bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity of seed storage protein patterns of Slovak accessions in jointed goatgrass (Aegilops cylindrica Host.)
Authors: Gregová Edita , Hauptvogel Pavol , Hauptvogel René , Vörösváry Gábor , Csizmadia Gábor Málnási
Published: June 2011

Variations in seed storage protein patterns were investigated for six accessions of jointed goatgrass (Aegilops cylindrica) populations collected from Slovakia within the framework of the bilateral Co-operation in Science and Technology between the Slovak Republic and Hungary. The study covered populations collected from the southwestern (localities: Sered and Dunajská Streda), southern (localities: Chlaba and Kamenica nad Hronom) and southeastern (localities: Cierna nad Tisou and Dobra) parts of Slovakia. Analysis of profiles of seed storage proteins – glutenins and gliadins – was carried out using acid polyacrylamide gel electrophoresis and sodium dodecyl sulphate polyacrylamide gel electrophoresis. All accessions have a uniform three-band high molecular weight glutenin pattern with CxCyDy subunit composition. The highest variations in gliadin bands among the populations were observed from Cierna nad Tisou. There were small differences among the populations from Chlaba and Dobra. The lowest variations were in populations from Sered, Dunajska Streda and Kamenica nad Hronom. The present investigation showed that these jointed goatgrass populations are valuable genetic resources for wheat crop improvement programmes.
Analysis of genetic diversity inCitrus
Authors: Luro François , Gatto Julia , Costantino Gilles , Pailly Olivier
Published: June 2011

Sugar and acidity levels are the main criteria of general fruit quality and for citrus juices pulp, in particular. The constituents of the acidity (organic acids) and the sweetness (glucose, fructose and sucrose) and the genes involved in their regulation have seldom been used to exploreCitrusgenetic diversity. We evaluated the juice composition of primary metabolic components for 87 varieties belonging to the eight majorCitrusspecies grown under the same environmental and cultivation conditions by HPLC. We investigated the sequence polymorphism of nine candidate genes encoding for key enzymes of sugars and organic acids metabolic pathways by single strand conformation polymorphism (SSCP). Whatever the biochemical or molecular analyses, the observed structure ofCitrusdiversity was organized around three groups corresponding to the ancestral species (mandarin, pummelo and citron). As expected, the secondary species were closely related to their putative ancestors except forCitrus aurantium. Biochemical diversity was strongly correlated to molecular SSCP diversity at the genus level but not at the intraspecific level. Compared with other molecular marker types, higher diversity has been observed with SSCP technology, which makes it suitable for future quantitative trait loci mapping approach on gene polymorphism in citrus pulp acidity and sweetness regulation.
The genetic make-up of the European landraces of the common bean
Authors: Angioi S. A. , Rau D. , Nanni L. , Bellucci E. , Papa R. , Attene G.
Published: June 2011

Here, we present a brief overview of the main studies conducted on the common bean (Phaseolus vulgarisL.) in Europe and other countries outside its centres of origin. We focus on the proportions of the Andean and Mesoamerican gene pools, and on the inter-gene pool hybridization events. In Europe, for chloroplast microsatellites, 67% of European germplasm is of Andean origin. Within Europe, interesting trends have been seen; indeed, the majority of the Andean type is found in the three macro-areas of the Iberian Peninsula, Italy and central-northern Europe, while, in eastern and south-eastern Europe, the proportion of the Mesoamerican type increased. On a local scale, the contribution of the Mesoamerican type is always low. On other continents, various situations are seen using different markers: in China and Brazil, the Mesoamerican gene pool prevails, while in an African sample, overall, both gene pools are equally represented, with differences in individual countries. The frequency of European bean genotypes deriving from at least one hybridization event was 44% with an uneven distribution. Interestingly, hybrids tend to have intermediate seed size in comparison with ‘pure’ Andean or Mesoamerican types. On other continents, very few hybrids are found, probably because of the different marker systems used.
Assessment of genetic diversity among Sri Lankan rice varieties by AFLP markers
Authors: Rajkumar Gowri , Weerasena Jagathpriya , Fernando Kumudu , Liyanage Athula
Published: June 2011

Sri Lanka has a valuable repository of germplasm collection due to the availability of a large number of different traditional and improved rice varieties. Molecular techniques can increase the effectiveness of traditional technologies in assessing genetic diversity. Amplified fragment length polymorphism (AFLP) was used to evaluate the genetic diversity among rice varieties available in the germplasm collection of Plant Genetic Resources Centre, Sri Lanka. AFLP analysis of rice varieties using ten different primer combinations yielded a total of 772 polymorphic bands (98.4%). Genetic similarities were estimated using Jaccard's (J) similarity coefficient. Unweighted pair group method with arithmetic mean (UPGMA)-based dendrogram was constructed. Genetic similarities varied from 0.073 to 0.565. Cluster analysis by genetic similarity divided the accessions into four main groups. The Cophenetic correlation with r = 0.781 indicated high confidence of AFLP data to group the varieties in UPGMA clusters. Principal component analysis further confirmed the patterns obtained by the cluster analysis. The results revealed very high genetic diversity at molecular level among the Sri Lankan rice varieties used in this study.
Molecular characterization of the European rice collection in view of association mapping
Authors: Courtois Brigitte , Greco Raffaella , Bruschi Gianluca , Frouin Julien , Ahmadi Nourollah , Droc Gaëtan , Hamelin Chantal , Ruiz Manuel , Evrard Jean-Charles , Katsantonis Dimitrios , Oliveira Margarida , Negrao Sonia , Cavigiolo Stefano , Lupotto Elisabetta , Piffanelli Pietro
Published: June 2011

