bluuebunny/crossref_metadata_2025_split huggingface dataset:
Derrida, Politics and Democracy to Come
Authors: Patton Paul 
Published: October 2007

AbstractDerrida's early reluctance to spell out political implications of deconstruction gave way during the course of the 1980s to a series of analyses of political concepts and issues. This article identifies the principal intellectual strategies of Derrida's political engagements and provides a detailed account of his concept of ‘democracy to come’. Finally, it suggests several points of contact between Derrida and recent liberal political philosophy, as well as some areas in which deconstructive analyses require further refinement if fruitful exchange is to occur.
From Local to Global to Transnational Civil Society: Re‐Framing Development Perspectives on the Non‐State Sector
Authors: McIlwaine Cathy 
Published: October 2007

AbstractThis article outlines the meanings of civil society covering theoretical and development policy debates. It traces the evolution of conceptualisations of civil society noting how diversity in type, function and scale are critical in understanding these changes. The role of non‐governmental organisations within development policy is explored highlighting how the euphoria over civil society has been tempered over time, reflecting how Gramscian interpretations have begun to replace neo‐Tocquevillian viewpoints. The article also examines how civil society operates over different scales from local to global to transnational, assessing and critiquing the rise of global civil society or what is more appropriately called ‘transnational civil society’. The article finishes by highlighting the importance of diasporic civil society in relation to migrant groups especially from a development viewpoint as well as the need for more research on this issue. Conceptually, the article argues for a more sophisticated Gramscian interpretation of civil society that also recognises the importance of spatiality in the complex interpenetration between an increasingly extra‐territorialised state and an increasingly transnational civil society. Thus, it presents a re‐framing of development perspectives on the non‐state sector from local to global to transnational scales.
Urban Heat Islands: Observations, Impacts, and Adaptation
Authors: Yow Donald M. 
Published: October 2007

AbstractUrban heat islands are a clear, well‐documented example of an anthropogenic modification to climate that has an atmospheric, biological, and economic impact. This review shows how field‐based and modeling studies continue to help unravel the factors that are responsible for heat island development and are providing a basis for the development and application of sustainable adaptation strategies. As urban areas continue to expand, there is a heightened awareness that scientific knowledge of the urban heat island must be more effectively communicated to architects, engineers, and planners and translated into intelligent urban design. Green roof technology is a case in point. This and other technologies are being slowly adopted, and research published since 2003 suggests that the pace with which many practical applications are put into practice should accelerate.
Analytic Formula for the Clear‐sky UV Index
Authors: Madronich Sasha 
Published: October 2007

AbstractAn approximate formula for the UV Index (UVI) under cloud‐free, unpolluted, low surface albedo conditions is:
image
where μo is the cosine of the solar zenith angle and Ω is the total vertical ozone column (in Dobson Units, DU). The dependence on μo and Ω is based on a simple physical model of biologically weighted atmospheric transmission in the UV‐B and UV‐A spectral bands, with coefficients tuned to a detailed radiative transfer model, and is accurate to 10% or better over 0–60° and 200–400 DU. Other factors (clouds, haze, ground, etc.) mostly conserve this dependence and scale simply.
Sociology and New Wars in the Era of Globalisation
Authors: Drake Michael S. 
Published: October 2007

AbstractThe sociology of war has used a number of analytical perspectives to explain why the end of the Cold War saw outbreaks of violence around the world in the form of ‘new wars’, rather than universal peace. Factors often considered are globalisation, nationalist ideology, political elites, the Revolution in Military Affairs, international crime and migration. Sociological analysis of these new wars often makes use of comparative historical sociology, but these are wars of state disintegration rather than of state formation. This summary undertakes a critical evaluation of different approaches, arguing that they mostly follow a model of war inherited from Clausewitz which conceives of war only as an encounter between two states and so cannot successfully explain new war, where armed forces no longer primarily fight each other but target civilians.
Media, Racism and Islamophobia: The Representation of Islam and Muslims in the Media
Authors: Saeed Amir 
Published: October 2007

