Showing papers by "Stanford University published in 2006"

Geant4 developments and applications

Abstract: Geant4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection. Its functionality and modeling capabilities continue to be extended, while its performance is enhanced. An overview of recent developments in diverse areas of the toolkit is presented. These include performance optimization for complex setups; improvements for the propagation in fields; new options for event biasing; and additions and improvements in geometry, physics processes and interactive capabilities

Quantum Spin Hall Effect and Topological Phase Transition in HgTe Quantum Wells

Abstract: We show that the quantum spin Hall (QSH) effect, a state of matter with topological properties distinct from those of conventional insulators, can be realized in mercury telluride–cadmium telluride semiconductor quantum wells. When the thickness of the quantum well is varied, the electronic state changes from a normal to an “inverted” type at a critical thickness d c . We show that this transition is a topological quantum phase transition between a conventional insulating phase and a phase exhibiting the QSH effect with a single pair of helical edge states. We also discuss methods for experimental detection of the QSH effect.

Mindset: The New Psychology of Success

Abstract: Every so often a truly groundbreaking idea comes along. This is one. Mindset explains: Why brains and talent don’t bring success How they can stand in the way of it Why praising brains and talent doesn’t foster self-esteem and accomplishment, but jeopardizes them How teaching a simple idea about the brain raises grades and productivity What all great CEOs, parents, teachers, athletes know Mindset is a simple idea discovered by world-renowned Stanford University psychologist Carol Dweck in decades of research on achievement and success—a simple idea that makes all the difference. In a fixed mindset, people believe their basic qualities, like their intelligence or talent, are simply fixed traits. They spend their time documenting their intelligence or talent instead of developing them. They also believe that talent alone creates success—without effort. They’re wrong. In a growth mindset, people believe that their most basic abilities can be developed through dedication and hard work—brains and talent are just the starting point. This view creates a love of learning and a resilience that is essential for great accomplishment. Virtually all great people have had these qualities. Teaching a growth mindset creates motivation and productivity in the worlds of business, education, and sports. It enhances relationships. When you read Mindset, you’ll see how.

Metagenomic Analysis of the Human Distal Gut Microbiome

Abstract: The human intestinal microbiota is composed of 10(13) to 10(14) microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed approximately 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction-amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Impacts of biodiversity loss on ocean ecosystem services.

Abstract: Human-dominated marine ecosystems are experiencing accelerating loss of populations and species, with largely unknown consequences. We analyzed local experiments, long-term regional time series, and global fisheries data to test how biodiversity loss affects marine ecosystem services across temporal and spatial scales. Overall, rates of resource collapse increased and recovery potential, stability, and water quality decreased exponentially with declining diversity. Restoration of biodiversity, in contrast, increased productivity fourfold and decreased variability by 21%, on average. We conclude that marine biodiversity loss is increasingly impairing the ocean's capacity to provide food, maintain water quality, and recover from perturbations. Yet available data suggest that at this point, these trends are still reversible.

Cancer stem cells--perspectives on current status and future directions: AACR Workshop on cancer stem cells.

Abstract: A workshop was convened by the AACR to discuss the rapidly emerging cancer stem cell model for tumor development and progression. The meeting participants were charged with evaluating data suggesting that cancers develop from a small subset of cells with self-renewal properties analogous to organ

