bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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

The 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

The 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

Familial 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

The 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

Phosphorylase 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

The 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.
“They Get You Out of Courage:” Persistent Deep Poverty Among Former Welfare‐Reliant Women
Authors: Blalock Lydia L. , Tiller Vicky R. , Monroe Pamel A.
Published: February 2004

We looked closely at families who remain in persistent deep poverty in the remote rural areas of one state, using welfare reform as the contextual backdrop. We examined the lives of 10 women who have participated in this qualitative research for over 6 years. The woman heading each family was a welfare program participant; she engaged (more or less) in the process mandated by the state for an orderly exit from welfare; and today she is caring for herself and her family without welfare. Human ecology and systems theories are used to help explain the choices made by these women as they often faced insurmountable barriers to finding and retaining jobs.
Women's Danger Management Strategies in an Inner‐City Housing Project*
Authors: Jarrett Robin L. , Jefferson Stephanie M.
Published: February 2004

The danger management strategies of low‐income African American women who live in a public housing community characterized by chronic violence are examined. Based on qualitative interviews with 18 single mothers, we explored the violent community dangers with which women contend, the nature of this violence, the strategies used to deal with community violence, and their benefits and costs to family and community life. Findings show that multiple types of violence characterized life in the community and that this violence has specific physical locations, a particular set of actors, and a temporal rhythm. Women's responses to violence were nonconfrontational and family focused in nature. These efforts were effective in keeping women and their children safe, but did not reduce the prevalence of violence.
Welfare Reform, Work‐Family Tradeoffs, and Child Well‐Being*
Authors: London Andrew S. , Scott Ellen K. , Edin Kathryn , Hunter Vicki
Published: February 2004

Welfare reform and related policy changes have altered the context in which welfare‐reliant women make choices about employment and family care. Using data from longitudinal qualitative interviews, we examined women's experiences of work‐family tradeoffs and how they think their employment affected their children. Women identified multiple co‐occurring costs and benefits of work for themselves and their children. Benefits included: increased income; increased self‐esteem, feelings of independence, and social integration; and the ability to model work and self‐sufficiency values for children. Costs included: working without increased income; overload, exhaustion, and stress; and less time and energy to be with, supervise, and support children. The relevance of these findings for family policy specialists and practitioners who work with low‐income families is discussed.
The Resilience and Strengths of Low‐Income Families
Authors: Orthner Dennis K. , Jones‐Sanpei Hinckley , Williamson Sabrina
Published: February 2004

This study examines indicators of family strength among a random sample of low‐income households with children. The Family Strength Index assesses strength according to economic, problem‐solving, communication, family cohesion, and social support assets. Variations in family strength are explained according to parental status and level of employment. Logistic regression is used to examine the contribution of assets to family outcomes. Findings indicate that relationship assets such as communication, problem solving, and social support predict positive outcomes for low‐income families.
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

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

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

In 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

Political 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.
A MAP kinase of the vascular wilt fungus Fusarium oxysporum is essential for root penetration and pathogenesis
Authors: Di Pietro Antonio , García‐Maceira Fe I. , Méglecz Emese , Roncero M. Isabel G.
Published: February 2004

The soil‐borne vascular wilt fungus Fusarium oxysporum infects a wide variety of plant species by directly penetrating roots, invading the cortex and colonizing the vascular tissue. We have identified fmk1, encoding a mitogen‐activated protein kinase (MAPK) of F. oxysporum that belongs to the yeast and fungal extracellular signal‐regulated kinase (YERK1) subfamily. Targeted mutants of F. oxysporum f. sp. lycopersici carrying an inactivated copy of fmk1 have lost pathogenicity on tomato plants but show normal vegetative growth and conidiation in culture. Colonies of the fmk1 mutants are easily wettable, and hyphae are impaired in breaching the liquid–air interface, suggesting defects in surface hydrophobicity. Fmk1 mutants also show reduced invasive growth on tomato fruit tissue and drastically reduced transcript levels of pl1 encoding the cell wall‐degrading enzyme pectate lyase. Conidia of the mutants germinating in the tomato rhizosphere fail to differentiate penetration hyphae, resulting in greatly impaired root attachment. The orthologous MAPK gene Pmk1 from the rice leaf pathogen Magnaporthe grisea complements invasive growth and partially restores surface hydrophobicity, root attachment and pathogenicity in an fmk1 mutant. These results demonstrate that FMK1 controls several key steps in the pathogenesis of F. oxysporum and suggest a fundamentally conserved role for the corresponding MAPK pathway in soil‐borne and foliar plant pathogens.
Regulation of RpoS by a novel small RNA: the characterization of RprA
Authors: Majdalani Nadim , Chen SuAnn , Murrow Jonathan , St John Kristin , Gottesman Susan
Published: February 2004

Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double‐stranded RNA stem–loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. The interaction of the rpoS mRNA with a small RNA, DsrA, disrupts the double‐strand pairing and allows high levels of translation initiation. We screened a multicopy library of Escherichia coli DNA fragments for novel activators of RpoS translation when DsrA is absent. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA, RprA is predicted to form three stem–loops and is highly conserved in Salmonella and Klebsiella species. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non‐essential. Mutations in the gene interfere with the induction of RpoS after osmotic shock when DsrA is absent, demonstrating a physiological role for RprA. The existence of two very different small RNA regulators of RpoS translation suggests that such additional regulatory RNAs are likely to exist, both for regulation of RpoS and for regulation of other important cellular components.
The alien flowering plants of Mexico
Authors: Villaseñor Jose L. , J. Espinosa‐Garcia Francisco
Published: February 2004

A list of 618 species of alien flowering plants recorded for Mexico is presented; they are distributed in 355 genera and 87 families. The families with the largest number of species are Poaceae (171), Fabaceae sensu lato (57), Asteraceae (56), and Brassicaceae (45). The representation of most families with alien species in Mexico agrees with the average distribution frequencies estimated by Pysek (1998) for 26 floras throughout the World. Exceptions are an under‐representation of Asteraceae and an over‐representation of Poaceae. Most alien species (78.9%) in Mexico have their origin in the Old World; South America ranks second with 9.6%. As defined by Richardson et al. (2000), 19.8% of the alien species could be considered casual aliens and 80.2% of them naturalized. The proportion of alien species relative to the 22,968 native flowering plant species recorded for Mexico is 2.7%.
Place prioritization for biodiversity conservation using probabilistic surrogate distribution data
Authors: Sarkar Sahotra , Pappas Christopher , Garson Justin , Aggarwal Anshu , Cameron Susan
Published: February 2004

We analyse optimal and heuristic place prioritization algorithms for biodiversity conservation area network design which can use probabilistic data on the distribution of surrogates for biodiversity. We show how an Expected Surrogate Set Covering Problem (ESSCP) and a Maximal Expected Surrogate Covering Problem (MESCP) can be linearized for computationally efficient solution. For the ESSCP, we study the performance of two optimization software packages (XPRESS and CPLEX) and five heuristic algorithms based on traditional measures of complementarity and rarity as well as the Shannon and Simpson indices of α‐diversity which are being used in this context for the first time. On small artificial data sets the optimal place prioritization algorithms often produced more economical solutions than the heuristic algorithms, though not always ones guaranteed to be optimal. However, with large data sets, the optimal algorithms often required long computation times and produced no better results than heuristic ones. Thus there is generally little reason to prefer optimal to heuristic algorithms with probabilistic data sets.
Impact of the invasive alien grass Melinis minutiflora at the savanna‐forest ecotone in the Brazilian Cerrado
Authors: Hoffmann William A. , Lucatelli Verusca M. P. C. , Silva Franciane J. , Azeuedo Isaac N. C. , Marinho Marcelo da S. , Albuquerque Ana Maria S. , Lopes Apoena de O. , Moreira Silvana P.
Published: February 2004

Exotic grasses are a serious threat to biodiversity in the cerrado savannas of central Brazil. Of particular concern is the possible role they may have in impeding tree regeneration at gallery (riverine) forest edges and increasing fire intensity, thereby driving gallery forest retreat. Here we quantify the effect of roads and distance from gallery forests on the abundance of the African grass Melinis minutiflora Beauv. and test for an effect of this species on woody plant regeneration and leaf area index. Melinis was present at approximately 70% of the sites near gallery forest edges, with its frequency declining sharply at greater distances from the edge. Melinis frequency was 2.8 times greater where roads were present nearby. Leaf area index (LAI) of the ground layer was 38% higher where Melinis was present than where it was absent. LAI was strongly correlated to fine fuel mass (r2 = 0.80), indicating higher fuel loads where Melinis was present. The abundance of tree and shrub species in the ground layer was negatively related to LAI and to the presence of Melinis. The greater fuel accumulation and reduced tree regeneration caused by Melinis may cause a net reduction in forest area by increasing fire intensity at the gallery forest edge and slowing the rate of forest expansion.
Latitudinal patterns in abundance and life‐history traits of the mole crabEmerita brasiliensison South American sandy beaches
Authors: Defeo Omar , Cardoso Ricardo S.
Published: February 2004

