bluuebunny/crossref_metadata_2025_split huggingface dataset:
A gene signature identified using a mouse model of androgen receptor‐dependent prostate cancer predicts biochemical relapse in human disease
Authors: Thompson Vanessa C. , Day Tanya K. , Bianco‐Miotto Tina , Selth Luke A. , Han Guangzhou , Thomas Mervyn , Buchanan Grant , Scher Howard I. , Nelson Colleen C. ,   the Australian Prostate Cancer BioResource, Greenberg Norman M. , Butler Lisa M. , Tilley Wayne D. 
Published: September 2011

AbstractMutations in the androgen receptor (AR) have been detected in experimental and clinical prostate tumors. Mice with enforced prostate‐specific expression of one such receptor variant, AR‐E231G, invariably develop prostatic intraepithelial neoplasia by 12 weeks and metastatic prostate cancer by 52 weeks. The aim of this study was to identify genes with altered expression in the prostates of AR‐E231G mice at an early stage of disease that may act as drivers of AR‐mediated tumorigenesis. The gene expression profile of AR‐E231G prostate tissue from 12‐week‐old mice was compared to an equivalent profile from mice expressing the AR‐T857A receptor variant (analogous to the AR‐T877A variant in LNCaP cells), which do not develop prostate tumors. One hundred and thirty‐two genes were differentially expressed in AR‐E231G prostates. Classification of these genes revealed enrichment for cellular pathways known to be involved in prostate cancer, including cell cycle and lipid metabolism. Suppression of two genes upregulated in the AR‐E231G model, ADM and CITED1, increased cell death and reduced proliferation of human prostate cancer cells. Many genes differentially expressed in AR‐E231G prostates are also deregulated in human tumors. Three of these genes, ID4, NR2F1 and PTGDS, which were expressed at consistently lower levels in clinical prostate cancer compared to nonmalignant tissues, formed a signature that predicted biochemical relapse (hazard ratio 2.2, p = 0.038). We believe that our findings support the value of this novel mouse model of prostate cancer to identify candidate therapeutic targets and/or biomarkers of human disease.
Calcium‐regulated transcriptional pathways in the normal and pathologic heart
Authors: Zarain‐Herzberg Angel , Fragoso‐Medina Jorge , Estrada‐Avilés Rafael 
Published: September 2011

AbstractThe cytosolic calcium concentration ([Ca2+]c) is key for the regulation of many cellular processes, such cell signaling and proliferation, metabolism, and muscle contraction. In cardiomyocytes, Ca2+ is an important regulator in many cellular functions such electrophysiological processes, excitation‐contraction coupling, regulation of contractile proteins activity, energy metabolism, cell death, and transcriptional regulation by the activation of Ca2+‐dependent transcriptional pathways. In cardiomyocytes, the two main Ca2+‐dependent pathways are the Ca2+/calmodulin‐calcineurin‐NFAT and the Ca2+/calmodulin‐dependent kinases‐MEF2. Both pathways are involved in the transcriptional control of many cardiac genes. Cardiac hypertrophy (CH) and heart failure (HF) are characterized by alterations in calcium handling such a low sarcoplasmic reticulum Ca2+ content, decreased rate of Ca2+ removal from the sarcoplasm, increased diastolic [Ca2+]c, and decreased systolic [Ca2+]c, all of them contributing to diminished contractibility and force generation in failing heart. At gene expression level, there are also many changes such decreased levels of SERCA2a and activation of a fetal gene expression program in cardiomyocytes. A variety of Ca2+‐dependent signaling pathways have been implicated in CH and HF, but whether these pathways are interrelated and whether there is specificity among them are still unclear and under investigation. The focus of this review is to make an analysis of the current knowledge about the role of Ca2+ signaling pathways in the regulation of cardiac gene expression making special emphasis in novel strategies to correct Ca2+ handling alterations by means of SERCA2a gene therapy. © 2011 IUBMB IUBMB Life, 2011.
Signaling epigenetics: Novel insights on cell signaling and epigenetic regulation
Authors: Arzate‐Mejía Rodrigo G. , Valle‐García David , Recillas‐Targa Félix 
Published: September 2011

