bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic profiling of 766 cancer‐related genes in archived esophageal normal and carcinoma tissues
Authors: Chen Jing , Guo Liping , Peiffer Daniel A. , Zhou Lixin , Chan Owen Tsan Mo , Bibikova Marina , Wickham‐Garcia Eliza , Lu Shih‐Hsin , Zhan Qimin , Wang‐Rodriguez Jessica , Jiang Wei , Fan Jian‐Bing
Published: February 2008

We employed the BeadArray™ technology to perform a genetic analysis in 33 formalin‐fixed, paraffin‐embedded (FFPE) human esophageal carcinomas, mostly squamous‐cell‐carcinoma (ESCC), and their adjacent normal tissues. A total of 1,432 single nucleotide polymorphisms (SNPs) derived from 766 cancer‐related genes were genotyped with partially degraded genomic DNAs isolated from these samples. This directly targeted genomic profiling identified not only previously reported somatic gene amplifications (e.g., CCND1) and deletions (e.g., CDKN2A and CDKN2B) but also novel genomic aberrations. Among these novel targets, the most frequently deleted genomic regions were chromosome 3p (including tumor suppressor genes FANCD2 and CTNNB1) and chromosome 5 (including tumor suppressor gene APC). The most frequently amplified genomic region was chromosome 3q (containing DVL3, MLF1, ABCC5, BCL6, AGTR1 and known oncogenes TNK2, TNFSF10, FGF12). The chromosome 3p deletion and 3q amplification occurred coincidently in nearly all of the affected cases, suggesting a molecular mechanism for the generation of somatic chromosomal aberrations. We also detected significant differences in germline allele frequency between the esophageal cohort of our study and normal control samples from the International HapMap Project for 10 genes (CSF1, KIAA1804, IL2, PMS2, IRF7, FLT3, NTRK2, MAP3K9, ERBB2 and PRKAR1A), suggesting that they might play roles in esophageal cancer susceptibility and/or development. Taken together, our results demonstrated the utility of the BeadArray technology for high‐throughput genetic analysis in FFPE tumor tissues and provided a detailed genetic profiling of cancer‐related genes in human esophageal cancer. © 2008 Wiley‐Liss, Inc.
Gastric cancer cells exploit CD4+ cell‐derived CCL5 for their growth and prevention of CD8+ cell‐involved tumor elimination
Authors: Sugasawa Hidekazu , Ichikura Takashi , Kinoshita Manabu , Ono Satoshi , Majima Takashi , Tsujimoto Hironori , Chochi Kentaro , Hiroi Sadayuki , Takayama Eiji , Saitoh Daizoh , Seki Shuhji , Mochizuki Hidetaka
Published: February 2008

The level of serum CCL5, a C‐C chemokine, is reportedly correlated with tumor progression in several cancers. We herein investigated the mechanisms by which CCL5 might contribute to tumor progression in gastric cancer. Serum CCL5 levels significantly correlated with tumor progression and prognosis in patients with gastric cancer. Immunohistochemistry showed that tumor‐infiltrating lymphocytes expressed CCL5, while the tumor cells expressed the CCL5 receptors. Fluorescent double staining showed that tumor‐infiltrating CD4+ cells rather than CD8+ cells preferentially expressed CCL5. Using gastric cancer cell lines (MKN45, KATO III), we examined CCL5 production by coculturing whole peripheral blood mononuclear cells (PBMCs), CD4+ cells, or CD8+ cells, with tumor cells. CD4+ cells cocultured with tumor cells remarkably enhanced CCL5 production in a direct cell–cell contact manner over other cocultured PBMCs, including CD8+ cells. Gastric cancer cell lines expressed CCL5 receptors and augmented their proliferation in response to CCL5 stimulation. Furthermore, we examined the effect of CCL5‐treated cancer cells on the cocultured PBMCs, focusing on the CD4+/CD8+ proportion and apoptosis. Coculture of CCL5‐treated gastric cancer cells with PBMCs resulted in a significant decrease in the proportion of CD8+ cells but not CD4+ cells, suggesting Fas‐FasL‐mediated apoptosis in CD8+ cells. In immunodeficient mice coinjected with KATO III and PBMCs, neutralization of CCL5 significantly suppressed tumor progression, resulting in a favorable outcome. In conclusion, gastric cancer cells might thus induce CD4+ T cells to secrete CCL5 and exploit it for their progression, as well as to aid in the prevention of CD8+ T cell‐involved tumor elimination. © 2008 Wiley‐Liss, Inc.
Species Composition and Distribution of Invasive Ponto‐Caspian Amphipods in the Off‐Channel Microhabitats of a Temperate, Lowland Dam Reservoir
Authors: Žytkowicz Jarosław , Kobak Jarosław , Kakareko Tomasz , Kentzer Andrzej
Published: February 2008

The Włocławek Dam Reservoir located on the lower Vistula River (central Poland) is part of the central corridor used by Ponto‐Caspian species to migrate in Europe. It provides a number of habitats suitable for sustaining populations of several non‐indigenous taxa. Four Ponto‐Caspian amphipod species were recorded in the reservoir: Chaetogammarus ischnus, Chelicorophium curvispinum, Dikerogammarus haemobaphes and Pontogammarus robustoides. We found significant differences in amphipod densities and species composition among various microhabitats in off‐channel areas. P. robustoides was the only amphipod species that occurred on very shallow (<1 m) sandy bottom near the shore. It inhabited also other sites but its share in the total number of amphipods and abundance decreased with the distance from the shore. Furthermore, at sites more distant from shore its affinity for plant substratum was higher. D. haemobaphes, C. ischnus and C. curvispinum clearly preferred sites distant from shore, overgrown by macrophytes or covered by mussel shells. Furthermore, the abundance of C. ischnus was negatively correlated with the presence of P. robustoides. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
In vitro gene expression analysis of hepatotoxic drugs in rat primary hepatocytes
Authors: Suzuki Hiromi , Inoue Tomoaki , Matsushita Tomochika , Kobayashi Kazuko , Horii Ikuo , Hirabayashi Yoko , Inoue Tohru
Published: February 2008