AbstractThis article examines the representation of Islam and Muslims in the British press. It suggests that British Muslims are portrayed as an ‘alien other’ within the media. It suggests that this misrepresenatation can be linked to the development of a ‘racism’, namely, Islamphobia that has its roots in cultural representations of the ‘other’. In order to develop this arguement, the article provies a summary/overview of how ethnic minorities have been represented in the British press and argues that the treatment of British Muslims and Islam follows these themes of ‘deviance’ and ‘un‐Britishness’.
Protective effects of a combination of quercetin and vitamin E against cyclosporine A‐induced oxidative stress and hepatotoxicity in rats
Authors: Mostafavi–Pour Zohreh , Zal Fatemeh , Monabati Ahmad , Vessal Mahmood 
Published: October 2007

Aim: Cyclosporine A (CsA) is the most widely used immunosuppressive drug in transplant surgery. It is able to generate reactive oxygen species (ROS) and cause lipid peroxidation (thiobarbituric acid‐reacting substances [TBARS]), which will directly result in CsA hepatotoxicity.Methods: In this study, the potential of quercetin (Q) and vitamin E (E), in attenuating CsA‐induced liver dysfunction in rats was investigated. Male Sprague–Dawley rats were divided into six groups and treated with either olive oil, ethanol + olive oil, CsA, CsA + E, CsA + Q, or CsA + E + Q for both 4 and 8 weeks. Hepatotoxicity was assessed by morphological alterations in tissue architecture and by reduced serum total protein and increased serum alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase.Results: The results indicated that CsA treatment increases TBARS and decreases activities of catalase (CAT) and glutathione peroxidase (GPx) in the rat liver. The co‐administration of E and Q with CsA treatment improved both liver morphology changes and function. A combination of these antioxidants significantly reduced TBARS and increased CAT and GPx activities in the hepatic tissue.Conclusion: Our data demonstrates that E + Q plays a protective role against the imbalance elicited by CsA between the production of free radicals and antioxidant defence systems, and suggests that a combination of these two antioxidants may find clinical application where cellular damage is a consequence of ROS.
Culture-Dependent and -Independent Characterization of Microbial Communities Associated with a Shallow Submarine Hydrothermal System Occurring within a Coral Reef off Taketomi Island, Japan
Authors: Hirayama Hisako , Sunamura Michinari , Takai Ken , Nunoura Takuro , Noguchi Takuro , Oida Hanako , Furushima Yasuo , Yamamoto Hiroyuki , Oomori Tamotsu , Horikoshi Koki 
Published: October 2007

ABSTRACTMicrobial communities in a shallow submarine hydrothermal system near Taketomi Island, Japan, were investigated using cultivation-based and molecular techniques. The main hydrothermal activity occurred in a craterlike basin (depth, ∼23 m) on the coral reef seafloor. The vent fluid (maximum temperature, >52°C) contained 175 μM H2S and gas bubbles mainly composed of CH4(69%) and N2(29%). A liquid serial dilution cultivation technique targeting a variety of metabolism types quantified each population in the vent fluid and in a white microbial mat located near the vent. The most abundant microorganisms cultivated from both the fluid and the mat were autotrophic sulfur oxidizers, including mesophilicThiomicrospiraspp. and thermophilicSulfurivirga caldicuralii. Methane oxidizers were the second most abundant organisms in the fluid; one novel type I methanotroph exhibited optimum growth at 37°C, and another novel type I methanotroph exhibited optimum growth at 45°C. The number of hydrogen oxidizers cultivated only from the mat was less than the number of sulfur and methane oxidizers, although a novel mesophilic hydrogen-oxidizing member of theEpsilonproteobacteriawas isolated. Various mesophilic to hyperthermophilic heterotrophs, including sulfate-reducingDesulfovibriospp., iron-reducingDeferribactersp., and sulfur-reducingThermococcusspp., were also cultivated. Culture-independent 16S rRNA gene clone analysis of the vent fluid and mat revealed highly diverse archaeal communities. In the bacterial community,S. caldicuraliiwas identified as the predominant phylotype in the fluid (clonal frequency, 25%). Both bacterial clone libraries indicated that there were bacterial communities involved in sulfur, hydrogen, and methane oxidation and sulfate reduction. Our results indicate that there are unique microbial communities that are sustained by active chemosynthetic primary production rather than by photosynthetic production in a shallow hydrothermal system where sunlight is abundant.
Sequence Characterization and Comparative Analysis of Three Plasmids Isolated from EnvironmentalVibriospp
Authors: Hazen Tracy H. , Wu Dongying , Eisen Jonathan A. , Sobecky Patricia A. 
Published: October 2007

