Showing papers by "University of Hawaii at Manoa published in 2013"

Recent global-warming hiatus tied to equatorial Pacific surface cooling

Abstract: Despite the continued increase in atmospheric greenhouse gas concentrations, the annual-mean global temperature has not risen in the twenty-first century, challenging the prevailing view that anthropogenic forcing causes climate warming. Various mechanisms have been proposed for this hiatus in global warming, but their relative importance has not been quantified, hampering observational estimates of climate sensitivity. Here we show that accounting for recent cooling in the eastern equatorial Pacific reconciles climate simulations and observations. We present a novel method of uncovering mechanisms for global temperature change by prescribing, in addition to radiative forcing, the observed history of sea surface temperature over the central to eastern tropical Pacific in a climate model. Although the surface temperature prescription is limited to only 8.2% of the global surface, our model reproduces the annual-mean global temperature remarkably well with correlation coefficient r = 0.97 for 1970-2012 (which includes the current hiatus and a period of accelerated global warming). Moreover, our simulation captures major seasonal and regional characteristics of the hiatus, including the intensified Walker circulation, the winter cooling in northwestern North America and the prolonged drought in the southern USA. Our results show that the current hiatus is part of natural climate variability, tied specifically to a La-Nina-like decadal cooling. Although similar decadal hiatus events may occur in the future, the multi-decadal warming trend is very likely to continue with greenhouse gas increase.

Revisiting the scaling relations of black hole masses and host galaxy properties

Abstract: New kinematic data and modeling efforts in the past few years have substantially expanded and revised dynamical measurements of black hole masses (M ?) at the centers of nearby galaxies. Here we compile an updated sample of 72 black holes and their host galaxies, and present revised scaling relations between M ? and stellar velocity dispersion (?), V-band luminosity (L), and bulge stellar mass (M bulge), for different galaxy subsamples. Our best-fitting power-law relations for the full galaxy sample are log10(M ?) = 8.32 + 5.64log10(?/200 km s?1), log10(M ?) = 9.23 + 1.11log10(L/1011 L ?), and log10(M ?) = 8.46 + 1.05log10(M bulge/1011 M ?). A log-quadratic fit to the M ?-? relation with an additional term of ?2 [log10(?/200 km s?1)]2 gives ?2 = 1.68 ? 1.82 and does not decrease the intrinsic scatter in M ?. Including 92 additional upper limits on M ? does not change the slope of the M ?-? relation. When the early- and late-type galaxies are fit separately, we obtain similar slopes of 5.20 and 5.06 for the M ?-? relation but significantly different intercepts?M ? in early-type galaxies are about two times higher than in late types at a given sigma. Within early-type galaxies, our fits to M ?(?) give M ? that is about two times higher in galaxies with central core profiles than those with central power-law profiles. Our M ?-L and M ?-M bulge relations for early-type galaxies are similar to those from earlier compilations, and core and power-law galaxies yield similar L- and M bulge-based predictions for M ?. When the conventional quadrature method is used to determine the intrinsic scatter in M ?, our data set shows weak evidence for increased scatter at M bulge < 1011 M ? or LV < 1010.3 L ?, while the scatter stays constant for 1011 < M bulge < 1012.3 M ? and 1010.3 < LV < 1011.5 L ?. A Bayesian analysis indicates that a larger sample of M ? measurements would be needed to detect any statistically significant trend in the scatter with galaxy properties.

Large-scale genotyping identifies 41 new loci associated with breast cancer risk

Abstract: Breast cancer is the most common cancer among women Common variants at 27 loci have been identified as associated with susceptibility to breast cancer, and these account for ∼9% of the familial risk of the disease We report here a meta-analysis of 9 genome-wide association studies, including 10,052 breast cancer cases and 12,575 controls of European ancestry, from which we selected 29,807 SNPs for further genotyping These SNPs were genotyped in 45,290 cases and 41,880 controls of European ancestry from 41 studies in the Breast Cancer Association Consortium (BCAC) The SNPs were genotyped as part of a collaborative genotyping experiment involving four consortia (Collaborative Oncological Gene-environment Study, COGS) and used a custom Illumina iSelect genotyping array, iCOGS, comprising more than 200,000 SNPs We identified SNPs at 41 new breast cancer susceptibility loci at genome-wide significance (P < 5 × 10(-8)) Further analyses suggest that more than 1,000 additional loci are involved in breast cancer susceptibility

