bluuebunny/crossref_metadata_2025_split huggingface dataset:
A benchmarking study of two trauma centres highlighting limitations when standardising mortality for comorbidity
Authors: Budd Henry R , Almond Laurence M , Oakley Peter A , McKenzie Gilbert , Danne Peter 
Published: January 2008

Abstract

Introduction
A continuous process of trauma centre evaluation is essential to ensure the development and progression of trauma care at regional, national and international levels. Evaluation may be by comparison between pooled datasets or by direct benchmarking between centres. This study attempts to benchmark mortality at two trauma centres standardising this for multiple case-mix factors, which includes the prevalence of individual background pre-existing diseases within the study population.

Methods
Trauma patients with an Injury Severity Score (ISS) >15 admitted to the two centres in 2001 and 2002 were included in the study with the exception of those who died in the emergency department. Patient characteristics were analysed in terms of 18 case-mix factors including Glasgow Coma Scale on arrival, Injury Severity Score and the presence or absence of 9 co-morbidity types, and patient outcome was compared based on in-hospital mortality before and after standardisation.

Results
Crude mortality was greater at UHNS (18.2 vs 14.5%) with a non-significant odds ratio of 1.31 prior to adjusting for case-mix (P = 0.171). Adjustment for case mix using logistic regression analysis altered the odds ratio to 1.64, which was not significant (P = 0.069).

Discussion
This study did not demonstrate any significant difference in the outcome of patients treated at either hospital during the study period. More importantly it has raised several important methodological issues pertinent to researchers undertaking registry based benchmarking studies. Data at the two registries was collected by personnel with differing backgrounds, in formats that were not completely compatible and was collected for patients that met different admissions criteria. The inclusion of a meaningful analysis of pre-existing disease was limited by the availability of robust data and sample size. We suggest greater communication between trauma research coordinators to ensure equivalent data collection and facilitate future benchmarking studies.
The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation
Authors: Wu Shirley , Liang Mike P , Altman Russ B 
Published: January 2008

AbstractStructural genomics efforts have led to increasing numbers of novel, uncharacterized protein structures with low sequence identity to known proteins, resulting in a growing need for structure-based function recognition tools. Our method, SeqFEATURE, robustly models protein functions described by sequence motifs using a structural representation. We built a library of models that shows good performance compared to other methods. In particular, SeqFEATURE demonstrates significant improvement over other methods when sequence and structural similarity are low.
Platelet–lymphocyte cross-talk
Authors: Li Nailin 
Published: January 2008

AbstractPlatelets and lymphocytes reciprocally regulate mutual functions, i.e., platelet–lymphocyte cross-talk. The heterotypic interactions have emerged as important regulatory mechanisms in the pathophysiological processes of thrombosis, inflammation, immunity, and atherosclerosis. Platelets influence lymphocyte function via direct cell–cell contact and/or soluble mediators. Hence, platelets enhance adhesion and cell migration of TH, T cytolytic (TC), NK, and B cells. Platelets affect other functional aspects of lymphocyte subpopulations in a complex manner. They may attenuate cytokine secretion and immunosuppressive responses of TH cells and enhance TC cell proliferation and cytotoxicity. Platelets promote isotype shifting and antibody production of B cells but ameliorate cytolytic activity of NK cells. On the other hand, lymphocytes can also regulate platelet aggregation and secretion, as well as the effector cell function of platelets in immune defense. The two cell types collaborate in transcellular phospholipid metabolism, CD40–CD40 ligand-mediated intercellular signaling, and their involvements in atherogenesis. The research perspectives of platelet–lymphocyte cross-talk have also been addressed.
TFF3-Based Candidate Gene Discrimination of Benign and Malignant Thyroid Tumors in a Region with Borderline Iodine Deficiency
Authors: Krause Kerstin , Eszlinger Markus , Gimm Oliver , Karger Stefan , Engelhardt Cornelia , Dralle Henning , Fuhrer Dagmar , Führer-Sakel Dagmar 
Published: January 2008

