bluuebunny/crossref_metadata_2025 huggingface dataset:
Stage‐specific alterations of the genome, transcriptome, and proteome during colorectal carcinogenesis
Authors: Habermann Jens K. , Paulsen Ulrike , Roblick Uwe J. , Upender Madhvi B. , McShane Lisa M. , Korn Edward L. , Wangsa Danny , Krüger Stefan , Duchrow Michael , Bruch Hans‐Peter , Auer Gert , Ried Thomas
Published: October 2006

To identify sequential alterations of the genome, transcriptome, and proteome during colorectal cancer progression, we have analyzed tissue samples from 36 patients, including the complete mucosa‐adenoma‐carcinoma sequence from 8 patients. Comparative genomic hybridization (CGH) revealed patterns of stage specific, recurrent genomic imbalances. Gene expression analysis on 9K cDNA arrays identified 58 genes differentially expressed between normal mucosa and adenoma, 116 genes between adenoma and carcinoma, and 158 genes between primary carcinoma and liver metastasis (P < 0.001). Parallel analysis of our samples by CGH and expression profiling revealed a direct correlation of chromosomal copy number changes with chromosome‐specific average gene expression levels. Protein expression was analyzed by two‐dimensional gel electrophoresis and subsequent mass spectrometry. Although there was no direct match of differentially expressed proteins and genes, the majority of them belonged to identical pathways or networks. In conclusion, increasing genomic instability and a recurrent pattern of chromosomal imbalances as well as specific gene and protein expression changes correlate with distinct stages of colorectal cancer progression. Chromosomal aneuploidies directly affect average resident gene expression levels, thereby contributing to a massive deregulation of the cellular transcriptome. The identification of novel genes and proteins might deliver molecular targets for diagnostic and therapeutic interventions. © Wiley‐Liss, Inc.
A FISH comparison of variant derivatives of the recurrent dic(17;20) of myelodysplastic syndromes and acute myeloid leukemia: Obligatory retention of genes on 17p and 20q may explain the formation of dicentric chromosomes
Authors: MacKinnon Ruth N. , Patsouris Cris , Chudoba Ilse , Campbell Lynda J.
Published: October 2006

The dic(17;20) is a recurrent unbalanced translocation occurring rarely in myelodysplastic syndromes and acute myeloid leukemia. We have studied eleven cases with the dic(17;20) or a more complex derivative, all of which showed deletion of 17p and 20q material. The tumor suppressor gene TP53 was not always lost, supporting a more distal gene as the target of these 17p deletions. All derivatives could be interpreted as having initially been formed as a dicentric chromosome, those with a larger amount of material between the centromeres having undergone further rearrangement to stabilize the chromosome while retaining proximal 17p and proximal 20q material. We propose that critical sequences on both 17p and 20q proximal to the sites of deletion must be retained during the critical 17p and 20q deletions. This would explain the excess of dicentric chromosomes resulting from 17;20 translocation, and the apparent stabilization of the unstable derivatives by further rearrangements which preserve 17p and 20q material. © 2006 Wiley‐Liss, Inc.
Gene expression in 16q is associated with survival and differs between Sørlie breast cancer subtypes
Authors: Wennmalm Kristian , Calza Stefano , Ploner Alexander , Hall Per , Bjöhle Judith , Klaar Sigrid , Smeds Johanna , Pawitan Yudi , Bergh Jonas
Published: October 2006

We have investigated the relationship between gene expression and chromosomal positions in 402 breast cancer patients. Using an overrepresentation approach based on Fisher's exact test, we identified disproportionate contributions of specific chromosomal positions to genes associated with survival. Our major finding is that the gene expression in the long arm of chromosome 16 stands out in its relationship to survival. This arm contributes 36 (18%) and 55 (11%) genes to lists negatively associated with recurrence‐free survival (set to sizes 200 and 500). This is a highly disproportionate contribution from the 313 (2%) genes in this arm represented on the used Affymetrix U133A and B microarray platforms (Bonferroni corrected Fisher test: P < 2.2 × 10−16). We also demonstrate differential expression in 16q across tumor subtypes, which suggests that the ERBB2, basal, and luminal B tumors progress along a high grade–poor prognosis path, while luminal A and normal‐like tumors progress along a low grade–good prognosis path, in accordance with a previously proposed model of tumor progression. We conclude that important biological information can be extracted from gene expression data in breast cancer by studying non‐random connections between chromosomal positions and gene expression. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045‐2257/suppmat. © 2006 Wiley‐Liss, Inc.
A preliminary metabolomic analysis of older adults with and without depression
Authors: Paige Lisa A. , Mitchell Matthew W. , Krishnan K. Ranga R. , Kaddurah‐Daouk Rima , Steffens David C.
Published: October 2006

Background

Metabolomics, the global science of biochemistry, is an emerging field that enables detection and quantification of small molecules involved in metabolic and signaling pathways. Metabolic signatures for disease and its treatment could provide valuable biomarkers and insights about disease mechanisms. In this pilot study, we evaluate the potential of metabolomics in the study of older depressed patients.

Methods

We performed a metabolomic analysis of blood plasma from nine depressed, 11 remitted, and ten never‐depressed older adults. Approximately 800 metabolites were analyzed, with comparisons made among the three groups.