Prevalence of Earth-size planets orbiting Sun-like stars

Abstract: Determining whether Earth-like planets are common or rare looms as a touchstone in the question of life in the universe. We searched for Earth-size planets that cross in front of their host stars by examining the brightness measurements of 42,000 stars from National Aeronautics and Space Administration’s Kepler mission. We found 603 planets, including 10 that are Earth size () and receive comparable levels of stellar energy to that of Earth (). We account for Kepler’s imperfect detectability of such planets by injecting synthetic planet–caused dimmings into the Kepler brightness measurements and recording the fraction detected. We find that 11 ± 4% of Sun-like stars harbor an Earth-size planet receiving between one and four times the stellar intensity as Earth. We also find that the occurrence of Earth-size planets is constant with increasing orbital period (P), within equal intervals of logP up to ∼200 d. Extrapolating, one finds % of Sun-like stars harbor an Earth-size planet with orbital periods of 200–400 d.

The critical role of extreme heat for maize production in the United States

Abstract: Statistical studies of rainfed maize yields in the United States(1) and elsewhere(2) have indicated two clear features: a strong negative yield response to accumulation of temperatures above 30 degrees C (or extreme degree days (EDD)), and a relatively weak response to seasonal rainfall. Here we show that the process-based Agricultural Production Systems Simulator (APSIM) is able to reproduce both of these relationships in the Midwestern United States and provide insight into underlying mechanisms. The predominant effects of EDD in APSIM are associated with increased vapour pressure deficit, which contributes to water stress in two ways: by increasing demand for soil water to sustain a given rate of carbon assimilation, and by reducing future supply of soil water by raising transpiration rates. APSIM computes daily water stress as the ratio of water supply to demand, and during the critical month of July this ratio is three times more responsive to 2 degrees C warming than to a 20% precipitation reduction. The results suggest a relatively minor role for direct heat stress on reproductive organs at present temperatures in this region. Effects of elevated CO2 on transpiration efficiency should reduce yield sensitivity to EDD in the coming decades, but at most by 25%.

Observation of a charged charmoniumlike structure in e+ e- → (D* D*)± π∓ at √s = 4.26 GeV.

Abstract: We study the process e(+)e(-) -> pi(+)pi(-) J/psi at a center-of-mass energy of 4.260 GeV using a 525 pb(-1) data sample collected with the BESIII detector operating at the Beijing Electron Positron Collider. The Born cross section is measured to be (62.9 +/- 1.9 +/- 3.7) pb, consistent with the production of the Y(4260). We observe a structure at around 3.9 GeV/c(2) in the pi(+/-) J/psi mass spectrum, which we refer to as the Z(c)(3900). If interpreted as a new particle, it is unusual in that it carries an electric charge and couples to charmonium. A fit to the pi(+/-) J/psi invariant mass spectrum, neglecting interference, results in a mass of (3899.0 +/- 3.6 +/- 4.9) MeV/c(2) and a width of (46 +/- 10 +/- 20) MeV. Its production ratio is measured to be R = (sigma(e(+)e(-) -> pi(+/-) Z(c)(3900)(-/+) -> pi(+)pi(-) J/psi)/sigma(e(+)e(-) -> pi(+)pi(-) J/psi)) = (21.5 +/- 3.3 +/- 7.5)%. In all measurements the first errors are statistical and the second are systematic.

