bluuebunny/crossref_metadata_2025 huggingface dataset:
Biogeography of the nearshore rocky‐reef fishes at the southern and Baja California islands
Authors: Pondella Daniel J. , Gintert Brooke E. , Cobb Jana R. , Allen Larry G.
Published: January 2005

Aim  To examine the uniqueness and relationship of islands in the San Diegan Province using reef fishes.

Location  Pacific coast of Baja and Southern California.

Methods  Quantitative scuba surveys and statistics were used. Between June 2000 and August 2002, the nearshore rocky‐reef fishes of eight southern California and Baja California islands were quantitatively surveyed. The islands surveyed were: Santa Cruz, San Nicolas, Santa Barbara, Santa Catalina, San Clemente, North Coronado, San Martin and San Benito. These islands span the latitudinal range of offshore islands within the San Diegan marine province. This regional scale approach provided not only the first quantitative description of rocky‐reef fishes at five of these islands, but also allowed comparisons with known biogeographical patterns.

Results  Here we discuss the distribution and abundance of 84 conspicuous rocky‐reef fishes from 35 families. In general, the richness, diversity and composition of fish assemblages at these islands were found to reflect previously described biogeographical processes. The rocky reef fish assemblages of all islands in the survey were found to be significantly distinctive form each other. Phenetic analyses revealed two clusters. San Clemente, Santa Catalina and North Coronado clustered as a warm‐water assemblage in the middle of the San Diegan Province. The remaining islands grouped together as a cold‐water assemblage, despite the geographically disjunct position of the islands within this cluster. The relatedness of islands was independent of distance. Examination of the most common fish species at all islands revealed that while some conformed to the north–south trending density distributions predicted by previous investigators, the distribution of others could not be explained by latitude or temperature regimes. No single pattern explained the density of fishes at all islands. Both the rock croaker, Pareques sp., and flag cabrilla, Epinephelus labriformis, were observed at San Benito during these surveys, representing northern range extensions and may be indicators of the warming trend observed in this marine province.

Main conclusion  For nearshore rocky‐reef fishes, the islands of the San Diegan marine province are distinct and their interrelatedness is independent of the distance between them.
Geographic range size, seedling ecophysiology and phenotypic plasticity in AustralianAcaciaspecies
Authors: Pohlman Catherine L. , Nicotra Adrienne B. , Murray Brad R.
Published: January 2005

Aim The degree to which eco‐physiological traits critical to seedling establishment are related to differences in geographic range size among species is not well understood. Here, we first tested the idea that seedling eco‐physiological attributes associated with establishment differ between narrowly distributed and geographically widespread plant species. Secondly, we tested the notion that species occupying wide geographic ranges have greater phenotypic plasticity in response to the environment than contrasted species with more restricted distributions.

Location Eastern Australia.

Methods We compared five pairs of geographically restricted and widespreadAcaciaspecies grown under glasshouse conditions for differences in seedling relative growth rate and associated allocational, morphological and physiological traits. We then examined whether widespread species displayed greater phenotypic plasticity in these traits than narrowly distributed species in response to changes in soil water availability.

Results Neither relative growth rate nor any measure of biomass accumulation or allocation differed significantly between seedlings of narrowly distributed and widespread species. In addition, the plasticity of biomass allocation was not greater in widespread species. However, the leaflets of widespread species had higher photosynthetic capacity and greater plasticity of water use efficiency than the leaflets of narrowly distributed species.

Main conclusions We demonstrated fundamental differences in the physiology and plasticity of leaflets of widespread and narrowly distributed species. The greater plasticity of these seedling leaflet traits may allow widespreadAcaciaspecies to utilize a wider range of environmental conditions in relation to soil moisture than restrictedAcaciaspecies. However, we did not find corresponding differences in mean or plasticity of seedling growth and allocational traits. In general, we suggest that relationships between rarity and species traits are both context and taxon specific.
A Model of Toxoplasmosis Incidence in the UK: Evidence Synthesis and Consistency of Evidence
Authors: Welton N. J. , Ades A. E.
Published: January 2005

We present a Bayesian evidence synthesis model combining data on seroprevalence, seroconversion and tests of recent infection, to produce estimates of current incidence of toxoplasmosis in the UK. The motivation for the study was the need for an estimate of current average incidence in the UK, with a realistic assessment of its uncertainty, to inform a decision model for a national screening programme to prevent congenital toxoplasmosis. The model has a hierarchical structure over geographic region, a random-walk model for temporal effects and a fixed age effect, with one or more types of data informing the regional estimates of incidence. Inference is obtained by using Markov chain Monte Carlo simulations. A key issue in the synthesis of evidence from multiple sources is model selection and the consistency of different types of evidence. Alternative models of incidence are compared by using the deviance information criterion, and we find that temporal effects are region specific. We assess the consistency of the various forms of evidence by using cross-validation where practical, and posterior and mixed prediction otherwise, and we discuss how these measures can be used to assess different aspects of consistency in a complex evidence structure. We discuss the contribution of the various forms of evidence to estimated current average incidence.
Hierarchical Modelling of Orthopaedic Hip Replacement Damage Accumulation and Reliability
Authors: Wilson Simon P.
Published: January 2005

