Showing papers by "University of California, Davis published in 2004"

The metacommunity concept: a framework for multi-scale community ecology

Abstract: The metacommunity concept is an important way to think about linkages between different spatial scales in ecology. Here we review current understanding about this concept. We first investigate issues related to its definition as a set of local communities that are linked by dispersal of multiple potentially interacting species. We then identify four paradigms for metacommunities: the patch-dynamic view, the species-sorting view, the mass effects view and the neutral view, that each emphasizes different processes of potential importance in metacommunities. These have somewhat distinct intellectual histories and we discuss elements related to their potential future synthesis. We then use this framework to discuss why the concept is useful in modifying existing ecological thinking and illustrate this with a number of both theoretical and empirical examples. As ecologists strive to understand increasingly complex mechanisms and strive to work across multiple scales of spatio-temporal organization, concepts like the metacommunity can provide important insights that frequently contrast with those that would be obtained with more conventional approaches based on local communities alone.

Mild cognitive impairment--beyond controversies, towards a consensus: report of the International Working Group on Mild Cognitive Impairment.

Abstract: The First Key Symposium was held in Stockholm, Sweden, 2-5 September 2003. The aim of the symposium was to integrate clinical and epidemiological perspectives on the topic of Mild Cognitive Impairment (MCI). A multidisciplinary, international group of experts discussed the current status and future directions of MCI, with regard to clinical presentation, cognitive and functional assessment, and the role of neuroimaging, biomarkers and genetics. Agreement on new perspectives, as well as recommendations for management and future research were discussed by the international working group. The specific recommendations for the general MCI criteria include the following: (i) the person is neither normal nor demented; (ii) there is evidence of cognitive deterioration shown by either objectively measured decline over time and/or subjective report of decline by self and/or informant in conjunction with objective cognitive deficits; and (iii) activities of daily living are preserved and complex instrumental functions are either intact or minimally impaired.

Docetaxel and estramustine compared with mitoxantrone and prednisone for advanced refractory prostate cancer

Abstract: background Mitoxantrone-based chemotherapy palliates pain without extending survival in men with progressive androgen-independent prostate cancer. We compared docetaxel plus estramustine with mitoxantrone plus prednisone in men with metastatic, hormoneindependent prostate cancer. methods We randomly assigned 770 men to one of two treatments, each given in 21-day cycles: 280 mg of estramustine three times daily on days 1 through 5, 60 mg of docetaxel per square meter of body-surface area on day 2, and 60 mg of dexamethasone in three divided doses before docetaxel, or 12 mg of mitoxantrone per square meter on day 1 plus 5 mg of prednisone twice daily. The primary end point was overall survival; secondary end points were progression-free survival, objective response rates, and post-treatment declines of at least 50 percent in serum prostate-specific antigen (PSA) levels. results Of 674 eligible patients, 338 were assigned to receive docetaxel and estramustine and 336 to receive mitoxantrone and prednisone. In an intention-to-treat analysis, the median overall survival was longer in the group given docetaxel and estramustine than in the group given mitoxantrone and prednisone (17.5 months vs. 15.6 months, P=0.02 by the log-rank test), and the corresponding hazard ratio for death was 0.80 (95 percent confidence interval, 0.67 to 0.97). The median time to progression was 6.3 months in the group given docetaxel and estramustine and 3.2 months in the group given mitoxantrone and prednisone (P<0.001 by the log-rank test). PSA declines of at least 50 percent occurred in 50 percent and 27 percent of patients, respectively (P<0.001), and objective tumor responses were observed in 17 percent and 11 percent of patients with bidimensionally measurable disease, respectively (P=0.30). Grade 3 or 4 neutropenic fevers (P=0.01), nausea and vomiting (P<0.001), and cardiovascular events (P=0.001) were more common among patients receiving docetaxel and estramustine than among those receiving mitoxantrone and prednisone. Pain relief was similar in both groups. conclusions The improvement in median survival of nearly two months with docetaxel and estramustine, as compared with mitoxantrone and prednisone, provides support for this approach in men with metastatic, androgen-independent prostate cancer.

