Showing papers by "University of California, Irvine published in 2008"

Restoring the Density-Gradient Expansion for Exchange in Solids and Surfaces

Abstract: Popular modern generalized gradient approximations are biased toward the description of free-atom energies. Restoration of the first-principles gradient expansion for exchange over a wide range of density gradients eliminates this bias. We introduce a revised Perdew-Burke-Ernzerhof generalized gradient approximation that improves equilibrium properties of densely packed solids and their surfaces.

A discriminatively trained, multiscale, deformable part model

Abstract: This paper describes a discriminatively trained, multiscale, deformable part model for object detection. Our system achieves a two-fold improvement in average precision over the best performance in the 2006 PASCAL person detection challenge. It also outperforms the best results in the 2007 challenge in ten out of twenty categories. The system relies heavily on deformable parts. While deformable part models have become quite popular, their value had not been demonstrated on difficult benchmarks such as the PASCAL challenge. Our system also relies heavily on new methods for discriminative training. We combine a margin-sensitive approach for data mining hard negative examples with a formalism we call latent SVM. A latent SVM, like a hidden CRF, leads to a non-convex training problem. However, a latent SVM is semi-convex and the training problem becomes convex once latent information is specified for the positive examples. We believe that our training methods will eventually make possible the effective use of more latent information such as hierarchical (grammar) models and models involving latent three dimensional pose.

Coronary calcium as a predictor of coronary events in four racial or ethnic groups.

Abstract: BACKGROUND In white populations, computed tomographic measurements of coronary-artery calcium predict coronary heart disease independently of traditional coronary risk factors. However, it is not known whether coronary-artery calcium predicts coronary heart disease in other racial or ethnic groups. METHODS We collected data on risk factors and performed scanning for coronary calcium in a population-based sample of 6722 men and women, of whom 38.6% were white, 27.6% were black, 21.9% were Hispanic, and 11.9% were Chinese. The study subjects had no clinical cardiovascular disease at entry and were followed for a median of 3.8 years. RESULTS There were 162 coronary events, of which 89 were major events (myocardial infarction or death from coronary heart disease). In comparison with participants with no coronary calcium, the adjusted risk of a coronary event was increased by a factor of 7.73 among participants with coronary calcium scores between 101 and 300 and by a factor of 9.67 among participants with scores above 300 (P<0.001 for both comparisons). Among the four racial and ethnic groups, a doubling of the calcium score increased the risk of a major coronary event by 15 to 35% and the risk of any coronary event by 18 to 39%. The areas under the receiver-operating-characteristic curves for the prediction of both major coronary events and any coronary event were higher when the calcium score was added to the standard risk factors. CONCLUSIONS The coronary calcium score is a strong predictor of incident coronary heart disease and provides predictive information beyond that provided by standard risk factors in four major racial and ethnic groups in the United States. No major differences among racial and ethnic groups in the predictive value of calcium scores were detected.

Nitrogen limitation of net primary productivity in terrestrial ecosystems is globally distributed.

Abstract: Our meta-analysis of 126 nitrogen addition experiments evaluated nitrogen (N) limitation of net primary production (NPP) in terrestrial ecosystems. We tested the hypothesis that N limitation is widespread among biomes and influenced by geography and climate. We used the response ratio (R approximately equal ANPP(N)/ANPP(ctrl)) of aboveground plant growth in fertilized to control plots and found that most ecosystems are nitrogen limited with an average 29% growth response to nitrogen (i.e., R = 1.29). The response ratio was significant within temperate forests (R = 1.19), tropical forests (R = 1.60), temperate grasslands (R = 1.53), tropical grasslands (R = 1.26), wetlands (R = 1.16), and tundra (R = 1.35), but not deserts. Eight tropical forest studies had been conducted on very young volcanic soils in Hawaii, and this subgroup was strongly N limited (R = 2.13), which resulted in a negative correlation between forest R and latitude. The degree of N limitation in the remainder of the tropical forest studies (R = 1.20) was comparable to that of temperate forests, and when the young Hawaiian subgroup was excluded, forest R did not vary with latitude. Grassland response increased with latitude, but was independent of temperature and precipitation. These results suggest that the global N and C cycles interact strongly and that geography can mediate ecosystem response to N within certain biome types.

