bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic profiling of animal models mimicking skeletal muscle disorders
Authors: Doran Philip , Gannon Joan , O'Connell Kathleen , Ohlendieck Kay 
Published: August 2007

AbstractOver the last few decades of biomedical research, animal models of neuromuscular diseases have been widely used for determining pathological mechanisms and for testing new therapeutic strategies. With the emergence of high‐throughput proteomics technology, the identification of novel protein factors involved in disease processes has been decisively improved. This review outlines the usefulness of the proteomic profiling of animal disease models for the discovery of new reliable biomarkers, for the optimization of diagnostic procedures and the development of new treatment options for skeletal muscle disorders. Since inbred animal strains show genetically much less interindividual differences as compared to human patients, considerably lower experimental repeats are capable of producing meaningful proteomic data. Thus, animal model proteomics can be conveniently employed for both studying basic mechanisms of molecular pathogenesis and the effects of drugs, genetic modifications or cell‐based therapies on disease progression. Based on the results from comparative animal proteomics, a more informed decision on the design of clinical proteomics studies could be reached. Since no one animal model represents a perfect pathobiochemical replica of all of the symptoms seen in complex human disorders, the proteomic screening of novel animal models can also be employed for swift and enhanced protein biochemical phenotyping.
Nine steps to proteomic wisdom: A practical guide to using protein‐protein interaction networks and molecular pathways as a framework for interpreting disease proteomic profiles
Authors: Isserlin Ruth , Emili Andrew 
Published: August 2007

AbstractA major aim of proteomic profiling of disease is to uncover the mechanistic basis of a given pathology. High‐throughput experimental techniques continue to advance rapidly, but are still plagued by high rates of false negatives, false positives, and other spurious findings. By reducing a disease profile to a subset of differentially expressed proteins and determining functional over‐representation, one can often make a reasonable first‐pass assessment as to what might be happening in disease. Integrating mRNA expression patterns together with prior knowledge of protein‐protein interaction networks and biological pathway information goes a step further, providing clues into the core processes that are aberrant in the disease state, and indicating which cellular functions are activated or repressed as a maladaptive pathophysiological response. This multi‐step framework allows one to hypothesize as to possible cause and effect of pathology, and highlights potentially instructive pathways or sub‐networks for subsequent experimental validation. Indeed, efficiently exploiting data regarding the myriad of physical and genetic interactions among expressed gene products, in parallel with the systematic sampling of genetic variation among diverse human populations, promises to revolutionize our current understanding of disease action at a deeper molecular level.
Exploring the proteome of meningococcal outer membrane vesicle vaccines
Authors: Wheeler Jun X. , Vipond Caroline , Feavers Ian M. 
Published: August 2007

AbstractNeisseria meningitidis, one of the principal causes of bacterial meningitis and septicemia, continues to present a challenge for vaccine developers. While significant progress has been made in the development and implementation of conjugate vaccines, which are based on the capsular polysaccharide of the organism, this approach has failed to produce a vaccine against organisms expressing a serogroup B capsule. The completion of the first meningococcal genome sequences in 2000 provided new ways of meeting this challenge. One approach has been to learn more about meningococcal biology and pathogenesis through exploring its proteome. This article reviews the results of ten recent studies of the meningococcal proteome and compares the different methodologies employed. Not surprisingly, given the renewed impetus to develop a comprehensive vaccine and the continuing clinical development of outer membrane vesicle vaccines, many of these studies focus on the proteome of the outer membrane fraction. As in other areas of proteome research, the direct comparison of data from different studies is hampered by the lack of standardization of separation technologies and data formats. Nevertheless, proteomic analysis, especially when combined with detailed knowledge of meningococcal population structures, represents a powerful tool in the development of vaccines against this important pathogen.
Lysosomal proteomics and disease
Authors: Sleat David E. , Jadot Michel , Lobel Peter 
Published: August 2007

