bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole genome amplification (WGA) for archiving and genotyping of clinical isolates ofCryptosporidiumspecies
Authors: BOUZID MAHA , HEAVENS DARREN , ELWIN KRISTIN , CHALMERS RACHEL M. , HADFIELD STEPHEN J. , HUNTER PAUL R. , TYLER KEVIN M.
Published: September 2009

Clinical and environmental isolates of pathogens are often unique and may be unculturable, yielding a very limited amount of DNA for genetic studies.Cryptosporidiumin particular are difficult to propagate. Whole genome amplification (WGA) is a valuable technique for amplifying genomic material. In this study, we tested 5 WGA commercial kits usingCryptosporidiumclinical isolates. DNA of 5C. hominisand 5C. parvumclinical isolates andC. parvumIOWA reference strain were used. The majority of the samples were amplified by all of the kits tested. The integrity and fidelity of the amplified genomic DNA were assessed by sequence analysis of several PCR products of varying length. We found evidence that one kit in particular may be more error prone while another seemed the more suitable kit forCryptosporidiumclinical samples, generating high molecular weight DNA from all the samples with high fidelity. Thus WGA was found to be a useful technique for producing amplified DNA suitable for downstream genotyping techniques and archiving ofCryptosporidiumclinical isolates.
Echinococcusmetacestodes as laboratory models for the screening of drugs against cestodes and trematodes
Authors: HEMPHILL A. , STADELMANN B. , SCHOLL S. , MÜLLER J. , SPILIOTIS M. , MÜLLER N. , GOTTSTEIN B. , SILES-LUCAS M.
Published: September 2009

Among the cestodes,Echinococcus granulosus,Echinococcus multilocularisandTaenia soliumrepresent the most dangerous parasites. Their larval stages cause the diseases cystic echinococcosis (CE), alveolar echincoccosis (AE) and cysticercosis, respectively, which exhibit considerable medical and veterinary health concerns with a profound economic impact. Others caused by other cestodes, such as species of the generaMesocestoidesandHymenolepis, are relatively rare in humans. In this review, we will focus onE. granulosusandE. multilocularismetacestode laboratory models and will review the use of these models in the search for novel drugs that could be employed for chemotherapeutic treatment of echinococcosis. Clearly, improved therapeutic drugs are needed for the treatment of AE and CE, and this can only be achieved through the development of medium-to-high throughput screening approaches. The most recent achievements in thein vitroculture and genetic manipulation ofE. multiloculariscells and metacestodes, and the accessability of theE. multilocularisgenome and EST sequence information, have rendered theE. multilocularismodel uniquely suited for studies on drug-efficacy and drug target identification. This could lead to the development of novel compounds for the use in chemotherapy against echinococcosis, and possibly against diseases caused by other cestodes, and potentially also trematodes.
Culture for genetic manipulation of developmental stages of Schistosoma mansoni
Authors: MANN VICTORIA H. , MORALES MARIA E. , RINALDI GABRIEL , BRINDLEY PAUL J.
Published: September 2009

Genomes of the major human helminth parasites, and indeed many others of agricultural significance, are now the research focus of intensive genome sequencing and annotation. A draft genome sequence of the filarial parasite Brugia malayi was reported in 2007 and draft genomes of two of the human schistosomes, Schistosoma japonicum and S. mansoni reported in 2009. These genome data provide the basis for a comprehensive understanding of the molecular mechanisms involved in schistosome nutrition and metabolism, host-dependent development and maturation, immune evasion and invertebrate evolution. In addition, new potential vaccine candidates and drug targets will likely be predicted. However, testing these predictions is often not straightforward with schistosomes because of the difficulty and expense in maintenance of the developmental cycle. To facilitate this goal, several developmental stages can be maintained in vitro for shorter or longer intervals of time, and these are amenable to manipulation. Our research interests focus on experimental studies of schistosome gene functions, and more recently have focused on development of transgenesis and RNA interference with the longer term aim of heritable gene manipulation. Here we review methods to isolate and culture developmental stages of Schistosoma mansoni, including eggs, sporocysts, schistosomules and adults, in particular as these procedures relate to approaches for gene manipulation. We also discuss recent advances in genetic manipulation of schistosomes including the deployment of square wave electroporation to introduce reporter genes into cultured schistosomes.
Biological, ultrastructural effect and subcellular localization of aromatic diamidines in Trypanosoma cruzi
Authors: BATISTA D. G. J. , PACHECO M. G. O. , KUMAR A. , BRANOWSKA D. , ISMAIL M. A. , HU L. , BOYKIN D. W. , SOEIRO M. N. C.
Published: September 2009

