bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pierre Bourdieu, the ‘cultural turn’ and the practice of international history
Authors: JACKSON PETER 
Published: January 2008

AbstractThe rise of the ‘cultural turn’ has breathed new life into the practice of international history over the past few decades. Cultural approaches have both broadened and deepened interpretations of the history of international relations. This article focuses on the use of culture as an explanatory methodology in the study of international history. It outlines the two central criticisms often made of this approach. The first is that it suffers from a lack of analytical rigour in both defining what culture is and understanding how it shapes individual and collective policy decisions. The second is that it too often leads to a tendency to exaggerate the importance of the cultural predispositions of individual or collective actors at the expense of the wider structures within which policymaking takes place. The article provides a brief outline of the social theory of Pierre Bourdieu – which focuses on the interaction between the cultural orientations of social actors and the structural environment that conditions their strategies and decisions. It then argues that Bourdieu’s conceptual framework can provide the basis for a more systematic approach to understanding the cultural roots of policymaking and that international historians would benefit from engagement with his approach.
Molecular mechanisms for myocardial mitochondrial dysfunction in the metabolic syndrome
Authors: Bugger Heiko , Dale Abel E. 
Published: January 2008

The metabolic syndrome represents a cluster of abnormalities, including obesity, insulin resistance, dyslipidaemia and Type 2 diabetes, that increases the risk of developing cardiovascular diseases, such as coronary artery disease and heart failure. The heart failure risk is increased even after adjusting for coronary artery disease and hypertension, and evidence is emerging that changes in cardiac energy metabolism might contribute to the development of contractile dysfunction. Recent findings suggest that myocardial mitochondrial dysfunction may play an important role in the pathogenesis of cardiac contractile dysfunction in obesity, insulin resistance and Type 2 diabetes. This review will discuss potential molecular mechanisms for these mitochondrial abnormalities.
Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus
Authors: Liao Yu-Chieh , Lee Min-Shi , Ko Chin-Yu , Hsiung Chao A. 
Published: January 2008

Abstract
Motivation: Continual and accumulated mutations in hemagglutinin (HA) protein of influenza A virus generate novel antigenic strains that cause annual epidemics.
Results: We propose a model by incorporating scoring and regression methods to predict antigenic variants. Based on collected sequences of influenza A/H3N2 viruses isolated between 1971 and 2002, our model can be used to accurately predict the antigenic variants in 1999–2004 (agreement rate = 91.67%). Twenty amino acid positions identified in our model contribute significantly to antigenic difference and are potential immunodominant positions.
Contact: hsiung@nhri.org.tw
Supplementary information: The supplementary information includes 62 amino acid sequences of H3N2 viruses and 277 pair-wise antigenic distances.
A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake
Authors: Kremling A. , Bettenbrock K. , Gilles E. D. 
Published: January 2008

Abstract
Motivation: In Escherichia coli, the phosphoenolpyruvate: carbohydrate phosphotransferase system acts like a sensory element which is able to measure the flux through glycolysis. Since the output of the sensor, the phosphorylated form of protein EIIA, is connected to the activity of the global transcription factor Crp, the kinetic and structural properties of the system are important for the understanding of the overall cellular behavior.
Results: A family of mathematical models is presented, varying with respect to their degree of complexity (number of reactions that are taken into account, number of parameters) that show a structurally and quantitatively robust behavior. The models describe a set of experimental data that relates the output of the sensor to the specific growth rate. A central element that is responsible for the structural robustness is a feed-forward loop in the glycolysis, namely the activation of the pyruvate kinase reaction by a metabolite of the upper part of the glycolysis. The robustness is shown for variations of the measured data as well as for variations of the parameters.
Availability: MATLAB files for model simulations are available on http://www.mpi-magdeburg.mpg.de/people/kre/robust/ A short description of the files provided on this site can be found in the Supporting information.
Contact: kremling@mpi-magdeburg.mpg.de
Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification
Authors: Khatun Jainab , Hamlett Eric , Giddings Morgan C. 
Published: January 2008

