bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanowastes and the environment: Using mercury as an example pollutant to assess the environmental fate of chemicals adsorbed onto manufactured nanomaterials
Authors: Gao Jie , Bonzongo Jean-Claude J , Bitton Gabriel , Li Ying , Wu Chang-Yu 
Published: March 2008

Abstract
Emerging nanotechnologies hold great promise for creating new means of detecting pollutants, cleaning polluted waste streams, and recovering materials before they become wastes, thereby protecting environmental quality. Studies focusing on the different advantages of nanoscience and nanotechnology abound in the literature, but less research effort seems to be directed toward studying the fate and potential impacts of wastes that will be generated by this technology. Using a combination of biogeochemical and toxicological methods, we conducted a preliminary investigation of the potential environmental fate of Hg as an example pollutant bound to nanomaterials used in treatment of gas effluents. Methylation of Hg sorbed onto SiO2-TiO2 nano-composites was used as a proxy for Hg bioavailability to sedimentary microorganisms, and the FluoroMetPLATE™ assay was used to assess the toxicity of both virgin and Hg-loaded SiO2-TiO2 nanocomposites. Our results show that the bioavailability of Hg sorbed onto SiO2-TiO2 nanocomposites to sedimentary microorganisms is pH dependent, with decreasing reaction rates as the pH increases from 4 to 6. Toxicity tests conducted using liquid extracts obtained by leaching of Hg-loaded SiO2-TiO2 nanocomposites with the synthetic precipitation leaching procedure solution showed an average inhibition of 84% (vs 57% for virgin SiO2-TiO2 nanocomposites). These results suggest that Hg sorbed onto engineered nanoparticles could become bioavailable and toxic if introduced into natural systems. Accordingly, studies focusing on the environmental implications of nanomaterials should include determination of the fate and impacts of pollutants that enter the environment bound to engineered nanomaterials.
Using fluorescent aromatic compounds in bile from juvenile salmonids to predict exposure to polycyclic aromatic hydrocarbons
Authors: Meador James P , Buzitis Jon , Bravo Claudia F 
Published: March 2008

Abstract
We provide data from four different studies in which fish were fed polycyclic aromatic hydrocarbons (PAHs) that were used to develop a predictive relationship between dose (μg/g fish/d) and metabolites of PAHs in bile. Juvenile salmonids were fed various doses of total PAH that were applied as a mixture to fish pellets. The number of PAHs in each mixture ranged from 10 to 21 different low- and high-molecular-weight compounds, and their relative proportions and abundance were based on stomach concentrations observed for field-collected fish. Although we examined both the phenanthrene (PHN) and benzo[a]pyrene signals for the fluorescent aromatic compounds (FACs) in bile, the PHN signal exhibited the highest correlation and was considered to be the better choice for predicting exposure. A large database of PHN FAC values for field-collected fish was examined and used to predict dose by the method of inverse prediction. The goal of the present study was to develop a predictive relationship that would allow estimation of an exposure dose for an observed value of PHN FACs from juvenile salmonids sampled in the field. This dose would then be used to estimate adverse effects based on toxicity results from laboratory studies. Additional analyses were performed to determine ventilation doses from water concentrations of total PAH and then relate those to PHN FAC values.
Estrogenic effects of polychlorinated biphenyls and relation to cytochrome P4501A activity in the endangered goodeid fishAmeca splendens
Authors: Vega-López Armando , Jiménez-Orozco F. Alejandro , Ramón-Gallegos Eva , García-Latorre Ethel , Domínguez-López M. Lilia 
Published: March 2008

AbstractThe present study examines the relationships between cytochrome P4501A (CYP1A) activity and vitellogenin (VTG) induction in Ameca splendens elicited by a polychlorinated biphenyl (PCB) mixture. Ethoxyresorufin-O-deethylase (EROD) activity, mRNA levels of VTG, and VTG induction were evaluated in male and female fish exposed for 1, 2, 4, 8, and 16 d to a commercial PCB mixture. Polychlorinated biphenyls induced higher EROD in both sexes and this induction was higher in females than in males. Maximum EROD and VTG induction occurred on day 1 in females, while in males these maxima occurred on days 8 and 16. A correlation between EROD and VTG induction was found only in males (p &lt; 0.001), and VTG induction was also higher in males than in females (p &lt; 0.01). Exposure to PCBs elicited increases in VTG expression and induction over time in males, while in females these decreased at the end of the exposure period. Deficiencies in the feedback mechanisms of male A. splendens exposed in the wild to xenoestrogens such as PCBs have probably contributed to alter the sex ratio of wild populations of this species.
Uncertainty analysis of dioxin-like polychlorinated biphenyls–related toxic equivalents in fish
Authors: Bhavsar Satyendra P , Hayton Alan , Jackson Donald A 
Published: March 2008

