bluuebunny/crossref_metadata_2025_split huggingface dataset:
On low dimensional case in the fundamental asset pricing theorem with transaction costs
Authors: Grigoriev Pavel G. 
Published: August 2005

Summary
The well-known Harrison–Plisse theorem claims that in the classical discrete time model of the financial market with finite Ω there is no arbitrage iff there exists an equivalent martingale measure. The famous Dalang–Morton–Willinger theorem extends this result for an arbitrary Ω. Kabanov and Stricker [KS01] generalized the Harrison–Pliska theorem for the case of the market with proportional transaction costs. Nevertheless the corresponding extension of the Kabanov and Stricker result to the case of non-finite Ω fails, the corresponding counter-example with 4 assets was constructed by Schachermayer [S04].
The main result of this paper is that in the special case of 2 assets the Kabanov and Stricker theorem can be extended for an arbitrary Ω. This is quite a surprising result since the corresponding cone of hedgeable claims ÂT is not necessarily closed.
Functional Connection Between the Clb5 Cyclin, the Protein Kinase C Pathway and the Swi4 Transcription Factor in Saccharomyces cerevisiae
Authors: Queralt Ethel , Igual J Carlos 
Published: August 2005

Abstract
The rsf12 mutation was isolated in a synthetic lethal screen for genes functionally interacting with Swi4. RSF12 is CLB5. The clb5 swi4 mutant cells arrest at G2/M due to the activation of the DNA-damage checkpoint. Defects in DNA integrity was confirmed by the increased rates of chromosome loss and mitotic recombination. Other results suggest the presence of additional defects related to morphogenesis. Interestingly, genes of the PKC pathway rescue the growth defect of clb5 swi4, and pkc1 and slt2 mutations are synthetic lethal with clb5, pointing to a connection between Clb5, the PKC pathway, and Swi4. Different observations suggest that like Clb5, the PKC pathway and Swi4 are involved in the control of DNA integrity: there is a synthetic interaction between pkc1 and slt2 with rad9; the pkc1, slt2, and swi4 mutants are hypersensitive to hydroxyurea; and the Slt2 kinase is activated by hydroxyurea. Reciprocally, we found that clb5 mutant is hypersensitive to SDS, CFW, latrunculin B, or zymolyase, which suggests that, like the PKC pathway and Swi4, Clb5 is related to cell integrity. In summary, we report numerous genetic interactions and phenotypic descriptions supporting a close functional relationship between the Clb5 cyclin, the PKC pathway, and the Swi4 transcription factor.
Replication Origin of Mitochondrial DNA in Insects
Authors: Saito Shigeru , Tamura Koichiro , Aotsuka Tadashi 
Published: August 2005

Abstract
The precise position of the replication origin (OR) of mtDNA was determined for insect species belonging to four different orders (four species of Drosophila, Bombyx mori, Triborium castaneum, and Locusta migratoria, which belong to Diptera, Lepidoptera, Coleoptera, and Orthoptera, respectively). Since the free 5′ ends of the DNA strands of mtDNA are interpreted as the OR, their positions were mapped at 1-nucleotide resolution within the A + T-rich region by using the ligation-mediated PCR method. In all species examined, the free 5′ ends were found within a very narrow range of several nucleotides in the A + T-rich region. For four species of Drosophila, B. mori, and T. castaneum, which belong to holometabolous insects, although the OR's were located at different positions, they were located immediately downstream of a series of thymine nucleotides, the so-called T-stretch. These results strongly indicate that the T-stretch is involved in the recognition of the OR of mtDNA at least among holometabolous insects. For L. migratoria (hemimetabolous insect), on the other hand, none of the long stretches of T's was found in the upstream portion of the OR, suggesting that the regulatory sequences involved in the replication initiation process have changed through insect evolution.
Protein–nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure
Authors: Lejeune Diane , Delsaux Nicolas , Charloteaux Benoît , Thomas Annick , Brasseur Robert 
Published: August 2005

