bluuebunny/crossref_metadata_2025 huggingface dataset:
Managing Politics and Consumption in Business Improvement Districts: The Geographies of Political Activism on Burlington, Vermont's Church Street Marketplace
Authors: Clough Nathan L. , Vanderbeck Robert M.
Published: November 2006

Business improvement districts (BIDs), which are formed when spaces that are legally public are put under private or semi-private forms of administration, have become increasingly prominent features of many cities internationally. This paper provides an in-depth, empirically grounded analysis of the practices of political activism and issue advocacy in one widely admired BID (Church Street Marketplace, Burlington, Vermont) in light of recent theoretical concerns about the decline of 'public' space within the current neo-liberal context of privatisation. The paper examines the ways in which various kinds of political activity are constructed by Marketplace management as either assets or liabilities, and how different forms of activism are differentially regulated and policed in pursuit of maintaining the carefully themed environment of the BID. The research raises important questions about the extent to which downtown (and other) spaces that have been (re)organised as BIDs can fulfil the role of public space in democratic societies.
The New Metropolitan Reality in the US: Rethinking the Traditional Model
Authors: Hanlon Bernadette , Vicino Thomas , Short John Rennie
Published: November 2006

This paper critically evaluates the traditional metropolitan model of an urban core and a homogeneous suburban ring. Using place data from the US Bureau of the Census from 1980 to 2000, it examines 1639 suburbs from a sample of 13 metropolitan areas in the US. Poor, manufacturing, Black and immigrant suburbs are identified to show that metropolitan areas are less a simple dichotomous structure and more a mosaic of very diverse suburban places. The results suggest the need for more subtle frameworks in order better to understand the structure of contemporary metropolitan areas.
Facilitating Structures for Neighbourhood Regeneration in the UK: The Contribution of the Housing Action Trusts
Authors: Hull Angela
Published: November 2006

This paper revisits the data collected for the mid-term evaluation of the six Housing Action Trusts (HATs) to throw light on the theory of change embodied in this neighbourhood regeneration model. The analysis employs Ostrom's theoretical framework to understand the role that HAT residents played in the regeneration of their neighbourhoods and how specific structuring mechanisms helped to bring about change. The similarities and differences that have surfaced between the HATs and the New Deal for Community partnerships at their mid-point are compared. The analysis concludes that formal structures to empower residents are insufficient on their own and that empowerment comes through specific customised training for employment, decision-making rights and a culture of commitment from skilled support staff.
Determinants of House Price: A Decision Tree Approach
Authors: Fan Gang-Zhi , Ong Seow Eng , Koh Hian Chye
Published: November 2006

The hedonic-based regression approach has been utilised extensively to investigate th relationship between house prices and housing characteristics. However, this approach is subject t criticisms arising from potential problems relating to fundamental model assumptions an estimation such as the identification of supply and demand, market disequilibrium, the selectio of independent variables, the choice of functional form of hedonic equation and marke segmentation. This study introduces and utilises an alternative approach-the decision tre approach, which is an important statistical pattern recognition tool. Using the Singapore resal public housing market as a case study, the article demonstrates the usefulness of this techniqu in examining the relationship between house prices and housing characteristics, identifying th significant determinants of housing prices and predicting housing prices. The built tree show that homebuyers are more concerned about the basic housing characteristics of two- and three room flats or four-room flats such as floor area, model type and flat age. However, homebuyer of five-room flats pay more attention to floor level in addition to the basic housin characteristics. In addition, homebuyers of executive apartments are less concerned about basi quantitative characteristics and have higher housing consumption expectations and pay mor attention to 'quality' and service characteristics such as recreational facilities and the livin environment.
Monitoring seasonal and long‐term changes in test performance in elite swimmers
Authors: Anderson Megan E. , Hopkins William G. , Roberts Alan D. , Pyne David B.
Published: November 2006

The purpose of this study was to characterize changes and variability in test performance of swimmers within and between seasons over their elite competitive career. Forty elite swimmers (24 male, 16 female) performed a 7×200‐m incremental swimming step test several times each 6‐month season (10±5 tests, spanning 0.5–6.0 y). Mixed linear modeling provided estimates of percent change in the mean and individual responses (within‐athlete variation as a coefficient of variation) for measures based on submaximal performance (fixed 4‐mM lactate), maximal performance (the seventh step) and lean mass (from skinfolds and body mass). Submaximal and maximal swim speed increased within each season from pre to taper phase by ∼2.2% for females and ∼1.5% for males (95% confidence limits ±1.0%), with variable contributions from stroke rate and stroke length. Most of the gains in speed were lost in the off‐season, leaving a net average annual improvement of ∼1.0% for females and ∼0.6% for males (±1.0%). For submaximal and maximal speed, individual variation between phases was ±2.2% and the typical measurement error was ±0.80%. Step test and anthropometric measures can be used to confidently monitor progressions in swimmers in an elite training program within and between seasons.
Truth makers for judgement calls
Authors: Mumford Stephen
Published: November 2006

Truths of sport seem to admit a certainty that is not to be found in other domains. I offer a diagnosis of this phenomenon. Awards in sport have a performative force: the making of an award thereby deems that it so. There are other elements, however, that have equal importance. There is an epistemic element in that umpire or referee must make a judgement about the award. This must be based on the metaphysical element, which is some fact or state of affairs in the world. Such a tripartite account allows that referees can make mistakes or that they can deliberately make an unjustified award. Because such awards are performatives, however, such facts about sport will not typically admit rational doubt.
SAGA: a subgraph matching tool for biological graphs
Authors: Tian Yuanyuan , McEachin Richard C. , Santos Carlos , States David J. , Patel Jignesh M.
Published: November 2006

