bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis and characterization of novel h‐HTBN/PEG PU copolymers for tissue engineering: degradation, phase behavior, and mechanical properties
Authors: Luo Yan‐Ling , Nan Yun‐Fei , Xu Feng , Chen Ya‐Shao , Di Hong‐Wei 
Published: December 2009

AbstractThe phase behavior of the as‐prepared polyether polyurethane (PU) elastomers was investigated by dynamic mechanical analysis (DMA), polarized optical microscope (POM), and atomic force microscopy (AFM). This PU copolymers were composed of different compositions of two soft segments, poly(ethylene glycol) (PEG) and hydrolytically modified hydroxyl‐terminated poly(butadiene‐co‐acrylonitrile) (h‐HTBN) oligomers. The microphase separation behavior is confirmed to occur between soft and hard segments as well as soft and soft segments as the h‐HTBN is incorporated into the PU system, depending on soft‐soft and/or soft‐hard microdomain composition, molecular weight (MW) of PEG, and hydrolysis time of HTBN. The driving force for this phase separation is mainly due to the formation of inter‐ and intramolecular hydrogen bonding interaction. The PU‐70, PU‐50 samples with non‐reciprocal composition seem to exhibit larger microphase separation than any other PU ones. The hydrolysis degradation, thermal stability, and mechanical properties of the copolymers were assessed by gravimetry, scanning electron microscope (SEM), thermal gravity analysis (TGA), and tensile test, respectively. The experimental results indicated that the incorporation of h‐HTBN soft segment into PEG as well as low MW of PEG leads to increased thermal and degradable stability based on the intermolecular hydrogen bond interaction. The PU‐70 and PU‐50 copolymers exhibit better mechanical properties such as high flexibility and high ductility because of their larger microphase separation architecture with the hard domains acting as reinforcing fillers and/or physical crosslinking agents dispersed in the soft segment matrix. Copyright © 2009 John Wiley & Sons, Ltd.
Functional proteomic and structural insights into molecular targets related to the growth inhibitory effect of tanshinone IIA on HeLa cells
Authors: Pan Tai‐Long , Hung Yu‐Chiang , Wang Pei‐Wen , Chen Shui‐Ten , Hsu Teng‐Kuei , Sintupisut Nardnisa , Cheng Chao‐Sheng , Lyu Ping‐Chiang 
Published: January 2010

AbstractCertain antitumor agents have recently been extracted from the roots of Salvia miltiorrhiza Bunge. The diterpene derivative, tanshinone IIA, possesses cytotoxic activity against several human carcinoma cell lines. It also inhibits invasion and metastasis of cancer cells. In the present study, we isolated tanshinone IIA from S. miltiorrhiza, and it exhibited strong growth inhibition against human cervical cancer cells in dose‐ and time‐dependent manners with a 50% cell growth inhibition value of 2.5 μg/mL (8.49 μM). Flow cytometric analysis of cell cycle progression revealed that G2/M arrest was initiated after a 24 h exposure to the drug. It also resulted in DNA fragmentation and degradation of poly (ADP‐ribose) polymerase indicating that tanshinone IIA may be a potential antitumor agent. Furthermore, we performed a comprehensive proteomic analysis to survey global protein changes induced by tanshinone IIA treatment on HeLa cells. Significant changes in the levels of cytoskeleton proteins as well as stress‐associated proteins were observed. Immunoblot analysis and immunofluorescence staining were used to confirm the levels of protein expression. Overexpression of the vimentin rescued these tanshinone IIA‐induced events. Computational docking methods indicated that tanshinone IIA could stably bind to the β‐subunit of the microtubule protein. An interaction network analysis of these 12 proteins using MetaCore™ software suggested that tanshinone IIA treatment regulated the expressions of proteins involved in apoptotic processes, spindle assembly, and p53 activation, including vimentin, Maspin, α‐ and β‐tubulin, and GRP75. Taken together, our results suggest that tanshinone IIA strongly inhibited the growth of cervical cancer cells through interfering in the process of microtubule assembly, leading to G2/M phase arrest and sequent apoptosis. The success of this large‐scale effort was assessed by a bioinformatics analysis of proteins through predictions of protein domains and possible functional roles. The possible contributions of these proteins to the cytotoxicity of tanshinone IIA provide potential opportunities for the development of cancer therapeutics.
Proteomic analysis of symbiosome membranes in Cnidaria–dinoflagellate endosymbiosis
Authors: Peng Shao‐En , Wang Yu‐Bao , Wang Li‐Hsueh , Chen Wan‐Nan Uang , Lu Chi‐Yu , Fang Lee‐Shing , Chen Chii‐Shiarng 
Published: January 2010

