bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches
Authors: Diotel Nicolas , Rodriguez Viales Rebecca , Armant Olivier , März Martin , Ferg Marco , Rastegar Sepand , Strähle Uwe 
Published: December 2014

ABSTRACTThe zebrafish has become a model to study adult vertebrate neurogenesis. In particular, the adult telencephalon has been an intensely studied structure in the zebrafish brain. Differential expression of transcriptional regulators (TRs) is a key feature of development and tissue homeostasis. Here we report an expression map of 1,202 TR genes in the telencephalon of adult zebrafish. Our results are summarized in a database with search and clustering functions to identify genes expressed in particular regions of the telencephalon. We classified 562 genes into 13 distinct patterns, including genes expressed in the proliferative zone. The remaining 640 genes displayed unique and complex patterns of expression and could thus not be grouped into distinct classes. The neurogenic ventricular regions express overlapping but distinct sets of TR genes, suggesting regional differences in the neurogenic niches in the telencephalon. In summary, the small telencephalon of the zebrafish shows a remarkable complexity in TR gene expression.The adult zebrafish telencephalon has become a model to study neurogenesis. We established the expression pattern of more than 1200 transcription regulators (TR) in the adult telencephalon. The neurogenic regions express overlapping but distinct sets of TR genes suggesting regional differences in the neurogenic potential. J. Comp. Neurol. 523:1202–1221, 2015. © 2015 Wiley Periodicals, Inc.
Roles of histone H3K27 trimethylase Ezh2 in retinal proliferation and differentiation
Authors: Iida Atsumi , Iwagawa Toshiro , Baba Yukihiro , Satoh Shinya , Mochizuki1 Yujin , Nakauchi Hiromitsu , Furukawa Takahisa , Koseki Haruhiko , Murakami Akira , Watanabe Sumiko 
Published: December 2014

ABSTRACTThe histone modification H3K27me3 regulates transcription negatively, and Jmjd3 and Ezh2 demethylate and methylate H3K27me3 and H3K27, respectively. We demonstrated previously that Jmjd3 plays pivotal roles in the differentiation of subsets of bipolar (BP) cells by regulating H3K27me3 levels at the Bhlhb4 and Vsx1 loci, both of which are transcription factors essential for the maturation of BP cell subsets. In this study, we examined the role of Ezh2 in retinal development using retina‐specific Ezh2 conditional knockout mice (Ezh2‐CKO). The eyes of the Ezh2‐CKO mice were microphthalemic, and the proliferation of retinal cells was diminished postnatally in Ezh2‐CKO. Differentiation of all examined retinal subsets was observed with higher proportion of BP cell subsets, which was determined by immunostaining using specific retinal markers. The onsets of Müller glia and rod photoreceptor differentiation were accelerated. The expression of Bhlhb4 was increased in postnatal retinas, which was accompanied by the loss of H3K27me3 modifications at these genetic loci. Decreased expression of proneural genes in postnatal stage was observed. As reported previously in other Ezh2‐KO tissues, increased expression of Arf/Ink4a was observed in the Ezh2‐CKO retinas. The ectopic expression of Arf or Ink4a in the retina suppressed proliferation and increased apoptosis. In addition, earlier onset of Müller glia differentiation was observed in Ink4a‐expressing cells. These results support an important role for histone H3K27me3 modification in regulating the proliferation and maturation of certain subsets of interneurons in the retina. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 75: 947–960, 2015
The influence of activity on axon pathfinding in the optic tectum
Authors: Kita Elizabeth M. , Scott Ethan K. , Goodhill Geoffrey J. 
Published: December 2014

