bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined analysis of transcriptome and proteome data as a tool for the identification of candidate biomarkers in renal cell carcinoma
Authors: Seliger Barbara , Dressler Sven P. , Wang Ena , Kellner Roland , Recktenwald Christian V. , Lottspeich Friedrich , Marincola Francesco M. , Baumgärtner Maja , Atkins Derek , Lichtenfels Rudolf 
Published: February 2009

AbstractResults obtained from expression profilings of renal cell carcinoma using different “ome”‐based approaches and comprehensive data analysis demonstrated that proteome‐based technologies and cDNA microarray analyses complement each other during the discovery phase for disease‐related candidate biomarkers. The integration of the respective data revealed the uniqueness and complementarities of the different technologies. While comparative cDNA microarray analyses though restricted to up‐regulated targets largely revealed genes involved in controlling gene/protein expression (19%) and signal transduction processes (13%), proteomics/PROTEOMEX‐defined candidate biomarkers include enzymes of the cellular metabolism (36%), transport proteins (12%), and cell motility/structural molecules (10%). Candidate biomarkers defined by proteomics and PROTEOMEX are frequently shared, whereas the sharing rate between cDNA microarray and proteome‐based profilings is limited. Putative candidate biomarkers provide insights into their cellular (dys)function and their diagnostic/prognostic value but still warrant further validation in larger patient numbers. Based on the fact that merely three candidate biomarkers were shared by all applied technologies, namely annexin A4, tubulin α‐1A chain, and ubiquitin carboxyl‐terminal hydrolase L1, the analysis at a single hierarchical level of biological regulation seems to provide only limited results thus emphasizing the importance and benefit of performing rather combinatorial screenings which can complement the standard clinical predictors.
Serum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool?
Authors: Callesen Anne K. , Madsen Jonna S. , Vach Werner , Kruse Torben A. , Mogensen Ole , Jensen Ole N. 
Published: February 2009

AbstractSerum protein profiling by MS is a promising method for early detection of disease. Important characteristics for serum protein profiling are preanalytical factors, analytical reproducibility and high throughput. Problems related to preanalytical factors can be overcome by using standardized and rigorous sample collection and sample handling protocols. The sensitivity of the MS analysis relies on the quality of the sample; consequently, the blood sample preparation step is crucial to obtain pure and concentrated samples and enrichment of the proteins and peptides of interest. This review focuses on the serum sample preparation step prior to protein profiling by MALDI MS analysis, with particular focus on various SPE methods. The application of SPE techniques with different chromatographic properties such as RP, ion exchange, or affinity binding to isolate specific subsets of molecules (subproteomes) is advantageous for increasing resolution and sensitivity in the subsequent MS analysis. In addition, several of the SPE sample preparation methods are simple and scalable and have proven easy to automate for higher reproducibility and throughput, which is important in a clinical proteomics setting.
The art of observing rare protein species in proteomes with peptide ligand libraries
Authors: Boschetti Egisto , Righetti Pier Giorgio 
Published: February 2009

AbstractThe present review deals with the use of combinatorial ligand libraries, composed by hexapeptides, in the capture and concentration of the low‐abundance proteome. This method, first reported in 2005, is compared with other current methodologies aimed at exploring the “deep proteome”, such as: depletion of high‐abundance proteins (especially in sera and cerebrospinal fluid) by individual or combined antibodies (up to 20 against the most abundant species); narrow (1‐pH‐unit) IPGs (zoom gels) and prefractionation with multicompartment electrolyzers or with Off‐Gel electrophoresis. The physico‐chemical properties of the hexapeptide library are also explored, namely in assessing the proper length of the baits and the behavior of shorter oligopeptides, down to capture elicited by single amino acids. A number of examples on the use of this library is given, such as the analysis of biological fluids (human sera, urine, bile, cerebrospinal fluid) and of cell lysates (platelets, red blood cells). In all cases, it was possible to detected from three to five times as many proteins as compared to control, untreated samples. Perhaps the most spectacular results were obtained with the erythrocyte proteome, where 1570 proteins could be identified in the “minority” proteome, representing only 2% of the total cell lysate. Another interesting area of application regards the concentration and detection of trace impurities contaminanting r‐DNA proteins meant for human consumption: several host proteins, never reported before, could be revealed for the first time. Other nonhuman samples are currently under investigation, such as egg‐white (where no less than 148 unique gene products could be identified), egg yolk (with 255 unique species) and latex from Hevea brasiliensis. It is anticipated that the ligand library could be a most useful tool for detecting biomarkers for different pathologies and for drug treatment. As a future outlook, one could envision the synthesis of specialized libraries able to capture given classes of proteins (e.g., phospho‐ and glyco‐proteins). Additionally, the library could be used in association with other techniques currently in vogue, such as zoom gels, Off‐Gels, and the like.
Immuno‐MALDI‐TOF MS: New perspectives for clinical applications of mass spectrometry
Authors: Sparbier Katrin , Wenzel Thomas , Dihazi Hassan , Blaschke Sabine , Müller Gerhard‐Anton , Deelder André , Flad Thomas , Kostrzewa Markus 
Published: February 2009

