bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and implementation of aggregate functions in the DLV
system
Authors: FABER WOLFGANG , PFEIFER GERALD , LEONE NICOLA , DELL'ARMI TINA , IELPA GIUSEPPE
Published: May 2008

Disjunctive logic programming (DLP) is a very expressive formalism. It allows for
expressing every property of finite structures that is decidable in the
complexity class ΣP2(=NPNP). Despite this high expressiveness, there
are some simple properties, often arising in real-world applications, which
cannot be encoded in a simple and natural manner. Especially properties that
require the use of arithmetic operators (like sum, times, or count) on a set or
multiset of elements, which satisfy some conditions, cannot be naturally
expressed in classic DLP. To overcome this deficiency, we extend DLP by
aggregate functions in a conservative way. In particular, we avoid the
introduction of constructs with disputed semantics, by requiring aggregates to
be stratified. We formally define the semantics of the extended language (called ), and illustrate how it can be profitably used for representing
knowledge. Furthermore, we analyze the computational complexity of , showing that the addition of aggregates does not bring a higher
cost in that respect. Finally, we provide an implementation of in DLV—a state-of-the-art DLP system—and
report on experiments which confirm the usefulness of the proposed extension
also for the efficiency of computation.
Preferred extensions as stable models
Authors: NIEVES JUAN CARLOS , CORTÉS ULISES , OSORIO MAURICIO
Published: May 2008

Given an argumentation frameworkAF, we introduce a mapping function that constructs a disjunctive logic programP, such that the preferred extensions ofAFcorrespond to the stable models ofP, after intersecting each stable model with the relevant atoms. The given mapping function is of polynomial size w.r.t.AF.

In particular, we identify that there is a direct relationship between the minimal models of a propositional formula and the preferred extensions of an argumentation framework by working on representing the defeated arguments. Then we show how to infer the preferred extensions of an argumentation framework by using UNSAT algorithms and disjunctive stable model solvers. The relevance of this result is that we define a direct relationship between one of the most satisfactory argumentation semantics and one of the most successful approach of nonmonotonic reasoning i.e., logic programming with the stable model semantics.
Crossing the Ocean and Back Again with Piven and Cloward
Authors: Tarrow Sidney
Published: May 2008

Poor People's Movements: Why They Succeed, How They Fail. By Frances Fox Piven and Richard A. Cloward. New York: Pantheon Books, 1977. 381 pages.
The Praxis ofPoor People's Movements: Strategy and Theory in Dissensus Politics
Authors: Schram Sanford F.
Published: May 2008

Poor People's Movements: Why They Succeed, How They Fail. By Frances Fox Piven and Richard A. Cloward. New York: Pantheon Books, 1977. 381 pages.
The Success of Poor People's Movements: Empirical Tests and the More Elaborate Model
Authors: Lefkowitz Joel
Published: May 2008

Poor People's Movements: Why They Succeed, How They Fail. By Frances Fox Piven and Richard A. Cloward. New York: Pantheon Books, 1977. 381 pages.
The Mismatch Negativity
Authors: Näätänen Risto
Published: May 2008

In the present article, I will selectively review some of the recent research on the brain substrates of central-auditory processing using the mismatch negativity (MMN) and its magnetoencephalographic equivalent MMNm, trying to identify some of the most promising trends in this research work. Although the early MMN research dealt almost exclusively with basic cognitive-neuroscience issues, more recently, the usefulness of the MMN phenomenon with regard to a large number of clinical and other applied issues has also been realized. Nine research lines or issues with particular promise will be identified, many of which are of a clinical/applied nature. Cognitive brain research using the MMN, an automatic electric response to any discriminable change in auditory stimulation, has continued for three decades and seems continuously to gain in number, inspired by novel findings, there now being approximately 1,000 articles in English-language international journals using, or referring to, the MMN. There are several highly promising research lines or issues: (1) the MMN as an index of early cognitive development, (2) the MMN as an index of the functional condition of the NMDA-receptor system, (3) the MMN as an index of the different brain pathologies underlying schizophrenia, (4) the role of the MMN in genetic research of psychopathology, (5) the extremely wide range of MMN deficiency across different clinical conditions and diseases, (6) the MMN in prediction of coma outcome, (7) the MMN as an index of primitive sensory intelligence in audition, and (8) the MMN as an index of brain mechanisms of speech perception and understanding. These findings, in particular (8), extend the interpretation of the MMN, currently mainly confined to sensory representations, to involve auditory memory in general.
Mismatch Negativity
Authors: Schröger Erich
Published: May 2008

Since its discovery by Näätänen and colleagues in 1978, the mismatch negativity (MMN) has been used as an index of auditory sensory memory. The present paper explicates various possibilities of how MMN can assess memory functions, it reveals possible traps when interpreting MMN as an index of auditory memory, and it reviews recent developments of paradigms showing that memory on a short time-scale, consolidation of memory traces, and even implicit memory can be probed with MMN.
Language in the Mismatch Negativity Design
Authors: Shtyrov Yury , Pulvermüller Friedemann
Published: May 2008

