Status of and performance estimates for QCDOC

QCDOC is a supercomputer designed for high scalability at a low cost per node. We discuss the status of the project and provide performance estimates for large machines obtained from cycle accurate simulation of the QCDOC ASIC.Comment: 3 pages 1 figure. Lattice2002(machines

The nucleon's strange electromagnetic and scalar matrix elements

Quenched lattice QCD simulations and quenched chiral perturbation theory are used together for this study of strangeness in the nucleon. Dependences of the matrix elements on strange quark mass, valence quark mass and momentum transfer are discussed in both the lattice and chiral frameworks. The combined results of this study are in good agreement with existing experimental data and predictions are made for upcoming experiments. Possible future refinements of the theoretical method are suggested.Comment: 24 pages, 9 figure

Hardware and software status of QCDOC

QCDOC is a massively parallel supercomputer whose processing nodes are based on an application-specific integrated circuit (ASIC). This ASIC was custom-designed so that crucial lattice QCD kernels achieve an overall sustained performance of 50% on machines with several 10,000 nodes. This strong scalability, together with low power consumption and a price/performance ratio of $1 per sustained MFlops, enable QCDOC to attack the most demanding lattice QCD problems. The first ASICs became available in June of 2003, and the testing performed so far has shown all systems functioning according to specification. We review the hardware and software status of QCDOC and present performance figures obtained in real hardware as well as in simulation.Comment: Lattice2003(machine), 6 pages, 5 figure

Chapter 11 - Agriculture, forestry and other land use (AFOLU)