AbstractWe analyzed structural features of 11,038 direct atomic contacts (either electrostatic, H‐bonds, hydrophobic, or other van der Waals interactions) extracted from 139 protein–DNA and 49 protein–RNA nonhomologous complexes from the Protein Data Bank (PDB). Globally, H‐bonds are the most frequent interactions (∼50%), followed by van der Waals, hydrophobic, and electrostatic interactions. From the protein viewpoint, hydrophilic amino acids are over‐represented in the interaction databases: Positively charged amino acids mainly contact nucleic acid phosphate groups but can also interact with base edges. From the nucleotide point of view, DNA and RNA behave differently: Most protein–DNA interactions involve phosphate atoms, while protein–RNA interactions involve more frequently base edge and ribose atoms. The increased participation of DNA phosphate involves H‐bonds rather than salt bridges. A statistical analysis was performed to find the occurrence of amino acid–nucleotide pairs most different from chance. These pairs were analyzed individually. Finally, we studied the conformation of DNA in the interaction sites. Despite the prevalence of B‐DNA in the database, our results suggest that A‐DNA is favored in the interaction sites. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Structural insights into the cellular retinaldehyde‐binding protein (CRALBP)
Authors: Liu Tianyun , Jenwitheesuk Ekachai , Teller David C. , Samudrala Ram 
Published: August 2005

AbstractCellular retinaldehyde‐binding protein (CRALBP) is an essential protein in the human visual cycle without a known three‐dimensional structure. Previous studies associate retinal pathologies to specific mutations in the CRALBP protein. Here we use homology modeling and molecular dynamics methods to investigate the structural mechanisms by which CRALBP functions in the visual cycle. We have constructed two conformations of CRALBP representing two states in the process of ligand association and dissociation. Notably, our homology models map the pathology‐associated mutations either directly in or adjacent to the putative ligand‐binding cavity. Furthermore, six novel residues have been identified to be crucial for the hinge movement of the lipid‐exchange loop in CRALBP. We conclude that the binding and release of retinoid involve large conformational changes in the lipid‐exchange loop at the entrance of the ligand‐binding cavity. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Foliage randomness and light interception in 3‐D digitized trees: an analysis from multiscale discretization of the canopy
Authors: SINOQUET HERVÉ , SONOHAT GABRIELA , PHATTARALERPHONG JESSADA , GODIN CHRISTOPHE 
Published: August 2005

ABSTRACTLight models for vegetation canopies based on the turbid medium analogy are usually limited by the basic assumption of random foliage dispersion in the canopy space. The objective of this paper was to assess the effect of three possible sources of non‐randomness in tree canopies on light interception properties. For this purpose, four three‐dimensional (3‐D) digitized trees and four theoretical canopies – one random and three built from fractal rules – were used to compute canopy structure parameters and light interception, namely the sky‐vault averaged STAR (Silhouette to Total Area Ratio). STAR values were computed from (1) images of the 3‐D plants, and (2) from a 3‐D turbid medium model using space discretization at different scales. For all trees, departure from randomness was mainly due to the spatial variations in leaf area density within the canopy volume. Indeed STAR estimations, based on turbid medium assumption, using the finest space discretization were very close to STAR values computed from the plant images. At this finest scale, foliage dispersion was slightly clumped, except one theoretical fractal canopy, which showed a marked regular dispersion. Taking into account a non‐infinitely small leaf size, whose effect is theoretically to shorten self‐shading, had a minor effect on STAR computations. STAR values computed from the 3‐D turbid medium were very sensitive to plant lacunarity, a parameter introduced in the context of fractal studies to characterize the distribution of gaps in porous media at different scales. This study shows that 3‐D turbid medium models based on space discretization are able to give correct estimation of light interception by 3‐D isolated trees, provided that the 3‐D grid is properly defined, that is, discretization maximizes plant lacunarity.
Consequences of vancomycin‐resistant Enterococcus in liver transplant recipients: a matched control study
Authors: Gearhart Michelle , Martin Jill , Rudich Steve , Thomas Mark , Wetzel Dave , Solomkin Joseph , Hanaway Michael J , Aranda‐Michel Jaime , Weber Fred , Trumball Leslie , Bass Maryetta , Zavala Ed , Steve Woodle E , Buell Joseph F 
Published: August 2005