AbstractCells must be able to respond rapidly and precisely not only to changes in their external environment but also to developmental and differentiation cues to determine when to divide, die, or acquire a particular cell fate. Signal transduction pathways are responsible for the integration and interpretation of most of such signals into specific transcriptional states. Those states are achieved by the modulation of chromatin structure that activates or represses transcription at particular loci. Although a large variety of signal transduction pathways have already been described, much less is known about the crosstalk between signal transduction and its consequent changes in chromatin structure and, therefore, gene expression. Here we present some examples of the relationship between chromatin‐associated proteins and important signal transduction pathways during critical processes like development, differentiation, and disease. There is a great diversity of epigenetic mechanisms that have unexpected interactions with signaling pathways to establish transcriptional programs. Moreover, there are also particular cases where signaling pathways directly affect important components of the epigenetic machinery. Based on such examples, we further propose future research directions linking cell signaling and epigenetics. It is foreseeable that analyzing the relationship between cell signaling and epigenetics will be a huge area for future development that will help us understand the complex process by which a cell is able to induce transcriptional changes in response to external and internal signals. © 2011 IUBMB IUBMB Life, 2011
Molecular control of cell differentiation and programmed cell death during digit development
Authors: Chimal‐Monroy Jesús , Abarca‐Buis René Fernando , Cuervo Rodrigo , Díaz‐Hernández Martha , Bustamante Marcia , Rios‐Flores Jesús Alberto , Romero‐Suárez Silvina , Farrera‐Hernández Alejandro 
Published: September 2011

AbstractDuring the hand plate development, the processes of cell differentiation and control of cell death are relevant to ensure a correct shape of the limb. The progenitor cell pool that later will differentiate into cartilage to form the digits arises from undifferentiated mesenchymal cells beneath the apical ectodermal ridge (AER). Once these cells abandon the area of influence of signals from AER and ectoderm, some cells are committed to chondrocyte lineage forming the digital rays. However, if the cells are not committed to chondrocyte lineage, they will form the prospective interdigits that in species with free digits will subsequently die. In this work, we provide the overview of the molecular interactions between different signaling pathways responsible for the formation of digit and interdigit regions. In addition, we briefly describe some experiments concerning the most important signals responsible for promoting cell death. Finally, on the basis that the interdigital tissue has chondrogenic potential, we discuss the hypothesis that apoptotic‐promoting signals might also act as antichondrogenic factors and chondrogenic factors might operate as anti‐apoptotic factors. © 2011 IUBMB IUBMB Life, 2011
Site specificity of OH α‐H abstraction reaction for a β‐hairpin peptide: An ab initio study
Authors: Lin Ren‐Jie , Jang Soonmin , Wu Chen‐Chang , Liu Ya‐Ling , Li Feng‐Yin 
Published: September 2011

AbstractA β‐hairpin peptide (PDB ID 1UAO) was modeled to explore the backbone oxidation of a protein by an OH radical to abstract one α‐H atom with ab initio calculation at the B3LYB/6‐31G(d) without any constraint. Three glycine residues located at three different sites in 1UAO were used to examine the possible site specificity of this backbone oxidation. The pre‐ and post‐reactive complexes along with their associated transition states were located and verified by the intrinsic reaction coordinate method. The reaction profile of these α‐H abstraction reactions was constructed. The effects of the aqueous solution were estimated by the conductor‐like polarizable continuum model (CPCM) model. Rate constants were calculated with transition state theory. The reaction rate of the OH α‐H abstraction varies among these three different sites. The differences among these three sites were rationalized in terms of the molecular and electronic structures of the reactive complexes along the reaction pathway. The explicit solvation effect was estimated through the similar abstraction of a zwitterionic glycine with the combination of microsolvation and a CPCM model. Our results indicate that the α‐H abstraction at certain sites requires explicit salvation to obtain accurate results. A replica exchange molecular dynamics simulation was performed to demonstrate the structural change due to this type of abstraction. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Timing of Lateglacial vegetation dynamics and respective palaeoenvironmental conditions in southern Estonia: evidence from the sediment record of Lake Nakri
Authors: Amon Leeli , Veski Siim , Heinsalu Atko , Saarse Leili 
Published: September 2011

