bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimum altered regions in early prostate cancer progression identified by high resolution whole genome tiling path BAC array comparative hybridization
Authors: Watson Spencer K. , Woolcock Bruce W. , Fee John N. , Bainbridge Terry C. , Webber Douglas , Kinahan Thomas J. , Lam Wan L. , Vielkind Juergen R. 
Published: March 2009

AbstractBACKGROUNDCarcinoma of the prostate (CaP) is a serious health problem. The altered molecular mechanisms that lead to this disease are poorly understood.METHODSSpecimens from radical prostatectomies and blood were collected from 18 CaP surgery patients. For CGH studies, 20 CaP‐related samples (16 Gleason grade 3, 3 higher grades, 1 BPH sample) and 18 samples of patient‐matched normal epithelial cells were obtained by laser‐assisted microdissection from frozen sections of the 18 prostatectomy specimens. High resolution SMRT aCGH was used to compare genomic profiles of prostatic samples to patient‐matched blood and pooled female DNA. TMPRSS2‐ERG fusion transcript analysis was performed by RT‐PCR in relation to alterations detected at the TMPRSS2 locus.RESULTSOur comprehensive aCGH approach allowed us to define 35 regions of recurrent alterations while excluding germline copy number polymorphisms. Novel regions identified include 2q14.2, containing INHBB, and 17q21.31. The TMPRSS2 locus at 21q22.3 may be a hotspot for rearrangements with 75% of the alterations resulting in the expression of a TMPRSS2‐ERG fusion transcript. Differences in fusion expression in different areas in an individual tumor focus and expression in adjacent normal epithelium supported intrafocal heterogeneity and field cancerization, respectively. Both features challenge our efforts to develop more objective markers for diagnosis and prediction of the severity of CaP.CONCLUSIONThe high‐density array enabled precise mapping of genomic alterations and consequently definition of minimum altered regions smaller than previously reported thus facilitating identification of those genes that contribute to the cancer transformation process. Prostate 69: 961–975, 2009. © 2009 Wiley‐Liss, Inc.
Conventions on multioperator sites: An efficient risk management tool
Authors: Gaucher R. , Dolladille O. 
Published: March 2009

AbstractUntil the end of the 20th century, single user sites were the norm in Europe, but in the last 10 years the situation has changed. Today, especially in the chemical industry, sites are operated by several companies with facilities close to one another.Beyond business interests, multioperator sites can offer great advantages to deal with environment, safety, security, and emergency management. But, this change generates new risks because of the interdependence between different companies and calls for a new organization of risk management at site scale.For managing overall risk, it is necessary to define a minimum of common rules. In particular, companies should be encouraged to conclude clear and efficient contracts between themselves. These contracts under private law are very flexible and can be easily updated to accompany the development of sites.The aim of this article is to highlight the main issues brought by this new kind of organization and to present INERIS' conclusions on appropriate contracts between operators (conventions) and efficient risk management on each site. © 2009 American Institute of Chemical Engineers Process Saf Prog 2010
Recommended management of steroid‐induced osteoporosis
Authors: Shukla Santwana , Tuck Stephen 
Published: March 2009

AbstractGlucocorticoids are responsible for a quarter of osteoporosis cases and doses as low as 2.5mg prednisolone daily increase the risk of bone loss. Here the authors discuss the pathogenesis and recommended management of glucocorticoid‐induced osteoporosis. Copyright © 2009 Wiley Interface Ltd
The optical properties of Cd1–xMnxTe (0 < x < 0.55) solid solutions in monocrystals and thin polycrystalline films
Authors: Caraman Iuliana , Bibire Gabriel Lazar Luminita , Lazar Iuliana , Stamate Marius , Rusu Dragos 
Published: March 2009

AbstractThe optical absorption spectra at the fundamental absorption edge of Cd1–xMnxTe (0 ≤ x ≤ 0.5) at 78‐300 K have been studied. Single crystals were grown by Bridgman method. At 293 K, the fundamental absorption red edge in crystals with x ≤ 0.5 is determined by the exciton absorption. The fundamental absorption edge has the specific shape of crystals with high impurity levels density. The absorption spectra in the domain of the fundamental absorption band of Cd1–xMnxTe solid solutions in thin films prepared by discrete (“flash”) evaporation of synthesized single crystals and by physical vapor deposition (using Cd0.5Mn0.5Te as source material) are investigated. The optical gap of Cd1–xMnxTe films prepared by discrete evaporation is equal to ∼2.0 eV and 2.13 eV at temperatures 293 K and 78 K, respectively. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Analysis of the co‐doping effect of manganese and lanthanide elements in SrGa2S4 by the relativistic DV‐Xα calculation
Authors: Nomura Shigetaka , Takizawa Takeo , Kai Munenori , Ando Shizutoshi 
Published: March 2009