No vaccines or safe chemotherapy are available for Chagas disease. Pentamidine and related di-cations are DNA minor groove-binders with broad-spectrum anti-protozoal activity. Therefore our aim was to evaluate the in vitro efficacy of di-cationic compounds – DB1645, DB1582, DB1651, DB1646, DB1670 and DB1627 – against bloodstream trypomastigotes (BT) and intracellular forms of Trypanosoma cruzi. Cellular targets of these compounds in treated parasites were also analysed by fluorescence and transmission electron microscopy (TEM). DB1645, DB1582 and DB1651 were the most active against BT showing IC50 values ranging between 0·15 and 6·9 μm. All compounds displayed low toxicity towards mammalian cells and DB1645, DB1582 and DB1651 were also the most effective against intracellular parasites, with IC50 values ranging between 7·3 and 13·3 μm. All compounds localized in parasite nuclei and kDNA (with greater intensity in the latter structure), and DB1582 and DB1651 also concentrated in non-DNA-containing cytoplasmic organelles possibly acidocalcisomes. TEM revealed alterations in mitochondria and kinetoplasts, as well as important disorganization of microtubules. Our data provide further information regarding the activity of this class of compounds upon T. cruzi which should aid future design and synthesis of agents that could be used for Chagas disease therapy.
Molecular phylogenetic and morphological analysis of haemosporidian parasites (Haemosporida) in a naturally infected European songbird, the blackcapSylvia atricapilla, with description ofHaemoproteus pallidulussp. nov.
Authors: KRIŽANAUSKIENĖ ASTA , PÉREZ-TRIS JAVIER , PALINAUSKAS VAIDAS , HELLGREN OLOF , BENSCH STAFFAN , VALKIŪNAS GEDIMINAS
Published: September 2009

The blackcap (Sylvia atricapilla) is a common Palearctic migratory warbler, and haemosporidian parasites are common in this species. However, genetic and phenotypic diversity of haemosporidians in warblers has been insufficiently investigated and poorly linked. We addressed this issue by combining molecular and microscopy data for detection of pigment-forming haemosporidians of the generaHaemoproteusandPlasmodium. Blood samples from 498 blackcaps were collected at 7 different sites in Europe and investigated for these parasites by polymerase chain reaction (PCR)-based techniques and microscopic examination. In all, 56% of the birds were infected by at least 1 out of 25 distinct mitochondrial cytochromeb(cytb) gene lineages of these haemosporidians. It is concluded that the blackcap is infected not only with blackcap specific haemosporidians, but also withHaemoproteus majoris, which is a host generalist and common in birds belonging to the Paridae.Haemoproteus pallidulussp. nov. is described based on morphology of its blood stages and segments of the cytband dihydrofolate reductase/thymidylate synthase (DHFR-TS) genes. This study provides evidence that genetic diversity of haemosporidian parasites might be positively correlated with migratory strategies of their avian hosts; it also contributes to the value of both microscopy and molecular diagnostics of avian blood parasites.
Modeling of blade sharpness and compression cut of biomaterials
Authors: Zhou Debao , McMurray Gary
Published: September 2009

To realize the automation of biomaterial cutting, the interaction between the blade and biomaterial deserves insight understanding. In this paper, a blade-compression cutting model is developed. The influences from the material properties, deformation, and blade properties on the cutting force are thoroughly explained. An approach to describe the sharpness of a blade is provided and its applicability is experimentally demonstrated. Based on the material property and knife sharpness property, the required force to realize compression cut can be predicted. This provides the reference force trajectory for the automation of biomaterial compression cutting.
Visual motor control of a 7DOF redundant manipulator using redundancy preserving learning network
Authors: Kumar Swagat , P. Premkumar , Dutta Ashish , Behera Laxmidhar
Published: September 2009

This paper deals with the design and implementation of a visual kinematic control scheme for a redundant manipulator. The inverse kinematic map for a redundant manipulator is a one-to-many relation problem; i.e. for each Cartesian position, multiple joint angle vectors are associated. When this inverse kinematic relation is learnt using existing learning schemes, a single inverse kinematic solution is achieved, although the manipulator is redundant. Thus a new redundancy preserving network based on the self-organizing map (SOM) has been proposed to learn the one-to-many relation using sub-clustering in joint angle space. The SOM network resolves redundancy using three criteria, namely lazy arm movement, minimum angle norm and minimum condition number of image Jacobian matrix. The proposed scheme is able to guide the manipulator end-effector towards the desired target within 1-mm positioning accuracy without exceeding physical joint angle limits. A new concept of neighbourhood has been introduced to enable the manipulator to follow any continuous trajectory. The proposed scheme has been implemented on a seven-degree-of-freedom (7DOF) PowerCube robot manipulator successfully with visual position feedback only. The positioning accuracy of the redundant manipulator using the proposed scheme outperforms existing SOM-based algorithms.
Complete dynamic modelling of a moving base 6-dof parallel manipulator
Authors: Lopes António M.
Published: September 2009

In this paper a new approach based on the generalized momentum is used to obtain the dynamic model of a six degrees-of-freedom (dof) parallel manipulator. First, the system dynamic equations are obtained supposing the manipulator base platform is fixed. Afterwards, the dynamic model is extended to the case of a moving base platform. This could be important in a macro/micro robotic application, where a small manipulator is attached in series to a big manipulator. Simulation results of a macro/micro robotic system are presented and the contribution of the base platform motion to the total actuating forces is shown.
Asymptotic models for curved rods derived from nonlinear elasticity by Γ-convergence
Authors: Scardia Lucia
Published: September 2009

