bluuebunny/crossref_metadata_2025 huggingface dataset:
Size-Selected Ag Nanoparticles with Five-Fold Symmetry
Authors: Gracia-Pinilla MiguelÁngel , Ferrer Domingo , Mejía-Rosales Sergio , Pérez-Tijerina Eduardo
Published: May 2009

Silver nanoparticles were synthesized using the inert gas aggregation technique. We found the optimal experimental conditions to synthesize nanoparticles at different sizes: 1.3 ± 0.2, 1.7 ± 0.3, 2.5 ± 0.4, 3.7 ± 0.4, 4.5 ± 0.9, and 5.5 ± 0.3 nm. We were able to investigate the dependence of the size of the nanoparticles on the synthesis parameters. Our data suggest that the aggregation of clusters (dimers, trimer, etc.) into the active zone of the nanocluster source is the predominant physical mechanism for the formation of the nanoparticles. Our experiments were carried out in conditions that kept the density of nanoparticles low, and the formation of larges nanoparticles by coalescence processes was avoided. In order to preserve the structural and morphological properties, the impact energy of the clusters landing into the substrate was controlled, such that the acceleration energy of the nanoparticles was around 0.1 eV/atom, assuring a soft landing deposition. High-resolution transmission electron microscopy images showed that the nanoparticles were icosahedral in shape, preferentially oriented with a five-fold axis perpendicular to the substrate surface. Our results show that the synthesis by inert gas aggregation technique is a very promising alternative to produce metal nanoparticles when the control of both size and shape are critical for the development of practical applications.
Short Term External Debt and Economic Growth—Granger Causality: Evidence from Latin America and the Caribbean
Authors: Butts Hector C.
Published: May 2009

In this paper the direction of the causality relationship between economic growth and short-term external debt was investigated for 27 Latin American and Caribbean countries over the period 1970–2003. The empirical results suggest the existence of bidirectional causality relationships between the two variables for several countries, which means that the performance of both variables is interrelated. The main finding is that in the short- and long- runs Granger causality from economic growth to short-term external debt is present in 13 Latin American and Caribbean countries. With the evidence suggesting, in the majority of estimated cases, economic growth Granger caused short-term external debt, short-term policy decisions related to capacity absorption enhancement should be encouraged in Latin America and the Caribbean. Further work in this regard is encouraged in the form of panel studies or specific individual case studies inclusive of foreign trade linkage parameters to capture the potential effects of omitted variables.
Les kystes intraprostatiques: à propos de trois observations
Authors: Hadj Slimen M. , Fakhfakh H. , Charfi W. , Tlijani J. , Ketata H. , Bahloul A. , Mhiri M. N.
Published: May 2009

Introduction

Les kystes intraprostatiques sont considérés comme une affection rare, actuellement de découverte de plus en plus fréquente grace au développement des moyens d’imagerie. Certaines formes peuvent être responsables d’infertilité chez l’homme. Les auteurs se proposent d’étudier les différents aspects cliniques, diagnostiques et thérapeutiques des différents types de kystes intraprostatiques.

Matériel et méthodes

Entre 2002 et 2007, nous avons colligé trois cas de kyste intraprostatique en dehors des kystes utriculaires chez des hommes âgés de 32, 36 et 39 ans.

Résultats

Le motif de consultation était une infertilité primaire (deux cas) et des douleurs pelviennes (deux cas). Le toucher rectal a révélé une masse rénitente de la prostate dans deux cas. Le spermogramme a été perturbé dans deux cas. Le diagnostic a été confirmé par une échographie prostatique. Une ponction de première intention a été réalisée dans un cas avec récidive secondaire. Deux patients ont eu une urétroscopie montrant l’absence de communication entre le kyste et la lumière urétrale. Une résection du dôme saillant a été réalisée. L’évolution a été favorable dans tous les cas, avec amélioration du spermogramme et dissipation de la symptomatologie, sans aucune récidive.

Conclusion

Les kystes intraprostatiques représentent une pathologie bénigne d’origine le plus souvent congénitale. L’imagerie représente un élément capital dans le diagnostic et permet parfois de guider un geste thérapeutique. Le traitement n’est pas encore bien codifié, mais les kystes symptomatiques et/ou compliqués d’une hypofertilité peuvent bénéficier d’un traitement par voie endoscopique efficace et peu invasif.
Le sperme « inflammatoire »: ses relations avec la fertilité
Authors: Zorn B.
Published: May 2009

Objectifs

L’inflammation du sperme résulte d’une infection bactérienne ou virale du tractus urogénital male (TUGM); elle est souvent cliniquement silencieuse. Le dilemme existe quant aux rapports de cause à effet entre leucocytes, marqueurs de l’inflammation et mauvaise qualité du sperme. Nous nous sommes intéressés aux modifications des spermatozoïdes à l’échelon moléculaire en rapport avec l’inflammation.

Matériel et méthodes

Cette étude repose sur une revue de la littérature et des résultats personnels. Chez 200 hommes, partenaires de couples infertiles au spermogramme normal, nous avons étudié la condensation nucléaire et les dérivés actifs de l’oxygène (DAO) déterminés par cytométrie en flux après marquage à l’acridine orange et au dihydroéthidium en fonction des taux d’élastase du plasma séminal.

