bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic mapping and functional analysis in a breast cancer metastasis model using whole-genome promoter tiling microarrays
Authors: Rodenhiser David I , Andrews Joseph , Kennette Wendy , Sadikovic Bekim , Mendlowitz Ariel , Tuck Alan B , Chambers Ann F 
Published: July 2008

Abstract
Introduction
Breast cancer metastasis is a complex, multi-step biological process. Genetic mutations along with epigenetic alterations in the form of DNA methylation patterns and histone modifications contribute to metastasis-related gene expression changes and genomic instability. So far, these epigenetic contributions to breast cancer metastasis have not been well characterized, and there is only a limited understanding of the functional mechanisms affected by such epigenetic alterations. Furthermore, no genome-wide assessments have been undertaken to identify altered DNA methylation patterns in the context of metastasis and their effects on specific functional pathways or gene networks.

Methods
We have used a human gene promoter tiling microarray platform to analyze a cell line model of metastasis to lymph nodes composed of a poorly metastatic MDA-MB-468GFP human breast adenocarcinoma cell line and its highly metastatic variant (468LN). Gene networks and pathways associated with metastasis were identified, and target genes associated with epithelial–mesenchymal transition were validated with respect to DNA methylation effects on gene expression.

Results
We integrated data from the tiling microarrays with targets identified by Ingenuity Pathways Analysis software and observed epigenetic variations in genes implicated in epithelial–mesenchymal transition and with tumor cell migration. We identified widespread genomic hypermethylation and hypomethylation events in these cells and we confirmed functional associations between methylation status and expression of the CDH1, CST6, EGFR, SNAI2 and ZEB2 genes by quantitative real-time PCR. Our data also suggest that the complex genomic reorganization present in cancer cells may be superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes.

Conclusion
This is the first whole-genome approach to identify genome-wide and gene-specific epigenetic alterations, and the functional consequences of these changes, in the context of breast cancer metastasis to lymph nodes. This approach allows the development of epigenetic signatures of metastasis to be used concurrently with genomic signatures to improve mapping of the evolving molecular landscape of metastasis and to permit translational approaches to target epigenetically regulated molecular pathways related to metastatic progression.
Mutations of CXorf6 are associated with a range of severities of hypospadias
Authors: Kalfa Nicolas , Liu Benchun , Ophir Klein , Audran Francoise , Wang Ming-Hsieh , Mei Cao , Sultan Charles , Baskin Laurence S 
Published: July 2008

ObjectiveMutations in chromosome X open reading frame 6 (CXorf6), a recently described candidate gene involved in the development of male genitalia, have been found in patients with complex 46,XY disorders of sexual development (46,XY DSD) including micropenis, bifid scrotum, and penoscrotal hypospadias. The objective of this work was to identify genomic variants of CXorf6 in patients with isolated hypospadias, severe or non-severe.Design and methodsForty-one patients with glandular to perineal hypospadias and thirty controls were studied. Direct sequencing for coding exons 3–6 of CXorf6 and their flanking splice sites was performed on DNA extracted from foreskin collected from surgery. Secondary and tertiary structures of the protein were predicted using NNpredict and Protein Homology/analogY Recognition Engine engines.ResultsFour mutations (9.7% of cases) were identified. One missense mutation (1295T>C, V432A) and two deletions (325delG, predicted to cause a stop codon L121X) occurred in patients with penoscrotal and proximal hypospadias. One patient with subcoronal hypospadias had CAG-repeat amplification in the second polyglutamine domain of CXorf6. Secondary structure prediction indicated that this insertion occurred in a helix element of the protein. The tertiary structure prediction showed an alteration of the shape of the protein and crowding between domains.ConclusionCXorf6 mutations are associated with isolated hypospadias of varying severity. However, the pathophysiology of these mutations and the function of the CXorf6 gene product remain to be investigated.
Thoracic stenosis causing lateral compression of the spinal cord in two immature Dogues de Bordeaux
Authors: Pratt J. N. J. , Smith P. M. , Jeffery N. D. , Stalin C. E. 
Published: July 2008

SummaryThis case report describes a novel developmental vertebral malformation in two young Dogues de Bordeaux, which was diagnosed by magnetic resonance imaging. Both dogs were treated surgically with reasonable success.
Synthesis, Characterization, Two‐Photon Absorption, and Optical Limiting Properties of Ladder‐Type Oligo‐p‐phenylene‐Cored Chromophores
Authors: Zheng Qingdong , Gupta Sandesh K. , He Guang S. , Tan Loon‐Seng , Prasad Paras N. 
Published: July 2008