A Review on Recent Advances in Doppler Radar Sensors for Noncontact Healthcare Monitoring

Abstract: This paper reviews recent advances in biomedical and healthcare applications of Doppler radar that remotely detects heartbeat and respiration of a human subject. In the last decade, new front-end architectures, baseband signal processing methods, and system-level integrations have been proposed by many researchers in this field to improve the detection accuracy and robustness. The advantages of noncontact detection have drawn interests in various applications, such as energy smart home, baby monitor, cardiopulmonary activity assessment, and tumor tracking. While many of the reported systems were bench-top prototypes for concept verification, several portable systems and integrated radar chips have been demonstrated. This paper reviews different architectures, baseband signal processing, and system implementations. Validations of this technology in a clinical environment will also be discussed.

Insights into bilaterian evolution from three spiralian genomes

Abstract: Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology1, 2, 3. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.

Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array

Abstract: Prostate cancer is the most frequently diagnosed cancer in males in developed countries. To identify common prostate cancer susceptibility alleles, we genotyped 211,155 SNPs on a custom Illumina array (iCOGS) in blood DNA from 25,074 prostate cancer cases and 24,272 controls from the international PRACTICAL Consortium. Twenty-three new prostate cancer susceptibility loci were identified at genome-wide significance (P < 5 × 10(-8)). More than 70 prostate cancer susceptibility loci, explaining ∼30% of the familial risk for this disease, have now been identified. On the basis of combined risks conferred by the new and previously known risk loci, the top 1% of the risk distribution has a 4.7-fold higher risk than the average of the population being profiled. These results will facilitate population risk stratification for clinical studies.

Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer

Abstract: TERT-locus SNPs and leukocyte telomere measures are reportedly associated with risks of multiple cancers. Using the Illumina custom genotyping array iCOG, we analyzed similar to 480 SNPs at the TERT locus in breast (n = 103,991), ovarian (n = 39,774) and BRCA1 mutation carrier (n = 11,705) cancer cases and controls. Leukocyte telomere measurements were also available for 53,724 participants. Most associations cluster into three independent peaks. The minor allele at the peak 1 SNP rs2736108 associates with longer telomeres (P = 5.8 x 10(-7)), lower risks for estrogen receptor (ER)-negative (P = 1.0 x 10(-8)) and BRCA1 mutation carrier (P = 1.1 x 10(-5)) breast cancers and altered promoter assay signal. The minor allele at the peak 2 SNP rs7705526 associates with longer telomeres (P = 2.3 x 10(-14)), higher risk of low-malignant-potential ovarian cancer (P = 1.3 x 10(-15)) and greater promoter activity. The minor alleles at the peak 3 SNPs rs10069690 and rs2242652 increase ER-negative (P = 1.2 x 10(-12)) and BRCA1 mutation carrier (P = 1.6 x 10-14) breast and invasive ovarian (P = 1.3 x 10(-11)) cancer risks but not via altered telomere length. The cancer risk alleles of rs2242652 and rs10069690, respectively, increase silencing and generate a truncated TERT splice variant.

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition.

Abstract: Although the function of DNA methylation in gene promoter regions is well established in transcriptional repression, the function of the evolutionarily conserved widespread distribution of DNA methylation in gene body regions remains incompletely understood. Here, we show that DNA methylation is enriched in included alternatively spliced exons (ASEs), and that inhibition of DNA methylation results in aberrant splicing of ASEs. The methyl-CpG-binding protein MeCP2 is enriched in included ASEs, particularly those that are also highly methylated, and inhibition of DNA methylation disrupts specific targeting of MeCP2 to exons. Interestingly, ablation of MeCP2 results in increased histone acetylation and aberrant ASE-skipping events. We further show that inhibition of histone deacetylase (HDAC) activity leads to exon skipping that shows a highly significant degree of overlap with that caused by MeCP2 knockdown. Together, our data indicate that intragenic DNA methylation operates in exon definition to modulate alternative RNA splicing and can enhance exon recognition via recruitment of the multifunctional protein MeCP2, which thereby maintains local histone hypoacetylation through the subsequent recruitment of HDACs.

