bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling change: new opportunities in the analysis of microgenetic data
Authors: Cheshire Andrea , Muldoon Kevin P. , Francis Brian , Lewis Charlie N. , Ball Linden J.
Published: February 2007

Despite the increasing use of the microgenetic methodology to examine change, the techniques employed to analyse microgenetic data remain fairly unsophisticated. This paper reviews the existing ways of analysing such data and describes their limitations. We use two recent studies to illustrate how modelling can avoid these problems and reveal important aspects of children's cognitive development. The first example illustrates the use of quasi‐binomial modelling to examine 6‐ and 7‐year olds' analogical reasoning development. This method offered insights into the way in which children develop, in terms of the rate and path of change, and how different instructional cues can affect their performance. The second study employs a random effects logistic model to analyse the development of preschoolers' counting skills. This technique was employed to examine different influences on children's use of counting to compare quantities. We argue that the key benefit of such modelling approaches is that they are able to tap into the process of change whilst not compromising statistical assumptions. Copyright © 2007 John Wiley & Sons, Ltd.
TAP expression reduces IL‐10 expressing tumor infiltrating lymphocytes and restores immunosurveillance against melanoma
Authors: Zhang Qian‐Jin , Seipp Robyn P. , Chen Susan S. , Vitalis Timothy Z. , Li Xiao‐Lin , Choi Kyung‐Bok , Jeffries Andrew , Jefferies Wilfred A.
Published: February 2007

Many immune therapeutic strategies are under development for melanoma to treat metastatic disease and prevent disease reoccurrence. However, human melanoma cells are often deficient in antigen processing and this appears to play a role in their expansion and escape from immunosurveillance. For example, expression of the transporters associated with antigen processing (TAP1 and TAP2) is down‐regulated in the mouse melanoma cell line B16F10. This results in a lack of tumor‐associated antigen processing, low surface expression of MHC Class I molecules and low immunogenicity. We observe that restoration of TAP1 expression by transfection resurrects the processing and presentation of viral antigens, and the melanoma‐associated antigen, TRP‐2. Immunization with irradiated B16F10/rTAP1 transfected cells generates CTLs that are capable of killing B16F10/rTAP1 transfected targets and B16F10 targets deficient in TAP1. Furthermore, B16F10/rTAP1 transfectants grow at a significantly slower rate in mice than B16F10 cells. In an experimental model that closely recapitulates the clinical situation, treatment of B16F10 tumors in mice with a vaccinia virus vector expressing TAP1 also significantly decreases tumor growth in vivo. Furthermore, tumors treated with vaccinia TAP1 had significantly reduced numbers of immunosuppressive, CD3+/IL‐10 positive, tumor infiltrating lymphocytes. Therefore, TAP1 expression restores both antigen presentation and immunogenicity in B16F10 melanoma cells and concomitantly reduces immunosuppressive IL‐10 production at the local tumor site, thereby increasing immunosurveillance mechanisms against tumors. © 2007 Wiley‐Liss, Inc.
Biliary tract cancer and stones in relation to chronic liver conditions: A population‐based study in Shanghai, China
Authors: Hsing Ann W. , Gao Yu‐Tang , McGlynn Katherine A. , Niwa Shelley , Zhang Mingdong , Han Tian‐Quan , Wang Bing‐Sheng , Chen Jinbo , Sakoda Lori C. , Shen Ming‐Chang , Zhang Bai‐He , Deng Jie , Rashid Asif
Published: February 2007

Biliary tract cancers are relatively rare but fatal tumors. Apart from a close link with gallstones and cholangitis, risk factors for biliary tract cancer are obscure. Chronic liver conditions, including liver cirrhosis, have been linked to a higher risk of biliary tract cancer. In a population‐based case‐control study conducted in Shanghai, China, we investigated the relationships of a history of chronic hepatitis and liver cirrhosis as well as a family history of liver cancer with biliary tract cancer risk. The study included 627 patients with biliary tract cancers (368 gallbladder, 191 bile duct and 68 ampulla of Vater), 1,037 patients with biliary stones (774 gallbladder stones and 263 bile duct stones) and 959 healthy subjects randomly selected from the population. Bile duct cancer was associated with self‐reports of chronic liver conditions, including a history of chronic hepatitis (OR = 2.0, 95% CI 0.9–4.4), liver cirrhosis (OR = 4.7, 95% CI 1.9–11.7) and a family history of primary liver cancer (OR = 2.0, 95% CI 1.0–3.9). The excess risk persisted after adjustment for gallstones and were more pronounced among subjects without gallstones (OR = 5.0, 95% CI 1.3–20.0 and OR = 4.9, 95% 2.0–12.2, respectively). History of liver conditions was also associated with an excess of biliary stones (OR = 1.9, 95% CI 1.2–3.0). No association was found for cancers of the gallbladder and ampulla of Vater. A history of chronic hepatitis and cirrhosis may be risk factors for extraheptic bile duct cancer. Given that chronic infection with hepatitis B virus (HBV) is the most common cause of liver disease in China, serologic markers of HBV need to be measured in future studies to examine the link between HBV and bile duct cancer. © 2007 Wiley‐Liss, Inc.
Fluorescence spectroscopy of an in vitro model of human cervical precancer identifies neoplastic phenotype
Authors: Martin Sarah F. , Wood Andrew D. , McRobbie Michelle M. , Mazilu M. , McDonald Michael P. , Samuel Ifor D.W. , Herrington C. Simon
Published: February 2007

