bluuebunny/crossref_metadata_2025 huggingface dataset:
Parallelization of a dynamic SVD clustering algorithm and its application in information retrieval
Authors: Seshadri Karthick , Iyer K. Viswanathan
Published: July 2010

We describe an implementation of a parallel document clustering scheme based on latent semantic indexing, which uses singular value decomposition. Given a set of documents, the clustering algorithm is dynamic in the sense that it automatically infers the number of clusters to be output. The parallel version has been implemented on a LAN and on a dual‐core system. Experimental evaluation of the algorithm shows an average speed‐up of 6.22 for the LAN implementation and an average speed‐up of 3.71 for the dual‐core implementation, while still maintaining a precision and recall in the range [0.85, 1]. To put these implementations in the context of information retrieval, we use the parallel clustering algorithm and develop a document similarity search system. The similarity search system shows good performance in terms of precision and recall. Copyright © 2010 John Wiley & Sons, Ltd.
Architectural layer recovery for software system understanding and evolution
Authors: Scanniello Giuseppe , D'Amico Anna , D'Amico Carmela , D'Amico Teodora
Published: July 2010

This paper presents an approach to identify software layers for the understanding and evolution of software systems implemented with any object‐oriented programming language. The approach first identifies relations between the classes of a software system and then uses a link analysis algorithm (i.e. the Kleinberg algorithm) to group them into layers. Additionally to assess the approach and the underlying techniques, the paper also presents a prototype of a supporting tool and the results from a case study. Copyright © 2010 John Wiley & Sons, Ltd.
WSB: a broker‐centric framework for quality‐driven web service discovery
Authors: Al‐Masri Eyhab , Mahmoud Qusay H.
Published: July 2010

Web service interfaces can be discovered through several means, including service registries, search engines, service portals, and peer‐to‐peer networks. But discovering Web services in such heterogeneous environments is becoming a challenging task and raises several concerns, such as performance, reliability, and robustness. In this paper, we introduce the Web Service Broker (WSB) framework that provides a universal access point for discovering Web services. WSB uses a crawler to collect the plurality of Web services disseminated throughout the Web, continuously monitor the behavior of Web services in delivering the expected functionality, and enable clients to articulate service queries tailored to their needs. The framework features ranking algorithms we have developed which are capable of ranking services according to Quality of Web Service parameters. WSB can be seamlessly integrated into the existing service‐oriented architectures. Copyright © 2010 John Wiley & Sons, Ltd.
Support for enterprise consolidation of I/O bound services
Authors: Kvalnes Åge , Johansen Dag , Halvorsen Pål , Griwodz Carsten
Published: July 2010

In this article, we evaluate the performance effects of I/O bound workloads on a specific virtual machine, an important component of an enterprise cloud computing infrastructure. In particular, we demonstrate that (1) the I/O workload of one guest system may adversely affect the I/O performance of another for the XEN hypervisor and (2) the general I/O performance is degraded due to various overheads. Next, we have devised a light‐weight, complementary, backwards‐compatible alternative to hypervisor‐based virtualization techniques called BONSAI. Our software provides low‐overhead I/O performance isolation by transparently applying traffic shaping to system calls in a cost‐effective manner. Using this system, I/O resource consumption can be controlled at a very fine granularity. Furthermore, using video streaming experiments, where we limit the I/O bandwidth available to each service, we show that we are able to achieve the required level of resource isolation on a per process basis with only a negligible CPU overhead and without reducing the I/O performance. Copyright © 2010 John Wiley & Sons, Ltd.
Mitochondrial tRNA mutations and disease
Authors: Yarham John W. , Elson Joanna L. , Blakely Emma L. , McFarland Robert , Taylor Robert W.
Published: July 2010

Mitochondrial (mt‐) tRNA (MTT) gene mutations are an important cause of human morbidity and are associated with a wide range of pathology, from isolated organ‐specific diseases such as myopathy or hearing loss, through to multisystem disorders with encephalopathy, gastrointestinal dysmotility, and life‐threatening cardiomyopathy. Our understanding of how MTT mutations cause disease remains poor and progress has been hampered by the complex interaction of genotype with phenotype that can result in patients who harbor the same mutation exhibiting starkly contrasting phenotypes, whereas other (genetically heterogeneous) patients manifest clinically identical syndromes. A further complexity is the highly polymorphic nature of mitochondrial DNA (mtDNA), which must temper any reflex assumptions of pathogenicity for novel MTT substitutions. Nevertheless significant progress is being made and we shall review the methods employed to identify and characterize MTT mutations as pathogenic. Also important is our understanding of the molecular processes involved and we shall discuss the data available on two of the most studied MTT mutations (m.8344A > G and m.3243A > G) as well as other potential pathogenic mechanisms. Knowledge of factors influencing the inheritance of MTT mutations, and therefore the likelihood of disease transmission, is of particular importance to female patients. At present, the factors determining transmission remain elusive, but we shall examine several possible mechanisms and discuss the evidence for each. Finally, a number of different yeast and mouse models are currently used to investigate mitochondrial disease and we will assess the importance of and difficulties associated with each model as well as the future of possible therapies for patients with mitochondrial disease. Copyright © 2010 John Wiley & Sons, Inc.