We study the problem of the rigorous derivation of one-dimensional models for a thin curved beam starting from three-dimensional nonlinear elasticity. We describe the limiting models obtained for different scalings of the energy. In particular, we prove that the limit functional corresponding to higher scalings coincides with the one derived by dimension reduction starting from linearized elasticity.
Applications of Riccati-type inequalities to asymptotic theory of elliptic problems
Authors: Usami Hiroyuki
Published: September 2009

We show how one-dimensional generalized Riccati-type inequalities can be employed to analyse asymptotic behaviour of solutions of elliptic problems. We give Liouville-type theorems as well as necessary conditions for the existence of solutions of specified asymptotic behaviour of nonlinear elliptic problems.
Influence of the Hardy potential in a semilinear heat equation
Authors: Abdellaoui Boumediene , Peral Ireneo , Primo Ana
Published: September 2009

This paper deals with the influence of the Hardy potential in a semilinear heat equation. Precisely, we consider the problem

where Ω⊂ℝN, N≥3, is a bounded regular domain such that 0∈Ω, p>1, and u0≥0, f≥0 are in a suitable class of functions.

There is a great difference between this result and the heat equation (λ=0); indeed, if λ>0, there exists a critical exponent p+(λ) such that for p≥p+(λ) there is no solution for any non-trivial initial datum.

The Cauchy problem, Ω=ℝN, is also analysed for 1
1+2/N, which is the Fujita exponent for the heat equation (λ=0).
Stability of periodic optical solitons for a nonlinear Schrödinger system
Authors: Pava Jaime Angulo , Ferreira Ademir Pastor
Published: September 2009

This paper is concerned with the existence and nonlinear stability of periodic travelling-wave solutions for a nonlinear Schrödinger-type system arising in nonlinear optics. We show the existence of smooth curves of periodic solutions depending on the dnoidal-type functions. We prove stability results by perturbations having the same minimal wavelength, and instability behaviour by perturbations of two or more times the minimal period. We also establish global well posedness for our system by using Bourgain's approach.
Filtration-preserving mappings and centralizers within graded Lie algebras
Authors: Bendersky M. , Chen G. , Churchill R. C.
Published: September 2009

We use spectral sequence techniques to compute centralizers of elements within graded Lie algebras, and the methods are then applied to the calculation of unique normal forms of elements within one-parameter matrix Lie
algebras. A finiteness criterion for unique normal forms is presented.
Duality and compactness results in high-contrast homogenization of incompressible two-dimensional elasticity problems
Authors: Manceau David
Published: September 2009

We study incompressible two-dimensional elasticity problems with high-contrast coefficients. The Keller–Dykhne duality relations are extended to the case of Hooke's laws which are equicoercive and uniformly bounded in L1 but not in L∞. A compactness result is obtained for Hooke's laws which are uniformly bounded from above and such that their inverses are bounded in L1 but not in L∞, with a refinement in the periodic case. Moreover, we establish a compactness result in $L^2_\mathrm{loc}$ for a sequence of two-dimensional vector-valued functions in $H^1_0$ which are only bounded in L2.
A foodborne norovirus outbreak at a manufacturing company
Authors: ZOMER T. P. , DE JONG B. , KÜHLMANN-BERENZON S. , NYRÉN O. , SVENUNGSSON B. , HEDLUND K. O. , ANCKER C. , WAHL T. , ANDERSSON Y.
Published: September 2009

Over 400 office workers from the same unit of a manufacturing company in Stockholm County, Sweden, fell ill with gastroenteritis. A retrospective cohort study of office workers in the affected unit demonstrated that canteen visitors on one day had an increased risk of illness [risk ratio (RR) 27·1, 95% confidence interval (CI) 15·7–46·8] compared to non-visitors. A second study, investigating canteen visitors' consumption of particular food items, showed that both tomatoes from the salad buffet (RR 5·6, 95% CI 3·2–9·6) and hamburgers (RR 4·9, 95% CI 2·4–9·8) were the most likely vehicles of infection. Norovirus GI.3 (Desert Shield) was identified in stool samples from three office workers and from a food handler who prepared the tomatoes for the salad buffet and hamburger ingredients before vomiting at the workplace on 12 November. The outbreak could have been prevented if the food items prepared by the food handler some hours before vomiting had not been served.
Recovery After Psychosis (RAP): A Compassion Focused Programme for Individuals Residing in High Security Settings
Authors: Laithwaite Heather , O'Hanlon Martin , Collins Padraig , Doyle Patrick , Abraham Lucy , Porter Shauneen , Gumley Andrew
Published: September 2009

