Abstract: What the biological cell, organ, or barrier actually “sees” when interacting with a nanoparticle dispersed in a biological medium likely matters more than the bare material properties of the particle itself. Typically the bare surface of the particle is covered by several biomolecules, including a select group of proteins drawn from the biological medium. Here, we apply several different methodologies, in a time-resolved manner, to follow the lifetime of such biomolecular “coronas” both in situ and isolated from the excess plasma. We find that such particle−biomolecule complexes can be physically isolated from the surrounding medium and studied in some detail, without altering their structure. For several nanomaterial types, we find that blood plasma-derived coronas are sufficiently long-lived that they, rather than the nanomaterial surface, are likely to be what the cell sees. From fundamental science to regulatory safety, current efforts to classify the biological impacts of nanomaterials (currently acc...

Estimating the technology of cognitive and noncognitive skill formation

Abstract: This paper formulates and estimates multistage production functions for children's cognitive and noncognitive skills. Skills are determined by parental environments and investments at different stages of childhood. We estimate the elasticity of substitution between investments in one period and stocks of skills in that period to assess the benefits of early investment in children compared to later remediation. We establish nonparametric identification of a general class of production technologies based on nonlinear factor models with endogenous inputs. A by-product of our approach is a framework for evaluating childhood and schooling interventions that does not rely on arbitrarily scaled test scores as outputs and recognizes the differential effects of the same bundle of skills in different tasks. Using the estimated technology, we determine optimal targeting of interventions to children with different parental and personal birth endowments. Substitutability decreases in later stages of the life cycle in the production of cognitive skills. It is roughly constant across stages of the life cycle in the production of noncognitive skills. This finding has important implications for the design of policies that target the disadvantaged. For most configurations of disadvantage it is optimal to invest relatively more in the early stages of childhood than in later stages.

Effect of thermal processing on anthocyanin stability in foods; mechanisms and kinetics of degradation

Abstract: Anthocyanins are the most abundant flavonoid constituents of fruits and vegetables. The conjugated bonds in their structures, which absorb light at about 500 nm, are the basis for the red, blue and purple colours of fruits, vegetables and their products. Anthocyanin pigments readily degrade during thermal processing which can have a dramatic impact on colour quality and may also affect nutritional properties. This review attempts to summarize some important aspects of anthocyanin degradation during thermal processing. Conclusions regarding the mechanisms and kinetics of anthocyanin degradation during heat treatment are postulated based on current findings.

T cells in multiple sclerosis and experimental autoimmune encephalomyelitis

Abstract: Multiple sclerosis (MS) is a demyelinating inflammatory disorder of the central nervous system (CNS), which involves autoimmune responses to myelin antigens. Studies in experimental autoimmune encephalomyelitis (EAE), an animal model for MS, have provided convincing evidence that T cells specific for self-antigens mediate pathology in these diseases. Until recently, T helper type 1 (Th1) cells were thought to be the main effector T cells responsible for the autoimmune inflammation. However more recent studies have highlighted an important pathogenic role for CD4(+) T cells that secrete interleukin (IL)-17, termed Th17, but also IL-17-secreting γδ T cells in EAE as well as other autoimmune and chronic inflammatory conditions. This has prompted intensive study of the induction, function and regulation of IL-17-producing T cells in MS and EAE. In this paper, we review the contribution of Th1, Th17, γδ, CD8(+) and regulatory T cells as well as the possible development of new therapeutic approaches for MS based on manipulating these T cell subtypes.

Cyclometalation Using d-Block Transition Metals: Fundamental Aspects and Recent Trends