Résultats

Dans la littérature, on a décrit une relation positive entre infection et exacerbation de l’apoptose des spermatozoïdes avec augmentation de la nécrose et diminution du potentiel de membrane mitochondriale. Nous avons retrouvé une corrélation positive entre le taux de spermatozoïdes avec ADN dénaturé et celui d’élastase. Ce taux passait de 8,6 % à un taux d’élastase entre 0 et 100 μg/l à 15,7 % pour un taux d’élastase entre 100 et 250 μg/l, cette augmentation ne dépendant pas de la sécrétion de DAO. Le taux de spermatozoïdes avec ADN dénaturé se normalisait pour des taux d’élastase supérieurs à 600 μg/l.

Discussion et conclusion

Les modifications de l’ADN ou des membranes des spermatozoïdes n’influencent pas automatiquement les caractéristiques classiques du sperme ni ne réduisent la fertilité male. Elles peuvent cependant retentir négativement sur la capacitation et la réaction acrosomique, avec absence de fécondation ou mauvais développement embryonnaire. Avant de traiter, on tiendra compte du lieu et de la durée de l’inflammation ainsi que des lésions occasionnées sur les spermatozoïdes.
Les conceptions andrologiques de Galien (129–201)
Authors: Karamanou M. , Diamantis A. , Ploumpidis D. , Androutsos G.
Published: May 2009

Galien, après Hippocrate, est le plus grand représentant de la médecine grecque et occidentale. Pendant 15 siècles, l’autorité de la médecine galénique fut incontestable. Dans les Œuvres de Galien, l’andrologie occupe une place considérable.
DNA hypomethylation as Achilles’ heel of tumorigenesis: A working hypothesis
Authors: Shvachko L.P.
Published: May 2009

There are at least two findings that show DNA hypomethylation plays a key role in carcinogenesis. The first major evidence is that DNA hypomethylation induces target chromosomal and genomic instability with cancer manifestations. The second reason that cancer progression is associated with deepening DNA hypomethylation. Nevertheless, the evolution of this crucial epigenomic alteration in the somatic cellular malignant transformation remains unclear.

From some of the experimental data to be present, a key role of DNA hypomethylation in early development of epigenetic somatic cancer biology is proposed. We have observed the significant increasing of genome ploidy at the level of peripheral blood lymphocytes taken from the patients with different solid carcinomas. Similarly, 5‐azacytidine demethylating DNA treatment of cultured healthy lymphocytes induces increased nuclear DNA content. We argue that somatic lymphocyte ploidy induced by genomic DNA hypomethylation during carcinogenesis is related to global demethylation and decondensation of mitotic constitutive pericentromeric heterochromatin. This results in disturbances of pericentromeric heterochromatin that are expressed in nuclear heterochromatinization on the basis of extrachromosomal chromomerization.

On the basis of literature searches and experimental findings, it is proposed that DNA hypomethylation plays the role of an initiator in epigenetic somatic cancer biology.
In search of a theoretical approach to the analysis of the ‘Colour revolutions’: Transition studies and discourse theory
Authors: Zherebkin Maksym
Published: May 2009

The article aims to identify a theoretical framework which would be able to provide explanation for the cases of political mobilization during the ‘Colour revolutions’ in Georgia, Ukraine and Kyrgyzstan. It reviews the existing literature on the topic, which is predominantly oriented by the ‘transition paradigm’. The major shortcomings of this literature are identified: the privileging of either structure or agency when accounting for social change, a strong emphasis on the role of elites and insufficient attention to collective agency. Accordingly, I argue that the methodology of poststructuralist discourse theory may importantly supplement the ‘transitological’ framework owing to its ability to conceptualize the dynamic interdependence between structure and agency, as well as the formation of collective political identities.
The ghosts of the past: 20 years after the fall of communism in Europe
Authors: Rabikowska Marta
Published: May 2009

Twenty years after the fall of communism in Europe, the post-Soviet countries have not achieved a similar stage of democratic development. They have shown to be too diverse and historically too independent to follow one path of consolidation. This volume questions the premises of transitology, homogeneity, and path dependency theories and suggests an insight into the continuities and discontinuities within particular contexts of the given countries (Russia, Belarus, Estonia, Georgia, Ukraine, Poland and others). The latter quite often collide with each other and with the Western democratic values, thus putting a concept of a harmonious dialogue or a definite democratic solution for Europe into doubt. This volume challenges one-directional analyses of both communism and capitalism and offers an examination of their inner contrasts and contradictions that are a part of transitions to democracy. The irreconcilable differences between the two systems of ideologies determined by universalisms, such as utilitarianism, liberalism, harmony, and productivity, were derived from the post-Enlightenment heritage of the humanist ideals which today cannot be acknowledged without criticism. To grasp the dynamics of the post-Soviet countries that are developing their own democratic models requires looking into their political struggles, social fissures and complexities within their past and present, rather than observing them from the epistemological standpoint. Such a standpoint is criticised in this volume for seeing those countries as locked in one homogenous totalitarian paradigm. The abstractness of the universalist and utopian concept of transition imposed on concrete social relations is criticised, while the theoriticisation of democratic ideals is related to the political legitimisation.
ON LIE-LIKE COMPLEX FILIFORM LEIBNIZ ALGEBRAS
Authors: OMIROV B. A. , RAKHIMOV I. S.
Published: May 2009