A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics

Abstract: Since the 1900s, the link between soil biotic activity, soil organic matter (SOM) decomposition and stabilization, and soil aggregate dynamics has been recognized and intensively been studied. By 1950, many studies had, mostly qualitatively, investigated the influence of the five major factors (i.e. soil fauna, microorganisms, roots, inorganics and physical processes) on this link. After 1950, four theoretical mile-stones related to this subject were realized. The first one was when Emerson [Nature 183 (1959) 538] proposed a model of a soil crumb consisting of domains of oriented clay and quartz particles. Next, Edwards and Bremner [J. Soil Sci. 18 (1967) 64] formulated a theory in which the solid-phase reaction between clay minerals, polyvalent cations and SOM is the main process leading to microaggregate formation. Based on this concept, Tisdall and Oades [J. Soil Sci. 62 (1982) 141] coined the aggregate hierarchy concept describing a spatial scale dependence of mechanisms involved in micro- and macroaggregate formation. Oades [Plant Soil 76 (1984) 319] suggested a small, but very important, modification to the aggregate hierarchy concept by theorizing the formation of microaggregates within macroaggregates. Recent research on aggregate formation and SOM stabilization extensively corroborate this modification and use it as the base for furthering the understanding of SOM dynamics. The major outcomes of adopting this modification are: (1) microaggregates, rather than macroaggregates protect SOM in the long term; and (2) macroaggregate turnover is a crucial process influencing the stabilization of SOM. Reviewing the progress made over the last 50 years in this area of research reveals that still very few studies are quantitative and/or consider interactive effects between the five factors. The quantification of these relationships is clearly needed to improve our ability to predict changes in soil ecosystems due to management and global change. This quantification can greatly benefit from viewing aggregates as dynamic rather than static entities and relating aggregate measurements with 2D and 3D quantitative spatial information.

Behavioral syndromes: an ecological and evolutionary overview.

Abstract: Recent studies suggest that populations and species often exhibit behavioral syndromes; that is, suites of correlated behaviors across situations. An example is an aggression syndrome where some individuals are more aggressive, whereas others are less aggressive across a range of situations and contexts. The existence of behavioral syndromes focuses the attention of behavioral ecologists on limited (less than optimal) behavioral plasticity and behavioral carryovers across situations, rather than on optimal plasticity in each isolated situation. Behavioral syndromes can explain behaviors that appear strikingly non-adaptive in an isolated context (e.g. inappropriately high activity when predators are present, or excessive sexual cannibalism). Behavioral syndromes can also help to explain the maintenance of individual variation in behavioral types, a phenomenon that is ubiquitous, but often ignored. Recent studies suggest that the behavioral type of an individual, population or species can have important ecological and evolutionary implications, including major effects on species distributions, on the relative tendencies of species to be invasive or to respond well to environmental change, and on speciation rates. Although most studies of behavioral syndromes to date have focused on a few organisms, mainly in the laboratory, further work on other species, particularly in the field, should yield numerous new insights.

Anterior cingulate conflict monitoring and adjustments in control

Abstract: Conflict monitoring by the anterior cingulate cortex (ACC) has been posited to signal a need for greater cognitive control, producing neural and behavioral adjustments. However, the very occurrence of behavioral adjustments after conflict has been questioned, along with suggestions that there is no direct evidence of ACC conflict-related activity predicting subsequent neural or behavioral adjustments in control. Using the Stroop color-naming task and controlling for repetition effects, we demonstrate that ACC conflict-related activity predicts both greater prefrontal cortex activity and adjustments in behavior, supporting a role of ACC conflict monitoring in the engagement of cognitive control.

Not by genes alone: How culture transformed human evolution.

