bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical significance of minimal residual disease quantification in adult patients with standard-risk acute lymphoblastic leukemia
Authors: Brüggemann Monika , Raff Thorsten , Flohr Thomas , Gökbuget Nicola , Nakao Makoto , Droese Jo , Lüschen Silke , Pott Christiane , Ritgen Matthias , Scheuring Urban , Horst Heinz-August , Thiel Eckhard , Hoelzer Dieter , Bartram Claus R. , Kneba Michael ,   for the German Multicenter Study Group for Adult Acute Lymphoblastic Leukemia
Published: September 2005

AbstractAdult patients with acute lymphoblastic leukemia (ALL) who are stratified into the standard-risk (SR) group due to the absence of adverse prognostic factors relapse in 40% to 55% of the cases. To identify complementary markers suitable for further treatment stratification in SR ALL, we evaluated the predictive value of minimal residual disease (MRD) and prospectively monitored MRD in 196 strictly defined SR ALL patients at up to 9 time points in the first year of treatment by quantitative polymerase chain reaction (PCR). Frequency of MRD positivity decreased from 88% during early induction to 13% at week 52. MRD was predictive for relapse at various follow-up time points. Combined MRD information from different time points allowed definition of 3 risk groups (P < .001): 10% of patients with a rapid MRD decline to lower than 10-4 or below detection limit at day 11 and day 24 were classified as low risk and had a 3-year relapse rate (RR) of 0%. A subset of 23% with an MRD of 10-4 or higher until week 16 formed the high-risk group, with a 3-year RR of 94% (95% confidence interval [CI] 83%-100%). The remaining patients whose RR was 47% (31%-63%) represented the intermediate-risk group. Thus, MRD quantification during treatment identified prognostic subgroups within the otherwise homogeneous SR ALL population who may benefit from individualized treatment.
Mathematical design of prokaryotic clone-based microarrays
Authors: Pieterse Bart , Quirijns Elisabeth J , Schuren Frank HJ , van der Werf Mariët J 
Published: September 2005

Abstract
Background
Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. Since the generation of a genomic DNA library is a random process, it is beforehand uncertain which genes are represented. Nevertheless, the genome coverage of such an array, which depends on different variables like the insert size and the number of clones in the library, can be predicted by mathematical approaches. When applying the classical formulas that determine the probability that a certain sequence is represented in a DNA library at the nucleotide level, massive amounts of clones would be necessary to obtain a proper coverage of the genome.

Results
This paper describes the development of two complementary equations for determining the genome coverage at the gene level. The first equation predicts the fraction of genes that is represented on the array in a detectable way and cover at least a set part (the minimal insert coverage) of the genomic fragment by which these genes are represented. The higher this minimal insert coverage, the larger the chance that changes in expression of a specific gene can be detected and attributed to that gene. The second equation predicts the fraction of genes that is represented in spots on the array that only represent genes from a single transcription unit, which information can be interpreted in a quantitative way.

Conclusion
Validation of these equations shows that they form reliable tools supporting optimal design of prokaryotic clone-based microarrays.
Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data
Authors: Baty Florent , Bihl Michel P , Perrière Guy , Culhane Aedín C , Brutsche Martin H 
Published: September 2005

Abstract

Background
A recent publication described a supervised classification method for microarray data: Between Group Analysis (BGA). This method which is based on performing multivariate ordination of groups proved to be very efficient for both classification of samples into pre-defined groups and disease class prediction of new unknown samples. Classification and prediction with BGA are classically performed using the whole set of genes and no variable selection is required. We hypothesize that an optimized selection of highly discriminating genes might improve the prediction power of BGA.

Results
We propose an optimized between-group classification (OBC) which uses a jackknife-based gene selection procedure. OBC emphasizes classification accuracy rather than feature selection. OBC is a backward optimization procedure that maximizes the percentage of between group inertia by removing the least influential genes one by one from the analysis. This selects a subset of highly discriminative genes which optimize disease class prediction. We apply OBC to four datasets and compared it to other classification methods.

Conclusion
OBC considerably improved the classification and predictive accuracy of BGA, when assessed using independent data sets and leave-one-out cross-validation.