Background:The aim of the study was to evaluate the effectiveness of a recovery group intervention based on compassionate mind training, for individuals with psychosis. In particular, the objective was to improve depression, to develop compassion towards self, and to promote help seeking.Method:A within-subjects design was used. Participants were assessed at the start of group, mid-group (5 weeks), the end of the programme and at 6 week follow-up. Three group programmes were run over the course of a year. Nineteen participants commenced the intervention and 18 completed the programme.Results:Significant improvements were found on the Social Comparison Scale; the Beck Depression Inventory; Other As Shamer Scale; the Rosenberg Self-Esteem Inventory and the General Psychopathology Scale from the Positive and Negative Syndrome Scale.Conclusions:The results provide initial indications of the effectiveness of a group intervention based on the principles of compassionate focused therapy for this population. The findings of this study, alongside implications of further research are discussed.
Beyond Laterality: A Critical Assessment of Research on the Neural Basis of Metaphor
Authors: SCHMIDT GWENDA L. , KRANJEC ALEXANDER , CARDILLO EILEEN R. , CHATTERJEE ANJAN
Published: September 2009

Metaphors are a fundamental aspect of human cognition. The major neuropsychological hypothesis that metaphoric processing relies primarily on the right hemisphere is not confirmed consistently. We propose ways to advance our understanding of the neuropsychology of metaphor that go beyond simple laterality. Neuropsychological studies need to more carefully control confounding lexical and sentential factors, and consider the role of different parts of speech as they are extended metaphorically. They need to incorporate recent theoretical frameworks such as the career of metaphor theory, and address factors such as novelty. We also advocate the use of new methods such as voxel-based lesion-symptom mapping, which permits precise and formal tests of hypotheses correlating behavior with lesions sites. Finally, we outline a plausible model for the neural basis of metaphor. (JINS, 2010, 16, 1–5.)
Neuropsychological functioning as a predictor of employment activity in a longitudinal study of HIV-infected adults contemplating workforce reentry
Authors: CHERNOFF ROBERT A. , MARTIN DAVID J. , SCHROCK DARYL A. , HUY MELISSA P.
Published: September 2009

Cognitive deficits are associated with HIV disease, and HIV-related cognitive deficits have been associated with declines in everyday functioning and vocational status. We administered a baseline neuropsychological (NP) test battery designed to assess estimated full-scale IQ, achievement, attention/concentration, executive function, language, mental speed, motor function, nonverbal memory, verbal memory, and visual-spatial function to a sample of 174 disabled, HIV-positive individuals enrolled in a randomized, controlled trial of a vocational-rehabilitation program. We then used these NP scores to predict employment at the end of participants’ study participation, using both hierarchical multiple regression and ordinal logistic regression models. The hierarchical multiple regression analyses did not predict participants’ employment activities at the end of study participation. In the ordinal logistic regression model, executive functioning weakly predicted employment status at the end of study participation and inspection of the predicted classifications revealed that 63% of the participants were incorrectly classified using this model. These results suggest that although predicting workforce reentry from NP testing may be statistically significant, NP testing may be of limited clinical value for informing the workforce reentry of disabled people with HIV who are interested in returning to work. (JINS, 2010, 16, 38–48.)
Soilless cultivation for high-quality vegetables with biogas manure in China: Feasibility and benefit analysis
Authors: Liu Wen Ke , Yang Qi-Chang , Du Lianfeng
Published: September 2009

Vegetables, the indispensable staple produce providing humans with many beneficial substances, are readily contaminated by nitrate, heavy metals and pesticides during conventional cultivation. In particular, off-season vegetables grown in protected systems with low light intensity do tend to accumulate more nitrate in tissues due to excess N fertilization driven by farmers' desire for high yields. Over-the-limit accumulation of the harmful substances in vegetables constitutes a serious hazard to human health globally. Soilless cultivation, currently a fraction of vegetable cultivation in China, is a promising cultivation method to decrease the accumulation of harmful substances through nutrient solution regulation and environmental factor control. However, conventional inorganic nutrient solutions present few quality benefits besides plant nutrition for the widely acknowledged formulations. Currently, high-quality vegetables are urgently desired by humans globally, but they are difficult to grow for lack of an effective and practical cultivation method to lower the accumulation of harmful substances and to improve nutritional quality simultaneously. Although some attempts have been made, few commercial formulations have been applied in practice. Biogas manure (biogas slurry and biogas dregs) is a by-product of biogas production. It has been shown to be a good fertilizer with abundant nutrients, amino acids and bioactive substances. In China, as a product of the recycling process of agricultural wastes, biogas manure is an ever-growing resource due to the rapid development of biogas projects. Therefore, the need to utilize biogas manure is an urgent issue that relates both to environment protection and nutrient resources utilization. In this paper, the updated research results on yield and the quality effects of vegetables cultivated with biogas dregs and the solutions modified from biogas slurry in China are summarized, highlighting the feasibility and benefits of biogas manure in high-quality vegetable production. It is concluded that biogas manure is an effective nutrient source for high-quality vegetable production based on its synergistic effects and effectiveness in yield and quality improvement (particularly depression effects on nitrate accumulation), and stress resistance. However, deliberate component regulations need to be developed for better yield and quality of vegetables under soilless cultivation due to the large variability of components of biogas manure caused by various combinations of fermentative materials.
Uniform and nonuniform V‐shaped planar arrays for 2‐D direction‐of‐arrival estimation
Authors: Filik T. , Tuncer T. E.
Published: September 2009