Chronic Health Conditions in Adult Survivors of Childhood Cancer

Abstract: Background Only a few small studies have assessed the long-term morbidity that follows the treatment of childhood cancer. We determined the incidence and severity of chronic health conditions in adult survivors. Methods The Childhood Cancer Survivor Study is a retrospective cohort study that tracks the health status of adults who received a diagnosis of childhood cancer between 1970 and 1986 and compares the results with those of siblings. We calculated the frequencies of chronic conditions in 10,397 survivors and 3034 siblings. A severity score (grades 1 through 4, ranging from mild to life-threatening or disabling) was assigned to each condition. Cox proportional-hazards models were used to estimate hazard ratios, reported as relative risks and 95% confidence intervals (CIs), for a chronic condition. Results Survivors and siblings had mean ages of 26.6 years (range, 18.0 to 48.0) and 29.2 years (range, 18.0 to 56.0), respectively, at the time of the study. Among 10,397 survivors, 62.3% had at least one chronic condition; 27.5% had a severe or life-threatening condition (grade 3 or 4). The adjusted relative risk of a chronic condition in a survivor, as compared with siblings, was 3.3 (95% CI, 3.0 to 3.5); for a severe or life-threatening condition, the risk was 8.2 (95% CI, 6.9 to 9.7). Among survivors, the cumulative incidence of a chronic health condition reached 73.4% (95% CI, 69.0 to 77.9) 30 years after the cancer diagnosis, with a cumulative incidence of 42.4% (95% CI, 33.7 to 51.2) for severe, disabling, or life-threatening conditions or death due to a chronic condition. Conclusions Survivors of childhood cancer have a high rate of illness owing to chronic health conditions.

Cryopyrin activates the inflammasome in response to toxins and ATP

Abstract: A crucial part of the innate immune response is the assembly of the inflammasome, a cytosolic complex of proteins that activates caspase-1 to process the proinflammatory cytokines interleukin (IL)-1beta and IL-18. The adaptor protein ASC is essential for inflammasome function, binding directly to caspase-1 (refs 3, 4), but the triggers of this interaction are less clear. ASC also interacts with the adaptor cryopyrin (also known as NALP3 or CIAS1). Activating mutations in cryopyrin are associated with familial cold autoinflammatory syndrome, Muckle-Wells syndrome and neonatal onset multisystem inflammatory disease, diseases that are characterized by excessive production of IL-1beta. Here we show that cryopyrin-deficient macrophages cannot activate caspase-1 in response to Toll-like receptor agonists plus ATP, the latter activating the P2X7 receptor to decrease intracellular K+ levels. The release of IL-1beta in response to nigericin, a potassium ionophore, and maitotoxin, a potent marine toxin, was also found to be dependent on cryopyrin. In contrast to Asc-/- macrophages, cells deficient in the gene encoding cryopyrin (Cias1-/-) activated caspase-1 and secreted normal levels of IL-1beta and IL-18 when infected with Gram-negative Salmonella typhimurium or Francisella tularensis. Macrophages exposed to Gram-positive Staphylococcus aureus or Listeria monocytogenes, however, required both ASC and cryopyrin to activate caspase-1 and secrete IL-1beta. Therefore, cryopyrin is essential for inflammasome activation in response to signalling pathways triggered specifically by ATP, nigericin, maitotoxin, S. aureus or L. monocytogenes.

For most large underdetermined systems of linear equations the minimal 1-norm solution is also the sparsest solution

Abstract: We consider linear equations y = Φx where y is a given vector in ℝn and Φ is a given n × m matrix with n 0 so that for large n and for all Φ's except a negligible fraction, the following property holds: For every y having a representation y = Φx0by a coefficient vector x0 ∈ ℝmwith fewer than ρ · n nonzeros, the solution x1of the 1-minimization problem is unique and equal to x0. In contrast, heuristic attempts to sparsely solve such systems—greedy algorithms and thresholding—perform poorly in this challenging setting. The techniques include the use of random proportional embeddings and almost-spherical sections in Banach space theory, and deviation bounds for the eigenvalues of random Wishart matrices. © 2006 Wiley Periodicals, Inc.

Efficient sparse coding algorithms

Abstract: Sparse coding provides a class of algorithms for finding succinct representations of stimuli; given only unlabeled input data, it discovers basis functions that capture higher-level features in the data. However, finding sparse codes remains a very difficult computational problem. In this paper, we present efficient sparse coding algorithms that are based on iteratively solving two convex optimization problems: an L1-regularized least squares problem and an L2-constrained least squares problem. We propose novel algorithms to solve both of these optimization problems. Our algorithms result in a significant speedup for sparse coding, allowing us to learn larger sparse codes than possible with previously described algorithms. We apply these algorithms to natural images and demonstrate that the inferred sparse codes exhibit end-stopping and non-classical receptive field surround suppression and, therefore, may provide a partial explanation for these two phenomena in V1 neurons.