In this paper we propose an approach to classifying a subclass of filiform Leibniz algebras. This subclass arises from the naturally graded filiform Lie algebras. We reconcile and simplify the structure constants of such a class. In the arbitrary fixed dimension case an effective algorithm to control the behavior of the structure constants under adapted transformations of basis is presented. In one particular case, the precise formulas for less than 10 dimensions are given. We provide a computer program in Maple that can be used in computations as well.
Differences in population parameters and behaviour of the herbivorous fishSarpa salpabetween protected and unprotected seagrass meadows in the north-western Mediterranean
Authors: Raventos N. , Ferrari B. , Planes S.
Published: May 2009

Population parameters and behaviour of the herbivorous fishSarpa salpa, present differences between protected and non-protected seagrass meadows of the north-western Mediterranean Sea. Larger individuals are more abundant inside protected areas, where their grazing pressure on seagrass is disproportionately greater than that of smaller fish feeding on algae and seagrass in unprotected areas. The feeding rate (bites per minute per individual) of smaller fish in unprotected areas is relatively high; however, the denser populations of larger fish in protected areas consume more forage because individual mouth gape is greater and larger fish remove more forage per bite. All these differences suggest a higher impact on seagrass meadows inside protected areas.
The role of macrophages in inflammatory bowel diseases
Authors: Heinsbroek Sigrid E.M. , Gordon Siamon
Published: May 2009

The small and large intestine contain the largest number of macrophages in the body and these cells are strategically located directly underneath the epithelial layer, enabling them to sample the lumen. Such intestinal macrophages have a different phenotype from other tissue macrophages in that they ingest and may kill microbes but they do not mediate strong pro-inflammatory responses upon microbial recognition. These properties are essential for maintaining a healthy intestine. It is generally accepted that tolerance to the intestinal flora is lost in inflammatory bowel diseases, and genes involved in microbial recognition, killing and macrophage activation have already been associated with these diseases. In this review, we shed light on the intestinal macrophage and how it influences intestinal immunity.
The Simon Effect with Conventional Signals
Authors: Pellicano Antonello , Lugli Luisa , Baroni Giulia , Nicoletti Roberto
Published: May 2009

The Simon effect consists of a faster and a more accurate performance when spatial responses correspond to irrelevant-spatial stimuli than when they do not. The time course of the Simon effect was investigated using centrally presented conventional signals (arrows and spatial words) conveying spatial information through iconic-symbolic (Experiments 1 and 2) and semantic (Experiment 3) codes. Time-demanding object-inherent and semantic spatial codes were generated for arrows and words, respectively. This resulted in Simon effects increasing in size across increasing response times (RTs). However, different onsets of the Simon effect were displayed across RT distributions. For arrows, the Simon effect was already significant at the fastest RT intervals, providing clear evidence that they are distinctively more effective directional indicators compared to words.
Anticipation Selectively Enhances Interference Exerted by Pictures of Negative Valence
Authors: Kleinsorge Thomas
Published: May 2009

Recent evidence suggests that anticipation of negatively valenced pictures strongly increases interference exerted by the actual presentation of these pictures, while anticipation of positively valenced pictures leaves the impact of the actual presentation of positive pictures unaffected. However, there is some ambiguity as to whether anticipation of negative valence generally increases the impact of all emotional stimuli, or whether the effect of anticipation is specific for stimuli of negative valence. In the present experiments, different anticipation conditions were contrasted that differed with respect to the specificity of the information on which anticipations could be based. The data show that all anticipation conditions that entailed the possibility of the presentation of unpleasant stimuli selectively enhanced the impact of negatively valenced stimuli without affecting the impact of positively valenced stimuli.
Optimizing Distributed Practice
Authors: Cepeda Nicholas J. , Coburn Noriko , Rohrer Doug , Wixted John T. , Mozer Michael C. , Pashler Harold
Published: May 2009

More than a century of research shows that increasing the gap between study episodes using the same material can enhance retention, yet little is known about how this so-called distributed practice effect unfolds over nontrivial periods. In two three-session laboratory studies, we examined the effects of gap on retention of foreign vocabulary, facts, and names of visual objects, with test delays up to 6 months. An optimal gap improved final recall by up to 150%. Both studies demonstrated nonmonotonic gap effects: Increases in gap caused test accuracy to initially sharply increase and then gradually decline. These results provide new constraints on theories of spacing and confirm the importance of cumulative reviews to promote retention over meaningful time periods.
Stop Task After-Effects
Authors: Enticott Peter G. , Bradshaw John L. , Bellgrove Mark A. , Upton Daniel J. , Ogloff James R.P.
Published: May 2009

In the stop task, response time to the go signal is increased when the immediately preceding trial involves the presentation of a stop signal. A recent explanation suggests that these “after-effects” are due to mechanisms that occur prior to the completion of response selection processes, but it is possible that they instead may reflect a slowed motor response (i.e., deliberate slowing after response selection). The participants completed a novel stop task that allows a differentiation between the time taken to prepare a movement (which incorporates response selection processes) and the time taken to execute a movement (i.e., speed of motor response). If mechanisms underlying stop task after-effects occur prior to the completion of response selection processes, then slowing should only occur during movement preparation. Movement preparation and execution time during go trials were analysed according to the characteristics of the preceding trial. Slowing after a stop trial was found during movement preparation time (regardless of inhibition success on that stop trial), and it further increased during this period when the primary task stimulus was repeated. There was also evidence for general after-effects during movement execution time, but no effect of repetition. These findings support the current theoretical accounts that suggest that repetition-based stop task after-effects are attributable to a mechanism that occurs prior to the completion of response selection processes, and also indicate a possible switch to a more conservative response set (as in signal detection theory terms) that results in deliberate slowing of movement.
Navon Letters Affect Face Learning and Face Retrieval
Authors: Lewis Michael B. , Mills Claire , Hills Peter J. , Weston Nicola
Published: May 2009

