bluuebunny/crossref_metadata_2025_split huggingface dataset:
The methylator phenotype in microsatellite stable colorectal cancers is characterized by a distinct gene expression profile
Authors: Ferracin M , Gafà R , Miotto E , Veronese A , Pultrone C , Sabbioni S , Lanza G , Negrini M 
Published: February 2008

AbstractThe CpG island methylator phenotype (CIMP) in colorectal tumours can be recognized by an increased frequency of aberrant methylation in a specific set of genomic loci. Because of the strong association of CIMP with high microsatellite instability (MSI‐H), the identification of CIMP+ tumours within microsatellite stable (MSS) colorectal cancers may not be straightforward. To overcome this potential limitation, we have built an improved seven‐locus set of methylation markers that includes CACNA1G, IGF2, RUNX3, HTR6, RIZ1, MINT31, and MAP1B. This new set of CIMP markers revealed a bimodal distribution of methylation frequencies in a group of 95 MSS colorectal cancers, which allowed a clearer separation between CIMP classes. Correlation of MSS CIMP+ tumours with bio‐pathological traits revealed significant associations with location to the proximal colon, mucinous histology, BRAF mutation, and chromosomal stability. A potential trend towards an adverse prognosis of CIMP+ cases was associated with the high frequency of BRAF mutations present within this cohort of tumours. Microarray analysis revealed that CIMP+ tumours are characterized by a unique expression profile, a result that confirms that CIMP+ tumours represent a truly distinct molecular class within MSS colorectal cancers. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
PATZ1 gene has a critical role in the spermatogenesis and testicular tumours
Authors: Fedele M , Franco R , Salvatore G , Paronetto MP , Barbagallo F , Pero R , Chiariotti L , Sette C , Tramontano D , Chieffi G , Fusco A , Chieffi P 
Published: February 2008

AbstractPATZ1 is a recently discovered zinc finger protein that, due to the presence of the POZ domain, acts as a transcriptional repressor affecting the basal activity of different promoters. To gain insights into its biological role, we generated mice lacking the PATZ1 gene. Male PATZ1−/− mice were unfertile, suggesting a crucial role of this gene in spermatogenesis. Consistently, most of adult testes from these mice showed only few spermatocytes, associated with increased apoptosis, and complete absence of spermatids and spermatozoa, with the subsequent loss of tubular structure. The analysis of PATZ1 expression, by northern blot, western blot and immunohistochemistry, revealed its presence in Sertoli cells and, among the germ cells, exclusively in the spermatogonia. Since PATZ1 has been indicated as a potential tumour suppressor gene, we also looked at its expression in tumours deriving from testicular germ cells (TGCTs). Although expression of PATZ1 protein was increased in these tumours, it was delocalized in the cytoplasm, suggesting an impaired function. These results indicate that PATZ1 plays a crucial role in normal male gametogenesis and that its up‐regulation and mis‐localization could be associated to the development of TGCTs. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Glutamate and schizophrenia: new insights, new treatments
Authors: Greener Mark 
Published: February 2008

AbstractThere is increasing evidence to suggest that dopamine may not be as central to the pathogenesis of schizophrenia as previously believed. Here, Mark Greener provides an overview of studies supporting the primary role of glutamate in the development of schizophrenia and discusses its potential as a novel therapeutic target. Copyright © 2008 Wiley Interface Ltd
Ring‐chain interconversion of sulforhodamine‐amine conjugates involves an unusually labile CN bond and allows measurement of sulfonamide ionization kinetics
Authors: Corrie John E. T. , Eccleston John F. , Ferenczi Michael A. , Moore Madeleine H. , Turkenburg Johan P. , Trentham David R. 
Published: February 2008

