bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural investigation of high‐transmittance aluminum oxynitride films deposited by ion beam sputtering
Authors: Wang Paul W. , Hsu Jin‐Cherng , Lin Yung‐Hsin , Chen Huang‐Lu
Published: October 2010

Aluminum oxynitride films were deposited by ion beam sputtering technique at room temperature. The optical properties and morphologies of the aluminum oxynitride films were studied and reported previously. It was found that the optical properties are closely related to the O contents in the films. In this study, the structures of the films were investigated by X‐ray diffractometer and XPS. Three oxidation states of N1s in oxynitride films, N+, N2+ and N3+, were clearly deduced from N1s spectra in the amorphous films fabricated under various oxygen partial pressures (PO2). To our knowledge, three oxidation states of N1s have not been simultaneously observed and reported in the aluminum oxynitride films previously. Corresponding bonding variations in Al2p and O1s spectra indicated more oxygen in oxynitride in the film as PO2 increases. Three aluminum oxynitride networks, AlO2N, AlO2.5N and AlO3N were deduced. Optical properties of aluminum oxynitride films resemble those of AlN and Al2O3 films when PO2 is low and high during the deposition. The refractive indices and extinction coefficients of the aluminum oxynitride films can be adjusted by using proper PO2 during the film depositions. Copyright © 2010 John Wiley & Sons, Ltd.
Testing Hardy–Weinberg equilibrium: An objective Bayesian analysis
Authors: Consonni Guido , Moreno El�as , Venturini Sergio
Published: October 2010

We analyze the general (multiallelic) Hardy–Weinberg equilibrium problem from an objective Bayesian testing standpoint. We argue that for small or moderate sample sizes the answer is rather sensitive to the prior chosen, and this suggests to carry out a sensitivity analysis with respect to the prior. This goal is achieved through the identification of a class of priors specifically designed for this testing problem. In this paper, we consider the class of intrinsic priors under the full model, indexed by a tuning quantity, the training sample size. These priors are objective, satisfy Savage's continuity condition and have proved to behave extremely well for many statistical testing problems. We compute the posterior probability of the Hardy–Weinberg equilibrium model for the class of intrinsic priors, assess robustness over the range of plausible answers, as well as stability of the decision in favor of either hypothesis. Copyright © 2010 John Wiley & Sons, Ltd.
Code Bad Smells: a review of current knowledge
Authors: Zhang Min , Hall Tracy , Baddoo Nathan
Published: October 2010

Fowler et al. identified 22 Code Bad Smells to direct the effective refactoring of code. These are increasingly being taken up by software engineers. However, the empirical basis of using Code Bad Smells to direct refactoring and to address ‘trouble’ in code is not clear, i.e., we do not know whether using Code Bad Smells to target code improvement is effective. This paper aims to identify what is currently known about Code Bad Smells. We have performed a systematic literature review of 319 papers published since Fowler et al. identified Code Bad Smells (2000 to June 2009). We analysed in detail 39 of the most relevant papers. Our findings indicate that Duplicated Code receives most research attention, whereas some Code Bad Smells, e.g., Message Chains, receive little. This suggests that our knowledge of some Code Bad Smells remains insufficient. Our findings also show that very few studies report on the impact of using Code Bad Smells, with most studies instead focused on developing tools and methods to automatically detect Code Bad Smells. This indicates an important gap in the current knowledge of Code Bad Smells. Overall this review suggests that there is little evidence currently available to justify using Code Bad Smells. Copyright © 2010 John Wiley & Sons, Ltd.
Nestin Is Required for the Proper Self-Renewal of Neural Stem Cells
Authors: Park Donghyun , Xiang Andy Peng , Mao Frank Fuxiang , Zhang Li , Di Chun-Guang , Liu Xiao-Mei , Shao Yuan , Ma Bao-Feng , Lee Jae-Hyun , Ha Kwon-Soo , Walton Noah , Lahn Bruce T.
Published: October 2010

The intermediate filament protein, nestin, is a widely employed marker of multipotent neural stem cells (NSCs). Recent in vitro studies have implicated nestin in a number of cellular processes, but there is no data yet on its in vivo function. Here, we report the construction and functional characterization of Nestin knockout mice. We found that these mice show embryonic lethality, with neuroepithelium of the developing neural tube exhibiting significantly fewer NSCs and much higher levels of apoptosis. Consistent with this in vivo observation, NSC cultures derived from knockout embryos show dramatically reduced self-renewal ability that is associated with elevated apoptosis but no overt defects in cell proliferation or differentiation. Unexpectedly, nestin deficiency has no detectable effect on the integrity of the cytoskeleton. Furthermore, the knockout of Vimentin, which abolishes nestin's ability to polymerize into intermediate filaments in NSCs, does not lead to any apoptotic phenotype. These data demonstrate that nestin is important for the proper survival and self-renewal of NSCs, and that this function is surprisingly uncoupled from nestin's structural involvement in the cytoskeleton.
Preliminary experience with the combined use of recombinant bone morphogenetic protein and bisphosphonates in the treatment of congenital pseudarthrosis of the tibia
Authors: Birke Oliver , Schindeler Aaron , Ramachandran Manoj , Cowell Chris T. , Munns Craig F. , Bellemore Michael , Little David G.
Published: October 2010

Purpose

Congenital pseudarthrosis of the tibia (CPT) is a rare but serious disorder in children. No single approach has clearly emerged as superior in terms of operative procedure, fixation, optimal time for surgery or adjunctive pharmaceutical intervention. CPT is frequently associated with neurofibromatosis type 1 (NF1), a condition featuring deficient bone anabolism and excessive catabolism. We have therefore combined the use of bone morphogenetic proteins (BMP) with bisphosphonates (BP) as an adjunct to surgical intervention.

