bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stringent environmental control in pregnancy and early life: the long‐term effects on mite, cat and dog allergen
Authors: Simpson A. , Simpson B. , Custovic A. , Craven M. , Woodcock A. 
Published: April 2004

SummaryBackground As part of a primary prevention of asthma study, we measured the effect of environmental control measures on Der p 1, Fel d 1 and Can f 1 over a 3.5‐year period.Methods High‐risk infants (both parents atopic) without pets, were randomized to the Active group (n = 142, vinyl flooring in child's room, allergen‐impermeable cot mattress, hot‐washable toy, mite allergen‐impermeable encasings to parental bed and to child's bed when older, high filtration vacuum cleaner, hot‐washing of bedding) or the Control group (n = 136, no intervention), in early pregnancy. Dust samples from the parental mattress, living room floor, child's mattress and floor at baseline (pregnancy), birth and at 3 years were analysed for Der p 1, Fel d 1 and Can f 1.Results A total of 278 families completed the baseline visit, 259 the birth visit and 239 the 3‐year visit. In the Active group at 3 years, 58% remained compliant with all measures likely to reduce the child's exposure to allergen and 77% of parents still used encasings on their bed. Levels of Der p 1, Fel d 1 and Can f 1 were significantly lower in the Active group in the child's floor and the child's mattress at 3 years compared to the Control group (P < 0.001). For the parental mattress, the levels of Der p 1 and Fel d 1 were lower in the Active group (P < 0.001) and there was a strong trend towards a lower level for Can f 1. There was no difference in the levels of any of the allergens between the groups in the living room floor. Childrens' bedrooms with no detectable mite, cat or dog allergen were significantly more common in the Active than the Control group (25 vs. 2, P < 0.001).Conclusions Environmental control measures are effective in substantially reducing levels of Der p 1, Fel d 1 and Can f 1 in homes without pets in the long term and are acceptable to families. The effect of this environmental manipulation on the development of sensitization and allergic disease remains to be seen.
Effect of pollinator on haploid production in durum wheat crossed with maize and pearl millet
Authors: GARCIA‐LLAMAS C. , RAMIREZ M. C. , BALLESTEROS J. 
Published: April 2004

AbstractThe aim of this work was to analyse the influence of the male parent on the production of embryos and haploid plants in durum wheat crossed with maize and pearl millet, to find a proper trait to identify the most efficient pollinators and to evaluate the mixtures of pollen. Two genotypes of durum wheat, low and high responding, were crossed with eight pollen samples: (i) three maize hybrids, (ii) three pearl millet inbred lines, (iii) a mixture of maize pollen and (iv) another mixture of pearl millet pollen. No significant differences on embryos and haploid plant production were observed among the four samples of maize pollen, but there were clear genotypic differences for the production of haploids between genotypes of pearl millet. The best pearl millet genotype produced significantly more haploid plants than the other two and the mixture of pollen. There was no correlation between the production of embryos and haploid plants. Therefore, the production of haploid plants must be the criterion to identify superior pollinators. In addition, a mixture of pollen is inappropriate except when using genotypes previously identified as good pollinators.
Pyramiding of insect‐ and disease‐resistance genes into an elite indica, cytoplasm male sterile restorer line of rice,‘Minghui 63′
Authors: Jiang G. H. , Xu C. G. , Tu J. M. , Li X. H. , He Y. Q. , Zhang Q. F. 
Published: April 2004