Resistance, resilience, and redundancy in microbial communities

Abstract: Although it is generally accepted that plant community composition is key for predicting rates of ecosystem processes in the face of global change, microbial community composition is often ignored in ecosystem modeling. To address this issue, we review recent experiments and assess whether microbial community composition is resistant, resilient, or functionally redundant in response to four different disturbances. We find that the composition of most microbial groups is sensitive and not immediately resilient to disturbance, regardless of taxonomic breadth of the group or the type of disturbance. Other studies demonstrate that changes in composition are often associated with changes in ecosystem process rates. Thus, changes in microbial communities due to disturbance may directly affect ecosystem processes. Based on these relationships, we propose a simple framework to incorporate microbial community composition into ecosystem process models. We conclude that this effort would benefit from more empirical data on the links among microbial phylogeny, physiological traits, and disturbance responses. These relationships will determine how readily microbial community composition can be used to predict the responses of ecosystem processes to global change.

Plant species traits are the predominant control on litter decomposition rates within biomes worldwide

Abstract: Worldwide decomposition rates depend both on climate and the legacy of plant functional traits as litter quality. To quantify the degree to which functional differentiation among species affects their litter decomposition rates, we brought together leaf trait and litter mass loss data for 818 species from 66 decomposition experiments on six continents. We show that: (i) the magnitude of species-driven differences is much larger than previously thought and greater than climate-driven variation; (ii) the decomposability of a species' litter is consistently correlated with that species' ecological strategy within different ecosystems globally, representing a new connection between whole plant carbon strategy and biogeochemical cycling. This connection between plant strategies and decomposability is crucial for both understanding vegetation-soil feedbacks, and for improving forecasts of the global carbon cycle.

Stoichiometry of soil enzyme activity at global scale

Abstract: Extracellular enzymes are the proximate agents of organic matter decomposition and measures of these activities can be used as indicators of microbial nutrient demand. We conducted a global-scale meta-analysis of the seven-most widely measured soil enzyme activities, using data from 40 ecosystems. The activities of b-1,4-glucosidase, cellobiohydrolase, b-1,4-N-acetylglucosaminidase and phosphatase g )1 soil increased with organic matter concentration; leucine aminopeptidase, phenol oxidase and peroxidase activities showed no relationship. All activities were significantly related to soil pH. Specific activities, i.e. activity g )1 soil organic matter, also varied in relation to soil pH for all enzymes. Relationships with mean annual temperature (MAT) and precipitation (MAP) were generally weak. For hydrolases, ratios of specific C, N and P acquisition activities converged on 1 : 1 : 1 but across ecosystems, the ratio of C : P acquisition was inversely related to MAP and MAT while the ratio of C : N acquisition increased with MAP. Oxidative activities were more variable than hydrolytic activities and increased with soil pH. Our analyses indicate that the enzymatic potential for hydrolyzing the labile components of soil organic matter is tied to substrate availability, soil pH and the stoichiometry of microbial nutrient demand. The enzymatic potential for oxidizing the recalcitrant fractions of soil organic material, which is a proximate control on soil organic matter accumulation, is most strongly related to soil pH. These trends provide insight into the biogeochemical processes that create global patterns in ecological stoichiometry and organic matter storage.

Remote plethysmographic imaging using ambient light

Abstract: Plethysmographic signals were measured remotely (>1m) using ambient light and a simple consumer level digital camera in movie mode. Heart and respiration rates could be quantified up to several harmonics. Although the green channel featuring the strongest plethysmographic signal, corresponding to an absorption peak by (oxy-) hemoglobin, the red and blue channels also contained plethysmographic information. The results show that ambient light photo-plethysmography may be useful for medical purposes such as characterization of vascular skin lesions (e.g., port wine stains) and remote sensing of vital signs (e.g., heart and respiration rates) for triage or sports purposes.

Age differences in sensation seeking and impulsivity as indexed by behavior and self-report: evidence for a dual systems model.