The article considers neurophysiological and psycholinguistic motivations for applying mismatch negativity (MMN) to studying the language function, briefly reviews the current evidence in the field, and offers some further directions for research in this area. MMN, a well-known index of automatic acoustic change detection, has also been found to be a sensitive indicator of long-term memory traces for native language sounds (phonemes, syllables). When comparing MMNs to words and meaningless pseudowords, we found larger amplitudes for words than for meaningless items. This was interpreted as a neurophysiological signature of word-specific memory circuits/cell assemblies activated in the human brain in a largely automatic and attention-independent fashion. This lexical enhancement of the word-elicited MMN has now been replicated by different groups using different languages and methodologies. We have also demonstrated that, using MMN, it is possible to register differences in the brain response to individual words and even to different aspects of referential semantics, confirming that the cortical memory circuits of individual lexical items can be revealed by the MMN. In other studies, we found evidence that the mismatch negativity reflects automatic syntactic processing commencing as early as ~100 ms after relevant information becomes available in the acoustic input. More recently, MMN responses were found to be sensitive to semantic context integration processes. In summary, neurophysiological imaging of the MMN response provides a unique opportunity to see subtle spatio-temporal dynamics of the neural processes underlying the language function in the human cortex in lexical, semantic, and syntactic domains.
Audiovisual Events in Sensory Memory
Authors: Besle Julien , Caclin Anne , Mayet Romaine , Delpuech Claude , Lecaignard Françoise , Giard Marie-Hélène , Morlet Dominique
Published: May 2008

The functional properties of the auditory sensory memory have been extensively studied using the mismatch negativity (MMN) component of the auditory event-related potential (ERP) and its magnetic counterpart recorded using magneto-encephalography (MEG). It has been found that distinct auditory features (such as frequency or intensity) are encoded separately in sensory memory. Nevertheless, the conjunction of these features (auditory “gestalts”) can also be encoded in auditory sensory memory. Here we investigated how auditory and visual features of bimodal events are represented in sensory memory by recording audiovisual MMNs in two different audiovisual oddball paradigms. The results of a first ERP experiment showed that the sensory memory representations of auditory and visual features of audiovisual events lie within the temporal and occipital cortex, respectively, yet with possible interactions between the processing of the unimodal features. In a subsequent MEG experiment, we found some evidence that audiovisual feature conjunctions could also be represented in sensory memory. These results, thus, extend to the audiovisual domain a number of properties of sensory memory already established within the auditory system.
The Role of Early Auditory Discrimination Deficits in Language Disorders
Authors: Kujala Teija
Published: May 2008

Language impairments can have a devastating effect on the individual’s life. Brain damage such as stroke may cause varying degrees of impaired language. Even milder language problems, such as developmental dyslexia or specific language impairment, can have long-lasting detrimental effects on the individual’s life, affecting both success at school as well as motivation and even self-esteem. In recent years, the mismatch negativity (MMN) has been intensively applied to study the neural basis of language impairments. These studies have shown that the MMN, which reflects the early stages of cortical sound discrimination, is abnormal in a large variety of language impairments. Furthermore, a close relationship between the MMN and some language disorders is suggested by significant correlations between the MMN and language test results. Further support is provided by follow-up studies suggesting that the MMN parameters may predict future language problems in children and by investigations indicating that intervention programs with an ameliorating effect also concurrently change the MMN. However, when interpreting the implications of MMN results it is important to acknowledge that this response specifically reflects early stages of auditory discrimination and should, therefore, be combined with measures probing the further steps of auditory processing for a more complete picture of the underlying deficits of language. The current review addresses how the MMN can be used in determining auditory impairments in language disorders such as aphasia, dyslexia, autism spectrum, and specific language impairment.
Multicollinearity and Missing Constraints
Authors: Kelava Augustin , Moosbrugger Helfried , Dimitruk Polina , Schermelleh-Engel Karin
Published: May 2008

Multicollinearity complicates the simultaneous estimation of interaction and quadratic effects in structural equation modeling (SEM). So far, approaches developed within the Kenny-Judd (1984 ) tradition have failed to specify additional and necessary constraints on the measurement error covariances of the nonlinear indicators. Given that the constraints comprise, in part, latent linear predictor correlations, multicollinearity poses a problem for such approaches. Klein and Moosbrugger’s (2000 ) latent moderated structural equations approach (LMS) approach does not utilize nonlinear indicators and should therefore not be affected by this problem. In the context of a simulation study, we varied predictor correlation and the number of nonlinear effects in order to compare the performance of three approaches developed for the estimation of simultaneous nonlinear effects: Ping’s (1996 ) two-step approach, a correctly extended Jöreskog-Yang (1996 ) approach, and LMS. Results show that in contrast to the Jöreskog-Yang approach and LMS, the two-step approach produces biased parameter estimates and false inferences under heightened multicollinearity. Ping’s approach resulted in overestimated interaction effects and underestimated quadratic effects.
Effect of the Number of Response Categories on the Reliability and Validity of Rating Scales
Authors: Lozano Luis M. , García-Cueto Eduardo , Muñiz José
Published: May 2008

