bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urban stormwater thermal gene expression models for protection of sensitive receiving streams
Authors: Sattar A.M.A. , Gharabaghi B. , Sabouri F. , Thompson A.M. 
Published: March 2017

AbstractThermal impact of typical high‐density residential, industrial, and commercial land uses is a major concern for the health of aquatic life in urban watersheds, especially in smaller, cold, and cool‐water streams. This is the first study of its kind that provides simple easy‐to‐use equations, developed using gene expression programming (GEP) that can guide the assessment and the design of urban stormwater management systems to protect thermally sensitive receiving streams. We developed 3 GEP models using data collected during 3 years (2009–2011) from 4 urban catchments; the first GEP model predicts event mean temperature at the inlet of the pond; the second model predicts the stormwater temperature at the outlet of the pond; and the third model predicts the temperature of the stormwater after flowing through a cooling trench and before discharging to the receiving stream. The new models have high correlation coefficients of 0.90–0.94 and low prediction uncertainty of less than 4% of the median value of the predicted runoff temperatures. Sensitivity analysis shows that climatic factors have the highest influence on the thermal enrichment followed by the catchment characteristics and the key design variables of the stormwater pond and the cooling trench. The general method presented here is easily transferable to other regions of the world (but not necessarily the exact equations developed here); also through sensitivity and parametric analysis, we gained insight on the key factors and their relative importance in modelling thermal enrichment of urban stromwater runoff.
Spatially explicit bioaccumulation modeling in aquatic environments: Results from 2 demonstration sites
Authors: von Stackelberg Katherine , Williams Marc A , Clough Jonathan , Johnson Mark S 
Published: March 2017

Abstract

Bioaccumulation models quantify the relationship between sediment and water exposure concentrations and resulting tissue levels of chemicals in aquatic organisms and represent a key link in the suite of tools used to support decision making at contaminated sediment sites. Predicted concentrations in the aquatic food web provide exposure estimates for human health and ecological risk assessments, which, in turn, provide risk-based frameworks for evaluating potential remedial activities and other management alternatives based on the fish consumption pathway. Despite the widespread use of bioaccumulation models to support remedial decision making, concerns remain about the predictive power of these models. A review of the available literature finds the increased mathematical complexity of typical bioaccumulation model applications is not matched by the deterministic exposure concentrations used to drive the models. We tested a spatially explicit exposure model (FishRand) at 2 nominally contaminated sites and compared results to estimates of bioaccumulation based on conventional, nonspatial techniques, and monitoring data. Differences in predicted fish tissue concentrations across applications were evident, although these demonstration sites were only mildly contaminated and would not warrant management actions on the basis of fish consumption. Nonetheless, predicted tissue concentrations based on the spatially explicit exposure characterization consistently outperformed conventional, nonspatial techniques across a variety of model performance metrics. These results demonstrate the improved predictive power as well as greater flexibility in evaluating the impacts of food web exposure and fish foraging behavior in a heterogeneous exposure environment. Integr Environ Assess Manag 2017;13:1023–1037. © 2017 SETAC

Key Points
We demonstrate the advantages of a probabilistic, spatially explicit bioaccumulation modeling framework. We identify how fish foraging behavior intersects with heterogeneity in exposure concentrations in aquatic environments. Spatially explicit methods take advantage of GIS. Probabilistic methods combined with GIS better inform decision making.
Osteogenic differentiation of mesenchymal stem cells using hybrid nanofibers with different configurations and dimensionality
Authors: Gugutkov Dencho , Awaja Firas , Belemezova Kalina , Keremidarska Milena , Krasteva Natalia , Kyurkchiev Stanimir , Gallego‐Ferrer Gloria , Seker Sukran , Elçin Ayşe Eser , Elçin Yaşar Murat , Altankov George 
Published: March 2017