Motivation: With the rapid increase in the availability of biological graph datasets, there is a growing need for effective and efficient graph querying methods. Due to the noisy and incomplete characteristics of these datasets, exact graph matching methods have limited use and approximate graph matching methods are required. Unfortunately, existing graph matching methods are too restrictive as they only allow exact or near exact graph matching. This paper presents a novel approximate graph matching technique called SAGA. This technique employs a flexible model for computing graph similarity, which allows for node gaps, node mismatches and graph structural differences. SAGA employs an indexing technique that allows it to efficiently evaluate queries even against large graph datasets.

Results: SAGA has been used to query biological pathways and literature datasets, which has revealed interesting similarities between distinct pathways that cannot be found by existing methods. These matches associate seemingly unrelated biological processes, connect studies in different sub-areas of biomedical research and thus pose hypotheses for new discoveries. SAGA is also orders of magnitude faster than existing methods.

Availability: SAGA can be accessed freely via the web at . Binaries are also freely available at this website.

Contact:  jignesh@eecs.umich.edu

Supplementary material: Supplementary material is available at .
Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
Authors: Kim Jaebum , Sinha Saurabh
Published: November 2006

Motivation: A quantitative study of molecular evolutionary events such as substitutions, insertions and deletions from closely related genomes requires (1) an accurate multiple sequence alignment program and (2) a method to annotate the insertions and deletions that explain the ‘gaps’ in the alignment. Although the former requirement has been extensively addressed, the latter problem has received little attention, especially in a comprehensive probabilistic framework.

Results: Here, we present Indelign, a program that uses a probabilistic evolutionary model to compute the most likely scenario of insertions and deletions consistent with an input multiple alignment. It is also capable of modifying the given alignment so as to obtain a better agreement with the evolutionary model. We find close to optimal performance and substantial improvement over alternative methods, in tests of Indelign on synthetic data. We use Indelign to analyze regulatory sequences in Drosophila, and find an excess of insertions over deletions, which is different from what has been reported for neutral sequences.

Availability: The Indelign program may be downloaded from the website

Supplementary information: Supplementary material is available at Bioinformatics online.

Contact:  sinhas@uiuc.edu
Network neighborhood analysis with the multi-node topological overlap measure
Authors: Li Ai , Horvath Steve
Published: November 2006

Motivation: The goal of neighborhood analysis is to find a set of genes (the neighborhood) that is similar to an initial ‘seed’ set of genes. Neighborhood analysis methods for network data are important in systems biology. If individual network connections are susceptible to noise, it can be advantageous to define neighborhoods on the basis of a robust interconnectedness measure, e.g. the topological overlap measure. Since the use of multiple nodes in the seed set may lead to more informative neighborhoods, it can be advantageous to define multi-node similarity measures.

Results: The pairwise topological overlap measure is generalized to multiple network nodes and subsequently used in a recursive neighborhood construction method. A local permutation scheme is used to determine the neighborhood size. Using four network applications and a simulated example, we provide empirical evidence that the resulting neighborhoods are biologically meaningful, e.g. we use neighborhood analysis to identify brain cancer related genes.

Availability: An executable Windows program and tutorial for multi-node topological overlap measure (MTOM) based analysis can be downloaded from the webpage ().

Contact:  shorvath@mednet.ucla.edu

Supplementary information: Supplementary material is available at Bioinformatics online.
p63 regulates proliferation and differentiation of developmentally mature keratinocytes
Authors: Truong Amy B. , Kretz Markus , Ridky Todd W. , Kimmel Robin , Khavari Paul A.
Published: November 2006

p63 is a multi-isoform p53 family member required for epidermal development. Contrasting roles for p63 in either the initial commitment to the stratified epithelial cell fate or in stem cell-based self-renewal have been proposed. To investigate p63 function in a post-developmental context, we used siRNAs directed against p63 to down-regulate p63 expression in regenerating human epidermis. Loss of p63 resulted in severe tissue hypoplasia and inhibited both stratification and differentiation in a cell-autonomous manner. Although p63-deficient cells exhibited hypoproliferation, differentiation defects were not due to tissue hypoplasia. Simultaneous p63 and p53 knockdown rescued the cell proliferation defect of p63 knockdown alone but failed to restore differentiation, suggesting that defects in epidermal proliferation and differentiation are mediated via p53-dependent and -independent mechanisms, respectively. Furthermore, ΔNp63 isoforms are the main mediators of p63 effects, although TAp63 isoforms may contribute to late differentiation. These data indicate that p63 is required for both the proliferative and differentiation potential of developmentally mature keratinocytes.
Hedgehog/Ras interactions regulate early stages of pancreatic cancer
Authors: Pasca di Magliano Marina , Sekine Shigeki , Ermilov Alexandre , Ferris Jenny , Dlugosz Andrzej A. , Hebrok Matthias
Published: November 2006