The clinical diagnosis of cervical neoplasia by spectroscopic methods is potentially a reliable, fast and cost‐effective alternative to the conventional smear test. However, it is currently limited by significant inter‐patient variation in the spectroscopic properties of the cervix. Characterisation of suitable in vitro models of the spectroscopic changes that take place during neoplastic progression may prove to be a significant step towards the successful development of reliable in vivo systems. In this study, we used organotypic epithelial raft culture as an in vitro model of cervical tissue to analyse changes in the fluorescence properties of surface squamous epithelium that are associated with the development of neoplastic disease. Collagen plugs lined by primary human keratinocytes (PHKs) were used to model the normal cervical epithelium, and plugs lined by cells of the SiHa line were used as a model of neoplastic cervical tissue. Fluorescence emission spectra of these rafts were recorded at excitation wavelengths in the 250–330 nm range, complementing previous work published at longer wavelengths. Normalised, truncated emission spectra were analysed using multivariate principal component analysis. We successfully distinguished between in vitro models of normal and neoplastic cervical tissue and demonstrated a differential effect of acetic acid, which enhances the discrimination of normal from neoplastic tissue. Identification of these differences between in vitro organotypic epithelial rafts may ultimately aid the discrimination of cervical lesions in vivo. © 2007 Wiley‐Liss, Inc.
Reproductive and hormonal factors and risk of lung cancer in women: A prospective cohort study
Authors: Kabat Geoffrey C. , Miller Anthony B. , Rohan Thomas E.
Published: February 2007

Several lines of evidence suggest that endocrine factors may play a role in the development of lung cancer, but the evidence is limited and inconsistent. We investigated the association of reproductive and hormonal factors with risk of lung cancer in the National Breast Screening Study, which included 89,835 Canadian women aged 40–59 years at recruitment between 1980 and 1985. Linkages to national cancer and mortality databases provided data on cancer incidence and deaths from all causes, respectively, with follow‐up ending between 1998 and 2000. Cox proportional hazards models were used to estimate hazard ratios (HR) and 95% confidence intervals (95% CI) for the association between hormonal factors and lung cancer. During a mean of 16.4 years of follow‐up, we observed 750 incident lung cancer cases. After adjustment for covariates, parous women were not at increased risk of lung cancer (HR = 1.18, 95% CI 0.94–1.47) relative to nulliparous women; however, there was a modest increase in risk with increasing parity, reaching a HR of 1.42, 95% CI 1.06–1.88 in women who had 5 or more live births (p for trend 0.02). Among parous women, age at first live birth was inversely associated with risk. Women who had their first live birth at age 30 or older were at reduced risk relative to women who had their first live birth below age 23 (HR 0.68, 95% CI 0.50–0.93, p for trend 0.004). These associations did not differ by age at enrollment (40–49 vs. 50–59 years old), but were somewhat strengthened when attention was restricted to never smokers. Ever use of exogenous hormones showed little association with lung cancer risk; however, long‐term users of hormone replacement therapy were at slightly increased risk. Our results add to the limited existing evidence that certain reproductive and hormonal factors may be associated with lung cancer risk in women. © 2007 Wiley‐Liss, Inc.
Second primary malignancies in females with primary fallopian tube cancer
Authors: Riska Annika , Pukkala Eero , Scélo Ghislaine , Mellemkjaer Lene , Hemminki Kari , Weiderpass Elisabete , McBride Mary L. , Pompe‐Kirn Vera , Tracey Elizabeth , Brewster David H. , Kliewer Erich V. , Tonita Jon M. , Kee‐Seng Chia , Jonasson Jon G. , Martos Carmen , Boffetta Paolo , Brennan Paul
Published: February 2007

Primary fallopian tube cancer (PFTC) is a rare disease, and its aetiological factors are poorly understood. Studies on PFTC in the setting of 2nd primary malignant neoplasms can provide clues on aetiology and also define the possible side effects of different treatment modalities for PFTC. A cohort of 2,084 cases with first PFTC was extracted from the data from 13 cancer registries from Europe, Canada, Australia and Singapore and followed for second primary cancers within the period 1943–2000. Standardized incidence ratios (SIRs) were calculated and Poisson regression analyses were done to find out the RRs related to age at, period of and time since the PFTC diagnosis. There were 118 cancer cases observed after first PFTC (SIR 1.4, 95%CI 1.1–1.6). Elevated SIRs were seen for colorectal cancer (1.7, 95%CI 1.0–2.6), for breast cancer (1.5, 95%CI 1.1–2.2), for bladder cancer (2.8, 95%CI 1.0–6.0), for lung cancer (1.8, 95% CI 0.9–3.2) and for nonlymphoid leukaemia (3.7, 95%CI 1.0–9.4). Significant risk increases were detected for colorectal cancer during the 2nd to 5th year after the first PFTC diagnosis, for breast cancer in follow‐up 10+ and for nonlymphoid leukaemia during the 2nd to 10th year. The clustering of cancers of the lung and bladder in PFTC patients may suggest shared smoking aetiology. The excess of colorectal and breast cancers after PFTC may indicate a genetic aetiology. © 2007 Wiley‐Liss, Inc.
Airborne exposures and risk of gastric cancer: A prospective cohort study
Authors: Sjödahl Krister , Jansson Catarina , Bergdahl Ingvar A. , Adami Johanna , Boffetta Paolo , Lagergren Jesper
Published: February 2007