ABSTRACTThe horizontal transfer of genes by mobile genetic elements such as plasmids and phages can accelerate genome diversification ofVibriospp., affecting their physiology, pathogenicity, and ecological character. In this study, sequence analysis of three plasmids fromVibriospp. previously isolated from salt marsh sediment revealed the remarkable diversity of these elements. Plasmids p0908 (81.4 kb), p23023 (52.5 kb), and p09022 (31.0 kb) had a predicted 99, 64, and 32 protein-coding sequences and G+C contents of 49.2%, 44.7%, and 42.4%, respectively. A phylogenetic tree based on concatenation of the host 16S rRNA andrpoAnucleotide sequences indicated p23023 and p09022 were isolated from strains most closely related toV. mediterraneiandV. campbellii, respectively, while the host of p0908 forms a clade withV. fluvialisandV. furnissii. Many predicted proteins had amino acid identities to proteins of previously characterized phages and plasmids (24 to 94%). Predicted proteins with similarity to chromosomally encoded proteins included RecA, a nucleoid-associated protein (NdpA), a type IV helicase (UvrD), and multiple hypothetical proteins. Plasmid p0908 had striking similarity to enterobacteria phage P1, sharing genetic organization and amino acid identity for 23 predicted proteins. This study provides evidence of genetic exchange betweenVibrioplasmids, phages, and chromosomes among diverseVibriospp.
Collateral Ability of the Circle of Willis in Patients With Unilateral Internal Carotid Artery Occlusion
Authors: Hendrikse Jeroen , Hartkamp Monique J. , Hillen Berend , Mali Willem P.T.M. , Grond Jeroen van der 
Published: October 2007

Background and Purpose—The circle of Willis is regarded as the major source of collateral flow in patients with severe carotid artery disease. The purpose of the present study was to assess whether the presence of border zone infarcts is related to the collateral ability of the circle of Willis in symptomatic (transient ischemic attack, minor stroke) and asymptomatic patients with unilateral occlusion of the internal carotid artery (ICA).Methods—Fifty-one patients (35 symptomatic, 16 asymptomatic) and 53 control subjects were investigated. Patients had unilateral occlusion of the ICA and contralateral ICA stenosis between 0% and 69%. The directions of flow, on the side of the ICA occlusion, and the size of the component vessels in the circle of Willis were investigated with MR angiography.Results—On average, 92% of the patients without border zone infarcts (n=26) had willisian collateral flow compared with 60% of patients with border zone infarcts (n=25;P<0.05). This increase in collateral flow was caused by the high prevalence of collateral flow via the posterior communicating artery in patients without border zone infarcts (50% versus 12%;P<0.05). No statistically significant relation was found between the pattern of collateral flow via the circle of Willis and the presence of clinical symptoms. Nevertheless, asymptomatic patients with ICA occlusion demonstrated an increased diameter of the anterior communicating artery (P<0.05).Conclusions—In patients with unilateral ICA occlusion, the presence of collateral flow via the posterior communicating artery in the circle of Willis is associated with a low prevalence of border zone infarcts. Asymptomatic patients with an ICA occlusion do not have an increased collateral function of the circle of Willis.
Common variation in the C-terminal region of the fibrinogen β-chain: effects on fibrin structure, fibrinolysis and clot rigidity
Authors: Ajjan Ramzi , Lim Bernard C. B. , Standeven Kristina F. , Harrand Robert , Dolling Sarah , Phoenix Fladia , Greaves Richard , Abou-Saleh Radwa H. , Connell Simon , Smith D. Alastair M. , Weisel John W. , Grant Peter J. , Ariëns Robert A. S. 
Published: October 2007

