bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chelate effect: The importance of reorganization energy
Authors: Davydova E. I. , Sevastianova T. N. , Timoshkin A. Y. , Suvorov A. V. , Frenking G. 
Published: June 2004

AbstractThe chelate effect has been theoretically studied at the Becke's three‐parameter exchange functional and the gradient‐corrected functional of Lee, Yang, and Paar/double‐ζ polarization level of theory. The influence of ligand, metal, and halogen nature on the chelate effect was analyzed for complexes of group 14 element tetrahalides with monodentate and bidentate nitrogen‐containing donors. It is shown that the large reorganization energy of the 2,2′‐bipyridine ligand (≈32 kJ mol‐1) shadows the chelate effect. The same conclusion holds for other ligands, which undergo significant reorganization upon complex formation. 1,10‐Phenanthroline does not have such a large reorganization energy, and its complexes are therefore more stable in the gas phase than are complexes with bipyridine. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Physics: Frightful, but fun. Pupils' and teachers' views of physics and physics teaching
Authors: Angell Carl , Guttersrud Øystein , Henriksen Ellen K. , Isnes Anders 
Published: June 2004

AbstractThere is widespread concern for the situation of school physics regarding recruitment, contents, teaching methods, etc. In this study based on questionnaire and focus group data, we explore how upper secondary pupils and teachers perceive physics as a subject, how they experience physics instruction, and how physics compares to other subjects.Our study shows that pupils find physics interesting, but difficult and work‐intensive; formalistic in nature, but still describing the world and everyday phenomena. Pupils express that “exoti” topics like astrophysics are closer to their life‐world than mechanics etc. Whereas teachers complain about pupils' poor mathematics skills, pupils do not see this as a major problem. Physics instruction is still dominated by traditional content knowledge and seems to attract and reward pupils with this orientation. Pupils have a relatively weak understanding of the central role of experiments in science. Generally, pupils appear conservative in their views on teaching and learning; however, they would like stronger emphasis on qualitative and pupil‐centred approaches.Based on our findings, we suggest that an upper secondary physics education preparing pupils for tomorrow's society should be characterized by variety, both within and among courses, integration of mathematics in the physics courses, more pupil‐centred instruction, and a stronger emphasis on knowledge in context. © 2004 Wiley Periodicals, Inc.Sci Ed88:683–706, 2004
Problem‐based learning: Using students' questions to drive knowledge construction
Authors: Chin Christine , Chia Li‐Gek 
Published: June 2004

AbstractThis study employed problem‐based learning for project work in a year 9 biology class. The purpose of the study was to investigate (a) students' inspirations for their self‐generated problems and questions, (b) the kinds of questions that students asked individually and collaboratively, and (c) how students' questions guided them in knowledge construction. Data sources included observation and field notes, students' written documents, audiotapes and videotapes of students working in groups, and student interviews. Sources of inspiration for students' problems and questions included cultural beliefs and folklore; wonderment about information propagated by advertisements and the media; curiosity arising from personal encounters, family members' concerns, or observations of others; and issues arising from previous lessons in the school curriculum. Questions asked individually pertained to validation of common beliefs and misconceptions, basic information, explanations, and imagined scenarios. The findings regarding questions asked collaboratively are presented as two assertions. Assertion 1 maintained that students' course of learning were driven by their questions. Assertion 2 was that the ability to ask the “right'' questions and the extent to which these could be answered, were important in sustaining students' interest in the project. Implications of the findings for instructional practice are discussed. © 2004 Wiley Periodicals, Inc. Sci Ed 88:707–727, 2004
Complete deterministic stream X-machine testing
Authors: Ipate Florentin 
Published: June 2004

Abstract.

