bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kings versus Bandits: Anti-colonialism in a Bandit Narrative
Authors: Mayaram Shail 
Published: February 2004

AbstractDebate and controversy have bedevilled the subject of social banditry. The early writing on social banditry saw it as primitive rebellion, as prepolitical and antithetical to class consciousness. Another approach identified it with weak state formation. The literature on South Asia saw social banditry as absent having been eroded by the institutional structure of caste. This article examines and critiques some of these theses on banditry. It argues, firstly, that social banditry can be simultaneous with a phase of intensified state formation. The specific theme investigated here is the interaction of the king, peasant and bandit in an Indian kingdom under late colonialism. A window to this universe is opened up by a folk epic from the oral tradition of a community of Muslims called the Meos. Far from being prepolitical, banditry raises crucial questions with respect to authority and legitimacy. This narrative not only interrogates the legitimacy of kingship, it also challenges the authority of the colonial state. Secondly, the article challenges the argument of South Asian exceptionalism to banditry that is perhaps easier to refute. Thirdly, as this article demonstrates, banditry need not relate to a pre-industrial capitalist world. Our bandit narrative indicates the reverberations of industrialism and attendant exchange relations and institutions in the colony even though it belongs to an area of ‘indirect’ rule.
Ôba Osamu
Authors: Loewe Michael 
Published: February 2004

AbstractA leading Japanese scholar of Chinese history who was based in Kansai, Ôba Osamu (1927–2002) spent a highly productive career, holding appointments from 1953 onwards at Seishin Joshi Daigaku, Ryûkoku Daigaku and Osaka Daigaku. A Professor of Kansai Daigaku in 1965, he later served there as the head of the Faculty of Letters (Bungaku bu) and at one time as Director of the University Library. Outside Japan he held short-term appointments, or was invited to be a visiting scholar, at a number of centres of learning, including some in China (Liaoning, Shandong, Hong Kong and Beijing), the United States of America (Princeton), Belgium (Leuven) and the United Kingdom (Cambridge and London). He held the title of Guest Professor in the Archaeological Research Institute, Gansu, and at the Chinese Academy of Social Sciences, Beijing.
The role of geometric complementarity in secondary structure packing: A systematic docking study
Authors: Jiang Sulin , Tovchigrechko Andrei , Vakser Ilya A. 
Published: February 2004

AbstractA strong similarity between the major aspects of protein folding and protein recognition is one of the emerging fundamental principles in protein science. A crucial importance of steric complementarity in protein recognition is a well‐established fact. The goal of this study was to assess the importance of the steric complementarity in protein folding, namely, in the packing of the secondary structure elements. Although the tight packing of protein structures, in general, is a well‐known fact, a systematic study of the role of geometric complementarity in the packing of secondary structure elements has been lacking. To assess the role of the steric complementarity, we used a docking procedure to recreate the crystallographically determined packing of secondary structure elements in known protein structures by using the geometric match only. The docking results revealed a significant percentage of correctly predicted packing configurations. Different types of pairs of secondary structure elements showed different degrees of steric complementarity (from high to low: β–β, loop–loop, α–α, and α–β). Interestingly, the relative contribution of the steric match in different types of pairs was correlated with the number of such pairs in known protein structures. This effect may indicate an evolutionary pressure to select tightly packed elements of secondary structure to maximize the packing of the entire structure. The overall conclusion is that the steric match plays an essential role in the packing of secondary structure elements. The results are important for better understanding of principles of protein structure and may facilitate development of better methods for protein structure prediction.
Atomic resolution analysis of the catalytic site of an aspartic proteinase and an unexpected mode of binding by short peptides
Authors: Erskine Peter T. , Coates Leighton , Mall Sanjay , Gill Raj S. , Wood Steve P. , Myles Dean A.A. , Cooper Jon. B. 
Published: February 2004

AbstractThe X‐ray structures of native endothiapepsin and a complex with a hydroxyethylene transition state analog inhibitor (H261) have been determined at atomic resolution. Unrestrained refinement of the carboxyl groups of the enzyme by using the atomic resolution data indicates that both catalytic aspartates in the native enzyme share a single negative charge equally; that is, in the crystal, one half of the active sites have Asp 32 ionized and the other half have Asp 215 ionized. The electron density map of the native enzyme refined at 0.9 Å resolution demonstrates that there is a short peptide (probably Ser‐Thr) bound noncovalently in the active site cleft. The N‐terminal nitrogen of the dipeptide interacts with the aspartate diad of the enzyme by hydrogen bonds involving the carboxyl of Asp 215 and the catalytic water molecule. This is consistent with classical findings that the aspartic proteinases can be inhibited weakly by short peptides and that these enzymes can catalyze transpeptidation reactions. The dipeptide may originate from autolysis of the N‐terminal Ser‐Thr sequence of the enzyme during crystallization.
Surface plasmon resonance studies of wild‐type and AV77 tryptophan repressor resolve ambiguities in super‐repressor activity
Authors: Finucane Michael D. , Jardetzky Oleg 
Published: February 2004

