bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphology of Titanium Nanocluster Films Prepared by Gas Aggregation Cluster Source
Authors: Drábik Martin , Choukourov Andrei , Artemenko Anna , Kousal Jaroslav , Polonskyi Oleksandr , Solař Pavel , Kylián Ondřej , Matoušek Jindřich , Pešička Josef , Matolínová Iva , Slavínská Danka , Biederman Hynek 
Published: April 2011

AbstractTitanium nanocluster films were prepared using a gas aggregation cluster source based on a planar magnetron following a Haberland concept and using Ar as a working gas. The films were deposited in dependence on the argon pressure inside the cluster source and on the magnetron current. Prior to the analysis, deposited metal nanocluster films were allowed to oxidize in air at room temperature. Selected nanocluster films were annealed in air at 420 °C. The films were studied by TEM, SEM, and AFM in order to describe their morphology and topography. Crystal structure of the nanoclusters was estimated from electron diffraction patterns by SAD analysis. Chemical composition of the film surface was determined by XPS. Special attention was paid to describing the changes in the nanocluster films connected with ageing. magnified image
A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer
Authors: Remily‐Wood Elizabeth R. , Liu Richard Z. , Xiang Yun , Chen Yi , Thomas C. Eric , Rajyaguru Neal , Kaufman Laura M. , Ochoa Joana E. , Hazlehurst Lori , Pinilla‐Ibarz Javier , Lancet Jeffrey , Zhang Guolin , Haura Eric , Shibata David , Yeatman Timothy , Smalley Keiran S. M. , Dalton William S. , Huang Emina , Scott Ed , Bloom Gregory C. , Eschrich Steven A. , Koomen John M. 
Published: April 2011

AbstractPurpose: The Quantitative Assay Database (QuAD), http://proteome.moffitt.org/QUAD/, facilitates widespread implementation of quantitative mass spectrometry in cancer biology and clinical research through sharing of methods and reagents for monitoring protein expression and modification.Experimental design: Liquid chromatography coupled to multiple reaction monitoring (LC‐MRM) mass spectrometry assays are developed using SDS‐PAGE fractionated lysates from cancer cell lines. Pathway maps created using GeneGO Metacore provide the biological relationships between proteins and illustrate concepts for multiplexed analysis; each protein can be selected to examine assay development at the protein and peptide levels.Results: The coupling of SDS‐PAGE and multiple reaction monitoring mass spectrometry screening has been used to detect 876 peptides from 218 cancer‐related proteins in model systems including colon, lung, melanoma, leukemias, and myeloma, which has led to the development of 95 quantitative assays including stable‐isotope‐labeled peptide standards. Methods are published online and peptide standards are made available to the research community. Protein expression measurements for heat shock proteins, including a comparison with ELISA and monitoring response to the HSP90 inhibitor, 17‐(dimethylaminoethylamino)‐17‐demethoxygeldanamycin (17‐DMAG), are used to illustrate the components of the QuAD and its potential utility.Conclusions and Clinical Relevance: This resource enables quantitative assessment of protein components of signaling pathways and biological processes and holds promise for systematic investigation of treatment responses in cancer.
Utility of formalin‐fixed, paraffin‐embedded liver biopsy specimens for global proteomic analysis in nonalcoholic steatohepatitis
Authors: Bell Lauren N. , Saxena Romil , Mattar Samer G. , You Jinsam , Wang Mu , Chalasani Naga 
Published: April 2011