Identifying the local letters of a Navon letter (a large letter made up of smaller different letters) prior to recognition causes impairment in accuracy, while identifying the global letters of a Navon letter causes an enhancement in recognition accuracy ( Macrae & Lewis, 2002 ). This effect may result from a transfer-inappropriate processing shift (TIPS) ( Schooler, 2002 ). The present experiment extends research on the underlying mechanism of this effect by exploring this Navon effect on face learning as well as face recognition. The results of the two experiments revealed that when the Navon task used at retrieval was the same as that used at encoding then the performance accuracy is enhanced, whereas when the processing operations mismatch at retrieval and at encoding, this impairs recognition accuracy. These results provide support for the TIPS explanation of the Navon effect.
The Brief Implicit Association Test
Authors: Sriram N. , Greenwald Anthony G.
Published: May 2009

The Brief Implicit Association Test (BIAT) consists of two blocks of trials with the same four categories and stimulus-response mappings as the standard IAT, but with 1/3 the number of trials. Unlike the standard IAT, the BIAT focuses the subject on just two of each block’s four categories. Experiments 1 and 2 demonstrated that attitude BIATs had satisfactory validity when good (but not bad) was a focal category, and that identity IATs had satisfactory validity when self (but not other) was a focal category. Experiment 2 also showed that a good-focal attitude BIAT and a self-focal identity BIAT were psychometrically similar to standard IAT measures of the same constructs. Experiment 3 presented each of six BIATs twice, showing that procedural variables had no more than minor influences on the resulting implicit measures. Experiment 4 further demonstrated successful use of the BIAT to measure implicit stereotypes.
Adjoint models of mantle convection with seismic, plate motion, and stratigraphic constraints: North America since the Late Cretaceous
Authors: Spasojevic Sonja , Liu Lijun , Gurnis Michael
Published: May 2009

We apply adjoint models of mantle convection to North America since the Late Cretaceous. The present‐day mantle structure is constrained by seismic tomography and the time‐dependent evolution by plate motions and stratigraphic data (paleoshorelines, borehole tectonic subsidence, and sediment isopachs). We infer values of average upper and lower mantle viscosities, provide a synthesis of North American vertical motions (relative sea level) from the Late Cretaceous to the present, and reconstruct the geometry of the Farallon slab back to the Late Cretaceous. In order to fit Late Cretaceous marine inundation and borehole subsidence, the adjoint model requires a viscosity ratio across 660 km discontinuity of 15:1 (reference viscosity of 1021 Pa s), which is consistent with values previously inferred by postglacial rebound studies. The dynamic topography associated with subduction of the Farallon slab is localized in western North America over Late Cretaceous, representing the primary factor controlling the widespread flooding. The east coast of the United States is not stable; rather, it has been experiencing continuous dynamic subsidence over the Cenozoic, coincident with an overall eustatic fall, explaining a discrepancy between sea level derived from the New Jersey coastal plain and global curves. The east coast subsidence further constrains the mantle viscosity structure and requires an uppermost mantle viscosity of 1020 Pa s. Imposed constraints require that the Farallon slab was flat lying during Late Cretaceous, with an extensive zone of shallow dipping Farallon subduction extending beyond the flat‐lying slab farther east and north by up to 1000 km than previously suggested.
Global maps of the CRUST 2.0 crustal components stripped gravity disturbances
Authors: Tenzer Robert , Hamayun K. , Vajda Peter
Published: May 2009

We use the CRUST 2.0 crustal model and the EGM08 geopotential model to compile global maps of the gravity disturbances corrected for the gravitational effects (attractions) of the topography and of the density contrasts of the oceans, sediments, ice, and the remaining crust down to the Moho discontinuity. Techniques for a spherical harmonic analysis of the gravity field are used to compute both the gravity disturbances and the topographic and bathymetric corrections with a spectral resolution complete to degree 180 of the spherical harmonics. The ice stripping correction is computed with a spectral resolution complete to degree 90. The sediment and consolidated crust stripping corrections are computed in spatial form by forward modeling their respective attractions. All data are evaluated on a 1 × 1 arc degree grid at the Earth's surface and provided in Data Sets S1–S5 in the auxiliary material for the scientific community for use in global geophysical studies. The complete crust‐stripped gravity disturbances (globally having a range of 1050 mGal) contain the gravitational signal coming dominantly from the global mantle lithosphere (upper mantle) morphology and density composition and partially from the sublithospheric density heterogeneities. Large errors are expected because of uncertainties of the CRUST 2.0 model (i.e., deviations of the CRUST 2.0 model density from the real Earth's crustal density heterogeneities and the Moho relief uncertainties).
Landscape structure control on soil CO2 efflux variability in complex terrain: Scaling from point observations to watershed scale fluxes
Authors: Riveros‐Iregui Diego A. , McGlynn Brian L.
Published: May 2009