We describe the modelling of crack initiation and growth in a group of orthopaedic hip replacements. A hierarchical model is proposed and fitted with Bayesian methods, implemented by the Gibbs sampler. Our interest is in predicting the failure of the replacements, which is predominately caused by crack activity in the cement that fixates the metal prosthesis to the bone. Simulation from the model based on posterior distribution samples allows us to approx-imate the reliability function and to assess the effect on reliability of the properties of the replacement. We discuss the ideas behind this approach, which can be generalized to any group of physical systems and any function of their state that interests us.
Pharmacoepidemiology of anabolic androgenic steroids: a review
Authors: Thiblin Ingemar , Petersson Anna
Published: January 2005

Non‐prescribed use of anabolic androgenic steroids (AAS) has been associated with a number of physical and psychiatric/behavioural complications, some of which are potentially lethal. Here, we review both observational and experimental studies on human subjects concerned with such side‐effects. The only physical complication of AAS use that receives definitive support from such investigations is unfavourable changes in blood lipid profiles. Support for various psychiatric complications has also been provided by a number of cross‐sectional studies, most involving comparisons between weight‐training individuals who use or do not use AAS. Certain of these complications, in particular hypomania and increased aggressiveness, have been confirmed in some, but not all, randomized controlled studies. Epidemiological attempts to determine whether AAS use triggers violent behaviour have failed, primarily because of high rates of non‐participation. Studies regarding the prevalence of AAS use in different populations typically report life‐time prevalences of 1–5% among adolescents. However, the life‐time prevalence (i.e. use on at least one occasion) is of doubtful relevance in attempting to estimate the number of individuals at risk for side‐effects, as most of these complications appear to develop during prolonged use of AAS. Furthermore, it is reasonable to assume that the symptoms and signs of AAS use are often overlooked by healthcare professionals, so that the number of cases of possible AAS‐related complications is virtually unknown. These limitations, together with an apparently low prevalence of prolonged AAS use among the general population, indicate that future epidemiological research in this area should focus on retrospective case–control studies and, perhaps, also on prospective cohort studies of populations selected for a high prevalence of AAS use, rather than attempting to perform large‐scale population‐based studies.
Protective effect of taurine against alendronate‐induced gastric damage in rats
Authors: Şener Göksel , Şehirli Özer , Cetinel Sule , Midillioğlu Şükrü , Gedik Nursal , Ayanoğlu‐Dülger Gül
Published: January 2005

Alendronate (ALD) causes serious gastrointestinal adverse effects. The aim of this study was to investigate whether taurine (TAU), a semi‐essential amino acid and an antioxidant, improves the alendronate‐induced gastric injury. Rats were administered 20 mg/kg ALD by gavage for 4 days, either alone or following treatment with TAU (50 mg/kg, i.p.). On the last day of treatment, following drug administration, pylorus ligation was performed and 2 h later, rats were killed and stomachs were removed. Gastric acidity and tissue ulcer index values, lipid peroxidation and glutathione (GSH) levels, myeloperoxidase (MPO) activity as well as the histologic appearance of the stomach tissues were determined. Chronic oral administration of ALD induced significant gastric damage, increasing lipid peroxidation, MPO activity and collagen content, as well as decreasing tissue GSH levels. Treatment with TAU prevented the damage and also the changes in biochemical parameters. Findings of the present study suggest that ALD induces oxidative gastric damage by a local irritant effect, and that TAU ameliorates this damage by its antioxidant and/or membrane‐stabilizing effects.
G protein‐coupled receptors: a count of 1001 conformations
Authors: Vauquelin G. , Van Liefde I.
Published: January 2005

G protein‐coupled receptors (GPCRs) were initially regarded to adopt an inactive and an active conformation and to activate a single type of G protein. Studies with recombinant cell systems have led to a more complex picture. First, GPCRs can activate distinct G protein species. Second, GPCR multistate models have been invoked to explain their complex behaviour in the presence of agonists, antagonists and other binding partners. The occurrence of intermediate receptor conformational states during GPCR activation and antagonist binding is suggested by fluorescence measurements and studies with constitutively active receptor mutants and insurmountable antagonists. Different agonists may trigger distinct effector pathways through a single receptor by dictating its preference for certain G proteins (i.e. ‘agonist trafficking’). Structural modification and exogenous and endogenous (e.g. other cellular proteins, lipids) allosteric modulators also affect ligand–GPCR interaction and receptor activation. These new developments in GPCR research could lead to the development of more selective therapeutic drugs.
Multiple‐brooding in birds of prey: South African Black Sparrowhawks Accipiter melanoleucus extend the boundaries
Authors: CURTIS ODETTE , MALAN GERARD , JENKINS ANDREW , MYBURGH NICO
Published: January 2005

