bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for positive selection on Mycobacterium tuberculosis within patients
Authors: Tanaka Mark M 
Published: September 2004

Abstract
Background
While the pathogenesis and epidemiology of tuberculosis are well studied, relatively little is known about the evolution of the infectious agent Mycobacterium tuberculosis, especially at the within-host level. The insertion sequence IS6110 is a genetic marker that is widely used to track the transmission of tuberculosis between individuals. This and other markers may also facilitate our understanding of the disease within patients.

Results
This article presents three lines of evidence supporting the action of positive selection on M. tuberculosis within patients. The arguments are based on a comparison between empirical findings from molecular epidemiology, and population genetic models of evolution. Under the hypothesis of neutrality of genotypes, 1) the mutation rate of the marker IS6110 is unusually high, 2) the time it takes for substitutions to occur within patients is too short, and 3) the amount of polymorphism within patients is too low.

Conclusions
Empirical observations are explained by the action of positive selection during infection, or alternatively by very low effective population sizes. I discuss the possible roles of antibiotic treatment, the host immune system and extrapulmonary dissemination in creating opportunities for positive selection.
Characterization of a novel large deletion and single point mutations in the BRCA1gene in a Greek cohort of families with suspected hereditary breast cancer
Authors: Belogianni Ioulia , Apessos Angela , Mihalatos Markos , Razi Evangelia , Labropoulos Stefanos , Petounis Andreas , Gaki Vasiliki , Keramopoulos Antonios , Pandis Nikos , Kyriacou Kyriacos , Hadjisavvas Andreas , Kosmidis Paris , Yannoukakos Drakoulis , Nasioulas Georgios 
Published: September 2004

Abstract
Background
Germline mutations in BRCA1 and BRCA2 predispose to breast and ovarian cancer. A multitude of mutations have been described and are found to be scattered throughout these two large genes. We describe analysis of BRCA1 in 25 individuals from 18 families from a Greek cohort.

Methods
The approach used is based on dHPLC mutation screening of the BRCA1 gene, followed by sequencing of fragments suspected to carry a mutation including intron – exon boundaries. In patients with a strong family history but for whom no mutations were detected, analysis was extended to exons 10 and 11 of the BRCA2 gene, followed by MLPA analysis for screening for large genomic rearrangements.

Results
A pathogenic mutation in BRCA1 was identified in 5/18 (27.7 %) families, where four distinct mutations have been observed. Single base putative pathogenic mutations were identified by dHPLC and confirmed by sequence analysis in 4 families: 5382insC (in two families), G1738R, and 5586G > A (in one family each). In addition, 18 unclassified variants and silent polymorphisms were detected including a novel silent polymorphism in exon 11 of the BRCA1 gene. Finally, MLPA revealed deletion of exon 20 of the BRCA1 gene in one family, a deletion that encompasses 3.2 kb of the gene starting 21 bases into exon 20 and extending 3.2 kb into intron 20 and leads to skipping of the entire exon 20. The 3' breakpoint lies within an AluSp repeat but there are no recognizable repeat motifs at the 5' breakpoint implicating a mechanism different to Alu-mediated recombination, responsible for the majority of rearrangements in the BRCA1 gene.

Conclusions
We conclude that a combination of techniques capable of detecting both single base mutations and small insertions / deletions and large genomic rearrangements is necessary in order to accurately analyze the BRCA1 gene in patients at high risk of carrying a germline mutation as determined by their family history. Furthermore, our results suggest that in those families with strong evidence of linkage to the BRCA1 locus in whom no point mutation has been identified re-examination should be carried out searching specifically for genomic rearrangements.
Microarrays in ecological research: A case study of a cDNA microarray for plant-herbivore interactions
Authors: Held Matthias , Gase Klaus , Baldwin Ian T 
Published: September 2004

Abstract
Background
Microarray technology allows researchers to simultaneously monitor changes in the expression ratios (ERs) of hundreds of genes and has thereby revolutionized most of biology. Although this technique has the potential of elucidating early stages in an organism's phenotypic response to complex ecological interactions, to date, it has not been fully incorporated into ecological research. This is partially due to a lack of simple procedures of handling and analyzing the expression ratio (ER) data produced from microarrays.