This article is categorized under:

RNA in Disease and Development > RNA in Disease
Effects of Seal Oil and Tuna‐Fish Oil on Platelet Parameters and Plasma Lipid Levels in Healthy Subjects
Authors: Mann Neil J. , O’Connell Stella L. , Baldwin Kylie M. , Singh Indu , Meyer Barbara J.
Published: July 2010

Fish are a rich source of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), two long‐chain polyunsaturated n‐3 fatty acids (LC n‐3 PUFA) with cardiovascular benefits. A related but less‐investigated LC n‐3 PUFA, docosapentaenoic acid (DPA), is more common in seal oil and pasture‐fed red meats. This study compared indicators of platelet function and plasma lipids in healthy volunteers given supplements containing these different fatty acids (FA) for 14 days. Subjects, randomised into three groups of ten, consumed capsules of tuna oil (210 mg EPA, 30 mg DPA, 810 mg DHA), seal oil (340 mg EPA, 230 mg DPA, 450 mg DHA) or placebo (sunola) oil. Supplementary LC n‐3 PUFA levels were approximately 1 g/day in both fish and seal oil groups. Baseline dietary FA and other nutrient intakes were similar in all groups. Both fish and seal oil elevated platelet DHA levels (P < 0.01). Seal oil also raised platelet DPA and EPA levels (P < 0.01), and decreased p‐selectin (P = 0.01), a platelet activation marker negatively associated with DPA (P = 0.03) and EPA (P < 0.01) but not DHA. Plasma triacylglycerol decreased (P = 0.03) and HDL‐cholesterol levels increased (P = 0.01) with seal oil only. Hence, seal oil may be more efficient than fish oil at promoting healthy plasma lipid profiles and lowering thrombotic risk, possibly due to its high DPA as well as EPA content.
Évaluation des effets prosexuels des extraits de Bridelia ferruginea chez le rat mâle naïf
Authors: Watcho P. , Nchegang B. , Nguelefack T.B. , Kamanyi A.
Published: July 2010

Bridelia ferruginea(BF, Euphorbiaceae) est un arbre dont les écorces du tronc et les feuilles sont utilisées en médecine traditionnelle pour remédier à plusieurs problèmes et en particulier l’impuissance masculine. La présente étude vise à identifier les effets prosexuels (fréquences d’érection, de monte, d’intromission et d’éjaculation) des extraits aqueux (100 mg/kg) et éthanolique (100 mg/kg) des écorces du tronc de BF administrés par voie orale à des rats Wistar adultes mâles (intacts ou castrés) sexuellement inexpérimentés pendant zéro, un et sept jours. Le comportement sexuel des rats normaux recevant une administration unique de l’extrait aqueux de BF (100 mg/kg) a été aussi évalué après prétraitement par le L-omega-nitro-arginine methyl ester (Lω-NAME, 10 mg/kg), l’halopéridol (10 mg/kg) ou l’atropine (10 mg/kg). Les animaux témoins ont reçu per os de l’eau distillée (10 ml/kg) pour le témoin neutre et une injection sous-cutanée de testostérone propionate (20 mg/kg par jour pendant trois jours avant le début du test) pour le témoin positif. Les résultats de l’étude montrent que la durée du traitement a un impact significatif (p< 0,05) sur les fréquences d’érection pénienne, de monte et d’intromission aussi bien chez les rats normaux que chez les animaux castrés. Une tendance à l’augmentation des paramètres de performance sexuelle a été aussi observée. La fréquence d’intromission des rats intacts était plus élevée (p< 0,05–0,01) à J1 et particulièrement chez les rats recevant l’extrait aqueux de BF. Chez les rats castrés, par contre, seuls les animaux traités par la testostérone ont présenté une augmentation statistique (p< 0,01–0,001) des paramètres copulatoires. Les effets prosexuels de l’extrait aqueux de BF étaient abolis par l’atropine et l’halopéridol, tandis qu’une préadministration de Lω-NAME était sans effet sur l’activité copulatoire des animaux. Ces effets stimulants sexuels de BF pourraient être attribués à la présence des flavonoïdes et des stérols, substances bioactives qui agiraient par voie dopaminergique et/ou cholinergique, et soutiennent l’intérêt de l’emploi de BF en médecine traditionnelle comme stimulant sexuel.
Multiple recognition systems adopting four different glycotopes at the same domain for the Agaricus bisporus agglutinin–glycan interactions
Authors: Wu Albert M. , Liu Jia-Hau , Gong Yu-Ping , Li Chia-Chen , Chang En-Tzu
Published: July 2010

For the GalNAcα1→ specific Agaricus bisporus agglutinin (ABA) from an edible mushroom, the mechanism of polyvalent Galβ1→3/4GlcNAcβ1→ complex in ABA–carbohydrate recognition has not been well defined since Gal and GlcNAc are weak ligands. By enzyme‐linked lectinosorbent and inhibition assays, we show that the polyvalent Galβ1→3/4GlcNAcβ1→ in natural glycans also play vital roles in binding and we propose that four different intensities of glycotopes (Galβ1‐3GalNAcα1‐, GalNAcα1‐Ser/Thr and Galβ1‐3/4GlcNAcβ1‐) construct three recognition systems at the same domain. This peculiar concept provides the most comprehensive mechanism for the attachment of ABA to target glycans and malignant cells at the molecular level.
3′–5′ tRNAHis guanylyltransferase in bacteria
Authors: Heinemann Ilka U. , Randau Lennart , Tomko Robert J. , Söll Dieter
Published: July 2010

