bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of supercritical fluid extraction use in whole sediment toxicity identification evaluations
Authors: Burgess Robert M , Hawthorne Steven B , Perron Monique M , Cantwell Mark G , Grabanski Carol B , Miller David J , Ho Kay T , Pelletier Marguerite A 
Published: December 2010

Abstract
Supercritical fluid extraction (SFE) with pure CO2 was assessed as a confirmatory tool in phase III of whole sediment toxicity identification evaluations (TIEs). The SFE procedure was assessed on two reference sediments and three contaminated sediments by using a combination of toxicological and chemical measurements to quantify effectiveness. Sediment toxicity pre- and post-SFE treatment was quantified with a marine amphipod (Ampelisca abdita) and mysid (Americamysis bahia), and nonionic organic contaminants (NOCs) polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) were measured in sediments, overlying waters, and interstitial waters. In general, use of SFE with the reference sediments was successful, with survival averaging 91% in post-SFE treatments. Substantial toxicity reductions and contaminant removal from sediments and water samples generated from extracted sediments of up to 99% in two of the contaminated sediments demonstrated SFE effectiveness. Furthermore, toxicological responses for these SFE-treated sediments showed comparable results to those from the same sediments treated with the powdered coconut charcoal addition manipulation. These data demonstrated the utility of SFE in phase III of a whole sediment TIE. Conversely, in one of the contaminated sediments, the SFE treatments had no effect on sediment toxicity, whereas sediment concentrations of PCBs and PAHs were reduced. We propose that, for some sediments, the SFE treatment may result in the release of otherwise nonbioavailable cationic metals that subsequently cause toxicity to test organisms. Overall, SFE treatment was found to be effective for reducing the toxicity and concentrations of NOCs in some contaminated sediments. However, these studies suggest that SFE treatment may enhance toxicity with some sediments, indicating that care must be taken when applying SFE and interpreting the results. Environ. Toxicol. Chem. 2011; 30:819–827. © 2010 SETAC
Oxidative stress response of Forster's terns (Sterna forsteri) and Caspian terns (Hydroprogne caspia) to mercury and selenium bioaccumulation in liver, kidney, and brain
Authors: Hoffman David J , Eagles-Smith Collin A , Ackerman Joshua T , Adelsbach Terrence L , Stebbins Katherine R 
Published: December 2010

Abstract
Bioindicators of oxidative stress were examined in prebreeding and breeding adult and chick Forster's terns (Sterna forsteri) and in prebreeding adult Caspian terns (Hydroprogne caspia) in San Francisco Bay, California. Highest total mercury (THg) concentrations (mean ± standard error; µg/g dry wt) in liver (17.7 ± 1.7), kidney (20.5 ± 1.9), and brain (3.0 ± 0.3) occurred in breeding adult Forster's terns. The THg concentrations in liver were significantly correlated with hepatic depletion of reduced glutathione (GSH), increased oxidized glutathione (GSSG):GSH ratio, and decreased hepatic gamma-glutamyl transferase (GGT) activity in adults of both tern species. Prefledging Forster's tern chicks with one-fourth the hepatic THg concentration of breeding adults exhibited effects similar to adults. Total mercury–related renal GSSG increased in adults and chicks. In brains of prebreeding adults, THg was correlated with a small increase in glucose-6–phosphate dehydrogenase (G-6-PDH) activity, suggestive of a compensatory response. Brain THg concentrations were highest in breeding adult Forster's terns and brain tissue exhibited increased lipid peroxidation as thiobarbituric acid-reactive substances, loss of protein bound thiols (PBSH), and decreased activity of antioxidant enzymes, GSSG reductase (GSSGrd), and G-6-PDH. In brains of Forster's tern chicks there was a decrease in total reduced thiols and PBSH. Multiple indicator responses also pointed to greater oxidative stress in breeding Forster's terns relative to prebreeding terns, attributable to the physiological stress of reproduction. Some biondicators also were related to age and species, including thiol concentrations. Enzymes GGT, G-6-PDH, and GSSGred activities were related to species. Our results indicate that THg concentrations induced oxidative stress in terns, and suggest that histopathological, immunological, and behavioral effects may occur in terns as reported in other species. Environ. Toxicol. Chem. 2011; 30:920–929. © 2010 SETAC
Mining gold dust under the genome wide significance level: a two‐stage approach to analysis of GWAS
Authors: Shi Gang , Boerwinkle Eric , Morrison Alanna C. , Gu C. Charles , Chakravarti Aravinda , Rao D.C. 
Published: December 2010

