bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating monitoring methods to guide adaptive management of a threatened amphibian (Litoria aurea)
Authors: Bower Deborah S. , Pickett Evan J. , Stockwell Michelle P. , Pollard Carla J. , Garnham James I. , Sanders Madeleine R. , Clulow John , Mahony Michael J. 
Published: March 2014

AbstractPrompt detection of declines in abundance or distribution of populations is critical when managing threatened species that have high population turnover. Population monitoring programs provide the tools necessary to identify and detect decreases in abundance that will threaten the persistence of key populations and should occur in an adaptive management framework which designs monitoring to maximize detection and minimize effort. We monitored a population of Litoria aurea at Sydney Olympic Park over 5 years using mark–recapture, capture encounter, noncapture encounter, auditory, tadpole trapping, and dip‐net surveys. The methods differed in the cost, time, and ability to detect changes in the population. Only capture encounter surveys were able to simultaneously detect a decline in the occupancy, relative abundance, and recruitment of frogs during the surveys. The relative abundance of L. aurea during encounter surveys correlated with the population size obtained from mark–recapture surveys, and the methods were therefore useful for detecting a change in the population. Tadpole trapping and auditory surveys did not predict overall abundance and were therefore not useful in detecting declines. Monitoring regimes should determine optimal survey times to identify periods where populations have the highest detectability. Once this has been achieved, capture encounter surveys provide a cost‐effective method of effectively monitoring trends in occupancy, changes in relative abundance, and detecting recruitment in populations.
Human antigen‐specific CD4+CD25+CD134+CD39+ T cells are enriched for regulatory T cells and comprise a substantial proportion of recall responses
Authors: Seddiki Nabila , Cook Laura , Hsu Denise C. , Phetsouphanh Chansavath , Brown Kai , Xu Yin , Kerr Stephen J. , Cooper David A. , Munier C. Mee Ling , Pett Sarah , Ananworanich Jintanat , Zaunders John , Kelleher Anthony D. 
Published: March 2014

Human Ag‐specific CD4+ T cells can be detected by their dual expression of CD134 (OX40) and CD25 after a 44 hours stimulation with cognate Ag. We show that surface expression of CD39 on Ag‐specific cells consistently identifies a substantial population of CD4+CD25+CD134+CD39+ T cells that have a Treg‐cell‐like phenotype and mostly originate from bulk memory CD4+CD45RO+CD127lowCD25highCD39+ Treg cells. Viable, Ag‐specific CD25+CD134+CD39+ T cells could be expanded in vitro as cell lines and clones, and retained high Forkhead Box Protein 3, CTLA‐4 and CD39 expression, suppressive activity and Ag specificity. We also utilised this combination of cell surface markers to measure HIV‐Gag responses in HIV+ patients before and after anti‐retroviral therapy (ART). Interestingly, we found that the percentage of CD39− cells within baseline CD4+ T‐cell responses to HIV‐Gag was negatively correlated with HIV viral load pre‐ART and positively correlated with CD4+ T‐cell recovery over 96 weeks of ART. Collectively, our data show that Ag‐specific CD4+CD25+CD134+CD39+ T cells are highly enriched for Treg cells, form a large component of recall responses and maintain a Treg‐cell‐like phenotype upon in vitro expansion. Identification and isolation of these cells enables the role of Treg cells in memory responses to be further defined and provides a development pathway for novel therapeutics.
Airflow and aeolian sediment transport patterns within a coastal trough blowout during lateral wind conditions
Authors: Smyth Thomas Andrew George , Jackson Derek , Cooper Andrew 
Published: March 2014