Fibrinogen BβArg448Lys is a common polymorphism, positioned within the carboxyl terminus of the Bβ-chain of the molecule. Studies suggest that it is associated with severity of coronary artery disease and development of stroke. The effects of the amino acid substitution on clot structure remains controversial, and the aim of this study was to investigate the effect(s) of this polymorphism on fibrin clot structure using recombinant techniques. Permeation, turbidity, and scanning electron microscopy showed that recombinant Lys448 fibrin had a significantly more compact structure, with thin fibers and small pores, compared with Arg448. Clot stiffness, measured by means of a novel method using magnetic tweezers, was significantly higher for the Lys448 compared with the Arg448 variant. Clots made from recombinant protein variants had similar lysis rates outside the plasma environment, but when added to fibrinogen-depleted plasma, the fibrinolysis rates for Lys448 were significantly slower compared with Arg448.
This study demonstrates for the first time that clots made from recombinant BβLys448 fibrinogen are characterized by thin fibers and small pores, show increased stiffness, and appear more resistant to fibrinolysis. Fibrinogen BβArg448Lys is a primary example of common genetic variation with a significant phenotypic effect at the molecular level.
RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses
Authors: Zhu Dianhui , Fox George E , Chakravarty Sugoto 
Published: October 2007

Abstract

Background
Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is essential for epidemiology, diagnostics, and vaccine development. Strain recognition based on similarity scores between target sequences and sequences of homology matched reference strains is often time consuming and ambiguous. This is especially true if only partial target sequences are available or if different ssRNA virus families are jointly analyzed. In such cases, knowledge of residues that uniquely distinguish among known reference strains is critical for rapid and unambiguous strain identification. Conventional sequence comparisons are unable to identify such capsid residues due to high sequence divergence among the ssRNA virus reference strains. Consequently, automated general methods to reliably identify strains using strain distinguishing residues are not currently available.

Results
We present here RECOVIR ("recognize viruses"), a software tool to automatically detect strains of caliciviruses and picornaviruses by comparing their capsid residues with built-in databases of residues that uniquely distinguish among known reference strains of these viruses. The databases were created by constructing partitioned phylogenetic trees of complete capsid sequences of these viruses. Strains were correctly identified for more than 300 complete and partial target sequences by comparing the database residues with the aligned residues of these sequences. It required about 5 seconds of real time to process each sequence. A Java-based user interface coupled with Perl-coded computational modules ensures high portability of the software. RECOVIR currently runs on Windows XP and Linux platforms. The software generalizes a manual method briefly outlined earlier for human caliciviruses.

Conclusion
This study shows implementation of an automated method to identify virus strains using databases of capsid residues. The method is implemented to detect strains of caliciviruses and picornaviruses, two of the most highly divergent ssRNA virus families, and therefore, especially difficult to identify using a uniform method. It is feasible to incorporate the approach into classification schemes of caliciviruses and picornaviruses and to extend the approach to recognize and classify other ssRNA virus families.
Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture
Authors: Bruce Stephen J , Gardiner Brooke B , Burke Les J , Gongora M Milena , Grimmond Sean M , Perkins Andrew C 
Published: October 2007

Abstract

Background
Expression profiling of embryonic stem (ES) cell differentiation in the presence of serum has been performed previously. It remains unclear if transcriptional activation is dependent on complex growth factor mixtures in serum or whether this process is intrinsic to ES cells once the stem cell program has been inactivated. The aims of this study were to determine the transcriptional programs associated with the stem cell state and to characterize mesoderm differentiation between serum and serum-free culture.