AbstractWe propose a two‐stage approach to analyze genome‐wide association data in order to identify a set of promising single‐nucleotide polymorphisms (SNPs). In stage one, we select a list of top signals from single SNP analyses by controlling false discovery rate. In stage two, we use the least absolute shrinkage and selection operator (LASSO) regression to reduce false positives. The proposed approach was evaluated using simulated quantitative traits based on genome‐wide SNP data on 8,861 Caucasian individuals from the Atherosclerosis Risk in Communities (ARIC) Study. Our first stage, targeted at controlling false negatives, yields better power than using Bonferroni‐corrected significance level. The LASSO regression reduces the number of significant SNPs in stage two: it reduces false‐positive SNPs and it reduces true‐positive SNPs also at simulated causal loci due to linkage disequilibrium. Interestingly, the LASSO regression preserves the power from stage one, i.e., the number of causal loci detected from the LASSO regression in stage two is almost the same as in stage one, while reducing false positives further. Real data on systolic blood pressure in the ARIC study was analyzed using our two‐stage approach which identified two significant SNPs, one of which was reported to be genome‐significant in a meta‐analysis containing a much larger sample size. On the other hand, a single SNP association scan did not yield any significant results.Genet. Epidemiol. 32:111‐118, 2011.© 2010 Wiley‐Liss, Inc.
Inferring genetic causal effects on survival data with associated endo‐phenotypes
Authors: Lipman Peter J. , Liu Kuang‐Yu , Muehlschlegel Jochen Daniel , Body Simon , Lange Christoph 
Published: December 2010

AbstractAge‐at‐onset phenotypes are important traits in genetic association analyses. Often, intermediate phenotypes that are related to the age‐at‐onset phenotype are also associated with the marker loci that are associated with the age‐at‐onset phenotype. In order to understand the genetic etiology of the observed associations, statistical methodology is needed to distinguish between a direct genetic effect on the age‐at‐onset phenotype and an indirect effect induced by the genetic association with the endo‐phenotype that is correlated with the age‐at‐onset phenotype. In this communication, we introduce a new statistical approach to detect causal genetic effects on survival data in the presence of genetic associations with secondary phenotypes that might influence survival as well and thereby induce seemingly causal relationships. Derived using causal inference methodology, the proposed method is based on standard statistical methodology and can be implemented straight‐forwardly, using standard software. Using simulation studies, the theoretical properties of the approach are verified and the power is assessed under realistic scenarios. The practical relevance of the approach is illustrated by an application to survival after cardiac surgery, where genetic components of myocardial infarctions are determined to not influence post‐surgery hospital duration except through the MI‐pathway. Genet. Epidemiol. 32:119‐124, 2011.  © 2010 Wiley‐Liss, Inc.
Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method
Authors: Bruckner Stefan , Boresch Stefan 
Published: December 2010

AbstractWe investigate the relative efficiency of thermodynamic integration, three variants of the exponential formula, also referred to as thermodynamic perturbation, and Bennett's acceptance ratio method to compute relative and absolute solvation free energy differences. Our primary goal is the development of efficient protocols that are robust in practice. We focus on minimizing the number of unphysical intermediate states (λ‐states) required for the computation of accurate and precise free energy differences. Several indicators are presented which help decide when additional λ‐states are necessary. In all tests Bennett's acceptance ratio method required the least number of λ‐states, closely followed by the “double‐wide” variant of the exponential formula. Use of the exponential formula in only strict “forward” or “backward” mode was not found to be competitive. Similarly, the performance of thermodynamic integration in terms of efficiency was rather poor. We show that this is caused by the use of the trapezoidal rule as method of numerical quadrature. A systematic study focusing on the optimization of thermodynamic integration is presented in a companion paper. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
O(NlogN) Continuous electrostatics method for fast calculation of solvation energies of biomolecules
Authors: Fedichev P. O. , Getmantsev E. G. , Menshikov L. I. 
Published: December 2010