Abstract
Background: With the advent of microarray technology, increasing numbers of marker genes are proposed to distinguish benign and malignant thyroid lesions. However, most markers await confirmation through independent studies. In this paper, we re-evaluate the diagnostic potential of 10 proposed candidate genes in benign and malignant thyroid pathologies in a region with borderline iodine deficiency.
Methods: Quantitative real-time PCR was performed for CCND2, PLAB, PCSK2, HGD1, TFF3, B4GALT, LGALS3, ETS1, ADM3, and TG in 150 thyroid specimens, including 52 benign thyroid nodules (28 follicular adenoma and 24 adenomatous nodules), 52 corresponding normal thyroid tissues, 20 follicular carcinomas, 20 papillary carcinomas, and six undifferentiated carcinomas.
Results: On a single-gene basis, significant differences in mRNA expression were found for TFF3, PLAB, and ADM3 in benign thyroid nodules and thyroid malignancy. Using two-marker gene sets, we identified 11 combinations, which allowed both a distinction of benign and malignant thyroid nodules and a discrimination of follicular adenoma and carcinoma. However, for cancer prediction, analysis of a minimum of six genes per sample was necessary and allowed correct prediction of a benign thyroid lesion and thyroid cancer with 94% accuracy in the most discriminative set (TFF3/PLAB/TG/ADM3/HGD1/LGALS3).
Conclusion: We confirm the applicability of a number of recently proposed marker genes for the distinction of benign and malignant thyroid tumor and suggest that their diagnostic usefulness is independent of the iodide supply. We propose that the most discriminative marker set identified in our validation study together with marker combinations proposed by other investigators should now be evaluated in multicenter trials.
Assessing the biological relevance of exposing freshwater organisms to atrazine and molinate in environmentally realistic exposure test systems
Authors: Phyu Yin Latt , Warne Michael St. J , Lim Richard P 
Published: January 2008

Abstract
Assessing the toxicity of chemicals in treated laboratory water may not accurately represent the toxicity of chemicals in natural aquatic systems. In natural water, dissolved organic matter, suspended particulate matter, and sediment play key roles in the sorption of contaminants from the water. Our previously published series of papers illustrated that the presence of sediment in aquatic toxicity testing systems significantly (p &lt; 0.05) reduced the bioavailability of the herbicides atrazine and molinate to five Australian freshwater organisms. It is not clear whether the reduced bioavailability means that the trigger values (TVs) in the current Australian and New Zealand water quality guidelines, which are calculated using toxicity data from water-only toxicity tests, provide appropriate environmental protection. Several new sets of TVs were derived in the present study and were compared to each other and to the current Australian and New Zealand TVs for atrazine and molinate. The current Australian and New Zealand TVs for atrazine and molinate provided appropriate protection to Australian freshwater species. Australian freshwater species have a sensitivity distribution similar to those of overseas species to atrazine and molinate.
Interaction of stilbene compounds with human and rainbow trout estrogen receptors
Authors: Simmons Denina Bobbie Dawn , Trudeau Vance Lionel , Marlatt Vicki Lee , Moon Thomas William , Sherry James P , Metcalfe Chris David 
Published: January 2008

Abstract
Compounds with stilbene structures are widely used as pharmaceuticals and personal care products (PPCPs) and are present in plants. A suite of stilbene-related compounds, including PPCPs and plant-derived compounds were tested in vitro for interactions with the human and rainbow trout estrogen receptors and in vivo with rainbow trout using vitellogenin levels as a biomarker. Among the compounds with antagonistic activity, the common structural similarity was (in addition to the stilbene backbone) the presence of 4-hydroxy substitution. Stilbene-related compounds found to act as inhibitors at the estrogen receptor included the plant-derived compound resveratrol and two formulations of fluorescent whitening agents used in detergents, 4,4′-bis(2-sulfostyryl)biphenyl and diaminostilbene-1. In the yeast estrogenicity screening assay, the concentrations which caused a 50% inhibition in estrogenic response (IC50s) with the human estrogen receptor ranged from 2.56 × 10−6 to 2.56 × 10−6 M. In the rainbow trout estrogen receptor assay, the IC50s ranged from 7.75 × 10−8 to 1.11 × 10−5 M. However, in the in vivo rainbow trout vitellogenin assay, tamoxifen was the only stilbene of the compounds tested to have a significant effect as an inhibitor of estrogenicity.
Fonofos poisons raptors and waterfowl several months after granular application
Authors: Elliott John E , Birmingham Anna L , Wilson Laurie K , McAdie Malcolm , Trudeau Suzanne , Mineau Pierre 
Published: January 2008

