bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Model of Multiple Zonal Jets in the Oceans: Dynamical and Kinematical Analysis
Authors: Berloff P. , Kamenkovich I. , Pedlosky J. 
Published: April 2009

Abstract
Multiple alternating zonal jets observed in the ocean are studied with an idealized quasigeostrophic zonal-channel model, with the supercritical, zonal background flow imposed. Both eastward and westward background flows with vertical shear are considered. The underlying nonlinear dynamics is illuminated with analysis of the vertical-mode interactions and time-mean eddy fluxes.
Interactions between the vertical modes are systematically studied. The barotropic component of the jets is maintained by both barotropic–barotropic and baroclinic–baroclinic time-mean interactions; thus, the barotropic component of the jets cannot be accurately simulated with a randomly forced barotropic model. The roles of the vertical-mode interactions in driving the baroclinic component of the jets are also characterized. Not only the first but also the second baroclinic mode is found to be important for maintaining the baroclinic component of the jets, whereas the barotropic component of the jets is maintained mostly by the barotropic and first baroclinic modes.
The properties of the eddy forcing were systematically studied. It is shown that the baroclinic component of the jets is maintained by Reynolds stress forcing and resisted by form stress forcing only in the eastward background flow. In the westward background flow, the jets are maintained by form stress forcing and resisted by Reynolds stress forcing.
The meridional scaling and kinematical properties of the jets are studied as well as the roles of meridional boundaries. The Rhines scaling for meridional spacing of the jets is not generally confirmed, and it is also shown that there are multiple stable equilibria with different numbers of the time-mean jets. It is also found that the jets are associated with alternating weak barriers to the meridional material transport, but the locations of these barriers are not unique and depend on the direction of the background flow and depth. Finally, if the channel is closed with meridional walls, then the jets become more latent but the eddy forcing properties do not change qualitatively.
Hybrid Rossby-Shelf Modes in a Laboratory Ocean
Authors: Bokhove Onno , Ambati Vijaya 
Published: April 2009

Abstract
Idealized laboratory experiments reveal the existence of forced–dissipative hybrid Rossby-shelf modes. The laboratory ocean consists of a deeper ocean (accommodating basin-scale Rossby modes) and a coastal step shelf (accommodating trapped shelf modes). Planetary Rossby modes are mimicked in the laboratory via a uniform topographic slope in the north–south direction. Hybrid modes are found as linear modes in numerical calculations, and similar streamfunction patterns exist in streak photography of the rotating tank experiments. These numerical calculations are based on depth-averaged potential vorticity dynamics with Ekman forcing and damping. Preliminary nonlinear calculations explore the deficiencies observed between reality and the linear solutions. The aim of the work is twofold: to show that idealized hybrid Rossby-shelf modes exist in laboratory experiments and to contribute in a general sense to the discussion on the coupling and energy exchange associated with hybrid modes between shallow coastal seas and deep-ocean basins.
A New Look at Richardson Number Mixing Schemes for Equatorial Ocean Modeling
Authors: Zaron Edward D. , Moum James N. 
Published: April 2009

Abstract
A reexamination of turbulence dissipation measurements from the equatorial Pacific shows that the turbulence diffusivities are not a simple function of the gradient Richardson number. A widely used mixing scheme, the K-profile parameterization, overpredicts the turbulent vertical heat flux by roughly a factor of 4 in the stably stratified region between the surface mixed layer and the Equatorial Undercurrent (EUC). Additionally, the heat flux divergence is of the incorrect sign in the upper 80 m. An alternative class of parameterizations is examined that expresses the mixing coefficients in terms of the large-scale kinetic energy, shear, and Richardson number. These representations collapse the turbulence diffusivities above and below the Equatorial Undercurrent, and a tuned version is able to reproduce the vertical turbulence heat flux within the 50–180-m depth range. Kinetic energy is not Galilean invariant, so the collapse of the data with the new parameterization suggests that oceanic turbulence responds to boundary forcing at depths well below the surface mixed layer.
Thermally Driven Flows at an Asymmetric Valley Exit: Observations and Model Studies at the Lech Valley Exit
Authors: Spengler Thomas , Schween Jan H. , Ablinger Markus , Zängl Günther , Egger Joseph 
Published: April 2009

