bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shaping biological knowledge: applications in proteomics
Authors: Lisacek F. , Chichester C. , Gonnet P. , Jaillet O. , Kappus S. , Nikitin F. , Roland P. , Rossier G. , Truong L. , Appel R. 
Published: March 2004

AbstractThe central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small‐scale studies. We analyse proteomics data while following both a data‐driven (focus on proteins smaller than 10 kDa) and a hypothesis‐driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies. Copyright © 2004 John Wiley & Sons, Ltd.
A fragment of 21 ORFs around the direct repeat (DR) region of Mycobacterium tuberculosis is absent from the other sequenced mycobacterial genomes: implications for the evolution of the DR region
Authors: Caimi Karina , Cataldi Angel 
Published: March 2004

AbstractThe direct repeat (DR) region is a singular locus of the Mycobacterium tuberculosis complex genome. This region consists of 36 bp repetitive sequences separated by non‐repetitive unique spacer sequences. Around this region there are several genes coding for proteins of unknown function. To determine whether the M. smegmatis, M. avium, M. marinum and M. leprae genomes contain sequences and ORFs similar to those of the DR locus of the M. tuberculosis complex, we analysed the corresponding regions in these species. As a first step, some conserved genes that flank the DR genes [Rv2785c (rpsO), Rv2786c (ribF), Rv2790c (ltp1), Rv2793c (truB), Rv2800, Rv2825, Rv2828, Rv2831 (echA16), Rv2838 (rbfA) and Rv2845 (proS)] were used as markers to locate the corresponding orthologues in M. smegmatis, M. avium, M. marinum and M. leprae in silico. Most of these M. tuberculosis marker genes have highly similar orthologues located in the same order and orientation in the other mycobacteria. In contrast, no orthologues were found for ORFs Rv2801–Rv2824, suggesting that these genes are unique to M. tuberculosis within the genus Mycobacterium. We observed that in M. smegmatis and M. avium, Rv2800 and Rv2825 are adjacent. This observation was experimentally confirmed by PCR. In conclusion, as the DR locus and the ORFs around it are absent in M. smegmatis and M. avium and, as it is possible that these species are older than M. tuberculosis, we postulated that the DR locus was acquired by the M. tuberculosis complex species or by an ancestor bacterium. Copyright © 2004 John Wiley & Sons, Ltd.
Phylogenetics in the bioinformatics culture of understanding
Authors: Allaby Robin G. , Woodwark Mathew 
Published: March 2004

AbstractBioinformatics, as a relatively young discipline, has grown up in a world of high‐throughput large volume data that requires automatic analysis to enable us to stay on top of it all. As a response, the bioinformatics discipline has developed strategies to find patterns in a ‘low signal : noise ratio’ environment. While the need to process large amounts of information and extract hypotheses is both laudable and inescapable, the pressures that such requirements have introduced can lead to short cuts and misapprehensions. This is particularly the case with reference to assumptions about the underlying evolutionary theories that are implicitly invoked by the algorithms utilised in the analysis pipelines. The classic example is the misuse of the term ‘homologous’ to mean ‘similar’ or even ‘functionally similar’, rather than the correct definition of ‘having the same evolutionary origin’, which may or may not imply similarity of function. In this review, we outline some of the common phylogenetic questions from a bioinformatics perspective that can be better addressed with a deeper understanding of evolutionary principles and show, with examples from the amidohydrolase and Toll families, that quite different conclusions can be drawn if such approaches are taken. This review focuses on the importance of the underlying evolutionary biology, rather than assessing the merits of different phylogenetic techniques. The relative merits of a priori and a posteriori inclusion of biological information are discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Three novel pigmentation mutants generated by genome‐wide random ENU mutagenesis in the mouse
Authors: Tsipouri Vicky , Curtin John A. , Nolan Pat M. , Vizor Lucie , Parsons Claire A. , Clapham Colin M. , Latham Ian D. , Rooke Lesley J. , Martin Jo E. , Peters Jo , Hunter A. Jackie , Rogers Derek , Rastan Sohaila , Brown Steve D.M. , Fisher Elizabeth M.C. , Spurr Nigel K. , Gray Ian C. 
Published: March 2004