AbstractThe interactions of wild‐type (WT) and AV77 tryptophan repressor (TR) with several operators have been studied using surface plasmon resonance. The use of this real‐time method has been able to settle several outstanding issues in the field, in a way that has heretofore not been possible. We resolve the issue of the super‐repressor status of the AV77 aporepressor and find that in contrast to early studies, which found no significant difference in the binding constants in vitro to those of the WT, that there is indeed a clear difference in the binding constant that can simply account for the phenotype. Accordingly, there is no need for alternative proposals invoking complex equilibria with in vivo components not found in the in vitro experiments. In addition, we find that the AV77 holorepressor–DNA complex is much more stable than the equivalent WT complex, which has not been apparent from either in vitro or equilibrium binding experiments.
Library analysis of SCHEMA‐guided protein recombination
Authors: Meyer Michelle M. , Silberg Jonathan J. , Voigt Christopher A. , Endelman Jeffrey B. , Mayo Stephen L. , Wang Zhen‐Gang , Arnold Frances H. 
Published: February 2004

AbstractThe computational algorithm SCHEMA was developed to estimate the disruption caused when amino acid residues that interact in the three‐dimensional structure of a protein are inherited from different parents upon recombination. To evaluate how well SCHEMA predicts disruption, we have shuffled the distantly‐related β‐lactamases PSE‐4 and TEM‐1 at 13 sites to create a library of 214 (16,384) chimeras and examined which ones retain lactamase function. Sequencing the genes from ampicillin‐selected clones revealed that the percentage of functional clones decreased exponentially with increasing calculated disruption (E = the number of residue–residue contacts that are broken upon recombination). We also found that chimeras with low E have a higher probability of maintaining lactamase function than chimeras with the same effective level of mutation but chosen at random from the library. Thus, the simple distance metric used by SCHEMA to identify interactions and compute E allows one to predict which chimera sequences are most likely to retain their function. This approach can be used to evaluate crossover sites for recombination and to create highly mosaic, folded chimeras.
Identification of S‐sulfonation and S‐thiolation of a novel transthyretin Phe33Cys variant from a patient diagnosed with familial transthyretin amyloidosis
Authors: Lim Amareth , Prokaeva Tatiana , McComb Mark E. , Connors Lawreen H. , Skinner Martha , Costello Catherine E. 
Published: February 2004

AbstractFamilial transthyretin amyloidosis (ATTR) is an autosomal dominant disorder associated with a variant form of the plasma carrier protein transthyretin (TTR). Amyloid fibrils consisting of variant TTR, wild‐type TTR, and TTR fragments deposit in tissues and organs. The diagnosis of ATTR relies on the identification of pathologic TTR variants in plasma of symptomatic individuals who have biopsy proven amyloid disease. Previously, we have developed a mass spectrometry‐based approach, in combination with direct DNA sequence analysis, to fully identify TTR variants. Our methodology uses immunoprecipitation to isolate TTR from serum, and electrospray ionization and matrix‐assisted laser desorption/ionization mass spectrometry (MS) peptide mapping to identify TTR variants and posttranslational modifications. Unambiguous identification of the amino acid substitution is performed using tandem MS (MS/MS) analysis and confirmed by direct DNA sequence analysis. The MS and MS/MS analyses also yield information about posttranslational modifications. Using this approach, we have recently identified a novel pathologic TTR variant. This variant has an amino acid substitution (Phe → Cys) at position 33. In addition, like the Cys10 present in the wild type and in this variant, the Cys33 residue was both S‐sulfonated and S‐thiolated (conjugated to cysteine, cysteinylglycine, and glutathione). These adducts may play a role in the TTR fibrillogenesis.
Identification of protein biochemical functions by similarity search using the molecular surface database eF‐site
Authors: Kinoshita Kengo , Nakamura Haruki 
Published: February 2004

AbstractThe identification of protein biochemical functions based on their three‐dimensional structures is strongly required in the post‐genome‐sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database eF‐site (electrostatic surface of functional‐site in proteins). Using this system, functional sites similar to those of phosphoenoylpyruvate carboxy kinase were detected in several mononucleotide‐binding proteins, which have different folds. We also applied our method to a hypothetical protein, MJ0226 from Methanococcus jannaschii, and detected the mononucleotide binding site from the similarity to other proteins having different folds.
Glucoamylase‐like domains in the α‐ and β‐subunits of phosphorylase kinase
Authors: Pallen Mark J. 
Published: February 2004