Availability
The R code is freely available [see Additional file 1] as well as supplementary information [see Additional file 2].
Genetic chimerism of Vitis viniferacv. Chardonnay 96 is maintained through organogenesis but not somatic embryogenesis
Authors: Bertsch Christophe , Kieffer Flore , Maillot Pascale , Farine Sibylle , Butterlin Gisèle , Merdinoglu Didier , Walter Bernard 
Published: September 2005

Abstract

Background
Grapevine can be a periclinal chimera plant which is composed at least of two distinct cell layers (L1, L2). When the cell layers of this plant are separated by passage through somatic embryogenesis, regenerated plants could show distinct DNA profiles and a novel phenotype which proved different from that of the parent plant.

Results
Genetically Chardonnay clone 96 is a periclinal chimera plant in which is L1 and L2 cell layers are distinct. Plants obtained via organogenesis through meristematic bulks are shown to be composed of both cell layers. However, plants regenerated through somatic embryogenesis starting from anthers or nodal explants are composed only of L1 cells. These somaclones do not show phenotypic differences to the parental clone up to three years after regeneration. Interestingly, the only somaclone showing an atypical phenotype (asymmetric leave) shows a genotypic modification.

Conclusion
These results suggest that the phenotype of Chardonnay 96 does not result from an interaction between the two distinct cell layers L1 and L2. If phenotype conformity is further confirmed, somatic embryogenesis will result in true-to-type somaclones of Chardonnay 96 and would be well suitable for gene transfer.
GB virus-C – a virus without a disease: We cannot give it chronic fatigue syndrome
Authors: Jones James F , Kulkarni Prasad S , Butera Salvatore T , Reeves William C 
Published: September 2005

Abstract

Background
Chronic fatigue syndrome (CFS) is an illness in search of an infectious etiology. GB virus-C (GBV-C) virus is a flavivirus with cell tropism and host defense induction qualities compatible with a role in producing the syndrome. The GBV-C genome is detectable in 4% of the population and 12% of the population is seropositive. The present study evaluated the association between infection with GBV and CFS.

Methods
We used a commercial EIA to detect antibodies against the GBV-C E2 protein and a quantitative real-time RT-PCR assay to detect active GBV-C infection. Sera were from a case control study of CFS in Atlanta, Georgia. The Fisher's exact two-tailed test was used for statistical analysis.

Results
Two of 12 CFS patients and one of 21 controls were seropositive for prior GBV-C infection and one control had viral RNA detected, indicating active infection. The results are not statistically different.

Conclusion
We found no evidence that active or past infection with GBV is associated with CFS.
Plasma lipid profiles and risk of cardiovascular disease in occupational lead exposure in Abeokuta, Nigeria
Authors: Ademuyiwa Oladipo , Ugbaja Regina Ngozi , Idumebor Florence , Adebawo Olugbenga 
Published: September 2005

Abstract
In order to investigate the effects of lead exposure on risk of cardiovascular disease during occupational exposure to this metal, plasma cholesterol and its fractions as high-density liporotein (HDL), low-density liporotein (LDL) and triglyceride were determined in various artisans in Abeokuta, Nigeria who have been shown to be occupationally exposed to lead and these were related to blood lead levels. Increased risk of cardiovascular disease was observed in the artisans. Total cholesterol in the artisans was between 1.5 and 2.0 times higher in the artisans than that present in controls while LDL cholesterol was between 1.6 and 2.4 times higher in the artisans when compared with control subjects [p < 0.001]. HDL cholesterol and triglyceride levels were not affected [p > 0.05]. A significant positive correlation was observed between blood lead and total cholesterol on one hand [r = 0.372; p = 3.0 × 10-5] and blood lead and LDL cholesterol on the other hand [r = 0.283; p = 0.001]. LDL/HDL cholesterol ratio was also higher in the artisans when compared with control. Blood pressure (systolic and diastolic) and other anthropometric parameters were not significantly different between the artisans and the control subjects [p > 0.05]. Results suggest that lead exposure increases cholesterol synthesis and transport to peripheral tissues whereas reverse cholesterol transport to the liver is not affected.
Using the intraoperative hand held probe without lymphoscintigraphy or using only dye correlates with higher sensory morbidity following sentinel lymph node biopsy in breast cancer: A review of the literature
Authors: Kim Suk Chul , Kim Dong Wook , Moadel Renee M , Kim Chun K , Chatterjee Samprit , Shafir Michail K , Travis Arlene , Machac Josef , Krynyckyi Borys R 
Published: September 2005