Results

Metabolites that were altered in currently depressed patients when compared with controls included several fatty acids, glycerol and gamma‐aminobutyric acid (GABA). Analyses comparing concentrations in remitted and currently depressed patients revealed a pattern of metabolite alterations similar to the control vs currently depressed analyses. One difference observed in the remitted patients relative to the depressed patients was elevation of the concentration of the ketone 3‐hydroxybutanoic acid.

Conclusion

These observations suggest that the depressed state may be associated with alterations in the metabolism of lipids and neurotransmitters, and that treatment with antidepressants adjusts some of the aberrant pathways in disease so that the patients in remission have a metabolic profile more similar to controls than to the depressed population. These results will need to be examined and validated in larger longitudinal cohorts. Copyright © 2006 John Wiley & Sons, Ltd.
Prophylactic transdermal treatment with physostigmine and scopolamine against soman intoxication in guinea‐pigs
Authors: Meshulam Yacov , Davidovici Rachel , Wengier Ada , Levy Aharon
Published: October 2006

This study was designed to evaluate the prophylactic efficacy of transdermally administered physostigmine (PHY) against soman exposure using guinea‐pigs. Transdermal PHY pad (3 cm2 kg−1; 60 μg cm−2), containing a vehicle based on propionic acid, was applied onto the dorsal back of the animals, 24 h before exposure to the organophosphate. At the time of exposure, PHY concentrations in brain and plasma were ca. 3.6 ng g−1 and 4.1 ng ml−1, respectively. Brain and whole blood cholinesterase (ChE) activity was inhibited to 70% and 47% of the original activity, respectively. Transdermal PHY by itself protected up to 70% of the animals exposed to 1.5 LD50 of soman (100% mortality was recorded in the control group). Combining transdermal PHY with Scopoderm provided full protection against 1.5 LD50 of soman (protection of 70% against 3 LD50). When the prophylactic treatment was combined with post‐exposure therapy (atropine, 10 mg kg−1; toxogonin, 10 mg kg−1) 1 min after 5 LD50 of soman, protection of 90% of the animals was achieved.
Nasal mucus clearance in rats: Differences with sex and phase of the oestrous cycle
Authors: Saldiva P. H. N. , Parada M. A. C. , Macchione M. , Paiva P. S. O. , Guimarães E. T. , Lorenzi G. , Martins M. A. , Montes G. S. , Balbani A. P. , King M.
Published: October 2006

We studied the changes in airway mucus rheology and clearability, as well as in morphometric indices, between male rats and females in either the oestrous or dioestrous phases of the oestrous cycle. Three‐month‐old Wistar rats were studied and the phases of the oestrous cycle were determined based on analysis of vaginal smears stained by a modified Shorr's procedure. Nasal mucus samples were analysed by means of magnetic rheometry and determination of in vitro transport rate in the frog palate preparation. In situ clearance on the exposed nasal septum was also determined. The mucociliary velocity in situ was significantly affected by both sex and the oestrous cycle phase. In female rats, dioestrous phase clearance was significantly slower than the oestrous phase one. Clearance in male rats was faster than that of both the phases studied in females. Mucus rigidity of females in the oestrous phase was more rigid than that of females in the dioestrous phase and that of males. Mucus viscosity/elasticity ratio for deformations performed at high frequencies was greater for females in comparison with males. Cough clearability computed on the basis of rheological parameters was predicted to be more favourable in females. There were no significant differences between the three groups in mucociliary clearance in vitro. Morphometric studies of the nasal epithelium showed that epithelial and glandular volumes did not exhibit sex‐ or oestrous‐phase‐related differences, but the amount of epithelial acidic glycoproteins was lower in females in the oestrous phase in comparison with males and those in the dioestrous phase, the same trend being observed in the glands of the lamina propria. The finding of significant differences of mucus rheology and mucus airway histochemistry may be important in explaining differences between sexes in the susceptibility to the effects of airborne noxious stimulants, as suggested by some epidemiological data.
Semiautomated quantification of cytotoxic damage induced in cultured insect cells exposed to commercial bacillus thuringiensis biopesticides
Authors: Tayabali Azam F. , Seligy Verner L.
Published: October 2006

A convenient in vitro bioassay based on semiautomated quantification of live‐cell reduction of tetrazolium dyes ‐ 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl tetrazolium bromide (MIT) and 2,3‐bis(2‐methoxy‐4‐nitro‐5‐sulphophenyl)‐2H‐tetrazolium‐5‐corboxanilide sodium salt (XTT) – to formazan was developed and used to evaluate cytotoxic effects of two commercial insecticides (BT) derived from Bacillus thuringiensis subsp. kurstaki (Btk). Comparison of two target insect cell lines MGI (Trichoplusia ni, cabbage looper midgut) and Sf9 (Spodoptera frugiperda, fall army worm oocyte) revealed similar cell‐dependent responses in mitochondrial‐associated electron transport activity. The 50% inhibition of formazan production (ID50) obtained by exposing these cells to 20 μM 2,4‐dinitrophenol or 5 mM sodium azide occurred in the range 10−7–10−6 International Units (IU) of BT cell−1 24 h−1. Damage to cell adhesion and cytoarchitecture, revealed by light and electron microscopic analysis, increased with BT exposure and dose. MTT was superior to XTT as a cytotoxic indicator in kinetic studies related to spores, a major component of BT. Unless blocked by antibiotic (gentamicin), vegetative growth resulting from spore germination was the major cause of toxicity. The ID50 exposure time using vegetative Btk cells was ∼0.1–0.2 times that required for BT spores, with or without intact parasporal proteins present. This difference in exposure is an indirect measure of the time required for spores to germinate and produce vegetative cells. The assay methodology developed here, if linked with suitable target and non‐target animal cell types, should have broad application for conducting standardizable estimates of cytotoxic potential of any microbe‐based biotechnology product.
Effects of short‐term occupational exposure to lead on erythrocyte glucose‐6‐phosphate dehydrogenase activity and serum cholesterol
Authors: Cocco Pierluigi , Salis Stefano , Anni Maristella , Cocco Maria E. , Flore Costantino , Ibba Antonio
Published: October 2006

