bluuebunny/crossref_metadata_2025_split huggingface dataset:
T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory
Authors: Monnier Stéphanie , Cox David G , Albion Tim , Canzian Federico 
Published: October 2005

Abstract
Background
Single Nucleotide Polymorphism (SNP) genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System (LIMS) need tools to organize the data flow.

Results
We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements.

Conclusion
We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories whithout a more sophisticated and expensive system, such as a LIMS.
Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis
Authors: Enault François , Suhre Karsten , Claverie Jean-Michel 
Published: October 2005

Abstract
Background
The large amount of completely sequenced genomes allows genomic context analysis to predict reliable functional associations between prokaryotic proteins. Major methods rely on the fact that genes encoding physically interacting partners or members of shared metabolic pathways tend to be proximate on the genome, to evolve in a correlated manner and to be fused as a single sequence in another organism.

Results
The new "Gene Function Predictor", linked to the web server Phydbac proposes putative associations between Escherichia coli K-12 proteins derived from a combination of these methods. We show that associations made by this tool are more accurate than linkages found in the other established databases. Predicted assignments to GO categories, based on pre-existing functional annotations of associated proteins are also available. This new database currently holds 9,379 pairwise links at an expected success rate of at least 80%, the 6,466 functional predictions to GO terms derived from these links having a level of accuracy higher than 70%.

Conclusion
The "Gene Function Predictor" is an automatic tool that aims to help biologists by providing them hypothetical functional predictions out of genomic context characteristics. The "Gene Function predictor" is available at http://www.igs.cnrs-mrs.fr/phydbac/indexPS.html.
Prosthetic valve endocarditis caused by Pseudomonas luteola
Authors: Casalta Jean-Paul , Fournier Pierre-Edouard , Habib Gilbert , Riberi Alberto , Raoult Didier 
Published: October 2005

Abstract

Background

Pseudomonas luteola has been recognized as an uncommon cause of bacteremia and of infections in patients with underlying medical disorders

Case presentation
We isolated P. luteola from blood cutures in a patient with prosthetic valve endocarditis developed 16 months after cardiac surgery.

Conclusion

P. luteola is a rare opportunistic agent, with a propensity of infecting valvular prostheses.
Clinico-morphological patterns of breast cancer including family history in a New Delhi hospital, India-A cross-sectional study
Authors: Saxena Sunita , Rekhi Bharat , Bansal Anju , Bagga Ashok , Chintamani  , Murthy Nandagudi S 
Published: October 2005

Abstract

Background
Breast cancer is the second most common malignancy among women, next to cervix cancer. Understanding its pathogenesis, morphological features and various risk-factors, including family history holds a great promise for the treatment, early detection and prevention of this cancer.

Patients and methods
In an attempt to evaluate the clinico-morphological patterns of breast cancer patients, including their family history of breast and/or other cancers, a detailed analysis of 569 breast cancer cases diagnosed during the years 1989–2003 was carried out. Mean and standard deviation and Odds ratios along with 95% confidence intervals were estimated. χ2/Fisher's exact test were employed to test for proportions.

Results
Mean age of the patient at presentation was 47.8 years, ranging from 13–82 years. Among the various histo-morphological types, Infiltrating duct carcinoma (IDC) was found to be commonest type i.e. in 502 cases (88.2%), followed by infiltrating lobular carcinoma (ILC) in 21 cases (3.7%) and other types forming 9(1%). Out of 369 cases where TNM staging was available, stage IIIB (35.2%) was the commonest. Lymph node positivity was observed in 296 cases (80.2%). Out of 226 cases evaluated for presence of family history, 47 cases (20.7%) revealed positive family history of cancer, among which breast or ovarian cancer were the commonest type (72.0%). Patients below 45 years of age had more frequent occurrence of family history as compared to above 45 years. Amongst familial cases, Infiltrating duct carcinoma was the commonest form accounting for 68.8% cases while ILC was found to be in a higher proportion (12.5%) as compared to non- familial cases (5.4%).

