bluuebunny/crossref_metadata_2025 huggingface dataset:
Plant foods and the risk of cerebrovascular diseases: a potential protection of fruit consumption
Authors: Mizrahi Anna , Knekt Paul , Montonen Jukka , Laaksonen Maarit A. , Heliövaara Markku , Järvinen Ritva
Published: July 2009

Studies on the association between plant foods and cerebrovascular diseases have given contradictory results suggesting the existence of some effect-modifying factors. The present study determines whether the consumption of plant foods (i.e. fruits and berries, vegetables, and cereals) predicts a decreased cerebrovascular disease incidence in a population with low fruit and vegetable and high wholegrain intake. This cohort study on 3932 men and women was based on data from the Finnish Mobile Clinic Health Examination Survey, conducted in 1968–72. The participants were 40–74 years of age and free of cardiovascular diseases at baseline. Data on the plant food consumption were derived from a 1-year dietary history interview. During a 24-year follow-up 625 cases of cerebrovascular diseases occurred, leading to either hospitalisation or death. An inverse association was found between fruit consumption and the incidence of cerebrovascular diseases, ischaemic stroke and intracerebral haemorrhage. The adjusted relative risks (RR) between the highest and lowest quartiles of intake of any cerebrovascular disease, ischaemic stroke and intracerebral haemorrhage were 0·75 (95 % CI 0·59, 0·94), 0·73 (95 % CI 0·54, 1·00) and 0·47 (95 % CI 0·24, 0·92), respectively. These associations were primarily due to the consumption of citrus fruits and occurred only in men. Total consumption of vegetables or cereals was not associated with the cerebrovascular disease incidence. The consumption of cruciferous vegetables, however, predicted a reduced risk of cerebrovascular diseases (RR 0·79; 95 % CI 0·63, 0·99), ischaemic stroke (RR 0·67; 95 % CI 0·49, 0·92) and intracerebral haemorrhage (RR 0·49; 95 % CI 0·25, 0·98). In conclusion, the consumption of fruits, especially citrus, and cruciferous vegetables may protect against cerebrovascular diseases.
DIOPHANTINE APPROXIMATION BY PRIMES
Authors: MATOMÄKI KAISA
Published: July 2009

We show that whenever δ > 0 and constants λisatisfy some necessary conditions, there are infinitely many prime triplesp1,p2,p3satisfying the inequality |λ0+ λ1p1+ λ2p2+ λ3p3| < (maxpj)−2/9+δ. The proof uses Davenport–Heilbronn adaption of the circle method together with a vector sieve method.
COMPARISON THEOREMS ON THE OSCILLATION AND ASYMPTOTIC BEHAVIOUR OF HIGHER-ORDER NEUTRAL DIFFERENTIAL EQUATIONS
Authors: KARPUZ BAŞAK , ÖCALAN ÖZKAN , ÖZTÜRK SERMIN
Published: July 2009

In this work, oscillatory and asymptotic behaviours of all solutions of higher-order neutral differential equations are compared with first-order delay differential equations, depending on two different ranges of the coefficient associated with the neutral part. Some simple examples are given to compare our results with the existing results in the literature and to illustrate the significance and applicability of our new results. Our results generalise, improve and correct some of the existing results in the literature.
Striking Deaths: Lethal Contestation and the “Exceptional” Character of the American Labor Movement, 1870–1970
Authors: Lipold Paul F. , Isaac Larry W.
Published: July 2009

The decades between the Great Railway Strike of 1877 and the post-World- War-II institutionalization of organized labor in the US have been impressionistically characterized by labor scholars as the most violent and bloody to be found in any Western, democratic nation. A variety of different forms of labor repression have been identified and studied. Yet because of a lack of systematic data, none have been able to examine directly the incidence and contours of the ultimate form of violent repression in collective contention. We create the conceptual space for pursuing bloodshed and a new data set featuring deaths resulting from labor strikes as a new and promising direction in the American exceptionalism debate and in studies of comparative strikes. Through a painstaking search of the historical record, we produce the first systematic quantitative gauge of striking deaths between 1870 and 1970. These data permit a mapping of fatalities resulting from labor strikes across time, geographical region, and industry. After describing configurations of strike-based mortality, we suggest what these patterned variations may mean and identify additional questions that these data may help resolve in subsequent studies. We urge comparable data collections in other countries that would permit direct comparative-historical assessments of the magnitude and role of bloodshed in different labor movements.
“I Fear You Will Think Me Too Presumtuous in My Demands but Necessity Has No Law”: Clothing in English Pauper Letters, 1800–1834
Authors: King Steven
Published: July 2009

This article investigates the way in which the English poor used the rhetoric of clothing in their engagement with local officials as they attempted to secure poor relief. Using letters written about or by the dependent poor from a wide selection of English communities, the article suggests that the poor employed concepts such as raggedness, lost clothing, nakedness, compromised dignity, and community presence and the link between poor clothing and unemployment, to assert their deservingness. An exemplar of a series of letters from the same person is used to explore how paupers developed the rhetoric of clothing over a sustained period of correspondence, suggesting that paupers had a keen appreciation of the impact of compromised clothing in their negotiations with officials. Ultimately, this paper will argue, paupers and officials had a shared concept of minimal clothing standards and a shared linguistic register for linking clothing and deservingness.
“Dens of Iniquity and Holes of Wickedness”: George Lippard and the Queer City
Authors: UNGER MARY
Published: July 2009

