bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Migmatite Area Around Bettyhill, Sutherland
Authors: Cheng Yu-Chi , Read H. H. 
Published: October 2009

Summary
The Migmatization of pelitic, semipelitic, siliceous and hornblendic (Durcha type) rocks of the Moine Series is a record of a lengthy series of metasomatic changes brought about by the activity of alkaline solutions. Pelitic gneisses are converted by soda-metasomatism into permeation-gneisses. Semipelitic granulites give rise to augen-migmatites through the action of potash-bearing fluids. Siliceous and hornblendic rocks are relatively resistant to change. Various types of granite-gneisses arise from the different sedimentary parents. Many sheets of pegmatite, granite and aplite are shown by their field relations to have been formed by the gradual metasomatism of the country rocks, probably by the long-continued passage of fluids along certain channels.
I. Introduction
The area which forms the subject of this paper is about l0 square miles in extent and forms a narrow strip along the north coast of Sutherland, from the River Naver eastwards to near Kirktomy. This small region provides excellent examples of the migmatization of the various lithological types of the Moine Series and its associated intrusions. It consists of numerous small injection zones varying greatly both in width and length, most of them being roughly parallel to the regional foliation. Though the beds are affected by small faults and thrusts, their strike is sufficiently persistent and the lithological characters of comparatively thin layers are sufficiently constant to permit the tracing in the field of the changes in a number of zones in response to different degrees of migmatization. It has thus been possible to prove beyond reasonable doubt the
"Equation missing" -Stability Approach to Variational Iteration Method for Solving Integral Equations
Authors: Saadati R. , Vaezpour S. M. , Rhoades B. E. 
Published: October 2009

AbstractWe consider "Equation missing"-stability definition according to Y. Qing and B. E. Rhoades (2008) and we show that the variational iteration method for solving integral equations is "Equation missing"-stable. Finally, we present some text examples to illustrate our result.
Spatial inking
Authors: Figal Günter 
Published: October 2009

AbstractThis paper is an attempt to solve a key problem of phenomenology. The problem is given with the double role of the revealing capacity for which phenomena are present. On the one hand, this capacity must be prior to all phenomena, because it allows phenomena to show themselves and thus to be what they essentially are. On the other hand, the revealing capacity must be situated in the midst of phenomena; it must belong to the phenomenal world in order to have access to it. This problem has been discussed in different versions by Husserl, Heidegger, and Merleau-Ponty, but in every version it remains aporetic. The problem can be solved by conceiving the capacity, which reveals phenomena, as spatial. The paper shows how the essential priority of the revealing capacity as well as its situatedness in the midst of phenomena has spatial character. Phenomenology thus is spatial thinking.
Modelling sanitary demands for occupant loads in shopping centres of Hong Kong
Authors: Mui KW , Wong LT , Lam HS 
Published: October 2009

This paper presents a quantitative mathematical model of sanitary demands from occupants in shopping complexes. In-situ measurements and interview surveys with occupants were conducted in typical local shopping malls in order to determine the model parameters for their visiting patterns, load patterns, demand patterns and their preferred or acceptable duration for waiting and using water closets (WCs). The model is used to assess the probable acceptance of sanitary facilities towards the acceptable amount of time for waiting at a typical female washroom designed for an occupant load of 600 occupants in a shopping mall. The results showed that the current sanitary provisions for female washrooms in local shopping malls could meet occupants’ minimum expectation, while with an additional 33% of WC, the sanitary would fully satisfy ‘all’ occupants in terms of amount of time for waiting. Practical applications: This paper presents a quantitative mathematical model of sanitary demands from a group of building occupants. This model is applied to evaluate the performance of sanitary provisions at typical female washrooms in Hong Kong shopping malls and to quantify the provisions required to achieve the most acceptable amount of time for waiting to their users.
Prediction of Major Adverse Cardiac Events in Vascular Surgery: Are Cardiac Risk Scores of Any Practical Value?
Authors: Parmar Chetan D. , Torella Francesco 
Published: October 2009