There is an unexplained male predominance among patients with gastric cancer, and many carcinogens are found in male‐dominated dusty occupations. However, the relation between occupational exposures and risk of gastric cancer remains unclear. To investigate whether airborne occupational exposures might influence the risk of noncardia gastric cancer, we used a large, prospective cohort study of male Swedish construction workers. These workers were, during the period 1971–1993, regularly invited to health examinations by a nationwide occupational health service organization. Data on job titles and other variables were collected through self‐administered questionnaires and forms completed by the health organization's staff. Industrial hygienists assessed 12 specific airborne occupational exposures for 200 job titles. Gastric cancer, death or emigration occurring during follow‐up in 1971–2002 were identified by linkage to the Swedish registers of Cancer, Causes of Death and Total Population, respectively. Incidence rate ratios (IRR) and 95% confidence intervals (CI), adjusted for attained age, tobacco smoking, calendar period and body mass, were derived from Cox regression. Among 256,357 cohort members, contributing 5,378,012 person‐years at risk, 948 noncardia gastric cancers were identified. Increased risk of this tumor was found among workers exposed to cement dust (IRR 1.5 [95% CI 1.1–2.1]), quartz dust (IRR 1.3 [95% CI 1.0–1.7]) and diesel exhaust (IRR 1.4 [95% CI 1.1–1.9]). Dose‐response relations were observed for these exposures. No consistent positive associations were found regarding exposure to asbestos, asphalt fumes, concrete dust, epoxy resins, isocyanates, metal fumes, mineral fibers, organic solvents or wood dust. In conclusion, this study provides some support to the hypothesis that specific airborne exposures increase the risk of noncardia gastric cancer. © 2007 Wiley‐Liss, Inc.
MIDGE/hNIS vaccination generates antigen‐associated CD8+IFN‐γ+ T cells and enhances protective antitumor immunity
Authors: Choi Yun , Jeon Yong‐Hyun , Kang Joo‐Hyun , Chung June‐Key , Schmidt Manuel , Kim and Chul‐Woo
Published: February 2007

Human sodium iodide symporter (hNIS) is a transmembrane protein that actively transports iodide ions into thyroid cells. hNIS is over‐expressed in some cases of the thyroid cancers compared with the surrounding normal tissues and has been considered to be an attractive target for immunotherapy. The aim of this study is to determine the feasibility of utilizing the hNIS antigenic protein in enhanced‐antigen‐associated immunotherapy using image analysis with a gamma counter. To accomplish this, minimalistic immunogenically defined gene expression (MIDGE), either plain or coupled to a nuclear localization signal (NLS) peptide, was used as a vector system. Vaccination with MIDGE/hNIS, MIDGE/hNIS‐NLS and pcDNA3.1/hNIS produced a significant increase in the number of hNIS‐associated IFN‐γ‐secreting CD8+ T cells, with MIDGE/hNIS having the strongest effect. In addition, immunization with the hNIS encoding vectors induced antigen‐mediated antitumor activity against NIS‐expressing CT26 tumors in vivo, with the highest tumor free rate (100%) and lowest tumor growth being observed up to 40 days after the CT26/NIS tumor challenge with MIDGE/hNIS than those resulting from other immunization groups. Tumor progression could be followed noninvasively and repetitively by monitoring levels of hNIS gene expression in the tumors using scintigraphic image analysis. Overall, hNIS has a potential use as an antigen for immunization approaches, and vaccination with MIDGE/hNIS vectors is an effective means of generating hNIS‐associated immune responses in mice. © 2007 Wiley‐Liss, Inc.
Submicron poly(L‐lactic acid) pillars affect fibroblast adhesion and proliferation
Authors: Milner Keith R. , Siedlecki Christopher A.
Published: February 2007

Controlling cell adhesion and proliferation on synthetic polymers is key to tissue engineering scaffold development. It is accepted that surface topography influences cell response but the mechanisms behind this remain unclear. In this work, cell response is assessed to topographies larger than focal complexes (FXs) but smaller than focal adhesions (FAs). Poly(L‐lactic acid) was patterned with 400‐ and 700‐nm pillars via replication molding. Human fibroblast adhesion and proliferation were assessed. The development of focal contacts and actin microfilaments were evaluated via immunofluorescence. Cell interactions with surface topography were observed via scanning electron microscopy. Initial fibroblast adhesion (<1 day) increased with texture as 400 nm > 700 nm > smooth, but proliferation (>1 day) decreased with texture. Increased FX formation was observed on textured surfaces. However, FAs were narrower on textured surfaces compared with smooth materials and confined to interpillar regions. SEM showed that fibroblasts deformed the 400‐nm pillars. It is hypothesized that surface texture mediated FX formation and increased cell adhesion, possibly via increased material surface area. Texture geometry limited maturation of FXs to FAs, decreasing proliferation. We conclude that surface texture can alter cell adhesion and proliferation and propose geometric constraint as a mechanism for this process. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
In vivo experiments with tracheostoma tissue connector prototypes
Authors: Olivier ten Hallers E. J. , Van der Houwen Eduard B. , Marres Henri A. M. , Rakhorst Gerhard , Jansen John A. , Schutte Harm K. , Van Kooten Theo G. , Van Loon Jan‐Paul , Verkerke Gijsbertus J.
Published: February 2007

