bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benthic macroinvertebrates as indicators of biological condition below hydropower dams on west slope Sierra Nevada streams, California, USA
Authors: Rehn Andrew C. 
Published: May 2008

AbstractOver 50 hydropower dams in California will undergo relicensing by the Federal Energy Regulatory Commission (FERC) in the next 15 years. An interpretive framework for biological data collected by relicensing studies is lacking. This study developed a multi‐metric index of biotic integrity (IBI) to assess biological condition below hydropower diversion dams on west slope Sierra Nevada streams based on benthic macroinvertebrates (BMIs). Ten streams were sampled above the upstream influence of peak reservoir storage and at five downstream sites sequentially spaced 500 m apart. Reference conditions were defined by screening upstream study sites and 77 other regional streams using quantitative GIS land use analysis, reach‐scale physical habitat (PHAB) data and water chemistry data. Eighty‐two metrics were evaluated for inclusion in the IBI based on three criteria: (1) good discrimination between reference and first downstream sites with some indication of recovery over the distance sampled; (2) sufficient range for scoring; (3) minimal correlation with other discriminating metrics. The IBI showed good discrimination between reference and downstream sites with partial recovery as distance downstream increased, and was validated with an independent dataset. Individual metrics, IBI scores and multivariate ordination axes were poorly correlated with PHAB variables across sites. When only reference and first downstream sites were evaluated, decreased IBI scores were related to lower habitat variability and substrate coarsening below dams. Lower IBI scores below dams were most strongly associated with altered hydrologic regime, especially non‐fluctuating flows as defined by the flow constancy/predictability index. Flow restoration experiments would be valuable in developing management actions that achieve a sustainable balance between conflicting human and ecological needs for freshwater. Copyright © 2008 John Wiley & Sons, Ltd.
The order of the largest complete minor in a random graph
Authors: Fountoulakis Nikolaos , Kühn Daniela , Osthus Deryk 
Published: May 2008

AbstractLet ccl(G) denote the order of the largest complete minor in a graph G (also called the contraction clique number) and let Gn,p denote a random graph on n vertices with edge probability p. Bollobás, Catlin, and Erdős (Eur J Combin 1 (1980), 195–199) asymptotically determined ccl(Gn,p) when p is a constant. Łuczak, Pittel and Wierman (Trans Am Math Soc 341 (1994) 721–748) gave bounds on ccl(Gn,p) when p is very close to 1/n, i.e. inside the phase transition. We show that for every ε > 0 there exists a constant C such that whenever C/n < p < 1 ‐ ε then asymptotically almost surely ccl(Gn,p) = (1 ± ε)n/
$ \sqrt{\rm {log}_{b}(np)} $, where b := 1/(1 ‐ p). If p = C/n for a constant C > 1, then ccl(Gn,p) = Θ($ \sqrt{n} $). This extends the results in (Bollobás, Catlin, and P. Erdős, Eur J Combin 1 (1980), 195–199) and answers a question of Krivelevich and Sudakov (preprint, 2006). © 2008 Wiley Periodicals, Inc. Random Struct. Alg., 2008
Reinforcement of rigid PVC/wood‐flour composites with multi‐walled carbon nanotubes
Authors: Faruk Omar , Matuana Laurent M. 
Published: May 2008

AbstractMulti‐walled carbon nanotubes (CNT) were compounded with PVC by a melt blending process based on fusion behaviors of PVC. The effects of CNT content on the flexural and tensile properies of the PVC/CNT composites were evaluated in order to optimize the CNT content. The optimized CNT‐reinforced PVC was used as a matrix in the manufacture of wood‐plastic composites. Flexural, electrical, and thermal properties of the PVC/wood‐flour composites were evaluated as a function of matrix type (nonreinforced vs. CNT‐reinforced). The experimental results indicated that rigid PVC/wood‐flour composites with properties similar to those of solid wood can be made by using CNT‐reinforced PVC as a matrix. The CNT‐reinforced PVC did not influence the electrical and thermal conductivity of the PVC/wood‐flour composites. J. VINYL ADDIT. TECHNOL., 2008. © 2008 Society of Plastics Engineers.
Analysis of thermally abused soybean oils for cyclic monomers
Authors: Meltzer J. B. , Frankel E. N. , Bessler T. R. , Perkins E. G. 
Published: May 2008