AbstractPhosphorylase kinase is a four‐subunit enzyme involved in the regulation of glycogen breakdown. The traditional textbook view is that only the γ subunit has enzymatic activity, whereas the other three subunits have a regulatory role. Evidence from homology searches and sequence alignments, however, shows that the α‐ and β‐subunits possess amino‐terminal glucoamylase‐like domains and suggests that they might possess a previously overlooked amylase activity. If true, this would have important implications for the understanding, diagnosis, and management of glycogen storage diseases. There is thus a clear need to test this hypothesis through enzymatic assays and structural studies.
Exploring the nonlinear geometry of protein homology
Authors: Farnum Michael A. , Xu Huafeng , Agrafiotis Dimitris K. 
Published: February 2004

AbstractThe explosion of biological data resulting from genomic and proteomic research has created a pressing need for data analysis techniques that work effectively on a large scale. An area of particular interest is the organization and visualization of large families of protein sequences. An increasingly popular approach is to embed the sequences into a low‐dimensional Euclidean space in a way that preserves some predefined measure of sequence similarity. This method has been shown to produce maps that exhibit global order and continuity and reveal important evolutionary, structural, and functional relationships between the embedded proteins. However, protein sequences are related by evolutionary pathways that exhibit highly nonlinear geometry, which is invisible to classical embedding procedures such as multidimensional scaling (MDS) and nonlinear mapping (NLM). Here, we describe the use of stochastic proximity embedding (SPE) for producing Euclidean maps that preserve the intrinsic dimensionality and metric structure of the data. SPE extends previous approaches in two important ways: (1) It preserves only local relationships between closely related sequences, thus allowing the map to unfold and reveal its intrinsic dimension, and (2) it scales linearly with the number of sequences and therefore can be applied to very large protein families. The merits of the algorithm are illustrated using examples from the protein kinase and nuclear hormone receptor superfamilies.
The decline of a regional fishing nation: The case of Ghana and West Africa
Authors: Atta‐Mills John , Alder Jackie , Rashid Sumaila Ussif 
Published: February 2004

Abstract Inadequate trade policies, globalization of the fishing industry, dominance of Europe's distant water fleets, declarations of exclusive economic zones (EEZs) by neighbouring West African nations, overfishing and a lack of good governance contributed to the decline of Ghana as a regional fishing nation, a position it had held since the 18th century. The prohibitive cost of access arrangements limited Ghana's access to distant waters. The country's marine environments have been impacted by overexploitation of stocks and the use of destructive methods. Subsistence fishing has become the sole means of survival for many fishers. The decline of the fishing sector has limited the country's ability to meet domestic demand and threatened the economic and food security of many Ghanaians. The article traces the early history of Ghana's fisheries, their gradual decline during the last four decades, and outlines recommendations for policy changes to address the situation and steer the nation on a course towards sustainable fisheries.
Irrigation and collective action: A study in method with reference to the Shiwalik Hills, Haryana
Authors: Kurian Mathew , Dietz Ton 
Published: February 2004

Abstract In recent years decentralized development approaches have gained prominence in the agricultural sector. A host of community based watershed management projects have been implemented that encourage community organizations to undertake management of previously government controlled irrigation systems and forests. Community organizations have been given the responsibility of managing water distribution, collection of irrigation service fees and undertaking routine maintenance of irrigation infrastructure. In this context, analysis of irrigation management has concluded that groups that are relatively homogeneous may fare better than heterogeneous groups in facilitating collective action. However, this article argues that analysis of the influence of group heterogeneity on collective action is complicated because of its multi‐dimensional nature and the presence of non‐monotonic effects in mechanisms linking heterogeneity and collective outcomes. The article discusses the importance of context specification in analysis of group heterogeneity through a discussion of elements of a joint management contract in Haryana (India), identification of key variables with a potential to explain collective action in irrigation management and construction of household endowment and water interest scores to account for the influence of group heterogeneity in facilitating collective action. In the process of applying household endowment and water interest scores, the authors highlight the role of local ecological variation and non‐farm employment in influencing collective action. Proper specification of local context enables the researchers to rely on household endowment and water interest scores to predict conflicts and potential for irrigation service provision and compliance with irrigation service rules.
City in Change: Globalization, Local Politics and Urban Movements in Contemporary Stockholm
Authors: Stahre Ulf 
Published: February 2004

