bluuebunny/crossref_metadata_2025_split huggingface dataset:
Down syndrome maternal serum marker screening after 18 weeks' gestation
Authors: Muller Françoise , Dreux Sophie , Oury Jean‐François , Luton Dominique , Uzan Serge , Uzan Michèle , Levardon Michel , Dommergues Marc 
Published: November 2002

AbstractWomen having access to prenatal care late in pregnancy may still wish to benefit from maternal serum screening for Down syndrome. Therefore, we established reference values for α‐feto protein (AFP) and free β‐human chorionic gonadotrophin (β‐hCG), and assessed the diagnostic value of maternal serum marker screening at 18–35 weeks' gestation based upon a series of 4072 sera from unaffected pregnancies and 118 sera from pregnant women with fetuses affected by Down syndrome. Using a 1/250 risk cut‐off, a detection rate of 72.9% (95% CI = 71.5–74.3%) was achieved with a false‐positive rate of 7.51% (95% CI = 6.71–8.3%). This was not significantly different from the percentages observed in our 14–17 weeks routine screening (50 596 patients): 71.9% (95% CI = 71.5–72.3%) and 6.48% (95% CI = 6.28–6.68%), respectively. Detection and screen‐positive rates were, respectively, 51.3% (95% CI = 35.6–67.0%) and 5.95% (95% CI = 5.12–6.68%) in women aunder 35 years of age, and 84.8% (95% CI = 76.9–92.7%) and 24% (95% CI = 20.7–27.3%) in women aged 35 years and over. In conclusion, maternal serum marker screening is feasible at 18 weeks' gestation and later, which may be of interest in selected cases. Copyright © 2002 John Wiley & Sons, Ltd.
Rapid diagnosis of triploidy of maternal origin using fluorescent PCR and DNA fragment analysis in the third trimester of pregnancy
Authors: Bán Zoltán , Nagy Bálint , Papp Csaba , Tóth‐Pál Ernö , Papp Zoltán 
Published: November 2002

AbstractObjectivesTriploidy is a common cause of spontaneous abortion in the very early stages of pregnancy. It is very rare for a prenatal diagnostic center to discover triploidy in the third trimester of pregnancy. A pregnant woman in the third trimester was referred to our genetic counselling clinic because of abnormal ultrasound findings. We planned to test for the most common chromosomal abnormalities.MethodsWe performed ultrasound examination, chorionic villus sampling, karyotyping and fluorescent‐polymerase chain reaction (F‐PCR) and fragment analysis.ResultsWe diagnosed a 69,XXX karyotype fetus in the 31st week of gestation, based on a short tandem repeat (STR) pattern typical for triploidy, which was confirmed by karyotyping. The comparison of the fetal and parental STR patterns showed maternal origin of the extra haploid chromosome set.ConclusionsSTR analysis of fluorescent‐PCR and DNA fragment analysis is a rapid and reliable alternative to karyotyping for detection of certain aneuploidies. The method is also suitable for the determination of the origin of the extra chromosome set. Copyright © 2002 John Wiley & Sons, Ltd.
Currarino triad: concurrent US and MRI diagnosis in the fetus and the mother
Authors: Eliáš P. , Žižka J. , Balíček P. 
Published: November 2002

AbstractWe report an unusual case of the complete Currarino triad diagnosed in a fetus at 21 weeks' gestation by means of prenatal ultrasonography (US). The highly suspicious findings in the fetus were accompanied by analogous US findings in the mother who suffered from mild symptoms of up to that time unrecognized Currarino triad. Consecutively, magnetic resonance imaging (MRI) confirmed the findings simultaneously in the fetus and in her mother. This is the first report describing the prenatal diagnosis of Currarino triad without the background of positive family history. To our knowledge, the prenatal MRI findings of Currarino triad have not yet been published. Copyright © 2002 John Wiley & Sons, Ltd.
Global robust stabilization of nonlinear systems subject to input constraints
Authors: Suárez Rodolfo , Solís‐Daun Julio , Álvarez‐Ramírez José 
Published: November 2002

