bluuebunny/crossref_metadata_2025_split huggingface dataset:
Energy Exchange in Isometric Contraction of Vascular Smooth Muscle Induced by K‐ions
Authors: Beviz Andras , Lundholm Lennart , Mohme‐Lundholm Ella 
Published: December 2008

AbstractActa physiol scand. 1969. 00. 000–000. – On isometric contraction of isolated mesenteric arteries induced by K‐ions in anaerobic, glucose‐free suspension solution the increase in tension after 1 min was accompanied by a significant decrease in the content of adenosine triphosphate (0.21 ± 0.07 μmoles/g), creatine phosphate (0.30 ± 0–08 μmoles/g) and an increased lactate content (0.25 ±0.10 μmoles/g) of the vascular muscle. In the presence of 0.5 % glucose, essentially the same effect was observed on the contents of energy‐rich phosphate esters, while the effect on the lactate content varied. Three min after the addition of K+ someresynthesis of energy‐rich phosphate compounds had taken place, but the synthesis was relatively slow. The series elastic component was relatively large in mesenteric arteries. Therefore even on isometric contraction the muscle performed work on stretching of this component. After correction of this “internal” work the LP ratio L.P/H was calculated to be 4.8, i. e. about 1/2 of that demonstrated by Hill (1958) in thermoelectrical determinations in isometrically contracted skeletal muscle from the frog. In glucose‐free solution a significant correlation was found between the tension developed and the content of energy‐rich phosphate compounds in muscle.
Release of Histamine and Formation of Smooth‐Muscle Stimulating Principles in Guinea‐Pig Lung Tissue Induced by Antigen and Bee Venom Phosphatidase A
Authors: Fredholm Bo , Strandberg Kjell 
Published: December 2008

AbstractRelease of histamine and formation of smooth‐muscle stimulating principles (spasmogenic lipids) occurred when minced guinea‐pig lung tissue was exposed to antigen or to bee venom phosphatidase A. In agreement with earlier reports the anaphylactic histamine release was a rapid process, and it could be inhibited by anoxia in the absence of glucose, and by potassium cyanide, ninhydrin and A’‐ethyl‐maleimide. The histamine release induced by phosphatidase A was not influenced by these inhibitors or by anoxia, and the release was slower than in anaphylaxis. The spasmogenic lipids formed had similar chromatographic and biological properties to those reported for the corresponding principles formed in anaphylaxis, and the process of formation was inhibited by oxygen lack and by the above enzyme inhibitors. One noteworthy feature of the spasmogenic lipid formation was that the inhibition caused by anoxia could not be counteracted by glucose. The results support earlier hypotheses regarding the mode of action of phosphatidase A on guinea‐pig lung tissue. It is suggested that mast cells are not necessarily involved in the formation of spasmogenic lipids occurring in connection with histamine release induced by phosphatidase A in the guinea‐pig lung. The bee venom fraction F II, which liberates histamine from rat tissues by a mechanism resembling that of compound 48/80, did not cause release of histamine or formation of spasmogenic lipids from the guinea‐pig lung tissue in concentrations up to 100 mug/ml.
The liberalization and (re)regulation of Dutch gambling markets: National consequences of the changing European context
Authors: Kingma Sytze F. 
Published: December 2008

AbstractThis paper deals with the liberalization of Dutch gambling markets, in particular the (re)regulation of these markets after 2002. It is argued that during the 1990s a neo‐liberal “risk regime” of gambling regulation replaced the traditional moralizing and restrictive gambling policies. However, this risk regime has recently been challenged by the development of Internet gambling, the discussions about the “Services Directive” in the European Parliament and cases brought to the European Court of Justice. These circumstances are redefining the European context for national gambling policies and gambling organizations. Together with a growing risk awareness, this has caused the Dutch government to reconsider its gambling policies. This paper outlines the basic features of the risk regime of gambling regulation, and makes clear that after a decade of great leniency and tremendous market growth, the Dutch gambling markets, including casinos, lotteries and slot machines, were confronted with serious backwashes.
Even clubs can’t do without legitimacy: Why the anti‐money laundering blacklist was suspended
Authors: Hülsse Rainer 
Published: December 2008