Pancreatic ductal adenocarcinoma (PDA) constitutes a lethal disease that affects >30,000 people annually in the United States. Deregulation of Hedgehog signaling has been implicated in the pathogenesis of PDA. To gain insights into the role of the pathway during the distinct stages of pancreatic carcinogenesis, we established a mouse model in which Hedgehog signaling is activated specifically in the pancreatic epithelium. Transgenic mice survived to adulthood and developed undifferentiated carcinoma, indicating that epithelium-specific Hedgehog signaling is sufficient to drive pancreatic neoplasia but does not recapitulate human pancreatic carcinogenesis. In contrast, simultaneous activation of Ras and Hedgehog signaling caused extensive formation of pancreatic intraepithelial neoplasias, the earliest stages of human PDA tumorigenesis, and accelerated lethality. These results indicate the cooperation of Hedgehog and Ras signaling during the earliest stages of PDA formation. They also mark Hedgehog pathway components as relevant therapeutic targets for both early and advanced stages of pancreatic ductal neoplasia.
Smad4 is dispensable for normal pancreas development yet critical in progression and tumor biology of pancreas cancer
Authors: Bardeesy Nabeel , Cheng Kuang-hung , Berger Justin H. , Chu Gerald C. , Pahler Jessica , Olson Peter , Hezel Aram F. , Horner James , Lauwers Gregory Y. , Hanahan Douglas , DePinho Ronald A.
Published: November 2006

SMAD4 is inactivated in the majority of pancreatic ductal adenocarcinomas (PDAC) with concurrent mutational inactivation of the INK4A/ARF tumor suppressor locus and activation of the KRAS oncogene. Here, using genetically engineered mice, we determined the impact of SMAD4 deficiency on the development of the pancreas and on the initiation and/or progression of PDAC—alone or in combination with PDAC-relevant mutations. Selective SMAD4 deletion in the pancreatic epithelium had no discernable impact on pancreatic development or physiology. However, when combined with the activated KRASG12D allele, SMAD4 deficiency enabled rapid progression of KRASG12D-initiated neoplasms. While KRASG12D alone elicited premalignant pancreatic intraepithelial neoplasia (PanIN) that progressed slowly to carcinoma, the combination of KRASG12D and SMAD4 deficiency resulted in the rapid development of tumors resembling intraductal papillary mucinous neoplasia (IPMN), a precursor to PDAC in humans. SMAD4 deficiency also accelerated PDAC development of KRASG12D INK4A/ARF heterozygous mice and altered the tumor phenotype; while tumors with intact SMAD4 frequently exhibited epithelial-to-mesenchymal transition (EMT), PDAC null for SMAD4 retained a differentiated histopathology with increased expression of epithelial markers. SMAD4 status in PDAC cell lines was associated with differential responses to transforming growth factor-β (TGF-β) in vitro with a subset of SMAD4 wild-type lines showing prominent TGF-β-induced proliferation and migration. These results provide genetic confirmation that SMAD4 is a PDAC tumor suppressor, functioning to block the progression of KRASG12D-initiated neoplasms, whereas in a subset of advanced tumors, intact SMAD4 facilitates EMT and TGF-β-dependent growth.
Spreading of antibody reactivity to non-thyroid antigens during experimental immunization with human thyroglobulin
Authors: Thrasyvoulides A , Liakata E , Lymberi P
Published: November 2006

Intermolecular spreading of antibody reactivity has been implicated in the evolution of autoimmune disease. In this study, spreading of antibody reactivity to non-thyroid autoantigens after experimental immunization with thyroglobulin (Tg) was investigated. For this purpose, two rabbits were injected with human Tg six times (stages 1–6) every 3 weeks. Animals were also bled before priming. Antisera were tested by enzyme-linked immunosorbent assay (ELISA) for reactivity to several non-thyroid antigens: bovine serum albumin (BSA), native DNA (nDNA), human myosin, human globular (G) and filamentous (F) actin and porcine tubulin. Tg-immunized animals developed the following serological reactivity pattern: (a) high reactivity to myosin from stage 2 onward, (b) significant reactivity to F-actin, remaining high up to stage 6, (c) reactivity to BSA with a peak at stage 3, (d) a small increase of reactivity to G-actin at stage 3 and (e) no increase of reactivity to nDNA and tubulin. The study of affinity-purified anti-Tg antibodies and the use of competitive assays revealed that reactivity to F-actin was not due to cross-reaction with Tg. On the contrary, reactivity to myosin during the first stages of immunization was due to cross-reaction with Tg, while at stage 6 it became myosin-specific. Reactivity to BSA at stage 3 was also due to cross-reaction with Tg. We conclude that at least part of the induced anti-Tg antibodies may result from the expansion of B cell clones producing polyreactive natural autoantibodies, and polyreactivity of anti-Tg antibodies during the first stages of Tg-immunization may be responsible for the intermolecular spreading of antibody response.
Innate immunity mediated by epidermal keratinocytes promotes acquired immunity involving Langerhans cells and T cells in the skin
Authors: Sugita K , Kabashima K , Atarashi K , Shimauchi T , Kobayashi M , Tokura Y
Published: November 2006

