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Showing papers by "Stony Brook University published in 2004"


Journal ArticleDOI
TL;DR: Evidence-based recommendations can be made regarding many aspects of the acute management of sepsis and septic shock that will hopefully translate into improved outcomes for the critically ill patient.
Abstract: To develop management guidelines for severe sepsis and septic shock that would be of practical use for the bedside clinician, under the auspices of the Surviving Sepsis Campaign, an international effort to increase awareness and improve outcome in severe sepsis. The process included a modified Delphi method, a consensus conference, several subsequent smaller meetings of subgroups and key individuals, teleconferences, and electronic-based discussion among subgroups and among the entire committee. The modified Delphi methodology used for grading recommendations built upon a 2001 publication sponsored by the International Sepsis Forum. We undertook a systematic review of the literature graded along 5 levels to create recommendation grades from A–E, with A being the highest grade. Pediatric considerations were provided to contrast adult and pediatric management. Participants included 44 critical care and infectious disease experts representing 11 international organizations. A total of 46 recommendations plus pediatric management considerations. Evidence-based recommendations can be made regarding many aspects of the acute management of sepsis and septic shock that will hopefully translate into improved outcomes for the critically ill patient. The impact of these guidelines will be formally tested and guidelines updated annually, and even more rapidly when some important new knowledge becomes available.

3,703 citations


Journal ArticleDOI
03 Dec 2004-Science
TL;DR: The DRM's utility is shown by documenting close correspondences between the DRM reports of 909 employed women and established results from experience sampling, and an analysis of the hedonic treadmill shows its potential for well-being research.
Abstract: The Day Reconstruction Method (DRM) assesses how people spend their time and how they experience the various activities and settings of their lives, combining features of time-budget measurement and experience sampling. Participants systematically reconstruct their activities and experiences of the preceding day with procedures designed to reduce recall biases. The DRM's utility is shown by documenting close correspondences between the DRM reports of 909 employed women and established results from experience sampling. An analysis of the hedonic treadmill shows the DRM's potential for well-being research.

2,933 citations


Journal ArticleDOI
03 Sep 2004-Science
TL;DR: The evidence supports a model in which Argonaute contributes “Slicer” activity to RISC, providing the catalytic engine for RNAi.
Abstract: Gene silencing through RNA interference (RNAi) is carried out by RISC, the RNA-induced silencing complex. RISC contains two signature components, small interfering RNAs (siRNAs) and Argonaute family proteins. Here, we show that the multiple Argonaute proteins present in mammals are both biologically and biochemically distinct, with a single mammalian family member, Argonaute2, being responsible for messenger RNA cleavage activity. This protein is essential for mouse development, and cells lacking Argonaute2 are unable to mount an experimental response to siRNAs. Mutations within a cryptic ribonuclease H domain within Argonaute2, as identified by comparison with the structure of an archeal Argonaute protein, inactivate RISC. Thus, our evidence supports a model in which Argonaute contributes "Slicer" activity to RISC, providing the catalytic engine for RNAi.

2,704 citations


Journal ArticleDOI
23 Jul 2004-Science
TL;DR: It is shown that large-scale copy number polymorphisms (CNPs) (about 100 kilobases and greater) contribute substantially to genomic variation between normal humans.
Abstract: The extent to which large duplications and deletions contribute to human genetic variation and diversity is unknown. Here, we show that large-scale copy number polymorphisms (CNPs) (about 100 kilobases and greater) contribute substantially to genomic variation between normal humans. Representational oligonucleotide microarray analysis of 20 individuals revealed a total of 221 copy number differences representing 76 unique CNPs. On average, individuals differed by 11 CNPs, and the average length of a CNP interval was 465 kilobases. We observed copy number variation of 70 different genes within CNP intervals, including genes involved in neurological function, regulation of cell growth, regulation of metabolism, and several genes known to be associated with disease.

