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Showing papers by "University of Hawaii at Manoa published in 2009"


Journal ArticleDOI
Patrick S. Schnable1, Doreen Ware2, Robert S. Fulton3, Joshua C. Stein2  +156 moreInstitutions (18)
20 Nov 2009-Science
TL;DR: The sequence of the maize genome reveals it to be the most complex genome known to date and the correlation of methylation-poor regions with Mu transposon insertions and recombination and how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state is reported.
Abstract: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

3,761 citations


Journal ArticleDOI
25 Nov 2009-Cell
TL;DR: Reduction of lysyl oxidase-mediated collagen crosslinking prevented MMTV-Neu-induced fibrosis, decreased focal adhesions and PI3K activity, impeded malignancy, and lowered tumor incidence, and data show how collagenCrosslinking can modulate tissue fibrosis and stiffness to force focal adhesion, growth factor signaling and breast malignancies.

3,396 citations


Journal ArticleDOI
TL;DR: In this paper, two types of El Nino events are classified based on spatial patterns of the sea surface temperature (SST) anomaly, namely cold tongue (CT) and warm pool (WP) events.
Abstract: In this study, two types of El Nino events are classified based on spatial patterns of the sea surface temperature (SST) anomaly. One is the cold tongue (CT) El Nino, which can be regarded as the conventional El Nino, and the other the warm pool (WP) El Nino. The CT El Nino is characterized by relatively large SST anomalies in the Nino-3 region (5°S–5°N, 150°–90°W), while the WP El Nino is associated with SST anomalies mostly confined to the Nino-4 region (5°S–5°N, 160°E–150°W). In addition, spatial patterns of many atmospheric and oceanic variables are also distinctively different for the two types of El Nino events. Furthermore, the difference in the transition mechanism between the two types of El Nino is clearly identified. That is, the discharge process of the equatorial heat content associated with the WP El Nino is not efficient owing to the spatial structure of SST anomaly; as a result, it cannot trigger a cold event. It is also demonstrated that zonal advective feedback (i.e., zonal adve...

1,144 citations


Journal ArticleDOI
TL;DR: This paper found that countries with higher literacy rate, better institutions, higher per capita income, higher degree of openness to trade, and higher levels of government spending are better able to withstand the initial disaster shock and prevent further spillovers into the macro-economy.

987 citations


Journal ArticleDOI
TL;DR: In this paper, the authors evaluate black carbon (BC) model predictions from the AeroCom model intercomparison project by considering the diversity among year 2000 model simulations and comparing model predictions with available measurements.
Abstract: . We evaluate black carbon (BC) model predictions from the AeroCom model intercomparison project by considering the diversity among year 2000 model simulations and comparing model predictions with available measurements. These model-measurement intercomparisons include BC surface and aircraft concentrations, aerosol absorption optical depth (AAOD) retrievals from AERONET and Ozone Monitoring Instrument (OMI) and BC column estimations based on AERONET. In regions other than Asia, most models are biased high compared to surface concentration measurements. However compared with (column) AAOD or BC burden retreivals, the models are generally biased low. The average ratio of model to retrieved AAOD is less than 0.7 in South American and 0.6 in African biomass burning regions; both of these regions lack surface concentration measurements. In Asia the average model to observed ratio is 0.7 for AAOD and 0.5 for BC surface concentrations. Compared with aircraft measurements over the Americas at latitudes between 0 and 50N, the average model is a factor of 8 larger than observed, and most models exceed the measured BC standard deviation in the mid to upper troposphere. At higher latitudes the average model to aircraft BC ratio is 0.4 and models underestimate the observed BC loading in the lower and middle troposphere associated with springtime Arctic haze. Low model bias for AAOD but overestimation of surface and upper atmospheric BC concentrations at lower latitudes suggests that most models are underestimating BC absorption and should improve estimates for refractive index, particle size, and optical effects of BC coating. Retrieval uncertainties and/or differences with model diagnostic treatment may also contribute to the model-measurement disparity. Largest AeroCom model diversity occurred in northern Eurasia and the remote Arctic, regions influenced by anthropogenic sources. Changing emissions, aging, removal, or optical properties within a single model generated a smaller change in model predictions than the range represented by the full set of AeroCom models. Upper tropospheric concentrations of BC mass from the aircraft measurements are suggested to provide a unique new benchmark to test scavenging and vertical dispersion of BC in global models.

