bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic study of DBA/2J mice retina: Down‐regulation of Integrin β7 correlated with retinal ganglion cell death
Authors: Kanamoto Takashi , Ue Takahiro , Yokoyama Tomoko , Souchelnytskyi Nazariy , Kiuchi Yoshiaki 
Published: September 2009

AbstractTo identify and determine the function of the proteins associated with the death of retinal ganglion cells (RGCs) in DBA/2J mice, an animal model of glaucoma, retinas of DBA/2J mice, were analyzed by proteomics at 5‐, 7‐, and 11‐months‐of‐age. The proteins showing significant alterations were selected for identification by MS and 18 proteins were differentially expressed and the identified proteins included cell membrane receptors and proteins associated with intracellular signaling pathways. Among of identified proteins, the expression of Integrin β7 at 7‐months‐of‐age was decreased by about 89% of that at 5‐months‐of‐age. Integrin β7 was expressed in the RGCs. The effect of glutamate toxicity on the expression pattern of Integrin β7 in a RGC line was also investigated and the glutamate‐induced death of RGC was inhibited by the RNA knockdown of Integrin β7. Our data showed also that the expression of 18 proteins in the DBA/2J was significantly altered in DBA2 mice and down‐regulation of Integrin β7 may have a protective effect on glutamate‐induced death of RGCs.
Proteopathogen, a protein database for studying Candida albicans – host interaction
Authors: Vialás Vital , Nogales‐Cadenas Rubén , Nombela César , Pascual‐Montano Alberto , Gil Concha 
Published: September 2009

AbstractThere exist, at present, public web repositories for management and storage of proteomic data and also fungi‐specific databases. None of them, however, is focused to the specific research area of fungal pathogens and their interactions with the host, and contains proteomics experimental data. In this context, we present Proteopathogen, a database intended to compile proteomics experimental data and to facilitate storage and access to a range of data which spans proteomics workflows from description of the experimental approaches leading to sample preparation to MS settings and peptides supporting protein identification. Proteopathogen is currently focused on Candida albicans and its interaction with macrophages; however, data from experiments concerning different pathogenic fungi species and other mammalian cells may also be found suitable for inclusion into the database. Proteopathogen is publicly available at http://proteopathogen.dacya.ucm.es
Recent advances in yeast organelle and membrane proteomics
Authors: Premsler Thomas , Zahedi René Peiman , Lewandrowski Urs , Sickmann Albert 
Published: September 2009

AbstractYeast proteome research comprises two different aspects: with respect to systemic fungal infections (fungemias), invasive candidiasis, for instance by Candida albicans, is among the most common causes of morbidity and mortality particularly in the expanding population of immunocompromised patients, which rises a high medical and pharmaceutical interest in this facultative pathogenic organism. Apart from its clinical relevance, yeast research moreover provides an indispensable source of knowledge regarding fundamental biochemical processes of eukaryotic cells. In this context, the budding yeast Saccharomyces cerevisiae is, in addition to its multiple industrial applications, one of the most extensively used microorganisms and serves as the best understood eukaryotic model system so far. Consequently, numerous studies have focused on gaining insight into the yeast proteome, with protein MS providing a very efficient technology to cope with this task since it enables both protein identification and differential quantification of cellular material. In this review we present an overview of recent advances in yeast organelle and membrane proteomics focusing on the cell wall, plasma membrane, mitochondria and vacuole.
Improving soil protein extraction for metaproteome analysis and glomalin‐related soil protein detection
Authors: Chen Shaoning , Rillig Matthias C. , Wang Wei 
Published: September 2009

AbstractSoil contains low amounts of protein but high amounts of interfering substances. Current extraction methods for soil protein cannot produce high‐quality samples suitable for proteomic analysis. To resolve the problem, we devised a sequential extraction method, through sequentially extracting soil in citrate and SDS buffers, followed by phenol extraction. The method allows for obtaining applicable 1‐D and 2‐D protein profiles with various agricultural soils and detecting glomalin‐related soil protein. The method may be a valuable tool for soil proteomics.
Quantitative proteomics in biological research
Authors: Wilm Matthias 
Published: September 2009