Abstract: ion and completion of the cyclometalation reaction are feasible and produce the cyclometalated complex 205. Notably, addition of a strong acid reverts the cyclometalation and regenerates the agostic species 204. Small changes in the rhodium precursor significantly modify the product outcome and lead at fast rates to the cyclometalated complex 203, that is, the final oxidative addition product S. Similarly, alkene C-H bond activation has been observed to occur readily in a PCP ligand setting.348 Milstein and co-workers developed a procedure for preparing the cyclometalated PCP, PCN, or PCO pincer complexes 209 by rhodium-mediated cleavage of a strong Caryl-Calkyl bond (Scheme 87).32,349,350 Kinetically, Calkyl-H bond activation is competitive and complex 208 is formed as a second product at essentially similar rates. However, C-C bond cleavage appears to be the thermodynamically more favored process. Obviously, the higher energy required for Caryl-Calkyl bond activation (bond dissociation energy 427 kJ mol-1) compared to C-H bond breaking (368 kJ mol-1) is compensated by the stronger Rh-Caryl bond and the formation of two fiverather than six-membered metallacycles. Because rhodium-mediated Caryl-Calkyl and Calkyl-H bond activations in 206 are thermodynamically and kinetically very similar processes,351 subtle changes in the ligand parameters strongly affect the reaction outcome. For example, PPh2 donors induce C-H bond cleavage to afford 208d exclusively at ambient temperatures. C-C activation and formation of 209d is only induced upon heating under H2 atmosphere,352 presumably because these conditions allow the product selectivity to be controlled thermodynamically. In contrast, bulky PtBu2 donors as in 206a promote C-C bond activation already at room temperature, and the aryl complex 209a is the only product observed. Similarly, replacing one phosphine donor by a harder NEt2 group or the use of less basic phosphinite donors results in selective C-C bond cleavage at room temperature. These preferences suggest steric factors to play a more dominant role than electronic differences in determining the C-C vs C-H selectivity. Steric congestion induced by the donor substituents has been proposed to arrange the orbitals of the metal center to be directed toward the C-C bond rather than toward the C-H bond.353 Kinetic investigations have identified the coordination compound 207 as a common intermediate of Calkyl-H and the Caryl-Calkyl bond activation. On the basis of the similar rates for both cleavage processes and because of the absence of any detectable intermediate, formation of 207 and not C-H or C-C bond activation appears to be rate-limiting. While displacement of a weakly bound olefin ligand in the metal precursor may be fast, formation of the 8-membered metallacycle in 207 may be less favored, especially due to the potential for forming diand polymeric coordination compounds. It is worth noting that, upon substituting the PCP pincer ligand to a PCN donor array, the coordination complex 207c becomes stable at low temperature and has been spectroscopically characterized.354 As a consequence, the rate-determining step is shifted to a later stage on the reaction coordinate. Notably, slight modifications in the metal precursor, that is, utilization of [Rh(C2H4)(CO)(solv)2]BF4 instead of [RhCl(C2H4)2]2, alters the stability of the intermediates and produces complex 210 (Scheme 88).355 This complex may be represented by an agostic interaction of the C-C bond with the rhodium center, or alternatively by an arenium structure including an sp3-hybridized ipso carbon. Because of only weak Cipso-Rh interactions in solution (e.g., the absence of any 103Rh coupling), the agostic description is favored. The different product outcome has been presumed to originate from the reduced electron density at the cationic rhodium(I) center due to the strongly withdrawing CO ligand and the relatively weak Rh-N bond. This configuration Scheme 87 Scheme 86 Cyclometalation Using d-Block Transition Metals Chemical Reviews, 2010, Vol. 110, No. 2 603

Beyond catalysis: N-heterocyclic carbene complexes as components for medicinal, luminescent, and functional materials applications.

Abstract: This tutorial review compiles the advances that have been achieved in using transition metal complexes containing N-heterocyclic carbene ligands as components for materials. Applications of metal carbene complexes in fields different from catalysis are remarkably scarce. During the last few years, promising results have been accomplished in particular by utilizing such complexes as antimicrobial and cytotoxic agents, as photoactive sites in luminescent materials, for self-assembly into liquid crystalline materials and metallosupramolecular structures, and as synthons for molecular switches and conducting polymeric materials. These initial achievements clearly underline the great potential of N-heterocyclic carbene complexes in various fields of materials science.

Towards an agronomic assessment of N2O emissions: a case study for arable crops

Abstract: Agricultural soils are the main anthropogenic source of nitrous oxide (N2O), largely because of nitrogen (N) fertilizer use. Commonly, N2O emissions are expressed as a function of N application rate. This suggests that smaller fertilizer applications always lead to smaller N2O emissions. Here we argue that, because of global demand for agricultural products, agronomic conditions should be included when assessing N2O emissions. Expressing N2O emissions in relation to crop productivity (expressed as above-ground N uptake: ‘yield-scaled N2O emissions') can express the N2O efficiency of a cropping system. We show how conventional relationships between N application rate, N uptake and N2O emissions can result in minimal yield-scaled N2O emissions at intermediate fertilizer-N rates. Key findings of a meta-analysis on yield-scaled N2O emissions by non-leguminous annual crops (19 independent studies and 147 data points) revealed that yield-scaled N2O emissions were smallest (8.4 g N2O-N kg-1N uptake) at application rates of approximately 180–190 kg N ha-1 and increased sharply after that (26.8 g N2O-N kg-1 N uptake at 301 kg N ha-1). If the above-ground N surplus was equal to or smaller than zero, yield-scaled N2O emissions remained stable and relatively small. At an N surplus of 90 kg N ha-1 yield-scaled emissions increased threefold. Furthermore, a negative relation between N use efficiency and yield-scaled N2O emissions was found. Therefore, we argue that agricultural management practices to reduce N2O emissions should focus on optimizing fertilizer-N use efficiency under median rates of N input, rather than on minimizing N application rates.

