bluuebunny/crossref_metadata_2025_split huggingface dataset:
Moving proteins from the cytosol into mitochondria
Authors: Chacinska A. , Rehling P. 
Published: October 2004

Mitochondria of the yeast Saccharomyces cerevisiae contain at least 750 different proteins, which perform diverse roles. Most of these proteins (approx. 99%) are translated on cytosolic ribosomes, and their import into mitochondria is essential for mitochondrial function. Proteinaceous machineries of great complexity, the so-called translocases, in the mitochondrial membranes mediate the import of these proteins.
RNA interference and double-stranded-RNA-activated pathways
Authors: Sledz C.A. , Williams B.R.G. 
Published: October 2004

RNAi (RNA interference) has become a powerful tool to determine gene function. Different methods of expressing the short ds (double-stranded) RNA intermediates required for interference in mammalian systems have been developed, including the introduction of si (short interfering) RNAs by direct transfection or driven from transfected plasmids or lentiviral vectors encoding sh (short hairpin) RNAs. Although RNAi relies upon a high degree of specificity, recent findings suggest that off-target non-specific effects can be encountered. We found that transfection of siRNAs can results in an interferon-mediated activation of the JAK/STAT (Janus kinase/signal transducer and activator of transcription) pathway and global up-regulation of interferon-stimulated genes. This effect is mediated in part by the dsRNA-dependent protein kinase PKR, as this kinase is activated by the 21 bp siRNA, and is required in response to the siRNAs. However, the transcription factor IRF3 (interferon-regulatory factor 3) is also activated by siRNA as a primary response, resulting in the stimulation of genes independent of an interferon response. In cells deficient in IRF3, this response is blunted, but can be restored by re-introduction of IRF3. Thus siRNAs induce complex signalling responses in target cells, leading to effects beyond the selective silencing of specific genes.
Use of mass spectrometry-based lipidomics to probe PITPα (phosphatidylinositol transfer protein α) function inside the nuclei of PITPα+/+ and PITPα−/− cells
Authors: Hunt A.N. , Alb J.G. , Koster G. , Postle A.D. , Bankaitis V.A. 
Published: October 2004

The mammalian phospholipid exchange protein PITPα (phosphatidylinositol transfer protein alpha), found in both extranuclear and endonuclear compartments, is thought in part to facilitate nuclear import of the PtdIns (phosphatidylinositol) consumed in the generation of proliferation-associated endonuclear diacylglycerol accumulations. Unlike phosphatidylcholine, endonuclear PtdIns is not synthesized in situ. However, despite progressive postnatal lethality of PITPα ablation in mice, PITPα−/− MEF (mouse embryonic fibroblasts) lack an obviously impaired proliferative capacity. We used ESI-MS (tandem electrospray ionization-MS) to monitor incorporation of the deuterated phospholipid precursors, choline-d9 and inositol-d6, into molecular species of whole cell and endonuclear phosphatidylcholine and PtdIns over 24 h to assess the contribution of PITPα to the nuclear import of PtdIns into MEF cells. In cells labelled for 1, 3, 6, 12 and 24 h fractional inositol-d6 incorporation into whole-cell PtdIns species was consistently higher in PITPα−/− MEF implying greater flux through its biosynthetic pathway. Moreover, endonuclear accumulation of PtdIns-d6 was apparent in the PITPα−/− cells and mirrored that in PITPα+/+ cells. Together, these results suggest that the essential endonuclear PtdIns import via PITPα can be accommodated by other mechanisms.
Immunodetection of UCP1 in rat thymocytes
Authors: Carroll A.M. , Haines L.R. , Pearson T.W. , Brennan C. , Breen E.P. , Porter R.K. 
Published: October 2004

Thymi were dissected from rats and connective tissue was removed. Mitochondria were purified from isolated thymocytes and immunoblot analysis was performed using an antibody specific for uncoupling protein 1, which detected a 32.5 kDa protein associated with mitochondria from the thymocytes. This implies that rat thymocytes contain uncoupling protein 1.
Cross sections and transport coefficients for electrons in Zn vapour
Authors: R D White  , R P McEachran  , R E Robson  , M T Elford  , K Bartschat  
Published: October 2004