AbstractProteomics has enabled the direct investigation of biological material, at first through the analysis of individual proteins, then of lysates from cell cultures, and finally of extracts from tissues and biopsies from entire organisms. Its latest manifestation – quantitative proteomics – allows deeper insight into biological systems. This article reviews the different methods used to extract quantitative information from mass spectra. It follows the technical developments aimed toward global proteomics, the attempt to characterize every expressed protein in a cell by at least one peptide. When applications of the technology are discussed, the focus is placed on yeast biology. In particular, differential quantitative proteomics, the comparison between an experiment and its control, is very discriminating for proteins involved in the process being studied. When trying to understand biological processes on a molecular level, differential quantitative proteomics tends to give a clearer picture than global transcription analyses. As a result, MS has become an even more indispensable tool for biochemically motivated biological research.
When less can yield more – Computational preprocessing of MS/MS spectra for peptide identification
Authors: Renard Bernhard Y. , Kirchner Marc , Monigatti Flavio , Ivanov Alexander R. , Rappsilber Juri , Winter Dominic , Steen Judith A. J. , Hamprecht Fred A. , Steen Hanno 
Published: September 2009

AbstractThe effectiveness of database search algorithms, such as Mascot, Sequest and ProteinPilot is limited by the quality of the input spectra: spurious peaks in MS/MS spectra can jeopardize the correct identification of peptides or reduce their score significantly. Consequently, an efficient preprocessing of MS/MS spectra can increase the sensitivity of peptide identification at reduced file sizes and run time without compromising its specificity. We investigate the performance of 25 MS/MS preprocessing methods on various data sets and make software for improved preprocessing of mgf/dta‐files freely available from http://hci.iwr.uni‐heidelberg.de/mip/proteomics or http://www.childrenshospital.org/research/steenlab.
Comparative study of electronic structure and optical properties of a series of Pt(II) complexes containing different electron‐donating and ‐withdrawing groups: a DFT study
Authors: Li Xiao‐Na , Wu Zhi‐Jian , Zhang Hong‐Jie 
Published: September 2009

AbstractWe report a quantum‐chemistry study of electronic structures and spectral properties of a series of Pt(II) complexes containing different substituents (CH3 (1), OCH3 (2), NO2 (3), CF3 (4), and COOH (5)). 1 and 2 have been previously synthesized in experiment, while 3–5 are artificial complexes that we suggest can be used to investigate the electron‐withdrawing effect on charge injection, transport, absorption, and phosphorescence properties. The results reveal that the stronger electron‐donating and ‐withdrawing groups show stronger absorption intensity, while the phosphorescence efficiency is generally higher for complexes containing electron‐donating substituents. 1 and 2 are easier for hole injection, while 3–5 are easier for electron injection. The enhanced electron injection abilities of 3–5 will confine more excitons in the light‐emitting layer (EML) and may not result in lower electroluminescence (EL) efficiency than 1 and 2. These results suggest that the three artificial complexes may be new emitters in organic light‐emitting diodes (OLEDs). Copyright © 2009 John Wiley & Sons, Ltd.
Characterization of Atmospheric Pressure Microplasma Jet Source and its Application to Bacterial Inactivation
Authors: Kim Sun Ja , Chung Tae Hun , Bae Se Hwan , Leem Sun Hee 
Published: September 2009

AbstractAtmospheric pressure microplasma jet sources driven by radio‐frequency wave of 13.56 MHz and by low frequency continuous wave of several kHz ac were fabricated and characterized. The source consists of an ac‐driven copper wire (needle) surrounded by dielectric layer that are placed in a glass tube, and a ground plane electrode (pin‐to‐plane electrode configuration). The basic physical and chemical properties of the plasma jet sources, such as optical emission spectrum, gas temperature, and power deposition were investigated. With various geometrical and operational parameters changed, plasma jets showed different discharge characteristics. The geometrical parameters include the length of the pin wire exposed to the plasma, the distance between the pin to the outlet of the glass tube, and the distance between the pin and the plane electrode. The operational parameters include the applied voltage (amplitude and frequency) and the gas flow rate. As an example of biomedical application of the microplasma jets, the bacterial inactivation experiment was performed. Plasma power (or applied voltage), treatment time, and needle‐to‐sample distance were varied and the bacterial inactivation effects of these parameters were observed.magnified image
Phase diagram of the three‐dimensional anisotropic Heisenberg anti‐ferromagnetic model
Authors: Rocha J. C. S. , Costa B. V. 
Published: September 2009