Randomized gossip algorithms

Abstract: Motivated by applications to sensor, peer-to-peer, and ad hoc networks, we study distributed algorithms, also known as gossip algorithms, for exchanging information and for computing in an arbitrarily connected network of nodes. The topology of such networks changes continuously as new nodes join and old nodes leave the network. Algorithms for such networks need to be robust against changes in topology. Additionally, nodes in sensor networks operate under limited computational, communication, and energy resources. These constraints have motivated the design of "gossip" algorithms: schemes which distribute the computational burden and in which a node communicates with a randomly chosen neighbor. We analyze the averaging problem under the gossip constraint for an arbitrary network graph, and find that the averaging time of a gossip algorithm depends on the second largest eigenvalue of a doubly stochastic matrix characterizing the algorithm. Designing the fastest gossip algorithm corresponds to minimizing this eigenvalue, which is a semidefinite program (SDP). In general, SDPs cannot be solved in a distributed fashion; however, exploiting problem structure, we propose a distributed subgradient method that solves the optimization problem over the network. The relation of averaging time to the second largest eigenvalue naturally relates it to the mixing time of a random walk with transition probabilities derived from the gossip algorithm. We use this connection to study the performance and scaling of gossip algorithms on two popular networks: Wireless Sensor Networks, which are modeled as Geometric Random Graphs, and the Internet graph under the so-called Preferential Connectivity (PC) model.

A Comparison and Evaluation of Multi-View Stereo Reconstruction Algorithms

Abstract: This paper presents a quantitative comparison of several multi-view stereo reconstruction algorithms. Until now, the lack of suitable calibrated multi-view image datasets with known ground truth (3D shape models) has prevented such direct comparisons. In this paper, we first survey multi-view stereo algorithms and compare them qualitatively using a taxonomy that differentiates their key properties. We then describe our process for acquiring and calibrating multiview image datasets with high-accuracy ground truth and introduce our evaluation methodology. Finally, we present the results of our quantitative comparison of state-of-the-art multi-view stereo reconstruction algorithms on six benchmark datasets. The datasets, evaluation details, and instructions for submitting new models are available online at http://vision.middlebury.edu/mview.

CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells

Abstract: Regulatory T (T reg) cells are critical regulators of immune tolerance. Most T reg cells are defined based on expression of CD4, CD25, and the transcription factor, FoxP3. However, these markers have proven problematic for uniquely defining this specialized T cell subset in humans. We found that the IL-7 receptor (CD127) is down-regulated on a subset of CD4+ T cells in peripheral blood. We demonstrate that the majority of these cells are FoxP3+, including those that express low levels or no CD25. A combination of CD4, CD25, and CD127 resulted in a highly purified population of T reg cells accounting for significantly more cells that previously identified based on other cell surface markers. These cells were highly suppressive in functional suppressor assays. In fact, cells separated based solely on CD4 and CD127 expression were anergic and, although representing at least three times the number of cells (including both CD25+CD4+ and CD25−CD4+ T cell subsets), were as suppressive as the “classic” CD4+CD25hi T reg cell subset. Finally, we show that CD127 can be used to quantitate T reg cell subsets in individuals with type 1 diabetes supporting the use of CD127 as a biomarker for human T reg cells.

Generating Typed Dependency Parses from Phrase Structure Parses

Abstract: This paper describes a system for extracting typed dependency parses of English sentences from phrase structure parses. In order to capture inherent relations occurring in corpus texts that can be critical in real-world applications, many NP relations are included in the set of grammatical relations used. We provide a comparison of our system with Minipar and the Link parser. The typed dependency extraction facility described here is integrated in the Stanford Parser, available for download.

Microbial biogeography : putting microorganisms on the map

Abstract: We review the biogeography of microorganisms in light of the biogeography of macroorganisms A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity However, recent studies also dispute the idea that 'everything is everywhere' We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world

Motivations for play in online games.

Abstract: An empirical model of player motivations in online games provides the foundation to understand and assess how players differ from one another and how motivations of play relate to age, gender, usage patterns, and in-game behaviors. In the current study, a factor analytic approach was used to create an empirical model of player motivations. The analysis revealed 10 motivation subcomponents that grouped into three overarching components (achievement, social, and immersion). Relationships between motivations and demographic variables (age, gender, and usage patterns) are also presented.