In South Europe, rice is grown as an irrigated crop in river deltas where it plays an important role in soil desalinization. Specific varieties are needed for these tough conditions. We analyzed the genetic structure of a set of 305 varieties coming from the European Rice Germplasm Collection (ERGC) with 90 single nucleotide polymorphisms and compared it with a reference set representative of the diversity of Oryza sativa (mini-Germplasm Bank (GB)). These accessions had been characterized for their grain type and growth cycle duration. The polymorphism information contents of the ERGC were lower than those of the mini-GB, indicating a narrower genetic basis. Indeed, almost all ERGC accessions belong to the japonica group. Within the japonica group, both a dendrogram and a Bayesian clustering identified two major clusters. The first cluster encompassed tropical japonicas and American varieties from USA and Argentina characterized by long and narrow grains and medium to long duration. On a finer level, tropical japonicas appear separated from the other accessions. The second cluster is composed of European varieties mostly early or medium in duration and Asian temperate accessions, with a subgrouping based on grain format. A set of 200 accessions was composed for association mapping studies on traits such as salt tolerance.
Genetic diversity among Italian melon inodorus (Cucumis melo L.) germplasm revealed by ISSR analysis and agronomic traits
Authors: Sestili S. , Giardini A. , Ficcadenti N.
Published: June 2011

The genetic relationships among 13 melon inodorus populations that were collected in southern Italy were assessed using 100 inter-simple-sequence repeat (ISSR) primers and 15 morphological traits. The dihaploid line Nad-1 and the cultivar Charentais-T, both of which belong to the botanical variety cantalupensis, were used as reference accessions in the molecular analysis. A total of 358 polymorphic bands were obtained from 39 of the 100 ISSR primers used, and 15 phenotypic traits were scored and used for genetic-similarity calculations and cluster analysis. The resulting dendrograms based on the ISSR and phenotypic data allowed almost all of the melon genotypes to be distinguished on the basis of the skin colour of the fruits. Mantel's test revealed a good correlation between the morphological and molecular data in their ability to detect genetic relationships among melon ecotypes (r = 0.50, P = 0.99). The data obtained confirm the effectiveness of this approach, and open new perspectives to reveal possible molecular associations with the phenotypic traits analysed.
SCAR markers of the R-genes and germplasm of wild Solanum species for breeding late blight-resistant potato cultivars
Authors: Sokolova Ekaterina , Pankin Artem , Beketova Maria , Kuznetsova Maria , Spiglazova Svetlana , Rogozina Elena , Yashina Isol'da , Khavkin Emil
Published: June 2011

New races of Phytophthora infestans rapidly defeat potato late blight (LB) resistance based on Solanum demissum germplasm, and breeders search for new sources of durable LB resistance. We developed and verified six sequence characterized amplified region markers recognizing the race-specific genes R1 and R3 of S. demissum and the broad-spectrum resistance gene RB of S. bulbocastanum and the germplasms of these species and used them to screen 209 accessions of 21 wild Solanum species. In addition to S. demissum, homologues of R1 and R3 were found in several species of series Demissa,Longipedicellata and diploid Tuberosa; R3 homologues were also detected in S. bulbocastanum,S. cardiophyllum and S. ehrenbergii. The RB homologues were found in a wider range of Solanum species. The markers of R1 and R3 genes reliably discerned between germplasms of S. tuberosum ssp. tuberosum and wild sources of LB resistance. Following introgression, the species-specific markers of demissum and bulbocastanum germplasm were rapidly lost, whereas the markers of R1 and R3 genes lasted through several meiotic generations and were maintained at high frequencies in modern potato cultivars. The presence of these markers in demissoid potato cultivars was significantly associated with LB resistance, presuming that both genes contribute to overall defence response.
Seed longevity in oilseed rape (Brassica napus L.) – genetic variation and QTL mapping
Authors: Nagel Manuela , Rosenhauer Maria , Willner Evelin , Snowdon Rod J. , Friedt Wolfgang , Börner Andreas
Published: June 2011

Although oilseed rape has become one of the most important oil crops in Europe, little is known regarding the viability of its seed under conditions of long-term storage. We report here an examination of oilseed rape seed longevity performed on a set of 42 accessions housed at the German ex situ genebank at IPK, Gatersleben. A comparison of germination between the accessions stored for 26 years showed that viability was in part genetically determined, since it ranged between 42 and 98%. An attempt was made to define the genetic basis of viability by subjecting a mapping population of doubled haploids to three artificial ageing treatments. Quantitative trait loci (QTL) were detected on six chromosomes: N6, N7, N8, N15, N16 and N18. The chromosomal locations of these QTL were compared with their syntenic regions in Arabidopsis thaliana in order to explore what genes might underlie genetic variation for longevity.
Allele variation in loci for adaptive response in Bulgarian wheat cultivars and landraces and its effect on heading date
Authors: Kolev Stanislav , Vassilev Dimitar , Kostov Kostadin , Todorovska Elena
Published: June 2011