AbstractThe electronic states of manganese and lanthanide elements in SrGa2S4 are calculated by the relativistic discrete variational Xα method using a FORTRAN program of DVSCATR in order to investigate the mechanism allowing the 3d‐3d transition of Mn in SrGa2S4 by co‐doping a lanthanide element. We use a spherical cluster model of the D2 symmetry which consists of 45 atoms of Sr9Ga12S24, representing SrGa2S4, in our calculation. Doping a lanthanide to SrGa2S4 is represented by substituting a Sr atom with a lanthanide atom (indicated by ‘Ln’) at the cluster centre as (LnSr8)Ga12S24. Two types of co‐doping models are prepared as (LnMn2Sr6)Ga12S24 for MnSr and (LnSr8)(Mn4Ga8)S24 for MnGa with keeping the D2 symmetry. As a result of the self‐consistent charge (SCC) calculation, the averaged distance between a lanthanide atom at the cluster centre and surrounding eight sulphur atoms has to be set as 70 to 80% of that between the original Sr‐S combinations. Calculated electronic states show that the Ln(5d) and Mn(4s,4p) atomic orbitals are highly mixed, and in the lower energy range, the Mn(4s,4p) and Mn(3d) are also highly mixed. This hybridization cascade can explain the co‐doping effect as that the electrons optically excited to the unoccupied states relating to the Ln(5d) would finaly relax to the 3d‐3d transition of Mn. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The anisotropy of the optical properties of ternary semiconductors formed by elements of III and VI groups
Authors: Cuculescu Elmira , Evtodiev Igor , Caraman Iuliana 
Published: March 2009

AbstractThe GaSxSe1‐x and GaSexTe1‐x single crystals with the composition parameter x in the range of 0 ≤ x ≤ 0.3 and 0.7 ≤ x ≤ 1 respectively have been obtained. The absorption and photoluminescence (PL) measurements have been carried out for two polarizations: E ∥ C and E ⊥ C (E is the electrical field vector of light wave and C is the crystallographic axis normal to the cleaved plane). The anisotropy of optical absorption reveals itself on the low energy wing of the n =1 free exciton band. The anisotropy coefficient increases with the temperature decrease. The edge of the absorption band is determined by direct n =1 excitons for E ⊥ C polarization and by indirect transitions at low absorption coefficient for E ∥ C polarization. The photoluminescence spectra of GaS0.2Se0.8 crystals at 78 K in E ∥ C and E ⊥ C polarizations are identical to those of GaSe. The high energy photoluminescence band is determined by the radiative emission of direct bounded excitons. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Characteristics of chemical bond and vacancy formation in chalcopyrite‐type CuInSe2 and related compounds
Authors: Maeda Tsuyoshi , Wada Takahiro 
Published: March 2009

AbstractWe studied characteristics of chemical bond and vacancy formation in chalcopyrite‐type CuInSe2 (CIS) by first principles calculations. The chalcopyrite‐type CIS has two kinds of chemical bonds, Cu‐Se and In‐Se. The Cu‐Se bond is a weak covalent bonding because electrons occupy both bonding and antibonding orbitals of Cu 3d and Se 4p and occupy only the bonding orbital (a1) of Cu 4s and Se 4p and do not occupy the antibonding orbital (a1*) of Cu 4s and Se 4p. On the other hand, the In‐Se bond has a partially covalent and partially ionic character because the In 5s orbital covalently interacts with Se 4p; the In 5p orbital is higher than Se 4p and so the electron in the In 5p orbital moves to the Se 4p orbital. The average bond order of the Cu‐Se and In‐Se bonds can be calculated to be 1/4 and 1, respectively. The bond order of Cu‐Se is smaller than that of In‐Se. The characteristics of these two chemical bonds are related to the formation of Cu and In vacancies in CIS. The formation energy of the Cu vacancy is smaller than that of the In vacancy under both Cu‐poor and In‐poor conditions. The displacement (Δl) of the surrounding Se atoms after the formation of the Cu vacancy is smaller than the Δl after the formation of the In vacancy. The interesting and unique characteristics of CIS are discussed on the basis of the characteristics of the chemical bond. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Thin film deposition of complex chalcogenide gradient layers by sputtering methods
Authors: Dittrich Herbert , Stadler Andreas , Topa Dan , Schimper Hermann‐Josef , Basch Angelika 
Published: March 2009