Background: Disease-specific preoperative scoring systems are often used to predict postoperative cardiac complications. We retrospectively evaluated the accuracy of 2 cardiac risk scores in the prediction of major adverse cardiac events (MACE) after vascular surgery. Methods: Consecutive procedures were ‘‘scored’’ according to the Revised Cardiac Risk Index (RCRI) and the Eagle criteria. Two ‘‘generic’’ risk scoring systems, ASA (American Society of Anesthesiology) grade and the physiology Portsmouth POSSUM (P-POSSUM) score, were also documented for comparison. Results: After 344 surgical procedures, 18 patients suffered a MACE (5.2%; 95% CI = 2.8-7.58-4 fatal). The RCRI (AUC 95% CI = 0.68 [0.57-0.83], P = .009) and the Eagle criteria (AUC 95% CI = 0.73 [0.57-0.8], P = .001) were no better than P-POSSUM (AUC 95% CI = 0.82 [0.73-0.91], P < .001) and ASA grade (AUC 95% CI = 0.67 (0.56-0.78), P = 0.016) in predicting MACE. Of the variables included in the 2 cardiac scoring systems, only age and history of ischemic heart disease were associated with MACE in our patients. Conclusion: Cardiac risk scores were no better than generic risk scoring systems in predicting MACE. Poor performance may be due to differences between our patient population and those in which the scores were developed and to improved perioperative management of cardiac risk.
Characterization of a rituximab variant with potent antitumor activity against rituximab-resistant B-cell lymphoma
Authors: Li Bohua , Zhao Lei , Guo Huaizu , Wang Chong , Zhang Xunming , Wu Lan , Chen Lin , Tong Qing , Qian Weizhu , Wang Hao , Guo Yajun 
Published: October 2009

AbstractDespite widespread use of the anti-CD20 monoclonal antibody (mAb), rituximab, in treating B-cell lymphomas, its efficacy remains variable and often modest. A better understanding of rituximab-mediated killing mechanisms is essential to develop more effective therapeutic agents. In this study, we modulated the binding property of rituximab by introducing several point mutations in its complementarity-determining regions. The data showed that changing the binding avidity of rituximab in the range from 10−8 to 10−10 M could regulate its antibody-dependent cellular cytotoxicity but not affect its complement-dependent cytotoxicity and apoptosis-inducing activity in B-lymphoma cells. Contradictory to previous findings, we found that the complement-dependent cytotoxicity potency of CD20 mAb was independent of the off-rate. Despite still being a type I CD20 mAb, a rituximab triple mutant (H57DE/H102YK/L93NR), which had a similar binding avidity to a double mutant (H57DE/H102YK), was unexpectedly found to have extremely potent apoptosis-inducing activity. Moreover, this triple mutant, which was demonstrated to efficiently initiate both caspase-dependent and -independent apoptosis, exhibited potent in vivo therapeutic efficacy, even in the rituximab-resistant lymphoma model, suggesting that it might be a promising therapeutic agent for B-cell lymphomas.
Evidence of serum immunoglobulin abnormalities up to 9.8 years before diagnosis of chronic lymphocytic leukemia: a prospective study
Authors: Tsai Huei-Ting , Caporaso Neil E. , Kyle Robert A. , Katzmann Jerry A. , Dispenzieri Angela , Hayes Richard B. , Marti Gerald E. , Albitar Maher , Ghia Paolo , Rajkumar S. Vincent , Landgren Ola 
Published: October 2009

AbstractImmune-related deficiencies are well-known complications of chronic lymphocytic leukemia (CLL). Although recent data indicate that almost all CLL patients are preceded by a monoclonal B-cell lymphocytosis precursor state, patterns of immune defects preceding CLL diagnosis are unclear. We identified 109 persons who developed CLL from the prospective and nationwide Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial with 77 469 participants, with serially collected prediagnostic serum samples. We assayed monoclonal (M)–proteins, κ/λ free light chains (FLCs) in prediagnostic obtained up to 9.8 years before CLL diagnosis. The prevalence of an abnormal FLC ratio, M-protein, and hypogamma-globulinemia before CLL diagnosis was 38% (95% confidence interval, 29%-47%), 13% (7%-21%), and 3% (1%-8%), respectively. M-proteins and abnormal FLC ratios were detected up to 9.8 years before CLL diagnosis in a total of 48 persons (44%). Hypogammaglobulinemia was not present until 3 years before the diagnosis of CLL. Among 37 patients with information on tumor cell immunophenotype, an association between immunophenotype and involved FLC (P = .024, Fisher exact test) was observed. Among 61 persons with a normal FLC ratio and without an M-protein, 17 had elevated κ and/or λ FLC levels, indicating polyclonal B-cell activation in 17 of 109 (16%) patients. These findings support a role for chronic immune stimulation in CLL genesis.
STAR NET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data
Authors: Jupiter Daniel , Chen Hailin , VanBuren Vincent 
Published: October 2009

Abstract

Background
Although expression microarrays have become a standard tool used by biologists, analysis of data produced by microarray experiments may still present challenges. Comparison of data from different platforms, organisms, and labs may involve complicated data processing, and inferring relationships between genes remains difficult.