Multiple‐brooding (raising more than one brood of young in quick succession) occurs infrequently in raptors and is generally restricted to either smaller species with shorter nesting periods, co‐operative breeders or species capable of capitalizing on conditions of prolonged food abundance whenever they occur. This paper presents the first recorded cases of multiple‐brooding in the Black Sparrowhawk Accipiter melanoleucus from two distinct locales in South Africa. In the Western Cape (Cape Peninsula), four attempts to multiple‐brood were recorded in four different years, involving three distinct pairs of birds, and in KwaZulu–Natal (Eshowe), three distinct pairs of Sparrowhawks successfully multiple‐brooded on several occasions over a 5‐year study period. These results establish the Black Sparrowhawk as one of only two relatively large, monogamous raptor species, and the only specialist bird‐eating raptor, in which multiple‐brooding has been recorded with any frequency. The species’ capacity to thrive in human‐modified environments (i.e. alien plantations) and particularly to exploit associated foraging opportunities (e.g. high densities of doves and pigeons in suburban areas) may, at least partly, account for the instances of multiple‐brooding reported here. We suggest that biologists be more vigilant for cases of multiple‐brooding in raptors, as it is possible that this trait is more common than originally thought and has previously been overlooked.
Comparison of migratory tendency in European Quail Coturnix c. coturnix, domestic Japanese Quail Coturnix c. japonica and their hybrids
Authors: DERÉGNAUCOURT SEBASTIEN , GUYOMARC’H JEAN‐CHARLES , BELHAMRA MOHAMED
Published: January 2005

Since the 1970s, the decline of the occidental populations of European Quail Coturnix c. coturnix, a partial migrant Galliform species, has driven the release of domestic Japanese Quail Coturnix c. japonica into the wild as game birds. Recent experiments suggest that reproductive isolating mechanisms have not developed to prevent hybridization between European and Japanese Quail. To assess the potential impact of hybridization between the subspecies in the wild, this study aims to compare the migratory characteristics of captive European Quail, domestic Japanese Quail, F1 hybrids and a backcross. In a laboratory experiment, birds hatched in summer and reared under a natural photoperiod were transferred during winter to an artificial photoperiod (light–dark) of 14 : 10 h. Behavioural (migratory restlessness, crowing activity in males) and physiological (sexual development, fat accumulation, body mass) measures were recorded. Domestic Japanese Quail showed no migratory tendency in response to the increased day length. F1 hybrids showed rapid sexual development and few of them exhibited the typical profile of a migrant bird. Backcrosses showed great variation in their response, comparable with those of the European Quail. Therefore, hybridization could lead to an increased proportion of quail showing sedentary rather than migratory behaviour. Furthermore, hybrids that do show migratory behaviour have the potential to facilitate Japanese gene flow into areas where the release of domestic Quail as game birds is not yet practised.
First pairing in Snow GeeseAnser caerulescens: at what age and at what time of year does it occur?
Authors: GANTER BARBARA , BOYD W. SEAN , BARANYUK VASILY V. , COOKE FRED
Published: January 2005

In migratory birds, the place and time of pair formation are important parameters for population structure and dynamics. Geese are not only migratory but also exhibit long‐term monogamy, and therefore the first pairing event in a bird's lifetime is of particular importance. Through behavioural observations of young, known‐age, marked birds conducted on the wintering grounds during three winter seasons we investigated two aspects of the timing of first pair formation in the Wrangel Island population of Snow GeeseAnser caerulescens: (1) the age at which birds first form pair bonds, and (2) the seasonal pattern of first pair formation. Wrangel Island Snow Geese paired considerably later in life than Snow Geese from a low‐Arctic population: almost none of the birds formed pairs in their second winter, and many were still in sibling groups for at least part of that season. The proportion of birds in pairs continued to increase until at least 5 years of age. Most pairing took place during the observation periods, and in general the proportion of birds in pair bonds increased gradually throughout the winter season. The amount of pairing during spring migration or summer varied annually and among cohorts, indicating that even very young birds may be able to form pair bonds quickly if conditions on the breeding grounds are unusually favourable. Pairing later and remaining in family groups longer may be a response to breeding conditions in this high‐Arctic colony. Here, productivity is typically low due to harsh weather and predation, whereas Snow Geese breeding in the low Arctic are less restricted and form pairs and start to breed when younger. The fact that most, but not all, pairing takes place on the wintering grounds helps explain why a previous study found a certain amount of gene flow between the two Wrangel Island subpopulations with separate wintering grounds.
Pair bond and breeding success in Blue TitsParus caeruleusand Great TitsParus major
Authors: PAMPUS MIRIAM , SCHMIDT KARL‐HEINZ , WILTSCHKO WOLFGANG
Published: January 2005