558 citations


Journal ArticleDOI
TL;DR: In this article, a longitudinal study examines the effects of distributed leadership on school improvement and growth in student math achievement in 195 elementary schools in one state over a 4-year period.
Abstract: Although there has been sizable growth in the number of empirical studies of shared forms of leadership over the past decade, the bulk of this research has been descriptive. Relatively few published studies have investigated the impact of shared leadership on school improvement. This longitudinal study examines the effects of distributed leadership on school improvement and growth in student math achievement in 195 elementary schools in one state over a 4-year period. Using multilevel latent change analysis, the research found significant direct effects of distributed leadership on change in the schools’ academic capacity and indirect effects on student growth rates in math. The study supports a perspective on distributed leadership that aims at building the academic capacity of schools as a means of improving student learning outcomes.

514 citations


Journal ArticleDOI
TL;DR: In this article, the authors present a best evidence synthesis of the published evidence on the burden and determinants of neck pain and its associated disorders in the general population, concluding that "neck pain is common and is more prevalent among women and prevalence peaked in middle age".

508 citations


Journal ArticleDOI
TL;DR: The feasibility of a new approach to magnetic recording based on shingled writing and two-dimensional readback and signal-processing and the significant challenges that must be overcome are examined.
Abstract: This paper proposes a new approach to magnetic recording based on shingled writing and two-dimensional readback and signal-processing. This approach continues the use of conventional granular media but proposes techniques such that a substantial fraction of one bit of information is stored on each grain. Theoretically, areal-densities of the order of 10 Terabits per square inch may be achievable. In this paper we examine the feasibility of this two-dimensional magnetic recording (TDMR) and identify the significant challenges that must be overcome to achieve this vision.

504 citations


Journal ArticleDOI
TL;DR: In this article, the capacity fading of an 18650 LiFePO4-based lithium ion cell was studied using the dynamic stress test (DST) schedule in a cycle life evaluation.