AbstractBackgroundThere are no studies that have directly investigated the incremental reduction in sensory morbidity that lymphoscintigraphy images (LS) and triangulated body marking or other skin marking techniques provide during sentinel lymph node biopsy (SLNB) compared to using only the probe without LS and skin marking or using only dye. However, an indirect assessment of this potential for additional sensory morbidity reduction is possible by extracting morbidity data from studies comparing the morbidity of SLNB to that of axillary lymph node dissection.MethodsA literature search yielded 13 articles that had data on sensory morbidity at specific time points on pain, numbness or paresthesia from SLNB that used radiotracer and probe or used only dye as a primary method of finding the sentinel node (SN). Of these, 10 utilized LS, while 3 did not utilize LS. By matching the data in studies not employing LS to the studies that did, comparisons regarding the percentage of patients experiencing pain, numbness/paresthesia after SLNB could be reasonably attempted at a cutoff of 9 months.ResultsIn the 7 studies reporting on pain after 9 months (> 9 months) that used LS (1347 patients), 13.8% of patients reported these symptoms, while in the one study that did not use LS (143 patients), 28.7% of patients reported these symptoms at > 9 months (P < 0.0001). In the 6 studies reporting on numbness and/or paresthesia at > 9 months that used LS (601 patients), 12.5% of patients reported these symptoms, while in the 3 studies that did not use LS (229 patients), 23.1% of patients reported these symptoms at > 9 months (P = 0.0002). Similar trends were also noted for all these symptoms at ≤ 9 months.ConclusionBecause of variations in techniques and time of assessing morbidity, direct comparisons between studies are difficult. Nevertheless at a minimum, a clear trend is present: having the LS images and skin markings to assist during SLNB appears to yield more favorable morbidity outcomes for the patients compared to performing SLNB with only the probe or performing SLNB with dye alone. These results are extremely pertinent, as the main reason for performing SLNB itself in the first place is to achieve reduced morbidity.
Smoking and reproduction: The oviduct as a target of cigarette smoke
Authors: Talbot Prue , Riveles Karen 
Published: September 2005

AbstractThe oviduct is an exquisitely designed organ that functions in picking-up ovulated oocytes, transporting gametes in opposite directions to the site of fertilization, providing a suitable environment for fertilization and early development, and transporting preimplantation embryos to the uterus. A variety of biological processes can be studied in oviducts making them an excellent model for toxicological studies. This review considers the role of the oviduct in oocyte pick-up and embryo transport and the evidence that chemicals in both mainstream and sidestream cigarette smoke impair these oviductal functions. Epidemiological data have repeatedly shown that women who smoke are at increased risk for a variety of reproductive problems, including ectopic pregnancy, delay to conception, and infertility. In vivo and in vitro studies indicate the oviduct is targeted by smoke components in a manner that could explain some of the epidemiological data. Comparisons between the toxicity of smoke from different types of cigarettes, including harm reduction cigarettes, are discussed, and the chemicals in smoke that impair oviductal functioning are reviewed.
Amino acid residues that are important for Hyal2 function as a receptor for jaagsiekte sheep retrovirus
Authors: Duh Fuh-Mei , Dirks Clarissa , Lerman Michael I , Miller A Dusty 
Published: September 2005

Abstract

Background
Infection by jaagsiekte sheep retrovirus (JSRV) and by enzootic nasal tumor virus (ENTV) depends on cell-surface expression of the virus entry receptor, hyaluronidase 2 (Hyal2). Human Hyal2 binds the envelope (Env) proteins of these viruses and is functional as a receptor, but Hyal2 from mice does not bind Env nor does it mediate entry of either virus. Here we have explored the amino acid determinants that account for the difference in receptor function.