AbstractpH‐dependent interconversion between ring and chain forms of sultams/sulfonamides derived from conjugates of sulforhodamines with amines, and the associated sulfonamide ionization, have been studied by a combination of equilibrium and kinetic methods. The colorless, ring‐closed sultam form is favored at alkaline pH with an apparent pKa of 7.37 for the color change of the methylamine conjugate of Sulforhodamine B. The ring‐closed form is also favored at very low pH (apparent pKa ∼ 0.68) by protonation of both diethylamino substituents. The kinetics of interconversion between open and closed forms were measured at 4°C over the pH range 0–13. The observed rate constant ranges over nine orders of magnitude from 4.8 × 10−4 s−1 at pH 1 to 2.27 × 106 s−1 at pH ≥ 12. Above pH 2, the data are accommodated by a mechanism that includes cleavage of the sultam CN bond in the ring opening step with a sulfonamide anion as the leaving group, and in the reverse reaction, OH−‐dependent ionization of the sulfonamide at 4.8 (±2.0) × 109 M−1 s−1. Below pH 2, H+‐dependent protonation occurs at 1.4 (±0.4) × 10−3 M−1 s−1. X‐ray crystallography of a related N‐methylsultam showed that the labile, endocyclic CN bond is significantly longer than the exocyclic NCH3 bond (1.509 Å and 1.445 Å, respectively). Laser‐induced ring opening of the closed form has potential application as an orientation probe of biological macromolecules. Copyright © 2008 John Wiley & Sons, Ltd.
Synthesis of a novel poly(para‐phenylene ethynylene) for highly selective and sensitive sensing mercury (II) ions
Authors: Li Cuihong , Zhou Chunjie , Zheng Haiyan , Yin Xiaodong , Zuo Zicheng , Liu Huibiao , Li Yuliang 
Published: February 2008

AbstractA new poly(p‐phenylene ethynylene) derivative with pendant 2,2′‐bipyridyl groups and glycol units (PPE‐bipy) has been prepared, and its metal ion sensing properties were investigated. The polymer of PPE‐bipy exhibited high selectivity for Hg2+ as compared with Li+, Na+, K+, Ba2+, Ca2+, Mg2+, Al3+, Mn2+, Ag+, Zn2+, Pb2+, Ni2+, Cd2+, Cu2+, Co,2+ and Fe3+ in THF/EtOH (1:1, v/v) solution. The fluorescence of PPE‐bipy was efficiently quenched by Hg2+ ions, and the detection limit was found to be 8.0 nM in a THF/EtOH (1:1, v/v) solvent system. PPE‐bipy also showed a selective chromogenic behavior toward Hg2+ ions by changing the color of the solution from slight yellow to colorless, which can be detected with the naked eye. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1998–2007, 2008
Initialization behavior at various target molecular weight RAFT‐mediated methyl acrylate polymerizations
Authors: van den Dungen Eric T. A. , Matahwa Howard , McLeary James B. , Sanderson Ronald D. , Klumperman Bert 
Published: February 2008

AbstractIn the reversible addition‐fragmentation chain transfer (RAFT) mediated polymerization of methyl acrylate, a selective reaction is observed in the early stages of the polymerization. This initialization process was earlier observed in in situ 1H NMR spectroscopy experiments where extremely low target molar masses were chosen (around DP = 5). Here, for the first time, the presence of the initialization process is identified as the cause of an induction period under typical conditions of a RAFT‐mediated polymerization. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2500–2509, 2008
Ultrafast SET‐LRP of methyl acrylate at 25 °C in alcohols
Authors: Lligadas Gerard , Percec Virgil 
Published: February 2008

AbstractAlcohols are known to promote the disproportionation of Cu(I)X species into nascent Cu(0) and Cu(II)X. Therefore, alcohols are expected to be excellent solvents that facilitate the single‐electron transfer mediated living radical polymerization (SET‐LRP) mediated by nascent Cu(0) species. This publication demonstrates the ultrafast SET‐LRP of methyl acrylate initiated with bis(2‐bromopropionyloxy)ethane and catalyzed by Cu(0)/Me6‐TREN in methanol, ethanol, 1‐propanol, and tert‐butanol and in their mixture with water at 25 °C. The structural analysis of the resulting polymers by a combination of 1H NMR and MALDI‐TOF MS demonstrates the synthesis of perfectly bifunctional α,ω‐dibromo poly(methyl acrylate)s by SET‐LRP in alcohols. Moreover, this work provides an expansion of the list of solvents available for SET‐LRP. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2745–2754, 2008
Polyethylene terephthalate–multiwall nanotubes nanocomposites: Effect of nanotubes on the conformations, crystallinity and crystallization behavior of PET
Authors: Tzavalas Spiros , Mouzakis Dionysis E. , Drakonakis Vasilis , Gregoriou Vasilis G. 
Published: February 2008

