bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissipative particle dynamics for complex geometries using non‐orthogonal transformation
Authors: Abu‐Nada Eiyad , Kumar Anurag , Asako Yutaka , Faghri Mohammad 
Published: January 2011

AbstractDissipative particle dynamics (DPD) was applied to fluid flow in irregular geometries using non‐orthogonal transformation, where an irregular domain is transformed into a simple rectangular domain. Transformation for position and velocity was used to relate the physical and computational domains. This approach was described by simulating fluid flow inside a two‐dimensional convergent–divergent nozzle. The nozzle geometry is controlled by the contraction ratio (CR) in the middle of the channel. The range of Reynolds number and CR, in this paper, was Re = 10hbox−−200 and CR = 0.8 and 0.6, respectively. The DPD results were validated against in‐house computational fluid dynamic (CFD) finite volume code based on the stream function vorticity approach. The results revealed an excellent agreement between DPD and CFD. The maximum deviation between the DPD and CFD results was within 2%. Local and average coefficients of friction was calculated and it compared well with the CFD results. Copyright © 2011 John Wiley & Sons, Ltd.
Methods for Biochemical Model Decomposition and Quantitative Submodel Comparison
Authors: Mizera Andrzej , Czeizler Elena , Petre Ion 
Published: January 2011

AbstractComparing alternative models for a given biochemical system is in general a very difficult problem: the models may focus on different aspects of the same system and may consist of very different species and reactions. The numerical setups of the models also play a crucial role in the quantitative comparison. When the alternative designs are submodels of a reference model, for example, knockdown mutants of a model, the problem of comparing them becomes simpler: they all have very similar, although not identical, underlying reaction networks, and the biological constraints are given by those in the reference model. In the first part of our study, we review several known methods for model decomposition and for quantitative comparison of submodels. We describe knockdown mutants, elementary flux modes, control‐based decomposition, mathematically controlled comparison and its extension, local submodel comparison and a discrete approach for comparing continuous submodels. In the second part of the paper we present a new statistical method for comparing submodels, which complements the methods presented in the review. The main difference between our approach and the known methods is related to the important question of how to chose the numerical setup in which to perform the comparison. In the case of the reviewed methods, the comparison is made in the numerical context of the reference model, i.e., in each of the alternative models both the kinetics of the reactions and the initial values of all variables are chosen to be identical to those from the reference model. We propose in this paper a different approach, better suited for response networks, where each alternative model is assumed to start from its own steady state under basal conditions. We demonstrate our approach with a case study focusing on the heat shock response in eukaryotes.
RNA Interference‐Based Computing in Mammalian Cells
Authors: Benenson Yaakov 
Published: January 2011

AbstractDevelopment of synthetic biological pathways is contingent upon the availability of general‐purpose, programmable tools to process molecule‐encoded information in live cells. A few years ago we introduced a comprehensive design framework for biological computing in mammalian cells that utilizes the RNA interference (RNAi) pathway. Our method exploits the relatively simple structural requirements of the RNAi to engineer increasingly complex molecular logic circuits. This led to a scalable and intuitive method to perform logic integration of transcription factors, and first steps toward sensing and integrating mRNA signals.
Hydrostatic pressure independently increases elastin and collagen co‐expression in small‐diameter engineered arterial constructs
Authors: Crapo Peter M. , Wang Yadong 
Published: January 2011

AbstractPrior studies have demonstrated that smooth muscle cell (SMC) proliferation, migration, and extracellular matrix production increase with hydrostatic pressure in vitro. We have engineered highly compliant small‐diameter arterial constructs by culturing primary adult baboon arterial SMCs under pulsatile perfusion on tubular, porous, elastomeric scaffolds composed of poly(glycerol sebacate) (PGS). This study investigates the effect of hydrostatic pressure on the biological and mechanical properties of PGS‐based engineered arterial constructs. Pressure was raised using a downstream needle valve during perfusion while preserving flow rate and pulsatility, and constructs were evaluated by pressure–diameter testing and biochemical assays for collagen and elastin. Pressurized constructs contained half as much insoluble elastin as baboon common carotid arteries but were significantly less compliant, while constructs cultured at low hydrostatic pressure contained one‐third as much insoluble elastin as baboon carotids and were similar in compliance. Hydrostatic pressure significantly increased construct burst pressure, collagen and insoluble elastin content, and soluble elastin concentration in culture medium. All arteries and constructs exhibited elastic recovery during pressure cycling. Hydrostatic pressure did not appear to affect radial distribution of SMCs, collagens I and III, and elastin. These results provide insights into the control of engineered smooth muscle tissue properties using hydrostatic pressure. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 2011.
Covalently immobilized glycosaminoglycans enhance megakaryocyte progenitor expansion and platelet release
Authors: Kishore Vipuil , Eliason James F. , Matthew Howard W. T. 
Published: January 2011