AbstractThree mutant mice with pigmentation phenotypes were recovered from a genome‐wide random mouse chemical mutagenesis study. White toes (Whto; MGI:1861986), Belly spot and white toes (Bswt; MGI:2152776) and Dark footpads 2 (Dfp2; MGI:1861991) were identified following visual inspection of progeny from a male exposed to the point mutagen ethylnitrosourea (ENU). In order to rapidly localize the causative mutations, genome‐wide linkage scans were performed on pooled DNA samples from backcross animals for each mutant line. Whto was mapped to proximal mouse chromosome (Mmu) 7 between Cen (the centromere) and D7Mit112 (8.0 cM from the centromere), Bswt was mapped to centric Mmul between D1Mit214 (32.1 cM) and D1Mit480 (32.8 cM) and Dfp2 was mapped to proximal Mmu4 between Cen and D4Mit18 (5.2 cM). Whto, Bswt and Dfp2 may provide novel starting points in furthering the elucidation of genetic and biochemical pathways relevant to pigmentation and associated biological processes. Copyright © 2004 John Wiley & Sons, Ltd.
TRANSPATH®—a high quality database focused on signal transduction
Authors: Choi Claudia , Krull Mathias , Kel Alexander , Kel‐Margoulis Olga , Pistor Susanne , Potapov Anatolij , Voss Nico , Wingender Edgar 
Published: March 2004

AbstractTRANSPATH® can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyser. Therefore, three modules have been created: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder™, which provides several different types of network visualization and hence faciliates understanding; the third is ArrayAnalyzer™, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH® to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH® is the inclusion of transcription factor–gene relations, which are transferred from TRANSFAC®, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. More information is available at www.biobase.de/pages/products/databases.html. Copyright © 2004 John Wiley & Sons, Ltd.
Classification of chemical compounds to support complex queries in a pathway database
Authors: Wittig Ulrike , Weidemann Andreas , Kania Renate , Peiss Christian , Rojas Isabel 
Published: March 2004

AbstractData quality in biological databases has become a topic of great discussion. To provide high quality data and to deal with the vast amount of biochemical data, annotators and curators need to be supported by software that carries out part of their work in an (semi‐) automatic manner. The detection of errors and inconsistencies is a part that requires the knowledge of domain experts, thus in most cases it is done manually, making it very expensive and time‐consuming. This paper presents two tools to partially support the curation of data on biochemical pathways. The tool enables the automatic classification of chemical compounds based on their respective SMILES strings. Such classification allows the querying and visualization of biochemical reactions at different levels of abstraction, according to the level of detail at which the reaction participants are described. Chemical compounds can be classified in a flexible manner based on different criteria. The support of the process of data curation is provided by facilitating the detection of compounds that are identified as different but that are actually the same. This is also used to identify similar reactions and, in turn, pathways. Copyright © 2004 John Wiley & Sons, Ltd.
The ESF Programme on Functional Genomics workshop on ‘Data Integration in Functional Genomics: Application to Biological Pathways’
Authors: Binz Pierre‐Alain , Hermjakob Henning , van der Vet Paul 
Published: March 2004

AbstractWe report from the second ESF Programme on Functional Genomics workshop on Data Integration, which covered topics including the status of biological pathways databases in existing consortia; pathways as part of bioinformatics infrastructures; design, creation and formalization of biological pathways databases; generating and supporting pathway data and interoperability of databases with other external databases and standards. Key issues emerging from the discussions were the need for continued funding to cover maintenance and curation of databases, the importance of quality control of the data in these resources, and efforts to facilitate the exchange of data and to ensure the interoperability of databases. Copyright © 2004 John Wiley & Sons, Ltd.
Differential mRNA expression and protein localization of the SAP90/PSD‐95–associated proteins (SAPAPs) in the nervous system of the mouse
Authors: Welch Jeffrey M. , Wang Dongqing , Feng Guoping 
Published: March 2004

