bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tectonic implications of new age data for the Meratus Complex of south Kalimantan, Indonesia
Authors: Wakita Koji , Miyazaki Kazuhiro , Zulkarnain Iskandar , Sopaheluwakan Jan , Sanyoto Prihardjo 
Published: January 2004

Cretaceous subduction complexes surround the southeastern margin of Sundaland in Indonesia. They are widely exposed in several localities, such as Bantimala (South Sulawesi), Karangsambung (Central Java) and Meratus (South Kalimantan).The Meratus Complex of South Kalimantan consists mainly of mélange, chert, siliceous shale, limestone, basalt, ultramafic rocks and schists. The complex is uncomformably covered with Late Cretaceous sedimentary‐volcanic formations, such as the Pitap and Haruyan Formations.Well‐preserved radiolarians were extracted from 14 samples of siliceous sedimentary rocks, and K–Ar age dating was performed on muscovite from 6 samples of schist of the Meratus Complex. The radiolarian assemblage from the chert of the complex is assigned to the early Middle Jurassic to early Late Cretaceous. The K–Ar age data from schist range from 110 Ma to 180 Ma. Three samples from the Pitap Formation, which unconformably covers the Meratus Complex, yield Cretaceous radiolarians of Cenomanian or older.These chronological data as well as field observation and petrology yield the following constraints on the tectonic setting of the Meratus Complex.(1) The mélange of the Meratus Complex was caused by the subduction of an oceanic plate covered by radiolarian chert ranging in age from early Middle Jurassic to late Early Cretaceous.(2) The Haruyan Schist of 110–119 Ma was affected by metamorphism of a high pressure–low temperature type caused by oceanic plate subduction. Some of the protoliths were high alluminous continental cover or margin sediments. Intermediate pressure type metamorphic rocks of 165 and 180 Ma were discovered for the first time along the northern margin of the Haruyan Schist.(3) The Haruyan Formation, a product of submarine volcanism in an immature island arc setting, is locally contemporaneous with the formation of the mélange of the Meratus Complex.
Auditory Hallucinations in Nonpsychotic Children: Diagnostic Considerations
Authors: Mertin Peter , Hartwig Steve 
Published: January 2004

Background:  Auditory hallucinations in childhood and adolescence are not necessarily an indication of psychosis, but are more frequently associated with a range of other mental health problems. Although not specifically linked to abuse as an aetiological factor, the literature reporting on hallucinations in children alludes to a range of family dysfunction and disruption.Method:  This study reports on the auditory hallucinations of 13 children referred to a community‐based child and family mental health service exhibiting a variety of emotional and behavioural difficulties. The presence of the hallucinations was generally revealed during the course of the initial assessment.Results:  None of the children were considered psychotic at initial presentation; however, all were experiencing high levels of stress and/or anxiety in their lives. Following the initial assessments children were given diagnoses ranging from generalised anxiety disorder, through adjustment disorder, to posttraumatic stress disorder. The hallucinations gradually disappeared over the course of therapy. Two case studies describe the hallucinations and family histories in more detail.Conclusions:  The present study adds further confirmation of the presence of auditory hallucinations in nonpsychotic children. The clinical presentation of the children in the present study indicates an association between hallucinations and high levels of stress and anxiety, suggesting that mental health professionals should enquire more routinely about auditory hallucinations, particularly with those children from abusive and violent backgrounds.
Cognitive Therapy for Children, Young People and Families: Considering Service Provision
Authors: Derisley Jo 
Published: January 2004

Background:  This article presents a case for the development of cognitive therapy services for children, adolescents and their families.Method:  The theoretical basis of cognitive therapy is described, and illustrated with a case. The article continues by exploring the context for service development, with a specific emphasis on evaluating the evidence‐base for using cognitive therapy with children and adolescents. Consideration is also given to adapting cognitive therapy to the child's developmental level, and the evidence for the efficacy of cognitive‐behavioural family approaches.Conclusions:  The article concludes by arguing that there is a need to address mental health difficulties in young people by providing effective treatment approaches. The development of cognitive therapy services would support the further evaluation of this therapeutic approach.
Limited conformational space for early-stage protein folding simulation
Authors: Bryliński M. , Jurkowski W. , Konieczny L. , Roterman I. 
Published: January 2004