Allele composition at the major growth habit (Ppd-D1,Vrn-1, Rht-1andRht8) loci was determined in 52 Bulgarian bread wheat cultivars and landraces, using recently developed diagnostic molecular markers. The study showed that Bulgarian wheat germplasm varies for photoperiod, vernalization and height-reducing genes. The photoperiod-sensitive allele (Ppd-D1b)was the most frequent one in the old cultivars and landraces (90.9%), while the photoperiod-insensitive allele (Ppd-D1a) showed the highest frequency in the modern cultivars (96.71%). The alleles conferring winter growth habit (vrn-A1,vrn-B1andvrn-D1) were more common in both the old (72.7%) and the modern (93.3%) wheat genotypes. The spring alleleVrn-A1cwas not detected in Bulgarian germplasm, while the spring alleleVrn-B1was found only in the old genotypes (13.6%). The semi-dwarfing alleleRht-B1bwas observed in several modern cultivars. Seven allele variants were found in the microsatellite locusXgwm261, closely located to theRht8gene. Among them, alleles of 164, 212 and 216 bp length were specific for the old genotypes studied, while alleles of 192 and 202 bp length were specific for the modern ones. The allele combinationRht-B1b//192 or 202 bp allele (Xgwm261locus)//Ppd-D1a//vrn-A1/vrn–B1/vrn-D1was detected in most of the early-heading modern cultivars. Our study emphasizes on the plasticity of the adaptive response of bread wheat cultivars sown in Bulgaria, as well as on the effect of variation for major growth habit on some yield and reproductive characteristics.
Making Sense of Entertainment
Authors: Bartsch Anne , Beth Oliver Mary
Published: June 2011

This contribution explores the relationship of emotion and cognition in entertainment experience. Drawing on the reflective model of aesthetic experience ( Cupchik, 1995 ) and the concept of appreciation ( Oliver & Bartsch, 2010 ), we propose a multi-level view of affective processing that includes simple affect schemata as well as more elaborate forms of sociomoral reasoning that build on this basic layer of emotional meaning. To better understand how affective factors can stimulate or impede cognitive elaboration processes, we review research on motivated cognition that has dealt with the influence of arousal, valence, and personal relevance on cognitive depth. The role of affect in defensive information processing (i.e., the motivated neglect or denial of information) is also considered. Specifically, we discuss how research on motivated cognition can help explain thought-provoking entertainment experiences, and the potential of such experiences to stimulate self-reflection and personal growth.
Appreciation of Entertainment
Authors: Oliver Mary Beth , Bartsch Anne
Published: June 2011

The purpose of this article is to examine the experience of appreciation to media entertainment as a unique audience response that can be differentiated from enjoyment. To those ends, the first section provides a conceptualization of appreciation in which we outline how we are using the term and how it is distinct from questions of emotional valence. The second section discusses the types of entertainment portrayals and depictions that we believe are most likely to elicit feelings of appreciation. Here, we suggest that appreciation is most evident for meaningful portrayals that focus on human virtue and that inspire audiences to contemplate questions concerning life’s purpose. In the final section we consider the affective and cognitive components of appreciation, arguing that mixed-affective responses (rather than bi-polar conceptualizations of affective valence) better capture the experience of appreciation and its accompanying feelings states such as inspiration, awe, and tenderness.
The Complicated Relationship Between Media and Morality
Authors: Bilandzic Helena
Published: June 2011

This contribution reflects content and effects of moral messages in media from a narrative perspective. Building on Tamborini’s (2011) Model of Moral Intuition and Media Enjoyment, several issues are raised: First, the difficulty of conceptually and empirically defining “morality” in media entertainment is elaborated. Several options of moral ambiguity arising from the narrative structure of a story are sketched. Then, the link between processing moral content and positive media experiences such as enjoyment and appreciation is considered. Finally, issues of effects, especially on the long-term, are raised and implications for empirical questions are discussed.
Extending the Mental Number Line
Authors: Nuerk Hans-Christoph , Moeller Korbinian , Klein Elise , Willmes Klaus , Fischer Martin H.
Published: June 2011

Multi-digit number processing is ubiquitous in our everyday life – even in school, multi-digit numbers are computed from the first year onward. Yet, many problems children and adults have are about the relation of different digits (for instance with fractions, decimals, or carry effects in multi-digit addition). Cognitive research has mainly focused on single-digit processing, and there is no comprehensive review of the different multi-digit number processing types and effects. The current review aims to fill this gap. First, we argue that effects observed in single-digit tasks cannot simply be transferred to multi-digit processing. Next, we list 16 effect types and processes which are specific for multi-digit number processing. We then discuss the development of multi-digit number processing, its neurocognitive correlates, its cultural or language-related modulation, and finally some models for multi-digit number processing. We finish with conclusions and perspectives about where multi-digit number processing research may or should be heading in following years.
The Processing of Two-Digit Numbers Depends on Task Instructions
Authors: Reynvoet Bert , Notebaert Karolien , Van den Bussche Eva
Published: June 2011