Abstract:  Background:  Liver transplant recipients are at high risk for multi‐drug resistant infections because of broad‐spectrum antibiotic and immunosuppression. This study evaluates the clinical and financial impact of vancomycin resistant Enterococcus (VRE) in liver transplant recipients.Methods:  Liver transplant recipients with VRE from 1995 to 2002 were identified and matched (age, gender, UNOS status, liver disease and transplant date) to controls. Demographics, clinical factors, co‐infections, antibiotic use, length of stay, abdominal surgeries, biliary complications, survival and resource utilization were compared with matched controls.Results:  Nineteen patients were found to have 28 VRE infections via evaluation of microbiologic culture results of all liver transplant patients in the transplant registry. Thirty‐eight non‐VRE patients served as matched controls. The four most common sites VRE was cultured from included blood (35%), peritoneal fluid (35%), bile (20%), and urine (12%). Median time from transplant to infection was 48 d (range of 4–348). No significant differences in demographics were observed. The VRE group had a higher incidence of prior antibiotic use than the non‐VRE group (95% vs. 34%; p < 0.05). The VRE group also experienced more abdominal surgery (20/19 vs. 3/38; p = 0.029), biliary complications (9/19 vs. 9/38; p = 0.018) and a longer length of stay (42.5 vs. 21.7 d; p = .005). Survival in the VRE group was lower (52% vs. 82%; p = 0.048). Six of the 19 VRE patients were treated with linezolid for eight infection episodes, and four of six patients survived. Eight patients were treated with quinupristin/dalfopristin for nine infections, and two of eight survived. Increased cost of care was observed in the VRE group. Laboratory costs were higher in the VRE group ($6500 vs. 1750; p = 0.02) as well.Conclusion:  VRE was associated with prior antibiotic use, multiple abdominal surgeries, biliary complications and resulted in decreased survival compared to non‐VRE control patients. VRE patients also utilized more hospital resources. Linezolid showed a trend toward improved survival.
Alteration and resilience of the soil microbial community following compost amendment: effects of compost level and compost‐borne microbial community
Authors: Saison Carine , Degrange Valérie , Oliver Robert , Millard Peter , Commeaux Claire , Montange Denis , Le Roux Xavier 
Published: August 2005

SummaryCompost amendment has been reported to impact soil microbial activities or community composition. However, little information is available on (i) to what extent compost amendment concurrently affects the activity, size and composition of soil microbial community, (ii) the relative effect of the addition of a material rich in organic matter versus addition of compost‐borne microorganisms in explaining the effects of amendment and (iii) the resilience of community characteristics. We compared five treatments in microcosms: (i) control soil (S), (ii) soil + low level of compost (Sc), (iii) soil + high level of compost (SC), (iv) sterilized soil + high level of compost [(S)C] and (v) soil + high level of sterilized compost [S(C)]. The actual C mineralization rate, substrate‐induced respiration, size of microbial community (biomass and heterotrophic cells number), and structure of total microbial (phospholipid fatty acids) and bacterial (automated ribosomal intergenic spacer analysis, A‐RISA) communities were surveyed during 6 months after amendment. Our results show that (i) compost amendment affected the activity, size and composition of the soil microbial community, (ii) the effect of compost amendment was mainly due to the physicochemical characteristics of compost matrix rather than to compost‐borne microorganisms and (iii) no resilience of microbial characteristics was observed 6–12 months after amendment with a high amount of compost.
New diagnostic techniques
Authors: Feuilhade de Chauvin M 
Published: August 2005

ABSTRACTObjectives  To review current diagnostic strategies. To review alternative diagnostic techniques.Results  The pathogen(s) responsible for onychomycosis must be identified to optimize treatment. Mycological examination is currently the most common diagnostic technique. This typically involves clearing with potassium hydroxide followed by microscopy. This direct test rapidly differentiates between living and dead hyphae. Sensitivity can be enhanced by using dimethyl sulfoxide (DMSO) or stains such as Chlorazol Black E. However, microscopy must always be combined with culture, allowing correct species identification. Accurate diagnosis depends on the expertise of laboratory staff and biologists and on the quality of the nail sample: samples should always be taken from the most proximal infected area.In the absence of experienced mycological laboratories, new laboratory techniques have been developed. Histological analysis by nail plate clipping has been shown to be an easy and efficient method for diagnosis. However, nail clipping is not an optimal technique for fungal culture and a large proportion of nonpathogenic but contaminant moulds can grow on culture medium. Moreover, histological analysis provides no information about causal agent or vitality. In vivo confocal microscopy and flow cytometry are powerful but complicated and costly techniques, making them unsuitable for routine use. Finally, polymerase chain reaction (PCR) (low proportion of positive results) and PCR–restriction fragment length polymorphism (PCR–RFLP) (suitable even for patients receiving antifungals) techniques have been developed. These molecular methods are cost‐intensive and require highly skilled staff, meaning they are reserved exclusively for laboratories that process numerous nail samples.Conclusion  In conclusion, mycological examination remains the gold standard technique; it provides the most information, at a reasonable cost with little inconvenience to the patient.
Metaphors and Models: The ASR Bubble in the Floridan Aquifer
Authors: Vacher H.L. , Hutchings William C. , Budd David A. 
Published: August 2005