AbstractA recent trend in proteomic studies has been to analyze macromolecular complexes such as subcellular organelles instead of complete cells or tissues. This “divide and conquer” approach circumvents some of the formidable problems associated with whole proteome analyses and allows focus on a subset of proteins that may be involved in a particular process or disease of interest. One organelle that has been the focus of considerable attention in proteomic studies is the lysosome, an acidic, membrane‐delimited compartment that plays an essential role in the degradation and recycling of biological macromolecules. Lysosomal proteomics have been driven in part by the well‐established involvement of this organelle in numerous human diseases, but also by the availability of approaches to selectively visualize and/or isolate subsets of lysosomal proteins. In terms of clinical application, proteomic studies of the lysosome have led to the identification of gene defects in three human hereditary diseases. This review summarizes past progress, current limitations and future directions in the field of lysosomal proteomics.
Thermal Decomposition of NTO: An Explanation of the High Activation Energy
Authors: Sinditskii Valery P. , Smirnov Sergei P. , Egorshev Viacheslav Yu. 
Published: August 2007

AbstractBurning rate characteristics of the low‐sensitivity explosive 5‐nitro‐1,2,4‐triazol‐3‐one (NTO) have been investigated in the pressure interval of 0.1–40 MPa. The temperature distribution in the combustion wave of NTO has been measured at pressures of 0.4–2.1 MPa. Based on burning rate and thermocouple measurements, rate constants of NTO decomposition in the molten layer at 370–425 °C have been derived from a condensed‐phase combustion model (k=8.08⋅1013⋅exp(−19420/T) s−1. NTO vapor pressure above the liquid (ln P=−9914.4/T+14.82) and solid phases (ln P=−12984.4/T+20.48) has been calculated. Decomposition rates of NTO at low temperatures have been defined more exactly and it has been shown that in the interval of 180–230 °C the decomposition of solid NTO is described by the following expression: k=2.9⋅1012⋅exp(−20680/T). Taking into account the vapor pressure data obtained, the decomposition of NTO in the gas phase at 240–250 °C has been studied. Decomposition rate constants in the gaseous phase have been found to be comparable with rate constants in the solid state. Therefore, a partial decomposition in the gas cannot substantially increase the total rate. High values of the activation energy for solid‐state decomposition of NTO are not likely to be connected with a sub‐melting effect, because decomposition occurs at temperatures well below the melting point. It has been suggested that the abnormally high activation energy in the interval of 230–270 °C is a consequence of peculiarities of the NTO transitional process rather than strong bonds in the molecule. In this area, the NTO molecule undergoes isomerization into the aci‐form, followed by C3‐N2 heterocyclic bond rupture. Both processes depend on temperature, resulting in an abnormally high value of the observed activation energy.
Serum PSA half‐life as a predictor of survival for hormone‐refractory prostate cancer patients: Modelization using a standardized set of response criteria
Authors: Banu Eugeniu , Banu Adela , Medioni Jacques , Levy Eric , Thiounn Nicolas , Mejean Arnaud , Andrieu Jean‐Marie , Oudard Stephane 
Published: August 2007

AbstractOBJECTIVEChanges of serum prostate‐specific antigen (PSA) during chemotherapy have been validated as a marker of response for hormone‐refractory prostate cancer (HRPC) patients. We retrospectively established new response criteria to assess the risk of death.METHODSTwo hundred fifty‐six chemonaive HRPC patients treated with chemotherapy were included in the analysis. According to PSA half‐life (HL) dynamics, three response categories were defined: responders (R), late‐progressors (LP) and initial‐progressors (IP), that were compared with Working Group (WG) criteria. PSA HL time to failure (TTF) and overall survival (OS) were estimated and compared between HT categories. Multivariate regression analysis was performed to isolate the impact on OS of these response categories. A new predictor of survival, delta‐time PSA interval (ΔT) was described.RESULTSPSA HL categories were strongly related with WG criteria (P = 0.0001). PSA HL TTF differed among PSA HL categories: 4.2, 2.3, and 0.9 months for R, LP, and IP patients, respectively, and their respective median OS were 27, 19.7, and 12.3 months (P = 0.0001). For ΔT ≥ 3 versus <3 months, median OS significantly differed: 24.9 months versus 13.2 months (P = 0.0001).CONCLUSIONSPSA HL dynamics during chemotherapy were able to accurately predict survival, earlier than WG‐defined progression criteria. This criterion should be prospectively evaluated in randomized trials for HRPC patients in order to better estimate the risk of death. Prostate 67: 1543–1549, 2007. © 2007 Wiley‐Liss, Inc.
A prospective randomized trial comparing contrast‐enhanced targeted versus systematic ultrasound guided biopsies: Impact on prostate cancer detection
Authors: Mitterberger Michael , Horninger Wolfgang , Pelzer Alexandre , Strasser Hannes , Bartsch Georg , Moser Patrizia , Halpern Ethan J. , Gradl Johann , Aigner Friedrich , Pallwein Leo , Frauscher Ferdinand 
Published: August 2007

