bluuebunny/crossref_metadata_2025_split huggingface dataset:
IMAC/TiO2 enrich for peptide modifications other than phosphorylation: Implications for chromatographic choice and database searching in phosphoproteomics
Authors: Worthington Jenny , Cutillas Pedro R. , Timms John F. 
Published: September 2011

AbstractProtein regulation by reversible phosphorylation is fundamental in nature, and large‐scale phosphoproteomic analyses are becoming routine in proteomics laboratories. These analyses utilise phosphopeptide separation and enrichment techniques linked to LC‐MS/MS. Herein, we report that IMAC and TiO2 also enrich for non‐phosphorylated modified peptides such as acetylated, deamidated and carbamylated peptides. Urea and digestion conditions commonly used in phosphoproteomic workflows are the likely sources of the induced modifications (deamidation and carbamylation) and can easily modify phosphopeptides. Including these variable modifications in database searches increased the total number of identified phosphopeptides by 15%. We also show that strong cation exchange fractionation provides poor resolution of phosphopeptides and actually enriches these alternatively modified peptides. By switching to reverse‐phase chromatography, we show a significant improvement in the number of identified phosphopeptides. We recommend that the users of phosphopeptide enrichment strategies avoid using urea as a denaturant and that careful consideration is given to chromatographic conditions and the types of variable modifications used in database searches. Thus, the capacity of IMAC and TiO2 to enrich phosphopeptides bearing modifications other than phosphorylation is a previously unappreciated property of these chromatographies with practical implications for the field of phosphoproteomics.
The selective inhibitory effect of a synthetic tanshinone derivative on prostate cancer cells
Authors: Xu Defeng , Lin Tzu‐Hua , Zhang Caixia , Tsai Yu‐Chieh , Li Shaoshun , Zhang Jing , Yin Min , Yeh Shuyuan , Chang Chawnshang 
Published: September 2011

AbstractBACKGROUNDAndrogen receptor (AR) is the main therapeutic target for the treatment of prostate cancer (PCa). Anti‐androgens to reduce or prevent androgens binding to AR are widely used to suppress AR‐mediated PCa growth; however, the androgen depletion therapy (ADT) is only effective for a short period of time. Here we tested PTS33, a new sodium derivative of cryptotanshinone, which can effectively inhibit the DHT‐induced AR transactivation and PCa cell growth, and then explored the effects of PTS33 on inhibiting the expressions of AR target genes and proteins.METHODSPCa cells, LNCaP, CWR22Rv1, C4‐2, PC‐3, and DU145, were treated with PTS33 and luciferase assay was used to evaluate the ability of each to regulate AR transactivation. RT‐PCR was used to evaluate the mRNA levels of AR target genes such as PSA, TMPRSS2, and TMEPA1. Western blot was used to determine AR, PSA, estrogen receptor alpha (ERα), glucocorticoid receptor (GR), and progesterone receptor (PR) protein expression. Cell growth and IC50 were determined by MTT assay after 48 hr treatment.RESULTSOur data showed that PTS33 selectively inhibits AR activities, but PTS33 does not repress the activities of other nuclear receptors, including ERα, GR, and PR. At a low concentration, 2 µM of PTS33 effectively suppresses the growth of AR‐positive PCa cells, and has little effect on AR‐negative PCa cells. Furthermore, our data indicated that PTS33 could modulate AR transactivation and suppress the AR target genes (PSA, TMPRSS2, and TMEPA1) expression in both androgen responsive PCa LNCaP cells and castration‐resistant C4‐2 cells. In addition, PTS33 can also inhibit estrogen/Δ5‐androstenediol induced AR activities. The mechanistic studies indicate that PTS33 can inhibit AR function by suppression of AR protein expression, the AR N–C interaction, and AR–coregulator interaction.CONCLUSIONSPTS33 has shown a good efficacy to inhibit AR transactivation, block AR regulated gene expression, and reduce cell growth in AR positive PCa cells. The structure of PTS33 could be used as a base for development of novel AR signaling inhibitors to treat PCa. Prostate 72:803–816, 2012. © 2011 Wiley Periodicals, Inc.
Radioresistance of prostate cancer cells with low proteasome activity
Authors: Della Donna Lorenza , Lagadec Chann , Pajonk Frank 
Published: September 2011