In this paper, isotropic and directional uniform and nonuniform V‐shaped arrays are considered for azimuth and elevation direction‐of‐arrival (DOA) angle estimation simultaneously. It is shown that the uniform isotropic V‐shaped arrays (UI V arrays) have no angle coupling between the azimuth and elevation DOA. The design of the UI V arrays is investigated, and closed form expressions are presented for the parameters of the UI V arrays and nonuniform V arrays. These expressions allow one to find the isotropic V angle for different array types. The DOA performance of the UI V array is compared with the uniform circular array (UCA) for correlated signals and in case of mutual coupling between array elements. The modeling error for the sensor positions is also investigated. It is shown that V array and circular array have similar robustness for the position errors while the performance of UI V array is better than the UCA for correlated source signals and when there is mutual coupling. Nonuniform V‐shaped isotropic arrays are investigated which allow good DOA performance with limited number of sensors. Furthermore, a new design method for the directional V‐shaped arrays is proposed. This method is based on the Cramer‐Rao Bound for joint estimation where the angle coupling effect between the azimuth and elevation DOA angles is taken into account. The design method finds an optimum angle between the linear subarrays of the V array. The proposed method can be used to obtain directional arrays with significantly better DOA performance.
A Frequency‐Agile Distributed Sensor System to address space weather effects upon ionospherically dependent systems
Authors: Rice D. D. , Eccles J. V. , Sojka J. J. , Raitt J. W. , Brady J. , Hunsucker R. D.
Published: September 2009

The outstanding problem faced by operational systems that utilize the ionosphere is that ionospheric weather variability is comparable to the ionospheric climate variability. However, the number of simultaneous measurements is orders of magnitude too few to resolve the weather scales that are impacting systems. We describe a prototype distributed array of affordable passive radio beacon monitors combined with a central data repository and a data‐model analysis system called the Frequency‐Agile Distributed Sensor System (FADSS). By monitoring signals from terrestrial VLF/HF radio beacons the FADSS tracks changes in the D, E, or F regions and makes appropriate modifications to the ionospheric specification in near real time. These observations provide fundamental seasonal and diurnal climatology and weather affecting the lower ionosphere. They demonstrate space weather effects on communications over the VLF through HF range, even during quiet solar minimum conditions.
Evolving deformation along a transform plate boundary: Example from the Dead Sea Fault in northern Israel
Authors: Weinberger Ram , Gross Michael R. , Sneh Amihai
Published: September 2009

We analyzed geologic structures adjacent to the Dead Sea Fault (DSF) along the margins of the Sinai and Arabian plates in northern Israel in order to investigate the style and sequence of deformation associated with a transform plate boundary. The field area, located between the Hula basin in northern Israel and the Lebanese restraining bend in southern Lebanon, is divided into distinct structural blocks by a series of distributed faults that comprise this approximately N‐S trending section of the DSF. Cretaceous and Tertiary rocks within and adjacent to the structural blocks are folded into broad anticlines and synclines, with more intense localized shortening manifested by tight folds and thrust duplexes. Kinematic analyses of folds, faults, and veins provide evidence for two directions of regional shortening: (1) NW‐SE shortening responsible for the formation of NE‐SW trending fold axes and left‐lateral strike‐slip motion along N‐S trending faults and (2) E‐W shortening as indicated by N‐S trending fold axes, N‐S striking thrust faults, and extensional calcite‐filled veins that strike E‐W. Crosscutting relations and U‐Th ages of the vein material suggest that the E‐W phase of transform‐normal shortening represents the most recent and presently active phase of deformation. The structural analysis provides evidence for the transition from an early (Miocene–lower Pliocene) phase of pure strike‐slip motion to a late (Pleistocene to Recent) phase of convergent strike slip. The latter phase is characterized by strain partitioning, which is manifested by discrete left‐lateral strike‐slip motion across weak N‐S faults and the development of a fold‐thrust belt in response to transform‐normal shortening. Analogous to the strain partitioning observed in southern California, we suggest that blind thrust faults adjacent to the DSF in the study area may pose a seismic risk to populations in northern Israel and southern Lebanon.
Modeling California's high‐elevation hydropower systems in energy units
Authors: Madani Kaveh , Lund Jay R.
Published: September 2009

This paper presents a novel approach for modeling high‐elevation hydropower systems. Conservation of energy and energy flows (rather than water volume or mass flows) is used as the basis for modeling more than 135 high‐elevation high‐head hydropower sites throughout California. The unusual energy basis for reservoir modeling allows for development of hydropower operations models for a large number of plants to estimate large‐scale system behavior without the expense and time needed to develop traditional streamflow and reservoir volume‐based models in absence of storage and release capacity, penstock head, and efficiency information. Potential applications of the developed Energy‐Based Hydropower Optimization Model (EBHOM) include examination of the effects of climate change and energy prices on system‐wide generation and hydropower revenues. An extensive comparison of the EBHOM with a traditional hydropower optimization model used in California produced similar results and indicated good reliability of EBHOM's predictions.
Proxy calibration to instrumental data set: Implications for paleoceanographic reconstructions
Authors: Abrantes F. , Lopes C. , Rodrigues T. , Gil I. , Witt L. , Grimalt J. , Harris I.
Published: September 2009

