bluuebunny/crossref_metadata_2025 huggingface dataset:
The capacity for multistability in small gene regulatory networks
Authors: Siegal-Gaskins Dan , Grotewold Erich , Smith Gregory D
Published: September 2009

Background

Recent years have seen a dramatic increase in the use of mathematical modeling to gain insight into gene regulatory network behavior across many different organisms. In particular, there has been considerable interest in using mathematical tools to understand how multistable regulatory networks may contribute to developmental processes such as cell fate determination. Indeed, such a network may subserve the formation of unicellular leaf hairs (trichomes) in the model plant Arabidopsis thaliana.

Results

In order to investigate the capacity of small gene regulatory networks to generate multiple equilibria, we present a chemical reaction network (CRN)-based modeling formalism and describe a number of methods for CRN analysis in a parameter-free context. These methods are compared and applied to a full set of one-component subnetworks, as well as a large random sample from 40,680 similarly constructed two-component subnetworks. We find that positive feedback and cooperativity mediated by transcription factor (TF) dimerization is a requirement for one-component subnetwork bistability. For subnetworks with two components, the presence of these processes increases the probability that a randomly sampled subnetwork will exhibit multiple equilibria, although we find several examples of bistable two-component subnetworks that do not involve cooperative TF-promoter binding. In the specific case of epidermal differentiation in Arabidopsis, dimerization of the GL3-GL1 complex and cooperative sequential binding of GL3-GL1 to the CPC promoter are each independently sufficient for bistability.

Conclusion

Computational methods utilizing CRN-specific theorems to rule out bistability in small gene regulatory networks are far superior to techniques generally applicable to deterministic ODE systems. Using these methods to conduct an unbiased survey of parameter-free deterministic models of small networks, and the Arabidopsis epidermal cell differentiation subnetwork in particular, we illustrate how future experimental research may be guided by network structure analysis.
Tyrosine Kinase Inhibitor Enhances the Bioavailability of Oral Irinotecan in Pediatric Patients With Refractory Solid Tumors
Authors: Furman Wayne L. , Navid Fariba , Daw Najat C. , McCarville M. Beth , McGregor Lisa M. , Spunt Sheri L. , Rodriguez-Galindo Carlos , Panetta John C. , Crews Kristine R. , Wu Jianrong , Gajjar Amar J. , Houghton Peter J. , Santana Victor M. , Stewart Clinton F.
Published: September 2009

Purpose

To assess the maximum-tolerated dosages (MTDs), and dose-limiting toxicities (DLTs) of the epidermal growth factor receptor inhibitor gefitinib and of intravenous (IV) irinotecan when administered together in children with refractory solid tumors. To assess the effect of gefitinib on the pharmacokinetics of IV irinotecan and on the bioavailability of a single oral dose of irinotecan.

Patients and Methods

IV irinotecan (15 or 20 mg/m2) was given daily for 5 days of 2 consecutive weeks. Oral gefitinib (150 or 112.5 mg/m2) was concomitantly given daily for 12 or 21 days. A single oral dose of irinotecan was given on day 9 of course 2 to allow pharmacokinetic analysis.

Results

The study enrolled 29 patients with recurrent solid tumors. The 21-day regimen of oral gefitinib with irinotecan was not tolerated. Diarrhea was the most common DLT. The MTD of the combination regimen was 15 mg/m2/d of IV irinotecan for 5 days of 2 consecutive weeks and 112.5 mg/m2/d of gefitinib given for 12 days. Gefitinib increased the bioavailability of oral irinotecan by four-fold over that observed in historical controls (median, 0.09 v 0.42; P < .000001), reducing the apparent clearance (an inverse measure of exposure) of irinotecan and SN-38 by 37% and 38%, respectively (P < .0001). A partial response was observed in a patient with refractory Ewing sarcoma.

Conclusion

IV irinotecan given with 12 days of oral gefitinib is well tolerated in children. We observed one partial response. Gefitinib significantly enhances the bioavailability of oral irinotecan. This combination warrants further investigation, particularly with orally administered irinotecan.
Effect of Exercise on Postmenopausal Sex Hormone Levels and Role of Body Fat: A Randomized Controlled Trial
Authors: Monninkhof Evelyn M. , Velthuis Miranda J. , Peeters Petra H.M. , Twisk Jos W.R. , Schuit Albertine J.
Published: September 2009

Purpose

To examine the effects of a 1-year exercise intervention on sex hormone levels in postmenopausal women and whether any effects are mediated by changes in body fat composition.

Methods

We randomly assigned 189 sedentary postmenopausal women (age 50 to 69 years, body mass index of 22 to 40 kg/m2) to an exercise intervention (n = 96) or a control group (n = 93). The intervention combined aerobic and strength training and comprised supervised group sessions and home-based exercises (a total of 2.5 h/wk). Between-group differences in sex hormone levels (at baseline and 4 and 12 months) were examined with generalized estimating equations.

Results

In total, 183 women (97%) completed the study. Overall, the exercise intervention did not result in favorable effects on sex hormone levels. Among women who lost more than 2% body fat, declines in all estrogens were not significantly different between exercisers and controls. Androgen levels decreased significantly in the exercise group who lost body fat compared with their peers in the control group. Furthermore, this study confirmed that fat loss was significantly associated with declines in postmenopausal estrogen levels. Although not significant, a similar trend was observed for the androgens.