AbstractCyclic monomers derived from the intramolecular condensation of the C18 polyunsaturated fatty acids have been reported to elicit toxic responses when fed to laboratory animals at low dietary levels. This study was undertaken to quantitate the cyclic monomers formed by thermal oxidation induced during deep fat frying to assess the potential toxicity of commonly used vegetable oils. Two separate experiments were designed to study the effects of unsaturation and both intermittent and continuous heating on cyclic monomer formation. Both lightly hydrogenated soybean oil (iodine value [IV]=107) and refined, bleached and deodorized soybean oil were studied. The heated oil sustained substantial chemical and physical alterations, as indicated by IV decreases from 10–15 units, increases in free fatty acids of 5–10‐fold and in noneluted material of 18–21%. Selected samples were completely hydrogenated and analyzed for cyclic monomers by gas chromatography. Under chromatographic conditions sufficiently sensitive to detect a cyclic monomer standard at less than 0.5% by weight, no cyclic monomers were detected in any of the heated oil samples. However, after concentration by low temperature crystallization of the hydrogenated samples to remove a major portion of the saturated components interfering in cyclic monomer resolution, about 0.3–0.6% cyclic acids, as well as 0.4–0.9% polar materials, were detected in the heated soybean oils. Components appearing in the gas chromatogram with the same retention time as those in a cyclic monomer standard were further identified by gas chromatography‐mass spectrometry as disubstituted cyclic C‐18 acids.
Nickel‐catalyzed hydrogenation of soybean oil: I. Kinetic, equilibrium and mass transfer determinations
Authors: Susu Alfred A. , Ogunye A. F. 
Published: May 2008

AbstractThe kinetic and equilibrium constants were determined for the hydrogenation of soybean oil on a commercial nickel catalyst in a 300‐ml Parr batch reactor. These constants were used to calculate the hydrogen gas absorption coefficients by coupling mass transfer with reaction rate based on a Langmuir Hinshelwood model. The activation energy for the rate‐determining step was 23 kcal/g mol whereas the adsorption energy for hydrogen was −12.5 kcal/g mol. The gas absorption coefficients varied between 0.3 to 0.7 min−1 as the temperature ranged between 140–180 C.
Investigations on the conditions for hydrogenation of fatty oils with polymer anchored pd‐phosphine complexes
Authors: Andersson C. , Larsson R. 
Published: May 2008

AbstractPalladium chloride has been anchored to phosphinated, cross‐linked polystyrene by substitution of the pyridine ligand in Cl2Pd‐(NC5H5)2with the polymeric phosphine. By analytical and infrared studies of the prepared catalyst, it has been shown that the main species formed in the matrix is the half‐substituted complex Cl2Pd‐(NC5H5)P‐PS (P‐PS=polymeric benzyldiphenylphosphine). This polymer‐bound palladium complex has been tested together with two other preparations, both of which are bisphosphine complexes, as catalysts for hydrogenation of soybean oil. The results show that the presence of the mixed phosphine‐pyridine complex is necessary for catalytic activity under ambient conditions. The monoene fraction of the oil is hydrogenated very slowly, but the polyene fraction is reduced quickly. Relatively large amounts oftrans‐isomers are formed, however, in the reaction. It has been noted that the activation of the catalyst is coupled to a release of pyridine from the catalyst. It is proposed that after the release of pyridine, further reactions take place inside the polymer which cause the catalyst to be active under mild conditions.
Rapeseed meal in animal nutrition: II. Nonruminant animals
Authors: Clandinin D. R. , Robblee A. R. 
Published: May 2008

AbstractOn the basis of our present knowledge regarding the use of rapeseed meal in rations for swine and poultry, it would appear that the usage levels for high glucosinolate and low glucosinolate rapeseed meals discussed in this paper should give excellent results in terms of performance.
Licochalcone A inhibits the formation and bone resorptive activity of osteoclasts
Authors: Kim Soon Nam , Kim Myung Hee , Min Yong Ki , Kim Seong Hwan 
Published: May 2008

