bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finite element approximation of a forward and backward anisotropic diffusion model in image denoising and form generalization
Authors: Ebmeyer Carsten , Vogelgesang Jens 
Published: July 2007

AbstractA new forward–backward anisotropic diffusion model is introduced. The two limit cases are the Perona‐Malik equation and the Total Variation flow model. A fully discrete finite element scheme is studied using C0‐piecewise linear elements in space and the backward Euler difference scheme in time. A priori estimates are proven. Numerical results in image denoising and form generalization are presented.© 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2008
Computational analysis of human protein interaction networks
Authors: Ramírez Fidel , Schlicker Andreas , Assenov Yassen , Lengauer Thomas , Albrecht Mario 
Published: July 2007

AbstractLarge amounts of human protein interaction data have been produced by experiments and prediction methods. However, the experimental coverage of the human interactome is still low in contrast to predicted data. To gain insight into the value of publicly available human protein network data, we compared predicted datasets, high‐throughput results from yeast two‐hybrid screens, and literature‐curated protein‐protein interactions. This evaluation is not only important for further methodological improvements, but also for increasing the confidence in functional hypotheses derived from predictions. Therefore, we assessed the quality and the potential bias of the different datasets using functional similarity based on the Gene Ontology, structural iPfam domain‐domain interactions, likelihood ratios, and topological network parameters. This analysis revealed major differences between predicted datasets, but some of them also scored at least as high as the experimental ones regarding multiple quality measures. Therefore, since only small pair wise overlap between most datasets is observed, they may be combined to enlarge the available human interactome data. For this purpose, we additionally studied the influence of protein length on data quality and the number of disease proteins covered by each dataset. We could further demonstrate that protein interactions predicted by more than one method achieve an elevated reliability.
Two‐dimensional wavepacket dynamics with quantum hydrodynamics
Authors: Matsumoto D. , Hayashi K. , Ida T. , Mizuno M. , Endo K. , Nishikawa K. 
Published: July 2007

AbstractWyatt and coworkers introduced a new approach (Wyatt, Quantum Dynamics with Trajectories Introduction to Quantum Hydrodynamics, Springer, New York, 2005; Lopreore and Wyatt, Phys Rev Lett, 1999, 82, 5190; Wyatt et al., J Chem Phys, 2001, 114, 5113; Lopreore and Wyatt, J Chem Phys, 2002, 116, 1228; Trahan and Wyatt, J Chem Phys, 2003, 118, 4784; Trahan et al., J Chem Phys, 2005, 122, 164104; Babyuk and Wyatt, J Chem Phys, 2006, 125, 64112) which is based on quantum hydrodynamics to the quantum wavepacket dynamics and applied to several systems including tunneling and nonadiabatic transition. This approach is expected to overcome some disadvantages of the conventional wavepacket dynamics, such as order‐N problem and use of absorbing potential. We applied this method to two‐dimensional model of quantum tunneling system and compared the new approach with the conventional wavepacket simulation since the validity of this method to multidimensional systems is not well known. In the simulation, we adopted two different model potentials (Model I and Model II) and calculated time dependence of the probability density and the tunneling probability in both models, where we showed explicitly that the results of the quantum hydrodynamics are identical with those of the conventional method. Using the moving grid and the regridding algorithm in the quantum hydrodynamics, we can effectively avoid order‐N problem and use of the absorbing potential. In addition to these computational advantages, the flux vector is easily obtained by the quantum hydrodynamics and these vectors field helps us to intuitively understand detailed tunneling dynamics. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Simultaneous detection of N‐terminal fragment ions in a protein mixture using a ruthenium(II) complex
Authors: Ito Akihiro , Okamura Taka‐aki , Yamamoto Hitoshi , Ueyama Norikazu , Yamaguchi Minoru , Kuyama Hiroki , Ando Eiji , Tsunasawa Susumu , Ake Kojiro , Masui Ryoji , Kuramitsu Seiki , Nakazawa Takashi , Norioka Shigemi 
Published: July 2007