Abstract
Motivation: The identification of peptides by tandem mass spectrometry (MS/MS) is a central method of proteomics research, but due to the complexity of MS/MS data and the large databases searched, the accuracy of peptide identification algorithms remains limited. To improve the accuracy of identification we applied a machine-learning approach using a hidden Markov model (HMM) to capture the complex and often subtle links between a peptide sequence and its MS/MS spectrum.
Model: Our model, HMM_Score, represents ion types as HMM states and calculates the maximum joint probability for a peptide/spectrum pair using emission probabilities from three factors: the amino acids adjacent to each fragmentation site, the mass dependence of ion types and the intensity dependence of ion types. The Viterbi algorithm is used to calculate the most probable assignment between ion types in a spectrum and a peptide sequence, then a correction factor is added to account for the propensity of the model to favor longer peptides. An expectation value is calculated based on the model score to assess the significance of each peptide/spectrum match.
Results: We trained and tested HMM_Score on three data sets generated by two different mass spectrometer types. For a reference data set recently reported in the literature and validated using seven identification algorithms, HMM_Score produced 43% more positive identification results at a 1% false positive rate than the best of two other commonly used algorithms, Mascot and X!Tandem. HMM_Score is a highly accurate platform for peptide identification that works well for a variety of mass spectrometer and biological sample types.
Availability: The program is freely available on ProteomeCommons via an OpenSource license. See http://bioinfo.unc.edu/downloads/ for the download link.
Contact: giddings@unc.edu, giddings@med.unc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Evidence for population structuring of blue whiting (Micromesistius poutassou) in the Northeast Atlantic
Authors: Was Anna , Gosling Elizabeth , McCrann Karen , Mork Jarle 
Published: January 2008

AbstractWas, A., Gosling, E., McCrann, K., and Mork, J. 2008. Evidence for population structuring of blue whiting (Micromesistius poutassou) in the Northeast Atlantic. – ICES Journal of Marine Science, 65: 216–225. Many marine fish species are characterized by large population sizes, strong migratory behaviour, high fecundity, and pelagic eggs and larvae that are subject to passive transport by ocean currents, all factors that tend to reduce the rate of development of genetic partitioning among localized populations. The blue whiting (Micromesistius poutassou) is a commercially important gadoid that exhibits all these characteristics, although to date there has been little evidence of genetic heterogeneity except at the latitudinal extremes of its range in the NE Atlantic. Genetic variation was analysed at five microsatellite loci in 16 samples, 14 comprising spawning adults, collected along the continental shelf from 44°N to 60°N, a distance of ∼1900 km. Although pairwise FST values were low (0.0–0.040; mean 0.0097), more than 40% of the estimates were significant, with Celtic Sea and Bay of Biscay samples significantly differentiated from samples from the Porcupine Bank, Hebridean Shelf, Sulisker Bank, and Papa Bank. There was also significant differentiation between samples taken in different years on Rockall Bank. Mantel tests revealed no significant isolation by distance. We used a landscape genetics approach, which combines spatial and genetic information, to detect barriers to gene flow. Four zones of lowered gene flow were identified, generally in concordance with hydrographic patterns, fish spawning behaviour, and the simulated transport of larvae in the NE Atlantic Ocean.
Functional Characterization of PaLAX1, a Putative Auxin Permease, in Heterologous Plant Systems
Authors: Hoyerová Klára , Perry Lucie , Hand Paul , Laňková Martina , Kocábek Tomáš , May Sean , Kottová Jana , Pačes Jan , Napier Richard , Zažímalová Eva 
Published: January 2008