AbstractSymbiosomes are specific intracellular membrane‐bound vacuoles containing microalgae in a mutualistic Cnidaria (host)–dinoflagellate (symbiont) association. The symbiosome membrane is originally derived from host plasma membranes during phagocytosis of the symbiont; however, its molecular components and functions are not clear. In order to investigate the protein components of the symbiosome membranes, homogenous symbiosomes were isolated from the sea anemone Aiptasia pulchella and their purities and membrane intactness examined by Western blot analysis for host contaminants and microscopic analysis using various fluorescent probes, respectively. Pure and intact symbiosomes were then subjected to biotinylation by a cell impermeant agent (Biotin‐XX sulfosuccinimidyl ester) to label membrane surface proteins. The biotinylated proteins, both Triton X‐100 soluble and insoluble fractions, were subjected to 2‐D SDS‐PAGE and identified by MS using an LC‐nano‐ESI‐MS/MS. A total of 17 proteins were identified. Based on their different subcellular origins and functional categories, it indicates that symbiosome membranes serve as the interface for interaction between host and symbiont by fulfilling several crucial cellular functions such as those of membrane receptors/cell recognition, cytoskeletal remodeling, ATP synthesis/proton homeostasis, transporters, stress responses/chaperones, and anti‐apoptosis. The results of proteomic analysis not only indicate the molecular identity of the symbiosome membrane, but also provide insight into the possible role of symbiosome membranes during the endosymbiotic association.
Screening for therapeutic targets of vorinostat by SILAC‐based proteomic analysis in human breast cancer cells
Authors: Zhou Qun , Chaerkady Raghothama , Shaw Patrick G. , Kensler Thomas W. , Pandey Akhilesh , Davidson Nancy E. 
Published: January 2010

AbstractHistone deacetylases (HDACs) play critical roles in silencing tumor suppressor genes. HDAC inhibitors reactivate tumor suppressor genes and inhibit tumor cell growth in vitro and in vivo, and several HDAC inhibitors are currently being evaluated in clinical trials for cancer therapy. A comprehensive analysis of proteins regulated by HDAC inhibitors would enhance our ability to define and characterize their essential therapeutic targets. Here, we employed stable isotope labeling with amino acids in cell culture‐based quantitative proteomics to identify acetylated proteins in human breast cancer cells. Treatment with the clinically relevant HDAC inhibitor, suberoylanilide hydroxamic acid (vorinostat), induces lysine acetylation of 61 proteins in MDA‐MB‐231 human breast cancer cells. Suberoylanilide hydroxamic acid not only induces lysine acetylation in chromatin‐associated proteins, but also acetylates previously unrecognized nonhistone proteins, including transcriptional factors and regulators, chaperones, cell structure proteins, and glycolytic enzymes in a time‐dependent manner. Knowledge of the full repertoire of acetylated proteins will provide a foundation for further defining the functions of HDACs in cancer cells.
Telomerase enzyme inhibition (TEI) and cytolytic therapy in the management of androgen independent osseous metastatic prostate cancer
Authors: Li Yingming , Malaeb Bahaa S. , Li Zhong‐ze , Thompson Melissa G. , Chen Zhi , Corey David R. , Hsieh Jer‐Tsong , Shay Jerry W. , Koeneman Kenneth S. 
Published: December 2009