Recently, a lot of research has focused on resolving whether two-digit numbers are processed holistically or compositionally. This has led to inconsistent results. In the present study we investigated effects of task instructions. Subjects performed magnitude or parity judgments on targets preceded by masked primes containing parts of the target at a task-congruent (3#_37) or task-incongruent (#3_37) position. Priming effects were influenced by the instructions: In the magnitude task, the priming effects were primarily mediated by the congruency of the decade digit, whereas in the parity task they were elicited by the congruency of the unit digit, which is in line with a flexible compositional processing style. These and previous findings show that two-digit numbers can be processed in a very flexible way, depending on the task context.
The Upper Rhine Graben (URG) revisited: Miocene transtension and transpression account for the observed first‐order structures
Authors: Rotstein Y. , Schaming M.
Published: June 2011

Although the Upper Rhine Graben (URG) has been studied extensively for years, the origin of some of its first‐order structures is still under debate, particularly the relatively young uplift of the Vosges Mountains (VM) and Black Forest Mountains (BFM). Their uplift appears to be temporally related to the change of the URG into a continental transform, the rapid subsidence of its deep northern basin, and the onset of erosional and nondepositional phase south of the Northern Basin. Recent observations from newly released seismic reflection data, coupled with older geologic and seismic observations, are used to explain this correlation. We suggest that when the URG turned into a continental transform during the early Miocene, not only was its northern basin transtensionally subsiding as previously suggested, but the VM and BFM were transpressionally uplifted. Transpression became weaker with growing distance from the Alpine front, and north of Baden‐Baden the transpression is expressed only by down‐buckling of the sediments, forming a deep, elongated syncline. The largest uplifts and erosion associated with this event occurred along both boundaries of the southern URG. However, the center of the graben was also affected to some extent, causing widespread erosion of pre‐early Miocene sediments and subsequent nondeposition. The arcuate Vosges and Black Forest fault systems, which formed the boundary faults of the URG during the Oligocene, became mechanically unfavorable during the Miocene transpressional regime. Instead, more linear normal faults took over as the dominant boundary faults, forming the western and eastern Rhine Fault systems and assuming a strike‐slip component of motion.
Benchmarking quantitative precipitation estimation by conceptual rainfall‐runoff modeling
Authors: Heistermann Maik , Kneis David
Published: June 2011

Hydrologic modelers often need to know which method of quantitative precipitation estimation (QPE) is best suited for a particular catchment. Traditionally, QPE methods are verified and benchmarked against independent rain gauge observations. However, the lack of spatial representativeness limits the value of such a procedure. Alternatively, one could drive a hydrological model with different QPE products and choose the one which best reproduces observed runoff. Unfortunately, the calibration of conceptual model parameters might conceal actual differences between the QPEs. To avoid such effects, we abandoned the idea of determining optimum parameter sets for all QPE being compared. Instead, we carry out a large number of runoff simulations, confronting each QPE with a common set of random parameters. By evaluating the goodness‐of‐fit of all simulations, we obtain information on whether the quality of competing QPE methods is significantly different. This knowledge is inferred exactly at the scale of interest—the catchment scale. We use synthetic data to investigate the ability of this procedure to distinguish a truly superior QPE from an inferior one. We find that the procedure is prone to failure in the case of linear systems. However, we show evidence that in realistic (nonlinear) settings, the method can provide useful results even in the presence of moderate errors in model structure and streamflow observations. In a real‐world case study on a small mountainous catchment, we demonstrate the ability of the verification procedure to reveal additional insights as compared to a conventional cross validation approach.
Streamflow generation in a large, alpine watershed in the southern Rocky Mountains of Colorado: Is streamflow generation simply the aggregation of hillslope runoff responses?
Authors: Frisbee Marty D. , Phillips Fred M. , Campbell Andrew R. , Liu Fengjing , Sanchez Steve A.
Published: June 2011

Spatial and temporal trends in stream chemistry were investigated in a large (1600 km2) alpine watershed in the southern Rocky Mountains of Colorado to help understand mechanisms of streamflow generation. We observed linear increases of concentrations of chemical constituents in streamflow as accumulated drainage area increased along the main channel of Saguache Creek. We tested two conceptual models of streamflow generation against our stream chemistry observations. One model is essentially two‐dimensional and treats streamflow generation at the large watershed scale as the aggregation of runoff responses from individual hillslopes, primarily surface and shallow subsurface flow paths. Alternatively, a fully three‐dimensional conceptual model treats streamflow generation as being controlled by a distribution of large‐scale groundwater flow paths as well as surface and shallow subsurface flow paths. The structure and magnitude of groundwater contributions in streamflow as a function of increasing scale provided a key distinction between these two conceptual models. End‐member mixing analysis and measurements of hydraulic head gradients in streambeds were used to quantify basin‐scale groundwater contributions to streamflow with increasing spatial scale in the Saguache Creek watershed. Our data show that groundwater contributions are important in streamflow generation at all scales and, more importantly, that groundwater contributions to streamflow do increase with increasing watershed scale. These results favor the three‐dimensional conceptual model in which long groundwater flow paths provide a streamflow generation process at large scales that is not operative at smaller scales. This finding indicates that large watersheds may be more than simply the aggregation of hillslopes and small catchments.
Dividing the waters: An empirical analysis of interstate compact allocation of transboundary rivers
Authors: Katz David L. , Moore Michael R.
Published: June 2011