AbstractPurpose: To compare the proteomic profiles of formalin‐fixed, paraffin‐embedded (FFPE) liver biopsy material and matched frozen liver tissue from patients with nonalcoholic steatohepatitis (NASH).Experimental design: A label‐free mass spectrometry‐based approach was used to profile global protein expression in FFPE and frozen liver biopsy specimens from five patients with NASH.Results: Eight hundred and sixty proteins were identified with >75% confidence: 225 common proteins were identified in both the FFPE and frozen tissues, and an additional 142 and 493 proteins were identified in the FFPE and frozen tissues, respectively. Functional analyses revealed a general, nonspecific reduction in the number of proteins identified in FFPE tissue compared with frozen tissue. No bias toward proteins located in any specific subcellular compartments or implicated in any particular biological functions was observed. The relative abundance of several proteins with functions relating to the pathogenesis of NASH (peroxiredoxin‐1, fatty acid binding protein 1, fatty acid synthase, vimentin, catalase, and glutathione S‐transferase A1) was similar in FFPE and frozen liver tissues.Conclusions and clinical relevance: FFPE liver biopsy material from NASH patients can be used for global proteomic analysis and biomarker identification studies, although a universal reduction in the number of identified proteins compared with frozen tissue is likely.
De novo protein structure prediction by dynamic fragment assembly and conformational space annealing
Authors: Lee Juyong , Lee Jinhyuk , Sasaki Takeshi N. , Sasai Masaki , Seok Chaok , Lee Jooyoung 
Published: April 2011

AbstractAb initio protein structure prediction is a challenging problem that requires both an accurate energetic representation of a protein structure and an efficient conformational sampling method for successful protein modeling. In this article, we present an ab initio structure prediction method which combines a recently suggested novel way of fragment assembly, dynamic fragment assembly (DFA) and conformational space annealing (CSA) algorithm. In DFA, model structures are scored by continuous functions constructed based on short‐ and long‐range structural restraint information from a fragment library. Here, DFA is represented by the full‐atom model by CHARMM with the addition of the empirical potential of DFIRE. The relative contributions between various energy terms are optimized using linear programming. The conformational sampling was carried out with CSA algorithm, which can find low energy conformations more efficiently than simulated annealing used in the existing DFA study. The newly introduced DFA energy function and CSA sampling algorithm are implemented into CHARMM. Test results on 30 small single‐domain proteins and 13 template‐free modeling targets of the 8th Critical Assessment of protein Structure Prediction show that the current method provides comparable and complementary prediction results to existing top methods. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Crystal structure of the novel PaiA N‐acetyltransferase from Thermoplasma acidophilum involved in the negative control of sporulation and degradative enzyme production
Authors: Filippova E.V. , Shuvalova L. , Minasov G. , Kiryukhina O. , Zhang Y. , Clancy S. , Radhakrishnan I. , Joachimiak A. , Anderson W.F. 
Published: April 2011

AbstractGCN5‐related N‐acetyltransferases (GNATs) are the most widely distributed acetyltransferase systems among all three domains of life. GNATs appear to be involved in several key processes, including microbial antibiotic resistance, compacting eukaryotic DNA, controlling gene expression, and protein synthesis. Here, we report the crystal structure of a putative GNAT Ta0374 from Thermoplasma acidophilum, a hyperacidophilic bacterium, that has been determined in an apo‐form, in complex with its natural ligand (acetyl coenzyme A), and in complex with a product of reaction (coenzyme A) obtained by cocrystallization with spermidine. Sequence and structural analysis reveals that Ta0374 belongs to a novel protein family, PaiA, involved in the negative control of sporulation and degradative enzyme production. The crystal structure of Ta0374 confirms that it binds acetyl coenzyme A in a way similar to other GNATs and is capable of acetylating spermidine. Based on structural and docking analysis, it is expected that Glu53 and Tyr93 are key residues for recognizing spermidine. Additionally, we find that the purification His‐Tag in the apo‐form structure of Ta0374 prevents binding of acetyl coenzyme A in the crystal, though not in solution, and affects a chain‐flip rotation of “motif A” which is the most conserved sequence among canonical acetyltransferases. Proteins 2011; © 2011 Wiley‐Liss, Inc.
FISH HABITAT OPTIMIZATION TO PRIORITIZE RIVER RESTORATION DECISIONS
Authors: Null S. E. , Lund J. R. 
Published: April 2011