Genetic evidence implicates the immune system and cholesterol metabolism in the aetiology of Alzheimer's disease.

Abstract: Background 1Late Onset Alzheimer's disease (LOAD) is the leading cause of dementia. Recent large genome-wide association studies (GWAS) identified the first strongly supported LOAD susceptibility genes since the discovery of the involvement of APOE in the early 1990s. We have now exploited these GWAS datasets to uncover key LOAD pathophysiological processes. Methodology We applied a recently developed tool for mining GWAS data for biologically meaningful information to a LOAD GWAS dataset. The principal findings were then tested in an independent GWAS dataset. Principal Findings We found a significant overrepresentation of association signals in pathways related to cholesterol metabolism and the immune response in both of the two largest genome-wide association studies for LOAD. Significance Processes related to cholesterol metabolism and the innate immune response have previously been implicated by pathological and epidemiological studies of Alzheimer's disease, but it has been unclear whether those findings reflected primary aetiological events or consequences of the disease process. Our independent evidence from two large studies now demonstrates that these processes are aetiologically relevant, and suggests that they may be suitable targets for novel and existing therapeutic approaches.

The ABC of physical activity for health: A consensus statement from the British Association of Sport and Exercise Sciences

Abstract: Our understanding of the relationship between physical activity and health is constantly evolving. Therefore, the British Association of Sport and Exercise Sciences convened a panel of experts to review the literature and produce guidelines that health professionals might use. In the ABC of Physical Activity for Health, A is for All healthy adults, B is for Beginners, and C is for Conditioned individuals. All healthy adults aged 18-65 years should aim to take part in at least 150 min of moderate-intensity aerobic activity each week, or at least 75 min of vigorous-intensity aerobic activity per week, or equivalent combinations of moderate- and vigorous-intensity activities. Moderate-intensity activities are those in which heart rate and breathing are raised, but it is possible to speak comfortably. Vigorous-intensity activities are those in which heart rate is higher, breathing is heavier, and conversation is harder. Aerobic activities should be undertaken in bouts of at least 10 min and, ideally, should be performed on five or more days a week. All healthy adults should also perform muscle-strengthening activities on two or more days a week. Weight training, circuit classes, yoga, and other muscle-strengthening activities offer additional health benefits and may help older adults to maintain physical independence. Beginners should work steadily towards meeting the physical activity levels recommended for all healthy adults. Even small increases in activity will bring some health benefits in the early stages and it is important to set achievable goals that provide success, build confidence, and increase motivation. For example, a beginner might be asked to walk an extra 10 min every other day for several weeks to slowly reach the recommended levels of activity for all healthy adults. It is also critical that beginners find activities they enjoy and gain support in becoming more active from family and friends. Conditioned individuals who have met the physical activity levels recommended for all healthy adults for at least 6 months may obtain additional health benefits by engaging in 300 min or more of moderate-intensity aerobic activity per week, or 150 min or more of vigorous-intensity aerobic activity each week, or equivalent combinations of moderate- and vigorous-intensity aerobic activities. Adults who find it difficult to maintain a normal weight and adults with increased risk of cardiovascular disease or type 2 diabetes may in particular benefit from going beyond the levels of activity recommended for all healthy adults and gradually progressing towards meeting the recommendations for conditioned individuals. Physical activity is beneficial to health with or without weight loss, but adults who find it difficult to maintain a normal weight should probably be encouraged to reduce energy intake and minimize time spent in sedentary behaviours to prevent further weight gain. Children and young people aged 5-16 years should accumulate at least 60 min of moderate-to-vigorous-intensity aerobic activity per day, including vigorous-intensity aerobic activities that improve bone density and muscle strength.