Legal scholars and jurists have identified several criteria (e.g., hydrology, climate, population, and historical water use) to guide equitable allocation of transboundary rivers among riparian claimants. Are these criteria used in practice, such that a quantitative pattern emerges from actual water‐sharing agreements regarding factors affecting allocations? To address this, we study interstate compacts, the principal mechanism for allocating the waters of transboundary rivers within the United States. We develop a georeferenced data set and construct variables representing conditions in state‐based watersheds of 14 rivers at the times of compact ratification. A state's water allocation share of a compact serves as the dependent variable, and a set of explanatory variables is derived from legal and political theories. We estimate allocation shares using both ordinary least squares (OLS) and bootstrap regressions, and we apply two alternative specifications of the factors affecting compact allocations, one with and one without political variables. Estimated coefficients on variables for land area, population, prior water use, riparian position, and Congressional committee chair are statistically significant in the OLS regressions. The preferred OLS specification, which includes political variables, provides a good fit (R2= 0.84). We also find that OLS and bootstrap regressions have a similar ability to predict state allocation shares. We discuss how the results could be used as a reference point in negotiations over new compacts or international river treaties and as a basis to identify existing compacts with statistical outliers.
Radiocarbon‐age differences among coexisting planktic foraminifera shells: The Barker Effect
Authors: Broecker Wally , Clark Elizabeth
Published: June 2011

For slowly accumulating sediments, a major contrast exists in the radiocarbon‐age differences among coexisting shells of planktic foraminifera between those experiencing little dissolution and those experiencing significant dissolution. In the former, the ages generally agree to within a couple of hundred years. In the latter, age differences as large as 1000 years are common. The most likely explanation appears to be the Barker Effect, which involves the preferential fragmentation of dissolution‐prone G. sacculifer and G. ruber. The whole shells of these species picked for radiocarbon dating have shorter residence times in the bioturbation zone than those for dissolution‐resistant species (including benthics). As low accumulation rate sediment cores often fail to yield reliable radiocarbon‐based ocean ventilation ages, where possible, such studies should be conducted on high accumulation rate cores.
Tocotrienol Vitamin E Protects against Preclinical Canine Ischemic Stroke by Inducing Arteriogenesis
Authors: Rink Cameron , Christoforidis Greg , Khanna Savita , Peterson Laura , Patel Yojan , Khanna Suchin , Abduljalil Amir , Irfanoglu Okan , Machiraju Raghu , Bergdall Valerie K , Sen Chandan K
Published: June 2011

Vitamin E consists of tocopherols and tocotrienols, in which α-tocotrienol is the most potent neuroprotective form that is also effective in protecting against stroke in rodents. As neuroprotective agents alone are insufficient to protect against stroke, we sought to test the effects of tocotrienol on the cerebrovascular circulation during ischemic stroke using a preclinical model that enables fluoroscopy-guided angiography. Mongrel canines (mean weight=26.3±3.2 kg) were supplemented with tocotrienol-enriched (TE) supplement (200 mg b.i.d, n=11) or vehicle placebo ( n=9) for 10 weeks before inducing transient middle cerebral artery (MCA) occlusion. Magnetic resonance imaging was performed 1 hour and 24 hours post reperfusion to assess stroke-induced lesion volume. Tocotrienol-enriched supplementation significantly attenuated ischemic stroke-induced lesion volume ( P<0.005). Furthermore, TE prevented loss of white matter fiber tract connectivity after stroke as evident by probabilistic tractography. Post hoc analysis of cerebral angiograms during MCA occlusion revealed that TE-supplemented canines had improved cerebrovascular collateral circulation to the ischemic MCA territory ( P<0.05). Tocotrienol-enriched supplementation induced arteriogenic tissue inhibitor of metalloprotease 1 and subsequently attenuated the activity of matrix metalloproteinase-2. Outcomes of the current preclinical trial set the stage for a clinical trial testing the effects of TE in patients who have suffered from transient ischemic attack and are therefore at a high risk for stroke.
Ionizing shocks in argon. Part II: Transient and multi-dimensional effects
Authors: Kapper M. G. , Cambier J.-L.
Published: June 2011

We extend the computations of ionizing shocks in argon to the unsteady and multi-dimensional, using a collisional-radiative model and a single-fluid, two-temperature formulation of the conservation equations. It is shown that the fluctuations of the shock structure observed in shock-tube experiments can be reproduced by the numerical simulations and explained on the basis of the coupling of the nonlinear kinetics of the collisional-radiative model with wave propagation within the induction zone. The mechanism is analogous to instabilities of detonation waves and also produces a cellular structure commonly observed in gaseous detonations. We suggest that detailed simulations of such unsteady phenomena can yield further information for the validation of nonequilibrium kinetics.
Two-center black holes duality-invariants for stu model and its lower-rank descendants
Authors: Ferrara Sergio , Marrani Alessio , Orazi Emanuele , Stora Raymond , Yeranyan Armen
Published: June 2011

We classify 2-center extremal black hole charge configurations through duality-invariant homogeneous polynomials, which are the generalization of the unique invariant quartic polynomial for single-center black holes based on homogeneous symmetric cubic special Kä hler geometries. A crucial role is played by a horizontal $SL(p,\mathbb {R})$SL(p,R) symmetry group, which classifies invariants for p-center black holes. For p = 2, a (spin 2) quintet of quartic invariants emerge. We provide the minimal set of independent invariants for the rank-3 $\mathcal {N}=2$N=2, d = 4 stu model, and for its lower-rank descendants, namely, the rank-2 st2 and rank-1 t3 models; these models, respectively, exhibit seven, six, and five independent invariants. We also derive the polynomial relations among these and other duality invariants. In particular, the symplectic product of two charge vectors is not independent from the quartic quintet in the t3 model, but rather it satisfies a degree-16 relation, corresponding to a quartic equation for the square of the symplectic product itself.
Little–Parks oscillations at low temperatures: Gigahertz resonator method
Authors: Belkin Andrey , Brenner Matthew , Aref Thomas , Ku Jaseung , Bezryadin Alexey
Published: June 2011