AbstractApplication of umbilical cord blood (UCB) transplantation in adults as a treatment post‐chemotherapy is hampered due to delayed platelet recovery. A potential solution suggested is the transfusion of ex vivo expanded megakaryocytes (Mks) from hematopoietic stem cells (HSCs). Alternatively, large‐scale production of platelets in vitro has also been attempted with the goal of transfusing them into patients with thrombocytopenia. Glycosaminoglycans (GAGs) have been shown to influence the proliferation and differentiation of HSCs. This study sought to examine the effects of immobilized GAGs on the expansion, apoptosis, and platelet release activity of CD41a+ Mk progenitors in vitro. Freshly isolated HSCs from UCB were cultured in serum‐free media supplemented with thrombopoietin on GAG‐derivatized chitosan membranes for 17 days. Controls consisted of uncoated and chitosan‐coated wells. Wells were demidepopulated at periodic intervals and analyzed by flow cytometry. Heparin and dermatan sulfate surfaces significantly enhanced total cell and Mk cell expansion (p < 0.05) compared to both the controls. The apoptotic Mk fraction was significantly lower on GAG surfaces (p < 0.05) compared to the polystyrene control during the early stages of the culture (days 7 and 11). However, by day 17, the apoptotic Mk fraction was comparable on all surfaces. The cumulative number of platelets generated on dermatan sulfate and heparan sulfate surfaces was significantly higher (p < 0.05) than on both the controls. These results suggest that immobilized GAGs delay Mk apoptosis and thereby enhance Mk expansion and platelet production. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 2011.
Donor survey to assess facial flushing during automated red cell collections and medication use
Authors: Eder Anne F. , Mitchell Tanya , Dy Beth , Herron Ross M. , Ellen Wissel Mary , Lightfoot Thomas , Jo Drew Mary , Mair David ,   American Red Cross Regional Blood Centers
Published: January 2011

AbstractBackground: We conducted a donor survey to assess the occurrence of facial flushing and other symptoms during automated 2‐U red cell collections (2RBC) and plateletpheresis (PLT) procedures and evaluated the possible association of the reactions with angiotensin‐converting enzyme (ACE) inhibitors or with the collection technology. Methods: An online survey was developed using Zoomerang to capture details of the donors' experience and medication use after 2RBC or PLT donations in regional blood centers of the American Red Cross. Results: Between 12/16/09 and 4/19/10, 1,299 donors in five American Red Cross blood center regions completed an online survey (739 2RBC, 4.2% total registrations; 560 PLT, 2.3% total registrations). Facial flushing was reported by 29 donors, and was more likely associated with 2RBC than PLT procedures (3.0% vs. 1.3%, P = 0.03). Facial flushing with 2RBC donation was reported by eight of 72 (11%) donors on ACE inhibitors; and 14 of 667 (2%) donors who were not taking ACE inhibitors (P = 0.001). The incidence of facial flushing reactions with PLT donation was less than 2% whether donors reported ACEI inhibitor use or not. More than 95% of the donors reported their intent to donate again, regardless of symptoms. Conclusion: Facial flushing was more often reported by 2RBC donors taking ACE inhibitors than other donors [11% vs. 2%; P = 0.001]; and was uncommon among PLT donors, irrespective of ACE inhibitor use (<2%). All blood donors should be informed of the potential for common, minor side effects of the collection procedure and the possible but rare occurrence of more medically serious complications. J. Clin. Apheresis, 2011. © 2011 Wiley‐Liss, Inc.
Single region of interest versus multislice T2* MRI approach for the quantification of hepatic iron overload
Authors: Meloni Antonella , Luciani Antongiulio , Positano Vincenzo , De Marchi Daniele , Valeri Gianluca , Restaino Gennaro , Cracolici Eliana , Caruso Vincenzo , Dell'Amico Maria Chiara , Favilli Brunella , Lombardi Massimo , Pepe Alessia 
Published: January 2011