The effect of short‐term occupational exposure to lead on erythrocyte glucose‐6‐phosphate dehydrogenase (G6PD) activity and serum cholesterol was studied in 40 male workers of a lead and zinc foundry. All parameters were measured just before employment and after 172 ± 21.3 days of work. Genetic deficiency of erythrocyte G6PD was observed in 5/40 subjects. Among G6PD normal subjects, increases in enzyme activity followed any change (increase or decrease) in blood lead. At the pre‐employment test, serum cholesterol parameters did not show any correlation with G6PD activity or blood lead, and they were not affected by exposure. Cholesterol values observed among all the G6PD‐deficient subjects were within the range of the rest of the study population.
Neutralization of ciliary neurotrophic factor reduces astrocyte production from transplanted neural stem cells and promotes regeneration of corticospinal tract fibers in spinal cord injury
Authors: Ishii Ken , Nakamura Masaya , Dai HaiNing , Finn Tom P. , Okano Hideyuki , Toyama Yoshiaki , Bregman Barbara S.
Published: October 2006

Transplantation of neural stem cells (NSC) into lesioned spinal cord offers the potential to increase regeneration by replacing lost neurons or oligodendrocytes. The majority of transplanted NSC, however, typically differentiate into astrocytes that may exacerbate glial scar formation. Here we show that blocking of ciliary neurotrophic factor (CNTF) with anti‐CNTF antibodies after NSC transplant into spinal cord injury (SCI) resulted in a reduction of glial scar formation by 8 weeks. Treated animals had a wider distribution of transplanted NSC compared with the control animals. The NSC around the lesion coexpressed either nestin or markers for neurons, oligodendrocytes, or astrocytes. Approximately 20% fewer glial fibrillary acidic protein‐positive/bromodeoxyuridine (BrdU)‐positive cells were seen at 2, 4, and 8 weeks postgrafting, compared with the control animals. Furthermore, more CNPase+/BrdU+ cells were detected in the treated group at 4 and 8 weeks. These CNPase+ or Rip+ mature oligodendrocytes were seen in close proximity to host corticospinal tract (CST) and 5HT+ serotonergic axon. We also demonstrate that the number of regenerated CST fibers both at the lesion and at caudal sites in treated animals was significantly greater than that in the control animals at 8 weeks. We suggest that the blocking of CNTF at the beginning of SCI provides a more favorable environment for the differentiation of transplanted NSC and the regeneration of host axons. © 2006 Wiley‐Liss, Inc.
Strategic implementation: a comparison of three methodologies
Authors: Ritson Neil , O'Neill Maureen
Published: October 2006

This paper presents the outcomes of a live consultancy project. Since the introduction of performance measures, much of the public sector has found itself having to change. It must find a way to introduce effective change to achieve the targets it is set.

The quasi‐experimental empirical study was structured around three models of change: Strategic Information Systems, Theory of Constraints, and Organizational Development. Each model was used to achieve three separate changes in a district hospital in the North West of England.

The conclusions from the research suggest that the theory of constraints (TOC) has all the components necessary to achieve effective change. It copes well with the public sector culture, especially in negotiating and overcoming resistance to change.

Copyright © 2006 John Wiley & Sons, Ltd.
Controlled pilot study of the effects of neuromuscular therapy in patients with Parkinson's disease
Authors: Craig Lauren H. , Svircev Anna , Haber Michael , Juncos Jorge L.
Published: October 2006

The objectives of this study is to examine the effects of neuromuscular therapy (NMT) on motor and nonmotor symptoms in Parkinson's disease (PD). Thirty‐six subjects with PD were randomly assigned to NMT or music relaxation (MR, or active control). Subjects received treatment twice a week for 4 weeks. Testing was conducted at baseline, after final treatment, and 8 days after final treatment. Primary outcome measures were the Motor subscale of the United Parkinson Disease Rating Scale (UPDRS) and the Clinical Global Impression scale (CGI‐Change). Secondary outcome measures included a PD‐specific quality of life scale (PDQ‐39), quantitative measures of motor function, and severity scales for anxiety and depression symptoms. NMT resulted in a significant and sustained improvement in the Motor subscale of the UPDRS (P ≤ 0.0001), most notable in the tremor scores. Also improved 1 week after the last treatment were the CGI scores (P = 0.007) and the finger‐tapping speed (P = 0.001). The MR active control group had a slight improvement in tremor but evidenced no other change in motor function. Both groups exhibited a modest improvement in quality of life immediately after the last treatment. This effect was sustained for 8 days only in the MR group. In the nonmotor domains, the MR group evidenced improvements in mood (P = 0.001) and anxiety (P = 0.002), whereas NMT had no effect on mood (P = 0.09), and its initial effect on anxiety (P = 0.0009) dissipated after 8 days (P = 0.40). Group differences for UPDRS motor score and patient CGI‐Change were superior in the NMT compared to the MR group. There was no group difference in PDQ‐39 scores or in nonmotor measures. The findings suggest that NMT can improve motor and selected nonmotor symptoms in PD and that this effect is more durable for the motor symptoms. The results of this pilot study warrant larger controlled studies to examine dose range, durability, and mechanisms of NMT in PD function. © 2006 Movement Disorder Society
A computational model for fracturing porous media
Authors: Al‐Khoury R. , Sluys L. J.
Published: October 2006