One of the strengths of using
stream X-machines
to specify a system is that, under certain well defined conditions, it is possible to produce a test set that is guaranteed to determine the correctness of an implementation. However, the existing method assumes that the implementation of each processing function is proved to be correct before the actual testing can take place, so it only test the system
integration
. This paper presents a new method for generating test sets from a deterministic stream X-machine specification that generalises the existing integration testing method. This method no longer requires the implementations of the processing functions to be proved correct prior to the actual testing. Instead, the testing of the processing functions is performed along with the integration testing.
Increased expression of tumor necrosis factor‐α converting enzyme and tumor necrosis factor‐α in peripheral blood mononuclear cells in patients with advanced congestive heart failure
Authors: Satoh Mamoru , Iwasaka Junji , Nakamura Motoyuki , Akatsu Tomonari , Shimoda Yudai , Hiramori Katsuhiko 
Published: May 2004

AbstractBackground:Tumor necrosis factor‐α converting enzyme (TACE) has recently been identified as a metalloproteinase‐disintegrin, which converts pro‐tumor necrosis factor‐α (TNF‐α) to the mature form, and is an important mediator in the pathogenesis of CHF.Aims:In order to establish the importance of TACE in the regulation of TNF‐α synthesis in peripheral blood mononuclear cells (PBMC), we analyzed mRNAs and protein‐positive cells of both TACE and TNF‐α in PBMC obtained from patients with congestive heart failure (CHF).Methods and results:PBMC were obtained from 46 patients with CHF and 22 controls. PBMC were activated by phorbol 12‐myristate 13‐acetate and ionomycin and assessed for TACE and TNF‐α mRNAs by real‐time RT‐PCR, intracellular TACE and TNF‐α levels by flow cytometry, and TNF‐α secretion by supernatant ELISA. Levels of TACE and TNF‐α mRNAs, intracellular TACE and TNF‐α, and supernatant TNF‐α were higher in CHF than in controls (P<0.001). There was a positive correlation between TACE and TNF‐α levels in CHF patients (mRNA: r=0.60, P<0.001, intracellular protein levels: r=0.76, P<0.001). When the CHF group was divided into two subgroups by NYHA functional class (I and II vs. III and IV), levels of TACE and TNF‐α were significantly higher in severe CHF patients (NYHA III or IV) than in mild CHF patients (NYHA I or II) (mRNA: P<0.001; intracellular protein levels: P<0.001).Conclusion:These results demonstrate that in patients with CHF, and especially those with severe CHF, TACE expression in PBMC increases with TNF‐α expression. These observations suggest that TACE in PBMC is an important regulator of TNF‐α maturation, meaning that TACE may be a potential target for the inhibition of cellular TNF‐α production in CHF.
Examination of type I/type II alcoholism typology in a Greek hospital treatment population
Authors: Lykouras Lefteris , Moussas George , Botsis Alexander 
Published: May 2004

AbstractObjectiveThe study aims at testing the validity of two types of classification of male alcoholism in a Greek hospital treatment sample.MethodThe study population was drawn from male patients with alcohol dependence admitted to the Alcohol Treatment Unit of the Psychiatric Hospital of Attica. Seventy-three patients comprised the study sample after exclusion of subjects with alcohol dependence suffering from a comorbid serious medical condition, schizophrenic disorder, bipolar disorder, drug dependence or abuse, organic mental disorder or inability to read. The alcoholics were grouped in type I and II adopting the criterion of age-of-onset used by von Knorring et al. (1985). Impulsivity, suicide risk and violence risk were measured by means of the impulse control scale (ICS), the suicide risk scale (SRS) and the past feelings and acts of violence scale (PFAVS).ResultsFifty patients with alcohol dependence were defined as late-onset and 23 as early-onset. Compared to late-onset patients, early-onset individuals with alcohol dependence had more familial alcoholism (P = 0.032); they were in a higher rate unmarried (P = 0.001), had no stable job before entry in the Unit (P = 0.007) and scored higher on ICS (P = 0.046) and SRS (P = 0.024).ConclusionThe present study confirms type I/type II dichotomy of male alcoholism and also shows that the age-of-onset is a valid classification criterion.
Effect of cortical thickness and cancellous bone density on the holding strength of internal fixator screws
Authors: Seebeck J. , Goldhahn J. , Städele H. , Messmer P. , Morlock M. M. , Schneider E. 
Published: May 2004