In this paper we present details of the following:ab initiocalculations of a set of electron impact cross sections for atomic Zn; andtransport coefficients and distribution functions for an electron swarm in Zn vapour, obtained from a multiterm solution of Boltzmann's equation using these cross sections, over a range of reduced fields,E/N, and gas temperatures of practical interest.Our work has been motivated, in part, by recent suggestions that zinc could be an attractive replacement for mercury in making high-pressure gas discharge lamps more environment-friendly (Born M2001J. Phys. D: Appl. Phys.34909; Born M2002Plasma Sources Sci. Technol.11A55). Current models of such lamps require a knowledge of the plasma electrical conductivity, which can be calculated from the (e, Zn) cross sections and mobility coefficients presented in this paper.
ColorHOR—novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome
Authors: Paar Vladimir , Pavin Nenad , Rosandić Marija , Glunčić Matko , Basar Ivan , Pezer Robert , Žinić Sonja Durajlija 
Published: October 2004

Abstract
Motivation: GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR consensus lengths have not been reported so far. Given the fast growth of sequence databases in the centromeric region, it is of increasing interest to have efficient tools for computational identification and analysis of HORs from known sequences.
Results: We develop a graphical user interface method, ColorHOR, for fast computational identification of HORs in a given genomic sequence, without requiring a priori information on the composition of the genomic sequence. ColorHOR is based on an extension of the key-string algorithm and provides a color representation of the order and orientation of HORs. For the key string, we use a robust 6 bp string from a consensus alpha satellite and its representative nature is tested. ColorHOR algorithm provides a direct visual identification of HORs (direct and/or reverse complement). In more detail, we first illustrate the ColorHOR results for human chromosome 1. Using ColorHOR we determine for the first time the HOR annotation of the GenBank sequence of the whole human genome. In addition to some HORs, corresponding to those determined previously biochemically, we find new HORs in chromosomes 4, 8, 9, 10, 11 and 19. For the first time, we determine exact consensus lengths of HORs in 10 chromosomes. We propose that the HOR assignment obtained by using ColorHOR be included into the GenBank database.
Availability: The program with graphical user interface application for ColorHOR is freely available at http://www.hazu.hr/KSA/colorHOR.html. It can be run on any platform on which wxPython is supported.
Contact: paar@hazu.hr
Supplementary information: http://www.hazu.hr/KSA/colorHOR.html.
Local correlation of expression profiles with gene annotations—proof of concept for a general conciliatory method
Authors: Pinto F. R. , Cowart L. Ashley , Hannun Yusuf A. , Rohrer B. , Almeida J. S. 
Published: October 2004

AbstractMotivation: Integrated analysis of expression data and gene ontology annotations is a prime example of biological data that need co-explanatory interpretation. This particular application is used to validate a new method for integrated analysis of varied biological information.Results: The proposed method consists of determining local correlation coefficients and the corresponding P-values calculated per biological entity. This measure considers the combined intensity and significance of the agreement or disagreement, between two data sources about the same biological entity. The method is applied to the integrated analysis of gene expression and annotation of two gene sets, one from yeast and other from mouse. The potential of the method to generate accurate mechanistic hypothesis is also demonstrated. Specially, negative correlation results pose a new kind of biological hypothesis. Method performance was compared with annotation enrichment methods, and optimal conditions for the superiority of local correlation results are discussed.Availability: The matlab functions described in this article are available at http://bioinformatics.musc.edu/~frpinto/Contact: almeidaj@musc.eduSupplementary information: Further information, tables and figures are available at http://bioinformatics.musc.edu/~frpinto/
Fast and accurate database homology search using upper bounds of local alignment scores
Authors: Itoh Masumi , Goto Susumu , Akutsu Tatsuya , Kanehisa Minoru 
Published: October 2004