AbstractThe wild‐rice‐derived dominant gene Xa21 conferring multi‐race resistance to bacterial blight and a fused Bt gene cry1Ab/cry1Ac conferring resistance to lepidopteran insects were individually introduced into the same genetic background of an elite indica cytoplasm male sterile (CMS) restorer line ‘Minghui 63′. The line showed the desirable insect‐ and disease‐resistant phenotypes. To maximize the effect, the two genes were also pyramided into the same recipient plant of ‘Minghui 63’ by marker‐assisted selection. After being subjected to natural infestation of leaf‐folders and yellow stem borers and inoculation of Xoo strain mixtures, the pyramiding line and its derived hybrids showed high levels of resistance against both insect damage and disease. Furthermore, data from field trials demonstrated that the hybrids made by crossing this pyramiding line with the CMS lines ‘Zhenshan 97A’ and ‘Maxie A’ retained a similar level of yield under conditions without chemical spray, indicating that the pyramiding genes have a yield‐stabilizing effect on the recipient line and its hybrids.
Interspecific hybrids of sunflower as a source of Sclerotinia resistance
Authors: Rönicke S. , Hahn V. , Horn R. , Grone I. , Brahm L. , Schnabl H. , Friedt W. 
Published: April 2004

Abstract Sclerotinia sclerotiorum is considered the most devastating pathogen of sunflower grown in humid environments. In this study, progenies of partial hybrids between Helianthus maximiliani, a wild species that has been shown to be resistant to S. sclerotiorum, and H. annuus were characterized by amplified fragment length polymorphism (AFLP) analysis to identify whether there are introgressions from H. maximiliani into the cultivated sunflower at the molecular level. Wild species‐specific fragments as well as fragments not found in either parent were detected. Progenies tended to cluster together according to the original partial hybrids in the dendrogram by the use of bootstrap procedures. The progenies were studied for their reaction to S. sclerotiorum using artificial inoculation of sunflower heads. Some of the progenies showed a higher level of resistance compared with resistant inbred lines. It was possible to identify two AFLP‐fragments which seem to be linked to Sclerotinia resistance.
Breeding for high yield and fibre quality in coloured cotton
Authors: Dutt Y. , Wang X. D. , Zhu Y. G. , Li Y. Y. 
Published: April 2004

AbstractIn the present study, three types of coloured fibre cottons, i.e. white, brown and green, were compared for their fibre quality and yield. The comparison of fibre quality suggested that coloured fibre cotton was inferior as compared with white fibre cotton. To understand the effect of cellulose, mineral elements [nitrogen (N), phosphorus (P) and potassium (K)] and pH of fibre cells on the quality of fibre, these components were studied at different fibre cell developed stages in all three fibre cotton types. The cellulose content is closely associated with the quality of fibre. The higher fibre quality of white fibre cotton might be the result of the high cellulose content in it compared with coloured fibre cotton. A rapid and slow decrease in pH in white and coloured cottons, respectively, might have some effects on fibre elongation. Among the mineral contents, potassium is positively correlated with the fibre quality traits. The pigment development patterns in brown and green fibre cottons are not similar. In green fibre cotton it takes more time to deepen in colour as compared with brown fibre cotton. Possible strategies for the improvement in quality of coloured fibre cotton are discussed. The results of heterosis studies in coloured fibre cotton suggest that heterosis could improve yield and quality of coloured fibre cotton. In the present study, the hybrids between ZJU12A x ZJU05R and ZJU18A x ZJU01R, having an acceptable lint colour types plus better fibre quality and high yield performance, may be exploited further for their heterotic advantages.
Identification of resistance gene analogue markers closely linked to wheat powdery mildew resistance gene Pm31
Authors: XIE C. , SUN Q. , NI Z. , YANG T. , NEVO E. , FAHIMA T. 
Published: April 2004

AbstractSpecific oligonucleotide primers, designed for the sequences of known plant disease resistance genes, were used to amplify resistance gene analogues (RGAs) from wheat genomic DNA. This method was applied in a bulked segregant analysis to screen for the RGA markers linked to the powdery mildew resistance gene Pm31, introgressed into common wheat from wild emmer. Two RGA markers (RGA200 and RGA390) were found to be closely linked to Pm31 and completely co‐segregating with the marker allele of Xpsp3029 linked to Pm31, with a genetic distance of 0.6 cM. These two RGA markers were then integrated into the formerly established microsatellite map of Pm31 region. The result showed the effectiveness of the RGA approach for developing molecular markers linked to disease resistance genes and demonstrated the efficiency of denaturing polyacrylamide‐gel electrophoresis for detecting polymerase chain reaction polymorphism.
Effect of PI‐HAART on the prevalence of oral lesions in HIV‐1 infected patients. A Greek study
Authors: Nicolatou‐Galitis O , Velegraki A , Paikos S , Economopoulou P , Stefaniotis T , Papanikolaou IS , Kordossis T 
Published: April 2004