This article examines George Lippard's portrayal of “queer space” in his 1845 novel The Quaker City. Despite William Penn's meticulous urban grid rooted in the democratic ideals of national space, Lippard presents Philadelphia's landscape as unruly, illogical, and transgressive. The novel's manor of vice, Monk Hall, is as twisted as the city streets, facilitating behaviors and experiences unregulated by hegemonic forces. I argue that by perverting the places of his novel, Lippard creates ruptures in the ideological underpinnings of a national geography. In so doing, he attempts to enact a radical social critique to reconstitute the Philadelphia of Penn's egalitarian plan. Yet while Lippard's exposé reveals Philadelphia's illicit elite, his sensational narrative undercuts any social transformation he may have imagined.
Long-term relationships among early first language skills, second language aptitude, second language affect, and later second language proficiency
Authors: SPARKS RICHARD L. , PATTON JON , GANSCHOW LEONORE , HUMBACH NANCY
Published: July 2009

Fifty-four students were followed over 10 years beginning in first grade to determine best predictors of oral and written second language (L2) proficiency. Predictor variables included measures of first language (L1) skill administered in first through fifth grades, L1 academic aptitude, L2 aptitude (Modern Language Aptitude Test), and L2 affect (motivation, anxiety). All participants completed 2 years of L2 study in high school. Findings revealed strong correlations between early L1 skills and later L2 proficiency, but the Modern Language Aptitude Test was the best predictor of overall L2 proficiency and most L2 proficiency subtests. However, L1 word decoding was the best predictor of L2 word decoding skills. Early L1 skills, L2 motivation, or L2 anxiety added a small amount of variance to the prediction models. Findings suggested that language-related variables are the most robust predictors of L2 proficiency. Results are discussed in the context of long-term cross linguistic transfer of early L1 skills to later L2 aptitude and L2 proficiency.
Associational resistance to a tropical leaf-miner: does neighbour identity matter?
Authors: Orians Colin M. , Björkman Christer
Published: July 2009

Associational resistance occurs when host plants experience reduced attack when in the presence of other plant species (Atsatt & O'Dowd 1976, Tahvanainen & Root 1972). The issue is most studied in agriculture and forestry because of the potential benefits to pest control (Andow 1991, Brown & Ewel 1987, Tahvanainen & Root 1972), but recent research indicates that associational resistance may be relatively common in natural systems as well (Hjältén et al. 1993, Karban 2007, Vehviläinen et al. 2007, Wise et al. 2009; but see Östergård & Ehrlén 2005, White & Whitham 2000), especially against specialist herbivores (Hambäck et al. 2000, 2003; Stenberg et al. 2007).
Terrestrial and understorey insectivorous birds of a Peruvian cloud forest: species richness, abundance, density, territory size and biomass
Authors: Kikuchi David W.
Published: July 2009

Terrestrial insectivorous birds in a cloud-forest on the north-western slope of the Peruvian Andes were described in terms of species richness, abundance, density, territory size and biomass. Abundance, density and territory size were also characterized for several understorey insectivores. The three terrestrial insectivore species, all in the genusGrallaria, had 35.25 territories on a 26.2-ha plot, defended territories of (mean ± SD) 1.65 ± 1.34 ha, dwelled at an average density of 4.4 ± 2.7 pairs per 10 ha per species and constituted a biomass of 2470 g per 10 ha. Eight understorey insectivore species had 122.75 territories on the plot, held territories 0.86 ± 0.62 ha in size, and lived at an average density of 5.0 ± 2.7 pairs per 10 ha per species. Six of the 11 species studied each occupied over 50% of the plot. Data on terrestrial insectivores from this study were compared with data from other Neotropical plots to examine how properties of guild structure relate to one another. Increasing densities, smaller territory sizes and higher biomasses appeared to be linked with decreasing species richness and increasing elevation, suggesting consistent patterns of covariance.
Mountains of Sublimity, Mountains of Fatigue: Towards a History of Speechlessness in the Alps
Authors: Felsch Philipp
Published: July 2009

Argument

The discovery of the Alps in the second half of the eighteenth century spawned an aesthetics of sublimity that enabled overwhelmed beholders of mountains to overcome their confusion symbolically by transforming initial speechlessness into pictures and words. When travelers ceased to be content with beholding mountains, however, and began climbing them, the sublime shudder turned into something else. In the snowy heights, all attempts to master symbolically the challenging landscape was thwarted by vertigo, somnolence, and fatigue. After 1850, physiologists intervened, using the Alpine terrain as a laboratory landscape that was ideally suited to examine one of the most threatening concerns offin de siècleindustrial societies: fatigue. This essay examines how the picturesque voyage turned into an experimental physiology of fatigue, and how the “wordless subjectivity” of romantic travelers turned into the “wordless objectivity” of life scientists.
Mountains Made in Switzerland: Facts and Concerns in Nineteenth-Century Cartography
Authors: Speich Daniel
Published: July 2009