AbstractUse of a bis(terpyridine)ruthenium(II) derivative as an N‐terminal labeling reagent resulted in the simultaneous detection and individual determination of all the N‐terminal fragments of the proteins in a mixture without requiring any separation. All of the N‐termini of the guanidinated proteins were labeled selectively by the ruthenium complex (<Ru>‐CO‐labeling). After chymotryptic digestion, the fragments were analyzed by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) and post‐source decay (PSD). The <Ru>‐CO moiety exclusively enhanced N‐terminal fragment ions in mass spectra and enabled easy N‐terminal sequencing. In a mixture containing three different proteins (lysozyme, ubiquitin, and insulin), all of the N‐terminal fragment ions labeled with the ruthenium complex were found to produce uniformly intense peaks without the detection of the other unlabeled fragments. The N‐terminal sequences of these ions were determined individually by PSD analysis. Application to unknown proteins from Thermus thermophilus HB8 with two‐dimensional electrophoretic separation resulted in the successful determination of the N‐terminal sequence and easy identification of the target protein. Copyright © 2007 John Wiley & Sons, Ltd.
Quantitative analysis of a proteome by N‐terminal stable‐isotope labelling of tryptic peptides
Authors: Fedjaev Michael , Trudel Stephanie , Tjon‐A‐Pan Natascha , Parmar Amanda , Posner Barry I. , Levy Emile , Nifant'ev Ilya , Pshezhetsky Alexey V. 
Published: July 2007

AbstractCovalent modification of peptides and proteins with compounds containing stable isotopes (isotope tagging) has become an essential tool to detect dynamic changes in the proteome following external or internal influence; however, using terminal amino groups for global isotope labelling of tryptic peptides is challenged by the similar reactivity of the amino groups of lysine residues. We describe a new quantitative method based on selective tagging of the terminal amino groups of tryptic peptides with pentafluorophenyl esters containing stable isotopes. The labelled peptides were resolved by two‐dimensional nanoflow liquid chromatography on weak anion‐exchange and reversed‐phase columns and then identified and quantified by tandem mass spectrometry. The method was applied to compare the proteomes of plasma membranes from proliferating and differentiated human colorectal adenocarcinoma (Caco‐2) cells and endosomes purified from the livers of rats stimulated with insulin and epidermal growth factor. The comparison of the results obtained by isotope tagging and biochemical assays demonstrate that global isotope tagging with pentafluorophenyl esters allows accurate quantification of complex protein samples. Copyright © 2007 John Wiley & Sons, Ltd.
Creating Nanopatterns of His‐Tagged Proteins on Surfaces by Nanoimprint Lithography Using Specific NiNTA‐Histidine Interactions
Authors: Maury Pascale , Escalante Maryana , Péter Mária , Reinhoudt David N. , Subramaniam Vinod , Huskens Jurriaan 
Published: July 2007

AbstractDirected assembly of the DsRed FT protein is demonstrated on self‐assembled monolayers (SAMs) on silicon substrates patterned by nanoimprint lithography. Initially, the DsRed protein is attached using electrostatic interactions on both topographical (polymer) templates with an amino functionalization and on chemically patterned (flat) substrates. In a second experiment, a patterned NiNTA SAM is used in order to attach the DsRed FT protein via supramolecular interactions, taking advantage of the histidine functionalization of the DsRed FT protein. The NTA SAM is formed on silicon oxide using a multistep covalent process. Patterning of the NTA SAM is performed using nanoimprint lithography. The DsRed FT protein is attached on the patterned NTA layer after treating this with a NiII solution. Moreover, the histidine‐NiNTA binding may be reversed by removing the Ni using EDTA or by competition using imidazole. The regeneration and reuse of the substrate by subsequently attaching and removing two different histidine‐functionalized proteins from the patterned NTA is shown by fluorescence microscopy.
Oto, a generic and extensible tool for marking programming assignments
Authors: Tremblay G. , Guérin F. , Pons A. , Salah A. 
Published: July 2007