Objective:  To investigate the association between the prevalence of oral lesions and highly active antiretroviral therapy (HAART) including a protease inhibitor (PI).Design:  Prospective study.Patients and methods:  Ninety‐five consecutive patients, attending an AIDS Unit, in Greece entered the study. Fourty‐four patients were receiving PI‐ HAART, 14 patients were on double antiretroviral therapy, and 37 patients were not receiving antiretroviral therapy at the time of oral examination.Oral lesions were diagnosed by established presumptive clinical criteria.Main outcome measures:  Oral lesions were scored. CD4 counts and viral load were determined and related to the prevalence of oral lesions.Results:  Oral lesions, and specifically oral candidiasis, were significantly reduced (P < 0.001) in patients receiving PI‐HAART. Oral lesions were significantly increased in patients with CD4 counts <200 cells μl−1 and viral load >20 000 copies ml−1 (P < 0.001). The percentage of patients, with lesions on PI‐HAART, and with CD4 < 200 and viral load >20 000 was 1.5 times lower (37.5%vs 58.8%, P < 0.001) than that of patients not receiving antiretroviral therapy, but with similar immune and viremic status.Conclusions:  Oral lesions were significantly reduced in patients on PI‐HAART. A direct anticandidal effect of PI was suggestive and seemed to have accounted, beyond the HAART‐related immune reconstitution, for the reduction of candidiasis and all other oral lesions.
Is the incidence of oral and pharyngeal cancer increasing in Finland? An epidemiological study of 17 383 cases in 1953–1999
Authors: Tarvainen L , Suuronen R , Lindqvist C , Malila N 
Published: April 2004

Objective:  The aim of this study was to describe the occurrence of oral and pharyngeal cancer in Finland over the last half century.Materials and methods:  The study included all lip, oral and pharyngeal cancer cases diagnosed in Finland and reported to the nation‐wide Finnish Cancer Registry between 1953 and 1999.Results:  The study comprised 17 383 new cancer cases: 11 666 in males and 5717 in females. Of these, 83% were squamous cell carcinomas. By the end of the study, 1999, the mean age at diagnosis had increased to 63 years for males and 67 for females. The age‐adjusted incidence of oral and pharyngeal cancer decreased in males from 12.5 per 105 to 8.4 per 105 while it increased in females from 3.0 per 105 to 3.9 per 105. This was because of a decrease in lip cancer incidence in males, while the incidence of tongue, mouth and salivary gland cancers increased in both genders. The annual number of new oral cancer cases increased, however, in both genders.Conclusion:  The incidence of lip cancer decreased in males, probably because of a decrease in smoking and in outdoor work. The incidence of intra‐oral cancers increased in both genders, possibly because of increased alcohol consumption.
Isolation and characterization of subgingival staphylococci from periodontitis patients and controls
Authors: Murdoch FE , Sammons RL , Chapple ILC 
Published: April 2004