AbstractThis paper investigates a detailed well‐dated Lateglacial floristic colonisation in the eastern Baltic area, ca. 14 000–9000 cal. a BP, using palynological, macrofossil, loss‐on‐ignition, and 14C data. During 14 000–13 400 cal. a BP, primarily treeless pioneer tundra vegetation existed. Tree birch (Betula sect. Albae) macro‐remains and a high tree pollen accumulation rate indicate the presence of forest‐tundra with birch and possibly pine (Pinus sylvestris L.) trees during 13 400–12 850 cal. a BP. Palaeobotanical data indicate that the colonisation and development of forested areas were very rapid, arising within a period of less than 50 years. Thus far, there are no indications of conifer macrofossils in Estonia to support the presence of coniferous forests in the Lateglacial period. Signs of Greenland Interstadial 1b cooling during 13 100 cal. a BP are distinguishable. Biostratigraphic evidence indicates that the vegetation was again mostly treeless tundra during the final colder episode of the Lateglacial period associated with Greenland Stadial 1, approximately 12 850–11 650 cal. a BP. This was followed by onset of the Holocene vegetation, with the expansion of boreal forests, in response to rapid climatic warming. Copyright © 2011 John Wiley & Sons, Ltd.
Hydrogen Abstraction Followed by Nitroxide‐Mediated Polymerization: Synthesis of 2,7‐Dibromofluorene‐Labeled Polystyrene
Authors: Butcher William E. , Tillman Eric S. 
Published: September 2011

AbstractChromophore end‐labeled polystyrene is synthesized using nitroxide‐mediated polymerization (NMP) by decomposing 2‐2′‐azoisobutyronitrile (AIBN) or benzoyl peroxide (BPO) in the presence of fluorene or fluorene derivatives. End‐labeling is dependent on the thermally produced radical species selectively abstracting a hydrogen atom from the 9‐position of the fluorene species prior to initiation of styrene. From gel permeation chromatography (GPC) data and UV–Vis analysis, it is found that AIBN initiation, compared to BPO, leads to a more controlled polymerization system, producing polymers with predictable molecular weights, narrower polydispersity index (PDI) values (<1.3), and higher amounts of fluorene end‐labeling. In terms of the reaction parameters, no consistent trend is observed as a function of the timing of styrene's addition or the temperature at which the hydrogen abstraction phase is performed. Analysis of the chromophore content by UV–Vis spectroscopy demonstrated that the presence of bromine atoms on the 2‐ and 7‐position of the fluorene species leads to higher percent labeling of the chromophore species, presumably due to a more facile abstraction of the hydrogen at the 9‐position.
Global attractor for a three‐species predator‐prey model with cross‐diffusion
Authors: Guo Haojie , Zheng Sining 
Published: September 2011

AbstractThis paper studies a three‐species predator‐prey model with cross‐diffusion. In a previous paper 11 of Pang and Wang, it was proved that the system admits global classical solutions if the exponents in cross diffusion term satisfy m, l ≥ 1. In the present paper, we continue considering the asymptotic behavior of the solutions, and obtain that the system possesses a global attractor in fact, if the cross diffusion exponents are even larger with m, l ≥ 2.
A note on the unirationality of a moduli space of double covers
Authors: Jaya NN Iyer , Müller–Stach Stefan 
Published: September 2011

AbstractIn this note we look at the moduli space \documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}${\mathcal R}_{3,2}$\end{document} of double covers of genus three curves, branched along 4 distinct points. This space was studied by Bardelli, Ciliberto and Verra in 1. It admits a dominating morphism \documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}${\mathcal R}_{3,2} \rightarrow {\mathcal A}_4$\end{document} to Siegel space. We show that there is a birational model of \documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}${\mathcal R}_{3,2}$\end{document} as a group quotient of a product of two Grassmannian varieties. This gives a proof of the unirationality of \documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}${\mathcal R}_{3,2}$\end{document} and hence a new proof for the unirationality of \documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}${\mathcal A}_4$\end{document}.
Structure elucidation of two new unusual monoterpene glycosides from Euphorbia decipiens, by 1D and 2D NMR experiments
Authors: Demirkiran Ozlem , Topcu Gulacti , Hussain Javid , Uddin Ahmad Viqar , Choudhary M. Iqbal 
Published: September 2011