503 citations


Journal ArticleDOI
Shahana Ahmed1, Gilles Thomas2, Maya Ghoussaini1, Catherine S. Healey1, Manjeet K. Humphreys1, Radka Platte1, Jonathan J. Morrison1, Melanie Maranian1, Karen A. Pooley1, Robert Luben1, Diana Eccles3, D. Gareth Evans4, Olivia Fletcher, Nichola Johnson, Isabel dos Santos Silva, Julian Peto, Michael R. Stratton5, Nazneen Rahman, Kevin B. Jacobs2, Kevin B. Jacobs6, Ross L. Prentice7, Garnet L. Anderson7, Aleksandar Rajkovic8, J. David Curb9, Regina G. Ziegler2, Christine D. Berg2, Saundra S. Buys10, Catherine A. McCarty11, Heather Spencer Feigelson12, Eugenia E. Calle12, Michael J. Thun12, W. Ryan Diver12, Stig E. Bojesen13, Børge G. Nordestgaard13, Henrik Flyger13, Thilo Dörk14, Peter Schürmann14, Peter Hillemanns14, Johann H. Karstens14, Natalia Bogdanova14, Natalia Antonenkova, Iosif V. Zalutsky, Marina Bermisheva14, S. A. Fedorova15, Elza Khusnutdinova, Daehee Kang16, Keun-Young Yoo16, Dong Young Noh16, Sei Hyun Ahn16, Peter Devilee17, Christi J. van Asperen17, R.A.E.M. Tollenaar17, Caroline Seynaeve18, Montserrat Garcia-Closas2, Jolanta Lissowska19, Louise A. Brinton2, Beata Peplonska20, Heli Nevanlinna21, Tuomas Heikkinen21, Kristiina Aittomäki21, Carl Blomqvist21, John L. Hopper22, Melissa C. Southey22, Letitia D. Smith23, Amanda B. Spurdle23, Marjanka K. Schmidt24, Annegien Broeks24, Richard van Hien24, Sten Cornelissen24, Roger L. Milne25, Gloria Ribas25, Anna González-Neira25, Javier Benitez25, Rita K. Schmutzler26, Barbara Burwinkel27, Barbara Burwinkel28, Claus R. Bartram28, Alfons Meindl29, Hiltrud Brauch30, Hiltrud Brauch31, Christina Justenhoven30, Christina Justenhoven31, Ute Hamann27, Jenny Chang-Claude27, Rebecca Hein27, Shan Wang-Gohrke32, Annika Lindblom33, Sara Margolin33, Arto Mannermaa34, Veli-Matti Kosma34, Vesa Kataja34, Janet E. Olson35, Xianshu Wang35, Zachary S. Fredericksen35, Graham G. Giles36, Graham G. Giles22, Gianluca Severi36, Gianluca Severi22, Laura Baglietto22, Laura Baglietto36, Dallas R. English22, Dallas R. English25, Susan E. Hankinson37, David G. Cox37, Peter Kraft37, Lars J. Vatten38, Kristian Hveem38, Merethe Kumle, Alice J. Sigurdson2, Michele M. Doody2, Parveen Bhatti2, Bruce H. Alexander39, Maartje J. Hooning18, Ans M.W. van den Ouweland18, Rogier A. Oldenburg18, Mieke Schutte18, Per Hall33, Kamila Czene33, Jianjun Liu40, Yuqing Li40, Angela Cox41, Graeme Elliott41, Ian W. Brock41, Malcolm W.R. Reed41, Chen-Yang Shen42, Chen-Yang Shen43, Jyh Cherng Yu44, Giu Cheng Hsu44, Shou Tung Chen, Hoda Anton-Culver45, Argyrios Ziogas45, Irene L. Andrulis46, Julia A. Knight46, Jonathan Beesley23, Ellen L. Goode35, Fergus J. Couch35, Georgia Chenevix-Trench23, Robert N. Hoover2, Bruce A.J. Ponder47, Bruce A.J. Ponder1, David J. Hunter37, Paul D.P. Pharoah1, Alison M. Dunning1, Stephen J. Chanock2, Douglas F. Easton1 
TL;DR: Strong evidence is found for additional susceptibility loci on 3p and 17q and potential causative genes include SLC4A7 and NEK10 on3p and COX11 on 17q.
Abstract: Genome-wide association studies (GWAS) have identified seven breast cancer susceptibility loci, but these explain only a small fraction of the familial risk of the disease. Five of these loci were identified through a two-stage GWAS involving 390 familial cases and 364 controls in the first stage, and 3,990 cases and 3,916 controls in the second stage. To identify additional loci, we tested over 800 promising associations from this GWAS in a further two stages involving 37,012 cases and 40,069 controls from 33 studies in the CGEMS collaboration and Breast Cancer Association Consortium. We found strong evidence for additional susceptibility loci on 3p (rs4973768: per-allele OR = 1.11, 95% CI = 1.08-1.13, P = 4.1 x 10(-23)) and 17q (rs6504950: per-allele OR = 0.95, 95% CI = 0.92-0.97, P = 1.4 x 10(-8)). Potential causative genes include SLC4A7 and NEK10 on 3p and COX11 on 17q.

480 citations



Journal ArticleDOI
TL;DR: This review summarizes recent insights into properties of individual selenoproteins such as tissue distribution, subcellular localization, and regulation of expression as well as potential roles the different seleniproteins play in human health and disease.
Abstract: Selenium (Se) is a nutritional trace mineral essential for various aspects of human health that exerts its effects mainly through its incorporation into selenoproteins as the amino acid, selenocysteine. Twenty-five selenoprotein genes have been identified in humans and several selenoproteins are broadly classified as antioxidant enzymes. As progress is made on characterizing the individual members of this protein family, however, it is becoming clear that their properties and functions are quite diverse. This review summarizes recent insights into properties of individual selenoproteins such as tissue distribution, subcellular localization, and regulation of expression. Also discussed are potential roles the different selenoproteins play in human health and disease.

Journal ArticleDOI
TL;DR: In this article, the authors investigated the mechanisms for the second peak of the tropical Indian Ocean (TIO) sea surface temperature (SST) with a lag of one season.
Abstract: El Nino induces a basin-wide increase in tropical Indian Ocean (TIO) sea surface temperature (SST) with a lag of one season. The north IO (NIO), in particular, displays a peculiar double-peak warming with the second peak larger in magnitude and persisting well through the summer. Motivated by recent studies suggesting the importance of the TIO warming for the Northwest Pacific and East Asian summer monsoons, the present study investigates the mechanisms for the second peak of the NIO warming using observations and general circulation models. This analysis reveals that internal air-sea interaction within the TIO is key to sustaining the TIO warming through summer. During El Nino, anticyclonic wind curl anomalies force a downwelling Rossby wave in the south TIO through Walker circulation adjustments, causing a sustained SST warming in the tropical southwest IO (SWIO) where the mean thermocline is shallow. During the spring and early summer following El Nino, this SWIO warming sustains an antisymmetric pattern of atmospheric anomalies with northeasterly ( northwesterly) wind anomalies north ( south) of the equator. Over the NIO as the mean winds turn into southwesterly in May, the northeasterly anomalies force the second SST peak that persists through summer by reducing the wind speed and surface evaporation. Atmospheric general circulation model experiments show that the antisymmetric atmospheric pattern is a response to the TIO warming, suggestive of their mutual interaction. Thus, ocean dynamics and Rossby waves in particular are important for the warming not only locally in SWIO but also on the basin-scale north of the equator, a result with important implications for climate predictability and prediction.

