Showing papers by "Australian National University published in 2008"

The Reticular Chemistry Structure Resource (RCSR) Database of, and Symbols for, Crystal Nets

Abstract: During the past decade, interest has grown tremendously in the design and synthesis of crystalline materials constructed from molecular clusters linked by extended groups of atoms. Most notable are metal-organic frameworks (MOFs), in which polyatomic inorganic metal-containing clusters are joined by polytopic linkers. (Although these materials are sometimes referred to as coordination polymers, we prefer to differentiate them, because MOFs are based on strong linkages that yield robust frameworks.) The realization that MOFs could be designed and synthesized in a rational way from molecular building blocks led to the emergence of a discipline that we call reticular chemistry. MOFs can be represented as a special kind of graph called a periodic net. Such descriptions date back to the earliest crystallographic studies but have become much more common recently because thousands of new structures and hundreds of underlying nets have been reported. In the simplest cases (e.g., the structure of diamond), the atoms in the crystal become the vertices of the net, and bonds are the links (edges) that connect them. In the case of MOFs, polyatomic groups act as the vertices and edges of the net. Because of the explosive growth in this area, a need has arisen for a universal system of nomenclature, classification, identification, and retrieval of these topological structures. We have developed a system of symbols for the identification of three periodic nets of interest, and this system is now in wide use. In this Account, we explain the underlying methodology of assigning symbols and describe the Reticular Chemistry Structure Resource (RCSR), in which about 1600 such nets are collected and illustrated in a database that can be searched by symbol, name, keywords, and attributes. The resource also contains searchable data for polyhedra and layers. The database entries come from systematic enumerations or from known chemical compounds or both. In the latter case, references to occurrences are provided. We describe some crystallographic, topological, and other attributes of nets and explain how they are reported in the database. We also describe how the database can be used as a tool for the design and structural analysis of new materials. Associated with each net is a natural tiling, which is a natural partition of space into space-filling tiles. The database allows export of data that can be used to analyze and illustrate such tilings.

Nonlinear Complementary Filters on the Special Orthogonal Group

Abstract: This paper considers the problem of obtaining good attitude estimates from measurements obtained from typical low cost inertial measurement units. The outputs of such systems are characterized by high noise levels and time varying additive biases. We formulate the filtering problem as deterministic observer kinematics posed directly on the special orthogonal group SO (3) driven by reconstructed attitude and angular velocity measurements. Lyapunov analysis results for the proposed observers are derived that ensure almost global stability of the observer error. The approach taken leads to an observer that we term the direct complementary filter. By exploiting the geometry of the special orthogonal group a related observer, termed the passive complementary filter, is derived that decouples the gyro measurements from the reconstructed attitude in the observer inputs. Both the direct and passive filters can be extended to estimate gyro bias online. The passive filter is further developed to provide a formulation in terms of the measurement error that avoids any algebraic reconstruction of the attitude. This leads to an observer on SO(3), termed the explicit complementary filter, that requires only accelerometer and gyro outputs; is suitable for implementation on embedded hardware; and provides good attitude estimates as well as estimating the gyro biases online. The performance of the observers are demonstrated with a set of experiments performed on a robotic test-bed and a radio controlled unmanned aerial vehicle.

The status of the world's land and marine mammals: diversity, threat, and knowledge

Abstract: Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action.

The genome of the model beetle and pest Tribolium castaneum.