AbstractBACKGROUNDWe performed a prospective randomized trial comparing 5 contrast‐enhanced color Doppler (CECD) ultrasound (US) targeted biopsy cores to 10 gray‐scale US guided systematic biopsy (SB) cores to determine the impact on the cancer detection rate.METHODSWe prospectively randomized 100 prostate specific antigen (PSA) screening volunteers with an elevated PSA (≥1.25 ng/ml and free‐to‐total PSA < 18%) to undergo contrast‐enhanced targeted or SB. Contrast‐enhanced targeted biopsies with a limited number of five cores were performed into hypervascular areas of the peripheral zone (PZ) during administration of the US contrast agent SonoVue® (Bracco, Italy). A subjective grading of the vascularity from 0 to 3 was used: grade 0, no color signal; 1, low density; 2, medium density; and 3, high density of color signals. Ten SBs were obtained in a standard spatial distribution. Cancer detection rates were compared in the groups.RESULTSCancer was detected in 16/50 subjects (32%) by targeted biopsy, and in 13/50 patients (26%) with SB. The cancer detection rate was significantly better for the targeted approach (P < 0.04, McNemar). The detection rate for targeted biopsy cores (15.6% or 39/250 cores) was significantly better than for SB cores (6.8% or 34/500 cores, P < 0.001, McNemar).CONCLUSIONSCECD targeted biopsy detected more cancers than SB with a reduced number of biopsy cores. Prostate 67: 1537–1542, 2007. © 2007 Wiley‐Liss, Inc.
Are aromatic carbon donor hydrogen bonds linear in proteins?
Authors: Nanda Vikas , Schmiedekamp Ann 
Published: August 2007

AbstractProteins fold and maintain structure through the collective contributions of a large number of weak, noncovalent interactions. The hydrogen bond is one important category of forces that acts on very short distances. As our knowledge of protein structure continues to expand, we are beginning to appreciate the role that weak carbon‐donor hydrogen bonds play in structure and function. One property that differentiates hydrogen bonds from other packing forces is propensity for forming a linear donor‐hydrogen‐acceptor orientation. To ascertain if carbon‐donor hydrogen bonds are able to direct acceptor linearity, we surveyed the geometry of interactions specifically involving aromatic sidechain ring carbons in a data set of high resolution protein structures. We found that while donor–acceptor distances for most carbon donor hydrogen bonds were tighter than expected for van der Waals packing, only the carbons of histidine showed a significant bias for linear geometry. By categorizing histidines in the data set into charged and neutral sidechains, we found only the charged subset of histidines participated in linear interactions. B3LYP/6‐31G**++ level optimizations of imidazole and indole–water interactions at various fixed angles demonstrates a clear orientation dependence of hydrogen bonding capacity for both charged and neutral sidechains. We suggest that while all aromatic carbons can participate in hydrogen bonding, only charged histidines are able to overcome protein packing forces and enforce linear interactions. The implications for protein modeling and design are discussed. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Thermal annealing effects on the TL response of beta‐irradiated HPHT Ib type synthetic diamond
Authors: Preciado‐Flores S. , Meléndrez R. , Chernov V. , Soto‐Puebla D. , Pedroza‐Montero M. , Barboza‐Flores M. 
Published: August 2007