AbstractThe discovery of novel biomarkers by means of advanced detection tools based on proteomic analysis technologies necessitates the development of improved diagnostic methods for application in clinical routine. On the basis of three different application examples, this review presents the limitations of conventional routine diagnostic assays and illustrates the advantages of immunoaffinity enrichment combined with MALDI‐TOF MS. Applying this approach increases the specificity of the analysis supporting a better diagnostic recognition, sensitivity, and differentiation of certain diseases. The use of MALDI‐TOF MS as detection method facilitates the identification of modified peptides and proteins providing additional information. Further, employing respective internal standard peptides allows for relative and absolute quantitation which is mandatory in the clinical context. Although MALDI‐TOF MS is not yet established for clinical routine diagnostics this technology has a high potential for improvement of clinical diagnostics and monitoring therapeutic efficacy.
Strategy for surveying the proteome using affinity proteomics and mass spectrometry
Authors: Wingren Christer , James Peter , Borrebaeck Carl A. K. 
Published: February 2009

AbstractAntibody‐based microarrays is a rapidly evolving technology that has gone from the first proof‐of‐concept studies to more demanding proteome profiling applications, during the last years. Miniaturized microarrays can be printed with large number of antibodies harbouring predetermined specificities, capable of targeting high‐ as well as low‐abundant analytes in complex, nonfractionated proteomes. Consequently, the resolution of such proteome profiling efforts correlate directly to the number of antibodies included, which today is a key limiting factor. To overcome this bottleneck and to be able to perform in‐depth global proteome surveys, we propose to interface affinity proteomics with MS‐based read‐out, as outlined in this technical perspective. Briefly, we have defined a range of peptide motifs, each motif being present in 5–100 different proteins. In this manner, 100 antibodies, binding 100 different motifs commonly distributed among different proteins, would potentially target a protein cluster of 104 individual molecules, i.e. around 50% of the nonredundant human proteome. Notably, these motif‐specific antibodies would be directly applicable to any proteome in a specie independent manner and not biased towards abundant proteins or certain protein classes. The biological sample is digested, exposed to these immobilized antibodies, whereby motif‐containing peptides are specifically captured, enriched and subsequently detected and identified using MS.
Randomized controlled trial of mindfulness‐based stress reduction (MBSR) for survivors of breast cancer
Authors: Lengacher Cecile A. , Johnson‐Mallard Versie , Post‐White Janice , Moscoso Manolete S. , Jacobsen Paul B. , Klein Thomas W. , Widen Raymond H. , Fitzgerald Shirley G. , Shelton Melissa M. , Barta Michelle , Goodman Matthew , Cox Charles E. , Kip Kevin E. 
Published: February 2009