AbstractThis article uses the case of anti‐money laundering regulation to investigate international club organisations’ efforts to secure compliance with their rules. As these rules can hardly claim much legitimacy, one would expect that they are complied with only if the club organisation uses side‐payments or coercion. Indeed, the Financial Action Task Force against Money‐Laundering (FATF), the international standard setter in that field, has used blacklisting to force non‐members into compliance. But although it had greatly improved compliance, the blacklist was suspended again after a short period of time. Why? This article argues that this was due to allegations of the blacklist being illegitimate. The FATF reacted by withdrawing the blacklist and also by engaging in various legitimatory practices, because even club organisations need legitimacy if they want to achieve results. Only if the rules are considered legitimate, will there be actual, and not just formal compliance. Hence this article denies the existence of a dilemma between legitimacy and effectiveness (the conventional view), suggesting that only legitimate rules can be effective.
The Rise of the Megachurches and Changes in Religious Culture: Review Article
Authors: Ellingson Stephen 
Published: December 2008

AbstractMegachurches represent an emerging and powerful force within American Religion. These large, Protestant churches that average at least 2,000 attendees per week are reshaping religion locally, regionally, and nationally as well as at the denominational and congregational levels. Megachurch leaders have been leaders in religious innovation since the 1970s, ushering in major changes in church architecture, ritual practices, polity, and marketing. In this essay, I review the nascent literature on megachurches. First, I discuss the major descriptive findings from several surveys and case studies of megachurches. Second, I examine scholars’ efforts to explain how and why megachurches have emerged and grown over the past forty years. Finally, I suggest several lines of future inquiry that may allow sociologists of religion to extend or refine existing cultural and market based theories of religious change and church‐sect theory.
Wiresweep Reduction via Direct Cavity Injection During Encapsulation
of Stacked Chip-Scale Packages
Authors: Brand Jason M. , Ruggero Salvatore A. , Shah Amip J. 
Published: December 2008

Abstract
As packaging continues to offer challenges with variable stacked die configurations of increasing complexity, traditional transfer mold encapsulation faces challenges in defining a robust process window. A major concern is the problem of “wiresweep,” wherein deformation of the wirebond during the mold process can potentially cause shortcircuiting. Several prior studies have focused on qualifying the effects of various wirebond and mold process parameters on package wiresweep, but most of these studies are restricted to single (discrete) die packages. This paper attempts to fill this gap of knowledge by experimenting with a variety of test vehicles with different stacking configurations. Specifically, the effects of varying loop height, stack height, and mold compound type are quantified in terms of maximum wiresweep. We find that loop height can have a considerable effect on wiresweep, with the maximum wiresweep being reduced by half (from around 6% to less than 3%) simply by reducing the loop height. Additionally, the study finds that for a given mold process, higher die stacks tend to increase wiresweep, although a threshold stack height exists beyond which further stacking can reduce wiresweep. Lastly, the data suggest that the choice of mold compound can adversely impact wiresweep, especially for test vehicles with traditionally high wiresweep. Having identified these trends, semianalytical models from the literature are used to investigate the cause behind these observations. The analysis suggests that the mold front velocity has the major root impact on package wiresweep. To validate this hypothesis, the series of tests conducted earlier is repeated for a compression mold process, which provides greater control over the mold front velocity. As predicted by the model, significant reduction in wiresweep is achieved. Thus, the compression mold process seems to offer the opportunity for reducing wiresweep without any compromise in the complexity of the die stack.
Phase 1/2 study of fractionated 131I-rituximab in low-grade B-cell lymphoma: the effect of prior rituximab dosing and tumor burden on subsequent radioimmunotherapy
Authors: Illidge Tim M. , Bayne Mike , Brown Nicholas S. , Chilton Samantha , Cragg Mark S. , Glennie Martin J. , Du Yong , Lewington Valerie , Smart James , Thom James , Zivanovic Maureen , Johnson Peter W. M. 
Published: December 2008

Abstract
The effect of induction therapy with multiple doses of rituximab on the subsequent efficacy and toxicity of anti-CD20 radioimmunotherapy is unknown. We evaluated a novel protocol using 4 weekly infusions of 375 mg/m2 rituximab followed by 2 fractions of 131I-rituximab, preceded by a 100-mg/m2 predose of rituximab, in relapsed indolent B-cell lymphoma. Induction therapy with rituximab significantly increased the effective half-life of 131I-rituximab (P = .003) and high serum levels of rituximab after induction therapy correlated with increased effective half-life of the radioimmunoconjugate (P = .009). Patients with large tumor burdens experienced significant increases in the effective half-life of 131I-rituximab between delivery of the first and second fractions (P = .007). Induction therapy with multiple doses of rituximab did not appear to compromise the clinical efficacy or increase toxicity of subsequent 131I-rituximab radioimmunotherapy. The overall response rate was 94%, with complete response rate 50%. The median time to progression was 20 months, significantly longer than for the last qualifying chemotherapy (P = .001). Fractionation of 131I-rituximab allowed cumulative whole-body doses of more than 120 cGy, approximately 60% greater than those previously achieved with a single administration of a murine radioimmunconjugate, to be delivered without significant hematologic toxicity.
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions
Authors: Lee Sheng-An , Chan Cheng-hsiung , Tsai Chi-Hung , Lai Jin-Mei , Wang Feng-Sheng , Kao Cheng-Yan , Huang Chi-Ying F 
Published: December 2008

Abstract

Background
The rapid growth of protein-protein interaction (PPI) data has led to the emergence of PPI network analysis. Despite advances in high-throughput techniques, the interactomes of several model organisms are still far from complete. Therefore, it is desirable to expand these interactomes with ortholog-based and other methods.

