bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of regional and global climatic oscillations on Croatian climate
Authors: Bice David , Montanari Alessandro , Vučetić Višnja , Vučetić Marko 
Published: July 2011

AbstractWe apply spectral analysis and sliding window correlations to monthly, seasonal, and annual climatological data from station records throughout Croatia going back to 1859 in order to investigate the potential influences of a set of important climatic drivers, including solar variability, and ocean–atmosphere oscillations in both the Pacific realm (El Niño‐Southern Oscillation, ENSO and Pacific Decadal Oscillation, PDO) and the Atlantic realm (Atlantic Multidecadal Oscillation, AMO and North Atlantic Oscillation, NAO). In addition to a general long‐term warming and drying, there are significant interannual to decadal scale variations. Positive phases of AMO correspond to higher Croatian temperatures and also times of greater interannual temperature variability. Higher frequency variations in NAO are positively correlated with temperature such that a negative phase of NAO is associated with lower Croatian temperatures. The strength of NAO's influence is modulated by the long‐term cycles of AMO; stronger during positive decadal‐scale phases of AMO. ENSO exerts a weaker influence on temperatures, and is only significant during positive phases of the PDO. NAO has a strong influence on Croatian winter precipitation, with negative NAO phases corresponding to higher precipitation, modulated by the longer term phases of AMO. Although weaker and less consistent, ENSO also influences Croatian winter precipitation, modulated by longer term cycles of the PDO. Both NAO and ENSO show signs of frequency‐dependent correlation; NAO is influential at cycles of 8–9 and 2.4 yr in the Adriatic–Dinaric part of Croatia, while ENSO is especially influential at a 3.6 yr cycle in the Pannonian region. The influence of solar variability is apparently much weaker than that of NAO and ENSO, yet there is a remarkably coherent correlation between amplitude modulation of winter precipitation in the Pannonian region and the sunspot record. Copyright © 2011 Royal Meteorological Society
The effectiveness of extreme rainfall alerts in predicting surface water flooding in England and Wales
Authors: Hurford, A. P. , Priest S. J. , Parker D. J. , Lumbroso D. M. 
Published: July 2011

AbstractThe extreme rainfall alert (ERA) pilot was a response to the Pitt Review's recommendation that ‘the Met Office and Environment Agency (EA) provide an early assessment of the costs, benefits and feasibility of techniques which can predict where rain will fall and where surface water flooding will occur’. In April 2009, the ERA became an operational service provided to the EA professional partners and Category 1 and 2 responders—organizations with legal responsibilities to respond to flooding. ERAs are intended as a first step towards warnings for surface water flooding (SWF). This article assesses the effectiveness of the ERA pilot at predicting SWF. ERAs relating to three case study areas and issued during the pilot were compared with reports of SWF, identified from the data available relating to all sources of flooding. While data were found to be lacking in quality and consistency, it is possible to provide an initial assessment of the effectiveness of the ERA pilot. The existing ERA rainfall thresholds do not relate directly to SWF in all areas. As the ERA service specifically intends to warn for rainfall likely to cause severe SWF in urban areas, it is impossible to draw strong conclusions without further investigating the magnitude of flooding which occurred both when an ERA was and was not issued. As SWF magnitude and extent data were extremely sparse, it is recommended that systematic collection of comprehensive data relating to flood events should be implemented nationally. This will facilitate more accurate investigations of the links between rainfall intensity and SWF, which it is vital to understand in order to provide the most effective surface water flood warnings possible. Copyright © 2011 Royal Meteorological Society
Genome‐wide transcriptional profiling analysis of all trans retinoic acid‐treated tongue carcinoma SCC‐9 cells
Authors: Dai Yaohui , Wang Juan , Xia Juan , Hong Yun , Chen Na , Cheng Bin 
Published: July 2011