Subtropical High predictability establishes a promising way for monsoon and tropical storm predictions

Abstract: Monsoon rainfall and tropical storms (TSs) impose great impacts on society, yet their seasonal predictions are far from successful. The western Pacific Subtropical High (WPSH) is a prime circulation system affecting East Asian summer monsoon (EASM) and western North Pacific TS activities, but the sources of its variability and predictability have not been established. Here we show that the WPSH variation faithfully represents fluctuations of EASM strength (r = –0.92), the total TS days over the subtropical western North Pacific (r = –0.81), and the total number of TSs impacting East Asian coasts (r = –0.76) during 1979–2009. Our numerical experiment results establish that the WPSH variation is primarily controlled by central Pacific cooling/warming and a positive atmosphere-ocean feedback between the WPSH and the Indo-Pacific warm pool oceans. With a physically based empirical model and the state-of-the-art dynamical models, we demonstrate that the WPSH is highly predictable; this predictability creates a promising way for prediction of monsoon and TS. The predictions using the WPSH predictability not only yields substantially improved skills in prediction of the EASM rainfall, but also enables skillful prediction of the TS activities that the current dynamical models fail. Our findings reveal that positive WPSH–ocean interaction can provide a source of climate predictability and highlight the importance of subtropical dynamics in understanding monsoon and TS predictability.

A 500-kiloton airburst over Chelyabinsk and an enhanced hazard from small impactors

Abstract: The damage caused by the asteroid 17–20 metres in diameter that exploded over Chelyabinsk, Russia, on 15 February 2013 is estimated here to have an energy equivalent to about 500 kilotons of TNT. The fireball that streaked across the skies above Chelyabinsk in Russia on 15 February 2013 is providing astronomers with a wealth of information. Two papers in this issue present detailed reconstructions of the Chelyabinsk event. From an analysis of videos, Jiři Borovicka et al. determined the trajectory and velocity of the superbolide with high precision. Its orbit was similar to that of the 2-kilometre-diameter asteroid 86039 (1999 NC43), suggesting that the two bodies may be part of the same asteroid family. And they show that it broke into small pieces between the altitudes of 45 and 30 kilometres. In the companion paper, Peter Brown et al. analysed the damage caused by the airburst which they estimate was equivalent in energy to the detonation of 400 to 600 kilotons of TNT. They suggest that the number of impactors with diameters of tens of metres was an order of magnitude higher than current estimates, shifting much of the residual impact risk to these sizes. Most large (over a kilometre in diameter) near-Earth asteroids are now known, but recognition that airbursts (or fireballs resulting from nuclear-weapon-sized detonations of meteoroids in the atmosphere) have the potential to do greater damage1 than previously thought has shifted an increasing portion of the residual impact risk (the risk of impact from an unknown object) to smaller objects2. Above the threshold size of impactor at which the atmosphere absorbs sufficient energy to prevent a ground impact, most of the damage is thought to be caused by the airburst shock wave3, but owing to lack of observations this is uncertain4,5. Here we report an analysis of the damage from the airburst of an asteroid about 19 metres (17 to 20 metres) in diameter southeast of Chelyabinsk, Russia, on 15 February 2013, estimated to have an energy equivalent of approximately 500 (±100) kilotons of trinitrotoluene (TNT, where 1 kiloton of TNT = 4.185×1012 joules). We show that a widely referenced technique4,5,6 of estimating airburst damage does not reproduce the observations, and that the mathematical relations7 based on the effects of nuclear weapons—almost always used with this technique—overestimate blast damage. This suggests that earlier damage estimates5,6 near the threshold impactor size are too high. We performed a global survey of airbursts of a kiloton or more (including Chelyabinsk), and find that the number of impactors with diameters of tens of metres may be an order of magnitude higher than estimates based on other techniques8,9. This suggests a non-equilibrium (if the population were in a long-term collisional steady state the size-frequency distribution would either follow a single power law or there must be a size-dependent bias in other surveys) in the near-Earth asteroid population for objects 10 to 50 metres in diameter, and shifts more of the residual impact risk to these sizes.

