bluuebunny/crossref_metadata_2025 huggingface dataset:
The quantile regression approach to efficiency measurement: insights from Monte Carlo simulations
Authors: Liu Chunping , Laporte Audrey , Ferguson Brian S.
Published: August 2008

In the health economics literature there is an ongoing debate over approaches used to estimate the efficiency of health systems at various levels, from the level of the individual hospital – or nursing home – up to that of the health system as a whole. The two most widely used approaches to evaluating the efficiency with which various units deliver care are non‐parametric data envelopment analysis (DEA) and parametric stochastic frontier analysis (SFA). Productivity researchers tend to have very strong preferences over which methodology to use for efficiency estimation. In this paper, we use Monte Carlo simulation to compare the performance of DEA and SFA in terms of their ability to accurately estimate efficiency. We also evaluate quantile regression as a potential alternative approach. A Cobb–Douglas production function, random error terms and a technical inefficiency term with different distributions are used to calculate the observed output. The results, based on these experiments, suggest that neither DEA nor SFA can be regarded as clearly dominant, and that, depending on the quantile estimated, the quantile regression approach may be a useful addition to the armamentarium of methods for estimating technical efficiency. Copyright © 2008 John Wiley & Sons, Ltd.
Sentinel node biopsy in patients with cutaneous melanoma of the head and neck: Recurrence and survival study
Authors: Gomez‐Rivera Fernando , Santillan Alfredo , McMurphey Andrea Barber , Paraskevopoulos George , Roberts Dianna B. , Prieto Victor G. , Myers Jeffrey N.
Published: August 2008

Background.

Controversy remains regarding the benefits of sentinel lymph node (SLN) biopsy for predicting survival in cutaneous melanoma of the head and neck (CMHN).

Methods.

We analyzed the factors associated with the recurrence and survival of CMHN patients treated in our institution.

Results.

One hundred thirteen patients underwent SLN biopsy for CMHN in a 12‐year period. SLN identification was successful in 96%, with a median of 3 SLNs per patient. Positive‐SLNs were identified in 21%. With a median follow‐up of 34 months, 28% recurred. Disease‐free survival (DFS) and overall survival (OS) rates were 66% and 78% in patients with SLN‐negative, and 39% and 62% in SLN‐positive disease. In multivariate analysis, greater Breslow‐thickness was associated with decreased DFS rate (HR 2.07, CI 1.04–4.09), and age >60 years (HR 3.53, CI 1.32–9.4) with lower 5‐year OS rate.

Conclusion.

Primary tumor thickness and age were associated with decreased survival, whereas SLN status showed a trend for prognostic significance in CMHN. © 2008 Wiley Periodicals, Inc. Head Neck, 2008
Survivin and epidermal growth factor receptor expression in surgically treated oropharyngeal squamous cell carcinoma
Authors: Preuss Simon Florian , Weinell Antje , Molitor Markus , Semrau Robert , Stenner Markus , Drebber Uta , Wedemeyer Inga , Hoffmann Thomas K. , Guntinas‐Lichius Orlando , Klussmann Jens Peter
Published: August 2008

Background.

The epidermal growth factor receptor (EGFR) and the inhibitor of apoptosis protein survivin play important roles in the regulation of cellular proliferation and survival in squamous cell carcinomas. Their correlation in oropharyngeal squamous cell carcinoma (OSCC) has not been evaluated yet.

Methods.

In this multicenter study, we analyzed the expression of survivin and EGFR in tissue specimens from 73 selected patients with OSCC using immunohistochemistry.

Results.

Higher cytoplasmic survivin scores were significantly correlated with high scores of EGFR expression (p = .013). Nuclear survivin expression was associated with a poor overall survival rate with an estimated 3‐year overall survival probability of 17.3% versus 87.4% for non‐nuclear expression of survivin (p <.001). Multivariate analysis revealed that nuclear survivin expression was an independent negative prognostic factor (p = .008).

Conclusion.

Considering the strong impact of nuclear survivin expression on survival, the survivin expression should be prospectively evaluated to select patients with an increased risk for disease recurrence. © 2008 Wiley Periodicals, Inc. Head Neck, 2008
Definitive radiotherapy in the management of paragangliomas arising in the head and neck: A 35‐year experience
Authors: Hinerman Russell W. , Amdur Robert J. , Morris Christopher G. , Kirwan Jessica , Mendenhall William M.
Published: August 2008

Background.

An evaluation of the treatment results for 104 patients with 121 paragangliomas of the temporal bone, carotid body, and/or glomus vagale who were treated with radiation therapy (RT) at the University of Florida between 1968 and 2004.

Methods.

Eighty‐nine paragangliomas (86%) were treated with conventional megavoltage techniques, 15 (14%) patients with stereotactic fractionated radiation therapy, 6 (6%) patients with stereotactic radiosurgery (SRS), and 11 (11%) patients with intensity‐modulated radiation therapy (IMRT).

Results.

There were 6 local recurrences. One recurrence was salvaged with additional RT. The actuarial local control and cause‐specific survival rates at 10 years were 94% and 95%. The overall local control rate for all 121 lesions was 95%; the ultimate local control rate was 96%. The incidence of treatment‐related complications was low.

Conclusion.

Fractionated RT offers a high probability of tumor control with minimal risks for patients with paragangliomas of the temporal bone and neck. © 2008 Wiley Periodicals, Inc. Head Neck, 2008
Comparison of perioperative management and outcome of parathyroidectomy between older and younger patients
Authors: Bachar Gideon , Gilat Hanna , Mizrachi Aviram , Shimon Ilan , Feinmesser Raphael , Kaizerman Igor , Shpitzer Thomas
Published: August 2008

Background.

