bluuebunny/crossref_metadata_2025_split huggingface dataset:
A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example
Authors: Balandraud N , Gouret P , Danchin EGJ , Blanc M , Zinn D , Roudier J , Pontarotti P 
Published: November 2005

Abstract

Background
large scale and reliable proteins' functional annotation is a major challenge in modern biology. Phylogenetic analyses have been shown to be important for such tasks. However, up to now, phylogenetic annotation did not take into account expression data (i.e. ESTs, Microarrays, SAGE, ...). Therefore, integrating such data, like ESTs in phylogenetic annotation could be a major advance in post genomic analyses. We developed an approach enabling the combination of expression data and phylogenetic analysis. To illustrate our method, we used an example protein family, the peptidyl arginine deiminases (PADs), probably implied in Rheumatoid Arthritis.

Results
the analysis was performed as follows: we built a phylogeny of PAD proteins from the NCBI's NR protein database. We completed the phylogenetic reconstruction of PADs using an enlarged sequence database containing translations of ESTs contigs. We then extracted all corresponding expression data contained in EST database This analysis allowed us 1/ To extend the spectrum of homologs-containing species and to improve the reconstruction of genes' evolutionary history. 2/ To deduce an accurate gene expression pattern for each member of this protein family. 3/ To show a correlation between paralogous sequences' evolution rate and pattern of tissular expression.

Conclusion
coupling phylogenetic reconstruction and expression data is a promising way of analysis that could be applied to all multigenic families to investigate the relationship between molecular and transcriptional evolution and to improve functional annotation.
A non-parametric framework for estimating threshold limit values
Authors: Salanti Georgia , Ulm Kurt 
Published: November 2005

Abstract

Background
To estimate a threshold limit value for a compound known to have harmful health effects, an 'elbow' threshold model is usually applied. We are interested on non-parametric flexible alternatives.

Methods
We describe how a step function model fitted by isotonic regression can be used to estimate threshold limit values. This method returns a set of candidate locations, and we discuss two algorithms to select the threshold among them: the reduced isotonic regression and an algorithm considering the closed family of hypotheses. We assess the performance of these two alternative approaches under different scenarios in a simulation study. We illustrate the framework by analysing the data from a study conducted by the German Research Foundation aiming to set a threshold limit value in the exposure to total dust at workplace, as a causal agent for developing chronic bronchitis.

Results
In the paper we demonstrate the use and the properties of the proposed methodology along with the results from an application. The method appears to detect the threshold with satisfactory success. However, its performance can be compromised by the low power to reject the constant risk assumption when the true dose-response relationship is weak.

Conclusion
The estimation of thresholds based on isotonic framework is conceptually simple and sufficiently powerful. Given that in threshold value estimation context there is not a gold standard method, the proposed model provides a useful non-parametric alternative to the standard approaches and can corroborate or challenge their findings.
Hypothyroidism attenuates protein tyrosine nitration, oxidative stress and renal damage induced by ischemia and reperfusion: effect unrelated to antioxidant enzymes activities
Authors: Tenorio-Velázquez Verónica M , Barrera Diana , Franco Martha , Tapia Edilia , Hernández-Pando Rogelio , Medina-Campos Omar Noel , Pedraza-Chaverri José 
Published: November 2005