The Likert-type format is one of the most widely used in all types of scales in the field of social sciences. Nevertheless, there is no definitive agreement on the number of response categories that optimizes the psychometric properties of the scales. The aim of the present work is to determine in a systematic fashion the number of response alternatives that maximizes the fundamental psychometric properties of a scale: reliability and validity. The study is carried out with data simulated using the Monte Carlo method. We simulate responses to 30 items with correlations between them ranging from 0.2 to 0.9. We also manipulate sample size, analyzing four different sizes: 50, 100, 200, and 500 cases. The number of response options employed ranges from two to nine. The results show that as the number of response alternatives increases, both reliability and validity improve. The optimum number of alternatives is between four and seven. With fewer than four alternatives the reliability and validity decrease, and from seven alternatives onwards psychometric properties of the scale scarcely increase further. Some applied implications of the results are discussed.
Distribution of escaping ions produced by non‐specular reflection at the stationary quasi‐perpendicular shock front
Authors: Gedalin M. , Liverts M. , Balikhin M. A.
Published: May 2008

Field‐aligned and gyrophase bunched ion beams are observed in the foreshock of the Earth bow shock. One of the mechanisms proposed for their production is non‐specular reflection at the shock front. We study the distributions which are formed at the stationary quasi‐perpendicular shock front within the same process which is responsible for the generation of reflected ions and transmitted gyrating ions. The test particle motion analysis in a model shock allows one to identify the parameters which control the efficiency of the process and the features of the escaping ion distribution. These parameters are: the angle between the shock normal and the upstream magnetic field, the ratio of the ion thermal velocity to the flow velocity upstream, and the cross‐shock potential. A typical distribution of escaping ions exhibits a bimodal pitch angle distribution (in the plasma rest frame).
A nested model study of the Loop Current generated variability and its impact on the West Florida Shelf
Authors: Barth A. , Alvera‐Azcárate A. , Weisberg R. H.
Published: May 2008

A West Florida Shelf model based on the Regional Ocean Modeling System (ROMS) is nested in the North Atlantic Hybrid Coordinate Ocean Model (NAT HYCOM). The focus of this work is the study of the impact of the Loop Current on the West Florida Shelf. In order to assess the model's accuracy, it is compared quantitatively to in situ temperature and velocity measurements on the shelf. A series of sensitivity experiments are conducted to determine the appropriate wind forcing, sea surface temperature relaxation, and mixing scheme. By the inclusion of the Loop Current, we are able to study the propagation of an anticyclonic vortex detaching from the Loop Current. We found that the ambient gradient of potential vorticity is able to explain the vortex path and speed. The statistics of such Loop Current generated flow features were examined by including a tracer marking Loop Current water. This allows to track the Loop Current water on the West Florida Shelf and to quantify the amount of Loop Current water reaching the shelf.
Evaluation of the OMI cloud pressures derived from rotational Raman scattering by comparisons with other satellite data and radiative transfer simulations
Authors: Vasilkov Alexander , Joiner Joanna , Spurr Robert , Bhartia Pawan K. , Levelt Pieternel , Stephens Graeme
Published: May 2008

In this paper we examine differences between cloud pressures retrieved from the Ozone Monitoring Instrument (OMI) using the ultraviolet rotational Raman scattering (RRS) algorithm and those from the thermal infrared (IR) Aqua/MODIS. Several cloud data sets are currently being used in OMI trace gas retrieval algorithms including climatologies based on IR measurements and simultaneous cloud parameters derived from OMI. From a validation perspective, it is important to understand the OMI retrieved cloud parameters and how they differ with those derived from the IR. To this end, we perform radiative transfer calculations to simulate the effects of different geophysical conditions on the OMI RRS cloud pressure retrievals. We also quantify errors related to the use of the Mixed Lambert‐Equivalent Reflectivity (MLER) concept as currently implemented of the OMI algorithms. Using properties from the Cloudsat radar and MODIS, we show that radiative transfer calculations support the following: (1) The MLER model is adequate for single‐layer optically thick, geometrically thin clouds, but can produce significant errors in estimated cloud pressure for optically thin clouds. (2) In a two‐layer cloud, the RRS algorithm may retrieve a cloud pressure that is either between the two cloud decks or even beneath the top of the lower cloud deck because of scattering between the cloud layers; the retrieved pressure depends upon the viewing geometry and the optical depth of the upper cloud deck. (3) Absorbing aerosol in and above a cloud can produce significant errors in the retrieved cloud pressure. (4) The retrieved RRS effective pressure for a deep convective cloud will be significantly higher than the physical cloud top pressure derived with thermal IR.
Validation of Aura Microwave Limb Sounder stratospheric ozone measurements
Authors: Froidevaux L. , Jiang Y. B. , Lambert A. , Livesey N. J. , Read W. G. , Waters J. W. , Browell E. V. , Hair J. W. , Avery M. A. , McGee T. J. , Twigg L. W. , Sumnicht G. K. , Jucks K. W. , Margitan J. J. , Sen B. , Stachnik R. A. , Toon G. C. , Bernath P. F. , Boone C. D. , Walker K. A. , Filipiak M. J. , Harwood R. S. , Fuller R. A. , Manney G. L. , Schwartz M. J. , Daffer W. H. , Drouin B. J. , Cofield R. E. , Cuddy D. T. , Jarnot R. F. , Knosp B. W. , Perun V. S. , Snyder W. V. , Stek P. C. , Thurstans R. P. , Wagner P. A.
Published: May 2008