This paper presents a new computational model for simulating a fracturing process in a porous medium using the finite element method. Two independent numerical techniques are used for describing this process. The partition of unity method is used for describing the fracturing process, and the double porosity model is used for describing the resulting fluid flow. A key feature of the model is the coupling of these two independent numerical techniques, which provide the means for a better simulation of the involved physical and mechanical processes. The paper focuses on the numerical formulation of the model. The capability of the model is illustrated by means of numerical examples, which examine the behaviour of a 1D porous medium under different boundary conditions. The numerical results show that the very complicated physical and mechanical processes of the fracturing porous media can be simulated properly and efficiently. Copyright © 2006 John Wiley & Sons, Ltd.
Optimal control of a water reservoir with expected value–variance criteria
Authors: Karbowski Andrzej , Magiera Przemysław
Published: October 2006

The article presents how to solve a reservoir management problem, which has been formulated as a two‐criteria stochastic optimal control problem. Apart from the expected value of a performance index, its variance is also considered. Three approaches are described: a method based on the Lagrange function; a method based on the ordinary moment of the second order (finite time horizon); and a method based on linear programming (infinite time horizon). In the second part of the article, they are assessed in a case study concerning a reservoir in the southern part of Poland. Copyright © 2006 John Wiley & Sons, Ltd.
Sex steroids modulate α1‐adrenoceptor‐stimulated Ca2+ elevation in human cultured prostatic stromal cells
Authors: Nguyen S.T. , Prakash R. , Anderson C.J. , Frydenberg M. , Haynes J.M.
Published: October 2006

BACKGROUND

Benign prostatic hyperplasia is an age‐ and androgen‐dependent condition of urethral compression caused by prostatic contractility and glandular enlargement. In this study we investigate whether testosterone, dihydrotestosterone and estradiol modulate the ability of human cultured prostatic stromal cells (HCPSCs) to respond to the adrenoceptor agonists, noradrenaline (30 µM) and phenylephrine (100 µM), the protein kinase C activating phorbol ester, phorbol diacetate (PDA, 10 µM), and the L‐type Ca2+ channel activator, (−)‐Bay K8644 (Bay K, 10 µM) with elevations of intracellular Ca2+ ([Ca2+]i).

METHODS

Cells were loaded with the Ca2+ sensitive fluorophore, FURA‐2AM (10 µM) and changes in intracellular Ca2+ determined before and 8–12 min after ligand addition.

RESULTS

Compared to steroid‐free (SF) controls, the incubation of HCPSC with testosterone (30 and 300 pM) significantly increased responses to both noradrenaline and phenylephrine. Responses to Bay K were significantly reduced between 30 nM to 300 pM but responses to PDA were not greatly affected. Compared to SF the addition of estradiol (E2, 100 pM) did not affect responses to phenylephrine. The concomitant addition of dihydrotestosterone (DHT) and E2 (to give ratios from 1:1 to 1,000:1) elevated the responses to noradrenaline and phenylephrine at the extreme ranges. Responses to PDA and Bay K generally increased as DHT:E2 approached unity.

CONCLUSIONS

These results indicate that sex steroids modulate the activities of HCPSCs through the regulation of both receptors and signal transduction processes. Prostate 67:74–82, 2007. © 2006 Wiley‐Liss, Inc.
Computational diagnosis of protein conformational diseases: Short molecular dynamics simulations reveal a fast unfolding of r‐LDL mutants that cause familial hypercholesterolemia
Authors: Cuesta‐López S. , Falo F. , Sancho J.
Published: October 2006

The molecular basis of conformational diseases frequently resides in mutant proteins constituting a subset of the vast mutational space. While the subtleties of protein structure point to molecular dynamics (MD) techniques as promising tools for an efficient exploration of such a space, the average size of proteins and the time scale of unfolding events make this goal difficult with present computational capabilities. We show here, nevertheless, that an efficient approach is already feasible for modular proteins. Familial hypercholesterolemia (FH) is a conformational disease linked to mutations in the gene encoding the low density lipoprotein receptor. A high percentage of these mutations has been found in the seven small modular binding repeats of the receptor. Taking advantage of its small size, we have performed an in depth MD study of the fifth binding repeat. Fast unfolding dynamics have been observed in the absence of a structural bound calcium ion, which agrees with its reported essential role in the stability of the module. In addition, several mutations detected in FH patients have been analyzed, starting from the native conformation. Our results indicate that in contrast with the wild type protein and an innocuous control mutant, disease‐related mutants experience, in short simulation times (2–8 ns), gross departures from the native state that lead to unfolded conformations and, in some cases, to binding site desorganization deriving in calcium release. Computational diagnosis of mutations leading to conformational diseases seems thus feasible, at least for small or modular pathogenic proteins. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Theoretical structure of the low‐laying electronic states of the molecule YBr
Authors: Abdul‐Al S. , Korek M. , Allouche A. R. , Aubert Frécon M.
Published: October 2006