Journal ArticleDOI
TL;DR: In this article, a service-dominant logic-based conceptualization of relationship is proposed to better understand the role of relationship in value creation and its correspondence to transactions and products.
Abstract: Purpose – The purpose of this paper is to propose and elaborate on a service‐dominant‐logic‐based conceptualization of relationship that transcends traditional conceptualizations.Design/methodology/approach – The paper consists of a review of traditional conceptualizations of relationship, a review of service‐dominant logic foundational premises that are useful in reframing the concept, and supporting views from the institutional economics and business ecosystems literature.Findings – A transcending, service‐dominant‐logic‐based conceptualization of relationship as a general term representing the network‐with‐and‐within‐network nature of value creation, with transactions as “temporal isolates” of relationships is suggested.Originality/value – This higher‐order conceptualization of relationship provides a foundation for better understanding the role of relationship in value creation, as well as its correspondence to transactions and products.

Journal ArticleDOI
TL;DR: Depressed symptoms and suicidal ideation in medical trainees (medical students and residents) are assessed to highlight the importance of ongoing mental health assessment, treatment, and education for medicalTrainees.
Abstract: Background This multisite, anonymous study assessed depressive symptoms and suicidal ideation in medical trainees (medical students and residents). Method In 2003–2004, the authors surveyed medical trainees at six sites. Surveys included content from the Center for Epidemiologic Studies–Depression scale (CES-D) and the Primary Care Evaluation of Mental Disorders (PRIME-MD) (measures for depression), as well as demographic content. Rates of reported major and minor depression and of suicidal ideation were calculated. Responses were compared by level of training, gender, and ethnicity. Results More than 2,000 medical students and residents responded, for an overall response rate of 89%. Based on categorical levels from the CES-D, 12% had probable major depression and 9.2% had probable mild/moderate depression. There were significant differences in depression by trainee level, with a higher rate among medical students; and gender, with higher rates among women ( 2 10.42, df 2, and P .005 and 2 22.1, df 2, and P .001, respectively). Nearly 6% reported suicidal ideation, with differences by trainee level, with a higher rate among medical students; and ethnicity, with the highest rate among black/African American respondents and the lowest among Caucasian respondents ( 2 5.19, df 1, and P .023 and 2 10.42, df 3, and P .015, respectively). Conclusions Depression remains a significant issue for medical trainees. This study highlights the importance of ongoing mental health assessment, treatment, and education for medical trainees.