Abstract
The toxic equivalent (TEQ) concept is widely used to assess toxicity potential of a dioxin-like chemical mixture. The TEQ approach converts concentrations of various dioxin-like compounds into a single concentration that is toxicologically equivalent to the most toxic dioxin compound, 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), using toxic equivalency factors (TEFs). It has been shown that in the absence of costly measurements of dioxin-like polychlorinated biphenyls (dl-PCBs) in fish, relatively inexpensive measurements of total PCB can be utilized to estimate dl-PCB–related TEQ (i.e., TEQdl-PCB). The present study assesses the impacts of uncertainties in dl-PCB measurements and estimates, and mammalian TEFs on TEQdl-PCB using the Monte Carlo technique. The analysis suggests that measurement errors for dl-PCBs translate into up to 1.3-fold uncertainty in TEQdl-PCB, while uncertainties in estimates of dl-PCBs generally produce up to a threefold uncertainty in TEQdl-PCB. In contrast, the uncertainty due to TEFs normally ranges 10- to 13-fold and spans over 30- to 40-fold under extreme cases. For 2005 TEFs, PCB-126 is the dominating contributor to uncertainty in TEQdl-PCB. When we considered uncertainties in the TEFs and estimated dl-PCB concentrations simultaneously, there was little increase in uncertainty in TEQdl-PCB that was already produced by the TEFs only. These results indicate that the dl-PCB composition in fish and/or the relationship between total PCB and TEQdl-PCB can be utilized to estimate TEQdl-PCB with reasonable confidence.
Metal Analysis
Authors: Wrobel Katarzyna , Wrobel Kazimierz , Caruso Joseph A. 
Published: March 2008

Abstract
Measuring the concentration levels of trace and ultratrace elements in different samples is an important analytical task in environmental, biological, clinical, as well as industrial studies. Furthermore, the increasing recognition of species‐dependent behavior of elements in a given system has imposed the need for speciation analysis. Thus, the identification and/or quantification of individual compounds is required for elements in their naturally occurring forms, those produced and/or emitted from different anthropogenic activities, as well as the products of species degradation or biotransformation. The two most commonly used tools to deal with such analyses are plasma‐spectrometry techniques, namely inductively coupled plasma optical emission spectrometry (ICP‐OES) and inductively coupled plasma mass spectrometry (ICP‐MS). The suitability of these two techniques relies on their multielemental capabilities, high selectivity, wide dynamic range, high sample throughput, absence of chemical interferences, and easy coupling with different separation techniques. Consequently, applications of these techniques encompass both the determination of total element concentration and the specific detection of elements in different speciation schemes. In this article, the technical background of ICP‐OES and ICP‐MS is introduced, highlighting the capabilities and limitations of each technique. Different sample introduction systems are briefly presented and some applications for element analysis in inorganic and organometallic chemistry are reviewed.
Nuclear Magnetic Resonance (
NMR
) Spectroscopy of Metallobiomolecules
Authors: Bren Kara L. 
Published: March 2008