AbstractBACKGROUNDRecurrent prostate cancer can be osseous, androgen independent and lethal. The purpose is to discern the efficacy of synthetic small molecule telomerase enzyme inhibitors (TEI) alone or in combination with other cytotoxic therapies in controlling metastatic osseous prostate cancer.METHODSC4‐2B was pre‐treated with a match or mismatch TEI for 6 weeks and then inoculated into nude mice subcutaneously or intraosseously. In a separate experiment, untreated C4‐2B was injected into femur of nude mice. The mice were divided into seven systemic “combination” treatment groups of control, Ad‐BSP‐E1a virus, docetaxel, mismatch and match TEI. Serum PSA was followed longitudinally. Histology analyses and histomorphometry were performed. Repeated measure analysis was applied for statistical analysis and Bonferroni method was used in multiple comparisons.RESULTSIn the pre‐treated study, the PSA of match treated cells in subcutaneous or intraosseous model was significantly lower than mismatch TEI or PBS treated group (P < 0.05). Histology revealed increased fibrosis, apoptosis and decreased PSA staining in the match TEI treated subcutaneous xenografts. In the combination treatment study, the PSA was significantly lower in single/double treatment and triple treatment than control (P < 0.05). Histology revealed that triple therapy mice had normal femur architecture. Histomorphometrics revealed that the area of femur tumor and woven bone was significantly positively correlated (P = 0.007).CONCLUSIONSMultiple lines of data point toward the efficacy of systemically administered telomerase inhibitors. Combining cytotoxic regimens with telomerase inhibitors could be beneficial in controlling prostate cancer. Clinical trials are warranted to explore the efficacy of TEI in prostate cancer. Prostate 70: 616–629, 2010. © 2009 Wiley‐Liss, Inc.
ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data
Authors: Winkler Robert 
Published: January 2010

AbstractElectrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI‐MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI‐MS data. The resulting software ESIprot was tested with ESI‐MS data of six intact reference proteins between 12.4 and 66.7 kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between −0.2 and 1.2 Da, the relative errors below 30 ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. The program code was released under the open‐source GPLv3 license to support future developments of mass spectrometry software. Copyright © 2010 John Wiley & Sons, Ltd.
Application of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry for the study of Helicobacter pylori
Authors: Ilina Elena N. , Borovskaya Alexandra D. , Serebryakova Marina V. , Chelysheva Vera V. , Momynaliev Kuvat T. , Maier Thomas , Kostrzewa Markus , Govorun Vadim M. 
Published: January 2010

AbstractThe characteristics of matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry based investigation of extremely variable bacteria such as Helicobacter pylori were studied. H. pylori possesses a very high natural variability. Accurate tools for species identification and epidemiological characterization could help the scientific community to better understand the transmission pathways and virulence mechanisms of these bacteria. Seventeen clinical as well as two laboratory strains of H. pylori were analyzed by the MALDI Biotyper method for rapid species identification. Mass spectra collected were found containing 7–13 significant peaks per sample, and only six protein signals were identical for more than half of the strains. Four of them could be assigned to ribosomal proteins RL32, RL33, RL34, and RL36. The reproducible peak with m/z 6948 was identified as a histidine‐rich metal‐binding polypeptide by tandem mass spectrometry (MS/MS). In spite of the evident protein heterogeneity of H. pylori the mass spectra collected for a particular strain under several cultivations were highly reproducible. Moreover, all clinical strains were perfectly identified as H. pylori species through comparative analysis using the MALDI Biotyper software (Bruker Daltonics, Germany) by pattern matching against a database containing mass spectra from different microbial strains (n = 3287) including H. pylori 26695 and J99. The results of this study allow the conclusion that the MALDI‐TOF direct bacterial profiling is suited for H. pylori identification and could be supported by mass spectra fragmentation of the observed polypeptide if necessary. Copyright © 2010 John Wiley & Sons, Ltd.
A parametric mixture model for clustering multivariate binary data
Authors: Tamhane Ajit C. , Qiu Dingxi , Ankenman Bruce E 
Published: December 2009