Journal ArticleDOI
Rosalind A. Eeles1, Zsofia Kote-Jarai, Ali Amin Al Olama2, Graham G. Giles3, Graham G. Giles4, Michelle Guy, Gianluca Severi4, Gianluca Severi3, Kenneth Muir5, John L. Hopper3, Brian E. Henderson6, Christopher A. Haiman6, Johanna Schleutker7, Freddie C. Hamdy8, David E. Neal2, Jenny L Donovan9, Janet L. Stanford10, Janet L. Stanford11, Elaine A. Ostrander12, Sue A. Ingles6, Esther M. John13, Stephen N. Thibodeau14, Daniel J. Schaid14, Jong Y. Park15, Amanda B. Spurdle16, Judith A. Clements17, Joanne L. Dickinson18, Christiane Maier, Walther Vogel, Thilo Dörk19, Timothy R. Rebbeck20, Kathleen A. Cooney21, Lisa A. Cannon-Albright22, Pierre O. Chappuis23, Pierre Hutter, Maurice P. Zeegers24, Radka Kaneva25, Hong Wei Zhang26, Yong-Jie Lu27, William D. Foulkes28, Dallas R. English3, Daniel Leongamornlert, Malgorzata Tymrakiewicz, Jonathan J. Morrison2, Audrey Ardern-Jones1, Amanda L. Hall1, Lynne T. O'Brien, Rosemary A. Wilkinson, Edward J. Saunders, Elizabeth Page1, Emma J. Sawyer, Stephen M. Edwards, David P. Dearnaley1, Alan Horwich1, Robert Huddart1, Vincent Khoo1, Chris Parker1, Nicholas Van As1, C. R. J. Woodhouse1, Alan Thompson1, Tim Christmas1, Chris Ogden1, Colin Cooper, Melissa C. Southey3, Artitaya Lophatananon5, Jo Fen Liu5, Laurence N. Kolonel29, Loic Le Marchand29, Tiina Wahlfors7, Teuvo L.J. Tammela, Anssi Auvinen7, Sarah J Lewis9, Angela Cox30, Liesel M. FitzGerald11, Liesel M. FitzGerald18, Joseph S. Koopmeiners11, Joseph S. Koopmeiners10, Danielle M. Karyadi12, Erika M. Kwon12, Mariana C. Stern6, Roman Corral6, Amit Joshi6, Ahva Shahabi6, Shannon K. McDonnell14, Thomas A. Sellers15, Julio M. Pow-Sang15, Suzanne K. Chambers, Joanne F. Aitken31, Robert A. Gardiner31, Jyotsna Batra17, Mary-Anne Kedda17, Felicity Lose17, Felicity Lose16, Andrea M. Polanowski18, Briony Patterson18, Jürgen Serth19, Andreas Meyer19, Manuel Luedeke, Klara Stefflova20, Anna M. Ray21, Ethan M. Lange32, J. M. Farnham22, Humera Khan33, C. Slavov, Atanaska Mitkova25, Guangwen Cao26, Douglas F. Easton2 
TL;DR: The study is extended to evaluate promising associations in a second stage in which 43,671 SNPs are genotyped in 3,650 PrCa cases and 3,940 controls and in a third stage involving an additional 16,229 cases and 14,821 controls from 21 studies.
Abstract: Prostate cancer (PrCa) is the most frequently diagnosed cancer in males in developed countries To identify common PrCa susceptibility alleles, we previously conducted a genome-wide association study in which 541,129 SNPs were genotyped in 1,854 PrCa cases with clinically detected disease and in 1,894 controls We have now extended the study to evaluate promising associations in a second stage in which we genotyped 43,671 SNPs in 3,650 PrCa cases and 3,940 controls and in a third stage involving an additional 16,229 cases and 14,821 controls from 21 studies In addition to replicating previous associations, we identified seven new prostate cancer susceptibility loci on chromosomes 2, 4, 8, 11 and 22 (with P = 16 x 10(-8) to P = 27 x 10(-33))

Journal ArticleDOI
TL;DR: In this paper, a carbon cycle model was used to constrain the initial carbon pulse to a magnitude of 3,000 C or less, with an isotopic composition lighter than −50‰.
Abstract: About 55 million years ago global surface temperatures increased by 5–9 ∘C within a few thousand years, following a pulse of carbon released to the atmosphere. Analysis of existing data with a carbon cycle model indicates that this carbon pulse was too small to cause the full amount of warming at accepted values for climate sensitivity. The Palaeocene–Eocene Thermal Maximum (about 55 Myr ago) represents a possible analogue for the future and thus may provide insight into climate system sensitivity and feedbacks1,2. The key feature of this event is the release of a large mass of 13C-depleted carbon into the carbon reservoirs at the Earth’s surface, although the source remains an open issue3,4. Concurrently, global surface temperatures rose by 5–9 ∘C within a few thousand years5,6,7,8,9. Here we use published palaeorecords of deep-sea carbonate dissolution10,11,12,13,14 and stable carbon isotope composition10,15,16,17 along with a carbon cycle model to constrain the initial carbon pulse to a magnitude of 3,000 Pg C or less, with an isotopic composition lighter than −50‰. As a result, atmospheric carbon dioxide concentrations increased during the main event by less than about 70% compared with pre-event levels. At accepted values for the climate sensitivity to a doubling of the atmospheric CO2 concentration1, this rise in CO2 can explain only between 1 and 3.5 ∘C of the warming inferred from proxy records. We conclude that in addition to direct CO2 forcing, other processes and/or feedbacks that are hitherto unknown must have caused a substantial portion of the warming during the Palaeocene–Eocene Thermal Maximum. Once these processes have been identified, their potential effect on future climate change needs to be taken into account.