ABSTRACTThis paper examines and ranks restoration alternatives for improving fish habitat by evaluating tradeoffs between fish production and restoration costs. Optimization modelling is used to maximize out‐migrating coho salmon (Oncorhynchus kisutch) from a natal stream and is applied as a case study in California's Shasta River. Restoration activities that alter flow and water temperature conditions are the decision variables in the model and include relocating a major diversion, increasing riparian shading, increasing instream flow, restoring a cool‐water spring and removing a dam. A budget constraint limits total restoration expenditures. This approach combines simple fish population modelling with flow and water quality modelling to explore management strategies and aid decision making. Previous fish habitat optimization research typically uses single restoration strategies, usually by altering reservoir releases or modifying outlet structures. Our method enlarges the solution space to more accurately represent extensive and integrated solutions to fish habitat problems. Results indicate that restoration alternatives can be prioritized by fish habitat improvement and restoration cost. For the Shasta River case study, considerable habitat restoration investments were required before fish productivity increased substantially. This exercise illustrates the potential of ecological optimization for highlighting promising restoration approaches and dismissing poor alternatives. Copyright © 2011 John Wiley & Sons, Ltd.
Strontium Enhances Osteogenic Differentiation of Mesenchymal Stem Cells and In Vivo Bone Formation by Activating Wnt/Catenin Signaling
Authors: Yang Fan , Yang Dazhi , Tu Jie , Zheng Qixin , Cai Lintao , Wang Liping 
Published: April 2011

Abstract
Strontium ranelate is a newly approved drug that can reduce the risk of vertebral fracture, which is attributed to its dual function in increasing the bone formation and decreasing the bone resorption. Strontium-containing hydroxyapatite was also demonstrated to stimulate the osteoblast activity and inhibit the osteoclast activity. However, the molecular mechanisms of strontium underlying such beneficial effects were still not fully understood. In this study, we investigated the effects of strontium on the osteogenic differentiation of human mesenchymal stem cells (MSCs) and its related mechanism; its osteogenic potential was also evaluated using a calvarial defect model in rats. We found that strontium could enhance the osteogenic differentiation of the MSCs, with upregulated extracellular matrix (ECM) gene expression and activated Wnt/β-catenin pathway. After transplanting the collagen-strontium-substituted hydroxyapatite scaffold into the bone defect region, histology and computed tomography scanning revealed that in vivo bone formation was significantly enhanced; the quantity of mature and remodeled bone substantially increased and ECM accumulated. Interestingly, strontium induced an increase of β-catenin expression in newly formed bone area. In this study, we showed for the first time that strontium could stimulate the β-catenin expression in vitro and in vivo, which might contribute to the enhanced osteogenic differentiation of MSCs and in vivo bone formation.
Concise Review: Transplantation of Human Hematopoietic Cells for Extracellular Matrix Protein Deficiency in Epidermolysis Bullosa
Authors: Tolar Jakub , Blazar Bruce R. , Wagner John E. 
Published: April 2011

Abstract
The skin is constantly exposed to environmental insults and requires effective repair processes to maintain its protective function. Wound healing is severely compromised in people with congenital absence of structural proteins of the skin, such as in dystrophic epidermolysis bullosa, a severe congenital mechanobullous disorder caused by mutations in collagen type VII. Remarkably, stem cell transplantation can ameliorate deficiency of this skin-specific structural protein in both animal models and in children with the disorder. Healthy donor cells from the hematopoietic graft migrate to the injured skin; simultaneously, there is an increase in the production of collagen type VII, increased skin integrity, and reduced tendency to blister formation. How hematogenous stem cells from bone marrow and cord blood can alter skin architecture and wound healing in a robust, clinically meaningful way is unclear. We review the data and the resulting hypotheses that have a potential to illuminate the mechanisms for these effects. Further modifications in the use of stem cell transplantation as a durable source of extracellular matrix proteins may make this regenerative medicine approach effective in other cutaneous and extracutaneous conditions.
Concise Review: Contribution of Cancer Stem Cells to Neovascularization
Authors: Ping Yi-Fang , Bian Xiu-Wu 
Published: April 2011