Data from 939 nests of the Blue TitParus caeruleusand 1008 nests of the Great TitP. majorfrom nestboxes provided in superabundance in mixed forest study sites between 1976 and 2001 were analysed to examine the effects of mate retention on breeding success and the relationship between mate fidelity and site fidelity. Most birds retained their former partner (76% in Great Tits and 65% in Blue Tits). The probability of a pair divorcing was affected by male age in Great Tits, divorce being more likely in pairs with first‐year males. Great Tit pairs breeding together for a second season bred earlier, but had no higher breeding success than pairs breeding together for the first time. In Blue Tits laying date and start of incubation tended to be earlier in pairs breeding together for a second season, but hatching and fledging dates were not earlier than in other pairs. Great Tit pairs breeding together for two consecutive seasons bred earlier in the second season than in the first, but breeding success did not differ significantly between years. In both species, breeding performance did not differ between pairs that divorced after a season and pairs that stayed together. Thus breeding success did not determine whether a pair divorced or bred together again. Neither Blue Tits nor Great Tits improved their breeding performance through divorce. Blue Tit females even had fewer fledglings in the year after divorce than in the year before. Mate retention affected breeding site fidelity. Blue Tit females had greater breeding dispersal distances between consecutive years when re‐mating than when breeding again with the same mate. In Great Tits both males and females dispersed more when re‐mating than when retaining the former partner, suggesting that mate retention increased the chance of retaining the breeding site. In both species, breeding dispersal distances did not differ between pairs that divorced and pairs in which one mate disappeared. Because no major advantage of mate retention was evident, we suggest that mate retention evolved under different conditions than those found in study sites with high breeding densities and a superabundance of artificial nesting sites.
Development of chicks and predispersal behaviour of young in the Eagle Owl Bubo bubo
Authors: PENTERIANI V. , DELGADO M. M. , MAGGIO C. , ARADIS A. , SERGIO F.
Published: January 2005

Little quantitative information on the development and behaviour of chicks and young is available for many species, despite the crucial importance of such data and the sensitivity of this stage in a bird's life. For Eagle Owls Bubo bubo, despite the large amount of scientific literature on this species, much basic information is lacking. This study provides a photographic and morphometric guide for age estimation of nestlings and fledglings, as well as data on the call behaviour of young, and patterns of movements during the post‐fledging dependence period. The most remarkable event in chick development is the rapid increase in mass, and size gain, during the first 30 and 40–45 days, respectively. Because after this time morphometric differences become less evident, young‐feather development is more useful for ageing. Patterns of chick call behaviour showed that the time spent calling increased with age and, from 110 days of age, chick vocalizations were usually uniformly distributed through the whole night and most synchronized at sunset and sunrise (the maximum recorded number of vocalizations per chick and per night was 1106 calls). During the post‐fledging dependence period, radiotagged Owls moved widely, up to 1500 m from the nest after the age of 80–90 days. During such movements, the mean distance among siblings increased with age, from 168 m on average for juveniles less than 100 days old, to 489 m for those older than 100 days. Definitive dispersal started when young were about 150–160 days old. Information on chick call behaviour and movements is crucial for unbiased census and nest checking, as well as for the definition of young post‐fledging areas. Knowledge of the latter is very important in terms of conservation and management (especially for those species that move largely around their nest before dispersal) owing to the high mortality that can occur during this period.
Frequency and consequences of feather holes in Barn SwallowsHirundo rustica
Authors: PAP PÉTER LÁSZLÓ , TÖKÖLYI JÁCINT , SZÉP TIBOR
Published: January 2005

The relationship between feather quality, estimated through the prevalence and intensity of feather holes, and the breeding performance and survival of the Barn SwallowHirundo rusticawas studied over a 5‐year period. In addition, we present some indirect data on the role of chewing lice in producing the feather holes. The balanced distribution of feather holes (high prevalence, low aggregation) corresponds with the pattern of distribution of lice on colonial birds, and in the Barn Swallow. Feather holes were significantly and positively associated with the arrival dates of the birds, as both males and females with an increased number of feather holes started laying later. Females that survived the winter had significantly fewer holes than non‐surviving females, whereas there was no difference in feather hole number between surviving and non‐surviving males. Given that there was no association between the number of feather holes and body condition indices, except for the tail length of male Barn Swallows, we suggest that the negative effect of feather holes on the fitness of the birds is mainly apparent during periods of intensive locomotor activity, such as migration. Alternatively, if feather holes are an indicator of quality, those birds with a high intensity of feather holes may have been of poor quality. These birds may have been less able to cope with the environmental conditions, resulting in the lower survival and later arrival of the birds to the breeding grounds. The negative relationship between the length of the outermost tail feathers of males and the incidence of feather holes suggests that the tail is a condition‐dependent secondary sexual characteristic.
Selection of arboreal termitaria for nesting by cooperatively breeding Micronesian KingfishersTodiramphus cinnamominus reichenbachii
Authors: KESLER DYLAN C. , HAIG SUSAN M.
Published: January 2005

Limited nest‐site availability appears to be an important factor in the evolution of delayed dispersal and cooperative breeding in some cavity‐nesting species. The cooperatively breeding Pohnpei subspecies of Micronesian KingfisherTodiramphus cinnamominusreichenbachii excavates nest cavities from the nests of arboreal termitesNasutitermesspp., or termitaria. In this first published description of nest‐sites for this subspecies, we used surveys, remote sensing and radiotelemetry to evaluate the relationship between nest‐site availability and co‐operation. Results illustrate that nest termitaria are higher in the forest canopy, larger in volume and occur in areas with more contiguous canopy cover than unused termitaria. Nest termitaria were selected independently of the proximity to forest edges and territory boundaries, and we found no difference in characteristics of termitaria used by cooperative groups and breeding pairs. Logistic regression modelling indicated that termitaria with nest‐like characteristics were not limited in abundance, suggesting that neither the prospects of inheriting nesting resources nor limited nest‐site abundance are probable explanations for delayed dispersal in the Pohnpei subspecies of Micronesian Kingfisher.
Overexpressed Sod1p acts either to reduce or to increase the lifespans and stress resistance of yeast, depending on whether it is Cu2+‐deficient or an active Cu,Zn‐superoxide dismutase
Authors: Harris Nicholas , Bachler Marcus , Costa Vitor , Mollapour Mehdi , Moradas‐Ferreira Pedro , Piper Peter W.
Published: January 2005