AbstractIn this article contemporary city change in Stockholm is first described against a background of theories on global cities. Stockholm cannot be seen as a global city, but displays many typical signs of the ongoing development in global cities. In the article this is shown by examining the situation in Stockholm regarding the economic structure, especially the expanding IT‐sector, social and economic polarization, local politics and the efforts to improve the infrastructure. In the change of the city social movements have been very active. Since the 1960s three different kinds of movements have existed, which are described and analysed against a background of theories on social movements. The first of these, the so‐called neighbourhood movement, emerged at the end of the 1960s and had all the typical signs of the so‐called ‘new’ social movements of that time. In the 1990s a new environmental movement acted mainly against proposed big traffic‐routes. This movement reflected in its structure some important features of today's society: fragmentation, individualization and globalization. At the end of the 1990s a third movement emerged as a reaction against the new competitive urban politics and the ongoing change of the city. Finally, the modifying impact that movements and local factors in Stockholm have had on globalization is discussed, as well as the difficulty in estimating the impact of movements on local politics.L'article décrit d'abord l'évolution urbaine contemporaine à Stockholm, en fonction des théories sur les villes planétaires. Même si la capitale suédoise n'est pas censée en faire partie, elle présente nombre des caractéristiques du développement actuel de ces grandes villes mondiales. L'article le montre en examinant sa situation en matière de structure économique (en particulier, l'expansion de son secteur technologique informatique), de polarisation sociale et économique, de politique locale et d'efforts d'amélioration des infrastructures. Les mouvements sociaux ont largement contribuéà l'évolution urbaine. Depuis 1960, ils sont intervenus sous trois formes, décrites et analysées par rapport aux théories des mouvements sociaux. La première, le ‘mouvement de quartier’, est apparue à la fin des années 1960 et présentait tous les signes typiques des dits ‘nouveaux’ mouvements sociaux de l'époque. Dans les années 1990, c'est un mouvement environnemental qui a agi surtout à l'encontre des grands itinéraires de circulation proposés, révélant par sa structure quelques caractéristiques importantes de la société actuelle: fragmentation, individualisation et mondialisation. A la fin des années 1990, un troisième mouvement est né en réaction à la nouvelle politique urbaine concurrentielle et à l'évolution vécue par la ville. Pour finir sont discutées l'incidence, sur la mondialisation, des mouvements et des facteurs locaux propres à Stockholm, ainsi que la difficulté d'évaluer l'impact des mouvements sur la politique locale.
Urban Elites in England: New Models of Executive Governance
Authors: Leach Steve , Wilson David 
Published: February 2004

AbstractPolitical leadership has become a much more explicit and widespread feature of English urban governance than it was 20 years ago. It has become particularly high profile since the Labour Government came into power in 1997 and sponsored legislation (Local Government Act 2000) which required all English local authorities to replace or modify the existing committee system of decision‐making by adopting one of four prescribed options, the thrust of which was to strengthen executive governance. This article considers the legislative drivers for change against the backdrop of long‐established cultural traditions, most notably the continued dominance of the party group which, in many ways, is inimical to the exercise of individual political leadership. It is argued that the way local authorities develop new models of executive governance reflects the local political culture. In other words the ‘locality effect’ assumes considerable importance when considering new patterns of executive governance in urban England. This article explores the interplay between the changing operational and institutional context and the resilient traditions of party group behaviour. It concludes that, while over a period of time there is likely to be considerable change in the patterns of urban political leadership, the rate of progress to that end will be highly differential.Au Royaume‐Uni, le leadership politique est devenu une caractéristique de la gouvernance urbaine bien plus nette et courante qu'il y a vingt ans. Elle est proéminente depuis l'accession au pouvoir du gouvernement travailliste en 1997, lequel a soutenu une législation (Local Government Act, 2000) exigeant de toutes les autorités locales britanniques qu'elles remplacent ou modifient leur système décisionnel de commissions en adoptant l'une des quatre options établies visant au renforcement de la gouvernance exécutive. L'article s'intéresse aux moteurs législatifs du changement sur fond de longues traditions culturelles, notamment de dominance persistante du groupe du parti qui, à bien des égards, est hostile à l'exercice d'un leadership politique personnel. La manière dont les autorités locales élaborent des modèles originaux de gouvernance pour l'exécutif traduit la culture politique locale. Autrement dit, ‘l'incidence locale’ revêt une importance considérable lorsqu'on s'attache aux nouveaux modèles de gouvernance exécutive dans l'Angleterre urbaine. L'article explore l'interaction entre le contexte opérationnel et institutionnel évolutif et les traditions résistantes du comportement de parti. En conclusion, si les modèles de leadership politique urbain connaîtront sans doute une vaste transformation au fil des années, la vitesse de progression de celle‐ci sera très diversifiée.