ABSTRACTBlowouts are depressions that occur on coastal dunes, deserts and grasslands. The absence of vegetation in blowouts permits high speed winds to entrain and remove sediment. Whereas much research has examined patterns of wind flow and sediment transport on the stoss slopes and lee of sand dunes, no study has yet investigated the connections between secondary air‐flow structures and sediment transport in a blowout where zones of streamline compression, expansion and steering are less clearly delineated. In this study we investigated the variability of sediment flux and its relation to near‐surface wind speed and turbulence within a trough blowout during wind flow that was oblique to the axis of the blowout. Wind flow was measured using six, three‐dimensional (3D) ultrasonic anemometers while sediment flux by eight sand traps, all operating at 25 Hz.Results demonstrated that sediment flux rates were highly variable throughout the blowout deflation basin, even over short distances (< 0.5 m). Where flow was steadiest, flux was greatest. Consequently the highest rates of sediment transport were recorded on the erosional wall crest where flow was compressed and accelerated. The strength of correlation between sediment flux and wind parameter improved with an increase in averaging interval, from 10 seconds to 1 minute. At an interval of 10 seconds, however, wind speed correlated best with flux at seven of eight traps, whereas at an interval of one minute Turbulent Kinetic Energy (TKE) provided the best correlation with flux at six of the eight traps. Correlation between sediment flux and wind parameters was best in the centre of the blowout and poorest on the erosional wall crest. The evidence from this paper suggests, for the first time, that TKE may be a better predictor of sediment transport at minute scale averaging intervals, particularly over landforms where wind flow is highly turbulent. Copyright © 2014 John Wiley & Sons, Ltd.
Cholinesterase activity of muscle tissue from freshwater fishes: Characterization and sensitivity analysis to the organophosphate methyl-paraoxon
Authors: Lopes Renato Matos , Filho Moacelio Veranio Silva , de Salles João Bosco , Bastos Vera Lúcia Freire Cunha , Bastos Jayme Cunha 
Published: March 2014

Abstract

The biochemical characterization of cholinesterases (ChE) from different teleost species has been a critical step in ensuring the proper use of ChE activity levels as biomarkers in environmental monitoring programs. In the present study, ChE from Oreochromis niloticus, Piaractus mesopotamicus, Leporinus macrocephalus, and Prochilodus lineatus was biochemically characterized by specific substrates and inhibitors. Moreover, muscle tissue ChE sensitivity to the organophosphate pesticide methyl-paraoxon was evaluated by determining the inhibition kinetic constants for its progressive irreversible inhibition by methyl-paraoxon as well as the 50% inhibitory concentration (IC50) for 30 min for each species. The present results indicate that acetylcholinesterase (AChE) must be present in the muscle from P. mesopotamicus, L. macrocephalus, and P. lineatus and that O. niloticus possesses an atypical cholinesterase or AChE and butyrylcholinesterase (BChE). Furthermore, there is a large difference regarding the sensitivity of these enzymes to methyl-paraoxon. The determined IC50 values for 30 min were 70 nM (O. niloticus), 258 nM (P. lineatus), 319 nM (L. macrocephalus), and 1578 nM (P. mesopotamicus). The results of the present study also indicate that the use of efficient methods for extracting these enzymes, their kinetic characterization, and determination of sensitivity differences between AChE and BChE to organophosphate compounds are essential for the determination of accurate ChE activity levels for environmental monitoring programs. Environ Toxicol Chem 2014;33:1331–1336. © 2014 SETAC
Developing a foundation for eco-epidemiological assessment of aquatic ecological status over large geographic regions utilizing existing data resources and models
Authors: Kapo Katherine E. , Holmes Christopher M. , Dyer Scott D. , de Zwart Dick , Posthuma Leo 
Published: March 2014

Abstract

Eco-epidemiological studies utilizing existing monitoring program data provide a cost-effective means to bridge the gap between the ecological status and chemical status of watersheds and to develop hypotheses of stressor attribution that can influence the design of higher-tier assessments and subsequent management. The present study describes the process of combining existing data and models to develop a robust starting point for eco-epidemiological analyses of watersheds over large geographic scales. Data resources from multiple federal and local agencies representing a range of biological, chemical, physical, toxicological, and other landscape factors across the state of Ohio, USA (2000–2007), were integrated with the National Hydrography Dataset Plus hydrologic model (US Environmental Protection Agency and US Geological Survey). A variety of variable reduction, selection, and optimization strategies were applied to develop eco-epidemiological data sets for fish and macroinvertebrate communities. The relative importance of landscape variables was compared across spatial scales (local catchment, watershed, near-stream) using conditional inference forests to determine the scales most relevant to variation in biological community condition. Conditional inference forest analysis applied to a holistic set of environmental variables yielded stressor–response hypotheses at the statewide and eco-regional levels. The analysis confirmed the dominant influence of state-level stressors such as physical habitat condition, while highlighting differences in predictive strength of other stressors based on ecoregional and land-use characteristics. This exercise lays the groundwork for subsequent work designed to move closer to causal inference. Environ Toxicol Chem 2014;33:1665–1677. © 2014 SETAC
Field survey of Canadian background soils: Implications for a new mathematical gas chromatography–flame ionization detection approach for resolving false detections of petroleum hydrocarbons in clean soils
Authors: Kelly-Hooper Francine , Farwell Andrea J. , Pike Glenna , Kennedy Jocelyn , Wang Zhendi , Grunsky Eric C. , Dixon D. George 
Published: March 2014