An ab initio CASSCF and MRCI (single and double excitation plus Davidson correction) calculation have been performed for the molecule YBr. The potential energy curves of 20 electronic states in the representation 2s+1Λ(+/−) (neglecting the spin‐orbit effects) and 41 states in the representation Ω(+/−) [including the spin‐orbit (SO) effects] have been calculated along with the corresponding spectroscopic constants. The SO effects are taken into account via a semi‐empirical SO pseudo‐potential for the yttrium atom, while they have been neglected for bromine. Very good agreement is displayed by comparing the present results with those obtained experimentally, up to now, of the three states X1Σ+, (1)2Π, and (2)1Σ+. New results have been obtained for 17 states 2s+1Λ(+/−), and their SO components yet not observed or calculated. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Spectroscopic constants and molecular properties of rare‐gas diatomic molecule in Lennard‐Jones potential: Ab initio and density functional study
Authors: Bera N. C. , Bhattacharyya I. , Das A. K.
Published: October 2006

Ab initio and density functional theory (DFT) are applied to study the spectroscopic constants, molecular properties, and nature of force between two rare gas atoms of the weakly bound diatomic molecules He2, Ne2, Ar2, HeNe, and HeAr in the Lennard‐Jones potential. A simple method is developed to calculate the spectroscopic constants of these molecules. The calculated spectroscopic constants and molecular properties agree very well with the experimental and theoretical results wherever available. Most of the spectroscopic constants and molecular properties are reported for the first time. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
A rapid water toxicity screening test based on oxygen uptake of pseudomonas putida
Authors: Slabbert J. L. , Grabow W. O. K.
Published: October 2006

Oxygen uptake of Pseudomonas putida was employed for the rapid screening of toxicants in water. Oxygen uptake was measured over a 10 minute period at constant temperature by means of a biological oxygen monitoring system connected to a potentiometric recorder. Sublethal concentrations of selected chemicals inhibited or stimulated oxygen uptake. A P. putida growth inhibition test proved more sensitive to most individual chemicals than the oxygen uptake assay, but yields results only after some 7 hours. Industrial effluent in low concentrations and domestic wastewater, stimulated both oxygen uptake and growth of P. putida. Higher concentrations of industrial effluent and a laboratory mixture of selected toxicants inhibited both growth and oxygen uptake at equal levels of sensitivity. Sensitivity compared favourably with that of other rapid bioassays, and various toxicants were detected at concentrations well below those allowed in industrial effluents. Since the P. putida oxygen uptake assay is relatively sensitive, simple, economical and exceptionally fast, it should prove useful for the rapid testing of many wastewaters and even excessive contamination of drinking‐water supplies while it may serve a valuable purpose as part of a battery of bioassays containing slower tests.
Poterioochromonas malhamensis—a unicellular alga as test system in ecotoxicology, toxicology, and pharmacology
Authors: Röderer Gerhard
Published: October 2006

The unicellular freshwater alga Poterioochromonas malhamensis is presented as a screening test system for studying general and specific toxic effects of xenobiotics. The algae are grown in suspension culture in organic substrate and have various characteristics (e.g. fast growth, vegetative reproduction, mobility, etc.) which allow the detection of effects on viability and cell reproduction by light microscopical observation and counting. In addition, the cells exhibit three microtubule‐dependent processes: lorica formation, mitosis and cytokinesis. Using two light microscopical tests adapted to this system (lorica formation test and nuclear phase accumulation test) information about possible interactions of a given test compound with mitotic and/or cytoplasmic microtubules of the algae can be obtained within a comparatively short time (3 hr. and 24 hr. incubation, respectively).
A multispecies toxicity assessment procedure using flow microcalorimetry: Comparison with other toxicity evaluation methods
Authors: Beaubien A. , Lapierre L. , Bouchard A. , Jolicoeur C.
Published: October 2006

The acute toxicity of various contaminants and effluents towards a heterogenous aerobic culture has been determined using flow microcalorimetry. The toxicity of these contaminants and effluents was also evaluated towards a marine bacteria (type Photobacterium phosphoreum, Microtox test), a green algae (Selenastrum capricornutum, inhibition of growth) and a small crustacean (Daphnia magna, inhibition of mobility). The 50% (IC50) or 20% (IC20) inhibitory concentrations were obtained for each toxicity test, and compared to each other. The results of the present study suggest that, under proper conditions, a mixed aerobic culture could yield toxicity estimates comparable to those obtained from a combination of single species tests.
Herbicide toxicity and microbial responses in soil
Authors: Mahendru P. , Dubey P. S.
Published: October 2006

The question mark placed on a few herbicides because of their longer persistence in Black Cotton soil made this ecotoxicological assessment necessary. Since microbial responses can be used as an indicator of herbicide toxicity, soil respiration, dehydrogenase, and viable bacterial counts were used as the parameters to assess herbicide toxicity. Basalin, Lasso, and Tafazine are used in Black Cotton Soil of Southwest part of India. Soils treated with 1,5, and 25 ppm (w/w) and assessed 1, ε, 11, 16, and 21 days later, indicated a significant inhibitory effect on microbial activity measured in terms of these parameters. The improvement in soil quality started after 16–21 days in Basalin treated soil only. Further, there exists a correlation between soil respiration and number of bacterial colonies, and soil respiration and dehydrogenase activity. The study warrants a rigorous screening of all the recommended preemergence herbicides in Black Cotton soil of this fertile area.
A new, short term, sensitive, bacterial assay kit for the detection of toxicants
Authors: Reinhartz A. , Lampert I. , Herzberg M. , Fish F.
Published: October 2006

We present and evaluate a new bacterial test suitable for the detection of toxicants in water, chemicals, pharmaceuticals, foodstuff, food additives and cosmetics. It is a simple, rapid (1–1.5 hours), colorimetric assay which does not require special equipment, and can easily be carried out under field conditions.