A systematic approach to protein glycosylation analysis: a path through the maze

Abstract: Protein glycosylation is an important post-translational modification. It is a feature that enhances the functional diversity of proteins and influences their biological activity. A wide range of functions for glycans have been described, from structural roles to participation in molecular trafficking, self-recognition and clearance. Understanding the basis of these functions is challenging because the biosynthetic machinery that constructs glycans executes sequential and competitive steps that result in a mixture of glycosylated variants (glycoforms) for each glycoprotein. Additionally, naturally occurring glycoproteins are often present at low levels, putting pressure on the sensitivity of the analytical technologies. No universal method for the rapid and reliable identification of glycan structure is currently available; hence, research goals must dictate the best method or combination of methods. To this end, we introduce some of the major technologies routinely used for structural N- and O-glycan analysis, describing the complementary information that each provides.

European Society of Hypertension International Protocol revision 2010 for the validation of blood pressure measuring devices in adults

Abstract: The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland, dabl Ltd., Blackrock Co., Dublin, Ireland, Hypertension Center, Third University Department of Medicine, Sotiria Hospital, Athens, Greece, Istituto Scientifico Ospedale San Luca, IRCCS, Instituto Auxologico Italiano, Milan, Italy, Societe Francaise d’Hypertension Arterielle, Filiale de la Societe Francaise de Cardiolgie, Paris, France, The Department of Clinical Pharmacology and Therapeutics, Tohoku University Graduate School of Pharmaceutical Science and Medicine, Sendai, Japan, Centre for Epidemiological Studies and Clinical Trials, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China, University Clinic Bonn, Department of Internal Medicine, Bonn, Germany and Guy’s and St Thomas’ Hospitals, London, UK

Effects of β blockers and calcium-channel blockers on within-individual variability in blood pressure and risk of stroke

Abstract: Summary Background Analyses of some randomised trials show that calcium-channel blockers reduce the risk of stroke more than expected on the basis of mean blood pressure alone and that β blockers are less effective than expected. We aimed to investigate whether the effects of these drugs on variability in blood pressure might explain these disparities in effect on stroke risk. Methods The Anglo-Scandinavian Cardiac Outcomes Trial Blood Pressure Lowering Arm (ASCOT-BPLA) compared amlodipine-based regimens with atenolol-based regimens in 19 257 patients with hypertension and other vascular risk factors and the Medical Research Council (MRC) trial compared atenolol-based and diuretic-based regimens versus placebo in 4396 hypertensive patients aged 65–74 years. We expressed visit-to-visit variability of blood pressure during follow-up in the two trials as standard deviation (SD) and as transformations uncorrelated with mean blood pressure. For ASCOT-BPLA, we also studied within-visit variability and variability on 24 h ambulatory blood-pressure monitoring (ABPM). Results In ASCOT-BPLA, group systolic blood pressure (SBP) SD was lower in the amlodipine group than in the atenolol group at all follow-up visits (p Interpretation The opposite effects of calcium-channel blockers and β blockers on variability of blood pressure account for the disparity in observed effects on risk of stroke and expected effects based on mean blood pressure. To prevent stroke most effectively, blood-pressure-lowering drugs should reduce mean blood pressure without increasing variability; ideally they should reduce both. Funding None.

Signalling ballet in space and time

Abstract: The discovery of molecular signalling machines such as Ras nanoclusters, spatial activity gradients and flexible network circuitries involving transcriptional feedback, are beginning to reveal the design principles of spatiotemporal organization that are crucial for signalling network function and cell fate decisions.

A genome-wide scan for common alleles affecting risk for autism

Abstract: Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.

Handling of the generation of primary events in Gauss, the LHCb simulation framework

Abstract: The LHCb simulation application. Gauss, consists or two independent phases, the generation of the primary event and the tracking of particles produced in the experimental setup. For the LHCh experimental program it is particularly important to model IS meson decays: the KvtGcn code developed in CLEO and BaBah has been chosen and customized for non-coherent B production as necuring in pp collisions at the LHC, The initial proton-proto n collision is provided by a different generator engine, currently PYTHIA 6 for massive prwluclion of signal and generic pp collisions events. Beam gas events, background events originating from proton halo, cosmics and calibration events for different detectors can be generated in addition to pp collisions. Different generator packages as available in the physics community or specifically developed in LHCb are used for the different purposes. Running conditions affecting the events generated such as the size of the luminous region, the number of collisions occuring in a bunch crossing and the number of spill-over events from neighbouring bunches are modeled via dedicated algorithms appropriately configured. The design of the generator phase of Gauss will be described: a modular structure with well defined interfaces specific to the various tasks, e.g. pp collisions, particles' decays, selections, etc. has been chosen. Different implementations are available for the various tasks allowing selecting and combining them as most appropriate at run time as in the case of Pythia 6 im pp collisions or HIJING for beam gas. The advantages of such structure, allowing for example to adopt transparently new generators packages will be discussed.