Abstract
Motivation: The problem of early-stage protein folding is critical for protein structure prediction. The model presented introduces a common definition of protein structures which may be treated as the possible in silico early-stage form of the polypeptide chain. Limitation of the conformational space to the ellipse path on the Ramachandran map was tested as a possible sub-space to represent the early-stage structure for simulation of protein folding. The proposed conformational sub-space was developed on the basis of the backbone conformation, with side-chain interactions excluded.
Results: The ellipse-path-limited conformation of BPTI was created using the criterion of shortest distance between Phi, Psi angles in native form of protein and the Phi, Psi angles belonging to the ellipse. No knots were observed in the structure created according to ellipse-path conformational sub-space. The energy minimization procedure applied to ellipse-path derived conformation directed structural changes toward the native form of the protein with SS-bonds system introduced to the procedure.
Availability: Program ‘Ellipse’ to create the ellipse-path derived structure available on request: myroterm@cyf-kr.edu.pl
Minimal cut sets in biochemical reaction networks
Authors: Klamt Steffen , Gilles Ernst Dieter 
Published: January 2004

Abstract
Motivation: Structural studies of metabolic networks yield deeper insight into topology, functionality and capabilities of the metabolisms of different organisms. Here, we address the analysis of potential failure modes in metabolic networks whose occurrence will render the network structurally incapable of performing certain functions. Such studies will help to identify crucial parts in the network structure and to find suitable targets for repressing undesired metabolic functions.
Results: We introduce the concept of minimal cut sets for biochemical networks. A minimal cut set (MCS) is a minimal (irreducible) set of reactions in the network whose inactivation will definitely lead to a failure in certain network functions. We present an algorithm which enables the computation of the MCSs in a given network related to user-defined objective reactions. This algorithm operates on elementary modes. A number of potential applications are outlined, including network verifications, phenotype predictions, assessing structural robustness and fragility, metabolic flux analysis and target identification in drug discovery. Applications are illustrated by the MCSs in the central metabolism of Escherichia coli for growth on different substrates.
Availability: Computation and analysis of MCSs is an additional feature of the FluxAnalyzer (freely available for academic users upon request, special contracts for industrial companies; see web page below).
Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer
Graph-based clustering for finding distant relationships in a large set of protein sequences
Authors: Kawaji Hideya , Takenaka Yoichi , Matsuda Hideo 
Published: January 2004

Abstract
Motivation: Clustering of protein sequences is widely used for the functional characterization of proteins. However, it is still not easy to cluster distantly-related proteins, which have only regional similarity among their sequences. It is therefore necessary to develop an algorithm for clustering such distantly-related proteins.
Results: We have developed a time and space efficient clustering algorithm. It uses a graph representation where its vertices and edges denote proteins and their sequence similarities above a certain cutoff score, respectively. It repeatedly partitions the graph by removing edges that have small weights, which correspond to low sequence similarities. To find the appropriate partitions, we introduce a score combining the normalized cut and a locally minimal cut capacities. Our method is applied to the entire 40 703 human proteins in SWISS-PROT and TrEMBL. The resulting clusters shows a 76% recall (20 529 proteins) of the 26 917 classified by InterPro. It also finds relationships not found by other clustering methods.
Availability: The complete result of our algorithm for all the human proteins in SWISS-PROT and TrEMBL, and other supplementary information are available at http://motif.ics.es.osaka-u.ac.jp/Ncut-KL/
PGTdb: a database providing growth temperatures of prokaryotes
Authors: Huang Shir-Ly , Wu Li-Cheng , Liang Han-Kuen , Pan Kuan-Ting , Horng Jorng-Tzong , Ko Ming-Tat 
Published: January 2004