AbstractMarking programming assignments in programming courses involves a lot of work: each program must be tested, the source code must be read and evaluated, etc. With the large classes encountered nowadays, the feedback provided to students through marking is thus rather limited, and often late. Tools providing support for marking programming assignments do exist, ranging from support for administrative aspects through automation of program testing or support for source code evaluation based on metrics. In this paper, we introduce a tool, called Oto, that provides support for submission and marking of assignments. Oto aims at reducing the workload associated with the marking task. Oto also aims at providing timely feedback to the students, including feedback before the final submission. Furthermore, the tool has been designed to be generic and extensible, so that the marking process for a specific assignment can easily be customized and the tool can be extended with various marking components (modules) that allows it to deal with various aspects of marking (testing, style, structure, etc.) and with programs written in various programming languages. Copyright © 2007 John Wiley & Sons, Ltd.
FIRE/J—optimizing regular expression searches with generative programming
Authors: Karakoidas Vassilios , Spinellis Diomidis 
Published: July 2007

AbstractRegular expressions are a powerful tool for analyzing and manipulating text. Their theoretical background lies within automata theory and formal languages. The FIRE/J (fast implementation of regular expressions for Java) regular expression library is designed to provide maximum execution speed while remaining portable across different machine architectures. To achieve that, FIRE/J transforms each regular expression into a tailor‐made class file, which is compiled directly to Java virtual machine (JVM) bytecodes. The library is compatible with the POSIX standard. Copyright © 2007 John Wiley & Sons, Ltd.
Chemical Composition and Structure of Granule Periphery and Envelope Remnant of Rice Starches as Revealed by Chemical Surface Gelatinization
Authors: Wang Ya‐Jane , Kuo Meng‐I , Wang Linfeng , Patindol James 
Published: July 2007

AbstractIn this work the contribution of molecular structures to the swelling behavior of rice starches was investigated. Rice starches with different amylose contents (0 ‐ 23.4 %) were gelatinized to various degrees (approximately 10, 20, and 50 %) with 13 M aqueous LiCl, and the surface‐gelatinized starch and ungelatinized remaining granules were separated and characterized. The native starches were heated at 85 or 95°C for 30 min in excess water, and the granule envelope remnants were recovered by centrifugation for further characterization. The remaining granules after surface removal exhibited a lower gelatinization temperature and enthalpy, and swelled to a greater extent upon heating than the native counterpart. The amylopectin molecules in granule envelope remnants obtained at 95°C had larger Mw (weight‐average molar mass) and Rz (z‐average gyration radius) than those in remnants obtained at 85°C. The chemical composition and structure of granule envelope remnants obtained at 85°C were different from those obtained at 95°C for the same rice starch cultivar. The results imply that starch periphery may not be responsible for maintaining starch granule integrity during gelatinization and swelling. It is proposed that the composition and structure of the granule envelope remnant that maintains granule integrity are not constant but dynamic. The formation of a semi‐permeable membrane‐like surface structure during gelatinization and swelling is proposed to be a result of molecule entanglement after gelatinization.
Mechanisms of progression of chronic kidney disease
Authors: Fogo Agnes B. 
Published: July 2007

AbstractChronic kidney disease (CKD) occurs in all age groups, including children. Regardless of the underlying cause, CKD is characterized by progressive scarring that ultimately affects all structures of the kidney. The relentless progression of CKD is postulated to result from a self-perpetuating vicious cycle of fibrosis activated after initial injury. We will review possible mechanisms of progressive renal damage, including systemic and glomerular hypertension, various cytokines and growth factors, with special emphasis on the renin–angiotensin–aldosterone system (RAAS), podocyte loss, dyslipidemia and proteinuria. We will also discuss possible specific mechanisms of tubulointerstitial fibrosis that are not dependent on glomerulosclerosis, and possible underlying predispositions for CKD, such as genetic factors and low nephron number.
Interferon‐gamma and lipopolysaccharide stimulation increases matrix metalloproteinase‐9 expression and enhances invasion activity in ras/myc‐transformed serum‐free mouse embryo cells
Authors: Kidachi Yumi , Yamaguchi Hideaki , Umetsu Hironori , Ryoyama Kazuo 
Published: July 2007