The aim of this study was to compare the clinical status, surgical course, and outcomes of patients with primary hyperparathyroidism (PHPT), over the age of 70, with younger patients.

Methods.

Between 1996 and 2006, 951 patients underwent parathyroidectomies for PHPT, of whom 190 were over the age of 70. Patient data were collected from chart reviews and a computerized database.

Results.

Fewer older patients were asymptomatic at presentation. No between‐group differences in serum calcium were seen; however, parathyroid hormone (PTH) levels were higher in the older group. Hospitalization time was longer for the elderly. Duration of surgery, surgical success rates, and postoperative complications were similar between the 2 groups.

Conclusion.

Surgical treatment of PHPT has both physiological benefits and helps to preserve quality of life. Our findings suggest that there is no practical difference in perioperative management and surgical outcomes for older patients. Surgeons should consider parathyroidectomy in PHPT patients regardless of age. © 2008 Wiley Periodicals, Inc. Head Neck, 2008
Sirolimus as a potential radiosensitizer in squamous cell cancer of the head and neck
Authors: Shinohara Eric T. , Maity Amit , Jha Neha , Lustig Robert A.
Published: August 2008

Background.

An estimated 34,000 cases of squamous cell carcinomas of the head and neck (HNSCC) will be diagnosed in 2007 with 7500 estimated deaths. Radiation is commonly used to treat these patients. Preclinical studies have suggested that sirolimus may be an effective radiosensitizer in HNSCC.

Methods.

The present case report describes a patient, status post liver transplant, who was switched to sirolimus for immunosupression. The patient subsequently underwent radiation therapy for a T2N0M0 SCC of the larynx.

Results.

The patient had an unusually early response to radiation, with a clinical complete response after 7 fractions of radiation. However, the patients also had toxicity earlier than expected and required a break from radiation after 11 fractions.

Conclusions.

To the authors' knowledge, this is the first observation to suggest that sirolimus is an effective radiosensitizer in patients with HNSCC. We hope that our results will create interest in future clinical studies. © 2008 Wiley Periodicals, Inc. Head Neck, 2009
Molecular mechanisms of hepatocellular carcinoma
Authors: Aravalli Rajagopal N. , Steer Clifford J. , Cressman Erik N. K.
Published: August 2008

Hepatocellular carcinoma (HCC) typically has poor prognosis, because it is often diagnosed at an advanced stage. Heterogeneous phenotypic and genetic traits of affected individuals and a wide range of risk factors have classified it a complex disease. HCC is not amenable to standard chemotherapy and is resistant to radiotherapy. In most cases, surgical resection and liver transplantation remain the only curative treatment options. Therefore, development of novel, effective therapies is of prime importance. Extensive research over the past decade has identified a number of molecular biomarkers as well as cellular networks and signaling pathways affected in liver cancer. Recent studies using a combination of “omics” technologies, microRNA studies, combinatorial chemistry, and bioinformatics are providing new insights into the gene expression and protein profiles during various stages of the disease. In this review, we discuss the contribution of these newer approaches toward an understanding of molecular mechanisms of HCC and for the development of novel cancer therapeutics. (Hepatology 2008;48:2047-2063.)
The removal of phosphorus from reject water in a municipal wastewater treatment plant using iron ore
Authors: Ivanov Volodymyr , Kuang Shengli , Stabnikov Viktor , Guo Chenghong
Published: August 2008

BACKGROUND: Reject water (return liquor) from dewatering of anaerobically digested activated sludge in municipal wastewater treatment plants contains from 10 to 50% of the phosphorus load when being recycled to the aeration tank. Phosphorus removal from reject water could be an effective way to decrease phosphorus loads entering the aeration tank. An innovative approach involves the replacement of iron salts, which are commonly used for phosphorus removal, with ferrous ions produced by iron‐reducing bacteria from iron ore. The aim of the research was to examine the feasibility of phosphorus removal from return liquor using bioreduction of iron ore.

RESULTS: Ferrous production, phosphate and organic carbon removal rates were determined as a function of different iron ore particle sizes in batch experiments. Iron‐reducing bacteria ensured the production of ferrous ions from iron ore up to concentrations of 550 mg L−1. The ferrous production rate was linearly dependent on the calculated specific surface area of the iron ore particles. The phosphorus concentration in the reject water was reduced by 90% during bioreduction of iron ore. The phosphorus removal rate did not depend on specific surface area of iron ore particles when the particle size of iron ore was smaller than 7 mm. The organic carbon removal rate did not seem to be dependent on iron ore particle size.