Results
Analysis of human-mouse Hyal2 chimeric proteins showed that amino acid differences responsible for the difference in Hyal2 receptor activity were localized to the central third of Hyal2. Human Hyal2 mutants containing single or double amino acid replacements with the respective mouse amino acids were generated across this region and were assayed for activity. None of the single or double mutation reduced the receptor activity of human Hyal2 by more than 10-fold, whereas mouse Hyal2 activity is reduced 1,000-fold from that of human Hyal2. While the 3-dimensional structures of mammalian Hyal2 proteins are unknown, bee venom hyaluronidase shows significant amino acid similarity to human and mouse Hyal2 and its structure has been determined. Many mutations having the largest negative effects on human Hyal2 function mapped to a small region of the bee venom hyaluronidase close to but not overlapping the active site of the enzyme, suggesting that this site represents the binding site for Env. Analysis of synonymous and non-synonymous nucleotide substitutions in the coding sequences of multiple mammalian Hyal2 proteins shows that the proteins are undergoing strong selection for amino acid conservation. We found no evidence for positive selection of amino acid changes that might reflect evolution of mammalian hosts to resist JSRV or ENTV infection.

Conclusion
These results show that the greatly reduced receptor activity of mouse Hyal2 in comparison to that of human Hyal2 is determined by multiple amino acid changes acting in concert. In particular, no one amino acid change blocks infection. However, the most important amino acids map to a small patch on a predicted 3-dimensional Hyal2 structure, which may represent the binding site for Env.
Effect of a small molecule inhibitor of nuclear factor-κB nuclear translocation in a murine model of arthritis and cultured human synovial cells
Authors: Wakamatsu Kyoko , Nanki Toshihiro , Miyasaka Nobuyuki , Umezawa Kazuo , Kubota Tetsuo 
Published: September 2005

AbstractA small cell-permeable compound, dehydroxymethylepoxyquinomicin (DHMEQ), does not inhibit phosphorylation and degradation of IκB (inhibitor of nuclear factor-κB [NF-κB]) but selectively inhibits nuclear translocation of activated NF-κB. This study aimed to demonstrate the antiarthritic effect of this novel inhibitor of the NF-κB pathwayin vivoin a murine arthritis model andin vitroin human synovial cells. Collagen-induced arthritis was induced in mice, and after onset of arthritis the mice were treated with DHMEQ (5 mg/kg body weight per day). Using fibroblast-like synoviocyte (FLS) cell lines established from patients with rheumatoid arthritis (RA), NF-κB activity was examined by electrophoretic mobility shift assays. The expression of molecules involved in RA pathogenesis was determined by RT-PCR, ELISA, and flow cytometry. The proliferative activity of the cells was estimated with tritiated thymidine incorporation. After 14 days of treatment with DHMEQ, mice with collagen-induced arthritis exhibited decreased severity of arthritis, based on the degree of paw swelling, the number of swollen joints, and radiographic and histopathologic scores, compared with the control mice treated with vehicle alone. In RA FLS stimulated with tumor necrosis factor-α, activities of NF-κB components p65 and p50 were inhibited by DHMEQ, leading to suppressed expression of the key inflammatory cytokine IL-6, CC chemokine ligand-2 and -5, matrix metalloproteinase-3, intercellular adhesion molecule-1, and vascular cell adhesion molecule-1. The proliferative activity of the cells was also suppressed. This is the first demonstration of an inhibitor of NF-κB nuclear translocation exhibiting a therapeutic effect on established murine arthritis, and suppression of inflammatory mediators in FLS was thought to be among the mechanisms underlying such an effect.
Explicit equilibrium modeling of transcription-factor binding and gene regulation
Authors: Granek Joshua A , Clarke Neil D 
Published: September 2005

AbstractWe have developed a computational model that predicts the probability of transcription factor binding to any site in the genome. GOMER (generalizable occupancy model of expression regulation) calculates binding probabilities on the basis of position weight matrices, and incorporates the effects of cooperativity and competition by explicit calculation of coupled binding equilibria. GOMER can be used to test hypotheses regarding gene regulation that build upon this physically principled prediction of protein-DNA binding.
Attachment representations in mothers with abnormal illness behaviour by proxy
Authors: Adshead Gwen , Bluglass Kerry 
Published: September 2005