2,572 citations


Journal ArticleDOI
TL;DR: In this article, the prevalence and distribution of age-related macular degeneration (AMD) in the United States by age, race/ethnicity, and gender was estimated.
Abstract: Objective: To estimate the prevalence and distribution of age-related macular degeneration (AMD) in the United States by age, race/ethnicity, and gender.Methods: Summary prevalence estimates of drusen 125 pin or larger, neovascular AMD, and geographic atrophy were prepared separately for black and white persons in 5-year age intervals starting at 40 years. The estimated rates were based on a meta-analysis of recent population-based studies in the United States, Australia, and Europe. These rates were applied to 2000 US Census data and to projected US population figures for 2020 to estimate the number of the US population with drusen and AMD.Results: The overall prevalence of neovascular AMD and/or geographic atrophy in the US population 40 years and older is estimated to be 1.47% (95% confidence interval, 1.38%-1.55%), with 1.75 million citizens having AMD. The prevalence of AMD increased dramatically with age, with more than 15% of the white women older than 80 years having neovascular AMD and/or geographic atrophy. More than 7 million individuals had drusen measuring 125 pin or larger and were, therefore, at substantial risk of developing AMD. Owing to the rapidly aging population, the number of persons having AMD will increase by 50% to 2.95 million in 2020. Age-related macular degeneration was far more prevalent among white than among black persons.Conclusion: Age-related macular degeneration affects more than 1.75 million individuals in the United States. Owing to the rapid aging of the US population, this number will increase to almost 3 million by 2020.

2,389 citations


Journal ArticleDOI
TL;DR: The chasm that has developed between ecology and historical biogeography is described, some of the important questions that have fallen into it and how it might be bridged, and a model that can help explain the latitudinal gradient of species richness is expanded.
Abstract: Ecology and historical (phylogeny-based) biogeography have much to offer one another, but exchanges between these fields have been limited. Historical biogeography has become narrowly focused on using phylogenies to discover the history of geological connections among regions. Conversely, ecologists often ignore historical biogeography, even when its input can be crucial. Both historical biogeographers and ecologists have more-or-less abandoned attempts to understand the processes that determine the large-scale distribution of clades. Here, we describe the chasm that has developed between ecology and historical biogeography, some of the important questions that have fallen into it and how it might be bridged. To illustrate the benefits of an integrated approach, we expand on a model that can help explain the latitudinal gradient of species richness.

1,572 citations


Journal ArticleDOI
TL;DR: The question, are aliens generally responsible for widespread extinctions?
Abstract: The link between species invasions and the extinction of natives is widely accepted by scientists as well as conservationists, but available data supporting invasion as a cause of extinctions are, in many cases, anecdotal, speculative and based upon limited observation. We pose the question, are aliens generally responsible for widespread extinctions? Our goal is to prompt a more critical synthesis and evaluation of the available data, and to suggest ways to take a more scientific, evidence-based approach to understanding the impact of invasive species on extinctions. Greater clarity in our understanding of these patterns will help us to focus on the most effective ways to reduce or mitigate extinction threats from invasive species.

1,390 citations


Journal ArticleDOI
TL;DR: A detailed performance evaluation shows that with intelligent channel and bandwidth assignment, equipping every wireless mesh network node with just 2 NICs operating on different channels can increase the total network goodput by a factor of up to 8 compared with the conventional single-channel ad hoc network architecture.
Abstract: The IEEE 802.11 Wireless LAN standards allow multiple non-overlapping frequency channels to be used simultaneously to increase the aggregate bandwidth available to end-users. Such bandwidth aggregation capability is routinely used in infrastructure mode operation, where the traffic to and from wireless nodes is distributed among multiple interfaces of an access point or among multiple access points to balance the traffic load. However, bandwidth aggregation is rarely used in the context of multi-hop 802.11-based LANs that operate in the ad hoc mode. Most past research efforts that attempt to exploit multiple radio channels require modifications to the MAC protocol and therefore do not work with commodity 802.11 interface hardware. In this paper, we propose and evaluate one of the first multi-channel multi-hop wireless ad-hoc network architectures that can be built using standard 802.11 hardware by equipping each node with multiple network interface cards (NICs) operating on different channels. We focus our attention on wireless mesh networks that serve as the backbone for relaying end-user traffic from wireless access points to the wired network. The idea of exploiting multiple channels is particularly appealing in wireless mesh networks because of their high capacity requirements to support backbone traffic. To reap the full performance potential of this architecture, we develop a set of centralized channel assignment, bandwidth allocation, and routing algorithms for multi-channel wireless mesh networks. A detailed performance evaluation shows that with intelligent channel and bandwidth assignment, equipping every wireless mesh network node with just 2 NICs operating on different channels can increase the total network goodput by a factor of up to 8 compared with the conventional single-channel ad hoc network architecture.