CONCLUSION: Removal of phosphate using iron ore can be more economical than conventional chemical precipitation of phosphate using iron salts because of the lower cost of iron ore. Copyright © 2008 Society of Chemical Industry
Antibody immobilization on magnetic particles
Authors: Roque A. C. A. , Bispo S. , Pinheiro A. R. N. , Antunes J. M. A. , Gonçalves D. , Ferreira H. A.
Published: August 2008

Magnetic particles (MNPs) offer attractive possibilities in biotechnology. MNPs can get close to a target biological entity, as their controllable sizes range from a few nanometres up to tens of nanometres, and their surface can be modified to add affinity and specificity towards desired molecules. Additionally, they can be manipulated by an external magnetic field gradient. In this work, the study of ferric oxide (Fe3O4) MNPs with different coating agents was conducted, particularly in terms of strategies for antibody attachment at the surfaces (covalent and physical adsorption) and the effects of blocking buffer composition and incubation times on the specific and non‐specific interactions observed. The considered biological model system consisted of a coating antibody (goat IgG), bovine serum albumin (BSA) as blocking agent, and a complementary antibody labelled with FITC (anti‐goat IgG). The detection of antibody binding was followed by fluorescence microscopy and the intensity of the signals quantified. The ratio between the mean grey values of negative and positive controls, as well as the maximum intensity attainable in positive controls, were considered in the evaluation of the assays efficiency. The covalent immobilization of the coating antibody was more successful as opposed to protein adsorption. For covalent immobilization, silica‐coated MNPs, a 5% (w/v) concentration of BSA in the blocking buffer and incubation times of 1 h produced the best results in terms of assay sensitivity. However, when conducting the assay for incubation periods of 10 min, the fluorescence signal was reduced by 44% but the assay specificity was maintained. Copyright © 2008 John Wiley & Sons, Ltd.
Synthesis and thermal decomposition kinetics of the complexes [Sm(o‐NBA)3bipy]2·2H2O and [Sm(o‐BrBA)3bipy]2· 2H2O
Authors: Zhang Hai Yan , Zhang Jian Jun , Ren Ning , Bai Ji Hai , Wang Shu Ping , Wang Rui Fen
Published: August 2008

Two new complexes [Sm(o‐NBA)3bipy]2·2H2O (1) and [Sm(o‐BrBA)3bipy]2·2H2O (2) (where o‐NBA is o‐nitrobenzoic acid, o‐BrBA is o‐bromobenzoic acid, and bipy is 2,2′‐bipyridine) were prepared and characterized by elemental analysis, IR, UV, and molar conductance, respectively. The thermal decomposition behaviors of the two complexes were investigated by means of TG–DTG and IR techniques. The thermal decomposition kinetics was studied by using advanced double equal‐double steps method, nonlinear integral isoconversional method, and nonlinear differential isoconversional method. The kinetic parameters of the second‐step process for the two complexes were obtained, respectively. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 607–616, 2008
Quantitative proteome analysis reveals annexin A3 as a novel biomarker in lung adenocarcinoma
Authors: Liu YF , Xiao ZQ , Li MX , Li MY , Zhang PF , Li C , Li F , Chen YH , Yi H , Yao HX , Chen Z‐C
Published: August 2008

Metastasis is a common phenomenon and the major lethal cause of lung adenocarcinoma (AdC). To discover novel potential biomarkers associated with lymph node metastasis and prognosis in lung AdC, we assessed differences in protein expression between primary lung AdC with (LNM AdC) and without lymph node metastasis (non‐LNM AdC) using a quantitative proteomic approach. Laser capture microdissection was performed to purify the cancer cells from primary lung AdC tissues. The differential proteins between the pooled microdissected non‐LNM AdC and LNM AdC tissues were identified by two‐dimensional difference gel electrophoresis (2D‐DIGE) coupled with mass spectrometry (MS). In this study, twenty proteins were found to be differentially expressed in two types of lung AdC. ANXA3, significantly up‐regulated in LNM AdC compared with non‐LNM AdC, was validated by western blotting. Immunohistochemistry showed that ANXA3 over‐expression was frequently observed in LNM AdCs and matched lymph node metastases compared with non‐LNM AdCs. ANXA3 over‐expression was significantly associated with advanced clinical stage (p < 0.001) and lymph node metastasis (p < 0.001) and increased relapse rate (p < 0.001) and decreased overall survival (p < 0.001) in lung AdCs. Cox regression analysis indicated ANXA3 over‐expression was an independent prognostic factor. Our results indicate that ANXA3 might serve as a novel biomarker for lymph node metastasis and prognosis in lung AdC, and play an important role in lung AdC progression. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Outcomes of the POG 9340/9341/9342 trials for children with high‐risk neuroblastoma: A report from the Children's Oncology Group
Authors: Zage Peter E. , Kletzel Morris , Murray Kevin , Marcus Robert , Castleberry Robert , Zhang Yang , London Wendy B. , Kretschmar Cynthia
Published: August 2008

Background

From 1993 to 1995, the Pediatric Oncology Group (POG) enrolled patients with high‐risk neuroblastoma on three sequential, conjoined studies: a phase II induction window (9340), followed by intensive multiagent induction chemotherapy (9341), and subsequent myeloablative therapy with autologous stem cell rescue (9342). We report here the outcomes of patients treated on these studies.

Patients and Methods

Patients were between 1 and 21 years old with high‐risk neuroblastoma. Phase II window therapy consisted of two courses of either paclitaxel, topotecan, or cyclophosphamide with topotecan. Induction therapy consisted of at least five cycles of intensive chemotherapy, followed by myeloablative therapy with purged autologous stem cell reinfusion. Patient responses, treatment toxicities, and overall and event‐free survival rates were calculated.

Results

Eighty‐four percent of patients responded to induction chemotherapy, with 39% achieving complete response. Toxicities were primarily hematologic. The 7‐year EFS and OS rates for all eligible patients on POG 9341 were 23 ± 4% and 28 ± 4%, respectively. The 7‐year EFS and OS rates for patients treated on POG 9342 were 27 ± 6% and 29 ± 6%, respectively.