The study examined the feasibility of screening for hepatotoxicity by an in vitro gene expression analysis using rat primary hepatocytes and Affymetrix Rat Toxicology U34 arrays. Hepatocytes were exposed for 6 or 24 h to eight drugs, with different mechanisms of hepatotoxicity, at one third of the cytotoxic concentration TC50, i.e. acetaminophen, cyclophosphamide, clofibrate, chlorpromazine, lithocholic acid, cisplatin, diclofenac and disulfiram. The types of transcriptional changes observed in this study were generally consistent with previously reported in vivo data, although there were some differences. In hierarchical cluster analysis, drugs formed clusters depending on their mode of toxicity against cells. The number of transcripts affected by the cholestatic hepatotoxicants (lithocholic acid and chlorpromazine) or the drugs that rarely cause of hepatotoxicity (cisplatin, diclofenac and disulfiram) were limited compared with the other drugs (acetaminophen, clobifibrate and cyclophosphamide), where they did not induce transcriptional changes apparently related to toxicity. It is concluded that in vitro gene expression analysis of hepatocytes using microarray is a useful tool for evaluating the toxicological profile of drugs and in screening for the direct toxicity of drugs against hepatocytes. Copyright © 2008 John Wiley & Sons, Ltd.
Enhanced visualization of histological samples with an adjustable RGB contrast system with application for tissue used in photodynamic therapy
Authors: Barrionuevo Wilma Regina , Filho Edson Cesar Marques , Bagnato Vanderlei Salvador
Published: February 2008

The analysis of histological sections has long been a valuable tool in the pathological studies. The interpretation of tissue conditions, however, relies directly on visual evaluation of tissue slides, which may be difficult to interpret because of poor contrast or poor color differentiation. The Chromatic Contrast Visualization System (CCV) combines an optical microscope with electronically controlled light‐emitting diodes (LEDs) in order to generate adjustable intensities of RGB channels for sample illumination. While most image enhancement techniques rely on software post‐processing of an image acquired under standard illumination conditions, CCV produces real‐time variations in the color composition of the light source itself. The possibility of covering the entire RGB chromatic range, combined with the optical properties of the different tissues, allows for a substantial enhancement in image details. Traditional image acquisition methods do not exploit these visual enhancements which results in poorer visual distinction among tissue structures. Photodynamic therapy (PDT) procedures are of increasing interest in the treatment of several forms of cancer. This study uses histological slides of rat liver samples that were induced to necrosis after being exposed to PDT. Results show that visualization of tissue structures could be improved by changing colors and intensities of the microscope light source. PDT‐necrosed tissue samples are better differentiated when illuminated with different color wavelengths, leading to an improved differentiation of cells in the necrosis area. Due to the potential benefits it can bring to interpretation and diagnosis, further research in this field could make CCV an attractive technique for medical applications. Microsc. Res. Tech., 2008. © 2008 Wiley‐Liss, Inc.
Synthesis and evaluation of [O‐methyl‐11C]4‐[3‐[4‐(2‐methoxyphenyl)‐ piperazin‐1‐yl]propoxy]‐4‐aza‐tricyclo[5.2.1.02,6]dec‐8‐ene‐3,5‐dione as a 5‐HT1A receptor agonist PET ligand
Authors: Majo Vattoly J. , Parsey Ramin V. , Prabhakaran Jaya , Mann J. John , Dileep Kumar J. S.
Published: February 2008

4‐[3‐[4‐(2‐Methoxyphenyl)piperazin‐1‐yl]propoxy]‐4‐aza‐tricyclo[5.2.1.02,6]dec‐8‐ene‐3,5‐dione (4), a potent and selective 5‐HT1A agonist, was labeled by 11C‐methylation of the corresponding desmethyl analogue 3 with 11C‐methyl triflate. The precursor molecule 3 was synthesized from commercially available endo‐N‐hydroxy‐5‐norbornene‐2,3‐dicarboximide in two steps with an overall yield of 40%. Radiosynthesis of 11C‐4 was achieved in 35 min in 20±5% yield (n=6) at the end of synthesis with a specific activity of 2600±250 Ci/mmol. In vivo positron emission tomography (PET) studies in baboon revealed rapid uptake of the tracer into the brain. However, lack of specific binding indicates that 11C‐4 is not useful as a 5‐HT1A agonist PET ligand for clinical studies. Copyright © 2008 John Wiley & Sons, Ltd.
Significant summer rainfall in the Canadian Prairie Provinces: modes and mechanisms 2000–2004
Authors: Raddatz R. L. , Hanesiak J. M.
Published: February 2008

This study analysed nearly 1000 significant (≥10 mm in 24 h) summer rain events that occurred within the boundaries of the Canadian Prairie Provinces from 2000 to 2004. The objective of this examination was to identify the mode of each event (i.e. solely or partially convective versus non‐convective), and its primary forcing mechanism (i.e. source of lift). Daily rainfall and lightning maps revealed that most of the significant rain events (79%) were solely or partially convective (i.e. lightning was recorded during the event), while 88% of the total rain area, a measure of the impact of each event, was from events with moist deep convection. Average monthly percentages varied. In June, 74% of the events were solely or partially convective, in July 85%, and in August 79%. In June, 84% of the rain area was from events that were solely or partially convective, in July 93%, and in August 86%.