AbstractOur main purpose in this paper is to further address the global stabilization problem for affine systems by means of bounded feedback control functions, taking into account a large class of control value sets:p,r‐weighted balls ℬ︁mr(p), with 1<p⩽∞, defined viap,r‐weighted gauge functions. Observe thatp=∞ is allowed, so thatm‐dimensionalr‐hyperboxes ℬ︁mr(∞)≔[−r1−,r1+]×⋅⋅⋅×[−rm−,rm+],rj±>0 are also considered. Working along the line of Artstein–Sontag's approach, we construct an explicit formula for a one‐parameterized family of continuous feedback controls taking values in ℬ︁rm(p) that globally asymptotically stabilize an affine system, provided an appropriatecontrol Lyapunov functionis known. The designed family of controls issuboptimalwith respect to the robust stability margin for uncertain systems. The problem of achieving disturbance attenuation for persistent disturbances is also considered. Copyright © 2002 John Wiley & Sons, Ltd.
ERRATA
Authors: LÉVESQUE M. , LEMAY S. , CHOUINARD S. , BLANCHET P. , BÉDARD M.-A. , RICHER F. , ZAWACKI T. , SWEET L. , PAUL R. , MOSER D. , COHEN R. , MANLY JENNIFER J. , JACOBS DIANE M. , TOURADJI PEGAH , SMALL SCOTT A. , STERN YAAKOV 
Published: November 2002

First erratum: The following is a correction for an error that
occurred in the Journal of the International Neuropsychological
Society, Vol. 8, No. 2. An abstract titled
“Parkinson's Disease Affects the Attentional Control of
Unpracticed Movements,” by M. Lévesque, S. Lemay, S.
Chouinard, P. Blanchet, M.-A. Bédard, and F. Richer, was
accidently left out. This abstract was supposed to appear on p. 230
after C. Boulet et al., in the Executive Function subsection of Poster
4, which was a part of the Friday Morning, February 16, group of sessions.Second erratum: The following is a correction for an error that
occurred in Journal of the International Neuropsychological Society,
8:2. On page 276, the abstract at the bottom of the left column has
a laterality error, and “right” was supposed to appear instead
of “left.”Third erratum: The following is a correction for an error that occurred
in the Journal of the International Neuropsychological Society,
Vol. 8, No. 3. The error occurred in the article titled
“Reading level attenuates differences in neuropsychological tests
performance between African American and White Elders,” pp.
341–348, by Manly et al. On page 343, under the subheading
“Reading Level,” the last line in the paragraph should state
the age range as 65–74 and not 70–75 years.Cambridge University Press and the authors regret the inconvenience
that these inadvertent errors may have caused.
MethPrimer: designing primers for methylation PCRs
Authors: Li Long-Cheng , Dahiya Rajvir 
Published: November 2002

Abstract
Motivation: DNA methylation is an epigenetic mechanism of gene regulation. Bisulfite- conversion-based PCR methods, such as bisulfite sequencing PCR (BSP) and methylation specific PCR (MSP), remain the most commonly used techniques for methylation mapping. Existing primer design programs developed for standard PCR cannot handle primer design for bisulfite-conversion-based PCRs due to changes in DNA sequence context caused by bisulfite treatment and many special constraints both on the primers and the region to be amplified for such experiments. Therefore, the present study was designed to develop a program for such applications.
Results: MethPrimer, based on Primer3, is a program for designing PCR primers for methylation mapping. It first takes a DNA sequence as its input and searches the sequence for potential CpG islands. Primers are then picked around the predicted CpG islands or around regions specified by users. MethPrimer can design primers for BSP and MSP. Results of primer selection are delivered through a web browser in text and in graphic view.
Availability: MethPrimer is freely accessible at the following Web address http://itsa.ucsf.edu/~urolab/methprimer
Contact: longli@itsa.ucsf.eduurologylab@aol.com
* To whom correspondence should be addressed.
Nonparametric methods for identifying differentially
expressed genes in microarray data
Authors: Troyanskaya Olga G. , Garber Mitchell E. , Brown Patrick O. , Botstein David , Altman Russ B. 
Published: November 2002