AbstractNovel, hybrid fibrinogen/polylactic acid (FBG/PLA) nanofibers with different configuration (random vs aligned) and dimensionality (2‐D vs 3‐D environment) were used to control the overall behavior and the osteogenic differentiation of human adipose‐derived mesenchymal stem cells (ADMSCs). Aligned nanofibers in both the 2‐D and 3‐D configurations are proved to be favored for osteodifferentiation. Morphologically, we found that on randomly configured nanofibers, the cells developed a stellate‐like morphology with multiple projections; however, time‐lapse analysis showed significantly diminished cell movements. Conversely, an elongated cell shape with advanced cell spreading and extended actin cytoskeleton accompanied with significantly increased cell mobility were observed when cells attached on aligned nanofibers. Moreover, a clear tendency for higher alkaline phosphatase activity was also found on aligned fibers when ADMSCs were switched to osteogenic induction medium. The strongest accumulation of Alizarin red (AR) and von Kossa stain at 21 days of culture in osteogenic medium were found on 3‐D aligned constructs while the rest showed lower and rather undistinguishable activity. Quantitative reverse transcription‐polymerase chain reaction analysis for Osteopontin (OSP) and RUNX 2 generally confirmed this trend showing favorable expression of osteogenic genes activity in 3‐D environment particularly in aligned configuration. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2065–2074, 2017.
Identification of Chloride Intracellular Channel Protein 3 as a Novel Gene Affecting Human Bone Formation
Authors: Brum Andrea M , van der Leije Cindy S , Schreuders‐Koedam Marijke , Verhoeven Jeroen , Janssen Mark , Dekkers Dick HW , Demmers Jeroen AA , Eijken Marco , van de Peppel Jeroen , van Leeuwen Johannes PTM , van der Eerden Bram CJ 
Published: March 2017

ABSTRACTOsteoporosis is a common skeletal disorder characterized by low bone mass leading to increased bone fragility and fracture susceptibility. The bone building cells, osteoblasts, are derived from mesenchymal stromal cells (MSCs); however, with increasing age osteogenic differentiation is diminished and more adipocytes are seen in the bone marrow, suggesting a shift in MSC lineage commitment. Identification of specific factors that stimulate osteoblast differentiation from human MSCs may deliver therapeutic targets to treat osteoporosis. The aim of this study was to identify novel genes involved in osteoblast differentiation of human bone marrow–derived MSCs (hMSCs). We identified the gene chloride intracellular channel protein 3 (CLIC3) to be strongly upregulated during MSC‐derived osteoblast differentiation. Lentiviral overexpression of CLIC3 in hMSCs caused a 60% increase of matrix mineralization. Conversely, knockdown of CLIC3 in hMSCs using two short‐hairpin RNAs (shRNAs) against CLIC3 resulted in a 69% to 76% reduction in CLIC3 mRNA expression, 53% to 37% less alkaline phosphatase (ALP) activity, and 78% to 88% less matrix mineralization compared to scrambled control. Next, we used an in vivo human bone formation model in which hMSCs lentivirally transduced with the CLIC3 overexpression construct were loaded onto a scaffold (hydroxyapatite‐tricalcium‐phosphate), implanted under the skin of NOD‐SCID mice, and analyzed for bone formation 8 weeks later. CLIC3 overexpression led to a 15‐fold increase in bone formation (0.33% versus 5.05% bone area relative to scaffold). Using a Clic3‐His‐tagged pull‐down assay and liquid chromatography–mass spectrometry (LS/MS)‐based proteomics analysis in lysates of osteogenically differentiated hMSCs, we showed that CLIC3 interacts with NIMA‐related kinase 9 (NEK9) and phosphatidylserine synthase 1 (PTDSS1) in vitro, and this finding was supported by immunofluorescent analysis. In addition, inhibition of NEK9 or PTDSS1 gene expression by shRNAs inhibited osteoblast differentiation and mineralization. In conclusion, we successfully identified CLIC3 to be a lineage‐specific gene regulating osteoblast differentiation and bone formation through its interaction with NEK9 and PTDSS1. © The Authors. JBMR Plus is published by Wiley Periodicals, Inc. on behalf of the American Society for Bone and Mineral Research.
V‐ATPases Containing a3 Subunit Play a Direct Role in Enamel Development in Mice
Authors: Johnson Lisa , Ganss Bernhard , Wang Andrew , Zirngibl Ralph A. , Johnson Danielle E. , Owen Celeste , Bradley Grace , Voronov Irina 
Published: March 2017