1,318 citations


Journal ArticleDOI
TL;DR: In this paper, the prevalence of diabetic retinopathy among adults 40 years and older in the United States was estimated by pooled analysis of data from 8 population-based eye surveys.
Abstract: Objective: To determine the prevalence of diabetic retinopathy among adults 40 years and older in the United States.Methods: Pooled analysis of data from 8 population-based eye surveys was used to estimate the prevalence, among persons with diabetes mellitus (DM), of retinopathy and of vision-threatening retinopathy-defined as proliferative or severe nonproliferative retinopathy and/or macular edema. Within strata of age, race/ethnicity, and gender, US prevalence rates were estimated by multiplying these values by the prevalence of DM reported in the 1999 National Health Interview Survey and the 2000 US Census population.Results: Among an estimated 10.2 million US adults 40 years and older known to have DM, the estimated crude prevalence rates for retinopathy and vision-threatening retinopathy were 40.3% and 8.2%, respectively. The estimated US general population prevalence rates for retinopathy and vision-threatening retinopathy were 3.4% (4.1 million persons) and 0.75% (899000 persons). Future projections suggest that diabetic retinopathy will increase as a public health problem, both with aging of the US population and increasing age-specific prevalence of DM over time.Conclusion: Approximately 4.1 million US adults 40 years and older have diabetic retinopathy; 1 of every 12 persons with DM in this age group has advanced, vision-threatening retinopathy.

1,092 citations


Journal ArticleDOI
TL;DR: In this paper, the authors analyzed the relationship between the total far-IR luminosity, a tracer of the star formation rate, and the global HCN line luminosity (a measure of the total dense molecular gas content).
Abstract: HCN luminosity is a tracer of dense molecular gas, n(H(2)) greater than or similar to3 x 10(4) cm(-3), associated with star-forming giant molecular cloud (GMC) cores. We present the results and analysis of our survey of HCN emission from 65 infrared galaxies, including nine ultraluminous infrared galaxies (ULIGs, L(IR) greater than or similar to 10(12) L(circle dot)), 22 luminous infrared galaxies (LIGs, 10(11) L(circle dot) < L(IR) less than or similar to 10(12) L(circle dot)), and 34 normal spiral galaxies with lower IR luminosity (most are large spiral galaxies). We have measured the global HCN line luminosity, and the observations are reported in Paper I. This paper analyzes the relationships between the total far-IR luminosity (a tracer of the star formation rate), the global HCN line luminosity (a measure of the total dense molecular gas content), and the CO luminosity (a measure of the total molecular content). We find a tight linear correlation between the IR and HCN luminosities L(IR) and L(HCN) (in the log-log plot) with a correlation coefficient R = 0.94, and an almost constant average ratio L(IR)/L(HCN) = 900 L(circle dot) (K km s(-1) pc(2))(-1). The IR-HCN linear correlation is valid over 3 orders of magnitude including ULIGs, the most luminous objects in the local universe. The direct consequence of the linear IR-HCN correlation is that the star formation law in terms of dense molecular gas content has a power-law index of 1.0. The global star formation rate is linearly proportional to the mass of dense molecular gas in normal spiral galaxies, LIGs, and ULIGs. This is strong evidence in favor of star formation as the power source in ultraluminous galaxies since the star formation in these galaxies appears to be normal and expected given their high mass of dense star-forming molecular gas.

1,063 citations


Journal ArticleDOI
TL;DR: Information from natural history collections about the diversity, taxonomy and historical distributions of species worldwide is becoming increasingly available over the Internet, and its utility and limitations are critically reviewed.
Abstract: Information from natural history collections (NHCs) about the diversity, taxonomy and historical distributions of species worldwide is becoming increasingly available over the Internet. In light of this relatively new and rapidly increasing resource, we critically review its utility and limitations for addressing a diverse array of applications. When integrated with spatial environmental data, NHC data can be used to study a broad range of topics, from aspects of ecological and evolutionary theory, to applications in conservation, agriculture and human health. There are challenges inherent to using NHC data, such as taxonomic inaccuracies and biases in the spatial coverage of data, which require consideration. Promising research frontiers include the integration of NHC data with information from comparative genomics and phylogenetics, and stronger connections between the environmental analysis of NHC data and experimental and field-based tests of hypotheses.

Journal ArticleDOI
TL;DR: The combination of mechanical barriers based on non-woven nanofibrous biodegradable scaffolds and their capability for local delivery of antibiotics increases their desired utility in biomedical applications, particularly in the prevention of post-surgical adhesions and infections.

Journal ArticleDOI
TL;DR: Using a tumor xenograft model, it is shown that Ras-dependent CXCL-8 secretion is required for the initiation of tumor-associated inflammation and neovascularization and a novel mechanism by which the Ras oncogene can elicit a stromal response that fosters cancer progression.

Journal ArticleDOI
29 Dec 2004-Cell
TL;DR: This study represents the most comprehensive definition of transcription factor binding sites in a metazoan species.