Conclusion

This study confirms that fat loss is associated with changes in postmenopausal sex hormone levels and suggests that exercise may be effective in inducing favorable changes in these hormones.
Identification and Validation of a Gene Expression Signature That Predicts Outcome in Adult Men With Germ Cell Tumors
Authors: Korkola James E. , Houldsworth Jane , Feldman Darren R. , Olshen Adam B. , Qin Li-Xuan , Patil Sujata , Reuter Victor E. , Bosl George J. , Chaganti R.S.K.
Published: September 2009

Purpose

Germ cell tumor (GCT) is the most common malignancy in young adult men. Currently, patients are risk-stratified on the basis of clinical presentation and serum tumor markers. The introduction of molecular markers could improve outcome prediction.

Patients and Methods

Expression profiling was performed on 74 nonseminomatous GCTs (NSGCTs) from cisplatin-treated patients (ie, training set) and on 34 similarly treated patients with NSGCTs (ie, validation set). A gene classifier was developed by using prediction analysis for microarrays (PAM) for the binary end point of 5-year overall survival (OS). A predictive score was developed for OS by using the univariate Cox model.

Results

In the training set, PAM identified 140 genes that predicted 5-year OS (cross-validated classification rate, 60%). The PAM model correctly classified 90% of patients in the validation set. Patients predicted to have good outcome had significantly longer survival than those with poor predicted outcome (P < .001). For the OS end point, a 10-gene model had a predictive accuracy (ie, concordance index) of 0.66 in the training set and a concordance index of 0.83 in the validation set. Dichotomization of the samples on the basis of the median score resulted in significant differences in survival (P = .002). For both end points, the gene-based predictor was an independent prognostic factor in a multivariate model that included clinical risk stratification (P < .01 for both).

Conclusion

We have identified gene expression signatures that accurately predict outcome in patients with GCTs. These predictive genes should be useful for the prediction of patient outcome and could provide novel targets for therapeutic intervention.
Multicenter Phase II Trial of YM155, a Small-Molecule Suppressor of Survivin, in Patients With Advanced, Refractory, Non–Small-Cell Lung Cancer
Authors: Giaccone Giuseppe , Zatloukal Petr , Roubec Jaromir , Floor Karijn , Musil Jaromir , Kuta Milan , van Klaveren Rob J. , Chaudhary Subhash , Gunther Adrie , Shamsili Setareh
Published: September 2009

Purpose

To evaluate the antitumor activity and safety of YM155, a novel, small-molecule suppressor of survivin, as single-agent therapy in patients with previously treated, advanced non–small-cell lung cancer (NSCLC).

Patients and Methods

Patients with stage IIIb/IV NSCLC who had experienced treatment failure during one or two prior chemotherapy regimens (at least one of which was platinum based) received YM155 as a continuous intravenous infusion (4.8 mg/m2/d) over 168 hours followed by observation for 14 days in 21-day treatment cycles. The primary end point was objective tumor response rate (ORR). Secondary end points included duration of stable disease (SD), progression-free survival (PFS), overall survival (OS), safety and pharmacokinetic profiles, and pharmacodynamic evaluations.

Results

Thirty-seven patients received YM155. Two patients achieved a confirmed partial response, with an ORR of 5.4% (95% CI, 0.7% to 18.2%). An additional 14 patients (37.8%) achieved SD resulting in a disease control rate of 43.2% (95% CI, 27.1% to 60.5%). Median duration of PFS was 1.7 months (95% CI, 1.3 to 2.8 months). Median duration of OS was 6.6 months (95% CI, 4 to 12.2 months), with a 1-year survival rate of 35.1%. Treatment with YM155 was well tolerated with the majority of treatment discontinuations not treatment related.

Conclusion

YM155 exhibited modest single-agent activity in patients with refractory, advanced NSCLC. A favorable safety/tolerability profile was reported. Further evaluation of YM155 in combination with chemotherapy and other targeted agents may be warranted.
Randomized Phase II Study Comparing Two Schedules of Everolimus in Patients With Recurrent/Metastatic Breast Cancer: NCIC Clinical Trials Group IND.163
Authors: Ellard Susan L. , Clemons Mark , Gelmon Karen A. , Norris Brian , Kennecke Hagen , Chia Stephen , Pritchard Kathleen , Eisen Andrea , Vandenberg Ted , Taylor Marianne , Sauerbrei Eric , Mishaeli Moshe , Huntsman David , Walsh Wendy , Olivo Martin , McIntosh Lynn , Seymour Lesley
Published: September 2009

Purpose

To evaluate the safety and efficacy of oral everolimus, a mammalian target of rapamycin (mTOR) inhibitor, in two different schedules in minimally pretreated patients with metastatic breast cancer and to explore for possible biologic correlates of response.

Patients and Methods

Patients who received no or one prior chemotherapy regimen for metastatic breast cancer were entered onto this multicenter, noncomparative, randomized phase II study of everolimus 10 mg daily versus 70 mg weekly; the multinomial end points of response and progression were evaluated at 8 weeks. A two-stage accrual design was used, with 15 evaluable patients in each schedule in stage 1. Only daily therapy met criteria for continuing, and another 15 patients were added. pAKT, PTEN, carbonic anhydrase 9, estrogen receptor (ER), progesterone receptor, and human epidermal growth factor receptor 2 (HER2) were evaluated for possible correlation with response.

Results

The most common drug-related toxicities were fatigue, rash, anorexia, diarrhea, stomatitis, cough, and pneumonitis. Pneumonitis occurred at higher than expected rates and seemed to be schedule dependent, with the highest incidence on the daily schedule. Response rate with daily therapy was 12% (95% CI, 3.4% to 28.2%) compared with 0% (95% CI, 0.0% to 20.6%) for weekly therapy. Twenty-seven percent of patients on daily therapy discontinued treatment compared with 13% on weekly therapy (16% v 6% with pneumonitis, respectively). No biologic correlates of response could be identified, although there were trends favoring benefit in ER-positive and HER2-negative metastatic breast cancer.