AbstractWe report the development of a new, fast, surface‐based method for numerical calculations of the solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size, both in time and memory requirements, produces explicit values for the reaction field potential and stable values of the polar energy within only a few percent error margin practically for any molecular configurations. The method works well both for large and small molecules and thus gives stable energy differences for quantities such as the polar energy contributions to molecular complex formation energies. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Short interspersed elements (SINEs) of squamate reptiles (Squam1 and Squam2): Structure and phylogenetic significance
Authors: Grechko Vernata V. , Kosushkin Sergei A. , Borodulina Olga R. , Butaeva Fatima G. , Darevsky Ilya S. 
Published: December 2010

AbstractShort interspersed elements (SINEs) are important nuclear molecular markers of the evolution of many eukaryotes. However, the SINEs of squamate reptile genomes have been little studied. We first identified two families of SINEs, termed Squam1 and Squam2, in the DNA of meadow lizard Darevskia praticola (Lacertidae) by performing DNA hybridization and PCR. Later, the same families of retrotransposons were found using the same methods in members of another 25 lizard families (from Iguania, Scincomorpha, Gekkota, Varanoidea, and Diploglossa infraorders) and two snake families, but their abundances in these taxa varied greatly. Both SINEs were Squamata‐specific and were absent from mammals, birds, crocodiles, turtles, amphibians, and fish. Squam1 possessed some characteristics common to tRNA‐related SINEs from fish and mammals, while Squam2 belonged to the tRNAAla group of SINEs and had a more unusual and divergent structure. Squam2‐related sequences were found in several unannotated GenBank sequences of squamate reptiles. Squam1 abundance in the Polychrotidae, Agamidae, Leiolepididae, Chamaeleonidae, Scincidae, Lacertidae, Gekkonidae, Varanidae, Helodermatidae, and two snake families were 102–104 times higher than those in other taxa (Corytophanidae, Iguanidae, Anguidae, Cordylidae, Gerrhosauridae, Pygopodidae, and Eublepharidae). A less dramatic degree of copy number variation was observed for Squam2 in different taxa. Several Squam1 copies from Lacertidae, Chamaeleonidae, Gekkonidae, Varanidae, and Colubridae were sequenced and found to have evident orthologous features, as well as taxa‐specific autapomorphies. Squam1 from Lacertidae and Chamaeleonidae could be divided into several subgroups based on sequence differences. Possible applications of these SINEs as Squamata phylogeny markers are discussed. J. Exp. Zool. (Mol. Dev. Evol.) 316:212–226, 2011. © 2010 Wiley‐Liss, Inc.
Localization of burn mark under an abnormal topography on MOSFET chip surface using liquid crystal and emission microscopy tools
Authors: Lau C. K. , Sim K. S. , Tso C. P. 
Published: December 2010

AbstractThis article focuses on the localization of burn mark in MOSFET and the scanning electron microscope (SEM) inspection on the defect location. When a suspect abnormal topography is shown on the die surface, further methods to pin‐point the defect location is necessary. Fault localization analysis becomes important because an abnormal spot on the chip surface may and may not have a defect underneath it. The chip surface topography can change due to the catastrophic damage occurred at layers under the chip surface, but it could also be due to inconsistency during metal deposition in the wafer fabrication process. Two localization techniques, liquid crystal thermography and emission microscopy, were performed to confirm that the abnormal topography spot is the actual defect location. The tiny burn mark was surfaced by performing a surface decoration at the defect location using hot hydrochloric acid. SEM imaging, which has the high magnification and three‐dimensional capabilities, was used to capture the images of the burn mark. SCANNING 33: 13–20, 2011. © 2010 Wiley Periodicals, Inc.
Computational systems biology of aging
Authors: Kriete Andres , Lechner Mark , Clearfield Drew , Bohmann Dirk 
Published: December 2010