AbstractLicochalcone A on the formation and bone resorptive activity of osteoclasts up to 5 μM significantly inhibited the receptor activator of nuclear factor κB (NF‐κB) ligand (RANKL)‐induced activity of tartrate‐resistant acid phosphatase (TRAP) activity and formation of osteoclasts without any effect on cell viability. Interestingly, licochalcone A was shown to inhibit the RANKL‐induced activation of extracellular signal‐regulated kinase, translocation of NF‐κB into nucleus and mRNA expression of Fra‐2. Licochalcone A also inhibited the bone resorptive activity of mature osteoclasts and the expression of bone resorption‐related genes. Inhibitory effects of licochalcone A on the formation and bone resorptive activity of mouse bone marrow macrophage‐derived osteoclasts were also observed. In conclusion, licochalcone A has the potential to inhibit the formation of osteoclasts as well as the bone resorptive activity of mature osteoclasts.
Effects of small interfering RNAs targeting MAPK1 on gene expression profile in HeLa cells as revealed by microarray analysis
Authors: Huang Chen , Liu Li‐Ying , Li Zong‐Fang , Wang Pei , Ni Lei , Song Li‐Ping , Xu De‐Hui , Song Tu‐Sheng 
Published: May 2008

AbstractThe mitogen activated protein kinases (MAPK) signaling cascade plays an important role in cell life. We proved that small interfering RNAs targeting MAPK1 (siRNA‐2) could inhibit HeLa cell growth, but the effects of siRNA‐2 on gene expression profile were unclear. Using Affymetrix GeneChip HG‐U133A 2.0, we identified the long‐term changes for 48 h in gene expression profile in HeLa cell treated by siRNA‐2. The results showed that expressions of 181 genes were altered by siRNA‐2 and were divided into two groups: (i) one group showed downregulation by siRNA‐2, including the proliferation associated genes, small G protein, cytoskeleton associated protein and extracellular matrix associated protein; and (ii) the other group showed upregulation by siRNA‐2, including interferon response genes, OAS family, TRIM family and apoptosis associated genes. The results of Real‐time quantitative PCR for MAPK1, NUP188, P38, STAT1, STAT2, MPL and OAS1 were consistent with that of gene chip. Two networks were found to react substantially to the downregulation of MAPK1 by siRNA‐2. One of the networks regulates cell growth through cell‐cycle control, apoptosis and cytoskeleton. The other network is related to interferon‐like response. Our findings suggest that siRNA‐mediated downregulation of MAPK1 could be an attractive strategy for cancer therapy.
Interhemispheric compensation: A hypothesis of TMS-induced effects on language-related areas
Authors: Andoh Jamila , Martinot Jean-Luc 
Published: May 2008

AbstractRepetitive transcranial magnetic stimulation (rTMS) applied over brain regions responsible for language processing is used to curtail potentially auditory hallucinations in schizophrenia patients and to investigate the functional organisation of language-related areas. Variability of effects is, however, marked across studies and between subjects. Furthermore, the mechanisms of action of rTMS are poorly understood.Here, we reviewed different factors related to the structural and functional organisation of the brain that might influence rTMS-induced effects. Then, by analogy with aphasia studies, and the plastic-adaptive changes in both the left and right hemispheres following aphasia recovery, a hypothesis is proposed about rTMS mechanisms over language-related areas (e.g. Wernicke, Broca). We proposed that the local interference induced by rTMS in language-related areas might be analogous to aphasic stroke and might lead to a functional reorganisation in areas connected to the virtual lesion for language recovery.
Early reduction in prefrontal theta QEEG cordance value predicts response to venlafaxine treatment in patients with resistant depressive disorder
Authors: Bares Martin , Brunovsky Martin , Kopecek Miloslav , Novak Tomas , Stopkova Pavla , Kozeny Jiri , Sos Peter , Krajca Vladimir , Höschl Cyril 
Published: May 2008

AbstractIntroductionPrevious studies of patients with unipolar depression have shown that early decrease of prefrontal EEG cordance in theta band can predict clinical response to various antidepressants. We have now examined whether decrease of prefrontal quantitative EEG (QEEG) cordance value after 1 week of venlafaxine treatment predicts clinical response to venlafaxine in resistant patients.MethodWe analyzed 25 inpatients who finished 4-week venlafaxine treatment. EEG data were monitored at baseline and after 1 week of treatment. QEEG cordance was computed at three frontal electrodes in theta frequency band. Depressive symptoms and clinical status were assessed using Montgomery–Åsberg Depression Rating Scale (MADRS), Beck Depression Inventory-Short Form (BDI-S) and Clinical Global Impression (CGI).ResultsEleven of 12 responders (reduction of MADRS ≥50%) and only 5 of 13 non-responders had decreased prefrontal QEEG cordance value after the first week of treatment (p = 0.01). The decrease of prefrontal cordance after week 1 in responders was significant (p = 0.03) and there was no significant change in non-responders. Positive and negative predictive values of cordance reduction for response were 0.7 and 0.9, respectively.ConclusionThe reduction of prefrontal theta QEEG cordance value after first week of treatment might be helpful in the prediction of response to venlafaxine.
Preference‐based quality of life in patients with Alzheimer's disease
Authors: Karlawish Jason H. , Zbrozek Art , Kinosian Bruce , Gregory Annemarie , Ferguson Allison , Glick Henry A. 
Published: May 2008