Conclusion

Oral everolimus has activity in metastatic breast cancer that is schedule dependent. Daily therapy with 10 mg is worthy of further study in this patient population.
Preoperative Multimodality Therapy Improves Disease-Free Survival in Patients With Carcinoma of the Rectum: NSABP R-03
Authors: Roh Mark S. , Colangelo Linda H. , O'Connell Michael J. , Yothers Greg , Deutsch Melvin , Allegra Carmen J. , Kahlenberg Morton S. , Baez-Diaz Luis , Ursiny Carol S. , Petrelli Nicholas J. , Wolmark Norman
Published: September 2009

Purpose

Although chemoradiotherapy plus resection is considered standard treatment for operable rectal carcinoma, the optimal time to administer this therapy is not clear. The NSABP R-03 (National Surgical Adjuvant Breast and Bowel Project R-03) trial compared neoadjuvant versus adjuvant chemoradiotherapy in the treatment of locally advanced rectal carcinoma.

Patients and Methods

Patients with clinical T3 or T4 or node-positive rectal cancer were randomly assigned to preoperative or postoperative chemoradiotherapy. Chemotherapy consisted of fluorouracil and leucovorin with 45 Gy in 25 fractions with a 5.40-Gy boost within the original margins of treatment. In the preoperative group, surgery was performed within 8 weeks after completion of radiotherapy. In the postoperative group, chemotherapy began after recovery from surgery but no later than 4 weeks after surgery. The primary end points were disease-free survival (DFS) and overall survival (OS).

Results

From August 1993 to June 1999, 267 patients were randomly assigned to NSABP R-03. The intended sample size was 900 patients. Excluding 11 ineligible and two eligible patients without follow-up data, the analysis used data on 123 patients randomly assigned to preoperative and 131 to postoperative chemoradiotherapy. Surviving patients were observed for a median of 8.4 years. The 5-year DFS for preoperative patients was 64.7% v 53.4% for postoperative patients (P = .011). The 5-year OS for preoperative patients was 74.5% v 65.6% for postoperative patients (P = .065). A complete pathologic response was achieved in 15% of preoperative patients. No preoperative patient with a complete pathologic response has had a recurrence.

Conclusion

Preoperative chemoradiotherapy, compared with postoperative chemoradiotherapy, significantly improved DFS and showed a trend toward improved OS.
Value engineering for railway construction projects: Cost driver analysis
Authors: Kwok E C S , Anderson P M , Ng S H S
Published: September 2009

Railway construction projects involve major capital investments, and a slight variance in design could lead to a significant change in the total project cost. To achieve value for money, it is necessary to optimize the design as far as possible. However, in reducing costs, it is important that key project objectives such as system capacity and operational flexibility are not sacrificed. In this article, a value engineering methodology, with particular emphasis on maintaining project objectives and requirements, is introduced. It involves identifying major cost drivers, devising explicit knowledge representations for these cost drivers, and analysing how they could be optimized without compromising key requirements such as the passenger-carrying capacity. The methodology is illustrated using real-world examples taken from the West Rail project in Hong Kong, which was originally conceived to be a twelve-car railway and subsequently optimized to become a seven-car system initially, with provisions to grow into an eight-car and then a nine-car configuration, without compromising the planned carrying capacity. The savings achieved were in the order of billions of Hong Kong dollars. One novel aspect of the proposed methodology is the development of a structured representation for a cost driver, through which non-obvious but significant savings could be derived.
Evaluation of reaction scheme at high initial temperature condition bypassing low-temperature reaction
Authors: Ando H , Kuwahara K
Published: September 2009

By using ‘contribution matrices’, the authors had clarified that a major reaction path during the thermal ignition preparation phase of dimethyl ether and n-heptane was a set of reactions named the ‘H2O2 reaction loop’, and suggested it may be a universal rule that the heat accumulated by this loop plays a dominant role in preparing a thermal ignition. In the present study, this suggestion was verified by using a fuel with a higher octane number, iso-octane, and by changing the initial temperature. It was verified in all cases that the ignition delay, a period of the thermal ignition preparation phase, depends on the H2O2 concentration at the beginning of this phase. Reaction path analyses showed that higher initial temperature conditions and skipping reactions in the low-temperature oxidation (LTO or cool flame) and negative temperature coefficient (NTC) range result in lower H2O2 concentrations and lower heat release during the thermal ignition preparation phase. Fuels with low and high octane number show similar ignition characteristics when the initial temperature is higher than NTC range temperatures. When a low-octane-number fuel reacts at a lower initial temperature than NTC range temperatures, the fuel is given an ‘H2O2 bonus by LTO’.
Equity in the distribution of community pharmacies in England: Impact of regulatory reform
Authors: Wagner Andrew , Hann Mark , Noyce Peter , Ashcroft Darren
Published: September 2009

Objectives:

To examine whether relaxation of control of entry regulations for community pharmacy contracts in England, introduced in 2005, affected the distribution of community pharmacies relative to population need indicators.

Methods:

Community pharmacy locations and population need indicators were used to calculate three summary measures of distributional equity across Primary Care Trust (PCT) areas (n = 152): the Gini coefficient, Atkinson Index and community pharmacies per PCT population. The indicators were adjusted for need using data from NHS GP contract Quality and Outcomes Framework disease registers, deprivation, all-cause mortality and elderly population rates.