Conclusion
Among the various determining factors for development of breast cancer and for its early detection, family history of cancer forms one of the major risk factor. It is important to take an appropriate history for eliciting information pertaining to occurrence of cancers amongst the patients' relatives there by identifying the high risk group. Educating the population about the risk factors would be helpful in early detection of breast cancer.
Association between anti-nucleophosmin and anti-cardiolipin antibodies in (NZW × BXSB)F1mice and human systemic lupus erythematosus
Authors: Lartigue Aurelia , Drouot Laurent , Jouen Fabienne , Charlionet Roland , Tron François , Gilbert Danièle 
Published: October 2005

AbstractWe showed previously that nucleophosmin (NPM), a nucleolar phosphoprotein, is recognized by sera from (NZW × BXSB)F1 (WB) mice, a model of systemic lupus erythematosus (SLE) and anti-phospholipid syndrome. In the present study we analysed the prevalence and kinetics of anti-NPM autoantibodies in WB mice by a solid-phase ELISA with recombinant human (rh) NPM as the antigen and showed that most male WB mouse sera had anti-NPM antibodies that were responsible for their indirect immunofluorescence staining pattern on Hep-2 cells. Anti-NPM antibodies were significantly associated with anti-cardiolipin (aCL) antibodies. This antibody profile mirrored that observed in certain human SLE sera because anti-NPM antibodies were detected in 28% of the sera from patients with SLE and were similarly associated with aCL antibodies. The demonstration that rhNPM bound to cardiolipin (CL) in vitro and increased the CL-binding activity of a WB-derived aCL monoclonal antibody indicates that NPM can interact with CL to form SLE-related immunogenic particles that might be responsible for the concomitant production of anti-NPM and aCL antibodies.
Die quantitative Analyse von Markerproteinen im Urin Quantitative analysis of marker proteins in urine
Authors: Regeniter Axel , Scholer André , Siede Werner H. 
Published: October 2005

Zusammenfassung
Die Analyse von spezifischen Proteinen im zweiten Morgenurin, bezogen auf den Kreatiningehalt der Probe, erlaubt heute nicht nur den Nachweis oder den Ausschluss von Nierenerkrankungen, sondern darüber hinaus auch die Differenzierung und Verlaufskontrolle von Nephropathien.
Störungen lassen sich aufgrund ihres Markerproteinprofils in solche mit hauptsächlich glomerulärem oder tubulärem Anteil und zusätzlich in weitere Untergruppen einteilen.
Im Zusammenhang mit den Teststreifenresultaten kann die Quelle einer Blutung mit spezifischen Quotienten näher eingegrenzt und Kontaminationen können von tatsächlichen renalen Proteinurien unterschieden werden.
Eine Plausibilitätsprüfung und Interpretation der erhaltenen Ergebnisse ist unbedingt erforderlich. Da eineVielzahl von Regeln überprüft werden muss, ist eine Berechnung und Darstellung der Ergebnisse nur mit Hilfe von wissensbasierten Systemen in Kombination mit einer grafischen Befunddarstellung sinnvoll.
Differentialdiagnose renaler Erkrankungen mit der Urinprotein-Elektrophorese (SDS-PAGE) Differential diagnosis of renal diseases by urinary protein electrophoresis (SDS-PAGE)
Authors: Becker Andreas , Boesken Wolf H. 
Published: October 2005

Zusammenfassung
Die SDS-Discelektrophorese (SDS-PAGE) trennt Proteine nach dem Molekulargewicht und erlaubt die qualitative und semiquantitative Analyse der mit dem Urin ausgeschiedenen Eiweiße. Im Gegensatz zur Einzelproteinanalyse werden keine Konzentrationen von Markerproteinen gemessen, sondern es werden alle im Urin vorhandenen Proteine mit einem Molekulargewicht zwischen etwa 10 und 800 kDa dargestellt. Da die pathophysiologischen Prozesse im Nephron sich im Wesentlichen in der molekularen Größe der Urineiweiße widerspiegeln, lassen die elektrophoretischen Muster Rückschlüsse auf das Vorliegen einer glomerulären und/oder tubulären Schädigung und auf prä- und postrenale Prozesse zu. Sie ermöglichen somit die Bestimmung der Lokalisation der Erkrankung am Nephron, nicht aber die Diagnose der zugrunde liegenden Ursache. Im klinischen Alltag gibt die Untersuchung damit wertvolle Hinweise auf die Natur der Erkrankung und leistet Hilfestellung bei der Entscheidung, ob eine Biopsie zur weiteren Abklärung erforderlich ist. Daneben liefert sie insbesondere bei Verlaufsuntersuchungen Hinweise in Bezug auf die Prognose und lässt bei Veränderungen im Verlauf Remissionen, Rezidive und Progression erkennen.
Fallbericht eines falsch-positiven Hepatitis C-Virus-diagnostischen Befundes mit weitreichenden Folgen Case report on a false positive hepatitis C diagnostic result with far-reaching consequences
Authors: Rabenau Holger F. , Werwatz Gudrun , Teuber Gerlinde , Gottschalk Rene , Wicker Sabine , Berger Annemarie , Wilhelm Doerr Hans 
Published: October 2005