Yeast overexpressing SOD1, the gene for Cu,Zn‐superoxide dismutase (Cu,Zn‐Sod), was used to determine how Sod1p overexpression influences the chronological lifespan [the survival of non‐dividing stationary (G0) phase cells over time], the replicative lifespan (the number of buds produced by actively dividing yeast cells) and stress resistance. Increasing the level of active Cu,Zn‐Sod in yeast was found to require either growth in the presence of high copper, or the simultaneous overexpression of both SOD1 and CCS1 (the latter being the gene that encodes the chaperone dedicated to Cu2+‐loading of Sod1p in vivo). Dual SOD1 + CCS1 overexpression elevated the levels of Cu,Zn‐Sod activity six‐ to eight‐fold in vegetative cultures. It also increased the optimized survival of stationary cells up to two‐fold, showing this chronological lifespan is ultimately limited by oxidative stress. In contrast, several detrimental effects resulted when the SOD1 gene was overexpressed in the absence of either high copper or a simultaneous overexpression of CCS1. Both the chronological and the replicative lifespans were shortened; the cells displayed an abnormally high level of endogenous oxidative stress, resulting in a high rate of spontaneous mutation. Such harmful effects were all reversed through the overexpression of CCS1. It is apparent therefore that they relate to the incomplete Cu2+‐loading of the overexpressed Sod1p, most probably accumulation of a Cu2+‐deficient Sod1p to appreciable levels in vivo. The same events may generate the detrimental effects that are frequently, though not universally, observed when Cu,Zn‐Sod overexpression is attempted in metazoans.
Activation of the PI3K/Akt signal transduction pathway and increased levels of insulin receptor in protein repair‐deficient mice
Authors: Farrar Christine , Houser Carolyn R. , Clarke Steven
Published: January 2005

Protein l‐isoaspartate (d‐aspartate) O‐methyltransferase is an enzyme that catalyses the repair of isoaspartyl damage in proteins. Mice lacking this enzyme (Pcmt1–/– mice) have a progressive increase in brain size compared with wild‐type mice (Pcmt1+/+ mice), a phenotype that can be associated with alterations in the PI3K/Akt signal transduction pathway. Here we show that components of this pathway, including Akt, GSK3β and PDK‐1, are more highly phosphorylated in the brains of Pcmt1–/– mice, particularly in cells of the hippocampus, in comparison with Pcmt1+/+ mice. Examination of upstream elements of this pathway in the hippocampus revealed that Pcmt1–/– mice have increased activation of insulin‐like growth factor‐I (IGF‐I) receptor and/or insulin receptor. Western blot analysis revealed an approximate 200% increase in insulin receptor protein levels and an approximate 50% increase in IGF‐I receptor protein levels in the hippocampus of Pcmt1–/– mice. Higher levels of the insulin receptor protein were also found in other regions of the adult brain and in whole tissue extracts of brain, liver, heart and testes of both juvenile and adult Pcmt1–/– mice. There were no significant differences in plasma insulin levels for adult Pcmt1–/– mice during glucose tolerance tests. However, they did show higher peak levels of blood glucose, suggesting a mild impairment in glucose tolerance. We propose that Pcmt1–/– mice have altered regulation of the insulin pathway, possibly as a compensatory response to altered glucose uptake or metabolism or as an adaptive response to a general accumulation of isoaspartyl protein damage in the brain and other tissues.
Large Sulfur Bacteria and the Formation of Phosphorite
Authors: Schulz Heide N. , Schulz Horst D.
Published: January 2005

Phosphorite deposits in marine sediments are a long-term sink for an essential nutrient, phosphorus. Here we show that apatite abundance in sediments on the Namibian shelf correlates with the abundance and activity of the giant sulfur bacterium
Thiomargarita namibiensis
, which suggests that sulfur bacteria drive phosphogenesis. Sediments populated by
Thiomargarita
showed sharp peaks of pore water phosphate (≤300 micromolar) and massive phosphorite accumulations (≥50 grams of phosphorus per kilogram). Laboratory experiments revealed that under anoxic conditions,
Thiomargarita
released enough phosphate to account for the precipitation of hydroxyapatite observed in the environment.
Cryo-Electron Tomography Reveals the Cytoskeletal Structure of
Spiroplasma melliferum
Authors: Kürner Julia , Frangakis Achilleas S. , Baumeister Wolfgang
Published: January 2005