Abstract
The summertime thermal circulation in the region of an asymmetric valley exit is investigated by means of observations and high-resolution model simulations. The northeastward-oriented Alpine Lech Valley opening into the Bavarian Alpine foreland has an eastern slope exceeding the western slope by about 15 km. Northerly winds along the eastern slope are frequently observed, reaching substantial strength during fair weather conditions. A field experiment has been conducted to explore this phenomenon and to pinpoint the connection of the northeasterly flow to the Lech Valley wind circulation. Numerical simulations have also been carried out to support the interpretation of the observations. It is found that the northerlies owe their existence to the dominantly easterly flow along the foothills of the Alps, which is partly induced by the Alpine heat low but may be strengthened by favorable synoptic conditions. Examples for both situations will be discussed. The diurnal flow in the Lech Valley has little obvious impact on these northeasterlies. On days with moderate synoptic easterly flow, a wake is present on the lee of the eastern slope of the exit region, accompanied by a shear zone along the edge of the wake. This shear zone is forced southward during the daytime because of thermally initiated pressure gradients between the Alpine foreland and the Alps, leading to sudden wind changes in the exit area at the time of its passage.
Co-Morbid Social Phobia in Schizophrenia
Authors: Mazeh Doron , Bodner Ehud , Weizman Ronit , Delayahu Yael , Cholostoy Alexander , Martin Tatiana , Barak Yoram 
Published: April 2009

Background: The co-morbid occurrence of anxiety disorders and schizophrenia has recently begun to be investigated. Social anxiety may be especially important to diagnose and manage among patients with schizophrenia. Aim: To investigate the prevalence and correlates of social phobia in patients with schizophrenia. Method: Diagnosis of schizophrenia and schizoaffective disorders as well as co-morbid anxiety disorders was established according to DSM-IV and the Structured Clinical Interview for Diagnosis (SCID-P Hebrew version). Severity of psychotic symptoms and social anxiety symptoms was assessed with the Positive and Negative Symptom Scale (PANSS) and the Liebowitz Social Anxiety Scale (LSAS). Results: The cohort studied included 117 patients with schizophrenia. Thirteen patients were diagnosed as suffering from co-morbid social phobia (11%). There was a tendency for patients with co-morbid social phobia to have higher severity PANSS total score. There was a significant correlation between the score of the LSAS `fear' and PANSS positive subscales. Avoidance scores were higher among patients with negative signs. Conclusion: Co-morbidity of schizophrenia and social anxiety disorder is not rare among patients with schizophrenia. Treatment implications need be further investigated.
Quality of Life in Opium-Addicted Patients With Coronary Artery Disease as Measured With WHOQOL-BREF
Authors: Najafi Mahdi , Sheikhvatan Mehrdad , Montazeri Ali , Sheikhfathollahi Mahmood 
Published: April 2009

Objective: Several factors can influence the quality of life in patients with coronary artery disease (CAD). The goal of this research was to measure quality of life in opium-addicted patients with CAD in order to assess the effect of CAD risk factors on their quality of life. Method: The WHOQOL-BREF questionnaire was completed through interviews with 275 patients who underwent isolated coronary artery bypass surgery in Tehran Heart Centre between May and September 2006. Results: No significant differences were found in the mean scores of the four domains of quality of life between the addicted and non-addicted patients. Furthermore, the evaluation of QOL in the groups with CAD risk factors showed that the mean QOL domains were statistically similar between opium addicted and non-opium addicted patients. In the addicted group, men had a higher psychological health score than women. A previous history of myocardial infarction reduced the psychological score in this group. Also, in the addicted patients with a history of diabetes mellitus, social functioning was better than that of the non-diabetics. Conclusions: The different domains of quality of life in our opium-addicted and non-addicted patients with CAD were similar; and among all the major risk factors for coronary artery disease, only female gender and a previous history of myocardial infarction could influence quality of life in the opium-addicted patients.
CXCR7 heterodimerizes with CXCR4 and regulates CXCL12-mediated G protein signaling
Authors: Levoye Angélique , Balabanian Karl , Baleux Françoise , Bachelerie Françoise , Lagane Bernard 
Published: April 2009