AbstractTwo new unusual monoterpene glycosides, (Z)‐3,6‐dimethyl‐3‐(β‐D‐O‐glucosylmethylene)cyclohept‐4‐ene‐1‐one (1) and 3,6‐dimethyl‐3‐(β‐D‐O‐glucosylmethylene)cycloheptanone (2) have been isolated along with five known compounds, 3‐hydroxy‐4‐methoxybenzoic acid, 6,7‐dihydroxycoumarin, luteolin, apigenin 5‐O‐αl‐L‐rhamnoside, and pinocembrin‐7‐O‐rutinoside from ethyl acetate extract of Euphorbia decipiens. The structures of the isolated compounds were elucidated by extensive 1D‐ and 2D‐NMR, and mass spectroscopic analyses. Copyright © 2011 John Wiley & Sons, Ltd.
Potential role of reduced basolateral potassium (IKCa3.1) channel expression in the pathogenesis of diarrhoea in ulcerative colitis
Authors: Al‐Hazza Adel , Linley John E , Aziz Qadeer , MacLennan Kenneth A , Hunter Malcolm , Sandle Geoffrey I 
Published: September 2011

AbstractDiarrhoea in ulcerative colitis (UC) mainly reflects impaired colonic Na+ and water absorption. Colonocyte membrane potential, an important determinant of electrogenic Na+ absorption, is reduced in UC. Colonocyte potential is principally determined by basolateral IK (KCa3.1) channel activity. To determine whether reduced Na+ absorption in UC might be associated with decreased IK channel expression and activity, we used molecular and patch clamp recording techniques to evaluate IK channels in colon from control patients and patients with active UC. In control patients, immunolabelling revealed basolateral IK channels distributed uniformly along the surface‐crypt axis, with substantially decreased immunolabelling in patients with active UC, although IK mRNA levels measured by quantitative PCR were similar in both groups. Patch clamp analysis indicated that cell conductance was dominated by basolateral IK channels in control patients, but channel abundance and overall activity were reduced by 53% (p = 0.03) and 61% (p = 0.04), respectively, in patients with active UC. These changes resulted in a 75% (p = 0.003) decrease in the estimated basolateral membrane K+ conductance in UC patients compared with controls. Levels of IK channel immunolabelling and activity in UC patients in clinical remission were similar to those in control patients. We conclude that a substantial decrease in basolateral IK channel expression and activity in active UC most likely explains the epithelial cell depolarization observed in this disease, and decreases the electrical driving force for electrogenic Na+ transport, thereby impairing Na+ absorption (and as a consequence, Cl− and water absorption) across the inflamed mucosa. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers
Authors: Yip Stephen , Butterfield Yaron S , Morozova Olena , Chittaranjan Suganthi , Blough Michael D , An Jianghong , Birol Inanc , Chesnelong Charles , Chiu Readman , Chuah Eric , Corbett Richard , Docking Rod , Firme Marlo , Hirst Martin , Jackman Shaun , Karsan Aly , Li Haiyan , Louis David N , Maslova Alexandra , Moore Richard , Moradian Annie , Mungall Karen L , Perizzolo Marco , Qian Jenny , Roldan Gloria , Smith Eric E , Tamura‐Wells Jessica , Thiessen Nina , Varhol Richard , Weiss Samuel , Wu Wei , Young Sean , Zhao Yongjun , Mungall Andrew J , Jones Steven JM , Morin Gregg B , Chan Jennifer A , Cairncross J Gregory , Marra Marco A 
Published: September 2011

AbstractOligodendroglioma is characterized by unique clinical, pathological, and genetic features. Recurrent losses of chromosomes 1p and 19q are strongly associated with this brain cancer but knowledge of the identity and function of the genes affected by these alterations is limited. We performed exome sequencing on a discovery set of 16 oligodendrogliomas with 1p/19q co‐deletion to identify new molecular features at base‐pair resolution. As anticipated, there was a high rate of IDH mutations: all cases had mutations in either IDH1 (14/16) or IDH2 (2/16). In addition, we discovered somatic mutations and insertions/deletions in the CIC gene on chromosome 19q13.2 in 13/16 tumours. These discovery set mutations were validated by deep sequencing of 13 additional tumours, which revealed seven others with CIC mutations, thus bringing the overall mutation rate in oligodendrogliomas in this study to 20/29 (69%). In contrast, deep sequencing of astrocytomas and oligoastrocytomas without 1p/19q loss revealed that CIC alterations were otherwise rare (1/60; 2%). Of the 21 non‐synonymous somatic mutations in 20 CIC‐mutant oligodendrogliomas, nine were in exon 5 within an annotated DNA‐interacting domain and three were in exon 20 within an annotated protein‐interacting domain. The remaining nine were found in other exons and frequently included truncations. CIC mutations were highly associated with oligodendroglioma histology, 1p/19q co‐deletion, and IDH1/2 mutation (p < 0.001). Although we observed no differences in the clinical outcomes of CIC mutant versus wild‐type tumours, in a background of 1p/19q co‐deletion, hemizygous CIC mutations are likely important. We hypothesize that the mutant CIC on the single retained 19q allele is linked to the pathogenesis of oligodendrogliomas with IDH mutation. Our detailed study of genetic aberrations in oligodendroglioma suggests a functional interaction between CIC mutation, IDH1/2 mutation, and 1p/19q co‐deletion. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
A Comparative Study of Matrix‐ and Nano‐assisted Laser Desorption/Ionisation Time‐of‐Flight Mass Spectrometry of Isolated and Synthetic Lignin
Authors: Yoshioka Koichi , Ando Daisuke , Watanabe Takashi 
Published: September 2011