Abstract: Humans are a striking anomaly in the natural world. While we are similar to other mammals in many ways, our behavior sets us apart. Our unparalleled ability to adapt has allowed us to occupy virtually every habitat on earth, and our societies are larger, more complex, and more cooperative than any other mammal's. In "Not by Genes Alone", Peter J. Richerson and Robert Boyd argue that only a Darwinian theory of cultural evolution can explain these unique characteristics. "Not by Genes Alone" offers a radical interpretation of human evolution, arguing that our ecological dominance and our singular social systems stem from a psychology uniquely adapted to create complex culture. Richerson and Boyd consider culture to be essential to human adaptation, as much a part of human biology as bipedal locomotion. Drawing on work in the fields of anthropology, political science, sociology, and economics - and building their case with such fascinating examples as kayaks, clever knots, and yams that require twelve men to carry them - Richerson and Boyd convincingly demonstrate that culture and biology are inextricably linked. In abandoning the nature-versus-nurture debate as fundamentally misconceived, "Not by Genes Alone" is a truly original and groundbreaking theory of the role of culture in evolution and a book to be reckoned with for generations to come.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Abstract: We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

A Revised Approach to Ice Microphysical Processes for the Bulk Parameterization of Clouds and Precipitation

Abstract: A revised approach to cloud microphysical processes in a commonly used bulk microphysics parameterization and the importance of correctly representing properties of cloud ice are discussed. Several modifications are introduced to more realistically simulate some of the ice microphysical processes. In addition to the assumption that ice nuclei number concentration is a function of temperature, a new and separate assumption is developed in which ice crystal number concentration is a function of ice amount. Related changes in ice microphysics are introduced, and the impact of sedimentation of ice crystals is also investigated. In an idealized thunderstorm simulation, the distribution of simulated clouds and precipitation is sensitive to the assumptions in microphysical processes, whereas the impact of the sedimentation of cloud ice is small. Overall, the modifications introduced to microphysical processes play a role in significantly reducing cloud ice and increasing snow at colder temperatures and ...

Behavioral syndromes: An integrative overview

Abstract: A behavioral syndrome is a suite of correlated behaviors expressed either within a given behavioral context (e.g., correlations between foraging behaviors in different habitats) or across different contexts (e.g., correlations among feeding, antipredator, mating, aggressive, and dispersal behaviors). For example, some individuals (and genotypes) might be generally more aggressive, more active or bold, while others are generally less aggressive, active or bold. This phenomenon has been studied in detail in humans, some primates, laboratory rodents, and some domesticated animals, but has rarely been studied in other organisms, and rarely examined from an evolutionary or ecological perspective. Here, we present an integrative overview on the potential importance of behavioral syndromes in evolution and ecology. A central idea is that behavioral correlations generate tradeoffs; for example, an aggressive genotype might do well in situations where high aggression is favored, but might be inappropriate...

De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signalling

Abstract: NF-kappaB transcription factors mediate the effects of pro-inflammatory cytokines such as tumour necrosis factor-alpha and interleukin-1beta. Failure to downregulate NF-kappaB transcriptional activity results in chronic inflammation and cell death, as observed in A20-deficient mice. A20 is a potent inhibitor of NF-kappaB signalling, but its mechanism of action is unknown. Here we show that A20 downregulates NF-kappaB signalling through the cooperative activity of its two ubiquitin-editing domains. The amino-terminal domain of A20, which is a de-ubiquitinating (DUB) enzyme of the OTU (ovarian tumour) family, removes lysine-63 (K63)-linked ubiquitin chains from receptor interacting protein (RIP), an essential mediator of the proximal TNF receptor 1 (TNFR1) signalling complex. The carboxy-terminal domain of A20, composed of seven C2/C2 zinc fingers, then functions as a ubiquitin ligase by polyubiquitinating RIP with K48-linked ubiquitin chains, thereby targeting RIP for proteasomal degradation. Here we define a novel ubiquitin ligase domain and identify two sequential mechanisms by which A20 downregulates NF-kappaB signalling. We also provide an example of a protein containing separate ubiquitin ligase and DUB domains, both of which participate in mediating a distinct regulatory effect.