AbstractThe stromal cell-derived factor-1/CXCL12 chemokine engages the CXCR4 and CXCR7 receptors and regulates homeostatic and pathologic processes, including organogenesis, leukocyte homeostasis, and tumorigenesis. Both receptors are widely expressed in mammalian cells, but how they cooperate to respond to CXCL12 is not well understood. Here, we show that CXCR7 per se does not trigger Gαi protein–dependent signaling, although energy transfer assays indicate that it constitutively interacts with Gαi proteins and undergoes CXCL12-mediated conformational changes. Moreover, when CXCR4 and CXCR7 are coexpressed, we show that receptor heterodimers form as efficiently as receptor homodimers, thus opening the possibility that CXCR4/CXCR7 heterodimer formation has consequences on CXCL12-mediated signals. Indeed, expression of CXCR7 induces conformational rearrangements within preassembled CXCR4/Gαi protein complexes and impairs CXCR4-promoted Gαi-protein activation and calcium responses. Varying CXCR7 expression levels and blocking CXCL12/CXCR7 interactions in primary T cells suggest that CXCR4/CXCR7 heterodimers form in primary lymphocytes and regulate CXCL12-promoted chemotaxis. Taken together, these results identify CXCR4/CXCR7 heterodimers as distinct functional units with novel properties, which can contribute to the functional plasticity of CXCL12.
Receptor targeting of hemoglobin mediated by the haptoglobins: roles beyond heme scavenging
Authors: Nielsen Marianne Jensby , Moestrup Søren Kragh 
Published: April 2009

AbstractHaptoglobin, the haptoglobin-hemoglobin receptor CD163, and the heme oxygenase-1 are proteins with a well-established function in the clearance and metabolism of “free” hemoglobin released during intravascular hemolysis. This scavenging system counteracts the potentially harmful oxidative and NO-scavenging effects associated with “free” hemoglobin, and, furthermore, elicits an anti-inflammatory response. In the late primate evolution, haptoglobin variants with distinct functions have arisen, including haptoglobin polymers and the haptoglobin-related protein. The latter associates with a subspecies of high-density lipoprotein (HDL) particles playing a crucial role in the innate immunity against certain trypanosome parasites. Recent studies have elucidated this fairly sophisticated immune defense mechanism that takes advantage of a trypanosomal haptoglobin-hemoglobin receptor evolved to supply the parasite with heme. Because of the high resemblance between haptoglobin and haptoglobin-related protein, the receptor also takes up the complex of hemoglobin and the HDL-bound haptoglobin-related protein. This tricks the parasite into internalizing another HDL-associated protein and toxin, apolipoprotein L-I, that kills the parasite. In conclusion, variant human homologous hemoglobin-binding proteins that collectively may be designated the haptoglobins have diverted from the haptoglobin gene. On hemoglobin and receptor interaction, these haptoglobins contribute to different biologic events that go beyond simple removal from plasma of the toxic hemoglobin.
Differential efficacy of bortezomib plus chemotherapy within molecular subtypes of diffuse large B-cell lymphoma
Authors: Dunleavy Kieron , Pittaluga Stefania , Czuczman Myron S. , Dave Sandeep S. , Wright George , Grant Nicole , Shovlin Margaret , Jaffe Elaine S. , Janik John E. , Staudt Louis M. , Wilson Wyndham H. 
Published: April 2009