Abstract
Summary: Included in Prokaryotic Growth Temperature database (PGTdb) are a total of 1334 temperature data from 1072 prokaryotic organisms, Bacteria and Archaea. PGTdb integrates microbial growth temperature data from literature survey with their nucleotide/protein sequence and protein structure data from related databases. A direct correlation is observed between the average growth temperature of an organism and the melting temperature of proteins from the organism. Therefore, this database is useful not only for microbiologists to obtain cultivation condition, but also for biochemists and structure biologists to study the correlation between protein sequences/structures and their thermostability. In addition, the taxonomy and ribosomal RNA sequence(s) of an organism are linked through NCBI Taxonomy and the Ribosomal RNA Operon Copy Number Database umdb, respectively. PGTdb is the only integrated database on the Internet to provide the growth temperature data of the prokaryotes and the combined information of their nucleotide/protein sequences, protein structures, taxonomy and phylogeny.
Availability: http://pgtdb.csie.ncu.edu.tw
FGDP: functional genomics data pipeline for automated, multiple microarray data analyses
Authors: Grant Jeffrey D. , Somers Luke A. , Zhang Yue , Manion Frank J. , Bidaut Ghislain , Ochs Michael F. 
Published: January 2004

Abstract
Summary: Gene expression microarrays and oligonucleotide GeneChips™ have provided biologists with a means of measuring, in a single experiment, the expression levels of entire genomes under a variety of conditions. As with any nascent field, there is no single accepted method for analyzing the new data types, with new methods appearing monthly. Investigators using the new technology must constantly seek access to the latest tools and explore their data in multiple ways. The functional genomics data pipeline provides an integrated, extendable analysis environment permitting multiple, simultaneous analyses to be automatically performed and provides a web server and interface for presenting results.
Availability: Source code and executables are available under the GNU public license at http://bioinformatics.fccc.edu/
YETI: Yeast Exploration Tool Integrator
Authors: Orton R. J. , Sellers W. I. , Gerloff D. L. 
Published: January 2004

Abstract
Summary: Yeast Exploration Tool Integrator (YETI) is a novel bioinformatics tool for the integrated visualization and analysis of functional genomic data sets from the budding yeast Saccharomyces cerevisiae.
Availability: YETI is freely available for use over the WWW, or download under license, at http://www.bru.ed.ac.uk/~orton/yeti.html
A strategy for assembling the maize (Zea mays L.) genome
Authors: Emrich Scott J. , Aluru Srinivas , Fu Yan , Wen Tsui-Jung , Narayanan Mahesh , Guo Ling , Ashlock Daniel A. , Schnable Patrick S. 
Published: January 2004

Abstract
Summary: Because the bulk of the maize (Zea mays L.) genome consists of repetitive sequences, sequencing efforts are being targeted to its ‘gene-rich’ fraction. Traditional assembly programs are inadequate for this approach because they are optimized for a uniform sampling of the genome and inherently lack the ability to differentiate highly similar paralogs.
Results: We report the development of bioinformatics tools for the accurate assembly of the maize genome. This software, which is based on innovative parallel algorithms to ensure scalability, assembled 730 974 genomic survey sequences fragments in 4 h using 64 Pentium III 1.26 GHz processors of a commodity cluster. Algorithmic innovations are used to reduce the number of pairwise alignments significantly without sacrificing quality. Clone pair information was used to estimate the error rate for improved differentiation of polymorphisms versus sequencing errors. The assembly was also used to evaluate the effectiveness of various filtering strategies and thereby provide information that can be used to focus subsequent sequencing efforts.
Multi-species comparative mapping in silico using the COMPASS strategy
Authors: Liu Lei , Gong George , Liu Yong , Natarajan Shreedhar , Larkin Denis M. , Everts-van der Wind Annelie , Rebeiz Mark , Beever Jonathan E. 
Published: January 2004