ABSTRACTVacuolar H+‐ATPases (V‐ATPases) are ubiquitous multisubunit proton pumps responsible for organellar pH maintenance. Mutations in the a3 subunit of V‐ATPases cause autosomal recessive osteopetrosis, a rare disease due to impaired bone resorption. Patients with osteopetrosis also display dental anomalies, such as enamel defects; however, it is not clear whether these enamel abnormalities are a direct consequence of the a3 mutations. We investigated enamel mineralization, spatiotemporal expression of enamel matrix proteins and the a3 protein during tooth development using an osteopetrotic mouse model with a R740S point mutation in the V‐ATPase a3 subunit. Histology revealed aberrations in both crown and root development, whereas SEM analysis demonstrated delayed enamel mineralization in homozygous animals. Enamel thickness and mineralization were significantly decreased in homozygous mice as determined by μCT analysis. The expression patterns of the enamel matrix proteins amelogenin, amelotin, and odontogenic ameloblast‐associated protein (ODAM) suggested a delay in transition to the maturation stage in homozygous animals. Protein expression of the a3 subunit was detected in ameloblasts in all three genotypes, suggesting that a3‐containing V‐ATPases play a direct role in amelogenesis, and mutations in a3 delay transition from the secretory to the maturation stage, resulting in hypomineralized and hypoplastic enamel. J. Cell. Biochem. 118: 3328–3340, 2017. © 2017 Wiley Periodicals, Inc.
Morphogenesis and developmental ultrastructure of Nicotiana tabacum short glandular trichomes
Authors: Uzelac Branka , Janošević Dušica , Stojičić Dragana , Budimir Snežana 
Published: March 2017

AbstractThe anatomy and ultrastructure of the short glandular trichomes occurring on young expanding leaves of Nicotiana tabacum were investigated using light and transmission electron microscopy. The objective of the present research was to characterize the cellular changes that occur during morphogenesis of short glandular trichomes, from initiation to senescence. Ultrastructural analysis of their secretory cells revealed characteristics common to gland cells: numerous mitochondria in highly organized cytoplasm, large nuclei, and an elaborate network of endoplasmic reticulum. Initial changes in nuclear and plastidial organization were observed at a more advanced secretory stage, marking the onset of senescence. During trichome senescence, gradual reduction of the cytoplasm density occurred along with structural changes of the plastids and the tonoplast. As a result of inward blebbing of the cytoplasm into the vacuole, membrane bound vesicular structures appeared in the vacuolar space. At the late secretory stage, marked by an increase in vacuolation and extraplasmic space, degenerative changes included further fragmentation of the cytoplasm and deterioration of the tonoplast. Multimembrane myelin bodies observed in the vacuolar space were indicative of membrane digestion although plasma membrane did not appear massively degraded.
Feasibility of 3D navigator‐triggered magnetic resonance cholangiopancreatography with combined parallel imaging and compressed sensing reconstruction at 3T
Authors: Seo Nieun , Park Mi‐Suk , Han Kyunghwa , Kim Dongeun , King Kevin F. , Choi Jin‐Young , Kim Honsoul , Kim Hye Jin , Lee Minsu , Bae Heejin , Kim Myeong‐Jin 
Published: March 2017

PurposeTo assess the feasibility of 3D navigator‐triggered magnetic resonance cholangiopancreatography (MRCP) with combined parallel imaging (PI) and compressed sensing (CS).Materials and MethodsWith Institutional Review Board approval, 30 consecutive patients who underwent MRCP for suspected pancreaticobiliary disease were prospectively recruited. All patients underwent 3D navigator‐triggered MRCP with conventional PI alone, and with combined PI and CS using a 3T machine. The acquisition time and relative duct‐to‐periductal contrast ratios (RCs) at three biliary segments were quantitatively compared between the two MRCP methods. Qualitative image parameters were independently evaluated by two blinded radiologists, and were compared between two methods using the Wilcoxon signed‐rank test.ResultsThe mean acquisition time of MRCP with combined PI and CS (131.87 ± 33.60 sec) was significantly shorter compared with that of MRCP with PI (253.63 ± 56.08 sec; P < 0.001). The RC obtained using MRCP with combined PI and CS at two segments was slightly lower compared to that obtained using MRCP with PI (P = 0.007 and 0.002). Both reviewers found no significant differences in duct visualization, overall image quality, and degree of artifacts between the two methods (P ≥ 0.063; P = 0.637; and P = 0.752, respectively). Lesion conspicuity and confidence in duct abnormalities were comparable between two MRCP methods in both readers (P = 0.564 and P > 0.999).ConclusionCombined PI and CS reconstruction is feasible for 3D navigator‐triggered MRCP, providing image quality comparable to that of MRCP with PI alone, in about half the acquisition time.Level of Evidence: 2Technical Efficacy: Stage 1J. Magn. Reson. Imaging 2017;46:1289–1297.
Identification and characterization of fluvastatin metabolites in rats by UHPLC/Q‐TOF/MS/MS and in silico toxicological screening of the metabolites
Authors: Chavan Balasaheb B. , Kalariya Pradipbhai D. , Nimbalkar Rakesh D. , Garg Prabha , Srinivas R. , Kumar Talluri M. V. N. 
Published: March 2017