The Earth Observing System (EOS) Microwave Limb Sounder (MLS) aboard the Aura satellite has provided essentially daily global measurements of ozone (O3) profiles from the upper troposphere to the upper mesosphere since August of 2004. This paper focuses on validation of the MLS stratospheric standard ozone product and its uncertainties, as obtained from the 240 GHz radiometer measurements, with a few results concerning mesospheric ozone. We compare average differences and scatter from matched MLS version 2.2 profiles and coincident ozone profiles from other satellite instruments, as well as from aircraft lidar measurements taken during Aura Validation Experiment (AVE) campaigns. Ozone comparisons are also made between MLS and balloon‐borne remote and in situ sensors. We provide a detailed characterization of random and systematic uncertainties for MLS ozone. We typically find better agreement in the comparisons using MLS version 2.2 ozone than the version 1.5 data. The agreement and the MLS uncertainty estimates in the stratosphere are often of the order of 5%, with values closer to 10% (and occasionally 20%) at the lowest stratospheric altitudes, where small positive MLS biases can be found. There is very good agreement in the latitudinal distributions obtained from MLS and from coincident profiles from other satellite instruments, as well as from aircraft lidar data along the MLS track.
Factors controlling the interannual variability in the carbon balance of a southern boreal black spruce forest
Authors: Krishnan Praveena , Black T. Andrew , Barr Alan G. , Grant Nicholas J. , Gaumont‐Guay David , Nesic Zoran
Published: May 2008

Factors controlling the seasonal and interannual variability of net ecosystem productivity (FNEP), gross ecosystem photosynthesis (Pg), ecosystem respiration (Re) and evapotranspiration (E) of a mature boreal black spruce forest in central Saskatchewan, Canada were investigated using eight years (1999–2006) of continuous eddy covariance measurements. During 2000–2006, which included a three‐year drought, the forest was a weak sink for CO2 with annual FNEP ranging from 27 to 80 g C m‐2 (56 ± 21 g C m−2 a−1). The beginning of the growing season occurred when daily mean air temperature exceeded 4°C and the near surface soil temperature equaled or exceeded 0°C. The length of the growing season varied from 186 to 232 days. During the extreme drought year (2003), the smaller reduction in annual Pg than in Re resulted in highest FNEP of the record. Annual FNEP decreased slightly with increasing soil water content; however, there was evidence of increased FNEP due to high water table conditions in 2004 because of the slightly higher decrease in Re than Pg. Although bulk surface conductance (gs) decreased significantly during the dry conditions in 2003, the associated increase in D prevented a significant drop in E, which resulted in only a slight decline in evaporative fraction and almost no change in water use efficiency. Interannual variation inPg, Re and FNEP in the early growing season (April–June) and late growing season (July–September) was controlled by air temperature and soil water content, respectively. However, spring (April–May) mean air temperature was the main factor determining the interannual variation in annual FNEP. The effect of late growing season soil water content on annual Pg and Re was greater than its effect on annual FNEP. The results emphasize the need to consider soil moisture conditions as well as temperature when simulating the response of the carbon balance components of this ecosystems to climate change.
Radiative influences on ice crystal and droplet growth within mixed‐phase stratus clouds
Authors: Lebo Z. J. , Johnson N. C. , Harrington J. Y.
Published: May 2008

This study uses a box model and a Lagrangian microphysical parcel model to investigate the influences of radiative heating and cooling on the vapor diffusional growth of liquid drops and ice crystals within mixed‐phase clouds. Without radiative effects, the combined influences of drop and ice vapor diffusion lead to slight supersaturations with respect to liquid despite the rapid growth of ice. This allows drops grown on aerosol particles with a critical radius of at least 2.5 μm to continue growing while drops grown on smaller aerosols evaporate (if activation occurs) leading to a broader drop size distribution. Longwave radiation allows drops with radii >10 μm to grow simultaneously with the ice with some drops exceeding 25 μm in radius. Both the box model and the parcel model suggest that longwave cooling reduces, whereas solar heating increases, glaciation time‐scales. Although the maximum possible reduction in the glaciation time‐scale due to longwave cooling is as much as 45%, the parcel model shows that reductions on the order of 5 to 15% are more likely. Moreover, infrared cooling increases, and solar heating decreases, the temperature at which the Bergeron process is a maximum. Model simulations suggest the conclusion that radiative influences are most substantial for ice concentrations between 5 and 50 ℓ−1, precisely when the glaciation time‐scale is on the order of the in‐cloud time‐scale.
Modeling the particle flux effect on distribution of 230Th in the equatorial Pacific
Authors: Siddall Mark , Anderson Robert F. , Winckler Gisela , Henderson Gideon M. , Bradtmiller Louisa I. , McGee David , Franzese Allison , Stocker Thomas F. , Müller Simon A.
Published: May 2008