AbstractIt is known that room temperature beta‐irradiated Ib type diamond generates a non‐reproducible TL glow curve shape, due to mobility of the impurity‐vacancy (I –V) and interstitials (I) defects in the 30–800 °C temperature range. This situation may hinder the use of this type of diamond material in dose assessment applications. The recurring heating of the Ib type diamond sample changes the defects concentration and consequently the intensity of the TL glow peaks associated to the characteristic temperature annealing stages. In the present work we have performed thermal annealing (TA) treatment on an Ib type diamond in the 100–800 °C range previous to beta irradiation. It was observed that after the 800 °C annealing treatment the TL glow curve showed 3–5% reproducibility, in contrast to the non‐reproducible TL observed in non‐annealed diamond, and remained the same after two months of successive TL read outs. Moreover, the 800 °C annealing treatment assured a linear integrated TL dose behavior, a significant improvement over non‐annealed samples that could facilitate the employment of Ib type synthetic diamond in dosimetric applications. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Radiation hardness of diamond and silicon sensors compared
Authors: de Boer Wim , Bol Johannes , Furgeri Alex , Müller Steffen , Sander Christian , Berdermann Eleni , Pomorski Michal , Huhtinen Mika 
Published: August 2007

AbstractThe radiation hardness of silicon charged particle sensors is compared with single crystal and polycrystalline diamond sensors, both experimentally and theoretically. It is shown that for Si‐ and C‐sensors, the NIEL hypothesis, which states that the signal loss is proportional to the Non‐Ionizing Energy Loss, is a good approximation to the present data. At incident proton and neutron energies well above 0.1 GeV the radiation damage is dominated by the inelastic cross section, while at non‐relativistic energies the elastic cross section prevails. The smaller inelastic nucleon‐carbon cross section and the light nuclear fragments imply that at high energies diamond is an order of magnitude more radiation hard than silicon, while at energies below 0.1 GeV the difference becomes significantly smaller. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Thermal conductivity of CoSb3 nano‐composites grown via a novel solvothermal nano‐plating technique
Authors: Ji X. , He J. , Alboni P. , Su Z. , Gothard N. , Zhang B. , Tritt Terry M. , Kolis J. W. 
Published: August 2007

AbstractWe have utilized a solvothermal nano‐plating technique to grow nano‐structured CoSb3 directly onto the surface of micron‐sized CoSb3 particles that were subsequently hot pressed and densified into a homogeneous skutterudite nano‐composite. We herein present results for three samples: a bulk sample to serve as a reference, and two samples with solvothermally grown nano‐structures of 5 wt% and 20 wt%, respectively. All three samples used the same bulk starting materials. The thermal conductivity was measured via two independent techniques (steady state and laser flash) and both show a systematic reduction in the thermal conductivity with an increasing amount of nano‐structures. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Deep‐level characterization of emissive interface states in Alq3‐based OLEDs
Authors: Nakano Yoshitaka , Noda Koji , Fujikawa Hisayoshi , Morikawa Takeshi 
Published: August 2007

AbstractWe have succesfully investigated emissive interface states in fabricated indium‐tin‐oxide (ITO)/N,N′‐di‐1‐naphthyl‐N,N′‐diphenyl‐1,1′‐biphenyl‐4,4′diamine (α‐NPD)/tris(8‐hydroxyquinoline) aluminum (Alq3)/LiF/Al organic light‐emitting diodes (OLEDs) by a modified deep‐level optical spectroscopy (DLOS) technique. In the vicinity of the α‐NPD/Alq3 emissive interface, a discrete trap level was found to be located at ∼1.77 eV below the conduction band of Alq3, in addition to band‐to‐band transitions of carriers from α‐NPD to Alq3. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Restoration of the immune functions in aged mice by supplementation with a new herbal composition, HemoHIM
Authors: Park Hae‐Ran , Jo Sung‐Kee , Jung Uhee , Yee Sung‐Tae 
Published: August 2007

AbstractThe effect of a new herbal composition, HemoHIM, on immune functions was examined in aged mice, in which various immune responses had been impaired. The composition HemoHIM was prepared by adding the ethanol‐insoluble fraction to the total water extract of a mixture of three edible herbs, Angelica Radix, Cnidium Rhizoma and Paeonia Radix. Supplementation to the aged mice with HemoHIM restored the proliferative response and cytokine production of splenocytes with a response to ConA. Also, HemoHIM recovered the NK cell activity which had been impaired in the aged mice. Meanwhile aging is known to reduce the Th1‐like function, but not the Th2‐like function, resulting in a Th1/Th2 imbalance. HemoHIM restored the Th1/Th2 balance in the aged mice through enhanced IFN‐γ and IgG2a production, and conversely a reduced IL‐4 and IgG1 production. It was found that one factor for the Th1/Th2 imbalance in the aged mice was a lower production of IL‐12p70. However, HemoHIM restored the IL‐12p70 production in the aged mice. These results suggested that HemoHIM was effective for the restoration of impaired immune functions of the aged mice and therefore could be a good recommendation for immune restoration in elderly humans. Copyright © 2007 John Wiley & Sons, Ltd.
Improvement of the duty cycle of an orthogonal acceleration time‐of‐flight mass spectrometer using ion gates
Authors: Brenton A. G. , Krastev T. , Rousell D. J. , Kennedy M. A. , Craze A. S. , Williams C. M. 
Published: August 2007