The assay is based on the ability of toxicants to inhibit thede novosynthesis of an inducible enzyme, e.g., β‐galactosidase, by a rough mutant ofE. coli, which is highly sensitive to a wide spectrum of toxic substances, such as pesticides, mycotoxins and heavy metals. The test is performed under stress conditions for the bacterium, since under such conditions better sensitivity for low concentrations of analytes is obtained. In the assay, serial dilutions of the sample are mixed with the stressed bacteria and a cocktail containing the specific inducer for the chromogenic enzyme and essential factors, required for the recovery of the bacteria from their‐stressed condition. The ability of cells to synthesize β‐galactosidase under these conditions depends on their ability to recover from the stress. Toxic materials interfere and/or inhibit the recovery process and with it the synthesis of β‐galactosidase. The amount of thede novosynthesized enzyme is determined by a colorimetric reaction.

We have developed a commercial kit based on the assay. The kit is field oriented and easy to operate. The kit contains the bacteria in a lyophilized form and all the reagents have been stabilized so that the kit may be stored under normal refrigeration for a long period of time.
Technical methods section ATP‐TOX system—a bacterial toxicity screening procedure
Authors: Xu Hao , Dutka B. J.
Published: October 2006

When rapidly growing bacterial cells are exposed to low concentrations of toxicants, growth inhibition usually occurs. However, some toxicants not only inhibit bacterial growth but also affect the luciferase activity during ATP determinations. Thus, the observed light output reduction of a test bacterial system is the net result of both bacterial growth and luciferase inhibition. Based on this information, a new toxicity screening test was developed, the ATP‐TOX System.
Prediction of permissible concentrations of copper from microcosm toxicity tests
Authors: Pratt James R. , Niederlehner B. R. , Bowers Nancy , Jr. John Cairns
Published: October 2006

Microcosm toxicity tests using naturally derived protozoan communities were used to estimate permissible concentrations of copper. In tests with copper sulfate, taxonomic richness of communities was adversely affected at concentrations ≧12.7 μg/L after 21 days. Colonization was also affected at ≧12.7 μg Cu/L. Concentrations affecting taxonomic composition, chlorophyll and biomass concentrations, and nutrient retention ranged from ≦6.6 to ≧59.5 μg Cu/L. A Cu concentration expected to affect only 5% of taxa (EC05) adversely was predicted from test data as 3.2 (1.6–4.8) μg Cu/L. A similar estimate of a 5% effect level based on single‐species chronic toxicity test data was 4.9 (2.2ndash;7.1) μg Cu/L. Results of a test with combined effluents containing Cu were similar, with differences in colonization apparent at ≧18.0 μg Cu/L. Reductions in individual populations were apparent at 8.7 μg Cu/L. Estimates of permissible concentrations derived from these tests were reasonable when compared to the revised numerical water quality criteria (8.2 μg Cu/L at a hardness of 65 ppm). In addition, they fell above selected literature reports of Cu levels in clean systems (<2 μg/L) and below levels associated with damage in natural systems (>23 μg/L), thus seeming to be a reasonable basis for management decisions.
The effect of ionic solutes on EC50 values measured using the microtox test
Authors: Hinwood A. L. , McCormick M. J.
Published: October 2006

The Microtox test uses the marine luminescent bacterium, Photobacterium phosphoreum. To provide the organism with osmotic protection, sodium chloride (2.0%) is usually added to freshwater samples before analysis. This procedure is shown to cause a dramatic lowering of measured toxicity where ionic compounds are the major toxicants present. The reason for this is the consequent variation in ionic strength upon addition of NaCl rather than formation of less‐toxic chloro complexes. Data are given for the toxicants Zn, Cd, Cu, NH4+, and phenol.

It was found that measurements on aqueous samples could be made without adjustment provided that the salinity was in the range of 1.0–7.0%. Freshwaters can also be analyzed without adjustment of ionic strength by adding sucrose (20.4%) to provide the necessary osmotic protection.

It is therefore recommended that the ionic strength of aqueous samples should not be altered as part of the test and that receiving waters should be used as the diluent wherever possible.
Ecotoxicological risk assessment of chemicals by measurements of nitrification combined with a computer simulation model of the N‐cycle
Authors: Mathes K. , Schulz‐Berendt V. M.
Published: October 2006

The N‐cycle of an Aldicarb‐contaminated [2.5 g · m−2 (a.i.)] soil cover of a newly graded rubble dump was investigated in order to judge the alterations of microbial nitrogen transformations at the ecosystem level. The pesticide reduced the kinetic parameters of nitrification (maximum activity and division rate) markedly, indicating severe damage to the nitrifying population of the soil during the first 16 weeks after its application. The degree of nitrification varied depending on the incubation conditions. Incubations in the field and under laboratory conditions without substrate addition showed negligible effects, whereas incubation with the addition of (NH4)2SO4 led to an intolerable reduction in nitrification.