Abstract: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

A Double-Negative Feedback Loop between ZEB1-SIP1 and the microRNA-200 Family Regulates Epithelial-Mesenchymal Transition

Abstract: Epithelial to mesenchymal transition occurs during embryologic development to allow tissue remodeling and is proposed to be a key step in the metastasis of epithelial-derived tumors. The miR-200 family of microRNAs plays a major role in specifying the epithelial phenotype by preventing expression of the transcription repressors, ZEB1/deltaEF1 and SIP1/ZEB2. We show here that miR-200a, miR-200b, and the related miR-429 are all encoded on a 7.5-kb polycistronic primary miRNA (pri-miR) transcript. We show that the promoter for the pri-miR is located within a 300-bp segment located 4 kb upstream of miR-200b. This promoter region is sufficient to confer expression in epithelial cells and is repressed in mesenchymal cells by ZEB1 and SIP1 through their binding to a conserved pair of ZEB-type E-box elements located proximal to the transcription start site. These findings establish a double-negative feedback loop controlling ZEB1-SIP1 and miR-200 family expression that regulates cellular phenotype and has direct relevance to the role of these factors in tumor progression.

Nutritional Control of Reproductive Status in Honeybees via DNA Methylation

Abstract: Fertile queens and sterile workers are alternative forms of the adult female honeybee that develop from genetically identical larvae following differential feeding with royal jelly. We show that silencing the expression of DNA methyltransferase Dnmt3, a key driver of epigenetic global reprogramming, in newly hatched larvae led to a royal jelly-like effect on the larval developmental trajectory; the majority of Dnmt3 small interfering RNA-treated individuals emerged as queens with fully developed ovaries. Our results suggest that DNA methylation in Apis is used for storing epigenetic information, that the use of that information can be differentially altered by nutritional input, and that the flexibility of epigenetic modifications underpins, profound shifts in developmental fates, with massive implications for reproductive and behavioral status.

Assisted colonization and rapid climate change.

Abstract: Moving species outside their historic ranges may mitigate loss of biodiversity in the face of global climate change.

Amino acid transport across mammalian intestinal and renal epithelia.

Abstract: The transport of amino acids in kidney and intestine is critical for the supply of amino acids to all tissues and the homeostasis of plasma amino acid levels. This is illustrated by a number of inherited disorders affecting amino acid transport in epithelial cells, such as cystinuria, lysinuric protein intolerance, Hartnup disorder, iminoglycinuria, dicarboxylic aminoaciduria, and some other less well-described disturbances of amino acid transport. The identification of most epithelial amino acid transporters over the past 15 years allows the definition of these disorders at the molecular level and provides a clear picture of the functional cooperation between transporters in the apical and basolateral membranes of mammalian epithelial cells. Transport of amino acids across the apical membrane not only makes use of sodium-dependent symporters, but also uses the proton-motive force and the gradient of other amino acids to efficiently absorb amino acids from the lumen. In the basolateral membrane, antiporters cooperate with facilitators to release amino acids without depleting cells of valuable nutrients. With very few exceptions, individual amino acids are transported by more than one transporter, providing backup capacity for absorption in the case of mutational inactivation of a transport system.

Parental investment, sexual selection and sex ratios

Abstract: Conventional sex roles imply caring females and competitive males. The evolution of sex role divergence is widely attributed to anisogamy initiating a self-reinforcing process. The initial asymmetry in pre-mating parental invest- ment (eggs vs. sperm) is assumed to promote even greater divergence in post- mating parental investment (parental care). But do we really understand the process? Trivers (Sexual Selection and the Descent of Man 1871-1971 (1972), Aldine Press, Chicago) introduced two arguments with a female and male perspective on whether to care for offspring that try to link pre-mating and post-mating investment. Here we review their merits and subsequent theoretical develop- ments. The first argument is that females are more committed than males to providing care because they stand to lose a greater initial investment. This, however, commits the 'Concorde Fallacy' as optimal decisions should depend on future pay-offs not past costs. Although the argument can be rephrased in terms of residual reproductive value when past investment affects future pay-offs, it remains weak. The factors likely to change future pay-offs seem to work against females providing more care than males. The second argument takes the reasonable premise that anisogamy produces a male-biased operational sex ratio (OSR) leading to males competing for mates. Male care is then predicted to be less likely to evolve as it consumes resources that could otherwise be used to increase competitiveness. However, given each offspring has precisely two genetic parents (the Fisher condition), a biased OSR generates frequency- dependent selection, analogous to Fisherian sex ratio selection, that favours increased parental investment by whichever sex faces more intense competi- tion. Sex role divergence is therefore still an evolutionary conundrum. Here we review some possible solutions. Factors that promote conventional sex roles are sexual selection on males (but non-random variance in male mating success must be high to override the Fisher condition), loss of paternity because of female multiple mating or group spawning and patterns of mortality that generate female-biased adult sex ratios (ASR). We present an integrative model that shows how these factors interact to generate sex roles. We emphasize the need to distinguish between the ASR and the operational sex ratio (OSR). If mortality is higher when caring than competing this diminishes the likelihood of sex role divergence because this strongly limits the mating success of the earlier deserting sex. We illustrate this in a model where a change in relative mortality rates while caring and competing generates a shift from a mammalian type breeding system (female-only care, male-biased OSR and female-biased ASR) to an avian type system (biparental care and a male-biased OSR and ASR).