AbstractComputational systems biology is expected to make major contributions to unravel the complex molecular mechanisms underlying the progression of aging in cells, tissues, and organisms. The development of computational approaches is, however, challenged by a wide spectrum of aging mechanisms participating on different levels of biological organization. The tight connectivity between the molecular constituents, functions, and cell states requires frameworks and strategies that extend beyond current practice to model, simulate, and predict the progression of aging and the emerging aging phenotypes. We provide a general overview of the specific computational tasks and opportunities in aging research, and discuss some illustrative systems level concepts in more detail. One example provided here is the assembly of a conceptual whole cell model that considers the temporal dynamics of the aging process grounded on molecular mechanisms. Another application is the assembly of interactomes, such as protein networks that allow us to analyze changes in network topology and interaction of proteins that have been implicated in aging with other cellular constituents and processes. We introduce the necessary key steps to build these applications and discuss their merits and future extensions for aging research. WIREs Syst Biol Med 2011 3 414–428 DOI: 10.1002/wsbm.126This article is categorized under:

Physiology > Mammalian Physiology in Health and Disease
Where gene discovery turns into systems biology: genome‐scale RNAi screens in Drosophila
Authors: Neumüller Ralph A. , Perrimon Norbert 
Published: December 2010

AbstractSystems biology aims to describe the complex interplays between cellular building blocks which, in their concurrence, give rise to the emergent properties observed in cellular behaviors and responses. This approach tries to determine the molecular players and the architectural principles of their interactions within the genetic networks that control certain biological processes. Large‐scale loss‐of‐function screens, applicable in various different model systems, have begun to systematically interrogate entire genomes to identify the genes that contribute to a certain cellular response. In particular, RNA interference (RNAi)‐based high‐throughput screens have been instrumental in determining the composition of regulatory systems and paired with integrative data analyses have begun to delineate the genetic networks that control cell biological and developmental processes. Through the creation of tools for both, in vitro and in vivo genome‐wide RNAi screens, Drosophila melanogaster has emerged as one of the key model organisms in systems biology research and over the last years has massively contributed to and hence shaped this discipline. WIREs Syst Biol Med 2011 3 471–478 DOI: 10.1002/wsbm.127This article is categorized under:

Laboratory Methods and Technologies > RNA Methods
Genome‐wide approaches in the study of microRNA biology
Authors: Wilbert Melissa L. , Yeo Gene W. 
Published: December 2010

AbstractMicroRNAs (miRNAs), a class of ∼21–23 nucleotide long non‐coding RNAs (ncRNAs), have critical roles in diverse biological processes that encompass development, proliferation, apoptosis, stress response, and fat metabolism. miRNAs recognize their target mRNA transcripts by partial sequence complementarity and collectively have been estimated to regulate the majority of human genes. Consequently, misregulation of miRNAs or disruption of their target sites in genes has been implicated in a variety of human diseases ranging from cancer metastasis to neurological disorders. With the development and availability of genomic technologies and computational approaches, the field of miRNA biology has advanced tremendously over the last decade. Here we review the genome‐wide approaches that have allowed for the discovery of new miRNAs, the characterization of their targets, and a systems‐level view of their impact. WIREs Syst Biol Med 2011 3 491–512 DOI: 10.1002/wsbm.128This article is categorized under:

Laboratory Methods and Technologies > Genetic/Genomic Methods
Cardiac function and disease: emerging role of small ubiquitin‐related modifier
Authors: Wang Jun 
Published: December 2010

AbstractSmall ubiquitin‐related modifiers, or SUMOs, have emerged as versatile regulators of many biological functions that do so by covalent attachment to a variety of substrates via enzymatic reactions. SUMO conjugation has also been shown to be involved in a number of human pathogenic processes. More recent advances in the SUMO field have indicated a potential role for SUMO conjugation pathway in cardiogenesis. This advanced review will describe the basic features of the SUMO conjugation pathway and will summarize the most recent studies implicating the influence of the sumoylation pathway in cardiac function under both physiological and pathological conditions. WIREs Syst Biol Med 2011 3 446–457 DOI: 10.1002/wsbm.130This article is categorized under:

Developmental Biology > Developmental Processes in Health and Disease
Network biology: a direct approach to study biological function
Authors: Emmert‐Streib Frank , Glazko Galina V. 
Published: December 2010