Methods

Between 2002 and 2008 we administered BMP-7 (OP-1) at the time of surgery followed by BP (pamidronate or zoledronic acid) in eight Crawford type IV CPT cases in seven patients (six with a confirmed diagnosis of NF1) with a median age of 7 years (range 2 years 11 months to 12 years) at surgery.

Results

In six of eight cases, this approach led to primary healing after a mean of 5.5 months (range 4–7 months). One of these cases represented 17 months after primary healing of a proximal CPT with a new further distal fracture that required multiple operations to finally unite at 19 months. The two remaining cases ultimately reached union after multiple operations at 14 and 30 months, respectively, but required recent treatment for refractures.

Conclusion

Based on these clinical data (primary healing in 6/8 cases) and prior pre-clinical findings, we propose that BP therapy may be helpful in preserving the BMP-induced bone formation by inhibiting the osteoclastic bone loss. Key factors to achieve union in CPT include sufficient fixation, meticulous resection of the dysplastic tissue and the establishment of a net anabolic environment for bone healing. Whether our biological concept of balancing the anabolic and catabolic responses with BMP and BP improves healing rates in the complex treatment of NF1 CPT remains uncertain and warrants larger prospective multicentre trials.
Origins and Rationale for the African American Economic Summit
Authors: Jackson Fatimah L. C.
Published: October 2010

African American economists and related social scientists have an indispensible role to play in providing culturally-informed insight into the role of economic disadvantage in the current crisis in African American health, incarceration, wealth, housing, and education. The African American Economic Summit co-sponsored by the Institute of African American Research at the University of North Carolina at Chapel Hill and the Research Network on Racial and Ethnic Inequality at Duke University brought together over 30 experts who provided insights into the roots of the current economic status of African Americans, its broad impact on the quality of African American life, and possible remedial solutions. This volume reports on the deliberations in this first Summit.
A computer-assisted depression intervention in primary care
Authors: Levin W. , Campbell D. R. , McGovern K. B. , Gau J. M. , Kosty D. B. , Seeley J. R. , Lewinsohn P. M.
Published: October 2010

Background

The clinical benefit for depression of an interactive computer-assisted cognitive-behavioral program on CD-ROM, the Wellness Workshop (WW), was evaluated in a randomized controlled trial.

Method

A total of 191 individuals referred by primary-care physicians were randomly assigned to a control group, where physician-directed treatment as usual (TAU) was provided, or to a treatment group, where TAU was supplemented with the WW CD-ROM, delivered by mail (WW+TAU). Data were collected at baseline, at 6 weeks' post-intervention, and at a 6-month follow-up assessment. Participants were given a strong incentive by a reimbursement of $75 for completion of each assessment. Measures included symptom ratings obtained via structured clinical diagnostic interviews, as well as a battery of self-report questionnaires on symptoms specifically targeted by the intervention.

Results

Analysis of results demonstrated evidence for skill acquisition for improving dysfunctional thinking and reducing anxiety. Among those who met diagnostic criteria for depression, WW+TAU participants were three times more likely to remit at 6 weeks' post-test than TAU participants.

Conclusions

The evidence supports the conclusion that the WW intervention added benefit to traditional care for depression. No placebo comparison group was included and the WW+TAU participants received slightly more attention (a supportive telephone contact, ⩽5 min from a psychologist 2 weeks after receiving the program). Overall, the findings add support to the accumulating evidence for the potential clinical benefit of computer-assisted behavioral health interventions.
Effects of education, literacy, and dementia on the Clock Drawing Test performance
Authors: KIM HOYOUNG , CHEY JEANYUNG
Published: October 2010

The Clock Drawing Test (CDT) has been recognized as an effective tool for dementia detection. This study investigated the clock drawing performance of 240 non-demented elderly Korean people with a wide-range of educational levels and 28 patients with mild dementia of the Alzheimer’s type (DAT). We examined the effects of demographic factors, including education, and established norms for the elderly population. We found that the educational attainment and literacy status of older people influenced performance on the CDT significantly (p < .001). Furthermore, qualitative error analysis revealed that normal participants with low educational background committed errors similar to errors of the DAT patients. The DAT patients performed significantly worse than the non-demented participants in the CDT Total score (p < .001). However, the CDT has better criterion validity in participants with more than 6 years of education. In conclusion, the CDT performance in older people who are either illiterate or with 6 or less years of education should be interpreted with caution. Conceptual errors in the CDT can be the result of not only dementia but also lack of education. (JINS, 2010, 16, 1138–1146.)
Kardiale Niedrigdosis-Computertomographie
Authors: Karlo  , Stinn  , Leschka  , Alkadhi  , Stolzmann
Published: October 2010

Die kardiale Computertomographie hat sich zu einer sehr robusten und genauen Methode zur kardialen Abklärung entwickelt, was jedoch auch zu einer zunehmenden Strahlenexposition führte. In den letzten Jahren wurden zahlreiche technische Entwicklungen und Algorithmen entwickelt, um die Strahlendosis der kardialen CT zu reduzieren. Die wichtigsten Massnahmen zur Strahlendosisreduktion sollen in diesem Artikel näher erläutert werden. Dazu gehören die korrekte Indikationsstellung, verschiedene EKG-Synchronisierungstechniken, die Reduktion der Röhrenspannung und Untersuchungen mit hohem Tischvorschub (sog. Pitch).
Akute Nackenschmerzen bei einem älteren Patienten
Authors: Pfeiffer Zehnder
Published: October 2010