AbstractThe supramolecular anchoring/signaling complex at the postsynaptic density of glutamatergic synapses has been proposed to play a key role in regulating synaptic function and plasticity. One class of proteins present in the complex is the SAP90/PSD‐95‐associated protein family (SAPAPs). The SAPAPs, identified by their direct interaction with PSD‐95 family proteins, were initially proposed to function in the anchoring/signaling complex as linker proteins between glutamate receptor binding proteins and the cytoskeleton. However, recent studies have indicated that the SAPAPs also bind to signaling molecules and may thus have multiple roles at synapses. Four homologous genes encoding SAPAP proteins have been previously identified. As a first step toward understanding the physiological function of the SAPAPs, we have investigated in detail, at both the mRNA and protein levels, the localization of the individual SAPAP genes in the adult murine nervous system. We find that the SAPAP mRNAs are highly, yet differentially, expressed in many regions of the brain, including the hippocampus and cerebellum. Furthermore, SAPAP3 mRNA is targeted to dendrites, whereas SAPAP1, ‐2, and ‐4 mRNAs are detected mainly in cell bodies. The SAPAP proteins are localized at synapses in a manner consistent with mRNA expression. Surprisingly, in addition to glutamatergic synapse localization, antibody staining also reveals that the SAPAP proteins are localized at cholinergic synapses, including neuronal cholinergic synapses and the neuromuscular junction. Together, these results indicate that the SAPAPs are general components of excitatory synapses and that each of these proteins may perform a distinct function. J. Comp. Neurol. 472:24–39, 2004. © 2004 Wiley‐Liss, Inc.
The population of bipolar cells in the rabbit retina
Authors: MacNeil Margaret A. , Heussy John K. , Dacheux Ramon F. , Raviola Elio , Masland Richard H. 
Published: March 2004

AbstractThe population of bipolar cells in the rabbit retina was studied using Golgi impregnation and photocatalyzed filling of single cells with dihydrorhodamine, a quantitative sampling technique. The Golgi method revealed the morphology and stratification of cells in detail. The photofilling method allowed us to estimate the frequency of the cell types. From a sample of 243 Golgi‐impregnated bipolar cells and 107 photofilled cells, we identified 1 type of rod bipolar cell and 12 types of cone bipolar cells. An analysis based on retinal coverage indicates that this number of types could be contained within the number of bipolar cells known to exist. The dendrites of most cone bipolars contacted all the cones within the individual cone bipolar cell's dendritic field. Types of bipolar cell were encountered at roughly similar frequency, without any one type predominating. The rabbit retina thus contains about a dozen parallel and roughly equipotent through‐pathways. J. Comp. Neurol. 472:73–86, 2004. © 2004 Wiley‐Liss, Inc.
Cuii in Liquid Ammonia: An Approach by Hybrid Quantum‐Mechanical/Molecular‐Mechanical Molecular Dynamics Simulation
Authors: Schwenk Christian F. , Rode Bernd M. 
Published: March 2004

AbstractTo investigate the solvation structure of the Cuii ion in liquid ammonia, ab initio quantum‐mechanical/molecular‐mechanical (QM/MM) molecular dynamics (MD) simulations were carried out at Hartree Fock (HF) and hybrid density functional theory (B3 LYP) levels. A sixfold‐coordinated species was found to be predominant in the HF case whereas five‐ and sixfold‐coordinated complexes were obtained in a ratio 2:1 from the B3 LYP simulation. In contrast to hydrated Cuii, which exhibits a typical Jahn–Teller distortion, the geometrical arrangement of ligand molecules in the case of ammonia can be described as a [2+4] ([2+3]) configuration with 4 (3) elongated copper–nitrogen bonds. First shell solvent exchange reactions at picosecond rate took place in both HF and B3 LYP simulations, again in contrast to the more stable sixfold‐coordinated hydrate. NH3 ligands apparently lead to strongly accelerated dynamics of the Cuii solvate due to the “inverse” [2+4] structure with its larger number of elongated copper–ligand bonds. Several dynamical properties, such as mean ligand residence times or ion–ligand stretching frequencies, prove the high lability of the solvated complex.
Preparation and investigation of (CuInSe2)x(2ZnSe)1‐x and (CuInTe2)x(2ZnTe)1‐x solid solution crystals
Authors: Bodnar I. V. , Gremenok V. F. , Schmitz W. , Bente K. , Doering Th. 
Published: March 2004