AbstractPurposeTo evaluate the effectiveness of the single ROI approach for the detection of hepatic iron burden in thalassemia major (TM) patients in respect to a whole liver measurement.Materials and MethodsFive transverse hepatic slices were acquired by a T2* gradient‐echo sequence in 101 TM patients and 20 healthy subjects. The T2* value was calculated in a single region of interest (ROI) defined in the medium‐hepatic slice. Moreover, the T2* value was extracted on each of the eight ROIs defined in the functionally independent segments. The mean hepatic T2* value was calculated.ResultsFor patients, the mean T2* values over segments VII and VIII were significantly lower. This pattern was substantially preserved in the two groups identified considering the T2* normal cutoff. All segmental T2* values were correlated with the single ROI T2* value. After the application of a correction map based on T2* fluctuations in the healthy subjects, no significant differences were found in the segmental T2* values.ConclusionHepatic T2* variations are low and due to artifacts and measurement variability. The single ROI approach can be adopted in the clinical arena, taking care to avoid the susceptibility artifacts, occurring mainly in segments VII and VIII. J. Magn. Reson. Imaging 2011;33:348–355. © 2011 Wiley‐Liss, Inc.
Off‐resonance Raman analysis of wurtzite CdS ground to the nanoscale: structural and size‐related effects
Authors: Chi T. T. K. , Gouadec G. , Colomban Ph. , Wang G. , Mazerolles L. , Liem N. Q. 
Published: January 2011

AbstractDifferent techniques were used to follow the transformation of CdS platelets during grinding and under hydrostatic pressure. X‐ray diffraction and transmission electron microscopy revealed that the platelets included zinc blende (cubic) CdS nanodomains dispersed in a wurtzite (hexagonal) single‐crystalline matrix. Extended grinding led to a decrease of the grain size and to a progressive transformation of the hexagonal stacking into a cubic one. The same phase transition was observed up to 9 GPa under hydrostatic pressure.Off‐resonance Raman spectra collected at different stages of the transition led us to connect band groups that were usually overlooked (in resonance conditions) or considered separately. They all probe the stacking disorder and their intensity can be related to the density of stacking faults. Off‐resonance Raman spectroscopy offers a way of probing the optical properties of CdS (and, more generally, layered semiconductors) as a function of the structure and of the confinement of vibrations by structural defects. Copyright © 2011 John Wiley & Sons, Ltd.
Soil salinity development in the yellow river delta in relation to groundwater dynamics
Authors: Fan X. , Pedroli B. , Liu G. , Liu Q. , Liu H. , Shu L. 
Published: January 2011

AbstractThe Yellow River Delta occupies an important position in the global ecosystem because of its valuable wetland habitat resources for migratory birds on the Eastern Pacific migration route. However, it has suffered from severe land degradation because of soil salinization. This paper assesses the distribution maps of saline soils during the past two decades, using field observations at three points in time using remote sensing images for the same periods, in combination with spatial models. Soil salinization appears to have expanded from the coastline to inland areas of the Yelow River Delta at a surprising speed during that period. The spatio‐temporal dynamics of the groundwater table and total dissolved solids (TDS) during the last 20 years were analyzed using maps based on Kriging interpolation. Kriging helped substantially to improve the accurateness of the predicted values of soil salt content, using a random subsample of the observation points as validation basis. Correlation analysis of the spatial data revealed that the distribution and evolution of saline soils are closely related to the dynamics of groundwater: the aggravation of soil salinization is associated with a rising groundwater table and increasing TDS. Insufficient recharge of the groundwater with fresh surface water due to reduced Yellow River discharge and subsequent seawater intrusion are therefore serious environmental problems in the Yellow River Delta ecosystem. Copyright © 2011 John Wiley & Sons, Ltd.
Homogeneous Sulfation of Xylan from Different Sources
Authors: Daus Stephan , Petzold‐Welcke Katrin , Kötteritzsch Manuela , Baumgaertel Anja , Schubert Ulrich S. , Heinze Thomas 
Published: January 2011

AbstractXylan sulfates have been prepared under homogeneous reaction conditions in DMF/LiCl applying SO3/pyridine and SO3/DMF. The degree of substitution (DSSulfate) of the products obtained was determined by elemental analysis. DSSulfate reached values of up to 1.90 applying a molar ratio of 3 mol sulfating agent per anhydroxylose unit. The structure of the xylans and of the xylan sulfates was studied in detail by one‐ and two‐dimensional NMR spectroscopy and MALDI‐TOF mass spectrometry. magnified image
Iterative solutions for zeros of multivalued accretive operators
Authors: Song Yisheng 
Published: January 2011