Journal ArticleDOI
21 Oct 2004-Nature
TL;DR: It is reported that DNA damage checkpoint activation by a DSB requires the cyclin-dependent kinase CDK1 (Cdc28) in budding yeast, andCDK1 is also required for DSB-induced homologous recombination at any cell cycle stage.
Abstract: A single double-strand break (DSB) induced by HO endonuclease triggers both repair by homologous recombination and activation of the Mec1-dependent DNA damage checkpoint in budding yeast. Here we report that DNA damage checkpoint activation by a DSB requires the cyclin-dependent kinase CDK1 (Cdc28) in budding yeast. CDK1 is also required for DSB-induced homologous recombination at any cell cycle stage. Inhibition of homologous recombination by using an analogue-sensitive CDK1 protein results in a compensatory increase in non-homologous end joining. CDK1 is required for efficient 5' to 3' resection of DSB ends and for the recruitment of both the single-stranded DNA-binding complex, RPA, and the Rad51 recombination protein. In contrast, Mre11 protein, part of the MRX complex, accumulates at unresected DSB ends. CDK1 is not required when the DNA damage checkpoint is initiated by lesions that are processed by nucleotide excision repair. Maintenance of the DSB-induced checkpoint requires continuing CDK1 activity that ensures continuing end resection. CDK1 is also important for a later step in homologous recombination, after strand invasion and before the initiation of new DNA synthesis.

Journal ArticleDOI
05 Aug 2004-Neuron
TL;DR: Low-affinity LRP/Aβ interaction and/or Aβ-induced LRP loss at the BBB mediate brain accumulation of neurotoxic Aβ in transgenic mice and patients with cerebrovascular β-amyloidosis.

Journal Article
TL;DR: In this article, the authors used oligonucleotide-based DNA microarrays to analyze transcriptional changes resulting from constitutive Ras signaling and found that Ras signaling leads to a significant induction of Interleukin-8 (IL-8) mRNA, which is accompanied by a corresponding increase in protein levels.
Abstract: 1749 Ras proteins are important regulators of cell proliferation and their constitutive activation is a key event in cancer development. To discover novel effector pathways that might contribute to the oncogenic properties of Ras, we used oligonucleotide-based DNA microarrays to analyze transcriptional changes resulting from constitutive Ras signaling. We performed the expression analyses with HeLa stable cell lines expressing activated RasG12→V transgenes under a tetracycline responsive promoter (Tet-Off™ Expression System). This system not only mediates tight on/off regulation of gene expression; it also permits the titration of protein levels on a single cell basis allowing the study of dose dependent aspects of gene activity. Ras signaling leads to a significant induction of Interleukin-8 (IL-8) mRNA, which is accompanied by a corresponding increase in protein levels. IL-8 is a chemotactic factor for leukocytes and closely associated with the initiation of an acute inflammatory response. Analysis of signal transduction pathways that link Ras to IL-8 up-regulation suggests a direct effect of Ras on the IL-8 promoter, mediated by the synergistic activation of both MAPK-cascades and the PI3K > NFκB pathway. In addition, the Ras-induced accumulation of IL-8 protein is dependent on the activation of p38 MAP-kinase through a post-transcriptional mechanism involving an increase in IL-8 mRNA stability. Investigation of the functional importance of IL-8 in the context of tumorigenesis shows that IL-8 plays a decisive role in RasV12-mediated acceleration of tumor growth in a nude mouse xenograft model. Ablation of IL-8 function is accompanied by a significant reduction in tumor size. This effect is not due to decreased cell proliferation rates, since we observe no change in the mitogenic index of tumors after inhibition of IL-8. However, tumors devoid of functional IL-8 show a marked reduction in vascularization accompanied by vast tissue necrosis. These observations can be correlated with an IL-8-mediated initiation of an early inflammatory reaction in developing neoplasms that triggers tumor vascularization. In addition, IL-8 may act directly to support angiogenesis by promoting endothelial cell proliferation and migration. These results provide a novel mechanism by which tumor cells harboring oncogenic Ras can appropriate inflammatory mediators to recruit immune cells to the tumor site and facilitate neo-angiogenesis, thus setting the stage for subsequent progression to malignancy.

Journal ArticleDOI
TL;DR: In this paper, the authors review the present status of global analyses of neutrino oscillations and discuss the robustness of the oscillation interpretation against departures from the Standard Solar Model and the possible existence of non-standard neutrinos physics.
Abstract: We review the present status of global analyses of neutrino oscillations, taking into account the most recent neutrino data including the latest KamLAND and K2K updates presented at Neutrino 2004, as well as state-of-the-art solar and atmospheric neutrino flux calculations. We give the two-neutrino solar + KamLAND results, and the two-neutrino atmospheric + K2K oscillation regions, discussing in each case the robustness of the oscillation interpretation against departures from the Standard Solar Model and the possible existence of non-standard neutrino physics. Furthermore, we give the best-fit values and allowed ranges of the three-flavour oscillation parameters from the current worlds' global neutrino data sample and discuss in detail the status of the small parameters α ≡ ΔmSOL2/ΔmATM2 as well as sin2 θ13, which characterize the strength of CP violating effects in neutrino oscillations. We also update the degree of rejection of four-neutrino interpretations of the LSND evidence in view of the most recent developments.