AbstractBackgroundAll trans retinoic acid (ATRA) is used as standard of care in promyelocytic leukemia. Not much is known about the gene expression profile in ATRA‐treated tongue cancer cells. We performed a genome‐wide transcriptional profiling of ATRA‐treated tongue cancer cells to understand the pathways that mediate ATRA action in tongue cancer.MethodsWe measured the effects of ATRA on the proliferation of SCC‐9 human tongue carcinoma cells. The differential gene expression profile was measured by microarray analysis of untreated and ATRA‐treated cells and expression of key genes was validated by real‐time RT‐PCR.ResultsATRA treatment (24 and 48 hr) significantly inhibited SCC‐9 cell proliferation in a dose‐dependent manner. SCC‐9 cells treated for 48 hr with ATRA showed upregulation of 276 genes, including ANGPTL4, GDF15, ICAM1 and TUSC4, and downregulation of 43 genes, including CXCL10. Validation by real‐time PCR showed a significant upregulation of intracellular adhesion molecule 1 (ICAM1) and downregulation of CXCL10 and IL32.ConclusionsATRA had an anti‐tumor effect in tongue cancer cells. This effect is likely mediated via upregulation of ICAM1 and downregulation of CXCL10 and IL32. J. Surg. Oncol. 2011; 104:830–835. © 2011 Wiley Periodicals, Inc.
In vitro Characterization of an Electroactive Carbon‐Nanotube‐Based Nanofiber Scaffold for Tissue Engineering
Authors: Mackle Joseph N. , Blond David J.‐P. , Mooney Emma , McDonnell Caitlin , Blau Werner J. , Shaw Georgina , Barry Frank P. , Murphy J. Mary , Barron Valerie 
Published: July 2011

AbstractIn an effort to reduce organ replacement and enhance tissue repair, there has been a tremendous effort to create biomechanically optimized scaffolds for tissue engineering applications. In contrast, the development and characterization of electroactive scaffolds has attracted little attention. Consequently, the creation and characterization of a carbon nanotube based poly(lactic acid) nanofiber scaffold is described herein. After 28 d in physiological solution at 37 °C, a change in the mass, chemical properties and polymer morphology is seen, while the mechanical properties and physical integrity are unaltered. No adverse cytotoxic affects are seen when mesenchymal stem cells are cultured in the presence of the scaffold. Taken together, these data auger well for electroactive tissue engineering.magnified image
Covalent Heparin Modification of a Polysulfone Flat Sheet Membrane for Selective Removal of Low‐Density Lipoproteins: A Simple and Versatile Method
Authors: Li Jing , Huang Xiao‐Jun , Ji Jing , Lan Ping , Vienken Jörg , Groth Thomas , Xu Zhi‐Kang 
Published: July 2011

AbstractA simple, convenient and economical method for the heparinization of PSf membranes is described, with the aim of preparing an LDL adsorber for simultaneous LDL apheresis and hemodialysis. An atmospheric pressure glow discharge generator is used to activate the PSf membrane surface, with subsequent chemical binding of heparin in the presence of EDC and NHS. ATR‐FTIR spectroscopy and XPS measurements confirm successful surface modification. The PSf‐Hep membrane shows good blood compatibility, with a relatively low amount and normal morphology of adherent platelets. ELISA results indicate that the PSf‐Hep membrane exhibits excellent selective affinity for LDL in single and binary protein solutions, suggesting potential applications in hemodialysis with simultaneous LDL removal.magnified image
Truly Nonionic Polymer Shells for the Encapsulation of Living Cells
Authors: Carter Jessica L. , Drachuk Irina , Harbaugh Svetlana , Kelley‐Loughnane Nancy , Stone Morley , Tsukruk Vladimir V. 
Published: July 2011

AbstractEngineering surfaces of living cells with natural or synthetic compounds can mediate intercellular communication and provide a protective barrier from hostile agents. We report on truly nonionic hydrogen‐bonded LbL coatings for cell surface engineering. These ultrathin, highly permeable polymer membranes are constructed on living cells without the cationic component typically employed to increase the stability of LbL coatings. Without the cytotoxic cationic PEI pre‐layer, the viability of encapsulated cells drastically increases to 94%, in contrast to 20% viability in electrostatically‐bonded LbL shells. Moreover, the long‐term growth of encapsulated cells is not affected, thus facilitating efficient function of protected cells in hostile environment.magnified image
Synthesis and Characterization of an Amphiphilic Blue‐Light‐Emitting Glycosylated Poly(naphthalene/phenylene) Copolymer
Authors: Nagy Miklós , Rácz Dávid , Daróczi Lajos , Lukács Balázs , Jóna István , Zsuga Miklós , Kéki Sándor 
Published: July 2011

AbstractThe preparation and self‐assembly of poly(2‐glucopyranosyl‐1,6‐naphthalene‐1,4‐phenylene), P16NP2Glu, an amphiphilic, blue‐light‐emitting copolymer, is reported. The copolymer is soluble in polar solvents such as methanol/THF mixtures and even in water. The emission spectrum of P16NP2Glu shows a maximum at ≈400 nm for solutions containing the above solvents. Owing to the highly polar nature of the glucopyranose rings of P16NP2Glu, the formation of aggregates is observed. Uniform‐size nanospheres capable of emitting blue light are prepared in the solid phase. The critical micelle concentration and micelle sizes are determined by light‐scattering measurements. It is found that the emission maximum and fluorescence quantum yields depend on the aggregate formation of the copolymer.magnified image
A Fully Polymeric Mouldable Microfluidic Device. Part 1: The Process of Design
Authors: Neerincx Peter E. , Denteneer Roel P. J. , Meijer Han E. H. 
Published: July 2011