The consequences of these experimental results on the NO3 ‐N and NH4+‐N content of the soil solution were analyzed by simulating the N‐cycle using different sets of parameters (climatic factors, initial conditions). The results indicate that combining field and laboratory studies of microbial populations with a computer simulation model of the N‐cycle improves ecotoxicological risk assessment.
Cellular effects of cyanobacterial peptide toxins
Authors: Eriksson J. E. , Meriluoto J. A. O. , Kujari H. P. , Al‐Layl K. Jamel , Codd G. A.
Published: October 2006

Peptide toxins from the cyanobacteria Microcystic aeruginosa, Oscillatoria agardhii, Nodularia spumigena, and Anabaena flos‐aquae were isolated. Of these, only the cyclic peptide of Microcystis has been characterized structurally and toxicologically in detail. Preliminary studies of the other peptide toxins have indicated that they may be structurally related to the toxins of Microcystis. The morphological and ultrastructural effects of these toxins were studied using freshly isolated hepatocytes. The toxins caused identical morphological alterations in the hepatocytes. Numerous surface swellings appeared on the cell surface and finally the normal cell morphology was totally disrupted. During this process, however, the viability of the cells was not affected. These results are viewed in the light of recent results showing that these toxins could exhibit a specific interaction with the actin part of the cytoskeleton. The overall results indicate that all four toxins may be toxicologically closely related.
Microbiology of recreational and therapeutic whirlpools
Authors: Highsmith Anita K. , McNamara Ann Marie
Published: October 2006

Over half of the reported outbreaks of whirlpool‐associated dermatitis and folliculitis have been caused by Pseudomonas aeruginosa, serotype 011. Illness caused by Staphylococcus aureus, Legionella pneumophila, Mycobacterium, Streptococci, and Acanthamoeba have been infrequently reported. The presence of microorganisms in water is not the only factor involved in infection transmission. Other factors in disease may be individual host susceptibility, immersion time, bather load, gender, and use of clothing. A bather's risk for P. aeruginosa dermatitis or folliculitis appears to depend on immersion in water colonized by P. aeruginosa, skin hydration with altered skin flora, and toxic reactions to extracellular enzymes or exotoxins produced by P. aeruginosa. Outbreaks of illness appear to be directly related to inadequate operational and maintenance procedures. Chemical and physical parameters should be routinely monitored. Microbiologic sampling of whirlpool water is not advised except in outbreak investigations.
Removal of High Phenol Concentrations with Adapted Activated Sludge in Suspended Form and Entrapped in Calcium Alginate/Cross‐Linked Poly(N‐vinyl pyrrolidone) Hydrogels
Authors: Hernández‐Esparza Margarita , Doria‐Serrano M. Carmen , Acero‐Salinas Gabriela , Ruiz‐Treviño F. Alberto
Published: October 2006

The present work evaluates the aerobic removal of 0.25–2 g/L of phenol by adapted activated sludge in batch and continuous reactors, in suspended form and trapped in polymeric hydrogel beads of calcium alginate(1%) and cross‐linked poly(N‐vinyl pyrrolidone), x‐PVP (4%). The mechanical and chemical resistance of the entrapping hydrogel was also evaluated in three different media: (I) rich in phosphate and ammonium ions; (II) using alternate P and N sources, and (III) without nutrients. The adapted consortium removed phenol concentrations up to 2 g/L more efficiently in the immobilized systems. A decrease in phenol removal rate was observed as the food/microorganisms (F/M) ratio increased. A zero‐order kinetics was observed with phenol concentrations > 1 g/L and a first‐order kinetics at concentrations < 1 g/L. The best response (100% removal) was in the continuous reactors using type II medium, with a hydraulic residence time (HRT) of 12.5 h, an influent pH = 5, and an F/M ratio below 0.25. The immobilizing matrix deteriorated after 170 h of use in continuous reactors, especially with media I and II, probably due to the attrition forces, to chemical weakness of the material, and to the pressure of the bacterial growth inside the bead.
Composition control in metal-organic vapor-phase epitaxy grown InGaAs nanowhiskers
Authors: Regolin I. , Khorenko V. , Prost W. , Tegude F.-J. , Sudfeld D. , Kästner J. , Dumpich G.
Published: October 2006

InGaAs nanowhiskers were grown by metal-organic vapor-phase epitaxy on (111)B GaAs substrates using the vapor-liquid-solid growth mode. The diameter of nanowhiskers was defined by monodisperse gold nanoparticles deposited on the GaAs substrate from the liquid phase. By adjusting the triethylgallium to trimethylindium flow ratio, InxGa1−xAs whiskers with various compositions were realized. The composition characterization of the grown whiskers was done by high-resolution x-ray diffractometry. A detailed analysis of measured spectra allowed resolving the presence of an InGaAs three-dimensional layer between whiskers. High-resolution transmission electron microscopy investigation revealed the lattice constant of the grown whisker structures, which agrees with the whisker composition defined by x-ray diffractometry. Finally, low-temperature photoluminescence measurements of the realized InGaAs whiskers were carried out.
Investigations of electron injection in a methanofullerene thin film transistor
Authors: von Hauff Elizabeth , Parisi Jürgen , Dyakonov Vladimir
Published: October 2006