Journal ArticleDOI
S. S. Adler1, S. Afanasiev2, Christine Angela Aidala1, N. N. Ajitanand3  +337 moreInstitutions (41)
TL;DR: In this paper, the authors measured the centrality dependence of transverse momentum distributions and particle yields at the PHENIX experiment at the Relativistic Heavy Ion Collider (HIC).
Abstract: The centrality dependence of transverse momentum distributions and yields for ${\ensuremath{\pi}}^{\ifmmode\pm\else\textpm\fi{}},{K}^{\ifmmode\pm\else\textpm\fi{}},p$, and $\overline{p}$ in $\text{Au}+\text{Au}$ collisions at $\sqrt{{s}_{NN}}=200\phantom{\rule{0.3em}{0ex}}\text{GeV}$ at midrapidity are measured by the PHENIX experiment at the Relativistic Heavy Ion Collider. We observe a clear particle mass dependence of the shapes of transverse momentum spectra in central collisions below $\ensuremath{\sim}2\phantom{\rule{0.3em}{0ex}}\text{GeV}∕c$ in ${p}_{T}$. Both mean transverse momenta and particle yields per participant pair increase from peripheral to midcentral and saturate at the most central collisions for all particle species. We also measure particle ratios of ${\ensuremath{\pi}}^{\ensuremath{-}}∕{\ensuremath{\pi}}^{+}$, ${K}^{\ensuremath{-}}∕{K}^{+}$, $\overline{p}∕p$, $K∕\ensuremath{\pi}$, $p∕\ensuremath{\pi}$, and $\overline{p}∕\ensuremath{\pi}$ as a function of ${p}_{T}$ and collision centrality. The ratios of equal mass particle yields are independent of ${p}_{T}$ and centrality within the experimental uncertainties. In central collisions at intermediate transverse momenta $\ensuremath{\sim}1.5--4.5\phantom{\rule{0.3em}{0ex}}\text{GeV}∕c$, proton and antiproton yields constitute a significant fraction of the charged hadron production and show a scaling behavior different from that of pions.

Journal ArticleDOI
TL;DR: A meta-analysis of 95 studies was conducted to investigate the relations of heart rate (HR) and electrodermal activity (EDA) with aggression, psychopathy, and conduct problems, revealing a complex constellation of interactive effects.
Abstract: A meta-analysis of 95 studies was conducted to investigate the relations of heart rate (HR) and electrodermal activity (EDA) with aggression, psychopathy, and conduct problems Analyses revealed a complex constellation of interactive effects, with a failure in some cases of autonomic patterns to generalize across antisocial spectrum behavior constructs Low resting EDA and low task EDA were associated with psychopathy/sociopathy and conduct problems However, EDA reactivity was positively associated with aggression and negatively associated with psychopathy/sociopathy Low resting HR and high HR reactivity were associated with aggression and conduct problems Physiology--behavior relations varied with age and stimulus valence in several cases Empirical and clinical implications are discussed

Journal ArticleDOI
16 Apr 2004-Science
TL;DR: Two mesoscale experiments, designed to investigate the effects of iron enrichment in regions with high and low concentrations of silicic acid, were performed in the Southern Ocean, demonstrating iron's pivotal role in controlling carbon uptake and regulating atmospheric partial pressure of carbon dioxide.
Abstract: The availability of iron is known to exert a controlling influence on biological productivity in surface waters over large areas of the ocean and may have been an important factor in the variation of the concentration of atmospheric carbon dioxide over glacial cycles. The effect of iron in the Southern Ocean is particularly important because of its large area and abundant nitrate, yet iron-enhanced growth of phytoplankton may be differentially expressed between waters with high silicic acid in the south and low silicic acid in the north, where diatom growth may be limited by both silicic acid and iron. Two mesoscale experiments, designed to investigate the effects of iron enrichment in regions with high and low concentrations of silicic acid, were performed in the Southern Ocean. These experiments demonstrate iron's pivotal role in controlling carbon uptake and regulating atmospheric partial pressure of carbon dioxide.

