bluuebunny/crossref_metadata_2025_split huggingface dataset:
An interlaboratory comparison of ITS2-PCR for the identification of yeasts, using the ABI Prism 310 and CEQ8000 capillary electrophoresis systems
Authors: De Baere Thierry , Van Keerberghen Anne , Van Hauwe Peter , De Beenhouwer Hans , Boel An , Verschraegen Gerda , Claeys Geert , Vaneechoutte Mario 
Published: March 2005

Abstract
Background
Currently, most laboratories identify yeasts routinely on the basis of morphology and biochemical reactivity. This approach has quite often limited discriminatory power and may require long incubation periods. Due to the increase of fungal infections and due to specific antifungal resistence patterns for different species, accurate and rapid identification has become more important. Several molecular techniques have been described for fast and reliable identification of yeast isolates, but interlaboratory exchangeability of identification schemes of molecular techniques has hardly been studied. Here, we compared amplified ITS2 fragment length determination by an ABI Prism 310 (Applied Biosystems, Foster City, Ca.) capillary electrophoresis system with that obtained by a CEQ8000 (Beckman Coulter, Fullerton, Ca.) capillary electrophoresis system.

Results
Although ITS2 size estimations on both systems differed and separate libraries had to be constructed for each system, both approaches had the same discriminatory power with regard to the 44 reference strains, identical identifications were obtained for 39/ 40 clinical isolates in both laboratories and strains from 51 samples were correctly identified using CEQ8000, when compared to phenotypic identification.

Conclusion
Identification of yeasts with ITS2-PCR followed by fragment analysis can be carried out on different capillary electrophoresis systems with comparable discriminatory power.
Data mining of the transcriptome of Plasmodium falciparum: the pentose phosphate pathway and ancillary processes
Authors: Bozdech Zbynek , Ginsburg Hagai 
Published: March 2005

Abstract
The general paradigm that emerges from the analysis of the transcriptome of the malaria parasite Plasmodium falciparum is that the expression clusters of genes that code for enzymes engaged in the same cellular function is coordinated. Here the consistency of this perception is examined by analysing specific pathways that metabolically-linked. The pentose phosphate pathway (PPP) is a fundamental element of cell biochemistry since it is the major pathway for the recycling of NADP+ to NADPH and for the production of ribose-5-phosphate that is needed for the synthesis of nucleotides. The function of PPP depends on the synthesis of NADP+ and thiamine pyrophosphate, a co-enzyme of the PPP enzyme transketolase. In this essay, the transcription of gene coding for enzymes involved in the PPP, thiamine and NAD(P)+ syntheses are analysed. The genes coding for two essential enzymes in these pathways, transaldolase and NAD+ kinase could not be found in the genome of P. falciparum. It is found that the transcription of the genes of each pathway is not always coordinated and there is usually a gene whose transcription sets the latest time for the full deployment of the pathway's activity. The activity of PPP seems to involve only the oxidative arm of PPP that is geared for maximal NADP+ reduction and ribose-5-phosphate production during the early stages of parasite development. The synthesis of thiamine diphosphate is predicted to occur much later than the expression of transketolase. Later in the parasite cycle, the non-oxidative arm of PPP that can use fructose-6-phosphate and glyceraldehyde-3-phosphate supplied by glycolysis, becomes fully deployed allowing to maximize the production of ribose-5-phosphate. These discrepancies require direct biochemical investigations to test the activities of the various enzymes in the developing parasite. Notably, several transcripts of PPP enzyme-coding genes display biphasic pattern of transcription unlike most transcripts that peak only once during the parasite cycle. The physiological meaning of this pattern requires further investigation.
Anti-Sa antibodies and antibodies against cyclic citrullinated peptide are not equivalent as predictors of severe outcomes in patients with recent-onset polyarthritis
Authors: Boire Gilles , Cossette Pierre , de Brum-Fernandes Artur J , Liang Patrick , Niyonsenga Théophile , Zhou Zhijie J , Carrier Nathalie , Daniel Claude , Ménard Henri-A 
Published: March 2005