We investigated the spatial and temporal variability of soil CO2 efflux across 62 sites of a 393‐ha complex watershed of the northern Rocky Mountains. Growing season (83 day) cumulative soil CO2 efflux varied from ∼300 to ∼2000 g CO2 m−2, depending upon landscape position, with a median of 879.8 g CO2 m−2. Our findings revealed that highest soil CO2 efflux rates were observed in areas with persistently high soil moisture (riparian meadows), whereas lower soil CO2 efflux rates were observed on forested uplands (98% of watershed area). Furthermore, upslope accumulated area (UAA), a surrogate measure of the lateral redistribution of soil water, was positively correlated with seasonal soil CO2 efflux at all upland sites, increasing in explanatory power when sites were separated by the major aspects of the watershed (SE/NW). We used the UAA–soil CO2 efflux relationship to upscale measured CO2 efflux to the entire watershed and found watershed‐scale soil CO2 efflux of 799.45 ± 151.1 g CO2 m−2 over 83 days. These estimates compared well with independent eddy covariance estimates of nighttime ecosystem respiration measured over the forest. We applied this empirical model to three synthetic watersheds with progressively reduced complexity and found that seasonal estimates of soil CO2 efflux increased by 50, 58, and 98%, demonstrating the importance of landscape structure in controlling CO2 efflux magnitude. Our study represents an empirical quantification of seasonal watershed‐scale soil CO2 efflux and demonstrates that UAA (i.e., landscape position) and drainage patterns are important controls on the spatial organization of large‐scale (∼km2) soil CO2 efflux, particularly in semiarid, subalpine ecosystems.
A relationship between rain radar reflectivity and height elevation variance of ringwaves due to the impact of rain on the sea surface
Authors: Sobieski P. , Craeye C. , Bliven L. F.
Published: May 2009

Raindrops impacting the rough sea modify its surface and its backscattering coefficient. This roughness change essentially depends on the rain content in very large drops, which is highly variable from one drop size distribution model to another. However, it has been observed that the radar reflectivity of raindrops has a drop size dependence very similar to that of the ringwaves induced by rain on the surface. From a numerical analysis on various drop size distributions, rain rates, and frequencies from 3 to 35 GHz, a relationship between the sea surface elevation variance of ringwaves resulting from drop impact and the rain radar reflectivity Z is established. It is found to be weakly dependent on the raindrop size distribution model. This link is expected to lead to better estimates of the surface roughness, and in turn, via electromagnetic scattering models, it could improve algorithms for near nadir rain radar retrieval.
Characteristics of counter‐Sq SFE (SFE*) at the dip equator CPMN stations
Authors: Yamazaki Y. , Yumoto K. , Yoshikawa A. , Watari S. , Utada H.
Published: May 2009

The solar flare effect (SFE) at dip equatorial latitudes sometimes shows the counter‐Sq variation around local noon. In this paper, we refer to this type of SFE as SFE*. Observations obtained by the Circum‐pan Pacific Magnetometer Network (CPMN) reveal some previously unknown characteristics of SFE*. Some of these features are the following: (1) the counter‐Sq SFE variation is observed in limited longitude (local time) and latitude sectors (i.e., LT ≈ 1030–1300, ∣DipLat.∣ ≲ 1.5°), (2) outside this limited region, the amplitude of SFE(H) and preflare Sq(H) have a linear relationship, and (3) SFE* is observed during the significant depression of the horizontal magnetic field at dip equatorial latitudes, which indicates the presence of westward electric fields whose origin remains to be understood.
Nitrogen regulates chitinase gene expression in a marine bacterium
Authors: Delpin Marina W , Goodman Amanda E
Published: May 2009

Ammonium concentration and nitrogen source regulate promoter activity and use for the transcription of chiA, the major chitinase gene of Pseudoalteromonas sp. S91 and S91CX, an S91 transposon lacZ fusion mutant. The activity of chiA was quantified by β-galactosidase assay of S91CX cultures containing different ammonium concentrations (NH4+; 0, 9.5 or 191 mm) and with different nitrogen sources (N-acetylglucosamine (GlcNAc) or glutamate (glt)). S91 chiA expression was found to depend on both the NH4+ concentration and source of nitrogen in marine minimal medium (MMM). Pseudoalteromonas sp. S91 and S91CX can use either GlcNAc or glt as a sole source of carbon in MMM containing a standard concentration of 9.5 mm NH4+. Adding excess NH4+, 20 times the standard concentration, to MMM significantly reduced chiA activity below that found in the presence of either GlcNAc or glt. When no NH4+ was added to MMM, S91CX was also able to use either GlcNAc or glt as a source of nitrogen; under these conditions chiA activity was significantly increased. Under all conditions tested, GlcNAc induced chiA activity significantly more than glt. Regulation of bacterial chitinases by nitrogen has not been previously reported. Transcriptional start point analysis of S91 chiA, using 5′RACE (ligation-anchored PCR), showed that during growth in MMM supplemented with (1) maltose (solely a carbon source for S91), chiA transcription occurred from only one putative σ70-dependent promoter; (2) the chitin monomer GlcNAc, transcription initiated from two putative σ54-dependent promoters and (3) glt, transcription initiated from all three putative promoters.
TMS, phosphenes and visual mental imagery: A mini-review and a theoretical framework
Authors: Bokkon Istvan , Kirby Matthew , D'Angiulli Amedeo
Published: May 2009