AbstractBACKGROUNDProstate cancer is frequently treated with radiotherapy. While treatment results are in general excellent, some patients relapse and current systemic therapies are not curative, thus, underlining the need for novel targeted therapies. Proteasome inhibitors have been suggested as promising new agents against solid tumors including prostate cancer but initial results from clinical trials are disappointing.METHODSIn this study we tested if prostate cancer cells are heterogeneous with regard to their intrinsic 26S proteasome activity, which could explain the lack of clinical responses to bortezomib. PC‐3 and DU145 prostate cancer cells and an imaging system for proteasome activity were used to identify individual cells with low proteasome activity. Clonogenic survival assays, a sphere‐forming assay and an in vivo limiting dilution assay were used to characterize radiation sensitivity, self‐renewal capacity, and tumorigenicity of the different subsets of cells.RESULTSWe identified a small population of cells with intrinsically low 26S proteasome activity. Fractionated radiation enriched for these cells and clonogenic survival assays and sphere‐forming assays revealed a radioresistant phenotype and increased self‐renewal capacity.CONCLUSIONSWe conclude that low 26S proteasome activity identifies a radioresistant prostate cancer cell population. This population of cells could be responsible for the clinical resistance of advanced prostate cancer to proteasome inhibitors and radiation. Prostate 72:868–874, 2012. © 2011 Wiley Periodicals, Inc.
XMRV accelerates cellular proliferation, transformational activity, and invasiveness of prostate cancer cells by downregulating p27Kip1
Authors: Pandhare‐Dash Jui , Mantri Chinmay K. , Gong Yuanying , Chen Zhenbang , Dash Chandravanu 
Published: September 2011

AbstractBACKGROUNDXenotropic murine leukemia virus‐related retrovirus (XMRV) is a recently discovered gammaretrovirus that was originally detected in prostate tumors. However, a causal relationship between XMRV and prostate cancer remains controversial due to conflicting reports on its etiologic occurrence. Even though gammaretroviruses are known to induce cancer in animals, a mechanism for XMRV‐induced carcinogenesis remains unknown. Several mechanisms including insertional mutagenesis, proinflammatory effects, oncogenic viral proteins, immune suppression, and altered epithelial/stromal interactions have been proposed for a role of XMRV in prostate cancer. However, biochemical data supporting any of these mechanisms are lacking. Therefore, our aim was to evaluate a potential role of XMRV in prostate carcinogenesis.METHODSGrowth kinetics of prostate cancer cells are conducted by MTT assay. In vitro transformation and invasion was carried out by soft agar colony formation, and Matrigel cell invasion assay, respectively. p27Kip1 expression was determined by Western blot and MMP activation was evaluated by gelatin‐zymography. Up‐regulation of miR221 and miR222 expression was examined by real‐time PCR.RESULTSWe demonstrate that XMRV infection can accelerate cellular proliferation, enhance transformation, and increase invasiveness of slow growing prostate cancer cells. The molecular basis of these viral induced activities is mediated by the downregulation of cyclin/cyclin dependent kinase inhibitor p27Kip1. Downstream analyses illustrated that XMRV infection upregulates miR221 and miR222 expression that target p27Kip1 mRNA.CONCLUSIONSWe propose that downregulation of p27Kip1 by XMRV infection facilitates transition of G1 to S, thereby accelerates growth of prostate cancer cells. Our findings implicate that if XMRV is present in humans, then under appropriate cellular microenvironment it may serve as a cofactor to promote cancer progression in the prostate. Prostate 72:886–897, 2012. © 2011 Wiley Periodicals, Inc.
On the molecular structure of human neuroserpin polymers
Authors: Santangelo Maria Grazia , Noto Rosina , Levantino Matteo , Cupane Antonio , Ricagno Stefano , Pezzullo Margherita , Bolognesi Martino , Mangione Maria Rosalia , Martorana Vincenzo , Manno Mauro 
Published: September 2011

AbstractThe polymerization of serpins is at the root of a large class of diseases; the molecular structure of serpin polymers has been recently debated. In this work, we study the polymerization kinetics of human neuroserpin by Fourier Transform Infra Red spectroscopy and by time‐lapse Size Exclusion Chromatography. First, we show that two distinct neuroserpin polymers, formed at 45 and 85°C, display the same isosbestic points in the Amide I′ band, and therefore share common secondary structure features. We also find a concentration independent polymerization rate at 45°C suggesting that the polymerization rate‐limiting step is the formation of an activated monomeric species. The polymer structures are consistent with a model that predicts the bare insertion of portions of the reactive center loop into the A β‐sheet of neighboring serpin molecule, although with different extents at 45 and 85°C. Proteins 2012; © 2011 Wiley Periodicals, Inc.
Pulse duration impact on laser structured ZnO:Al
Authors: Sämann Marc , Schubert Markus B. 
Published: September 2011

