bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of prostaglandin receptors in mitochondria on apoptosis of human lung carcinoma cell line A549
Authors: Fang K.M. , Shu W.H. , Chang H.C. , Wang J.J. , Mak O.T. 
Published: October 2004

PGs (prostaglandins) are synthesized through the cyclo-oxygenase (COX-1 and -2) pathway in a variety of cells in response to various physiological stimuli. All cells require at least one pathway for apoptosis, and mitochondrial play a central role in regulation of apoptosis. In a previous study, incubation of A549 cells with NS-398 (a COX-2-specific inhibitor) induced apoptosis and inhibited cell proliferation, and the concentrations of different PGs between various cellular compartments were found to be changed. To determine whether PG receptors are involved in this regulation, Western-blot analyses were performed specific for PGE2 (EP receptors) and PGF2α (FP receptor) receptors, which were expressed in A549 cells. Western-blot analysis revealed that mitochondria that were isolated from A549 cells expressed EP receptors (EP2, EP3 and EP4), whereas FP receptors were undetectable. EP receptors (EP1, EP3 and EP4) and FP receptors were detected from A549 cell membrane. These results suggest that the change of PG production in A549-cells-induced cancer cell apoptosis might be related to the different expressions of EP and FP receptors in cell and mitochondrial membrane.
Relational patterns of gene expression via non-metric multidimensional scaling analysis
Authors: Taguchi Y.-h. , Oono Y. 
Published: October 2004

Abstract
Motivation: Microarray experiments result in large-scale data sets that require extensive mining and refining to extract useful information. We demonstrate the usefulness of (non-metric) multidimensional scaling (MDS) method in analyzing a large number of genes. Applying MDS to the microarray data is certainly not new, but the existing works are all on small numbers (&lt;100) of points to be analyzed. We have been developing an efficient novel algorithm for non-metric MDS (nMDS) analysis for very large data sets as a maximally unsupervised data mining device. We wish to demonstrate its usefulness in the context of bioinformatics (unraveling relational patterns among genes from time series data in this paper).
Results: The Pearson correlation coefficient with its sign flipped is used to measure the dissimilarity of the gene activities in transcriptional response of cell-cycle-synchronized human fibroblasts to serum. These dissimilarity data have been analyzed with our nMDS algorithm to produce an almost circular relational pattern of the genes. The obtained pattern expresses a temporal order in the data in this example; the temporal expression pattern of the genes rotates along this circular arrangement and is related to the cell cycle. For the data we analyze in this paper we observe the following. If an appropriate preparation procedure is applied to the original data set, linear methods such as the principal component analysis (PCA) could achieve reasonable results, but without data preprocessing linear methods such as PCA cannot achieve a useful picture. Furthermore, even with an appropriate data preprocessing, the outcomes of linear procedures are not as clear-cut as those by nMDS without preprocessing.
Availability: The FORTRAN source code of the method used in this analysis (pure nMDS) is available at http://www.granular.com/MDS/
Contact: tag@granular.com
Supplementary information: http://www.granular.com/MDS/B1_2005.
Inferring pathways from gene lists using a literature-derived network of biological relationships
Authors: Rajagopalan Dilip , Agarwal Pankaj 
Published: October 2004

Abstract
Motivation: A number of omic technologies such as transcriptional profiling, proteomics, literature searches, genetic association, etc. help in the identification of sets of important genes. A subset of these genes may act in a coordinated manner, possibly because they are part of the same biological pathway. Interpreting such gene lists and relating them to pathways is a challenging task. Databases of biological relationships between thousands of mammalian genes can help in deciphering omics data. The relationships between genes can be assembled into a biological network with each protein as a node and each relationship as an edge between two proteins (or nodes). This network may then be searched for subnetworks consisting largely of interesting genes from the omics experiment. The subset of genes in the subnetwork along with the web of relationships between them helps to decipher the underlying pathways. Finding such subnetworks that maximally include all proteins from the query set but few others is the focus for this paper.
Results: We present a heuristic algorithm and a scoring function that work well both on simulated data and on data from known pathways. The scoring function is an extension of a previous study for a single biological experiment. We use a simple set of heuristics that provide a more efficient solution than the simulated annealing method. We find that our method works on reasonably complex curated networks containing ∼9000 biological entities (genes and metabolites), and ∼30 000 biological relationships. We also show that our method can pick up a pathway signal from a query list including a moderate number of genes unrelated to the pathway. In addition, we quantify the sensitivity and specificity of the technique.
Contact: dilip_rajagopalan@gsk.com
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
Authors: Yu Yi-Kuo , Altschul Stephen F. 
Published: October 2004