Results:

Numbers of community pharmacies increased by 397 (4%) between 2005 and 2007 with three supermarket chains accounting for 152 (38%) of new pharmacies. Over one-quarter of PCTs experienced increases of 5% or more in community pharmacies per capita between 2005 and 2007. Gini and Atkinson indicators showed small increases in distributional equity across all population needs indicators.

Conclusion:

Deregulation was associated with more community pharmacies per capita and a small increase in geographic equity of community pharmacy distribution at PCT level. Future research should continue to monitor how pharmacy distribution changes over time and assess the extent to which the new regulatory framework has allowed clustering of pharmacies which could result in increased inequity below PCT level.
In vivo detection of RNA-binding protein interactions with cognate RNA sequences by fluorescence resonance energy transfer
Authors: Huranová Martina , Jablonski Joseph A. , Benda Aleš , Hof Martin , Staněk David , Caputi Massimo
Published: September 2009

Expression of the nascent RNA transcript is regulated by its interaction with a number of proteins. The misregulation of such interactions can often result in impaired cellular functions that can lead to cancer and a number of diseases. Thus, our understanding of RNA–protein interactions within the cellular context is essential for the development of novel diagnostic and therapeutic tools. While there are many in vitro methods that analyze RNA–protein interactions in vivo approaches are scarce. Here we established a method based on fluorescence resonance energy transfer (FRET), which we term RNA-binding mediated FRET (RB-FRET), which determines RNA–protein interaction inside cells and tested it on hnRNP H protein binding to its cognate RNA. Using two different approaches, we provide evidence that RB-FRET is sensitive enough to detect specific RNA–protein interactions in the cell, providing a powerful tool to study spatial and temporal localization of specific RNA–protein complexes.
Complex architecture and regulated expression of the Sox2ot locus during vertebrate development
Authors: Amaral Paulo P. , Neyt Christine , Wilkins Simon J. , Askarian-Amiri Marjan E. , Sunkin Susan M. , Perkins Andrew C. , Mattick John S.
Published: September 2009

The Sox2 gene is a key regulator of pluripotency embedded within an intron of a long noncoding RNA (ncRNA), termed Sox2 overlapping transcript (Sox2ot), which is transcribed in the same orientation. However, this ncRNA remains uncharacterized. Here we show that Sox2ot has multiple transcription start sites associated with genomic features that indicate regulated expression, including highly conserved elements (HCEs) and chromatin marks characteristic of gene promoters. To identify biological processes in which Sox2ot may be involved, we analyzed its expression in several developmental systems, compared to expression of Sox2. We show that Sox2ot is a stable transcript expressed in mouse embryonic stem cells, which, like Sox2, is down-regulated upon induction of embryoid body (EB) differentiation. However, in contrast to Sox2, Sox2ot is up-regulated during EB mesoderm-lineage differentiation. In adult mouse, Sox2ot isoforms were detected in tissues where Sox2 is expressed, as well as in different tissues, supporting independent regulation of expression of the ncRNA. Sox2dot, an isoform of Sox2ot transcribed from a distal HCE located >500 kb upstream of Sox2, was detected exclusively in the mouse brain, with enrichment in regions of adult neurogenesis. In addition, Sox2ot isoforms are transcribed from HCEs upstream of Sox2 in other vertebrates, including in several regions of the human brain. We also show that Sox2ot is dynamically regulated during chicken and zebrafish embryogenesis, consistently associated with central nervous system structures. These observations provide insight into the structure and regulation of the Sox2ot gene, and suggest conserved roles for Sox2ot orthologs during vertebrate development.
Path-Reduced Costs for Eliminating Arcs in Routing and Scheduling
Authors: Irnich Stefan , Desaulniers Guy , Desrosiers Jacques , Hadjar Ahmed
Published: September 2009

In many branch-and-price algorithms, the column generation pricing problem consists of computing feasible paths in a network. In this paper, we show how, in this context, path-reduced costs can be used to remove some arcs from the underlying network without compromising optimality, and we introduce a bidirectional search technique to compute these reduced costs. This arc elimination method can lead to a substantial speedup of the pricing process and the overall branch-and-price algorithm. Special attention is given to variants of shortest-path problems with resource constraints. Computational results obtained for the vehicle routing problem with time windows show the efficiency of the proposed method.
The Opinions of Manufacturers of Resin-Based Composite Materials towards the Repair of Failing Composite Restorations
Authors: Blum Igor R , Jagger Daryll C , Newton J Tim , Wilson Nairn HF
Published: September 2009

Aim

To investigate the opinions of manufacturers of resin-based composite (RBC) towards the repair of their materials.

Methods

Representatives of 20 manufacturers of RBC were electronically mailed a questionnaire seeking information on aspects of the repair of direct composite restorations.

Results

The response rate was 100%. The findings indicated that although the majority of respondents regarded repair as a viable option for managing failing direct RBC restorations, marked variations were found to exist regarding recommendations for and contra-indications to performing repairs of RBC restorations.

Conclusions

Within the limitations of the current study, the following conclusions can be drawn: (1) the majority of manufacturers of RBC materials are aware and in favour of repair as opposed to replacement of defective composite restorations; (2) there is a need for manufacturers to produce guidelines for repair of their materials; and (3) there is a need for robust randomised controlled dental practice-based clinical studies in the field of repair of composite restorations.
Evaluation of the End User (Dentist) Experience of Undertaking Clinical Audit in a PCT-Led NHS Modernisation Agency Pilot Scheme
Authors: Cannell Phillip J
Published: September 2009

Introduction

A new dental contract was introduced in the National Health Service (NHS) General Dental Services (GDS) in April 2006. Responsibility for clinical audit activities was devolved to Primary Care Trusts (PCTs) as part of their clinical governance remit. In July 2003, an NHS Modernisation Agency pilot scheme for clinical audit was launched by Southend PCT.