AbstractWe demonstrate a laser structuring process for aluminum doped ZnO with a line‐shaped Nd:YAG ultraviolet laser. This process yields a pyramid‐like surface texture with structure depths of d = 1.3 µm, which enhances light trapping in solar cells by diffraction of near infrared radiation. We investigate the impact of laser pulse duration from $ 25\,{\rm ns}\; \le \; \tau _{\rm P} \; \le \;60\;{\rm ns} $ on the optical transmittance and electrical conductivity of laser structured ZnO:Al. Formation of the surface texture proceeds via capillary waves. Increasing laser pulse duration causes oxygen effusion during the melt phase, and thereby impairs charge carrier mobility of the laser structured films.magnified imagea) Line‐focused Nd:YAG UV laser locally melts ZnO:Al and b) induces capillary waves. c) Line‐scanning forms wave structures, d) second scan after 90° rotation yields 2D pattern.(© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Magnetic vortex excitation dependence on the magnetic free layer and size of spin‐valve nanocontacts
Authors: Eggeling Moritz , Dimopoulos Theodoros , Heer Rudolf , Brückl Hubert 
Published: September 2011

AbstractIn this Letter we report on the spin‐torque‐driven magnetic switching and dynamic excitations in spin‐valve, circular nanocontacts, incorporating an unpinned CoFe/Ru/CoFe artificial antiferromagnet as polarizer. Our investigation concentrates on the influence of the magnetic free layer moment and of the nanocontact size on these spin‐torque related phenomena. Two multilayers are therefore investigated, one with an amorphous CoFeB and the other with a CoFe/CoFeB free layer. The nanocontact radii range from 40–130 nm. Both multilayers show clear current‐induced magnetic switching for small in‐plane magnetic fields. On the other hand, sub‐gigahertz dynamic spectra, related to magnetic vortex precession, are only observed for multilayers employing the CoFeB free layer and only for contact radii below 100 nm. The current and frequency dependence of the oscillation on the point contact radius and magnetic field is discussed. Multiple excitation modes are shown to exist at zero or small magnetic fields as a result of a highly inhomogeneous magnetic state below the nanocontact. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Polymer‐Coated Nanoparticles: A Universal Tool for Biolabelling Experiments
Authors: Zhang Feng , Lees Emma , Amin Faheem , Rivera_Gil Pilar , Yang Fang , Mulvaney Paul , Parak Wolfgang J. 
Published: September 2011

AbstractWater solubilization of nanoparticles is a fundamental prerequisite for many biological applications. To date, no single method has emerged as ideal, and several different approaches have been successfully utilized. These ‘phase‐transfer’ strategies are reviewed, indicating key advantages and disadvantages, and a discussion of conjugation strategies is presented. Coating of hydrophobic nanoparticles with amphiphilic polymers provides a generic pathway for the phase transfer of semiconductor, magnetic, metallic, and upconverting nanoparticles from nonpolar to polar environments. Amphiphilic polymers that include maleimide groups can be readily functionalized with chemical groups for specific applications. In the second, experimental part, some of the new chemical features of such polymer‐capped nanoparticles are demonstrated. In particular, nanoparticles to which a pH sensitive fluorophore has been attached are described, and their use for intracellular pH‐sensing demonstrated. It is shown that the properties of analyte‐sensitive fluorophores can be tuned by using interactions with the underlying nanoparticles.
Metastable Bi8Ni8S by Reductive Pseudomorphosis of Bi8Ni8SI2
Authors: Kaiser Martin , Isaeva Anna , Skrotzki Richard , Schwarz Ulrich , Ruck Michael 
Published: September 2011