Abstract
Cancer stem cells (CSCs), a special subpopulation of tumor cells, are considered as tumor initiating cells. More recently, these cells have also been identified as initiators of tumor neovascularization. A better understanding of the contribution of CSCs to neovascularization should elucidate the mechanisms of cancer initiation and progression as well as establish new concepts for cancer diagnosis and treatment. In this review, we discuss the evidence for the roles of CSCs in tumor vascularization, including production of proangiogenic factors, transdifferentiation into vascular mural cells such as endothelial and smooth muscle-like cells, and formation of nonendothelium-lined vasculogenic mimicry. In addition, the potential therapeutic significance of targeting CSCs is envisaged.
Toll-Like Receptor-3-Activated Human Mesenchymal Stromal Cells Significantly Prolong the Survival and Function of Neutrophils
Authors: Cassatella Marco A. , Mosna Federico , Micheletti Alessandra , Lisi Veronica , Tamassia Nicola , Cont Caterina , Calzetti Federica , Pelletier Martin , Pizzolo Giovanni , Krampera Mauro 
Published: April 2011

AbstractBone marrow-derived mesenchymal stromal cells (BM-MSCs) are stromal precursors endowed with extensive immunomodulative properties. In this study, we aimed to assess whether Toll-like receptor-3 (TLR3)- and TLR4-activated BM-MSC influence human neutrophil (PMN) responses under coculture conditions. We show that TLR3 triggering by polyinosinic:polycytidylic acid dramatically amplifies, in a more significant manner than TLR4 triggering by lipopolysaccharide, the antiapoptotic effects that resting BM-MSC constitutively exert on PMN under coculture conditions, preserving a significant fraction of viable and functional PMN up to 72 hours. In addition, TLR3- and TLR4-activated BM-MSC enhance respiratory burst ability and CD11b expression by PMN. The coculture in the absence of cell contact and the incubation of PMN in supernatants harvested from TLR3- and TLR4-activated BM-MSC yield comparable results in terms of increased survival and immunophenotypic changes, thus suggesting the involvement of endogenous soluble factors. Neutralizing experiments reveal that the biological effects exerted on PMN by TLR3-activated BM-MSC are mediated by the combined action of interleukin 6, interferon-β (IFN-β), and granulocyte macrophage colony-stimulating factor (GM-CSF), while those exerted by TLR4-activated BM-MSC mostly depend on GM-CSF. MSC isolated from thymus, spleen, and subcutaneous adipose tissue behaves similarly. Finally, the effects exerted by TLR3- or TLR4-stimulated BM-MSC on PMN are conserved even after the previous priming of BM-MSC with IFN-γ and tumor necrosis factor-α. Our data highlight a novel mechanism by which MSC sustain and amplify the functions of PMN in response to TLR3- and TLR4-triggering and may consequently contribute to inflammatory disorders.
Thread algebra for poly-threading
Authors: Bergstra J. A. , Middelburg C. A. 
Published: April 2011

Abstract
It is a fact of life that sequential programs are often fragmented. Consequently, fragmented program behaviours are frequently found. We consider this phenomenon in the setting of thread algebra. We extend basic thread algebra with poly-threading, the barest mechanism for sequencing of threads that are taken for program fragment behaviours. This mechanism is the counterpart of program overlaying at the level of program behaviours. We relate the resulting theory to the process theory known as ACP and use it to describe analytic execution architectures suited for fragmented programs. We also consider the case where the steps of fragmented program behaviours are interleaved in the ways of non-distributed and distributed multi-threading.
Retrospective Comparison of Clinical Outcomes between Endovenous Laser and Saphenous Vein‐sparing Surgery for Treatment of Varicose Veins
Authors: Chan Chih‐Yang , Chen Tzu‐Chun , Hsieh Yung‐Kun , Huang Jih‐Hsin 
Published: April 2011