NEURAL MECHANISMS OF ADDICTION: The Role of Reward-Related Learning and Memory

Abstract: Addiction is a state of compulsive drug use; despite treatment and other attempts to control drug taking, addiction tends to persist. Clinical and laboratory observations have converged on the hypothesis that addiction represents the pathological usurpation of neural processes that normally serve reward-related learning. The major substrates of persistent compulsive drug use are hypothesized to be molecular and cellular mechanisms that underlie long-term associative memories in several forebrain circuits (involving the ventral and dorsal striatum and prefrontal cortex) that receive input from midbrain dopamine neurons. Here we review progress in identifying candidate mechanisms of addiction.

Toward a Psychology of Human Agency

Abstract: This article presents an agentic theory of human development, adaptation, and change. The evolutionary emergence of advanced symbolizing capacity enabled humans to transcend the dictates of their immediate environment and made them unique in their power to shape their life circumstances and the courses their lives take. In this conception, people are contributors to their life circumstances, not just products of them. Social cognitive theory rejects a duality between human agency and social structure. People create social systems, and these systems, in turn, organize and influence people's lives. This article discusses the core properties of human agency, the different forms it takes, its ontological and epistemological status, its development and role in causal structures, its growing primacy in the coevolution process, and its influential exercise at individual and collective levels across diverse spheres of life and cultural systems.

A Direct Empirical Proof of the Existence of Dark Matter

Abstract: We present new weak lensing observations of 1E0657-558 (z = 0.296), a unique cluster merger, that enable a direct detection of dark matter, independent of assumptions regarding the nature of the gravitational force law. Due to the collision of two clusters, the dissipationless stellar component and the fluid-like X-ray emitting plasma are spatially segregated. By using both wide-field ground based images and HST/ACS images of the cluster cores, we create gravitational lensing maps which show that the gravitational potential does not trace the plasma distribution, the dominant baryonic mass component, but rather approximately traces the distribution of galaxies. An 8{sigma} significance spatial offset of the center of the total mass from the center of the baryonic mass peaks cannot be explained with an alteration of the gravitational force law, and thus proves that the majority of the matter in the system is unseen.

Central nervous system control of food intake and body weight

Abstract: The capacity to adjust food intake in response to changing energy requirements is essential for survival. Recent progress has provided an insight into the molecular, cellular and behavioural mechanisms that link changes of body fat stores to adaptive adjustments of feeding behaviour. The physiological importance of this homeostatic control system is highlighted by the severe obesity that results from dysfunction of any of several of its key components. This new information provides a biological context within which to consider the global obesity epidemic and identifies numerous potential avenues for therapeutic intervention and future research.

CONSTRUCTING 21st-CENTURY TEACHER EDUCATION

Abstract: Much of what teachers need to know to be successful is invisible to lay observers, leading to the view that teaching requires little formal study and to frequent disdain for teacher education programs. The weakness of traditional program models that are collections of largely unrelated courses reinforce this low regard. This article argues that we have learned a great deal about how to create stronger, more effective teacher education programs. Three critical components of such programs include tight coherence and integration among courses and between course work and clinical work in schools, extensive and intensely supervised clinical work integrated with course work using pedagogies linking theory and practice, and closer, proactive relationships with schools that serve diverse learners effectively and develop and model good teaching. Also, schools of education should resist pressures to water down preparation, which ultimately undermine the preparation of entering teachers, the reputation of schools of education, and the strength of the profession.

A mutation in Orai1 causes immune deficiency by abrogating CRAC channel function

Abstract: Antigen stimulation of immune cells triggers Ca2+ entry through Ca2+ release-activated Ca2+ (CRAC) channels, promoting the immune response to pathogens by activating the transcription factor NFAT. We have previously shown that cells from patients with one form of hereditary severe combined immune deficiency (SCID) syndrome are defective in store-operated Ca2+ entry and CRAC channel function. Here we identify the genetic defect in these patients, using a combination of two unbiased genome-wide approaches: a modified linkage analysis with single-nucleotide polymorphism arrays, and a Drosophila RNA interference screen designed to identify regulators of store-operated Ca2+ entry and NFAT nuclear import. Both approaches converged on a novel protein that we call Orai1, which contains four putative transmembrane segments. The SCID patients are homozygous for a single missense mutation in ORAI1, and expression of wild-type Orai1 in SCID T cells restores store-operated Ca2+ influx and the CRAC current (I(CRAC)). We propose that Orai1 is an essential component or regulator of the CRAC channel complex.