Genome-wide association studies identify four ER negative-specific breast cancer risk loci

Abstract: Estrogen receptor (ER)-negative tumors represent 20-30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry. The etiology and clinical behavior of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), 2p24.1 (P = 4.6 × 10(-8)) and 16q12.2 (FTO, P = 4.0 × 10(-8)), were associated with ER-negative but not ER-positive breast cancer (P > 0.05). These findings provide further evidence for distinct etiological pathways associated with invasive ER-positive and ER-negative breast cancers.

The Complexity of Context: A Service Ecosystems Approach for International Marketing:

Abstract: To strengthen the theoretical foundations of international marketing (IM), the authors propose a framework for conceptualizing the complexity of the context that frames international and global exchange systems. In particular, they apply a service ecosystems approach, which is grounded in service-dominant logic and its foundational premise that service is the basis of all exchange. The proposed framework provides insight into the nature of context, a distinguishing feature of IM. The authors argue that the embeddedness of social networks and the multiplicity of institutions within a service ecosystem influence the complexity of context. They articulate the way the (co)creation of value influences and is influenced by the enactment of practices and the integration of resources through various levels (micro, meso, and macro) of interaction and institutions. They introduce the concept of “value in cultural context” to emphasize the influence of the symbolic and social components of context. The arti...

Observation of a Charged Charmoniumlike Structure Z(c) (4020) and Search for the Z(c) (3900) in e(+)e(-) -> pi(+) pi(-)h(c)

Abstract: We study e(+)e(-) -> pi(+) pi(-)h(c) at center-of-mass energies from 3.90 to 4.42 GeV by using data samples collected with the BESIII detector operating at the Beijing Electron Positron Collider. The Born cross sections are measured at 13 energies and are found to be of the same order of magnitude as those of e(+)e(-) -> pi(+) pi(-) J/Psi but with a different line shape. In the pi(+/-)h(c) mass spectrum, a distinct structure, referred to as Z(c)(4020) is observed at 4. 02 GeV/c(2). The Z(c)(4020) carries an electric charge and couples to charmonium. A fit to the pi(+/-)h(c) invariant mass spectrum, neglecting possible interferences, results in a mass of (4022.9 +/- 0.8 +/- 2.7) MeV/c(2) and a width of (7.9 +/- 2.7 +/- 2.6) MeV for the Z(c)(4020), where the first errors are statistical and the second systematic. The difference between the parameters of this structure and the Z(c) (4025) observed in the D*(D) over bar* final state is within 1.5 sigma, but whether they are the same state needs further investigation. No significant Z(c)(3900) signal is observed, and upper limits on the Z(c)(3900) production cross sections in pi +/- h(c) at center-of-mass energies of 4.23 and 4.26 GeVare set.

The epidemiology of hepatitis C virus in Egypt: a systematic review and data synthesis.

Abstract: Egypt has the highest prevalence of hepatitis C virus (HCV) in the world, estimated nationally at 14.7%. Our study’s objective was to delineate the evidence on the epidemiology of HCV infection among the different population groups in Egypt, and to draw analytical inferences about the nature of HCV transmission in this country. We conducted a systematic review of all data on HCV prevalence and incidence in Egypt following PRISMA guidelines. The main sources of data included PubMed and Embase databases. We also used a multivariate regression model to infer the temporal trend of HCV prevalence among the general population and high risk population in Egypt. We identified 150 relevant records, four of which were incidence studies. HCV incidence ranged from 0.8 to 6.8 per 1,000 person-years. Overall, HCV prevalence among pregnant women ranged between 5-15%, among blood donors between 5-25%, and among other general population groups between 0-40%. HCV prevalence among multi-transfused patients ranged between 10-55%, among dialysis patients between 50-90%, and among other high risk populations between 10% and 85%. HCV prevalence varied widely among other clinical populations and populations at intermediate risk. Risk factors appear to be parenteral anti-schistosomal therapy, injections, transfusions, and surgical procedures, among others. Results of our time trend analysis suggest that there is no evidence of a statistically significant decline in HCV prevalence over time in both the general population (p-value: 0.215) and high risk population (p-value: 0.426). Egypt is confronted with an HCV disease burden of historical proportions that distinguishes this nation from others. A massive HCV epidemic at the national level must have occurred with substantial transmission still ongoing today. HCV prevention in Egypt must become a national priority. Policymakers, and public health and medical care stakeholders need to introduce and implement further prevention measures targeting the routes of HCV transmission.