Abstract
Nuclear magnetic resonance (NMR) spectroscopy provides information on the structure and dynamics of metallobiomolecules at atomic resolution. A range of metal‐binding sites in biomolecules can be studied by NMR, although the methods used require consideration of the properties of the metal site. Diamagnetic metal‐binding sites are probed using conventional NMR approaches appropriate for analyzing interactions between ions and macromolecules. Weak metal binding as is common in RNAs may require use of mimics that bind more strongly and/or that provide a specific spectroscopic handle. Paramagnetic metals induce hyperfine shifting and linebroadening that serve as signals of metal binding, but may also require adjustments to standard NMR methodologies. Hyperfine shifting takes place through scalar or dipolar mechanisms, and these effects in turn reveal details of metal site structure and metal electronic structure. Paramagnetic effects on chemical shifts are also used to refine structures of metallobiomolecules. Resonance broadening resulting from the hyperfine interaction is related to unpaired electron–nucleus distance as well as properties of the metal ion and thus can be a restraint on structure. The high magnetic anisotropy of some paramagnetic biomolecules can cause the molecule to take a preferential orientation within the applied magnetic field to allow observation of residual dipolar couplings, which reveal relative angular orientations of bond vectors. The study of the many effects of paramagnetic centers on NMR spectra has advanced the field of biomolecular solution structure determination as these efforts have introduced new restraints used in calculating structures. NMR is also valuable for analyzing biomolecule dynamics and chemical exchange processes. A related application is analysis of interactions between metallobiomolecules and ligands, or other macromolecules. Application of NMR to metallobiomolecules has provided a means to study phenomena difficult to observe using other methods such as interactions between proteins, electron self‐exchange reactions, and biomolecule dynamics over a wide range of time scales. NMR methodology continues to advance rapidly and is expected to continue to exert a large influence on our understanding of metal sites in biomolecules.
Perturbed Angular Correlations of γ‐rays (PAC) Spectroscopy
Authors: Hemmingsen Lars , Butz Tilman 
Published: March 2008

AbstractIn this article, we give an elementary introduction to the theory and applications of perturbed angular correlation of γ‐rays (PAC) spectroscopy. In most applications in bioinorganic and inorganic chemistry the nuclear quadrupole interaction (NQI) is measured, providing a spectroscopic fingerprint of the local electronic and molecular structure and dynamics at the PAC probe site. The focus is on selected illustrative applications of PAC spectroscopy in bioinorganic chemistry: (i) local structure at metal ion binding sites in the bacterial mercury sensor MerR; de novo designed proteins; alcohol dehydrogenase–pH dependence; carboxypeptidase A—crystalline state versus solution; and carboxypeptidase A–during the hydrolysis of substrate; (ii) trapping intermediates in reactions using rapid freeze quenching; (iii) in vivo experiments on Cd(II) binding to biomolecules in cyanobacteria; (iv) cooperativity of metal ion binding in multinuclear sites; (v) dynamics of protein folding; (vi) rotational diffusion of biomolecules as a tool to monitor protein–protein interactions; (vii) exchange dynamics; and (viii) internal dynamics in proteins.Examples from inorganic chemistry and solid state physics are included for cases where the information derived is different from that already presented in the examples from bioinorganic chemistry: (i) magnetic properties of metals; (ii) defects trapped by the impurity PAC probe atom; (iii) temperature and pressure dependence of the EFG in metals; (iv) amorphous metals, alloys and internal oxidation; (v) metal surfaces and interfaces; (vi) semiconductors; (vii) phase transitions; (viii) charge density waves in transition metal dichalcogenides; (ix) intercalation reactions in 2H‐TaS2; (x) structure and bonding; (xi) single crystal experiments.
Rapid Scan, Stopped‐Flow Kinetics
Authors: Wang Rui‐Yong 
Published: March 2008

AbstractOne of the most frequently used rapid kinetics techniques is the stopped‐flow method. A major strength of rapid mixing methods is that they can be readily combined with a wide range of detection methods. Applications of stopped‐flow techniques, mainly stopped‐flow absorbance and fluorescence spectrometry, in the fields of inorganic and bioinorganic chemistry include kinetic measurement of ligand substitution, ligand binding and dissociation, redox reactions, and so on. The kinetic and thermodynamic parameters can be calculated with the aid of stopped‐flow methods. The general procedures for kinetic and thermodynamic studies by using stopped‐flow techniques are also discussed.
Electron Transfer: Chemical Roles of Water
Authors: Balabin Ilya A. , Beratan David N. , Skourtis Spiros S. 
Published: March 2008

AbstractWater plays multiple roles in biological electron transfer (ET): energy bath, polarizable medium that defines the reaction coordinate, electronic coupling bridge, and intimate participant in molecular recognition. This article explores these many faces of water in ET. Links are drawn to reactions in photosynthesis, oxidative phosphorylation, proton‐coupled ET, and DNA damage and repair.
Natural Products in Plants: Chemical Diversity
Authors: Leslie Gunatilaka A. 
Published: March 2008