AbstractFrom 1994 to 1999 in the Lower Fraser Valley region of southwest Canada, fonofos (Dyfonate G) was recommended for control of introduced wireworm (Agriotes spp.) pests on potato and other root crops. As part of a wildlife-monitoring program, we collected 15 raptors, including 12 bald eagles (Haliaeetus leucocephalus), found dead or debilitated on or near agricultural lands with severely inhibited brain and/or plasma cholinesterase activity and fonofos residues in ingesta. Bird remains, in nine cases waterfowl, were identified in the ingesta samples. Another seven bald eagles had severe cholinesterase inhibition, but without evidence of fonofos residues. During two winters from 1996 to 1998, 420 ha of potato fields, half of which had been treated the previous spring with fonofos and the remainder untreated, were searched weekly for evidence of wildlife mortality. Search efficiency was assessed with placed duck carcasses. Waterfowl outnumbered other species in field-use counts and comprised the greatest proportion of birds found dead. We found 211 wildlife remains, most scavenged; 35 intact carcasses were suitable for postmortem examination and/or toxicology analyses. Cholinesterase activity was assayed in brains of 18 waterfowl, five of which had severely depressed activity (average inhibition 74%; range, 69–78%). The gastrointestinal tract of a mallard found in a field treated with granular product contained 49 μg/g fonofos residues, linking waterfowl mortality with labelled use of the product. These findings demonstrate the risk of both primary and secondary poisoning by anticholinesterase insecticides where wildlife make intensive use of farmed fields.
Effect of prolonged exposition to pulp mill effluents on the invasive aquatic plantEgeria densaand other primary producers: A mesocosm approach
Authors: Palma Alvaro T , Silva Marcelo G , Muñoz Carlos A , Cartes Carolina , Jaksic Fabián M 
Published: January 2008

AbstractThe recent disappearance of the aquatic plant Egeria densa, a Brazilian native invasive species, from a wetland in southern Chile prompted several efforts to unveil the origin of this phenomenon. Because these changes occurred by the time a newly built pulp mill started its operations in the area, a reasonable doubt for a cause–effect relationship is plausible. We implemented a mesocosm approach to directly evaluate the effect of treated pulp mill effluents (PMEs) on several growth-related parameters of E. densa as well as other primary producers. We hypothesize that effluent, at a dilution similar to that detected in the zone of the wetland where the negative environmental impacts were evident, has a significant negative effect on this aquatic plant as well as on other primary producers inside a mesocosm system. After a prolonged (months) exposure to both 0% PME with pure river water and a 4 to 5% (v/v) dilution of treated PME, no effect on E. densa was measured. Furthermore, plants exposed to effluent exhibited a significantly greater general growth rate. Coincidently, chlorophyll a concentration in the water column and periphyton biomass also changed over time, but without any pattern attributable to the effluent. Values of the autotrophic index obtained from the periphyton growth pattern did not suggest enrichment of the system with organic matter. Our results only refer to the direct effect of mill effluents on several biotic responses, but they represent an important advance toward generation of the scientific knowledge necessary to understand how the ecosystem functions while receiving this and other unquantified sources of water.
Arsenate-induced toxicity: Effects on antioxidative enzymes and DNA damage in Vicia faba
Authors: Lin Aijun , Zhang Xuhong , Zhu Yong-Guan , Zhao Fang-Jie 
Published: January 2008