Objectives:  To isolate and characterize subgingival staphylococci from patients with periodontal disease and from periodontally healthy controls, to evaluate the periodontal environment as a potential source for systemic staphylococcal infections.Methods:  PeriopaperTM strips were used to isolate subgingival staphylococci from 28 patients with chronic periodontitis and 28 periodontally healthy age and sex‐matched controls. Staphylococci were identified by microbiological methods and antibiotic resistance profiles determined.Results:  Staphylococci were isolated from 54% diseased subgingival and 43% healthy subgingival sites in over 50% periodontitis patients and from 29% healthy subgingival sites in 54% controls. No significant differences in the frequency of isolation or numbers of staphylococci isolated from diseased and healthy sites were noted. Staphylococcus epidermidis was the predominant oral species. Seventy per cent (115 of 165) of all isolates were penicillin‐resistant.Conclusions:  Subgingival staphylococci are present in both periodontitis patients and controls. In periodontitis there is an increased risk of bacteraemia because of the increased dentogingival surface area. The dental and periodontal health of patients at risk from haematogenous infections should therefore be maintained at a high level. Antibiotic resistance profiles of the oral staphylococcal isolates suggest that amoxicillin may no longer be a suitable antibiotic for prophylaxis against systemic infections such as prosthetic valve endocarditis.
Autoantibodies Profile in the Sera of Patients with Sjogren]s Syndrome: The ANA Evaluation—A Homogeneous, Multiplexed System
Authors: Gilburd Boris , Abu-Shakra Mahmoud , Shoenfeld Yehuda , Giordano Andrea , Bocci Elena Bartoloni , delle Monache Francesco , Gerli Roberto 
Published: April 2004

Background: Flow‐based, multiplex bead arrays (MBA)
have been
developed for a variety of applications including the detection of antibodies
to extractable nuclear antigens (ENA). It offers a rapid and sensitive
method to assess multiple analyses in a single tube/well.Purpose: To evaluate the Athena Multi‐Lyte ANA Test
System utilizes
Luminex Corporation′s MBA technology for the detection of antinuclear
antibodies (ANA) and
ENA antibodies in the sera of patients with Sjogren′s syndrome (SS).Methods: MBA assay was used to detect ANA and
ENA antibodies in the
sera of 37 patients with SS and 96 sera from healthy subjects.Results: All patients were women. Their mean age was 48.7 years
and the mean disease duration was 7.27 years. ANA was found in 3 (3%)
sera of healthy subjects by the AtheNA system and in 2 (2%) sera by the
ELISA kit. A 99% concordance between the 2 assays was found. A 94.6%
concordance between
the 2 assays was found by testing the sera of patients with SS for ANA.By the AtheNA system, none of the sera of 37
patients with SS had autoantibodies reacting with Sm, Jo‐1, dsDNA
or histones. Anti‐RNP antibody was found in 5.4% of the sera and 2.7%
of the sera reacted with Scl‐70 and histones. Anti‐SS/A and anti‐SS/B were
identified in 84 and 76% of the sera, respectively.Conclusion: The AtheNa Multi‐Lyte ANA Test System offers
a sensitive and specific result for the detection of ANA and
ENA antibodies in the sera of patients with SS.
SCANMS: adjusting for multiple comparisons in sliding window neutrality tests
Authors: Ardell David H. 
Published: April 2004

Abstract
Summary: A Perl utility called SCANMS was written that operates on parametric bootstrap data generated by Hudson's simulator MS. SCANMS simulates sliding window analysis of Tajima's D or Fu and Li's D* or F* over the replicates and generates the empirical joint distribution of window minima and maxima. This distribution may then be used to calculate achieved significance values or significance cutoffs that account for multiple comparisons in sliding window analysis of real data.
Availability: SCANMS is available free of charge under the terms of the Academic Free License 2.0 and may be downloaded from http://www.lcb.uu.se/~dave/SCANMS
ProMode: a database of normal mode analyses on protein molecules with a full-atom model
Authors: Wako Hiroshi , Kato Masaki , Endo Shigeru 
Published: April 2004