BackgroundThis study was developed to evaluate the feasibility, reliability, and validity of use of patients' ratings of health preference measures as outcomes for cost‐effectiveness analyses in persons with very mild to moderate Alzheimer's disease (AD).MethodsPatients and caregivers completed ratings of the EuroQol‐5D system (EQ‐5D) and the Health Utilities Index Mark 2 (HUI2) and instruments that assess cognition, mood, insight, AD‐specific and generic health‐related quality of life (QOL) and activities of daily living.ResultsPatients' HUI2 scores were reliable. EQ‐5D scores were somewhat less so. Patients rated their utility high, with overall EQ‐5D and HUI2 scores greater than 0.8. Neither the EQ‐5D nor the HUI2 scores had a relationship with severity of cognitive impairment. Both the EQ‐5D and the HUI2 had expected relationships with patient‐rated measures of QOL, function, mood, and specific subscales we hypothesized should be associated with patient preferences. Patient insight into functional and cognitive impairments had little association with their health preference scores.ConclusionsAD patients' scores on the EQ‐5D and the HUI2 have many of the characteristics of valid preference measures. However, the proportions of persons who do not perceive any disability, the lack of association with the caregivers' ratings of activities of daily living, limited associations with insight, and no association with their Mini‐Mental State Exam scores suggest that patients' reports of disability might reflect legitimate self‐perceptions of mood and function that are associated with comorbidities rather than with AD.
Applying VaR to REITs: A comparison of alternative methods
Authors: Lu Chiuling , Wu Sheng‐Ching , Ho Lan‐Chih 
Published: May 2008

AbstractThis study employs five methods to calculate the VaR of twelve REITs portfolios and evaluates the accuracy of these methods. Firstly, we find that the VaR varies among individual portfolios. The Hotel REITs has consistently the largest VaR. The low‐leveraging portfolio tends to have the largest VaR measured by the parametric methods, while the high leveraging portfolio has the largest VaR calculated by the non‐parametric methods. Secondly, each method performs differently at different confidence levels, and no method dominates the others. At the 95% confidence level, the EWMA method performs relatively well. The EQWMA and the two non‐parametric methods perform equivalently and slightly overestimate VaRs. The EQWMAT method ranks the bottom and significantly overestimates VaRs for all portfolios. At the 99% confidence level, the EQWMA method performs the best. The EQWMAT and the two non‐parametric methods perform equivalently and may overestimate VaR for all portfolios. The EWMA method turns out to be the worst and tends to underestimate the VaR. These findings may provide more insights for institutional real estate investors.
An efficient method to identify differentially expressed genes in microarray experiments
Authors: Qin Huaizhen , Feng Tao , Harding Scott A. , Tsai Chung-Jui , Zhang Shuanglin 
Published: May 2008

AbstractMotivation: Microarray experiments typically analyze thousands to tens of thousands of genes from small numbers of biological replicates. The fact that genes are normally expressed in functionally relevant patterns suggests that gene-expression data can be stratified and clustered into relatively homogenous groups. Cluster-wise dimensionality reduction should make it feasible to improve screening power while minimizing information loss.Results: We propose a powerful and computationally simple method for finding differentially expressed genes in small microarray experiments. The method incorporates a novel stratification-based tight clustering algorithm, principal component analysis and information pooling. Comprehensive simulations show that our method is substantially more powerful than the popular SAM and eBayes approaches. We applied the method to three real microarray datasets: one from a Populus nitrogen stress experiment with 3 biological replicates; and two from public microarray datasets of human cancers with 10 to 40 biological replicates. In all three analyses, our method proved more robust than the popular alternatives for identification of differentially expressed genes.Availability: The C++ code to implement the proposed method is available upon request for academic use.Contact: shuzhang@mtu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
DAnTE: a statistical tool for quantitative analysis of -omics data
Authors: Polpitiya Ashoka D. , Qian Wei-Jun , Jaitly Navdeep , Petyuk Vladislav A. , Adkins Joshua N. , Camp David G. , Anderson Gordon A. , Smith Richard D. 
Published: May 2008