Abstract
Motivation: The completion of human and mouse genome sequences provides a valuable resource for decoding other mammalian genomes. The comparative mapping by annotation and sequence similarity (COMPASS) strategy takes advantage of the resource and has been used in several genome-mapping projects. It uses existing comparative genome maps based on conserved regions to predict map locations of a sequence. An automated multiple-species COMPASS tool can facilitate in the genome sequencing effort and comparative genomics study of other mammalian species.
Results: The prerequisite of COMPASS is a comparative map table between the reference genome and the predicting genome. We have built and collected comparative maps among five species including human, cattle, pig, mouse and rat. Cattle–human and pig–human comparative maps were built based on the positions of orthologous markers and the conserved synteny groups between human and cattle and human and pig genomes, respectively. Mouse–human and rat–human comparative maps were based on the conserved sequence segments between the two genomes. With a match to human genome sequences, the approximate location of a query sequence can be predicted in cattle, pig, mouse and rat genomes based on the position of the match relatively to the orthologous markers or the conserved segments.
Availability: The COMPASS-tool and databases are available at http://titan.biotec.uiuc.edu/COMPASS/
A comparative phylogenetic approach for dating whole genome duplication events
Authors: Chapman Brad A. , Bowers John E. , Schulze Stefan R. , Paterson Andrew H. 
Published: January 2004

Abstract
Motivation: Whole genome duplications have played a major role in determining the structure of eukaryotic genomes. Current evidence revealing large blocks of duplicated chromatin yields new insights into the evolutionary history of species, but also presents a major challenge for researchers attempting to utilize comparative genomics techniques. Understanding the timing of duplication events relative to divergence among taxa is critical to accurate and comprehensive cross-species comparisons.
Results: We describe a large-scale approach to estimate the timing of duplication events in a phylogenetic context. The methodology has been previously utilized for analysis of Arabidopsis and Saccharomyces duplication events. This new implementation provides a more flexible and reusable framework for these analyses. Scripts written in the Python programming language drive a number of freely available bioinformatics programs, creating a no-cost tool for researchers. The usefulness of the approach is demonstrated through genome-scale analysis of Arabidopsis and Oryza (rice) duplications.
Availability: Software and documentation are freely available from http://plantgenome.agtec.uga.edu/bioinformatics/dating/
Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA
Authors: Cavaluzzi Michael J , Borer Philip N 
Published: January 2004

AbstractUltraviolet absorption provides the nearly universal basis for determining concentrations of nucleic acids. Values for the UV extinction coefficients of DNA and RNA rely on the mononucleotide values determined 30–50 years ago. We show that nearly all of the previously published extinction coefficients for the nucleoside-5′-monophosphates are too large, and in error by as much as 7%. Concentrations based on complete hydrolysis and the older set of values are too low by ∼4% for typical RNA and 2–3% for typical DNA samples. We also analyzed data in the literature for the extinction coefficients of unpaired DNA oligomers. Robust prediction of concentrations can be made using 38 µg/A260 unit for single-stranded DNA (ssDNA) having non-repetitive sequences and 40–80% GC. This is superior to currently used predictions that account for nearest-neighbor frequency or base composition. The latter result in concentrations that are 10–30% too low for typical ssDNA used as primers for PCR and other similar techniques. Methods are described here to accurately measure concentrations of nucleotides by nuclear magnetic resonance. NMR can be used to accurately determine concentrations (and extinction coefficients) of biomolecules within 1%.
Induction of Salt and Osmotic Stress Tolerance by Overexpression of an Intracellular Vesicle Trafficking Protein AtRab7 (AtRabG3e)
Authors: Mazel Alexander , Leshem Yehoram , Tiwari Budhi Sagar , Levine Alex 
Published: January 2004