Fallbeschreibung eines 85-jährigen Patienten mit akuten nächtlich betonten subokzipitalen Nackenschmerzen, hochgradig eingeschränkter HWS-Beweglichkeit und erhöhten Entzündungsparametern. Die Symptome und der MRT-Befund täuschten initial eine infektiöse Spondylitis mit Weichteilabszessbildung im Densbereich vor. Nach fehlendem Ansprechen auf eine intravenöse Antibiotikatherapie wurde eine Computertomographie der HWS durchgeführt, wobei sich typische Verkalkungen im Ligamentum transversum atlantis zeigten und zur Diagnose eines Crowned Dens-Syndroms, der hochzervikalen Manifestation der CPPD-Kristallablagerungskrankheit führten. Bei ungenügendem Ansprechen auf NSAR konnte nach peroraler Steroidgabe eine rasche Symptomfreiheit erreicht werden.
A coupled stochastic space‐time intermittent random cascade model for rainfall downscaling
Authors: Kang Boosik , Ramírez Jorge A.
Published: October 2010

Analysis of Next Generation Weather Radar rainfall data indicates that for the central United States, rainfall exhibits a composite behavior with respect to its spatial and temporal scaling characteristics. Our data analysis shows that rainfall fluctuations at spatial scales smaller than a reference scale exhibit self‐similarity and that at scales larger than the reference scale, rainfall fluctuations are scale dependent. Accordingly, we present a new methodology for downscaling large‐scale rainfall consistent with this composite character of rainfall variability. The new downscaling model is a composite of a stochastic space‐time submodel that preserves the spatial and temporal dependency characteristics at scales larger than the reference scale and an intermittent random cascade submodel that preserves the statistical self‐similarity and spatial intermittency at scales smaller than the reference scale. The new model is applied to downscale summer daily rainfall for the central United States from a scale of 256 km to a scale of 2 km. We show that the new model reproduces quite well the intermittency and self‐similarity features and the interscale and across‐scale correlation structures of observed rainfall with a relatively low computational burden.
Relation between length‐of‐day variation and angular momentum of geophysical fluids
Authors: Chao Benjamin F. , Yan Haoming
Published: October 2010

The remarkable relation well observed between variation in the length of day (ΔLOD) and variation in the axial atmospheric angular momentum (ΔAAM) (plus the oceanic counterpart, to a much lesser extent) is a consequence of the conservation of angular momentum on planet Earth. Quantification of the exact ΔLOD‐ΔAAM relation, which we seek in the present study, depends significantly on the extent to which the core participates, or is dynamically coupled with the mantle, in transmission of the axial ΔAAM from the mantle to the core. If, after conversion to the equivalent ΔLOD assuming core‐mantle decoupling (as in current standard practice), the calculated axial ΔAAM (according to atmospheric general circulation models [GCMs]) is systematically greater than the observed ΔLOD, then we can conclude the presence, and, furthermore, estimate the strength, of the said dynamic core‐mantle coupling. However, in this study we find the opposite instead, that the calculated ΔAAM (plus the small oceanic counterpart) is smaller than the observed ΔLOD by 10%–20% consistently across the intraseasonal and seasonal time scales. Our main logical conclusion is that the atmospheric GCMs in general underpredict the ΔAAM, by at least 10%–20% at the mentioned time scales, a fact of importance with respect to the assessment of GCMs. Therefore, the systematic discrepancy found between the ΔAAM‐predicted and the observed ΔLOD masks the relevant information on core‐mantle coupling that we seek.
On the use of Advanced Microwave Sounding Unit‐A and ‐B measurements for studying the monsoon variability over West Africa
Authors: Eymard Laurence , Karbou F. , Janicot S. , Chouaib N. , Pinsard F.
Published: October 2010

The advanced microwave sounding unit (AMSU) ‐A and ‐B sensors provide observations of humidity and temperature that are relevant for meteorological and climate studies. The use of these observations in numerical weather prediction models has increased in the past 10 years because of some improvements in data assimilation. However, an appropriate use of AMSU measurements apart from assimilation context is rather difficult and depends for the most part on how successfully the instrumental characteristics are accounted for. In particular, atmosphere humidity and temperature variations can be completely hidden by features because of the effect of the observation zenith angle. In this paper, 8 years of AMSU‐A and ‐B observations have been corrected from the observations zenith angle effect and have been used to study temperature and humidity variations over West Africa. Comparisons have been made between AMSU observations and selected atmospheric fields from European Centre for Medium‐Range Weather Forecasts analyses as well as outgoing longwave radiation estimates. It has been found that observations from AMSU‐A channel 5 can be used to monitor the heat low evolution and that AMSU‐B observations from channels 3 and 5 are well adapted to study the humidity variations in direct link with the African monsoon from intraseasonal to interannual scales.
Three‐dimensional velocity structure of the northern Hikurangi margin, Raukumara, New Zealand: Implications for the growth of continental crust by subduction erosion and tectonic underplating
Authors: Bassett Daniel , Sutherland Rupert , Henrys Stuart , Stern Tim , Scherwath Martin , Benson Adrian , Toulmin Suzannah , Henderson Mark
Published: October 2010