AbstractPET‐nanotube composite samples were manufactured by mixing neat PET with a PET‐multiwall carbon nanotube masterbatch. Fourier transform infrared (FTIR) spectroscopy was utilized to monitor the gauche and trans conformations of the polymeric chains with respect to the nanotube content. The crystallinity as well as the crystallization behavior of the polymer were studied via differential scanning calorimetry (DSC). An increase of the trans conformations and crystallinity was recorded at low NT contents followed by a sharp decrease at 1 wt % of nanotubes, further addition of nanotubes led once again to increase of the trans conformations and crystallinity. This behavior was attributed to the aggregations formation which as shown via transmission electron microscopy (TEM) was initiated at concentrations above 0.5 wt %. Discordance between the FTIR and DSC results in the case of the PET sample showed that the later bears relatively more trans non‐crystalline conformers than the nanocomposite samples. Thus it appears that the nanotubes incorporate the trans non‐crystalline segments into the crystalline phase. This work has shown that even a minor addition of carbon nanotubes (even 0.1 wt %) alters the crystallization behavior of the polymer dramatically, yielding a novel nanocomposite material rather than a simple mixture of two ingredients. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 668–676, 2008
Fine structure of PVDF nanofiber fabricated by electrospray deposition
Authors: Danno T. , Matsumoto H. , Nasir M. , Shimizu S. , Minagawa M. , Kawaguchi J. , Horibe H. , Tanioka A. 
Published: February 2008

AbstractThe fine structure of poly(vinylidene fluoride) (PVDF) nanofiber prepared by electrospray deposition (ESD) has been investigated by wide angle X‐ray diffraction (WAXD) and infrared spectroscopy (IR). The β‐phase crystal was dominant in the crystalline region. The degree of crystallinity of 0.54 for the nanofiber, determined by Ruland's method, was almost identical to that for a melt pressed sheet of PVDF. The disorder parameter k was 4, which is significantly smaller than the value of 6 for the melt pressed sheet of PVDF. Molecular orientation along the fiber axis was observed by the polarized infrared spectra of the uniaxially aligned nanofiber. These results suggest that the PVDF nanofiber possesses a fiber structure which is by no means inferior to that of practical fibers. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 558–563, 2008
Templated synthesis of silver nanoparticles in amphiphilic poly(vinylidene fluoride‐co‐chlorotrifluoroethylene) comb copolymer
Authors: Koh Joo Hwan , Kim Yong Woo , Park Jung Tae , Kim Jong Hak 
Published: February 2008

AbstractIn this study, poly(vinylidene fluoride‐co‐chlorotrifluoroethylene)‐graft‐poly(oxyethylene methacrylate), P(VDF‐co‐CTFE)‐g‐POEM, an amphiphilic comb copolymer with hydrophobic P(VDF‐co‐CTFE) backbone and hydrophilic POEM side chains at 73:27 wt % was synthesized. The POEM side chains were grafted from the P(VDF‐co‐CTFE) mainchain backbone via atom transfer radical polymerization (ATRP) using direct initiation of the chlorine atoms in CTFE units. Synthesis of microphase‐separated P(VDF‐co‐CTFE)‐g‐POEM comb copolymer was successful, as confirmed by nuclear magnetic resonance (1H NMR), FTIR spectroscopy, and transmission electron microscopy (TEM). Nanocomposite films were prepared using the comb copolymer as a template film and the in situ reduction of AgCF3SO3 precursor to silver nanoparticles under UV irradiation. Silver nanoparticles with 4–8 nm in average size were in situ created in the solid state template film, as revealed by TEM, UV–visible spectroscopy, and wide angle X‐ray scattering (WAXS). Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) presented the selective incorporation and the in situ growth of silver nanoparticles within the hydrophilic POEM domains of microphase‐separated comb copolymer film. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 702–709, 2008
Stimulus response and molecular structural modification of polyacrylamide gel in nitric acid: A study by Raman, FTIR, and photoluminescence techniques
Authors: Sivanantham M. , Kesavamoorthy R. , Sairam T. N. , Sabharwal K. N. , Raj Baldev 
Published: February 2008