Abstract: It has been hypothesized that sensation seeking and impulsivity, which are often conflated, in fact develop along different timetables and have different neural underpinnings, and that the difference in their timetables helps account for heightened risk taking during adolescence. In order to test these propositions, the authors examined age differences in sensation seeking and impulsivity in a socioeconomically and ethnically diverse sample of 935 individuals between the ages of 10 and 30, using self-report and behavioral measures of each construct. Consistent with the authors' predictions, age differences in sensation seeking, which are linked to pubertal maturation, follow a curvilinear pattern, with sensation seeking increasing between 10 and 15 and declining or remaining stable thereafter. In contrast, age differences in impulsivity, which are unrelated to puberty, follow a linear pattern, with impulsivity declining steadily from age 10 on. Heightened vulnerability to risk taking in middle adolescence may be due to the combination of relatively higher inclinations to seek excitement and relatively immature capacities for self-control that are typical of this period of development.

Nitrogen additions and microbial biomass: a meta-analysis of ecosystem studies

Abstract: Nitrogen (N) enrichment is an element of global change that could influence the growth and abundance of many organisms. In this meta-analysis, I synthesized responses of microbial biomass to N additions in 82 published field studies. I hypothesized that the biomass of fungi, bacteria or the microbial community as a whole would be altered under N additions. I also predicted that changes in biomass would parallel changes in soil CO2 emissions. Microbial biomass declined 15% on average under N fertilization, but fungi and bacteria were not significantly altered in studies that examined each group separately. Moreover, declines in abundance of microbes and fungi were more evident in studies of longer durations and with higher total amounts of N added. In addition, responses of microbial biomass to N fertilization were significantly correlated with responses of soil CO2 emissions. There were no significant effects of biomes, fertilizer types, ambient N deposition rates or methods of measuring biomass. Altogether, these results suggest that N enrichment could reduce microbial biomass in many ecosystems, with corresponding declines in soil CO2 emissions.

ergm: A Package to Fit, Simulate and Diagnose Exponential-Family Models for Networks.

Abstract: We describe some of the capabilities of the ergm package and the statistical theory underlying it. This package contains tools for accomplishing three important, and interrelated, tasks involving exponential-family random graph models (ERGMs): estimation, simulation, and goodness of t. More precisely, ergm has the capability of approximating a maximum likelihood estimator for an ERGM given a network data set; simulating new network data sets from a tted ERGM using Markov chain Monte Carlo; and assessing how well a tted ERGM does at capturing characteristics of a particular network data set.

Scalable and efficient provable data possession

Abstract: Storage outsourcing is a rising trend which prompts a number of interesting security issues, many of which have been extensively investigated in the past. However, Provable Data Possession (PDP) is a topic that has only recently appeared in the research literature. The main issue is how to frequently, efficiently and securely verify that a storage server is faithfully storing its client's (potentially very large) outsourced data. The storage server is assumed to be untrusted in terms of both security and reliability. (In other words, it might maliciously or accidentally erase hosted data; it might also relegate it to slow or off-line storage.) The problem is exacerbated by the client being a small computing device with limited resources. Prior work has addressed this problem using either public key cryptography or requiring the client to outsource its data in encrypted form.In this paper, we construct a highly efficient and provably secure PDP technique based entirely on symmetric key cryptography, while not requiring any bulk encryption. Also, in contrast with its predecessors, our PDP technique allows outsourcing of dynamic data, i.e, it efficiently supports operations, such as block modification, deletion and append.

The minimum information about a genome sequence (MIGS) specification.

Abstract: With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

Consciousness and Anesthesia

Abstract: When we are anesthetized, we expect consciousness to vanish But does it always? Although anesthesia undoubtedly induces unresponsiveness and amnesia, the extent to which it causes unconsciousness is harder to establish For instance, certain anesthetics act on areas of the brain's cortex near the midline and abolish behavioral responsiveness, but not necessarily consciousness Unconsciousness is likely to ensue when a complex of brain regions in the posterior parietal area is inactivated Consciousness vanishes when anesthetics produce functional disconnection in this posterior complex, interrupting cortical communication and causing a loss of integration; or when they lead to bistable, stereotypic responses, causing a loss of information capacity Thus, anesthetics seem to cause unconsciousness when they block the brain's ability to integrate information

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains

Abstract: In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb-repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation, followed by ultra high-throughput sequencing. We find that bivalent domains can be segregated into two classes—the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only). PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters. We also used computational genomics to search for sequence determinants of Polycomb binding. This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes, and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes in pluripotent cells.