AbstractBackgroundIt has been established that hypothyroidism protects rats against renal ischemia and reperfusion (IR) oxidative damage. However, it is not clear if hypothyroidism is able to prevent protein tyrosine nitration, an index of nitrosative stress, induced by IR or if antioxidant enzymes have involved in this protective effect. In this work it was explored if hypothyroidism is able to prevent the increase in nitrosative and oxidative stress induced by IR. In addition the activity of the antioxidant enzymes catalase, glutathione peroxidase, and superoxide dismutase was studied. Control and thyroidectomized (HTX) rats were studied 24 h of reperfusion after 60 min ischemia.MethodsMale Wistar rats weighing 380 ± 22 g were subjected to surgical thyroidectomy. Rats were studied 15 days after surgery. Euthyroid sham-operated rats were used as controls (CT). Both groups of rats underwent a right kidney nephrectomy and suffered a 60 min left renal ischemia with 24 h of reperfusion. Rats were divided in four groups: CT, HTX, IR and HTX+IR. Rats were sacrificed and samples of plasma and kidney were obtained. Blood urea nitrogen (BUN) and creatinine were measured in blood plasma. Kidney damage was evaluated by histological analysis. Oxidative stress was measured by immunohistochemical localization of protein carbonyls and 4-hydroxy-2-nonenal modified proteins. The protein carbonyl content was measured using antibodies against dinitrophenol (DNP)-modified proteins. Nitrosative stress was measured by immunohistochemical analysis of 3-nitrotyrosine modified proteins. The activity of the antioxidant enzymes catalase, glutathione peroxidase, and superoxide dismutase was measured by spectrophotometric methods. Multiple comparisons were performed with ANOVA followed by Bonferroni t test.ResultsThe histological damage and the rise in plasma creatinine and BUN induced by IR were significantly lower in HTX+IR group. The increase in protein carbonyls and in 3-nitrotyrosine and 4-hydroxy-2-nonenal modified proteins was prevented in HTX+IR group. IR-induced decrease in renal antioxidant enzymes was essentially not prevented by HTX in HTX+IR group.ConclusionHypothyroidism was able to prevent not only oxidative but also nitrosative stress induced by IR. In addition, the antioxidant enzymes catalase, glutathione peroxidase, and superoxide dismutase seem not to play a protective role in this experimental model.
TOIB Study. Are topical or oral ibuprofen equally effective for the treatment of chronic knee pain presenting in primary care: a randomised controlled trial with patient preference study. [ISRCTN79353052]
Authors: Cross Pamela L , Ashby Deborah , Harding Geoff , Hennessy Enid M , Letley Louise , Parsons Suzanne , Spencer Anne E , Underwood Martin ,   the TOIB Study Team
Published: November 2005

Abstract

Background
Many older people have chronic knee pain. Both topical and oral non- steroidal anti-inflammatory drugs (NSAIDs) are commonly used to treat this. Oral NSAIDS are effective, at least in the short term, but can have severe adverse effects. Topical NSAIDs also appear to be effective, at least in the short term. One might expect topical NSAIDs both to be less effective and to have fewer adverse effects than oral NSAIDs. If topical NSAIDs have fewer adverse effects this may outweigh both the reduction in effectiveness and the higher cost of topical compared to oral treatment. Patient preferences may influence the comparative effectiveness of drugs delivered via different routes.

Methods
TOIB is a randomised trial comparing topical and oral ibuprofen, with a parallel patient preference study. We are recruiting people aged 50 or over with chronic knee pain, from 27 MRC General Practice Research Framework practices across the UK. We are seeking to recruit 283 participants to the RCT and 379 to the PPS. Participants will be followed up for up to two years (with the majority reaching one year). Outcomes will be assessed by postal questionnaire, nurse examination, laboratory tests and medical record searches at one and two years or the end of the study.

Discussion
This study will provide new evidence on the overall costs and benefits of treating chronic knee pain with either oral or topical ibuprofen. The use of a patient preference design is unusual, but will allow us to explore how preference influences response to a medication. In addition, it will provide more information on adverse events. This study will provide evidence to inform primary care practitioners, and possibly influence practice.
Mapping and characterization of the amplicon near APOA2 in 1q23 in human sarcomas by FISH and array CGH
Authors: Kresse Stine H , Berner Jeanne-Marie , Meza-Zepeda Leonardo A , Gregory Simon G , Kuo Wen-Lin , Gray Joe W , Forus Anne , Myklebost Ola 
Published: November 2005

Abstract

Background
Amplification of the q21-q23 region on chromosome 1 is frequently found in sarcomas and a variety of other solid tumours. Previous analyses of sarcomas have indicated the presence of at least two separate amplicons within this region, one located in 1q21 and one located near the apolipoprotein A-II (APOA2) gene in 1q23. In this study we have mapped and characterized the amplicon in 1q23 in more detail.

Results
We have used fluorescence in situ hybridisation (FISH) and microarray-based comparative genomic hybridisation (array CGH) to map and define the borders of the amplicon in 10 sarcomas. A subregion of approximately 800 kb was identified as the core of the amplicon. The amplification patterns of nine possible candidate target genes located to this subregion were determined by Southern blot analysis. The genes activating transcription factor 6 (ATF6) and dual specificity phosphatase 12 (DUSP12) showed the highest level of amplification, and they were also shown to be over-expressed by quantitative real-time reverse transcription PCR (RT-PCR). In general, the level of expression reflected the level of amplification in the different tumours. DUSP12 was expressed significantly higher than ATF6 in a subset of the tumours. In addition, two genes known to be transcriptionally activated by ATF6, glucose-regulated protein 78 kDa and -94 kDa (GRP78 and GRP94), were shown to be over-expressed in the tumours that showed over-expression of ATF6.