AbstractThe prognostic value of two antibodies targeting citrullinated antigens, anti-Sa and anti-cyclic citrullinated peptide (CCP), present at inclusion, was evaluated prospectively in a cohort of 165 consecutive patients with recent-onset or early polyarthritis (EPA) followed for up to 30 months. Patients were treated according to current Good Clinical Practice standards. Predefined outcomes were severe arthritis and persistent arthritis. At inclusion, a median of 3 months after disease onset, 133 (81%) patients fulfilled at least four American College of Rheumatology criteria for rheumatoid arthritis and 30 (18%) had erosive changes on radiographs of hands and feet. Disease-modifying anti-rheumatic drugs were used in close to 80% of the patients at 30 months. Joint damage increased linearly over time, whereas disease activity declined markedly and remained low at each follow-up. Autoantibodies were identified in 76 (46%) patients: rheumatoid factor (RF) in 68 (41%), anti-CCP in 53 (33%), and anti-Sa in 46 (28%). All three antibodies were correlated, but anti-Sa antibodies best predicted severity at 18 and 30 months. RF and anti-CCP performed less well. For both outcomes, anti-Sa alone performed better than any combination of antibodies. The presence of any autoantibody identified about 50 to 60% of the patients with poor outcomes. In multivariate analysis, anti-Sa (odds ratio (OR) 8.83), the presence of erosions at inclusion (OR 3.47) and increasing age (OR 1.06/year) were significantly associated with severity, whereas RF and anti-CCP were not significant predictors. Persistent arthritis was present in up to 84% of patients; autoantibodies were specific but poorly sensitive predictors of this outcome. We conclude that assays for antibodies against citrullinated antigens differ in their ability to predict poorer outcomes in patients with EPA. In our EPA cohort treated in accordance with current standards, detection of anti-Sa but not of RF or anti-CCP antibodies, in combination with clinical and radiological variables present at the first encounter, allowed the identification of a subgroup of EPA patients suffering more rapid and more severe joint damage over 30 months.
Derivation of an ambient water quality criterion for mercury: Taking account of site-specific conditions
Authors: Moore Dwayne R. J. , Teed R. Scott , Richardson G. Mark 
Published: March 2005

Abstract
Mercury is considered to bea seriousr risk to wildlife. As a result, the Great Lakes Water Quality Initiative and others have developed ambient water quality criteria (AWQC) for the protection of wildlife. These AWQC have been controversial, however, because the AWQC were single values that did not account for site-specific conditions, derivation of the AWQC relied on a single no-observed-adverse-effect level, and the AWQC had an unknown level of conservatism because of reliance on both average and conservative assumptions and uncertainty factors. Rather than develop a single-value AWQC for total mercury, we derived an AWQC model that explicitly incorporates factors controlling bioavailability, methylation rates, and bioaccumulation in the aquatic environment (e.g., pH, dissolved organic carbon). To derive our AWQC model, field data were collected from 31 lakes in Ontario and an additional 10 lakes in Nova Scotia (North America). In the field study, levels of total and methylmercury in water and fish as well as levels of key water quality variables were determined. We conducted multiple-regression analysis to derive a model that estimates mercury levels in prey of mink. Mink are very sensitive to mercury exposure. An independent dataset consisting of 51 water bodies in the United States was then used to confirm the validity and robustness of the AWQC model. Next, we combined the results of chronic-feeding studies with similar protocols and endpoints in a meta-analysis to derive a dose–response curve for mink exposed to mercury in the diet. In the final step, we used a probabilistic risk model to estimate the concentrations of methylmercury in water that would lead to levels in fish sufficient for a 10% probability of exceeding the lethal dose affecting 5% of the mink population. The result is an AWQC equation for mercury for the protection of wildlife that can be used with a variety of site-specific conditions.
Influence of salinity on the bioaccumulation and photoinduced toxicity of fluoranthene to an estuarine shrimp and oligochaete
Authors: Weinstein John E. 
Published: March 2005