BackgroundAbnormal illness behaviour by proxy (also known as factitious illness by proxy or Munchhausen syndrome by proxy) is a type of child maltreatment, the origins of which are poorly understood.AimsTo describe attachment representations in a cohort of mothers demonstrating abnormal illness behaviour by proxy.MethodSixty-seven mothers who had shown this behaviour took part in a semi-structured interview assessing their attachment representations.ResultsOnly 12 mothers (18%) were rated secure in terms of their own childhood attachments. There was evidence of unresolved trauma or loss reactions in 40 mothers (60%). Eighteen mothers (27%) gave unusually disorganised and incoherent accounts of attachment relationships in their own childhoods. The frequency of these attachment categories is higher than in normal non-clinical samples.ConclusionsInsecure attachment is a risk factor for this type of child maltreatment. Therapeutic interventions could be offered in relation to unresolved traumatic stress or bereavement responses. Further study of similar groups, such as mothers with sick children or mothers with histories of traumatic experience, would be a useful next step.
Retirement intentions of consultant psychiatrists
Authors: Eagles John M. , Addie Karen , Brown Tom 
Published: September 2005

Aims and MethodThrough a postal survey we sought to determine the current retirement intentions of consultant psychiatrists working in Scotland. Consultants were asked their likely date of retirement, whether they might return as a locum and what might induce them to retire later.ResultsFull data were returned by 180 consultants. The mean planned age at retirement was 58.0 years. Women intended to retire significantly earlier than men. Most respondents could be persuaded to retire later through changes in services, conditions or job content; only 7% regarded their proposed retirement date as immutable.Clinical ImplicationsEarly retirement among consultants is likely to contribute to an even more seriously understaffed service. It is necessary to seek national and individual changes to the factors that give rise to early retirement in psychiatry.
Using special interest sessions to design and implement a fatigue management group for people with multiple sclerosis
Authors: Sutherland Jane K. , Cowan Paula 
Published: September 2005

Aims and MethodSpecial interest sessions are a means of developing additional clinical interests in higher specialist training. We investigated the educational value of developing a group treatment programme for people with multiple sclerosis as well as its benefits for participants.ResultsFeedback from those attending the groups indicated the programme was rated highly or very highly. There was a trend towards improvement in quality of life measures.Clinical ImplicationsThe group programme provided an excellent opportunity for shared interdisciplinary learning. The use of special interest sessions in psychiatry was important in building relationships with a department without direct psychiatric input and allowed the psychiatric trainee to acquire specific disease knowledge.
Increased Osteoclast Activity in the Presence of Increased Homocysteine Concentrations
Authors: Herrmann Markus , Widmann Thomas , Colaianni Graziana , Colucci Silvia , Zallone Alberta , Herrmann Wolfgang 
Published: September 2005

AbstractBackground: Increased plasma homocysteine (HCY) may be an independent risk factor for osteoporotic fractures and therefore may also adversely affect bone metabolism. We analyzed the effect of HCY on human osteoclast (OC) activity.Methods: We cultured peripheral blood mononuclear cells from 17 healthy male donors [median (SD) age, 30 (5) years] for 20 days with 25 μg/L macrophage-colony-stimulating factor (days 0–11), 20 μg/L receptor-activator of nuclear factor-κB ligand (days 6–20), and 4 different concentrations of HCY (0, 10, 50, and 100 μmol/L; days 0–20). For control purposes, cysteine and glutathione were tested in equimolar concentrations. OCs were identified as large, multinucleated cells with tartrate-resistant acid phosphatase (TRAP) activity and surface vitronectin receptors. We quantified OC activity by measuring TRAP activity. We analyzed cathepsin K (CP-K) activity in 9 donor samples and estimated the dentine-resorbing activity on standard dentine slices in 3 samples.Results: After 20 days of culture, most cells were fully differentiated OCs. TRAP activity increased with increasing HCY concentrations (P &lt;0.001). HCY concentrations of 10, 50, and 100 μmol/L stimulated TRAP activity by 20%, 15%, and 42%. Additionally, HCY stimulated CP-K activity (P = 0.005): in the presence of 100 μmol/L HCY, CP-K activity was ∼38% higher than in controls (P = 0.002). Bone-resorbing activity was significantly increased in cultures with 50 and 100 μmol/L HCY. Cysteine and glutathione significantly decreased TRAP and CP-K activity.Conclusions: Increased HCY concentrations specifically stimulate OC activity in vitro, suggesting a mechanistic role of HCY for bone resorption. Future studies clarifying the mechanistic role of increased HCY concentrations in osteoporosis could have interesting therapeutic implications.