The normalization of sediment accumulation rates by 230Th is increasingly used to constrain particle rain rates because 230Th is produced at a known rate in the water column and removed relatively quickly to the sediment. Several recent contributions have questioned this approach and suggested that the preferential removal of 230Th in areas of high particle flux, the “particle flux effect,” introduces a systematic bias in the 230Th normalization technique. We use a circulation model that includes a description of particle scavenging to show that the particle flux effect cannot explain observations of high 230Th accumulation in equatorial Pacific sediments (relative to 230Th production in the water column). We further consider the possible variation of particle rain rates over time. We find only a minimal sensitivity in the particle flux effect due to increases in the particle rain rate at the equatorial Pacific by a factor of up to 10. This situation exists because the residence time of 230Th in the water column is too short to permit significant lateral transport with reasonable isopycnal mixing coefficients. We conclude that the increased rates of 230Th accumulation found in equatorial Pacific sediments deposited during the Last Glacial Maximum cannot have been caused by the particle flux effect.
Radiation belt electron precipitation due to VLF transmitters: Satellite observations
Authors: Sauvaud J.‐A. , Maggiolo R. , Jacquey C. , Parrot M. , Berthelier J.‐J. , Gamble R. J. , Rodger Craig J.
Published: May 2008

In the Earth's inner magnetosphere, the distribution of energetic electrons is controlled by pitch‐angle scattering by waves. A category of Whistler waves originates from powerful ground‐based VLF transmitter signals in the frequency range 10–25 kHz. These transmissions are observed in space as waves of very narrow bandwidth. Here we examine the significance of the VLF transmitter NWC on the inner radiation belt using DEMETER satellite global observations at low altitudes. We find that enhancements in the ∼100–600 keV drift‐loss cone electron fluxes at L values between 1.4 and 1.7 are linked to NWC operation and to ionospheric absorption. Waves and particles interact in the vicinity of the magnetic equatorial plane. Using Demeter passes across the drifting cloud of electrons caused by the transmitter; we find that ∼300 times more 200 keV electrons are driven into the drift‐loss cone during NWC transmission periods than during non‐transmission periods. The correlation between the flux of resonant electrons and the Dst index shows that the electron source intensity is controlled by magnetic storm activity.
Global energy dissipation rate of deep‐ocean low‐frequency flows by quadratic bottom boundary layer drag: Computations from current‐meter data
Authors: Sen Ayon , Scott Robert B. , Arbic Brian K.
Published: May 2008

The global energy dissipation rate of deep‐ocean low‐frequency flows by quadratic bottom boundary layer drag is estimated in three ways. First, an average over the dissipations computed from the near‐bottom velocities recorded by 290 moored current meters is multiplied by the World Ocean area. Second, near‐global maps of surface velocities derived from satellite altimetry data are used to estimate the bias due to the sparse spatial coverage of the moorings. Third, a relationship between bottom and surface flows, computed over the mooring locations, is used to estimate global maps of bottom flows from the surface data. All three methods suggest that at least 0.2 TW of the wind‐power input into geostrophic flows is dissipated in deep water by quadratic bottom drag. Implications for the oceanic overturning circulation, and for oceanic mesoscale eddy dynamics, are briefly discussed.
Impact of small ice crystal assumptions on ice sedimentation rates in cirrus clouds and GCM simulations
Authors: Mitchell David L. , Rasch Philip , Ivanova Dorothea , McFarquhar Greg , Nousiainen Timo
Published: May 2008

In the prediction of climate change, the greatest uncertainty lies in the representation of clouds. Ice clouds are particularly challenging, and to date there is no accepted method for measuring the smaller ice crystals (D < 60 μm). This study examines the sensitivity of a global climate model to different assumptions regarding the number concentrations of small ice crystals when they are allowed to affect ice sedimentation rates. When their concentrations are relatively high, the GCM predicts a 12% increase in cloud ice amount and a 5.5% increase in cirrus cloud coverage globally. This produces a net cloud forcing of −5 W m−2 in the tropics and warms the upper tropical troposphere over 3°C. Ice crystal concentration differences assumed were modest in comparison to corresponding measurement uncertainties, revealing a potentially large source of uncertainty in the prediction of global climate.
Quantification of gravity wave forcing in driving the stratospheric Quasi‐Biennial Oscillation
Authors: Antonita T. Maria , Ramkumar Geetha , Kishore Kumar Karanam , Sunil Kumar S. V.
Published: May 2008

Using long‐term Rayleigh lidar temperature observations during April 1998–April 2005 in the lower stratospheric region, momentum flux divergence of the gravity waves of periods 0.5–1 and 2–4 hours are estimated over Gadanki (13.5°N, 79.2°E), India. Monthly mean zonal winds from NCEP/NCAR reanalysis data over Gadanki at two pressure levels 10 and 20 hPa are used to study the characteristics of the Quasi‐Biennial Oscillation (QBO) and its month‐to‐month acceleration. This observed mean flow acceleration is compared with that estimated from the momentum flux divergence of gravity waves, which led to a better insight into the role of gravity waves in driving the QBO. The present analysis reveals that the contribution of gravity waves towards the westerly phase of QBO varies from ∼10–60% while that during easterly phase from ∼10–30%. The present study thus quantifies the role of gravity waves in driving the easterly and westerly phases of QBO.
Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions
Authors: Martin-Cuadrado Ana-Belen , Rodriguez-Valera Francisco , Moreira David , Alba José C , Ivars-Martínez Elena , Henn Matthew R , Talla Emmanuel , López-García Purificación
Published: May 2008

