bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endocytosis of Environmental and Engineered Micro‐ and Nanosized Particles
Authors: Gehr Peter , Clift Martin J.D , Brandenberger Christina , Lehmann Andrea , Herzog Fabian , Rothen‐Rutishauser Barbara 
Published: July 2011

AbstractThere are many studies with cells to find out how particles interact with them. In contrast to micronsized particles, which are actively taken up by phagocytosis or macropinocytosis, nanosized particles may be taken up by cells through different endocytic pathways or by another, yet to be defined mechanism. There is increasing evidence that it is the nanosized particles, which are a particular risk because of their high content of organic chemicals and their pro‐oxidative potential due to the high surface‐to‐volume ratio of the particles as compared to the bulk material. It is the goal of this article to create an understanding for the interaction of particles with biological systems, with particular consideration of the interaction of nanoparticles (NPs) with lung cells. One is attempting to understand, how NPs interact with cellular membranes, as it is hardly known, how they are taken up by cells, how they are trafficking in cells, and how they interact with subcellular compartments, such as with mitochondria or with the nucleus. Cells tend to defend themselves against any foreign material, which is taken up. In general, they try to eliminate particulate intruders and this is what they usually manage with micronsized particles. However, with NPs it is different. NPs may not be eliminated easily, and, hence may stimulate the cells to react in an unfavorable way. What we can learn is that NPs behave differently than microparticles. © 2011 American Physiological Society.Compr Physiol1:1159‐1174, 2011.
Pathophysiology of the Diabetic Kidney
Authors: Vallon Volker , Komers Radko 
Published: July 2011

AbstractDiabetes mellitus contributes greatly to morbidity, mortality, and overall health care costs. In major part, these outcomes derive from the high incidence of progressive kidney dysfunction in patients with diabetes making diabetic nephropathy a leading cause of end‐stage renal disease. A better understanding of the molecular mechanism involved and of the early dysfunctions observed in the diabetic kidney may permit the development of new strategies to prevent diabetic nephropathy. Here we review the pathophysiological changes that occur in the kidney in response to hyperglycemia, including the cellular responses to high glucose and the responses in vascular, glomerular, podocyte, and tubular function. The molecular basis, characteristics, and consequences of the unique growth phenotypes observed in the diabetic kidney, including glomerular structures and tubular segments, are outlined. We delineate mechanisms of early diabetic glomerular hyperfiltration including primary vascular events as well as the primary role of tubular growth, hyperreabsorption, and tubuloglomerular communication as part of a “tubulocentric” concept of early diabetic kidney function. The latter also explains the “salt paradox” of the early diabetic kidney, that is, a unique and inverse relationship between glomerular filtration rate and dietary salt intake. The mechanisms and consequences of the intrarenal activation of the renin‐angiotensin system and of diabetes‐induced tubular glycogen accumulation are discussed. Moreover, we aim to link the changes that occur early in the diabetic kidney including the growth phenotype, oxidative stress, hypoxia, and formation of advanced glycation end products to mechanisms involved in progressive kidney disease. © 2011 American Physiological Society.Compr Physiol1:1175‐1232, 2011.
Exercise and Muscular Dystrophy: Implications and Analysis of Effects on Musculoskeletal and Cardiovascular Systems
Authors: Barnabei Matthew S. , Martindale Joshua M. , Townsend DeWayne , Metzger Joseph M. 
Published: July 2011

AbstractThe muscular dystrophies are a heterogeneous collection of progressive, inherited diseases of muscle weakness and degeneration. Although these diseases can vary widely in their etiology and presentation, nearly all muscular dystrophies cause exercise intolerance to some degree. Here, we focus on Duchenne muscular dystrophy (DMD), the most common form of muscular dystrophy, as a paradigm for the effects of muscle disease on exercise capacity. First described in the mid‐1800s, DMD is a rapidly progressive and lethal muscular dystrophy caused by mutations in the dystrophin gene. Dystrophin is a membrane‐associated cytoskeletal protein, the loss of which causes numerous cellular defects including mechanical instability of the sarcolemma, increased influx of extracellular calcium, and cell signaling defects. Here, we discuss the physiological basis for exercise intolerance in DMD, focusing on the molecular and cellular defects caused by loss of dystrophin and how these manifest as organ‐level dysfunction and reduced exercise capacity. The main focus of this article is the defects present in dystrophin‐deficient striated muscle. However, discussion regarding the effects of dystrophin loss on other tissues, including vascular smooth muscle is also included. Collectively, the goal of this article is to summarize the current state of knowledge regarding the mechanistic basis for exercise intolerance in DMD, which may serve as an archetype for other muscular dystrophies and diseases of muscle wasting. © 2011 American Physiological Society.Compr Physiol1:1353‐1363, 2011.
Oxidants and Redox Signaling in Acute Lung Injury
Authors: Sarma J. Vidya , Ward Peter A. 
Published: July 2011