The present study reports the in vivo and in vitro identification and characterization of metabolites of fluvastatin, the 3‐hydroxy‐3‐methyl‐glutaryl‐coenzyme A reductase inhibitor, using liquid chromatography–mass spectrometry (LC–MS). In vitro studies were conducted by incubating the drug with human liver microsomes and rat liver microsomes. In vivo studies were carried out by administration of the drug in the form of suspension to the Sprague–Dawley rats followed by collection of urine, faeces and blood at different time points up to 24 h. Further, samples were prepared by optimized sample preparation method, which includes freeze liquid extraction, protein precipitation and solid phase extraction. The extracted and concentrated samples were analysed using ultrahigh‐performance liquid chromatography–quadruple time‐of‐flight tandem mass spectrometry. A total of 15 metabolites were observed in urine, which includes hydroxyl, sulphated, desisopropyl, dehydrogenated, dehydroxylated and glucuronide metabolites. A few of the metabolites were also present in faeces and plasma samples. In in vitro studies, a few metabolites were observed that were also present in in vivo samples. All the metabolites were characterized using ultrahigh‐performance liquid chromatography–quadruple time‐of‐flight tandem mass spectrometry in combination with accurate mass measurement. Finally, in silico toxicity studies indicated that some of the metabolites show or possess carcinogenicity and skin sensitization. Several metabolites that were identified in rats are proposed to have toxicological significance on the basis of in silico evaluation. However, these metabolites are of no human relevance. Copyright © 2017 John Wiley & Sons, Ltd.
Shallow gas development and grassland songbirds: The importance of perches
Authors: Rodgers Jennifer Anne , Koper Nicola 
Published: March 2017

ABSTRACTGrassland bird species have declined more than birds of any other region in North America and industrial development may exert further pressure on these species. We evaluated effects of conventional natural gas infrastructure on the relative abundances of grassland songbirds in southeastern Alberta, Canada at sites with shallow gas well pad densities ranging from 0 to 16 pads/258 ha (0–24 well heads/258 ha). Conventional gas wells have a relatively small footprint and minimal associated noise and maintenance activities, allowing us to focus on effects of the infrastructure itself and vegetation surrounding wells. We conducted fixed‐radius point counts and vegetation sampling at 34 sites in 2010 and 40 sites in 2011. We used generalized linear mixed models and information theory to evaluate effects of infrastructure on birds. Relative abundances of vesper sparrow (Pooecetes gramineus) and western meadowlark (Sturnella neglecta) increased near gas wells, whereas abundance of the threatened Sprague's pipit (Anthus spragueii) declined. Vegetation near infrastructure was shorter and sparser than locations farther from wells, but discrepancies with avian habitat preferences suggest that, in contrast to conclusions of previous studies, vegetation structure could not explain responses to infrastructure by birds. Instead, gas wells may have acted as artificial shrubs because they attracted species that use vegetation for perching but were avoided by species that avoid shrubs. Our results suggest that observed effects were a direct result of the presence of wells and associated fencing, and thus risk mitigation should focus on reducing the extent of aboveground infrastructure. © 2017 The Wildlife Society.
Utility of radio‐telemetry data for improving statistical population reconstruction
Authors: Berg Sergey S. , Erb John D. , Fieberg John R. , Forester James D. 
Published: March 2017