AbstractThe traditional latent class analysis (LCA) uses a mixture model with binary responses on each subject that are independent conditional on cluster membership. However, in many practical applications, the responses are correlated because they are observed on the same subject; this is known as local dependence. In this paper, we extend the LCA model to allow for local dependence in each cluster to improve clustering accuracy. The clustering problem is hard because of its unsupervised learning nature (the true cluster memberships and even the true number of clusters are unknown), the difficulty of estimating a correlation matrix for each cluster and the paucity of information in binary data. Therefore, we follow a parametric approach in which we fit a mixture model whose components follow multivariate Bernoulli distributions (one for each cluster). An extension of a family of parametric models by Oman and Zucker1is adopted for this purpose and the maximum likelihood estimation method is used for fitting. The Bayesian information criterion (BIC) due to Schwarz2is employed to select the number of clusters. Subjects are classified to clusters using the maximum posterior rule. The proposed method is tested and compared with the LCA method via simulation and by applying both methods to two real data sets. Significant improvement is demonstrated relative to the LCA method. Copyright © 2009 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 3: 3‐19, 2010
Co‐clustering numerical data under user‐defined constraints
Authors: Pensa Ruggero G. , Boulicaut Jean‐Francois , Cordero Francesca , Atzori Maurizio 
Published: December 2009

AbstractIn the generic setting of objects × attributes matrix data analysis, co‐clustering appears as an interesting unsupervised data mining method. A co‐clustering task provides a bi‐partition made of co‐clusters: each co‐cluster is a group of objects associated to a group of attributes and these associations can support expert interpretations. Many constrained clustering algorithms have been proposed to exploit the domain knowledge and to improve partition relevancy in the mono‐dimensional clustering case (e.g. using the must‐link and cannot‐link constraints on one of the two dimensions). Here, we consider constrained co‐clustering not only for extended must‐link and cannot‐link constraints (i.e. both objects and attributes can be involved), but also for interval constraints that enforce properties of co‐clusters when considering ordered domains. We describe an iterative co‐clustering algorithm which exploits user‐defined constraints while minimizing a given objective function. Thanks to a generic setting, we emphasize that different objective functions can be used. The added value of our approach is demonstrated on both synthetic and real data. Among others, several experiments illustrate the practical impact of this original co‐clustering setting in the context of gene expression data analysis, and in an original application to a protein motif discovery problem. Copyright © 2009 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 3: 38‐55, 2010
Constrained overlapping clusters: minimizing the negative effects of bridge‐nodes
Authors: Scripps Jerry , Tan Pang‐Ning 
Published: December 2009

AbstractThis paper presents a new approach to form overlapping clusters of objects by balancing the effects of incompleteness, impurity, and overlap. Incompleteness results from similar objects separated into different clusters while impurity arises when a cluster contains dissimilar objects. Overlap is caused by nodes that appear in more than one cluster. The key to balancing these effects is the identification of bridge‐nodes. We show the limitations of traditional clustering algorithms in handling bridge‐nodes and demonstrate the intractability of minimizing all three effects. Approximation algorithms based on graph mincut and genetic algorithm are proposed to minimize these effects. Our results with real data sets show significant improvement over traditional methods with regard to incompleteness, impurity, and overlap. Copyright © 2009 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 3: 20‐37, 2010
Life-Sparing Effect of Human Cord Blood-Mesenchymal Stem Cells in Experimental Acute Kidney Injury
Authors: Morigi Marina , Rota Cinzia , Montemurro Tiziana , Montelatici Elisa , Lo Cicero Viviana , Imberti Barbara , Abbate Mauro , Zoja Carla , Cassis Paola , Longaretti Lorena , Rebulla Paolo , Introna Martino , Capelli Chiara , Benigni Ariela , Remuzzi Giuseppe , Lazzari Lorenza 
Published: January 2010