Journal ArticleDOI
TL;DR: In this paper, the authors review the present status of global analyses of neutrino oscillations and discuss the robustness of the oscillation interpretation against departures from the Standard Solar Model and the possible existence of non-standard neutrinos physics.
Abstract: We review the present status of global analyses of neutrino oscillations, taking into account the most recent neutrino data including the latest KamLAND and K2K updates presented at Neutrino2004, as well as state-of-the-art solar and atmospheric neutrino flux calculations. We give the two-neutrino solar + KamLAND results, as well as two-neutrino atmospheric + K2K oscillation regions, discussing in each case the robustness of the oscillation interpretation against departures from the Standard Solar Model and the possible existence of non-standard neutrino physics. Furthermore, we give the best fit values and allowed ranges of the three-flavour oscillation parameters from the current worlds' global neutrino data sample and discuss in detail the status of the small parameters $\alpha \equiv \Dms/\Dma$ as well as $\sin^2\theta_{13}$, which characterize the strength of CP violating effects in neutrino oscillations. We also update the degree of rejection of four-neutrino interpretations of the LSND anomaly in view of the most recent developments.

Journal ArticleDOI
15 Jul 2004-Nature
TL;DR: This analysis implies that the threshold-dependent interpretation of maternal morphogen concentration is not sufficient to determine shifting gap domain boundary positions, and suggests that establishing and interpreting positional information are not independent processes in the Drosophila blastoderm.
Abstract: Morphogen gradients contribute to pattern formation by determining positional information in morphogenetic fields. Interpretation of positional information is thought to rely on direct, concentration-threshold-dependent mechanisms for establishing multiple differential domains of target gene expression. In Drosophila, maternal gradients establish the initial position of boundaries for zygotic gap gene expression, which in turn convey positional information to pair-rule and segment-polarity genes, the latter forming a segmental pre-pattern by the onset of gastrulation. Here we report, on the basis of quantitative gene expression data, substantial anterior shifts in the position of gap domains after their initial establishment. Using a data-driven mathematical modelling approach, we show that these shifts are based on a regulatory mechanism that relies on asymmetric gap-gap cross-repression and does not require the diffusion of gap proteins. Our analysis implies that the threshold-dependent interpretation of maternal morphogen concentration is not sufficient to determine shifting gap domain boundary positions, and suggests that establishing and interpreting positional information are not independent processes in the Drosophila blastoderm.

Journal ArticleDOI
TL;DR: It is suggested that it is the tendency of lineages to maintain their ancestral ecological niche and their failure to adapt to new environments which frequently isolates incipient species and begins the process of speciation.
Abstract: Evolutionary biologists have often suggested that ecology is important in speciation, in that natural selection may drive adaptive divergence between lineages that inhabit different environments. I suggest that it is the tendency of lineages to maintain their ancestral ecological niche (phylogenetic niche conservatism) and their failure to adapt to new environments which frequently isolates incipient species and begins the process of speciation. Niche conservatism may be an important and widespread component of allopatric speciation but is largely unstudied. The perspective outlined here suggests roles for key microevolutionary processes (i.e., natural selection, adaptation) that are strikingly different from those proposed in previous literature on ecology and speciation. Yet, this perspective is complementary to the traditional view because it focuses on a different temporal stage of the speciation process.

Journal ArticleDOI
TL;DR: The first commercial Li-ion rechargeable battery contains the layered materials LiCoO2 and graphite as the cathode and anode (or negative electrode), respectively, which is the current standard in many applications including cell phones and laptops.
Abstract: Lithium intercalation or insertion materials have been widely investigated in the search for new electrode materials for use in high-voltage rechargeable batteries.1-6 The first commercial Li-ion rechargeable battery contains the layered materials LiCoO2 (Figure 1) and graphite as the cathode (or positive electrode) and anode (or negative electrode), respectively.7 Although this battery is the current standard in many applications including cell phones and laptops, its slow charge and discharge rates and cost have prevented its use in applications that require cheap high power and capacity, such as hybrid electric vehicles and electric vehicles. The toxicity of Co is also an issue. A wide variety of materials have been studied,5,6 which include doped LiCoO2 phases, layered compounds based on the LiCoO2 structure (e.g., LiNiO2 8 and LiNi0.5Mn0.5O2 9,10),