Results
We describe an analysis of the sources of variation in ERs from 73 hybridized cDNA microarrays, each with 234 herbivory-elicited genes from the model ecological expression system, Nicotiana attenuata, using procedures that are commonly used in ecologic research. Each gene is represented by two independently labeled PCR products and each product was arrayed in quadruplicate. We present a robust method of normalizing and analyzing ERs based on arbitrary thresholds and statistical criteria, and characterize a "norm of reaction" of ERs for 6 genes (4 of known function, 2 of unknown) with different ERs as determined across all analyzed arrays to provide a biologically-informed alternative to the use of arbitrary expression ratios in determining significance of expression. These gene-specific ERs and their variance (gene CV) were used to calculate array-based variances (array CV), which, in turn, were used to study the effects of array age, probe cDNA quantity and quality, and quality of spotted PCR products as estimates of technical variation. Cluster analysis and a Principal Component Analysis (PCA) were used to reveal associations among the transcriptional "imprints" of arrays hybridized with cDNA probes derived from mRNA from N. attenuata plants variously elicited and attacked by different herbivore species and from three congeners: N. quadrivalis, N. longiflora and N. clevelandii. Additionally, the PCA revealed the contribution of individual gene ERs to the associations among arrays.

Conclusions
While the costs of 'boutique' array fabrication are rapidly declining, familiar methods for the analysis of the data they create are still missing. The case history illustrated here demonstrates the ease with which this powerful technology can be adapted to ecological research.
Mitoxantrone pleurodesis to palliate malignant pleural effusion secondary to ovarian cancer
Authors: Barbetakis Nikolaos , Vassiliadis Michalis , Kaplanis Konstantinos , Valeri Rosalia , Tsilikas Christodoulos 
Published: September 2004

Abstract
Background
Advanced ovarian cancer is the leading non-breast gynaecologic cause of malignant pleural effusion. Aim of this study was to assess the efficacy of mitoxantrone sclerotherapy as a palliative treatment of malignant pleural effusions due to ovarian cancer.

Methods
Sixty women with known ovarian cancer and malignant recurrent symptomatic pleural effusion were treated with chest tube drainage followed by intrapleural mitoxantrone sclerotherapy. Survival, complications and response to pleurodesis were recorded. The data are expressed as the mean ± SEM and the median.

Results
The mean age of the entire group was 64 ± 11,24 years. The mean interval between diagnosis of ovarian cancer and presentation of the effusion was 10 ± 2,1 months. Eighteen patients (30%) had pleural effusion as the first evidence of recurrence. The mean volume of effusion drained was 1050 ± 105 ml and chest tube was removed within 4 days in 75% of patients. There were no deaths related to the procedure. Side effects of chemical pleurodesis included fever (37–38,5°C) chest pain, nausea and vomiting. At 30 days among 60 treated effusions, there was an 88% overall response rate, including 41 complete responses and 12 partial responses. At 60 days the overall response was 80% (38 complete responses and 10 partial responses). The mean survival of the entire population was 7,5 ± 1,2 months.

Conclusions
Mitoxantrone is effective in the treatment of malignant pleural effusion secondary to ovarian cancer without causing significant local or systemic toxicity.
Single group study to evaluate the feasibility and complications of radiofrequency ablation and usefulness of post treatment position emission tomography in lung tumours
Authors: Kang Shijun , Luo Rongcheng , Liao Wangjun , Wu Hubing , Zhang Xuelin , Meng Yuru 
Published: September 2004

Abstract
Background
There is genuine need to develop interventional treatment options for management of lung tumors. Radiofrequency ablation (RFA) is one such alternative being promoted to treat lung tumors recently. Larger studies should help define RFA's further development. Furthermore fluorodeoxyglucose positron emission tomography (PET) has been reported to be an accurate indicator of treatment response in variety of tumors. This study focuses on the evaluating the feasibility of RFA and usefulness of PET scan in lung tumors after RFA procedure.