Conclusions

These studies were the first attempt by POG to use autologous stem cell transplantation for neuroblastoma treatment in a cooperative group setting. Toxicities and outcomes were comparable to contemporary cooperative group studies. The phase II induction window had no detectable effect on outcomes. New strategies are needed to improve survival for this devastating disease. Pediatr Blood Cancer 2008;51:747–753. © 2008 Wiley‐Liss, Inc.
Preparation and characterization of polyimide/silica‐barium titanate nanocomposites
Authors: Gao Lingxiang , Liu Qiuping , Gao Ziwei , Lin Yang
Published: August 2008

The silica‐barium titanate (SiO2‐BaTiO3) nanocomposites coated with polyimide had been synthesized successfully by a dispersion polymerization method. The conformation, structure, and size of SiO2‐BaTiO3 nanocomposites coated with polyimide were investigated by using FT‐IR, EDAX, XRD,TEM, SEM, and TGA. The results indicate that there is a thin layer polymer of SiO2‐BaTiO3 nanocomposites surface, in which the polymer thickness is about 10 nm and the size of them are about 50–60 nm, and the particles are well‐dispersed with even particle size. In addition, the crystal structure of BaTiO3 is stable in preparing composite process and the chemical bond is formed between the inorganic phase and the polymer matrix. POLYM. COMPOS., 2008. © 2008 Society of Plastics Engineers
Melt‐processed polyaniline nanofibers/LDPE/EAA conducting composites
Authors: Su Chang , Wang Gengchao , Huang Farong , Li Xingwei
Published: August 2008

The melt‐processable polyaniline nanofibers doped with superfluous dodecylbenzenesulfonic acid (PANI‐DBSA) were synthesized using the interfacial polymerization and thermal doping technique. Conducting composites composed of PANI‐DBSA nanofibers, low‐density polyethylene (LDPE), and ethylene‐acrylic acid copolymer (EAA) as compatibilizer were prepared by melt processing. The effects of PANI‐DBSA nanofibers on the electrical conductivity, and mechanical properties, and morphological structure of the composites were investigated. As a result, the conducting composites had lower percolation threshold (4 wt%) due to the easy formation of conducting paths for fibrillar‐like PANI‐DBSA in the LDPE matrix, which was also confirmed by the frequency dependence of the real part of the AC conductivity. The Scanning electron microscopy (SEM) images indicated that the PANI‐DBSA nanofibers were dispersed uniformly in the matrix. The mechanical properties of the composites were improved at the low PANI‐DBSA load (about 1 wt%), but they were deteriorated at high PANI‐DBSA content. POLYM. COMPOS., 2008. © 2008 Society of Plastics Engineers
Quantitative analysis of the intramacrophagic Brucella suis proteome reveals metabolic adaptation to late stage of cellular infection
Authors: Al Dahouk Sascha , Jubier‐Maurin Véronique , Scholz Holger C. , Tomaso Herbert , Karges Wolfram , Neubauer Heinrich , Köhler Stephan
Published: August 2008

A 2‐D DIGE approach allowed the characterization of the intramacrophagic proteome of the intracellular pathogen Brucella suis at the late stage of in vitro infection by efficient discrimination between bacterial and host cell proteins. Using a subtraction model, a total of 168 proteins showing altered concentrations in comparison with extracellularly grown, stationary‐phase bacteria were identified. The majority of the 44 proteins significantly regulated at this stage of infection were involved in bacterial metabolism and 40% were present in lowered concentrations, supporting the hypothesis of an adaptive response by quantitative reduction of processes participating in energy, protein, and nucleic acid metabolism. In the future, the 2‐D DIGE‐based approach will permit to decipher specifically and quantitatively the intracellular proteomes of various pathogens during adaptation to their specific host cell environments.
Identification of Apolipoprotein AI as a serum biomarker of chronic kidney disease in liver transplant recipients, using proteomic techniques
Authors: O'Riordan Aisling , Johnston Olwyn , McMorrow Tara , Wynne Kieran , Maguire Patricia , Hegarty John E. , McCormick Aidan , Watson Alan J. , Cagney Gerard , Gallagher William M. , Ryan Michael P.
Published: August 2008

Chronic kidney disease (CKD) is a common complication post‐orthotopic liver transplantation (OLT). Development of CKD is detected by monitoring serum urea and creatinine, however disease can occasionally be at an advanced stage before they become abnormal. Therefore, more accurate parameters are required. In order to identify novel biomarkers of CKD, serum was obtained from 47 OLT recipients with CKD (glomerular filtration rate <60 mL/min) and 23 with normal renal function (glomerular filtration rate >90 mL/min). Using the proteomic technique SELDI‐TOF‐MS, three protein biomarkers (55.6 kDa, 9.5 kDa and 11.4 kDa) were identified that, together, could stratify patients into cases or controls with a sensitivity and specificity of 93.6 and 91.3%, respectively. The area under the curve was 0.94. The primary splitter of the groups at 55.6 kDa was an alternative version of a molecule at 27.8 kDa, which was subsequently identified by 1‐D SDS‐PAGE and LC‐ESI‐MS/MS to be Apolipoprotein AI. Protein expression was shown to be reduced in CKD, by both ELISA (p = 0.057) and Western blot analysis (p = 0.003). Apolipoprotein AI is a novel, accurate marker of CKD post‐OLT. It does require further validation in a large, more diverse patient population but could potentially improve detection of CKD.
MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method
Authors: Perdih Andrej , Hodoscek Milan , Solmajer Tom
Published: August 2008