Results
ES cells were differentiated as embryoid bodies in 10% FBS or serum-free media containing BMP4 (2 ng/ml), and expression profiled using 47 K Illumina(R) Sentrix arrays. Statistical methods were employed to define gene sets characteristic of stem cell, epiblast and primitive streak programs. Although the initial differentiation profile was similar between the two culture conditions, cardiac gene expression was inhibited in serum whereas blood gene expression was enhanced. Also, expression of many members of the Kruppel-like factor (KLF) family of transcription factors changed dramatically during the first few days of differentiation. KLF2 and KLF4 co-localized with OCT4 in a sub-nuclear compartment of ES cells, dynamic changes in KLF-DNA binding activities occurred upon differentiation, and strong bio-informatic evidence for direct regulation of many stem cell genes by KLFs was found.

Conclusion
Down regulation of stem cell genes and activation of epiblast/primitive streak genes is similar in serum and defined media, but subsequent mesoderm differentiation is strongly influenced by the composition of the media. In addition, KLF family members are likely to be important regulators of many stem cell genes.
Saccharomyces cerevisiae: a versatile eukaryotic system in virology
Authors: Galao Rui P , Scheller Nicoletta , Alves-Rodrigues Isabel , Breinig Tanja , Meyerhans Andreas , Díez Juana 
Published: October 2007

AbstractThe yeastSaccharomyces cerevisiaeis a well-established model system for understanding fundamental cellular processes relevant to higher eukaryotic organisms. Less known is its value for virus research, an area in whichSaccharomyces cerevisiaehas proven to be very fruitful as well. The present review will discuss the main achievements of yeast-based studies in basic and applied virus research. These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production.
Gene expression profiling of cuticular proteins across the moult cycle of the crab Portunus pelagicus
Authors: Kuballa Anna V , Merritt David J , Elizur Abigail 
Published: October 2007

AbstractBackgroundCrustaceans represent an attractive model to study biomineralization and cuticle matrix formation, as these events are precisely timed to occur at certain stages of the moult cycle. Moulting, the process by which crustaceans shed their exoskeleton, involves the partial breakdown of the old exoskeleton and the synthesis of a new cuticle. This cuticle is subdivided into layers, some of which become calcified while others remain uncalcified. The cuticle matrix consists of many different proteins that confer the physical properties, such as pliability, of the exoskeleton.ResultsWe have used a custom cDNA microarray chip, developed for the blue swimmer crabPortunus pelagicus, to generate expression profiles of genes involved in exoskeletal formation across the moult cycle. A total of 21 distinct moult-cycle related differentially expressed transcripts representing crustacean cuticular proteins were isolated. Of these, 13 contained copies of the cuticle_1 domain previously isolated from calcified regions of the crustacean exoskeleton, four transcripts contained a chitin_bind_4 domain (RR consensus sequence) associated with both the calcified and un-calcified cuticle of crustaceans, and four transcripts contained an unannotated domain (PfamB_109992) previously isolated fromC. pagurus. Additionally, cryptocyanin, a hemolymph protein involved in cuticle synthesis and structural integrity, also displays differential expression related to the moult cycle. Moult stage-specific expression analysis of these transcripts revealed that differential gene expression occurs both among transcripts containing the same domain and among transcripts containing different domains.ConclusionThe large variety of genes associated with cuticle formation, and their differential expression across the crustacean moult cycle, point to the complexity of the processes associated with cuticle formation and hardening. This study provides a molecular entry path into the investigation of the gene networks associated with cuticle formation.