AbstractA method to control the duty cycle of a time‐of‐flight mass spectrometer is described. The method relies on one or more ion gates placed in the beam path that have the function to transmit or stop the beam. These ion gates can switch from the open state to the closed state in tens of nanoseconds and effectively select portions of the mass range. The method is useful in circumstances where recording the complete mass spectrum is not an essential requirement, for example, in the analysis of known compounds where sensitivity and speed of operation are more important. It will be of benefit for applications in separation sciences with techniques involving fast chromatographic separations, where hundreds of mass spectra may be required per second. In such circumstances analytical identification may require only a limited number of masses (or mass regions) to be continuously monitored. Improvement of the duty cycle is particularly important for orthogonal‐acceleration time‐of‐flight (oa‐TOF) mass spectrometry instruments whose performance suffers from a low duty cycle. The duty cycle is not a constant for an instrument design but is a mass‐dependent function and is least for smaller masses. The method described here is capable of raising the duty cycle to 100%. A theory is developed for one or more ion gate arrangements, for both linear‐ and reflectron‐TOF systems. For a two‐gate system the relationship between the positions of the first and second gates is described by a ‘2/3 rule’. Experimental results are shown for one‐gate and two‐gate operation, both in linear and in reflectron modes of operation, on an oa‐TOF system built in‐house. Copyright © 2007 John Wiley & Sons, Ltd.
SIA spotlight on Asia
Authors: Chu Paul K. , Wu X. L. , Xie X. N. , Wee A. T. S. 
Published: August 2007

AbstractThere has been rapid development in science and technology in Asia in recent decades, including in the fields of surface and interface sciences. This has been facilitated by the sustained economic growth in the region, especially the growth of the semiconductor, electronic, chemical, coating and biomedical industries. Accompanying this growth is the increased use of more sophisticated analytical techniques, especially in the field of surface and interface analysis. This article reviews a selection of papers from Asia, published in major international journals in the last two years. Short reviews of each paper are presented in three sections: (i) Characterization and techniques, (ii) Materials and processing and (iii) Nanoscience and nanotechnology. Copyright © 2007 John Wiley & Sons, Ltd.
Modal ductility factors of one‐story inelastic structures with simple eccentricity
Authors: Georgoussis George K. 
Published: August 2007

AbstractA simple procedure is presented for constructing modal capacity curves of one‐story monosymmetric models with elastoplastic resisting elements. These curves may be used for an approximate decomposition of the equations of motion of the assumed structural models, when subjected to ground motions. The motive of applying a modal decomposition on inelastic structures is the simplicity and the consequent attractiveness of the response spectrum technique as applied in linear structures. By applying a modal decomposition on eccentric one‐story inelastic systems, modal ductility demands may be determined for the various resisting elements and the total demands may be estimated by an appropriate combination rule. The modal capacity curves are constructed by performing a nonlinear pushover analysis using the inertia force eccentricities of each mode. As at each loading step the modal eccentricity reflects the current state of stiffness, the incremental floor movement consists of a rotation about the corresponding natural center of vibration and this simplifies the calculation of displacements throughout the loading history. The method of constructing modal capacity curves is outlined for systems with different structural parameters: uncoupled lateral frequency, uncoupled torsional‐to‐lateral frequency ratio, stiffness eccentricity and relative values of element strength. A parametric analysis is also presented, based on a three‐element single mass model that has been extensively used in the past for similar analyses. In particular, two types of model structure are examined: systems with element strengths proportional to their stiffness and systems with element strengths determined by the static equilibrium of the eccentric model. The results of the present work are in good agreement with the findings of studies published in the past. Copyright © 2007 John Wiley & Sons, Ltd.