AbstractThe bimetallic subsulfide Bi8Ni8S was synthesized by reduction of Bi8Ni8SI2withn‐BuLi. Bi8Ni8S is metastable and decomposes exothermically at about 180 °C. In a pseudomorphosis, the shiny black crystals of the precursor were preserved, while the iodide ions were extracted and the pre‐formed$\rm^1_\infty$[Bi8Ni8S] fragments rearranged into a pseudo‐hexagonal rod packing [space groupPbam,a= 1750.14(7) pm,b= 1007.7(2) pm,c= 419.6(3) pm]. The rods have an effective diameter of about 1 nm and consist of an outer octagonal tube of bismuth atoms and an inner octagonal tube of nickel atoms. This arrangement markedly resembles the columnar Ta4Te4Si structure type. The difference comes with the disulfide groups that reside on the central axis. Interatomic distances inside the rods are almost not affected by the reduction, and thus the electronic band structure is not much altered. Yet, the additional electrons raise the Fermi level into a local maximum of the density of states and occupy predominantly antibonding Ni–Ni and S–S states. The dominant Bi–Ni multicenter bonding is accompanied by localized two‐center bonds between nickel atoms. The charges of the nickel atoms as well as ELI‐D basin populations of Ni–Ni and Ni–Bi bonds change considerably, indicating that the tube is (un)charging quite flexibly and acts as an electron reservoir. In contrast to the iodide precursor, the weak Pauli paramagnetism of Bi8Ni8S is slightly enhanced and spin correlations are observed below 20 K.
Experiments in program verification using Event-B
Authors: Hallerstede Stefan , Leuschel Michael 
Published: September 2011

Abstract
The Event-B method can be used to model all sorts of discrete event systems, among them sequential programs. In this article we describe our experiences with using Event-B by way of two examples. We present a simple model of a factorial program, explaining the method, and a more intricate model of the Quicksort algorithm, providing some insights into strengths and weaknesses of Event-B. The two models are interspersed with our observations and some suggestions of how, we believe, Event-B could evolve. This evaluation of Event-B is intended to serve for determining directions for the evolution of Event-B and judging progress. It is our hope that the observations and suggestions can also be put to use for similar modelling formalisms, such as Z, ASM or VDM.
Polyacrylamide Gel Injections for Breast Augmentation: Management of Complications in 106 Patients, a Multicenter Study
Authors: Unukovych Dmytro , Khrapach Vasyl , Wickman Marie , Liljegren Annelie , Mishalov Volodymyr , Patlazhan Gennadiy , Sandelin Kerstin 
Published: September 2011

AbstractBackgroundPolyacrylamide gel (PAAG) was first manufactured in Ukraine in the late 1980s and introduced as a biomaterial for “breast augmentation without surgery.” Since it is prohibited in most countries, PAAG injections are rare nowadays, but their consequences and long‐term complications can be crucial.MethodsWe identified 106 patients consecutively operated on for PAAG complications at three teaching Ukrainian hospitals between 1998 and 2009. All relevant sociodemographic, clinical, and treatment characteristics were collected. Forty‐five (42%) patients were available for clinical follow‐up.ResultsThe majority (88%) had had bilateral PAAG injections. The mean volume of injected PAAG was 230 ml/breast (range = 50–400). Mean age at injection was 29 years (range = 17–49) and the mean time from the injection to complications was 6.1 years (SD = 4.1). Symptoms preceding debridement were pain in 85 patients (80%), breast hardening in 79 (74%), breast deformity in 77 (73%), lumps in 57 (54%), gel migration in 39 (37%), fistulas in 17 (16%), and gel leakage in 12 (11%). The surgical interventions in 199 breasts included gel evacuation alone in 107 (54%) or in combination with partial mastectomy in 65 (33%), partial mastectomy and partial pectoralis muscle resection in 12 (6%), or subcutaneous mastectomy in 15 (7%). Of the 199 operated breasts, 86 (43%) immediate and 58 (29%) delayed implant‐based breast reconstructions were performed.ConclusionInjections of PAAG can cause irreversible damage to the breast necessitating complex debridement procedures, even mastectomy and breast reconstruction. Despite numerous surgical interventions, gel remnants are still found on subsequent breast imaging. Although PAAG is prohibited in many countries, different types of injections with unknown long‐term effects are currently being used. Making the public aware of the problems of injectables for breast augmentation is warranted.
Mixing events in a stratified jet subject to surface wind and buoyancy forcing
Authors: Pham Hieu T. , Sarkar Sutanu 
Published: September 2011