Patients and methods
Between November 1999 and May 2002, 50 patients with primary or metastasis pulmonary tumors underwent RFA procedure. The electrode was guided to the target areas using computerized tomography (CT). Tumors smaller than 3.5 cm were given single RFA, while tumors larger than 3.5 cm received RFA to multiple sites. Maximum 4 lesions or 6 target areas were treated during one operating procedure. Whole body and/or lung PET images were acquired; identical site CT images and chest X-ray were taken 1 week before and after RFA.

Results
Of the 50 patients, 17 had single lesions while rest had multiple lesions. Tumors smaller than 3.5 cm were completely dissipated after RFA. In tumors larger than 3.5 cm, the part within 3.5 cm diameter dissipated. While CT showed that tumor image became larger 1 to 2 weeks after RFA procedure. PET demonstrated tumor destruction in 70% cases, compared to 38% in CT.

Conclusion
The present study shows RFA to be safe and effective treatment option for lung tumors. PET is superior to CT in evaluation the effectiveness of RFA treatment shortly after the procedure.
Retroviruses 2004: Review of the 2004 Cold Spring Harbor Retroviruses conference
Authors: Freed Eric O , Ross Susan R 
Published: September 2004

AbstractFor the past several decades, retrovirologists from around the world have gathered in late May at the Cold Spring Harbor Laboratories in New York to present their studies in formal talks and posters, and to discuss their ongoing research informally at the bar or on the beach. As organizers of the 2004 Cold Spring Harbor Retroviruses Conference, we have been asked by the editors of Retrovirology to prepare a review of the meeting for publication on-line. Our goal in this review is not to provide a detailed description of data presented at the meeting but rather to highlight some of the significant developments reported this year. The review is structured in a manner that parallels the organization of the meeting; beginning with the entry phase of the replication cycle, proceeding with post-entry events, assembly and release, integration, reverse transcription, pathogenesis/host factors, RNA-related events (transcription, processing, export, and packaging) and finishing with antivirals. While the most striking developments this year involved post-entry events and assembly/release, significant progress was made towards elucidating a number of aspects of the retroviral replication cycle.
Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillusspecies
Authors: Rey Michael W , Ramaiya Preethi , Nelson Beth A , Brody-Karpin Shari D , Zaretsky Elizabeth J , Tang Maria , de Leon Alfredo Lopez , Xiang Henry , Gusti Veronica , Clausen Ib Groth , Olsen Peter B , Rasmussen Michael D , Andersen Jens T , Jørgensen Per L , Larsen Thomas S , Sorokin Alexei , Bolotin Alexander , Lapidus Alla , Galleron Nathalie , Ehrlich S Dusko , Berka Randy M 
Published: September 2004

Abstract
Background
Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium that is used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. This species is closely related to the well studied model organism Bacillus subtilis, and produces an assortment of extracellular enzymes that may contribute to nutrient cycling in nature.

Results
We determined the complete nucleotide sequence of the B. licheniformis ATCC 14580 genome which comprises a circular chromosome of 4,222,336 base-pairs (bp) containing 4,208 predicted protein-coding genes with an average size of 873 bp, seven rRNA operons, and 72 tRNA genes. The B. licheniformis chromosome contains large regions that are colinear with the genomes of B. subtilis and Bacillus halodurans, and approximately 80% of the predicted B. licheniformis coding sequences have B. subtilis orthologs.

Conclusions
Despite the unmistakable organizational similarities between the B. licheniformis and B. subtilis genomes, there are notable differences in the numbers and locations of prophages, transposable elements and a number of extracellular enzymes and secondary metabolic pathway operons that distinguish these species. Differences include a region of more than 80 kilobases (kb) that comprises a cluster of polyketide synthase genes and a second operon of 38 kb encoding plipastatin synthase enzymes that are absent in the B. licheniformis genome. The availability of a completed genome sequence for B. licheniformis should facilitate the design and construction of improved industrial strains and allow for comparative genomics and evolutionary studies within this group of Bacillaceae.
Using mesoscale model winds for correcting wind‐drift errors in radar estimates of surface rainfall
Authors: Mittermaier Marion P. , Hogan Robin J. , Illingworth Anthony J. 
Published: September 2004