Journal ArticleDOI
TL;DR: This work proposes a comprehensive research agenda for tackling the problem of plant invasions into mountain ecosystems, including documentation of mountain invasion patterns at multiple scales, experimental studies, and an assessment of the impacts of non-native species in these systems.
Abstract: Most studies of invasive species have been in highly modified, lowland environments, with comparatively little attention directed to less disturbed, high-elevation environments. However, increasing evidence indicates that plant invasions do occur in these environments, which often have high conservation value and provide important ecosystem services. Over a thousand non-native species have become established in natural areas at high elevations worldwide, and although many of these are not invasive, some may pose a considerable threat to native mountain ecosystems. Here, we discuss four main drivers that shape plant invasions into high-elevation habitats: (1) the (pre-)adaptation of non-native species to abiotic conditions, (2) natural and anthropogenic disturbances, (3) biotic resistance of the established communities, and (4) propagule pressure. We propose a comprehensive research agenda for tackling the problem of plant invasions into mountain ecosystems, including documentation of mountain invasion patterns at multiple scales, experimental studies, and an assessment of the impacts of non-native species in these systems. The threat posed to high-elevation biodiversity by invasive plant species is likely to increase because of globalization and climate change. However, the higher mountains harbor ecosystems where invasion by non-native species has scarcely begun, and where science and management have the opportunity to respond in time.

Posted Content
TL;DR: In this article, the authors demonstrate that the omission of the previous month's stock returns can lead to a negatively biased estimate of the cross-sectional relation between idiosyncratic risk and expected stock returns.
Abstract: The empirical evidence on the cross-sectional relation between idiosyncratic risk and expected stock returns is mixed. We demonstrate that the omission of the previous month's stock returns can lead to a negatively biased estimate of the relation. The magnitude of the omitted variable bias depends on the approach to estimating the conditional idiosyncratic volatility. Although a negative relation exists when the estimate is based on daily returns, it disappears after return reversals are controlled for. Return reversals can explain both the negative relation between value-weighted portfolio returns and idiosyncratic volatility and the insignificant relation between equal-weighted portfolio returns and idiosyncratic volatility. In contrast, there is a significantly positive relation between the conditional idiosyncratic volatility estimated from monthly data and expected returns. This relation remains robust after controlling for return reversals.

Journal ArticleDOI
TL;DR: Selenoproteins are proteins containing selenium in the form of the 21st amino acid, selenocysteine, which has roles in a variety of cell processes and diseases.
Abstract: Selenoproteins are proteins containing selenium in the form of the 21st amino acid, selenocysteine. Members of this protein family have many diverse functions, but their synthesis is dependent on a common set of cofactors and on dietary selenium. Although the functions of many selenoproteins are unknown, several disorders involving changes in selenoprotein structure, activity or expression have been reported. Selenium deficiency and mutations or polymorphisms in selenoprotein genes and synthesis cofactors are implicated in a variety of diseases, including muscle and cardiovascular disorders, immune dysfunction, cancer, neurological disorders and endocrine function. Members of this unusual family of proteins have roles in a variety of cell processes and diseases.


Journal ArticleDOI
TL;DR: In this article, a season-reliant empirical orthogonal function (S-EOF) analysis is applied to seasonal mean precipitation over East Asia for the period of 1979-2004.
Abstract: A season-reliant empirical orthogonal function (S-EOF) analysis is applied to seasonal mean precipitation over East Asia for the period of 1979-2004. The first two dominant modes account for 44% of the total interannual variance, corresponding to post-ENSO and ENSO turnabout years, respectively. The first mode indicates that in El Nino decaying summer, an anomalous anticyclone appears over the western North Pacific (WNP). This anticyclone is associated with strong positive precipitation anomalies from central China to southern Japan. In the following fall, enhanced convection appears over the WNP as a result of the un- derlying warm SST anomalies caused by the increase of the shortwave radiative flux in the preceding sum- mer. A dry condition appears over southeastern China. The anomalous precipitation pattern persists throughout the subsequent winter and spring. The second mode shows that during the El Nino developing summer the anomalous heating over the equatorial central Pacific forces a cyclonic vorticity over the WNP. This strengthens the WNP monsoon. Meanwhile, an anomalous anticyclone develops in the northern Indian Ocean and moves eastward to the South China Sea and the WNP in the subsequent fall and winter. This leads to the increase of precipitation over southeastern China. The anticyclone and precipitation anomalies are maintained in the following spring through local air-sea interactions. The diagnosis of upper-level velocity potential and midlevel vertical motion fields reveals a season- dependent Indian Ocean forcing scenario. The Indian Ocean basinwide warming during the El Nino mature winter and the subsequent spring does not have a significant impact on anomalous circulation in the WNP, because convection over the tropical Indian Ocean is suppressed by the remote forcing from the equatorial central-eastern Pacific. The basinwide warming plays an active role in impacting the WNP anomalous an- ticyclone during the ENSO decaying summer through atmospheric Kelvin waves or Hadley circulation.