AbstractGene expression profiling of diffuse large B-cell lymphoma (DLBCL) has revealed distinct molecular subtypes that include germinal center B cell–like (GCB) and activated B cell–like (ABC) DLBCL. ABC DLBCL has a worse survival after upfront chemotherapy and is characterized by constitutive activation of the antiapoptotic nuclear factor–kappa B (NF-κB) pathway, which can inhibit chemotherapy. We hypothesized that inhibition of NF-κB might sensitize ABC but not GCB DLBCL to chemotherapy and improve outcome. As the proteasome inhibitor bortezomib can inhibit NF-κB through blocking IκBα degradation, we investigated bortezomib alone followed by bortezomib and doxorubicin-based chemotherapy in recurrent DLBCL. Tumor tissue was analyzed by gene expression profiling and/or immunohistochemistry to identify molecular DLBCL subtypes. As a control, we showed that relapsed/refractory ABC and GCB DLBCL have equally poor survivals after upfront chemotherapy. Bortezomib alone had no activity in DLBCL, but when combined with chemotherapy, it demonstrated a significantly higher response (83% vs 13%; P < .001) and median overall survival (10.8 vs 3.4 months; P = .003) in ABC compared with GCB DLBCL, respectively. These results suggest bortezomib enhances the activity of chemotherapy in ABC but not GCB DLBCL, and provide a rational therapeutic approach based on genetically distinct DLBCL subtypes. This trial is registered with http://www.ClinicalTrials.gov under identifier NCT00057902.
Hepcidin, the hormone of iron metabolism, is bound specifically to α-2-macroglobulin in blood
Authors: Peslova Gabriela , Petrak Jiri , Kuzelova Katerina , Hrdy Ivan , Halada Petr , Kuchel Philip W. , Soe-Lin Shan , Ponka Prem , Sutak Robert , Becker Erika , Huang Michael Li-Hsuan , Suryo Rahmanto Yohan , Richardson Des R. , Vyoral Daniel 
Published: April 2009

AbstractHepcidin is a major regulator of iron metabolism. Hepcidin-based therapeutics/diagnostics could play roles in hematology in the future, and thus, hepcidin transport is crucial to understand. In this study, we identify α2-macroglobulin (α2-M) as the specific hepcidin-binding molecule in blood. Interaction of 125I-hepcidin with α2-M was identified using fractionation of plasma proteins followed by native gradient polyacrylamide gel electrophoresis and mass spectrometry. Hepcidin binding to nonactivated α2-M displays high affinity (Kd 177 ± 27 nM), whereas hepcidin binding to albumin was nonspecific and displayed nonsaturable kinetics. Surprisingly, the interaction of hepcidin with activated α2-M exhibited a classical sigmoidal binding curve demonstrating cooperative binding of 4 high-affinity (Kd 0.3 μM) hepcidin-binding sites. This property probably enables efficient sequestration of hepcidin and its subsequent release or inactivation that may be important for its effector functions. Because α2-M rapidly targets ligands to cells via receptor-mediated endocytosis, the binding of hepcidin to α2-M may influence its functions. In fact, the α2-M–hepcidin complex decreased ferroportin expression in J774 cells more effectively than hepcidin alone. The demonstration that α2-M is the hepcidin transporter could lead to better understanding of hepcidin physiology, methods for its sensitive measurement and the development of novel drugs for the treatment of iron-related diseases.
Data-driven normalization strategies for high-throughput quantitative RT-PCR
Authors: Mar Jessica C , Kimura Yasumasa , Schroder Kate , Irvine Katharine M , Hayashizaki Yoshihide , Suzuki Harukazu , Hume David , Quackenbush John 
Published: April 2009

Abstract

Background
High-throughput real-time quantitative reverse transcriptase polymerase chain reaction (qPCR) is a widely used technique in experiments where expression patterns of genes are to be profiled. Current stage technology allows the acquisition of profiles for a moderate number of genes (50 to a few thousand), and this number continues to grow. The use of appropriate normalization algorithms for qPCR-based data is therefore a highly important aspect of the data preprocessing pipeline.

Results
We present and evaluate two data-driven normalization methods that directly correct for technical variation and represent robust alternatives to standard housekeeping gene-based approaches. We evaluated the performance of these methods against a single gene housekeeping gene method and our results suggest that quantile normalization performs best. These methods are implemented in freely-available software as an R package qpcrNorm distributed through the Bioconductor project.

Conclusion
The utility of the approaches that we describe can be demonstrated most clearly in situations where standard housekeeping genes are regulated by some experimental condition. For large qPCR-based data sets, our approaches represent robust, data-driven strategies for normalization.
Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation
Authors: Exarchos Konstantinos P , Exarchos Themis P , Papaloukas Costas , Troganis Anastassios N , Fotiadis Dimitrios I 
Published: April 2009

Abstract

Background
Polypeptides are composed of amino acids covalently bonded via a peptide bond. The majority of peptide bonds in proteins is found to occur in the trans conformation. In spite of their infrequent occurrence, cis peptide bonds play a key role in the protein structure and function, as well as in many significant biological processes.