AbstractIn this paper we discuss the dualism of gene networks and their role in systems biology. We argue that gene networks (1) can serve as a conceptual framework, forming a fundamental level of a phenomenological description, and (2) are a means to represent and analyze data. The latter point does not only allow a systems analysis but is even amenable for a direct approach to study biological function. Here we focus on the clarity of our main arguments and conceptual meaning of gene networks, rather than the causal inference of gene networks from data.WIREs Syst Biol Med2011 3 379–391 DOI: 10.1002/wsbm.134This article is categorized under:Biological Mechanisms > Regulatory Biology
Adaptation of cells to new environments
Authors: Brooks Aaron N. , Turkarslan Serdar , Beer Karlyn D. , Yin Lo Fang , Baliga Nitin S. 
Published: December 2010

AbstractThe evolutionary success of an organism is a testament to its inherent capacity to keep pace with environmental conditions that change over short and long periods. Mechanisms underlying adaptive processes are being investigated with renewed interest and excitement. This revival is partly fueled by powerful technologies that can probe molecular phenomena at a systems scale. Such studies provide spectacular insight into the mechanisms of adaptation, including rewiring of regulatory networks via natural selection of horizontal gene transfers, gene duplication, deletion, readjustment of kinetic parameters, and myriad other genetic reorganizational events. Here, we discuss advances in prokaryotic systems biology from the perspective of evolutionary principles that have shaped regulatory networks for dynamic adaptation to environmental change.WIREs Syst Biol Med2011 3 544–561 DOI: 10.1002/wsbm.136This article is categorized under:Biological Mechanisms > Cell FatesLaboratory Methods and Technologies > Genetic/Genomic MethodsPhysiology > Organismal Responses to EnvironmentBiological Mechanisms > Regulatory Biology
Are extremity musculoskeletal injuries in children related to obesity and social status? A prospective observational study in a district general hospital
Authors: Pullagura Mohan , Gopisetti Sharmila , Bateman Belinda , van Kampen Maria 
Published: December 2010

Background Obesity is one of the several independent risk factors for the risk of fractures. Major epidemiological studies also suggested the social status of the patients to be a confounding factor. We aimed to look at the influence of obesity on fractures and to determine if the social status of the patients is a confounding factor. Methods This is an observational study of 560 children with musculoskeletal injuries who presented over a period of 8 months and the data were collected prospectively. Obesity status and social deprivation index were estimated. Results The prevalence of overweight and obese children was 29.9%. Twenty-four percent of the boys and 31% of the girls were obese ( P = 0.2). In the group of most deprived areas, the prevalence of obesity increased to 40% in those needing admission for intervention. Conclusions Although there is a slight increase in obesity, there is no suggestion of increased rate of fractures in deprived areas. Upper limb injuries were more predominant, with distal radius fracture being the most common injury. Boys sustain fractures twice as often as girls. There is a tendency to increasing obesity with increasing age.
The contrasting effects of negative word of mouth in the post‐consumption stage
Authors: Chan Haksin , Cui Selina 
Published: December 2010

AbstractWe explore the effects of negative word of mouth (NWOM) from worse‐off or similar others in the post‐consumption stage. In four experiments, we show that the ramifications of NWOM are more complex than portrayed in the literature. Specifically, we demonstrate that attribute‐based NWOM has a negative (i.e., aggravating) effect on dissatisfied consumers, whereas experience‐based NWOM has a positive (i.e., alleviating) effect. Thought‐listing data reveal distinct processes underlying the contrasting effects. On one hand, these results are consistent with the predictions of attitude polarization and downward comparison research. On the other hand, they are explainable in terms of the disconfirmation model.
Pyrosequencing/Sanger Plant Genome Assembly (Limitations, Problems And Solutions) - On The Way To Cucumber (Cucumis sativus L. cv. Borszczagowski) Draft Genome Sequence Publishing
Authors: Woycicki Rafal , Przybecki Zbigniew 
Published: December 2010

AbstractGenome sequencing give us an opportunity to broaden the range and improve the quality of omics studies. New sequencing technologies make it possible to achieve the sequencing reads fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects.We focus here on the wide range of approaches undertaken to assemble the draft cucumber (Cucumis sativus L. cv. Borszczagowski) genome done by using 12x coverage of pyrosequencing Titanium chemistry shotgun paired and unpaired reads combined with Sanger reads.