bluuebunny/crossref_metadata_2025_split huggingface dataset:
A model diagram layout extension for SBML
Authors: Gauges Ralph , Rost Ursula , Sahle Sven , Wegner Katja 
Published: May 2006

Abstract
Motivation: Since the knowledge about processes in living cells is increasing, modelling and simulation techniques are used to get new insights into these complex processes. During the last few years, the SBML file format has gained in popularity and support as a means of exchanging model data between the different modelling and simulation tools. In addition to specifying the model as a set of equations, many modern modelling tools allow the user to create and to interact with the model in the form of a reaction graph. Unfortunately, the SBML file format does not provide for the storage of this graph data along with the mathematical description of the model.
Results: Therefore, we developed an extension to the SBML file format that makes it possible to store such layout information which describes position and size of objects in the graphical representation.
Availability: The complete specification can be found on ( (SBML Layout Extension documentation, 2005). Additionally, a complete implementation exists as part of libSBML (2006, ).
Contact: Ralph.Gauges@eml-r.villa-bosch.de
Supplementary information: Supplementary data are available on Bioinformatics online.
Steroids, triterpenoids and molecular oxygen
Authors: Summons Roger E , Bradley Alexander S , Jahnke Linda L , Waldbauer Jacob R 
Published: May 2006

There is a close connection between modern-day biosynthesis of particular triterpenoid biomarkers and presence of molecular oxygen in the environment. Thus, the detection of steroid and triterpenoid hydrocarbons far back in Earth history has been used to infer the antiquity of oxygenic photosynthesis. This prompts the question: were these compounds produced similarly in the past? In this paper, we address this question with a review of the current state of knowledge surrounding the oxygen requirement for steroid biosynthesis and phylogenetic patterns in the distribution of steroid and triterpenoid biosynthetic pathways.The hopanoid and steroid biosynthetic pathways are very highly conserved within the bacterial and eukaryotic domains, respectively. Bacteriohopanepolyols are produced by a wide range of bacteria, and are methylated in significant abundance at the C2 position by oxygen-producing cyanobacteria. On the other hand, sterol biosynthesis is sparsely distributed in distantly related bacterial taxa and the pathways do not produce the wide range of products that characterize eukaryotes. In particular, evidence for sterol biosynthesis by cyanobacteria appears flawed. Our experiments show that cyanobacterial cultures are easily contaminated by sterol-producing rust fungi, which can be eliminated by treatment with cycloheximide affording sterol-free samples.Sterols are ubiquitous features of eukaryotic membranes, and it appears likely that the initial steps in sterol biosynthesis were present in their modern form in the last common ancestor of eukaryotes. Eleven molecules of O2are required by four enzymes to produce one molecule of cholesterol. Thermodynamic arguments, optimization of function and parsimony all indicate that an ancestral anaerobic pathway is highly unlikely.The known geological record of molecular fossils, especially steranes and triterpanes, is notable for the limited number of structural motifs that have been observed. With a few exceptions, the carbon skeletons are the same as those found in the lipids of extant organisms and no demonstrably extinct structures have been reported. Furthermore, their patterns of occurrence over billion year time-scales correlate strongly with environments of deposition. Accordingly, biomarkers are excellent indicators of environmental conditions even though the taxonomic affinities of all biomarkers cannot be precisely specified. Biomarkers are ultimately tied to biochemicals with very specific functional properties, and interpretations of the biomarker record will benefit from increased understanding of the biological roles of geologically durable molecules.
Queering gender: anima/animus and the paradigm of emergence
Authors: McKenzie Susan 
Published: May 2006