Conclusion

ATF6 and DUSP12 seem to be the most likely candidate target genes for the 1q23 amplification in sarcomas. Both genes have possible roles in promoting cell growth, which makes them interesting candidate targets.
The pp24 phosphoprotein of Mason-Pfizer monkey virus contributes to viral genome packaging
Authors: Bohl Christopher R , Brown Shanna M , Weldon Robert A 
Published: November 2005

Abstract

Background
The Gag protein of Mason-Pfizer monkey virus, a betaretrovirus, contains a phosphoprotein that is cleaved into the Np24 protein and the phosphoprotein pp16/18 during virus maturation. Previous studies by Yasuda and Hunter (J. Virology. 1998. 72:4095–4103) have demonstrated that pp16/18 contains a viral late domain required for budding and that the Np24 protein plays a role during the virus life cycle since deletion of this N-terminal domain blocked virus replication. The function of the Np24 domain, however, is not known.

Results
Here we identify a region of basic residues (KKPKR) within the Np24 domain that is highly conserved among the phosphoproteins of various betaretroviruses. We show that this KKPKR motif is required for virus replication yet dispensable for procapsid assembly, membrane targeting, budding and release, particle maturation, or viral glycoprotein packaging. Additional experiments indicated that deletion of this motif reduced viral RNA packaging 6–8 fold and affected the transient association of Gag with nuclear pores.

Conclusion
These results demonstrate that the Np24 domain plays an important role in RNA packaging and is in agreement with evidence that suggests that correct intracellular targeting of Gag to the nuclear compartment is an fundamental step in the retroviral life cycle.
Is albumin administration in the acutely ill associated with increased mortality? Results of the SOAP study
Authors: Vincent Jean-Louis , Sakr Yasser , Reinhart Konrad , Sprung Charles L , Gerlach Herwig , Ranieri V Marco ,   the 'Sepsis Occurrence in Acutely Ill Patients' investigators
Published: November 2005

Abstract
Introduction
Albumin administration in the critically ill has been the subject of some controversy. We investigated the use of albumin solutions in European intensive care units (ICUs) and its relationship to outcome.

Methods
In a cohort, multicenter, observational study, all patients admitted to one of the participating ICUs between 1 May and 15 May 2002 were followed up until death, hospital discharge, or for 60 days. Patients were classified according to whether or not they received albumin at any time during their ICU stay.

Results
Of 3,147 admitted patients, 354 (11.2%) received albumin and 2,793 (88.8%) did not. Patients who received albumin were more likely to have cancer or liver cirrhosis, to be surgical admissions, and to have sepsis. They had a longer length of ICU stay and a higher mortality rate, but were also more severely ill, as manifested by higher simplified acute physiology score (SAPS) II and sequential organ failure assessment (SOFA) scores than the other patients. A Cox proportional hazard model indicated that albumin administration was significantly associated with decreased 30-day survival. Moreover, in 339 pairs matched according to a propensity score, ICU and hospital mortality rates were higher in the patients who had received albumin than in those who had not (34.8 versus 20.9% and 41.3 versus 27.7%, respectively, both p < 0.001).

Conclusion
Albumin administration was associated with decreased survival in this population of acutely ill patients. Further prospective randomized controlled trials are needed to examine the effects of albumin administration in sub-groups of acutely ill patients.
An in vitro study of Hoechst 33342 redistribution and its effects on cell viability
Authors: Mohorko N , Kregar-Velikonja N , Repovs G , Gorensek M , Bresjanac M 
Published: November 2005