The MAPPINGS III Library of Fast Radiative Shock Models

Abstract: We present a new library of fully-radiative shock models calculated with the MAPPINGS iii shock and photoionization code. The library consists of grids of models with shock velocities in the range vs=100-1000 km s −1 and magnetic parameters B/ p n of 10 −4 -10 µG cm 3/2 for five different atomic abundance sets, and for a pre-shock density of 1.0 cm −3 . Additionally, Solar abundance model grids have been calculated for densities of 0.01, 0.1, 10, 100, and 1000 cm −3 with the same range in vs and B/ p n. Each model includes components of both the radiative shock and its photoionized precursor, ionized by the EUV and soft X-ray radiation generated in the radiative gas. We present the details of the ionization structure, the column densities, and the luminosities of the shock and its precursor. Emission line ratio predictions are separately given for the shock and its precursor as well as for the composite shock+precursor structure to facilitate comparison with observations in cases where the shock and its precursor are not resolved. Emission line ratio grids for shock and shock+precursor are presented on standard line ratio diagnostic diagrams, and we compare these grids to observations of radio galaxies and a sample of AGN and star forming galaxies from the Sloan Digital Sky Survey. This library is available online, along with a suite of tools to enable the analysis of the shocks and the easy creation of emission line ratio diagnostic diagrams. These models represent a significant increase in parameter space coverage over previously available models, and therefore provide a unique tool in the diagnosis of emission by shocks. Subject headings: hydrodynamics - shock waves - ISM: abundances,- Galaxies: Nuclei, Galaxies: Seyfert - infrared: ISM, Ultraviolet: ISM, X-rays: ISM

Optimised KD-trees for fast image descriptor matching

Abstract: In this paper, we look at improving the KD-tree for a specific usage: indexing a large number of SIFT and other types of image descriptors. We have extended priority search, to priority search among multiple trees. By creating multiple KD-trees from the same data set and simultaneously searching among these trees, we have improved the KD-treepsilas search performance significantly.We have also exploited the structure in SIFT descriptors (or structure in any data set) to reduce the time spent in backtracking. By using Principal Component Analysis to align the principal axes of the data with the coordinate axes, we have further increased the KD-treepsilas search performance.

A gene expression atlas of the model legume Medicago truncatula.

Abstract: Legumes played central roles in the development of agriculture and civilization, and today account for approximately one-third of the world's primary crop production. Unfortunately, most cultivated legumes are poor model systems for genomic research. Therefore, Medicago truncatula, which has a relatively small diploid genome, has been adopted as a model species for legume genomics. To enhance its value as a model, we have generated a gene expression atlas that provides a global view of gene expression in all major organ systems of this species, with special emphasis on nodule and seed development. The atlas reveals massive differences in gene expression between organs that are accompanied by changes in the expression of key regulatory genes, such as transcription factor genes, which presumably orchestrate genetic reprogramming during development and differentiation. Interestingly, many legume-specific genes are preferentially expressed in nitrogen-fixing nodules, indicating that evolution endowed them with special roles in this unique and important organ. Comparative transcriptome analysis of Medicago versus Arabidopsis revealed significant divergence in developmental expression profiles of orthologous genes, which indicates that phylogenetic analysis alone is insufficient to predict the function of orthologs in different species. The data presented here represent an unparalleled resource for legume functional genomics, which will accelerate discoveries in legume biology.