Abstract
The effect of salinity on the photoinduced toxicity of waterborne fluoranthene to larvae of the grass shrimp (Palaemonetes pugto) and tubificid oligochaete worms (Monopylephorus rubrontveus) was studied in a laboratory system under simulated sunlight. In the grass shrimp toxicity tests, five concentrations of fluoranthene (0, 3.6, 7.3, 13.8, and 29.0 μg/L) and four salinities (6.9, 14.5, 21.2, and 28.6‰) were achieved. In the oligochaete toxicity tests, five concentrations of fluoranthene (0, 0.8, 1.4, 3.3, and 7.7 μg/L) and four salinities (7.1, 13.3, 20.5, and 27.6‰) were achieved. Salinity had no effect on either the photoinduced toxicity or the bioaccumulation of fluoranthene in the grass shrimp. However, the highest level of salinity decreased the median lethal time for the oligochaete. Bioaccumulation of fluoranthene was inversely related to salinity for the oligochaete. Additional experiments demonstrated an inverse relationship between salinity and short-term osmotic weight change in the oligochaete. Weight of the grass shrimp larvae was not affected by salinity. These findings show that salinity can influence the toxicity and bioaccumulation of fluoranthene in some estuarine organisms. The influence of salinity on these populations may be related to physiological responses associated with internal osmotic volume changes. Thus, salinity needs to be taken into account when assessing the risk of photoactivated polycyclic aromatic hydrocarbon (PAH) to at least some estuarine species.
A strategy to reduce the numbers of fish used in acute ecotoxicity testing of pharmaceuticals
Authors: Hutchinson Thomas H. , Barrett Sarah , Buzby Mary , Constable David , Hartmann Andreas , Hayes Eileen , Huggett Duane , Laenge Reinhard , Lillicrap Adam D. , Straub Jürg Oliver , Thompson Roy S. 
Published: March 2005

Abstract
The pharmaceutical industry gives high priority to animal welfare in the process of drug discovery and safety assessment. In the context of environmental assessments of active pharmaceutical ingredients (APIs), existing U.S. Food and Drug Administration and draft European regulations may require testing of APIs for acute ecotoxicity to algae, daphnids, and fish (base-set ecotoxicity data used to derive the predicted no-effect concentration [PNECwater] from the most sensitive of three species). Subject to regulatory approval, it is proposed that testing can be moved from fish median lethal concentration (LC50) testing (typically using ⩾42 fish/API) to acute threshold tests using fewer fish (typically 10 fish/API). To support this strategy, we have collated base-set ecotoxicity data from regulatory studies of 91 APIs (names coded for commercial reasons). For 73 of the 91 APIs, the algal median effect concentration (EC50) and daphnid EC50 values were lower than or equal to the fish LC50 data. Thus, for approximately 80% of these APIs, algal and daphnid acute EC50 data could have been used in the absence offish LC50 data to derive PNECwater values. For the other 18 APIs, use of an acute threshold test with a step-down factor of 3.2 is predicted to give comparable PNECwater outcomes. Based on this preliminary scenario of 91 APIs, this approach is predicted to reduce the total number offish used from 3,822 to 1,025 (∼73%). The present study, although preliminary, suggests that the current regulatory requirement for fish LC50 data regarding APIs should be succeeded by fish acute threshold (step-down) test data, thereby achieving significant animal welfare benefits with no loss of data for PNECwater estimates.
Immunocompetence of juvenile chinook salmon against Listonella anguillarum following dietary exposure to polycyclic aromatic hydrocarbons
Authors: Palm Roger C. , Powell David B. , Skillman Ann , Godtfredsen Kathy 
Published: March 2005

Abstract
Juvenile chinook salmon (Oncorhynchus tschawytscha) were fed a mixture of 14 polycyclic aromatic hydrocarbon (PAH) compounds that reflected the PAH composition of salmon stomach contents in an urban estuary of Puget Sound, Washington (USA). Following a 28-d dietary exposure, a standardized Listonella anguillarum challenge model was used to determine whether PAH exposure (16, 64, and 252 mg/kg wet wt feed) causes reduced disease resistance under the conditions examined in this study. To assess innate immunity, five replicate groups of fish per dose were acclimated for one week, exposed to a lethal concentration 60 of bacteria, and monitored for 14 d. In a parallel experiment, the effects of PAH exposure on the acquired immune response were examined by immersion vaccinating fish against L. anguillarum and allowing specific immunity to develop for three weeks prior to challenge. All mortalities were aseptically sampled to confirm L. anguillarum infections. No significant differences in fish length, weight, or coefficient of condition were observed. These controlled laboratory experiments suggest that dietary exposures to an environmentally relevant mixture of PAH compounds do not alter the immunocompetence or growth of juvenile chinook salmon.
Photoinduced lethal and sublethal toxicity of retene, a polycyclic aromatic hydrocarbon derived from resin acid, to coregonid larvae
Authors: Vehniäinen Eeva-Riikka , Häkkinen Jani , Oikari Aimo 
Published: March 2005