Demographic and life‐history attributes of the mole crabEmerita brasiliensiswere analysed along 2700 km of the Atlantic coast of South America, including sandy beaches at the southernmost limit (Uruguay) and at the core of its geographical range (Brazil). Population features varied markedly within this range and exhibited systematic geographical patterns of variation. Abundance significantly increased from temperate to subtropical beaches, and the same held true for the asymptotic weight of males. Conversely, length at maturity and asymptotic weight of females increased from subtropical to temperate beaches, being inversely related to sea water temperature. Macroecological patterns in abundance and body weight showed the first large‐scale evidence of scaling of population density to body size for a sandy beach population. Mortality rates (both sexes) followed a nonlinear increase from low‐density temperate beaches to high‐density subtropical beaches. The effect of habitat quality and availability could explain discontinuities in the species distribution within its range, and also differential responses in life‐history attributes at a local scale. Asymmetries and converse latitudinal trends between sexes suggest that there is not a single general factor determining large‐scale patterns in life‐history traits of this species. Our results reinforce the view that density‐dependent and environmental factors operating together regulate sandy beach populations. The need to develop macroecological studies in sandy beach ecology is highlighted, as knowledge acquired from local to large spatial scales throws light on population structure and regulation mechanisms.
Alien species reflecting history: medieval castles in Germany
Authors: Dehnen‐Schmutz Katharina
Published: February 2004

Ninety‐seven alien plant species were found in habitats provided by rocks and walls around 56 castles in Germany. Compared to Central European agriophytes (i.e. alien species naturalised in natural vegetation), the flora adjacent to castles had more species introduced before 1500. More alien species introduced earlier were found at castles built earlier compared to castles built later. Fifty percent of the species introduced before and during the Middle Ages were usable plants at that time, compared to 20% of usable plants among the native species in the same habitats. Species introduced earlier were mainly used for medication and nutrition, whereas later introductions were used for ornamental purposes. Compared to the total alien flora of Germany, there were more useable species at the castles, nearly the same percentage of ornamentals and fewer plants without use. These results imply that the species composition of alien species growing in the vicinity of medieval castles today may be traced back to the historical reasons for their introduction to these places.
A simple C‐reactive protein measurement for the differentiation between tuberculous and malignant pleural effusion
Authors: Chierakul Nitipatana , Kanitsap Apichart , Chaiprasert Angkana , Viriyataveekul Ronnachai
Published: February 2004

Objective:  The aim of this study was to determine the validity of pleural fluid C‐reactive protein (CRP) concentrations and/or pleural fluid to serum CRP ratio for differentiating tuberculous pleuritis (TBP) from malignant pleural effusion (MPE) in patients presenting with lymphocytic exudative pleural effusions.

Methodology:  A cross‐sectional study was conducted on 161 patients with pleural effusion who underwent diagnostic evaluation at Siriraj Hospital, Bangkok, Thailand, between April 2001 and March 2002. The complete biochemical analysis of pleural fluid, cultures of pleural fluid, and pathological examinations of pleural fluid and pleural tissue were performed. The CRP concentrations were then measured in stored sera and pleural fluid samples from patients with a lymphocytic exudative pleural effusion and with a definite diagnosis.

Results:  Among the 148 patients with lymphocytic exudative pleural effusions, 55 were diagnosed with TBP, 60 with MPE, and 33 with non‐specific pleuritis. Pleural fluid and serum CRP levels were significantly higher in the TBP group than in the MPE group (54.58 ± 4.50 mg/L and 106.93 ± 9.54 mg/L vs 12.66 ± 3.52 mg/L and 49.66 ± 8.84 mg/L, respectively, P < 0.001). The ratio of pleural fluid to serum CRP was significantly higher in the TBP group than in the MPE group (0.52 ± 0.18 vs 0.30 ± 0.16, P < 0.001). The optimum cut‐off value for pleural fluid CRP level of ≥30 mg/dL had a sensitivity of 72% with 93% specificity, and the pleural fluid to serum CRP ratio cut‐off value of 0.45 had a sensitivity of 60% with 89% specificity. A correlation between serum and pleural fluid CRP levels was observed in TBP patients but not in MPE patients.