AbstractThis paper reports on the two‐photon absorption (TPA) and related up‐converted emission properties of a novel series of chromophores containing ladder‐type oligo‐p‐phenylenes with various π‐conjugation lengths. The design and synthesis of these ladder‐type two‐photon chromophores are first discussed. An increase in the π‐conjugated length of the ladder‐type oligo‐p‐phenylene for these chromophores leads to an increase in TPA cross‐section together with an increased fluorescence quantum yield. These chromophores exhibit high fluorescence quantum yields because of the rigid planar structure of the ladder‐type oligomers. The chromophore with an enhanced TPA cross‐section together with an increased fluorescence quantum yield would provide significant benefits for two‐photon excited fluorescence based applications. An improved optical limiting behavior was also demonstrated using the ladder‐type pentaphenylene cored chromophore.
Postthaw survival of rhesus macaque sperm: variation in the response of individual males to different freezing protocols
Authors: Gagliardi Christine , Myers Leann , Kubisch H. Michael 
Published: July 2008

AbstractThis study was designed to assess the effects of various cryopreservation protocols on the postthaw survival of rhesus macaque sperm. Multiple ejaculates of five mature males were collected and frozen by each of four different methods. Cryopreservation significantly reduced motility in all samples, regardless of the method, and the response of different ejaculates of the same male to each method proved to be consistent. The freezing method was a significant factor in determining the immediate postthaw motility, although this effect disappeared after 4 hr. Moreover, there was a significant interaction between individual males and freezing method suggesting that developing a single freezing protocol that is universally suitable may be difficult. Am. J. Primatol. 70:1093–1096, 2008. © 2008 Wiley‐Liss, Inc.
Investigations of the Growth Kinetics of Capped CdSe and CdS Nanocrystals by a Combined Use of Small Angle X‐ray Scattering and Other Techniques
Authors: Varghese Neenu , Biswas Kanishka , Rao C. N. R. 
Published: July 2008

AbstractThe growth of capped CdSe and CdS nanocrystals formed by the reaction of selenium or sulfur with cadmium stearate in toluene solution in the presence of dodecanethiol or trioctylphosphine oxide and tetralin, has been investigated by a variety of techniques to obtain reliable data. Whereas small angle X‐ray scattering has provided statistically satisfactory data on the variation of size distribution with time, TEM has been used as a direct probe of the particle size, although with a limited sampling size. UV/Vis and photoluminescence spectroscopies have also provided information about the time evolution of the average diameter (D) of the nanocrystals. By employing all these techniques, we have obtained the D(t) data and fitted then to various growth models. Although certain qualitative observations suggest growth of the nanocrystals to be controlled by diffusion‐limited Ostwald ripening, we have found it is necessary to include the surface reaction term in the growth equation. Thus, the growth of CdSe and CdS nanocrystals has contributions from both diffusion and surface reaction, with a D3+D2 type behavior, independent of the capping agent.
Solphos: A New Family of Efficient Biaryl Diphosphine Ligands
Authors: Kesselgruber Martin , Lotz Matthias , Martin Pierre , Melone Gianpietro , Müller Markus , Pugin Benoît , Naud Frédéric , Spindler Felix , Thommen Marc , Zbinden Paul , Blaser Hans‐Ulrich 
Published: July 2008

AbstractSolphos (7,7′‐bis(diarylphosphino)‐3,3′,4,4′‐tetrahydro‐4,4′‐dimethyl‐8,8′‐bis‐2H‐1,4‐benzoxazine) is a new modular atropisomeric biaryl ligand with a very attractive activity profile. A technically feasible synthesis is described allowing the synthesis of various derivatives of enantiopure ligand on a technical scale. Very good catalytic performances have been demonstrated for the following transformations: Ru‐catalyzed hydrogenation of various β‐keto esters (95–99 % ee, s/c up to 100 000), of acetyl acetone (>99 % ee, dl/meso>98:2), and of an exocyclic α,β‐unsaturated acid (98.6 % ee, s/c 250). In several cases, the nature of the PAr2 moiety had a significant effect on the enantioselectivity. Furthermore, Rh and Ir Solphos complexes achieved high enantioselectivities for a novel synthesis of 3,3‐disubstituted phthalides and the reductive coupling of alkynes with N‐sulfonyl imines, respectively.
Stereoselective Synthesis of Cyclopropanes Based on a 1,2‐Chirality Transfer
Authors: Muehling Olaf , Wessig Pablo 
Published: July 2008