AbstractStrong convergence of two iterative schemes is proved to approach some zero of multivalued accretive operators in a Banach space. The first one is a regularization method for Rockafellar's proximal point algorithm of the resolvent and the second one is a kind of Halpern type iteration process of the resolvent. © 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim
Upregulation of the EP1 receptor for prostaglandin E2 promotes skin tumor progression
Authors: Surh Inok , Rundhaug Joyce , Pavone Amy , Mikulec Carol , Abel Erika , Fischer Susan M. 
Published: January 2011

AbstractProstaglandin E2 (PGE2) has been shown to promote the development of murine skin tumors. EP1 is 1 of the 4 PGE2 G‐protein‐coupled membrane receptors expressed by murine keratinocytes. EP1 mRNA levels were increased ∼2‐fold after topical treatment with 12‐O‐tetradecanoylphorbol‐13‐acetate (TPA) or exposure to ultraviolet (UV) light, as well as increased ∼3‐ to 12‐fold in tumors induced by 7,12‐dimethyl‐benz[a]anthracene (DMBA) initiation/TPA promotion or by UV exposure. To determine the effect of EP1 levels on tumor development, we generated BK5.EP1 transgenic mice that overexpress EP1 in the basal layer of the epidermis. Skins of these mice were histologically indistinguishable from wild type (WT) mice and had similar levels of proliferation after TPA treatment. Using a DMBA/TPA carcinogenesis protocol, BK5.EP1 mice had a reduced tumor multiplicity compared to WT mice, likely due to the observed down‐regulation of protein kinase C (PKC). However, the BK5.EP1 mice had an ∼8‐fold higher papilloma to carcinoma conversion rate. When DMBA/anthralin was used, BK5.EP1 mice produced more tumors than WT mice, as well as a ninefold increase in carcinomas, indicating that the tumor response is dependent on the type of tumor promoter agent used. Additionally, although almost undetectable in WT mice, cyclooxygenase‐2 (COX‐2) was expressed in the untreated epidermis of BK5.EP1 mice. While TPA highly induced COX‐2 in WT mice, COX‐2 expression in the BK5.EP1 mice did not change after TPA treatment; PGE2 levels were likewise affected. These data indicate that EP1 is more important in tumor progression than in tumor promotion and that it indirectly regulates COX‐2 expression. © 2011 Wiley‐Liss, Inc.
Activation and up‐regulation of translation initiation factor 4B contribute to arsenic‐induced transformation
Authors: Zhang Yong , Wang Qing , Guo Xiaoling , Miller Robert , Guo Yinglu , Yang Hsin‐Sheng 
Published: January 2011

AbstractArsenic is a known human carcinogen. However, the mechanism of how arsenic induces cell transformation remains unclear. In this study, we demonstrated that long‐term exposure to sodium arsenite at low‐dose (2 µM) increases cell proliferation and neoplastic transformation in a mouse epidermal cell model, JB6 promotion‐susceptible cells. The phosphorylation of AKT and its downstream targets, 70‐kDa ribosomal protein S6 kinase (p70S6K) and translation initiation factor 4B (eIF4B), are increased in the arsenite treated cells, indicating that long‐term arsenite treatment activates AKT–p70S6K signaling pathway. In addition, long‐term exposure to arsenite up‐regulates eIF4B expression and increases the rate of translation. Knockdown of eIF4B expression resulted in inhibition of arsenic‐induced cell proliferation, transformation, and translation. Moreover, the expression of c‐Myc which is up‐regulated by long‐term arsenite treatment is inhibited by eIF4B knockdown. Taken together, these results indicate that activation and up‐regulation of eIF4B contributes to arsenic‐induced transformation in JB6 cells. Mol. Carcinog. © 2011 Wiley‐Liss, Inc.
Diclofenac, a selective COX‐2 inhibitor, inhibits DMH‐induced colon tumorigenesis through suppression of MCP‐1, MIP‐1α and VEGF
Authors: Kaur Jasmeet , Sanyal S.N. 
Published: January 2011