Conclusion:  In patients presenting with lymphocytic exudative pleural effusion, a simple marker of raised pleural fluid CRP level may be helpful in discriminating between TBP and MPE.
The effects of antioxidants on exercise‐induced lipid peroxidation in patients with COPD
Authors: Agacdiken Aysen , Basyigit Ilknur , Özden Meltem , Yildiz Fusun , Ural Dilek , Maral Hale , Boyaci Hasim , Ilgazli Ahmet , Komsuoglu Baki
Published: February 2004

Objective:  The oxidant–antioxidant balance plays an important role in the pathogenesis of COPD. The aim of the present study was to evaluate the effects of exercise, as an oxidative stress factor on the oxidant–antioxidant balance and to investigate whether short‐term antioxidant treatment affects lipid peroxidation products.

Methodology:  Twenty‐one stable COPD patients and 10 control subjects were included in the study. Symptom‐limited exercise tests were performed by all subjects. Blood was collected before and 1 h after exercise in control subjects and before, 1 and 3 h after exercise in COPD patients, for analysis of malondialdehyde (MDA), reduced glutathione (GSH) and vitamin E (VE) levels. VE and vitamin C treatments were added to the regular bronchodilator therapy in 10 COPD patients for 1 month. After the treatment period, an exercise test was performed and blood was collected again for MDA, GSH and VE levels.

Results:  Baseline GSH and VE levels were significantly lower in the COPD group when compared with the control subjects. There was no statistically significant difference in MDA levels between the two groups. In the COPD group, MDA levels 3 h after exercise were significantly higher than at baseline. In contrast there were no significant differences in MDA, VE and GSH levels in the control group after exercise. VE and MDA levels increased significantly after exercise in COPD patients but there was no difference in GSH levels. Baseline exercise time was significantly lower in the COPD group than in the controls. In 10 COPD patients who were given antioxidant therapy, their exercise time increased significantly and there was no increase in MDA and VE levels after the repeated exercise test.

Conclusions:  Antioxidant levels were significantly lower in COPD patients than in control subjects. In these patients, exercise results in more significant oxidative stress and lipid peroxidation than in control subjects and antioxidant therapy may decrease lipid peroxidation following exercise and improve exercise capacity.
Hospital‐acquired pneumonia in general wards of a Japanese tertiary hospital
Authors: Ohi Hideo , Yanagihara Katsunori , Miyazaki Yoshitsugu , Hirakata Yoichi , Tomono Kazunori , Kadota Jun‐ichi , Tashiro Takayoshi , Kohno Shigeru
Published: February 2004

Objective:  Hospital‐acquired pneumonia (HAP) is an important nosocomial disorder because both its mortality and morbidity are high. The Japanese Respiratory Society (JRS) has proposed a new guideline for the diagnosis and treatment of HAP. Clinical investigations of HAP were conducted to assess the current status of HAP in accordance with this guideline.

Methodology:  Inpatients who developed HAP in the Second Department of Internal Medicine, Nagasaki University Hospital, a tertiary hospital in Japan, were evaluated. The incidence of HAP was 1.86% (59 cases in 3176 admissions) from 1996 to 2000. In particular, the severity rating of HAP for 46 patients in accordance with the JRS guidelines, was assessed.

Results:  The mortality rate was 6.5% at this hospital, which is less than that reported by other investigators in the field. The frequency of bacteria isolated from clinical specimens was as follows: Haemophilus influenzae (20%), Pseudomonas aeruginosa (16.7%), and methicillin‐resistant Staphylococcus aureus (13.3%). Response rates were stratified by first‐line medications and the results were as follows: penicillins (33.3%), third‐generation cephems (44.4%), and carbapenems (66.7%).