AbstractA stereoselective route to enantiomerically enriched bicyclic cyclopropane derivatives 13 is described which is based on a conceptually novel 1,2‐chirality transfer approach. The hyperconjugative interaction of an electronically excited carbonyl group with the σ* orbital of an adjacent CX bond in the transition state of a hydrogen abstraction causes the preference of a certain conformation and consequently the differentiation between two diastereotopic methylene groups. The 1,2‐chirality transfer is completed by a subsequent HX elimination which destroys the only stereogenic center in the reactants 12. Furthermore, it was found that contrary enthalpic and entropic influences result in the existence of an inversion temperature T0. Upon crossing T0 the stereoselectivity is reversed. Considering this temperature dependency, chirality transfer efficiencies of up to 83 % could be achieved. The absolute configuration of most products could be unambiguously determined by VCD spectroscopy combined with DFT calculations.
Case–control study of oral and oropharyngeal cancer in whites and genetic variation in eight metabolic enzymes
Authors: Buch Shama C. , Nazar‐Stewart Valle , Weissfeld Joel L. , Romkes Marjorie 
Published: July 2008

AbstractBackground.Genetic variation in xenobiotic metabolizing enzymes may explain differing susceptibilities to the cancer causing effects of tobacco and alcohol.Methods.We compared 203 oral squamous cell carcinoma cases and 416 controls for single nucleotide polymorphisms (SNPs) in 8 genes (CYP1A1, CYP2E1, MPO, mEH, GSTM1, GSTT1, GSTP1, and NAT2). Except for NAT2, genotype frequencies were similar in the 2 groups. We classified subjects as fast or slow NAT2 acetylators genotyping 13 NAT2 SNPs.Results.Fast acetylators were overrepresented in cases (53.7%) compared with controls (43.9%; odds ratio (OR) 1.55, 95% confidence interval (CI) 1.08–2.20; p value = .03). Gene–gene interaction testing suggested several cancer‐NAT2 associations, with association strongest among persons without a CYP1A1 variant (*2C or *4) allele (OR 1.77, 95% CI 1.20–2.60, p value = .03) or with a variant MPO (463A) allele (OR 2.38, 95% CI 1.34–4.21, p value = .05).Conclusion.These results implicate fast NAT2 acetylation as a risk factor for oral cancer. © 2008 Wiley Periodicals, Inc. Head Neck 2008
Peroxynitrite damages U937 cell DNA via the intermediate formation of mitochondrial oxidants
Authors: Cantoni Orazio , Guidarelli Andrea 
Published: July 2008

AbstractEight years ago, we published in this journal the first evidence that peroxynitrite does not directly produce DNA single‐strand breakage in intact U937 cells (Guidarelli et al.,IUBMB Life, 50, 195–201). This event was rather attributed to the secondary reactive species produced at the mitochondrial level via a Ca2+‐dependent reaction, in which ubisemiquinone serves as an electron donor. Under these conditions, electrons are directly transferred to molecular oxygen and superoxide/H2O2, and the ensuing DNA damage can therefore be produced in a time‐ dependent manner for at least 30 min. Formation of H2O2and DNA single‐strand breaks was therefore dependent on interference with electron transport at the complex III level as well as on mitochondrial Ca2+accumulation. Further studies led to the demonstrations that peroxynitrite mobilizes Ca2+from the ryanodine receptor. Finally, in U937 cells, a pro‐monocytic cell line sharing with monocytes/macrophages the same signaling events to survive to peroxynitrite, mitochondrial H2O2promotes inhibition of survival via tyrosine phosphatase activation, leading to ERK1/2 dephosphorylation and thus to upstream inhibition of the survival signaling. © 2008 IUBMB IUBMB Life, 60(11): 753–756, 2008
Mapping nondominant voices into understanding stress‐coping mechanisms
Authors: Iwasaki Yoshitaka , Bartlett Judith , MacKay Kelly , Mactavish Jennifer , Ristock Janice 
Published: July 2008