Results
We perform a systematic analysis of regions in protein sequences that contain a proline cis peptide bond in order to discover non-random associations between the primary sequence and the nature of proline cis/trans isomerization. For this purpose an efficient pattern discovery algorithm is employed which discovers regular expression-type patterns that are overrepresented (i.e. appear frequently repeated) in a set of sequences. Four types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, iii) pattern discovery using a structural equivalency set and iv) pattern discovery using certain amino acids' physicochemical properties. The extracted patterns are carefully validated using a specially implemented scoring function and a significance measure (i.e. log-probability estimate) indicative of their specificity. The score threshold for the first three types of pattern discovery is 0.90 while for the last type of pattern discovery 0.80. Regarding the significance measure, all patterns yielded values in the range [-9, -31] which ensure that the derived patterns are highly unlikely to have emerged by chance. Among the highest scoring patterns, most of them are consistent with previous investigations concerning the neighborhood of cis proline peptide bonds, and many new ones are identified. Finally, the extracted patterns are systematically compared against the PROSITE database, in order to gain insight into the functional implications of cis prolyl bonds.

Conclusion

Cis patterns with matches in the PROSITE database fell mostly into two main functional clusters: family signatures and protein signatures. However considerable propensity was also observed for targeting signals, active and phosphorylation sites as well as domain signatures.
Profile analysis and prediction of tissue-specific CpG island methylation classes
Authors: Previti Christopher , Harari Oscar , Zwir Igor , del Val Coral 
Published: April 2009

Abstract

Background
The computational prediction of DNA methylation has become an important topic in the recent years due to its role in the epigenetic control of normal and cancer-related processes. While previous prediction approaches focused merely on differences between methylated and unmethylated DNA sequences, recent experimental results have shown the presence of much more complex patterns of methylation across tissues and time in the human genome. These patterns are only partially described by a binary model of DNA methylation. In this work we propose a novel approach, based on profile analysis of tissue-specific methylation that uncovers significant differences in the sequences of CpG islands (CGIs) that predispose them to a tissue- specific methylation pattern.

Results
We defined CGI methylation profiles that separate not only between constitutively methylated and unmethylated CGIs, but also identify CGIs showing a differential degree of methylation across tissues and cell-types or a lack of methylation exclusively in sperm. These profiles are clearly distinguished by a number of CGI attributes including their evolutionary conservation, their significance, as well as the evolutionary evidence of prior methylation. Additionally, we assess profile functionality with respect to the different compartments of protein coding genes and their possible use in the prediction of DNA methylation.

Conclusion
Our approach provides new insights into the biological features that determine if a CGI has a functional role in the epigenetic control of gene expression and the features associated with CGI methylation susceptibility. Moreover, we show that the ability to predict CGI methylation is based primarily on the quality of the biological information used and the relationships uncovered between different sources of knowledge. The strategy presented here is able to predict, besides the constitutively methylated and unmethylated classes, two more tissue specific methylation classes conserving the accuracy provided by leading binary methylation classification methods.
ACID: annotation of cassette and integron data
Authors: Joss Michael J , Koenig Jeremy E , Labbate Maurizio , Polz Martin F , Gillings Michael R , Stokes Harold W , Doolittle W Ford , Boucher Yan 
Published: April 2009

Abstract

Background
Although integrons and their associated gene cassettes are present in ~10% of bacteria and can represent up to 3% of the genome in which they are found, very few have been properly identified and annotated in public databases. These genetic elements have been overlooked in comparison to other vectors that facilitate lateral gene transfer between microorganisms.

Description
By automating the identification of integron integrase genes and of the non-coding cassette-associated attC recombination sites, we were able to assemble a database containing all publicly available sequence information regarding these genetic elements. Specialists manually curated the database and this information was used to improve the automated detection and annotation of integrons and their encoded gene cassettes. ACID (annotation of cassette and integron data) can be searched using a range of queries and the data can be downloaded in a number of formats. Users can readily annotate their own data and integrate it into ACID using the tools provided.

Conclusion
ACID is a community resource providing easy access to annotations of integrons and making tools available to detect them in novel sequence data. ACID also hosts a forum to prompt integron-related discussion, which can hopefully lead to a more universal definition of this genetic element.