Results
Orthologous pairs of 18 eukaryotic species were expanded and merged with experimental PPI datasets. The contributions of interologs from each species were evaluated. The expanded orthologous pairs enable the inference of interologs for various species. For example, more than 32,000 human interactions can be predicted. The same dataset has also been applied to the prediction of host-pathogen interactions. PPIs between P. falciparum calmodulin and several H. sapiens proteins are predicted, and these interactions may contribute to the maintenance of host cell Ca2+ concentration. Using comparisons with Bayesian and structure-based approaches, interactions between putative HSP40 homologs of P. falciparum and the H. sapiens TNF receptor associated factor family are revealed, suggesting a role for these interactions in the interference of the human immune response to P. falciparum.

Conclusion
The PPI datasets are available from POINT http://point.bioinformatics.tw/ and POINeT http://poinet.bioinformatics.tw/. Further development of methods to predict host-pathogen interactions should incorporate multiple approaches in order to improve sensitivity, and should facilitate the identification of targets for drug discovery and design.
Dynamic sensitivity analysis of biological systems
Authors: Wu Wu Hsiung , Wang Feng Sheng , Chang Maw Shang 
Published: December 2008

Abstract

Background
A mathematical model to understand, predict, control, or even design a real biological system is a central theme in systems biology. A dynamic biological system is always modeled as a nonlinear ordinary differential equation (ODE) system. How to simulate the dynamic behavior and dynamic parameter sensitivities of systems described by ODEs efficiently and accurately is a critical job. In many practical applications, e.g., the fed-batch fermentation systems, the system admissible input (corresponding to independent variables of the system) can be time-dependent. The main difficulty for investigating the dynamic log gains of these systems is the infinite dimension due to the time-dependent input. The classical dynamic sensitivity analysis does not take into account this case for the dynamic log gains.

Results
We present an algorithm with an adaptive step size control that can be used for computing the solution and dynamic sensitivities of an autonomous ODE system simultaneously. Although our algorithm is one of the decouple direct methods in computing dynamic sensitivities of an ODE system, the step size determined by model equations can be used on the computations of the time profile and dynamic sensitivities with moderate accuracy even when sensitivity equations are more stiff than model equations. To show this algorithm can perform the dynamic sensitivity analysis on very stiff ODE systems with moderate accuracy, it is implemented and applied to two sets of chemical reactions: pyrolysis of ethane and oxidation of formaldehyde. The accuracy of this algorithm is demonstrated by comparing the dynamic parameter sensitivities obtained from this new algorithm and from the direct method with Rosenbrock stiff integrator based on the indirect method. The same dynamic sensitivity analysis was performed on an ethanol fed-batch fermentation system with a time-varying feed rate to evaluate the applicability of the algorithm to realistic models with time-dependent admissible input.

Conclusion
By combining the accuracy we show with the efficiency of being a decouple direct method, our algorithm is an excellent method for computing dynamic parameter sensitivities in stiff problems. We extend the scope of classical dynamic sensitivity analysis to the investigation of dynamic log gains of models with time-dependent admissible input.
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
Authors: Yang Jin Ok , Hwang Sohyun , Oh Jeongsu , Bhak Jong , Sohn Tae-Kwon 
Published: December 2008

Abstract

Background
Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases.

Results
To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page http://diseasome.kobic.re.kr/, and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes.

Conclusion
Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals.
CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge
Authors: Gaikwad Jitendra , Khanna Varun , Vemulpad Subramanyam , Jamie Joanne , Kohen Jim , Ranganathan Shoba 
Published: December 2008

Abstract

Background
The customary medicinal plant knowledge possessed by the Australian Aboriginal people is a significant resource. Published information on it is scattered throughout the literature, in heterogeneous data formats, and is scattered among various Aboriginal communities across Australia, due to a multiplicity of languages. This ancient knowledge is at risk due to loss of biodiversity, cultural impact and the demise of many of its custodians. We have developed the Customary Medicinal Knowledgebase (CMKb), an integrated multidisciplinary resource, to document, conserve and disseminate this knowledge.