High‐resolution proxy data analyzed on two high‐sedimentation shallow water sedimentary sequences (PO287‐26B and PO287‐28B) recovered off Lisbon (Portugal) provide the means for comparison to long‐term instrumental time series of marine and atmospheric parameters (sea surface temperature (SST), precipitation, total river flow, and upwelling intensity computed from sea level pressure) and the possibility to do the necessary calibration for the quantification of past climate conditions. XRF Fe is used as proxy for river flow, and the upwelling‐related diatom genus Chaetoceros is our upwelling proxy. SST is estimated from the coccolithophore‐synthesized alkenones and U37k′ index. Comparison of the Fe record to the instrumental data reveals its similarity to a mean average run of the instrumentally measured winter (JFMA) river flow on both sites. The upwelling diatom record concurs with the upwelling indices at both sites; however, high opal dissolution, below 20–25 cm, prevents its use for quantitative reconstructions. Alkenone‐derived SST at site 28B does not show interannual variation; it has a mean value around 16°C and compares quite well with the instrumental winter/spring temperature. At site 26B the mean SST is the same, but a high degree of interannual variability (up to 4°C) appears to be determined by summer upwelling conditions. Stepwise regression analyses of the instrumental and proxy data sets provided regressions that explain from 65 to 94% of the variability contained in the original data, and reflect spring and summer river flow, as well as summer and winter upwelling indices, substantiating the relevance of seasons to the interpretation of the different proxy signals. The lack of analogs and the small data set available do not allow quantitative reconstructions at this time, but this might be a powerful tool for reconstructing past North Atlantic Oscillation conditions, should we be able to find continuous high‐resolution records and overcome the analog problem.
Carbon isotopic signatures of methanol and acetaldehyde emitted from biomass burning source
Authors: Yamada Keita , Hattori Ryota , Ito Yuji , Shibata Hiroki , Yoshida Naohiro
Published: September 2009

We present carbon isotopic signatures of methanol and acetaldehyde emitted from biomass burning sources using laboratory experiments. The respective δ13C of methanol and acetaldehyde emitted from burning experiments of five plant materials (three C3 and two C4 plants) were −20–−46‰ and −11–−25‰. The variation in δ13C of methanol depends on the δ13C of the fuel biomass and burning conditions, but the variation in δ13C of acetaldehyde depends on the δ13C of fuel biomass and is independent of burning conditions. Combining these observations with previously reported global distributions of fire types, burning conditions, amounts of biomass burned, vegetation types, and emission factors, we estimated the global isotopic signature for biomass burning source as −33 ± 16‰ for methanol.
Behavior of the Wyrtki Jet observed with surface drifting buoys and satellite altimeter
Authors: Qiu Yun , Li Li , Yu Weidong
Published: September 2009

Analyses of up‐to‐date data from satellite‐tracked surface drifters indicate that the Wyrtki Jets (WJ) of the equatorial Indian Ocean (EIO) are developed firstly in the central EIO between 75°E and 80°E and then propagate westward along the equator at speeds of about 0.7 m s−1. Climatologically, the fall jet is both stronger and wider than its spring counterpart. This westward propagation phenomenon is supported by altimetry observation. It is suggested that the westward propagation of the jets in the western EIO (55°–75°E) is primarily forced directly by the westward propagating zonal winds. Whereas in the eastern EIO (east to 80°E), propagation of the jet signals is ambiguous although the zonal wind pattern is observed moving east. It is also evident that the WJs are subject to strong interannual variability, which may associate with El Niño/Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD).
Partitioning of Si and O between liquid iron and silicate melt: A two‐phase ab‐initio molecular dynamics study
Authors: Zhang Yigang , Guo Guangjun
Published: September 2009

The magma ocean process in the early history of the Earth has a great influence on the light element identities and contents of the core which subsequently affect the energy of the geodynamo provided by the compositional convection and the inner core growth through their effect on the phase diagram of iron alloy. In the present work, a two‐phase ab‐initio molecular dynamics method is established to study the solubility of silicon and oxygen in liquid iron in equilibrium with silicate melt. The ab‐initio results are found to be in close agreement with experimental data. At the base of a deep magma ocean (39 GPa and 3116 K), liquid iron contains 2.7 wt% silicon and 0.5 wt% oxygen at the current bulk Earth composition. The oxygen content is low compared with its current estimate in the core, indicating a deeper magma ocean may need to be invoked.
Effect of zonal asymmetries in stratospheric ozone on simulated Southern Hemisphere climate trends
Authors: Waugh D. W. , Oman L. , Newman P. A. , Stolarski R. S. , Pawson S. , Nielsen J. E. , Perlwitz J.
Published: September 2009