MurD (UDP‐N‐acetylmuramoyl‐L‐alanine:D‐glutamate ligase), a three‐domain bacterial protein, catalyses a highly specific incorporation of D‐glutamate to the cytoplasmic intermediate UDP‐N‐acetyl‐muramoyl‐L‐alanine (UMA) utilizing ATP hydrolysis to ADP and Pi. This reaction is part of a biosynthetic path yielding bacterial peptidoglycan. On the basis of structural studies of MurD complexes, a stepwise catalytic mechanism was proposed that commences with a formation of the acyl‐phosphate intermediate, followed by a nucleophilic attack of D‐glutamate that, through the formation of a tetrahedral reaction intermediate and subsequent phosphate dissociation, affords the final product, UDP‐N‐acetyl‐muramoyl‐L‐alanine‐D‐glutamate (UMAG). A hybrid quantum mechanical/molecular mechanical (QM/MM) molecular modeling approach was utilized, combining the B3LYP QM level of theory with empirical force field simulations to evaluate three possible reaction pathways leading to tetrahedral intermediate formation. Geometries of the starting structures based on crystallographic experimental data and tetrahedral intermediates were carefully examined together with a role of crucial amino acids and water molecules. The replica path method was used to generate the reaction pathways between the starting structures and the corresponding tetrahedral reaction intermediates, offering direct comparisons with a sequential kinetic mechanism and the available structural data for this enzyme. The acquired knowledge represents new and valuable information to assist in the ongoing efforts leading toward novel inhibitors of MurD as potential antibacterial drugs. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Predicting drug resistance of the HIV‐1 protease using molecular interaction energy components
Authors: Hou Tingjun , Zhang Wei , Wang Jian , Wang Wei
Published: August 2008

Drug resistance significantly impairs the efficacy of AIDS therapy. Therefore, precise prediction of resistant viral mutants is particularly useful for developing effective drugs and designing therapeutic regimen. In this study, we applied a structure‐based computational approach to predict mutants of the HIV‐1 protease resistant to the seven FDA approved drugs. We analyzed the energetic pattern of the protease‐drug interaction by calculating the molecular interaction energy components (MIECs) between the drug and the protease residues. Support vector machines (SVMs) were trained on MIECs to classify protease mutants into resistant and nonresistant categories. The high prediction accuracies for the test sets of cross‐validations suggested that the MIECs successfully characterized the interaction interface between drugs and the HIV‐1 protease. We conducted a proof‐of‐concept study on a newly approved drug, darunavir (TMC114), on which no drug resistance data were available in the public domain. Compared with amprenavir, our analysis suggested that darunavir might be more potent to combat drug resistance. To quantitatively estimate binding affinities of drugs and study the contributions of protease residues to causing resistance, linear regression models were trained on MIECs using partial least squares (PLS). The MIEC‐PLS models also achieved satisfactory prediction accuracy. Analysis of the fitting coefficients of MIECs in the regression model revealed the important resistance mutations and shed light into understanding the mechanisms of these mutations to cause resistance. Our study demonstrated the advantages of characterizing the protease‐drug interaction using MIECs. We believe that MIEC‐SVM and MIEC‐PLS can help design new agents or combination of therapeutic regimens to counter HIV‐1 protease resistant strains. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Improving the prediction accuracy of residue solvent accessibility and real‐value backbone torsion angles of proteins by guided‐learning through a two‐layer neural network
Authors: Faraggi Eshel , Xue Bin , Zhou Yaoqi
Published: August 2008

This article attempts to increase the prediction accuracy of residue solvent accessibility and real‐value backbone torsion angles of proteins through improved learning. Most methods developed for improving the backpropagation algorithm of artificial neural networks are limited to small neural networks. Here, we introduce a guided‐learning method suitable for networks of any size. The method employs a part of the weights for guiding and the other part for training and optimization. We demonstrate this technique by predicting residue solvent accessibility and real‐value backbone torsion angles of proteins. In this application, the guiding factor is designed to satisfy the intuitive condition that for most residues, the contribution of a residue to the structural properties of another residue is smaller for greater separation in the protein‐sequence distance between the two residues. We show that the guided‐learning method makes a 2–4% reduction in 10‐fold cross‐validated mean absolute errors (MAE) for predicting residue solvent accessibility and backbone torsion angles, regardless of the size of database, the number of hidden layers and the size of input windows. This together with introduction of two‐layer neural network with a bipolar activation function leads to a new method that has a MAE of 0.11 for residue solvent accessibility, 36° for ψ, and 22° for ϕ. The method is available as a Real‐SPINE 3.0 server inhttp://sparks.informatics.iupui.edu. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Conductive nanodots on the surface of irradiated CaF2
Authors: Roll Tino , Meier Marion , Akcöltekin Sevilay , Klusmann Miriam , Lebius Henning , Schleberger Marika
Published: August 2008

CaF2(111) single crystal surfaces have been irradiated with fast heavy ions under oblique angles resulting in chains of nanosized hillocks. In order to characterize these nanodots with respect to their conductivity we have applied non‐contact atomic force microscopy using a magnetic tip. Measurements in ultra high vacuum as well as under ambient conditions reveal a clearly enhanced electromagnetic interaction between the magnetic tip and the nanodots. The dissipated energy per cycle is comparable to the value found for metals, indicating that the interaction of the ion with the target material leads to the creation of metallic Ca nanodots on the surface. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Phishwish: a simple and stateless phishing filter
Authors: Cook Debra L. , Gurbani Vijay K. , Daniluk Michael
Published: August 2008

