Showing papers by "University of California, Irvine published in 2007"

The cortical organization of speech processing

Abstract: Despite decades of research, the functional neuroanatomy of speech processing has been difficult to characterize. A major impediment to progress may have been the failure to consider task effects when mapping speech-related processing systems. We outline a dual-stream model of speech processing that remedies this situation. In this model, a ventral stream processes speech signals for comprehension, and a dorsal stream maps acoustic speech signals to frontal lobe articulatory networks. The model assumes that the ventral stream is largely bilaterally organized--although there are important computational differences between the left- and right-hemisphere systems--and that the dorsal stream is strongly left-hemisphere dominant.

Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems.

Abstract: The cycles of the key nutrient elements nitrogen (N) and phosphorus (P) have been massively altered by anthropogenic activities. Thus, it is essential to understand how photosynthetic production across diverse ecosystems is, or is not, limited by N and P. Via a large-scale meta-analysis of experimental enrichments, we show that P limitation is equally strong across these major habitats and that N and P limitation are equivalent within both terrestrial and freshwater systems. Furthermore, simultaneous N and P enrichment produces strongly positive synergistic responses in all three environments. Thus, contrary to some prevailing paradigms, freshwater, marine and terrestrial ecosystems are surprisingly similar in terms of N and P limitation.

Intracellular amyloid-β in Alzheimer's disease

Abstract: The primal role that the amyloid-beta (Abeta) peptide has in the development of Alzheimer's disease is now almost universally accepted. It is also well recognized that Abeta exists in multiple assembly states, which have different physiological or pathophysiological effects. Although the classical view is that Abeta is deposited extracellularly, emerging evidence from transgenic mice and human patients indicates that this peptide can also accumulate intraneuronally, which may contribute to disease progression.

The adaptive web: methods and strategies of web personalization

Abstract: I. Modeling Technologies.- User Models for Adaptive Hypermedia and Adaptive Educational Systems.- User Profiles for Personalized Information Access.- Data Mining for Web Personalization.- Generic User Modeling Systems.- Web Document Modeling.- II. Adaptation Technologies.- Personalized Search on the World Wide Web.- Adaptive Focused Crawling.- Adaptive Navigation Support.- Collaborative Filtering Recommender Systems.- Content-Based Recommendation Systems.- Case-Based Recommendation.- Hybrid Web Recommender Systems.- Adaptive Content Presentation for the Web.- Adaptive 3D Web Sites.- III. Applications.- Adaptive Information for Consumers of Healthcare.- Personalization in E-Commerce Applications.- Adaptive Mobile Guides.- Adaptive News Access.- IV. Challenges.- Adaptive Support for Distributed Collaboration.- Recommendation to Groups.- Privacy-Enhanced Web Personalization.- Open Corpus Adaptive Educational Hypermedia.- Semantic Web Technologies for the Adaptive Web.- Usability Engineering for the Adaptive Web.

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

Abstract: Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.

Mapping autism risk loci using genetic linkage and chromosomal rearrangements

Abstract: Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,181 [corrected] families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.

Efficient algorithms for Web services selection with end-to-end QoS constraints

Abstract: Service-Oriented Architecture (SOA) provides a flexible framework for service composition Using standard-based protocols (such as SOAP and WSDL), composite services can be constructed by integrating atomic services developed independently Algorithms are needed to select service components with various QoS levels according to some application-dependent performance requirements We design a broker-based architecture to facilitate the selection of QoS-based services The objective of service selection is to maximize an application-specific utility function under the end-to-end QoS constraints The problem is modeled in two ways: the combinatorial model and the graph model The combinatorial model defines the problem as a multidimension multichoice 0-1 knapsack problem (MMKP) The graph model defines the problem as a multiconstraint optimal path (MCOP) problem Efficient heuristic algorithms for service processes of different composition structures are presented in this article and their performances are studied by simulations We also compare the pros and cons between the two models

Oceanic methane biogeochemistry.