The Great Observatories Origins Deep Survey: Initial results from optical and near-infrared imaging

Abstract: This special issue of the Astrophysical Journal Letters is dedicated to presenting initial results from the Great Observatories Origins Deep Survey (GOODS) that are primarily, but not exclusively, based on multiband imaging data obtained with the Hubble Space Telescope and the Advanced Camera for Surveys (ACS). The survey covers roughly 320 arcmin2 in the ACS F435W, F606W, F814W, and F850LP bands, divided into two well-studied fields. Existing deep observations from the Chandra X-Ray Observatory and ground-based facilities are supplemented with new, deep imaging in the optical and near-infrared from the European Southern Observatory and from the Kitt Peak National Observatory. Deep observations with the Space Infrared Telescope Facility are scheduled. Reduced data from all facilities are being released worldwide within 3-6 months of acquisition. Together, this data set provides two deep reference fields for studies of distant normal and active galaxies, supernovae, and faint stars in our own Galaxy. This Letter serves to outline the survey strategy and describe the specific data that have been used in the accompanying letters, summarizing the reduction procedures and sensitivity limits.

Diclofenac residues as the cause of vulture population decline in Pakistan

Abstract: The Oriental white-backed vulture (OWBV; Gyps bengalensis) was once one of the most common raptors in the Indian subcontinent A population decline of >95%, starting in the 1990s, was first noted at Keoladeo National Park, India Since then, catastrophic declines, also involving Gyps indicus and Gyps tenuirostris, have continued to be reported across the subcontinent Consequently these vultures are now listed as critically endangered by BirdLife International In 2000, the Peregrine Fund initiated its Asian Vulture Crisis Project with the Ornithological Society of Pakistan, establishing study sites at 16 OWBV colonies in the Kasur, Khanewal and Muzaffargarh-Layyah Districts of Pakistan to measure mortality at over 2,400 active nest sites Between 2000 and 2003, high annual adult and subadult mortality (5-86%) and resulting population declines (34-95%) (ref 5 and MG, manuscript in preparation) were associated with renal failure and visceral gout Here, we provide results that directly correlate residues of the anti-inflammatory drug diclofenac with renal failure Diclofenac residues and renal disease were reproduced experimentally in OWBVs by direct oral exposure and through feeding vultures diclofenac-treated livestock We propose that residues of veterinary diclofenac are responsible for the OWBV decline

A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis.

Abstract: Rheumatoid arthritis (RA) is the most common systemic autoimmune disease, affecting ∼1% of the adult population worldwide, with an estimated heritability of 60%. To identify genes involved in RA susceptibility, we investigated the association between putative functional single-nucleotide polymorphisms (SNPs) and RA among white individuals by use of a case-control study design; a second sample was tested for replication. Here we report the association of RA susceptibility with the minor allele of a missense SNP in PTPN22 (discovery-study allelic P =6.6×10 −4 ; replication-study allelic P =5.6×10 −8 ), which encodes a hematopoietic-specific protein tyrosine phosphatase also known as "Lyp." We show that the risk allele, which is present in ∼17% of white individuals from the general population and in ∼28% of white individuals with RA, disrupts the P1 proline-rich motif that is important for interaction with Csk, potentially altering these proteins' normal function as negative regulators of T-cell activation. The minor allele of this SNP recently was implicated in type 1 diabetes, suggesting that the variant phosphatase may increase overall reactivity of the immune system and may heighten an individual carrier's risk for autoimmune disease.

The Language of Schooling: A Functional Linguistics Perspective

Abstract: Contents: Preface. Characterizing the Language of Schooling. Language and Context. Linguistic Features of Academic Registers. Writing School Genres. Functional Grammar in School Subjects. Language Development in School.