Zusammenfassung
Im vorliegenden Fall wird von einer Fehldiagnose auf der Grundlage eines falsch-reaktiven Anti-HCV-Tests und eines falsch-reaktiven HCV-Nukleinsäureamplifikationstests (NAT) berichtet, die bei einem 58-jährigen chirurgischen Oberarzt im Rahmen einer arbeitsmedizinischen Vorsorgeuntersuchung im krankenhauseigenen Labor gestellt wurde und zu einem knapp zweimonatigen Berufsverbot führte. Basis dieser Fehldiagnose war ein wiederholt schwach reaktiver HCV-Antikörper-ELISA, der mit einem Nukleinsäureamplifikationstest, der ebenfalls schwach positiv ausfiel, überprüft wurde. Ein Antikörperbestätigungs- bzw. Ergänzungstest (Immunoblot) wurde nicht durchgeführt. Die Fehldiagnose ist jedoch nicht durch einen Testfehler, sondern durch ein Missverständnis entstanden, indem beim Kliniker zwei Laborindizien zu einem Beweis aufsummiert wurden.
Effect of pH on the toxicity of nickel and other divalent metals to Burkholderia cepacia PR1301
Authors: Van Nostrand Joy D. , Sowder Andrew G. , Bertsch Paul M. , Morris Pamela J. 
Published: October 2005

Abstract
Nickel (Ni) is a common cocontaminant at many waste sites where the soils and sediments often are acidic, thereby influencing metal availability. Growth of Burkholderia cepacia PR1301 was not affected at 3.41 mM Ni at pH 5, but was inhibited by 73.2% at pH 6 and inhibited completely at pH 7 compared to growth without Ni. This pH effect was not observed in the Niresistant strains, Ralstonia metallidurans CH34 and 31A. Predicted Ni speciation did not explain the observed toxicity trends. Sorption of Ni to PR1 increased with increasing pH (1.49, 1.12, and 3.88 mg Ni/g dry weight at pH 5, 6, and 7, respectively), but was low at all three pH values, and most likely does not explain the observed pH effect. Growth inhibition of PR1 with increasing pH also was observed for other divalent cations, with growth observed at 4.24 mM Co, 2.22 mM Cd, and 3.82 mM Zn at pH 5 and 6, but totally inhibited at pH 7. These studies suggest that, at circumneutral pH, PR1 would be considered sensitive to Ni and other divalent cations, in spite of the ability to grow in higher concentrations at lower pH values.
Heterogeneity of natural organic matter amelioration of silver toxicity to Daphnia magna: Effect of source and equilibration time
Authors: Glover Chris N. , Playle Richard C. , Wood Chris M. 
Published: October 2005

Abstract
Despite the heterogeneity of natural organic matter (NOM) in the aquatic environment, current models that predict metal toxicity to aquatic biota treat these important metal-complexing agents in a homogeneous manner. In this investigation, the ability of 11 commercial and naturally isolated NOM samples to ameliorate silver toxicity to the freshwater crustacean Daphnia magna was examined. The commercially available Aldrich humic acid (AHA) increased the 48-h median lethal concentration for daphnid neonates from nominally NOM-free levels of 0.29 to 3.80 μg/L (at 6.9 mg C/L) in a concentration-dependent manner. Three of the tested samples exhibited similar protective effects, but the additional seven NOM samples displayed significantly stronger ameliorative actions. In fact, four samples of both commercial and naturally isolated origin demonstrated greater than fourfold increases in protection compared to that of AHA. Additional investigations showed that increased silver-AHA equilibration time resulted in decreased toxicity. Increased equilibration time also decreased whole-body silver accumulation at NOM levels less than 1 mg C/L. The present results suggest that heterogeneity of NOM and silver-NOM equilibration time will have to be accounted for in future models of silver toxicity to D. magna and that laboratory toxicity testing using NOM and metals should account for the effects of metal-NOM equilibration time.
Delineating copper accumulation pathways for the freshwater bivalve Corbicula using stable copper isotopes
Authors: Croteau Marie-Noéle , Luoma Samuel N. 
Published: October 2005