The First Catalog of Active Galactic Nuclei Detected by the Fermi Large Area Telescope

Abstract: We present the first catalog of active galactic nuclei (AGN) detected by the LAT, corresponding to 11 months of data collected in scientific operation mode. The First LAT AGN Catalog (1LAC) includes 671 gamma-ray sources located at high Galactic latitudes (|b| > 10 deg) that are detected with a test statistic (TS) greater than 25 and associated statistically with AGNs. Some LAT sources are associated with multiple AGNs, and consequently, the catalog includes 709 AGNs, comprising 300 BL Lacertae objects (BL Lacs), 296 flat-spectrum radio quasars (FSRQs), 41 AGNs of other types, and 72 AGNs of unknown type. We also classify the blazars based on their spectral energy distributions (SEDs) as archival radio, optical, and X-ray data permit. In addition to the format 1LAC sample, we provide AGN associations for 51 low-latitude LAT sources and AGN "affiliations" (unquantified counterpart candidates) for 104 high-latitude LAT sources without AGN associations. The overlap of the 1LAC with existing gamma-ray AGN catalogs (LBAS, EGRET, AGILE, Swift, INTEGRAL, TeVCat) is briefly discussed. Various properties--such as gamma-ray fluxes and photon power law spectral indices, redshifts, gamma-ray luminosities, variability, and archival radio luminosities--and their correlations are presented and discussed for the different blazar classes. We compare the 1LAC results with predictions regarding the gamma-ray AGN populations, and we comment on the power of the sample to address the question of the blazar sequence.

Pricing Carbon: The European Union Emissions Trading Scheme

Abstract: The European Union's Emissions Trading Scheme (EU ETS) is the world's largest market for carbon and the most significant multinational initiative ever taken to mobilize markets to protect the environment. It will be an important influence on the development and implementation of trading schemes in the US, Japan, and elsewhere. However, as is true of any pioneering public policy experiment, this scheme has generated much controversy. Pricing Carbon provides the first detailed description and analysis of the EU ETS, focusing on the first 'trial' period of the scheme (2005–7). Written by an international team of experts, it allows readers to get behind the headlines and come to a better understanding of what was done and what happened based on a dispassionate, empirically based review of the evidence. This book should be read by anyone who wants to know what happens when emissions are capped, traded, and priced.

Learning a New Land: Immigrant Students in American Society

Abstract: Carola Suarez-Orozco, Marcelo M. Suarez-Orozco and Irina Todorova, Learning a New Land: Immigrant Students in American Society Cambridge, MA: Harvard University Press, 2008, 440 pp., $29.95 hb. (IS...

Tracking the Evolution of Communities in Dynamic Social Networks

Abstract: Real-world social networks from a variety of domains can naturally be modelled as dynamic graphs. However, approaches to detecting communities have largely focused on identifying communities in static graphs. Recently, researchers have begun to consider the problem of tracking the evolution of groups of users in dynamic scenarios. Here we describe a model for tracking the progress of communities over time in a dynamic network, where each community is characterised by a series of significant evolutionary events. This model is used to motivate a community-matching strategy for efficiently identifying and tracking dynamic communities. Evaluations on synthetic graphs containing embedded events demonstrate that this strategy can successfully track communities over time in volatile networks. In addition, we describe experiments exploring the dynamic communities detected in a real mobile operator network containing millions of users.

Recommending twitter users to follow using content and collaborative filtering approaches

Abstract: Recently the world of the web has become more social and more real-time. Facebook and Twitter are perhaps the exemplars of a new generation of social, real-time web services and we believe these types of service provide a fertile ground for recommender systems research. In this paper we focus on one of the key features of the social web, namely the creation of relationships between users. Like recent research, we view this as an important recommendation problem -- for a given user, UT which other users might be recommended as followers/followees -- but unlike other researchers we attempt to harness the real-time web as the basis for profiling and recommendation. To this end we evaluate a range of different profiling and recommendation strategies, based on a large dataset of Twitter users and their tweets, to demonstrate the potential for effective and efficient followee recommendation.