Cognition and Anatomy in Three Variants of Primary Progressive Aphasia

Abstract: We performed a comprehensive cognitive, neuroimaging, and genetic study of 31 patients with primary progressive aphasia (PPA), a decline in language functions that remains isolated for at least 2 years. Detailed speech and language evaluation was used to identify three different clinical variants: nonfluent progressive aphasia (NFPA; n = 11), semantic dementia (SD; n = 10), and a third variant termed logopenic progressive aphasia (LPA; n = 10). Voxel-based morphometry (VBM) on MRIs showed that, when all 31 PPA patients were analyzed together, the left perisylvian region and the anterior temporal lobes were atrophied. However, when each clinical variant was considered separately, distinctive patterns emerged: (1) NFPA, characterized by apraxia of speech and deficits in processing complex syntax, was associated with left inferior frontal and insular atrophy; (2) SD, characterized by fluent speech and semantic memory deficits, was associated with anterior temporal damage; and (3) LPA, characterized by slow speech and impaired syntactic comprehension and naming, showed atrophy in the left posterior temporal cortex and inferior parietal lobule. Apolipoprotein E e4 haplotype frequency was 20% in NFPA, 0% in SD, and 67% in LPA. Cognitive, genetic, and anatomical features indicate that different PPA clinical variants may correspond to different underlying pathological processes.

Alien plants in checklists and floras: towards better communication between taxonomists and ecologists

Abstract: The number of studies dealing with plant invasions is increasing rapidly, but the accumulating body of knowledge has unfortunately also spawned increasing confusion about terminology. Invasions are a global phenomenon and comparison of geographically distant regions and their introduced biota is a crucially important methodological approach for elucidation of the determinants of invasiveness and invasibility. Comparative studies of alien floras provide substantial new insights to our understanding of general patterns of plant invasions. Such studies, using information in previously published floras and checklists, are fundamentally dependent on the quality of the assessment of particular species with respect to their taxonomic identity, time of immigration and invasion status. Three crucial decisions should be made when defining the status of a plant species in a given region: (1) whether the taxon is native or alien to that region (origin status); (2) what is its position in the invasion process, i.e., when was it introduced (residence status); and (3) what is the degree of its naturalization and possible invasion (invasion status). Standard floras differ hugely in their treatment of non-native species and those with appropriate categorization of alien species according to their status are rather rare. The present paper suggests definitions of terms associated with plant invasions and places these into the context of floras. Recommendations are outlined on how to deal with the issue of plant invasions in standard floras with the aim of contributing to a better understanding between taxonomists and ecologists and allowing more detailed comparative analyses of alien floras of various regions of the world.

International Zinc Nutrition Consultative Group (IZiNCG) technical document #1. Assessment of the risk of zinc deficiency in populations and options for its control.

Abstract: Chapter 1: Overview of Zinc Nutrition ............................................................................................................... S99 1.1 Biological functions of zinc ............................................................................................................................. S99 1.2 Tissue zinc distribution and reserves .............................................................................................................. S99 1.3 Zinc metabolism ........................................................................................................................................... S100 1.4 Importance of zinc for human health........................................................................................................... S101 1.5 Human zinc requirements............................................................................................................................. S105 1.5.1 Adult men ............................................................................................................................................. S106 1.5.2 Adult women......................................................................................................................................... S109 1.5.3 Children ................................................................................................................................................ S110 1.5.4 Pregnancy.............................................................................................................................................. S111 1.5.5 Lactation ............................................................................................................................................... S112 1.6 Dietary sources of zinc and suggested revisions of Recommended Daily Intakes .................................... S112 1.6.1 Dietary sources of zinc and factors affecting the proportion of zinc available for absorption ........ S112 1.6.2 Revised estimates of dietary requirements and recommended intakes for zinc ............................... S114 1.7 Zinc toxicity.................................................................................................................................................... S118 1.8 Causes of zinc deficiency and groups at high risk ....................................................................................... S121 1.9 Summary ........................................................................................................................................................ S123

Putting the self into self-conscious emotions: A theoretical model

Abstract: Self-conscious emotions (e.g., shame, pride) are fundamentally important to a wide range of psychological processes, yet they have received relatively little attention compared to other, more "basic" emotions (e.g., sadness, joy). This article outlines the unique features that distinguish self-conscious from basic emotions and then explains why generally accepted models of basic emotions do not adequately capture the self-conscious emotion process. The authors present a new model of self-conscious emotions, specify a set of predictions derived from the model, and apply the model to narcissistic self-esteem regulation. Finally, the authors discuss the model's broader implications for future research on self and emotion.