Abstract
Motivation: Amino acid substitution matrices play a central role in protein alignment methods. Standard log-odds matrices, such as those of the PAM and BLOSUM series, are constructed from large sets of protein alignments having implicit background amino acid frequencies. However, these matrices frequently are used to compare proteins with markedly different amino acid compositions, such as transmembrane proteins or proteins from organisms with strongly biased nucleotide compositions. It has been argued elsewhere that standard matrices are not ideal for such comparisons and, furthermore, a rationale has been presented for transforming a standard matrix for use in a non-standard compositional context.
Results: This paper presents the mathematical details underlying the compositional adjustment of amino acid or DNA substitution matrices.
Availability: Programs implementing the methods described are available from the authors upon request.
Contact: altschul@ncbi.nlm.nih.gov
Implementation of a gene expression index calculation method based on the PDNN model
Authors: Nielsen Henrik Bjørn , Gautier Laurent , Knudsen Steen 
Published: October 2004

AbstractSummary: Gene expression index calculations from Affymetrix GeneChips have been dominated by the Affymetrix MAS, dChip, and RMA methods. A new method to estimate the gene expression value utilizing the probe sequence information named position-dependent nearest-neighbor (PDNN) has been suggested by Zhang et al. (2003). Here we describe an open source implementation of the PDNN method for the statistical language R.Availability: The package can be downloaded from http://www.bioconductor.org/repository/devel/package/html/affypdnn.htmlContact: hbjorn@cbs.dtu.dk
Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites
Authors: Sabatti Chiara , Rohlin Lars , Lange Kenneth , Liao James C. 
Published: October 2004

AbstractMotivation: Gene expression arrays enable measurements of transcription values for a large number or all genes in the genome. In order to better interpret these resluts and to use them to reconstruct transcription networks, information on location of binding sites for regulatory proteins in the entire genome is needed. In particular, this represents an open problem in Escherichia coli.Results: We describe the first implementation of dictionary-style models to the study of transcription factors binding sites in an entire genome. Vocabulon's unique feature is that it can both reconstruct binding sites characterized by unknown motifs and impute locations of known binding sites in long sequences by simultaneous search. On one hand, the dictionary model specifies a probability for the entire sequence taking simultaneously into account all the possible binding sites. This greatly reduces the number of false positives. On the other hand, the possibility of refining motif description, as an increasig number of binding sites are identified, augments the sensitivity of the method. We illustrate these properties with examples in E.coli. The results of gene expression arrays are used both to guide the search and corroborate it.Availability: For copy of the Vocabulon program and other details please contact csabatti@mednet.ucla.eduContact: csabatti@mednet.ucla.edu
MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations
Authors: Ding Jing , Berleant Daniel 
Published: October 2004

Abstract
Summary: MEDLINE/PubMed is one of the most important information sources for bioinformatics text mining. However, there remain limitations in working with MEDLINE/PubMed citations. For example, PubMed imposes an upper limit of 10 000 for downloading PMID list or citations; and MEDLINE files are too large for most off-the-shelf XML parsers. We developed a Java package, MedKit, to work-around the limitations, as well as provide other useful functionalities, e.g. random sampling. Its four modules (querier, sampler, fetcher and parser) can work independently, or be pipelined in various combinations. It can be used as a stand-alone GUI application, or integrated into other text-mining systems. Text mining researchers and others may download and use the toolkit free for non-commercial purposes.
Availability: http://metnetdb.gdcb.iastate.edu/medkit
Contact: berleant@iastate.edu
Genomic Basis for Cell-Wall Diversity in Plants. A Comparative Approach to Gene Families in Rice and Arabidopsis
Authors: Yokoyama Ryusuke , Nishitani Kazuhiko 
Published: October 2004