Abstract
Motivation: Although information from protein dynamics simulation is important to understand principles of architecture of a protein structure and its function, simulations such as molecular dynamics and Monte Carlo are very CPU-intensive. Although the ability of normal mode analysis (NMA) is limited because of the need for a harmonic approximation on which NMA is based, NMA is adequate to carry out routine analyses on many proteins to compute aspects of the collective motions essential to protein dynamics and function. Furthermore, it is hoped that realistic animations of the protein dynamics can be observed easily without expensive software and hardware, and that the dynamic properties for various proteins can be compared with each other.
Results: ProMode, a database collecting NMA results on protein molecules, was constructed. The NMA calculations are performed with a full-atom model, by using dihedral angles as independent variables, faster and more efficiently than the calculations using Cartesian coordinates. In ProMode, an animation of the normal mode vibration is played with a free plug-in, Chime (MDL Information Systems, Inc.). With the full-atom model, the realistic three-dimensional motions at an atomic level are displayed with Chime. The dynamic domains and their mutual screw motions defined from the NMA results are also displayed. Properties for each normal mode vibration and their time averages, e.g. fluctuations of atom positions, fluctuations of dihedral angles and correlations between the atomic motions, are also presented graphically for characterizing the collective motions in more detail.
Availability: http://promode.socs.waseda.ac.jp
TIP: protein backtranslation aided by genetic algorithms
Authors: Moreira Andrés , Maass Alejandro 
Published: April 2004

Abstract
Summary: Several applications require the backtranslation of a protein sequence into a nucleic acid sequence. The degeneracy of the genetic code makes this process ambiguous; moreover, not every translation is equally viable. The usual answer is to mimic the codon usage of the target species; however, this does not capture all the relevant features of the ‘genomic styles’ from different taxa. The program TIP ‘ Traducción Inversa de Proteínas’) applies genetic algorithms to improve the backtranslation, by minimizing the difference of some coding statistics with respect to their average value in the target.
Availability: http://www.cmm.uchile.cl/genoma/tip/
Fragment assembly with short reads
Authors: Chaisson Mark , Pevzner Pavel , Tang Haixu 
Published: April 2004

Abstract
Motivation: Current DNA sequencing technology produces reads of about 500–750 bp, with typical coverage under 10×. New sequencing technologies are emerging that produce shorter reads (length 80–200 bp) but allow one to generate significantly higher coverage (30× and higher) at low cost. Modern assembly programs and error correction routines have been tuned to work well with current read technology but were not designed for assembly of short reads.
Results: We analyze the limitations of assembling reads generated by these new technologies and present a routine for base-calling in reads prior to their assembly. We demonstrate that while it is feasible to assemble such short reads, the resulting contigs will require significant (if not prohibitive) finishing efforts.
Availability: Available from the web at http://www.cse.ucsd.edu/groups/bioinformatics/software.html
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases
Authors: Swertz Morris A. , de Brock E. O. (Bert) , van Hijum Sacha A. F. T. , de Jong Anne , Buist Girbe , Baerends Richard J. S. , Kok Jan , Kuipers Oscar P. , Jansen Ritsert C. 
Published: April 2004

Abstract
Motivation: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory.
Results: Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects.
Availability: http://www.molgenis.nl
Gene annotation from scientific literature using mappings between keyword systems
Authors: Pérez Antonio J. , Perez-Iratxeta Carolina , Bork Peer , Thode Guillermo , Andrade Miguel A. 
Published: April 2004

Abstract
Motivation: The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied to gene data (e.g. searching a gene database for sequences related to a particular biological process). However, the association of keywords to genes or protein sequences is a difficult process that ultimately implies examination of the literature related to a gene.
Results: To support this task, we present a procedure to derive keywords from the set of scientific abstracts related to a gene. Our system is based on the automated extraction of mappings between related terms from different databases using a model of fuzzy associations that can be applied with all generality to any pair of linked databases. We tested the system by annotating genes of the SWISS-PROT database with keywords derived from the abstracts linked to their entries (stored in the MEDLINE database of scientific references). The performance of the annotation procedure was much better for SWISS-PROT keywords (recall of 47%, precision of 68%) than for Gene Ontology terms (recall of 8%, precision of 67%).
Availability: The algorithm can be publicly accessed and used for the annotation of sequences through a web server at http://www.bork.embl.de/kat