ABSTRACTStatistical population reconstruction using age‐at‐harvest and catch‐effort data has recently emerged as a robust and versatile approach to estimating the demographic dynamics of harvested populations of wildlife. Although there are clear benefits to incorporating radio‐telemetry data into reconstruction efforts, these data are costly and time‐consuming to collect. Managers that consider collecting these data alongside existing efforts could benefit from a comprehensive examination of how such benefits are influenced by the amount of radio‐telemetry data collected. Using a harvested population of American marten (Martes americana) in northeastern Minnesota, USA as a case study, we investigated the performance of population reconstruction using information on natural, harvest, or combined mortality derived from radio‐telemetry data collected over different numbers of years and with different numbers of animals collared each year. We simulated populations under a range of conditions and determined that incorporating radio‐telemetry data on natural and harvest mortality significantly improved model precision, and that each additional animal collared per year yielded a 0.50 ± 0.14% (SE) improvement in precision, whereas every additional year of radio‐telemetry data resulted in a 2.42 ± 0.70% improvement. Thus, including another year of radio‐telemetry resulted in similar gains in precision as including approximately 5 additional animals collared per year. In our applied marten example, incorporating radio‐telemetry data resulted in a significantly higher estimate of trapping vulnerability (0.20 vs. 0.058) and an overall smaller population size than reconstruction based solely on age‐at‐harvest and trapper effort data. These results illustrate the benefits of performing auxiliary studies, caution against relying on the results of population reconstruction based solely on age‐at‐harvest and hunter‐effort data, and demonstrate that improvements from incorporating radio‐telemetry data become evident even after as few as 2 years of data collection. © 2017 The Wildlife Society.
Seasonal variation and sexual difference of home ranges by takins
Authors: Yan Wen‐Bo , Zeng Zhi‐Gao , Gong Hui‐Sheng , He Xiang‐Bo , Liu Xin‐Yu , Ma Yi‐Sheng , Song Yan‐Ling 
Published: March 2017

ABSTRACTThe takin (Budorcas taxicolor) inhabits mountainous forests and exhibits seasonal migration along an altitudinal gradient. Its home range is largely unknown, yet this information is important to help guide the conservation of this threatened species. We conducted a global positioning system (GPS) radio‐tracking study to determine the home ranges of 10 takins in the middle range of the Qinling Mountains, China, from August 2013 to August 2015. Their annual home ranges averaged 69.7 km2 (range = 21.3–188.5 km2) using the 100% minimum convex polygon (MCP), and 25.3 km2 (range = 10.4–44.8 km2) using a 95% kernel density estimate (KDE) revealing variation among individuals. Because takins are sexually dimorphic, we predicted that males would have larger home ranges than females. However, annual and seasonal home ranges of females were as large as, or larger than, those of males. These results are attributed to body size, sex, reproduction, and grouping behavior. Home range sizes of takins varied seasonally with the smallest range in winter (MCP = F3,44 = 4.40, P = 0.009; KDE = F3,44 = 6.28, P = 0.001); this variation was caused by their migratory behavior and the seasonal environment. For effective conservation of takins, managers of the Nature Reserves should unify management and conserve habitats used at all elevations. © 2017 The Wildlife Society
Environmental multi‐scale effects on zooplankton inter‐specific synchrony
Authors: Buttay Lucie , Cazelles Bernard , Miranda Ana , Casas Gerardo , Nogueira Enrique , González‐Quirós Rafael 
Published: March 2017

AbstractKnowledge on the mechanisms that drive population dynamics and shape community structure is a key issue in ecology. Using wavelet methods, we analyzed 17‐yr of monthly time‐series of marine zooplankton (taxonomic composition, total abundance, and biomass) and their relationship with environmental factors (upwelling index and river outflow). The main mode of variation in all series was annual, and exhibited year‐to‐year variability. The dynamics of zooplankton aggregated properties showed a strong association with upwelling index and river outflow. The annual oscillation of biomass and abundance increased in 2000 corresponding to the highest amplitudes of environmental forcing. Concomitantly, enhanced synchrony was observed among the main taxonomic groups of zooplankton and among copepod species, the most relevant group in terms of occurrence and abundance. The degree of synchrony appeared to be correlated with the upwelling index and, more closely, with the duration of the upwelling events. The amplified seasonality of the environmental variables from 2000 to 2004, combined with a reduction of off‐shore exportation by shortening of upwelling events, favored retention in winter, and primary production in summer. These changes modulated community aggregated properties and affected the stability of the zooplankton community through an increase in inter‐specific synchrony allowing the community to shift to another state and likely a reorganization of the community size structure.