ABSTRACTIntroductionLignin is the second most abundant biopolymer next to cellulose. However, because of the complexity of the heterogeneous macromolecules, it is difficult to elucidate the polymeric structures of lignin by conventional analytical methods.ObjectiveTo obtain the detailed structures of lignin, we comparatively applied nano‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (NALDI‐TOF MS) and matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (MALDI‐TOF MS).MethodologySynthetic lignin from coniferyl alcohol and an isolated lignin from Pinus densiflora were subjected to NALDI‐ and MALDI‐TOF MS.ResultsWe first obtained NALDI‐TOF MS of synthetic and isolated lignin. Mass increments of 178 and 196 Da were observed in NALDI‐ and MALDI‐TOF mass spectra of the synthetic and isolated lignin. The mass intervals indicated that radical coupling forming β‐O‐4 bonds is the major pathway. Peaks in the low molecular mass region between m/z 500 and 800 were observed more extensively using NALDI‐TOF MS than MALDI‐TOF MS, which enabled detailed analysis of the interunit linkages in lignin.ConclusionOwing to the ionisation profile differentiation from MALDI‐TOF MS, NALDI‐TOF MS is useful for the structural analysis of lignin. Copyright © 2011 John Wiley & Sons, Ltd.
Biomaterials based on low cytotoxic vinyl esters for bone replacement application
Authors: Husár Branislav , Heller Christian , Schwentenwein Martin , Mautner Andreas , Varga Franz , Koch Thomas , Stampfl Jürgen , Liska Robert 
Published: September 2011

AbstractIn recent days, additive manufacturing technologies (AMT) based on photopolymerization have also found application in tissue engineering. Although acrylates and methacrylates have excellent photoreactivity and afford photopolymers with good mechanical properties, their cytotoxicity and degradation products disqualify them from medical use. Within this work, (meth)acrylate‐based monomers were replaced by vinyl esters with exceptional low cytotoxicity. The main focus of this paper lies on the determination of the photoreactivity and investigations concerning mechanical properties and degradation behavior of the new materials. Tested monomers provide sufficient photoreactivity for processing by AMT. Mechanical properties similar to natural bone could be obtained by adding suitable fillers like hydroxylapatite (HA). The right ratio of hydrophobic and hydrophilic monomers allows the tuning of the degradation behavior. Finally, with the optimum formulation, cellular 3D structures were built using digital light processing. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.
A critical local energy release rate criterion for fatigue fracture of elastomers
Authors: Mzabi Samy , Berghezan Daniel , Roux Stéphane , Hild Francois , Creton Costantino 
Published: September 2011

AbstractUsing Digital Image Correlation on high‐resolution images, the full strain field near the tip of a crack propagating under cyclic loading in an elastomer was characterized. We show unambiguously, and for the first time, the existence of a strongly localized and highly oriented process zone close to the crack tip and propose a simple physical model introducing a local energy release rate glocal = WunloadingH0, where Wunloading is the unloading strain energy density in uniaxial tension at the maximum strain measured at the crack tip, and H0 is the undeformed size of the highly stretched zone in the loading direction. Remarkably, the crack growth rate under cyclic loading is found to fall on a master curve as a function of glocal for three elastomers with different filler contents and crosslinking densities, while the same crack growth rate as a function of the applied macroscopic energy release rate G, differs by two orders of magnitude for the same three elastomers. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1518–1524, 2011