El Niño modulations over the past seven centuries

Abstract: The El Nino/Southern Oscillation exhibits considerable natural variability on interdecadal to centennial timescales making it difficult to understand how climate change affects it. A reconstruction now shows there has been anomalously high activity in the late twentieth century, relative to the past seven centuries. This is suggestive of a response to global warming, and will provide constraints to improve climate models and projections.

GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer

Abstract: Genome-wide association studies (GWAS) have identified four susceptibility loci for epithelial ovarian cancer (EOC), with another two suggestive loci reaching near genome-wide significance. We pooled data from a GWAS conducted in North America with another GWAS from the UK. We selected the top 24,551 SNPs for inclusion on the iCOGS custom genotyping array. We performed follow-up genotyping in 18,174 individuals with EOC (cases) and 26,134 controls from 43 studies from the Ovarian Cancer Association Consortium. We validated the two loci at 3q25 and 17q21 that were previously found to have associations close to genome-wide significance and identified three loci newly associated with risk: two loci associated with all EOC subtypes at 8q21 (rs11782652, P = 5.5 × 10(-9)) and 10p12 (rs1243180, P = 1.8 × 10(-8)) and another locus specific to the serous subtype at 17q12 (rs757210, P = 8.1 × 10(-10)). An integrated molecular analysis of genes and regulatory regions at these loci provided evidence for functional mechanisms underlying susceptibility and implicated CHMP4C in the pathogenesis of ovarian cancer.

Northern Hemisphere summer monsoon intensified by mega-El Niño/southern oscillation and Atlantic multidecadal oscillation

Abstract: Prediction of monsoon changes in the coming decades is important for infrastructure planning and sustainable economic development. The decadal prediction involves both natural decadal variability and anthropogenic forcing. Hitherto, the causes of the decadal variability of Northern Hemisphere summer monsoon (NHSM) are largely unknown because the monsoons over Asia, West Africa, and North America have been studied primarily on a regional basis, which is unable to identify coherent decadal changes and the overriding controls on planetary scales. Here, we show that, during the recent global warming of about 0.4 °C since the late 1970s, a coherent decadal change of precipitation and circulation emerges in the entirety of the NHSM system. Surprisingly, the NHSM as well as the Hadley and Walker circulations have all shown substantial intensification, with a striking increase of NHSM rainfall by 9.5% per degree of global warming. This is unexpected from recent theoretical prediction and model projections of the 21st century. The intensification is primarily attributed to a mega-El Nino/Southern Oscillation (a leading mode of interannual-to-interdecadal variation of global sea surface temperature) and the Atlantic Multidecadal Oscillation, and further influenced by hemispherical asymmetric global warming. These factors driving the present changes of the NHSM system are instrumental for understanding and predicting future decadal changes and determining the proportions of climate change that are attributable to anthropogenic effects and long-term internal variability in the complex climate system.

Genome of the long-living sacred lotus ( Nelumbo nucifera Gaertn.)

Abstract: Background: Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan. Results: The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101× and 5.2×. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment. Conclusions: The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.