Marine planktonic archaea are widespread and abundant in deep oceanic waters but, despite their obvious ecological importance, little is known about them. Metagenomic analyses of large genome fragments allow access to both gene content and genome structure from single individuals of these cultivation-reluctant organisms. We present the comparative analysis of 22 archaeal genomic clones containing 16S rRNA genes that were selected from four metagenomic libraries constructed from meso- and bathypelagic plankton of different oceanic regions (South Atlantic, Antarctic Polar Front, Adriatic and Ionian Sea; depths from 500 to 3000 m). We sequenced clones of the divergent archaeal lineages Group 1A (Crenarchaeota) and Group III (Euryarchaeota) as well as clones from the more frequent Group I Crenarchaeota and Group II Euryarchaeota. Whenever possible, we analysed clones that had identical or nearly identical 16S rRNA genes and that were retrieved from distant geographical locations, that is, that defined pan-oceanic operational taxonomic units (OTUs). We detected genes involved in nitrogen fixation in Group 1A Crenarchaeota, and genes involved in carbon fixation pathways and oligopeptide importers in Group I Crenarchaeota, which could confirm the idea that these are mixotrophic. A two-component system resembling that found in ammonia-oxidizing bacteria was found in Group III Euryarchaeota, while genes for anaerobic respiratory chains were detected in Group II Euryarchaeota. Whereas gene sequence conservation was high, and recombination and gene shuffling extensive within and between OTUs in Group I Crenarchaeota, gene sequence conservation was low and global synteny maintained in Group II Euryarchaeota. This implies remarkable differences in genome dynamics in Group I Crenarchaeota and Group II Euryarchaeota with recombination and mutation being, respectively, the dominant genome-shaping forces. These observations, along with variations in GC content, led us to hypothesize that the two groups of organisms have fundamentally different lifestyles.
Migraine and Ischemic Stroke: A Debated Question
Authors: Del Zotto Elisabetta , Pezzini Alessandro , Giossi Alessia , Volonghi Irene , Padovani Alessandro
Published: May 2008

Numerous epidemiologic observations reporting high prevalence of migraine among young individuals with stroke as well as dysfunction of cerebral arteries during migraine attacks prompt speculation on the existence of a comorbidity between the two disorders. The recent finding of silent infarct-like brain lesions in migraineurs reinforced this hypothesis and raised questions on whether migraine may be a progressive disorder rather than simply an episodic disorder. Stroke can occur during the course of migraine attacks with aura, supporting the assumption of a causal relation between the two diseases. Migraine may accentuate other existing risk factors for stroke, and both jointly increase the risk of cerebral ischemia outside of migraine attacks. In this regard, the role of migraine might be that of predisposing condition for cerebral ischemia. Migraine and ischemic stroke may be the end phenotype of common pathogenic mechanisms. Evidence of a migraine-stroke relation in cases of specific disorders, such as CADASIL (cerebral autosomal—dominant arteriopathy with subcortical infarcts and leukoencephalopathy) and MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes), strongly supports this concept. Finally, acute focal cerebral ischemia can trigger migraine attacks, and, thus, migraine may be the consequence of stroke. In this paper, we will review contemporary epidemiologic studies, discuss potential mechanisms of migraine-induced stroke and comorbid ischemic stroke, and pose new research questions.
Polysomnographic Sleep, Growth Hormone Insulin‐like Growth Factor‐I Axis, Leptin, and Weight Loss
Authors: Rasmussen Michael H. , Wildschiødtz Gordon , Juul Anders , Hilsted Jannik
Published: May 2008

Short sleep appears to be strongly associated with obesity and altered metabolic function, and sleep and growth hormone (GH) secretion seems interlinked. In obesity, both the GH‐insulin‐like‐growth‐factor‐I (GH‐IGF‐I) axis and sleep have been reported to be abnormal, however, no studies have investigated sleep in relation to the GH‐IGF‐I axis and weight loss in obese subjects. In this study polygraphic sleep recordings, 24‐h GH release, 24‐h leptin levels, free‐IGF‐I, total‐IGF‐I, IGF‐binding protein‐3 (IGFBP‐3), acid‐labile subunit (ALS), cortisol and insulin sensitivity were determined in six severely obese subjects (BMI: 41 ± 1 kg/m2, 32 ± 2 years of age), cross‐sectional at baseline, and longitudinal after a dramatically diet‐induced weight loss (36 ± 7 kg). Ten age‐ and gender‐matched nonobese subjects served as controls. Sleep duration (360 ± 17 vs. 448 ± 15 min/night; P < 0.01), 24‐h GH (55 ± 9 vs. 344 ± 55 mU/l·24 h; P < 0.01), free‐IGF‐I (2.3 ± 0.42 vs. 5.7 ± 1.2 μg/l; P < 0.01), and total‐IGF‐I (186 ± 21 vs. 301 ± 18 μg/l; P < 0.01) were significantly decreased and 24‐h leptin levels were increased (35 ± 5 vs. 12 ± 3 μg/l; P < 0.01) in obese subjects at pre‐weight loss compared with nonobese subjects After diet‐induced weight loss the differences in GH, free IGF‐I, and leptin were no longer present between previously obese and nonobese subjects, whereas a significant difference in sleep duration and total IGF‐I levels persisted. Rapid eye movement (REM) sleep, non‐REM sleep, IGFBP‐3, ALS, and cortisol levels were similar in obese and nonobese subjects. Sleep duration, 24‐h GH, and IGF‐I levels were decreased and 24‐h leptin levels were increased in obese subjects. We conclude that hyposomatotropism and hyperleptinemia in obesity are transient phenomena reversible with weight loss, whereas short sleep seems to persist after weight has been reduced dramatically.
Rapid purification of truncated Taq DNA polymerase Stoffel fragment by boiling lysis of bacterial expression cultures
Authors: Yang Zhengan , Ding Yumei , Zhang Yinghua , Liu Feihu
Published: May 2008