AbstractIn ternary chalcogenide systems, a lateral compositional gradient in deposited layers could help to reduce the experimental efforts drastically. At present, no sputtering method for these sulfosalt gradient layers is described. A method was developed to deposit ternary (SnS)x(Bi2S3)1‐x gradient layers by sputtering methods. Therefore, binary SnS and Bi2S3 sputter targets were prepared by uniaxial hot pressing. Halved targets were bonded together to form composite SnS/Bi2S3‐targets. Layer deposition was carried out on up to 50x100 mm2 glass and glass/Mo substrates using different sputter parameters and substrate temperatures. The (SnS)x(Bi2S3)1‐x gradient layers were characterised by microprobe, X‐ray diffraction, and UV/Vis/NIR spectrometry. The composition of the layers is determined laterally and the film structure and optical properties were correlated via the substrate coordinates. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Preface: Phys. Status Solidi C 6/3
Authors: Yang Deren , Kittler Martin 
Published: March 2009

AbstractThese proceedings contain the contributions of the 3rd Sino–German Symposium “The Silicon Age: Silicon for Microelectronics, Photonics and Photovoltaics”, which was held from 9 to 14 June 2008 in the HNA Hotel, Hangzhou, P.R. China. Nearly 30 scientists from Germany and China were invited to present their views about different aspects of silicon.In the silicon age, microelectronics has driven the high‐speed development of economy, science and technology in the world during the last century and affects now every aspect of our life. Solar cells based on crystalline Si are expected to cover more than 10% of the worldwide energy consumption in a few decades. Furthermore, there are intensive research activities regarding Si‐based photonics, including on‐chip integration of photonics in CMOS IC technology. In addition, new areas being connected with silicon are starting to appear, such as electrical biochips, micro‐opto‐electro‐mechanics or nanotechnology and nanoelectronics. Silicon, one can reasonably argue, is the most intensively studied solid element of all materials in the world. However, there is still a need for continuation of research and development regarding numerous aspects of Si, which are the field of work of many laboratories all over the world. Examples for such ‘hot’ areas are larger Si crystals/wafers, SiGe hetrostructures for high speed devices, Si‐based light emitters, application of Si in new micro‐opto‐electro‐mechanic devices etc.During the 3rd Sino–German symposium, the progress regarding crystalline silicon materials in different areas has been discussed. German and Chinese scientists from universities and research institutes presented their views about the various facets of silicon materials. The symposium provided a forum for a fruitful, intensive and open communication allowing the participants to build up or intensify relationships for a close cooperation in future.We would like to thank all participants of the symposium for their contributions and the Sino–German Science Centre in Beijing for the financial support of the symposium.October 2008
The effect of silyl and phenyl functional group end caps on the nonlinear optical properties of polyynes: A long‐range corrected density functional theory study
Authors: Song Jong‐Won , Watson Mark A. , Sekino Hideo , Hirao Kimihiko 
Published: March 2009

AbstractThe polarizabilities, α, second‐hyperpolarizabilities, γ, and γ scaling factors, c, of polyynes [i‐(Pr)3 Si–(CC)n–Si i‐(Pr)3, H–(CC)n–Si i‐(Pr)3, H–(CC)n‐Ph, and Ph–(CC)n–Ph: n = 1 to 8] end‐capped with triisopropylsilane (i‐(Pr)3 Si–; TIPS) and phenyl groups were calculated using HF and DFT using the recently developed LC‐BOP and LCgau‐BOP functionals. Comparison with the α and γ values of the uncapped polyynes shows that the TIPS and phenyl end caps do not increase the α and γ values by a simple additive constant, but instead seem to expand the effective conjugation length (n) of the polyyne backbone. Using a newly‐proposed power‐law function, γ = a + b(n + Δn)c, we found that a single phenyl or TIPS end cap has the effect of increasing n by approximately Δn = 1.35 or 0.83, respectively. In the case of the phenyl end caps, we confirm that this function gives a better fit to the data than the function γ = a + bnc, even with constant b and c values, determined from a fit to the uncapped polyyne γ values (γ = bnc). In the case of the TIPS end caps, the fit to γ = a + b(n + Δn)c gives a smaller Δn, but the assumption of constant b and c is less accurate. We also compared our c values to experimental data using the commonly used function γ = a + bnc. Our results are consistent with the experimental c values, in that the c values of Ph–(CC)n–Ph are higher than those of i‐(Pr)3 Si–(CC)n–Si i‐(Pr)3. Finally, using the power‐law, γ = a + b(n + Δn)c, we predict the, as yet undetermined, experimental c value of uncapped polyynes using the experimental γ values of Ph–(CC)n–Ph (Δn = 2.7), to be ∼4.88. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Comparison of geometric, electronic, and vibrational properties for all pentagon/hexagon‐bearing isomers of fullerenes C38, C40, and C42
Authors: Małolepsza Edyta , Lee Yuan‐Pern , Witek Henryk A. , Irle Stephan , Lin Chun‐Fu , Hsieh Horng‐Ming 
Published: March 2009