AbstractThe (CuInSe2)x(2ZnSe)1‐x and (CuInTe2)x(2ZnTe)1‐x solid solution crystals prepared by Bridgman method and chemical vapor transport have been studied. The nature of the crystalline phases, the local structure homogeneity and composition of these materials have been investigated by X‐ray diffraction (XRD) and Electron Probe Microanalysis (EPMA) methods. The analysis revealed the presence of chalcopyrite‐sphalerite phase transition between 0.6 ≤ X ≤ 0.7. Lattice constants, value of σ position parameter and bond length between atoms were also calculated. It was found that the lattice parameters exhibit a linear dependence versus composition. The transmission spectra of solid solution crystals in the region of the main absorption edge were studied. It was established that the optical band gap of these materials changes non‐linearly with the X composition. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Crystal growth of some urinary stone constituents: III. In‐vitro crystallization of L‐cystine and its characterization
Authors: Ramachandran E. , Natarajan S. 
Published: March 2004

AbstractL‐Cystine (‐SCH2· CHNH2· COOH), having the morphology of hexagonal plates, an amino acid constituent of urinary stone, is crystallized in silica gel under suitable pH conditions by double diffusion method. The grown crystals were characterized by density measurement, Fourier transform infra‐red spectroscopy, X‐ray powder diffraction and thermogravimetric analysis. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Crystallization of calcium sulfate dihydrate at different supersaturation ratios and different free sulfate concentrations
Authors: Abdel‐Aal E. A. , Rashad M. M. , El‐Shall H. 
Published: March 2004

AbstractFree Sulfate is a major parameter affecting gypsum crystallization during phosphoric acid production. Gypsum crystal size, shape and filtration rate are significantly affected by the concentration of free sulfate. It is, therefore, important to evaluate the effectiveness of different sulfate levels from 1.5% to 3.5% on induction time and gypsum morphology. The crystallization of gypsum was carried out under simulated conditions of phosphoric acid production by the dihydrate process. Calcium hydrogen phosphate and sulfuric acid were mixed with dilute phosphoric acid at 80 °C, and the turbidity of the reaction mixture was measured at different time periods to calculate the induction time of gypsum crystals formation. With increasing free sulfate concentration, the induction time was significantly decreased. Chemical processing of Central and South Florida phosphate concentrates under different concentrations of free sulfate from 1.5% to 5.5% was carried out. The change on crystal size distribution and filtration rate were traced with free sulfate concentrations. The results show that, filtration rate of phosphogypsum was correlated to the mean diameter of crystals. In addition, induction time and co‐crystallized (lattice) P2O5 % in gypsum are decreased with increasing free sulfate content from 1.5% to 3.5%. Morphology of formed gypsum crystals at different sulfate contents and different supersaturation ratios are investigated. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of substrate temperature on polycrystalline Cd0.9Zn0.1Te thin films studied by Raman scattering spectroscopy
Authors: Sridharan M. , Mekaladevi M. , Narayandass Sa. K. , Mangalaraj D. , Lee Hee Chul 
Published: March 2004

AbstractCd0.9Zn0.1Te thin films were prepared by vacuum evaporation onto well‐cleaned glass substrates maintained at 300, 373 and 473 K. X‐ray diffraction studies revealed that the films have zinc blende structure with preferential (111) orientation. Raman peak of the room temperature deposited film appeared at 140.30 cm‐1 and 159.65 cm‐1 were for the transverse optic (TO) and longitudinal optic (LO) phonons respectively. The XRD patterns of the higher substrate temperature deposited films exhibited an improvement in the crystallinity of the films. The Raman peak intensity increases and the FWHM decreases for the films deposited at higher substrate temperature. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical absorption spectra of LiNbO3, Fe:LiNbO3, and Zn:Fe:LiNbO3 single crystals grown by Bridgman method
Authors: Xia Haiping , Zeng Xianlin , Wang Jinhao , Zhang Jianli , Xu Jian , Zhang Yuepin , Nie Qiuhua 
Published: March 2004