Abstract: This review shows that thermodynamic and kinetic constraints largely prevent large-scale methanogenesis in the open ocean water column. One example of open-ocean methanogenesis involves anoxic digestive tracts and fecal pellet microenvironments; methane released during fecal pellet disaggregation results in the mixed-layer methane maximum. However, the bulk of the methane in the ocean is added by coastal runoff, seeps, hydrothermal vents, decomposing hydrates, and mud volcanoes. Since methane is present in the open ocean at nanomolar concentrations, and since the flux to the atmosphere is small, the ultimate fate of ocean methane additions must be oxidation within the ocean. As indicated in the Introduction and highlighted in Table 3, sources of methane to the ocean water column are poorly quantified. There are only a small number of direct water column methane oxidation rates, so sinks are also poorly quantified. We know that methane oxidation rates are sensitive to ambient methane concentrations, but we have no information on reaction kinetics and only one report of the effect of pressure on methane oxidation. Our perspective on methane sources and the extent of methane oxidation has been changed dramatically by new techniques involving gene probes, determination of isotopically depleted biomarkers, and recent 14C-CH4 measurements showing that methane geochemistry in anoxic basins is dominated by seeps providing fossil methane. The role of anaerobic oxidation of methane has changed from a controversial curiosity to a major sink in anoxic basins and sediments. © 2007 American Chemical Society.

Probabilistic Topic Models

Abstract: Many chapters in this book illustrate that applying a statistical method such as latent semantic analysis (LSA; Landauer & Dumais, 1997; Landauer, Foltz, & Laham, 1998) to large databases can yield insight into human cognition. The LSA approach makes three claims: that semantic information can be derived from a word-document co-occurrence matrix; that dimensionality reduction is an essential part of this derivation; and that words and documents can be represented as points in Euclidean space. This chapter pursues an approach that is consistent with the first two of these claims, but differs in the third, describing a class of statistical models in which the semantic properties of words and documents are expressed in terms of probabilistic topics.

Topics in semantic representation.

Abstract: Processing language requires the retrieval of concepts from memory in response to an ongoing stream of information. This retrieval is facilitated if one can infer the gist of a sentence, conversation, or document and use that gist to predict related concepts and disambiguate words. This article analyzes the abstract computational problem underlying the extraction and use of gist, formulating this problem as a rational statistical inference. This leads to a novel approach to semantic representation in which word meanings are represented in terms of a set of probabilistic topics. The topic model performs well in predicting word association and the effects of semantic association and ambiguity on a variety of language-processing and memory tasks. It also provides a foundation for developing more richly structured statistical models of language, as the generative process assumed in the topic model can easily be extended to incorporate other kinds of semantic and syntactic structure.

Present-day climate forcing and response from black carbon in snow

Abstract: and +0.049 (0.007–0.12) W m � 2 , respectively. Snow forcing from only fossil fuel + biofuel sources is +0.043 W m � 2 (forcing from only fossil fuels is +0.033 W m � 2 ), suggesting that the anthropogenic contribution to total forcing is at least 80%. The 1998 global land and sea-ice snowpack absorbed 0.60 and 0.23 W m � 2 , respectively, because of direct BC/snow forcing. The forcing is maximum coincidentally with snowmelt onset, triggering strong snow-albedo feedback in local springtime. Consequently, the ‘‘efficacy’’ of BC/snow forcing is more than three times greater than forcing by CO2. The 1998 and 2001 land snowmelt rates north of 50N are 28% and 19% greater in the month preceding maximum melt of control simulations without BC in snow. With climate feedbacks, global annual mean 2-meter air temperature warms 0.15 and 0.10C, when BC is included in snow, whereas annual arctic warming is 1.61 and 0.50C. Stronger highlatitude climate response in 1998 than 2001 is at least partially caused by boreal fires, which account for nearly all of the 35% biomass burning contribution to 1998 arctic forcing. Efficacy was anomalously large in this experiment, however, and more research is required to elucidate the role of boreal fires, which we suggest have maximum arctic BC/snow forcing potential during April–June. Model BC concentrations in snow agree reasonably well (r = 0.78) with a set of 23 observations from various locations, spanning nearly 4 orders of magnitude. We predict concentrations in excess of 1000 ng g � 1 for snow in northeast China, enough to lower snow albedo by more than 0.13. The greatest instantaneous forcing is over the Tibetan Plateau, exceeding 20 W m � 2 in some places during spring. These results indicate that snow darkening is an important component of carbon aerosol climate forcing.

Rapid evolution of flowering time by an annual plant in response to a climate fluctuation.