For significant rain events with convection, the most frequent forcing mechanisms were meso‐scale processes (28%), surface low‐pressure centres (16%), surface troughs (14%), and warm and cold fronts (both 14%). While meso‐scale forcing mechanisms were responsible for 28% of the significant rain events with convection, they generated just 11% of the rain area with convection. Surface low‐pressure centres, responsible for just 16% of the events with convection, produced 25% of the rain area with convection. The most frequent forcing mechanisms for significant rain events without convection were surface low‐pressure centres (25%), surface troughs (22%), cold fronts (19%), and cold lows (12%). The portion of the significant rain area without convection attributed to each of the synoptic forcing mechanisms was generally consistent with its relative frequency of occurrence. Copyright © 2008 Royal Meteorological Society
Effect of GDF‐7 deficiency on tail tendon phenotype in mice
Authors: Mikic Borjana , Entwistle Rachel , Rossmeier Kerri , Bierwert LouAnn
Published: February 2008

The subfamily of growth/differentiation factors (GDFs) known as GDFs 5, 6, and 7 appears to be involved in tendon maintenance and repair, although the precise nature of this role has yet to be elucidated. The aim of the present study was to examine the role of GDF‐7 in tendon maintenance by studying tail tendon fascicle gene expression, composition, and material property strain rate dependency in 16‐week‐old male and female GDF‐7 deficient mice. GDF‐7 deficiency did not affect the biochemical composition of tail tendon fascicles, nor did it significantly affect the tensile material properties obtained at either slow (5%/s) or fast (50%/s) strain rates. Further, no difference was found between genotypes in the strain rate sensitivity of any tensile material property. Consistent with the compositional analyses, QRT‐PCR data did not reveal any differences of twofold or greater in the gene expression levels of collagens I, III, V, nor in the proteoglycans decorin, fibromodulin, lumican, biglycan, versican, or aggrecan. Gdf5 expression was upregulated twofold in GDF‐7 deficient tail tendons, and Bmp7 expression was downregulated twofold. No notable differences in expression levels for Bmp1‐6 or Gdf6 were detected. GDF‐5 protein levels were 50% higher in GDF‐7 deficient tail tendon compared to wild type tail tendon. The results of this study support the intriguing possibility that compensation by Gdf‐5 may be at least in part responsible for the absence of a strong phenotype in GDF‐7 deficient mice. © 2008 Orthopaedic Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:834–839, 2008
Temporary distraction and compression of a diaphyseal osteotomy accelerates bone healing
Authors: Claes Lutz , Augat Peter , Schorlemmer Sandra , Konrads Christian , Ignatius Anita , Ehrnthaller Christian
Published: February 2008

Mechanical strain during callus distraction is known to stimulate osteogenesis. It is unclear whether this stimulus could be used to enhance the healing of a normal fracture without lengthening the bone. This study tested the hypothesis that a slow temporary distraction and compression of a diaphyseal osteotomy accelerates fracture healing. Fourteen sheep underwent a middiaphyseal osteotomy of the right tibia, stabilized by external fixation. An external fixator allowed either a temporary axial distraction (TD group; n = 6) or a constant fixation (C group; n = 8). Distraction began 7 days postoperatively at a rate of 0.5 mm twice per day for 2 days with subsequent shortening of 1.0 mm twice on the third day. The procedure was repeated four times. Fluorochrome labeling was performed postoperatively. After 8 weeks the sheep were sacrificed and healing was evaluated using densitometric, biomechanical, and histological methods. Bending stiffness of the tibiae after 8 weeks was 58% higher in the TD group than in the C group. The volume of the periosteal callus was significantly (p = 0.05) higher in the TD group (3.9 cm3) than in the C group (2.7 cm3). There was 20% more bone in the fracture gap of the TD group than the C group. There was a significantly higher bone formation rate in the TD group than in the C group. This study demonstrated the feasibility of fracture healing stimulation by the temporary application of distraction and compression. © 2008 Orthopaedic Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:772–777, 2008
Quadriceps and hamstrings muscle control in athletic males and females
Authors: Krishnan Chandramouli , Huston Kellen , Amendola Annunziato , Williams Glenn N.
Published: February 2008

The aim of this study was to investigate whether athletic males and females have differences in their quadriceps and hamstrings muscle control strategies. Twenty‐four people (12 males, 12 females) active in level I activities volunteered to participate. The subjects' muscle control strategies were studied using electromyography and a target matching protocol that assesses one's ability to produce force with control. The degree of control exhibited in the subjects' quadriceps and hamstrings muscle activation strategies was evaluated by calculating specificity indices for each muscle using circular statistics. Females displayed significantly lower specificity than males in their vastus medialis (p < 0.001), rectus femoris (p = 0.044), and lateral hamstrings (p = 0.001) muscle activity patterns, but similar specificity in their vastus lateralis and medial hamstrings activity patterns. Females also used a significantly higher magnitude of vastus lateralis (p < 0.001) and vastus medialis (p < 0.001) muscle activity than males to achieve the same relative force level. These findings indicate athletic males and females have differences in their knee muscle control strategies. © 2008 Orthopaedic Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:800–808, 2008
Friction properties of chemically modified starch
Authors: Biresaw Girma , Shogren Randal
Published: February 2008