On the optimality of multiantenna broadcast scheduling using zero-forcing beamforming

Abstract: Although the capacity of multiple-input/multiple-output (MIMO) broadcast channels (BCs) can be achieved by dirty paper coding (DPC), it is difficult to implement in practical systems. This paper investigates if, for a large number of users, simpler schemes can achieve the same performance. Specifically, we show that a zero-forcing beamforming (ZFBF) strategy, while generally suboptimal, can achieve the same asymptotic sum capacity as that of DPC, as the number of users goes to infinity. In proving this asymptotic result, we provide an algorithm for determining which users should be active under ZFBF. These users are semiorthogonal to one another and can be grouped for simultaneous transmission to enhance the throughput of scheduling algorithms. Based on the user grouping, we propose and compare two fair scheduling schemes in round-robin ZFBF and proportional-fair ZFBF. We provide numerical results to confirm the optimality of ZFBF and to compare the performance of ZFBF and proposed fair scheduling schemes with that of various MIMO BC strategies.

Stanley: The Robot that Won the DARPA Grand Challenge

Abstract: This article describes the robot Stanley, which won the 2005 DARPA Grand Challenge. Stanley was developed for high-speed desert driving without human intervention. The robot’s software system relied predominately on state-of-the-art AI technologies, such as machine learning and probabilistic reasoning. This article describes the major components of this architecture, and discusses the results of the Grand Challenge race.

Liquid-crystalline semiconducting polymers with high charge-carrier mobility.

Abstract: Organic semiconductors that can be fabricated by simple processing techniques and possess excellent electrical performance, are key requirements in the progress of organic electronics. Both high semiconductor charge-carrier mobility, optimized through understanding and control of the semiconductor microstructure, and stability of the semiconductor to ambient electrochemical oxidative processes are required. We report on new semiconducting liquid-crystalline thieno[3,2-b ]thiophene polymers, the enhancement in charge-carrier mobility achieved through highly organized morphology from processing in the mesophase, and the effects of exposure to both ambient and low-humidity air on the performance of transistor devices. Relatively large crystalline domain sizes on the length scale of lithographically accessible channel lengths (∼200 nm) were exhibited in thin films, thus offering the potential for fabrication of single-crystal polymer transistors. Good transistor stability under static storage and operation in a low-humidity air environment was demonstrated, with charge-carrier field-effect mobilities of 0.2–0.6 cm2 V−1 s−1 achieved under nitrogen.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

Abstract: Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.

Successful transduction of liver in hemophilia by AAV-Factor IX and limitations imposed by the host immune response

Abstract: We have previously shown that a single portal vein infusion of a recombinant adeno-associated viral vector (rAAV) expressing canine Factor IX (F.IX) resulted in long-term expression of therapeutic levels of F.IX in dogs with severe hemophilia B. We carried out a phase 1/2 dose-escalation clinical study to extend this approach to humans with severe hemophilia B. rAAV-2 vector expressing human F.IX was infused through the hepatic artery into seven subjects. The data show that: (i) vector infusion at doses up to 2 x 10(12) vg/kg was not associated with acute or long-lasting toxicity; (ii) therapeutic levels of F.IX were achieved at the highest dose tested; (iii) duration of expression at therapeutic levels was limited to a period of approximately 8 weeks; (iv) a gradual decline in F.IX was accompanied by a transient asymptomatic elevation of liver transaminases that resolved without treatment. Further studies suggested that destruction of transduced hepatocytes by cell-mediated immunity targeting antigens of the AAV capsid caused both the decline in F.IX and the transient transaminitis. We conclude that rAAV-2 vectors can transduce human hepatocytes in vivo to result in therapeutically relevant levels of F.IX, but that future studies in humans may require immunomodulation to achieve long-term expression.