The identity of the histidine specific transfer RNA (tRNAHis) is largely determined by a unique guanosine residue at position −1. In eukaryotes and archaea, the tRNAHis guanylyltransferase (Thg1) catalyzes 3′–5′ addition of G to the 5′‐terminus of tRNAHis. Here, we show that Thg1 also occurs in bacteria. We demonstrate in vitro Thg1 activity for recombinant enzymes from the two bacteria Bacillus thuringiensis and Myxococcus xanthus and provide a closer investigation of several archaeal Thg1. The reaction mechanism of prokaryotic Thg1 differs from eukaryotic enzymes, as it does not require ATP. Complementation of a yeast thg1 knockout strain with bacterial Thg1 verified in vivo activity and suggests a relaxed recognition of the discriminator base in bacteria.
Dihydropteridine reductase activity in the brainstem of intrauterine growth‐restricted rats
Authors: Manjarrez‐Gutierrez Gabriel , Gonzalez‐Ramirez Misael , Boyzo‐Montes de Oca Alfonso , Hernandez‐Rodriguez Jorge
Published: July 2010

The aim of this study was to determine whether intrauterine growth restriction produces an increase of dihydropteridine reductase activity as a compensatory mechanism that maintains the necessary concentration of cofactor, tetrahydrobiopterin, during accelerated brain serotonin biosynthesis. Intrauterine growth‐restricted offspring and controls were used. On days 1, 10, 15 and 21 of life, the brainstem was dissected andl‐tryptophan, serotonin, tryptophan‐5‐hydroxylase and dihydropteridine reductase activities were determined. Intrauterine growth‐restricted pups showed a significant increase ofl‐tryptophan, 5‐hydroxytryptamine, tryptophan‐5‐hydroxylase and also dihydropteridine activity in the brainstem in comparison to normal pups. These results confirm that intrauterine growth restriction produces an increase of serotonin biosynthesis in the brainstem. This is accompanied by an increase in dihydropteridine activity that appears to be a compensatory mechanism to maintain sufficient tetrahydrobiopterin for the donation of electrons during the accelerated synthesis of brain serotonin in intrauterine growth‐restricted rats.
Determinant functors on triangulated categories
Authors: Breuning Manuel
Published: July 2010

We study determinant functors which are defined on a triangulated category and take values in a Picard category. The two main results are the existence of a universal determinant functor for every small triangulated category, and a comparison theorem for determinant functors on a triangulated category with a non-degenerate bounded t-structure and determinant functors on its heart. For a small triangulated categoryΤwe give a natural definition of groupsK0(Τ) andK1(Τ) in terms of the universal determinant functor on Τ, and we show thatKi(Τ) ≅Ki(ε) fori= 0 and 1 ifΤhas a non-degenerate bounded t-structure with heartε.
Comparison of secondary invariants of algebraic K-theory
Authors: Kaad J.
Published: July 2010

In the context of 2-summable Fredholm modules, we prove that the Connes-Karoubi multiplicative character coincides with Brown's determinant invariant on algebraic K-theory.
cAMP-dependent protein kinase fromPlasmodium falciparum: an update
Authors: WURTZ NATHALIE , CHAPUS CHARLES , DESPLANS JEROME , PARZY DANIEL
Published: July 2010

One of the most important public health problems in the world today is the emergence and dissemination of drug-resistant malaria parasites.Plasmodium falciparumis the causative agent of the most lethal form of human malaria. New anti-malarial strategies are urgently required, and their design and development require the identification of potential therapeutic targets. However, the molecular mechanisms controlling the life cycle of the malaria parasite are still poorly understood. The published genome sequence ofP. falciparumand previous studies have revealed that several homologues of eukaryotic signalling proteins, such as protein kinases, are relatively conserved. Protein kinases are now widely recognized as important drug targets in protozoan parasites. Cyclic AMP-dependent protein kinase (PKA) is implicated in numerous processes in mammalian cells, and the regulatory mechanisms of the cAMP pathway have been characterized.P. falciparumcAMP-dependent protein kinase plays an important role in the parasite's life cycle and thus represents an attractive target for the development of anti-malarial drugs. In this review, we focus on theP. falciparumcAMP/PKA pathway to provide new insights and an improved understanding of this signalling cascade.
Microfluidic bioassay to characterize parasitic nematode phenotype and anthelmintic resistance
Authors: CHEN BAOZHEN , DEUTMEYER ALEX , CARR JOHN , ROBERTSON ALAN P. , MARTIN RICHARD J. , PANDEY SANTOSH
Published: July 2010