Argument

Cultural history has investigated the appropriation of mountain wilderness in considerable detail, without however systematically including the contributions of science and technology in the process. This paper suggests a way of filling this gap. It argues that cartography was instrumental in giving mountains their modern shape. In the course of the nineteenth century, mountains arguably gained a new factual existence at the intersection of new aesthetic, scientific, economic, and political concerns with landscape. Taking the case of Swiss cartography, the paper shows how mapmakers strived to represent this matter of concern in ever more perfect ways, culminating in the three-dimensional rendering of mountains as plaster reliefs. The paper concludes with the observation that this transformation is to a certain extent irreversible. The mountains made in Switzerland in the nineteenth century are probably here to stay.
Professionals on the Peak
Authors: Becker Catherine Nisbett
Published: July 2009

Argument

The administration of mountain expeditions from the ground created special managerial problems. The Harvard College Observatory's Boyden Expeditions of 1887–1890 sent men and materiel to three sites: Pike's Peak, Colorado; Mount Wilson, California; and Chosica, Peru. Their goal was to test sites in order to find a suitable site for a permanent Boyden station to conduct astrophysical work in service of Harvard's preexisting projects. The logistical difficulties of living on the mountainside combined with the organizational difficulties of administrating a station at a distance. The men who lived on the mountain were professionally vulnerable, and often cut off from their home observatory both by the weather conditions at their own altitude and local politics on the ground below them. Only when an unbroken line of communication could be established between the mountain station and the Harvard Observatory could the astronomers on both ends work together to create a successful expedition.
TRANSFER AND TRANSITION IN THE SLA OF ASPECT
Authors: Gabriele Alison
Published: July 2009

Previous studies have shown that it is particularly difficult for second language (L2) learners to overcome the effects of transfer when they need to unlearn specific aspects of the native language in the absence of explicit input that indicates which properties of the first language (L1) are ruled out by the L2 grammar (Inagaki, 2001; Westergaard, 2003; White, 1991a, 1991b). The present study focuses on the effects of transfer in the domain of aspectual semantics through an investigation of the interpretation of the present progressive in L2 English and the imperfective markerte-iruin L2 Japanese and examines whether L2 learners can rule out interpretations available in the L1 but not in the L2. Japanese learners of English (n= 101), English native-speaker controls (n= 23), English learners of Japanese (n= 31), and Japanese native-speaker controls (n= 33) completed an interpretation task in English or Japanese. The results show that the L2 Japanese learners were more successful than the L2 English learners in both acquiring the semantics of the imperfective in the L2 and ruling out interpretations available only in the L1. It is proposed that successful unlearning depends on both the grammatical complexity of the semantic target in the L2 and the transparency of the input cues available to the learner.
DECOMPOSITION OF INFLECTED WORDS IN A SECOND LANGUAGE
Authors: Neubauer Kathleen , Clahsen Harald
Published: July 2009

German participles offer a distinction between regular forms that are suffixed with –tand do not exhibit any stem changes and irregular forms that all have the ending –nand sometimes undergo (largely unpredictable) stem changes. This article reports the results from a series of psycholinguistic experiments (acceptability judgments, lexical decision, and masked priming) that investigate regular and irregular participle forms in adult native speakers of German in comparison to advanced adult second language (L2) learners of German with Polish as their first language (L1). The most striking L1-L2 contrasts were found for regular participles. Although the L1 group’s performance was influenced by the combinatorial structure of regular participle forms, this was not the case for the L2 group. These findings suggest that adult L2 learners are less sensitive to morphological structure than native speakers and rely more on lexical storage than on morphological parsing during processing.
TASK COMPLEXITY, FOCUS ON FORM, AND SECOND LANGUAGE DEVELOPMENT
Authors: Révész Andrea
Published: July 2009

Tasks have received increased attention in SLA research for the past decade, as has the role of focus on form. However, few empirical studies have investigated the relationship among tasks, focus-on-form techniques, and second language (L2) learning outcomes. To help address this gap, the present study examined how the task variable +/− contextual support combined with the focus-on-form technique known as recasting affects L2 morphosyntactic development. The participants were 90 adult learners of English as a foreign language, randomly assigned to one of five groups: four comparison groups and a control group. The comparison groups differed as to (a) whether they received recasts while describing photos and (b) whether they could see the photos while describing them. The control group only participated in the testing sessions. A pretest-posttest-delayed posttest design was employed to detect any improvement in participants’ ability to use the linguistic target, which was the past progressive form. Results from multifaceted Rasch measurement yielded two main findings. First, learners who received recasts but did not view photos outperformed learners who received recasts while viewing photos. Second, the group that viewed photos but did not receive recasts achieved greater L2 gains than the group who neither viewed photos nor received recasts.
Characterising equilibrium logic and nested logic programs: Reductions and complexity,
Authors: PEARCE DAVID , TOMPITS HANS , WOLTRAN STEFAN
Published: July 2009