Abstract
Motivation: Gene expression experiments provide a fast and systematic way to identify disease markers relevant to clinical care. In this study, we address the problem of robust identification of differentially expressed genes from microarray data. Differentially expressed genes, or discriminator genes, are genes with significantly different expression in two user-defined groups of microarray experiments. We compare three model-free approaches: (1) nonparametric t-test, (2) Wilcoxon (or Mann–Whitney) rank sum test, and (3) a heuristic method based on high Pearson correlation to a perfectly differentiating gene (‘ideal discriminator method’). We systematically assess the performance of each method based on simulated and biological data under varying noise levels and p-value cutoffs.
Results: All methods exhibit very low false positive rates and identify a large fraction of the differentially expressed genes in simulated data sets with noise level similar to that of actual data. Overall, the rank sum test appears most conservative, which may be advantageous when the computationally identified genes need to be tested biologically. However, if a more inclusive list of markers is desired, a higher p-value cutoff or the nonparametric t-test may be appropriate. When applied to data from lung tumor and lymphoma data sets, the methods identify biologically relevant differentially expressed genes that allow clear separation of groups in question. Thus the methods described and evaluated here provide a convenient and robust way to identify differentially expressed genes for further biological and clinical analysis.
Availability: By request from the authors.
Contact: russ.altman@stanford.edu
* To whom correspondence should be addressed.
An evaluation of β-turn prediction methods
Authors: Kaur Harpreet , Raghava G.P.S. 
Published: November 2002

Abstract
Motivation: β-turn is an important element of protein structure. In the past three decades, numerous β-turn prediction methods have been developed based on various strategies. For a detailed discussion about the importance of β-turns and a systematic introduction of the existing prediction algorithms for β-turns and their types, please see a recent review (Chou, Analytical Biochemistry, 286, 1–16, 2000). However at present, it is still difficult to say which method is better than the other. This is because of the fact that these methods were developed on different sets of data. Thus, it is important to evaluate the performance of β-turn prediction methods.
Results: We have evaluated the performance of six methods of β-turn prediction. All the methods have been tested on a set of 426 non-homologous protein chains. It has been observed that the performance of the neural network based method, BTPRED, is significantly better than the statistical methods. One of the reasons for its better performance is that it utilizes the predicted secondary structure information. We have also trained, tested and evaluated the performance of all methods except BTPRED and GORBTURN, on new data set using a 7-fold cross-validation technique. There is a significant improvement in performance of all the methods when secondary structure information is incorporated. Moreover, after incorporating secondary structure information, the Sequence Coupled Model has yielded better results in predicting β-turns as compared with other methods. In this study, both threshold dependent and independent (ROC) measures have been used for evaluation.
Contact: raghava@imtech.res.in
Supplementary information: http://imtech.res.in/raghava/betatpred/eval/
* To whom correspondence should be addressed.
Euclidian space and grouping of biological objects
Authors: Grishin Vyacheslav N. , Grishin Nick V. 
Published: November 2002

Abstract
Motivation: Biological objects tend to cluster into discrete groups. Objects within a group typically possess similar properties. It is important to have fast and efficient tools for grouping objects that result in biologically meaningful clusters. Protein sequences reflect biological diversity and offer an extraordinary variety of objects for polishing clustering strategies. Grouping of sequences should reflect their evolutionary history and their functional properties. Visualization of relationships between sequences is of no less importance. Tree-building methods are typically used for such visualization. An alternative concept to visualization is a multidimensional sequence space. In this space, proteins are defined as points and distances between the points reflect the relationships between the proteins. Such a space can also be a basis for model-based clustering strategies that typically produce results correlating better with biological properties of proteins.
Results: We developed an approach to classification of biological objects that combines evolutionary measures of their similarity with a model-based clustering procedure. We apply the methodology to amino acid sequences. On the first step, given a multiple sequence alignment, we estimate evolutionary distances between proteins measured in expected numbers of amino acid substitutions per site. These distances are additive and are suitable for evolutionary tree reconstruction. On the second step, we find the best fit approximation of the evolutionary distances by Euclidian distances and thus represent each protein by a point in a multidimensional space. The Euclidian space may be projected in two or three dimensions and the projections can be used to visualize relationships between proteins. On the third step, we find a non-parametric estimate of the probability density of the points and cluster the points that belong to the same local maximum of this density in a group. The number of groups is controlled by a σ-parameter that determines the shape of the density estimate and the number of maxima in it. The grouping procedure outperforms commonly used methods such as UPGMA and single linkage clustering.
Availability: The code of EESG program for Mathematica4 (Wolfram Research) as well as the details of the analysis are freely available at ftp://iole.swmed.edu/pub/EESG/.
Contact: grishin@chop.swmed.edu
* To whom correspondence should be addressed.
A motif of a microbial starch-binding domain found in human genethonin
Authors: Janeček Štefan 
Published: November 2002