AbstractObjectives: Considerable morbidity persists among survivors of breast cancer (BC) including high levels of psychological stress, anxiety, depression, fear of recurrence, and physical symptoms including pain, fatigue, and sleep disturbances, and impaired quality of life. Effective interventions are needed during this difficult transitional period.Methods: We conducted a randomized controlled trial of 84 female BC survivors (Stages 0–III) recruited from the H. Lee Moffitt Cancer and Research Institute. All subjects were within 18 months of treatment completion with surgery and adjuvant radiation and/or chemotherapy. Subjects were randomly assigned to a 6‐week Mindfulness‐Based Stress Reduction (MBSR) program designed to self‐regulate arousal to stressful circumstances or symptoms (n=41) or to usual care (n=43). Outcome measures compared at 6 weeks by random assignment included validated measures of psychological status (depression, anxiety, perceived stress, fear of recurrence, optimism, social support) and psychological and physical subscales of quality of life (SF‐36).Results: Compared with usual care, subjects assigned to MBSR(BC) had significantly lower (two‐sided p<0.05) adjusted mean levels of depression (6.3 vs 9.6), anxiety (28.3 vs 33.0), and fear of recurrence (9.3 vs 11.6) at 6 weeks, along with higher energy (53.5 vs 49.2), physical functioning (50.1 vs 47.0), and physical role functioning (49.1 vs 42.8). In stratified analyses, subjects more compliant with MBSR tended to experience greater improvements in measures of energy and physical functioning.Conclusions: Among BC survivors within 18 months of treatment completion, a 6‐week MBSR(BC) program resulted in significant improvements in psychological status and quality of life compared with usual care. Copyright © 2009 John Wiley & Sons, Ltd
Rapid degradation of ground ice in a ventilated talus slope: Flüela Pass, Swiss Alps
Authors: Phillips Marcia , Mutter Evelyn Zenklusen , Kern‐Luetschg Martina , Lehning Michael 
Published: February 2009

AbstractThe degradation of ground ice in talus deposits, which are important forms of debris storage in mountain environments, can cause mass movements, subsidence or instability of mountain infrastructure. Two 20 m deep boreholes instrumented with thermistors and located in a talus slope at 2400 m asl above a lake at Flüela Pass in the eastern Swiss Alps allow the analysis of the evolution of ground temperature and permafrost thickness between 2003 and 2008. The occurrence of intra‐talus ventilation can be discerned due to thermal anomalies within a layer of coarse blocks with large voids at around 15 m depth near the base of the slope and at 10 m depth mid‐slope. Intra‐talus ventilation is particularly effective in winter when subzero air temperatures coincide with snow depths less than 50 cm and reverses to a gravity discharge of intra‐talus air when air temperatures become positive. Despite the lack of annual variability in active layer depth, rapid permafrost degradation and thinning of ground ice (from 7 m thickness to 3.5 m in 4 years) is currently occurring. It is attributed to latent heat transfer from the moving air stream, caused by the flux of vapour from the relatively warm lake water table at 20 m depth and its condensation at the base of the permafrost body. Copyright © 2009 John Wiley & Sons, Ltd.
Parasitic angiosperms, semagenesis and general strategies for plant–plant signaling in the rhizosphere
Authors: Palmer Andrew G , Chen Michael C , Kinger Nikhar P , Lynn David G 
Published: February 2009

AbstractBACKGROUND: In addition to their roles in eukaryotic defense and development, reactive oxygen species (ROS) have recently been identified as critical for host attachment by the parasitic angiosperms. In a process known as semagenesis, ROS generated at the root tip of Striga asiatica (L.) Kuntze (Scrophulariaceae) function together with host peroxidases to oxidize monolignols at the host root surface. As a result, para‐benzoquinone products accumulate as both necessary and sufficient components for inducing development of the host attachment organ, the haustorium. This event constitutes the critical vegetative/pathogenic transition in the parasite.RESULTS: New evidence is presented that semagenesis occurs broadly in plant–plant signaling. Eudicotyledenous seedlings are more sensitive to the xenognostic benzoquinones than monocots, but general root development, including root elongation, root hair initiation and root hair growth, is impacted in both clades. Specific inhibitors of haustorial development in S. asiatica also inhibit benzoquinone‐mediated root development in the non‐parasites. These results suggest a common mechanism for benzoquinone perception.CONCLUSION: Semagenesis enriches our understanding of the mechanisms available for small‐molecule underground information exchange among plants. Critical differences in this process, as used by parasitic plants, are beginning to emerge and point towards new strategies for managing parasitic angiosperms in agricultural settings. Copyright © 2009 Society of Chemical Industry
Microstructure of CuFeS2–δ–CuInS2 alloys
Authors: Korzun B. V. , Fadzeyeva A. A. , Kloess G. , Bente K. 
Published: February 2009