Scaling environmental change through the community-level: a trait-based response-and-effect framework for plants

Abstract: Predicting ecosystem responses to global change is a major challenge in ecology. A critical step in that challenge is to understand how changing environmental conditions influence processes across levels of ecological organization. While direct scaling from individual to ecosystem dynamics can lead to robust and mechanistic predictions, new approaches are needed to appropriately translate questions through the community level. Species invasion, loss, and turnover all necessitate this scaling through community processes, but predicting how such changes may influence ecosystem function is notoriously difficult. We suggest that community-level dynamics can be incorporated into scaling predictions using a trait-based response-effect framework that differentiates the community response to environmental change (predicted by response traits) and the effect of that change on ecosystem processes (predicted by effect traits). We develop a response-and-effect functional framework, concentrating on how the relationships among species' response, effect, and abundance can lead to general predictions concerning the magnitude and direction of the influence of environmental change on function. We then detail several key research directions needed to better scale the effects of environmental change through the community level. These include (1) effect and response trait characterization, (2) linkages between response-and-effect traits, (3) the importance of species interactions on trait expression, and (4) incorporation of feedbacks across multiple temporal scales. Increasing rates of extinction and invasion that are modifying communities worldwide make such a research agenda imperative.

Recent Antarctic ice mass loss from radar interferometry and regional climate modelling

Abstract: Observed estimates of ice losses in Antarctica combined with regional modelling of ice accumulation in the interior suggest that East Antarctica is close to a balanced mass budget, but large losses of ice occur in the narrow outlet channels of West Antarctic glaciers and at the northern tip of the Antarctic peninsula.

Female and male antisocial trajectories: From childhood origins to adult outcomes

Abstract: This article reports on the childhood origins and adult outcomes of female versus male antisocial behavior trajectories in the Dunedin longitudinal study. Four antisocial behavior trajectory groups were identified among females and males using general growth mixture modeling and included life-course persistent (LCP), adolescent-onset, childhood-limited, and low trajectory groups. During childhood, both LCP females and males were characterized by social, familial and neurodevelopmental risk factors, whereas those on the adolescent-onset pathway were not. At age 32, women and men on the LCP pathway were engaging in serious violence and experiencing significant mental health, physical health, and economic problems. Females and males on the adolescent-onset pathway were also experiencing difficulties at age 32, although to a lesser extent. Although more males than females followed the LCP trajectory, findings support similarities across gender with respect to developmental trajectories of antisocial behavior and their associated childhood origins and adult consequences. Implications for theory, research, and practice are discussed.

Pattern Separation in the Human Hippocampal CA3 and Dentate Gyrus

Abstract: Pattern separation, the process of transforming similar representations or memories into highly dissimilar, nonoverlapping representations, is a key component of many functions ascribed to the hippocampus. Computational models have stressed the role of the hippocampus and, in particular, the dentate gyrus and its projections into the CA3 subregion in pattern separation. We used high-resolution (1.5-millimeter isotropic voxels) functional magnetic resonance imaging to measure brain activity during incidental memory encoding. Although activity consistent with a bias toward pattern completion was observed in CA1, the subiculum, and the entorhinal and parahippocampal cortices, activity consistent with a strong bias toward pattern separation was observed in, and limited to, the CA3/dentate gyrus. These results provide compelling evidence of a key role of the human CA3/dentate gyrus in pattern separation.

Coming of Age in Second Life: An Anthropologist Explores the Virtually Human

Abstract: Millions of people around the world today spend portions of their lives in online virtual worlds. Second Life is one of the largest of these virtual worlds. The residents of Second Life create communities, buy property and build homes, go to concerts, meet in bars, attend weddings and religious services, buy and sell virtual goods and services, find friendship, fall in love--the possibilities are endless, and all encountered through a computer screen. Coming of Age in Second Life is the first book of anthropology to examine this thriving alternate universe. Tom Boellstorff conducted more than two years of fieldwork in Second Life, living among and observing its residents in exactly the same way anthropologists traditionally have done to learn about cultures and social groups in the so-called real world. He conducted his research as the avatar "Tom Bukowski," and applied the rigorous methods of anthropology to study many facets of this new frontier of human life, including issues of gender, race, sex, money, conflict and antisocial behavior, the construction of place and time, and the interplay of self and group. Coming of Age in Second Life shows how virtual worlds can change ideas about identity and society. Bringing anthropology into territory never before studied, this book demonstrates that in some ways humans have always been virtual, and that virtual worlds in all their rich complexity build upon a human capacity for culture that is as old as humanity itself.