Abstract
Summary: The sequence of the starch-binding domain present in 10% of amylolytic enzymes of microbial origin and classified as the carbohydrate-binding module family 20, was identified in the equivalent part of sequence of human genethonin, a skeletal muscle protein of unknown function. The sequence identity between the starch-binding domain from Bacillus sp. strain 1011 cyclodextrin glucanotransferase and the corresponding segment of human genethonin was higher than 28%. The amino acid residues known to be involved in the raw starch binding were found to be conserved in the genethonin sequence. The three-dimensional structure of the genethonin ‘starch-binding domain’ was modelled and its eventual function briefly discussed.
Contact: stefan.janecek@savba.sk
Poxvirus Orthologous Clusters (POCs)
Authors: Ehlers Angelika , Osborne John , Slack Stephanie , Roper Rachel L. , Upton Chris 
Published: November 2002

Abstract
Summary: Poxvirus Orthologous Clusters (POCs) is a JAVA client–server application which accesses an updated database containing all complete poxvirus genomes; it automatically groups orthologous genes into families based on BLASTP scores for assessment by a human database curator. POCs has a user-friendly interface permitting complex SQL queries to retrieve interesting groups of DNA and protein sequences as well as gene families for subsequent interrogation by a variety of integrated tools: BLASTP, BLASTX, TBLASTN, Jalview (multiple alignment), Dotlet (Dotplot), Laj (local alignment), and NAP (nucleotide to amino acid alignment).
Availability: Direct access to the POCs database via the GENOME ANALYSIS link at the Poxvirus Bioinformatics Resource: http://www.poxvirus.org. The Software is available for download via HTTP at: http://athena.bioc.uvic.ca/pbr/POCs/pocs.html.
Contact: cupton@uvic.ca
Supplementary Information: Installation instructions, the User's Manual, screenshots, and examples are available at the POCs home page http://athena.bioc.uvic.ca/pbr/POCs/pocs.html. The software is free for non-commercial applications. For information on poxviruses see http://www.poxvirus.org.
* To whom correspondence should be addressed.
Biochemical Properties of
Neisseria gonorrhoeae
LgtE
Authors: Piekarowicz Andrzej , Stein Daniel C. 
Published: November 2002

ABSTRACT

A fragment of chromosomal DNA encoding the
lgtE
gene of
Neisseria gonorrhoeae
strain F62 was amplified by PCR and cloned into the expression vector pET15b. Functional LgtE was purified and its biochemical properties were determined. The purified enzyme was maximally active in buffer containing manganese; minimal activity was obtained in buffer containing other divalent cations. LgtE was only able to mediate the addition of UDP-galactose into neisserial lipooligosaccharides (LOSs). We used a variety of genetically defined and chemically verified LOS structures to determine acceptor specificity. LgtE was able to mediate the addition of galactose into a variety of LOS structures, indicating the this enzyme possesses broad acceptor specificity. Furthermore, it was able to add multiple galactose residues onto LOS. We also determined that this enzyme was capable of adding galactose onto both the α and β chains of neisserial LOS.
Requirement offlhAfor Swarming Differentiation, Flagellin Export, and Secretion of Virulence-Associated Proteins inBacillus thuringiensis
Authors: Ghelardi Emilia , Celandroni Francesco , Salvetti Sara , Beecher Douglas J. , Gominet Myriam , Lereclus Didier , Wong Amy C. L. , Senesi Sonia 
Published: November 2002