Abstract:  An exploration into the world of the queer others of gender and sexuality moves us beyond the binary opposition of male/masculinity and female/femininity in our understanding of gender and expands the meaning of gender and sexuality for all humans. A revision of Jungian gender theory that embraces all genders and sexualities is needed not only to inform our clinical work but also to allow us to bring Jungian thought to contemporary gender theory and to cultural struggles such as gay marriage.The cognitive and developmental neurosciences are increasingly focused on the importance of body biology and embodied experience to the emergence of mind. In my exploration of gender I ask how gender comes to be experienced in a developing body and how those embodied gender feelings elaborate into a conscious category in the mind, a gender position.My understanding of emergent mind theory suggests that one's sense of gender, like other aspects of the mind, emerges very early in development from a self‐organizing process involving an individual's particular body biology, the brain, and cultural environment. Gendered feeling, from this perspective, would be an emergent aspect of mind and not an archetypal inheritance, and the experiencing body would be key to gender emergence.A revised Jungian gender theory would transcend some of the limitations of Jung's anima/animus (A/A) gender thinking allowing us to contribute to contemporary gender theory in the spirit of another Jung; the Jung of the symbolic, the mythic, and the subtle body. This is the Jung who invites us to the medial place of the soul, bridging the realm of the physical body and the realm of the spirit.
Prospective analysis of treatment outcome and prognostic factors in patients with T‐cell lymphomas treated by CEOP‐B: single institutional study
Authors: Sung Hwa Jung , Kim Seok Jin , Seo Hee Yun , Sul Hye Ryoung , Choi Jong Gwon , Choi In Keun , Park Kyong Hwa , Oh Sang Cheul , Seo Jae Hong , Choi Chul Won , Kim Byung Soo , Shin Sang Won , Kim Yeul Hong , Kim Jun Suk 
Published: May 2006

SummaryThe important prognostic factors were evaluated for T‐cell non‐Hodgkin lymphoma (NHL) patients in a prospective study using the CEOP‐B protocol [a modified cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP)‐like regimen that uses epirubicin instead of doxorubicin with the addition of bleomycin]. Fifty‐two patients were enrolled in the study. The overall response rate was 63·5%. The median progression‐free survival (PFS) and median overall survival (OS) was 18·0 and 39·5 months respectively. The most common toxicity was neutropenia. The factors related to poor outcome were a high International Prognostic Index (IPI) and a high ‘B’ score (bone marrow involvement, B symptoms, bulky disease). We developed a new prognostic model, namely the Prognostic Group for T cell NHL (PGT) that included four groups: PGT1 (low IPI/low B score), PGT2 (low IPI/high B score), PGT3 (high IPI/Low B score) and PGT4 (high IPI/Low B score). OS and PFS (not reached, 48 months) in the PGT1 group were significantly longer than those (11·5 and 4·8 months) in PGT2. The same result was observed in the PGT3 and PGT4 groups. The CEOP‐B regimen was moderately active and tolerable for T‐cell NHL patients, and the PGT system might be useful for the prediction of long‐term survival of T‐cell NHL patients.
Abnormally short activated partial thromboplastin time values are associated with increased risk of recurrence of venous thromboembolism after oral anticoagulation withdrawal
Authors: Legnani Cristina , Mattarozzi Silvia , Cini Michela , Cosmi Benilde , Favaretto Elisabetta , Palareti Gualtiero 
Published: May 2006

SummaryThis study prospectively evaluated the relationship between activated partial thromboplastin time (aPTT) and risk of venous thromboembolism (VTE) recurrence after oral anticoagulant (OA) withdrawal in patients with a previous unprovoked VTE event. Six hundred twenty‐eight patients (331 males; median age: 67 years) were followed after OA interruption (mean follow‐up = 22 months). Three to four weeks from OA discontinuation patients were given a complete thrombophilic work‐out, including aPTT (automated aPTT). Recurrent symptomatic VTE events (objectively documented) occurred in 71/628 (11·3%, 6·8/100 person‐years) patients. The VTE recurrence rate was 17·5% and 7·5% in patients with aPTT in the lower (ratio ≤0·90) and in the upper (ratio >1·05) quartiles. The recurrence risk was more than twofold higher in patients with ratio ≤0·90 versus those of the reference category [Relative risk (RR): 2·38 (95% confidence interval (CI): 1·18–4·78)]. As expected, the increase in recurrence risk disappeared after adjustment for factor VIII, IX and XI levels [RR: 1·74 (95%CI: 0·43–2·76)]. In contrast, the risk was persistently increased in patients with a ratio ≤0·90 [RR: 2·07 (95%CI: 1·02–4·18)] after adjustment for age, gender and d‐dimer level. The aPTT predictive value was independent of the presence of inherited thrombophilic alterations. In conclusion, abnormally short aPTT values are associated with a significantly increased risk of VTE recurrence.
Essential elements of implementing a system of concurrent planning
Authors: Frame Laura , Berrick Jill Duerr , Coakley Jennifer Foulkes 
Published: May 2006