Traveltimes between shots from nine marine seismic reflection lines and nine onshore recorders were used to construct a 3‐D P wave velocity model of the northern Hikurangi subduction margin, New Zealand. From north to south between Raukumara Basin and Raukumara Peninsula, the Moho of the overriding plate increases in depth from 17 to ∼35 km. Low seismic P wave velocities of 3.5–5.0 km/s are localized within a ∼10 km thick prism in the lower crust of the overriding plate immediately updip of the intersection between the subduction thrust and Moho and beneath the topographic crest of East Cape Ridge and the Raukumara Range. Southward, this region of low seismic velocities and surface uplift increases in distance from the trench as the thickness of the crust in the overriding plate increases. We interpret this low‐velocity volume to be underplated sedimentary rocks and crustal materials that were tectonically eroded by subduction beneath the trench slope. The buoyancy and low strength of these subducted materials are proposed to assist the escape from a subduction channel near the base of the crust and drive local rock uplift. In the middle crust, our observations of very low velocity suggest high fluid‐filled porosities of 12%–18%, and the implied buoyancy anomaly may enhance underplating. At greater depths the process is driven by the contrast between upper crustal quartz‐feldspar mineralogy and the denser diabase or olivine‐rich lithologies of the lower crust and mantle. We estimate a rate of lower crustal underplating at the northern Hikurangi margin of 20 ± 7 km3 Ma−1 km−1 since 22 Ma. We suggest that underplating provides an efficient means of accreting subducted sediment and tectonically eroded material to the lower crust and that the flux of fore‐arc crustal rocks into the mantle at subduction zones may be systematically overestimated.
Geomagnetic activity triggered by interplanetary shocks
Authors: Yue C. , Zong Q. G. , Zhang H. , Wang Y. F. , Yuan C. J. , Pu Z. Y. , Fu S. Y. , Lui A. T. Y. , Yang B. , Wang C. R.
Published: October 2010

Interplanetary (IP) shocks can greatly disturb the Earth's magnetosphere, causing the global dynamic changes in the electromagnetic fields and the plasma. In order to investigate this, we have systematically analyzed 106 IP shock events based on OMNI data, GOES, and Los Alamos National Laboratory satellite observations during 1997−2007. It is revealed that the median value of IMF Bz keeps negative/positive prior to shock arrival and becomes more negative/positive following the shock arrival. The statistical analysis shows that IP shocks with southward interplanetary magnetic field (IMF) (46%) are likely to increase AE (AL, AU) and PC indices significantly. The amplitude of AE index increases from 200 to 600 nT, AU from 100 to 200 nT, AL from 50 to 400 nT, and PC from 1.5 to 3 approximately in 10 min, which could be a signature of geomagnetic activity/substorms onset (or substorm further intensification). Meanwhile, there is a strong injection of energetic electrons in the dawn region following the shock arrival and a strong depletion in the dusk region 30 min later, showing a clear dawn‐dusk asymmetry. On the other hand, there is only the typical shock compression effect for IP shocks with northward IMF (54%). The median value of AE index increased from 80 to 150 nT, AU from 50 to 90 nT, AL index decreased from −30 to −40 nT, and PC index increased from 0.6 to 1.2 in ∼10 min following the shock arrival. Both individual cases and statistical studies indicate that the magnetosphere‐ionosphere system must be preconditioned for a substorm‐like geomagnetic activity to be triggered by an IP shock with southward IMF impact, whereas IP shock with northward IMF precondition shows only compression effect.
Dynamics of the Patos Lagoon coastal plume and its contribution to the deposition pattern of the southern Brazilian inner shelf
Authors: Marques Wilian C. , Fernandes Elisa H. L. , Moraes Bruno C. , Möller Osmar O. , Malcherek Andreas
Published: October 2010

The southern Brazilian shelf (SBS) is a region influenced by fresh water. The initial deposition of suspended sediments carried by this fresh water presents important ecological consequences for the area. The aim of this study was to investigate the contribution of the Patos Lagoon coastal plume to the deposition pattern observed along the inner continental shelf by providing estimates of estuarine‐shelf suspended sediment exchange. The study was carried out through three‐dimensional numeric modeling experiments on coupled hydrodynamic and morphodynamic processes. Results were analyzed using the dynamic method proposed by Garvine (1995) to study persistent plumes. The results were also analyzed using wavelet analysis. Results showed that the Patos Lagoon coastal plume behaves as a hypopycnal plume covering the first meters of the water column. The Patos Lagoon presents a dominant ebb condition with a mean discharge of 2088 m3 s−1 and an exportation rate of suspended matter of approximately 1.3 × 107 t yr−1. In the adjacent coastal region deposition prevails in sheltered regions up to 10 m deep, with enrichment in silt reaching up to 10% in the deceleration region of the Patos Lagoon coastal plume. The dynamic balance indicates a behavior typical of small to average‐sized plumes, with a well‐developed displacement along the coast that is mainly controlled by the alongshore wind component. The Coriolis force and bed shear stress present significant contributions during periods of moderate to high freshwater discharge when large‐scale plumes are formed. Transversally to the coast the force balance is associated with the Coriolis effect and wind influence, with a less important contribution from bed shear stress. The inner continental shelf adjacent to the Patos Lagoon entrance is dominantly influenced by plume occurrence. In this region northeasterly winds induce the formation of southwestward currents near the coast. These currents deflect around jetties and generate recirculation zones to the south. The formation of a cyclonic eddy occurs in this area and creates convergence zones that intensify the vertical velocities promoting the deposition of suspended sediments.
The Effect of Basal Vasodilation on Hypercapnic and Hypocapnic Reactivity Measured using Magnetic Resonance Imaging
Authors: Bright Molly G , Donahue Manus J , Duyn Jeff H , Jezzard Peter , Bulte Daniel P
Published: October 2010