Evidence has accumulated recently that not only eukaryotes but also bacteria can have a cytoskeleton. We used cryo–electron tomography to study the three-dimensional structure of
Spiroplasma melliferum
cells in a close-to-native state at ∼4-nanometer resolution. We showed that these cells possess two types of filaments arranged in three parallel ribbons underneath the cell membrane. These two filamentous structures are built of the fibril protein and possibly the actin-like protein MreB. On the basis of our structural data, we could model the motility modes of these cells and explain how helical Mollicutes can propel themselves by means of coordinated length changes of their cytoskeletal ribbons.
How Obesity Causes Diabetes: Not a Tall Tale
Authors: Lazar Mitchell A.
Published: January 2005

The epidemic of obesity-associated diabetes is a major crisis in modern societies, in which food is plentiful and exercise is optional. The biological basis of this problem has been explored from evolutionary and mechanistic perspectives. Evolutionary theories, focusing on the potential survival advantages of “thrifty” genes that are now maladaptive, are of great interest but are inherently speculative and difficult to prove. Mechanistic studies have revealed numerous fat-derived molecules and a link to inflammation that, together, are hypothesized to underlie the obesity-diabetes connection and thereby represent prospective targets for therapeutic intervention.
Mitochondrial Dysfunction and Type 2 Diabetes
Authors: Lowell Bradford B. , Shulman Gerald I.
Published: January 2005

Maintenance of normal blood glucose levels depends on a complex interplay between the insulin responsiveness of skeletal muscle and liver and glucose-stimulated insulin secretion by pancreatic β cells. Defects in the former are responsible for insulin resistance, and defects in the latter are responsible for progression to hyperglycemia. Emerging evidence supports the potentially unifying hypothesis that both of these prominent features of type 2 diabetes are caused by mitochondrial dysfunction.
Ecological Change, Group Territoriality, and Population Dynamics in Serengeti Lions
Authors: Packer Craig , Hilborn Ray , Mosser Anna , Kissui Bernard , Borner Markus , Hopcraft Grant , Wilmshurst John , Mduma Simon , Sinclair Anthony R. E.
Published: January 2005

Territorial behavior is expected to buffer populations against short-term environmental perturbations, but we have found that group living in African lions causes a complex response to long-term ecological change. Despite numerous gradual changes in prey availability and vegetative cover, regional populations of Serengeti lions remained stable for 10- to 20-year periods and only shifted to new equilibria in sudden leaps. Although gradually improving environmental conditions provided sufficient resources to permit the subdivision of preexisting territories, regional lion populations did not expand until short-term conditions supplied enough prey to generate large cohorts of surviving young. The results of a simulation model show that the observed pattern of “saltatory equilibria” results from the lions' grouping behavior.
Mathematical Modeling of Planar Cell Polarity to Understand Domineering Nonautonomy
Authors: Amonlirdviman Keith , Khare Narmada A. , Tree David R. P. , Chen Wei-Shen , Axelrod Jeffrey D. , Tomlin Claire J.
Published: January 2005

Planar cell polarity (PCP) signaling generates subcellular asymmetry along an axis orthogonal to the epithelial apical-basal axis. Through a poorly understood mechanism, cell clones that have mutations in some PCP signaling components, including some, but not all, alleles of the receptor
frizzled
, cause polarity disruptions of neighboring wild-type cells, a phenomenon referred to as domineering nonautonomy. Here, a contact-dependent signaling hypothesis, derived from experimental results, is shown by reaction-diffusion, partial differential equation modeling and simulation to fully reproduce PCP phenotypes, including domineering nonautonomy, in the
Drosophila
wing. The sufficiency of this model and the experimental validation of model predictions reveal how specific protein-protein interactions produce autonomy or domineering nonautonomy.
Carotenoid Cation Formation and the Regulation of Photosynthetic Light Harvesting
Authors: Holt Nancy E. , Zigmantas Donatas , Valkunas Leonas , Li Xiao-Ping , Niyogi Krishna K. , Fleming Graham R.
Published: January 2005

Photosynthetic light harvesting in excess light is regulated by a process known as feedback deexcitation. Femtosecond transient absorption measurements on thylakoid membranes show selective formation of a carotenoid radical cation upon excitation of chlorophyll under conditions of maximum, steady-state feedback deexcitation. Studies on transgenic
Arabidopsis thaliana
plants confirmed that this carotenoid radical cation formation is correlated with feedback deexcitation and requires the presence of zeaxanthin, the specific carotenoid synthesized during high light exposure. These results indicate that energy transfer from chlorophyll molecules to a chlorophyllzeaxanthin heterodimer, which then undergoes charge separation, is the mechanism for excess energy dissipation during feedback deexcitation.
Deep-Ultraviolet Quantum Interference Metrology with Ultrashort Laser Pulses
Authors: Witte Stefan , Zinkstok Roel Th. , Ubachs Wim , Hogervorst Wim , Eikema Kjeld S. E.
Published: January 2005