ABSTRACTBacillus thuringiensisis being used worldwide as a biopesticide, although increasing evidence suggests that it is emerging as an opportunistic human pathogen. While phospholipases, hemolysins, and enterotoxins are claimed to be responsible forB. thuringiensisvirulence, there is no direct evidence to indicate that the flagellum-driven motility plays a role in parasite-host interactions. This report describes the characterization of a mini-Tn10mutant ofB. thuringiensisthat is defective in flagellum filament assembly and in swimming and swarming motility as well as in the production of hemolysin BL and phosphatidylcholine-preferring phospholipase C. The mutant strain was determined to carry the transposon insertion inflhA, a flagellar class II gene encoding a protein of the flagellar type III export apparatus. Interestingly, theflhAmutant ofB. thuringiensissynthesized flagellin but was impaired in flagellin export. Moreover, a protein similar to the anti-sigma factor FlgM that acts in regulating flagellar class III gene transcription was not detectable inB. thuringiensis, thus suggesting that the flagellar gene expression hierarchy ofB. thuringiensisdiffers from that described forBacillus subtilis. TheflhAmutant ofB. thuringiensiswas also defective in the secretion of hemolysin BL and phosphatidylcholine-preferring phospholipase C, although both of these virulence factors were synthesized by the mutant. Since complementation of the mutant with a plasmid harboring theflhAgene restored swimming and swarming motility as well as secretion of toxins, the overall results indicate that motility and virulence inB. thuringiensismay be coordinately regulated byflhA, which appears to play a crucial role in the export of flagellar as well as nonflagellar proteins.
Functions Required for Extracellular Quinolone Signaling by
Pseudomonas aeruginosa
Authors: Gallagher Larry A. , McKnight Susan L. , Kuznetsova Marina S. , Pesci Everett C. , Manoil Colin 
Published: November 2002

ABSTRACT

A set of 30 mutants exhibiting reduced production of the phenazine poison pyocyanin were isolated following transposon mutagenesis of
Pseudomonas aeruginosa
PAO1. The mutants could be subdivided into those with defects in the primary phenazine biosynthetic pathway and those with more pleiotropic defects. The largest set of pleiotropic mutations blocked the production of the extracellular
Pseudomonas
quinolone signal (PQS), a molecule required for the synthesis of secondary metabolites and extracellular enzymes. Most of these
pqs
mutations affected genes which appear to encode PQS biosynthetic functions, although a transcriptional regulator and an apparent response effector were also represented. Two of the genes required for PQS synthesis (
phnA
and
phnB
) had previously been assumed to encode phenazine biosynthetic functions. The transcription of one of the genes required for PQS synthesis (PA2587/
pqsH
) was regulated by the LasI/R quorum-sensing system, thereby linking quorum sensing and PQS regulation. Others of the pleiotropic phenazine-minus mutations appear to inactivate novel components of the quorum-sensing regulatory network, including one regulator (np20) previously shown to be required for virulence in neutropenic mice.
Functional Analysis of theBacillus subtilisZur Regulon
Authors: Gaballa Ahmed , Wang Tao , Ye Rick W. , Helmann John D. 
Published: November 2002

ABSTRACTTheBacillus subtiliszinc uptake repressor (Zur) regulates genes involved in zinc uptake. We have used DNA microarrays to identify genes that are derepressed in azurmutant. In addition to members of the two previously identified Zur-regulated operons (yciCandycdHI-yceA), we identified two other genes,yciAandyciB, as targets of Zur regulation. Electrophoretic mobility shift experiments demonstrated that all three operons are direct targets of Zur regulation. Zur binds to an ∼28-bp operator upstream of theyciAgene, as judged by DNase I footprinting, and similar operator sites are found preceding each of the previously described target operons,yciCandycdHI-yceA. Analysis of ayciA-lacZfusion indicates that this operon is induced under zinc starvation conditions and derepressed in thezurmutant. Phenotypic analyses suggest that the YciA, YciB, and YciC proteins may function as part of the same Zn(II) transport pathway. Mutation ofyciAoryciC, singly or in combination, had little effect on growth of the wild-type strain but significantly impaired the growth of theycdHmutant under conditions of zinc limitation. Since the YciA, YciB, and YciC proteins are not obviously related to any known transporter family, they may define a new class of metal ion uptake system. Mutant strains lacking all three identified zinc uptake systems (yciABC,ycdHI-yceA, andzosA) are dependent on micromolar levels of added zinc for optimal growth.