Journal ArticleDOI
TL;DR: As it develops into a comprehensive resource of known in vivo phosphorylation sites, it is expected that PhosphoSite will be a valuable tool for researchers seeking to understand the role of intracellular signaling pathways in a wide variety of biological processes.
Abstract: PhosphoSite is a curated, web-based bioinformatics resource dedicated to physiologic sites of protein phosphorylation in human and mouse. PhosphoSite is populated with information derived from published literature as well as high-throughput discovery programs. PhosphoSite provides information about the phosphorylated residue and its surrounding sequence, orthologous sites in other species, location of the site within known domains and motifs, and relevant literature references. Links are also provided to a number of external resources for protein sequences, structure, post-translational modifications and signaling pathways, as well as sources of phospho-specific antibodies and probes. As the amount of information in the underlying knowledgebase expands, users will be able to systematically search for the kinases, phosphatases, ligands, treatments, and receptors that have been shown to regulate the phosphorylation status of the sites, and pathways in which the phosphorylation sites function. As it develops into a comprehensive resource of known in vivo phosphorylation sites, we expect that PhosphoSite will be a valuable tool for researchers seeking to understand the role of intracellular signaling pathways in a wide variety of biological processes.

Journal ArticleDOI
03 Dec 2004-Science
TL;DR: The Mars Exploration Rover Opportunity has investigated the landing site in Eagle crater and the nearby plains within Meridiani Planum, and the rocks are interpreted to be a mixture of chemical and siliciclastic sediments formed by episodic inundation by shallow surface water, followed by evaporation, exposure, and desiccation.
Abstract: The Mars Exploration Rover Opportunity has investigated the landing site in Eagle crater and the nearby plains within Meridiani Planum. The soils consist of fine-grained basaltic sand and a surface lag of hematite-rich spherules, spherule fragments, and other granules. Wind ripples are common. Underlying the thin soil layer, and exposed within small impact craters and troughs, are flat-lying sedimentary rocks. These rocks are finely laminated, are rich in sulfur, and contain abundant sulfate salts. Small-scale cross-lamination in some locations provides evidence for deposition in flowing liquid water. We interpret the rocks to be a mixture of chemical and siliciclastic sediments formed by episodic inundation by shallow surface water, followed by evaporation, exposure, and desiccation. Hematite-rich spherules are embedded in the rock and eroding from them. We interpret these spherules to be concretions formed by postdepositional diagenesis, again involving liquid water.

Journal ArticleDOI
TL;DR: In this article, the authors report systematic HCN J = 1-0 (and CO) observations of a sample of 53 infrared and/or CO-bright and luminous galaxies, including seven ultraluminous infrared galaxies, nearly 20 luminous infrared and more than a dozen of the nearest normal spiral galaxies.
Abstract: We report systematic HCN J = 1-0 (and CO) observations of a sample of 53 infrared (IR) and/or CO-bright and/or luminous galaxies, including seven ultraluminous infrared galaxies, nearly 20 luminous infrared galaxies, and more than a dozen of the nearest normal spiral galaxies. This is the largest and most sensitive HCN survey of galaxies to date. All galaxies observed so far follow the tight correlation between the IR luminosity LIR and the HCN luminosity LHCN initially proposed by Solomon, Downes, & Radford, which is detailed in a companion paper. We also address here the issue of HCN excitation. There is no particularly strong correlation between LHCN and the 12 ?m luminosity; in fact, of all the four IRAS bands, the 12 ?m luminosity has the weakest correlation with the HCN luminosity. There is also no evidence of stronger HCN emission or a higher ratio of HCN and CO luminosities LHCN/LCO for galaxies with excess 12 ?m emission. This result implies that mid-IR radiative pumping, or populating, of the J = 1 level of HCN by a mid-IR vibrational transition is not important compared with the collisional excitation by dense molecular hydrogen. Furthermore, large velocity gradient calculations justify the use of HCN J = 1-0 emission as a tracer of high-density molecular gas (3 ? 104/? cm-3) and give an estimate of the mass of dense molecular gas from HCN observations. Therefore, LHCN may be used as a measure of the total mass of dense molecular gas, and the luminosity ratio LHCN/LCO may indicate the fraction of molecular gas that is dense.

Journal ArticleDOI
12 Nov 2004-Science
TL;DR: Quasi-classical trajectory calculations performed on a global potential energy surface for H2CO suggest that this second channel represents an intramolecular hydrogen abstraction mechanism: One hydrogen atom explores large regions of the potentialEnergy surface before bonding with the second H atom, bypassing the saddle point entirely.
Abstract: We present a combined experimental and theoretical investigation of formaldehyde (H2CO) dissociation to H2 and CO at energies just above the threshold for competing H elimination. High-resolution state-resolved imaging measurements of the CO velocity distributions reveal two dissociation pathways. The first proceeds through a well-established transition state to produce rotationally excited CO and vibrationally cold H2. The second dissociation pathway yields rotationally cold CO in conjunction with highly vibrationally excited H2. Quasi-classical trajectory calculations performed on a global potential energy surface for H2CO suggest that this second channel represents an intramolecular hydrogen abstraction mechanism: One hydrogen atom explores large regions of the potential energy surface before bonding with the second H atom, bypassing the saddle point entirely.