A simplified and low‐cost method, boiling lysis, was developed and used to purify the truncated DNA polymerase Stoffel fragment after overproduction of the enzyme in Escherichia coli. The method is based on the thermostable properties of the Stoffel fragment. Conditions such as the boiling time and number of cycles employed were identified as determinants with which to achieve a high yield and activity of this truncated Taq enzyme. Under established conditions, a period of 8 min consisting of two cycles of boiling and centrifuging was ideal for the purification of the Taq protein, followed by dibasic phosphate and ethanol extraction in a single type of storage buffer to remove contaminating nucleic acid. The whole purification process could be achieved within 1 or 2 h. A total yield of 80 mg of truncated Taq enzyme with an activity of 1.6×107 units was purified from l litre of bacterial culture. The purified Taq enzyme had a molecular mass of 61 kDa, a value consistent with the truncated DNA polymerase Stoffel fragment reported previously.
Effect of immobilized cell‐binding peptides on chitosan membranes for osteoblastic differentiation of mesenchymal stem cells
Authors: Lee Jue‐Yeon , Choo Jung‐Eun , Choi Young‐Sook , Shim In‐Kyong , Lee Seung‐Jin , Seol Yang‐Jo , Chung Chong‐Pyoung , Park Yoon‐Jeong
Published: May 2008

Two cell‐binding domains from FGF‐2 (fibroblast growth factor‐2) were shown to increase cell attachment and osteoblastic differentiation. Two synthetic peptides derived from FGF‐2, namely residues 36–41 (F36; PDGRVD) and 77–83 (F77; KEDGRLL), were prepared and their N‐termini further modified for ease of surface immobilization. Chitosan membranes were used in the present study as mechanical supportive biomaterials for peptide immobilization. Peptides could be stably immobilized on to the surface of chitosan membranes. The adhesion of mesenchymal stem cells to the peptide (F36 and F77)‐immobilized chitosan membrane was increased in a dose‐dependent manner and completely inhibited by soluble RGD (Arg‐Gly‐Asp) and anti‐integrin antibody, indicating the existence of an interaction between F36/F77 and integrin. Peptide‐immobilized chitosan supported human bone‐marrow‐derived mesenchymal‐stem‐cell differentiation into osteoblastic cells, as demonstrated by alkaline phosphate expression and mineralization. Taken together, the identified peptide‐immobilized chitosan membranes were able to support cell adhesion and osteoblastic differentiation; thus these peptides might be useful as bioactive agents for osteoblastic differentiation and surface‐modification tools in bone regenerative therapy.
Selection and characterization of Affibody® ligands to the transcription factor c‐Jun
Authors: Lundberg Emma , Brismar Hjalmar , Gräslund Torbjörn
Published: May 2008

c‐Jun is a highly oncogenic transcription factor involved in the development of different types of cancer. In the present study we have generated c‐Jun‐binding‐affinity proteins from a phage‐displayed library of so‐called ‘Affibody® ligands’, developed by combinatorial engineering of a non‐immunoglobulin‐based scaffold protein. Homodimeric c‐Jun protein was recombinantly produced in Escherichia coli and, prior to selection, the quality of the target protein was investigated by binding analyses, which indicated specific binding to a double‐stranded DNA hairpin construct containing a c‐Jun response element, but not to a control sequence. Isolated Affibody® variants from the phage selection were expressed in E. coli, purified by affinity chromatography and their interaction with c‐Jun was analysed. In biosensor analyses, one Affibody® ligand, denoted ZcJun518, was shown to interact with immobilized c‐Jun protein with an apparent dissociation constant of 5 μM. By constructing a head‐to‐tail homodimeric version of ZcJun518, its apparent affinity for c‐Jun could be increased threefold, suggesting co‐operativity effects in the binding to the immobilized c‐Jun protein. Further characterization of the ZcJun518 Affibody® molecule demonstrated, in both affinity‐capture and Western‐blotting experiments, its ability to interact selectively with c‐Jun, even when the c‐Jun target was present in a complex protein background consisting of a bacterial cell lysate. ZcJun518 could also be used to stain the c‐Jun‐overexpressing cell line C8161 visualized by confocal fluorescence microscopy. Results from competition experiments indicated that the binding epitope on c‐Jun for the ZcJun518 Affibody® molecule was separate from the binding sites of both a polyclonal antibody raised against the unstructured N‐terminal domain and a double‐stranded DNA hairpin containing a c‐Jun response element. The potential intracellular use of Affibody® ligands directed against transcription factors and other oncogenic factors is discussed.
Immunization with a recombinant fowlpox virus expressing a hepatitis C virus core–E1 polyprotein variant, protects mice and African green monkeys (Chlorocebus aethiops sabaeus) against challenge with a surrogate vaccinia virus
Authors: Alvarez‐Lajonchere Liz , Amador‐Cañizares Yalena , Frías Roberto , Milian Yoamel , Musacchio Alexis , Guerra Ivis , Acosta‐Rivero Nelson , Martínez Gillian , Castro Jorge , Puentes Pedro , Cosme Karelia , Dueñas‐Carrera Santiago
Published: May 2008