Starches of varying chemical structures were esterified with anhydrides, formulated into dry film lubricants with the addition of canola oil, and its friction properties investigated. In the absence of canola, chemically modified starch displayed a very high coefficient of friction (COF). Addition of canola resulted in a sharp decrease in COF, which decreased with increasing [canola] until it attained a minimum and constant value that was independent of the further increase in [canola]. This observation was attributed to the adsorption of the canola oil onto starch due to H‐bonding between the ester groups of the canola triglycerides and the free hydroxyl groups of starch. Analysis of the [canola] vs COF data using the Langmuir adsorption model showed stronger adsorption of canola to modified starch with a lower degree of substitution (DS). This was attributed to the availability of more free hydroxyl group adsorption sites on starches with lower DS than those with higher DS. Copyright © 2008 John Wiley & Sons, Ltd.
Improved additives for multiply alkylated cyclopentane‐based lubricants
Authors: Peterangelo Stephen C. , Gschwender Lois , Snyder Carl E. , Jones William R. , Nguyen QuynhGiao , Jansen Mark J.
Published: February 2008

Multiply alkylated cyclopentanes (MACs) are replacing heritage (mineral oil‐based) spacecraft lubricants because of their excellent performance and low volatility. While MACs have acquired an increasingly prominent role, soluble additives with similarly low volatility are lacking. In this study, the performance of specially designed candidate high‐molecular‐weight/low‐volatility phosphate additives was compared with the performance of conventional phosphate and lead naphthenate additives currently used in space. The candidate additives were equivalent or superior to the currently used additives in both conventional (atmospheric) and vacuum wear tests. Volatility studies revealed superior candidate additive performance compared with currently used additives. In addition, surface chemical analysis of the wear surfaces provided a better understanding of the anti‐wear protective films formed by these additives. Copyright © 2008 John Wiley & Sons, Ltd.
The DGF Rapeseed Oil Award – A tool to improve the quality of virgin edible rapeseed oil
Authors: Matthäus Bertrand , Brühl Ludger , Amoneit Frank
Published: February 2008

Virgin cold pressed rapeseed oils are becoming more popular in Germany. They are characterized by their specific taste and smell which resembles asparagus, cabbage or fresh, green vegetables in contrast to the refined oils. The quality of virgin rapeseed oils on the German market is very heterogeneous, resulting in a problem for the consumer to choose an oil with a pleasant taste and smell. The German Society for Fat Science (DGF) created in 2006 the DGF Rapeseed Oil Award for virgin rapeseed oils of excellent flavour in order to highlight good products and to bring the sensory quality of virgin rapeseed oil more into the focus of the producers. The paper describes the reasons, procedure and the performance of the DGF Rapeseed Oil Award and discusses the question whether the medal is suitable to improve the quality of the oils in the market and to thereby strengthen the confidence of the consumer in the product. Additionally the results of the years 2006 and 2007 are shown.
XRCC4 codon 247*A and XRCC4 promoter −1394*T related genotypes but not XRCC4 intron 3 gene polymorphism are associated with higher susceptibility for endometriosis
Authors: Hsieh Yao‐Yuan , Bau Da‐Tian , Chang Chi‐Chen , Tsai Chang‐Hai , Chen Chih‐Ping , Tsai Fuu‐Jen
Published: February 2008

DNA repair systems act to maintain genome integrity in the face of replication errors, environmental insults, and the cumulative effects of age. Genetic variants in DNA repair genes such as X‐ray repair cross‐complementing group 4 (XRCC4) might influence the ability to repair damaged DNA. Herein we aimed to investigate whether some XRCC4‐related polymorphisms were associated with endometriosis susceptibility. Women were divided: (1) severe endometriosis (rAFS stage IV, n = 136) and (2) nonendometriosis groups (n = 112). The polymorphisms of XRCC4 codon 247, XRCC4 promoter −1394, and XRCC4 intron 3 insertion/deletion (I/D) polymorphism were amplified by PCR and detected by electrophoresis after restriction enzyme (BBS I, Hinc II) digestions. Genotypes and allelic frequencies in both groups were compared. We observed that XRCC4 codon 247*A and XRCC4 promoter −1394*T related genotypes, but not XRCC4 intron 3 I/D polymorphism, are associated with higher susceptibility for endometriosis. Distributions of XRCC4 codon 247*C homozygote/heterozygote/A homozygote, and C/A allele in both groups were: (1) 89/9.5/1.5% and 93.7/6.3%; (2) 97.3/2.7/0%, and 98.7/1.3% (P < 0.05). Proportions of XRCC4 promoter −1394*T homozygote/heterozygote/G homozygote and T/G allele in both groups were: (1) 94.1/5.2/0.7% and 96.7/3.3%, and (2) 79.4/17.9/2.7% and 88.4/11.6% (P < 0.005). Proportions of XRCC4*I homozygote/heterozygote/D homozygote and A/C allele in both groups were: (1) 67.6/30.9/1.5% and 83.2/16.8%, and (2) 70.5/24.1/5.4% and 82.6/17.4% (nondifference). We conclude that XRCC4 codon 247*A and XRCC4 promoter −1394*T related genotypes and alleles, but not XRCC4 intron 3 I/D polymorphism, might be associated with endometriosis susceptibilities and pathogenesis. Mol. Reprod. Dev. 75: 946–951, 2008. © 2008 Wiley‐Liss, Inc.
Modification of actions of heat shock on development and apoptosis of cultured preimplantation bovine embryos by oxygen concentration and dithiothreitol
Authors: de Castro e Paula L.A. , Hansen P.J.
Published: February 2008