AbstractRas/myc‐transformed serum‐free mouse embryo (ras/myc SFME) cells were treated with interferon‐gamma (IFN‐γ, 100 units/ml) and/or lipopolysaccharide (LPS, 0.5 μg/ml) for 24 h to investigate the effects of these ligands on the expression of matrix metalloproteinase‐9 (MMP‐9) and tissue inhibitor of metalloproteinase‐1 (TIMP‐1). Aminoguanidine (AG, 1 mM; a nitric oxide synthase [NOS] inhibitor) was also added along with IFN‐γ and LPS to analyze a possible association of NO with invasiveness. Treatment of cells with IFN‐γ alone did not alter MMP‐9 mRNA expression or pro‐MMP‐9 production, but LPS alone and IFN‐γ + LPS co‐treatment enhanced them significantly. TIMP‐1 mRNA expression remained unchanged with or without treatment and the mRNA expression of MMP‐9 exceeded that of TIMP‐1 in LPS‐ or IFN‐γ + LPS‐treated cells. Co‐treatment of cells with IFN‐γ and LPS up‐regulated invasiveness and indicated a possible involvement of NO in the enhancement of invasiveness. These results suggest that ras/myc SFME cells respond to inflammatory and infectious conditions and that they may possibly modulate their characteristics as cancer cells due to their increase in MMP‐9 expression and invasion activity.
The peptidase inhibitor CGS‐26303 increases endothelin converting enzyme‐1 expression in endothelial cells through accumulation of big endothelin‐1
Authors: Raoch V , Martinez‐Miguel P , Arribas‐Gomez I , Rodriguez‐Puyol M , Rodriguez‐Puyol D , Lopez‐Ongil S 
Published: July 2007

Background and purpose:CGS‐26303 inhibits endothelin converting enzyme (ECE)‐1 more specifically than phosphoramidon. We have studied the effect of CGS‐26303 on ECE‐1 expression in bovine aortic endothelial cells.Methods:ECE‐1 activity and big endothelin (ET)‐1 levels were measured by ELISA, ECE‐1 expression using western and northern blot and promoter activity using transfection assays.Key results:ECE‐1 activity was completely inhibited by CGS‐26303 25 μ
M and phosphoramidon 100 μ
M. CGS‐26303 and phosphoramidon, though not thiorphan, a neutral endopeptidase (NEP) inhibitor, stimulated ECE‐1 expression in cells (maximal effect at 16 h, 25 μ
M). Cycloheximide abolished that effect. CGS‐26303 induced ECE‐1 mRNA expression and ECE‐1 promoter activity. CGS‐35066, a selective ECE‐1 inhibitor, mimicked the effects of CGS‐26303, suggesting that the effect was specific to ECE‐1 inhibition. Big ET‐1 accumulated in the cells and in the supernatants after CGS‐26303 treatment. Neither exogenously added ET‐1 nor the blockade of their receptors with bosentan modified ECE‐1 protein. When big ET‐1 was added to cells, significant increases in ECE‐1 protein content and ECE‐1 promoter activity were found. Bosentan did not block those effects. CGS‐26303 did not modify prepro‐ET‐1 expression. CGS‐26303 and big ET‐1 induced the same effects in human endothelial cells, at lower doses.Conclusions:These results suggest that the accumulation of big ET‐1 is responsible for the effects of CGS‐26303 on ECE‐1 and they did not depend on NEP blockade. Changes in ECE‐1 protein after the administration of CGS‐26303 could lead to a decreased response in long‐term treatments.British Journal of Pharmacology (2007) 152, 313–322; doi:10.1038/sj.bjp.0707398; published online 23 July 2007
Semiparametric functional mapping of quantitative trait loci governing long-term HIV dynamics
Authors: Wu Song , Yang Jie , Wu Rongling 
Published: July 2007

Abstract
Motivation: Functional mapping has proven to be powerful for characterizing quantitative trait loci (QTL) that control complex dynamic traits. More recently, functional mapping has been extended to identify the host QTL responsible for HIV dynamics by incorporating a parametric bi-exponential function for earlier stages of viral load trajectories. However, existing functional mapping cannot be used to map long-term HIV dynamics because no mathematical functions are available for later stages of HIV dynamic changes.
Results: We derived a statistical model for functional mapping of dynamic QTL through characterizing HIV load trajectories during a long-term period semiparametrically. The new model was constructed within the maximum likelihood framework and implemented with the EM-simplex algorithm. It allows for the test of differences in the genetic control of short- and long-term HIV dynamics and the characterization of the effects of viral-host genome interaction. Extensive simulation studies have been performed to test the statistical behavior of this model. The new model will provide an important tool for genetic and genomic studies of human complex diseases like HIV/AIDS and their pathological progression.
Availability: Available on request from the corresponding author.
Contact: rwu@stat.ufl.edu
Learning to extract relations for protein annotation
Authors: Kim Jee-Hyub , Mitchell Alex , Attwood Teresa K. , Hilario Melanie 
Published: July 2007