AbstractTwo series of alloys of the (CuFeS2–δ)1–x(CuInS2)x system with molar part of CuInS2 x = 0.01, 0.03, 0.125, 0.25, 0.375, 0.50, 0.625, 0.75, 0.95, 0.97 and 0.99 and δ being 0 and 0.10 were prepared from the CuFeS2–δ and CuInS2 starting ternary compounds. The samples were investigated by micro structural optics using freshly‐polished samples and XRPD. The studies confirmed two phase coexistences with microstructures dependent on the chemical composition. The geometric‐oriented arrangement of the α‐phase with the structure of CuInS2 is found in the (CuFeS2–δ)1–x(CuInS2)x system up to x equalling 0.50. It was established that the solvus of CuFeS2–δ exceeds 0.05 molar parts of CuInS2, while the solvus of CuInS2 does not exceed 0.03 molar parts of CuFeS2–δ. Additionally, stoichiometric composition of CuFeS2 exhibits a mixture of 3 coexisting phases of CuFeS2–δ, with δ from 0.14 to 0.28, bornite Cu5FeS4 and pyrrhotite Fe1–xS. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical and optical properties of Hg3In2Te6 single crystals
Authors: Maslyanchuk O. L. , Kosyachenko L. A. , German I. I. , Rarenko I. M. , Gnatyuk V. A. , Aoki T. 
Published: February 2009

AbstractThe basic properties of n‐Hg3In2Te6 single crystals with resistivity of 1‐2 Ω·cm are studied in their application for 1.55 μm wavelength photodiodes as optimal detectors for quartz fiber communications. The band gap of Hg3In2Te6 in the temperature range of 248‐353 K has been determined on the base of the optical transmission spectra. The absorption curves in the range of 0.4‐1.7 μm (at 300 K) have been obtained from the reflection spectra of polarized light. It is also shown that the electrical conductivity of the semiconductor is controlled by two types of donors with ionization energies of 0.063 and 0.18 eV, respectively, while the charge carrier mobility is predominantly affected by scattering at charged centers. The temperature dependence of the electron concentration in the temperature range from 100 to 370 K is quantitatively described on the base of the electroneutrality equation. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Luminescence properties of ZnGa2O4 and ZnAl2O4 spinels doped with Eu3+ and Tb3+ ions
Authors: Rusu E. , Ursaki V. , Novitschi G. , Vasile M. , Petrenco P. , Kulyuk L. 
Published: February 2009

AbstractSpinel‐type ZnGa2O4 and ZnAl2O4 powders doped with Eu3+ and Tb3+ ions, including dual doping, have been prepared by solid phase reactions and by deposition from chemical solutions. XRD analysis demonstrates the high quality of spinel grains constituting the powder. The luminescence shows that the rare earth ions are incorporated in the defect regions at the grain boundaries. The emission spectra of the samples with europium are characterized by an intense emission in red region due to the 5D0 → 7F1,2 transitions of Eu3+ ions, whereas in the case of terbium the highest intensity corresponds to the green emission due to the 5D4 → 7F5 transitions of Tb3+ ions. The possibility to change the color of the emission from green to red by the variation of Tb and Eu doping concentration is demonstrated. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
CuIn2n+1Se3n+2 single dot structures: creation and photosensitivity
Authors: Rud Yu. V. , Rud V. Yu. , Bodnar I. V. 
Published: February 2009

AbstractPhotosensitive single dot structures based on CuIn2n+1Se3n+2 (n = 0, 1, 2) bulk single crystals have been creation for the first time by means of electric‐discharge welding (EDW). The stationary current‐voltage characteristics and the photovoltaic properties of the structures based on CuInSe2, CuIn3Se5 and CuIn5Se8 ternary semiconductors have been studied, which show evidence for the rectification effect and photoconversion. The character of interband transitions is established and the energy bandgap variation in this type of ternary compounds is traced. It is concluded that EDW can be successfully used for the creation of photoconverters based on multi‐component semiconductors. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Preparation of Cu2ZnSnS4 thin films by sulfurization of co‐electroplated Cu‐Zn‐Sn precursors
Authors: Araki Hideaki , Kubo Yuki , Jimbo Kazuo , Maw Win Shwe , Katagiri Hironori , Yamazaki Makoto , Oishi Koichiro , Takeuchi Akiko 
Published: February 2009