With increasing resistance to anti-parasitic drugs, it has become more important to detect and recognize phenotypes of resistant isolates. Molecular methods of detecting resistant isolates are limited at present. Here, we introduce a microfluidic bioassay to measure phenotype using parameters of nematode locomotion. We illustrate the technique on larvae of an animal parasiteOesophagostomum dentatum.Parameters of sinusoidal motion such as propagation velocity, wavelength, wave amplitude, and oscillation frequency depended on the levamisole-sensitivity of the isolate of parasitic nematode. The levamisole-sensitive isolate (SENS) had a mean wave amplitude of 135μm, which was larger than 123μm of the levamisole-resistant isolate (LEVR). SENS had a mean wavelength of 373μm, which was less than 393μm of LEVR. The mean propagation velocity of SENS, 149μm s−1, was similar to LEVR, 143μm s−1. The propagation velocity of the isolates was inhibited by levamisole in a concentration-dependent manner above 0·5μm. TheEC50for SENS was 3μmand theEC50for LEVR was 10μm. This microfluidic technology advances present-day nematode migration assays and provides a better quantification and increased drug sensitivity. It is anticipated that the bioassay will facilitate study of resistance to other anthelmintic drugs that affect locomotion.
Oncospheral penetration glands are the source of the EG95 vaccine antigen against cystic hydatid disease
Authors: JABBAR A. , JENKINS D. J. , CRAWFORD S. , WALDUCK A. K. , GAUCI C. G. , LIGHTOWLERS M. W.
Published: July 2010

Immunohistochemistry and immunogold labelling techniques were used to localize the EG95 vaccine antigen inEchinococcus granulosusoncospheres. In non-activated oncospheres, the cytoplasm of 2 pairs of bilateral cells exhibited specific positive labelling for the presence of EG95. No surface localization was seen in non-activated or recently activated oncospheres. Besides the staining of 2 pairs of bilateral cells, there was also a generalized distribution of specific staining for EG95 throughout the parenchyma of activated oncospheres. Immunogold labelling of non-activated oncosphere revealed specific reactivity for EG95 involving 2 pairs of bilateral cells and the ultrastructural characteristics of these cells were consistent with them being penetration gland cells. No other oncospheral structures stained specifically for the presence of EG95. The absence of surface location of EG95 in oncospheres suggests that the parasite may not be susceptible to vaccine-induced antibody and complement mediated attack until some post-oncospheral development has occurred. Further studies would be required to determine when the EG95 antigen associates with the parasite's surface, thus making them susceptible to immune attack.
The pathway from glandular fever to chronic fatigue syndrome: can the cognitive behavioural model provide the map?
Authors: Moss-Morris R. , Spence M. J. , Hou R.
Published: July 2010

Background

The cognitive behavioural model of chronic fatigue syndrome (CFS) suggests that the illness is caused through reciprocal interactions between physiology, cognition, emotion and behaviour. The purpose of this study was to investigate whether the psychological factors operationalized in this model could predict the onset of CFS following an acute episode of infectious mononucleosis commonly known as glandular fever (GF).

Method

A total of 246 patients with GF were recruited into this prospective cohort study. Standardized self-report measures of perceived stress, perfectionism, somatization, mood, illness beliefs and behaviour were completed at the time of their acute illness. Follow-up questionnaires determined the incidence of new-onset chronic fatigue (CF) at 3 months and CFS at 6 months post-infection.

Results

Of the participants, 9.4% met the criteria for CF at 3 months and 7.8% met the criteria for CFS at 6 months. Logistic regression revealed that factors proposed to predispose people to CFS including anxiety, depression, somatization and perfectionism were associated with new-onset CFS. Negative illness beliefs including perceiving GF to be a serious, distressing condition, that will last a long time and is uncontrollable, and responding to symptoms in an all-or-nothing behavioural pattern were also significant predictors. All-or-nothing behaviour was the most significant predictor of CFS at 6 months. Perceived stress and consistently limiting activity at the time of GF were not significantly associated with CFS.

Conclusions

The findings from this study provide support for the cognitive behavioural model and a good basis for developing prevention and early intervention strategies for CFS.
SINGING THE SELF: THE AUTOBIOGRAPHY OF THE FIFTEENTH-CENTURY GERMAN SINGER AND COMPOSER JOHANNES VON SOEST
Authors: Pietschmann Klaus , Rozenski Steven
Published: July 2010

The German singer, composer and writer Johannes von Soest (1448–1506), also referred to as Steinwart or Steinwert, is the author of a vernacular autobiography in verse. One of the very few such documents written by a musician, it gives a highly personal insight into his career, which extended from his training as a chorister in Soest to the ducal chapel in Cleves and afterwards to Bruges (in the company of two unnamed English musicians), Aardenburg (Overijssel), Maastricht, possibly Cologne, Kassel and finally Heidelberg, where he was appointed as Kapellmeister. He subsequently decided to become a physician. The article includes a complete transcription of the text, whose original was destroyed during the Second World War, but has been preserved in Johann Carl von Fichard's rare edition of 1811, and a translation of the sections of musical interest. In an introduction his training and career choices are discussed, and his observations concerning musical practice are analysed.
BUXTEHUDE AND THE DANCE OF DEATH: THE CHORALE PARTITA AUF MEINEN LIEBEN GOTT (BUXWV 179) AND THE ARS MORIENDI IN THE SEVENTEENTH CENTURY
Authors: Rathey Markus
Published: July 2010