AbstractWe have isolated the cDNA of the gene PaLAX1 from a wild cherry tree (Prunus avium). The gene and its product are highly similar in sequences to both the cDNAs and the corresponding protein products of AUX/LAX-type genes, coding for putative auxin influx carriers. We have prepared and characterized transformed Nicotiana tabacum and Arabidopsis thaliana plants carrying the gene PaLAX1. We have proved that constitutive overexpression of PaLAX1 is accompanied by changes in the content and distribution of free indole-3-acetic acid, the major endogenous auxin. The increase in free indole-3-acetic acid content in transgenic plants resulted in various phenotype changes, typical for the auxin-overproducing plants. The uptake of synthetic auxin, 2,4-dichlorophenoxyacetic acid, was 3 times higher in transgenic lines compared to the wild-type lines and the treatment with the auxin uptake inhibitor 1-naphthoxyacetic acid reverted the changes caused by the expression of PaLAX1. Moreover, the agravitropic response could be restored by expression of PaLAX1 in the mutant aux1 plants, which are deficient in auxin influx carrier activity. Based on our data, we have concluded that the product of the gene PaLAX1 promotes the uptake of auxin into cells, and, as a putative auxin influx carrier, it affects the content and distribution of free endogenous auxin in transgenic plants.
Optimized Immune Response Elicited by a DNA Vaccine Expressing Pneumococcal Surface Protein A Is Characterized by a Balanced Immunoglobulin G1 (IgG1)/IgG2a Ratio and Proinflammatory Cytokine Production
Authors: Ferreira Daniela M. , Darrieux Michelle , Oliveira Maria Leonor S. , Leite Luciana C. C. , Miyaji Eliane N. 
Published: January 2008

ABSTRACT
We have previously shown that DNA immunization with PspA (pneumococcal surface protein A) DNA is able to elicit protection comparable to that elicited by immunization with PspA protein (with alum as adjuvant), even though the antibody levels elicited by DNA immunization are lower than those elicited by immunization with the protein. This work aims at characterizing the ability of sera to bind to the pneumococcal surface and to mediate complement deposition, using BALB/c wild-type and interleukin-4 knockout mice. We observed that higher anti-PspA levels correlated with intense antibody binding to the pneumococcal surface, while elevated complement deposition was observed with sera that presented balanced immunoglobulin G1 (IgG1)/IgG2a ratios, such as those from DNA-immunized mice. Furthermore, we demonstrated that gamma interferon and tumor necrosis factor alpha were strongly induced after intraperitoneal pneumococcal challenge only in mice immunized with the DNA vaccine. We therefore postulate that although both DNA and recombinant protein immunizations are able to protect mice against intraperitoneal pneumococcal challenge, an optimized response would be achieved by using a DNA vaccine and other strategies capable of inducing balanced Th1/Th2 responses.
Magnitude, Breadth, and Functional Profile of T-Cell Responses during Human Immunodeficiency Virus Primary Infection with B and BF Viral Variants
Authors: Turk Gabriela , Gherardi María Magdalena , Laufer Natalia , Saracco Mónica , Luzzi Renata , Cox Josephine H. , Cahn Pedro , Salomon Horacio 
Published: January 2008

ABSTRACTThe molecular pattern of the human immunodeficiency virus (HIV) epidemic in Argentina provides an appropriate scenario to study cellular immune responses in patients with non-clade B infection. We aimed to map T-cell responses in patients infected with BF recombinant variants and compare them with those of clade B patients. Sixteen recently infected patients were enrolled and grouped by viral subtype. Nef-specific responses were evaluated with a peptide matrix-based gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay using B and BF overlapping peptides. Cross-clade and clade-specific responses were found. A correlation between B versus BF Nef-specific responses was identified. Detailed analysis at the single-peptide level revealed that BF patients show a narrower response but greater magnitude. Nef immunodominant responses agreed with previous publications, although the B loop was targeted at an unexpectedly high frequency. The putative HLA allele(s) restricting each positive response was determined. Single-peptide level screening with two different peptide sets uncovered discordant responses (mostly caused by peptide offsetting) and allowed detection of increased breadth. Positive responses identified by ELISPOT assay were further studied by intracellular cytokine staining. These were almost exclusively mediated by CD8 T cells. Characterization of concordant responses revealed that cells show distinct functional profiles, depending on the peptide presented. Last, quality (in terms of polyfunctionality) of T cells was associated with better viral replication containment. Overall, interclade differences in the frequency of epitopes recognized, structural domains targeted, and magnitude of responses were identified. Screening T-cell responses with multiple sets increased sensitivity. Further support for the notion of polyfunctional CD8+T-cell requirement to better control viral replication is also provided.
Exercise-induced increases in NT-proBNP are not related to the exercise-induced immune response: Figure 1
Authors: Scharhag J , Meyer T , Auracher M , Müller M , Herrmann M , Gabriel H , Herrmann W , Kindermann W 
Published: January 2008