ABSTRACTThe relative importance of neural activity versus activity‐independent cues in shaping the initial wiring of the brain is still largely an open question. While activity is clearly critical for circuit rearrangements after initial connections have been made, whether it also plays a role in initial axon pathfinding remains to be determined. Here, we investigated this question using the guidance of zebrafish retinal ganglion cell axons to their targets in the tectum as a model. Recent results have implicated biased branching as a key feature of pathfinding in the zebrafish tectum. Using tetrodotoxin to silence neural activity globally, we found a decrease in the area covered by axon branches during pathfinding. After reaching the target, there were dynamic differences in axon length, area and the number of branches between conditions. However, other aspects of pathfinding were unaffected by silencing, including the ratio of branches directed toward the target, length, and number of branches, as well as turning angle, velocity, and number of growth cones per axon. These results challenge the hypothesis that neural connections develop in sequential stages of molecularly guided pathfinding and activity‐based refinement. Despite a maintenance of overall guidance, axon pathfinding dynamics can nevertheless be altered by activity loss. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 75: 608–620, 2015
Measurements of nanomaterials in environmentally relevant water matrices using liquid nebulization/differential mobility analysis
Authors: Mader Brian T. , Ellefson Mark E. , Wolf Susan T. 
Published: December 2014

Abstract

A liquid nebulization-differential mobility analysis methodology was evaluated for the measurement of the size distribution and quantitative mass concentration of nanomaterials in environmentally relevant aqueous media. The analysis time is 8 min, and the method requires little routine sample preparation and less than 8 mL of sample. The method can be used for rapid, direct analysis of nanomaterials in aqueous media with a particular application to dose verification in ecotoxicology studies, analysis of manufacturing process waste streams, and raw material analysis. Twelve reference materials having a diameter traceable to the National Institute of Standards and Technology were spiked into 6 different aqueous matrices that included drinking water, groundwater, industrial wastewater, as well as the algae and daphnia media used in ecotoxicology testing. Measurement of the diameter of a reference material was within the expected range for the reference material. Individual response factors for each reference material were determined in each medium and the accuracy and precision of the concentration measurements evaluated. In ecotoxicology test media, measurements of the concentration of nanoparticles having diameter ≥ 30 nm, had corresponding accuracies and precisions of 103% and 7%, respectively. Over 28 d 86% of the samples had concentrations within 20% of the initial concentration. The method limit of quantification depended primarily on matrix complexity and particle diameter; the limit of quantification ranged from 0.01 mg/L to 3 g/L. Environ Toxicol Chem 2015;34:833–842. © 2014 SETAC
Ammonia stress on the carbon metabolism of Ceratophyllum demersum
Authors: Gao Jingqing , Li Linshuai , Hu Zhiyuan , Zhu Songfeng , Zhang Ruiqin , Xiong Zhiting 
Published: December 2014

Abstract

In the present study, carefully controlled pH ranges (7 and 9) were used to distinguish between the effects of un-ionized NH3 and the NH4+ ion. The objective was to find the effect of different total ammonia nitrogen concentrations and pH values on the carbon metabolism of Ceratophyllum demersum. The authors investigated the effects of ammonia on the nonstructural carbohydrate content in shoots of C. demersum. Ammonia treatment decreased the contents of nonstructural carbohydrate, soluble sugar, sucrose, fructose, and starch in leaves. Meanwhile, increasing the pH value exacerbated the decline of the C. demersum nonstructural carbohydrate content. In addition, the activity of invertase was increased during the experiment. These results suggest that ammonia severely inhibits plant growth by disturbing nonstructural carbohydrate content. It has been suggested that ammonia has toxic effects on C. demersum and that the higher the pH in water, the more obvious the physiological responses that C. demersum exhibits. The results of the present study can provide some reference for studying the living conditions of submersed macrophytes under the stress of NH3. Environ Toxicol Chem 2015;34:843–849. © 2014 SETAC
Planktonic and biofilm-grown nitrogen-cycling bacteria exhibit different susceptibilities to copper nanoparticles
Authors: Reyes Vincent C. , Opot Stephen O. , Mahendra Shaily 
Published: December 2014