Conclusions:  Based on the results presented here, the severity rating proposed in this guideline for HAP appears reasonable, as the response rate for the first‐line antibiotic was better in Group II than in Groups III and IV. It will be important to analyse ‘clinical outcome’ in accordance with this guideline.
Blunted effect of the Kv channel inhibitor on pulmonary circulation in Tibetan sheep: A model for studying hypoxia and pulmonary artery pressure regulation
Authors: Ishizaki Takeshi , Sakai Akio , Koizumi Tomonori , Ruan Zonghai , Wang Zhan Gang
Published: February 2004

Objective:   The aim of this study was to assess the effect of 4‐aminopyridine, a Kv channel inhibitor, on the pulmonary circulation of Tibetan sheep. It has been reported that chronic hypoxia downregulates the 4‐aminopyridine (4AP)‐sensitive Kv channel (which governs the membrane potential (Em) of pulmonary vascular smooth muscle cells in pulmonary vessels) without a change in 4AP sensitivity.

Methodology:   Pulmonary haemodynamic indices and blood gas analyses were measured in six young male animals in an altitude chamber that was adjusted to simulated altitudes of 0 m, 2260 m, and 4500 m. Drip infusion of 4AP, 10 mg/h for 3 h, was started and continued during the study.

Results:   With the increase in altitude mean pulmonary artery pressure increased and mean Pao2 decreased. 4AP had no effect on the levels of mean PPA, mean pulmonary artery wedge pressure, cardiac output, and mean PaO2, mean PaCO2, and mean pH at any altitude but tended to alter heart rate and mean arterial pressure at altitudes of 2260 m and 4500 m.

Conclusion:   It is concluded that the 4AP‐sensitive Kv channel does not play a role in pulmonary vascular tone in high‐altitude active Tibetan sheep. Their pulmonary vascular oxygen sensing appears not to involve Kv channels.
Prediction of the maximal voluntary ventilation in healthy adult Chinese subjects
Authors: Kor Ai Ching , Ong Kian Chung , Earnest Arul , Wang Yee Tang
Published: February 2004

Objectives:  The aim of the present study was to investigate the relationship between the FEV1 and maximal voluntary ventilation (MVV) in healthy adult Chinese subjects, and to determine the validity of existing prediction equations of MVV for use in the Chinese population.

Methodology:  Ninety‐five healthy subjects (48 male and 47 female) stratified into five age groups (from 20 to 70 years) for both sexes were recruited from the general population. The FEV1 and MVV of these subjects were measured with a clinical spirometer. The MVV was determined using the closed‐circuit technique. The MVV was assessed for 12 s and values were calculated to obtain L/min. Multiple regression analysis was used to develop equations to predict MVV with age, height, FEV1 as well as with FEV1 alone as predictor variables. One‐sample t‐tests were used to compare the actual values of MVV for the subjects with their predicted values using equations from previous studies of MVV in healthy subjects.

Results:  Using FEV1 only, the following predictive equation was obtained: MVV = FEV1 × 45.12 − 15.85 (adjusted r2 = 0.792). Predicted MVV values using previously cited equations, including MVV = FEV1 × 35 or 40, were all significantly different from the actual MVV values of these subjects.

Conclusions:  The relationship between MVV and FEV1 among healthy adult Chinese subjects is described. Previously cited equations describing the relationship between FEV1 and MVV cannot be applied to healthy adult Chinese subjects.
Determinants of BMI in patients with COPD
Authors: Karadag Fisun , Karul Aslihan B. , Cildag Orhan , Altun Cagatay , Gurgey Ozgur
Published: February 2004

Objective:  COPD is characterized by significant chronic inflammation that is evident not only in the pulmonary compartment but also in the circulation. Peripheral blood features of COPD include markers of oxidative stress and altered circulating levels of inflammatory mediators and acute‐phase proteins. The presence of a systemic inflammatory response may influence quality of life by giving rise to weight loss, muscle wasting and tissue depletion. The aim of the present study was to evaluate the determinants of body mass and the value of serum tumour necrosis factor alpha (TNF‐α) as a marker of weight loss in COPD patients, and to correlate this with the burden of oxidative stress as measured by serum malonyldialdehyde (MDA) levels.

Methodology:  Fifty‐two male COPD patients (mean age 62.55 ± 6.81 years) were studied. After anthropometric measurements and standard spirometry, serum TNF‐α concentration was measured by enzyme‐linked immunosorbent assay using an hTNF‐α kit, and MDA was studied spectrophotometrically using the Yoshioka‐Kawada method.