Objective:To investigate if the exercise-induced immune response contributes to the exercise-induced increase in brain natriuretic peptide (BNP) in healthy athletes. This has previously been speculated, as elevated concentrations of BNP or N-terminal pro brain natriuretic peptide (NT-proBNP) in cardiovascular patients were found to be related to immune reactions and elevations in inflammatory cytokines such as interleukin 6 (IL-6).Methods:Stored serum samples were analysed for NT-proBNP concentrations of 14 healthy endurance athletes (mean age: 25 (SD 5) years; VO2peak67 (SD 6) ml/min/kg), who had been examined previously for exercise-induced immune reactions and their dependence on carbohydrate supplementation (6 or 12% carbohydrate vs placebo beverages) after three bouts of 4 h cycling at a given workload of 70% of the individual anaerobic threshold. Venous blood samples were taken before, immediately after, and 1 h and 1 day after exercise. Leucocyte subpopulations were determined immediately after blood sampling by flow cytometry. Serum samples for posterior analysis of C-reactive protein (CRP), IL-6, cortisol and NT-proBNP were stored at −80°C.Results:The exercise-induced increases in NT-proBNP (p<0.001) were not related to the exercise-induced immune response, although exercise induced marked (CHOS-dependent) increases in IL-6, CRP, cortisol, leucocytes, neutrophils, monocytes and natural killer cells.Conclusion:It is unlikely that the exercise-induced increases in NT-proBNP or BNP in healthy athletes are caused by the exercise-induced immune response. Therefore, exercise-induced increases in NT-proBNP or BNP in healthy athletes have to be differentiated from increases in cardiovascular patients with systemic inflammation.
Putting the Myth of Creatine Supplementation Leading to Muscle Cramps and Dehydration to Rest
Authors: Dalbo Vincent James , Roberts Mike , Kerksick Chad , Stout Jeff 
Published: January 2008

AbstractCreatine is one of the most popular athletic supplements with sales surpassing 400 million dollars in 2004. Due to the popularity and efficacy of creatine supplementation over 200 studies have examined the effects of creatine on athletic performance. Despite the abundance of research suggesting the effectiveness and safety of creatine a fallacy appears to exist in the general public driven by media claims and anecdotal reports that creatine supplementation can result in muscle cramps and dehydration. Although, a number of published studies have refuted these claims, a recent position statement by the American College of Sports Medicine (ACSM) in 2001 advised individuals who are managing their weight and exercising intensely or in hot environments to avoid creatine supplementation. Recent reports now suggest that creatine may enhance performance in hot and or humid conditions by maintaining hematocrit, aiding thermoregulation and reducing exercising heart rate and sweat rate. Creatine may also positively influence plasma volume during the onset of dehydration. Considering these new published findings, little evidence exists that creatine supplementation in the heat presents additional risk and should be taken into consideration as position statements and other related documents are published.Key Words:creatine supplementation, muscle cramping, dehydration
Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers
Authors: Stevens Ellen V. , Nishizuka Satoshi , Antony Smitha , Reimers Mark , Varma Sudhir , Young Lynn , Munson Peter J. , Weinstein John N. , Kohn Elise C. , Pommier Yves 
Published: January 2008