AbstractMotivation: It is widely recognized that homology search and ortholog clustering are very useful for analyzing biological sequences. However, recent growth of sequence database size makes homolog detection difficult, and rapid and accurate methods are required.Results: We present a novel method for fast and accurate homology detection, assuming that the Smith–Waterman (SW) scores between all similar sequence pairs in a target database are computed and stored. In this method, SW alignment is computed only if the upper bound, which is derived from our novel inequality, is higher than the given threshold. In contrast to other methods such as FASTA and BLAST, this method is guaranteed to find all sequences whose scores against the query are higher than the specified threshold. Results of computational experiments suggest that the method is dozens of times faster than SSEARCH if genome sequence data of closely related species are available.Availability: The programs for fast homolog detection can be downloaded from ftp://ftp.kuicr.kyoto-u.ac.jp/itoh/Contact: itoh@kuicr.kyoto-u.ac.jp
HyPhy: hypothesis testing using phylogenies
Authors: Pond Sergei L. Kosakovsky , Frost Simon D. W. , Muse Spencer V. 
Published: October 2004

AbstractSummary: The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution.Availability: http://www.hyphy.orgContact: muse@stat.ncsu.eduSupplementary information: HyPhydocumentation and tutorials are available at http://www.hyphy.org
A new approach to prediction of short-range conformational propensities in proteins
Authors: Gront Dominik , Kolinski Andrzej 
Published: October 2004

Abstract
Motivation: Knowledge-based potentials are valuable tools for protein structure modeling and evaluation of the quality of the structure prediction obtained by a variety of methods. Potentials of such type could be significantly enhanced by a proper exploitation of the evolutionary information encoded in related protein sequences. The new potentials could be valuable components of threading algorithms, ab-initio protein structure prediction, comparative modeling and structure modeling based on fragmentary experimental data.
Results: A new potential for scoring local protein geometry is designed and evaluated. The approach is based on the similarity of short protein fragments measured by an alignment of their sequence profiles. Sequence specificity of the resulting energy function has been compared with the specificity of simpler potentials using gapless threading and the ability to predict specific geometry of protein fragments. Significant improvement in threading sensitivity and in the ability to generate sequence-specific protein-like conformations has been achieved.
Availability: see: http://www.biocomp.chem.uw.edu.pl
Contact: dgront@chem.uw.edu.pl
PDBML: the representation of archival macromolecular structure data in XML
Authors: Westbrook John , Ito Nobutoshi , Nakamura Haruki , Henrick Kim , Berman Helen M. 
Published: October 2004

Abstract
Summary: The Protein Data Bank (PDB) has recently released versions of the PDB Exchange dictionary and the PDB archival data files in XML format collectively named PDBML. The automated generation of these XML files is driven by the data dictionary infrastructure in use at the PDB. The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files.
Availability: The current software translated XML schema file is located at http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd, and on the PDB mmCIF resource page at http://deposit.pdb.org/mmcif/. PDBML files are stored on the PDB beta ftp site at ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML
Contact: jwest@rcsb.rutgers.edu
Automatic extraction of gene/protein biological functions from biomedical text
Authors: Koike Asako , Niwa Yoshiki , Takagi Toshihisa 
Published: October 2004