Skin is an immunological organ consisting of epidermal cells, i.e. keratinocytes and Langerhans cells (LCs, antigen-presenting dendritic cells), and both innate and acquired immune systems operate upon exposure of the skin to various external microbes or their elements. To explore the relationship between innate and acquired immunities in the skin, we investigated whether Toll-like receptor (TLR) ligation of epidermal cells enhances the ability of LCs to present a specific antigen to T cells in mice. LC-containing epidermal cells were incubated with CpG oligonucleotide (TLR9 ligand) modified with trinitrophenyl hapten, and cultured with hapten-primed CD4+ T cells. TLR9 ligand was capable of enhancing the hapten-presenting ability of LCs when LC-enriched epidermal cells, but not purified LCs, were used as the LC source, suggesting that bystander keratinocytes play a role in the enhancement of LC function. Cultivation of freshly isolated epidermal cells with CpG promoted the expression of major histocompatibility complex (MHC) class II and CD86 molecules on LCs. CpG enhanced the production of interleukin (IL)-1α, granulocyte–macrophage colony-stimulating factor (GM-CSF) and tumour necrosis factor (TNF)-α by primarily cultured keratinocytes. The addition of a cocktail of neutralizing antibodies against these cytokines abrogated the CpG-promoted, antigen-presenting ability of LC-enriched epidermal cells. Moreover, the addition of culture supernatants from CpG-stimulated keratinocytes restored the ability of purified LCs. Our study demonstrated that although the direct effect of CpG on LCs is minimal, LC function can be up-regulated indirectly by cytokines released by CpG-stimulated keratinocytes. This also implies that innate immunity evoked by TLR ligation of keratinocytes enhances acquired immunity comprising LCs and T cells.
Effects of ultraviolet (UV) exclusion on the seasonal concentration of photosynthetic and UV‐screening pigments in Scots pine needles
Authors: MARTZ FRANÇOISE , SUTINEN MARJA‐LIISA , DEROME KIRSTI , WINGSLE GUNNAR , JULKUNEN‐TIITTO RIITTA , TURUNEN MINNA
Published: November 2006

The effects of ultraviolet (UV) radiation on the photosynthetic and UV‐screening pigments in needles of Scots pine (Pinus sylvestris L.) saplings were studied in a UV‐exclusion field chamber experiment in northern Finland (67°N) during 2001–2002. The chambers held filters that excluded both UVB and UVA, only UVB, transmitted all UV, or lacked filters. Analyses of control needles (no filter and polyethene filter) showed that the first changes to occur in spring (end of April) was an abrupt increase in the epoxidation state (EPS) of the xanthophyll cycle pigments, likely in relation with the beginning of the photosynthetic activity. The concentration of chlorophyll, lutein, neoxanthin, α‐carotene, β‐carotene, and the size of the xanthophyll cycle pool (violaxanthin+antheraxanthin+zeaxanthin=VAZ) changed only later when needles reached their summer photosynthesis state. Exclusion of UV radiation significantly affected the xanthophyll cycle but not the other photosynthetic pigments analysed. Interestingly, the effects on xanthophylls were dependent on the sampling date. Under UVA/B‐exclusion, the EPS was increased and VAZ pool size was unchanged in April, whereas EPS remained unchanged and the VAZ pool size was reduced in May and June. The existence of two sustained and active antenna modes during winter and summer could be an explanation for the specific UV‐exclusion effect in the different season. A high‐performance liquid chromatography analysis of soluble phenolics showed that the exclusion of UVA/B radiation caused a significant effect on five compounds out of 46 studied, without affecting the concentration of the total soluble phenolics. Under UVA/B‐exclusion, the concentration of three of them (secoisolariciresinol‐glucopyranoside, two unknown) was reduced while the concentration of dicoumaroyl‐astragalin and pinosylvin monomethylether was increased compared with both controls separately. In general, the exclusion of UVA/B caused a stronger effect than the exclusion of UVB on both photosynthetic and UV screening pigments. The effects of UV radiation on xanthophyll cycle pigments were season‐specific and detectable only under stressful spring conditions (freezing temperatures and high irradiance due to snow reflection). The effect on the xanthophyll cycle could be a direct consequence of UV treatments, or an indirect consequence of the changed flavonoid composition, or a combination of both.
Soils, a sink for N2O? A review
Authors: CHAPUIS‐LARDY LYDIE , WRAGE NICOLE , METAY AURÉLIE , CHOTTE JEAN‐LUC , BERNOUX MARTIAL
Published: November 2006

Soils are the main sources of the greenhouse gas nitrous oxide (N2O). The N2O emission at the soil surface is the result of production and consumption processes. So far, research has concentrated on net N2O production. However, in the literature, there are numerous reports of net negative fluxes of N2O, (i.e. fluxes from the atmosphere to the soil). Such fluxes are frequent and substantial and cannot simply be dismissed as experimental noise.

Net N2O consumption has been measured under various conditions from the tropics to temperate areas, in natural and agricultural systems. Low mineral N and large moisture contents have sometimes been found to favour N2O consumption. This fits in with denitrification as the responsible process, reducing N2O to N2. However, it has also been reported that nitrifiers consume N2O in nitrifier denitrification. A contribution of various processes could explain the wide range of conditions found to allow N2O consumption, ranging from low to high temperatures, wet to dry soils, and fertilized to unfertilized plots. Generally, conditions interfering with N2O diffusion in the soil seem to enhance N2O consumption. However, the factors regulating N2O consumption are not yet well understood and merit further study.