Preimplantation embryos exposed to elevated temperatures have reduced developmental competence. The involvement of reactive oxygen species in these effects has been controversial. Here we tested hypotheses that (1) heat shock effects on development and apoptosis would be greater when embryos were cultured in a high oxygen environment (air; oxygen concentration = ∼20.95%, v/v) than in a low oxygen environment (5% oxygen) and (2) that these effects would be reversed by addition of the antioxidant dithiothreitol (DTT). Heat shock of 41°C for 9 hr reduced development of two‐cell embryos and Day 5 embryos to the blastocyst stage embryos when in high oxygen. There was no effect of heat shock on development when embryos were in low oxygen. Furthermore, induction of TUNEL‐positive cells in Day 5 embryos by heat shock only occurred when embryos were in high oxygen. Addition of DTT to two‐cell embryos either did not reduce effects of a heat shock of 41°C for 15 hr on development or caused slight protection only. In contrast, treatment of Day 5 embryos with DTT reduced effects of heat shock on development and apoptosis. In summary, oxygen tension was shown to be a major determinant of the effects of heat shock on development and apoptosis in preimplantation bovine embryos. Protective effects of the antioxidant DTT were stage specific and more pronounced at later stages of development. Mol. Reprod. Dev. 75: 1338–1350, 2008. © 2008 Wiley‐Liss, Inc.
Mos 3′ UTR regulatory differences underlie species‐specific temporal patterns of Mos mRNA cytoplasmic polyadenylation and translational recruitment during oocyte maturation
Authors: Prasad C. Krishna , Mahadevan Mahendran , MacNicol Melanie C. , MacNicol Angus M.
Published: February 2008

The Mos proto‐oncogene is a critical regulator of vertebrate oocyte maturation. The maturation‐dependent translation of Mos protein correlates with the cytoplasmic polyadenylation of the maternal Mos mRNA. However, the precise temporal requirements for Mos protein function differ between oocytes of model mammalian species and oocytes of the frog Xenopus laevis. Despite the advances in model organisms, it is not known if the translation of the human Mos mRNA is also regulated by cytoplasmic polyadenylation or what regulatory elements may be involved. We report that the human Mos 3′ untranslated region (3′ UTR) contains a functional cytoplasmic polyadenylation element (CPE) and demonstrate that the endogenous Mos mRNA undergoes maturation‐dependent cytoplasmic polyadenylation in human oocytes. The human Mos 3′ UTR interacts with the human CPE‐binding protein and exerts translational control on a reporter mRNA in the heterologous Xenopus oocyte system. Unlike the Xenopus Mos mRNA, which is translationally activated by an early acting Musashi/polyadenylation response element (PRE)‐directed control mechanism, the translational activation of the human Mos 3′ UTR is dependent on a late acting CPE‐dependent process. Taken together, our findings suggest a fundamental difference in the 3′ UTR regulatory mechanisms controlling the temporal induction of maternal Mos mRNA polyadenylation and translational activation during Xenopus and mammalian oocyte maturation. Mol. Reprod. Dev. 75: 1258–1268, 2008. © 2008 Wiley‐Liss, Inc.
Molecular electron paramagnetic resonance imaging of melanin in melanomas: a proof‐of‐concept
Authors: Vanea Emilia , Charlier Nicolas , DeWever Julie , Dinguizli Mustapha , Feron Olivier , Baurain Jean‐François , Gallez Bernard
Published: February 2008

The incidence of malignant melanoma is increasing at an alarming rate. As the clinical outcome of the disease strongly depends on the localization of the lesion, early detection at the initial stages of development is critical. Here, we suggest spatial characterization of melanoma based on the presence of endogenous stable free radicals in melanin pigments. Taking into account the abundance of these naturally occurring free radicals in proliferating melanocytes and their localization pattern, we hypothesized that electron paramagnetic resonance (EPR) imaging could be a unique tool for mapping melanomas with high sensitivity and high resolution. The potential of EPR to image melanoma samples was demonstrated in vitro in animal and human samples. Using EPR systems operating at low frequency, we were also able to record in vivo EPR spectra and images from the melanin present in a subcutaneous melanoma implanted in a mouse. In addition to the proof‐of‐concept and the achievement of providing the first non‐invasive image of an endogenous radical, this technology may represent a key advance in improving the diagnosis of suspected melanoma lesions. Copyright © 2008 John Wiley & Sons, Ltd.
Convergence analysis of the Newton–Shamanskii method for a nonsymmetric algebraic Riccati equation
Authors: Lin Yiqin , Bao Liang
Published: February 2008

In this paper, we consider the nonsymmetric algebraic Riccati equation arising in transport theory. An important feature of this equation is that its minimal positive solution can be obtained via computing the minimal positive solution of a vector equation. We apply the Newton–Shamanskii method to solve the vector equation. Convergence analysis shows that the sequence of vectors generated by the Newton–Shamanskii method is monotonically increasing and converges to the minimal positive solution of the vector equation. Numerical experiments show that the Newton–Shamanskii method is feasible and effective, and outperforms the Newton method. Copyright © 2008 John Wiley & Sons, Ltd.
An improved numerical scheme for the sine‐Gordon equation in 2+1 dimensions
Authors: Bratsos A. G.
Published: February 2008