Aberrant mucin assembly in mice causes endoplasmic reticulum stress and spontaneous inflammation resembling ulcerative colitis.

Abstract: Background MUC2 mucin produced by intestinal goblet cells is the major component of the intestinal mucus barrier. The inflammatory bowel disease ulcerative colitis is characterized by depleted goblet cells and a reduced mucus layer, but the aetiology remains obscure. In this study we used random mutagenesis to produce two murine models of inflammatory bowel disease, characterised the basis and nature of the inflammation in these mice, and compared the pathology with human ulcerative colitis.

Genome analysis of the platypus reveals unique signatures of evolution

Abstract: We present a draft genome sequence of the platypus, Ornithorhynchus anatinus This monotreme exhibits a fascinating combination of reptilian and mammalian characters For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles Analysis of the first monotreme genome aligned these features with genetic innovations We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation

The Milky Way Tomography with SDSS. II. Stellar Metallicity

Abstract: In addition to optical photometry of unprecedented quality, the Sloan Digital Sky Survey (SDSS) is producing a massive spectroscopic database which already contains over 280,000 stellar spectra. Using eectiv e temperature and metallicity derived from SDSS spectra for 60,000 F and G type main sequence stars (0:2 < g r < 0:6), we develop polynomial models, reminiscent of traditional methods based on the UBV photometry, for estimating these parameters from the SDSS u g and g r colors. These estimators reproduce SDSS spectroscopic parameters with a root-mean-square scatter of 100 K for eectiv e temperature, and 0.2 dex for metallicity (limited by photometric errors), which are similar to random and systematic uncertainties in spectroscopic determinations. We apply this method to a photometric catalog of coadded SDSS observations and study the photometric metallicity distribution of 200,000 F and G type stars observed in 300 deg 2 of high Galactic latitude sky. These deeper (g < 20:5) and photometrically precise ( 0.01 mag) coadded data enable an accurate measurement of the unbiased metallicity distribution for a complete volume-limited sample of stars at distances between 500 pc and 8 kpc. The metallicity distribution can be exquisitely modeled using two components with a spatially varying number ratio, that correspond to disk and halo. The best-t number ratio of the two components is consistent with that implied by the decomposition of stellar counts proles into exponential disk and power-law halo components by Juri c et al. (2008). The two components also possess the kinematics expected for disk and halo stars. The metallicity of the halo component can be modeled as a spatially invariant Gaussian distribution with a mean of [F e=H] = 1:46 and a standard deviation of 0.3 dex. The disk metallicity distribution is non-Gaussian, with a remarkably small scatter (rms 0.16 dex) and the median smoothly decreasing with distance from the plane from 0:6 at 500 pc to 0:8 beyond several kpc. Similarly, we nd using proper motion measurements that a nonGaussian rotational velocity distribution of disk stars shifts by 50 km/s as the distance from the plane increases from 500 pc to several kpc. Despite this similarity, the metallicity and rotational velocity distributions of disk stars are not correlated (Kendall’s = 0:017 0:018). This absence of a correlation between metallicity and kinematics for disk stars is in a conict with the traditional decomposition in terms of thin and thick disks, which predicts a strong correlation ( = 0:30 0:04) at 1 kpc from the mid-plane. Instead, the variation of the metallicity and rotational velocity distributions can be modeled using non-Gaussian functions that retain their shapes and only shift as the distance from the mid-plane increases. We also study the metallicity distribution using a shallower (g < 19:5) but much larger sample of close to three million stars in 8500 sq. deg. of sky included in SDSS Data Release 6. The large sky coverage enables the detection of coherent substructures in the kinematics{ metallicity space, such as the Monoceros stream, which rotates faster than the LSR, and has a median metallicity of [F e=H] = 0:95, with an rms scatter of only 0.15 dex. We extrapolate our results to the performance expected from the Large Synoptic Survey Telescope (LSST) and estimate that LSST will obtain metallicity measurements accurate to 0.2 dex or better, with proper motion measurements accurate to 0.2-0.5 mas/yr, for about 200 million F/G dwarf stars within a distance limit of 100 kpc (g < 23:5). Subject headings: methods: data analysis | stars: statistics | Galaxy: halo, kinematics and dynamics, stellar content, structure