Abstract

The reference method for the Canada-wide standard (CWS) for petroleum hydrocarbons (PHCs) in soil provides laboratories with methods for generating accurate and reproducible soil analysis results. The CWS PHC tier 1 generic soil-quality guidelines apply to 4 carbon ranges/fractions: F1 (C6–C10), F2 (C10–C16), F3 (C16–C34), and F4 (&gt;C34). The methods and guidelines were developed and validated for soils with approximately 5% total organic carbon (TOC). However, organic soils have much higher TOC levels because of biogenic organic compounds (BOCs) originating from sources such as plant waxes and fatty acids. Coextracted BOCs can have elevated F2–F4 concentrations, which can cause false exceedances of PHC soil guidelines. The present study evaluated false PHC detections in soil samples collected from 34 background sites. The list of analytes included soil type, TOC, polycyclic aromatic hydrocarbons (PAHs), F2, F3, F4, F3a (C16–C22), and F3b (C22–C34). Soils with 3% to 41% TOC falsely exceeded the CWS PHC 300 mg/kg F3 coarse soil guideline. It was previously demonstrated that clean peat had F2:F3b ratios of less than 0.10, while crude oil spiked peat and spiked sand had higher ratios of greater than 0.10. In the present background study, all of the clean organic soils with at least 300 mg/kg F3 had F2:F3b ratios of less than 0.10, which indicated false guideline exceedances. Clean inorganic soils had low F3 concentrations, resulting in high F2:F3b ratios of greater than 0.10. Validation field studies are required to determine if the F2:F3b 0.10 PHC presence versus absence threshold value is applicable to crude oil- and diesel-contaminated sites. Environ Toxicol Chem 2014;33:1754–1760. © 2014 SETAC
Realistic environmental mixtures of micropollutants in surface, drinking, and recycled water: Herbicides dominate the mixture toxicity toward algae
Authors: Tang Janet Y.M. , Escher Beate I. 
Published: March 2014

Abstract

Mixture toxicity studies with herbicides have focused on a few priority components that are most likely to cause environmental impacts, and experimental mixtures were often designed as equipotent mixtures; however, real-world mixtures are made up of chemicals with different modes of toxic action at arbitrary concentration ratios. The toxicological significance of environmentally realistic mixtures has only been scarcely studied. Few studies have simultaneously compared the mixture effect of water samples with designed reference mixtures comprised of the ratios of analytically detected concentrations in toxicity tests. In the present study, the authors address the effect of herbicides and other chemicals on inhibition of photosynthesis and algal growth rate. The authors tested water samples including secondary treated wastewater effluent, recycled water, drinking water, and storm water in the combined algae assay. The detected chemicals were mixed in the concentration ratios detected, and the biological effects of the water samples were compared with the designed mixtures of individual detected chemicals to quantify the fraction of effect caused by unknown chemicals. The results showed that herbicides dominated the algal toxicity in these environmentally realistic mixtures, and the contribution by the non-herbicides was negligible. A 2-stage model, which used concentration addition within the groups of herbicides and non-herbicides followed by the model of independent action to predict the mixture effect of the two groups, could predict the experimental mixture toxicity effectively, but the concentration addition model for herbicides was robust and sufficient for complex mixtures. Therefore, the authors used the bioanalytical equivalency concept to derive effect-based trigger values for algal toxicity for monitoring water quality in recycled and surface water. All water samples tested would be compliant with the proposed trigger values associated with the appropriate guidelines. Environ Toxicol Chem 2014;33:1427–1436. © 2014 SETAC
Modeling oxyanion adsorption on ferralic soil, part 2: Chromate, selenate, molybdate, and arsenate adsorption
Authors: Pérez Claudio , Antelo Juan , Fiol Sarah , Arce Florencio 
Published: March 2014