Results:  The mean BMI was 24.82 ± 3.46. BMI was lower than normal (< 19) in six patients. Mean serum TNF‐α concentration was 14.99 ± 8.98 pg/mL and MDA was 0.93 ± 0.13 nmol/L. There was no significant correlation between serum MDA and TNF concentrations (P = 0.140). Serum TNF‐α and MDA concentrations were not correlated with severity of airflow obstruction or degree of hypoxaemia (P > 0.05 for all). BMI was negatively correlated with burden of smoking (pack‐years) (r = −0.392, P= 0.004); but not with pulmonary function, degree of hypoxaemia, serum TNF‐α or MDA levels. BMI was significantly lower in current smokers than ex‐smokers (P = 0.041); however, serum MDA and TNF levels were similar in both groups.

Conclusion:  The results of this study indicate that body mass is related to smoking status (both pack‐years and continuance of smoking) in COPD; however, serum TNF‐α concentration does not seem to be a good marker of weight loss in these patients.
The management of pleural space infections
Authors: Chapman Stephen J. , Davies Robert J. O.
Published: February 2004

Abstract:  Pleural infection is responsible for significant morbidity and mortality worldwide, and its clinical management is challenging. The diagnosis of empyema and tuberculous pleurisy may be difficult, and these conditions may be confused with other causes of exudative pleural effusions. Complicated parapneumonic effusion or empyema may present with ‘atypical’ clinical features; delays in diagnosis are common and may contribute to the high mortality of these infections. Pleural aspiration is the key diagnostic step; pleural fluid that is purulent or that has a pH < 7.2, or organisms on Gram stain or culture, is an indication for formal intercostal drainage. In order to achieve a definitive diagnosis of tuberculous pleurisy, Mycobacterium tuberculosis must be isolated in the culture of pleural fluid, pleural tissue or sputum; demonstration of granulomas in pleural tissue is also suggestive of tuberculosis. The use of pleural fluid biochemical markers, such as adenosine deaminase, in the diagnosis of tuberculous pleurisy varies among clinicians; the diagnostic value of such markers is affected by the background prevalence of tuberculosis and the likelihood of an alternative diagnosis. Uncertainties also remain regarding the treatment of pleural infection. Treatment of complicated parapneumonic effusion and empyema involves prolonged courses of antibiotics and attention to the patient's nutritional state. The role of intrapleural fibrinolytics and the optimal timing of surgical intervention are unknown. The lack of clear predictors of clinical outcome in empyema contributes to the difficulty in treating this condition. The pharmacological treatment of tuberculous pleurisy is the same as for pulmonary tuberculosis; the precise role of steroids in the treatment of tuberculous pleurisy remains uncertain.
Sputum carcinoembryonic antigen, neuron‐specific enolase and cytokeratin fragment 19 levels in lung cancer diagnosis
Authors: Kalomenidis Ioannis , Dimakou Katerina , Kolintza Androniki , Vlami Katerina , Papadakis Manos , Sotiropoulou Cristina , Orphanidou Dora , Roussos Charis , Papiris Spyros
Published: February 2004

Objective:  The aim of the present study was to examine the impact of sputum carcinoembryonic antigen (CEA), neuron‐specific enolase (NSE) and cytokeratin fragment 19 (CYFRA 21‐1) levels in lung cancer diagnosis and to compare the diagnostic usefulness of sputum assays with that of serum assays.

Methodology:  Forty‐seven patients with lung cancer and 62 with benign lung disease were studied. Tumour marker levels in sputum (sp.) and serum (ser) were measured by immunoradiometric assays.

Results:  Sputum and serum tumour marker levels were significantly higher in lung cancer than in benign disease. When the specificity was 95%, the sensitivity was 57%, 43%, 36%, 30%, 28% and 19%, for spCEA, serCYFRA 21‐1, spCYFRA 21‐1, serCEA, serNSE, and spNSE, respectively. Bayesian analysis showed that the best predictive values correspond to spCEA and serCYFRA 21‐1. The maximum overall gain was obtained in pretest probability of 0.35 for both spCEA and serCYFRA 21‐1, with predictive values of 84% and 80% for spCEA and serCYFRA 21‐1, respectively.

Conclusion:  Sputum tumour marker levels were no more useful than the serum levels in lung cancer diagnosis. SpCEA offered the best predictive values but these were still not sufficiently satisfactory for spCEA to be proposed for routine use.