AbstractThe self‐consistent‐charge density‐functional tight‐binding (SCC‐DFTB) method is employed for computing geometric, electronic, and vibrational properties for various topological isomers of small fullerenes. We consider all pentagon/hexagon‐bearing isomers of C38, C40, and C42 as the second part of a larger effort to catalogue the CC distance distributions, valence CCC angle distributions, electronic densities of states (DOSs), vibrational densities of states (VDOSs), and infrared (IR) and Raman spectra for fullerenes C20C180 [analogous data for C20C36 were published previously in Małolepsza et al., J Phys Chem A, 2007, 111, 6649]. Common features among the fullerenes are identified and properties characteristic for each specific fullerene cage size are discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Chestega: chess steganography methodology
Authors: Desoky Abdelrahman , Younis Mohamed 
Published: March 2009

AbstractSteganography is the science and art of avoiding the arousal of suspicion in covert communications. This paper presentsChessSteganography (Chestega), a novel methodology that exploits popular games like chess. Chestega conceals messages in chess related covers such as training documents, game analysis, news articles, etc. Unlike contemporary approaches, Chestega does not exploit noise to embed a message nor produce a detectable noise. Instead, authenticated data can be employed in the cover which makes it resilient to comparison attacks. Chestega is also a public approach that neither relies on the secrecy of its technique, nor need to employ a stega‐key. The paper demonstrates the feasibility of employing authenticated Chess Cover that is generated by Chessmaster 8000. Chestega is further validated through steganalysis. Copyright © 2009 John Wiley & Sons, Ltd.
Facile Plasma‐Enhanced Deposition of Ultrathin Crosslinked Amino Acid Films for Conformal Biometallization
Authors: Anderson Kyle D. , Slocik Joseph M. , McConney Michael E. , Enlow Jesse O. , Jakubiak Rachel , Bunning Timothy J. , Naik Rajesh R. , Tsukruk Vladimir V. 
Published: March 2009

AbstractA novel method for the facile fabrication of conformal, ultrathin, and uniform synthetic amino acid coatings on a variety of practical surfaces by plasma‐enhanced chemical vapor deposition is introduced. Tyrosine, which is utilized as an agent to reduce gold nanoparticles from solution, is sublimed into the plasma field and directly deposited on a variety of substrates to form a homogeneous, conformal, and robust polyamino acid coating in a one‐step, solvent‐free process. This approach is applicable to many practical surfaces and allows surface‐induced biometallization while avoiding multiple wet‐chemistry treatments that can damage many soft materials. Moreover, by placing a mask over the substrate during deposition, the tyrosine coating can be micropatterned. Upon its exposure to a solution of gold chloride, a network of gold nanoparticles forms on the surface, replicating the initial micropattern. This method of templated biometallization is adaptable to a variety of practical inorganic and organic substrates, such as silicon, glass, nitrocellulose, polystyrene, polydimethylsiloxane, polytetrafluoroethylene, polyethylene, and woven silk fibers. No special pretreatment is necessary, and the technique results in a rapid, conformal amino acid coating that can be utilized for further biometallization.
SOX15 and SOX7 Differentially Regulate the Myogenic Program in P19 Cells
Authors: Savage Josée , Conley Andrew J. , Blais Alexandre , Skerjanc Ilona S. 
Published: March 2009