We reviewed the existing research linking visual mental imagery and phosphenes induced by TMS. We examined and contrasted conditions (and parameters) under which intensity and amplitude of TMS application at various cortical sites along the ventral and dorsal visual pathways: 1) induces the experience of visual images during perception and mental imagery, 2) interferes with or facilitates perception and/or imagery in concurrent and dual task conditions, 3) correlates with self-reports such as vividness ratings, and 4) reduces or has other selective effects on phosphene threshold in concomitance with perception and imagery. We propose an interpretation of the results of this mini-review within a new biophysical framework for visual mental imagery based on Bokkon’s redox molecular model of explicit optical coding of visual information in early visual areas (V1) and the propagation of conscious visual content at other levels in the stream of visual processing and in other parts of the brain.
Literature Triage and Indexing in the Mouse Genome Informatics (MGI) Group
Authors: Babiuk Randal , Begley Dale , Bello Susan , Bradt Dirck , Burkart Donna , Dene Howard , Diehl Alexander , Drabkin Harold , Finger Jacqueline , Hayamizu Terry , Hill David , Knowlton Michelle , Krupke Debra , Lu Ira , Maltais Lois , McAndrews-Hill Monica , Meehan Terrence , Ni Li , Onda Hiroaki , Sitnikov Dmitry , Smith Constance , Smith Cynthia , Tomczuk Monika
Published: May 2009

The Mouse Genome Informatics (MGI; "http://www.informatics.jax.org":http://www.informatics.jax.org) group is comprised of several collaborating projects including the Mouse Genome Database (MGD) Project, the Gene Expression Database (GXD) Project, the Mouse Tumor Biology (MTB) Database Project, and the Gene Ontology (GO) Project. Literature identification and collection is performed cooperatively amongst the groups.In recent years many institutional libraries have transitioned from a focus largely on print holdings to one of electronic access to journals. This change has necessitated adaptation on the part of the MGI curatorial group. Whereas the majority of journals covered by the group used to be surveyed in paper form, those journals are now surveyed electronically. Approximately 160 journals have been identified as those most relevant to the various database groups. Each curator in the group has the responsibility of scanning several journals for articles relevant to any of the database projects. Articles chosen via this process are marked as to their potential significance for various projects. Each article is catalogued in a Master Bibliography section of the MGI database system and annotated to the database sections for which it has been identified as relevant. A secondary triage process allows curators from each group to scan the chosen articles and mark ones desired for their project if such annotation has been missed on the initial scan.Once articles have been identified for each database project a variety of processes are implemented to further categorize and index data from those articles. For example, the Alleles and Phenotype section of the MGD database indexes each article marked for MGD and in this indexing process they identify each mouse gene and allele examined in the article. The GXD database indexing process has a different focus. In this case articles are indexed with regard to the stage of development used in the study as well as the assay technique used. In each case the indexing gives an overview of the data held in the article and assists in the more extensive curation performed in the following step of the curation process. Indexing also provides each group with valuable information used to prioritize and streamline the overall curation process.The MGI projects are supported by NHGRI grants HG000330, HG00273, and HG003622, NICHD grant HD033745, and NCI grant CA089713.
Studying Biocuration Workflows
Authors: Burns Gully , Krallinger Martin , Cohen Kevin , Wu Cathy , Hirschman Lynette
Published: May 2009

As the first phase of a knowledge engineering study of biocuration workflows, we performed a preliminary task-modeling exercise on seven separate bioinformatics systems. This involved constructing UML activity diagrams from detailed interviews with curators in order to understand the organization of the process the biocurators used to populate their system. The objective of this work was to identify common patterns within the workflows where we might apply text mining methods to accelerate curation. We compiled a number of workflows in a common format but were largely unable to consolidate these structures into a formal structure that facilitated comparison across workflows. At present, more work is needed to perform this task.
Association of Two CETP Polymorphisms With HDL Levels in the Chinese Obese Population
Authors: Ruan Xiaoyang , Ma Lina , Wang Shuyu , Lindpaintner Klaus , Liu Xiangjun , Wang Binbin , Peng Zuoqi , Ma Xu , Cheng Maosheng , Zhang Jinghai , Liu Lisheng , Wang Xingyu
Published: May 2009

The association of two cholesterol ester transfer protein (CETP) polymorphisms, D442G and TAQIB (B1→B2), with high‐density lipoprotein (HDL) levels in 932 Chinese obese individuals (BMI ≥ 27) was investigated in comparison with normal controls (BMI ≤ 24). Independent association was demonstrated for TAQIB minor allele B2 and CETP442 minor allele G with elevated HDL levels. The CETP D442G polymorphism was associated with a much greater increase in HDL levels in subjects with BMI exceeding 27 kg/m2 (+5.42 mg/dl, P = 0.0007) compared to normal controls (+1.97 mg/dl, P = 0.275), and the increase in HDL reached the highest level among subjects with BMI exceeding 30 kg/m2 (+6.80 mg/dl, P = 0.016). TAQIB showed significant association with HDL levels only in normal BMI subgroup (P = 0.0017). TAQIB significantly interacted with serum triglyceride (TG) on modulating HDL levels (P = 0.027). The TAQIB–TG interaction effect remained marginally significant after controlling for BMI (P = 0.057). We conclude that D442G polymorphism is associated with more HDL elevation in obesity. TAQIB interacts with serum TG on modulating HDL levels, and the interaction is partly independent of BMI.
Genome‐wide Linkage Analysis of Multiple Metabolic Factors: Evidence of Genetic Heterogeneity
Authors: Cheng Ching‐Yu , Lee Kristine E. , Duggal Priya , Moore Emily L. , Wilson Alexander F. , Klein Ronald , Bailey‐Wilson Joan E. , Klein Barbara E.K.
Published: May 2009