AbstractAcute lung injury (ALI) and its more severe form of clinical manifestation, the acute respiratory distress syndrome is associated with significant dysfunction in air exchange due to inflammation of the lung parenchyma. Several factors contribute to the inflammatory process, including hypoxia (inadequate oxygen), hyperoxia (higher than normal partial pressure of oxygen), inflammatory mediators (such as cytokines), infections (viral and bacterial), and environmental conditions (such as cigarette smoke or noxious gases). However, studies over the past several decades suggest that oxidants formed in the various cells of the lung including endothelial, alveolar, and epithelial cells as well as lung macrophages and neutrophils in response to the factors mentioned above mediate the pathogenesis of ALI. Oxidants modify cellular proteins, lipids, carbohydrates, and DNA to cause their aberrant function. For example, oxidation of lipids changes membrane permeability. Interestingly, recent studies also suggest that spatially and temporally regulated production of oxidants plays an important role antimicrobial defense and immunomodulatory function (such as transcription factor activation). To counteract the oxidants an arsenal of antioxidants exists in the lung to maintain the redox status, but when overwhelmed tissue injury and exacerbation of inflammation occurs. We present below the current understanding of the pathogenesis of oxidant‐mediated ALI. © 2011 American Physiological Society.Compr Physiol1:1365‐1381, 2011.
Mechanisms of Exercise‐Induced Mitochondrial Biogenesis in Skeletal Muscle: Implications for Health and Disease
Authors: Hood David A. , Uguccioni Giulia , Vainshtein Anna , D'souza Donna 
Published: July 2011

AbstractMitochondria have paradoxical functions within cells. Essential providers of energy for cellular survival, they are also harbingers of cell death (apoptosis). Mitochondria exhibit remarkable dynamics, undergoing fission, fusion, and reticular expansion. Both nuclear and mitochondrial DNA (mtDNA) encode vital sets of proteins which, when incorporated into the inner mitochondrial membrane, provide electron transport capacity for ATP production, and when mutated lead to a broad spectrum of diseases. Acute exercise can activate a set of signaling cascades in skeletal muscle, leading to the activation of the gene expression pathway, from transcription, to post‐translational modifications. Research has begun to unravel the important signals and their protein targets that trigger the onset of mitochondrial adaptations to exercise. Exercise training leads to an accumulation of nuclear‐ and mtDNA‐encoded proteins that assemble into functional complexes devoted to mitochondrial respiration, reactive oxygen species (ROS) production, the import of proteins and metabolites, or apoptosis. This process of biogenesis has important consequences for metabolic health, the oxidative capacity of muscle, and whole body fitness. In contrast, the chronic muscle disuse that accompanies aging or muscle wasting diseases provokes a decline in mitochondrial content and function, which elicits excessive ROS formation and apoptotic signaling. Research continues to seek the molecular underpinnings of how regular exercise can be used to attenuate these decrements in organelle function, maintain skeletal muscle health, and improve quality of life. © 2011 American Physiological Society.Compr Physiol1:1119‐1134, 2011.
Where East not always meets West: Comparing the Sulha process to Western‐style mediation and arbitration
Authors: Pely Doron 
Published: July 2011

AbstractThe author uses literature and interviews to compare elements of the Muslim inter‐clan, mixed‐mode mediation and arbitration tradition of Sulha in Israel's Arab community with comparable elements of Western‐style mediation and arbitration practices. The author uncovers and analyzes the similarities and differences between specific Western‐style and Sulha mediation and arbitration elements, such as confidentiality, venting, and neutrality. Such insights may be helpful when considering possible synergies and points of divergence between Muslim and Western dispute‐resolution practices.
Examining structural components of peace agreements and their durability
Authors: Hoffman Evan , Bercovitch Jacob 
Published: July 2011