AbstractMotivation: With the rapid advancement of biomedical science and the development of high-throughput analysis methods, the extraction of various types of information from biomedical text has become critical. Since automatic functional annotations of genes are quite useful for interpreting large amounts of high-throughput data efficiently, the demand for automatic extraction of information related to gene functions from text has been increasing.Results: We have developed a method for automatically extracting the biological process functions of genes/protein/families based on Gene Ontology (GO) from text using a shallow parser and sentence structure analysis techniques. When the gene/protein/family names and their functions are described in ACTOR (doer of action) and OBJECT (receiver of action) relationships, the corresponding GO-IDs are assigned to the genes/proteins/families. The gene/protein/family names are recognized using the gene/protein/family name dictionaries developed by our group. To achieve wide recognition of the gene/protein/family functions, we semi-automatically gather functional terms based on GO using co-occurrence, collocation similarities and rule-based techniques. A preliminary experiment demonstrated that our method has an estimated recall of 54–64% with a precision of 91–94% for actually described functions in abstracts. When applied to the PUBMED, it extracted over 190 000 gene–GO relationships and 150 000 family–GO relationships for major eukaryotes.Availability: The extracted gene functions are available at http://prime.ontology.ims.u-tokyo.ac.jpContact: akoike@hgc.jp
Comparison of computational methods for the identification of cell cycle-regulated genes
Authors: de Lichtenberg Ulrik , Jensen Lars Juhl , Fausbøll Anders , Jensen Thomas S. , Bork Peer , Brunak Søren 
Published: October 2004

AbstractMotivation: DNA microarrays have been used extensively to study the cell cycle transcription programme in a number of model organisms. The Saccharomyces cerevisiae data in particular have been subjected to a wide range of bioinformatics analysis methods, aimed at identifying the correct and complete set of periodically expressed genes.Results: Here, we provide the first thorough benchmark of such methods, surprisingly revealing that most new and more mathematically advanced methods actually perform worse than the analysis published with the original microarray data sets. We show that this loss of accuracy specifically affects methods that only model the shape of the expression profile without taking into account the magnitude of regulation. We present a simple permutation-based method that performs better than most existing methods.Supplementary information: Results and benchmark sets are available at http://www.cbs.dtu.dk/cellcycleContact: brunak@cbs.dtu.dk
PDZBase: a protein–protein interaction database for PDZ-domains
Authors: Beuming Thijs , Skrabanek Lucy , Niv Masha Y. , Mukherjee Piali , Weinstein Harel 
Published: October 2004

Abstract
Summary: PDZBase is a database that aims to contain all known PDZ-domain-mediated protein–protein interactions. Currently, PDZBase contains approximately 300 such interactions, which have been manually extracted from &gt;200 articles. The database can be queried through both sequence motif and keyword-based searches, and the sequences of interacting proteins can be visually inspected through alignments (for the comparison of several interactions), or as residue-based diagrams including schematic secondary structure information (for individual complexes).
Availability: http://icb.med.cornell.edu/services/pdz/start.
Contact: pdzbase@med.cornell.edu.
Update on intrapartum fetal pulse oximetry
Authors: East Christine E , Colditz Paul B , Begg Lisa M , Brennecke Shaun P 
Published: October 2004

ABSTRACTThis article examines the current status of fetal pulse oximetry (FPO) as a means of intrapartum assessment of fetal wellbeing.FPO has been developed to a stage where it is a safe and accurate indicator of intrapartum fetal oxygenation. In general, sliding the FPO sensor along the examiner's fingers and through the cervix, to lie alongside the fetal cheek or temple is easy. The recent publication of a randomised controlled trial (RCT) of FPO versus conventional intrapartum monitoring has validated its use to reduce caesarean section rates for nonreassuring fetal status. An Australian multicentre RCT is currently underway. Maternal satisfaction rates with FPO are high.FPO may be used during labour when the electronic fetal heart rate trace is nonreassuring or when conventional monitoring is unreliable, such as with fetal arrhythmias. If the fetal oxygen saturation (FspO2) values are < 30%, prompt obstetric intervention is indicated, such as fetal scalp blood sampling or delivery. FspO2 monitoring should not form the sole basis of intrapartum fetal welfare assessment. Rather, the whole clinical picture should be considered.
Gestational diabetes versus obesity as risk factors for pregnancy‐induced hypertensive disorders and fetal macrosomia
Authors: van Hoorn Jessika , Dekker Gus , Jeffries Bill 
Published: October 2004