Cerebrovascular reactivity to vasodilatory hypercapnic and vasoconstrictive hypocapnic challenges is known to be altered in several hemodynamic disorders, which is often attributable to changes in smooth muscle-mediated vascular compliance. Recently, attenuated reactivity to hypercapnia but enhanced reactivity to hypocapnia was observed in patients with chronic stroke. We hypothesize that the latter observation could be explained by a change in the basal vascular tone. In particular, reduced cerebral perfusion pressure, as is prevalent in these patients, may cause vasodilation through autoregulatory mechanisms, and this compensatory baseline condition may alter reactivity to vasoconstrictive hypocapnic challenges. To test this hypothesis, a predilated vascular condition was created in young, healthy subjects ( n = 11; age = 23 to 36 years) using inhalation of 4% CO2. Using blood oxygenation level-dependent functional magnetic resonance imaging at 3 T, breath holding and cued deep breathing respiratory challenges were administered to assess hypercapnia and hypocapnia reactivity, respectively. During the predilated condition, vasoconstrictive reactivity to hypocapnia was significantly (21.1%, P = 0.016) enhanced throughout the gray matter, whereas there was no significant change (6.4%, P = 0.459) in hypercapnic vasodilatory reactivity. This suggests that baseline vasodilation may explain the enhanced hypocapnia reactivity observed in some stroke patients, and that hypocapnia challenges may help identify the level of vascular compliance in patients with reduced cerebral perfusion pressure.
Multiple Sites of Vasopressin Synthesis in the Injured Brain
Authors: Szmydynger-Chodobska Joanna , Zink Brian J , Chodobski Adam
Published: October 2010

Previous studies have indicated that the primary targets for vasopressin actions on the injured brain are the cerebrovascular endothelium and astrocytes, and that vasopressin amplifies the posttraumatic production of proinflammatory mediators. Here, the controlled cortical impact model of traumatic brain injury in rats was used to identify the sources of vasopressin in the injured brain. Injury increased vasopressin synthesis in the hypothalamus and cerebral cortex adjacent to the posttraumatic lesion. In the cortex, vasopressin was predominantly produced by activated microglia/macrophages, and, to a lesser extent, by the cerebrovascular endothelium. These data further support the pathophysiological role of vasopressin in brain injury.
Bioinformatics for Human Proteomics: Current State and Future Status
Authors: Bairoch Amos
Published: October 2010

We are entering a new era in the exploration of the human proteome.Advances in technologies are allowing researchers to map with a much better resolution and improved accuracy this very complex universe. Such an exploration also requires a compendium of adequate bioinformatics tools, data repositories and knowledge resources. We are going to describe what are the state of the art in term of data and knowledge resources for human proteins: from repositories of proteomics data such as PRIDE,PeptideAtlas or Peptidome, databases such as SRMAtlas and HPA and knowledgebase such as UniProtKB/Swiss-Prot.In September 2008, the UniProt/Swiss-Prot group achieved a major milestone: the first complete manual annotation of what is believed to be the full set of human proteins (derived from about 20'000 genes). This corpus of data is already quite rich in information pertinent to modern biomolecular medical research, but made us realize how large is the gap in our knowledge of human proteins in terms of functional information as well as protein characterization (PTMs, protein/protein interactions,subcellular locations, etc).This gap resides not only in the available experimental information, but also in the way this information has been stored, which is far from being sufficient to help researchers making sense of what all these human proteins do in our bodies! Therefore, in the framework of CALIPHO, a new interdisciplinary group created jointly by the University of Geneva and the Swiss Institute of Bioinformatics (SIB), we are developing neXtProt, a new human-centric protein knowledge resource.neXtProt is developed with the aim to help researchers answer pertinent questions relevant to human proteins. This requires answering 3 different challenges:1) Add to the corpus of data on human proteins that is already in Swiss-Prot, a lot of additional information. We will import in neXtProt data originating from a variety of high-throughput approaches such as microarray, antibodies, proteomics, siRNAs, interactomics, etc. All of these data sets must be carefully selected so as to only provide high-quality data as we want to avoid creating a noisy and dirty compendium.2) Organize the data in such a way that it is possible to make powerful queries in the most user-friendly environment. Here also, it is necessary to be able to capture the complexity and the heterogeneity of the data that will be available in neXtProt, yet make it easy for the user to forget this complexity!3) Build a software platform that will allows tools ranging from sequence analysis to text and data mining to be integrated in various research environments so as to answer specific needs of academic and industrial users.
Expression of the cannabinoid system in muscle: effects of a high-fat diet and CB1 receptor blockade
Authors: Crespillo Ana , Suárez Juan , Bermúdez-Silva Francisco J. , Rivera Patricia , Vida Margarita , Alonso Monica , Palomino Ana , Lucena Miguel A. , Serrano Antonia , Pérez-Martín Margarita , Macias Manuel , Fernández-Llébrez Pedro , Rodríguez de Fonseca Fernando
Published: October 2010