Aim

The aim of this study was to evaluate this scheme.

Methods

A qualitative research method was used. It used audiotape recorded semi-structured research interviews with eight general dental practitioners (GDPs) who had taken part in the scheme. The evaluation focused on dentists’ experiences of the scheme.

Results

Dentists appreciated the central PCT-based coordinator for the scheme and found that the streamlining of design, analysis and report writing within the audit projects enabled efficient use of time. The design by an outside agency appeared to add credibility to the scheme. Participants felt that comparability of data derived from clinical audit was enhanced by the scheme and could lead to comparison across PCT patch, regional or even national levels. The use of feedback mechanisms within the scheme was appreciated and thought to help produce maximum value from a clinical audit project. There was evidence of beneficial change occurring within practices and for patients.

Conclusions

This study provided an evaluation of a particular clinical audit scheme, several aspects of which differed from the traditional GDS scheme. Organisations proposing to undertake clinical audit activities in conjunction with dentistry in the future may benefit from incorporating elements of this scheme into their project design.
Image Analysis for the Quantification of a Developing Crack Network on a Drying Soil
Authors: Lakshmikantha M. R. , Prat P. C. , Ledesma A.
Published: September 2009

The paper presents a methodology for quantifying surface crack patterns that appear in cohesive soils under drying conditions due to environmental changes, using image analysis techniques. This has practical applications in the study of many geotechnical problems related to soil cracking such as the impact of permeability changes due to cracking in clay barriers, development of preferential flow paths for contaminant transport along cracks, decreasing bearing capacity, and others. The study of soil cracking may become even more relevant with the current climate change that may induce more frequent and severe droughts in many parts of the world, increasing the areas at risk of cracking. Qualitative and quantitative characterization of the crack patterns is needed to study the mechanical behavior of a cracking soil, how cracks generate and propagate. For this purpose a simple laboratory set-up has been developed for continuous monitoring of the processes of formation and propagation of cracks due to desiccation, and to study the final crack pattern. The paper describes a simple technique to process sequences of images obtained during the laboratory tests, and how image analysis can be used to quantify the parameters that characterize the evolving and final crack patterns.
The Effect of Incorporation of Gramicidin on the Translational Lipid Diffusion in Bicontinuous Cubic Monoolein/Water Mesophases
Authors: Pospiech E.-M. , Geil B. , Fujara F. , Winter Roland
Published: September 2009

The influence of incorporating the polypeptide gramicidin on the lateral mobility of the monoacylglyceride monoolein (MO) in its bicontinuous cubic lipid mesophases is studied applying static field gradient NMR. The effects of gramicidin on the topology, structure and phase behaviour of the system are characterized by small-angle x-ray scattering (SAXS) experiments. On the structural level the experiments show significant shifts in the boundaries of the various mesophases. Measurements of the translational dynamics are restricted to cubic mesophases, where the diffusion coefficients of lipid and additive are determined both by geometrical obstruction and by lipid-protein interaction effects.
Myoglobin and Apomyoglobin in their Native, Molten Globule and Acid-Denaturated States. A Dielectric Relaxation Study
Authors: Ajaj Yathrib , Wehner Mark , Weingärtner Hermann
Published: September 2009

The acid-induced unfolding of myoglobin and its haem-free derivative apo-myoglobin is studied by broadband dielectric relaxation spectroscopy at pH values near 5, 4 and 2, which reflect the transition N → MG → UA from the native state (N) via a molten globule state (MG) to an acid-unfolded state (UA). Spectral changes are singled out by considering difference spectra for the transitions N → MG and N → UA. A pronounced increase of the amplitude of the tumbling motion of holo-myoglobin and apo-myoglobin in the sequence N → MG→ UA reflects the increase of their electrical dipole moments by progressive unfolding. A distinct high-frequency shoulder of the tumbling mode indicates an enhanced internal protein dynamics in the unfolded states. The calculated Stokes radii confirm a compact nature of the MG state and a large increase in size of the UA state relative to the native state. In the native state the Stokes radii deduced from the dielectric spectra agree fairly well with those deduced from dynamic light scattering. In the MG state, and particularly in the UA state, the Stokes radii determined by light scattering are markedly larger than those determined by dielectric relaxation. The difference is attributed to aggregation of the unfolded species, which affects dynamic light scattering more than dielectric relaxation. In the high-frequency regime, the dielectric spectra indicate that unfolding enhances the number of water molecules showing bulk-like dynamics, but the effect is rather weak.
Were Tom and Huck On-Shelf? Public Libraries, Mark Twain, and the Formation of Accessible Canons, 1869–1910
Authors: Lear Bernadette A.
Published: September 2009