AbstractCu2ZnSnS4 (CZTS) thin films were prepared by sulfurization of electrodeposited Cu‐Zn‐Sn precursors. The Cu‐Zn‐Sn precursors were deposited on Mo‐coated glass substrates in a one‐step process from an electrolyte containing copper (II) sulfate pentahydrate, zinc sulfate heptahydrate, tin (II) chloride dehydrate and tri‐sodium citrate dehydrate. The precursors were sulfurized by annealing with sulfur at temperatures of 580 °C and 600 °C in an N2 atmosphere. X‐ray diffraction peaks attributable to CZTS were detected in the sulfurized films. Photovoltaic cells with the structure glass/Mo/CZTS/ CdS/ZnO:Al/Al were fabricated using the CZTS films by sulfurizing the electrodeposited precursors. The best photovoltaic cell performance was obtained with Zn‐rich samples. An open‐circuit voltage of 540 mV, a short‐circuit current of 12.6 mA/cm2 and an efficiency of 3.16% were achieved. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Chevron‐like twin pattern in crystals of solid oxide electrolytes
Authors: Tataryn T. , Savytskii D. , Vasylechko L. , Paulmann C. , Bismayer U. , Boysen H. 
Published: February 2009

AbstractA chevron‐like configuration of ferroelastic domain structure was observed in rhombohedral ZrO2:Sc2O3 (10 mol%) and orthorhombic La0.95Sr0.05Ga0.9Mg0.1O3‐δ crystals using the Laue method. In the first case it was formed by the intersection of W‐type domain walls (100)c, (001)c and (101)c. In the second case it was formed by the intersection of W‐type domain walls (01$ \bar 1 $)o, (21$ \bar 1 $)o and (2$ \bar 1 $1)o. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Single crystal X‐ray study of the modulated structure in Ga2XTe3 with the defect zinc‐blende structure
Authors: Kashida S. , Otaki Y. , Yanadori Y. , Seki Y. , Tadano M. 
Published: February 2009

AbstractGa2Te3 crystallizes into the zinc‐blende structure, where one third of the cation sites is vacant. Single crystal X‐ray diffraction studies on quenched and annealed Ga2Te3 and CuGaTe2 crystals are reported. The obtained diffraction maps show, other than the zinc‐blende type main reflections, satellite reflections at q1∼1/17[110]c in quenched Ga2Te3 crystals and q2∼1/20[210]c in annealed Ga2Te3 crystals, where the subscript c means the cubic sub‐lattice. The analysis of the satellite reflections shows that the modulation is two dimensional, and is ascribed to a coupled mode of the amplitude type modulation caused by Ga vacancies and the displacive modulation of surrounding Te atoms, which has the polarization vector along the <001>c direction. The nature of the atomic modulations is discussed and the origin of the modulation is ascribed to Jahn‐Teller type distortions around Ga vacancies. The experiments done on CuGaTe2 crystals indicate that the cation disorder compound sphalerite type CuGaTe2 contain the same modulated structure as Ga2Te3 crystals, but the cation ordered compound chalcopyrite type CuGaTe2 does not show the modulation. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of co‐doping of rare earth and transition metal ions on the photoluminescence in ZnGa2S4:Mn2+
Authors: Hidaka Chiharu , Hodotsuka Jun , Takizawa Takeo 
Published: February 2009

AbstractThe photoluminescence spectra of Mn2+ in ZnGa2S4 codoped with rare earth elements (REE) and transition metals have been investigated, respectively. First a La co‐doped sample is examined to find that it has the most enhanced effect on the Mn red‐emission. The effect of Mn and La concentrations on it is also investigated. When Mn or La concentration is varied, while the partner concentration is fixed, the red‐emission from the co‐doped sample has a peak at 2.0 mol% for both Mn and La cases. However, the peak shifts to the low energy side as Mn concentration increases though it stays constant when La concentration is varied. Next we have also measured PL spectra due to Mn2+ in the same compounds codoped with transition metals (TE: Ti,Cu,Cr,Fe,Co,Ni). It is found that these metals work as killers to the Mn red‐emission. We will discuss the role of REE and TE on the enhancement of the Mn red‐emission in ZnGa2S4. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Role of rare earth elements as co‐activators on both PL and afterglow of CaGa2S4:Eu
Authors: Hidaka Chiharu , Shiino Masaaki , Takizawa Takeo 
Published: February 2009

AbstractPhotoluminescence and afterglow spectra of Eu and rare earth elements (REE) doped CaGa2S4 have been measured. Nd, Dy and Ho ions are selected as sensitizers to make the afterglow (Eu green‐emission) long. The longest afterglow is observed at Eu and Ho co‐doping. We have also measured the dependence of the afterglow on Eu concentration. As Eu concentration decreases, the decay time is longer in the cases of Nd, Dy and Ho co‐doping. This is explained by the decrease in the probability of the life time of electrons in the electron reservoirs, as the distances between Eu and REE (Nd,Dy,Ho) ions are far from each other. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)