Equilibrium logic is an approach to non-monotonic reasoning that extends the stable-model and answer-set semantics for logic programs. In particular, it includes the general case ofnested logic programs, where arbitrary Boolean combinations are permitted in heads and bodies of rules, as special kinds of theories. In this paper, we present polynomial reductions of the main reasoning tasks associated with equilibrium logic and nested logic programs intoquantified propositional logic, an extension of classical propositional logic where quantifications over atomic formulas are permitted. Thus, quantified propositional logic is a fragment of second-order logic, and its formulas are usually referred to asquantified Boolean formulas(QBFs). We provide reductions not only for decision problems, but also for the central semantical concepts of equilibrium logic and nested logic programs. In particular, our encodings map a given decision problem into some QBF such that the latter is valid precisely in case the former holds. The basic tasks we deal with here are theconsistency problem,brave reasoningandskeptical reasoning. Additionally, we also provide encodings for testing equivalence of theories or programs under different notions of equivalence, viz.ordinary,stronganduniform equivalence. For all considered reasoning tasks, we analyse their computational complexity and give strict complexity bounds. Hereby, our encodings yield upper bounds in a direct manner. Besides this useful feature, our approach has the following benefits: First, our encodings yield auniform axiomatisationfor a variety of problems in a common language. Second, extant solvers for QBFs can be used as back-end inference engines to realise implementations of the encoded task in a rapid prototyping manner. Third, our axiomatisations also allow us to straightforwardly relate equilibrium logic with circumscription.
GREAT WALL?: OVERCOMING THE BOUNDARY BETWEEN EURO-AMERICAN AND SINO-JAPANESE SINOLOGIES
Authors: Kotera Atsushi
Published: July 2009

It is well known that the nations of Europe and North America take the lead in the majority of disciplines in the academic world today. In most fields, unless a scholarly work makes reference in some way or other to the findings of Euro-American research, it is not considered worthy of mention. It is not, however, so common for the accomplishments of Euro-American scholars to be taken up by Japanese and Chinese scholars working in the field of ancient Chinese history. Presumably one reason for this is that in East Asia, especially in Japan and China, there are long and rich traditions of scholarship on Chinese ancient history that reach back to premodern times. Yet to just what extent is the research of European and American scholars referenced in the introductory books and general surveys concerning ancient Chinese history that are published in Japan and China?
Global patterns of dissolved silica export to the coastal zone: Results from a spatially explicit global model
Authors: Beusen A. H. W. , Bouwman A. F. , Dürr H. H. , Dekkers A. L. M. , Hartmann J.
Published: July 2009

We present a multiple linear regression model developed for describing global river export of dissolved SiO2(DSi) to coastal zones. The model, with river basin spatial scale and an annual temporal scale, is based on four variables with a significant influence on DSi yields (soil bulk density, precipitation, slope, and area with volcanic lithology) for the predam situation. Cross validation showed that the model is robust with respect to the selected model variables and coefficients. The calculated global river export of DSi is 380 Tg a−1(340–427 Tg a−1). Most of the DSi is exported by global rivers to the coastal zone of the Atlantic Ocean (41%), Pacific Ocean (36%), and Indian Ocean (14%). South America and Asia are the largest contributors (25% and 23%, respectively). DSi retention in reservoirs in global river basins may amount to 18–19%.
Mössbauer modeling to interpret the spin state of iron in (Mg,Fe)SiO3 perovskite
Authors: Bengtson Amelia , Li Jie , Morgan Dane
Published: July 2009

The properties of (Mg,Fe)SiO3 perovskite at lower mantle conditions are still not well understood, and particular attention has recently been given to determining the Fe spin state. A major challenge in spin states studies is interpretation of Mössbauer spectra to determine the electronic structure of iron under extreme conditions. In this paper ab initio methods are used to predict quadrupole splitting values of high‐, intermediate‐ and low‐spin Fe2+ and Fe3+ in perovskite, as a function of pressure and composition. The calculations in (Mg0.75Fe0.25)SiO3 yield quadrupole splitting values in the range of 0.7–1.7 mm/s for all spin and valence states except high‐spin Fe2+, which has two possible quadrupole splittings, 2.3 and 3.3 mm/s. The unexpected multiple quadrupole splitting values for high‐spin Fe2+ are explained in terms of small changes in local structure and d‐orbital occupations. The computed results are applied to interpret existing perovskite Mössbauer data for iron's spin state.
A study of the sensitivity of ocean overturning circulation and climate to freshwater input in different regions of the North Atlantic
Authors: Smith Robin S. , Gregory Jonathan M.
Published: July 2009

The Atlantic meridional overturning circulation (AMOC) is an important component of the climate system. Models indicate that the AMOC can be perturbed by freshwater forcing in the North Atlantic. Using an ocean‐atmosphere general circulation model, we investigate the dependence of such a perturbation of the AMOC, and the consequent climate change, on the region of freshwater forcing. A wide range of changes in AMOC strength is found after 100 years of freshwater forcing. The largest changes in AMOC strength occur when the regions of deepwater formation in the model are forced directly, although reductions in deepwater formation in one area may be compensated by enhanced formation elsewhere. North Atlantic average surface air temperatures correlate linearly with the AMOC decline, but warming may occur in localised regions, notably over Greenland and where deepwater formation is enhanced. This brings into question the representativeness of temperature changes inferred from Greenland ice‐core records.
Evolution of electron pitch angle distribution due to interactions with whistler mode chorus following substorm injections
Authors: Su Zhenpeng , Zheng Huinan , Wang Shui
Published: July 2009