In his chorale partita Auf meinen lieben Gott (BuxWV 179) Dieterich Buxtehude combines the (sacred) genre of the chorale with the (secular) genre of a dance suite by modelling the variations of the partita on popular dances. This essay explores the Sitz im Leben of the composition and shows that it was part of a larger trend to turn hymn settings into keyboard pieces that borrowed stylistic features from contemporary dances. At the same time, the choice of the hymn has to be understood within the context of contemporary piety and the ars moriendi in particular. Both aspects converge in the musical and religious practices of the educated middle class in the second half of the seventeenth century in northern Germany.
Cup-length estimates for leaf-wise intersections
Authors: ALBERS PETER , MOMIN AL
Published: July 2010

We prove that on a restricted contact type hypersurface the number of leaf-wise intersections is bounded from below by a certain cup-length.
A potential geoconservation map of the Las Lagunas area, northern Peru
Authors: SEIJMONSBERGEN A. C. , SEVINK J. , CAMMERAAT L. H. , RECHARTE J.
Published: July 2010

The Andean páramo ecosystems host geodiversity of global importance, but also have important societal functions, including agricultural production and delivery of water to people and industry. Páramo geo-ecosystems are highly susceptible to environmental degradation because of their alpine relief, extreme climate and fragile soils. In contrast to other parts of the world, geodiversity assessment studies in the Andes are scarce. A geodiversity assessment method was adapted and used to produce a potential geoconservation map of the Andean páramo. The Las Lagunas area (Cajamarca, Northern Peru) has a rich archive of climate proxy data and landscape reconstruction, and plays a key role in the functioning of regional geo-ecosystems. Undisturbed proxies for climate change are contained in four Late-Glacial recessional complexes of its former local ice cap and in pollen records preserved in the post-glacial peat cover. These new findings were used to develop a refined chronostratigraphy of the Late-Glacial warming period in the Andes of Northern Peru. Geo-ecosystem functions (for example water and carbon storage) depend on the environmental vulnerability and disturbance of the landforms and deposits. Therefore, potential geoconservation areas that combine a high scientific value and environmental vulnerability with a low disturbance and low frequency of occurrence should be prioritized for geoconservation. Such a strategy should also optimize sustainable use of resources and development of these areas. Mountainous countries like Peru require future management strategies that recognize and incorporate potential geoconservation information in regional planning, to prevent unnecessary loss of irreplaceable soils, climate proxies and geo-ecosystem functions upon future changes in land use and climate.
Underspecification and asymmetries in voicing perception
Authors: Hwang So-One K. , Monahan Philip J. , Idsardi William J.
Published: July 2010

The purpose of our study is to show that phonological knowledge is an important basis for making predictions during speech perception. Taking the phonological constraint in English that coda obstruent clusters agree in their value for voicing, we conducted two experiments using vowel–stop–fricative sequences, where the task was to identify the fricative. Stimuli included sequences that were either congruent or incongruent. Consistent with models of featural underspecification for voiceless obstruents, our results indicate that only voiced stops induced predictions for an upcoming voiced fricative, eliciting processing difficulty when such predictions were not met. In contrast, voiceless stops appear to induce no equivalent predictions. These results demonstrate the important role of abstract phonological knowledge in online processing, and the asymmetries in our findings also suggest that only specified features are the basis for generating perceptual predictions about the upcoming speech signal.
When an interaction is both opaque and transparent: the paradox of fed counterfeeding
Authors: Kavitskaya Darya , Staroverov Peter
Published: July 2010

Opaque interactions have long been recognised as a challenge for Optimality Theory. We show that although there has been considerable effort to bring opacity into the scope of Optimality Theory, some types of process interactions are still problematic for the theory. Based on data from Tundra Nenets, we present and analyse a case offed counterfeedingin which a process A feeds a process B, and B counterfeeds A. We argue that such interactions present a challenge to Optimality Theory with Candidate Chains (OT-CC; McCarthy 2007) since the two interactions impose contradictory ranking requirements. We propose an extension of the theory that does not abandon its main assumptions and that makes fed counterfeeding analysable in OT-CC. This extension is based on the assumption that constraints can make reference to the position specified in a previous step in the derivation.
Finite-element approximation of coupled surface and grain boundary motion with applications to thermal grooving and sintering
Authors: BARRETT JOHN W. , GARCKE HARALD , NÜRNBERG ROBERT
Published: July 2010

We study the coupled surface and grain boundary motion in bi- and tricrystals in three-space dimensions, building on previous work by the authors on the simplified two-dimensional case. The motion of the interfaces, which in this paper are presented by two-dimensional hypersurfaces, is described by two types of normal velocities: motion by mean curvature and motion by surface diffusion. Three hypersurfaces meet at triple-junction lines, where junction conditions need to hold. Similarly, boundary conditions are prescribed where an interface meets an external boundary, and these conditions naturally give rise to contact angles. We present a variational formulation of the flows, which leads to a fully practical finite-element approximation that exhibits excellent mesh properties, with no mesh smoothing or remeshing required in practice. For the introduced parametric finite-element approximation we show well posedness and, in general, unconditional stability, i.e. there is no restriction on the chosen time-step size. Moreover, the induced discrete equations are linear and easy to solve. A generalisation to anisotropic surface energies is straightforward. Several numerical results in two- and three-space dimensions are presented, including simulations for thermal grooving and sintering. Three-dimensional simulations featuring quadruple junction points, non-standard boundary contact angles and fully anisotropic surface energies are also presented.
Long-term rehabilitation after stroke: where do we go from here?
Authors: Aziz NA
Published: July 2010