Stratospheric ozone is represented in most climate models by prescribing zonal‐mean fields. We examine the impact of this on Southern Hemisphere (SH) trends using a chemistry climate model (CCM): multi‐decadal simulations with interactive stratospheric chemistry are compared with parallel simulations using the same model in which the zonal‐mean ozone is prescribed. Prescribing zonal‐mean ozone results in a warmer Antarctic stratosphere when there is a large ozone hole, with much smaller differences at other times. As a consequence, Antarctic temperature trends for 1960 to 2000 and 2000 to 2050 in the CCM are underestimated when zonal‐mean ozone is prescribed. The impacts of stratospheric changes on the tropospheric circulation (i.e., summertime trends in the SH annular mode) are also underestimated. This shows that SH trends related to ozone depletion and recovery are underestimated when interactions between stratospheric ozone and climate are approximated by an imposed zonal‐mean ozone field.
Concurrent observations of the ultraviolet nitric oxide and infrared O2 nightglow emissions with Venus Express
Authors: Gérard J.‐C. , Cox C. , Soret L. , Saglam A. , Piccioni G. , Bertaux J.‐L. , Drossart P.
Published: September 2009

Two prominent features of the Venus nightside airglow are the nitric oxide δ and γ bands produced by radiative association of O and N atoms in the lower thermosphere and the O2 infrared emission generated by three‐body recombination of oxygen atoms in the upper mesosphere. The O2 airglow has been observed from the ground, during the Cassini flyby, and with VIRTIS on board Venus Express. It now appears that the global structure of the two emissions shows some similarities, but the statistical location of the region of strongest emission is not coincident. The Spectroscopy for Investigation of Characteristics of the Atmosphere of Venus (SPICAV) ultraviolet spectrograph has collected a large number of spectra of the Venus nitric oxide nightside airglow. Visible and Infrared Thermal Imaging Spectrometer (VIRTIS) images have been obtained at the limb and in the nadir‐viewing mode and have provided new information on the horizontal and vertical distribution of the emission. We present the first concurrent observations of the two emissions observed with Venus Express. We show that nadir observations generally indicate a low degree of correlation between the two emissions observed quasi‐simultaneously at a common location. A statistical study of limb profiles indicates that the altitude and the brightness of the two airglow layers generally do not covary. We suggest that this lack of correlation is explained by the presence of strong horizontal winds in the mesosphere‐thermosphere transition region. They carry the downflowing atoms over large distances in such a way that regions of enhanced NO emission generally do not coincide with zones of bright O2 airglow.
Compaction experiments on ice‐silica particle mixtures: Implication for residual porosity of small icy bodies
Authors: Yasui Minami , Arakawa Masahiko
Published: September 2009

To evaluate the residual porosity of small icy bodies, we performed compaction experiments on ice‐silica mixtures and studied the effects of silica content, temperature, and compaction time scale on residual porosity. To simulate the compositions of real icy bodies, we used ice‐silica mixtures with different silica volume fractions (0–0.29). The mixtures were compacted at a constant compression speed of 0.2 or 2.0 mm/min and the temperature was set to −10°C or a lower temperature (from −55 to −67°C). For the −10°C case, the mixtures were compressed to pressures of 30 MPa, while the lower temperature measurements were compressed to 80 MPa. In both cases, the residual porosity was found to be larger for higher silica fractions. At −10°C and 30 MPa, the residual porosity varied from 0.01 to 0.14 for silica fractions of 0–0.29, whereas for the −55 to −67°C and 80 MPa case, the corresponding residual porosities were 2–10 times larger. A two‐layer model was proposed to calculate the compaction curves of ice‐silica mixtures from the curves of the corresponding pure materials. We estimated the residual porosity of small icy bodies using this two‐layer model. From our calculations, we expect that icy bodies with diameters smaller than 700 km have residual porosity larger than 0.3 when the temperature is lower than −55°C.
Statistical description of slope‐dependent soil transport and the diffusion‐like coefficient
Authors: Furbish David Jon , Haff Peter K. , Dietrich William E. , Heimsath Arjun M.
Published: September 2009

For hillslopes undergoing “diffusive” soil transport, it is often assumed that the soil flux is proportional to the local land‐surface gradient, where the coefficient of proportionality is like a diffusion coefficient. Inasmuch as transport involves quasi‐random soil particle motions related to biomechanical mixing and similar dilational processes, a slope‐dependent relation arises from a balance between particle fluxes that tend to loft a soil and gravitational settling of particles into available pore space. A specialized form of the Fokker‐Planck equation adapted to such particle motions clarifies how the particle flux involves advective and diffusive parts. This in turn contributes to a kinematic description of the diffusion‐like coefficient. Ingredients of this coefficient include an active soil thickness, a characteristic particle size, the porosity in excess of a consolidated porosity, and the rate of particle activation as a function of depth. These last two ingredients, vertical porosity structure and activation rate, in effect characterize the magnitude and frequency of settling particle motions related to biological activity and thereby set the rate constant of the transport process. The significance of land‐surface slope is that it is a measure of the downslope component of slope‐normal lofting that is balanced by settling. Because the diffusion‐like coefficient contains the soil thickness, the analysis suggests that the soil flux is proportional to the “depth‐slope” product. The analysis is consistent with published profiles of soil creep displacement and with published estimates of soil flux obtained by downslope integration of soil production rates for hillslopes in California and Australia.
Geometric Representations of Language Taxonomies
Authors: Blanchard Philippe , Petroni Filippo , Serva Maurizio , Volchenkov Dimitri
Published: September 2009