Abstract: Ongoing climate change has affected the ecological dynamics of many species and is expected to impose natural selection on ecologically important traits. Droughts and other anticipated changes in precipitation may be particularly potent selective factors, especially in arid regions. Here we demonstrate the evolutionary response of an annual plant, Brassica rapa, to a recent climate fluctuation resulting in a multiyear drought. Ancestral (predrought) genotypes were recovered from stored seed and raised under a set of common environments with descendant (postdrought) genotypes and with ancestordescendant hybrids. As predicted, the abbreviated growing seasons caused by drought led to the evolution of earlier onset of flowering. Descendants bloomed earlier than ancestors, advancing first flowering by 1.9 days in one study population and 8.6 days in another. The intermediate flowering time of ancestordescendant hybrids supports an additive genetic basis for divergence. Experiments confirmed that summer drought selected for early flowering, that flowering time was heritable, and that selection intensities in the field were more than sufficient to account for the observed evolutionary change. Natural selection for drought escape thus appears to have caused adaptive evolution in just a few generations. A systematic effort to collect and store propagules from suitable species would provide biologists with materials to detect and elucidate the genetic basis of further evolutionary shifts driven by climate change. contemporary evolution global climate change life history theory local adaptation plant phenology

CO2 balance of boreal, temperate, and tropical forests derived from a global database

Abstract: Terrestrial ecosystems sequester 2.1 Pg of atmospheric carbon annually. A large amount of the terrestrial sink is realized by forests. However, considerable uncertainties remain regarding the fate of this carbon over both short and long timescales. Relevant data to address these uncertainties are being collected at many sites around the world, but syntheses of these data are still sparse. To facilitate future synthesis activities, we have assembled a comprehensive global database for forest ecosystems, which includes carbon budget variables (fluxes and stocks), ecosystem traits (e.g. leaf area index, age), as well as ancillary site information such as management regime, climate, and soil characteristics. This publicly available database can be used to quantify global, regional or biome-specific carbon budgets; to re-examine established relationships; to test emerging hypotheses about ecosystem functioning [e.g. a constant net ecosystem production (NEP) to gross primary production (GPP) ratio]; and as benchmarks for model evaluations. In this paper, we present the first analysis of this database. We discuss the climatic influences on GPP, net primary production (NPP) and NEP and present the CO2 balances for boreal, temperate, and tropical forest biomes based on micrometeorological, ecophysiological, and biometric flux and inventory estimates. Globally, GPP of forests benefited from higher temperatures and precipitation whereas NPP saturated above either a threshold of 1500 mm precipitation or a mean annual temperature of 10 degrees C. The global pattern in NEP was insensitive to climate and is hypothesized to be mainly determined by nonclimatic conditions such as successional stage, management, site history, and site disturbance. In all biomes, closing the CO2 balance required the introduction of substantial biome-specific closure terms. Nonclosure was taken as an indication that respiratory processes, advection, and non-CO2 carbon fluxes are not presently being adequately accounted for.

Fc receptor but not complement binding is important in antibody protection against HIV

Abstract: Many effective vaccines act by inducing neutralizing antibodies, and this approach is a top priority in work on HIV vaccines. But a new study suggests that anti-HIV antibodies are most effective when they act in two ways: through neutralization — killing the virus outright and blocking its entry into T cells — and by killing infected cells. The use of engineered versions of a neutralizing human antibody that protects against HIV in a monkey model shows that protection is dependent not only the antibody's neutralizing activity, but also on its interaction with Fc receptors on effector cells, which may act to reduce virus yield from infected cells. This work suggests that the best results might be achieved with vaccines that recruit both neutralizing antibodies and cell-mediated immunity via agents such as macrophages and cytokinins, rather than antibodies. Passively administered neutralizing antibodies have been shown to protect macaques against challenge by the HIV/SIV chimeric SHIV. The antiviral effects of the monoclonal antibody b12 are crucially dependent on antibody effector mechanisms. Most successful vaccines elicit neutralizing antibodies and this property is a high priority when developing an HIV vaccine1,2. Indeed, passively administered neutralizing antibodies have been shown to protect against HIV challenge in some of the best available animal models. For example, antibodies given intravenously can protect macaques against intravenous or mucosal SHIV (an HIV/SIV chimaera) challenge and topically applied antibodies can protect macaques against vaginal SHIV challenge3,4. However, the mechanism(s) by which neutralizing antibodies afford protection against HIV is not understood and, in particular, the role of antibody Fc-mediated effector functions is unclear. Here we report that there is a dramatic decrease in the ability of a broadly neutralizing antibody to protect macaques against SHIV challenge when Fc receptor and complement-binding activities are engineered out of the antibody. No loss of antibody protective activity is associated with the elimination of complement binding alone. Our in vivo results are consistent with in vitro assays indicating that interaction of Fc-receptor-bearing effector cells with antibody-complexed infected cells is important in reducing virus yield from infected cells. Overall, the data suggest the potential importance of activity against both infected cells and free virus for effective protection against HIV.