AbstractIn this study, we have identified novel roles for Sox15 and Sox7 as regulators of muscle precursor cell fate in P19 cells. To examine the role of Sox15 and Sox7 during skeletal myogenesis, we isolated populations of P19 cells with either gene stably integrated into the genome, termed P19[Sox15] and P19[Sox7]. Both SOX proteins were sufficient to upregulate the expression of the muscle precursor markers Pax3/7, Meox1, and Foxc1 in aggregated cells. In contrast to the P19[Sox7] cell lines, which subsequently differentiated into skeletal muscle, myogenesis failed to progress past the precursor stage in P19[Sox15] cell lines, shown by the lack of MyoD and myosin heavy chain (MHC) expression. P19[Sox15] clones showed elevated and sustained levels of the inhibitory factors Msx1 and Id1, which may account for the lack of myogenic progression in these cells. Stable expression of a Sox15 dominant-negative protein resulted in the loss of Pax3/7 and Meox1 transcripts, as well as myogenic regulatory factor (MRF) and MHC expression. These results suggest that Sox15, or genes that are bound by Sox15, are necessary and sufficient for the acquisition of the muscle precursor cell fate. On the other hand, knockdown of endogenous Sox15 caused a decrease in Pax3 and Meox1, but not MRF expression, suggesting that other factors can compensate in the absence of Sox15. Taken together, these results show that both Sox7 and Sox15 are able to induce the early stages of myogenesis, but only Sox7 is sufficient to initiate the formation of fully differentiated skeletal myocytes.Disclosure of potential conflicts of interest is found at the end of this article.
X‐ray tracing study of crystal spectrometers for WDXRS application
Authors: Tadić T. , Jakšić M. , Božičević I. 
Published: March 2009

AbstractConstruction of a high energy resolution crystal X‐ray spectrometer to be used for wavelength‐dispersive X‐ray emission spectroscopy (WDXRS) may result in different geometrical aberrations, such as systematic X‐ray line shifts and changes of the X‐ray line shape. Most of these aberrations can be reduced by careful design of a crystal spectrometer, keeping the efficiency of the spectrometer as high as possible. The availability of high‐resolution position‐sensitive detectors and small excitation beam sizes, and therefore a possible downsized Wavelength‐dispersive X‐ray (WDX) spectrometer, increase the need for reliable simulation of aberrations involved in WDXRS. Since the experimental investigation of the impact that WDX spectrometer design has on a particular aberration is rather time‐consuming, a numerical X‐ray tracing procedure, XTRACE, has been developed and applied for this purpose. Results are given in the form of virtual X‐ray energy spectra that have been affected by the most important aberrations. Copyright © 2009 John Wiley & Sons, Ltd.
De Novo Next Generation Sequencing of Plant Genomes
Authors: Rounsley Steve , Marri Pradeep Reddy , Yu Yeisoo , He Ruifeng , Sisneros Nick , Goicoechea Jose Luis , Lee So Jeong , Angelova Angelina , Kudrna Dave , Luo Meizhong , Affourtit Jason , Desany Brian , Knight James , Niazi Faheem , Egholm Michael , Wing Rod A. 
Published: March 2009

Abstract
The genome sequencing of all major food and bioenergy crops is of critical importance in the race to improve crop production to meet the future food and energy security needs of the world. Next generation sequencing technologies have brought about great improvements in sequencing throughput and cost, but do not yet allow for de novo sequencing of large repetitive genomes as found in most crop plants. We present a strategy that combines cutting edge next generation sequencing with “old school” genomics resources and allows rapid cost-effective sequencing of plant genomes.
Paleohydrology of the upper Laurentian Great Lakes from the late glacial to early Holocene
Authors: Breckenridge Andy , Johnson Thomas C. 
Published: March 2009

AbstractBetween 10,500 and 9000 cal yr BP, δ18O values of benthic ostracodes within glaciolacustrine varves from Lake Superior range from − 18 to − 22‰ PDB. In contrast, coeval ostracode and bivalve records from the Lake Huron and Lake Michigan basins are characterized by extreme δ18O variations, ranging from values that reflect a source that is primarily glacial (∼ − 20‰ PDB) to much higher values characteristic of a regional meteoric source (∼ − 5‰ PDB). Re-evaluated age models for the Huron and Michigan records yield a more consistent δ18O stratigraphy. The striking feature of these records is a sharp drop in δ18O values between 9400 and 9000 cal yr BP. In the Huron basin, this low δ18O excursion was ascribed to the late Stanley lowstand, and in the Lake Michigan basin to Lake Agassiz flooding. Catastrophic flooding from Lake Agassiz is likely, but a second possibility is that the low δ18O excursion records the switching of overflow from the Lake Superior basin from an undocumented northern outlet back into the Great Lakes basin. Quantifying freshwater fluxes for this system remains difficult because the benthic ostracodes in the glaciolacustrine varves of Lake Superior and Lake Agassiz may not record the average δ18O value of surface water.