A rational approximant of order 4, which is applied to a three‐time‐level recurrence relation, is used to transform the initial/boundary‐value problem associated with the two‐dimensional sine‐Gordon (SG) equation arising in the Josephson junctions problem. The resulting non‐linear system, which is analyzed for stability, is solved using an appropriate predictor–corrector (P–C) scheme, in which an explicit scheme of order 2 is used as predictor. For the implementation of the corrector, in order to avoid extended matrix evaluations, an auxiliary vector was successfully introduced. In this P–C scheme, a modification in the corrector has been proposed according to which the already evaluated corrected values are considered. The behavior of this P–C scheme is tested numerically on line and ring solitons known from the bibliography regarding the SG equation and conclusions for both undamped and damped problems are derived. Copyright © 2008 John Wiley & Sons, Ltd.
The Hu–Washizu variational principle for the identification of imperfections in beams
Authors: Caddemi S. , Di Paola M.
Published: February 2008

This paper presents a procedure for the identification of imperfections of structural parameters based on displacement measurements by static tests. The proposed procedure is based on the well‐known Hu–Washizu variational principle, suitably modified to account for the response measurements, which is able to provide closed‐form solutions to some inverse problems for the identification of structural parameter imperfections in beams. Copyright © 2008 John Wiley & Sons, Ltd.
Modal validation of sandwich shell finite elements based on a p‐order shear deformation theory including zigzag terms
Authors: Sulmoni Mattia , Gmür Thomas , Cugnoni Joël , Matter Marco
Published: February 2008

This paper describes a set of improved C0‐compatible composite shell finite elements for evaluating the global dynamic response (natural frequencies and mode shapes) of sandwich structures. Combining a through‐the‐thickness displacement approximation of variable high order with a first‐order zigzag function, the proposed finite elements are suited for modelling sandwich plates and doubly curved shells with a non‐uniform thickness and are more accurate than conventional models based on the first‐ and third‐order shear deformation theories, especially in sandwich panels with highly heterogeneous properties. The new finite element model is then validated by a comparison with the standard shell and 3D solid models. From these investigations, it can be concluded that adding a zigzag function even to high‐order polynomial approximations of the through‐the‐thickness displacement is a useful tool for refining the modelling of sandwich structures. In addition, the proposed formulation is sufficiently versatile to represent with the same level of accuracy the behaviour of thin‐to‐thick laminated shells as well as of strongly heterogeneous sandwich structures. Copyright © 2008 John Wiley & Sons, Ltd.
Synthesis and characterization of N‐substituted polyaniline with mesogen molecules
Authors: Gheybi Homa , Bagheri Massoumeh , Alizadeh Zahra , Entezami Ali Akbar
Published: February 2008

The N‐substituted polyaniline (PANi) was synthesized by incorporation of bromine‐terminated mesogens onto the emeraldine form of polyaniline. Firsty three liquid crystalline molecules containing biphenyl units were synthesized. These mesogenic molecules are named as: 6‐bromo‐ (4‐hexyloxy‐biphenyl‐4′‐oxy) hexane (C6C6Br), 5‐bromo‐(4‐hexyloxy‐biphenyl‐4′‐oxy) pentane (C6C5Br), 6‐bromo‐(4‐octyloxy‐biphenyl‐4′‐oxy) hexane (C8C6Br). Differential scanning calorimetry (DSC) in combination with polarizing optical microscopy (POM) were used to investigate the thermal properties of them. Optical microscopy showed focal conic texture characteristic of the Smectic A phase for (C6C5Br) and (C8C6Br). For (C6C6Br) smectic phase was determined. DSC experiments were also found in accord with mesophase formation. For the synthesis of N‐substituted polyaniline with these mesogen molecules, the emeraldine base polyaniline was reacted with BuLi to produce the N‐anionic polyaniline and then deprotonated polyaniline was reacted with bromine‐end mesogen to prepare mesogen‐substituted polyaniline through N‐substitution reaction. The degree of N‐substitution can be controlled by adjusting the molar feed ratio of mesogen to the number of repeat units of PANi. The microstructure and compositions of obtained polymers were characterized by FT‐IR, elemental analysis, DSC, and scanning electron microscopy (SEM). The cyclicvoltammetry show that the electroactivity of N‐substituted polyaniline is strongly dependent on the degree of N‐grafting. The solubility of mesogen‐substituted polyaniline in common organic solvents such as THF and chloroform was improved by increasing the degree of N‐substitution and also the samples are partially soluble in xylene. Liquid crystalline behavior of mesogen‐substituted polyanilines was investigated via POM, but no mesophase was observed. Copyright © 2008 John Wiley & Sons, Ltd.
Transplantation of human fetal mesenchymal stem cells improves glomerulopathy in a collagen type Iα2‐deficient mouse
Authors: Guillot PV , Cook HT , Pusey CD , Fisk NM , Harten S , Moss J , Shore I , Bou‐Gharios G
Published: February 2008

Fetal mesenchymal stem cell (fetal MSC) therapy has potential to treat genetic diseases with early onset, including those affecting the kidney and urinary tract. A collagen type Iα2‐deficient mouse has a deletion in the α2 chain of the procollagen type I gene, resulting in the synthesis of abnormal α1(I)3 homotrimers, which replace normal α1(I)2α2(I)1 heterotrimers and a glomerulopathy. We first confirmed that col1α2‐deficient homozygous mice show abnormal collagen deposition in the glomeruli, which increases in frequency and severity with postnatal age. Intrauterine transplantation of human MSCs from first trimester fetal blood led postnatally to a reduction of abnormal homotrimeric collagen type I deposition in the glomeruli of 4–12 week‐old col1α2‐deficient mice. Using bioluminescence imaging, in situ hybridization and immunohistochemistry in transplanted col1α2‐deficient mice, we showed that the damaged kidneys preferentially recruited donor cells in glomeruli, around mesangial cells. Real‐time RT–PCR demonstrated that this effect was seen at an engraftment level of 1% of total cells in the kidney, albeit higher in glomeruli. We conclude that intrauterine transplantation of human fetal MSCs improves renal glomerulopathy in a collagen type I‐deficient mouse model. These data support the feasibility of prenatal treatment for hereditary renal diseases. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Prenatal diagnosis of cystic fibrosis: the 18‐year experience of Brittany (western France)
Authors: Scotet Virginie , Duguépéroux Ingrid , Audrézet Marie‐Pierre , Blayau Martine , Boisseau Pierre , Journel Hubert , Parent Philippe , Férec Claude
Published: February 2008