Abstract

High levels of oxyanions are found in the soil environment, often as a result of human activity. At high concentrations, oxyanions can be harmful to both humans and wildlife. Information about the interactions between oxyanions and natural samples is essential for understanding the bioavailability, toxicity, and transport of these compounds in the environment. In the present study, the authors investigated the reactivity of different oxyanions (AsO4, MoO4, SeO4, and CrO4) at different pH values in 2 horizons of a ferralic soil. By combining available microscopic data on iron oxides with the macroscopic data obtained, the authors were able to use the charge distribution model to accurately describe the adsorption of these 4 oxyanions and thus to determine the surface speciation. The charge distribution model was previously calibrated and evaluated using phosphate adsorption/desorption data. The adsorption behavior on ferralic soil is controlled mainly by the natural iron oxides present, and it is qualitatively analogous to that exhibited by synthetic iron oxides. The highest adsorption was found for arsenate ions, whereas the lowest was found for selenate, with chromate and molybdate ions showing an intermediate behavior. Environ Toxicol Chem 2014;33:2217–2224. © 2014 SETAC
Effects of anionic polyacrylamide products on gill histopathology in juvenile rainbow trout (Oncorhynchus mykiss)
Authors: Kerr Jennifer L. , Lumsden John S. , Russell Spencer K. , Jasinska Edyta J. , Goss Greg G. 
Published: March 2014

Abstract
Anionic polyacrylamide (PAM) products are commonly used to remove suspended materials from turbid waters and to help mitigate soil erosion. In the present study, juvenile rainbow trout (Oncorhynchus mykiss) were exposed to 3 mg/L to 300 mg/L of 10 commercially available PAM products (Clearflow Water Lynx Polymer Log and Clearflow Soil Lynx Granular Polymer; Clearflow Enviro Systems Group), and gill histological parameters were measured following either 7 d or 30 d of polymer exposure. A cationic polymer product (≤0.38 mg/L MagnaFloc 368; Ciba Specialty Chemical) was also tested for comparison. Mild gill lesions were observed in fish exposed to polymer products. Lamellar fusion, interlamellar hyperplasia, epithelial lifting, mucous cell metaplasia, and cell counts of epithelial swelling and necrosis/apoptosis were minimal in fish exposed to environmentally relevant concentrations of anionic polymer (≤30 mg/L). Gill morphology was largely unaffected by exposure to concentrations up to 300 mg/L of many PAM products. Several anionic polymer products noticeably affected gill tissue by increasing epithelial hypertrophy, interlamellar hyperplasia, mucous cell metaplasia, and the frequency of necrotic cells. The severity of the lesions lessened with time, suggesting that fish may have experienced a short-term irritant effect. Similar levels of gill pathology were frequently observed in fish exposed to cationic polymer MagnaFloc 368 despite the concentration being 1000-fold lower than that of the PAM products. These observations highlight the increased toxicity of cationic polymers to aquatic life compared with anionic PAMs. Environ Toxicol Chem 2014;33:1552–1562. © 2014 SETAC
Discontinuous Galerkin finite element discretization of a strongly anisotropic diffusion operator
Authors: Pestiaux A. , Melchior S.A. , Remacle J.F. , Kärnä T. , Fichefet T. , Lambrechts J. 
Published: March 2014

SUMMARYThe discretization of a diffusion equation with a strong anisotropy by a discontinuous Galerkin finite element method is investigated. This diffusion term is implemented in the tracer equation of an ocean model, thanks to a symmetric tensor that is composed of diapycnal and isopycnal diffusions. The strong anisotropy comes from the difference of magnitude order between both diffusions. As the ocean model uses interior penalty terms to ensure numerical stability, a new penalty factor is required in order to correctly deal with the anisotropy of this diffusion. Two penalty factors from the literature are improved and established from the coercivity property. One of them takes into account the diffusion in the direction normal to the interface between the elements. After comparison, the latter is better because the spurious numerical diffusion is weaker than with the penalty factor proposed in the literature. It is computed with a transformed coordinate system in which the diffusivity tensor is diagonal, using its eigenvalue decomposition. Furthermore, this numerical scheme is validated with the method of manufactured solutions. It is finally applied to simulate the evolution of temperature and salinity due to turbulent processes in an idealized Arctic Ocean. Copyright © 2014 John Wiley & Sons, Ltd.
Effects of processing on the proximate and metal contents in three fish species from Nigerian coastal waters
Authors: Bassey Francisca I. , Oguntunde Fehintola C. , Iwegbue Chukwujindu M. A. , Osabor Vincent N. , Edem Christopher A. 
Published: March 2014