Current guidelines in stroke management are divided on the issue of providing further rehabilitation to stroke patients who have had stroke six months ago and longer. Whilst consensus considers that long-term rehabilitation is neither practical nor beneficial, rehabilitation remains vital in the complex management of longer-term stroke care, as it provides continuity from the formal rehabilitation intervention in the hospital setting. Longer-term rehabilitation is principally a community-based intervention, as it aims to assist the survivors to become more independent through social and leisure-based interventions. Available evidence is limited, with available studies heterogeneous and small in sample size. This review aims to look into the existing evidence, and discusses the feasibility and challenges in providing longer-term rehabilitation to stroke survivors.
Association of distributions of three types of germinal vesicle stage oocytes with the canine follicle location in the ovary
Authors: Wang L.X. , Wang S. , Hou J. , Hu R.L. , An X.R.
Published: July 2010

The objective of current study was to compare the nuclear configurations of canine oocytes recovered from between follicles after isolation. Follicles isolated were classified into follicle-S (follicles located in the ovarian surface) and follicle-I (follicles located inside the ovary) based on the follicle location in the ovary. Nuclear stages of canine oocytes recovered from follicle-S and follicle-I were examined by phase-contrast microscopy after isolation. Results demonstrated that canine GV stage oocytes can be classified into three types based on the status of the nuclear envelope, nucleolus, and chromatin: type A, type B, and type C. In follicle-S group, the majority (95.5%) of canine GV stage oocytes was of type B. All canine GV stage oocytes recovered from follicle-S (including type B and type C) were characterized by nuclear envelope disappearance prior to nucleolus collapse. In contrast, in follicle-I group, the majority (60.2%) of canine GV stage oocytes was of type C. Unexpectedly, a small proportion of canine GV stage oocytes from follicle-I (donated type A) were characterized by nuclear envelope disappearance following nucleolus collapse. In conclusion, nuclear configurations of each type of canine GV stage oocytes may differ from each other. Distributions of each type of canine GV stage oocytes may associate with the follicle location in the ovary.
Complete fluorescent fingerprints of extremophilic and photosynthetic microbes
Authors: Dartnell Lewis R. , Storrie-Lombardi Michael C. , Ward John M.
Published: July 2010

The work reported here represents a study into the total fluorescence exhibited by a broad selection of model, extremophilic and photosynthetic bacterial strains, over a great range of excitation and emission wavelengths from ultraviolet (UV) through visible to near infrared. The aim is to identify distinctive fluorescent features that may serve as detectable biosignatures of remnant microbial life on the Martian surface. A lab-bench fluorescence spectrometer was used to generate an excitation–emission matrix (EEM) for the unpigmented Escherichia coli, radiation-resistant Deinococcus radiodurans, Antarctic Dry Valley isolates Brevundimonas sp. MV.7 and Rhodococcus sp. MV.10, and the cyanobacterium Synechocystis sp. PCC 6803. Detailed EEMs, representing the fluorescence signature of each organism, are presented, and the most significant features suitable for biosignature surveys are identified, including small-molecule cellular metabolites, light-harvesting photosynthetic pigments and extracellular UV-screening compounds. E. coli exhibits the most intense emission from tryptophan, presumably due to the absence of UV-screening pigments that would shield the organism from short-wavelength light-exciting intracellular fluorescence. The efficacy of commonly available laser diodes for exciting cellular fluorescence is treated, along with the most appropriate filter wavelengths for imaging systems. The best combination of available laser diodes and PanCam filters aboard the ExoMars probe is proposed. The possibility of detecting fluorescence excited by solar UV radiation in freshly exposed surface samples by imaging when both sunlit and shadowed, perhaps by the body of the rover itself, is discussed. We also study how these biological fluorophore molecules may be degraded, and thus the potential biosignatures erased, by the high flux of far-ultraviolet light on Mars.
Strong linkages between dimethylsulphoniopropionate (DMSP) and phytoplankton community physiology in a large subtropical and tropical Atlantic Ocean data set
Authors: Bell Thomas G. , Poulton Alex J. , Malin Gill
Published: July 2010

We present an extensive data set of dimethylsulphide (DMS, n = 651) and dimethylsulphoniopropionate (DMSP, n = 590) from the Atlantic Meridional Transect program. These data are used to derive representative depth profiles that illustrate observed natural variations and can be used for DMS and DMSP model‐validation in oligotrophic waters. To further understand our data set, we interpret the data with a wide range of accompanying parameters that characterize the prevailing biogeochemical conditions and phytoplankton community physiology, activity, taxonomic composition, and capacity to cope with light stress. No correlations were observed with typical biomarker pigments for DMSP‐producing species. However, strong correlations were found between DMSP and primary production by cells >2 μm in diameter and between DMSP and some photo‐protective pigments. These parameters are measures of mixed phytoplankton communities, so we infer that such associations are likely to be stronger in DMSP‐producing organisms. Further work is warranted to develop links between community parameters, DMS, and DMSP at the global scale.
Multiple regimes of air‐sea carbon partitioning identified from constant‐alkalinity buffer factors
Authors: Omta Anne Willem , Goodwin Philip , Follows Michael J.
Published: July 2010