Although Hoechst 33342 (H342) is frequently used to label donor cells in cell transplantation research, it has been noted that it might secondarily label the host cells. Furthermore, its potential toxicity leading to cell death has been described. We studied the time course of H342 redistribution from the primary labeled rat bone marrow stromal cells (rBMSC) into the non-labeled rBMSC population over 7 days in culture; we evaluated the nuclear H342 fluorescence intensity as a possible criterion for distinguishing the primary from the secondary labeled cells, and determined the viability of rBMSC after an overnight incubation in 1 mg/mL of H342. H342 labeled / 50% of the initially non-labeled cells within the first 6 hours and almost 90% within a week.Nuclear fluorescence intensity was a reliable criterion for distinguishing primary and secondary labeled cells within the first 24 hours, but less so at later time points. The percentage of either apoptotic or necrotic cells did not rise acutely after the overnight incubation in 1 mg/mL of H342. Although a 12-hour incubation of rBMSC in 1 mg/mL of H342 did not cause acute cell death, H342 rapidly and extensively redistributed into non-labeled cells, which makes H342 a relatively unsuitable marker for cell transplantation research.
High-Dose Therapy and Autologous Blood Stem-Cell Transplantation Compared With Conventional Treatment in Myeloma Patients Aged 55 to 65 Years: Long-Term Results of a Randomized Control Trial From the Group Myelome-Autogreffe
Authors: Fermand Jean-Paul , Katsahian Sandrine , Divine Marine , Leblond Veronique , Dreyfus Francois , Macro Margaret , Arnulf Bertrand , Royer Bruno , Mariette Xavier , Pertuiset Edouard , Belanger Coralie , Janvier Maud , Chevret Sylvie , Brouet Jean Claude , Ravaud Philippe 
Published: November 2005

Purpose To study the impact of high-dose therapy (HDT) with autologous stem-cell support in patients with symptomatic multiple myeloma (MM) between the ages of 55 and 65 years. Patients and Methods One hundred ninety patients between 55 and 65 years old who had newly diagnosed stage II or III MM were randomly assigned to receive either conventional chemotherapy (CCT; ie, monthly courses of a regimen of vincristine, melphalan, cyclophosphamide, and prednisone) or HDT and autologous blood stem-cell transplantation (using either melphalan alone 200 mg/m2 intravenous [IV] or melphalan 140 mg/m2 IV plus busulfan 16 mg/kg orally as pretransplantation cytoreduction). Results Within a median follow-up of 120 months, median event-free survival (EFS) times were 25 and 19 months in the HDT and CCT groups, respectively. Median overall survival (OS) time was 47.8 months in the HDT group compared with 47.6 months in the CCT group. A trend to better EFS (P = .07) was observed in favor of HDT, whereas OS curves were not statistically different (P = .91). The period of time without symptoms, treatment, and treatment toxicity (TwiSTT) was significantly longer for the HDT patients than for the CCT patients (P = .03). Conclusion With a median follow-up time of approximately 10 years, this randomized trial confirmed a benefit of HDT in terms of EFS and TwiSTT but did not provide evidence for superiority of HDT over CCT in OS of patients aged 55 to 65 years with symptomatic newly diagnosed MM.
Human Sperm Sex Hormone-Binding Globulin Isoform: Characterization and Measurement by Time-Resolved Fluorescence Immunoassay
Authors: Selva David M. , Bassas Lluis , Munell Francina , Mata Ana , Tekpetey Francis , Lewis John G. , Hammond Geoffrey L. 
Published: November 2005

Abstract
Context: SHBG gene expression in human testis results in an SHBG isoform that accumulates in the sperm head.
Objective: The objective of this study was to further characterize the SHBG isoform in human sperm and to assess its biological relevance.
Design, Setting, and Patients: A time-resolved immunofluorometric assay was established to measure SHBG isoform concentrations in sperm samples from patients and sperm donors attending in vitro fertilization clinics.
Results and Conclusions: Molecular characterization of SHBG transcripts in human testis and sperm and biochemical analyses of the sperm SHBG isoform indicate that its smaller size compared with plasma SHBG is due to a lack of amino-terminal residues. The SHBG isoform is lost from sperm by one freeze and thaw cycle and during capacitation, which suggests it is located in or between the outer acrosomal and sperm plasma membranes. Sperm SHBG levels were proportional to the number of sperm analyzed and within assay variability in samples taken on different occasions from seven of nine individuals. Intra- and interassay variability (coefficient of variation) was 5.8 and 8.5%, respectively. Sperm SHBG levels ranged from 6–49 pm/106 sperm in 13 donor samples and did not correlate with serum SHBG levels. Sperm SHBG levels were lowest in fertile men and highest in patients with untreated varicocele, but these differences were not significant. Patients studied for couple infertility and those with surgically treated varicocele showed intermediate values. Sperm SHBG isoform levels correlate significantly with age and sperm motility and may influence sperm function in relation to male fertility.
Liquid-phase Epoxidation of Alkenes Using Molecular Oxygen Catalyzed by Vanadium Cation-exchanged Montmorillonite
Authors: Mitsudome Takato , Nosaka Naoya , Mori Kohsuke , Mizugaki Tomoo , Ebitani Kohki , Kaneda Kiyotomi 
Published: November 2005