Abstract
A glasshouse hydroponic experiment was conducted to investigate the toxicity of arsenate to broad bean (Vicia faba) plants when grown with external arsenate concentrations at 10 μmol/L. The treated plants showed no obvious symptoms of phytotoxicity, but shoot/root growth was inhibited. Lipid peroxidation in leaves and roots increased with the addition of arsenate, indicating oxidative stress. We investigated the responses to arsenate exposure in the activities of several representative antioxidant enzymes, including peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD), in plant tissues, and the DNA damage in plant leaves and root tips induced by arsenate in this plant was detected for the first time. Arsenate addition increased POD activity in the leaves significantly but decreased its activity in the roots in the 10 μmol/L treatment. Arsenate addition caused an induction of SOD and CAT activities in both leaves and roots, but not in roots at the arsenate concentration of 10 μmol/L. The DNA damage in V. faba was detected using Comet assay; in both leaves and roots, DNA damage increased with increasing arsenate concentrations, indicating genotoxicity of arsenate. These results indicate that arsenate toxicity causes oxidative stress in V. faba, which might be one of the mechanisms through which arsenic induces DNA damage.
Photodegradation of decabromodiphenyl ether in house dust by natural sunlight
Authors: Stapleton Heather M , Dodder Nathan G 
Published: January 2008

Abstract
Photolytic degradation of decabromodiphenyl ether (BDE 209) has been observed in several matrices such as solvent/water mixtures, sediments, and soil; however, no studies have investigated the degradation potential of BDE 209 in house dust. In the present study, both a natural and a BDE 209–spiked dust material were exposed to sunlight for 200 cumulative h. Degradation of BDE 209 was observed in both matrices but was 35% greater in the spiked dust relative to the natural dust material. The pseudo-first-order degradation rates were 2.3 × 10−3 and 1.7 × 10−3 per hour for the spiked and natural dust, respectively. During the 200-h exposure, as much as 38% of the original BDE 209 mass was degraded in the spiked dust, 25% of which could not be accounted for and was lost to unknown pathways and/or products. The remaining 13% was accounted for by the formation of lower brominated congeners. Debrominated products detected in the spiked dust included all three nonabrominated congeners (BDE 206, BDE 207, and BDE 208) and several octabrominated congeners (BDE 196, BDE 197, BDE 201, BDE 202, and BDE 203/200). In technical commercial octa-BDE mixtures, BDE 201 is a very small component (below detection limit to 0.8%), and BDE 202 is not detected. Therefore, the presence of these congeners in house dust may provide a marker of environmental debromination of BDE 209. The ratio of BDE 197 to BDE 201 may also be indicative of BDE 209 degradation. as the ratio of these two congeners appeared to reach a steady-state value (∼1) in both exposure scenarios in the present study.
Estimating metabolic biotransformation rates in fish from laboratory data
Authors: Arnot Jon A , Mackay Don , Bonnell Mark 
Published: January 2008

AbstractA method is proposed for estimating metabolic biotransformation rate constants for nonionic organic chemicals from measured laboratory bioconcentration and dietary bioaccumulation data in fish. Data have been selected based on a quality review to reduce uncertainty in the measured values. A kinetic mass balance model is used to estimate rates of chemical uptake and elimination. Biotransformation rate constants are essentially calculated as the difference between two quantities, a measured bio-concentration factor or elimination rate constant, and a model-derived bioconcentration factor or elimination rate constant estimated assuming no biotransformation. Model parameterization exploits key empirical data when they are available and assumes default values when study specific data are unavailable. Uncertainty analyses provide screening level assessments for confidence in the biotransformation rate constant estimates. The uncertainty analyses include the range for 95% of the predicted values and 95% confidence intervals for the calculated biotransformation values. Case studies are provided to illustrate the calculation and uncertainty methods. Biotransformation rate constants calculated by the proposed method are compared with other published estimates for 31 chemicals that range in octanol–water partition coefficients from approximately 101 to 108 and represent over four orders of magnitude in biotransformation potential. The comparison of previously published values with those calculated by the proposed method shows general agreement with 82% of the estimated values falling within a factor of three.
Acute and delayed effects of the neonicotinoid insecticide thiacloprid on seven freshwater arthropods
Authors: Beketov Mikhail A , Liess Matthias 
Published: January 2008