Abstract
Molecular profiling of markers involved in the activity of chemotherapeutic agents can shed light on the successes and failures of treatment in patients and can also provide a basis for individualization of therapy. Toward those ends, we have used reverse-phase protein lysate microarrays to evaluate expression of protein components of the nucleotide excision repair (NER) pathways. Those pathways strongly influence the anticancer activities of numerous drugs, including those that are the focus here, cisplatin and ecteinascidin 743 (Et-743; Yondelis, Trabectedin). Cisplatin is generally more active in cell types deficient in NER, whereas Et-743 tends to be less active in those cells. We measured protein expression and sensitivity to those drugs in 17 human ovarian and colon cancer cell lines (13 of them from the NCI-60 panel) and five xeroderma pigmentosum (XP) patient cell types, each containing a different NER defect. Of the NER proteins giving reliable signals, XPF and XPG showed the highest correlations of protein expression with drug activity across all three tissue-of-origin groups. When we compared protein expression data with mRNA expression data from Affymetrix U133A chips, we found no consistent correlation between the two across the cell lines studied, which reinforces the conclusion that protein measurements can give more interpretable mechanistic information than can transcript measurements. The work reported here provides motivation for larger proteomic studies with more cell types focused on potential biomarkers in additional pharmacologically pertinent pathways. [Mol Cancer Ther 2008;7(1):10–8]
Picturing Persian Victory: The Painted Battle Scene on the Munich Wood
Authors: Summerer Lâtife 
Published: January 2008

AbstractThe present article analyses the battle scene on the painted beam in Munich, which originally belonged to the ensemble of an extensively painted tomb chamber near Tatarlı, and reviews its interpretation as an historical depiction that was proposed by the first editor Peter Calmeyer. The author concludes that this battle scene bears no clear indications to connect it with a specific historical event; rather, it seems to depict an exemplary Persian victory over enemies, who are conveyed as a unified ethnic group by their uniform costumes and pointed caps.The article analyses the evidence of the iconography in detail with particular regard to the forms of narration and the context, and in the light of this review attempts to show alternative ways how this painted Persian victory may be viewed and interpreted.
An Achaemenid « Palace » at Qarajamirli (Azerbaijan) Preliminary Report on the Excavations in 2006
Authors: Gagoshidze Iulon , Knauß Florian , Babaev Ilyas 
Published: January 2008

AbstractExcavations on a small mound near the village Qarajamirli in western Azerbaijan provided remains of a monumental building, as well as quite a number of fragments of limestone column bases. The symmetrical ground plan of the building, the architectural sculpture and the pottery found on the floor closely follow Persian models from the Achaemenid era. Similar structures are known from Sary Tepe (Azerbaijan) and Gumbati (Georgia). These, as well as the building in Qarajamirli, can be interpreted as the residences of Persian officials, who left this area when the Achaemenid Empire collapsed. The painted pottery from the following period, when some peasants or herdsmen occasionally lived there, so far finds parallels only in Eastern Georgia.
Oriental Innovations in Samtskhe (Southern Georgia) in the 1st Millenium BC
Authors: Licheli Vakhtang 
Published: January 2008

AbstractThe only archaeological monument of the 1st Millennium BC in Southern Georgia (Samtskhe), which is systematically explored, is a multi-layer settlement and necropolis in Atskuri. The assemblages of the 6th-2nd centuries BC from Atskuri testify to the close relation with the Greek world on one side and with the Achaemenian cultural area on the other. Rich burials excavated in Atskuri in the last years contain numerous objects of Achaemenian type, which are mostly local imitations of Achaemenian objects. This material also shows that Achaemenian traditions continued to exist in Southern Georgia into the post-Achaemenian era.
Wall Painting from Dahaneh-ye Gholaman (Sistan)
Authors: Sajjadi S. Mansur Seyyed 
Published: January 2008

AbstractThe site of Dahaneh-ye Gholaman (Sistan, in the southeastern part of the Iranian Plateau) was discovered in the early 1960s by Umberto Scerrato of IsMEO (now IsIAO). It was a major urban center of the 6th to the 5th centuries BC. New excavations at Dahaneh-ye Gholaman started in October 2000. During the third campaign of excavations, traces of wall paintings and incised images have been identified in room 25. The most important scene shows a standing man, chariot rider, with a bow in his hand, shooting an animal, most probably a wild boar. In the same room and among a great variety of painted designs, which are only partly distinguishable, there are also remains of an image of a Bactrian camel.