During substorms, pitch angle distribution (PAD) of freshly injected plasma sheet electrons can develop into the typical pancake distribution from the nearly isotropic distribution, which has previously been suggested as the result of resonant scattering driven by electrostatic cyclotron harmonic (ECH) and whistler mode waves in the equatorial regions. In this paper, using the two‐dimensional bounce‐averaged Fokker‐Planck equation, we present a quantitative analysis of the electrons PAD evolution at L = 6 due to interactions with upper (ω/∣Ωe∣ > 0.5) and lower (ω/∣Ωe∣ < 0.5) band chorus based on the observed wave characteristics during substorms. It is found that the upper band chorus can efficiently scatter the electrons with energies 0.1–2 keV into loss cone and drive the electrons with energies above 2 keV toward loss cone. The lower band chorus can only cause precipitation loss of the electrons with energies above 1 keV by resonant scattering. The PADs of electrons with energies above 0.1 keV can develop into the pancake‐shaped distributions due to the combined resonant scattering by upper and lower band chorus, and the pancake index PI, defined as the flux ratio between 90° and 70°, can reach 6 after 5 hours since substorm injections. The PI variation timescale and amplitude are consistent with previous statistical results. The numerical results suggest that the resonant scattering of electrons by the whistler mode chorus waves can be a substantial mechanism responsible for the formation of a pancake distribution outside L = 6. Besides, the rapid precipitation of electrons (∼keV) driven by resonant scattering of chorus waves may also be responsible for the diffuse aurora.
Analysis quantifies effects of tides in Jupiter and lo
Authors: Miller Johanna
Published: July 2009

The planet and its moon distort each other, with consequences for lo’s volcanic activity and the orbits of Jupiter’s other moons.
Chaotic semiconductor lasers generate random numbers at high speed
Authors: Miller Johanna
Published: July 2009

Two groups have harnessed subnanosecond intensity fluctuations to produce unpredictable binary sequences.
Divisions heat up as Senate mulls carbon caps
Authors: Kramer David
Published: July 2009

Republicans warn that curbs on greenhouse gas will worsen recession.
Iron-based superconductors
Authors: Day Charles
Published: July 2009

For 22 years ceramic oxides of copper seemed to offer the only way to reach high-temperature superconductivity. Now, a new and unexpected route is being charted: through semimetal compounds of iron.
IL-1 antagonism reduces hyperglycemia and tissue inflammation in the type 2 diabetic GK rat
Authors: Ehses J. A. , Lacraz G. , Giroix M.-H. , Schmidlin F. , Coulaud J. , Kassis N. , Irminger J.-C. , Kergoat M. , Portha B. , Homo-Delarche F. , Donath M. Y.
Published: July 2009

Recent studies suggest an inflammatory process, characterized by local cytokine/chemokine production and immune cell infiltration, regulates islet dysfunction and insulin resistance in type 2 diabetes. However, the factor initiating this inflammatory response is not known. Here, we characterized tissue inflammation in the type 2 diabetic GK rat with a focus on the pancreatic islet and investigated a role for IL-1. GK rat islets, previously characterized by increased macrophage infiltration, displayed increased expression of several inflammatory markers including IL-1β. In the periphery, increased expression of IL-1β was observed primarily in the liver. Specific blockade of IL-1 activity by the IL-1 receptor antagonist (IL-1Ra) reduced the release of inflammatory cytokines/chemokines from GK islets in vitro and from mouse islets exposed to metabolic stress. Islets from mice deficient in IL-1β or MyD88 challenged with glucose and palmitate in vitro also produced significantly less IL-6 and chemokines. In vivo, treatment of GK rats with IL-1Ra decreased hyperglycemia, reduced the proinsulin/insulin ratio, and improved insulin sensitivity. In addition, islet-derived proinflammatory cytokines/chemokines (IL-1β, IL-6, TNFα, KC, MCP-1, and MIP-1α) and islet CD68+, MHC II+, and CD53+immune cell infiltration were reduced by IL-1Ra treatment. Treated GK rats also exhibited fewer markers of inflammation in the liver. We conclude that elevated islet IL-1β activity in the GK rat promotes cytokine and chemokine expression, leading to the recruitment of innate immune cells. Rather than being directly cytotoxic, IL-1β may drive tissue inflammation that impacts on both β cell functional mass and insulin sensitivity in type 2 diabetes.
Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in
Synechococcus elongatus
Authors: Ito Hiroshi , Mutsuda Michinori , Murayama Yoriko , Tomita Jun , Hosokawa Norimune , Terauchi Kazuki , Sugita Chieko , Sugita Mamoru , Kondo Takao , Iwasaki Hideo
Published: July 2009