Deficiency of Th17 cells in hyper IgE syndrome due to mutations in STAT3

Abstract: Hyper-immunoglobulin E syndrome (HIES) is a primary immune deficiency characterized by abnormal and devastating susceptibility to a narrow spectrum of infections, most commonly Staphylococcus aureus and Candida albicans. Recent investigations have identified mutations in STAT3 in the majority of HIES patients studied. Despite the identification of the genetic cause of HIES, the mechanisms underlying the pathological features of this disease remain to be elucidated. Here, we demonstrate a failure of CD4+ T cells harboring heterozygous STAT3 mutations to generate interleukin 17-secreting (i.e., T helper [Th]17) cells in vivo and in vitro due to a failure to express sufficient levels of the Th17-specific transcriptional regulator retinoid-related orphan receptor t. Because Th17 cells are enriched for cells with specificities against fungal antigens, our results may explain the pattern of infection susceptibility characteristic of patients with HIES. Furthermore, they underscore the importance of Th17 responses in normal host defense against the common pathogens S. aureus and C. albicans.

Should agricultural policies encourage land sparing or wildlife‐friendly farming?

Abstract: As the demands on agricultural lands to produce food, fuel, and fiber continue to expand, effective strategies are urgently needed to balance biodiversity conservation and agricultural production. “Land sparing” and “wildlife-friendly farming” have been proposed as seemingly opposing strategies to achieve this balance. In land sparing, homogeneous areas of farmland are managed to maximize yields, while separate reserves target biodiversity conservation. Wildlife-friendly farming, in contrast, integrates conservation and production within more heterogeneous landscapes. Different scientific traditions underpin the two approaches. Land sparing is associated with an island model of modified landscapes, where islands of nature are seen as separate from human activities. This simple dichotomy makes land sparing easily compatible with optimization methods that attempt to allocate land uses in the most efficient way. In contrast, wildlife-friendly farming emphasizes heterogeneity, resilience, and ecological inter...

Action potential generation requires a high sodium channel density in the axon initial segment.

Abstract: The axon initial segment (AIS) is a specialized region in neurons where action potentials are initiated. It is commonly assumed that this process requires a high density of voltage-gated sodium (Na(+)) channels. Paradoxically, the results of patch-clamp studies suggest that the Na(+) channel density at the AIS is similar to that at the soma and proximal dendrites. Here we provide data obtained by antibody staining, whole-cell voltage-clamp and Na(+) imaging, together with modeling, which indicate that the Na(+) channel density at the AIS of cortical pyramidal neurons is approximately 50 times that in the proximal dendrites. Anchoring of Na(+) channels to the cytoskeleton can explain this discrepancy, as disruption of the actin cytoskeleton increased the Na(+) current measured in patches from the AIS. Computational models required a high Na(+) channel density (approximately 2,500 pS microm(-2)) at the AIS to account for observations on action potential generation and backpropagation. In conclusion, action potential generation requires a high Na(+) channel density at the AIS, which is maintained by tight anchoring to the actin cytoskeleton.