ABSTRACTIn efforts to preserve foster children’s biological families and to promote the formation of alternative families in some situations, legislative efforts to promote ‘permanency’ have been gaining pace since the late 1990s. One policy and practice tool, concurrent planning (CP), simultaneously allows for the pursuit of reunification and adoption. This article examines six counties in California (USA) and their efforts towards implementation of the components of CP. Researchers used qualitative methods to explore policies and practices of CP. Key informants include social workers, social work supervisors, attorneys and judges. The study identifies and describes seven elements determined to be essential to the complete and successful implementation of CP. Implications for agency practice and family outcomes are discussed.
Impacts of climate warming and habitat loss on extinctions at species' low‐latitude range boundaries
Authors: FRANCO ALDINA M. A. , HILL JANE K. , KITSCHKE CLAUDIA , COLLINGHAM YVONNE C. , ROY DAVID B. , FOX RICHARD , HUNTLEY BRIAN , THOMAS CHRIS D. 
Published: May 2006

AbstractPolewards expansions of species' distributions have been attributed to climate warming, but evidence for climate‐driven local extinctions at warm (low latitude/elevation) boundaries is equivocal. We surveyed the four species of butterflies that reach their southern limits in Britain. We visited 421 sites where the species had been recorded previously to determine whether recent extinctions were primarily due to climate or habitat changes. Coenonympha tullia had become extinct at 52% of study sites and all losses were associated with habitat degradation. Aricia artaxerxes was extinct from 50% of sites, with approximately one‐third to half of extinctions associated with climate‐related factors and the remainder with habitat loss. For Erebia aethiops (extinct from 24% of sites), approximately a quarter of the extinctions were associated with habitat and three‐quarters with climate. For Erebia epiphron, extinctions (37% of sites) were attributed mainly to climate with almost no habitat effects. For the three species affected by climate, range boundaries retracted 70–100 km northwards (A. artaxerxes, E. aethiops) and 130–150 m uphill (E. epiphron) in the sample of sites analysed. These shifts are consistent with estimated latitudinal and elevational temperature shifts of 88 km northwards and 98 m uphill over the 19‐year study period. These results suggest that the southern/warm range margins of some species are as sensitive to climate change as are northern/cool margins. Our data indicate that climate warming has been of comparable importance to habitat loss in driving local extinctions of northern species over the past few decades; future climate warming is likely to jeopardize the long‐term survival of many northern and mountain species.
Eminent role of ICOS costimulation for T cells interacting with plasmacytoid dendritic cells
Authors: Janke Marko , Witsch Esther J. , Mages Hans W. , Hutloff Andreas , Kroczek Richard A. 
Published: May 2006

SummaryCD4+ CD45RO+ T cells could mature freshly isolated human plasmacytoid dendritic cells (PDC) in a superantigen‐driven culture in a similar way to recombinant interleukin‐3 (IL‐3). Mature PDC expressed significantly higher levels of inducible costimulator ligand (ICOS‐L), but similar levels of CD80 and CD86, when compared to mature monocyte‐derived DC (moDC). We therefore directly compared the capacities of mature PDC and moDC to activate T cells. A similar T helper type 1 (Th1)/Th2 pattern of cytokines was generated in both systems, but significantly higher levels of IL‐3, IL‐4 and IL‐10 were induced by PDC. In T cells interacting with PDC, the ICOS/ICOS‐L costimulatory pathway played a pre‐eminent role in the generation of IL‐3 and IL‐10, CD28 was central to the induction of IL‐2, and both pathways were equally important for the generation of other cytokines. In cocultures with moDC, the CD28 pathway was dominant over ICOS under all circumstances, except for the ICOS‐mediated release of IL‐10. In general, our data demonstrate an eminent role of ICOS in the interaction of T cells with PDC, and thus modify the current paradigm of CD28 dominance for the costimulation of T cells interacting with professional antigen‐presenting cells. In particular, our data highlight the role of ICOS in the generation of IL‐3, a factor central to the biology of human PDC.
PS80 interferes with the antiallergic effect of Cry‐consensus peptide, a novel recombinant peptide for immunotherapy of Japanese cedar pollinosis, at very low concentration through modulation of Th1/Th2 balance
Authors: Kozutsumi Daisuke , Tsunematsu Masako , Yamaji Taketo , Murakami Rika , Yokoyama Minehiko , Kino Kohsuke 
Published: May 2006