Frequent literature reports of net N2O consumption suggest that a soil sink could help account for the current imbalance in estimated global budgets of N2O. Therefore, a systematic investigation into N2O consumption is necessary. This should concentrate on the organisms, reactions, and environmental factors involved.
Salinity and sea level mediate elevated CO2 effects on C3–C4 plant interactions and tissue nitrogen in a Chesapeake Bay tidal wetland
Authors: ERICKSON JOHN E. , MEGONIGAL J. PATRICK , PERESTA GARY , DRAKE BERT G.
Published: November 2006

Elevated atmospheric carbon dioxide concentrations ([CO2]) generally increase plant photosynthesis in C3 species, but not in C4 species, and reduce stomatal conductance in both C3 and C4 plants. In addition, tissue nitrogen concentration ([N]) often fails to keep pace with enhanced carbon gain under elevated CO2, particularly in C3 species. While these responses are well documented in many species, implications for plant growth and nutrient cycling in native ecosystems are not clear. Here we present data on 18 years of measurement of above and belowground biomass, tissue [N] and total standing crop of N for a Scirpus olneyi‐dominated (C3 sedge) community, a Spartina patens‐dominated (C4 grass) community and a C3–C4‐mixed species community exposed to ambient and elevated (ambient +340 ppm) atmospheric [CO2] in natural salinity and sea level conditions of a Chesapeake Bay wetland. Increased biomass production (shoots plus roots) under elevated [CO2] in the S. olneyi‐dominated community was sustained throughout the study, averaging approximately 35%, while no significant effect of elevated [CO2] was found for total biomass in the C4‐dominated community. We found a significant decline in C4 biomass (correlated with rising sea level) and a concomitant increase in C3 biomass in the mixed community. This shift from C4 to C3 was accelerated by the elevated [CO2] treatment. The elevated [CO2] stimulation of total biomass accumulation was greatest during rainy, low salinity years: the average increase above the ambient treatment during the three wettest years (1994, 1996, 2003) was 2.9 t ha−1 but in the three driest years (1995, 1999, 2002), it was 1.2 t ha−1. Elevated [CO2] depressed tissue [N] in both species, but especially in the S. olneyi where the relative depression was positively correlated with salinity and negatively related with the relative enhancement of total biomass production. Thus, the greatest amount of carbon was added to the S. olneyi‐dominated community during years when shoot [N] was reduced the most, suggesting that the availability of N was not the most or even the main limitation to elevated [CO2] stimulation of carbon accumulation in this ecosystem.
Climate impacts on Mediterranean blue tit survival: an investigation across seasons and spatial scales
Authors: GROSBOIS VLADIMIR , HENRY PIERRE‐YVES , BLONDEL JACQUES , PERRET PHILIPPE , LEBRETON JEAN‐DOMINIQUE , THOMAS DONALD W. , LAMBRECHTS MARCEL M.
Published: November 2006

In some hole nesting passerine species, long‐term monitoring data are available for several geographically independent populations. Climate forcing can then be documented and predictions made on the scale of distribution ranges. Several demographic studies of Paridae report dramatic impacts of wintertime climatic factors. However, these studies were undertaken in populations located in the northern parts of the species' ranges. Studies on the survival of Paridae in their southern ranges are necessary in order to assess potential latitudinal variation in climate forcing on survival. Based on monitoring of individual adult blue tits (Parus caeruleus), the effects of climatic factors on annual survival were assessed in three distinct Mediterranean populations. In these regions, climatic conditions in early summer might be expected to have a strong impact because they can be extremely hot and dry and because at this time of year Paridae are subjected to intrinsic constraints that stem from energetically costly postbreeding moult, recovery from reproductive costs, and from population densities inflated by the new cohort of fledglings. The impact of climatic conditions in early summer was, thus, addressed in addition to that prevailing in winter. In order to consider a large number of local climatic variables while limiting statistical power loss, integrative indices of local climate were built using multivariate techniques. In addition, the NAO and three large‐scale factors that are closely linked with atmospheric and oceanic circulation in the intertropical zone were considered as potentially influential factors in winter and early summer. Relationships between blue tit survival and indices of local temperature and precipitation in winter and in early summer were detected. Adult survival also correlated with a large‐scale tropical index in early summer: rainfall in the Sahel. This is one of the first quantitative indications that fluctuations in summer climatic conditions explain a significant part of the temporal variation in adult survival in unconnected populations of a sedentary European vertebrate. Furthermore, the results support the hypothesis that summertime local climates in Western Europe are closely linked with atmospheric and oceanic circulation in the intertropical zone.
Niche pre‐emption increases with species richness in experimental plant communities
Authors: MWANGI PETER N. , SCHMITZ MARTIN , SCHERBER CHRISTOPH , ROSCHER CHRISTIANE , SCHUMACHER JENS , SCHERER‐LORENZEN MICHAEL , WEISSER WOLFGANG W. , SCHMID BERNHARD
Published: November 2006