A thin-film Fabry–Perot superconducting resonator is used to reveal the Little and Parks (LP) effect [Phys. Rev. Lett. 9, 9 (1962)], even at temperatures much lower than the critical temperature. A pair of parallel nanowires is incorporated into the resonator at the point of the supercurrent antinode. As the magnetic field is ramped, Meissner currents develop, changing the resonance frequency of the resonator. The LP oscillation is revealed as a periodic set of distorted parabolas observed in the transmission of the resonator and corresponds to the states of the wire loop having different vorticities. We also report a direct observation of single and double phase slip events.
A Boltzmann-weighted hopping model of charge transport in organic semicrystalline films
Authors: Kwiatkowski Joe J. , Jimison Leslie H. , Salleo Alberto , Spakowitz Andrew J.
Published: June 2011

We present a model of charge transport in polycrystalline electronic films, which considers details of the microscopic scale while simultaneously allowing realistically sized films to be simulated. We discuss the approximations and assumptions made by the model, and rationalize its application to thin films of directionally crystallized poly(3-hexylthiophene). In conjunction with experimental data, we use the model to characterize the effects of defects in these films. Our findings support the hypothesis that it is the directional crystallization of these films, rather than their defects, which causes anisotropic mobilities.
Kelvin probe microscopy and electronic transport in graphene on SiC(0001) in the minimum conductivity regime
Authors: Curtin A. E. , Fuhrer M. S. , Tedesco J. L. , Myers-Ward R. L. , Eddy C. R. , Gaskill D. K.
Published: June 2011

Ambient-environment Kelvin probe microscopy of many (10 μm)2 areas of single-layer graphene on SiC(0001) shows area-to-area rms surface potential variation of 12 meV. Electronic transport data are consistent with the minimum conductivity regime. Together the data indicate a highly uniform carrier concentration with a small magnitude (<1012 cm−2). We conclude that the previously reported large spread in carrier densities from Hall measurements on similar samples is an artifact of electron–hole puddling in the minimum conductivity regime.
Increased fraction of low-density structures in aqueous solutions of fluoride
Authors: Waluyo Iradwikanari , Huang Congcong , Nordlund Dennis , Weiss Thomas M. , Pettersson Lars G. M. , Nilsson Anders
Published: June 2011

X-ray absorption spectroscopy (XAS) and small angle x-ray scattering (SAXS) were utilized to study the effect of fluoride (F−) anion in aqueous solutions. XAS spectra show that F− increases the number of strong H-bonds, likely between F− and water in the first hydration shell. SAXS data show a low-Q scattering intensity increase similar to the effect of a temperature decrease, suggesting an enhanced anomalous scattering behavior in F− solutions. Quantitative analysis revealed that fluoride solutions have larger correlation lengths than chloride solutions with the same cations but shorter compared to pure water. This is interpreted as an increased fraction of tetrahedral low-density structures in the solutions due to the presence of the F− ions, which act as nucleation centers replacing water in the H-bonding network and forming stronger H-bonds, but the presence of the cations restricts the extension of strong H-bonds.
CO2 solvation free energy using quasi-chemical theory
Authors: Jiao Dian , Rempe Susan B.
Published: June 2011

Accumulation of greenhouse gases, especially carbon dioxide, is believed to be the key factor in global climate change. To develop effective ways to remove CO2 from the atmosphere, it is helpful to understand the mechanism of CO2 solvation first. Here we investigate the thermodynamics of CO2 hydration using quasi-chemical theory. Two approaches for estimating hydration free energy are carried out. Both agree reasonably well with experimental measurements. Analysis of the free energy components reveals that the weak hydration free energy results from a balance of unfavorable molecular packing and favorable chemical association.
Generalized Kubo relations and conditions for anomalous diffusion: Physical insights from a mathematical theorem
Authors: Kneller Gerald R.
Published: June 2011

The paper describes an approach to anomalous diffusion within the framework of the generalized Langevin equation. Using a Tauberian theorem for Laplace transforms due to Hardy, Littlewood, and Karamata, generalized Kubo relations for the relevant transport coefficients are derived from the asymptotic form of the mean square displacement. In a second step conditions for anomalous diffusion are derived for the asymptotic forms of the velocity autocorrelation function and the associated memory function. Both spatially unconfined and confined diffusion processes are considered. The results are illustrated with semi-analytical examples.
Hybrid density functional theory band structure engineering in hematite
Authors: Pozun Zachary D. , Henkelman Graeme
Published: June 2011