Abstract
Monocotyledons and dicotyledons are distinct, not only in their body plans and developmental patterns, but also in the structural features of their cell walls. The recent completion of the rice (Oryza sativa) genomic sequence and publication of the sequence data, together with the completed database of the Arabidopsis thaliana genome, provide the first opportunity to compare the full complement of cell-wall-related genes from the two distinct classes of flowering plants. We made this comparison by exploiting the fact that Arabidopsis and rice have type I and type II walls, respectively, and therefore represent the two extremes in terms of the structural features of plant cell walls. In this review article, we classify all cell-wall-related genes into 32 gene families, and generate their phylogenetic trees. Using these data, we can phylogenetically compare individual genes of particular interest between Arabidopsis and rice. This comparative genome approach shows that the differences in wall architecture in the two plant groups actually mirror the diversity of the individual gene families involved in the cell-wall dynamics of the respective plant species. This study also identifies putative rice orthologs of genes with well-defined functions in Arabidopsis and other plant species.
Caesarean delivery and outcome in very low birthweight infants
Authors: Paul David A , Sciscione Anthony , Leef Kathleen H , Stefano John L 
Published: October 2004

ABSTRACTObjectiveTo determine the relationship between mode of delivery, intraventricular haemorrhage (IVH), and mortality in very low birthweight (VLBW) infants.Study designA historical cohort study of infants admitted to a single level III neonatal intensive care unit during a five‐year period. Infants < 1500 g born by caesarean delivery (n = 400) were compared to those born by vaginal delivery (n = 305).ResultsAfter controlling for potential confounding variables including: gestational age, fetal presentation, and multiple birth, caesarean delivery was not associated with a decreased odds of IVH (odds ratio 1.2, 95% CI 0.7–2.0), severe IVH (1.9, 0.9–4.0), or mortality (1.2, 0.6–2.4).ConclusionsIn our population of very low birthweight infants, caesarean delivery is not associated with a decreased risk for mortality or intraventricular haemorrhage.
Risk factors for preterm delivery in patients demonstrating sonographic evidence of premature dilation of the internal os, prolapse of the membranes in the endocervical canal and shortening of the distal cervical segment by second trimester ultrasound
Authors: Benham Brady N , Balducci James , Atlas Robert O , Rust Orion A 
Published: October 2004

ABSTRACTObjectiveTo investigate the outcomes and risk factors associated with the second trimester sonographic findings of premature dilation of the internal cervical os, prolapse of the membranes into the endocervical canal and shortening of the distal segment.Study designRetrospective chart review to identify patients who met the following criteria: (i) gestational age between 16 and 24 weeks; (ii) a vaginal probe ultrasound documenting dilatation of the internal os, prolapsed membranes into the endocervical canal but not extending beyond the external os, and a shortened distal cervix; and (iii) no evidence of increased uterine activity.MethodsSonographic measurements obtained included: (i) the width of the internal os dilation; (ii) the depth of membranes prolapsed into endocervix (funneling); (iii) the distal cervical length;and (iv) the total cervical length. Patients were stratified into two groups according to gestational age at delivery: the preterm group (< 34 weeks) and the near‐term group (≥ 34 weeks).ResultsThirty‐seven patients had complete records for analysis and their pregnancies resulted in 47 live births. Eighteen patients were stratified to the near term group and 19 were stratified to the preterm group. There were no stillborn infants and 10 neonatal deaths. Ten patients received cerclage and seven patients delivered at < 34 weeks gestational age. Risk factors found to be significant for preterm delivery included a gestational age at diagnosis of ≥ 20 weeks gestation (p = 0.03), dilatation of the internal os > 1.3 cm (p = 0.04), and a composite Benham score ≥ 1.0 (p = 0.02).ConclusionsThe sonographic findings of premature dilatation of the internal os, prolapse of the membranes into the endocervical canal and shortening of the distal cervix are associated with a high rate of delivery < 34 weeks (51%) and neonatal death (27%).
Higher order multiple pregnancies in New South Wales 1990–1999
Authors: Roberts Christine L , Raynes‐Greenow Camille H , Algert Charles S , Peat Brian 
Published: October 2004