Abstract
A comparative investigation on the acute phototoxicity of retene to vendace (Coregonus albula) and whitefish (C. lavaretus), both having pelagial larvae in spring, was conducted. To test the concept of early warning of sublethal biomarkers in relation to lethality to posthatch stages, we examined the effects of ultraviolet-B (UV-B) and retene on the levels of cytochrome P4501A (CYP1A) and heat shock protein 70 (HSP70) by exposing the animals to elevated levels of these factors for 48 and 72 h, respectively. Whereas UV-B and retene on their own were not lethal, simultaneous retene and UV-B exposure caused very high mortality to both species. The median lethal concentration (LC50; i.e., the concentration at which half of the larvae died) of retene as a precursor was 41 μg/L for vendace and 15 to 16 μg/L, depending on the UV-B dose, for whitefish. Retene evoked substantial induction of CYP1A in larvae of both species, and UV-B induced CYP1A in whitefish. In vendace, no effect on HSP70 levels by any factor was observed. In whitefish, however, UV-B radiation and water retene alone upregulated HSP70, but no additive response was detected. The CYP1A is a biomarker of exposure to retene in both species. The HSP70 is an early warning signal of UV-B exposure in whitefish. As a species, vendace appears to be more resistant than whitefish to the phototoxicity of retene, as indicated by the higher tolerance.
Distribution of acidic and neutral drugs in surface waters near sewage treatment plants in the lower Great Lakes, Canada
Authors: Metcalfe Chris D. , Miao Xiu-Sheng , Koenig Brenda G. , Struger John 
Published: March 2005

Abstract
Prescription and nonprescription drugs have been detected in rivers and streams in Europe and the United States. Sewage treatment plants (STPs) are an important source of these contaminants, but few data exist on the spatial distribution of drugs in surface waters near STPs. Samples of surface water were collected in the summer and fall of 2000 at open-water sites in the lower Great Lakes (Lake Ontario and Lake Erie), at sites near the two STPs for the city of Windsor (ON, Canada), and at sites in Hamilton Harbour (ON, Canada), an embayment of western Lake Ontario that receives discharges from several STPs. In a follow-up study in the summer of 2002, samples of surface water and final effluent from adjacent STPs were collected from sites in Hamilton Harbour and Windsor. In addition, surface water and STP effluent samples were collected in Peterborough (ON, Canada). All samples of surface water and STP effluents were analyzed for selected acidic and neutral drugs. In the survey of Hamilton Harbour and Windsor conducted in 2000, acidic drugs and the antiepileptic drug carbamazepine were detected at ng/L concentrations at sites that were up to 500 m away from the STP, but the hydrological conditions of the receiving waters strongly influenced the spatial distribution of these compounds. Drugs were not detected at open-water locations in western Lake Erie or in the Niagara River near the municipality of Niagara-on-the-Lake (ON, Canada). However, clofibric acid, ketoprofen, fenoprofen, and carba-mazepine were detected in samples collected in the summer of 2000 at sites in Lake Ontario and at a site in the Niagara River (Fort Erie, ON, Canada) that were relatively remote from STP discharges. Follow-up studies in the summer of 2002 indicated that concentrations of acidic and neutral drugs in surface waters near the point of sewage discharge into the Little River (ON, Canada) STP were approximately equal to the concentrations in the final effluent from the STP. Caffeine and cotinine, a metabolite of nicotine, were generally present in STP effluents and surface waters contaminated by drugs. The antidepressant fluoxetine and the antibiotic trimethoprom were also detected in most STP effluents and some surface water samples. For the first time, the lipid regulating drug atorvastatin was detected in samples of STP effluent and surface water.
Insecticidal activity of synthetic pyrethroids, organophosphates, insect growth regulators, and other livestock parasiticides: An Australian perspective
Authors: Wardhaugh Keith G. 
Published: March 2005