Abstract
Vanadium cation-exchanged montmorillonite can efficiently catalyze the selective epoxidation of various alkenes and the oxygenation of adamantane using molecular oxygen as a sole oxidant.
Analysis of 237Np in spent fuel solutions
Authors: Morgenstern A. , Apostolidis C. , Ottmar H. , Mayer K. 
Published: November 2005

Summary
An experimental procedure has been developed for the analysis of neptunium in input solutions of spent nuclear fuel reprocessing. The method consists of selective chromatographic extraction of neptunium and plutonium using TEVA resin followed by determination of the ratio of [Np]/[Pu] on the column by high-resolution gamma spectrometry. Knowing the concentration of plutonium from routinely performed K-edge densitometry and X-ray fluorescence measurements, the concentration of Np can be evaluated. The method has been tested on simulated solutions and validated on spent fuel of known [Np]/[Pu] ratio.
The solubilisation of Ru and U from condensation particles released b overheated nuclear fuel and maturated in air and in argon
Authors: Froment P. , Cara J. , Ronneau C. 
Published: November 2005

SummaryThe emission of uranium and ruthenium oxides from overheated nuclear fuel is a complex phenomenon which depends on fuel matrix, temperature, oxygen potential of the atmosphere in contact and on emission sequence. Furthermore, secondary annealing (“maturation”) reactions of aerosol particles in the gas phase, immediately after emission, strongly influence the properties of particles before their dispersion in the reactor containment building and/or in the environment. Maturation influences surface and bulk gradient composition, particle size, and, as a consequence, weathering rates in the environment. This paper describes how emission and maturation conditions may affect the solubility rates of condensation particles released by overheated U and Ru oxides mixtures, in small-scale laboratory simulations. It will be demonstrated that the presence of Ru decreases the solubilisation rate of U.
Radiochemical separation of no-carrier-added radioniobium from zirconiu targets for application of90Nb-labelled compounds
Authors: Busse S. , Brockmann J. , Rösch Frank 
Published: November 2005

SummaryThe radioisotope90Nb is a positron emitter with a relatively high positron branching of 51% and a rather low β+-energy ofEmean= 662 keVEmax= 1.5 MeV) with potential for application in positron emission tomography (PET). Its half-life of 14.6 h makes it especially promising for the quantitative investigation of biological processes with slow distribution kinetics. An advantageous production route of90Nb is thenatZr(p,n)90Nb process. To separate nca (no-carrier-added) radioniobium from macroscopic amounts of irradiated zirconium targets, an effective two step separation procedure was developed. A liquid-liquid extraction using N-benzoyl-N-phenylhydroxylamine (BPHA) in CHCl3was applied first to separate the bulk of the zirconium matrix with a Zr separation coefficient of about 104, followed by anion-exchange chromatography for high grade purification of nca radioniobium. A sufficiently high decontamination factor of > 2 × 107and an overall radiochemical yield of nca90Nb of about 70% was achieved within about 3 hours.
Quantitative Trait Loci With Age-Specific Effects on Fecundity in Drosophila melanogaster
Authors: Leips Jeff , Gilligan Paul , Mackay Trudy F C 
Published: November 2005

Abstract
Life-history theory and evolutionary theories of aging assume the existence of alleles with age-specific effects on fitness. While various studies have documented age-related changes in the genetic contribution to variation in fitness components, we know very little about the underlying genetic architecture of such changes. We used a set of recombinant inbred lines to map and characterize the effects of quantitative trait loci (QTL) affecting fecundity of Drosophila melanogaster females at 1 and 4 weeks of age. We identified one QTL on the second chromosome and one or two QTL affecting fecundity on the third chromosome, but these QTL affected fecundity only at 1 week of age. There was more genetic variation for fecundity at 4 weeks of age than at 1 week of age and there was no genetic correlation between early and late-age fecundity. These results suggest that different loci contribute to the variation in fecundity as the organism ages. Our data provide support for the mutation accumulation theory of aging as applied to reproductive senescence. Comparing the results from this study with our previous work on life-span QTL, we also find evidence that antagonistic pleiotropy may contribute to the genetic basis of senescence in these lines as well.