In this study we investigate charge injection into a methanofullerene. The temperature and electric field dependent source-drain currents from contact limited [6,6]-phenyl C61-butyric acid methyl ester (PCBM) thin film transistors (TFTs) were analyzed. A form for the temperature and field dependent behavior of the parasitic contact resistances between metal and semiconductor was proposed based on a diffusion limited thermionic emission (DLTE) injection current and accounting for the disorder in the system. The temperature dependent current-voltage characteristics were initially modeled with a model for field effect behavior in amorphous organic semiconductors from the literature to determine material parameters. The initial fit resulted in discrepancies between the experimental data and the data predicted by the model. Modifying the model to account for the effects of contact resistances led to much better agreement between the experimental and predicted data. Based on these results, the DLTE injection current describes the injection process in PCBM TFTs well.
Interfacial structures of methanol:water mixtures at a hydrophobic interface probed by sum-frequency vibrational spectroscopy
Authors: Liu Wei-Tao , Zhang Luning , Shen Y. R.
Published: October 2006

Sum-frequency vibrational spectroscopy was used to study interfacial structure of methanol:water mixtures at an octyltrichlorosilane-covered hydrophobic surface. Methanol was found to adsorb preferentially than water at the interface with its methyl group tilted from the surface normal by ∼35° for all methanol concentrations. Redshift of the methanol symmetric stretch mode, gradual disappearance of the water dangling-OH mode, and blueshifts of the dangling and liquidlike bonded-OH modes were also observed as the methanol concentration increased. They could be understood from the change of the interfacial hydrogen-bonding network associated with the change of surface composition.
Investigation of the origin of the decrease in exchange biasing in Ga+ ion irradiated CoFe∕IrMn films
Authors: Wang Y. G. , McGrouther D. , McVitie S. , MacKenzie M. , Chapman J. N.
Published: October 2006

Irradiation of CoFe∕IrMn exchange biased bilayers by 30keV Ga+ ions leads to a reduction in the exchange biasing. Here we have used various imaging and analytical techniques including high resolution transmission electron microscopy and spectrum imaging based on electron energy-loss spectroscopy to determine how the physical structure of the multilayer changes as a function of irradiation dose. Element mixing across the interfaces is found to be the most important effect although significant grain growth is also observed. Computer simulation, incorporating the effects of collision cascades, can largely account for the experimental observations. The ways in which these changes lead to modification of the magnetic properties are discussed.
Hydrogen bonding and induced dipole moments in water: Predictions from the Gaussian charge polarizable model and Car-Parrinello molecular dynamics
Authors: Dyer Peter J. , Cummings Peter T.
Published: October 2006

We compare a new classical water model, which features Gaussian charges and polarizability (GCPM) with ab initio Car-Parrinello molecular dynamics (CPMD) simulations. We compare the total dipole moment, the total dipole moment distribution, and degree of hydrogen bonding at ambient to supercritical conditions. We also compared the total dipole moment calculated from both the electron density (partitioning the electron density among molecules based on a zero electron flux condition), and from the center of localized Wannier function centers (WFCs). Compared to CPMD, we found that GCPM overpredicts the dipole moment derived by partitioning the electron density and underpredicts that obtained from the WFCs, but exhibits similar trends and distribution of values. We also found that GCPM predicted similar degrees of hydrogen bonding compared to CPMD and has a similar structure.
Correlation between macroscopic properties and microscopic parameters versus stress in tetragonal Pb(Mg1∕3Nb2∕3)0.6Ti0.4O3 ferroelectric ceramics
Authors: Pruvost Sébastien , Lebrun Laurent , Sebald Gael , Seveyrat Laurence , Guyomar Daniel , Zhang Shujun , Shrout Thomas R.
Published: October 2006

The influence of domain switching on the evolution of macroscopic polarization in the ferroelectric Pb(Mg1∕3Nb2∕3)1−xTixO3 material was studied. Domain switching during the application of a compressive stress was evaluated using in situ x-ray diffraction. It was found that stress depolarization was controlled by 90° domain reorientation. Details on domain switching quantification were given for samples with their surface parallel to the polar axis. From x-ray data, the macroscopic polarization versus stress was also simulated, underlying a strong correlation between microscopic parameters and macroscopic properties. This simulation was based on the assumption that the dipolar moment of the unit cell does not change with stress. The x-ray diffraction was established as a viable nondestructive technique for the determination of remnant polarization.
Simulation of a tunable optically pumped terahertz intersubband laser with diluted magnetic semiconductors
Authors: Popadić Miloš , Milanović Vitomir , Ikonić Zoran , Indjin Dragan
Published: October 2006

A simulation of an optically pumped laser based on a ZnSe∕Zn1−yCdySe double quantum well with a Zn1−xMnxSe diluted magnetic semiconductor barrier is presented. Giant Zeeman splitting in diluted magnetic semiconductors leads to splitting of electronic states, which in turn leads to tunability of laser wavelength by external magnetic field. Tunability is predicted throughout the wavelength range between 60 and 72μm at low temperatures.
Bias-stimulated nucleation of silver prepared by pulsed arc deposition on silicon oxide
Authors: Romanyuk Andriy , Steiner Roland , Thommen Verena , Oelhafen Peter , Mathys Daniel
Published: October 2006

The nucleation and interface formation between Ag films and native silicon oxide have been studied with x-ray and ultraviolet photoelectron spectroscopies. Silver was deposited stepwise onto silicon native oxide by pulsed arc deposition technique onto grounded and biased substrates resulting in kinetic energy of incident silver ions of 95 and 720eV, respectively. We show that an increase in the kinetic energy of silver ions leads to more homogeneous nucleation and earlier coalescence of Ag films due to surface defect generation and preferential sputtering of oxygen. In addition, deposition from high energy beam results in the formation of an extended transition layer containing a mixture of Ag and Si oxide that might be beneficial in improving adhesion of Ag films.