Advances in understanding the cyanobacterial CO2-concentrating-mechanism (CCM): functional components, Ci transporters, diversity, genetic regulation and prospects for engineering into plants

Abstract: Cyanobacteria have evolved a significant environmental adaptation, known as a CO(2)-concentrating-mechanism (CCM), that vastly improves photosynthetic performance and survival under limiting CO(2) concentrations. The CCM functions to transport and accumulate inorganic carbon actively (Ci; HCO(3)(-), and CO(2)) within the cell where the Ci pool is utilized to provide elevated CO(2) concentrations around the primary CO(2)-fixing enzyme, ribulose bisphosphate carboxylase-oxygenase (Rubisco). In cyanobacteria, Rubisco is encapsulated in unique micro-compartments known as carboxysomes. Cyanobacteria can possess up to five distinct transport systems for Ci uptake. Through database analysis of some 33 complete genomic DNA sequences for cyanobacteria it is evident that considerable diversity exists in the composition of transporters employed, although in many species this diversity is yet to be confirmed by comparative phenomics. In addition, two types of carboxysomes are known within the cyanobacteria that have apparently arisen by parallel evolution, and considerable progress has been made towards understanding the proteins responsible for carboxysome assembly and function. Progress has also been made towards identifying the primary signal for the induction of the subset of CCM genes known as CO(2)-responsive genes, and transcriptional regulators CcmR and CmpR have been shown to regulate these genes. Finally, some prospects for introducing cyanobacterial CCM components into higher plants are considered, with the objective of engineering plants that make more efficient use of water and nitrogen.

Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota.

Abstract: The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesic-adapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.

Evaluation of theoretical conversion coefficients using BrIcc

Abstract: A new internal conversion coefficient database, BrIcc has been developed which integrates a number of tabulations on internal conversion electron (ICC) and electron–positron pair conversion coefficients (IPC), as well as Ω ( E 0 ) electronic factors. A critical review of general formulae and procedures to evaluate theoretical ICC and IPC values are presented, including the treatment of uncertainties in transition energy and mixing ratio in accordance with the Evaluated Nuclear Structure Data File. The default ICC table, based on the Dirac–Fock calculations using the so called “Frozen Orbital” approximation, takes into account the effect of atomic vacancies created in the conversion process. The table has been calculated for all atomic shells and to cover transition energies of 1–6000 keV and atomic numbers of Z = 5 –110. The software tools presented here are well suited for basic nuclear structure research and for a range of applications.

The segue stellar parameter pipeline. i. description and comparison of individual methods

Abstract: We describe the development and implementation of the Sloan Extension for Galactic Exploration and Understanding (SEGUE) Stellar Parameter Pipeline (SSPP) The SSPP is derived, using multiple techniques, radial velocities, and the fundamental stellar atmospheric parameters (effective temperature, surface gravity, and metallicity) for AFGK-type stars, based on medium-resolution spectroscopy and ugriz photometry obtained during the course of the original Sloan Digital Sky Survey (SDSS-I) and its Galactic extension (SDSS-II/SEGUE) The SSPP also provides spectral classification for a much wider range of stars, including stars with temperatures outside the window where atmospheric parameters can be estimated with the current approaches This is Paper I in a series of papers on the SSPP; it provides an overview of the SSPP, and tests of its performance using several external data sets Random and systematic errors are critically examined for the current version of the SSPP, which has been used for the sixth public data release of the SDSS (DR-6)

International study of temperature,heat and urban mortality: the ‘ISOTHURM’ project