AbstractInternal fixators are a new class of implants designed to preserve the periosteal blood supply of the bone. In contrast to conventional plate fixation in which the screws have spherical heads and are loaded mainly by axial pullout forces, screws in internal fixators are “locked” within the plate and therefore subjected to axial as well as bending loads. In this study the ultimate loads of screws of a commercially available internal fixator system were tested in a pullout (n = 72) and cantilever bending mode (n = 72) in metaphyseal and diaphyseal regions of four pairs of human tibiae with different bone qualities. Cortical thickness and cancellous bone density were determined at the screw insertion sites. Stepwise multiple linear regression revealed that cortical thickness and cancellous density can explain 93% and 98% of the variance of the ultimate load of the screws in an axial pullout and cantilever bending mode. Screws in internal fixators are better suited to transmit shear forces and thereby make better use of the strength potential of bone than screws used in conventional plate fixation: this is especially advantageous when bone strength is reduced, e.g. due to osteoporosis. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
Correcting the loss of cell-cycle synchrony in clustering analysis of microarray data using weights
Authors: Duan Fenghai , Zhang Heping 
Published: June 2004

Abstract
Motivation: Due to the existence of the loss of synchrony in cell-cycle data sets, standard clustering methods (e.g. k-means), which group open reading frames (ORFs) based on similar expression levels, are deficient unless the temporal pattern of the expression levels of the ORFs is taken into account.
Methods: We propose to improve the performance of the k-means method by assigning a decreasing weight on its variable level and evaluating the ‘weighted k-means’ on a yeast cell-cycle data set. Protein complexes from a public website are used as biological benchmarks. To compare the k-means clusters with the structures of the protein complexes, we measure the agreement between these two ways of clustering via the adjusted Rand index.
Results: Our results show the time-decreasing weight function—exp[−(1/2)(t2/C2)—]which we assign to the variable level of k-means, generally increases the agreement between protein complexes and k-means clusters when C is near the length of two cell cycles.
DBRF–MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants
Authors: Kyoda Koji , Baba Kotaro , Onami Shuichi , Kitano Hiroaki 
Published: June 2004

Abstract
Motivation: Large-scale gene expression profiles measured in gene deletion mutants are invaluable sources for identifying gene regulatory networks. Signed directed graph (SDG) is the most common representation of gene networks in genetics and cell biology. However, no practical procedure that deduces SDGs consistent with such profiles has been developed.
Results: We developed the DBRF–MEGN (difference-based regulation finding–minimum equivalent gene network) method in which an algorithm deduces the most parsimonious SDGs consistent with expression profiles of gene deletion mutants. Positive (or negative) directed edges representing positive (or negative) gene regulations are deduced by comparing the gene expression level between the wild-type and mutant. The most parsimonious SDGs are deduced using graph theoretical procedures. Compensation for excess removal of edges by restoring a minimum number of edges makes the method applicable to cyclic gene networks. Use of independent groups of edges greatly reduces the computational cost, thus making the method applicable to large-scale expression profiles. We confirmed the applicability of our method by applying it to the gene expression profiles of 265 Saccharomyces cerevisiae deletion mutants, and we confirmed our method's validity by comparing the pheromone response pathway, general amino acid control system, and copper and iron homeostasis system deduced by our method with those reported in the literature. Interpretation of the gene network deduced from the S. cerevisiae expression profiles by using our method led to the prediction of 132 transcriptional targets and modulators of transcriptional activity of 18 transcriptional regulators.
Availability: The software is available on request.
Supplementary information: http://www.so.bio.keio.ac.jp/dbrf-megn/
Mining gene expression data based on template theory
Authors: Yang Zheng Rong 
Published: June 2004