In cancer patients who have undergone total surgical removal of the larynx, ideally voice rehabilitation should be performed using a shunt valve (placed in a fistula of the tracheo–esophageal wall) and a tracheostoma valve (TSV) to enable hands‐free tracheo–esophageal speech. A tracheostoma is created by suturing the trachea into the lower anterior part of the neck, and a TSV is a device that can be placed at the stoma. Unfortunately, many patients are unable to use a TSV, mainly due to fixation difficulties. To improve the fixation of the TSV, tracheostoma tissue connector (TS‐TC) prototypes have been designed. Prototype 1 consisted of a titanium ring, inner diameter 30 mm, with a circular polypropylene mesh glued to it with silicone adhesive. Four holes had been drilled into the ring for the insertion of sub‐ and percutaneous screws. Prototype 2 consisted of a silicone rubber ring, inner diameter 30 mm, combined with polypropylene mesh and four titanium inserts that functioned as a base plate for the insertion of sub‐ and percutaneous screws. In adult female goats a tracheostoma was created and the prototypes were implanted. After 6 weeks of subcutaneous implantation, percutaneous screws were inserted. After twelve weeks, the experiment was terminated and the implants with the surrounding tissues were processed and examined histologically. The clinical appearance during weeks 7–12 varied from very poor to relatively good. Histologically, the implants showed a uniform inflammatory response. We found that all the tissue surrounding the screws showed signs of epithelial down growth. It was concluded that the two‐stage implantation procedure of our prototype TS‐TCs in this animal model was unsuccessful. Additional research efforts are necessary to improve tissue immobilization and to devise reliable fixation systems for TSVs. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
Alginate/polyethylene glycol blend fibers and their properties for drug controlled release
Authors: Wang Qun , Zhang Na , Hu Xianwen , Yang Jianhong , Du Yumin
Published: February 2007

Fibers of alginate and polyethylene glycol (PEG), with salicylic acid (SA) as model drug incorporated in different concentrations, were obtained by spinning their solution through a viscose‐type spinneret into a coagulating bath containing aqueous CaCl2 and ethanol. Chemical, morphological, and mechanical properties characterization were carried out, as well as the studies of the factors that influence the drug releasing from alginate/PEG fibers. These factors included the component ratio of alginate and PEG, the loaded amount of SA, the pH, and the ionic strength of the release solution and others. The best values of the tensile strength at 13.41 cN/tex and breaking elongation at 23.13% of blend fibers were obtained when the PEG content was 5 wt %; the water swelling ratio (WSR) of blend fibers increased as the composition of PEG was raised. The results of controlled release tests showed that the amount of SA released increased with an increase in the proportion of PEG present in the fiber. Moreover, the release rate of drug decreased as the amount of drug loaded in the fiber increased, but the cumulative release amount is increasing. The alginate/PEG fibers were also sensitive to pH and ionic strength. For pH 7.4 the drug release was faster compared to pH 1.0, being simultaneously accelerated by a higher ionic strength. All the results indicated that the alginate/PEG fiber was potentially useful in drug delivery systems. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
Branched chitosans: Effects of branching parameters on rheological and mechanical properties
Authors: Aggarwal Dinesh , Matthew Howard W.T.
Published: February 2007

Chitosan continues to be studied as a promising biomaterial for tissue repair and regeneration applications. However, chitosan structures show a large reduction in tensile strength in the wet state. Methods for improving the wet strength of chitosan materials may broaden its applicability as a tissue scaffold for applications requiring significant load bearing capacity. In this study, the role of molecular architecture in defining the mechanical properties of hydrated chitosan membranes was examined. Specifically, branched chitosan molecules were synthesized with a range of branch lengths and branch densities. Physical and mechanical properties were characterized using viscometry, FTIR spectroscopy, and tensile testing measurements, and the results were correlated with the postulated architecture of the linear and branched chitosan materials. Both branch density and branch length were found to influence the mechanical properties of chitosan membranes. For example, high‐molecular‐weight (600 kDa) chitosans grafted with 80 kDa branches exhibited up to twofold increases in both tensile strength and extensibility. FTIR results indicated that these increases correlated with enhanced levels of hydrogen bonding in the branched materials. Vascular smooth muscle cells cultured on cast membranes of the branched chitosans exhibited no differences in adhesion or spreading as compared to the linear polymer. The results indicate that the mechanical properties of chitosan materials can be improved by the induction of a branched molecular architecture. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
Nanostructural characteristics, mechanical properties, and osteoblast response of spark plasma sintered hydroxyapatite
Authors: Li H. , Khor K.A. , Chow V. , Cheang P.
Published: February 2007