Phase II Trial of Bevacizumab in Persistent or Recurrent Epithelial Ovarian Cancer or Primary Peritoneal Cancer: A Gynecologic Oncology Group Study

Abstract: Purpose Vascular endothelial growth factor (VEGF) seems to be a promoter of tumor progression for epithelial ovarian cancer (EOC) and primary peritoneal cancer (PPC). We conducted a phase II trial to assess the efficacy and tolerability of single-agent bevacizumab, an anti-VEGF monoclonal antibody. Patients and Methods Eligible patients had persistent or recurrent EOC/PPC after one to two prior cytotoxic regimens, measurable disease, and Gynecologic Oncology Group performance status of at least 2. Treatment consisted of bevacizumab 15 mg/kg intravenously every 21 days until disease progression or prohibitive toxicity. Primary end points were progression-free survival (PFS) at 6 months and clinical response. Results The study consisted of 62 eligible and assessable patients, median age 57 years, 41 (66.1%) having received two prior regimens and 36 (58.1%) considered platinum resistant. Grade 3 adverse events at least possibly related to bevacizumab were hematologic (1), GI (3), hypertension (6), thromboemb...

Reactive Oxygen Species: A Breath of Life or Death?

Abstract: New insights into cancer cell-specific biological pathways are urgently needed to promote development of rationally targeted therapeutics. Reactive oxygen species (ROS) and their role in cancer cell response to growth factor signaling and hypoxia are emerging as verdant areas of exploration on the road to discovering cancer's Achilles heel. One of the distinguishing and near-universal hallmarks of cancer growth is hypoxia. Unregulated cellular proliferation leads to formation of cellular masses that extend beyond the resting vasculature, resulting in oxygen and nutrient deprivation. The resulting hypoxia triggers a number of critical adaptations that enable cancer cell survival, including apoptosis suppression, altered glucose metabolism, and an angiogenic phenotype. Ironically, recent investigations suggest that oxygen depletion stimulates mitochondria to elaborate increased ROS, with subsequent activation of signaling pathways, such as hypoxia inducible factor 1alpha, that promote cancer cell survival and tumor growth. Because mitochondria are key organelles involved in chemotherapy-induced apoptosis induction, the relationship between mitochondria, ROS signaling, and activation of survival pathways under hypoxic conditions has been the subject of increased study. Insights into mechanisms involved in ROS signaling may offer novel avenues to facilitate discovery of cancer-specific therapies. Preclinical and clinical evaluation of agents that modify ROS signaling in cancer offers a novel avenue for intervention. This review will cover recent work in ROS-mediated signaling in cancer cells and its potential as a target for developmental therapeutics.

Are There Long‐Term Effects of Early Child Care?

Abstract: Effects of early child care on children's functioning from 4½ years through the end of 6th grade (M age=12.0 years) were examined in the National Institute of Child Health and Human Development Study of Early Child Care and Youth Development (n=1,364). The results indicated that although parenting was a stronger and more consistent predictor of children's development than early child-care experience, higher quality care predicted higher vocabulary scores and more exposure to center care predicted more teacher-reported externalizing problems. Discussion focuses on mechanisms responsible for these effects, the potential collective consequences of small child-care effects, and the importance of the ongoing follow-up at age 15.

Biological network comparison using graphlet degree distribution

Abstract: Motivation: Analogous to biological sequence comparison, comparing cellular networks is an important problem that could provide insight into biological understanding and therapeutics. For technical reasons, comparing large networks is computationally infeasible, and thus heuristics, such as the degree distribution, clustering coefficient, diameter, and relative graphlet frequency distribution have been sought. It is easy to demonstrate that two networks are different by simply showing a short list of properties in which they differ. It is much harder to show that two networks are similar, as it requires demonstrating their similarity in all of their exponentially many properties. Clearly, it is computationally prohibitive to analyze all network properties, but the larger the number of constraints we impose in determining network similarity, the more likely it is that the networks will truly be similar. Results: We introduce a new systematic measure of a network's local structure that imposes a large number of similarity constraints on networks being compared. In particular, we generalize the degree distribution, which measures the number of nodes 'touching' k edges, into distributions measuring the number of nodes 'touching' k graphlets, where graphlets are small connected non-isomorphic subgraphs of a large network. Our new measure of network local structure consists of 73 graphlet degree distributions of graphlets with 2--5 nodes, but it is easily extendible to a greater number of constraints (i.e. graphlets), if necessary, and the extensions are limited only by the available CPU. Furthermore, we show a way to combine the 73 graphlet degree distributions into a network 'agreement' measure which is a number between 0 and 1, where 1 means that networks have identical distributions and 0 means that they are far apart. Based on this new network agreement measure, we show that almost all of the 14 eukaryotic PPI networks, including human, resulting from various high-throughput experimental techniques, as well as from curated databases, are better modeled by geometric random graphs than by Erdos--Reny, random scale-free, or Barabasi--Albert scale-free networks. Availability: Software executables are available upon request. Contact: natasha@ics.uci.edu