Agriculture, Forestry, and Other Land Use (AFOLU) plays a central role for food security and sustainable development. Plants take up carbon dioxide (CO2) from the atmosphere and nitrogen (N) from the soil when they grow, re-distributing it among different pools, including above and below-ground living biomass, dead residues, and soil organic matter. The CO2 and other non-CO2 greenhouse gases (GHG), largely methane (CH4) and nitrous oxide (N2O), are in turn released to the atmosphere by plant respiration, by decomposition of dead plant biomass and soil organic matter, and by combustion. Anthropogenic land-use activities (e.g., management of croplands, forests, grasslands, wetlands), and changes in land use / cover (e.g., conversion of forest lands and grasslands to cropland and pasture, afforestation) cause changes superimposed on these natural fluxes. AFOLU activities lead to both sources of CO2 (e.g., deforestation, peatland drainage) and sinks of CO2 (e.g., afforestation, management for soil carbon sequestration), and to non-CO2 emissions primarily from agriculture (e.g., CH4 from livestock and rice cultivation, N2O from manure storage and agricultural soils and biomass burning. The main mitigation options within AFOLU involve one or more of three strategies: reduction / prevention of emissions to the atmosphere by conserving existing carbon pools in soils or vegetation that would otherwise be lost or by reducing emissions of CH4 and N2O; sequestration - enhancing the uptake of carbon in terrestrial reservoirs, and thereby removing CO2 from the atmosphere; and reducing CO2 emissions by substitution of biological products for fossil fuels or energy-intensive products. Demand-side options (e.g., by lifestyle changes, reducing losses and wastes of food, changes in human diet, changes in wood consumption), though known to be difficult to implement, may also play a role. Land is the critical resource for the AFOLU sector and it provides food and fodder to feed the Earth's population of ~7 billion, and fibre and fuel for a variety of purposes. It provides livelihoods for billions of people worldwide. It is finite and provides a multitude of goods and ecosystem services that are fundamental to human well-being. Human economies and quality of life are directly dependent on the services and the resources provided by land. Figure 11.1 shows the many provisioning, regulating, cultural and supporting services provided by land, of which climate regulation is just one. Implementing mitigation options in the AFOLU sector may potentially affect other services provided by land in positive or negative ways. In the Intergovernmental Panel on Climate Change (IPCC) Second Assessment Report (SAR) and in the IPCC Fourth Assessment Report (AR4), agricultural and forestry mitigation were dealt with in separate chapters. In the IPCC Third Assessment Report (TAR), there were no separate sectoral chapters on either agriculture or forestry. In the IPCC Fifth Assessment Report (AR5), for the first time, the vast majority of the terrestrial land surface, comprising agriculture, forestry and other land use (AFOLU), is considered together in a single chapter, though settlements (which are important, with urban areas forecasted to triple in size from 2000 global extent by 2030), are dealt with in Chapter 12. This approach ensures that all land-based mitigation options can be considered together; it minimizes the risk of double counting or inconsistent treatment (e.g., different assumptions about available land) between different land categories, and allows the consideration of systemic feedbacks between mitigation options related to the land surface. Considering AFOLU in a single chapter allows phenomena common across land-use types, such as competition for land and water, co-benefits, adverse side-effects and interactions between mitigation and adaptation to be considered consistently. The complex nature of land presents a unique range of barriers and opportunities, and policies to promote mitigation in the AFOLU sector need to take account of this complexity. In this chapter, we consider the competing uses of land for mitigation and for providing other services. Unlike the chapters on agriculture and forestry in AR4, impacts of sourcing bioenergy from the AFOLU sector are considered explicitly in a dedicated appendix. Also new to this assessment is the explicit consideration of food / dietary demand-side options for GHG mitigation in the AFOLU sector, and some consideration of freshwater fisheries and aquaculture, which may compete with the agriculture and forestry sectors, mainly through their requirements for land and / or water, and indirectly, by providing fish and other products to the same markets as animal husbandry. This chapter deals with AFOLU in an integrated way with respect to the underlying scenario projections of population growth, economic growth, dietary change, land-use change (LUC), and cost of mitigation. We draw evidence from both "bottom-up" studies that estimate mitigation potentials at small scales or for individual options or technologies and then scale up, and multi-sectoral "top-down" studies that consider AFOLU as just one component of a total multi-sector system response. In this chapter, we provide updates on emissions trends and changes in drivers and pressures in the AFOLU sector, describe the practices available in the AFOLU sector, and provide refined estimates of mitigation costs and potentials for the AFOLU sector, by synthesising studies that have become available since AR4. We conclude the chapter by identifying gaps in knowledge and data, providing a selection of Frequently Asked Questions, and presenting an Appendix on bioenergy to update the IPCC Special Report on Renewable Energy Sources and Climate Change Mitigation (SRREN)

How sharp is the chiral crossover phenomenon for realistic meson masses?

The mass dependence of the chiral phase transition is studied in the linear $SU(3)\times SU(3)$ sigma-model to leading order in a $1/N_f$-expansion, $N_f$ denoting the number of flavours. For realistic meson masses we find a smooth crossover between $T\sim181.5$ to 192.6~[MeV]. The crossover looks more rapid in the light quark condensate than in thermodynamic quantities like the energy and entropy densities. The change in the light quark condensate in this temperature interval is $\sim$~50\% of the zero-temperature condensate value, while the entropy density increases by ($5.5\pm0.8)\cdot10^{-3}$~[GeV$^3$]. Since the numerical error is particularly large in this region, we cannot rule out a finite latent heat smaller than 0.2~[GeV/fm$^3$]. The chiral transition is washed out for an average pseudoscalar meson octet mass of 203~[MeV]. This gives an upper bound on the first-order transition region in the meson mass parameter space. The corresponding ratio of critical to realistic light current quark masses $m^{crit}_{u,d}/m_{u,d}$ is estimated as $0.26\pm0.08$. This result is by an order of magnitude larger than the corresponding mean-field value. Therefore theComment: LaTeX, HD--TVP--94--16, Please contact authors via email for figure

Tectonic controls on post-subduction granite genesis and emplacement : the late Caledonian suite of Britain and Ireland