AbstractIn this work we use numerical Monte Carlo techniques to study the phase diagram of the three‐dimensional classical Heisenberg anti‐ferromagnetic (AF) model with single‐ion anisotropy model with an uniform magnetic field applied along the easy axis. Early experimental as well as theoretical calculations have shown that the phase diagram of the model is quite rich. We simulated the model on a simple cubic lattices using the Wang–Landau sampling and Metropolis algorithm. Finite size scaling theory is used to obtain the phase diagram. At low field and low temperature the system exhibits AF order separated from a spin‐flop (SF) phase by a first‐order line. As temperature grows a paramagnetic phase is reached by crossing a second‐order line both from the AF phase and from the SF phase. The critical exponents are obtained for each transition line. Contrary to early works we find that the line separating the SF phase from the paramagnetic phase is in the Ising class of universality.
Transparent, flexible and low‐resistive precision fabric electrode for organic solar cells
Authors: Castro Fernando A. , Chabrecek Peter , Hany Roland , Nüesch Frank 
Published: September 2009

AbstractWe report the use of conducting precision fabrics as transparent and flexible electrode for organic semiconductor‐based thin film devices. Precision fabrics have well‐defined mesh openings, excellent flexibility and are fabricated by high‐throughput roll‐to‐roll manufacturing. Optimized fabrics reached light transmittance over 95% throughout the visible and near infrared spectra. A significant part of the transmitted light is scattered, which is particularly advantageous for solar cell applications. Surface resistivity is as low as ∼3 Ohms/square, which decreases Ohmic losses when scaling up to large area devices. We demonstrate that solar cells fabricated onto these electrodes show very similar characteristics to those prepared on ITO. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A data clustering approach to discriminating impersonating devices in Wi‐Fi networks
Authors: Tao Zhiqi , Nath Baikunth , Lonie Andrew 
Published: September 2009

AbstractBy design, Wi‐Fi networks inherently lack reliable positional knowledge of the origin of individual network packets, and instead use the media access control (MAC) address of a received packet to assign packet identity. Given that there are a variety of tools that allow one to construct arbitrary network packets and transmit over a network, a potential security risk arises in that it is difficult to discriminate legitimate packets from packets generated by an intruder solely on the basis of packet content. We describe a data clustering approach to discriminating network nodes based on signal strength data measured from multiple angles through a distributed sensor network, and demonstrate that relatively little network data are sufficient for high discrimination accuracy. Copyright © 2009 John Wiley & Sons, Ltd.
Silica‐Templated Synthesis of Ordered Mesoporous Tungsten Carbide/Graphitic Carbon Composites with Nanocrystalline Walls and High Surface Areas via a Temperature‐Programmed Carburization Route
Authors: Wu Zhangxiong , Yang Yunxia , Gu Dong , Li Qiang , Feng Dan , Chen Zhenxia , Tu Bo , Webley Paul A. , Zhao Dongyuan 
Published: September 2009

AbstractOrdered mesostructured tungsten carbide and graphitic carbon composites (WC/C) with nanocrystalline walls are fabricated for the first time by a temperature‐programmed carburization approach with phosphotungstic acid (PTA) as a precursor and mesoporous silica materials as hard templates. The mesostructure, crystal phase, and amount of deposited graphitic carbon can be conveniently tuned by controlling the silica template (SBA‐15 or KIT‐6), carburizing temperature (700–1000 °C), the PTA‐loading amount, and the carburizing atmosphere (CH4 or a CH4/H2 mixture). A high level of deposited carbon is favorable for connecting and stabilizing the WC nanocrystallites to achieve high mesostructural regularity, as well as promoting the carburization reaction. Meanwhile, large pore sizes and high mesoporosity of the silica templates can promote WC‐phase formation. These novel, ordered, mesoporous WC/C nanocomposites with high surface areas (74–169 m2 g−1), large pore volumes (0.14–0.17 cm3 g−1), narrow pore‐size distributions (centered at about 3 nm), and very good oxidation resistance (up to 750°C) have potential applications in fuel‐cell catalysts and nanodevices.
Growth of Single‐Walled Carbon Nanotubes from Sharp Metal Tips
Authors: Rodríguez‐Manzo Julio A. , Janowska Izabela , Pham‐Huu Cuong , Tolvanen Antti , Krasheninnikov Arkady V. , Nordlund Kai , Banhart Florian 
Published: September 2009