The metabolic syndrome is a highly complex disease and has become one of the major public‐health challenges worldwide. We sought to identify genetic loci with potential influence on multiple metabolic factors in a white population in Beaver Dam, Wisconsin, and to explore the possibility of genetic heterogeneity by family history of diabetes (FHD). Three metabolic factors were generated using principal‐component factor analysis, and they represented: (i) glycemia, (ii) blood pressure, and (iii) combined (BMI, high‐density lipoprotein (HDL) cholesterol, and serum uric acid) factors. Multipoint model‐free linkage analysis of these factors with 385 microsatellite markers was performed on 1,055 sib‐pairs, using Haseman–Elston regression. Genome‐wide suggestive evidence of linkage was found at 30 cM on chromosome 22q (empirical P (Pe) = 0.0002) for the glycemia factor, at 188–191 cM on chromosome 1q (Pe = 0.0007) for the blood pressure factor, and at 82 cM on chromosome 17q (Pe = 0.0007) for the combined factor. Subset analyses of the families by FHD showed evidence of genetic heterogeneity, with divergent linkage signals in the subsets on at least four chromosomes. We found evidence of genetic heterogeneity by FHD for the three metabolic factors. The results also confirmed findings of previous studies that mapped components of the metabolic syndrome to a chromosome 1q region.
Diet‐induced Changes in Intra‐abdominal Adipose Tissue and CVD Risk in American Women
Authors: Katsoulis Konstantina , Blaudeau Tami E. , Roy Jane P. , Hunter Gary R.
Published: May 2009

The aim of the study was to determine what effect weight loss had on intra‐abdominal adipose tissue (IAAT) and cardiovascular disease (CVD) risk in 135 premenopausal overweight African‐American (AA) and European‐American (EA) women matched for BMI. Blood lipids, systolic blood pressure (SBP), diastolic BP (DBP), and IAAT (computed tomography determined) were examined prior to and after an 800 kcal/day diet producing 12 kg‐weight loss. Significant decreases in IAAT (∼38%), total cholesterol (TC; 3%), low‐density lipoproteins (LDLs: 6%), triglycerides (TGs: 27%), cholesterol/high‐density lipoprotein ratio (C/HDL ratio: 18%), SBP (3%), and DBP (3%) occurred while HDL increased (16%), following weight loss and 1 month energy balance. Significant interactions between time and race showed that AA women decreased TG and increased HDL proportionately less than EA women. After adjusting for ΔIAAT, none of the CVD variables significantly changed after weight loss with the exception of HDL and C/HDL ratio. After adjusting for ΔLF (leg fat), ΔTC, ΔTG, ΔLDL, and ΔC/HDL ratio were significantly different. Multiple regression showed that independent of each other, ΔIAAT was significantly and positively related to ΔTC (adjusted β = 0.24) and ΔTG (adjusted β = 0.47), and ΔLF was negatively related to ΔTC (adjusted β = −0.19) and ΔTG (adjusted β = −0.18). Overweight and premenopausal AA and EA women benefitted from weight loss by decreasing IAAT and improving CVD risk. The changes in IAAT were significantly related to blood lipids, but loss of LF seems to be related to reduced improvement in TC and TG. Based on these results, interventions should focus on changes on IAAT.
Serum Leptin Levels in Obese Males During Over‐ and Underfeeding
Authors: Cooper Jamie A. , Polonsky Kenneth S. , Schoeller Dale A.
Published: May 2009

Leptin levels in lean adults vary in response to short‐term alterations in energy balance. We tested whether leptin responded to short‐term changes in energy balance in obese males in a similar manner to lean individuals. We enrolled eight obese, healthy males in a 12‐day study composed of four consecutive dietary treatment periods of 3 days each: baseline eucaloric feeding followed by randomized crossover periods of overfeeding (130% of total energy expenditure (TEE)) or underfeeding (70% of TEE), separated by a eucaloric (100% of TEE) washout period. We measured TEE with doubly labeled water prior to baseline. Leptin levels were measured throughout the third day of each treatment and 24‐h weighted averaged were calculated. Subjects' ad libitum intake during a breakfast buffet following each treatment period was recorded. During underfeeding, leptin levels decreased by 21 ± 6% (P < 0.01) from the previous eucaloric period. During overfeeding, leptin levels increased by 25 ± 11% (P < 0.01) when subjects were underfed first, but did not increase (5 ± 8%, nonsignificant (n.s.)) when subjects were overfed first. Changes in ad libitum intake from baseline were calculated for each subject after over‐, under‐, and eucaloric feeding and did not to correlate with the changes in mesor leptin levels from baseline (R2 = 0.006, n.s). Leptin levels in obese males were acutely responsive to negative energy balance, but not to positive energy balance unless subjects were previously underfed. Consequently, leptin levels in obese males do not respond to changes in energy intake in a manner that would protect against weight gain.
Antiobesity Effects of yerba maté Extract (Ilex paraguariensis) in High‐fat Diet–induced Obese Mice
Authors: Arçari Demétrius P. , Bartchewsky Waldemar , dos Santos Tanila W. , Oliveira Karim A. , Funck Alexandre , Pedrazzoli José , de Souza Marina F.F. , Saad Mario J. , Bastos Deborah H.M. , Gambero Alessandra , Carvalho Patricia de O. , Ribeiro Marcelo L.
Published: May 2009