AbstractStudies at the intersection of cognitive science and linguistics have revealed the crucial role that metaphors play in shaping our thoughts about phenomena we cannot see. According to the domains interaction theory of cognition, a metaphoric expression sets up mappings between a target domain that we wish to understand and a familiar source domain. The source domain contains elements (“commonplaces”) that we manipulate mentally, like parts of an analogue model, to illuminate the target domain. This paper applies the structure of domains interaction theory to analyze the dynamics of a metaphor in hydrogeology: the so‐called bubble formed by water injected into an aquifer during aquifer storage and recovery (ASR). Of the four commonplaces of bubbles—(1) they are discrete; (2) they are geometrically simple; (3) they rise; and (4) they burst—we focus on the first two using both displacement and dispersion (tracer) models for both homogeneous and heterogeneous storage zones patterned from geological studies of the Suwannee Limestone of Sarasota County, Florida. The displacement model easily shows that “bottle brush” better represents the geometric complexity predicted from the known and inferred heterogeneity. There is virtually no difference, however, in the prediction of recovery efficiency using the dispersion model for a bubble (homogeneous flow zone) vs. bottle brush (heterogeneous flow zone). On the other hand, only the bottle brush reveals that unrecovered tracer is located preferentially in the low‐permeability layers that lie adjacent to high‐permeability channels in the flow zones.
Tandem machine learning for the identification of genes regulated by transcription factors
Authors: Dinakarpandian Deendayal , Raheja Venetia , Mehta Saumil , Schuetz Erin G , Rogan Peter K 
Published: August 2005

Abstract
Background
The identification of promoter regions that are regulated by a given transcription factor has traditionally relied upon the identification and distributions of binding sites recognized by the factor. In this study, we have developed a tandem machine learning approach for the identification of regulatory target genes based on these parameters and on the corresponding binding site information contents that measure the affinities of the factor for these cognate elements.

Results
This method has been validated using models of DNA binding sites recognized by the xenobiotic-sensitive nuclear receptor, PXR/RXRα, for target genes within the human genome. An information theory-based weight matrix was first derived and refined from known PXR/RXRα binding sites. The promoter region of candidate genes was scanned with the weight matrix. A novel information density-based clustering algorithm was then used to identify clusters of information rich sites. Finally, transformed data representing metrics of location, strength and clustering of binding sites were used for classification of promoter regions using an ensemble approach involving neural networks, decision trees and Naïve Bayesian classification. The method was evaluated on a set of 24 known target genes and 288 genes known not to be regulated by PXR/RXRα. We report an average accuracy (proportion of correctly classified promoter regions) of 71%, sensitivity of 73%, and specificity of 70%, based on multiple cross-validation and the leave-one-out strategy. The performance on a test set of 13 genes showed that 10 were correctly classified.