HCV (hepatitis C virus) is a worldwide health problem nowadays. No preventive vaccine is available against this pathogen, and therapeutic treatments currently in use have important drawbacks, including limited efficacy. In the present work a recombinant fowlpox virus, FPCoE1, expressing a truncated HCV core–E1 polyprotein, was generated. FPCoE1 virus generally failed to elicit a humoral immune response against HCV antigens in BALB/c mice. By contrast, mice inoculated with FPCoE1 elicited a positive interferon‐γ secretion response against HCV core in ex‐vivo ELISPOT (enzyme‐linked immunospot) assays. Remarkably, mice inoculated with FPCoE1 significantly controlled viraemia in a surrogate challenge model with vvRE, a recombinant vaccinia virus expressing HCV structural antigens. In fact, 40% of the mice had no detectable levels of vvRE in their ovaries. Administration of FPCoE1 in vervet monkeys [Chlorocebus (formerly Cercophitecus) aethiops sabaeus] induced lymphoproliferative response against HCV core and E1 proteins in 50% of immunized animals. Monkeys immunized with FPCoE1 had no detectable levels of vvRE in their blood, whereas monkeys inoculated with FP9, the negative control virus, had detectable levels of vvRE in blood up to 7 days after challenge. In conclusion, recombinant fowlpox virus FPCoE1 is able to induce an anti‐HCV immune response in mice and monkeys. This ability could be rationally employed to develop effective strategies against HCV infection by using FPCoE1 in combination with other vaccine candidates or antiviral treatments.
Small‐interfering‐RNA‐mediated silencing of human glutamate dehydrogenase induces apoptosis in neuroblastoma cells
Authors: Choi Myung‐Min , Kim Eun‐A , Huh Jae‐Wan , Choi Soo Young , Cho Sung‐Woo , Yang Seung‐Ju
Published: May 2008

In the nervous system, GDH (glutamate dehydrogenase) is enriched in astrocytes and is important for recycling glutamate, a major excitatory neurotransmitter. The function of hGDH (human GDH) may be important in neurodegenerative diseases such as Parkinson's disease. To test the effect of decreased hGDH expression, several vector‐based plasmidlinked hGDH siRNAs (small interfering RNAs) were expressed intracellularly in BE(2)C human neuroblastoma cells. Immunoblotting and reverse‐transcription–PCR confirmed that expression of hGDH protein and mRNA was knocked down by co‐transfection with phGDH‐siRNA vectors in BE(2)C human neuroblastoma cells. TUNEL (terminal uridine deoxynucleotidyl transferase dUTP nick‐end labelling) and DNA fragmentation assays 48 h after transfection of phGDH‐siRNAs revealed that inhibition of hGDH expression induced cellular apoptosis and activated phospho‐ERK1/2 (phospho‐extracellular‐signal‐regulated kinase 1/2). These findings show that inhibition of hGDH expression by siRNA is related to apoptosis in neuronal cells.
Transcriptome and proteome analysis of antibody‐producing mouse myeloma NS0 cells cultivated at different cell densities in perfusion culture
Authors: Krampe Britta , Swiderek Halina , Al‐Rubeai Mohamed
Published: May 2008

A combined gene and protein expression profiling was performed to gain a deeper insight into the intracellular response of the antibody‐producing GS‐NS0 cell line in continuous perfusion culture. Growth rate, production rate, metabolic activity and viability declined with increasing cell density, dilution rate and time. Transcriptome and proteome analyses of cells at three different densities revealed 53 genes and 47 proteins as having significantly altered expression levels at HCD (high cell density). The results showed an increased up‐regulation of genes/proteins involved in cellular energy production with increasing cell density. Furthermore, the intensified process triggered a cellular response to external stress stimuli, revealed by an overexpression of the genes/proteins implicated in cell‐cycle arrest [e.g. Rb1 (retinoblastoma 1 gene) and Cdkn1b (cyclin‐dependent kinase inhibitor 1B gene)] and in the induction of pro‐apoptotic genes/proteins [e.g. Tnfrsf (tumour necrosis factor receptor superfamily gene), Nfκbia (gene coding for nuclear factor‐κB inhibitor), HSP60 (heat‐shock protein of molecular mass 60 kDa) and heterogeneous nuclear ribonucleoprotein K]. Interestingly, we observed a down‐regulation of the transcription factor interferon regulatory factor 4 involved in the unfolded‐protein‐response process and protein disulfide‐isomerase family members responsible for protein folding and assembly. Additionally, subunits of proteasome complex were highly expressed at HCD. Microarray, real‐time quantitative reverse‐transcription PCR and Western‐blot analyses demonstrated a consistent trend of decrease in IgG heavy‐chain level with increasing cell density. HSP60, which inhibits apoptosis by complexing with pro‐apoptotic proteins such as Bax and Bak, was repressed at HCD. Overall, the data suggested that the balance among several factors involved in energy metabolism might be essential for fine‐tuning the cell choice between survival and apoptosis, leaning towards the side of apoptosis at HCD. The results provide significant information for cell‐engineering strategies and solutions to problems that prevail in HCD culture.