AbstractAdaptation to stress requires removal of existing molecules from various cellular compartments and replacing them with new ones. The transport of materials to and from the specific compartments involved in the recycling and deposition of macromolecules is carried out by an intracellular vesicle trafficking system. Here, we report the isolation of a vesicle trafficking-regulating gene, AtRabG3e (formerly AtRab7), from Arabidopsis. The gene was induced during programmed cell death after treatment of intact leaves with superoxide and salicylic acid or infection with necrogenic pathogens. Transgenic plants that expressed the AtRabG3e gene under the constitutive 35S promoter from cauliflower mosaic virus exhibited accelerated endocytosis in roots, leaves, and protoplasts. The transgenic plants accumulated sodium in the vacuoles and had higher amounts of sodium in the shoots. The transgenic plants also showed increased tolerance to salt and osmotic stresses and reduced accumulation of reactive oxygen species during salt stress. These results imply that vesicle trafficking plays an important role in plant adaptation to stress, beyond the housekeeping function in intracellular vesicle trafficking.
Binding of Sulfonylurea by AtMRP5, an Arabidopsis Multidrug Resistance-Related Protein That Functions in Salt Tolerance
Authors: Lee Eun Kyung , Kwon Minjae , Ko Jae-Heung , Yi Hochul , Hwang Moo Gak , Chang Soochul , Cho Myeon Haeng 
Published: January 2004

Abstract
Recently, a new member of the ABC transporter superfamily of Arabidopsis, AtMRP5, was identified and characterized. In the present work, we found that AtMRP5 can bind specifically to sulfonurea when it is expressed in HEK293 cells. We also present evidence for a new role of AtMRP5 in the salt stress response of Arabidopsis. We used reverse genetics to identify an Arabidopsis mutant (atmrp5-2) in which the AtMRP5 gene was disrupted by transferred DNA insertion. In root-bending assays using Murashige and Skoog medium supplemented with 100 mm NaCl, root growth of atmrp5-2 was substantially inhibited in contrast to the almost normal growth of wild-type seedlings. This hypersensitive response of the atmrp5-2 mutant was not observed during mannitol treatment. The root growth of the wild-type plant grown in Murashige and Skoog medium supplemented with the MRP inhibitor glibenclamide and NaCl was inhibited to a very similar extent as the root growth of atmrp5-2 grown in NaCl alone. The Na+-dependent reduction of root growth of the wild-type plant in the presence of glibenclamide was partially restored by diazoxide, a known K+ channel opener that reverses the inhibitory effects of sulfonylureas in animal cells. Moreover, the atmrp5-2 mutant was defective in 86Rb+ uptake. When seedlings were treated with 100 mm NaCl, atmrp5-2 seedlings accumulated less K+ and more Na+ than those of the wild type. These observations suggest that AtMRP5 is a putative sulfonylurea receptor that is involved in K+ homeostasis and, thus, also participates in the NaCl stress response.
Differential Expression of Sucrose Transporter and Polyol Transporter Genes during Maturation of Common Plantain Companion Cells
Authors: Ramsperger-Gleixner Martina , Geiger Dietmar , Hedrich Rainer , Sauer Norbert 
Published: January 2004

Abstract
The cDNAs of two sorbitol transporters, common plantain (Plantago major) polyol transporter (PLT) 1 and 2 (PmPLT1 and PmPLT2), were isolated from a vascular bundle-specific cDNA library from common plantain, a dicot plant transporting Suc plus sorbitol in its phloem. Here, we describe the kinetic characterization of these sorbitol transporters by functional expression in Brewer's yeast (Saccharomyces cerevisiae) and in Xenopus sp. oocytes and for the first time the localization of plant PLTs in specific cell types of the vascular tissue. In the yeast system, both proteins were shown to be uncoupler sensitive and could be characterized as low-affinity and low-specificity polyol symporters. The K m value for the physiological substrate sorbitol is 12 mm for PmPLT1 and even higher for PmPLT2, which showed an almost linear increase in sorbitol transport rates up to 20 mm. These data were confirmed in the Xenopus sp. system, where PmPLT1 was analyzed in detail and characterized as a H+ symporter. Using peptide-specific polyclonal antisera against PmPLT1 or PmPLT2 and simultaneous labeling with the monoclonal antiserum 1A2 raised against the companion cell-specific PmSUC2 Suc transporter, both PLTs were localized to companion cells of the phloem in common plantain source leaves. These analyses revealed two different types of companion cells in the common plantain phloem: younger cells expressing PmSUC2 at higher levels and older cells expressing lower levels of PmSUC2 plus both PLT genes. The putative role of these low-affinity transporters in phloem loading is discussed.