AbstractBackgroundThe purpose of the present study was to compare management of varicose veins by endovenous laser ablation (EVL) and a vein‐sparing procedure (CHIVA: Conservatrice et Hémodynamique de l’Insuffisance Veineuse en Ambulatoire) for management of varicose veins.MethodsData from 82 consecutive patients with great saphenous vein (GSV) reflux and primary varicose veins presenting to the vascular clinic at the Far Eastern Memorial Hospital between June and December 2005 were reviewed. Of these, 74 who met the inclusion criteria were included in this study. CHIVA was performed by a double division of the refluxing saphenous vein (i.e., proximal and distal ligation), and EVL was performed using 10–14 W beginning approximately 4 cm below the saphenofemoral junction to the level of the knee. Phlebectomy for significant branch varicose veins on the leg was routinely performed in all patients. Outcome measures included postoperative thrombophlebitis, bruising, pain, assessment of ultrasonographic and clinical symptoms (measured by the Venous Clinical Severity Score [VCSS]) and comparison of quality of life survey scores obtained preoperatively and postoperatively (measured by the Aberdeen Varicose Veins Score [AVVQ] and RAND‐36). Patients were examined one week post‐procedurally and again at 1, 3, 6, and 12 months.ResultsEndovenous laser ablation and CHIVA were performed on 54 and 20 patients, respectively. The EVL patients had significantly higher pain scores and bruising than the CHIVA group (p < 0.001). The VCSS of varicose, edema, pigmentation, and inflammation were significantly reduced after both EVL and CHIVA; however, patients treated by EVL had significantly more pain postoperatively than those treated by CHIVA (p = 0.003). Twenty‐two of 54 (40.7%) and 3 of 17 (17.6%) patients in the EVL and CHIVA groups, respectively, required sclerotherapy for residual varicosities (p = 0.026). Both groups benefited significantly from surgery in disease‐specific perceptions.ConclusionsThe CHIVA patients had less pain postoperatively and a significantly higher sclerotherapy‐free period compared to patients in the EVL group. Further follow‐up studies to compare long‐term results of various approaches to surgically managing varicose veins are needed.
A new synaptic player leading to autism risk: Met receptor tyrosine kinase
Authors: Judson Matthew C. , Eagleson Kathie L. , Levitt Pat 
Published: April 2011

AbstractThe validity for assigning disorder risk to an autism spectrum disorder (ASD) candidate gene comes from convergent genetic, clinical, and developmental neurobiology data. Here, we review these lines of evidence from multiple human genetic studies, and non-human primate and mouse experiments that support the conclusion that the MET receptor tyrosine kinase (RTK) functions to influence synapse development in circuits relevant to certain core behavioral domains of ASD. There is association of both common functional alleles and rare copy number variants that impact levels of MET expression in the human cortex. The timing of Met expression is linked to axon terminal outgrowth and synaptogenesis in the developing rodent and primate forebrain, and both in vitro and in vivo studies implicate this RTK in dendritic branching, spine maturation, and excitatory connectivity in the neocortex. This impact can occur in a cell-nonautonomous fashion, emphasizing the unique role that Met plays in specific circuits relevant to ASD.
Subsurface Structure Derived from Detailed Gravity and Magnetic Investigations along the Pala-Maneri Traverse of the Main Central Thrust, NW Himalaya
Authors: Seshunarayana T. , Prasad B. Rajendra , Prasad A.S.S.S.R.S. , Mysaiah D. 
Published: April 2011

Abstract
A detailed, integrated gravity and magnetic study across the Main Central Thrust (MCT) along the Pala- Maneri traverse in Uttaranchal, NW Himalaya was carried out. The gravity data was acquired using a CG-3 gravity meter with an accuracy of 0.005 mGal, while magnetic data was acquired using a proton precession magnetometer with a station interval of 20 m. Data was collected along a 11.7 km, NE–SW traverse from Pala to Maneri along the proposed route of a hydroelectric headrace tunnel. The measured variation in the gravity field was approximately 70 mGal, with two prominent highs recorded at distances of 0.5 km, 7.5 km and lows at 3.0 km, 10.5 km from Maneri. The gravity highs can be attributed to presence of high-density rocks along the thrust planes. The sharp gravity low recorded at 10.5 km distance possibly indicates a sympathetic fault of the MCT that is highly saturated with fluids (water). The broad gravity low between 2.5 km and 4.0 km distance is likely to represent the gravity signature of the MCT itself. The measured variation in the magnetic field was approximately 285 nT. The associated gravity and magnetic signatures located several faults along the traverse including presence of the MCT at Kumaltigad.