AbstractAngiogenesis is a physiological process involving growth of new blood vessels from pre‐existing ones; however, it also plays a critical role in tumor progression. It favors the transition from hyperplasia to neoplasia, that is, from a state of cellular multiplication to uncontrolled proliferation. Therefore targeting angiogenesis will be profitable as a mechanism to inhibit tumor's lifeline. Further, it is important to understand the cross‐communication between vascular endothelial growth factor (VEGF)—master switch in angiogenesis and other molecules in the neoplastic and pro‐inflammatory milieu. We studied the role of two important chemokines [monocyte chemoattractant protein (MCP)‐1 and macrophage inflammatory protein (MIP)‐lα] alongwith VEGF and matrix metalloproteinases (MMPs) in non‐steroidal anti‐inflammatory drugs (NSAIDs)‐induced chemopreventive effect in experimental colon cancer in rat. 1,2‐Dimethylhydrazine (DMH, 30 mg/kg body weight, subcutaneously (s.c.) once‐a‐week) for 18 wk was used as pro‐carcinogen and diclofenac (8 mg/kg body weight, orally daily) as the preferential cyclooxygenase‐2 (COX‐2) inhibitor. Expression of COX‐2 and VEGF was found to be significantly elevated in the DMH‐treated group as compared to the control, which was lowered notably by Diclofenac co‐administration with DMH. Gelatin zymography showed prominent MMP‐9 activity in the DMH‐treated rats, while the activity was nearly absent in all the other groups. Expression of MCP‐1 was found to be markedly increased whereas MIP‐1α expression was found to be decreased in colonic mucosa from DMH‐treated rats, which was reversed in the DMH + Diclofenac group. Our results indicate potential role of chemokines alongwith VEGF in angiogenesis in DMH‐induced cancer and its chemoprevention with diclofenac. Mol. Carcinog. ©2011 Wiley‐Liss, Inc.
CacyBP/SIP protein promotes proliferation and G1/S transition of human pancreatic cancer cells
Authors: Chen Xiong , Mo Ping , Li Xiaohua , Zheng Peichan , Zhao Lina , Xue Zengfu , Ren Gui , Han Guohong , Wang Xin , Fan Daiming 
Published: January 2011

AbstractCalcyclin‐binding protein or Siah‐1‐interacting protein (CacyBP/SIP), a component of the ubiquitin‐mediated proteolysis, could participate in beta‐catenin degradation, which was found to be related to the malignant phenotypes of pancreatic cancer previously. However, the role of CacyBP/SIP itself in pancreatic cancer has not been investigated. In the present study, CacyBP/SIP expression was assayed and manipulated to reveal the potential mechanism in pancreatic cancer carcinogenesis. Here, we show that CacyBP/SIP is over‐expressed in pancreatic cancer cells. Down‐regulation of CacyBP/SIP by small interference RNA (siRNA) severely suppresses the proliferation and tumorigenesis in pancreatic cancer. G1/S transition arrest induced by inhibition of CacyBP/SIP is at least partly mediated by down‐regulation of Cyclin E and CDK2 as well as up‐regulation of p27 and Rb. Collectively, CacyBP/SIP as an enhancer of pancreatic cancer malignance might develop into another possible therapeutic target. Mol. Carcinog. © 2011 Wiley‐Liss, Inc.
Grape seed extract upregulates p21 (Cip1) through redox‐mediated activation of ERK1/2 and posttranscriptional regulation leading to cell cycle arrest in colon carcinoma HT29 cells
Authors: Kaur Manjinder , Tyagi Alpna , Singh Rana P. , Sclafani Robert A. , Agarwal Rajesh , Agarwal Chapla 
Published: January 2011

AbstractAbnormalities in cell cycle progression provide unlimited replicative potential to cancer cells, and therefore targeting of key cell cycle regulators could be a sound cancer chemopreventive strategy. Earlier, we found that grape seed extract (GSE) increases Cip/p21 protein level and inhibits growth and induces apoptosis in human colon carcinoma HT29 cells both in vitro and in vivo. However, the mechanism of GSE‐induced p21 upregulation and its role in biological efficacy of GSE are not known, which were investigated here. GSE treatment of HT29 cells resulted in a strong dose‐ and time‐dependent phosphorylation of extracellular signal regulated kinase 1/2 (ERK1/2), consistent with p21 induction. The inhibition of sustained ERK1/2 activation by GSE using pharmacological inhibitors abrogated GSE‐induced p21 upregulation. Furthermore, pretreatment of cells with N‐acetylcysteine inhibited GSE‐induced ERK1/2 phosphorylation as well as p21 upregulation, suggesting the involvement of GSE‐induced oxidative stress as an upstream event. Consistent with this, GSE also decreased intracellular level of reduced glutathione. Next, we determined whether GSE‐induced signaling regulates p21 expression at transcriptional and/or translational levels. GSE was found to increase the stability of p21 message with resultant increase in p21 protein level, but it did not alter the protein stability to a great extent. Importantly, knock‐down of p21 abrogated GSE‐induced G1 arrest suggesting that p21 induction by GSE is essential for its G1 arrest effect. Together, our results for the first time identify a central role of p21 induction and associated mechanism in GSE‐induced cell cycle arrest in HT29 cells. Mol. Carcinog. © 2011 Wiley‐Liss, Inc.