This study aimed to fabricate bulk nanostructured hydroxyapatite (HA) pellets with improved properties using spark plasma sintering (SPS) for orthopedic applications. Spray‐dried nanostructured HA (nSD‐HA) powders were consolidated using the rapid SPS processing. The SPS processed nSD‐HA was characterized using Raman spectroscopy and field emission scanning electron microscopy (FESEM). Mechanical properties of the consolidates were also evaluated through indentation approach. The nanostructures (∼80 nm in grain size) of the starting powders were successfully retained after the SPS processing operated at 950°C with <15 min holding time. The SPS consolidated nSD‐HA showed promising mechanical properties, ∼118 GPa for Young's modulus, and up to 2.22 MPa m0.5 for fracture toughness. SPS holding time showed minor influence on the phases of the pellets. Furthermore, the spheroidized nanostructured HA retained the HA structure after the SPS consolidation. Preliminary cytotoxicity and cell attachment studies were also carried out using a human osteoblast cell line hFOB 1.19. Enhanced cell attachment and proliferation on the nanostructured pellets were revealed. The presence of the nanostructures accounts mainly for the enhanced mechanical properties and promoted proliferation of the osteoblast cells. This study suggests that the SPS technique is an appropriate process for fabrication of bulk nSD‐HA from nanostructured powder. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
Development of a useful technique to discriminate anterior cruciate ligament cells and mesenchymal stem cells—The application of cell electrophoresis
Authors: Lee I‐Chi , Wang Jyh‐Horng , Lee Yu‐Tsang , Young Tai‐Horng
Published: February 2007

Mesenchymal stem cells (MSCs) can differentiate into multiple nonhematopoietic cell lineages, including osteoblasts, chondrocytes, and ligament cells. The purpose of this study is to identify the difference between MSCs and anterior cruciate ligament (ACL) cells for the application of distinguishing these two cells during the process of MSCs differentiating into ACL cells. Although culture of MSCs and ACL cells have been studied extensively, it was found that these two cells could not be distinguished from their appearance, expression of surface antigens (including CD105, CD34, CD45, CD29, CD44, and CD71), α‐smooth muscle actin, and mRNAs for type I collagen, type III collagen, and tenascin‐C, based on a series of traditional methods for cell identification. Cell electrophoresis, measuring the electrophoretic mobility (EPM) of cells, was proposed to investigate the discrepancy in surface charge properties of MSCs and ACL cells. Surprisingly, the EPM value of MSCs is significantly greater than that of ACL cells (p < 0.001). Although cell electrophoresis cannot determine the specific surface protein, it can reflect the net surface charge density of cell membrane, which can be influenced by the dissociation of functional groups of peripheral membrane proteins. Therefore, it is suggested that cell electrophoresis, while simple and cheap in manipulation, can serve as a useful research tool to assist in identification of MSCs differentiating into ACL cells. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
Development of parallel density functional program using distributed matrix to calculate all‐electron canonical wavefunction of large molecules
Authors: Inaba Toru , Sato Fumitoshi
Published: February 2007

We developed a new parallel density‐functional canonical molecular‐orbital program for large molecules based on the resolution of the identity method. In this study, all huge matrices were decomposed and saved to the distributed local memory. The routines of the analytical molecular integrals and numerical integrals of the exchange‐correlation terms were parallelized using the single program multiple data method. A conventional linear algebra matrix library, ScaLAPACK, was used for matrix operations, such as diagonalization, multiplication, and inversion. Anderson's mixing method was adopted to accelerate the self‐consistent field (SCF) convergence. Using this program, we calculated the canonical wavefunctions of a 306‐residue protein, insulin hexamer (26,790 orbitals), and a 133‐residue protein, interleukin (11,909 orbitals) by the direct‐SCF method. In regard to insulin hexamer, the total parallelization efficiency of the first SCF iteration was estimated to be 82% using 64 Itanium 2 processors connected at 3.2 GB/s (SGI Altix3700), and the calculation successfully converged at the 17‐th SCF iteration. By adopting the update method, the computational time of the first and the final SCF loops was 229 min and 156 min, respectively. The whole computational time including the calculation before the SCF loop was 2 days and 17 h. This study put the calculations of the canonical wavefunction of 30,000 orbitals to practical use. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Electron correlation: The many‐body problem at the heart of chemistry
Authors: Tew David P. , Klopper Wim , Helgaker Trygve
Published: February 2007

The physical interactions among electrons and nuclei, responsible for the chemistry of atoms and molecules, is well described by quantum mechanics and chemistry is therefore fully described by the solutions of the Schrödinger equation. In all but the simplest systems we must be content with approximate solutions, the principal difficulty being the treatment of the correlation between the motions of the many electrons, arising from their mutual repulsion. This article aims to provide a clear understanding of the physical concept of electron correlation and the modern methods used for its approximation. Using helium as a simple case study and beginning with an uncorrelated orbital picture of electronic motion, we first introduce Fermi correlation, arising from the symmetry requirements of the exact wave function, and then consider the Coulomb correlation arising from the mutual Coulomb repulsion between the electrons. Finally, we briefly discuss the general treatment of electron correlation in modern electronic‐structure theory, focussing on the Hartree‐Fock and coupled‐cluster methods and addressing static and dynamical Coulomb correlation. © 2007 Wiley Periodicals, Inc. J Comput Chem 28: 1307–1320, 2007
A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase‐1
Authors: Tejero Ismael , González‐Lafont Àngels , Lluch José M.
Published: February 2007

This paper reports a specific reaction parameter (SRP) PM3/d model for iron that can reproduce the DFT/MM results of the hydrogen abstraction reaction from the C11 position of linoleic acid by the Soybean lipoxygenase‐1 enzyme. A suite of nonlinear optimization methods is outlined for semiempirical parameter development based on integrated evolutionary (genetic) and direction set minimization algorithms. The PM3/d‐SRP Fe parameters are derived along three consecutive steps. The final parameterization step includes the effect of the whole enzyme in order to get a better quantum mechanical/molecular mechanical description. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments
Authors: González‐díaz Humberto , Saíz‐urra Liane , Molina Reinaldo , González‐díaz Yenny , Sánchez‐gonzález Angeles
Published: February 2007