A test of climate, sun, and culture relationships from an 1810-year Chinese cave record.

Abstract: A record from Wanxiang Cave, China, characterizes Asian Monsoon (AM) history over the past 1810 years. The summer monsoon correlates with solar variability, Northern Hemisphere and Chinese temperature, Alpine glacial retreat, and Chinese cultural changes. It was generally strong during Europe's Medieval Warm Period and weak during Europe's Little Ice Age, as well as during the final decades of the Tang, Yuan, and Ming Dynasties, all times that were characterized by popular unrest. It was strong during the first several decades of the Northern Song Dynasty, a period of increased rice cultivation and dramatic population increase. The sign of the correlation between the AM and temperature switches around 1960, suggesting that anthropogenic forcing superseded natural forcing as the major driver of AM changes in the late 20th century.

Approaching the Capacity of Wireless Networks through Distributed Interference Alignment

Abstract: Recent results establish the optimality of interference alignment to approach the Shannon capacity of interference networks at high SNR. However, the extent to which interference can be aligned over a finite number of signalling dimensions remains unknown. Another important concern for interference alignment schemes is the requirement of global channel knowledge. In this work we provide examples of iterative algorithms that utilize the reciprocity of wireless networks to achieve interference alignment with only local channel knowledge at each node. These algorithms also provide numerical insights into the feasibility of interference alignment that are not yet available in theory.

statnet: Software Tools for the Representation, Visualization, Analysis and Simulation of Network Data.

Abstract: statnet is a suite of software packages for statistical network analysis. The packages implement recent advances in network modeling based on exponential-family random graph models (ERGM). The components of the package provide a comprehensive framework for ERGM-based network modeling, including tools for model estimation, model evaluation, model-based network simulation, and network visualization. This broad functionality is powered by a central Markov chain Monte Carlo (MCMC) algorithm. The coding is optimized for speed and robustness.

The burden and determinants of neck pain in the general population: results of the Bone and Joint Decade 2000-2010 Task Force on Neck Pain and Its Associated Disorders.

Abstract: STUDY DESIGN: Best evidence synthesis. OBJECTIVE: To undertake a best evidence synthesis of the published evidence on the burden and determinants of neck pain and its associated disorders in the general population. SUMMARY OF BACKGROUND DATA: The evidence on burden and determinants of neck has not previously been summarized. METHODS: The Bone and Joint Decade 2000-2010 Task Force on Neck Pain and Its Associated Disorders performed a systematic search and critical review of literature published between 1980 and 2006 to assemble the best evidence on neck pain. Studies meeting criteria for scientific validity were included in a best evidence synthesis. RESULTS: We identified 469 studies on burden and determinants of neck pain, and judged 249 to be scientifically admissible; 101 articles related to the burden and determinants of neck pain in the general population. Incidence ranged from 0.055 per 1000 person years (disc herniation with radiculopathy) to 213 per 1000 persons (self-reported neck pain). Incidence of neck injuries during competitive sports ranged from 0.02 to 21 per 1000 exposures. The 12-month prevalence of pain typically ranged between 30% and 50%; the 12-month prevalence of activity-limiting pain was 1.7% to 11.5%. Neck pain was more prevalent among women and prevalence peaked in middle age. Risk factors for neck pain included genetics, poor psychological health, and exposure to tobacco. Disc degeneration was not identified as a risk factor. The use of sporting gear (helmets, face shields) to prevent other types of injury was not associated with increased neck injuries in bicycling, hockey, or skiing. CONCLUSION: Neck pain is common. Nonmodifiable risk factors for neck pain included age, gender, and genetics. Modifiable factors included smoking, exposure to tobacco, and psychological health. Disc degeneration was not identified as a risk factor. Future research should concentrate on longitudinal designs exploring preventive strategies and modifiable risk factors for neck pain. Language: en