Abstract
The present review is restricted to the collation and evaluation of information describing the excretion profile and ecotoxicity of veterinary medicines developed specifically for the control of either internal or external parasites of livestock. It identifies numerous gaps in our knowledge and highlights our poor understanding of the environmental fate of many of these chemicals, especially those developed for the control of ticks, lice, and/or biting flies. Residues of most anthelmintics are largely harmless to dung-feeding arthropods, but those of many ectoparasiticides, especially the synthetic pyrethroids, are highly toxic to fly larvae and adult dung beetles. Organophosphates, because they are metabolized extensively and eliminated mostly in urine, are considered to be unlikely to have a major impact on the development or survival of dung-dwelling organisms. The present review stresses the need for better information regarding spatial and temporal usage patterns of veterinary parasiticides, and it examines the role of ecotoxicological models for evaluating their impact on populations of dung-dependent arthropods.
Factors influencing the sorption of oxytetracycline to soils
Authors: Jones Aaryn D. , Bruland Gregory L. , Agrawal Sheela G. , Vasudevan Dharni 
Published: March 2005

Abstract
Veterinary antibiotics such as oxytetracycline (OTC) increasingly are found in the environment and often come into direct contact with soils via the release of animal wastes. Oxytetracycline is known to sorb strongly to soils by interaction with soil organic matter, clay minerals, and metal oxides. However, current knowledge of the influence of soil properties on OTC sorption is limited, as is our ability to predict OTC sorption to soils. This work was aimed at identifying properties that most influence the extent of OTC sorption in a suite of soils from the eastern United States representing a wide range in soil properties. Thirty soils were well characterized, an OTC soil-water distribution coefficient (Kd) was determined for each soil, and statistical analyses were employed to determine appropriate soil descriptors of OTC sorption. Soil texture, cation exchange capacity, and iron oxide content seemed to most influence the extent of OTC sorption in soils with organic carbon (OC) content between 0 and 4%. Thus, the knowledge of these three soil properties would be key to anticipating the extent of OTC sorption and gaining insight into OTC fate within a given soil system. Notably, OC content appeared to influence OTC sorption only in a soil with 9% OC.
Fate of mercury accumulated by blowflies feeding on fish carcasses
Authors: Sarica José , Amyot Marc , Bey Julien , Hare Landis 
Published: March 2005

Abstract
Because fish represent the principal methylmercury (MeHg) pool in the water column of freshwater systems, MeHg released from their carcasses could represent an important flux to the environment. Necrophagous invertebrates such as fly larvae can play an important role in this Hg recycling. We studied Hg accumulation by blowflies (Diptera, Calliphoridae) feeding on beached fish carcasses in the field. We found that the MeHg these flies accumulated as larvae is retained in their pupal stage but is eliminated by the adult following emergence. We conclude that calliphorids possess an efficient mechanism for excreting the MeHg that they accumulate from carcasses.
Biofilm formation by algae as a mechanism for surviving on mine tailings
Authors: García-Meza J. Viridiana , Barrangue Christiane , Admiraal Wim 
Published: March 2005

Abstract
Photosynthetic biofilms successfully colonize the sediments of a mine tailings reservoir (Guanajuato, Mexico) despite the high metal concentrations that are present. To elucidate the mechanisms of biofilm survival despite metal ores, experiments were performed to evaluate the response of seminatural biofilms to Cu, Zn, and a combination of both metals at concentrations observed in the field. The biofilms were composed mostly of the chlorophyte Chlorococcum sp. and the cyanobacterium Phormidium sp., and their response to the two added metals was described by measurements of extracellular polymeric substances (EPS) and in vivo fluorescence. The photosynthetic efficiency and the minimal chlorophyll fluorescence of dark-adapted cells were measured by multiwavelength pulse amplitude–modulated fluorometry. The photosynthetic efficiency of light-adapted cells (ϕPSII) also was measured. Metal exposure increased the EPS production of biofilms, as visualized with confocal laser-scanning microscopy. Extracellular polymeric substances enhanced the extracellular metal accumulation from the first day of metal exposure. Metals provoked changes in the relative abundance of the dominant taxa because of a species-specific response to the metals when added individually. Metals affected the ϕpsii less than the total biomass, suggesting ongoing activity of the surviving biofilms. Survival of individual biofilm photosynthetic cells was found to resume from the embedding in the mucilaginous structure, which immobilizes the metals extracellularly. The survival of biofilms under mixed-metal exposure has practical applications in the remediation of mine tailings.