AbstractThe nucleation and growth of single‐walled carbon nanotubes is observed in situ in a transmission electron microscope. Carbon atoms are implanted into catalytically active metal particles by electron‐beam sputtering. The metal particles are then shaped with a focused electron beam. Once the particles have a region of high surface curvature, spontaneous nucleation and growth of single‐walled carbon nanotubes occurs on the metal particles. It is shown that the local solubility of carbon in the metal determines the nucleation of nanotubes. This is confirmed by atomistic computer simulations treating the solubility of carbon in a metal particle as a function of the size of the system.
In vivo Quantum‐Dot Toxicity Assessment
Authors: Hauck Tanya S. , Anderson Robin E. , Fischer Hans C. , Newbigging Susan , Chan Warren C. W. 
Published: September 2009

AbstractQuantum dots have potential in biomedical applications, but concerns persist about their safety. Most toxicology data is derived from in vitro studies and may not reflect in vivo responses. Here, an initial systematic animal toxicity study of CdSe–ZnS core–shell quantum dots in healthy Sprague–Dawley rats is presented. Biodistribution, animal survival, animal mass, hematology, clinical biochemistry, and organ histology are characterized at different concentrations (2.5–15.0 nmol) over short‐term (<7 days) and long‐term (>80 days) periods. The results show that the quantum dot formulations do not cause appreciable toxicity even after their breakdown in vivo over time. To generalize the toxicity of quantum dots in vivo, further investigations are still required. Some of these investigations include the evaluation of quantum dot composition (e.g., PbS versus CdS), surface chemistry (e.g., functionalization with amines versus carboxylic acids), size (e.g., 2 versus 6 nm), and shape (e.g., spheres versus rods), as well as the effect of contaminants and their byproducts on biodistribution behavior and toxicity. Combining the results from all of these studies will eventually lead to a conclusion regarding the issue of quantum dot toxicity.
Receptor‐Mediated Cellular Uptake of Folate‐Conjugated Fluorescent Nanodiamonds: A Combined Ensemble and Single‐Particle Study
Authors: Zhang Bailin , Li Yingqi , Fang Chia‐Yi , Chang Cheng‐Chun , Chen Chao‐Sheng , Chen Yi‐Ying , Chang Huan‐Cheng 
Published: September 2009

AbstractFluorescent nanodiamonds (FNDs) are nontoxic and photostable nanomaterials, ideal for long‐term in vivo imaging applications. This paper reports that FNDs with a size of ≈140 nm can be covalently conjugated with folic acid (FA) for receptor‐mediated targeting of cancer cells at the single‐particle level. The conjugation is made by using biocompatible polymers, such as polyethylene glycol, as crosslinked buffer layers. Ensemble‐averaged measurements with flow cytometry indicate that more than 50% of the FA‐conjugated FND particles can be internalized by the cells (such as HeLa cells) through receptor‐mediated endocytosis, as confirmed by competitive inhibition assays. Confocal fluorescence microscopy reveals that these FND particles accumulate in the perinuclear region. The absolute number of FNDs internalized by HeLa cells after 3 h of incubation at a particle concentration of 10 µg mL−1 is in the range of 100 particles per cell. The receptor‐mediated uptake process is further elucidated by single‐particle tracking of 35‐nm FNDs in three dimensions and real time during the endocytosis.
The future of general systems research: Obstacles, potentials, case studies
Authors: Troncale L. Raphael 
Published: September 2009