We present a hybrid density functional theory (DFT) study of doping effects in α-Fe2O3, hematite. Standard DFT underestimates the band gap by roughly 75% and incorrectly identifies hematite as a Mott-Hubbard insulator. Hybrid DFT accurately predicts the proper structural, magnetic, and electronic properties of hematite and, unlike the DFT+U method, does not contain d-electron specific empirical parameters. We find that using a screened functional that smoothly transitions from 12% exact exchange at short ranges to standard DFT at long range accurately reproduces the experimental band gap and other material properties. We then show that the antiferromagnetic symmetry in the pure α-Fe2O3 crystal is broken by all dopants and that the ligand field theory correctly predicts local magnetic moments on the dopants. We characterize the resulting band gaps for hematite doped by transition metals and the p-block post-transition metals. The specific case of Pd doping is investigated in order to correlate calculated doping energies and optical properties with experimentally observed photocatalytic behavior.
Oxygen adsorption on Pt/Ru(0001) layers
Authors: Jakob Peter , Schlapka Andreas , Gazdzicki Pawel
Published: June 2011

Chemical properties of epitaxially grown bimetallic layers may deviate substantially from the behavior of their constituents. Strain in conjunction with electronic effects due to the nearby interface represent the dominant contribution to this modification. One of the simplest surface processes to characterize reactivity of these substrates is the dissociative adsorption of an incoming homo-nuclear diatomic molecule. In this study, the adsorption of O2 on various epitaxially grown Pt films on Ru(0001) has been investigated using infrared absorption spectroscopy and thermal desorption spectroscopy. Pt/Ru(0001) has been chosen as a model system to analyze the individual influences of lateral strain and of the residual substrate interaction on the energetics of a dissociative adsorption system. It is found that adsorption and dissociative sticking depends dramatically on Pt film thickness. Even though oxygen adsorption proceeds in a straightforward manner on Pt(111) and Ru(0001), molecular chemisorption of oxygen on Pt/Ru(0001) is entirely suppressed for the Pt/Ru(0001) monolayer. For two Pt layers chemisorbed molecular oxygen on Pt terraces is produced, albeit at a very slow rate; however, no (thermally induced) dissociation occurs. Only for Pt layer thicknesses \documentclass[12pt]{minimal}\begin{document}$N_{\text{Pt}} \ge$\end{document}NPt≥ 3 sticking gradually speeds up and annealing leads to dissociation of O2, thereby approaching the behavior for oxygen adsorption on genuine Pt(111). For Pt monolayer films a novel state of chemisorbed O2, most likely located at step edges of Pt monolayer islands is identified. This state is readily populated which precludes an activation barrier towards adsorption, in contrast to adsorption on terrace sites of the Pt/Ru(0001) monolayer.
The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials
Authors: Lu Lanyuan , Voth Gregory A.
Published: June 2011

The potential of mean force (PMF) with respect to coarse-grained (CG) coordinates is often calculated in order to study the molecular interactions in atomistic molecular dynamics (MD) simulations. The multiscale coarse-graining (MS-CG) approach enables the computation of the many-body PMF of an atomistic system in terms of the CG coordinates, which can be used to parameterize CG models based on all-atom configurations. We demonstrate here that the MS-CG method can also be used to analyze the CG interactions from atomistic MD trajectories via PMF calculations. In addition, MS-CG calculations at different temperatures are performed to decompose the PMF values into energetic and entropic contributions as a function of the CG coordinates, which provides more thermodynamic information regarding the atomistic system. Two numerical examples, liquid methanol and a dimyristoylphosphatidylcholine lipid bilayer, are presented. The results show that MS-CG can be used as an analysis tool, comparable to various free energy computation methods. The differences between the MS-CG approach and other PMF calculation methods, as well as the characteristics and advantages of MS-CG, are also discussed.
Theoretical modeling of ionization energies of argon clusters: Nuclear delocalization effects
Authors: Svrčková Pavla , Vítek Aleš , Karlický František , Paidarová Ivana , Kalus René
Published: June 2011

Temperature dependence of vertical ionization energies is modeled for small argon clusters (N ⩽ 13) using classical parallel-tempering Monte Carlo methods and extended interaction models based on the diatomics-in-molecules approach. Quantum effects at the zero temperature are also discussed in terms of zero-point nuclear vibrations, either at the harmonic approximation level or at the fully anharmonic level using the diffusion Monte Carlo calculations. Both approaches lead to a considerable improvement of the theoretical predictions of argon clusters ionization energies and represent a realistic way of modeling of ionization energies for weakly bound and floppy complexes in general. A thorough comparison with a recent electron-impact experiment [O. Echt et al., J. Chem. Phys. 123, 084313 (2005)] is presented and a novel interpretation of the experimental data is proposed.
Spin polarized photoemission from strained Ge epilayers
Authors: Bottegoni Federico , Isella Giovanni , Cecchi Stefano , Ciccacci Franco
Published: June 2011

We report on spin polarized electron photoemission experiments on compressively strained Ge/SiGe/Si(001) layers. Spin polarization of conduction band electrons up to P=62% at T=120 K has been observed, well above the theoretical limit of P=50% valid for bulk materials. Such spin polarization increase, can be attributed to the strain-induced removal of the heavy-hole light-hole degeneracy in the valence band. A set of Ge epilayers with different strain levels has been characterized, achieving an experimental correlation between the measured polarization and the strain in the epilayer.
Surface plasmon enhanced broadband spectrophotometry on black silver substrates
Authors: Xu Zhida , Chen Yi , Gartia Manas R. , Jiang Jing , Liu Gang Logan
Published: June 2011