Public libraries are "accessible canons" for their communities. As part of their efforts to connect people and ideas, librarians purchase classic and bestselling books from "selective," "personal," "nonce," and other canons. They also create bibliographies, professional standards, and other tools that help shape reading habits. Thus libraries embody complex, ongoing processes of canon using and canon forming. This essay illustrates the canonical activities of American public libraries during the early years of the profession. It describes the American Library Association Catalog, local finding lists and accession records, and other primary sources that shed light on collection building during the late nineteenth and early twentieth centuries. Taking Mark Twain (Samuel Langhorne Clemens) as a case study, it presents statistics on library ownership during the author's lifetime from more than seven hundred communities across the United States. Tables focus on nine titles: The Innocents Abroad, Roughing It, The Gilded Age, The Adventures of Tom Sawyer, The Prince and the Pauper, Life on the Mississippi, Adventures of Huckleberry Finn, A Connecticut Yankee in King Arthur's Court, and The Tragedy of Pudd'nhead Wilson. Statistical analysis reveals that "controversial" items such as Huckleberry Finn were widely available in Gilded-Age and Progressive-era public libraries, thus calling into question some assumptions about censorship of Twain's work. Also, library holdings of some titles varied by decade and geography, demonstrating that libraries implemented "national" and "recognized" canons unevenly. In sum, the essay shifts attention toward the operationalization of literary canons and provides empirical evidence of Mark Twain's presence in the late-nineteenth- and early-twentieth-century literary landscape.
Effect of communal sewage sludge treatment on the Cu, Zn, Mn, Ni and Co fractions of the soil and on plant uptake in a pot experiment
Authors: Rékási Márk , Filep Tibor
Published: September 2009

A megengedett határértéket meghaladó fémtartalmú városi szennyvíziszapnak a kísérleti talajok (savanyú és karbonátos homok, ill. savanyú agyagos vályog és karbonátos vályog) Co, Ni, Mn, Cu és Zn frakcióira (mobilis: 1MNH4NO3-oldható, mobilizálható: ammónium-acetát+EDTA-oldható, „összes”: cc. HNO3+cc. H2O2roncsolás) és a tavaszi árpa szemtermésének elemtartalmára gyakorolt hatását vizsgáltuk tenyészedény-kísérletben. Az alkalmazott iszapterhelések a következők voltak: 0, 2,5, 5, 10 és 20 g iszap szárazanyag/kg légszáraz talaj. Az 5 iszapkezelés×4 talaj = 20 kezelés×4 ismétlés = 80 edényszámot tett ki. A kapott eredményeket az alábbiakban foglaljuk össze: – A talaj elemfrakciói és az árpaszem elemtartalma között regresszió-analízist végezve megállapítottuk, hogy az árpaszem és a talaj Co-, Ni-, Cu- és Zn-tartalmának kapcsolatát legjobban ezen elemek mobilis frakciójával jellemezhetjük. – Az iszappal kijuttatott elemek elenyésző hányada jelenik csak meg mobilis formában a talajban. Az eredmények azt mutatták, hogy minél gazdagabb a talaj a vizsgált elemekben, annál kisebb hányaduk van mobilis formában. A legnagyobb arányban a kijuttatott nikkel jelent mobilis elemként, átlagosan 3%-ban. A vizsgált elemek a Co és Mn kivételével a legnagyobb arányban a két homoktalajon, elsősorban a savanyú homokon voltak a mobilis frakcióban. A nyírlugosi talajon a legkisebb terheléssel kijuttatott Zn 19%-ban NH4NO3-oldható formában jelent meg. – A vizsgált elemek sorrendje a talajokon való megkötődés erőssége szerint a következő volt az adott kísérleti feltételek mellett: Mn > Zn > Cu > Ni = Co. – Az iszap pH-növelő hatásának eredményeképpen a vizsgált savanyú homoktalaj mobilis Co- és Mn-tartalma harmadára csökkent annak ellenére, hogy az „összes” elemtartalom nem változott szignifikánsan. Ez a csökkenés az árpaszem Co- és Mn-tartalmában is megmutatkozott. Ezért az iszapok szabadföldre történő elhelyezésénél az iszap elemtartalmán túl figyelembe kell venni egyéb paramétereit (pH, CaCO3%, szerves anyag) is, mert azok a talaj tulajdonságait és ezen keresztül a szennyező elemek oldódását befolyásolhatják. A fenti megállapítások megnyugtatóak a szennyvíziszapok mezőgazdasági hasznosítása szempontjából, de miután a kísérleti eredményeket extrém elemterhelés mellett kaptuk, hasonló munka elvégzése javasolható megengedett elemkoncentrációjú szennyvíziszappal is.
Radiocarbon age of buried humus layers in the Szigetköz region of Hungary
Authors: Szűcs Mihály , Szűcs Mihályné
Published: September 2009

A Szigetköz és a Mosoni-síkság eltemetett humuszos réteg folttérképének újabb pontosított változatát készítettük el 3 m mélységig terjedő fúrások segítségével. A jellemzőnek ítélt szelvények eltemetett humuszos rétegei mintáiból a radiokarbon kor vizsgálatokat az MTA ATOMKI Környezetanalitikai Laboratóriuma végezte. Több mint 2000 szelvény vizsgálata alapján megállapítottuk, hogy a szelvények kb. 25%-ában található eltemetett humuszos réteg, amelyeknek kevesebb, mint 20%-a van a felszín közelében. Azok a szelvények, amelyekben egynél több eltemetett humuszos réteget találunk a Dunaremetétől Lébényen át Győrzámolyig vezető félkör mentén helyezkednek el, délre eltávolodva a Mosoni-Duna jelenlegi vonalától. Ebben a sávban a talajképződést biztosító nyugalmi szakaszok után periodikusan visszatérő elöntések történtek. A félkör által határolt területen belül ilyen ciklikusság hatása nem volt megfigyelhető. A Duna és a Mosoni-Duna közelében az eltemetett humuszos rétegek kora 1–2 ezer év, távolabb a legrégebbi mért radiokarbon kor 4 ezer év körül volt. Ez közel azonos a Győr-tatai teraszvidéken egy lejtőhordalék talaj mélyen eltemetett humuszos rétegében mért korral. A Szigetközben a több eltemetett humuszos réteget tartalmazó zónában a periodikus nagy hordalékszállítási ciklusok 500–1000 évente ismétlődtek. A terület déli részén, Lébény környékén a viszonylag vékony, de ciklikusan megjelenő hordalékszállítások a korábbi 7–10 ezer éves hansági tőzegre rakódtak le. A vizsgálati adatok segíthetnek a terület földtani és emberi településtörténeti kutatásában is.
Competition for nutrients between weeds and green pea
Authors: Wágner Gábor , Nádasyné Ihárosi Erzsébet
Published: September 2009