Abstract: BACKGROUND: This study describes heat- and cold-related mortality in 12 urban populations in low- and middle-income countries, thereby extending knowledge of how diverse populations, in non-OECD countries, respond to temperature extremes. METHODS: The cities were: Delhi, Monterrey, Mexico City, Chiang Mai, Bangkok, Salvador, Sao Paulo, Santiago, Cape Town, Ljubljana, Bucharest and Sofia. For each city, daily mortality was examined in relation to ambient temperature using autoregressive Poisson models (2- to 5-year series) adjusted for season, relative humidity, air pollution, day of week and public holidays. RESULTS: Most cities showed a U-shaped temperature-mortality relationship, with clear evidence of increasing death rates at colder temperatures in all cities except Ljubljana, Salvador and Delhi and with increasing heat in all cities except Chiang Mai and Cape Town. Estimates of the temperature threshold below which cold-related mortality began to increase ranged from 15 degrees C to 29 degrees C; the threshold for heat-related deaths ranged from 16 degrees C to 31 degrees C. Heat thresholds were generally higher in cities with warmer climates, while cold thresholds were unrelated to climate. CONCLUSIONS: Urban populations, in diverse geographic settings, experience increases in mortality due to both high and low temperatures. The effects of heat and cold vary depending on climate and non-climate factors such as the population disease profile and age structure. Although such populations will undergo some adaptation to increasing temperatures, many are likely to have substantial vulnerability to climate change. Additional research is needed to elucidate vulnerability within populations. Language: en

China's changing energy intensity trend: A decomposition analysis

Abstract: China experienced a dramatic decline in energy intensity from the onset of economic reform in the late 1970s until 2000, but since then the rate of decline slowed and energy intensity actually increased in 2003. Most previous studies found that most of the decline was due to technological change, but disagreed on the role of structural change. To the best of our knowledge, no decomposition study has investigated the role of inter-fuel substitution in the decline in energy intensity or the causes of the rise in energy intensity since 2000. In this paper, we use logarithmic mean Divisia index (LMDI) techniques to decompose changes in energy intensity in the period 1980-2003. We find that: (1) technological change is confirmed as the dominant contributor to the decline in energy intensity; (2) structural change at the industry and sector (sub-industry) level actually increased energy intensity over the period of 1980-2003, although the structural change at the industry level was very different in the 1980s and in the post-1990 period; (3) structural change involving shifts of production between sub-sectors, however, decreased overall energy intensity; (4) the increase in energy intensity since 2000 is explained by negative technological progress; (5) inter-fuel substitution is found to contribute little to the changes in energy intensity.

Two levels of protection for the B cell genome during somatic hypermutation

Abstract: Somatic hypermutation, the mechanism by which activated B cells in the blood produce a diversity of immunoglobulin genes giving rise to high-affinity antibodies, plays a vital role in protecting the body from infection. Yet it also represents a major risk to genomic stability, with the potential to generate B-cell tumours if unchecked or wrongly directed. The somatic hypermutation reaction is initiated by activation induced deaminase (AID), and it is widely assumed that the risk of inappropriate hypermutation is averted by careful targeting of this enzyme. New work in mice suggests that this is not the case. Rather, AID deaminates a large fraction of the expressed genome, including numerous oncogenes linked to B-cell malignancies. Widespread mutation of the genome is averted in a surprising manner: by gene-specific, error-free DNA repair mediated by base excision and mismatch repair. Somatic hypermutation introduces point mutations into immunoglobulin genes in germinal centre B cells during an immune response. The reaction is initiated by cytosine deamination by the activation-induced deaminase (AID) and completed by error-prone processing of the resulting uracils by mismatch and base excision repair factors1. Somatic hypermutation represents a threat to genome integrity2 and it is not known how the B cell genome is protected from the mutagenic effects of somatic hypermutation nor how often these protective mechanisms fail. Here we show, by extensive sequencing of murine B cell genes, that the genome is protected by two distinct mechanisms: selective targeting of AID and gene-specific, high-fidelity repair of AID-generated uracils. Numerous genes linked to B cell tumorigenesis, including Myc, Pim1, Pax5, Ocab (also called Pou2af1), H2afx, Rhoh and Ebf1, are deaminated by AID but escape acquisition of most mutations through the combined action of mismatch and base excision repair. However, approximately 25% of expressed genes analysed were not fully protected by either mechanism and accumulated mutations in germinal centre B cells. Our results demonstrate that AID acts broadly on the genome, with the ultimate distribution of mutations determined by a balance between high-fidelity and error-prone DNA repair.