ABSTRACTObjectiveTo assess whether obesity and/or gestational diabetes mellitus (GDM) are independent risk factors for fetal macrosomia and/or pregnancy‐induced hypertensive disorders.DesignRetrospective computerised database review.SettingLyell McEwin Health Service, South Australia.SampleAll nulliparous women delivering singleton babies in the years 1999 and 2000Main outcome measuresBirth weights, the occurrence of fetal macrosomia, gestational hypertension and preeclampsia were compared between 258 normoglycaemic women (control group), 76 women with only an abnormal glucose challenge test, and 51 women with GDM.ResultsOnly GDM with fasting hyperglycaemia is a risk factor for macrosomia (risk ratio: 3.3 95% confidence limits 1.229–8.736). Smoking is associated with a decrease in the incidence of pregnancy‐induced hypertensive disorders.ConclusionsOur data strongly suggest that GDM and obesity are not independent risk factors for pregnancy‐induced hypertensive disorders.
The impact of intrapartum analgesia on labour and delivery outcomes in nulliparous women
Authors: Dickinson Jan E , Paech Michael J , McDonald Susan J , Evans Sharon F 
Published: October 2004

ABSTRACTObjectivesTo establish the spontaneous miscarriage rate and compare it with the procedure related miscarriage rate for amniocentesis and chorionic villus sampling (CVS) by experienced operators.DesignRetrospective audit over a two‐year period of all patients having a consultation for prenatal diagnosis before 12 weeks gestation.SettingA specialised obstetric and gynaecological ultrasound practice.PopulationA total of 2366 patients, mostly over 35 years of age.MethodsBetween 1 July 1995 and 30 June 1997, all patients having a prenatal consultation decided between amniocentesis, CVS or no invasive testing. The CVS was performed either transabdominally or transcervically, depending on the position of the uterus and placenta.Main outcome measuresDelivery, termination of pregnancy for chromosomal abnormality or miscarriage.ResultsOver the two‐year period, 2366 patients had a prenatal consultation and outcome data were available for all but 53 patients. After consultation, 346 patients decided not to have any prenatal testing and 29 (8.4%) of these had a spontaneous miscarriage. Amniocentesis was requested by 839 patients; however 10 miscarried before the scheduled procedure. After the amniocentesis, there were 13 terminations for chromosomal abnormality and three miscarriages. CVS was requested by 1128 patients; however, 23 miscarried before the scheduled procedure. Transabdominal CVS was performed in 665 patients, transcervical in 416 and in 24 cases the documentation of the method used was unclear. Eleven patients miscarried after the transabdominal CVS (1.65%) compared with nine patients miscarrying after the transcervical CVS (2.16%), which was not statistically significant (p = 0.27).ConclusionIn the group studied, the spontaneous miscarriage rate from nine weeks gestation is very high (8.4%). The procedure‐related loss rate from amniocentesis was less than 1 in 280. Transabdominal CVS appears to have a lower fetal loss rate than transcervical CVS, but much larger numbers are needed to prove this.
Strategies required to improve the management of chronic vulvar discomfort in Australia
Authors: Wines Nina 
Published: October 2004

SUMMARYObjectiveTo investigate factors required to improve the management of vulvar pain from a patient perspective.Sample and settingSixty patients in four different specialised vulvar clinics.MethodsWomen with chronic vulvar pain were asked to complete a questionnaire whilst waiting for specialist consultation by either a dermatologist, sexual health physican, psychologist or physiotherapist.ResultsThe average length of time patients had vulvar pain was 6.03 years, with a mean of 5.83 practitioners seen. Twenty‐seven per cent indicated that increased awareness of vulvodynia was required by gynaecologists and 74% suggested that increased general practitioner awareness was necessary to improve care. Accurate diagnosis, and understanding lifestyle implications were key elements of patient satisfaction, considered more important than any available treatment modality.ConclusionsCurrent services and skilled practitioners available for the management of chronic vulvar pain or vulvo dynia in Australia do not reflect the estimated prevalence of this condition. From this study it was concluded that the three most important factors required to improve quality of care in order of importance were increased practitioner awareness, research and the setting up of more specialized multi‐disciplinary clinics.