AbstractStimulus response of photopolymerized 1% and 0.5% N,N′‐methylene bisacrylamide (MBA) crosslinked 10% polyacrylamide (PAAm) hydrogels was studied in nitric acid. The hydrogels swelled exponentially to saturation in 13 h due to the osmotic pressure arising from diffusion of ions in to the gel. MBA (0.5%) gels swell more with larger time constant than 1% MBA gels due to lower bulk modulus. Diffusion coefficient of nitric acid in the hydrogel and polymer‐solvent interaction parameter were estimated from the swelling behavior and discussed. At longer times, the hydrogels deswelled linearly in nitric acid due to molecular modification of amide group by acidic hydrolysis. Degree of swelling and deswelling increase with nitric acid concentration. Raman and FTIR investigations revealed the formation of carboxylic acid due to acidic hydrolysis. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 710–720, 2008
Synthesis, characterization, and properties of monodispersed magnetite coated multi‐walled carbon nanotube/polypyrrole nanocomposites synthesized by in‐situ chemical oxidative polymerization
Authors: Wu Tzong‐Ming , Yen Shiang‐Jie , Chen Erh‐Chiang , Chiang Ray‐Kuang 
Published: February 2008

AbstractThis study describes the preparation of a nanocomposites fabricated from monodispersed 4‐nm iron oxide (Fe3O4) coated on the surface of carboxylic acid containing multi‐walled carbon nanotube (c‐MWCNT) and polypyrrole (PPy) by in situ chemical oxidative polymerization. High‐resolution transmission electron microscopy images and X‐ray diffraction (XRD) data indicate that the resulting Fe3O4 nanoparticles synthesized using the thermal decomposition are close to spherical dots with a particle size about 4 ± 0.2 nm. The resulting nanoparticles were further mixed with c‐MWCNT in an aqueous solution containing with anionic surfactant sodium bis(2‐ethylhexyl) sulfosuccinate to form one‐dimensional Fe3O4 coated c‐MWCNT template for further preparation of nanocomposite. Structural and morphological analysis using field‐emission scanning electron microscopy, high‐resolution transmission electron microscopy, and XRD showed that the fabricated Fe3O4 coated c‐MWCNT/PPy nanocomposites are one‐dimensional core (Fe3O4 coated c‐MWCNT)‐shell (PPy) structures. The conductivities of these Fe3O4 coated c‐MWCNT/PPy nanocomposites are about four times higher than those of pure PPy matrix. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 727–733, 2008
The UGT2B17 gene deletion is not associated with prostate cancer risk
Authors: Olsson Mats , Lindström Sara , Häggkvist Benjamin , Adami Hans‐Olov , Bälter Katarina , Stattin Pär , Ask Birgitta , Rane Anders , Ekström Lena , Grönberg Henrik 
Published: February 2008

AbstractBACKGROUNDDeletion polymorphism of the UDP‐glucuronosyltransferase 2B17 (UGT2B17) gene has been associated with an increased prostate cancer risk in two previous independent studies. Here we determine the risk in a large‐scale population‐based case–control study.METHODSGenotyping was conducted with a 5′‐nuclease activity assay to distinguish those with one or two UGT2B17 gene copies (ins/del and ins/ins) from individuals homozygous for the deletion (del/del) allele.RESULTSIn contrast to previous findings, no association between the UGT2B17 deletion polymorphism and prostate cancer risk was found. Furthermore the UGT2B17 gene deletion did not affect the risk for prostate cancer specific death.CONCLUSIONThe UGT2B17 deletion polymorphism does not play a major role in prostate cancer susceptibility as previously indicated. Prostate 68: 571–575, 2008. © 2008 Wiley‐Liss, Inc.
Prostate cancer in Mexican‐Americans: Identification of risk factors
Authors: Strom Sara S. , Yamamura Yuko , Flores‐Sandoval F. Nery , Pettaway Curtis A. , Lopez David S. 
Published: February 2008