Precision spectroscopy at ultraviolet and shorter wavelengths has been hindered by the poor access of narrow-band lasers to that spectral region. We demonstrate high-accuracy quantum interference metrology on atomic transitions with the use of an amplified train of phase-controlled pulses from a femtosecond frequency comb laser. The peak power of these pulses allows for efficient harmonic upconversion, paving the way for extension of frequency comb metrology in atoms and ions to the extreme ultraviolet and soft x-ray spectral regions. A proof-of-principle experiment was performed on a deep-ultraviolet (2 × 212.55 nanometers) two-photon transition in krypton; relative to measurement with single nanosecond laser pulses, the accuracy of the absolute transition frequency and isotope shifts was improved by more than an order of magnitude.
Creating Order from Random Fluctuations in Small Spin Ensembles
Authors: Budakian R. , Mamin H. J. , Chui B. W. , Rugar D.
Published: January 2005

We demonstrate the ability to create spin order by using a magnetic resonance force microscope to harness the naturally occurring statistical fluctuations in small ensembles of electron spins. In one method, we hyperpolarized the spin system by selectively capturing the transient spin order created by the statistical fluctuations. In a second method, we took a more active approach and rectified the spin fluctuations by applying real-time feedback to the entire spin ensemble. The created spin order can be stored in the laboratory frame for a period on the order of the longitudinal relaxation time of 30 seconds and then read out.
ESTABLISHING A RELIABLE JINI INFRASTRUCTURE FOR PARALLEL APPLICATIONS
Authors: BAKER MARK , SMITH GARRY
Published: January 2005

Java is becoming an increasingly popular language for developing distributed and parallel scientific and engineering applications. Jini is a Java-based infrastructure developed by Sun that can allegedly provide all the services necessary to support distributed applications. It is the aim of this paper to explore and investigate the services and properties that Jini actually provides and match these against the needs of high performance distributed and parallel applications written in Java. The motivation for this work is the need to develop a distributed infrastructure to support an MPI-like interface to Java known as MPJ.

In the first part of the paper we discuss the needs of MPJ, the parallel environment that we wish to support. In particular we look at aspects such as reliability and ease of use. We then move on to sketch out the Jini architecture and review the components and services that Jini provides. In the third part of the paper we critically explore a Jini infrastructure that could be used to support MPJ. Here we are particularly concerned with Jini's ability to support reliably a cocoon of MPJ processes executing in a heterogeneous envirnoment. In the final part of the paper we summarise our findings and report on future work being undertaken on Jini and MPJ.
ON THE USE OF COSCHEDULING IN FAST COMMUNICATION SYSTEMS
Authors: CHIOLA GIOVANNI , CIACCIO GIUSEPPE , ANGLANO COSIMO
Published: January 2005

Coscheduling of communication and computation is considered one of the crucial points to obtain good performance out of fast communication systems. Various techniques have been examined in literature ranging from strict "gang scheduling" of all processes possibly involved in message exchange to "implicit coscheduling" in which the communication support system may act on the scheduling of sending and receiving processes trying to improve performance without explicit coordination by special purpose message exchanges. Based on the experience in implementing the GAMMA communication system, we are convinced that some form of coscheduling is needed in order to obtain best performance in communication. However we believe that most of the approaches described in literature so far are too simplistic to be really effective. In this paper we point out and classify some of the major problems a system that attempts to coschedule communication and computation should address. We hope to clarify the goals of a coscheduler by taking some of the crucial characteristics of the communication into account. We also hope to be able to devise some more integrated and coherent strategies of coordination between process scheduling and choice of communication modes.
OPIOM: OFF-PROCESSOR IO WITH MYRINET
Authors: GEOFFRAY PATRICK
Published: January 2005

As processors become more powerful and clusters larger, users will exploit this increased power to progressively run larger and larger problems. Today's datasets in biology, physics or multimedia applications are huge and require high performance storage sub-systems. As a result, the hot spot of cluster computing is gradually moving from high performance computing to high performance IO. The solutions proposed by the parallel file-system community try to improve performance by working at the kernel level to enhance the regular IO design or by using a dedicated Storage Area Network like Fiber Channel.

We propose a new design to merge the communication network and the storage network at the best price. We have implemented it in OPIOM with the Myrinet interconnect: OPIOM moves data asynchronously from SCSI disks to the embedded memory of a Myrinet interface in order to send it to a remote node. This design presents attractive features: high performance and extremely low host overhead.
PLAYING INSIDE THE BLACK BOX: USING DYNAMIC INSTRUMENTATION TO CREATE SECURITY HOLES
Authors: MILLER BARTON P. , CHRISTODORESCU MIHAI , IVERSON ROBERT , KOSAR TEVFIK , MIRGORODSKII ALEXANDER , POPOVICI FLORENTINA
Published: January 2005

Programs running on insecure or malicious hosts have often been cited as ripe targets for security attacks. The enabling technology for these attacks is the ability to easily analyze and control the running program. Dynamic instrumentation provides the necessary technology for this analysis and control. As embodied in the DynInst API library, dynamic instrumentation allows easy construction of tools that can: (1) inspect a running process, obtaining structural information about the program; (2) control the execution of the program, (3) cause new libraries to be dynamically loaded into the process' address space; (4) splice new code sequences into the running program and remove them; and (5) replace individual call instructions or entire functions.