SummaryPolysorbate 80 (PS80 or Tween‐80) is often used as an additive to promote the rapid solubilization of pharmaceuticals in aqueous solutions. We investigated whether coinjection of a minimal amount of PS80 had a modulatory effect on the immunotherapeutic effects of Cry (Cryptomeria)‐consensus peptide, a novel peptide developed for the therapeutic management of Japanese cedar pollinosis, using a Cry j 1‐sensitized mouse model with experimental allergic rhinitis. Subcutaneous challenge with Cry‐consensus peptide plus 50 µg/ml of PS80 did not affect the antigen‐specific proliferation of splenocytes, but decreased the potency of Cry‐consensus peptide to inhibit antigen‐specific interleukin (IL)‐5 production by the cells significantly in comparison with challenge with Cry‐consensus peptide alone. However, there was no significant difference between the effect of Cry‐consensus peptide administration on interferon (IFN)‐γ production in the presence and absence of PS80, indicating that PS80 interfered with the T helper 1 (Th1)‐dominant T helper balance induced by Cry‐consensus peptide challenge. Moreover, the increase in the level of antigen‐specific immunoglobulin G2a (IgG2a) induced by Cry‐consensus peptide challenge was inhibited slightly but unambiguously by PS80 coinjection. These in vitro experiments indicated that PS80 induces Th2‐type differentiation of T helper cells through preferential inhibition of IFN‐γ expression relative to IL‐5 expression in splenocytes in a concentration‐dependent manner. In naïve mice, sensitization by Cry‐consensus peptide with PS80 induced antigen‐specific IL‐5 production more potently than sensitization by Cry‐consensus peptide alone, and when PS80 was added to bone marrow‐derived dendritic cells, the endocytosis of fluorescence‐labelled Cry‐consensus peptide was dramatically inhibited in a concentration‐dependent manner. Therefore, we conclude that PS80 has an immunomodulatory effect on the antigen‐specific response resulting in a shift towards Th2 predominance with respect to the antigen recognition stage. Taken together, our findings suggest that PS80 might decrease the efficacy of Cry‐consensus peptide through modulation of the efficiency of antigen endocytosis and/or of the direction of successive T helper cell differentiation.
Interventions with fathers of young children: systematic literature review
Authors: Magill‐Evans Joyce , Harrison Margaret J. , Rempel Gwen , Slater Linda 
Published: May 2006

Aim.  This paper reports a systematic review of the effectiveness of interventions for fathers with infants or toddlers.Background.  Nurses and other healthcare professionals work closely with families of infants and young children. This contact provides an opportunity to promote positive parent–child interactions and optimal child development. Previous research has demonstrated that interventions with mothers of infants can be effective in promoting sensitive, responsive parent–child interactions and positive child development. Recent research has indicated that fathers also contribute to child development, but little is known about what types of interventions with fathers are effective in promoting sensitive, responsive father–child interactions.Methods.  Literature from 1983 to 2003 in the Medline, CINAHL, and PsycINFO databases was searched to locate intervention studies published in English that included a control group or used a pretest and post‐test design; measured an aspect of father–child interaction; analysed father outcomes separately from mother outcomes; had a sample greater than one; and included infants or toddlers. Additional studies were located by cross‐checking reference lists.Results.  Fourteen papers describing 12 interventions met the inclusion criteria. The interventions included infant massage, observation and modelling of behaviour with infant, kangaroo care, participation with child in a preschool programme, discussion groups, and parent training programmes.Conclusion.  Although the number of intervention studies is limited, there is evidence that, if interventions involve active participation with or observation of the father's own child, the intervention may be effective in enhancing the father's interactions with the child and a positive perception of the child. There is less information on how interventions influence child development. More research is needed to determine the influence of interventions over time, the differential influence on mothers and fathers, and the optimal dose of intervention required.
Does the migration programme constrain dispersal and range sizes of migratory birds?
Authors: Thorup Kasper 
Published: May 2006