AbstractThe optical absorption spectra of LiNbO3 (LN), Fe:LiNbO3 (Fe:LN), and Zn:Fe:LiNbO3 (Zn:Fe:LN) single crystals grown by Bridgman method were measured and compared. The absorption characteristics of the samples and the effects of growth process conditions on the absorption spectra were investigated. The Fe, Zn and Li concentrations in the crystals were analyzed by inductively coupled plasma (ICP) spectrometry. The results indicated that the overall Fe ion and Fe2+ concentration in Fe:LN and Zn:Fe:LN crystals increased along the growing direction. The incorporation of ZnO in Fe:LN crystal induced increase of Fe2+ in the crystal. Among Fe‐doped and Zn:Fe‐codoped LN single crystals, 3 mol% ZnO doped Fe:LN had a biggest change of Fe2+ ion concentration from bottom to top part of crystal. The effects of technical conditions (atmosphere and thermal history) on Fe2+ ion concentration were discussed. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A new method for the investigation of orientation relationships in meteoritic plessite
Authors: Nolze G. , Geist V. 
Published: March 2004

AbstractThe orientation relationship (OR) between the bcc and fcc phase in the plessite microstructure of the iron meteorites Watson, Agpalilik and Gibeon has been analysed in a scanning electron microscope using electron back‐scattered diffraction (EBSD). A very strong OR exists, independently on the analysed plessite type and the observed spreading of single orientation data. The agreement between the experimental orientation distribution and existing models varies for each meteorite. The black plessite in the Agpalilik corresponds to the Nishiyama‐Wassermann model whereas the duplex plessite of the Gibeon meteorite shows an OR close to the Kurdjumov‐Sachs model. The Watson meteorite is strongly deformed so that a general OR is difficult to determine due to the blurred experimental orientation distribution. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Presence of pseudo‐peptide bond in the crystal structure of n‐(t‐butoxycarbonyl)‐ε‐n′‐benzyloxycarbony‐l‐lysyl‐l‐isoleucine (boc‐lys(obzl)‐ile)
Authors: Malathy Sony S. M. , Sukumar N. , Ponnuswamy M. N. , Jayakumar R. 
Published: March 2004

AbstractThe dipeptide Boc‐Lys(OBzl)‐Ile crystallizes in monoclinic space group P21 with cell parameters a = 5.003(1), b = 19.199(3), c = 15.270(2)Å, β =93.42(1)°, V = 1464.1(3)Å3, Z = 2, Dcal = 1.117 Mg/m3 at T = 293 K. The structure was solved by direct methods and refined by full‐matrix least‐squares procedure to a final R = 0.096 and wR = 0.101 using 1379 reflections. The peptide unit is in trans conformation and the molecule takes up an extended conformation. In the lysine side chain, delocalization of electrons and pseudo peptide bond formation is observed at the interaction site of benzyloxycarbonyl group. Both N‐H…O and main chain C‐H…O hydrogen bonds stabilize the molecules in the unit cell in a parallel β‐sheet fashion. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Application of unified voltage analysis for high‐ and low‐voltage distribution systems by power flow calculation using indication method between nodes
Authors: Okada Naotaka , Tanaka Kazuyuki 
Published: March 2004

AbstractIt has been noted that the voltage of connection points rises according to the reverse power flow when grid‐connected photovoltaic systems are concentrated in distribution systems in residential areas. When this happens, the photovoltaic system may control the power generation output to maintain a suitable voltage for the connection point. Designing a demand area power system aiming at free access to a distributed power supply for energy‐effective practical use requires a precise understanding of this problem. When analyzing photovoltaic systems mainly connected to low‐voltage systems, we looked for a method of analysis in which the high‐voltage systems and the low‐voltage single‐phase three‐wire systems are unified. This report concerns use of the indication method between nodes using power flow calculation, for the purpose of developing a technique of analyzing unified high‐voltage systems and low‐voltage single‐phase three‐wire systems. © 2004 Wiley Periodicals, Inc. Electr Eng Jpn, 147(3): 49–62, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/eej.10255