Journal ArticleDOI
23 Apr 2009-PLOS ONE
TL;DR: In this paper, a single cell sequencing approach was used to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms from the Gulf of Maine.
Abstract: The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91% and 78%, respectively. Only 0.24% of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.

Journal ArticleDOI
TL;DR: In this paper, the authors presented extensive early photometric and spectroscopic (optical and near-infrared) data on supernova (SN) 2008D as well as X-ray data analysis on the associated Swift Xray transient (XRT) 080109.
Abstract: We present extensive early photometric (ultraviolet through near-infrared) and spectroscopic (optical and near-infrared) data on supernova (SN) 2008D as well as X-ray data analysis on the associated Swift X-ray transient (XRT) 080109. Our data span a time range of 5 hr before the detection of the X-ray transient to 150days after its detection, and a detailed analysis allowed us to derive constraints on the nature of the SN and its progenitor; throughout we draw comparisons with results presented in the literature and find several key aspects that differ. We show that the X-ray spectrum of XRT 080109 can be fit equally well by an absorbed power law or a superposition of about equal parts of both power law and blackbody. Our data first established that SN 2008D is a spectroscopically normal SN Ib (i.e., showing conspicuous He lines) and showed that SN 2008D had a relatively long rise time of 18days and a modest optical peak luminosity. The early-time light curves of the SN are dominated by a cooling stellar envelope (for Δt0.1-4days, most pronounced in the blue bands) followed by 56Ni decay. We construct a reliable measurement of the bolometric output for this stripped-envelope SN, and, combined with estimates of E K and M ej from the literature, estimate the stellar radius R ⊙ of its probable Wolf-Rayet progenitor. According to the model of Waxman etal. and Chevalier & Fransson, we derive R W07⊙ = 1.2 0.7R ⊙ and R CF08⊙ = 12 7 R ⊙, respectively; the latter being more in line with typical WN stars. Spectra obtained at three and four months after maximum light show double-peaked oxygen lines that we associate with departures from spherical symmetry, as has been suggested for the inner ejecta of a number of SN Ib cores. © 2009. The American Astronomical Society. All rights reserved.

Journal ArticleDOI
TL;DR: The convergence of JSFP to a pure Nash equilibrium in congestion games, or equivalently in finite potential games, when players use some inertia in their decisions and in both cases of with or without exponential discounting of the historical data.
Abstract: We consider multi-player repeated games involving a large number of players with large strategy spaces and enmeshed utility structures. In these ldquolarge-scalerdquo games, players are inherently faced with limitations in both their observational and computational capabilities. Accordingly, players in large-scale games need to make their decisions using algorithms that accommodate limitations in information gathering and processing. This disqualifies some of the well known decision making models such as ldquoFictitious Playrdquo (FP), in which each player must monitor the individual actions of every other player and must optimize over a high dimensional probability space. We will show that Joint Strategy Fictitious Play (JSFP), a close variant of FP, alleviates both the informational and computational burden of FP. Furthermore, we introduce JSFP with inertia, i.e., a probabilistic reluctance to change strategies, and establish the convergence to a pure Nash equilibrium in all generalized ordinal potential games in both cases of averaged or exponentially discounted historical data. We illustrate JSFP with inertia on the specific class of congestion games, a subset of generalized ordinal potential games. In particular, we illustrate the main results on a distributed traffic routing problem and derive tolling procedures that can lead to optimized total traffic congestion.

Journal ArticleDOI
TL;DR: In this article, a universal modeling and simulation approach is presented to show that accurate battery pack simulation can be achieved if cell-to-cell variations were taken into account, using a single cell model, which was validated against experimental data and demonstrated with validity of high accuracy in predicting cell performance.