Abstract
Plants contain numerous natural products (secondary metabolites) that may not participate directly in their growth and development but play an important role in ecological interactions with other organisms. Despite immense chemical diversity, which originates from simple carbohydrates produced because of photosynthesis, plant natural products are formed from only a few biosynthetic building blocks that consist of acetate, mevalonate, and shikimate. These basic building blocks undergo a variety of biosynthetic transformations and combinations that lead to numerous classes of plant natural products including, but not limited to, carbohydrates, fatty acids and their esters, aromatic polyketides (phenols and quinones), terpenoids and steroids, phenyl propanoids (lignans and lignin, coumarins, flavonoids, and isoflavonoids), and alkaloids. Summarized in this article are representative members of these important classes of plant natural products with special emphasis on their chemical diversity. The article concludes with a brief discussion on recent methods for the maximization of chemical diversity and the production of natural products from plants.
Metabolism: Cellular Organization
Authors: Karp Peter D. 
Published: March 2008

Abstract
The field of pathway bioinformatics is concerned with the representation and the manipulation of metabolic information within computers. By organizing genome information into pathways, pathway bioinformatics places genes and their products into a mechanistic framework. This article describes how metabolic pathways are represented in a computer, and it describes the BioCyc (SRI International, Menlo Park, CA) collection of pathway/genome databases for several hundred organisms. Each BioCyc database describes the genome and the metabolic network of a single organism. This article describes computational algorithms for computing with pathway data. Pathway visualization algorithms help scientists comprehend this complex information space and facilitate analysis of large‐scale omics datasets. Pathway analysis algorithms predict the metabolic network of an organism from its genome, identify the genes coding for missing enzymes in metabolic pathways, and enable the comparison of metabolic networks from multiple organisms. They also allow the prediction of the metabolic capabilities of an organism and identify potential drug targets within the metabolic network.
Stem Cell Fates: Control by Small Molecules
Authors: Hilcove Simon , Xu Yue , Ding Sheng 
Published: March 2008

AbstractStem cells hold great promise for the treatment of many devastating diseases and will also provide new insights into the molecular mechanisms that control developmental and regenerative processes. Realization of the therapeutic potential of stem cells will require a better understanding of the signaling pathways that control stem cell fate as well as an improved ability to manipulate stem cell proliferation, differentiation and reprogramming. Cell‐based phenotypic and pathway screens of synthetic compounds have led recently to the discovery of several small molecules that can be used to control stem cell fate. Such molecules will not only provide new insights into stem cell biology but will also facilitate the development of therapeutic agents for regenerative medicine.
Protein and
DNA
Thermostability
Authors: Berezovsky Igor N. 
Published: March 2008

Abstract
Adaptation to different environmental temperatures establishes specific requirements on the stability of DNA and protein macromolecules. Organismal strategies of thermophilic adaptation, structure‐ and sequence‐based, and their physical origins provide a consistent picture of the evolution of protein thermostability. A strong correlation between the optimal growth temperature (OGT) and the frequency of ApG dinucleotides in both sense and antisense strands of genomic DNA along with the absence of any “thermophilic” bias in the nucleotide composition highlights a key role of base stacking in the thermostabilization of the DNA double helix. The codon bias provides an excess of ApG pairs, which ensures the thermophilic adaptation of genomic DNA. The concentration of seven amino acids, Ile, Val, Tyr, Trp, Arg, Glu, Leu (IVYWREL), serves as a universal proteomic predictor of the OGT prokaryotes. The IVYWREL combination manifests a generic “thermophilic” trend in amino acid composition: the increase of hydrophobic and charged residues at the expense of polar ones. This so‐called “from both ends of the hydrophobicity scale” trend is a result of the positive (stabilizing the native state) and the negative (destabilizing misfolded conformations) components of protein design. The pressure to preserve energies of important native and non‐native contacts results in a correlation in mutations of amino acid residues involved into these contacts. A comparison of energy (Myiazawa–Jernigan potential) and substitution (BLOSUM62) matrices reveals a high rate of substitutions between amino acids that strongly attract each other (native contacts) and between residues that strongly repel each other (non‐native contacts).
The role of working memory components in multimedia comprehension
Authors: Gyselinck Valérie , Jamet Eric , Dubois Véronique 
Published: March 2008