Landslide inventories and their statistical properties

Abstract: Landslides are generally associated with a trigger, such as an earthquake, a rapid snowmelt or a large storm. The landslide event can include a single landslide or many thousands. The frequency–area (or volume) distribution of a landslide event quantifies the number of landslides that occur at different sizes. We examine three well-documented landslide events, from Italy, Guatemala and the USA, each with a different triggering mechanism, and find that the landslide areas for all three are well approximated by the same three-parameter inverse-gamma distribution. For small landslide areas this distribution has an exponential ‘roll-over’ and for medium and large landslide areas decays as a power-law with exponent −2·40. One implication of this landslide distribution is that the mean area of landslides in the distribution is independent of the size of the event. We also introduce a landslide-event magnitude scale mL = log(NLT), with NLT the total number of landslides associated with a trigger. If a landslide-event inventory is incomplete (i.e. smaller landslides are not included), the partial inventory can be compared with our landslide probability distribution, and the corresponding landslide-event magnitude inferred. This technique can be applied to inventories of historical landslides, inferring the total number of landslides that occurred over geologic time, and how many of these have been erased by erosion, vegetation, and human activity. We have also considered three rockfall-dominated inventories, and find that the frequency–size distributions differ substantially from those associated with other landslide types. We suggest that our proposed frequency–size distribution for landslides (excluding rockfalls) will be useful in quantifying the severity of landslide events and the contribution of landslides to erosion. Copyright © 2004 John Wiley & Sons, Ltd.

The Collaborative Cross, a community resource for the genetic analysis of complex traits

Abstract: The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are less effective for studying intact polygenic networks and interactions among genes, environments, pathogens and other factors. The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease.

The wheat VRN2 gene is a flowering repressor down-regulated by vernalization.

Abstract: Plants with a winter growth habit flower earlier when exposed for several weeks to cold temperatures, a process called vernalization. We report here the positional cloning of the wheat vernalization gene VRN2, a dominant repressor of flowering that is down-regulated by vernalization. Loss of function of VRN2, whether by natural mutations or deletions, resulted in spring lines, which do not require vernalization to flower. Reduction of the RNA level of VRN2 by RNA interference accelerated the flowering time of transgenic winter-wheat plants by more than a month.

Serum albumin: relationship to inflammation and nutrition.

Abstract: Hypoalbuminemia is the result of the combined effects of inflammation and inadequate protein and caloric intake in patients with chronic disease such as chronic renal failure. Inflammation and malnutrition both reduce albumin concentration by decreasing its rate of synthesis, while inflammation alone is associated with a greater fractional catabolic rate (FCR) and, when extreme, increased transfer of albumin out of the vascular compartment. A vicious cascade of events ensues in which inflammation induces anorexia and reduces the effective use of dietary protein and energy intake and augments catabolism of the key somatic protein, albumin. Hypoalbuminemia is a powerful predictor of mortality in patients with chronic renal failure, and the major cause of death in this population is due to cardiovascular events. Inflammation is associated with vascular disease and likely causes injury to the vascular endothelium, and hypoalbuminemia as two separate expressions of the inflammatory process. Albumin has a myriad of important physiologic effects that are essential for normal health. However, simply administering albumin to critically ill patients with hypoalbuminemia has not been shown to improve survival or reduce morbidity. Thus the inference from these clinical studies suggests that the cause of hypoalbuminemia, rather than low albumin levels specifically, is responsible for morbidity and mortality.

Multiple-gate SOI MOSFETs

Abstract: In an ever increasing need for higher current drive and better short-channel characteristics, silicon-on-insulator MOS transistors are evolving from classical, planar, single-gate devices into three-dimensional devices with multiple gates (double-, triple- or quadruple-gate devices). The evolution and the properties of such devices are described and the emergence of a new class of MOSFETs, called triple-plus (3 + )-gate devices offer a practical solution to the problem of the ultimate, yet manufacturable, silicon MOSFET.