Abstract
Motivation: Protein annotation is a task that describes protein X in terms of topic Y. Usually, this is constructed using information from the biomedical literature. Until now, most of literature-based protein annotation work has been done manually by human annotators. However, as the number of biomedical papers grows ever more rapidly, manual annotation becomes more difficult, and there is increasing need to automate the process. Recently, information extraction (IE) has been used to address this problem. Typically, IE requires pre-defined relations and hand-crafted IE rules or annotated corpora, and these requirements are difficult to satisfy in real-world scenarios such as in the biomedical domain. In this article, we describe an IE system that requires only sentences labelled according to their relevance or not to a given topic by domain experts.
Results: We applied our system to meet the annotation needs of a well-known protein family database; the results show that our IE system can annotate proteins with a set of extracted relations by learning relations and IE rules for disease, function and structure from only relevant and irrelevant sentences.
Contact: jee.kim@cui.unige.ch
Polyploids, genome halving and phylogeny
Authors: Sankoff David , Zheng Chunfang , Zhu Qian 
Published: July 2007

Abstract
Motivation: Autopolyploidization and allopolyploidization events multiply the number of chromosomes and genomic content. Genome rearrangement phylogenetics requires that all genomes analyzed have the same set of orthologs, so that it is not possible to include diploid and polyploid genomes in the same phylogeny.
Results: We propose a framework for solving this difficulty by integrating the rearrangement median and genome halving algorithms. Though the framework is general, some problems remain open. We implement a heuristic solution to the prototypical case of a tree with one tetraploid and two diploid genomes, and apply it to study the evolution of cereals and of yeast.
Contact: sankoff@uottawa.ca
Spectrum: joint bayesian inference of population structure and recombination events
Authors: Sohn Kyung-Ah , Xing Eric P. 
Published: July 2007

Abstract
Motivation: While genetic properties such as linkage disequilibrium (LD) and population structure are closely related under a common inheritance process, the statistical methodologies developed so far mostly deal with LD analysis and structural inference separately, using specialized models that do not capture their statistical and genetic relationships. Also, most of these approaches ignore the inherent uncertainty in the genetic complexity of the data and rely on inflexible models built on a closed genetic space. These limitations may make it difficult to infer detailed and consistent structural information from rich genomic data such as populational single nucleotide polymorphisms (SNP) profiles.
Results: We propose a new model-based approach to address these issues through joint inference of population structure and recombination events under a non-parametric Bayesian framework; we present Spectrum, an efficient implementation based on our new model. We validated Spectrum on simulated data and applied it to two real SNP datasets, including single-population Daly data and the four-population HapMap data. Our method performs well relative to LDhat 2.0 in estimating the recombination rates and hotspots on these datasets. More interestingly, it generates an ancestral spectrum for representing population structures which not only displays sub-structure based on population founders but also reveals details of the genetic diversity of each individual. It offers an alternative view of the population structures to that offered by Structure 2.1, which ignores chromosome-level mutation and recombination with respect to founders.
Contact: epxing@cs.cmu.edu
Cotranslational protein folding—fact or fiction?
Authors: Deane Charlotte M. , Dong Mingqiang , Huard Fabien P.E. , Lance Braddon K. , Wood Graham R. 
Published: July 2007

Abstract
Motivation: Experimentalists have amassed extensive evidence over the past four decades that proteins appear to fold during production by the ribosome. Protein structure prediction methods, however, do not incorporate this property of folding. A thorough study to find the fingerprint of such sequential folding is the first step towards using it in folding algorithms, so assisting structure prediction.
Results: We explore computationally the existence of evidence for cotranslational folding, based on large sets of experimentally determined structures in the PDB. Our perspective is that cotranslational folding is the norm, but that the effect is masked in most classes. We show that it is most evident in α/β proteins, confirming recent findings. We also find mild evidence that older proteins may fold cotranslationally. A tool is provided for determining, within a protein, where cotranslation is most evident.
Contact: gwood@efs.mq.edu.au