Journal ArticleDOI
TL;DR: In this article, the effect of diabatic heating in outer spiral rainbands on the storm structure and intensity was studied using the cloud-resolving tropical cyclone model TCM4.
Abstract: A long-standing issue on how outer spiral rainbands affect the structure and intensity of tropical cyclones is studied through a series of numerical experiments using the cloud-resolving tropical cyclone model TCM4. Because diabatic heating due to phase changes is the main driving force of outer spiral rainbands, their effect on the tropical cyclone structure and intensity is evaluated by artificially modifying the heating and cooling rate due to cloud microphysical processes in the model. The view proposed here is that the effect of diabatic heating in outer spiral rainbands on the storm structure and intensity results mainly from hydrostatic adjustment; that is, heating (cooling) of an atmospheric column decreases (increases) the surface pressure underneath the column. The change in surface pressure due to heating in the outer spiral rainbands is significant on the inward side of the rainbands where the inertial stability is generally high. Outside the rainbands in the far field, where the iner...

Journal ArticleDOI
TL;DR: In this article, a depth-integrated, non-hydrostatic model with a semi-implicit finite difference scheme was proposed to model weakly dispersive wave propagation, transformation, breaking, and run-up.
Abstract: This paper describes the formulation, verification, and validation of a depth-integrated, non-hydrostatic model with a semi-implicit, finite difference scheme. The formulation builds on the nonlinear shallow-water equations and utilizes a non-hydrostatic pressure term to describe weakly dispersive waves. A momentum-conserved advection scheme enables modeling of breaking waves without the aid of analytical solutions for bore approximation or empirical equations for energy dissipation. An upwind scheme extrapolates the free-surface elevation instead of the flow depth to provide the flux in the momentum and continuity equations. This greatly improves the model stability, which is essential for computation of energetic breaking waves and run-up. The computed results show very good agreement with laboratory data for wave propagation, transformation, breaking, and run-up. Since the numerical scheme to the momentum and continuity equations remains explicit, the implicit non-hydrostatic solution is directly applicable to existing nonlinear shallow-water models. Copyright © 2008 John Wiley & Sons, Ltd.

Journal ArticleDOI
TL;DR: It is reported that TRPM2, in addition to its role as a plasma membrane channel, also functions as a Ca2+-release channel activated by intracellular ADPR in a lysosomal compartment, which is critically linked to hydrogen peroxide–induced β cell death.
Abstract: TRPM2 is a Ca 2+ -permeable cation channel that is specifically activated by adenosine diphosphoribose (ADPR). Channel activation in the plasma membrane leads to Ca 2+ influx and has been linked to apoptotic mechanisms. The primary agonist, ADPR, is produced both extra- and intracellularly and causes increases in intracellular calcium concentration ([Ca 2+ ] i ), but the mechanisms involved are not understood. Using short interfering RNA and a knockout mouse, we report that TRPM2, in addition to its role as a plasma membrane channel, also functions as a Ca 2+ -release channel activated by intracellular ADPR in a lysosomal compartment. We show that both functions of TRPM2 are critically linked to hydrogen peroxide–induced β cell death. Additionally, extracellular ADPR production by the ectoenzyme CD38 from its substrates NAD + (nicotinamide adenine dinucleotide) or cADPR causes IP 3 -dependent Ca 2+ release via P2Y and adenosine receptors. Thus, ADPR and TRPM2 represent multimodal signaling elements regulating Ca 2+ mobilization in β cells through membrane depolarization, Ca 2+ influx, and release of Ca 2+ from intracellular stores.

Journal ArticleDOI
TL;DR: In this paper, three mean dynamic topography maps derived with different methodologies are presented, combining sea level observed by the high-accuracy satellite radar altimetry with the geoid model of the Gravity Recovery and Climate Experiment (GRACE), which has recently measured the earth's gravity with unprecedented spatial resolution and accuracy.
Abstract: Presented here are three mean dynamic topography maps derived with different methodologies. The first method combines sea level observed by the high-accuracy satellite radar altimetry with the geoid model of the Gravity Recovery and Climate Experiment (GRACE), which has recently measured the earth’s gravity with unprecedented spatial resolution and accuracy. The second one synthesizes near-surface velocities from a network of ocean drifters, hydrographic profiles, and ocean winds sorted according to the horizontal scales. In the third method, these global datasets are used in the context of the ocean surface momentum balance. The second and third methods are used to improve accuracy of the dynamic topography on fine space scales poorly resolved in the first method. When they are used to compute a multiyear time-mean global ocean surface circulation on a 0.5° horizontal resolution, both contain very similar, new small-scale midocean current patterns. In particular, extensions of western boundary c...