Abstract

Proper characterization of nanoparticle (NP) interactions with environmentally relevant bacteria under representative conditions is necessary to enable their sustainable manufacture, use, and disposal. Previous nanotoxicology research based on planktonic growth has not adequately explored biofilms, which serve as the predominant mode of bacterial growth in natural and engineered environments. Copper nanoparticle (Cu-NP) impacts on biofilms were compared with respective planktonic cultures of the ammonium-oxidizing Nitrosomonas europaea, nitrogen-fixing Azotobacter vinelandii, and denitrifying Paracoccus denitrificans using a suite of independent toxicity diagnostics. Median inhibitory concentration (IC50) values derived from adenosine triphosphate (ATP) for Cu-NPs were lower in N. europaea biofilms (19.6 ± 15.3 mg/L) than in planktonic cells (49.0 ± 8.0 mg/L). However, in absorbance-based growth assays, compared with unexposed controls, N. europaea growth rates in biofilms were twice as resilient to inhibition than those in planktonic cultures. Similarly, relative to unexposed controls, growth rates and yields of P. denitrificans in biofilms exposed to Cu-NPs were 40-fold to 50-fold less inhibited than those in planktonic cells. Physiological evaluation of ammonium oxidation and nitrate reduction suggested that biofilms were also less inhibited by Cu-NPs than planktonic cells. Furthermore, functional gene expression for ammonium oxidation (amoA) and nitrite reduction (nirK) showed lower inhibition by NPs in biofilms relative to planktonic-grown cells. These results suggest that biofilms mitigate NP impacts, and that nitrogen-cycling bacteria in wastewater, wetlands, and soils might be more resilient to NPs than planktonic-based assessments suggest. Environ Toxicol Chem 2015;34:887–897. © 2014 SETAC
Do particle size and surface functionality affect uptake and depuration of gold nanoparticles by aquatic invertebrates?
Authors: Park Sujung , Woodhall James , Ma Guibin , Veinot Jonathan G.C , Boxall Alistair B.A. 
Published: December 2014

Abstract

Because of the widespread use of engineered nanoparticles (ENPs) in consumer and industrial products, it is inevitable that these materials will enter the environment. It is often stated that the uptake of ENPs into organisms in the environment is related to the particle size and surface functionality. To test this assumption, the present study investigated the uptake and depuration of gold nanoparticle (Au NPs) coated with either citrate (Au-citrate NPs), mercaptoundecanoic acid (Au-MUDA NPs), amino polyethylene glycol (PEG) thiol (Au-NH2 NPs), or PEG (Au-PEG NP) by the aquatic invertebrate Gammarus pulex. The studies were performed using a range of standard ecotoxicity media and natural waters, resulting in varying degrees of aggregation of the different NPs. Uptake of gold by G. pulex varied depending on the surface coatings, with Au-MUDA and Au-citrate NPs being taken up to a greater extent than Au-NH2 and Au-PEG NPs in all test media and natural waters. In all test media evaluated, higher amounts of amino and PEG-coated ENPs were eliminated compared with MUDA- and citrate-coated ENPs. No obvious relationships were seen between the aggregation state of the different Au NPs in treatment and uptake, suggesting that the widely accepted assumption that Au NP uptake is related to particle size does not hold for the range of aggregation states studied (67.1–178.8 nm). Positive correlations between particle number concentration in the media and uptake were observed, indicating that this factor might partly explain the differences in uptake of a particle from different media types. Environ Toxicol Chem 2015;34:850–859. © 2014 SETAC
Development and application of a multimetal multibiotic ligand model for assessing aquatic toxicity of metal mixtures
Authors: Santore Robert C. , Ryan Adam C. 
Published: December 2014

Abstract

A multimetal, multiple binding site version of the biotic ligand model (mBLM) has been developed for predicting and explaining the bioavailability and toxicity of mixtures of metals to aquatic organisms. The mBLM was constructed by combining information from single-metal BLMs to preserve compatibility between the single-metal and multiple-metal approaches. The toxicities from individual metals were predicted by assuming additivity of the individual responses. Mixture toxicity was predicted based on both dissolved metal and mBLM-normalized bioavailable metal. Comparison of the 2 prediction methods indicates that metal mixtures frequently appear to have greater toxicity than an additive estimation of individual effects on a dissolved metal basis. However, on an mBLM-normalized basis, mixtures of metals appear to be additive or less than additive. This difference results from interactions between metals and ligands in solutions including natural organic matter, processes that are accounted for in the mBLM. As part of the mBLM approach, a technique for considering variability was developed to calculate confidence bounds (called response envelopes) around the central concentration–response relationship. Predictions using the mBLM and response envelope were compared with observed toxicity for a number of invertebrate and fish species. The results show that the mBLM is a useful tool for considering bioavailability when assessing the toxicity of metal mixtures. Environ Toxicol Chem 2015;34:777–787. © 2014 SETAC
Pathway‐Based Association Study of Multiple Candidate Genes and Multiple Traits Using Structural Equation Models
Authors: Romdhani Hela , Hwang Heungsun , Paradis Gilles , Roy‐Gagnon Marie‐Helene , Labbe Aurelie 
Published: December 2014