AbstractFor operational radars at middle and high latitudes, even the lowest beam of a scan sequence may be above the melting layer for a considerable proportion of the total range. This means that surface rainfall estimates are inferred from measurements made in the snow and ice. Snow and ice are more susceptible to wind drift than rain because of the low fall speed of around 1 m s−1. Sampling these wind‐induced fall‐streak patterns results in a displacement of the radar‐rainfall field when compared to ground measurements. To date wind‐drift corrections have only been attempted in the rain, but corrections of around 2 km are generally smaller than the resolution of the grid on which the rainfall field is reported. Observational evidence from this study shows fall streaks in the snow can lead to displacements of the order of 10–20 km—a significant effect, especially in colder climates and seasons.In this paper a method for calculating and applying a wind‐drift correction between the top of the fall streak and the bright‐band height is presented. The forecast wind profile from the mesoscale version of the UK Met Office Unified Model is used to calculate the vertical shear of the horizontal wind. We assume the shear and the fall speed in the layer are constant. Results show that the method is able to reproduce observed displacements from high‐resolution radar data in the range–height plane. Assessing the effect of applying the method in plan view shows an improvement in the placement of rainfall at the ground, reflected by an increase in the calculated skill scores. The displacement can be corrected to within 20%. This also shows that whereas wind‐drift corrections in the rain have been found to be insignificant, corrections in the snow are not. Applying a wind‐drift correction also appears to reduce the variability of vertical profiles of reflectivity (VPR) when they are extracted along a fall‐streak path, and lead to a smaller reflectivity lapse rate locally. This would suggest that at least part of the reported variability in VPRs is due to wind effects. Copyright © 2004 Royal Meteorological Society
The shaman reborn in cyberspace, or evolving magico-spiritual techniques of consciousness-making
Authors: Eagar Manie 
Published: September 2004

With the expansion of consciousness comes new ways of seeing reality. The hypercontextual pretexts, contexts and subtexts created by the new technologies of virtual, immersive and cyber realities create boundaryless experiences that are analogous to the archaic techniques evolved through shamanic journeys designed to transcend all human boundaries.The magico-spiritual imagination, far from disappearing in our supposedly secular age, continues to feed the utopian dreams, apocalyptic visions, digital phantasms, and alien obsessions that populate today’s ‘technological unconscious’. The language and ideas of the information society have slipped into and even transformed the myriad worlds of contemporary spirituality. What is emerging is a networked framework for grappling with some of the impulses that are currently tearing us apart: spirit and the machine, modernity and nihilism, technology and the human. ‘We find ourselves trapped on a cyborg sandbank, caught between the old, smouldering campfire stories and the new networks of programming and control’ (Davis 1998: 131). We are ‘beached’ between the archaic sea of our magico-spiritual ancestors, freshly emerged from our proto-modern past, and spawned into the postmodern reality of fragmented selves, networked options, downloadable digitized consumerware and ‘technologies of ecstacy’.
Diurnal Differences in the Innermost Surface of the S2 Layer in Differentiating Tracheids of Cryptomeria japonica Corresponding to a Light-Dark Cycle
Authors: Hosoo Y. , Yoshida M. , Imai T. , Okuyama T. 
Published: September 2004

Summary
This paper describes the effect of light on the diurnal change in the innermost surface of developing
secondary walls. Cryptomeria japonica D. Don saplings were grown in two growth chambers, in
which temperature and relative humidity were kept constant and the light-dark phase of the photoperiod
varied. One chamber reproduced the natural light-dark phase, while the other reversed it.
Samples of differentiating xylem were collected during the dark period when the tangential strain,
used as an index of volumetric changes in differentiating cells, was high, and during the light period
when the tangential strain was low. The innermost surface of developing secondary walls in differentiating
tracheids was observed by field emission scanning electron microscopy. In the specimens
collected during the dark period, amorphous material was observed and the cell wall surface was
immunogold-labeled with an anti-glucomannan antiserum. In the specimens collected during the
light period, cellulose microfibrils were clearly evident, and amorphous material and immunogold
labeling were rarely observed. These results demonstrate that the diurnal changes in the innermost
surface of developing secondary walls correspond to the light-dark cycle over 24 h.
Delignification Mechanism during High-Boiling Solvent Pulping Part 3. Structural Changes in Lignin Analyzed by 13C-NMR Spectroscopy
Authors: Kishimoto T. , Ueki A. , Sano Y. 
Published: September 2004