In plant communities, invasion resistance may increase with diversity because empty niche space decreases simultaneously. However, it is not clear if this only applies to exotic species or also to native species arriving at a site with few other native species during community assembly. We tested the latter by transplanting four native species into experimental grassland communities varying in species richness form 1–16 (−60) species. In addition, we tested the hypothesis that invasion is less successful if the invading species belongs to a functional group that is already present in the community. The test invaders included a grass species (Festuca pratensis, FP), a short (Plantago lanceolata, PL) and a tall herb species (Knautia arvensis, KA), and a legume species (Trifolium pratense, TP). The same four functional groups also occurred alone or in all possible combinations in the different experimental communities. The overall performance of the transplants was negatively related to the logarithm of the species richness of host communities. Plant biomass declined by 58%, 90%, 84% and 62% in FP, PL, KA and TP, respectively, from monocultures to 16‐species mixtures, indicating lower invasiveness of the two herbs than of the grass and the legume. Resident grasses showed a strong negative effect on the performance of all test invaders, whereas resident small and tall herbs had neutral, and resident legumes had positive effects. The case of the legumes indicates that contributions to invasion resistance need not parallel invasiveness. Communities containing resident species of only one functional group were most inhibitive to transplants of the same functional group. These results indicate that invasion resistance of experimental plant communities is related to the degree of niche overlap between resident species and invaders. This niche overlap can be high due to generally low amounts of empty niche space in species‐rich resident communities or due to the occurrence of the same functional group as the one of the invader in the resident community. Stronger within‐ than between‐functional‐group invasion resistance may be the key mechanism underlying diversity effects on invasion resistance in grassland and other ecosystems at large.
Assessing the trade‐offs between crossover and parallel group designs in sleep research
Authors: BERRY CHARLES C. , MOORE POLLY , DIMSDALE JOEL E.
Published: November 2006

Sleep researchers invariably struggle with decisions regarding the optimal design for their studies. Whether such studies involve treatment for insomnia, obstructive sleep apnea, or any other sleep disorder, questions arise regarding the respective trade‐offs between a parallel group and a crossover design. This study analyzed the variance structure of commonly measured polysomnographic variables in an effort to describe the statistical impact of these alternate designs. The study examined the effects of opioids on sleep and employed multiple crossovers between placebo, MS‐contin, and methadone using a double‐blind, randomized crossover design. Thirty‐seven healthy subjects were studied. Four of the subjects were unable to complete the protocol for a variety of reasons, and polysomnogram data was unavailable for one subject. Data from 37 subjects provide the basis for this analysis. Despite dropouts, the crossover study was approximately four times as efficient as the parallel group design in terms of being able to recognize differences in deep sleep across these conditions. Other polysomnographic variables also favored the crossover design to varying extents. Despite the operational complexity of a crossover design, the statistical efficiency of this approach makes it a preferable approach for designing intervention studies in sleep research.
Total sleep deprivation can increase vestibulo‐ocular responses
Authors: QUARCK G. , VENTRE J. , ETARD O. , DENISE P.
Published: November 2006

The effect of sleep deprivation on the vestibular function is largely unknown. Some studies have found that postural balance or vestibular reflexes are decreased in sleep‐deprived subjects while others found no change. The aim of this study was to evaluate the effect of sleep deprivation on the vestibulo‐ocular reflex (VOR). Horizontal eye movements were recorded in healthy subjects during earth vertical axis rotation in darkness once after an ordinary night sleep and once after 26–29 h of sleep deprivation. In the first experiment (n = 8), for which rotation was a 60° s−1 velocity step, sleep deprivation induced a significant increase in VOR gain. In the second experiment (n = 12), for which rotation was sinusoidal (0.2 Hz ± 25° s−1), sleep deprivation induced no significant modification in VOR gain. The difference between the two studies was the abrupt onset of the step stimulation in comparison with the sinusoidal rotation. Because of its unexpected onset and the potential threat to postural balance, the step stimulation may activate the system specialized in reorienting attention towards salient or behaviourally relevant events. This system includes the right temporoparietal cortex, an area also involved in VOR control. A number of studies have found that sleep deprivation alters the activity of this cortical area during attentional tasks. It is therefore our hypothesis that the difference between the effects of these two vestibular stimulations results from a sleep deprivation‐induced modulation of the right temporoparietal cortex.
N‐terminal pro‐brain natriuretic peptide for detection of cardiovascular stress in patients with obstructive sleep apnea syndrome
Authors: VARTANY EDMOND , IMEVBORE MICHAEL , O'MALLEY MARY , MANFREDI CHRISTOPHER , PASQUARELLA CAROL , SCINTO LEONARD , FINE JONATHAN
Published: November 2006

Patients with obstructive sleep apnea syndrome (OSAS) have an elevated incidence of cardiovascular events that may be related to an increased ventricular load and hypoxemia caused by apneas and hypopneas. N‐terminal pro‐brain natriuretic peptide (NTproBNP) appears to be an excellent marker of myocardial stretch and could serve as an indicator of subclinical cardiac stress, thereby identifying a patient population at risk for cardiac effects from OSAS. Adult patients presenting with suspected OSAS and scheduled for nocturnal polysomnography were recruited. Patients with heart or renal failure or severe lung disease were excluded. NTproBNP was measured the evening before and the morning after sleep. Blood pressure (BP) was monitored intermittently throughout the night. Fifteen male and 15 female subjects with a mean ± SD body mass index of 38.2 ± 9.8 were studied. Mean Apnea–Hypopnea Index (AHI) was 38.4 ± 26, with 17 subjects having severe OSAS (AHI > 30). No subject had a significant rise in BP. NTproBNP values overnight decreased in 19 patients and rose in 11 (mean change 3.8 ± 33 pg mL−1), but only one patient had an abnormal morning value. Three patients had an abnormal NTproBNP value prior to sleep, but their levels decreased with sleep. No correlations were detected between the evening baseline or postsleep NTproBNP levels and OSAS. Monitoring pre‐ and postsleep NTproBNP levels revealed no association with the occurrence or degree of OSAS, making it unlikely that NTproBNP could serve as a marker of cardiac stress in OSAS patients with stable BP and without overt heart failure.
Screening for sleep‐related breathing disorders by transthoracic impedance recording integrated into a Holter ECG system
Authors: MUELLER ANDREAS , FIETZE INGO , VOELKER RICHARD , EDDICKS STEPHAN , GLOS MARTIN , BAUMANN GERT , THERES HEINZ
Published: November 2006