AbstractThis study reports key findings from a research project, which examined the stress and coping mechanisms of several nondominant groups of individuals. The groups were based in Winnipeg, Manitoba, Canada and included (a) Aboriginal individuals with diabetes, (b) individuals with disabilities, and (c) gays and lesbians. Our analyses of personal narratives and life stories have led to develop an interpretive map of findings that depicts mechanisms of how stress and coping operate. Specifically, the interpretive map consists of personal and structuralstressors, meanings of stress, and personal and structuralresources, as well as of two constructs termedintersectionalityandsocial exclusion. Not only are nondominant voices and lived experiences recognized and incorporated into an emergent interpretive map, but this map also articulates the complex ways in which multiple identities intersect (i.e., intersectionality) and the realities of being excluded socioeconomically, culturally, and politically among nondominant groups (i.e., social exclusion). © 2008 Wiley Periodicals, Inc.
How do implementation efforts relate to program adherence? examining the role of organizational, implementer, and program factors
Authors: Dariotis Jacinda K. , Bumbarger Brian K. , Duncan Larissa G. , Greenberg Mark T. 
Published: July 2008

AbstractWidespread replications of evidence‐based prevention programs (EBPPs) prompt prevention scientists to examine program implementation adherence in real world settings. Based on Chen's model (1990), we identified five key factors of the implementation system and assessed which characteristics related to program adherence. The sample included 32 EBPPs and results indicate that target recipient responsivity, program material quality, implementer prioritization, community collaborative system support, and parental support significantly relate to program adherence. Several differences reached statistical significance, thereby highlighting the importance of these variables and the need for future studies with larger sample sizes to identify factors related to program adherence adequately. © 2008 Wiley Periodicals, Inc.
Feasability of human endobronchial imaging with a linear‐array ultrasound catheter
Authors: Tranquart François , Palanchon Peggy , Cladé Odile , Bleuzen Aurore , Dinet Dominique , Magro Pascal , Diot Patrice 
Published: July 2008

AbstractPurpose.To explore the feasability of imaging lung masses with a novel endobronchial linear‐array transducer.Method.We used a linear‐array transducer of 7 F (2.3 mm in diameter) operating at a center frequency of 10 MHz for endobronchial imaging. We used the probe in 20 subjects with suspected lung cancer to identify and measure the tumor; to asses the tumor's sonographic characteristics, bronchial wall invasion, and presence of lymph nodes; to guide a transbronchial needle aspiration (TBNA); and to evaluate potential side effects.Results.In all patients, the tumor was identified and the relationship with the bronchial wall correctly evaluated through the depiction of a 3‐layer wall pattern. Bronchial wall invasion was suspected in 5 patients, small adjacent lymph nodes were detected in 3 patients, and a small pleural effusion was observed close to the lung lesion in 2 patients. The linear‐array probe allowed the guidance of successful TBNA with no complications.Conclusion.This feasibility study shows that the prototype probe can be used to depict pulmonary lesions and to guide biopsy nodes. Larger series are needed to validate its usefulness in clinical work‐ups and patients management. © 2008 Wiley Periodicals, Inc. J Clin Ultrasound, 2008
Development and validation of an HPLC method for the determination of benzodiazepines and tricyclic antidepressants in biological fluids after sequential SPE
Authors: Uddin Mohammad Nasir , Samanidou Victoria F. , Papadoyannis Ioannis N. 
Published: July 2008

AbstractA novel method for the simultaneous determination of six benzodiazepines (BZDs) and four tricyclic antidepressants (TCAs) in biological fluids by HPLC with UV detection at 240 nm has been developed. After a deproteinization step biological fluids were analyzed by direct injection. SPE on Nexus cartridges was also applied. Since two compounds, namely imipramine and diazepam, were coeluting, a sequential SPE protocol has been developed. BZDs were eluted by a mixture of methanol/ACN (1:1), followed by the elution of TCAs with methanol. Separation was performed on a Kromasil C8 column (250×4 mm2 id, 5 μm) using a mobile phase of 0.05 M CH3COONH4/ACN/methanol (initial composition 55:15:30 v/v/v) at a flow rate of 1.0 mL/min delivered by a gradient program within 15 min. Colchicine was used as the internal standard (4 ng/μL). The method was linear for all analytes up to 20 ng/μL, with coefficients of regression between 0.996 and 0.99996. LODs and LOQs were 0.08–1.17 and 0.28–3.91 ng/μL, respectively. Recovery was in the range of 92.8–108.7% for within‐day and 91.9–109.9% for between‐day assays, with RSD values lower than 10.0% for all matrices.
Self‐Assembly of Rod‐Coil Block Copolymers for Photovoltaic Applications
Authors: Sary Nicolas , Rubatat Laurent , Brochon Cyril , Hadziioannou Georges , Mezzenga Raffaele 
Published: July 2008