ABSTRACTThere is increasing interest in the joint analysis of multiple genetic variants from multiple genes and multiple correlated quantitative traits in association studies. The classical approach involves testing univariate associations between genotypes and phenotypes and correcting for multiple testing that results in loss of power to detect associations. In this paper, we propose modeling complex relationships between genetic variants in candidate genes and measured correlated traits using structural equation models (SEM), taking advantage of prior knowledge on clinical and genetic pathways. We adopt generalized structured component analysis (GSCA) as an approach to SEM and develop a single association test between multiple genetic variants in a gene and a set of correlated traits, taking into account all available data from other genes and other traits. The performance of this test is investigated by simulations. We apply the proposed method to the Quebec Child and Adolescent Health and Social Survey (1999) data to investigate genetic associations with cardiovascular disease‐related traits.
Olfactory performance and resting state functional connectivity in non‐demented drug naïve patients with Parkinson's disease
Authors: Sunwoo Mun Kyung , Cha Jungho , Ham Jee Hyun , Song Sook K. , Hong Jin Yong , Lee Jong‐Min , Sohn Young H. , Lee Phil Hyu 
Published: December 2014

AbstractOlfactory performance in Parkinson's disease (PD) is closely associated with subsequent cognitive decline. In the present study, we analyzed the olfaction‐dependent functional connectivity with a hypothesis that olfactory performance would influence functional connectivity within key brain areas of PD. A total of 110 nondemented drug‐naïve patients with PD were subdivided into three groups of high score (PD‐H, n = 23), middle score (PD‐M, n = 64), and low score (PD‐L, n = 23) based on olfactory performance. We performed the resting‐state functional connectivity with seed region of interest in the posterior cingulate cortex (PCC) and caudate. An analysis of functional connectivity revealed that PD‐L patients exhibited a significant attenuation of cortical functional connectivity with the PCC in the bilateral primary sensory areas, right frontal areas, and right parietal areas compared to PD‐H or PD‐M patients. Meanwhile, PD‐L patients exhibited a significant enhancement of striatocortical functional connectivity in the bilateral occipital areas and right frontal areas compared to PD‐H or PD‐M patients. In the voxel‐wise correlation analysis, olfactory performance was positively associated with cortical functional connectivity with the PCC in similar areas of attenuated cortical connectivity in PD‐L patients relative to PD‐H patients. On the other hand, the cortical functional connectivity with the caudate was negatively correlated with olfactory performance in similar areas of increased connectivity in PD‐L patients relative to PD‐H patients. The present study demonstrated that resting state functional connectivity exhibits a distinctive pattern depending on olfactory performance, which might shed light on a meaningful relationship between olfactory impairment and cognitive dysfunction in PD. Hum Brain Mapp 36:1716–1727, 2015. © 2014 Wiley Periodicals, Inc.
A S2O32−‐Enhanced Fluorogenic Chemosensor for Fe3+ in Aqueous Media Based on a Boron–Fluorine Derivative
Authors: Ping Shen , Mingxun Yan , Wei Zhang , Shuzhang Xiao , Changying Yang 
Published: December 2014

ABSTRACTA fluorescent “turn‐on” probe for Fe3+ was investigated in an aqueous system based on a boron 2‐(2′‐pyridyl) imidazole complex (BOPIM‐dma). BOPIM‐dma shows weak or no fluorescence in polar solvents due to twisted intramolecular charge transfer, but the addition of Fe3+ to BOPIM‐dma leads to fluorescence switch‐on responses. The binding is highly selective to Fe3+ over other metal ions, indicating that BOPIM‐dma is a chemodosimeter for Fe3+. Furthermore, the existence of S2O32− could much enhance and stabilize the emission significantly, indicating that the BOPIM‐dma/Fe3+/S2O32− complexes are a strong fluorescence system, and can be used as a sensitive detector for Fe3+, with the limit of detection of 6.0 × 10−7 mol L−1.
A site-specific ecological risk assessment for corn-associated insecticides
Authors: Whiting Sara A , Lydy Michael J 
Published: December 2014