Three‐dimensional (3D) protein structures now frequently lack functional annotations because of the increase in the rate at which chemical structures are solved with respect to experimental knowledge of biological activity. As a result, predicting structure‐function relationships for proteins is an active research field in computational chemistry and has implications in medicinal chemistry, biochemistry and proteomics. In previous studies stochastic spectral moments were used to predict protein stability or function (González‐Díaz, H. et al. Bioorg Med Chem 2005, 13, 323; Biopolymers 2005, 77, 296). Nevertheless, these moments take into consideration only electrostatic interactions and ignore other important factors such as van der Waals interactions. The present study introduces a new class of 3D structure molecular descriptors for folded proteins named the stochastic van der Waals spectral moments (oβk). Among many possible applications, recognition of kinases was selected due to the fact that previous computational chemistry studies in this area have not been reported, despite the widespread distribution of kinases. The best linear model found was Kact = −9.44°β0(c) +10.94°β5(c) −2.40°β0(i) + 2.45°β5(m) + 0.73, where core (c), inner (i) and middle (m) refer to specific spatial protein regions. The model with a high Matthew's regression coefficient (0.79) correctly classified 206 out of 230 proteins (89.6%) including both training and predicting series. An area under the ROC curve of 0.94 differentiates our model from a random classifier. A subsequent principal components analysis of 152 heterogeneous proteins demonstrated that βkcodifies information different to other descriptors used in protein computational chemistry studies. Finally, the model recognizes 110 out of 125 kinases (88.0%) in a virtual screening experiment and this can be considered as an additional validation study (these proteins were not used in training or predicting series). © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
On self duality of pathwidth in polyhedral graph embeddings
Authors: Fomin Fedor V. , Thilikos Dimitrios M.
Published: February 2007

Let G be a 3‐connected planar graph and G* be its dual. We show that the pathwidth of G* is at most 6 times the pathwidth of G. We prove this result by relating the pathwidth of a graph with the cut‐width of its medial graph and we extend it to bounded genus embeddings. We also show that there exist 3‐connected planar graphs such that the pathwidth of such a graph is at least 1.5 times the pathwidth of its dual. © 2007 Wiley Periodicals, Inc. J Graph Theory 55: 42–54, 2007
Efficient and practical syntheses of a stable labelled form of the non‐narcotic analgesic, bicifadine and its metabolites
Authors: Chen Zhengming , Yang Ji , Little Gillian , Keats Andrew
Published: February 2007

An efficient and practical synthesis of deuterium‐labelled bicifadine, together with 3 deuterium‐labelled bicifadine metabolites, was developed. The levels of deuterium incorporation are high, and the products were used as internal standards in bioanalytical method development and clinical bioanalysis. Copyright © 2007 John Wiley & Sons, Ltd.
Effect of thermal treatment on the proteins of amaranth isolates
Authors: Avanza M Victoria , Añón M Cristina
Published: February 2007

The effect of thermal treatment of proteins from Amaranthus hypochondriacus was studied. Two protein isolates were obtained from the defatted flour by water extraction at a pH of 9 (A9 isolate) and 11 (A11 isolate), followed by isoelectric precipitation at a pH of 5. Effect of thermal treatment (70 and 90 °C, during 3, 5, 10, 15 and 30 min) on A9 and A11 dispersions were analyzed by differential scanning calorimetry (DSC), polyacrylamide gel electrophoresis, UV spectrophotometry, superficial hydrophobicity and solubility in water. Thermal treatment induced the aggregate formation of high molecular mass stabilized by disulfide and non‐covalent bond. Thermal treatment at 70 °C produced a 30% denaturation in both, while at 90 °C A9 was more denatured than A11 (75% and 55% of denaturation, respectively). An increase in thermal stability was also detected by DSC in A9 treated at 90 °C. The denaturation process was accompanied at short heating times by an increase in UV absorbance and changes in superficial hydrophobicity. A decrease in water solubility (35–50%, depending on time–temperature conditions) was also observed for the A9 isolates. The results suggest that the A9 isolates, enriched in a globulin protein fraction, are more sensitive to thermal treatment than isolates A11 enriched in glutelin protein fraction. The changes shown by both isolates, indeed, could affect their functional properties and could definitely limit their use in food products. Copyright © 2007 Society of Chemical Industry
A comparison between the properties of seed, starch, flour and protein separated from chemically hardened and normal kidney beans
Authors: Kaur Maninder , Singh Narpinder
Published: February 2007