Complex relationships between different languages in a language family encoded in the lexicostatistic data can be subjected to a component analysis and represented geometrically, in terms of distances and angles. The fully automated method for construction of language taxonomy is tested on a sample of fifty languages of the Indo-European language group and applied to a sample of fifty languages of the Austronesian language group. The Anatolian and Kurgan hypotheses of the Indo-European origin and the 'express train' model of the Polynesian origin are thoroughly discussed.
Visual Analytics Technology Transition Progress
Authors: Schultz Jean , Cook Kristin A. , Whiting Mark A. , Lemon Doug , Greenblatt Howard
Published: September 2009

The authors provide a description of the transition process for visual analytic tools and contrast this with the transition process for more traditional software tools. This paper takes this difference into account and describes a user-oriented approach to technology transition including a discussion of key factors that should be considered and adapted to each situation. The progress made in transitioning visual analytic tools in the past 5 years is described and challenges that remain are enumerated.
The Science of Analytic Reporting
Authors: Chinchor Nancy , Pike William A.
Published: September 2009

The challenge of visually communicating analysis results is central to the ability of visual analytics tools to support decision making and knowledge construction. The benefit of emerging visual methods will be improved through more effective exchange of the insights generated through the use of visual analytics. This article outlines the major requirements for next-generation reporting systems in terms of eight major research needs: the development of best practices, design automation, visual rhetoric, context and audience, connecting analysis to presentation, evidence and argument, collaborative environments and interactive and dynamic documents. It also describes an emerging technology called Active Products that introduces new techniques for analytic process capture and dissemination.
The Science of Interaction
Authors: Pike William A. , Stasko John , Chang Remco , O'Connell Theresa A.
Published: September 2009

There is a growing recognition within the visual analytics community that interaction and inquiry are inextricable. It is through the interactive manipulation of a visual interface–the analytic discourse–that knowledge is constructed, tested, refined and shared. This article reflects on the interaction challenges raised in the visual analytics research and development agenda and further explores the relationship between interaction and cognition. It identifies recent exemplars of visual analytics research that have made substantive progress toward the goals of a true science of interaction, which must include theories and testable premises about the most appropriate mechanisms for human–information interaction. Seven areas for further work are highlighted as those among the highest priorities for the next 5 years of visual analytics research: ubiquitous, embodied interaction; capturing user intentionality; knowledge-based interfaces; collaboration; principles of design and perception; interoperability; and interaction evaluation. Ultimately, the goal of a science of interaction is to support the visual analytics and human–computer interaction communities through the recognition and implementation of best practices in the representation and manipulation of visual displays.
Scale and Complexity in Visual Analytics
Authors: Robertson George , Ebert David , Eick Stephen , Keim Daniel , Joy Ken
Published: September 2009

The fundamental problem that we face is that a variety of large-scale problems in security, public safety, energy, ecology, health care and basic science all require that we process and understand increasingly vast amounts and variety of data. There is a growing impedance mismatch between data size/complexity and the human ability to understand and interact with data. Visual analytic tools are intended to help reduce that impedance mismatch by using analytic tools to reduce the amount of data that must be viewed, and visualization tools to help understand the patterns and relationships in the reduced data. But visual analytic tools must address a variety of scalability issues if they are to succeed. In this paper, we characterize the scalability and complexity issues in visual analytics. We discuss some highlights on progress that has been made in the past 5 years, as well as key areas where more progress is needed.
Visual Analytics: Building a Vibrant and Resilient National Science
Authors: Wong Pak Chung , Thomas Jim
Published: September 2009

Five years after the science of visual analytics was formally established, we attempt to use two different studies to assess the current state of the community and evaluate the progress the community has made in the past few years. The first study involves a comparison analysis of intellectual and scholastic accomplishments recently made by the visual analytics community with two other visualization communities. The second study aims to measure the degree of community reach and internet penetration of visual-analytics-related resources. This article describes our efforts to harvest the study data, conduct analysis and make interpretations based on parallel comparisons with five other established computer science areas.
Data Transformations and Representations for Computation and Visualization
Authors: Kasik David J. , Ebert David , Lebanon Guy , Park Haesun , Pottenger William M.
Published: September 2009

At the core of successful visual analytics systems are computational techniques that transform data into concise, human comprehensible visual representations. The general process often requires multiple transformation steps before a final visual representation is generated. This article characterizes the complex raw data to be analyzed and then describes two different sets of transformations and representations. The first set transforms the raw data into more concise representations that improve the performance of sophisticated computational methods. The second transforms internal representations into visual representations that provide the most benefit to an interactive user. The end result is a computing system that enhances an end user's analytic process with effective visual representations and interactive techniques. While progress has been made on improving data transformations and representations, there is substantial room for improvement.