We demonstrate surface plasmon-induced enhancements in optical imaging and spectroscopy on silver coated silicon nanocones which we call black silver. The black silver with dense and homogeneous nanocone forest structure is fabricated with a mass-producible nanomanufacturing method. It can efficiently trap and convert incident photons into localized plasmons in broad wavelength range, permitting the enhancement in optical absorption from ultraviolet to near infrared range by 12 times, the visible fluorescence enhancement of ∼30 times and the Raman scattering enhancement factor up to ∼108. We show the potential of the black silver in high sensitivity and broadband optical sensing of molecules.
Measurement of SiO2/InZnGaO4 heterojunction band offsets by x-ray photoelectron spectroscopy
Authors: Douglas E. A. , Scheurmann A. , Davies R. P. , Gila B. P. , Cho Hyun , Craciun V. , Lambers E. S. , Pearton S. J. , Ren F.
Published: June 2011

X-ray photoelectron spectroscopy was used to measure the energy discontinuity in the valence band (ΔEv) of SiO2/InZnGaO4 (IGZO) heterostructures deposited by low temperature plasma enhanced chemical vapor deposition and sputtering at <50 °C, respectively. A value of ΔEv=1.43±0.15 eV was obtained by using the Ga and Zn 2p3 and In 3d3 and 3d5 energy levels as references. Given the experimental bandgap of 3.2 eV for the IGZO, this would indicate a conduction band offset ΔEC of 4.27 eV in this system.
Stable group theory and approximate subgroups
Authors: Hrushovski Ehud
Published: June 2011

We note a parallel between some ideas of stable model theory and certain topics in finite combinatorics related to the sum-product phenomenon. For a simple linear group

G
G

, we show that a finite subset

X
X

with

|

X

X

−
1

X

|

/

|

X

|

|X X ^{-1}X |/ |X|

bounded is close to a finite subgroup, or else to a subset of a proper algebraic subgroup of

G
G

. We also find a connection with Lie groups, and use it to obtain some consequences suggestive of topological nilpotence. Model-theoretically we prove the independence theorem and the stabilizer theorem in a general first-order setting.
Question answering systems in biology and medicine—the time is now
Authors: Wren Jonathan D.
Published: June 2011

Contact:  jdwren@gmail.com
Soil Suppressiveness Against the Disease Complex of the Soybean Cyst Nematode and Sudden Death Syndrome of Soybean
Authors: Westphal Andreas , Xing Lijuan
Published: June 2011

The ecology of the complex of soybean cyst nematode (SCN) and sudden death syndrome (SDS) of soybean was investigated under soybean monoculture in two field experiments from 2003 to 2007. Initially, susceptible soybean ‘Spencer’ was planted while inoculating Fusarium virguliforme into nonfumigated or preseason-fumigated plots (methyl bromide, MB, at 450 kg/ha), and SCN and SDS were monitored. In one field, SCN population densities declined in nonfumigated but increased in fumigated plots. After years of limited SDS in 2003 and 2004, SDS developed later in nonfumigated than fumigated plots. In 2006 in the greenhouse, nondisturbed or disturbed soil cores (10-cm diameter, 30-cm depth) from field plots received two two-level factors: (i) nonfumigated or fumigated (1,070 kg/ha MB); and (ii) noninoculated or inoculated with 9,000 second-stage juveniles of SCN. At harvest, nonfumigated cores from nonfumigated plots had fewer nematodes and less SDS regardless of disturbance or inoculation than the corresponding fumigated cores and any cores from fumigated plots. In the second field, SCN became detectable after 2003 during the monoculture in nonfumigated plots and lagged in fumigated plots; both treatments had low levels of SDS. Exploiting the suppressiveness of the first field could allow for biological control of SDS and SCN in soybean production.
Olpidium bornovanus-Mediated Germination of Ascospores of Monosporascus cannonballus: A Host-Specific Rhizosphere Interaction
Authors: Stanghellini Michael E. , Misaghi Iraj J.
Published: June 2011

Monosporascus cannonballus, a host-specific root-infecting ascomycete, is the causal agent of a destructive disease of melon (Cucumis melo L.) known as vine decline. Ascospores germinate only in the rhizosphere of melon plants growing in field soil. However, no germination occurs in the rhizosphere of melon plants if the field soil is heated to temperatures >50°C prior to infestation with ascospores. This observation suggested that germination is mediated by one or more heat-sensitive members of the soil microflora. Although bacteria or actinomycetes were heretofore suspected as the germination-inducing microbes, our data demonstrate that Olpidium bornovanus, an obligate, host-specific, root-infecting zoosporic fungus, is responsible. In four experiments conducted in autoclaved field soil amended with various population densities of culturally produced ascospores, significant ascospore germination was recorded only in the rhizosphere of cantaloupe seedlings colonized by O. bornovanus.
Vitaly Lazarevich Ginzburg. 4 October 1916 — 8 November 2009
Authors: Longair Malcolm S.
Published: June 2011

Vitaly Lazarevich Ginzburg played a leading role in many different aspects of theoretical physics during the Soviet era and after the dismantling of the Soviet Union in 1991. His research contributions were of the highest order, spanning a vast range of topics in theoretical physics and culminating in the award of the 2003 Nobel Prize in Physics, jointly with Alexei Alexeyevich Abrikosov and Anthony Leggett, for pioneering studies of superconductivity and superfluidity.