Tenyészedényes kísérletben vizsgáltuk a borsó és négy gyomnövénye tápanya- gokért folytatott kompetícióját. Az additív kísérleti módszert alkalmaztuk, mely során a kultúrnövény sűrűsége állandó, a gyomnövényeké változó. Mindegyik tenyészedényben 6 db korai érésű „Karlos” fajtájú borsónövényt neveltünk. A kísérletben szereplő gyomnövények a következők voltak: vadrepce (
Sinapis arvensis
L.), szőrös disznóparéj (
Amaranthus retroflexus
L.), fehér libatop (
Chenopodium album
L.) és a kakaslábfű (
Echinochloa crus-galli
L.P.B.). A gyomnövények versengését háromféle egyedszám mellett vizsgáltuk: 5, 10, ill. 15 db növény/tenyészedény. Kontrollként gyommentes, csak borsót tartalmazó edényeket használtunk. A növényeket 1,9 kg légszáraz talajt tartalmazó tenyészedényekben neveltük 4 ismétlésben, 13 kezeléssel, így összesen 52 tenyészedényünk volt. A keszthelyi Ramann-féle vályogos barna erdőtalaj a főbb tápelemekkel kielégítően ellátottnak minősült. A növényeket, a csírázást követő 6 hétig neveltük. A lebontást követően mértük a borsó és a gyomnövények friss, majd száraz hajtástömegét. A szárított növénymintákból tömény kénsavas feltárást követően határoztuk meg a nitrogén-, foszfor- és káliumtartalmat. A borsó tápanyagtartalmát a különböző gyomfajok és azok egyedszáma eltérő módon befolyásolták (2. táblázat). A gyomfajok növekedési üteme nem volt egységes, a
S. arvensis
fejlődött a leggyorsabban, a kísérlet végére a tenyészedény jelentős részét borította. Jól fejlődött az
E. crus-galli
is. Gyenge növekedést tapasztaltunk
A. retroflexus
és
C. album
növényeknél, ami befolyásolta biomassza produkcióikat. Ebből következik, hogy tápanyagfelvételük és kompetíciós képességük meglehetősen szerény volt. A gyomnövények intenzív tápelemfelvételük révén többnyire csökkentették a kultúrnövény tápanyagtartalmát. A
S. arvensis
akadályozta a legerősebben a kultúrnövény intenzív tápanyagfelvételét. A vadrepce P- és K-tartalmát nem befolyásolta az egyedsűrűsége. Az
A. retroflexus
N-, P- és K-tartalma az egyedsűrűség növelésével csökkent, tehát erős intraspecifikus kompetíciót tapasztaltunk.
Formation of controlled alumina films using Supercritical Fluids Chemical Deposition for electronic and telecommunication devices
Authors: Aymonier C. , Lamirand-Majimel M. , Bousquet C. , Moncade C. , Cansell F. , Maglione M. , Ellisalde C. , Heintz J.-M. , Silvain J.-F.
Published: September 2009

Alumina is one of the most widely used oxide ceramic material. It exists in many metastable forms, among which is the thermodynamically stable α phase, obtained upon severe thermal treatment. Sintering of alumina is generally performed in several stages: first, phase transitions towards the stable α phase followed by its densification. The first step is strongly dependent on the crystallinity of initial powders. By controlling this parameter, it is possible to optimize the sintering properties, in particular by decreasing the phase transition temperature. This effect has been studied for alumina elaborated in sub- and supercritical fluid media. This work highlights the possibilities to obtain, according to the nature of the fluid, different kinds of transition alumina: boehmite AlO(OH) or amorphous Al2O3. The sintering processes of these powders all lead to α-alumina, however, different microstructures and densities can be obtained. A significant shift towards lower λ/α phase transition temperature is also observed when amorphous alumina is considered, compared to boehmite. The transfer of this know-how to the design of core-shell nanoparticles and film deposition onto copper heat sinks is investigated to develop nanostructured ceramics for telecommunications and electronics.
Superhydrophobic Silicon Surfaces with Low Light Reflectivity
Authors: Xiu Yonghao , Liu Yan , Hess Dennis W. , Wong Chingping
Published: September 2009

Creation of superhydrophobic self-cleaning surfaces is an important objective for a variety of applications. Indeed, numerous routes to generate superhydrophobic surfaces have been proposed. In this paper, a facile way of forming superhydrophobic surfaces is reported that uses Au assisted HF/H2O2 etching of silicon wafers. The Au layer was deposited onto a silicon wafer via e-beam evaporation. By controlling the evaporation and etching times, the surface roughness can be manipulated and superhydrophobic surfaces with reduced light reflection can be generated. Contact angles were measured with a CCD camera equipped goniometer; these values determined the water repellency. Light reflection on the as prepared black surfaces was measured to assess the efficiency for low cost solar cell applications. This approach offers a new way both to theoretically study the surface roughness effect and to investigate engineering applications of self-cleaning surfaces in solar cells, MEMS, anti-bacteria coating, and microfluidic devices.
Synthesis and Characterization of LiFePO4/C Composite Obtained by One-Step Solid-State Reaction Using Solid PVA as Carbon Source
Authors: Yang Limei , Liang Guangchuan , Wang Li , Zhi Xiaoke , Ou Xiuqin
Published: September 2009