ABSTRACTObjectiveTo examine higher order multiple pregnancy and birth rates in NSW, and to describe trends in the characteristics and management of these births.DesignCross‐sectional analytic study.SettingNew South Wales, Australia.PopulationTwo hundred and ninety‐one women who gave birth to triplets, quadruplets or quintuplets (880 babies) from 1 January 1990 to 31 December 1999.MethodsData were obtained from the NSW Midwives Data Collection and rates over time were calculated.Main outcome measuresHigher order multiple birth and pregnancy rates (≥ 20 weeks), place of birth, mode of delivery, fetal death rates and Apgar scores.ResultsThere was no significant change in the number or rate of higher order multiple births in NSW during the 1990s with an average annual rate of 10.3/10,000 births or 3.5/10,000 pregnancies ≥ 20 weeks. Among women with higher order multiple pregnancies, those aged ≥ 35 years increased from 19% in 1990 to 47% in 1999. There was also a trend towards delivery in a perinatal centre from 56% to 70%, and vaginal birth from 18% to 28%. There were no significant changes in infant outcomes.ConclusionsThe increases in higher order multiple pregnancies observed in Australia in the 1980s, and into the 1990s in other countries, have not persisted in NSW, suggesting that guidelines for limiting the number of embryos/oocytes transferred in assisted reproductive technologies have been widely adopted.
The loss rates for invasive prenatal testing in a specialised obstetric ultrasound practice
Authors: Scott Fergus , Peters Helen , Boogert Tom , Robertson Robert , Anderson John , McLennan Andrew , Kesby Greg , Edelman David 
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.
A prospective observational study on the accuracy of patient self‐testing of urine at an antenatal clinic
Authors: Goh Judith TW , Krause Hannah 
Published: October 2004

ABSTRACTThis study was performed to assess whether assigning dipstick self‐testing of urine to antenatal women maintained accuracy and clinical relevance of the results. A total of 212 women were recruited from the routine antenatal clinic for the assessment of accuracy of self‐testing of urine. The women's results were compared to that of the one nurse who routinely performs dipstick testing at the antenatal clinic.Analysis of the results indicates that women tended to over estimate proteinuria.
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 randomized 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.
Ascertaining women's choice of title during pregnancy and childbirth
Authors: Denning Angela S , Tuttle Lynette K , Bryant Valerie J , Walker Susan P , Higgins John R 
Published: October 2004

ABSTRACTMethodsA questionnaire was administered to 958 women attending the antenatal clinic at Mercy Hospital for Women, Melbourne, to ascertain their choice of title during pregnancy. Midwifery, nursing and medical staff (376 in total) were also invited to respond to a similar questionnaire.ResultsThe response rate was 73.6% from the survey of all women who were overwhelmingly in favour of being called ‘patient’ as their first choice (34%), followed by ‘other’ (20%) and then ‘mother’ (19%). Virtually all women requesting ‘other’ wished to be called by their name. Women wishing to be called ‘patient’ for first choice did not significantly differ from the remainder of the study group in age, gestation, number of previous pregnancies, or number of children. When women from the Family Birth Centre (FBC) were analysed as a separate group, they had a clear preference to be called ‘other’ (unanimously, by their name) than the general antenatal population (odds ratio (OR) 5.1; 95% confidence interval (CI) 3.1, 8.3; p < 0.0001). The staff survey, with a response rate of 84%, also demonstrated that ‘patient’ was the most popular first choice for patient title. Medical staff were significantly more likely to choose ‘patient’ (OR 4.2, 95% CI 2.3, 7.7; p < 0.0001), though the term ‘patient’ was the preferred choice of all staff.
Prothrombin G20210A mutation is not associated with recurrent miscarriages
Authors: Chua Boon Ghee , Burrows Robert F 
Published: October 2004

ABSTRACTObjectiveTo assess the association between prothrombin G20210A mutation and recurrent miscarriages.Study designA literature review was performed in Medline identifying articles from 1966 to December 2000. Articles meeting inclusion criteria were systematically reviewed and included in a meta‐analysis.ResultsSix trials, all case‐controlled, were identified. These trials included 323 women with recurrent pregnancy loss. The odds ratio (OR) for heterozygous prothrombin mutation was 1.9 (95% confidence interval (CI) 0.98–4.14), and for homozygous prothrombin mutation was 3.76 (95% CI 0.75–18.77). The OR for prothrombin mutation and primary recurrent abortion was 2.19 (95% CI 0.61–7.89) and for prothrombin mutation and secondary recurrent abortion was 1.29 (95% CI 0.2–8.36).ConclusionThere is no evidence to support an association of prothrombin G20210A mutation with recurrent miscarriages.