Numerical studies have indicated that the steady‐state ocean‐atmosphere partitioning of carbon will change profoundly as emissions continue. In particular, the globally averaged Revelle buffer factor will first increase and then decrease at higher emissions. Furthermore, atmospheric carbon will initially grow exponentially with emission size, after which it will depend linearly on emissions at higher emission totals. In this article, we explain this behavior by means of an analytical theory based on simple carbonate chemistry. A cornerstone of the theory is a newly defined dimensionless factor, O. We show that the qualitative changes are connected with different regimes in ocean chemistry: if the air‐sea partitioning of carbon is determined by the carbonate ion, then the Revelle factor increases with emissions, whereas the buffer factor decreases with emission size, when dissolved carbon dioxide determines the partitioning. Currently, the ocean carbonate chemistry is dominated by the carbonate ion response, but at high total emissions, the response of dissolved carbon dioxide takes on this role.
Excitation mechanism of low‐latitude Pi2 pulsations: Cavity mode resonance or BBF‐driven process?
Authors: Nosé M.
Published: July 2010

There are two schools of thought regarding the excitation mechanism of low‐latitude Pi2 pulsations. One is the cavity mode resonance, which is established by fast mode waves that are emitted at substorm onset and form the standing oscillation within the plasmasphere. The other is the bursty bulk flow (BBF)‐driven process, in which periodical BBFs traveling from the magnetotail cause pressure pulses in the inner magnetosphere, generating Pi2 pulsations. This study intends to examine which of these two excitation mechanisms is more plausible. A working assumption is that in the case of the cavity mode resonance the wave period of Pi2 pulsations depends on the size and the plasma mass density of the plasmasphere, while in the case of the BBF‐driven process the wave period is controlled by the BBF period and is independent of the plasmaspheric parameters. We investigated long‐term variation in wave period of Pi2 pulsations observed at the Kakioka observatory for the period from March 1983 to October 2009. Multiple correlation analysis revealed that the Pi2 period is negatively correlated with the ΣKp index and positively correlated with ion mass in the near‐Earth plasma sheet or the F10.7 index. The ΣKp index is considered as a proxy for the size of the plasmasphere, and the plasma sheet ion mass or the F10.7 index can be considered as a proxy for the mass density of the plasmasphere, indicating that the Pi2 period is proportional to both the size and mass density of the plasmasphere. This result strongly supports the plasmaspheric cavity mode resonance as an excitation mechanism of low‐latitude Pi2 pulsations.
On the dynamics of wave‐mud interaction: A numerical study
Authors: Torres‐Freyermuth Alec , Hsu Tian‐Jian
Published: July 2010

Many previous studies consider wave attenuation over muddy seabeds and bottom boundary layer fluid‐mud transport as two distinct research topics. Hence, various processes related to the physics of wave‐mud interaction, such as turbulence‐sediment interactions, rheological stresses, and nonlinear wave‐wave interactions are incorporated rather artificially. The aim of this work is to present a new modeling approach which allows for the resolution of nonlinear wave propagation and bottom boundary layer mud transport with a single set of governing equations and closures. By adopting a fluid‐mud modeling framework, a well‐validated depth/phase‐resolving wave propagation model, based on the Reynolds‐Averaged Navier‐Stokes (RANS) equations, is extended to model cohesive sediment transport. The numerical model consists of a set of governing equations based on the equilibrium Eulerian approach accurate for the fine sediment limit. The numerical model reduces to the clear fluid RANS equations when the sediment concentration approaches zero. Hence, the model is able to calculate continuously and consistently the nonlinear wave propagation, wave boundary layer processes, and fluid‐mud transport without the need to prescribe the mud layer characteristics. Numerical simulations reveal several important physical processes that are critical for understanding the water‐wave dynamics over muddy seabeds: (i) an enhancement of the wave boundary layer thickness due to the presence of the fluid‐mud and rheological stress, which leads to a scaling relation between the enhanced wave boundary‐layer and the fluid‐mud layer and (ii) a direct wave amplitude dissipation due to rheological effects and clear evidences of low‐ and high‐frequency wave attenuation via nonlinear energy transfer.
An aircraft‐based upper troposphere lower stratosphere O3, CO, and H2O climatology for the Northern Hemisphere
Authors: Tilmes S. , Pan L. L. , Hoor P. , Atlas E. , Avery M. A. , Campos T. , Christensen L. E. , Diskin G. S. , Gao R.‐S. , Herman R. L. , Hintsa E. J. , Loewenstein M. , Lopez J. , Paige M. E. , Pittman J. V. , Podolske J. R. , Proffitt M. R. , Sachse G. W. , Schiller C. , Schlager H. , Smith J. , Spelten N. , Webster C. , Weinheimer A. , Zondlo M. A.
Published: July 2010