Driven to distraction: Extraneous events and underreaction to earnings news

Abstract: Psychological evidence indicates that it is hard to process multiple stimuli and perform multiple tasks at the same time. This paper tests the INVESTOR DISTRACTION HYPOTHESIS, which holds that the arrival of extraneous news causes trading and market prices to react sluggishly to relevant news about a firm. Our test focuses on the competition for investor attention between a firm's earnings announcements and the earnings announcements of other firms. We find that the immediate stock price and volume reaction to a firm's earnings surprise is weaker, and post-earnings announcement drift is stronger, when a greater number of earnings announcements by other firms are made on the same day. Distracting news has a stronger effect on firms that receive positive than negative earnings surprises. Industry-unrelated news has a stronger distracting effect than related news. A trading strategy that exploits post-earnings announcement drift is unprofitable for announcements made on days with little competing news.

Fuel efficiency and motor vehicle travel: the declining rebound effect

Abstract: It has long been realized that improving energy efficiency releases an economic reaction that partially offsets the original energy saving. As the energy efficiency of some process improves, the process becomes cheaper, thereby providing an incentive to increase its use. Thus total energy consumption changes less than proportionally to changes in physical energy efficiency. For motor vehicles, the process under consideration is use of fuel in producing vehicle-miles traveled (VMT). Our empirical specification is based on a simple aggregate model that simultaneously determines VMT, vehicles, and fuel efficiency. The coefficient on the lagged dependent variable implies considerable inertia in behavior, with people adjusting their travel in a given year by just 21 percent of the ultimate response to a permanent change. The equation exhibits only mild autocorrelation, giving people confidence that their specification accounts for most influences that move sluggishly over time.

Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest

Abstract: Our understanding of how saprotrophic and mycorrhizal fungi interact to re-circulate carbon and nutrients from plant litter and soil organic matter is limited by poor understanding of their spatiotemporal dynamics. In order to investigate how different functional groups of fungi contribute to carbon and nitrogen cycling at different stages of decomposition, we studied changes in fungal community composition along vertical profiles through a Pinus sylvestris forest soil. We combined molecular identification methods with 14C dating of the organic matter, analyses of carbon:nitrogen (C:N) ratios and 15N natural abundance measurements. Saprotrophic fungi were primarily confined to relatively recently (< 4 yr) shed litter components on the surface of the forest floor, where organic carbon was mineralized while nitrogen was retained. Mycorrhizal fungi dominated in the underlying, more decomposed litter and humus, where they apparently mobilized N and made it available to their host plants. Our observations show that the degrading and nutrient-mobilizing components of the fungal community are spatially separated. This has important implications for biogeochemical studies of boreal forest ecosystems.

Histone Deacetylase Inhibitors Enhance Memory and Synaptic Plasticity via CREB: CBP-Dependent Transcriptional Activation

Abstract: Histone deacetylase (HDAC) inhibitors increase histone acetylation and enhance both memory and synaptic plasticity. The current model for the action of HDAC inhibitors assumes that they alter gene expression globally and thus affect memory processes in a nonspecific manner. Here, we show that the enhancement of hippocampus-dependent memory and hippocampal synaptic plasticity by HDAC inhibitors is mediated by the transcription factor cAMP response element-binding protein (CREB) and the recruitment of the transcriptional coactivator and histone acetyltransferase CREB-binding protein (CBP) via the CREB-binding domain of CBP. Furthermore, we show that the HDAC inhibitor trichostatin A does not globally alter gene expression but instead increases the expression of specific genes during memory consolidation. Our results suggest that HDAC inhibitors enhance memory processes by the activation of key genes regulated by the CREB:CBP transcriptional complex.

Scaling up all pairs similarity search

Abstract: Given a large collection of sparse vector data in a high dimensional space, we investigate the problem of finding all pairs of vectors whose similarity score (as determined by a function such as cosine distance) is above a given threshold. We propose a simple algorithm based on novel indexing and optimization strategies that solves this problem without relying on approximation methods or extensive parameter tuning. We show the approach efficiently handles a variety of datasets across a wide setting of similarity thresholds, with large speedups over previous state-of-the-art approaches.