In the unicellular cyanobacterium
Synechococcus elongatus
PCC 7942, essentially all promoter activities are under the control of the circadian clock under continuous light (LL) conditions. Here, we used high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide
Synechococcus
gene expression in wild-type,
kaiABC
-null, and
kaiC
-overexpressor strains under LL and continuous dark (DD) conditions. In the wild-type strains, >30% of transcripts oscillated significantly in a circadian fashion, peaking at subjective dawn and dusk. Such circadian control was severely attenuated in
kaiABC
-null strains. Although it has been proposed that KaiC globally represses gene expression, our analysis revealed that dawn-expressed genes were up-regulated by
kaiC
-overexpression so that the clock was arrested at subjective dawn. Transfer of cells to DD conditions from LL immediately suppressed expression of most of the genes, while the clock kept even time in the absence of transcriptional feedback. Thus, the
Synechococcus
genome seems to be primarily regulated by light/dark cycles and is dramatically modified by the protein-based circadian oscillator.
Experimental and theoretical study of the diffraction properties of various crystals for the realization of a soft gamma-ray Laue lens
Authors: Barrière Nicolas , Rousselle Julien , von Ballmoos Peter , Abrosimov Nikolai V. , Courtois Pierre , Bastie Pierre , Camus Thierry , Jentschel Michael , Kurlov Vladimir N. , Natalucci Lorenzo , Roudil Gilles , Frisch Brejnholt Nicolai , Serre Denis
Published: July 2009

Crystals are the elementary constituents of Laue lenses, an emerging technology which could allow the realization of a space-borne telescope 10–100 times more sensitive than existing ones, in the 100 keV–1.5 MeV energy range. This paper addresses the development of efficient crystals for the realization of a Laue lens. In the theoretical part, 35 candidate crystals, both pure and two-component crystals, are considered. Their peak reflectivity at 100, 500 keV and 1 MeV is calculated assuming they are mosaic crystals. It is found that, by careful selection of crystals, it is possible to achieve a reflectivity above 30% over the whole energy range, and even up to 40% in the lower part of the energy range. In the experimental part, three different materials (Si1−xGexwith a gradient of composition, mosaic Cu and Au) have been measured at both ESRF and ILL using highly monochromatic beams ranging from 300 to 816 keV. The aim was to check their homogeneity, quality and angular spread (mosaicity). These crystals have shown outstanding performance, such as reflectivity up to 31% at ∼600 keV (Au) or 60% at 300 keV (SiGe) and angular spread as low as 15 arcsec for Cu, fulfilling very well the requirements for a Laue lens application. An unexpected finding is that there are important discrepancies with Darwin's model when a crystal is measured using various energies.
A combined fit of total scattering and extended X-ray absorption fine structure data for local-structure determination in crystalline materials
Authors: Krayzman V. , Levin I. , Woicik J. C. , Proffen Th. , Vanderah T. A. , Tucker M. G.
Published: July 2009

Reverse Monte Carlo (RMC) refinements of local structure using a simultaneous fit of X-ray/neutron total scattering and extended X-ray absorption fine structure (EXAFS) data were developed to incorporate an explicit treatment of both single- and multiple-scattering contributions to EXAFS. The refinement algorithm, implemented as an extension to the public domain computer softwareRMCProfile, enables accurate modeling of EXAFS over distances encompassing several coordination shells around the absorbing species. The approach was first tested on Ni, which exhibits extensive multiple scattering in EXAFS, and then applied to perovskite-like SrAl1/2Nb1/2O3. This compound crystallizes with a cubic double-perovskite structure but presents a challenge for local-structure determination using a total pair-distribution function (PDF) alone because of overlapping peaks of the constituent partial PDFs (e.g.Al—O and Nb—O or Sr—O and O—O). The results obtained here suggest that the combined use of the total scattering and EXAFS data provides sufficient constraints for RMC refinements to recover fine details of local structure in complex perovskites. Among other results, it was found that the probability density distribution for Sr in SrAl1/2Nb1/2O3adoptsTdpoint-group symmetry for the Sr sites, determined by the ordered arrangement of Al and Nb, as opposed to a spherical distribution commonly assumed in traditional Rietveld refinements.
Slow cooling of protein crystals
Authors: Warkentin Matthew , Thorne Robert E.
Published: July 2009

Cryoprotectant-free thaumatin crystals have been cooled from 300 to 100 K at a rate of 0.1 K s−1– 103–104times slower than in conventional flash cooling – while continuously collecting X-ray diffraction data, so as to follow the evolution of protein lattice and solvent properties during cooling. Diffraction patterns show no evidence of crystalline ice at any temperature. This indicates that the lattice of protein molecules is itself an excellent cryoprotectant, and with sodium potassium tartrate incorporated from the 1.5 Mmother liquor ice nucleation rates are at least as low as in a 70% glycerol solution. Crystal quality during slow cooling remains high, with an average mosaicity at 100 K of 0.2°. Most of the mosaicity increase occurs above ∼200 K, where the solvent is still liquid, and is concurrent with an anisotropic contraction of the unit cell. Near 180 K a crossover to solid-like solvent behavior occurs, and on further cooling there is no additional degradation of crystal order. The variation ofBfactor with temperature shows clear evidence of a protein dynamical transition near 210 K, and at lower temperatures the slope dB/dTis a factor of 3–6 smaller than has been reported for any other protein. These results establish the feasibility of fully temperature controlled studies of protein structure and dynamics between 300 and 100 K.
Models of uniformity for grain boundary distributions
Authors: Morawiec A.
Published: July 2009