The physicochemical, functional and thermal properties of starch, flour and protein isolates obtained from chemically hardened kidney beans were evaluated. A rapid chemical hardening procedure (soaking in acetate buffer, pH = 4.0, 37 °C, 6 h) was used to produce hardened kidney beans. Chemical hardening altered physicochemical, cooking, hydrating and textural properties of beans to a significant level (P < 0.05). Soaked and cooked chemically hardened beans had a higher value for different textural parameters than their normal counterparts. Chemical hardening increased cooking time (from 49 to 123 min) of beans and decreased swelling power and solubility of starch. The turbidity value of gelatinized starch suspensions from chemically hardened beans was significantly lower than that from normal beans. Chemical hardening of beans caused significant increase in transition temperatures (To, Tp, Tc) and enthalpy of gelatinization (ΔHgel) of both starch and flour. Chemically hardened bean starch showed significantly higher pasting temperature (94.9 °C) as compared to normal bean starch (83.2 °C). Flour and protein isolate from chemically hardened beans showed significantly lower water absorption, oil absorption, foaming capacity and gelling ability than those from normal beans. The onset temperature (Tm), peak denaturation temperature (Td) and heat of transition or enthalpy (ΔH) of protein isolate from hardened and normal beans did not differ significantly. Copyright © 2007 Society of Chemical Industry
Identification of dimer impurities in ampicillin and amoxicillin by capillary LC and tandem mass spectrometry
Authors: Lu Chi‐Yu , Feng Chia‐Hsien
Published: February 2007

A micro‐scale liquid chromatography electrospray ionization tandem mass spectrometric method was developed for the identification of polymerized impurities in ampicillin and amoxicillin in aqueous solution. Ampicillin and amoxicillin are broad‐spectrum antibiotics and widely used for the treatment of human and animal infections. In this study ampicillin, amoxicillin, and their dimers were trapped in a 5‐cm capillary column containing C18 sorbents. The analytes were separated on a reversed‐phase column and introduced into the mass spectrometer via a nanospray ion source. An isocratic mobile phase consisting of 1% formic acid‐acetonitrile (50 : 50, v/v) was used. For identification, the fragment ions of the analytes were monitored. The aim of the present study was to develop an optimized quality control method for the analysis of high molecular weight impurities of ampicillin and amoxicillin.
Environmental sustainability in economic development: A comment
Authors: Goodland R. J. A.
Published: February 2007

Although the linkages between economics and environment are absolute, they are not emphasized either by the economic or by the environmental professions. The economics of natural resources remains a minor unpopular theme in orthodox economics today. Similarly, the relationship of the economic subsystem to the overall ecosystem is only mentioned in most environmental science texts. Attention to the environmental dimensions of economic development burgeoned in the early 1970s and has yet to become systematic. There are encouraging signs that this is improving. The integration of economics and environmental studies has been the focus of several recent conferences and books, e.g. Brundtland, 1987; Conway, 1985; IIED, 1987; Jansson, 1984; Pearce, 1985 and at least two journals (Environmental Economics from 1976, and Ecology and Economics from 1987; excluding the vast literature mainly on pollution economics. This paper mentions four environmental aspects of economic development: the concept of sustainability, carrying capacity, ethics and irreversibility. It then focuses on one important irreversible—the loss of biodiversity—and outlines progress with the World Bank's policies in this regard.
Mechanism of UV‐Induced Gelation of Acryloyl‐Type Monomer and Polymer Solutions Using Persulfate as Photoinitiator
Authors: Ikkai Fumiyoshi , Adachi Eiki
Published: February 2007

An aqueous solution containing acryloyl‐type monomers or polymers undergoes gelation by UV irradiation in the presence of APS as UV‐photoinitiator. We investigate the mechanism of the UV‐induced gelation using LS and ESR. In LS, the dependence of the gelation time tgelation on the APS concentration CAPS is demonstrated for NIPAm solutions, and the relation between CAPS and tgelation fits a power law function, i.e., tgelation ∼ C, indicating that UV‐induced gelation progresses according to a radical polymerization mechanism. On the other hand, ESR data reveal that the UV‐induced cross‐linking reaction takes place at α‐carbon atoms in acryloyl‐type monomers and polymers.

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Parametrized Littlewood–Paley operators on Hardy and weak Hardy spaces
Authors: Ding Yong , Lu Shanzhen , Xue Qingying
Published: February 2007

In this paper, we give the boundedness of the parametrized Littlewood–Paley function $ \mu ^{*,\rho}_{\lambda} $ on the Hardy spaces and weak Hardy spaces. As the corollaries of the above results, we prove that $ \mu ^{*,\rho}_{\lambda} $ is of weak type (1, 1) and of type (p, p) for 1 < p < 2, respectively. This results are substantial improvement and extension of some known results. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optimal domains and integral representations ofLp(G)‐valued convolution operators via measures
Authors: Okada S. , Ricker W. J.
Published: February 2007

Given 1 ≤p< ∞, a compact abelian groupGand a measureμ∈M(G), we investigate the optimal domain of the convolution operator$ C^{(p)}_{\mu} $:f↦f∗︁μ(as an operator fromLp(G) to itself). This is the largest Köthe function space with order continuous norm into whichLp(G) is embedded and to which$ C^{(p)}_{\mu} $has a continuous extension, still with values inLp(G). Of course, the optimal domain depends onpandμ. Whereas$ C^{(p)}_{\mu} $is compact precisely whenμ∈M0(G), this is not always so for the extension of$ C^{(p)}_{\mu} $to its optimal domain (which is always genuinely larger thanLp(G) wheneverμ∈M0(G)). Several characterizations of precisely when the extension is compact are presented. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Smoking and cognitive function in Parkinson's disease
Authors: Weisskopf Marc G. , Grodstein Francine , Ascherio Alberto
Published: February 2007