Slowly fading super-luminous supernovae that are not pair-instability explosions

Abstract: Super-luminous supernovae(1-4) that radiate more than 1044 ergs per second at their peak luminosity have recently been discovered in faint galaxies at redshifts of 0.1-4. Some evolve slowly, resembling models of 'pair-instability' supernovae(5,6). Such models involve stars with original masses 140-260 times that of the Sun that now have carbon-oxygen cores of 65-130 solar masses. In these stars, the photons that prevent gravitational collapse are converted to electron-positron pairs, causing rapid contraction and thermonuclear explosions. Many solar masses of Ni-56 are synthesized; this isotope decays to Fe-56 via Co-56, powering bright light curves(7,8). Such massive progenitors are expected to have formed from metal-poor gas in the early Universe(9). Recently, supernova 2007bi in a galaxy at redshift 0.127 (about 12 billion years after the Big Bang) with a metallicity one-third that of the Sun was observed to look like a fading pair-instability supernova(1,10). Here we report observations of two slow-to-fade super-luminous supernovae that show relatively fast rise times and blue colours, which are incompatible with pair-instability models. Their late-time light-curve and spectral similarities to supernova 2007bi call the nature of that event into question. Our early spectra closely resemble typical fast-declining super-luminous supernovae(2,11,12), which are not powered by radio-activity. Modelling our observations with 10-16 solar masses of magnetar-energized(13,14) ejecta demonstrates the possibility of a common explosion mechanism. The lack of unambiguous nearby pair-instability events suggests that their local rate of occurrence is less than 6 x 10(-6) times that of the core-collapse rate.

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Abstract: Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species’ physiological capacities to withstand extreme anoxia and tissue freezing. Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. Conclusions: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle’s extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

Patterns of the seasonal response of tropical rainfall to global warming

Abstract: The response of tropical precipitation to global warming varies spatially and the factors controlling the spatial patterns of precipitation changes are unclear. An analysis of climate model simulations shows that warm regions are projected to become wetter in annual mean, whereas seasonally high rainfall anomalies are expected in regions that are currently wet.

Emplacement of continental flood basalt lava flows

Abstract: We propose that continental flood basalt (CFB) lavas were predominantly emplaced as inflated compound pahoehoe flow fields via prolonged, episodic eruptions Our most detailed observations come from the ∼14,7 Ma Roza flow field of the Columbia River Basalt (CRB) Group The Roza flow field seems to be typical of many flood basalt lavas Individual flows show a wide range of pahoehoe surface features and a three-part internal structure in vesicularity and other textural parameters This three-fold division into an upper crust, core, and basal crust appears to be diagnostic of the inflation process and is ubiquitous in basaltic lava flows over a remarkable range of sizes The pahoehoe surface features and indications of inflation are inconsistent with rapid emplacement of these lava flows Instead, we interpret the observations to imply that the Roza, and other CFB flows, were emplaced over an extended period of time From the thickness of the upper crust, which we suggest formed while the flow was actively inflating, and an empirical expression for the rate of crust growth of Hawaiian inflated sheet flows, we estimate that individual Roza flows were emplaced over 5 to 50 months and that the Roza flow field was constructed over a period of 6 to 14 years However, even with this longer eruption duration, the average lava effusion rate of ∼4000 m 3 /s is similar to that of the highest-effusion-rate eruption in recorded history (the 1783-4 Laki eruption in Iceland) Our observations of lava characteristics in other CRB flows and in the Deccan Traps suggest that this emplacement style is typical of many, if not most, CFB flows Initial estimates of the volatile release from the Roza eruption indicate that prodigious amounts of S, Cl, and F were injected into the upper troposphere and lowermost stratosphere; thus this single flood basalt eruption could have had a significant effect on the global atmosphere If other flood basalt eruptions produced similar amounts of volatiles, volatile release might provide a link between flood basalt eruptions and mass extinctions

Classical and quantum superintegrability with applications

Abstract: A superintegrable system is, roughly speaking, a system that allows more integrals of motion than degrees of freedom. This review is devoted to finite dimensional classical and quantum superintegrable systems with scalar potentials and integrals of motion that are polynomials in the momenta. We present a classification of second-order superintegrable systems in two-dimensional Riemannian and pseudo-Riemannian spaces. It is based on the study of the quadratic algebras of the integrals of motion and on the equivalence of different systems under coupling constant metamorphosis. The determining equations for the existence of integrals of motion of arbitrary order in real Euclidean space E2 are presented and partially solved for the case of third-order integrals. A systematic exposition is given of systems in two and higher dimensional space that allow integrals of arbitrary order. The algebras of integrals of motions are not necessarily quadratic but close polynomially or rationally. The relation between superintegrability and the classification of orthogonal polynomials is analyzed.