AbstractThis article argues that conducting experiments involving the ability to control and even manipulate the cognitive load in working memory (WM; storage and or processing load) should make it possible to identify the processes involved during the integration of information coming from multiple sources. Some experiments using the dual‐task paradigm are reviewed, and an original experiment using complex multimedia material is presented. Overall, the experiments show that even in cases where subjects have to navigate between different types of information and have to integrate various items of information, the verbal storage component of WM is important in permitting comprehension. Visuospatial WM is in addition involved as soon as visuospatial processing is required. Storage of verbal information does not however depend on the modality of presentation and the classical modality effect appears to depend on individual differences. Some theoretical and practical implications of these results are drawn. Copyright © 2008 John Wiley & Sons, Ltd.
Cognitive processes in children's multimedia text learning
Authors: Segers Eliane , Verhoeven Ludo , Hulstijn‐Hendrikse Nanneke 
Published: March 2008

AbstractThe cognitive processes underlying children's multimedia text learning were studied using a self‐paced task and authentic school texts with mostly representational pictures in an elementary school setting. Both the quantity and quality of learning were assessed immediately following intervention and 1 week later. In a within‐subjects design, all of the children were taught four lessons of a different format: (1) written presentation only; (2) written presentation accompanied by pictures; (3) oral presentation only and (4) oral presentation accompanied by pictures. With respect to the quantity of learning, a short‐term modality effect was found with oral presentation producing better results than written presentation when accompanied by pictures. A multimedia effect was found for only the oral conditions. With respect to the quality of the children's learning, an initial short‐term modality effect was found but reversed 1 week following intervention with no evidence of a multimedia effect. Copyright © 2008 John Wiley & Sons, Ltd.
Cognitive processes in comprehension of science texts: the role of co‐activation in confronting misconceptions
Authors: van den Broek Paul , Kendeou Panayiota 
Published: March 2008

AbstractIn this paper, we investigate the effects of readers' incorrect knowledge on the on‐line comprehension processes during reading of science texts, with an eye towards examining the conditions that encourage revision of such knowledge. We employed computational (Landscape Model) and empirical (think‐aloud and reading times) methods to compare comprehension processes by readers with correct and incorrect background knowledge, respectively. Science texts were presented in either regular or refutation versions; Prior research using off‐line methods suggests that refutation versions promote revision in readers with incorrect knowledge. The results of the current study indicate that incorrect knowledge systematically influences both type and content of processing. Moreover, simultaneous activation of correct and incorrect conceptions during reading plays an essential role in knowledge revision: The computational simulations show that refutation texts create optimal circumstances for co‐activation of the incorrect and correct conceptions and the empirical data show that such a co‐activation is associated with inconsistency detection and revision activities by the readers with incorrect knowledge. These findings provide insights in the effects of misconceptions on the on‐line text processing and have important implications for the development of methods for achieving revision during reading. Copyright © 2008 John Wiley & Sons, Ltd.
A Morphological Model for the Solvent‐Enhanced Conductivity of PEDOT:PSS Thin Films
Authors: Nardes Alexandre Mantovani , Janssen René A. J. , Kemerink Martijn 
Published: March 2008

AbstractThe well‐known enhanced conductivity of poly(3,4‐ethylenedioxythiophene):poly(4‐styrenesulfonate) (PEDOT:PSS) thin films that is obtained by addition of high‐boiling solvents like sorbitol to the aqueous dispersion used for film deposition is shown to be associated with a rearrangement of PEDOT‐rich clusters into elongated domains, as evidenced from STM and AFM. Consistently, temperature dependent conductivity measurements for sorbitol‐treated films reveal that charge transport occurs via quasi 1D variable range hopping (VRH), in contrast to 3D VRH for untreated PEDOT:PSS films. The typical hopping distance of 60–90 nm, extracted from the conductivity measurements is consistent with hopping between the 30–40 nm sized grains observed with scanning probe microscopy.