Abstract
Delineation of metal uptake routes in aquatic invertebrates is critical for characterizing bioaccumulation dynamics and assessing risks associated with metal exposure. Here we demonstrate that Cu stable isotopic ratios can be manipulated in both exposure media and algae to determine the efflux rate constant (ke) and to estimate Cu assimilation efficiency (AE) from ingested food in a freshwater bivalve (Corbicula fluminea). The Cu AE in Corbicula fed 65Cu-spiked Cryptomonas ozolini was 38%. Copper uptake routes had no significant influence on efflux; ke of 0.004 per day characterized the slowest component of efflux following short-term exposures to 65Cu in water or in both food and water. Incorporation of the physiological parameters for dietary and dissolved uptake as well as rate constants of loss into a bioaccumulation model allowed for assessing the relative contribution of water and food as Cu sources. At [65Cu2+] of 6.7 μg/L, Corbicula accumulated twice as much Cu from diet as from water. In most freshwater systems, the dietary pathway is likely to act as the major Cu uptake route for Corbicula. Extrapolation of our laboratory results to the San Francisco Bay—Delta (California, USA) indicated that our biodynamic model and the laboratory-derived parameters for dietary 65Cu uptake provided a realistic representation of the processes involved in Cu accumulation by the bivalve Corbicula.
Biotests and biosensors in ecotoxicological risk assessment of field soils polluted with zinc, lead, and cadmium
Authors: Kahru Anne , Ivask Angela , Kasemets Kaja , Pollumaa Lee , Kurvet Imbi , François Matthieu , Dubourguier Henri-Charles 
Published: October 2005

Abstract
The combined chemical and ecotoxicological hazard evaluations study was conducted on 60 smelter-influenced soils containing 1 to 13, 50 to 653, and 100 to 1,198 mg/kg of Cd, Pb, and Zn, respectively. For these soils (liquid-to-soil ratio = 10), water extractability of Zn, Cd, and Pb was less than 0.19% (median values). Acetic acid (0.11 M) extracted 23, 9.7, and 0.7% of Cd, Zn, and Pb, respectively. Although heavy metal concentrations in the studied soils were high, the toxic effects of water extracts were observed only in few samples and in few biotests (algae Selenastrum capricornutum and metal detector assay). For most of the aquatic test organisms (e.g., crustaceans, photobacteria), the bioavailable concentrations of metals in soil-water extracts were either subtoxic, or the adverse effects were compensated by soil nutrients, etc. However, analysis of the soils with recombinant Cd sensor Bacillus subtilis (pTOO24) showed that about 65% of these apparently subtoxic samples contained bioavailable Cd when analyzed in the suspension assay (detection limit 1.5 mg Cd/kg soil), indicating the desorption of Cd induced by direct contact of bacteria with soil particles. The median bioavailable fraction of Cd (1%) was 23-fold lower than the fraction extracted by acetic acid. The Pb-Cd sensor Staphylococcus aureus (pT0024) detected bioavailable Pb only in the suspensions of five of the most lead-polluted soils (&gt;417 mg Pb/kg): the median bioavailability of Pb was 0.42%. Consequently, the hazard assessment relying on total metal levels in soils should be revised by critical comparison with data obtained from bioassays. Development and use of biosensors (excellent tools for mechanistic studies and signaling hazard already at subtoxic level) should be encouraged.
Biotransformation of the polycyclic aromatic hydrocarbon pyrene in the marine polychaete Nereis virens
Authors: Jørgensen Anne , Giessing Anders M. B. , Rasmussen Lene Juel , Andersen Ole 
Published: October 2005