Conclusion
We have developed a machine learning approach for the successful detection of gene targets for transcription factors with high accuracy. The method has been validated for the transcription factor PXR/RXRα and has the potential to be extended to other transcription factors.
Suicide attempts in clinical trials with paroxetine randomised against placebo
Authors: Aursnes Ivar , Tvete Ingunn Fride , Gaasemyr Jorund , Natvig Bent 
Published: August 2005

AbstractBackgroundInclusion of unpublished data on the effects of antidepressants on children has suggested unfavourable risk-benefit profiles for some of the drugs. Recent meta-analyses of studies on adults have indicated similar effects. We obtained unpublished data for paroxetine that have so far not been included in these analyses.MethodsThe documentation for drug registration contained 16 studies in which paroxetine had been randomised against placebo. We registered the number of suicides, suicide attempts and ideation. We corrected for duration of medication and placebo treatment and used a standard Bayesian statistical approach with varying priors.ResultsThere were 7 suicide attempts in patients on the drug and 1 in a patient on placebo. We found that the probability of increased intensity of suicide attempts per year in adults taking paroxetine was 0.90 with a "pessimistic" prior, and somewhat less with two more neutral priors.ConclusionOur findings support the results of recent meta-analyses. Patients and doctors should be warned that the increased suicidal activity observed in children and adolescents taking certain antidepressant drugs may also be present in adults.
Role of N-Terminal Pro-B-Type Natriuretic Peptide in Risk Stratification in Patients Presenting in the Emergency Room
Authors: Möckel Martin , Müller Reinhold , Vollert Jörn O , Müller Christian , Carl Angelika , Peetz Dirk , Post Felix , Kohse J Klaus , Lackner Karl J 
Published: August 2005

Abstract
Background: Natriuretic peptides are promising markers in diagnosing acute and chronic heart failure and assessing prognosis in these patients. Increasing routine use to unselected patients is challenged by false-positive results. The aims of this study were to assess (a) the distributions of N-terminal B-type natriuretic peptide (NT-proBNP) values in various diagnostic groups, (b) factors that influence NT-proBNP, and (c) the value of NT-proBNP in risk stratification in unselected emergency room (ER) patients.
Methods: NT-proBNP was measured in 876 unselected consecutive patients [mean (SD) age, 58 (18) years; 53% male] attending the ERs of 2 university hospitals and 1 community hospital. Diagnoses, age, sex, hemoglobin, creatinine (CREA), C-reactive protein (CRP), troponin T, and intensity of care were documented. In a subset consisting of all 417 patients at 1 center, in-hospital follow-up was completed with respect to a complicated clinical course, including intensive care treatment and death.
Results: NT-proBNP was significantly increased in patients with cardiac diagnoses or histories compared with patients with only pulmonary or other diagnoses. In patients with other diagnoses, NT-proBNP values increased significantly with the number of atherosclerotic risk factors (P = 0.044). Age, renal function, CRP, and to a much lesser extent, hemoglobin significantly influenced NT-proBNP values. The amount of care was positively correlated with NT-proBNP (P &lt;0.001). Classification and regression tree analysis showed a superior impact of NT-proBNP for identification of high-risk patients.
Conclusions: NT-proBNP is a promising marker for identification of patients with structural heart disease in the ER and a suitable tool for risk stratification. Its use in the ER should be limited to clearly clinically defined patient groups at present to avoid a potential excess of additional diagnostic procedures in positive but asymptomatic patients.
Software-Entwicklung und Community-Kultivierung: ein integrativer Ansatz (Software-Development and Community-Cultivation: an Integrative Approach)
Authors: Jahnke Isa , Mattick Volker , Herrmann Thomas 
Published: August 2005

Zusammenfassung
Der Beitrag zeigt in einem integrativen Ansatz, welche technischen Entwicklungen zur sozialen Kultivierung einer Internet-unterstützten Community sinnvoll und notwendig sind. Anhand einer Fallstudie (Inpud-Community) wird einerseits die technische Entwicklung und andererseits die Bildung, Unterstützung und Förderung (Kultivierung) der sozialen Struktur beschrieben (soziotechnische Kultivierung). Wir möchten zeigen, dass klassische Software-Entwicklungs-Methoden für die Entwicklung von technischen Systemen zur Unterstützung der Community-Kultivierung durch die Berücksichtung von Lebensphasen-Modellen sinnvoll erweitert werden können. Dazu schlagen wir einen integrativen Ansatz vor, welcher die technische Entwicklung unter gleichzeitiger Berücksichtigung der Entwicklung des sozialen Systems unterstützt. Der Beitrag möchte damit eine Diskussion zur Vorgehensweise bei der Software-Entwicklung im Kontext einer soziotechnischen Community-Kultivierung anstoßen.