We definephishingas the practice of directing unsuspecting users to fraudulent websites with the intent of obtaining personal information to be used for illicit purpose by a spammer. We introduce a new anti‐phishing filter, phishwish, that has a number of advantages over existing phishing filters: it does not need to be trained, as is the case with Bayesian filters, nor does it consult centralized white or blacklists to determine whether an email is suspect. Phishwish uses a set of only 11 rules to determine the veracity of an incoming email; the results can be used to quarantine the email or to alert the user. We compare the performance of phishwish to SpamAssassin, a popular open source filter, as well as the Google phishing filters accessed from the Firefox browser. Our results indicate that phishwish outperforms existing filters in identifying phishing emails, even identifying those originated by the ‘rock phish’ gang, and that it aids in detection of zero‐day attacks that were not caught by existing filters. Copyright © 2008 John Wiley & Sons, Ltd.
Steam Purification for the Removal of Graphitic Shells Coating Catalytic Particles and the Shortening of Single‐Walled Carbon Nanotubes
Authors: Ballesteros Belén , Tobias Gerard , Shao Lidong , Pellicer Eva , Nogués Josep , Mendoza Ernest , Green Malcolm L.H.
Published: August 2008

Purification and shortening of single‐walled carbon nanotubes (SWNTs) is carried out by treatment with steam. During the steam purification the graphitic shells coating the catalytic metal particles are removed. Consequently, the exposed catalytic particles can be easily dissolved by treatment with hydrochloric acid. No damage to the carbon nanotube tubular structure is observed, even after prolonged treatment with steam. Samples are characterized by HRTEM, TGA, magnetic measurements, Raman spectroscopy, AFM, and XPS.
Student Opportunity: Short-Term Exposure to International Agriculture
Authors: Phillips Ronald L. , Magor Noel P. , Shires David , Leung Hei , McCouch Susan R. , Macintosh Duncan
Published: August 2008

Opportunities abound to apply crop science to solving many of the world’s food problems. International agricultural research centers (IARCs) provide a window through which students can see the need for improved agricultural productivity and briefly experience the rewards of working on difficult but important issues. In today’s world of highly technical graduate education, students find it difficult to obtain exposure to international agriculture due to the extreme constraints on their time. Programs for students that provide a short-term exposure to IARC strategies can have long-term benefits for the student as well as the international center. A short-term student exchange program between a US university and the International Rice Research Institute (IRRI) and a special course on rice (research to production) offered at IRRI provide students with unique insights for averting food riots in the future. Details of these educational efforts are described in this paper.
Florigen and the Photoperiodic Control of Flowering in Rice
Authors: Tsuji Hiroyuki , Tamaki Shojiro , Komiya Reina , Shimamoto Ko
Published: August 2008

Flowering time is a key trait for geographical and seasonal adaptation of plants and is an important consideration for rice breeders. Recently identified genetic factors provide new insights into this complex trait. The list of genes involved in flowering and their functions tells us that the molecular basis of day-length measurement includes both of the evolution of unique factors and the regulatory adaptation of conserved factors in rice. This information helped identify rice florigen, a mobile flowering signal. Our current view of flowering time regulation incorporates the presence of complex layers of gene networks integrated with the synthesis of florigen protein and its subsequent transport and perception.
THE DISCRETE COAGULATION EQUATIONS WITH MULTIPLE FRAGMENTATION
Authors: Laurençot Philippe
Published: August 2008

We present an alternative proof of the existence of density-conserving solutions to the discrete coagulation–fragmentation equations when the coagulation rates grow at most linearly. The proof relies on the study of the propagation of some moments of the solutions to approximating equations and simplifies the previous argument of Ball and Carr which involves rather delicate estimates. The case of multiple fragmentation is also considered, and the question of uniqueness as well.

AMS 2000 Mathematics subject classification: Primary 34A34; 82C22
CONFORMAL $\mathcal{s}$$\mathcal{l}$2 ENVELOPING ALGEBRAS AS AMBISKEW POLYNOMIAL RINGS
Authors: O’Neill Martin
Published: August 2008

We study a three parameter deformation $\mathcal{U}_{abc}$ of $\mathcal{U}(\mathfrak{sl}_2)$ introduced by Le Bruyn in 1995. Working over an arbitrary algebraically closed field of characteristic zero, we determine the centres, the finite-dimensional irreducible representations, and, when the parameter $a$ is not a non-trivial root of unity, the prime ideals of those $\mathcal{U}_{abc}$, with $ac\neq0$, which are conformal as ambiskew polynomial rings.

AMS 2000 Mathematics subject classification: Primary 16W35; 17B37. Secondary 16S36; 16S80
NORMAL SEMIGROUPS OF ENDOMORPHISMS OF PROPER INDEPENDENCE ALGEBRAS ARE IDEMPOTENT GENERATED
Authors: Araújo João
Published: August 2008

Let $\mathcal{A}$ be a proper independence algebra of finite rank, let $G$ be the group of automorphisms of $\mathcal{A}$, let $a$ be a singular endomorphism and let $a^G$ be the semigroup generated by all the elements $g^{-1}ag$, where $g\in G$. The aim of this paper is to prove that $a^G$ is a semigroup generated by its own idempotents.