AbstractThe effects of culinary practices such as boiling, frying, and grilling on the proximate compositions and concentrations of metals (Cd, Pb, Cr, Zn, Fe, Cu, Mn, Ni, and Hg) in commonly consumed fish species from the Nigerian coastal waters were investigated. The selected fish species were Polydactylus quadratifilis, Chrysicthys nigrodigitatus and Cynoglossus senegalensis. The culinary practices lead to increased protein, fat, and ash contents and decreased moisture contents of these fish species. The culinary practices resulted significant increase in the concentrations of most of the studied metals and decrease in the concentrations of Fe, Cr, and Pb in some fish types. The concentrations and estimated dietary intakes of Cd, Pb, Cr, Zn, Fe, Cu, Mn, Ni, and Hg from consumption of the processed fish were within their statutory safe limits. The individual metal target hazard quotient (THQ) values and the total THQs were less than 1 which indicates that no health risks would arise from the long‐term consumption of these fish species.
Tissue Crosstalk in Lung Development
Authors: Hines Elizabeth A. , Sun Xin 
Published: March 2014

ABSTRACTLung development follows a stereotypic program orchestrated by key interactions among epithelial and mesenchymal tissues. Deviations from this developmental program can lead to pulmonary diseases including bronchopulmonary dysplasia and pulmonary hypertension. Significant efforts have been made to examine the cellular and molecular basis of the tissue interactions underlying these stereotypic developmental processes. Genetically engineered mouse models, lung organ culture, and advanced imaging techniques are a few of the tools that have expanded our understanding of the tissue interactions that drive lung development. Intimate crosstalk has been identified between the epithelium and mesenchyme, distinct mesenchymal tissues, and individual epithelial cells types. For interactions such as the epithelial–mesenchymal crosstalk regulating lung specification and branching morphogenesis, the key molecular players, FGF, BMP, WNT, and SHH, are well established. Additionally, VEGF regulation underlies the epithelial–endothelial crosstalk that coordinates airway branching with angiogenesis. Recent work also discovered a novel role for SHH in the epithelial‐to‐mesenchymal (EMT) transition of the mesothelium. In contrast, the molecular basis for the crosstalk between upper airway cartilage and smooth muscle is not yet known. In this review we examine current evidence of the tissue interactions and molecular crosstalk that underlie the stereotypic patterning of the developing lung and mediate injury repair. J. Cell. Biochem. 115: 1469–1477, 2014. © 2014 Wiley Periodicals, Inc.
Sonographic detection of a patency capsule prior to capsule endoscopy: Case report
Authors: Kobayashi Yuka , Yamada Atsuo , Watabe Hirotsugu , Takahashi Ryota , Suzuki Hirobumi , Hirata Yoshihiro , Yamaji Yutaka , Yoshida Haruhiko , Koike Kazuhiko 
Published: March 2014

ABSTRACTTo avoid retention of the capsule used in capsule endoscopy (CE), the patency capsule (PC), a self‐disintegrating sham capsule, is administered prior to CE in patients suspected of small intestinal stenosis. If the PC is excreted intact within 30 hours of ingestion, the patient can undergo CE without retention. However, if the PC is not excreted within 30 hours, its location must be confirmed as in either the small intestine or the colon because of the potential for small intestinal stenosis in the former case. It is often difficult to confirm the location of the PC by abdominal radiograph. We report the case of one patient who did not excrete the PC within 30 hours and for whom it was difficult to distinguish whether the PC was in the small intestine or the colon on abdominal series. Abdominal sonography revealed the PC in the colon and subsequent CE was performed without complication. © 2014 Wiley Periodicals, Inc. J Clin Ultrasound 42:554–556, 2014