In patients with arrhythmias, coincidence with sleep‐related breathing disorders (SRBD) is high and of clinical relevance. Electrocardiogram‐derived (ECG) parameters have been developed for SRBD screening, but it has proved necessary to exclude patients with frequent arrhythmias. Holter‐based screening tools, easy to use, are therefore warranted. The goal of our study was to evaluate the diagnostic accuracy, with respect to SRBD detection, of transthoracic impedance recording (TTIR) integrated into a Holter System. Our investigation consisted of 2 phases. In phase 1 we compared the performance of TTIR to that of in‐hospital polysomnography (PSG) in 56 patients (46 male, mean age 57). In phase 2 we compared TTIR to results from an ambulatory polygraphy (PG) system in 180 patients (143 male, mean age 56). We scored apnea and hypopnea from P(S)G, and derived a respiratory‐disturbance index (P(S)G‐RDI). TTIR was analyzed semi‐automatically. Reduction of the impedance amplitude by more than 50% over 10 s was scored as apnea/hypopnea, with consequent calculation of TTIR‐RDI. In phase 1, 20 out of 56 patients revealed a PSG‐RDI > 10 h−1. TTIR‐RDI in 19 patients from this group was >10 h−1 (sensitivity 95%, specificity 97.2%, positive predictive value 95%, negative predictive value 97.2%, interclass correlation coefficient 0.98). In phase 2, 46 of 180 patients revealed a PSG‐RDI > 10 h−1. TTIR‐RDI in 37 out of this group was >10 h−1 (sensitivity 80.4%, specificity 92.5%, positive predictive value 78.7%, negative predictive value 93.2%, interclass correlation coefficient 0.92). TTIR integrated into a Holter ECG system and tested in a large patient cohort demonstrates acceptable high accuracy in detection of SRBD. Arrhythmia analysis and screening for SRBD can be performed in a single‐step approch.
A phylogenetic analysis of the correlates of sleep in birds
Authors: ROTH TIMOTHY C. , LESKU JOHN A. , AMLANER CHARLES J. , LIMA STEVEN L.
Published: November 2006

Quantitative comparative studies of sleep have focused exclusively on mammals. Such studies have repeatedly found strong relationships between the time spent in various sleep states and constitutive variables related to morphology, physiology, and life history. These studies influenced the development of several prominent hypotheses for the functions of sleep, but the applicability of these patterns and hypotheses to non‐mammalian taxa is unclear. Here, we present the first quantitative analysis of sleep in a non‐mammalian taxon (birds), focusing on the daily amount of time spent in slow‐wave sleep (SWS) and rapid‐eye movement (REM) sleep as determined by electrophysiological methods. We examined the relationships between constitutive and sleep variables in 23 avian species following earlier studies in mammals, but also considered an index of exposure to predators while asleep and controlled for shared evolutionary history among taxa. Overall, our results were very different from those obtained for mammals. Most remarkably, the relationships between both SWS time and REM sleep time and all constitutive variables were very weak and markedly non‐significant, even though we had adequate power to detect correlations typical of the mammalian data. Only an index of exposure to predation during sleep was significantly related to sleep time, which is the only result common to both birds and mammals. Our results suggest that further insight into the function(s) of sleep across the animal kingdom may require an expansion of sleep research beyond the current mammalian paradigm.
Comparative genomics and repetitive sequence divergence in the species of diploidNicotianasection Alatae
Authors: Yoong Lim K. , Kovarik Ales , Matyasek Roman , Chase Mark W. , Knapp Sandra , McCarthy Elizabeth , Clarkson James J. , Leitch Andrew R.
Published: November 2006

Combining phylogenetic reconstructions of species relationships with comparative genomic approaches is a powerful way to decipher evolutionary events associated with genome divergence. Here, we reconstruct the history of karyotype and tandem repeat evolution in species of diploidNicotianasection Alatae. By analysis of plastid DNA, we resolved two clades with high bootstrap support, one containingN. alata,N. langsdorffii,N. forgetianaandN. bonariensis(called then = 9 group) and another containingN. plumbaginifoliaandN. longiflora(called then = 10 group). Despite little plastid DNA sequence divergence, we observed, via fluorescentin situhybridization, substantial chromosomal repatterning, including altered chromosome numbers, structure and distribution of repeats. Effort was focussed on 35S and 5S nuclear ribosomal DNA (rDNA) and the HRS60 satellite family of tandem repeats comprising the elements HRS60, NP3R and NP4R. We compared divergence of these repeats in diploids and polyploids ofNicotiana. There are dramatic shifts in the distribution of the satellite repeats and complete replacement of intergenic spacers (IGSs) of 35S rDNA associated with divergence of the species in section Alatae. We suggest that sequence homogenization has replaced HRS60 family repeats at sub‐telomeric regions, but that this process may not occur, or occurs more slowly, when the repeats are found at intercalary locations. Sequence homogenization acts more rapidly (at least two orders of magnitude) on 35S rDNA than 5S rDNA and sub‐telomeric satellite sequences. This rapid rate of divergence is analogous to that found in polyploid species, and is therefore, in plants, not only associated with polyploidy.
ATR and ATM play both distinct and additive roles in response to ionizing radiation
Authors: Culligan Kevin M. , Robertson Clare E. , Foreman Julia , Doerner Peter , Britt Anne B.
Published: November 2006