We present a climatology of O3, CO, and H2O for the upper troposphere and lower stratosphere (UTLS), based on a large collection of high‐resolution research aircraft data taken between 1995 and 2008. To group aircraft observations with sparse horizontal coverage, the UTLS is divided into three regimes: the tropics, subtropics, and the polar region. These regimes are defined using a set of simple criteria based on tropopause height and multiple tropopause conditions. Tropopause‐referenced tracer profiles and tracer‐tracer correlations show distinct characteristics for each regime, which reflect the underlying transport processes. The UTLS climatology derived here shows many features of earlier climatologies. In addition, mixed air masses in the subtropics, identified by O3‐CO correlations, show two characteristic modes in the tracer‐tracer space that are a result of mixed air masses in layers above and below the tropopause (TP). A thin layer of mixed air (1–2 km around the tropopause) is identified for all regions and seasons, where tracer gradients across the TP are largest. The most pronounced influence of mixing between the tropical transition layer and the subtropics was found in spring and summer in the region above 380 K potential temperature. The vertical extent of mixed air masses between UT and LS reaches up to 5 km above the TP. The tracer correlations and distributions in the UTLS derived here can serve as a reference for model and satellite data evaluation.
Reduced space optimal interpolation of daily rain gauge precipitation in Switzerland
Authors: Schiemann R. , Liniger M. A. , Frei C.
Published: July 2010

The coarse spacing of automatic rain gauges complicates near‐real‐time spatial analyses of precipitation. We test the possibility of improving such analyses by considering, in addition to the in situ measurements, the spatial covariance structure inferred from past observations with a denser network. To this end, a statistical reconstruction technique, reduced space optimal interpolation (RSOI), is applied over Switzerland, a region of complex topography. RSOI consists of two main parts. First, principal component analysis (PCA) is applied to obtain a reduced space representation of gridded high‐resolution precipitation fields available for a multiyear calibration period in the past. Second, sparse real‐time rain gauge observations are used to estimate the principal component scores and to reconstruct the precipitation field. In this way, climatological information at higher resolution than the near‐real‐time measurements is incorporated into the spatial analysis. PCA is found to efficiently reduce the dimensionality of the calibration fields, and RSOI is successful despite the difficulties associated with the statistical distribution of daily precipitation (skewness, dry days). Examples and a systematic evaluation show substantial added value over a simple interpolation technique that uses near‐real‐time observations only. The benefit is particularly strong for larger‐scale precipitation and prominent topographic effects. Small‐scale precipitation features are reconstructed at a skill comparable to that of the simple technique. Stratifying the reconstruction method by the types of weather type classifications yields little added skill. Apart from application in near real time, RSOI may also be valuable for enhancing instrumental precipitation analyses for the historic past when direct observations were sparse.
Seismic activity triggered by water wells in the Paraná Basin, Brazil
Authors: Assumpção Marcelo , Yamabe Tereza H. , Barbosa José Roberto , Hamza Valiya , Lopes Afonso E. V. , Balancin Lucas , Bianchi Marcelo B.
Published: July 2010

Triggered seismicity is commonly associated with deep water reservoirs or injection wells where water is injected at high pressure into the reservoir rock. However, earth tremors related solely to the opening of groundwater wells are extremely rare. Here we present a clear case of seismicity induced by pore‐pressure changes following the drilling of water wells that exploit a confined aquifer in the intracratonic Paraná Basin of southeastern Brazil. Since 2004, shallow seismic activity, with magnitudes up to 2.9 and intensities V MM, has been observed near deep wells (120–200 m) that were drilled in early 2003 near the town of Bebedouro. The wells were drilled for irrigation purposes, cross a sandstone layer about 60–80 m thick and extract water from a confined aquifer in fractured zones between basalt flow layers. Seismic activity, mainly event swarms, has occurred yearly since 2004, mostly during the rainy season when the wells are not pumped. During the dry season when the wells are pumped almost continuously, the activity is very low. A seismographic network, installed in March 2005, has located more than 2000 microearthquakes. The events are less than 1 km deep (mostly within the 0.5 km thick basalt layer) and cover an area roughly 1.5 km × 5 km across. The seismicity generally starts in a small area and expands to larger distances with an equivalent hydraulic diffusivity ranging from 0.06 to 0.6 m2/s. Geophysical and geothermal logging of several wells in the area showed that water from the shallow sandstone aquifer enters the well at the top and usually forms waterfalls. The waterfalls flow down the sides of the wells and feed the confined, fractured aquifer in the basalt layer at the bottom. Two seismic areas are observed: the main area surrounds several wells that are pumped continuously during the dry season, and a second area near another well (about 10 km from the first area) that is not used for irrigation and not pumped regularly. The main area displays cyclic annual activity, but the second area does not. We explain the earthquake swarms as being triggered by pore pressure diffusion in the fractured basalt layer due to additional pressure from the newly connected surface aquifer. This reaches critically prestressed areas up to a few kilometers away from the wells. During periods of continuous pumping, the reduction of pore pressure in the confined aquifer stops the seismic activity. Our study suggests that this kind of activity may be more common than previously thought and implies that many other cases of small tremors associated with the drilling of water wells may have gone unnoticed.