AMS 2000 Mathematics subject classification: Primary 20M20; 20M10; 08A35
Coagulase-negative staphylococci isolated from bovine extramammary sites and intramammary infections in a single dairy herd
Authors: Taponen Suvi , Björkroth Johanna , Pyörälä Satu
Published: August 2008

Isolates of various species of coagulase-negative staphylococci (CNS) from extramammary swab samples were compared with isolates of bovine mastitis CNS species. Swab samples were taken from perineum skin and udder skin, teat apices and teat canals of lactating dairy cows of the research dairy herd of the University of Helsinki in 1999 and 2002. In addition, hands of herd staff and liners of teat cups were sampled for CNS. CNS isolates from milk samples of subclinical or clinical mastitis in the same herd were collected during 1998–2002. Species identification was performed using phenotyping (API Staph ID 32 test) and by constructing a 16 and 23S rRNA RFLP library (ribotyping). Based on phenotype, 84% of mastitis isolates and 57% of extramammary isolates were identified at species level with >90% probability. Ribotype patterns formed 24 clusters, and 15 of them included a CNS type strain. If the ribotype clusters contained isolates of both extramammary and mastitis origin, they were further typed using pulsed-field gel electrophoresis (PFGE). The predominant CNS species in mastitis, based both on phenotyping and genotyping, wereStaph. chromogenesandStaph. simulans. Phenotyping failed to identify half of the extramammary isolates. Based on phenotyping,Staph. equorumandStaph. sciuri, and based on ribotyping,Staph. succinusandStaph. xylosus, were the predominant CNS species in extramammary samples. The most common species in milk samples,Staph. chromogenes, was also isolated from several extramammary samples, and five out of ten pulsotypes were shared between mastitis and extramammary isolates, indicating that strains from udder skin are highly similar. The second commonest mastitis species,Staph. simulans, was isolated only from three extramammary samples, indicating thatStaph. simulansmay be more specifically associated with mastitis. Consequently, the origin of CNS mastitis may vary depending on the causing CNS species.
Differential expression of ABC transporters and their regulatory genes during lactation and dry period in bovine mammary tissue
Authors: Farke Carolin , Meyer Heinrich H D , Bruckmaier Rupert M , Albrecht Christiane
Published: August 2008

ATP-binding cassette (ABC) transporters play a pivotal role in human physiology, and mutations in these genes often result in severe hereditary diseases. ABC transporters are expressed in the bovine mammary gland but their physiological role in this organ remains elusive. Based on findings in the context of human disorders we speculated that candidate ABC transporters are implicated in lipid and cholesterol transport in the mammary gland. Therefore we investigated the expression pattern of selected genes that are associated with sterol transport in lactating and nonlactating mammary glands of dairy cows. mRNA levels from mammary gland biopsies taken during lactation and in the first and second week of the dry period were analysed using quantitative PCR. Five ABC transporter genes, namely ABCA1, ABCA7, ABCG1, ABCG2 and ABCG5, their regulating genes LXRα, PPARγ, SREBP1 and the milk proteins lactoferrin and α-lactalbumin were assessed. A significantly enhanced expression in the dry period was observed for ABCA1 while a significant decrease of expression in this period was detected for ABCA7, ABCG2, SREBP1 and α-lactalbumin. ABCG1, ABCG5, LXRα, PPARγ and lactoferrin expression was not altered between lactation and dry period. These results indicate that candidate ABC transporters involved in lipid and cholesterol transport show differential mRNA expression between lactation and the dry period. This may be due to physiological changes in the mammary gland such as immigration of macrophages or the accumulation of fat due to the loss of liquid in the involuting mammary gland. The current mRNA expression analysis of transporters in the mammary gland is the prerequisite for elucidating novel molecular mechanisms underlying cholesterol and lipid transfer into milk.
Performance of lactating dairy cows fed varying levels of total mixed ration and pasture
Authors: Vibart Ronaldo E , Fellner Vivek , Burns Joseph C , Huntington Gerald B , Green James T
Published: August 2008

Two, 8-week experiments, each using 30 lactating Holstein cows, were conducted to examine performance of animals offered combinations of total mixed ration (TMR) and high-quality pasture. Experiment 1 was initiated in mid October 2004 and Experiment 2 was initiated in late March 2005. Cows were assigned to either a 100% TMR diet (100:00, no access to pasture) or one of the following three formulated partial mixed rations (PMR) targeted at (1) 85% TMR and 15% pasture, (2) 70% TMR and 30% pasture and (3) 55% TMR and 45% pasture. Based on actual TMR and pasture intake, the dietary TMR and pasture proportions of the three PMR in Experiment 1 were 79% TMR and 21% pasture (79:21), 68% TMR and 32% pasture (68:32), and 59% TMR and 41% pasture (59:41), respectively. Corresponding proportions in Experiment 2 were 89% TMR and 11% pasture (89:11), 79% TMR and 21% pasture (79:21) and 65% TMR and 35% pasture (65:35), respectively. Reducing the proportion of TMR in the diets increased pasture consumption of cows on all PMR, but reduced total dry matter intake compared with cows on 100:00. An increase in forage from pasture increased the concentration of conjugated linoleic acids and decreased the concentration of saturated fatty acids in milk. Although milk and milk protein yields from cows grazing spring pastures (Experiment 2) increased with increasing intakes of TMR, a partial mixed ration that was composed of 41% pasture grazed in the fall (Experiment 1) resulted in a similar overall lactation performance with increased feed efficiency compared to an all-TMR ration.
T lymphocyte proliferative capacity and CD4+/CD8+ratio in primiparous and pluriparous lactating cows
Authors: Mehrzad Jalil , Zhao Xin
Published: August 2008