The ECS (endocannabinoid system) plays an important role in the onset of obesity and metabolic disorders, implicating central and peripheral mechanisms predominantly via CB1 (cannabinoid type 1) receptors. CB1 receptor antagonist/inverse agonist treatment improves cardiometabolic risk factors and insulin resistance. However, the relative contribution of peripheral organs to the net beneficial metabolic effects remains unclear. In the present study, we have identified the presence of the endocannabinoid signalling machinery in skeletal muscle and also investigated the impact of an HFD (high-fat diet) on lipid-metabolism-related genes and endocannabinoid-related proteins. Finally, we tested whether administration of the CB1 inverse agonist AM251 restored the alterations induced by the HFD. Rats were fed on either an STD (standard/low-fat diet) or an HFD for 10 weeks and then treated with AM251 (3 mg/kg of body weight per day) for 14 days. The accumulated caloric intake was progressively higher in rats fed on the HFD than the STD, resulting in a divergence in body weight gain. AM251 treatment reduced accumulated food/caloric intake and body weight gain, being more marked in rats fed on the HFD. CB2 (cannabinoid type 2) receptor and PPARα (peroxisome-proliferator-activated receptor α) gene expression was decreased in HFD-fed rats, whereas MAGL (monoglyceride lipase) gene expression was up-regulated. These data suggest an altered endocannabinoid signalling as a result of the HFD. AM251 treatment reduced CB2 receptor, PPARγ and AdipoR1 (adiponectin receptor 1) gene expression in STD-fed rats, but only partially normalized the CB2 receptor in HFD-fed rats. Protein levels corroborated gene expression results, but also showed a decrease in DAGL (diacylglycerol) β and DAGLα after AM251 treatment in STD- and HFD-fed rats respectively. In conclusion, the results of the present study indicate a diet-sensitive ECS in skeletal muscle, suggesting that blockade of CB1 receptors could work towards restoration of the metabolic adaption imposed by diet.
Procyanidin B3, an inhibitor of histone acetyltransferase, enhances the action of antagonist for prostate cancer cells via inhibition of p300-dependent acetylation of androgen receptor
Authors: Choi Kyung-Chul , Park SiYong , Lim Beom Jin , Sung Ah-Reum , Lee Yoo-Hyun , Shiota Masaki , Yokomizo Akira , Naito Seiji , Na Younghwa , Yoon Ho-Geun
Published: October 2010

Increasing evidence suggests that AR (androgen receptor) acetylation is critical for prostate cancer cell growth. In the present study, we identified Pro-B3 (procyanidin B3) as a specific HAT (histone acetyltransferase) inhibitor. Pro-B3 selectively inhibited the activity of HATs, but not other epigenetic enzymes. Pro-B3 substantially inhibited the p300-mediated AR acetylation, both in vitro and in vivo. Pro-B3 inhibited both p300-dependent and agonist-induced AR transcription. We demonstrate that the p300-mediated AR acetylation is critical for the hormone responsiveness of AR. Interestingly, B3 treatment efficiently enhanced the antagonist activity of flutamide through suppression of p300 HAT activity, demonstrating that relative p300 activity is critical for the antagonist action. Finally, Pro-B3 treatment inhibited acetylation-dependent prostate cell proliferation and expression of cell-cycle control genes, subsequently increasing cell death, indicating the functional importance of AR acetylation for prostate cancer cell growth.
Olive pollen allergen Ole e 8: identification in mature pollen and presence of Ole e 8‐like proteins in different pollens
Authors: Ledesma A. , Villalba M. , Vivanco F. , Rodríguez R.
Published: October 2010

In a first approach, Ole e 8, a novel Ca2+‐binding protein from olive pollen, was cloned and produced in Escherichia coli. We have obtained the natural form of Ole e 8 (nOle e 8) from the pollen and examined its immunologic equivalence with its recombinant form (rOle e 8). Size exclusion chromatography and a phenyl‐Sepharose CL‐4B affinity column were used to obtain nOle e 8 from the olive pollen. Inhibition assays by immunoblotting, using rOle e 8‐specific rabbit antiserum, were performed to analyze the immunologic equivalence between the natural and the recombinant allergen, as well as to detect its presence in other pollens. Recombinant and natural Ole e 8 resulted immunologically equivalents, since they completely inhibited the IgG binding of the polyclonal antiserum to each other. Ole e 8‐like proteins were detected in Oleaceae and Juniperus communis pollen, and might contribute to cross‐reactivity processes between taxonomically related pollens.
Eotaxin and CCR3 are up‐regulated in exacerbations of chronic bronchitis
Authors: Bocchino V. , Bertorelli G. , Bertrand C.P. , Ponath P.D. , Newman W. , Franco C. , Marruchella A. , Merlini S. , Del Donno M. , Zhuo X. , Olivieri D.
Published: October 2010

Background: Eosinophils and T lymphocytes represent constant features in the airways of subjects with exacerbated chronic bronchitis. Eotaxin is the most potent and selective eosinophil chemoattractant which can also attracts lymphocytes. The aim of the study was to evaluate the expression of eotaxin and its receptor, CCR3, in bronchial airways during exacerbation of chronic bronchitis.

Methods: By immunohistochemistry we studied eotaxin and CCR3 expression in the lamina propria of 14 subjects with acute exacerbation of chronic bronchitis, 20 asthmatics, and 8 healthy subjects. We determined the cell types expressing the CCR3 receptor by colocalization experiments. We finally studied the relationship between eotaxin and CCR3 and eosinophils and T lymphocytes.