AbstractIn search for new sources of mesenchymal stem cells (MSCs) for renal repair in acute kidney injury (AKI), we investigated the potential of human cord blood (CB)-MSCs to cure mice with AKI. Infusion of CB-MSCs in immunodeficient mice with cisplatin-induced AKI ameliorated both renal function and tubular cell injury, and prolonged survival. Transplanted CB-MSCs localized in peritubular areas, limited capillary alterations and neutrophil infiltration. Apoptosis reduced and tubular cell proliferation increased by virtue of stem cell capacity to produce growth factors. The reno-protective effect of CB-MSCs was further confirmed by their ability to inhibit oxidative damage and to induce the prosurvival factor Akt in tubular cells. The evidence that CB-MSCs in vitro increased the production of growth factors and inhibited IL-1β and TNFα synthesis when cocultured with damaged proximal tubular cells indicates a regenerative and anti-inflammatory action of stem cell treatment. Altogether these results highlight the potential of human CB-MSCs as future cell therapy for testing in human AKI.
Covalently linked wall proteins in ascomycetous fungi
Authors: Klis Frans M. , Brul Stanley , De Groot Piet W. J. 
Published: December 2009

AbstractThe covalently linked wall proteins of Saccharomyces cerevisiae and Candida albicans and to a lesser extent of Candida glabrata have been extensively studied. Here we describe some of their main structural features and discuss their conservation in other ascomycetous fungi. We also discuss the hybrid nature of many wall proteins and the frequent occurrence of families of wall proteins with a common multi‐domain structure. Finally, some quantitative data regarding wall proteins are presented. Copyright © 2009 John Wiley & Sons, Ltd.
The Middle Thyroid Vein: Anatomical and Surgical Aspects
Authors: Dionigi Gianlorenzo , Congiu Terenzio , Rovera Francesca , Boni Luigi 
Published: December 2009

AbstractBackgroundAn issue that has been overlooked in medical literature concerns the prevalence and topographic relationships of the middle thyroid vein (MTV), which have been studied, with a prospective approach, in patients with various thyroid diseases.MethodsMTV prevalence has been investigated in 394 consecutive lobes and a number of different variables (age, gender, thyroid pathology, gland weight) have been considered. Moreover, in cooperation with our Human Morphology Department, we brought to completion a dedicated anatomy report, with the clear objective of providing a detailed anatomic description of MTV.ResultsThe prevalence of MTV was 38% of the dissected lobes and 62% of operated patients. Most veins arise from the mid region of the thyroid lobe (80%): B, 3, and 2 positions in accordance with our scheme. As far as thyroid pathology is concerned, we found that the presence of MTV was more frequent in hyperthyroidism and large goiters (p < 0.05).ConclusionsA better understanding of the anatomic variability in MTV may be useful not only to minimize the risk of bleeding, but it also can help to perform a more accurate dissection with the goal of preserving the laryngeal nerves and parathyroid glands, especially because of its location and relationships with other adjacent structures.
Abnormal nonstoring capillary endothelium: a novel feature of Gaucher disease. Ultrastructural study of dermal capillaries
Authors: Hůlková Helena , Poupětová Helena , Harzer Klaus , Mistry Pramod , Aerts Johannes M. F. G. , Elleder Milan 
Published: January 2010

AbstractUltrastructural study of skin biopsies in two cases of Gaucher disease (GD) patients (types II and III) revealed hitherto unknown alteration of the blood capillary endothelial cells (ECs) featured by hypertrophy and numerous subplasmalemmal microvesicles underneath both the apical and basal membranes. There was also prominent apical membrane folding with formation of filiform and large cytoplasmic projections, with occasional transcapillary cytoplasmic bridges. Similar, though less frequently expressed, changes were manifested at the basal membrane by numerous cytoplasmic projections into the subendothelial space. Regressive changes with EC breakdown were rare. Lysosomal storage was always absent. Besides EC hypertrophy, there was also increased EC density in the capillary lumen, leading to pronounced changes in capillary architecture with loose or incomplete EC anchoring. There were also signs of EC sprouting. Some pericytes displayed an increase in size and number of cytoplasmic processes, which often extended into distant pericapillary regions. The spectrum of changes suggests that a significant positive growth effect on EC occurs in GD. The putative mechanisms triggered by GBA1 deficiency leading to EC involvement are discussed. The authors are well aware of the fact the results, based on a nontraditional type of bioptic samples, are preliminary, but they are worth following, as further ultrastructural and functional studies of blood endothelium in GD may open a novel field in molecular cell pathophysiology of the disorder: endothelial dysfunction.