AbstractEcotoxicological risk assessment of contaminants often is based on toxicity tests with continuous-exposure profiles. However, input of many contaminants (e.g., insecticides) to surface waters typically occurs in pulses rather than continuously. Neonicotinoids are a new group of insecticides, and little is known about their toxicity to nontarget freshwater organisms and potential effects on freshwater ecosystems. The aim of the present research was to assess effects of short-term (24-h) exposure to the neonicotinoid insecticide thiacloprid, including a postexposure observation period. A comparison of several freshwater insect and crustacean species showed an increase of sensitivity by three orders of magnitude in the following order: Daphnia magna &lt; Asellus aquaticus = Gammarus pulex &lt; Simpetrum striolatum &lt; Culex pipiens = Notidobia ciliaris = Simulium latigonium, with median lethal concentrations (LC50s) of 4,400, 153, 190, 31.2, 6.78, 5.47, and 5.76 μg/L, respectively (postexposure observation 11–30 d). Thiacloprid caused delayed lethal and sublethal effects, which were observed after 4 to 12 d following exposure. Reduction in LC50s found when postexposure observation was extended from 1 d to a longer period (11–30 d) was up to &gt;50-fold. Hence, delayed effects occurring after short-term exposure should be considered in risk assessment. The 5% hazardous concentration (HC5) of thiacloprid obtained in the present study (0.72 μg/L) is more than one order of magnitude below the currently predicted worst-case environmental concentrations in surface water. Concerning the selection of test organisms, we observed that the widely employed test organism D. magna is least sensitive among the arthropods tested and that, for neonicotinoid insecticides, an insect like the mosquito C. pipiens would be more suitable for predicting effects on sensitive species.
Variations of the Perforin Gene in Patients With Type 1 Diabetes
Authors: Orilieri Elisabetta , Cappellano Giuseppe , Clementi Rita , Cometa Angela , Ferretti Massimo , Cerutti Elisa , Cadario Francesco , Martinetti Miryam , Larizza Daniela , Calcaterra Valeria , D’Annunzio Giuseppe , Lorini Renata , Cerutti Franco , Bruno Graziella , Chiocchetti Annalisa , Dianzani Umberto 
Published: January 2008

OBJECTIVE—Perforin plays a key role in cell-mediated cytotoxicity. Mutations of its gene, PRF1, cause familial hemophagocytic lymphohistiocytosis but have also been associated with lymphomas and the autoimmune/lymphoproliferative syndrome. The aim of this work was to investigate the role of PRF1 variations in type 1 diabetes.
RESEARCH DESIGN AND METHODS—We typed for the N252S and A91V variations in an initial population of 352 type 1 diabetic patients and 816 control subjects and a second population of 365 patients and 964 control subjects. Moreover, we sequenced the coding sequence and intron-exons boundaries in 200 patients and 300 control subjects.
RESULTS—In both cohorts, allelic frequency of N252S was significantly higher in patients than in control subjects (combined cohorts: 1.5 vs. 0.4%; odds ratio 6.68 [95% CI 1.83–7.48]). Sequencing of the entire coding region detected one novel mutation in one patient, causing a P477A amino acid change not detected in 199 patients and 300 control subjects. Typing for HLA-DQA1 and DQB1 alleles showed that type 1 diabetes–predisposing DQα/DQβ heterodimers were less frequent in patients carrying N252S or P477A than in those carrying wild-type PRF1. We previously found that natural killer (NK) activity is not decreased in most N252S heterozygotes, but we detected one whose NK activity was normal at the age of 12 but strikingly low in early childhood. Here, we discovered that NK function was low in three heterozygotes in early childhood, one homozygous adult, and in the subject carrying P477A.
CONCLUSIONS—These data suggest that N252S and possibly other PRF1 variations are susceptibility factors for type 1 diabetes development.