AbstractThe fine-scale response of a subsurface stable stratified jet subject to the forcing of surface wind stress and surface cooling is investigated using direct numerical simulation. The initial velocity profile consists of a symmetric jet located below a surface layer driven by a constant wind stress. The initial density profile is well-mixed in the surface layer and linearly stratified in both upper and lower flanks of the jet. The minimum value of the gradient Richardson number in the upper flank of the jet exceeds the critical value of 0.25 for linear shear instability. Broadband finite-amplitude fluctuations are introduced to the surface layer to initiate the simulation. Turbulence is generated in the surface layer and deepens into the jet upper flank. Internal waves generated by the turbulent surface layer are observed to propagate downward across the jet. The momentum flux carried by the waves is significantly smaller than the Reynolds shear stress extracted from the background velocity. The wave energy flux is also smaller than the turbulence production by mean shear. Ejections of fluid parcels by horseshoe-like vortices cause intermittent patches of intense dissipation inside the jet upper flank where the background gradient Richardson number is larger than 0.25. Drag due to the wind stress is smaller than the drag caused by turbulent stress in the flow. Analysis of the mean and turbulent kinetic energy budgets suggests that the energy input by surface forcing is considerably smaller than the energy extracted from the initially imposed background shear in the surface layer.
Turbulent spots in oscillatory boundary layers
Authors: Mazzuoli Marco , Vittori Giovanna , Blondeaux Paolo 
Published: September 2011

AbstractDetailed knowledge of the dynamics of vortex structures in an oscillatory boundary layer is essential for the correct modelling of transport processes in many engineering problems and, in particular, of the pick-up and transport of sediments at the bottom of sea waves. In the present contribution, the formation of turbulent spots in an oscillatory boundary layer is investigated by means of direct numerical simulations. Two of the laboratory experiments of Carstensen, Sumer and Fredsøe are reproduced and, after a comparison of the numerical results with laboratory measurements, a detailed and quantitative characterization of the turbulent spots is also given on the basis of further simulations. The speeds of the head (${u}_{1H} $) and tail (${u}_{1T} $) of the spots are found to scale with the instantaneous free stream velocity ${U}_{e} $ and to be similar to those observed in steady boundary layers. The ratios ${u}_{1H} / {U}_{e} $ and ${u}_{1T} / {U}_{e} $ seem to increase with the Reynolds number (${R}_{\delta } $) while the streamwise expansion rate of the spots appears to be independent of ${R}_{\delta } $.
Credibility talk in public diplomacy
Authors: MOR BEN D. 
Published: September 2011

Abstract‘Politics has become a contest of competitive credibility’, argued Nye inSoft Power. Indeed, being perceived as honest and reliable is a necessary condition for obtaining and holding the attention of target audiences, as well as for effective persuasion, which is the objective of strategic communication. This task has become all the more difficult with the explosion of information sources and the discreditation efforts of opponents, but it is an essential element in the conduct of public diplomacy. How, then, do states and other international actors go about establishing their credibility while undermining that of opponents? This article employs rhetorical theory, impression management theory, and account theory to situate contests of credibility within the broader context of the accountability of social conduct. The theoretical part discusses the rhetorical strategies that actors use to credit their accounts and discredit those of their rivals. The empirical part addresses the debate between Israel and human rights groups over the Qana bombing incident of July 2006. The analysis of the blame imposition strategies used by Amnesty International and Human Rights Watch and the accounts offered by Israel, indicates the range and variability of credibility talk and the rules for crediting accounts that underlie it.
Fishing for a solution: can collaborative resource management reduce poverty and support conservation?
Authors: SOLOMON JENNIFER , JACOBSON SUSAN K. , LIU IVY 
Published: September 2011

SUMMARYProtected area management in developing countries faces the challenges of building support for conservation among neighbouring residents and monitoring the social and ecological impacts of conservation programming. This study examined a collaborative resource management (CRM) programme at Kibale National Park (Uganda) that permits residents to fish inside the Park. Like other integrated conservation and development programmes, the goals are to help alleviate poverty and encourage support for conservation and conservation-related behaviours. The programme's impact was empirically analysed using an 81 item personal survey, with 94 CRM fishers and 91 comparison group respondents, and additional data from semi-structured interviews and document review. Fishers’ annual income was significantly greater (median = US$ 376.02 yr−1) than that of the comparison group (median = US$ 196.19 yr−1;p< 0.001), and their tribal affiliation influenced earnings. Fishers indicated greater support for conservation (p< 0.01) than the comparison group. Although some CRM fishers deterred illegal activity, some may extract resources illegally. This study demonstrates that CRM is a viable tool for promoting support for conservation and increasing income, although monitoring of programme participants is needed to deter illegal behaviours and sustain the resource base.