Progress in experimental methods of serial sectioning and orientation determination opens new opportunities to study inter-crystalline boundaries in polycrystalline materials. In particular, macroscopic boundary parameters can now be measured automatically. With sufficiently large data sets, statistical analysis of interfaces between crystals is possible. The most basic and interesting issue is to find out the probability of occurrence of various boundaries in a given material. In order to define a boundary density function, a model of uniformity is needed. A number of such models can be conceived. It is proposed to use those derived from an assumed metric structure of the interface manifold. Some basic metrics on the manifold are explicitly given, and a number of notions and constructs needed for a strict definition of the boundary density function are considered. In particular, the crucial issue of the impact of symmetries is examined. The treatments of homo- and hetero-phase boundaries differ in some respects, and approaches applicable to each of these two cases are described. In order to make the abstract matter of the paper more accessible, a concrete boundary parameterization is used and some examples are given.
Meta‐analysis: deamidated gliadin peptide antibody and tissue transglutaminase antibody compared as screening tests for coeliac disease
Authors: LEWIS N. R. , SCOTT B. B.
Published: July 2009

Background  Following the appreciation of the importance of gliadin deamidation in the immunopathogenesis of coeliac disease, diagnostic tests based on antibodies to deamidated gliadin peptides have been developed and shown to have high sensitivity and specificity.

Aim  To compare the performance of the deamidated gliadin peptides antibody test with the current standard, the tissue transglutaminase antibody test, through a meta‐analysis of published studies.

Methods  Databases from 1998 to 2008 were searched for relevant studies. These were assessed for methodological quality and standard statistical tests were applied to compare particularly the sensitivity and specificity of the two tests for the diagnosis of coeliac disease.

Results  Most studies had methodological flaws, especially ascertainment bias. The pooled sensitivities for the deamidated gliadin peptides antibody and tissue transglutaminase antibody tests were 87.8% (95% CI, 85.6–89.9) and 93.0% (95% CI, 91.2–94.5) respectively and the pooled specificities were 94.1% (95% CI, 92.5–95.5) and 96.5% (95% CI, 95.2–97.5) respectively.

Conclusion  Although both tests perform well, the tissue transglutaminase antibody test outperforms the deamidated gliadin peptides antibody test and remains the preferred serological test for the diagnosis and/or exclusion of coeliac disease.
Biological measurements in a nationwide soil monitoring network
Authors: Rutgers M. , Schouten A. J. , Bloem J. , Van Eekeren N. , De Goede R. G. M. , Jagersop Akkerhuis G. A. J. M. , Van der Wal A. , Mulder C. , Brussaard L. , Breure A. M.
Published: July 2009

In the Netherlands soil biological measurements are undertaken in a nationwide monitoring programme. The measurements are combined in the Biological Indicator of Soil Quality (BISQ). About 300 locations were selected in a random stratified design comprising stringent combinations of land use and soil type. All locations were sampled in a six‐year cycle. In this contribution we describe the monitoring network and the BISQ and present average values for biomass, abundances and taxonomic diversity of various soil dwelling organisms derived from 10 years of measurements. We further highlight some results and discuss the possibilities in soil and land management policy frameworks for improving sustainable land management.
Coarse particulate organic matter dynamics in small streams: towards linking function to physical structure
Authors: RICHARDSON JOHN S. , HOOVER TRENT M. , LECERF ANTOINE
Published: July 2009

1. Organic matter derived from terrestrial vegetation (detritus) is a key basal resource in many food webs, including those of streams. Once detritus enters a stream, it is either retained or transported, but the rates of within‐reach retention depend on structural characteristics of the stream channel, physical properties of the detrital particles and hydrology. Each of these attributes varies in time and space and the magnitude of variation may be affected by structural changes wrought by land‐use. We developed a heuristic model framework in an attempt to find a minimal model that captures the essential temporal dynamics of coarse particulate detritus in small streams.

2. The dynamics of our minimal model are driven by several frequently measured variables. Rate of litter breakdown, average transport distance of a particle, discharge and temperature are the primary variables. In addition, we tested the effects of altering assumptions about the nature of particle type and the effect of channel roughness on transport rates.

3. The model produced patterns of detrital standing stocks generally similar to those measured by empirical studies in small streams. Discharge‐dependent transport relations are relatively rare, but our assumed pattern of a sigmoid relationship between transport and discharge produced reasonable outputs.

4. We parameterised the model using data for small streams in coastal British Columbia, Canada. The outputs of the model indicate that channel roughness has a more profound effect on small, mobile particles, such as conifer needles, than on angiosperm leaves, such as alder. The model also indicates that the largest proportion of detritus is broken downin situin all model scenarios.

5. A major limitation to this model and the literature is a scarcity of detail of leaf interception and entrainment processes in streams. Progress towards integrating ecosystem functions and the dynamics of hydromorphology require integrating these physical drivers with biological processes. We present our model to emphasise that progress towards generalisable models of detrital dynamics is possible if links between physical structure and function can be made explicit.
Low‐level effects of inert sediments on temperate stream invertebrates
Authors: LARSEN S. , ORMEROD S. J.
Published: July 2009

1. The delivery, entrainment and deposition of inert fine sediments are among the most significant contributors to stream and river impairment worldwide. Associated ecological effects have been observed frequently, but specific experiments to identify sensitivity and avoidance behaviour in stream organisms are few, particularly in headwaters.

2. In a field‐experiment, we added fine sand at low levels (c. 4–5 kg m−2) to 10 m reaches of two replicate headwater streams in the Usk catchment (Wales, U.K.) over two periods (autumn and summer). Upstream reaches were used as control in a classic before‐after‐control‐impact design. Invertebrate drift and benthic composition were measured for 2 days before and 1 day after sediment impact.