Objective

This study reports 18 years of experience in prenatal diagnosis (PD) of cystic fibrosis (CF) in a region where CF is frequent and the uptake of PD is common (Brittany, western France).

Method

All PDs made over the period 1989–2006 in women living in Brittany were collected.

Results

We recorded 268 PDs made in 1 in 4 risk couples, plus 22 PDs directly made following the sonographic finding of echogenic bowel. Most of the 268 PDs were done in couples already having CF child(ren) (n = 195, 72.8%). Close to one‐fifth followed cascade screening (n = 49, 18.3%), which identified 26 new 1 in 4 risk couples among the relatives of CF patients or of carriers identified through newborn screening (NBS). The remaining PDs were mainly made in couples whose 1 in 4 risk was evidenced following the diagnosis of echogenic bowel in a previous pregnancy (n = 22, 8.2%). Although patients' life expectancy has considerably improved, in our population the great majority of couples chose pregnancy termination when PD indicated that the foetus had CF (95.9%).

Conclusion

This study describes the distribution of PDs according to the context in which the 1 in 4 risk was discovered and highlights the real decisions of couples as regards pregnancy termination after a positive PD. Copyright © 2008 John Wiley & Sons, Ltd.
Ovarian cancer proteomics: Many technologies one goal
Authors: Narasimhan Kothandaraman , Changqing Zhao , Choolani Mahesh
Published: February 2008

The last decade has seen major changes in the technologies used to identify markers for diagnosing cancer. This review focuses on recent developments on the evolving field of biomarker discovery, and validation techniques using proteomics platforms for ovarian cancer. It is possible now to diagnose various disease conditions using microliter quantities of body fluids. Currently the major developments were made in three distinct areas: (i) protein profiling, (ii) high‐throughput validation techniques, and (iii) solid and liquid phase protein microarray platforms for analyzing candidate markers across subclasses and stages of cancers. The recent addition to the long list of technologies is metabolomics using metabolite profiling and informatics‐based filtering of information for biomarker discovery of ovarian cancer. Emerging technologies need to address ways to eliminate the limitations posed by the complex dynamic nature of body fluids as well as ways to enrich low‐abundance tumor markers if they were to become a successful biomarker discovery tool. These new technologies hold significant promise in identifying more robust markers for ovarian cancer. Since the prevalence of this disease in the population is low, the test must have a high specificity.
Oxidation of proteins: Basic principles and perspectives for blood proteomics
Authors: Barelli Stefano , Canellini Giorgia , Thadikkaran Lynne , Crettaz David , Quadroni Manfredo , Rossier Joël S. , Tissot Jean‐Daniel , Lion Niels
Published: February 2008

Protein oxidation mechanisms result in a wide array of modifications, from backbone cleavage or protein crosslinking to more subtle modifications such as side chain oxidations. Protein oxidation occurs as part of normal regulatory processes, as a defence mechanism against oxidative stress, or as a deleterious processes when antioxidant defences are overcome. Because blood is continually exposed to reactive oxygen and nitrogen species, blood proteomics should inherently adopt redox proteomic strategies. In this review, we recall the biochemical basis of protein oxidation, review the proteomic methodologies applied to analyse redox modifications, and highlight some physiological and in vitro responses to oxidative stress of various blood components.
Phosphoproteomics: A possible route to novel biomarkers of breast cancer
Authors: Metodiev Metodi , Alldridge Louise
Published: February 2008

Proteomics is rapidly transforming the way that cancer and other pathologies are investigated. The ability to identify hundreds of proteins and to compare their abundance in different clinical samples presents a unique opportunity for direct identification of novel disease markers. Furthermore, recent advances allow us to analyse and compare PTMs. This gives an additional dimension for defining a new class of protein biomarker based not only on abundance and expression but also on the occurrence of covalent modifications specific to a disease state or therapy response. Such modifications are often a consequence of the activation/inactivation of a particular disease related pathway. In this review we evaluate the available information on breast cancer related protein‐phosphorylation events, illustrating the rationale for investigating this PTM as a target for breast cancer research with eventual clinical relevance. We present a critical survey of the published experimental strategies to study protein phosphorylation on a system wide scale and highlight recent specific advances in breast cancer phosphoproteomics. Finally we discuss the feasibility of establishing novel biomarkers for breast cancer based on the detection of patterns of specific protein phosphorylation events.
Modulation of cancer cell line differentiation: A neglected proteomic analysis with potential implications in pathophysiology, diagnosis, prognosis, and therapy of cancer
Authors: Scatena Roberto , Bottoni Patrizia , Giardina Bruno
Published: February 2008