Abstract
In vivo and in vitro biotransformation of the polycyclic aromatic hydrocarbon (PAH) pyrene was investigated in the marine polychaete Nereis virens. Assays were designed to characterize phase I and II enzymes isolated from gut tissue. High-pressure liquid chromatography measurement of 1-hydroxypyrene, pyrene-1-glucuronide, pyrene-1-sulfate, and pyrene-1-glucoside appeared to be a sensitive method for estimating the activity of pyrene hydroxylase, glucuronosyl transferase, and sulfotransferase. Total pyrene in gut tissue after a 5-d exposure to 10 μg/g dry weight pyrene constituted 65% pyrene-1-glucuronide, 12% pyrene-1-sulfate, 2% pyrene-1-glucoside, 4% 1-hydroxypyrene, and 17% pyrene, indicating that glucuronidation is the prominent phase II pathway in this organism. Only pyrene hydroxylase activity was induced significantly after pre-exposure to sediment-associated pyrene (10 μg/g dry wt). Apparent kinetic parameters were determined for all enzymatic reactions. Glucuronidation was confirmed as being the prominent phase II reaction, based on its high apparent maximum velocity (Vmax(a)). Sulfation had the lowest apparent Michaelis constant (Km(a)), indicating high specificity. Apparent kinetic parameters for pyrene hydroxylase activity were changed after induction with pyrene. Induced worms showed increased Vmax(a) and decreased Km(a) compared to noninduced worms, indicating that the relative amount of the cytochrome P450 enzyme(s) responsible for pyrene hydroxylation is increased. Our findings show that N. virens has a high biotransformation capacity for PAHs, with inducible pyrene hydroxylase activity, and that the most prominent phase II pathway in this organism is glucuronidation.
Fate of gasoline oxygenates in conventional and multilevel wells of a contaminated groundwater table in düsseldorf, Germany
Authors: Rosell Mònica , Lacorte Sílvia , Forner Claudia , Rohns Hans-Peter , Irmscher Rudolf , Barceló Damiá 
Published: October 2005

Abstract
In a gasoline-contaminated site in Düsseldorf, Germany a two-year monitoring program was carried out to determine the presence, behavior, and fate of 12 gasoline additives in a total of 96 samples from 14 groundwater wells. The origin of contamination was suspected to be a gasoline spill at a gas station. Target compounds were methyl-tert-butyl ether (MTBE), its main degradation products, tert-butyl alcohol (TBA) and tert-butyl formate (TBF); other gasoline additives, oxygenate dialkyl ethers: Ethyl-tert-butyl ether (ETBE), tert-amyl methyl ether (TAME) and diisopropyl ether (DIPE); aromatics: Benzene, toluene, ethylbenzene and xylenes (BTEX), and other compounds causing odor problems: Dicyclopentadiene and trichloroethylene. Purge and trap coupled with gas chromatography-mass spectrometry permitted detection of ng/L concentrations. Ninety of the 96 samples analyzed contained MTBE at levels varying between 0.01 to 645 μ/L. Five contaminated hot spots were identified with levels up to U.S. Environmental Protection Agency (U.S. EPA) drinking water advisory values (20–40 μ/L) and one of them doubling Danish suggested toxicity level of 350 μ/L at a depth of 11 m. No significant natural attenuation was found in MTBE degradation, although samples with high levels of MTBE contained 0.1 to 440 μg/L of TBA. These levels were attributed to its presence in the contamination source more than MTBE degradation. tert-Butyl alcohol was found to be recalcitrant in groundwater. In all cases, BTEX were at low concentrations or not detected, showing less persistence than MTBE. The monitoring of the contamination plume showed that the distribution of the MTBE and TBA in the aquifer formed a similar vertical concentration profile that was influenced by the groundwater flow direction.
Field‐Scale Evaluation of Phosphorus Leaching in Acid Sandy Soils Receiving Swine Waste
Authors: Nelson Nathan O. , Parsons John E. , Mikkelsen Robert L. 
Published: October 2005

ABSTRACTAccurate descriptions of P leaching are important because excess P applied to soils can enter surface water via leaching and subsurface transport, thereby negatively impacting water quality. The objectives of this study were to monitor P leaching in soils with a long‐term history of waste application, relate soil solution P concentrations to soil P status, and quantify P leaching losses. Soil solution was monitored for 20 mo with samplers installed at 45‐, 90‐, and 135‐cm depths in two pits (1 × 3 × 1.5 m) in Autryville (loamy, siliceous, thermic Arenic Paleudults) and Blanton (loamy, siliceous, semiactive, thermic Grossarenic Paleudults) soils located in a grazed pasture in Sampson County, NC, which had received swine waste for >20 yr. Maximum soil solution P concentrations at 45 cm exceeded 18 mg L−1 in both soils. Soil solution P concentrations at 90 cm in the Blanton soil were similar to that at 45 cm indicating low P sorption. Soil solution P concentrations at 90 cm in the Autryville soil averaged 0.05 mg L−1 compared to 10 mg L−1 at 45 cm. A split‐line model related soil solution P concentration to the degree of phosphorus saturation (DPS), identifying a change point at 45% DPS. Phosphorus movement past 45 cm equaled or exceeded surplus P additions for both soils. Long‐term waste applications resulted in DPS > 90%, high soil solution P concentrations, and substantial vertical P movement. Phosphorus leaching should be considered when assessing long‐term risk of P loss from waste‐amended soils.