LiFePO4/C composite cathode materials were synthesized by one-step solid-state reaction using FePO4 as main raw materials and solid PVA (Polyvinyl Alcohol) as a reductive agent and carbon source. The sample was characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), particle size analysis and charge-discharge test. The results indicated that the carbon generated from the pyrogenation of PVA did not affect the olivine structure of the cathode materials but considerably improved its high-rate discharge ability and cycle performance. The initial discharge capacity of the sample was 149.7, 133.1, 120.6, 93.0 mAh/g at 0.2C, 1C, 2C, 5C respectively, and the discharge capacity could reach 90 mAh/g at 5C rates after 80 cycles. It is believed that the carbon coating could lead to small particle size and high electronic conductivity of active materials, thus leading to excellent electrochemical performance of LiFePO4/C cathode materials.
Improved Analytical Models for Single- and Multi-layer Silver Superlenses
Authors: Moore Ciaran P , Blaikie Richard John , Arnold Matthew D
Published: September 2009

Spatial-frequency transfer functions are regularly used to model the imaging performance of near-field �superlens� systems. However, these do not account for interactions between the object that is being imaged and the superlens itself. As the imaging in these systems is in the near field, such interactions are important to consider if accurate performance estimates are to be obtained. We present here a simple analytical modification that can be made to the transfer function to account for near-field interactions for objects consisting of small apertures in otherwise-continuous metal screens. The modified transfer functions are evaluated by comparison with full-field finite-element simulations for representative single-layer and multi-layer silver superlenses, and good agreement is found.
Effect of Partial Oxygen Pressure on Structural, Electrical, and Magneto transport Properties of Cobalt Doped Indium Oxide Thin Films
Authors: Ghosh Abhijit , Ukah N. , Gupta R K , Kahol P K , Ghosh K
Published: September 2009

Dilute magnetic semiconductors are ferromagnetic semiconductors recently discovered in nitride and oxide semiconductors by incorporating a small percentage of magnetic atoms into the semiconductors host. Recently it is reported that the structural and electrical properties of pure indium oxide can be modified by growth parameters. In this paper we investigate magneto-transport properties of Co-doped In2O3 dilute magnetic semiconductors thin films grown on sapphire and quartz substrates using pulsed laser deposition technique. The effect of partial oxygen pressure on structural, electrical, optical, and magneto-transport properties was discussed in details. The crystallinity of the films largely depends on growth temperature. Magneto-transport properties such as temperature dependent resistivity and magneto-resistance were found to be very sensitive to the micro-structural properties such as crystalinity as well as oxygen defect. The electrical carrier density of the films depends on oxygen pressure and a change of two orders of magnitude is observed. Depending on growth parameters, both positive and negative magneto-resistance is observed. Optical band-gap seems to vary with the growth partial oxygen pressure.
Universal Scaled Strength Behaviour for Micropillars and Nanoporous Materials
Authors: Derby Brian , Dou Rui
Published: September 2009

The strength of submicron FCC structure metal columns, σ, fabricated by FIB machining or electrodeposition, shows a strong correlation with specimen diameter, d, with σ/μ = A(d/b)−0.63, where A is a constant, μ is the single crystal shear modulus resolved onto the slip system and b is the Burgers' vector. The strength of BCC structure metals does not show such a well defined correlation with size across different metals but the data occupies the same region of parameter space as with the FCC metals. Nanoporous gold specimens show a similar size-correlated behaviour but with an exponent of −0.5. This may indicate different mechanisms operating in each case.
Piezoresponse Force Microscopy Characterization of PTO Thin Films
Authors: Morelli Alessio , Venkatesan Sriram , Palasantzas George , Kooi Bart J. , De Hosson Jeff
Published: September 2009

The piezoelectric properties of PTO thin films grown by pulsed laser deposition are investigated with piezoresponse force microscopy and transmission electron microscopy. The as-grown films exhibit upward polarization, and inhomogeneous distribution of piezoelectric characteristics. The data obtained reveal imprint during piezoresponse force microscopy measurements, nonlinearity in the piezoelectric deformation, and limited retention loss. Moreover, transmission electron microscopy shows the presence of defects near the film/substrate interface, which can be associated with the variations of piezoelectric properties.
Differential evolution algorithm for optimal design of water distribution networks
Authors: Suribabu C. R.
Published: September 2009

Water distribution networks are considered as the most important entity in the urban infrastructure system and need huge investment for construction. The inherent problem associated with cost optimisation in the design of water distribution networks is due to the nonlinear relationship between flow and head loss and availability of the discrete nature of pipe sizes. In the last few decades, many researchers focused on several stochastic methods of optimisation algorithms. The present paper is focused on the Differential Evolution algorithm (henceforth referred to as DE) and utilises a similar concept as the genetic algorithm to achieve a goal of optimisation of the specified objective function. A simulation–optimisation model is developed in which the optimization is done by DE. Four well-known benchmark networks were taken for application of the DE algorithm to optimise pipe size and rehabilitation of the water distribution network. The findings of the present study reveal that DE is a good alternative to the genetic algorithm and other heuristic approaches for optimal sizing of water distribution pipes.