The recent development of compounds that induce cell differentiation in various types of cancer cells has enabled the molecular mechanisms governing this kind of induced cancer regression to be investigated. Moreover, this approach to investigating the pathophysiology of neoplasia represents a promising experimental model for proteomic analysis of cancer cells. Modulating neoplastic cell differentiation grade may reveal cytodifferentiation‐related protein expression changes, and doing soin vitrohas the advantage of less biological variation. Hence, this analysis brings attention to molecular targets of the so‐called differentiating factors (i.e., retinoids, hybrid polar compounds, tyrosine kinase inhibitors,etc.) as well as proteins that are frequently associated with differentiation/dedifferentiation processes. Thein vitrostudy of these proteins and of their pathogenetic roles in cancer may ultimately result in the discovery of cancer biomarkers with diagnostic, prognostic, and therapeutic applications.
Exciting prospects for solids: Exact‐exchange based functionals meet quasiparticle energy calculations
Authors: Rinke Patrick , Qteish Abdallah , Neugebauer Jörg , Scheffler Matthias
Published: February 2008

Focussing on spectroscopic aspects of semiconductors and insulators we will illustrate how quasiparticle energy calculations in the G0W0 approximation can be successfully combined with density‐functional theory calculations in the exact‐ exchange optimised effective potential approach (OEPx) to achieve a first principles description of the electronic structure that overcomes the limitations of local‐ or gradient‐corrected DFT functionals (LDA and GGA). (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structure of gallium‐doped mayenite and its reduction behaviour
Authors: Palacios Luis , Bruque Sebastián , Aranda Miguel A. G.
Published: February 2008

The isovalent Al/Ga substitution in mayenite has been studied by preparing the (Ca12Al14–x Gax O32)O1□5 series. Single phase compounds can be prepared up to x = 1 and the structure of this compound has been studied by joint Rietveld analysis of neutron and X‐ray powder diffraction data. The results showed that gallium substitutes aluminium, which provokes the expansion of the unit cell, as expected. (Ca12Al13GaO32)O1□5 has been treated at high temperature under strong reducing conditions to prepare an electride derivative. Unfortunately, instead the reduction leaving electrons into the mayenite cages, the Ga‐doped mayenite undergoes decomposition. The initial compound transforms to Ca3Al2O6, (Ca12Al14O32)O1□5 and amorphous Ga metal, which is likely deposited on the mayenite crystal surfaces. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structure–charge mobility relation for hexabenzocoronene derivatives
Authors: Andrienko Denis , Kirkpatrick James , Marcon Valentina , Nelson Jenny , Kremer Kurt
Published: February 2008

Charge mobilities of several derivatives of discotic liquid crystals have been determined by combining three methods into one scheme: (i) quantum chemical methods for the calculation of molecular electronic structures and reorganization energies (ii) molecular dynamics for simulation of the relative positions and orientations of molecules in a columnar mesophase, and (iii) kinetic Monte Carlo simulations and Master Equation approach to simulate charge transport. Applying this scheme to differently substituted hexabenzocoronene derivatives we reproduce the trends and magnitudes of mobilities as measured by pulse‐radiolysis time‐resolved microwave conductivity (PR‐TRMC) and connect mobility directly to the microscopic morphology of the columns. Our study also shows that it is possible to understand and reproduce experimental charge transport parameters, and, in some cases, accurately predict them. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Stability analysis of graphene nanoribbons by molecular dynamics simulations
Authors: Dugan N. , Erkoç S¸.
Published: February 2008

In this work, stability of graphene nanoribbons are investigated using molecular dynamics. Simulations include heating armchair and zigzag‐edged nanoribbons of widths varying between one and nine hexagonal rings until the bonds between carbon atoms start to break. Breaking temperatures and binding energies per atom for different widths are presented for both armchair and zigzag‐edged cases. A nontrivial relation between stability and width is observed and discussed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A study of flexoelectric coupling associated internal electric field and stress in thin film ferroelectrics
Authors: Ma Wenhui
Published: February 2008

By discussions in the framework of tensor representations and phenomenological theory, general piezoelectricity equations that incorporate direct and inverse flexoelectric effects were analyzed and interlink between direct and inverse flexoelectricity discovered. Due to flexoelectric coupling, mechanical strain gradient is equivalent to internal electric field. In ferroelectrics above the Curie temperature, it was shown theoretically that strain gradient associated electric field leads to non‐zero polarization without external electric field. It was also shown theoretically that polarization (or electric field) gradient is an extra source of internal stress. Magnitudes of flexoelectricity associated internal electric field and stress were analyzed for heteroepitaxial thin films of barium strontium titanate. Flexoelectric coupling is expected to intensify with reducing lateral dimensions and thickness and get large enough at nanoscale to modify ferroelectric phase transitions and functional response. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic structure of oligoaniline doped by inorganic and organic acids
Authors: Yang Gang , Hou Wenhua , Feng Xiaomiao , Jiang Xuefan , Guo Jin
Published: February 2008

The electronic structure of doped‐oligoaniline with various dopants is investigated by means of DFT method. After doping by hydrochloric acid (HCl) and camphorsulfonic acid (HCSA), the alternation of bond‐lengths is decreased and the co‐planarity of adjacent aromatic rings is increased. The π‐conjugating effect is increased in the electronic nature of Ph‐N system because the electrons can be delocalized along the backbone of oligoaniline where the hydrogen bonds as a bridge transfer the electrons. The electronic structure of polaron and bipolaron conformation and their relative stability is discussed, indicating that the preferable conformation is dependant on various dopants. The calculation results reveal that there is a relatively stronger interaction between the organic dopant of HCSA and N atoms of PANI, and more charge transfer between PANI and HCSA is a reason for the fact that the conductivity of HCSA‐doped PANI is higher than that of HCl‐doped PANI. The doping mechanism is proposed based on the calculation results. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008