AbstractThis paper attempts to provide an evaluative and prescriptive overview of the young field of systems science as exemplified by one of its ‘specialties’ general systems theory (GST). Subjective observation and some data on seven vital signs are presented to measure the progress of the field over the last two decades. Thirty‐three specific obstacles inhibiting current research in systems science are presented. Suggestions for overcoming these obstacles are cited as a prescription for improved progress in the field. A sampling of some of the potential near‐term developments that may be expected in the three rather distinct areas of research on systems isomorphies, improvement of systems methodologies, and the utility of systems applications are illustrated with mini‐case studies. Throughout, there is an attempt to identify ‘key’ questions and practical mechanisms that might serve as a stimulus for research. Finally, a set of criteria defining a general theory of systems is suggested and illustrated with a case study. The paper concludes with a projection of the long‐term contributions that systems science may make toward a resolution of the growing chasm between high‐tech solutions and high‐value needs in human systems.
Systems research and the hierarchy of world systems: General systems in special chaos
Authors: Boulding Kenneth E. 
Published: September 2009

AbstractThe hierarchy of systems is described as parallel to the hierarchy of military titles: general systems as the universe; Major General Systems as the earth; the Major Systems of earth—physical, biological and social—each with its subsystems; ‘kernel’ systems, which try to describe the ‘core of the diverse major systems’ (these divide into ecological–evolutionary systems which have the quality of being ‘resurgent’) and ‘corporal’ systems, such as organisms and organizations. Then there are the ‘private’ systems, which are the ‘minute particulars’ of the real world. Cutting across this hierarchy are the ideologies, which might well be called ‘lieutenant’ systems, as they are in place of images of the more complex systems of the real world. The General Systems movement might help ideologies to become more realistic; it is showing some ecological resurgence, and it has to sustain both its ‘special’ aspect as mathematical modelling and its more general, philosophical aspect. It must also be aware that systems emerge from a matrix of chaos, and that all reality is not systematic.
Minimally Invasive Parathyroidectomy: Benefits and Requirements of Localization, Diagnosis, and Intraoperative PTH Monitoring. Long‐Term Results
Authors: Fraker Douglas L. , Harsono Hasly , Lewis Robert 
Published: September 2009

AbstractBackgroundSurgery is the only curative treatment for primary hyperparathyroidism. Initial parathyroidectomy procedures fail due to ectopic gland location and unappreciated multigland disease.MethodsAn evidence‐based literature review was performed, which surveyed all human studies in PubMed, searching for parathyroidectomy in humans between 1990 and 2009. Between 10 and 30% of patients have multigland disease caused by double adenomas or hyperplasia. Use of preoperative imaging studies and intraoperative PTH monitoring helps parathyroid surgeons overcome these obstacles.ResultsSestamibi nuclear scan and neck ultrasound identify 70–80% of abnormal glands in patients with single adenomas. The sensitivity of ultrasound or sestamibi to identify all abnormal glands in patients with multigland disease is extremely low. Intraoperative PTH monitoring should be utilized in all patients who undergo neck exploration for primary hyperparathyroidism to reduce failures due to multigland disease. Blood samples should be drawn from peripheral veins only and a postresection level 10–15 min after gland removal should have a >50% decrease from baseline preoperative levels, and also must go to the normal range for the PTH assay being used.ConclusionsContemporary prospective studies (level of evidence III/IV) show that by combining preoperative imaging and IOPTH it is possible to maximize performance of successful outpatient minimally invasive parathyroidectomy.
Verbal short-term memory deficits in Down syndrome: phonological, semantic, or both?
Authors: Raitano Lee Nancy , Pennington Bruce F. , Keenan Janice M. 
Published: September 2009

AbstractThe current study examined the phonological and semantic contributions to the verbal short-term memory (VSTM) deficit in Down syndrome (DS) by experimentally manipulating the phonological and semantic demands of VSTM tasks. The performance of 18 individuals with DS (ages 11–25) and 18 typically developing children (ages 3–10) matched pairwise on receptive vocabulary and gender was compared on four VSTM tasks, two tapping phonological VSTM (phonological similarity, nonword discrimination) and two tapping semantic VSTM (semantic category, semantic proactive interference). Group by condition interactions were found on the two phonological VSTM tasks (suggesting less sensitivity to the phonological qualities of words in DS), but not on the two semantic VSTM tasks. These findings suggest that a phonological weakness contributes to the VSTM deficit in DS. These results are discussed in relation to the DS neuropsychological and neuroanatomical phenotype.