Results

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2 is a new web-based tool that allows post hoc visual analysis of correlations that are derived from expression microarray data. S

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2 facilitates user discovery of putative gene regulatory networks in a variety of species (human, rat, mouse, chicken, zebrafish, Drosophila, C. elegans, S. cerevisiae, Arabidopsis and rice) by graphing networks of genes that are closely co-expressed across a large heterogeneous set of preselected microarray experiments. For each of the represented organisms, raw microarray data were retrieved from NCBI's Gene Expression Omnibus for a selected Affymetrix platform. All pairwise Pearson correlation coefficients were computed for expression profiles measured on each platform, respectively. These precompiled results were stored in a MySQL database, and supplemented by additional data retrieved from NCBI. A web-based tool allows user-specified queries of the database, centered at a gene of interest. The result of a query includes graphs of correlation networks, graphs of known interactions involving genes and gene products that are present in the correlation networks, and initial statistical analyses. Two analyses may be performed in parallel to compare networks, which is facilitated by the new H

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module.

Conclusion

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2 is a useful tool for developing new hypotheses about regulatory relationships between genes and gene products, and has coverage for 10 species. Interpretation of the correlation networks is supported with a database of previously documented interactions, a test for enrichment of Gene Ontology terms, and heat maps of correlation distances that may be used to compare two networks. The list of genes in a S

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network may be useful in developing a list of candidate genes to use for the inference of causal networks. The tool is freely available at http://vanburenlab.medicine.tamhsc.edu/starnet2.html, and does not require user registration.
Phylogenetic analysis of modularity in protein interaction networks
Authors: Erten Sinan , Li Xin , Bebek Gurkan , Li Jing , Koyutürk Mehmet 
Published: October 2009

AbstractBackgroundIn systems biology, comparative analyses of molecular interactions across diverse species indicate that conservation and divergence of networks can be used to understand functional evolution from a systems perspective. A key characteristic of these networks is their modularity, which contributes significantly to their robustness, as well as adaptability. Consequently, analysis of modular network structures from a phylogenetic perspective may be useful in understanding the emergence, conservation, and diversification of functional modularity.ResultsIn this paper, we propose a phylogenetic framework for analyzing network modules, with applications that extend well beyond network-based phylogeny reconstruction. Our approach is based on identification of modular network components from each network separately, followed by projection of these modules onto the networks of other species to compare different networks. Subsequently, we use the conservation of various modules in each network to assess the similarity between different networks. Compared to traditional methods that rely on topological comparisons, our approach has key advantages in (i) avoiding intractable graph comparison problems in comparative network analysis, (ii) accounting for noise and missing data through flexible treatment of network conservation, and (iii) providing insights on the evolution of biological systems through investigation of the evolutionary trajectories of network modules. We test our method, MOPHY, on synthetic data generated by simulation of network evolution, as well as existing protein-protein interaction data for seven diverse species. Comprehensive experimental results show that MOPHYis promising in reconstructing evolutionary histories of extant networks based on conservation of modularity, it is highly robust to noise, and outperforms existing methods that quantify network similarity in terms of conservation of network topology.ConclusionThese results establish modularity and network proximity as useful features in comparative network analysis and motivate detailed studies of the evolutionary histories of network modules.
A Perl procedure for protein identification by Peptide Mass Fingerprinting
Authors: Tiengo Alessandra , Barbarini Nicola , Troiani Sonia , Rusconi Luisa , Magni Paolo 
Published: October 2009

Abstract

Background
One of the topics of major interest in proteomics is protein identification. Protein identification can be achieved by analyzing the mass spectrum of a protein sample through different approaches. One of them, called Peptide Mass Fingerprinting (PMF), combines mass spectrometry (MS) data with searching strategies in a suitable database of known protein to provide a list of candidate proteins ranked by a score. To this aim, several algorithms and software tools have been proposed. However, the scoring methods and mainly the statistical evaluation of the results can be significantly improved.

Results
In this work, a Perl procedure for protein identification by PMF, called MsPI (Mass spectrometry Protein Identification), is presented. The implemented scoring methods were derived from the literature. MsPI implements a strategy to remove the contaminant masses present in the acquired spectra. Moreover, MsPI includes a statistical method to assign to each candidate protein, in addition to the scoring value, a p-value. Results obtained by MsPI on a dataset of 10 protein samples were compared with those achieved using two other software tools, i.e. Piums and Mascot. Piums implements one of the scoring methods available in MsPI, while Mascot is one of the most frequently used software tools in the protein identification field. MsPI scripts are available for downloading on the web site http://aimed11.unipv.it/MsPI.