Abstract
Motivation: It is understood that clustering genes are useful for exploring scientific knowledge from DNA microarray gene expression data. The explored knowledge can be finally used for annotating biological function for novel genes. Representing the explored knowledge in an efficient manner is then closely related to the classification accuracy. However, this issue has not yet been paid the attention it deserves.
Result: A novel method based on template theory in cognitive psychology and pattern recognition is developed in this study for representing knowledge extracted from cluster analysis effectively. The basic principle is to represent knowledge according to the relationship between genes and a found cluster structure. Based on this novel knowledge representation method, a pattern recognition algorithm (the decision tree algorithm C4.5) is then used to construct a classifier for annotating biological functions of novel genes. The experiments on five published datasets show that this method has improved the classification performance compared with the conventional method. The statistical tests indicate that this improvement is significant.
Availability: The software package can be obtained upon request from the author.
CoPS: Comprehensive Peptide Signature Database
Authors: Prakash Tulika , Khandelwal Mamta , Dasgupta Dipayan , Dash Debasis , Brahmachari Samir K. 
Published: June 2004

Abstract
Summary: We present the development of a Comprehensive database of 12 076 invariant Peptide Signatures (CoPS) derived from 52 bacterial genomes with a minimum occurrence in at least seven organisms. These peptides were observed in functionally similar proteins and are distributed over nearly 1250 different functional proteins. The database provides function, structure and occurrence in biochemical pathways of the proteins containing these signature peptides. It houses additional information on the signature peptides, such as identical match in other motif/pattern (e.g. PROSITE, BLOCKS, PRINTS and Pfam) databases and the database of interacting proteins, human proteome and mutation effect on these signature peptides. There is a wide applicability of this database in the identification of critical functional residues in proteins. The database also facilitates the identification of folding nucleus/structural determinants in proteins and functional assignment to yet unknown proteins. We demonstrate functional assignment to 2605 hypothetical proteins in bacterial genomes and 112 unknown proteins in human using this database.
Availability: The database can be freely accessed through the following URL: http://203.195.151.46/copsv2/index.html or http://203.90.127.70/copsv2/index.html
Supplementary information: http://203.195.151.46/copsv2/aboutcops.html and http://203.90.127.70/copsv2/aboutcops.html
ICBS: a database of interactions between protein chains mediated by β-sheet formation
Authors: Dou Yimeng , Baisnée Pierre-François , Pollastri Gianluca , Pécout Yann , Nowick James , Baldi Pierre 
Published: June 2004

Abstract
Motivation: Interchain β-sheet (ICBS) interactions occur widely in protein quaternary structures, interactions between proteins and protein aggregation. These interactions play a central role in many biological processes and in diseases ranging from AIDS and cancer to anthrax and Alzheimer's.
Results: We have created a comprehensive database of ICBS interactions that is updated on a weekly basis and allows entries to be sorted and searched by relevance and other criteria through a simple Web interface. We derive a simple ICBS index to quantify the relative contributions of the β-ladders in the overall interchain interaction and compute first- and second-order statistics regarding amino acid composition and pairing at different relative positions in the β-strands. Analysis of the database reveals a 15.8% prevalence of significant ICBS interactions, the majority of which involve the formation of antiparallel β-sheets and many of which involve the formation of dimers and oligomers. The frequencies of amino acids in ICBS interfaces are similar to those in intrachain β-sheet interfaces. A full range of non-covalent interactions between side chains complement the hydrogen-bonding interactions between the main chains. Polar amino acids pair preferentially with polar amino acids and non-polar amino acids pair preferentially with non-polar amino acids among antiparallel (i, j) pairs. We anticipate that the statistics and insights gained from the database will guide the development of agents that control interchain β-sheet interactions and that the database will help identify new protein interactions and targets for these agents.
Availability: The database is available at: http://www.igb.uci.edu/servers/icbs/
Supplementary Information: http://www.igb.uci.edu/servers/icbs/
Faster cyclic loess: normalizing RNA arrays via linear models
Authors: Ballman Karla V. , Grill Diane E. , Oberg Ann L. , Therneau Terry M. 
Published: June 2004