Rates of magma emplacement commonly vary as a function of tectonic setting. The late Caledonian granites of Britain and Ireland are associated with closure of the Iapetus Ocean and were emplaced into a varying regime of transpression and transtension throughout the Silurian and into the early Devonian. Here we evaluate a new approach for examining how magma volumes vary as a function of tectonic setting. Available radiometric ages from the late Caledonian granites are used to calculate probability density functions (age spectra), with each pluton weighted by outcrop area as a proxy for its volume. These spectra confirm an absence of magmatic activity during Iapetus subduction between c. 455 Ma and 425 Ma and a dominance of post-subduction magmas between c. 425 Ma and 380 Ma. We review possible reasons why, despite the widespread outcrop of the late Caledonian granites, magmatism appears absent during Iapetus subduction. These include shallow angle subduction or extensive erosion and tectonic removal of the arc. In contrast to previous work we find no strong difference in the age or major element chemistry of post-subduction granites across all terranes. We propose a common causal mechanism in which the down-going Iapetus oceanic slab peeled back and detached beneath the suture following final Iapetus closure. The lithospheric mantle was delaminated beneath the suture and for about 100 km back beneath the Avalonian margin. While magma generation is largely a function of gravitationally driven lithosphere delamination, strike-slip dominated kinematics in the overlying continental crust is what modulated granitic magma emplacement. Early Devonian (419–404 Ma) transtension permitted large volumes of granite emplacement, whereas the subsequent Acadian (late Early Devonian, 404–394 Ma) transpression reduced and eventually suppressed magma emplacement

Prediction of major depressive disorder following beta-blocker therapy in patients with cardiovascular diseases

Incident depression has been reported to be associated with poor prognosis in patients with cardiovascular disease (CVD), which might be associated with beta-blocker therapy. Because early detection and intervention can alleviate the severity of depression, we aimed to develop a machine learning (ML) model predicting the onset of major depressive disorder (MDD). A model based on L1 regularized logistic regression was trained against the South Korean nationwide administrative claims database to identify risk factors for the incident MDD after beta-blocker therapy in patients with CVD. We identified 50,397 patients initiating beta-blockers for CVD, with 774 patients developing MDD within 365 days after initiating beta-blocker therapy. An area under the receiver operating characteristic curve (AUC) of 0.74 was achieved. A history of non-selective beta-blockers and factors related to anxiety disorder, sleeping problems, and other chronic diseases were the most strong predictors. AUCs of 0.62–0.71 were achieved in the external validation conducted on six independent electronic health records and claims databases in the USA and South Korea. In conclusion, an ML model that identifies patients at high-risk for incident MDD was developed. Application of ML to identify susceptible patients for adverse events of treatment may serve as an important approach for personalized medicine

Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients

Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation

Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing.

BACKGROUND: Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases and 503 control participants. Candidate genes were subsequently validated for functions relevant to PD based on parallel RNA-interference (RNAi) screens in human cell culture and Drosophila and C. elegans models. RESULTS: Assuming autosomal recessive inheritance, we identify 27 genes that have homozygous or compound heterozygous loss-of-function variants in PD cases. Definitive replication and confirmation of these findings were hindered by potential heterogeneity and by the rarity of the implicated alleles. We therefore looked for potential genetic interactions with established PD mechanisms. Following RNAi-mediated knockdown, 15 of the genes modulated mitochondrial dynamics in human neuronal cultures and four candidates enhanced α-synuclein-induced neurodegeneration in Drosophila. Based on complementary analyses in independent human datasets, five functionally validated genes-GPATCH2L, UHRF1BP1L, PTPRH, ARSB, and VPS13C-also showed evidence consistent with genetic replication. CONCLUSIONS: By integrating human genetic and functional evidence, we identify several PD susceptibility gene candidates for further investigation. Our approach highlights a powerful experimental strategy with broad applicability for future studies of disorders with complex genetic etiologies