Conclusion
The performances of MsPI seem to be better than those of Piums and Mascot. In fact, on the considered dataset, MsPI includes in its candidate proteins list, the "true" proteins nine times over ten, whereas Piums includes in its list the "true" proteins only four time over ten. Even if Mascot also correctly includes in the candidates list the "true" proteins nine times over ten, it provides longer candidate lists, therefore increasing the number of false positives when the molecular weight of the proteins in the sample is approximatively known (e.g. by the 1-D/2-D electrophoresis gel). Moreover, being MsPI a Perl tool, it can be easily extended and customized by the final users.
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation
Authors: Alfieri Roberta , Barberis Matteo , Chiaradonna Ferdinando , Gaglio Daniela , Milanesi Luciano , Vanoni Marco , Klipp Edda , Alberghina Lilia 
Published: October 2009

Abstract

Background
The cell cycle is a complex process that allows eukaryotic cells to replicate chromosomal DNA and partition it into two daughter cells. A relevant regulatory step is in the G0/G1 phase, a point called the restriction (R) point where intracellular and extracellular signals are monitored and integrated.
Subcellular localization of cell cycle proteins is increasingly recognized as a major factor that regulates cell cycle transitions. Nevertheless, current mathematical models of the G1/S networks of mammalian cells do not consider this aspect. Hence, there is a need for a computational model that incorporates this regulatory aspect that has a relevant role in cancer, since altered localization of key cell cycle players, notably of inhibitors of cyclin-dependent kinases, has been reported to occur in neoplastic cells and to be linked to cancer aggressiveness.

Results
The network of the model components involved in the G1 to S transition process was identified through a literature and web-based data mining and the corresponding wiring diagram of the G1 to S transition drawn with Cell Designer notation. The model has been implemented in Mathematica using Ordinary Differential Equations. Time-courses of level and of sub-cellular localization of key cell cycle players in mouse fibroblasts re-entering the cell cycle after serum starvation/re-feeding have been used to constrain network design and parameter determination. The model allows to recapitulate events from growth factor stimulation to the onset of S phase. The R point estimated by simulation is consistent with the R point experimentally determined.

Conclusion
The major element of novelty of our model of the G1 to S transition is the explicit modeling of cytoplasmic/nuclear shuttling of cyclins, cyclin-dependent kinases, their inhibitor and complexes. Sensitivity analysis of the network performance newly reveals that the biological effect brought about by Cki overexpression is strictly dependent on whether the Cki is promoting nuclear translocation of cyclin/Cdk containing complexes.
Phenotypic and genotypic data integration and exploration through a web-service architecture
Authors: Nuzzo Angelo , Riva Alberto , Bellazzi Riccardo 
Published: October 2009

Abstract

Background
Linking genotypic and phenotypic information is one of the greatest challenges of current genetics research. The definition of an Information Technology infrastructure to support this kind of studies, and in particular studies aimed at the analysis of complex traits, which require the definition of multifaceted phenotypes and the integration genotypic information to discover the most prevalent diseases, is a paradigmatic goal of Biomedical Informatics. This paper describes the use of Information Technology methods and tools to develop a system for the management, inspection and integration of phenotypic and genotypic data.

Results
We present the design and architecture of the Phenotype Miner, a software system able to flexibly manage phenotypic information, and its extended functionalities to retrieve genotype information from external repositories and to relate it to phenotypic data. For this purpose we developed a module to allow customized data upload by the user and a SOAP-based communications layer to retrieve data from existing biomedical knowledge management tools. In this paper we also demonstrate the system functionality by an example application of the system in which we analyze two related genomic datasets.

Conclusion
In this paper we show how a comprehensive, integrated and automated workbench for genotype and phenotype integration can facilitate and improve the hypothesis generation process underlying modern genetic studies.
A scale space approach for unsupervised feature selection in mass spectra classification for ovarian cancer detection
Authors: Ceccarelli Michele , d'Acierno Antonio , Facchiano Angelo 
Published: October 2009

Abstract

Background
Mass spectrometry spectra, widely used in proteomics studies as a screening tool for protein profiling and to detect discriminatory signals, are high dimensional data. A large number of local maxima (a.k.a. peaks) have to be analyzed as part of computational pipelines aimed at the realization of efficient predictive and screening protocols. With this kind of data dimensions and samples size the risk of over-fitting and selection bias is pervasive. Therefore the development of bio-informatics methods based on unsupervised feature extraction can lead to general tools which can be applied to several fields of predictive proteomics.

Results
We propose a method for feature selection and extraction grounded on the theory of multi-scale spaces for high resolution spectra derived from analysis of serum. Then we use support vector machines for classification. In particular we use a database containing 216 samples spectra divided in 115 cancer and 91 control samples. The overall accuracy averaged over a large cross validation study is 98.18. The area under the ROC curve of the best selected model is 0.9962.

Conclusion
We improved previous known results on the problem on the same data, with the advantage that the proposed method has an unsupervised feature selection phase. All the developed code, as MATLAB scripts, can be downloaded from http://medeaserver.isa.cnr.it/dacierno/spectracode.htm