AbstractSummary: Two different approaches to obtain electron donor‐acceptor interfaces via self‐assembly of block copolymer systems are discussed, where the donor domains are formed by a π‐conjugated rod‐like polymer and the acceptor domains result from a coiled polymer modified by C60 fullerenes. In the first strategy, C60 is chemically grafted onto the coil polymer, typically a statistical copolymer of styrene and chloromethyl styrene. This has as major effect the increase in molecular weight and volume fraction of the coil block, which can markedly perturb the self‐assembled block copolymer final morphologies and eventually suppress any microseparated nanostructure in favour of fully isotropic homogeneous phases. We discuss how the presence of free homopolymer rods in the system can help recovering a microphase separated morphology suitable for photovoltaic applications. In the second approach we discuss the poly(diethylhexyl‐p‐phenylenevinylene‐b‐4‐vinylpyridine) (PPV‐P4VP) rod‐coil block copolymer system and we argue how supramolecular interactions among P4VP and free C60 can be exploited to blend rod‐coil block copolymers and C60 preserving the original lamellar phase.
Lead Sulfide Nanocrystal‐Polymer Composites for Optoelectronic Applications
Authors: Asunskis Daniel J. , Bolotin Igor L. , Wroble Amanda T. , Zachary Adam M. , Hanley Luke 
Published: July 2008

AbstractSummary: Nanocomposite films were prepared by two methods in which lead sulfide (PbS) nanocrystals were contained in an organic matrix. One method used a wet chemical synthesis of the nanocrystals in the direct presence of a polymer, where the polymer controlled nanocrystal growth. The second method was gaseous deposition of nanocrystals into the organic phase. The two methods were similar in that the nanocrystals in the composites were free from surfactant capping layers that otherwise would add an interfacial region between the nanocrystal and the organic matrix. The gaseous deposition technique had several advantages over the wet chemical synthesis in that it allowed direct control over nanocrystal size and density, improved flexibility in the choice of organic phase, and was compatible with lithographic methods.
Polymer Holography – New Theory of Image Growth
Authors: Havránek Antonín , Květoň Milan 
Published: July 2008

AbstractSummary: The image forming process in photopolymer holographic film has been studied thoroughly. Many grow‐curves, i.e. the curves describing the time dependence of the image grow, have been obtained by the special equipment (described in1) under varying conditions. The varying concerns both the changes in film composition and exposition. The S‐type form of the measured grow curves bring out some problem in interpreting them in the framework of the usual diffusion theories of photopolymer image growth. To overcome the problem we add the idea that polymer loses its mobility as it grows to the usual only diffusion theories and put down the more general immobilization‐diffusion theory.2
Synthesis of Polymethacrylates with Carbazole and Benzofuran Pendant Groups for Photovoltaic Applications
Authors: Bogdal Dariusz , Matras Katarzyna , Sanetra Jerzy , Pokladko Monika 
Published: July 2008

AbstractSummary: The article focuses on the photovoltaic devices made from copolymers of 2‐(carbazol‐9‐yl)ethyl methacrylate (CEM) with benzofuran‐2‐carboxylic acid 2‐(methacryloyloxy)ethyl 6‐(diethylamino)benzo[b]furan‐2‐carboxylate (MB) and poly(3‐decylthiophene) (PDT) or poly(3‐octylthiophene) (P3OT). Photovoltaic cell structure consisted of ITO/active materials/Al. The photophysics of such photoactive devices is based on the photo‐induced charge transfer from donor‐type semiconducting conjugated polymers to the acceptor‐type polymers. The monomer synthesis and polymerization as well as the device fabrication are presented. The copolymers can be spin‐coated from a solution at room temperature without subsequent processing and heat treatment. The photovoltaic properties of the devices are shown.
Light‐Induced Change of Charge Carrier Mobility in Semiconducting Polymers
Authors: Vala Martin , Weiter Martin , Zmeškal Oldřich , Nešpůrek Stanislav , Toman Petr 
Published: July 2008

AbstractSummary:Light‐driven devices based on reversible change of carrier mobility in semiconducting polymers were investigated. The mobility was altered using a photochromic spiropyran capable of a reversible change of permanent dipole moment and ionization potential. While the latter attribute may result in formation of chemical traps and is more important for matrices with similar ionization potential such as PVK, the former phenomenon results in formation of polar traps and is more pronounced in the case of lower‐band‐gap materials.