Abstract
Summary: Data Analysis Tool Extension (DAnTE) is a statistical tool designed to address challenges associated with quantitative bottom-up, shotgun proteomics data. This tool has also been demonstrated for microarray data and can easily be extended to other high-throughput data types. DAnTE features selected normalization methods, missing value imputation algorithms, peptide-to-protein rollup methods, an extensive array of plotting functions and a comprehensive hypothesis-testing scheme that can handle unbalanced data and random effects. The graphical user interface (GUI) is designed to be very intuitive and user friendly.
Availability: DAnTE may be downloaded free of charge at http://omics.pnl.gov/software/
Contact: rds@pnl.gov or proteomics@pnl.gov
Supplementary information: An example dataset with instructions on how to perform a series of analysis steps is available at http://omics.pnl.gov/software/
quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation
Authors: Neuenschwander Samuel , Hospital Frédéric , Guillaume Frédéric , Goudet Jérôme 
Published: May 2008

Abstract
Summary: quantiNemo is an individual-based, genetically explicit stochastic simulation program. It was developed to investigate the effects of selection, mutation, recombination and drift on quantitative traits with varying architectures in structured populations connected by migration and located in a heterogeneous habitat. quantiNemo is highly flexible at various levels: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography, mating system, etc. quantiNemo is coded in C++ using an object-oriented approach and runs on any computer platform.
Availability: Executables for several platforms, user's manual, and source code are freely available under the GNU General Public License at http://www2.unil.ch/popgen/softwares/quantinemo
Contact: samuel.neuenschwander@unil.ch
The “Old” Euonymus europaeus Agglutinin Represents a Novel Family of Ubiquitous Plant Proteins
Authors: Fouquaert Elke , Peumans Willy J. , Smith David F. , Proost Paul , Savvides Savvas N. , Van Damme Els J.M. 
Published: May 2008

Abstract
Molecular cloning of the “old” but still unclassified Euonymus europaeus agglutinin (EEA) demonstrated that the lectin is a homodimeric protein composed of 152 residue subunits. Analysis of the deduced sequence indicated that EEA is synthesized without a signal peptide and undergoes no posttranslational processing apart from the removal of a six-residue N-terminal peptide. Glycan array screening confirmed the previously reported high reactivity of EEA toward blood group B oligosaccharides but also revealed binding to high mannose N-glycans, providing firm evidence for the occurrence of a plant carbohydrate-binding domain that can interact with structurally different glycans. Basic Local Alignment Search Tool searches indicated that EEA shares no detectable sequence similarity with any other lectin but is closely related evolutionarily to a domain that was first identified in some abscisic acid- and salt stress-responsive rice (Oryza sativa) proteins, and, according to the available sequence data, might be ubiquitous in Spermatophyta. Hence, EEA can be considered the prototype of a novel family of presumably cytoplasmic/nuclear proteins that are apparently ubiquitous in plants. Taking into account that some of these proteins are definitely stress related, the present identification of the EEA lectin domain might be a first step in the recognition of the involvement and importance of protein-glycoconjugate interactions in some essential cellular processes in Embryophyta.
Core classification theory: a reply to Szostak
Authors: Hjørland Birger 
Published: May 2008

PurposeThe purpose of this paper is to provide an answer to a critique put forward by Szostak against a paper written by the present author.Design/methodology/approachThe paper is based on a literature‐based conceptual analysis based on Hjørland and Nissen Pedersen and Szostak. The main points in a core theory of classification are outlined and Szostak's criticism is examined and answered.FindingsThe paper demonstrates theoretical differences between the views adduced by Hjørland and Nissen Pedersen on the one side and by Szostak on the other.Practical implicationsTheoretical clarification is important for the future development of the field.Originality/valueThe paper should be seen as one among others developing an argument for a theoretical foundation of classification informed by the theory of knowledge.