AbstractBACKGROUNDThere is a paucity of information regarding prostate cancer (PCa) risk factors among Hispanics, the fastest‐growing ethnic group in the United States.METHODSThis population‐based case‐control study included 176 Texas men of Mexican descent with PCa and 174 age‐ and ethnicity‐matched controls. Demographic, lifetime occupational history, family history of cancer, lifestyle (e.g., smoking, alcohol, diet, and recreational physical activity) and anthropometric information were collected by personal interviews. Chemical exposure and physical activity were determined using job‐exposure matrices for each reported job.RESULTSLogistic regression models adjusted for relevant covariates were used to evaluate their independent effects. Compared to controls, cases were three times more likely to work in jobs with high agrichemical exposure (OR = 3.44, 95% CI 1.84–6.44), and 54% less likely to work in jobs with moderate/high occupational physical activity (OR = 0.46, 95% CI 0.28–0.77). In analyses stratified by stage, cases with organ‐confined PCa were three times more likely to have high agrichemical exposure (OR = 3.39, 9%CI 1.68–6.84), and 56% less likely to have moderate/high levels of occupational physical activity (OR = 0.44, 95% CI 0.26–0.76). Increased risk of being diagnosed with advanced PCa was associated with obesity at time of diagnosis (OR = 2.50, 95% CI 1.20–5.20) and high levels of agrichemical exposure (OR = 4.65, 95% CI 1.97–10.97), but not with occupational physical activity.CONCLUSIONSThis case‐control study, the first conducted in a homogeneous Hispanic population, identified modifiable PCa risk factors, such as physical activity and agrichemical exposure, which may be useful in developing interventions for this understudied population. Prostate 68: 563–570, 2008. © 2008 Wiley‐Liss, Inc.
Broadening of transgenic adenocarcinoma of the mouse prostate (TRAMP) model to represent late stage androgen depletion independent cancer
Authors: Jeet Varinder , Ow Kim , Doherty Eboney , Curley Ben , Russell Pamela J. , Khatri Aparajita 
Published: February 2008

AbstractBACKGROUNDThe transgenic adenocarcinoma of the mouse prostate (TRAMP) model closely mimics PC‐progression as it occurs in humans. However, the timing of disease incidence and progression (especially late stage) makes it logistically difficult to conduct experiments synchronously and economically. The development and characterization of androgen depletion independent (ADI) TRAMP sublines are reported.METHODSSublines were derived from androgen‐sensitive TRAMP‐C1 and TRAMP‐C2 cell lines by androgen deprivation in vitro and in vivo. Epithelial origin (cytokeratin) and expression of late stage biomarkers (E‐cadherin and KAI‐1) were evaluated using immunohistochemistry. Androgen receptor (AR) status was assessed through quantitative real time PCR, Western blotting, and immunohistochemistry. Coexpression of AR and E‐cadherin was also evaluated. Clonogenicity and invasive potential were measured by soft agar and matrigel invasion assays. Proliferation/survival of sublines in response to androgen was assessed by WST‐1 assay. In vivo growth of subcutaneous tumors was assessed in castrated and sham‐castrated C57BL/6 mice.RESULTSThe sublines were epithelial and displayed ADI in vitro and in vivo. Compared to the parental lines, these showed (1) significantly faster growth rates in vitro and in vivo independent of androgen depletion, (2) greater tumorigenic, and invasive potential in vitro. All showed substantial downregulation in expression levels of tumor suppressor, E‐cadherin, and metastatis suppressor, KAI‐1. Interestingly, the percentage of cells expressing AR with downregulated E‐cadherin was higher in ADI cells, suggesting a possible interaction between the two pathways.CONCLUSIONSThe TRAMP model now encompasses ADI sublines potentially representing different phenotypes with increased tumorigenicity and invasiveness. Prostate 68: 548–562, 2008. © 2008 Wiley‐Liss, Inc.
MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information
Authors: Wu Sitao , Zhang Yang 
Published: February 2008

AbstractWe develop a new threading algorithm MUSTER by extending the previous sequence profile–profile alignment method, PPA. It combines various sequence and structure information into single‐body terms which can be conveniently used in dynamic programming search: (1) sequence profiles; (2) secondary structures; (3) structure fragment profiles; (4) solvent accessibility; (5) dihedral torsion angles; (6) hydrophobic scoring matrix. The balance of the weighting parameters is optimized by a grading search based on the average TM‐score of 111 training proteins which shows a better performance than using the conventional optimization methods based on the PROSUP database. The algorithm is tested on 500 nonhomologous proteins independent of the training sets. After removing the homologous templates with a sequence identity to the target >30%, in 224 cases, the first template alignment has the correct topology with a TM‐score >0.5. Even with a more stringent cutoff by removing the templates with a sequence identity >20% or detectable by PSI‐BLAST with an E‐value <0.05, MUSTER is able to identify correct folds in 137 cases with the first model of TM‐score >0.5. Dependent on the homology cutoffs, the average TM‐score of the first threading alignments by MUSTER is 5.1–6.3% higher than that by PPA. This improvement is statistically significant by the Wilcoxon signed rank test with a P‐value < 1.0 × 10−13, which demonstrates the effect of additional structural information on the protein fold recognition. The MUSTER server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/MUSTER. Proteins 2008. © 2008 Wiley‐Liss, Inc.