AbstractThe authors address a question that is central to many ADR studies; namely, are some peace agreements really better designed than others, and, if so, will these agreements last longer? It is argued that peace ultimately rests on the parties choosing to cooperate with one another to uphold the terms of the agreement. Peace is thus framed as an ongoing, dynamic process involving constant renegotiation. Mediators, therefore, need to be forward‐looking and mindful of how to craft an agreement that has features that recognize the high likelihood that problems will arise after the formal signing.
High‐throughput quantitative analysis of HIV‐1 and SIV‐specific ADCC‐mediating antibody responses
Authors: Pollara Justin , Hart Lydia , Brewer Faraha , Pickeral Joy , Packard Beverly Z. , Hoxie James A. , Komoriya Akira , Ochsenbauer Christina , Kappes John C. , Roederer Mario , Huang Ying , Weinhold Kent J. , Tomaras Georgia D. , Haynes Barton F. , Montefiori David C. , Ferrari Guido 
Published: July 2011

AbstractWe have developed a high‐throughput platform to detect the presence of HIV‐1 and SIV‐specific ADCC‐mediating antibody responses. The assay is based on the hydrolysis of a cell‐permeable fluorogenic peptide substrate containing a sequence recognized by the serine protease, Granzyme B (GzB). GzB is delivered into target cells by cytotoxic effector cells as a result of antigen (Ag)‐specific Ab‐Fcγ receptor interactions. Within the target cells, effector cell‐derived GzB hydrolyzes the substrate, generating a fluorescent signal that allows individual target cells that have received a lethal hit to be identified by flow cytometry. Results are reported as the percentage of target cells with GzB activity (%GzB). Freshly isolated or cryopreserved PBMC and/or NK cells can be used as effector cells. CEM.NKR cells expressing the CCR5 co‐receptor are used as a target cells following: (i) coating with recombinant envelope glycoprotein, (ii) infection with infectious molecular clones expressing the Env antigens of primary and lab adapted viruses, or (iii) chronic infection with a variant of HIV‐1/IIIB, termed A1953. In addition, primary CD4+ T cells infected with HIV‐1 in vitro can also be used as targets. The assay is highly reproducible with a coefficient of variation of less than 25%. Target and effector cell populations, in the absence of serum/plasma, were used to calculate background (8.6 ± 2.3%). We determined that an initial dilution of 1:50 and 1:100 is required for testing of human and non‐human primate samples, respectively. This assay allows for rapid quantification of HIV‐1 or SIV‐specific ADCC‐mediating antibodies that develop in response to vaccination, or in the natural course of infection, thus providing researchers with a new methodology for investigating the role of ADCC‐mediating antibodies as correlates of control or prevention of HIV‐1 and SIV infection. © 2011 International Society for Advancement of Cytometry
Electrochemical Design of Ultrathin Palladium Coated Gold Nanoparticles as Nanostructured Catalyst for Amperometric Detection of Formaldehyde
Authors: Safavi Afsaneh , Farjami Fatemeh 
Published: July 2011

AbstractAn underpotential deposition (UPD) replacement tactic was employed to design a Pd overlayer on gold (Au) nanoparticles electrodeposited on a carbon ionic liquid electrode (CILE). Pd/Au/CILE was applied as an amperometric sensor for the determination of formaldehyde in aqueous solutions. The sensor displayed two linear ranges from 15 µM–1.4 mM and 1.4–56.7 mM of formaldehyde. The limit of detection was 3 µM of formaldehyde and the sensitivity of the sensor was 2.35 µA mM−1, using the calibration graph in the lower range. The presence of 20 mM of formic acid and methanol and 10 mM ethanol did not interfere with the determination of formaldehyde solution.
Electrochemical Determination of Tetracycline Using Molecularly Imprinted Polymer Modified Carbon Nanotube‐Gold Nanoparticles Electrode
Authors: Wang Hongtao , Zhao Huimin , Quan Xie , Chen Shuo 
Published: July 2011