T cells play a central role in specific immunity; their populations and phenotypes could be affected by number of lactation in high-yielding dairy cows. To investigate the effects of parity on the dynamics of T lymphocytes, lymphoproliferative capacity, T lymphocyte subsets and CD4+/CD8+ratio were studied in peripheral blood of primiparous and pluriparous dairy cows during mid–late lactation. A non-radioactive technique was also adapted for a detailed lymphoproliferation assay. Compared with the primiparous cows, the pluriparous cows exhibited weaker lymphoproliferative activity, larger number of CD4+cells and substantially greater CD4+/CD8+ratio in their blood circulation. The increase of the CD4+/CD8+ratio in the blood of pluriparous dairy cows was mainly due to the rise in the proportion of CD4+cells and decline in the proportion of CD8+cells. This increase of the CD4+/CD8+ratio coincided with the decrease of mitogen-induced proliferation capacity of T lymphocytes. Of four lymphocyte divisions or generations during the lymphoproliferation assay, maximal lymphocyte proliferation capacity at generation 3 in primiparous cows was markedly greater than in pluriparous cows. With an alternatively safer, faster and more reproducible assay (compared with3H-thymidine scintillation assay) we showed for the first time that aging in dairy cows leads to a decreased mitogen-induced lymphoproliferation and disturbed proportion between CD4+and CD8+T cells. This CD4+-CD8+imbalance together with diminished lymphoproliferative capacity may lead to a weaker T cytotoxic-mediated immunity and increased susceptibility to infectious diseases in pluriparous lactating cows. Our study also emphasizes further application of the methods in farm animals.
Molecular typing ofStaphylococcus aureusisolated from Italian dairy products on the basis of coagulase gene polymorphism, multiple-locus variable-number tandem-repeat and toxin genes
Authors: Stefano Morandi , Milena Brasca , Roberta Lodi , Lorenzo Brusetti
Published: August 2008

Coagulase gene restriction fragment length polymorphism (RFLP), six-locus variable-number tandem-repeat analysis patterns (MLVA) and detection of enterotoxin genes (se) (sea,sec,sed,seg,seh,sei,sejandsel) were used to determine the phylogenetic relationship among isolates ofStaphylococcus aureusisolated from dairy products from different regions of Italy. A total of 25Staph. aureuswere subtyped into 16 coagulase genotypes by RFLP, and MLVA revealed marked genomic variability. Furthermore, 17 of the isolates harboured at least one toxin gene, with the predominance ofsea,sedandsejamong cow isolates andsec-selamong the goat and sheep strains. Combined RFLP, MLVA polymorphism andsegenes were found to be useful techniques for discriminating several genetic variants inStaph. aureusisolates.
Democracy and distribution in highly unequal economies: the case of South Africa
Authors: Nattrass Nicoli , Seekings Jeremy
Published: August 2008

Given that incomes in South Africa are distributed very unequally, it might be expected that the establishment of representative democracy would result in the adoption of redistributive policies. Yet overall inequality has not declined since 1994. The electoral and party system provides uneven pressure for redistribution. The fact that poor South Africans have the vote ensures that some areas of public policy do help the poor. The post-apartheid government not only inherited a surprisingly redistributive set of social policies (welfare, education and health care), but has made changes that entail even more redistribution. But these policies do little to help a core section of the poor in South Africa: the unemployed, and especially households in which no one is working. Other public policies serve to disadvantage this marginalised constituency: labour market and other economic policies serve to steer the economy down a growth path that shuts out many of the unskilled and unemployed. The workings of these policies remain opaque, making it unlikely that poor citizens will use their vote to effect necessary policy reforms.
Evaluating the Truth and Reconciliation Commission
Authors: Stanley Elizabeth
Published: August 2008

Following a negotiated transition to democracy in South Africa, the Truth and Reconciliation Commission (TRC) was established to deal with crimes of the past regime. Despite the detail of submissions and the length of the Final Report, this article highlights the partiality of truth recognised by the Commission. The usefulness of acknowledged truth to deal with South Africa's past is shown to have been neutralised by wider concerns of social and criminal justice. In detailing the governmental reticence to provide reparations, the judicial disregard to pursue prosecutions, and the dismissal of responsibility for apartheid at a wider social level, the author argues that opportunities for reconciliation and developmental change are limited. Against the problems of crime, violence and unresolved land issues, the potential of the TRC to build a ‘reconciliatory bridge’ is called into question. The truth offered by the Commission increasingly appears of limited value.
Voting, violence and violations: peasant voices on the flawed elections in Hadiya, Southern Ethiopia
Authors: Tronvoll Kjetil
Published: August 2008

This article presents peasant grievances on the flawed 2000 elections in Hadiya zone, southern Ethiopia. For the first time in Ethiopia's electoral history, an opposition party managed to win the majority of the votes in one administrative zone. In the run-up to the elections, government cadres and officials intimidated and harassed candidates and members from the opposition Hadiya National Democratic Organisation (HNDO). Several candidates and members were arrested and political campaigning was restricted. On election day, widespread attempts at rigging the election took place, and violence was exerted in several places by government cadres and the police. Despite the government's attempt to curtail and control the elections in Hadiya, the opposition party mobilised the people in a popular protest to challenge the government party's political hegemony – and won. If this is an indication of a permanent shift of power relations in Hadiya, it is however, too early to say.