AbstractAim  It is generally believed that the migration programme constrains the dispersal and hence range sizes of migratory bird species. This conclusion is based on analyses of breeding ranges of migratory versus non‐migratory (resident) terrestrial bird species, and rests on the assumption that there are no ecological or evolutionary constraints on extending the non‐breeding range. To investigate this assumption, the abilities of migrant and resident terrestrial species to colonize new wintering areas were compared.Location  Three major wintering regions of long‐distance migrants: South America, sub‐Saharan Africa and the Indian Subcontinent.Methods  It was determined whether the relative numbers of residents and short‐ and long‐distance migrants were the same in those species that have dispersed to a novel wintering region as in the source species pools.Results  At the species level, long‐distance migratory species are more likely to have non‐breeding ranges that include more than one of the above regions than resident species. This indicates that the dispersal of migratory species is less constrained than that of resident species. The pattern holds irrespective of the inclusion or exclusion of species associated with coastal, freshwater and wetland habitats, and also holds for ecological groups such as aerial feeders. The pattern is most pronounced between the regions separated by the strongest dispersal barriers (South America and sub‐Saharan Africa).Main conclusions  It is unlikely that the migration programme per se constrains dispersal, but rather that difficulties in establishing new non‐breeding areas prevent range expansions in migrant species.
Comparative phylogeography of woodland reptiles in California: repeated patterns of cladogenesis and population expansion
Authors: FELDMAN CHRIS R. , SPICER GREG S. 
Published: May 2006

AbstractThe ultimate goal of comparative phylogeographical analyses is to infer processes of diversification from contemporary geographical patterns of genetic diversity. When such studies are employed across diverse groups in an array of communities, it may be difficult to discover common evolutionary and ecological processes associated with diversification. In order to identify taxa that have responded in a similar fashion to historical events, we conducted comparative phylogeographical analyses on a phylogenetically and ecologically limited set of taxa. Here, we focus on a group of squamate reptiles (snakes and lizards) that share similar ecological requirements and generally occupy the same communities in the western USA. At a gross level, deep genetic division in Contia tenuis, Diadophis punctatus, Elgaria multicarinata, the Charina bottae complex, and Lampropeltis zonata are often concordant in the Transverse Ranges, the Monterey Bay and Sacramento‐San Joaquin Delta region, and the southern Sierra Nevada in California. Molecular clock estimates suggest that major phyletic breaks within many of these taxa roughly coincide temporally, and may correspond to important geological events. Furthermore, significant congruence between the phylogeographies of E. multicarinata and L. zonata suggests that the succession of vicariance and dispersal events in these species progressed in concert. Such congruence suggests that E. multicarinata and L. zonata have occupied the same communities through time. However, across our entire multi‐taxon data set, the sequence of branching events rarely match between sympatric taxa, indicating the importance of subtle differences in life history features as well as random processes in creating unique genetic patterns. Lastly, coalescent and noncoalescent estimates of population expansion suggest that populations in the more southerly distributed clades of C. tenuis, D. punctatus, E. multicarinata, and L. zonata have been stable, while populations in more northerly clades appear to have recently expanded. This concerted demographic response is consistent with palaeontological data and previous phylogeographical work that suggests that woodland habitat has become more restricted in southern California, but more widespread in the North during Holocene warming. Future phylogeographical work focusing on allied and ecologically associated taxa may add insight into the ecological and evolutionary processes that yield current patterns of genetic diversity.