AbstractThis paper reports the use of a tetracycline (TC) sensor constructed from a combination of molecularly imprinted polymer (MIP) and gold nanoparticles modified multiwall carbon nanotubes (MWNTs‐GNPs). The results demonstrated that the amount of recognition sites in the polymer was significantly increased and the electron transfer ability of the sensor was improved. The relationship between the peak current and the TC concentration was linear in the range from 0.1 to 40 mg L−1, and the detection limit was 0.04 mg L−1 (S/N=3). The peak current to TC was 4.3, 6.2 and 6.8 times larger than that of oxytetracycline, chloramphenicol and nafcillin, respectively. Thus, the combination of MIP and MWNTs‐GNPs provides a sensitive and selective electrochemical detection method for tetracycline.
Carbon Nanotube‐Adsorbed Electrospun Nanofibrous Membranes as Coating for Electrochemical Sensors for Sulfhydryl Compounds
Authors: Li Fei , Scampicchio Matteo , Mannino Saverio 
Published: July 2011

AbstractA new method to modify electrodes with carbon nanotubes (CNT) was developed. Multiwalled carbon nanotubes (MWNT) were adsorbed on the electrospun nylon‐6 nanofibrous membranes (Ny‐6‐NFM) and used as a coating to modify conventional glassy carbon electrodes. The modified electrode was designed for the amperometric detection of sulfhydryl compounds with the potential held at +0.3 V vs. Ag/AgCl. The modified electrode showed a linear response for cysteine up to 0.4 mM (R2=0.997), with a sensitivity of 5.1 µA/mM and a detection limit of 15 µM. Other sulfhydryl compounds showed similar results. After use, the Ny‐6‐NFM was easily peeled off, leaving the bare electrode surface back to its original electrochemical behaviour. This is the first attempt to use a disposable membrane functionalized with MWNT for electroanalytical purposes.
Bile UPLC‐MS fingerprinting and bile acid fluxes during human liver transplantation
Authors: Legido‐Quigley Cristina , McDermott Lindsay , Vilca‐Melendez Hector , Murphy Gerard M. , Heaton Nigel , Lindon John C. , Nicholson Jeremy K. , Holmes Elaine 
Published: July 2011

AbstractBile flow restoration is a crucial step in the recovery process post transplantation of the liver. Here, metabolic trajectories based on changes in bile secretion – a known marker of functionality – have been utilised as an approach for discovering bile fluxes during transplantation. A total of ten liver transplants were monitored and from these 68 bile samples from both donors and recipients were collected and analysed using ultra‐performance LC‐MS in combination with multivariate statistical analysis. Based on the principal component scores constructed from the total bile fingerprint, differentiation of the bile acid concentrations before and after transplantation was detected. A trend was also observed, by constructing metabolic trajectories, whereby the post‐transplant profiles approached the position of pre‐transplant profiles within 30–60 min of the restoration of bile secretion function. The ten major conjugated bile acid salts were measured and a significant increase in concentrations of taurocholic acid and taurochenodeoxycholic acid were seen after transplantation. In addition, the ratios of secondary bile acids detected in gall bladder and hepatic bile were measured before and after transplantation. This study suggests that bile acid ratios in the donor liver at the pre‐transplant and post‐transplant stage may be important and that profiling of secreted bile after transplantation may aid clinical assessment and progress post‐transplantation.
Plasma biomarker identification in S‐adenosylhomocysteine hydrolase deficiency
Authors: Sedic Mirela , Kraljevic Pavelic Sandra , Cindric Mario , Vissers Johannes P. C. , Peronja Marija , Josic Djuro , Cuk Mario , Fumic Ksenija , Pavelic Krešimir , Baric Ivo 
Published: July 2011