Because the potential of yerba maté (Ilex paraguariensis) has been suggested in the management of obesity, the aim of the present study was to evaluate the effects of yerba maté extract on weight loss, obesity‐related biochemical parameters, and the regulation of adipose tissue gene expression in high‐fat diet–induced obesity in mice. Thirty animals were randomly assigned to three groups. The mice were introduced to standard or high‐fat diets. After 12 weeks on a high‐fat diet, mice were randomly assigned according to the treatment (water or yerba maté extract 1.0 g/kg). After treatment intervention, plasma concentrations of total cholesterol, high‐density lipoprotein cholesterol, triglyceride, low‐density lipoprotein (LDL) cholesterol, and glucose were evaluated. Adipose tissue was examined to determine the mRNA levels of several genes such as tumor necrosis factor‐α (TNF‐α), leptin, interleukin‐6 (IL‐6), C‐C motif chemokine ligand‐2 (CCL2), CCL receptor‐2 (CCR2), angiotensinogen, plasminogen activator inhibitor‐1 (PAI‐1), adiponectin, resistin, peroxisome proliferator‐activated receptor‐γ2 (PPAR‐γ2), uncoupling protein‐1 (UCP1), and PPAR‐γ coactivator‐1α (PGC‐1α). The F4/80 levels were determined by immunoblotting. We found that obese mice treated with yerba maté exhibited marked attenuation of weight gain, adiposity, a decrease in epididymal fat‐pad weight, and restoration of the serum levels of cholesterol, triglycerides, LDL cholesterol, and glucose. The gene and protein expression levels were directly regulated by the high‐fat diet. After treatment with yerba maté extract, we observed a recovery of the expression levels. In conclusion, our data show that yerba maté extract has potent antiobesity activity in vivo. Additionally, we observed that the treatment had a modulatory effect on the expression of several genes related to obesity.
Lateral organization of membrane proteins: tetraspanins spin their web
Authors: Charrin Stéphanie , le Naour François , Silvie Olivier , Milhiet Pierre-Emmanuel , Boucheix Claude , Rubinstein Eric
Published: May 2009

Despite high expression levels at the plasma membrane or in intracellular vesicles, tetraspanins remain among the most mysterious transmembrane molecules 20 years after their discovery. Several genetic studies in mammals and invertebrates have demonstrated key physiological roles for some of these tetraspanins, in particular in the immune response, sperm–egg fusion, photoreceptor function and the normal function of certain epithelia. Other studies have highlighted their ability to modulate cell migration and metastasis formation. Their role in the propagation of infectious agents has drawn recent attention, with evidence for HIV budding in tetraspanin-enriched plasma membrane domains. Infection of hepatocytic cells by two major pathogens, the hepatitis C virus and the malaria parasite, also requires the tetraspanin CD81. The function of tetraspanins is thought to be linked to their ability to associate with one another and a wealth of other integral proteins, thereby building up an interacting network or ‘tetraspanin web’. On the basis of the biochemical dissection of the tetraspanin web and recent analysis of the dynamics of some of its constituents, we propose that tetraspanins tightly regulate transient interactions between a variety of molecules and as such favour the efficient assembly of specialized structures upon proper stimulation.
How essential is cholesterol?
Authors: Stevenson Julian , Brown Andrew J.
Published: May 2009

Cholesterol is an apparently indispensable lipid for numerous processes required for cell proliferation. Levels of this molecule are primarily regulated at the transcriptional level by the SREBPs (sterol-regulatory-element-binding proteins) and LXR (liver X receptor). In this issue of the Biochemical Journal, Rodríguez-Acebes et al. show that a cholesterol precursor, desmosterol, can support cell proliferation in the absence of cholesterol in a murine macrophage-like model (J774-D cells). These cells are defective in DHCR24 (sterol-Δ24-reductase, or 3β-hydroxysterol Δ24-reductase), leading to desmosterol accumulation, and yet sterol homoeostasis appears to be normal with respect to SREBP processing and LXR activation. Other potentially cholesterol-dependent processes which were not the focus of this study are briefly discussed, such as lipid-raft-dependent cell signalling.
Affecting Life-Long Habits of School-Age Musicians
Authors: Palmer Catherine V.
Published: May 2009

The Musicians' Hearing Center at the University of Pittsburgh was established in 2003 with the purpose of impacting the Western Pennsylvania community of musicians and other noise-exposed individuals. The goal is to provide education empowering individuals of all ages to make choices regarding their noise exposures and to provide hearing protection as part of the overall solution when indicated. Encouraging life-long healthy hearing habits is at the core of the center’s mission. The recent data from the National Institutes of Health (NIH) indicating that school-age children are the fastest growing population of noise-exposed individuals suffering permanent hearing loss motivated the center to create a focus area on school-age children. After examining the likelihood of affecting various groups of children, the center decided to address this issue by targeting the life-long habits of school-age instrumental students and their teachers through an education and hearing protection program. This is a group of individuals who are known to have potentially damaging levels of sound exposure through a school activity and a group of individuals who are using their hearing for a specific purpose (i.e., making music). The program and various aspects of promoting and maintaining the program are described in the following article.