Journal ArticleDOI
Y. Ashie1, J. Hosaka1, K. Ishihara1, Yoshitaka Itow1, J. Kameda1, Yusuke Koshio1, A. Minamino1, C. Mitsuda1, M. Miura1, Shigetaka Moriyama1, Masayuki Nakahata1, Toshio Namba1, R. Nambu1, Y. Obayashi1, Masato Shiozawa1, Yasunari Suzuki1, Y. Takeuchi1, K. Taki1, Shinya Yamada1, Masaki Ishitsuka1, Takaaki Kajita1, K. Kaneyuki1, Shoei Nakayama1, A. Okada1, Ko Okumura1, T. Ooyabu1, C. Saji1, Y. Takenaga1, Shantanu Desai2, E. Kearns2, S. Likhoded2, J. L. Stone2, L. R. Sulak2, C. W. Walter2, W. Wang2, M. Goldhaber3, David William Casper4, J. P. Cravens4, W. Gajewski4, W. R. Kropp4, D. W. Liu4, S. Mine4, Michael B. Smy4, H. W. Sobel4, C. W. Sterner4, Mark R. Vagins4, K. S. Ganezer5, John Hill5, W. E. Keig5, J. S. Jang6, J. Y. Kim6, I. T. Lim6, R. W. Ellsworth7, S. Tasaka8, G. Guillian, A. Kibayashi, John G. Learned, S. Matsuno, D. Takemori, M. D. Messier9, Y. Hayato, A. K. Ichikawa, T. Ishida, T. Ishii, T. Iwashita, T. Kobayashi, Tomoyuki Maruyama, K. Nakamura, K. Nitta, Yuichi Oyama, Makoto Sakuda, Y. Totsuka, Atsumu Suzuki10, Masaya Hasegawa11, K. Hayashi11, T. Inagaki11, I. Kato11, H. Maesaka11, Taichi Morita11, Tsuyoshi Nakaya11, K. Nishikawa11, T. Sasaki11, S. Ueda11, Shoji Yamamoto11, Todd Haines12, Todd Haines4, S. Dazeley13, S. Hatakeyama13, R. Svoboda13, E. Blaufuss14, J. A. Goodman14, G. W. Sullivan14, D. Turcan14, Kate Scholberg15, Alec Habig16, Y. Fukuda17, C. K. Jung18, T. Kato18, Katsuhiro Kobayashi18, Magdalena Malek18, C. Mauger18, C. McGrew18, A. Sarrat18, E. Sharkey18, C. Yanagisawa18, T. Toshito19, Kazumasa Miyano20, N. Tamura20, J. Ishii21, Y. Kuno21, Y. Nagashima21, M. Takita21, Minoru Yoshida21, S. B. Kim22, J. Yoo22, H. Okazawa, T. Ishizuka23, Y. Choi24, H. Seo24, Y. Gando25, Takehisa Hasegawa25, Kunio Inoue25, J. Shirai25, A. Suzuki25, Masatoshi Koshiba1, Y. Nakajima26, Kyoshi Nishijima26, T. Harada27, Hirokazu Ishino27, R. Nishimura27, Y. Watanabe27, D. Kielczewska28, D. Kielczewska4, J. Zalipska28, H. G. Berns29, R. Gran29, K. K. Shiraishi29, A. L. Stachyra29, K. Washburn29, R. J. Wilkes29 
TL;DR: A dip in the L/E distribution was observed in the data, as predicted from the sinusoidal flavor transition probability of neutrino oscillation, which constrained nu(micro)<-->nu(tau) neutrinos oscillation parameters.
Abstract: Muon neutrino disappearance probability as a function of neutrino flight length $L$ over neutrino energy $E$ was studied. A dip in the $L/E$ distribution was observed in the data, as predicted from the sinusoidal flavor transition probability of neutrino oscillation. The observed $L/E$ distribution constrained ${\ensuremath{ u}}_{\ensuremath{\mu}}\ensuremath{\leftrightarrow}{\ensuremath{ u}}_{\ensuremath{\tau}}$ neutrino oscillation parameters; $1.9\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}3}l\ensuremath{\Delta}{m}^{2}l3.0\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}3}\text{ }\text{ }{\mathrm{e}\mathrm{V}}^{2}$ and ${sin }^{2}2\ensuremath{\theta}g0.90$ at 90% confidence level.