AbstractS‐Adenosylhomocysteine hydrolase (AHCY) deficiency is a rare congenital disorder in methionine metabolism clinically characterized by white matter atrophy, delayed myelination, slowly progressive myopathy, retarded psychomotor development and mildly active chronic hepatitis. In the present study, we utilized a comparative proteomics strategy based on 2‐DE/MALDI‐MS and LC/ESI‐MS to analyze plasma proteins from three AHCY‐deficient patients prior to and after receiving dietary treatment designed to alleviate disease symptoms. Obtained results revealed candidate biomarkers for the detection of myopathy specifically associated with AHCY deficiency, such as carbonic anhydrase 3, creatine kinase, and thrombospondin 4. Several proteins mediating T‐cell activation and function were identified as well, including attractin and diacylglycerol kinase α. Further validation and functional analysis of identified proteins with clinical value would ensure that these biomarkers make their way into routine diagnosis and management of AHCY deficiency.
Fractionation of the human plasma proteome for monoclonal antibody proteomics‐based biomarker discovery
Authors: Kovács András , Sperling Edit , Lázár József , Balogh Attila , Kádas János , Szekrényes Ákos , Takács László , Kurucz István , Guttman András 
Published: July 2011

AbstractmAb proteomics, a reversed biomarker discovery approach, is a novel methodology to recognize the proteins of biomarker potential, but requires subsequent antigen identification steps. While in case of high‐abundant proteins, it generally does not represent a problem, for medium or lower abundant proteins, the identification step requires a large amount of sample to assure the proper amount of antigen for the ID process. In this article, we report on the use of combined chromatographic and precipitation techniques to generate a large set of fractions representing the human plasma proteome, referred to as the Analyte Library, with the goal to use the relevant library fractions for antigen identification in conjunction with mAb proteomics. Starting from 500 mL normal pooled human plasma, this process resulted in 783 fractions with the average protein concentration of 1 mg/mL. First, the serum albumin and immunoglobulins were depleted followed by prefractionation by ammonium sulfate precipitation steps. Each precipitate was then separated by size exclusion chromatography, followed by cation and anion exchange chromatography. The 20 most concentrated ion exchange chromatography fractions were further separated by hydrophobic interaction chromatography. All chromatography and precipitation steps were carefully designed aiming to maintain the native forms of the intact proteins throughout the fractionation process. The separation route of vitamin D‐binding protein (an antibody proteomics lead) was followed in all major fractionation levels by dot blot assay in order to identify the library fraction it accumulated in and the identity of the antigen was verified by Western blot.
A nonparametric characterization of vertical ground motion effects
Authors: Tezcan Jale , Cheng Qiang 
Published: July 2011

SUMMARYDesign guidelines have traditionally oversimplified the vertical ground motion effects by defining a constant vertical‐to‐horizontal response spectral ratio (V/H). With the recognition that such practice is not always conservative, recent studies have proposed improvements to the representation of vertical seismic effects in design codes, based on empirical ground motion relations.Conventional empirical modeling requires selecting the functional form of the predictive model. Because of the complicated nature of ground motions, identification of the underlying function is a challenge. A related drawback to this approach is its high susceptibility to overfitting, especially with today's highly complex models.To address these issues, this paper proposes a nonparametric approach to characterize the vertical seismic effects. Using support vector machines, the V/H ratio is determined without an assumed functional form. The accuracy of the model is measured by adopting an epsilon‐insensitive residual function with a regularization term added to prevent overfitting.An example application using ground motion records from strike‐slip and normal faulting earthquakes is presented, and the results are compared with a current empirical model, for different magnitude, distance, and local soil conditions. The median V/H estimates from the two models are shown to be in good general agreement. The standard deviation estimates from the proposed model are consistently larger than the estimates from the empirical model.The results from this study show that the proposed method is a viable alternative and offers the opportunity to characterize vertical seismic effects without an assumed functional form. Copyright © 2011 John Wiley & Sons, Ltd.
Frequency domain substructural identification for arbitrary excitations
Authors: Zhang Z. , Koh C. G. , Perry M. J. 
Published: July 2011

SUMMARYStructural identification based on analysis of vibration signals is usually formulated as an optimization problem. Nevertheless, identifying a structural system as a whole often involves a great number of unknowns and degrees of freedom, resulting in considerable convergence difficulty and expensive evaluation of objective function. To handle these issues, this paper aims to propose a frequency domain substructural identification method applicable to arbitrary excitations. This is done by introducing the exponential window method in the formulation so that the effect caused by initial condition is alleviated without using zero padding. The proposed identification method is verified through both numerical and experimental studies. It is shown that significant reduction in computer time can be achieved in addition to remarkable identification accuracy. The experimental study also indicates that the proposed strategy is effective in identifying small structural changes. Copyright © 2011 John Wiley & Sons, Ltd.