Results: The number of eotaxin+ and CCR3+ cells was significantly higher in exacerbated chronic bronchitis (P < 0.003 and P < 0.002) and asthma (P < 0.002 and P < 0.0001) when compared to healthy subjects. CCR3 was mainly expressed by eosinophils and to a lesser extent by CD4+ and CD8+ lymphocytes. In exacerbated chronic bronchitis the number of CCR3+ cells was strongly correlated to the number of eosinophils (P < 0.0002, r = 0.85) and to the number of CD4+ lymphocytes (P < 0.05, r = 0.57).

Conclusion: Our study suggests that eotaxin and CCR3 are up‐regulated and could be involved in the eosinophil and CD4+ lymphocyte recruitment into the airways which occur during acute exacerbations of chronic bronchitis.
Permeability distribution in the Quaternary of the Upper Rhine glacio‐fluvial aquifer
Authors: Meinken Wolf , Stober Ingrid
Published: October 2010

An extraordinarily large and geographically extensive 3D dataset has allowed us to relate permeability to detailed geological features. Permeability data derived from several thousand pumptests in Quaternary sediments (thickness < 120 m) of the Upper Rhine valley vary from K= 4.5 × 10−7 m s−1 to K= 2.7 × 10−1 m s−1. The geometric mean of the data is K= 2.25 × 10−3 m s−1. The permeability distribution maps for four different stratigraphic levels show that the highest values are found in sections beneath recent and historic fluvial systems. Fossil fans of small rivers from the Black Forest can be identified in the Rhine valley on the basis of the permeability pattern. The average hydraulic conductivity decreases S–N along the flow direction which corresponds to a decrease in grain‐size of the fluvial sediments.
Absolute dating of brittle fault movements: Late Permian and late Jurassic extensional fault breccias in western Norway
Authors: Eide Elizabeth A. , Torsvik Trond H. , Andersen Torgeir B.
Published: October 2010

40Ar/39Ar geochronological and palaeomagnetic dating methods applied to fault breccias in western Norway have isolated two brittle reactivation episodes of the syn‐post‐Caledonian, extensional Nordfjord‐Sogn Detachment. These events, of latest Permian and latest Jurassic–Early Cretaceous ages, demonstrate temporal relationships between development of chemical remanent magnetism and partial resetting of Ar isotopic systems during distinct breccia‐forming episodes. A third event of Carboniferous age was also identified in the breccias with the 40Ar/39Ar technique and is a relict unroofing signature inherited from the fault wall‐rocks. These brittle faults are significant time markers and become relevant to interpretations of offshore seismic data which attempt to place ages on faults that have undergone multiple reactivation episodes.
An Eocene magmatic belt across central Tibet: mantle subduction triggered by the Indian collision?
Authors: Roger F. , Tapponnier P. , Arnaud N. , Schärer U. , Brunel M. , Zhiqin X. , Jingsui Y.
Published: October 2010

Mountain domes rising to ≈ 6600 m along Tibet’s Tanggula range herald the Eocene intrusion of calcalkaline granites into terranes accreted much earlier. Together with coeval, cogenetic volcanics, such intrusives, which have similar crystallization and cooling ages, may be part of an ESE‐trending belt cutting central Tibet in half. This magmatic belt may have marked a former northern boundary of the plateau, testifying to S‐directed subduction of the Asian mantle. Such subduction would have developed soon after India’s collision but long before the rise of the plateau’s present rims, along one of central Tibet’s Mesozoic sutures.
Major changes in volcano behaviour after a sector collapse: insights from Stromboli, Italy
Authors: Tibaldi Alessandro
Published: October 2010

In recent years, increasing numbers of volcanoes are being recognized as having undergone large sector collapses. How far such events can change the succeeding behaviour of the volcano is poorly known, despite the importance for natural hazards and economic applications. By analysing the last 100‐kyr geological history of Stromboli (Italy), which has involved multiple collapses, this paper illuminates the feedback effect between sector collapse and magma upwelling and emplacement. The collapsed zone of Stromboli is episodically unbuttressed, draining magma preferentially with formation of eruptive centres in the collapse amphitheatre and dyking along the collapse shoulders. After a collapse, there were no further linear eruptions across the cone on opposing middle–lower slopes, but these occurred again after rebuilding of the cone. The time‐averaged eruption rate increased immediately before the first collapse and remained higher during the succeeding period of frequent collapses.
Structural controls on sulphide deposition at the dyke–lava boundary, slow‐spreading ocean crust, Macquarie Island
Authors: Davidson Garry J. , Varne Rick , Brown Anthony V. , Connell Robert
Published: October 2010

Ocean Drilling Program hole 504B revealed an ocean crust hydrothermal sulphur anomaly on the dyke–lava transition, with implications for global sulphur sinks. Here we confirm the presence of the anomaly sporadically along 7.5 km of dyke–basalt contact on the Macquarie Ridge at Macquarie Island, a 39–9.7 Ma slow‐spreading setting. Background contact‐zone pyrite S contents average 1845 p.p.m. across ∼50 m. However, zones of small‐scale brittle faulting that commonly occur on and above the dyke–basalt contact average between 5000 and 11 000 p.p.m. S (20–30 m widths). These consist of steep ridge‐parallel faults and fault splays on the contact, overlain by up to 50 m of linked pyritic fault trellis. The contact zone faults are haloed by disseminated pyrite–chlorite, cross‐cut by quartz–chlorite–sphalerite and epidote‐cemented breccias, containing evidence of turbulent flow. The structural control on sulphur deposition is attributed to the active extensional slow spreading setting. With increasing extension, diffuse mixing across the contact was replaced by channellized flow and dynamic mixing in fault arrays. The magnitude of the dyke–lava transition sulphur sink must be reassessed to take account of this heterogeneity.
Buoyancy‐controlled eruption of magmas at Mt Etna
Authors: Corsaro Rosa Anna , Pompilio Massimo
Published: October 2010