The ATR and ATM protein kinases are known to be involved in a wide variety of responses to DNA damage. The Arabidopsis thaliana genome includes both ATR and ATM orthologs, and plants with null alleles of these genes are viable. Arabidopsis atr and atm mutants display hypersensitivity to γ‐irradiation. To further characterize the roles of ATM and ATR in response to ionizing radiation, we performed a short‐term global transcription analysis in wild‐type and mutant lines. We found that hundreds of genes are upregulated in response to γ‐irradiation, and that the induction of virtually all of these genes is dependent on ATM, but not ATR. The transcript of CYCB1;1 is unique among the cyclin transcripts in being rapidly and powerfully upregulated in response to ionizing radiation, while other G2‐associated transcripts are suppressed. We found that both ATM and ATR contribute to the induction of a CYCB1;1:GUS fusion by IR, but only ATR is required for the persistence of this response. We propose that this upregulation of CYCB1;1 does not reflect the accumulation of cells in G2, but instead reflects a still unknown role for this cyclin in DNA damage response.
Time of day modulates low‐temperature Ca2+ signals in Arabidopsis
Authors: Dodd Antony N. , Jakobsen Mia Kyed , Baker Andrew J. , Telzerow Anja , Hou Sui‐Wen , Laplaze Laurent , Barrot Laure , Scott Poethig R. , Haseloff Jim , Webb Alex A. R.
Published: November 2006

We tested the hypothesis that the circadian clock modulates Ca2+‐based signalling pathways, using low‐temperature (LT)‐induced Ca2+ signals. We investigated the relationship between diurnal and circadian modulation of LT‐induced increases in cytosolic‐free calcium ([Ca2+]cyt), and regulation of [Ca2+]cyt‐dependent outputs of the LT‐signalling network (RD29A transcript abundance and stomatal closure). We measured [Ca2+]cyt non‐invasively using aequorin, and targeted aequorin to the guard cell using a guard cell‐specific GAL4‐green fluorescent protein enhancer trap line. LT caused transient increases in whole plant and guard cell [Ca2+]cyt. In guard cells, the LT‐induced [Ca2+]cyt elevation preceded stomatal closure. In whole plants, the magnitude of LT‐induced [Ca2+]cyt transients, measured from the entire plant or specifically the guard cell, varied with the time of day: LT‐induced [Ca2+]cyt transients were significantly higher during the mid‐photoperiod than at the beginning or end. Diurnal variation in LT‐induced guard cell [Ca2+]cyt increases was not correlated to diurnal variation in LT‐induced stomatal closure. There was circadian modulation of LT‐induced whole plant [Ca2+]cyt increases, which were correlated to the circadian pattern of RD29A induction. In order to understand the significance of LT‐induced [Ca2+]cyt increases, we used a computer simulation to demonstrate that, in guard cells, LT‐induced [Ca2+]cyt increases measured from a population of cells are likely to represent the summation of cold‐induced single‐cell [Ca2+]cyt oscillations.
Alleviation of photoinhibition by calcium supplement in salt‐treated Rumex leaves
Authors: Chen Hua‐Xin , Li Peng‐Min , Gao Hui‐Yuan
Published: November 2006

By analysis of gas exchange and chlorophyll fluorescence, the effects of NaCl treatment and supplemental CaCl2 on photosynthesis, photosystem II (PSII) photochemistry and photoinhibition were investigated in Rumex leaves. Photosynthesis in Rumex leaves was strongly inhibited by 200 mM NaCl treatment. Such inhibition of photosynthesis was ameliorated by CaCl2 supplement. Neither NaCl treatment nor CaCl2 supplement had any significant effects on the PSII primary photochemical reaction in dark‐adapted leaves. In light‐adapted leaves, however, 200 mM NaCl treatment significantly decreased photochemical quenching (qp), efficiency of excitation energy capture by open PSII reaction centers (FV′/FM′) and quantum yield of PSII electron transport (ΦPSII). These decreases in qp, FV′/FM′ and ΦPSII were mitigated by CaCl2 supplement with the maximum of its effect appearing at a concentration of 8 mM CaCl2. A similar mitigating effect was shown in 200 mM NaCl‐treated Rumex leaves when susceptibility of PSII to photoinhibition was determined under high irradiance. It is suggested that the mitigation of photoinhibition in NaCl‐treated leaves is because of the amelioration of inhibition of photosynthesis.
Hierarchy amongst photosynthetic acclimation responses for plant fitness
Authors: Frenkel Martin , Bellafiore Stephane , Rochaix Jean‐David , Jansson Stefan
Published: November 2006

We have compared the seed production of Arabidopsis wild‐type and mutant plants impaired in the regulation of the photosynthetic light reactions grown under natural conditions in the field. Mutant plants (npq4) lacking feedback de‐excitation were, as previously demonstrated, severely affected in seed production. Seed sets of plants deficient in state transitions (stn7) were 19% smaller than those of wild‐type plants, whereas plants missing the STN8 kinase required for the phosphorylation of the core photosystem II reaction centre polypeptides (stn8) had a normal seed production. Plants lacking both STN7 and STN8 kinases were strongly affected, indicating that these mutations act synergistically. In contrast, npq4×stn7 double mutants had the same seed set as npq4 mutants.