Abstract
A site-specific ecological risk assessment (ERA) was conducted to examine the simultaneous use of genetically modified corn (Bt corn) with a neonicotinoid seed coating, clothianidin, and use of a granular insecticide, tefluthrin, to protect crops from pest damage. A field study was conducted on site, and exposure data from the literature were summarized to determine the matrices and exposure concentrations that nontarget species could typically experience within an agricultural ecosystem. To determine ecological effects on nontarget species, acute toxicity bioassays were conducted on earthworms (Eisenia fetida), amphipods (Hyalella azteca), and Elmid riffle beetle larvae (Ancyronyx spp.) in which the test species were exposed to single insecticides as well as the mixture of the 3 insecticides. In the risk characterization section of the ERA, stressor–response profiles for each species tested were compared with field distributions of the insecticides, and a margin of safety at the 10th percentile (MOS10) was calculated to estimate risk. No acute toxicity was observed in any of the 3 nontarget species after exposure to senescent Bt corn leaf tissue. Large MOS10 values were calculated for clothianidin to the nontarget species. When bioassays were compared with tefluthrin field distributions, very low MOS10 values were calculated for earthworms (0.06) and H. azteca (0.08) because the environmental concentrations often exceeded the stressor–response profile. No increased toxicity was observed when nontarget species were exposed to a mixture of the 3 insecticides. In summary, the genetically modified corn insecticidal proteins and clothianidin were not found at environmental concentrations exceeding benchmark values for ecological effects, but tefluthrin was consistently detected in the environment at levels that could be causing toxicity to nontarget species, especially if this pyrethroid is able to travel off site. Integr Environ Assess Manag 2015;11:445–458. © 2015 SETAC
Key Points
We employed the EPA framework to enhance our review of the use of 3 different insecticides commonly used together in corn production in the US. This is the first environmental risk assessment to evaluate three unique pesticides and mixtures of this type. The 3 insecticides examined in our risk assessment were the genetically modified protein used in corn production, Bt Cry1Ab; the neonicotinoid, clothianidin; and the pyrethroid, tefluthrin. Our findings will assist policy makers and scientists when making decisions on the ecological safety of employing this control method for corn production.
Beyond the throwaway society: A life cycle-based assessment of the environmental benefit of reuse
Authors: Castellani Valentina , Sala Serenella , Mirabella Nadia 
Published: December 2014

Abstract
In the context of a circular economy, sustainable consumption is often seen as the antithesis of current consumption patterns, which have led to the definition of the so-called throwaway society. Reuse may provide a preferred alternative to other waste management options, because it promotes resource efficiency and may significantly reduce environmental impacts. To appraise the environmental benefits related to reuse of goods, a methodology adopting life cycle assessment (LCA) has been developed. A standardized procedure has been developed, identifying reference products within product category subject to reuse, and collecting reliable inventory data as a basis for calculating environmental impact through LCA. A case study on a second-hand shop is presented, and the avoided impacts are quantified. Inventory data were taken both from the literature and directly from sales and surveys submitted to customers. The results are presented, highlighting: 1) for each product category, the average avoided impacts for 1 unit of reused product considered; and 2) for the overall activities of the second-hand shop, the cumulative avoided impacts in 1 yr. In the case study, the higher contribution to avoided impacts comes from the apparel sector, due to the high amount of items sold, followed by the furniture sector, because of the high amount of environmental impacts avoided by the reuse of each single item. Integr Environ Assess Manag 2015;11:373–382. © 2015 SETAC
Key Points
The proposed methodology defines a standardized procedure for assessing reuse practice in LCA, identifying reference products and collecting reliable inventory data. The reuse of large items is likely to provide higher environmental benefits, whereas small items generate lower benefits per item but are usually sold in larger amounts and provide higher environmental benefits as a whole The methodology 1) allows for the assessment of interventions of waste prevention and reuse, and 2) may help raise awareness of the environmental value of secondhand shops. The results highlight the need for future research focused on reducing uncertainties. This entails expanding current basket of reference products, including best- and worst-case product performance, and exploring various logistic options.