Buoyancy controls the ability of magma to rise, its ascent rate and the style of the eruptions. Geophysical, geological and petrological data have been integrated to evaluate the buoyancy of magmas at Mt Etna. The density difference between host rocks and magmas is mainly related to the amount of H2O dissolved in the magma and to the bubble‐liquid separation processes. In the depth interval 22–2 km b.s.l. highly hydrated (H2O ∼ 3%) basaltic magmas or mixtures of bubbles + liquid have positive buoyancy and rise rapidly. Conversely, bubble‐depleted liquids, with an intermediate H2O content (∼ 1.5%), having neutral buoyancy, will spread out and form magmatic reservoirs at different depths until cooling/crystallization further modify composition and density. These different processes account for the magma compositions, location of magmatic reservoirs as determined by geophysical methods, and the complex eruptive cycles (slow effusions, fire fountains and Plinian eruptions) that have been observed in the history of the volcano.
Isotope fractionation of neon during stepheating extraction?: a comment on ‘Re‐interpretation of the existence of a primitive plume under Australia based on neon isotope fractionation during step heating’ by Gautheron and Moreira (2003)
Authors: Matsumoto Takuya , Honda Masahiko , McDougall Ian , Yatsevich Igor , O'Reilly Suzanne Y.
Published: October 2010

Using a Rayleigh distillation fractionation model, we calculate that the maximum isotope fractionation potentially achievable is less than 5% during the early stages of gas release from a sample. Our calculation corrects the erroneous conclusions of Gautheron and Moreira (2003), who re‐interpreted the plume‐like neon isotopic compositions found in metasomatic apatite from a south‐eastern Australian xenolith (Matsumotoet al., 1997) to be the result of Rayleigh‐type isotope fractionation of originally MORB‐type neon during stepheating gas extraction. We stress that the modelling of neon isotopic fractionation by Gautheron and Moreira (2003) is incorrect, and that the finding of a plume‐like neon isotopic composition in the apatite by Matsumotoet al. (1997) remains a quite valid and robust conclusion.
Active extension of the Shanxi rift, north China: does it result from anticlockwise block rotations?
Authors: He Jiankun , Cai Dongsheng , Li Yanxing , Gong Zaisheng
Published: October 2010

The Shanxi rift is an intraplate extensional zone in the North China Block. Active extension has previously been considered to result from anticlockwise block rotation, with successive indentation of the Indian plate toward the Eurasian plate. However, GPS data show that the entire North China Block is moving coherently from WNW to ESE, indicating that no significant block rotations presently exist along the two sides of the rift. We use a viscoelastic model to predict that its active extension might be caused by intraplate deformation localization with lateral changes of the crustal rheological structures. A model result shows that for the ESE movement of the North China Block, the existing topographical loading and crustal weakness could have resulted in the obvious long‐term extension of the Shanxi rift even without different block rotations. The surface extension rate approximated from lateral inhomogeneous crustal models is ∼ 0.5–1.4 mm yr−1, consistent with observed geological and seismological extension rates.
The Drosophila Na,K‐ATPase α‐subunit gene: gene structure, promoter function and analysis of a cold‐sensitive recessive‐lethal mutation
Authors: Feng Yuanyi , Huynh Long , Takeyasu Kunio , Fambrough Douglas M.
Published: October 2010

The Drosophila Na,K‐ATPase (or sodium pump) α‐subunit gene was found to contain 10 exons and span approx. 25 kb. Two nearly adjacent transcriptional initiation sites were identified, and the 2085‐ nucleotide sequence upstream of the first transcriptional start was analysed for promoter activity in transfected Drosophila SL2 cells. This region was found to contain many cis‐acting elements that influence promoter activity, including elements that confer 2‐ to 3‐fold higher activity in SL2 cells cultured at 30°C versus 22°C. Temperature‐sensitive transcriptional regulation of the Na,K‐ATPase α‐subunit in Drosophila is a plausible mechanistic candidate for the factor driving temperature‐dependent up‐regulation of the Na,K‐ATPase α‐subunit described here for fly strains homozygous for single P‐element insertions in the α‐subunit gene. Four new P‐element insertion strains were identified in this study, each insertion site lying within the first intron of the Na,K‐ATPase α‐subunit gene. The insertion in strain 0462 resulted in cold‐sensitive recessive lethality; flies homozygous for the 0462 mutation could be rescued by growth at 29–30°C, a condition that partially corrected a deficiency in the level of Na,K‐ATPase α‐subunit. The high‐temperature rescue of homozygous 0462 flies appeared to result primarily from improved Na,K‐ATPase expression rather than an increase in the rate of ion transport per Na,K‐ATPase molecule. These observations point to a role for sodium‐pump activity in determining the range of temperature tolerance in Drosophila and demonstrate that relatively subtle changes in sodium‐pump expression can have major consequences in whole organisms.