Summary
Milled wood lignin as well as wood meal from todo fir (Abies sachalinensis MAST) was treated
with 70% aqueous 1,4-butanediol solution at 220°C without acid catalyst in order to elucidate the
delignification mechanism during high-boiling solvent (HBS) pulping. HBS lignin was recovered
from black liquor by precipitation, and was subjected to gel permeation chromatography and
quantitative 13C-NMR study. The average molecular weight of MWL decreased. The content of
phenolic hydroxyl groups in MWL increased from 0.28 to 0.68/OMe. The decrease in the content
of β-O-4 substructures was evident, which may be attributed to the homolytic cleavage of phenolic
β-aryl ethers. The changes in the content of β-5 and β-β substructures were rather small. The benzyl
ether formation of β-O-4 structures with 1,4-butanediol was also confirmed by 13C-NMR. However,
the signals corresponding to Hibbert's ketones were not observed, which suggests that acidolysis
was not an important degradation pathway during HBS pulping.
Delignification of Bamboo (Bambusa procera acher) Part 2. Characterisation of Kraft Black Liquors from Different Cooking Conditions
Authors: Vu T. H. M. , Alén R. , Pakkanen H. 
Published: September 2004

Summary
Bamboo (Bambusa procera acher) was delignified in a laboratory-scale digester by conventional
kraft pulping under varying conditions. Pulps with kappa numbers in the range 12.9–56.3 and viscosities
in the range 871–1319 ml g−1 were obtained. The chemical composition of the corresponding
black liquors was analysed with respect to their main organic and inorganic constituents. The
results indicated that the dry solids of the black liquor contained 40–44% lignin, 20–24% aliphatic
carboxylic acids, 4–7% polysaccharides and the residual matter (about 30%) consisted mainly
of inorganic constituents. Of the monosaccharide moieties detected in the polysaccharides, xylose
was predominant, suggesting that xylan was a major hemicellulose constituent in the black liquor.
The effect of effective alkali, sulphidity and H-factor of the cook on the formation of the individual
constituents in the black liquor is also discussed.
The Effect of Magnesium Ions and Chelants on Peroxide Bleaching
Authors: Lapierre L. , Berry R. , Bouchard J. 
Published: September 2004

Summary
We recently reported that during peroxide bleaching, magnesium is substantially more effective
when in a complex form with either pulp or a chelant. We also speculated that different magnesium
forms affected the catalytic activity of transition metals towards peroxide decomposition to
different degrees. As oxygen-delignified pulps still containing lignin were used, it was impossible
to separate the catalytic peroxide decomposition by transition metals from the peroxide reaction
with lignin, and thus to determine where in the pulp-liquor system magnesium or chelants, or both,
were deactivating transition metals. In this paper, we studied the peroxide decomposition kinetics
with different modes of addition of the P-stage chemicals in the presence of fully-bleached kraft
pulps which are virtually lignin-free, in alkaline filtrates, in P-stage filtrate and in water. We found
that most of the peroxide decomposition occurring during a P-stage applied to chemical pulps
takes place through interaction with transition metals in the pulp rather than with transition metals
in the soluble bulk phase. We also concluded that in any component of a peroxide bleaching
system, magnesium is extremely efficient at reducing the rate of peroxide decomposition, while a
chelant becomes more valuable when complexing magnesium.
Assessment of Wood-Cement Compatibility: A New Approach
Authors: Karade S. R. , Irle M. , Maher K. 
Published: September 2004

Summary
The influence of wood upon the setting of cement is generally assessed by conducting semi-adiabatic
hydration tests. The existing methods to quantify wood-cement compatibility are based on
the maximum hydration temperature (Tmax
), the time (tmax
) to reach it or the heat evolved in a
specified period. Results obtained by these methods at higher wood-cement ratios are not convincing
and show inconsistencies for various reasons. This paper discusses these reasons and suggests
an alternative method based on a maturity function. The results from the new calculation method
are compared with those of the existing methods and demonstrate the superiority of this new
method at higher wood-cement ratios.