Abstract
Motivation: Our goal was to develop a normalization technique that yields results similar to cyclic loess normalization and with speed comparable to quantile normalization.
Results: Fastlo yields normalized values similar to cyclic loess and quantile normalization and is fast; it is at least an order of magnitude faster than cyclic loess and approaches the speed of quantile normalization. Furthermore, fastlo is more versatile than both cyclic loess and quantile normalization because it is model-based.
Availability: The Splus/R function for fastlo normalization is available from the authors.
Command line tool for calculating theoretical MS spectra for given sequences
Authors: Boehm Andreas M. , Grosse-Coosmann Florian , Sickmann Albert 
Published: June 2004

Abstract
Summary: Scientists usually want to verify the ion matching process of algorithms that look up peptide sequences in DNA or protein databases. The verification step is often done numerically or visually. Not all search algorithms present the appropriate theoretical spectrum information within their results. Thus, the theoretical spectrum for each result should be calculated from the sequence of the matched peptide. We present an operating-system-independent command line tool for this purpose that can be integrated easily into complex as well as existing environments, and can be used to present the theoretical spectrum to the user in either graphical or tabular format by third party products.
Availability: The code is available via the website http://www.protein-ms.de.
BacTregulators: a database of transcriptional regulators in bacteria and archaea
Authors: Martínez-Bueno Manuel , Molina-Henares Antonio J. , Pareja Eduardo , Ramos Juan L. , Tobes Raquel 
Published: June 2004

Abstract
Motivation: The BacTregulators database is intended to collect and to integrate information on proteins belonging to defined families of transcriptional regulators in prokaryotes.
Results: The BacTregulators database currently contains data on two families of transcriptional regulators: AraC-XylS and TetR. The proteins included in the BacTregulators database have been identified by screening 123 genomes from archaea and bacteria and the SWISS-PROT and TrEMBL databases with profiles defining each family. As the result of an integration process, we have included 1326 different protein sequences from the AraC-XylS family and 1487 different protein sequences from the TetR family. The definition of an entry in BacTregulators is based on protein sequence, source organism, genome element and position in this genome element. The BacTregulators site allows the user to retrieve protein sequences, functional features and experimental evidence supporting the functions, references and the three-dimensional structure of the regulator when available. BacTregulators supplies an innovative tool that allows the researcher to obtain an integrated report that shows the data corresponding to other entries which are related by sequence similarity to the query entry. BacTregulators detects and classifies the regulators belonging to AraC-XylS and TetR families present in prokaryotic genomes, and thus contributes to a more accurate annotation of regulators in genomes. The information collected on each protein in the family can be useful to characterize a new regulator or compile information on the biological properties of a known regulator.
Availability: The BacTregulators is available at www.bactregulators.org
Supplementary information: www.bactregulators.org/supplementary/
Qxpak: a versatile mixed model application for genetical genomics and QTL analyses
Authors: Pérez-Enciso M. , Misztal I. 
Published: June 2004

Abstract
Motivation: Current methodology and software for quantitative trait loci (QTL) analyses do not use all available information and are inadequate to deal with the huge amount of QTL analyses to be needed in forecoming genetical genomics' studies.
Results: We show that a mixed model statistical framework provides a very flexible tool for QTL modeling in a variety of populations, be it a cross between inbred lines, a within population study, or experiments involving a mixture of populations or crosses. The software allows multitrait and multiQTL analyses, inclusion of infinitesimal genetic value and a batch multitrait option suitable for genetical genomics studies. It also allows massive association studies between single nucleotide polymorphisms and the trait(s) of interest.
Availability: A software (Qxpak), together with a manual and example files, is freely available for research purposes. So far, the compiled program is available for linux systems, the windows version will follow soon. See http://www.icrea.es/pag.asp?id=Miguel.Perez