3. Sediment addition significantly increased overall drift density (by 45%) and propensity (by 200%), with effects largest on the night following addition rather than immediately (i.e. within 9 h). The mayflies Baetis rhodani, B. muticus and Ecdyonurus spp., simuliid and chironomid dipterans, and helodid beetles were the strongest contributors.

4. There were no marked effects on benthic composition, but density declined in treated reaches by 30–60%, particularly in B. rhodani, Ecdyonurus spp. and Leuctra hippopus + L. moselyi.

5. All effects were consistent between both seasons and streams.

6. These data show how even low‐level, short‐term, increases in fine sediment loading to upland, stony streams can reduce overall benthic density through increased drift. We suggest that the likely cause of the delayed drift response was a change in habitat quality which prompted avoidance behaviour. Longer‐term experiments are required to assess whether these effects reduce fitness or explain the losses of some types of organisms observed recently in sediment‐impaired reaches of this and other catchments.
Response of grazing impacts of an algivorous fish (Pseudogastromyzon myersi: Balitoridae) to seasonal disturbance in Hong Kong streams
Authors: YANG GRACE Y. , DUDGEON DAVID
Published: July 2009

1. Manipulative experiments were carried out in four Hong Kong streams (two shaded, two unshaded) to investigate the impact of grazing by an algivorous fish, Pseudogastromyzon myersi, on benthic algal biomass and assemblage composition. Experiments were conducted and repeated during both the dry and wet seasons to determine whether spate‐induced disturbance modified any grazing effect. Treatments comprised fish exclusion and inclusion via closed and open cages, with a no‐cage treatment used as a control for the cage effect. Treatments were maintained for 4 weeks in each experimental run.

2. Grazing by P. myersi reduced benthic algal biomass and the organic matter content of periphyton in open cages and the no‐cage treatment relative to closed cages. The similarity between open‐cage and no‐cage treatments was evidence that the overall difference among treatments was caused by limiting fish access to closed cages and not merely an artifact of caging. Grazing effects were broadly similar in all streams, but there was a significant statistical interaction between treatments and seasons.

3. Analysis of dry‐season data matched the overall trend in inter‐treatment differences, confirming the effects of grazing by P. myersi on algal biomass and periphyton organic matter. Significant differences in algal assemblage composition between closed‐cage and no‐cage treatments during the dry season reflected reductions in the abundance of erect, stalked diatoms (Gomphonema) and filamentous cyanobacteria (Homeothrix). Removal of these vulnerable overstorey algae by P. myersi resulted in greater abundance of understorey diatoms (Achnanthes and Cocconeis) in the no‐cage treatment in all streams during the dry season. The composition of algal assemblages in open cages was intermediate between the other two treatments.

4. Although fish densities were greater in all streams during the wet season, spate‐induced disturbance obscured grazing effects and there were no significant differences among treatments attributable to fish grazing. Seasonal variation in impacts of P. myersi grazing provides support for the harsh‐benign hypothesis, and confirms that biotic factors are less important controls of stream algal biomass and assemblage structure during periods (i.e. the wet season in Hong Kong) when abiotic disturbances are frequent or intense.
Transport and settlement of organic matter in small streams
Authors: HOOVER TRENT M. , MARCZAK LAURIE B. , RICHARDSON JOHN S. , YONEMITSU NOBORU
Published: July 2009

1. After it enters streams, terrestrially derived organic matter (OM) rapidly absorbs water. Using field and laboratory experiments, we examined how this process affected the buoyancy, settling velocity, transport distance and retention locations of four types of organic matter typically found in Pacific coastal streams (‘flexible’ red alder leaves and three ‘stiff’ particle types – Douglas‐fir needles, red cedar fronds and Douglas‐fir branch pieces).

2. Immersion in water rapidly changed the physical characteristics of alder leaves, Douglas‐fir needles and red cedar fronds, which all reached constant still‐water settling velocities after only a few days of soaking. In contrast, the settling velocity of branch pieces continued to increase for 13 days, eventually reaching much higher values than any other OM type. Dried alder leaves became negatively buoyant after only two days of immersion, while other types took substantially longer (up to 24 days) before the specific gravity of all particles was >1.

3. We released saturated OM particles in an experimental channel and found that all particle types travelled further in a fast, shallow ‘riffle’ than a slow, deep ‘pool’. Comparisons with a passive settlement null model indicated that leaves were retained more rapidly than expected in the riffle (by large protruding stones), while the three stiff particle types travelled further than expected (probably due to turbulent suspension) and were retained when they settled in deeper water between larger stones. In pools, passive settlement appeared to dominate the retention of all OM types, with leaves travelling furthest.

4. These retention patterns corresponded well with those observed when saturated OM particles collected in the field were released in two pools and two riffles in a second‐order coastal stream.

5. When the experimental channel and in‐stream data were combined, the retention rates of the three stiff OM types were closely related to calculated Rouse numbers (Rouse number = particle settling velocity/shear velocity), whereas the retention rate of alder leaves was not. This suggests that different physical mechanisms are responsible for the retention of leaves and stiff OM types in shallow streams.