Description
CMKb is an online relational database for collating, disseminating, visualising and analysing initially public domain data on customary medicinal plants. The database stores information related to taxonomy, phytochemistry, biogeography, biological activities of customary medicinal plant species as well as images of individual species. The database can be accessed at http://biolinfo.org/cmkb. Known bioactive molecules are characterized within the chemoinformatics module of CMKb, with functions available for molecular editing and visualization.

Conclusion
CMKb has been developed as a prototype data resource for documenting, integrating, disseminating, analysing multidisciplinary customary medicinal plant data from Australia and to facilitate user-defined complex querying. Each species in CMKb is linked to online resources such as the Integrated Taxonomic Information System (ITIS), NCBI Taxonomy, Australia's SpeciesLinks-Integrated Botanical Information System (IBIS) and Google images. The bioactive compounds are linked to the PubChem database. Overall, CMKb serves as a single knowledgebase for holistic plant-derived therapeutics and can be used as an information resource for biodiversity conservation, to lead discovery and conservation of customary medicinal knowledge.
Predicting RNA-binding sites of proteins using support vector machines and evolutionary information
Authors: Cheng Cheng-Wei , Su Emily Chia-Yu , Hwang Jenn-Kang , Sung Ting-Yi , Hsu Wen-Lian 
Published: December 2008

Abstract

Background
RNA-protein interaction plays an essential role in several biological processes, such as protein synthesis, gene expression, posttranscriptional regulation and viral infectivity. Identification of RNA-binding sites in proteins provides valuable insights for biologists. However, experimental determination of RNA-protein interaction remains time-consuming and labor-intensive. Thus, computational approaches for prediction of RNA-binding sites in proteins have become highly desirable. Extensive studies of RNA-binding site prediction have led to the development of several methods. However, they could yield low sensitivities in trade-off for high specificities.

Results
We propose a method, RNAProB, which incorporates a new smoothed position-specific scoring matrix (PSSM) encoding scheme with a support vector machine model to predict RNA-binding sites in proteins. Besides the incorporation of evolutionary information from standard PSSM profiles, the proposed smoothed PSSM encoding scheme also considers the correlation and dependency from the neighboring residues for each amino acid in a protein. Experimental results show that smoothed PSSM encoding significantly enhances the prediction performance, especially for sensitivity. Using five-fold cross-validation, our method performs better than the state-of-the-art systems by 4.90%~6.83%, 0.88%~5.33%, and 0.10~0.23 in terms of overall accuracy, specificity, and Matthew's correlation coefficient, respectively. Most notably, compared to other approaches, RNAProB significantly improves sensitivity by 7.0%~26.9% over the benchmark data sets. To prevent data over fitting, a three-way data split procedure is incorporated to estimate the prediction performance. Moreover, physicochemical properties and amino acid preferences of RNA-binding proteins are examined and analyzed.

Conclusion
Our results demonstrate that smoothed PSSM encoding scheme significantly enhances the performance of RNA-binding site prediction in proteins. This also supports our assumption that smoothed PSSM encoding can better resolve the ambiguity of discriminating between interacting and non-interacting residues by modelling the dependency from surrounding residues. The proposed method can be used in other research areas, such as DNA-binding site prediction, protein-protein interaction, and prediction of posttranslational modification sites.
Extracting transcription factor binding sites from unaligned gene sequences with statistical models
Authors: Lu Chung-Chin , Yuan Wei-Hao , Chen Te-Ming 
Published: December 2008

Abstract

Background
Transcription factor binding sites (TFBSs) are crucial in the regulation of gene transcription. Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used to identify potential regulatory sequences, but the procedure can only map the probable protein-DNA interaction loci within 1–2 kb resolution. To find out the exact binding motifs, it is necessary to build a computational method to examine the ChIP-chip array binding sequences and search for possible motifs representing the transcription factor binding sites.

Results
We developed a program to find out accurate motif sites from a set of unaligned DNA sequences in the yeast genome. Compared with MDscan, the prediction results suggest that, overall, our algorithm outperforms MDscan since the predicted motifs are more consistent with previously known specificities reported in the literature and have better prediction ranks. Our program also outperforms the constraint-less Cosmo program, especially in the elimination of false positives.

Conclusion
In this study, an improved sampling algorithm is proposed to incorporate the binomial probability model to build significant initial candidate motif sets. By investigating the statistical dependence between base positions in TFBSs, the method of dependency graphs and their expanded Bayesian networks is combined. The results show that our program satisfactorily extract transcription factor binding sites from unaligned gene sequences.