With this technology, we have provided two demonstrations of its use: exposing vulnerabilities in a distributed scheduling system (Condor), and bypassing access to a license server by a word processor (Framemaker). The first demonstration shows the danger of remote execution of a job on a system of unknown pedigree, and the second demonstration shows the vulnerabilities of software license protection schemes. While these types of vulnerabilities have long been speculated, we show how, with the right tool (the DynInst API), they can be easily accomplished. Along with this discussion of vulnerabilities, we also discuss strategies for compensating for them.
A SCALABLE AND EFFICIENT STORAGE ALLOCATOR ON SHARED-MEMORY MULTIPROCESSORS
Authors: VEE VOON-YEE , HSU WEN-JING
Published: January 2005

An efficient dynamic storage allocator is important for time-critical parallel programs. In this paper, we present a fast and simple parallel allocator for fixed size blocks on shared-memory multiprocessors. We show both theoretically and empirically that the allocator incurs very low lock contention. The allocator is tested with parallel simulation applications with frequent allocation and release requests. The results confirm that our allocator is indeed very efficient.
ON THE NECESSITY OF FORMAL MODELS FOR REAL-TIME PARALLEL COMPUTATIONS
Authors: BRUDA STEFAN D. , AKL SELIM G.
Published: January 2005

We assume the multitape real-time Turing machine as a formal model for parallel real-time computation. Then, we show that, for any positive integer k, there is at least one language Lk which is accepted by a k-tape real-Turing machine, but cannot be accepted by a (k - 1)-tape real-time Turing machine. It follows therefore that the languages accepted by real-time Turing machines form an infinite hierarchy with respect to the number of tapes used. Although this result was previously obtained elsewhere, our proof is considerably shorter, and explicitly builds the languages Lk. The ability of the real-time Turing machine to model practical real-time and/or parallel computations is open to debate. Nevertheless, our result shows how a complexity theory based on a formal model can draw interesting results that are of more general nature than those derived from examples. Thus, we hope to offer a motivation for looking into realistic parallel real-time models of computation.
Enhance the Yield Shear Stress of Magnetorheological Fluids
Authors: TANG X. , ZHANG X. , TAO R.
Published: January 2005

To enhance the yield shear stress of magnetorheological (MR) fluids is an important task. Since thick columns have a yield stress much higher than a single-chain structure, we enhance the yield stress of an MR fluids by changing the microstructure of MR fluids. Immediately after a magnetic field is applied, we compress the MR fluid along the field direction. SEM images show that the particle chains are pushed together to form thick columns. The shear force measured after the compression indicates that the yield stress can reach as high as 800 kPa under a moderate magnetic field, while the same MR fluid has a yield stress of 80 kPa without compression. This enhanced yield stress increases with the magnetic field and compression pressure and has an upper limit well above 800 kPa. The method is also applicable to electrorheological fluids.
The Electrostatic Interaction between Coated Particles in Electrorheological Fluids
Authors: Men Shouqiang , Xu Xiaoyu , Lan Yucheng , Xu Sujuan , Lu Kunquan
Published: January 2005

A theoretical method is developed to calculate the interaction force between coated particles in a host liquid under an electric field. With the nonlinear conduction effect of the oil taken into consideration, the Poisson's equation of the potential φ is transformed into a Laplace's equation. At the same time, the multipolar expansion method is applied to solve the problem. By self-consistent calculation, the conductivity of the host liquid and the local field strength can be obtained simultaneously. On the basis of the model, a single chain structure spanning two parallel electrodes is dealt with. We find that the interaction between neighboring particles is strengthened when a dielectric layer is coated on the surface of the metallic spheres in comparison with that of the dielectric particles, and the interaction force is nearly independent on the dielectric constant of the coating layer except that the layer is a sort of insulator and its dielectric constant is rather small. Further, the interaction force in a dc field varies with the field strength more slowly than a parabola, and approaches a straight line in some cases, even has a maximum.
A THERMODYNAMIC APPROACH TO FIELD-INDUCED STRESSES IN ELECTRO- AND MAGNETOACTIVE COMPOSITES
Authors: SHKEL Y. M. , KLINGENBERG D. J.
Published: January 2005

An equilibrium thermodynamic approach is employed to derive a continuum-level expression for the field-induced stress in uniaxial anisotropic materials, such as electro- and magnetorheological suspensions. This model introduces new electro- and magnetostriction coefficients, which are material parameters that describe the strain dependence of the dielectric and permeability tensors as well as the field-induced stresses. An idealized microscopic model illustrates the relationships between microscopic parameters and the macroscopic magnetostriction coefficients. The model is used to determine the stresses in common applications; predictions from the continuum approach agree with direct calculations of the normal stress and static shear modulus of magnetorheological suspensions.
Structures of a Magnetorheological Fluid
Authors: Gulley G. L. , Tao R.
Published: January 2005

Molecular dynamics simulations were carried out to find the underlying structures of a Magnetorheological (MR) fluid while taking into account dipolar forces, viscous drag, and the Brownian force. Three different structures were found: the bct lattice, chains, and a liquid state. The conditions under which these structures are found is based on two parameters A and B which are the ratios of the dipolar force to the viscous drag force and the Brownian force to the dipolar force respectively.