The risk of dementia among Parkinson's disease (PD) patients is greatly elevated compared to controls, yet little is known about determinants of cognitive function among PD patients. We assessed the relation between cigarette smoking prior to disease onset and later cognitive function among PD patients (n = 286) and age‐ and sex‐matched controls (n = 1144) participating in the Nurses' Health Study and Health Professionals Follow‐up Study. Both groups completed telephone‐administered assessments of cognitive function. We used linear regression to calculate mean differences in cognitive test scores across smoking categories, adjusted for age, education, sex, age at onset of PD, and years since diagnosis. PD patients scored significantly worse on all tests than their matched controls. In analyses only among PD cases, but not among controls, current smokers at PD onset scored worse than never smokers on the Telephone Interview for Cognitive Status (difference = −0.82, 95% CI: −1.33, −0.30, P = 0.002) as well as on a global score combining results of all tests (difference = −0.36, 95% CI: −0.72, 0.01, P = 0.06). This difference was equivalent to the difference in global score observed among controls ∼10 years apart in age. Analyses of pack‐years of smoking prior to disease onset gave similar results. These findings, nested in prospective cohort studies, suggest that cigarette smoking prior to disease onset is associated with worse cognitive function in PD. © 2007 Movement Disorder Society
On the existence and stability of solutions for the micropolar fluids in exterior domains
Authors: Ferreira L. C. F. , Villamizar‐Roa E. J.
Published: February 2007

We prove the existence of a global strong solution in some class of Marcinkiewicz spaces for the micropolar fluid in an exterior domain of R3, with initial conditions being a non‐smooth disturbance of a steady solution. We also analyse the large time behaviour of those solutions and apply our results in the context of the Navier–Stokes equations. Copyright © 2007 John Wiley & Sons, Ltd.
Proteomic analysis of the major soluble components in Annurca apple flesh
Authors: Guarino Carmine , Arena Simona , De Simone Luciana , D'Ambrosio Chiara , Santoro Simona , Rocco Mariapina , Scaloni Andrea , Marra Mauro
Published: February 2007

Apple is one of the most worldwide‐consumed fruits and a number of cultivars, differing in organoleptic and nutritional characteristics, are available for the market. Annurca apple is a regional variety from Southern Italy, which is known for crispness, excellent taste and long shelf life of fruits. These features have renewed the interest in the investigation of their genetic potential and different studies have lead to their partial genetic and metabolic characterisation. In this study, we present the analysis of the protein repertoire of the pseudocarp tissues of three accessions of Malus x domestica Borkh. cv. Annurca, as first example of the systematic annotation of the apple proteome. Proteins were extracted from fruit tissues and resolved on 2‐DE gels; commonly expressed proteins were in‐gel digested and analysed by MALDI‐TOF‐MS and μLC‐ESI‐IT‐MS/MS approaches. Peptide MS and MS/MS data were searched against publicly available protein and EST databases, and 44 spots were identified and associated to 28 different species. They were related to important physiological processes such as energy production, ripening and stress response. The occurrence of allergens causative of widespread food allergy syndromes was also detected. Integration of genomic, metabolomic and proteomic data will be indispensable for future molecular characterisation and hence full exploitation of the peculiar organoleptic, nutritional and agronomic traits of local cultivars of fruits.
Quality and stability evaluation of disposable medical equipment
Authors: Schumacher Ilana , Tsiperman Evgeny , Tarnopolsky Alexander , Raskin Arthur , Sigler Erwin , Domb Abraham J.
Published: February 2007

The complexity and uniqueness of disposable medical devices (DMDs) requires thorough analytical investigation to ensure their quality and stability upon storage. Infusion sets were studied in this context. Chemical compositions of various parts of these medical devices were analyzed using spectroscopic and chromatographic techniques. Physical properties of the components were tested according to appropriate American Society for Testing and Materials (ASTM) procedures (swelling and leaching test, tensile strength and microhardness). Since degradation of polymers is often accompanied by a color change, the yellowing observed in the chosen items was considered as an indication of degradation. Swelling and microhardness tests indicative of a correlation between the plastics' shelf‐life and their degradation extent.

Analyses of extracts of the plastics in different solvents confirmed the presense of a common plasticizer diethylhexylphthalate (DEHP) and two widely used antioxidants butylated hydroxytoluene (BHT) and methylenebis(methyl‐t‐butylphenol) in different parts of the devices. The mentioned compounds were identified by high performance liquid chromatography (HPLC) and gas chromatography and mass spectrometry (GC/MS) techniques. The concentration of these compounds in the extracts may be correlated with aging of the examined parts of the infusion sets.

The quality of DMDs may deteriorate due to the field storage conditions. Development of qualititative and quantitative methods for evaluating this deterioration is essential for better quality control of these items. Copyright © 2007 John Wiley & Sons, Ltd.
Entering the Implementation Era A report on the HUPO‐PSI Fall workshop 25–27 September 2006, Washington DC, USA
Authors: Orchard Sandra , Taylor Chris F. , Jones Phil , Montechi‐Palazzo Luisa , Binz Pierre‐Alain , Jones Andrew R. , Pizarro Angel , Julian Randall K. , Hermjakob Henning
Published: February 2007

Since its conception in April 2002, the Human Proteome Organisation Proteomics Standards Initiative has contributed to the development of community standards for proteomics in a collaborative and very dynamic manner, resulting in the publication and increasing adoption of a number of interchange formats and controlled vocabularies. Repositories supporting these formats are being established or are already operational. In parallel with this, minimum reporting requirement have been developed and are now maturing to the point where they have been submitted for journal publication after prolonged exposure to community‐input via the PSI website.