AbstractMicrofluidic devices as used, e.g., in lab‐on‐a‐chip and micro‐total‐analysis systems, are frequently fabricated using silicon or polydimethylsiloxane (PDMS)‐based technologies, both with their known disadvantages. Here, we design a fully polymeric, multifunctional microfluidic reactor device, using an alternative fabrication method, the two‐component co‐injection moulding technology, in which different polymer combinations—generally a flexible and a rigid thermoplastic polymer—can be applied. The prototype device is based on an ambi‐symmetrical design, combining two identical shells, that are each folded to occupy a 160 × 90 mm2 space and subsequently stacked into a 4 (double) layer system. One microfluidic reactor unit includes six different in‐ and output connections, six peristaltic pumps (built up from three membranes each), eighteen volume‐neutral, recoverable control valves, two fluid storages, and two efficient, flow splitting, rotating and recombining, serpentine mixers. The mixers realize an almost perfect baker's transformation and possess ten elements that create 2 × 410 layers with an individual striation thickness of 0.5 nm in 10 s. The total reactor volume amounts 7 mL. The capacity of the peristaltic pumps, with their stroke of 0.5 mm, equals about 35 µL · s−1 at an actuation frequency of 5 Hz. Actuation occurs by air pressure. One microfluidic device can be endlessly connected to its replicas.magnified image
Predicting the Thermal Stability of Nitroaromatic Compounds Using Chemoinformatic Tools
Authors: Fayet Guillaume , Del Rio Alberto , Rotureau Patricia , Joubert Laurent , Adamo Carlo 
Published: July 2011

AbstractIn the framework of the European REACH regulation major attention was recently devoted to toxicological and ecotoxicological problems while little attention has been dedicated to other important applications concerning chemical hazards, for instance, explosive properties. In this work different chemoinformatic tools such as partial least squares, multilinear regressions, and decision trees have been used for the development of a novel quantitative structure‐property relationships to predict the heat of decomposition of a series of nitroaromatic compounds. Models were conceived in order to follow the regulatory requirements according to OECD principles for the validation of QSAR methods. Three models derived with MLR, PLS and decision tree techniques were developed, validated (internally and externally) and their applicability domains have been defined and analyzed. All models proved to be reliable with remarkable robustness in terms of full cross‐validation scheme and showed good predictive power toward the external validation set. These models also present a large applicability domain within nitrobenzene derivatives and are easy to implement and interpret in terms of subjacent mechanisms.
Molecular Dynamics Simulations Using Graphics Processing Units
Authors: Baker John A. , Hirst Jonathan D. 
Published: July 2011

AbstractIt is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation community augur well for the scale and scope of future computational studies of biomolecules.
Plasma nucleic acid analysis by massively parallel sequencing: pathological insights and diagnostic implications
Authors: Lo YM , Chiu Rossa WK 
Published: July 2011

AbstractOver the past 15 years there has been increasing interest in the biology and diagnostic applications of circulating DNA in the plasma of human subjects. In particular, DNA from a fetus, a tumour, a transplanted organ and injured tissues has been found in the plasma of pregnant women, cancer patients, transplant recipients and patients suffering from multiple pathologies, respectively. The advent of massively parallel sequencing has given us a quantitative and powerful tool for studying circulating DNA on a genome‐wide level. Using this approach, fetal chromosomal aneuploidies can be robustly detected using maternal plasma. Furthermore, a genome‐wide genetic map of a fetus can also be constructed using this approach. This method has also allowed one to identify tumour‐associated chromosomal translocations, which can then be detected in plasma. The direct application of massively parallel sequencing to the serum of cancer patients has also allowed quantitative aberrations that are associated with malignancy to be detected in serum. The use of massively parallel sequencing on the plasma of transplantation recipients has opened up an approach for detecting rejection. The application of circulating DNA sequencing has also opened up a new method for elucidating the quantitative aberration of circulating DNA in many pathological conditions. Such developments would provide new modalities for molecular diagnostics and would improve our understanding of the biology of circulating nucleic acids. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Low‐dose paclitaxel ameliorates fibrosis in the remnant kidney model by down‐regulating miR‐192
Authors: Sun Lin , Zhang Dongshan , Liu Fuyou , Xiang Xudong , Ling Guanghui , Xiao Li , Liu Yinghong , Zhu Xuejing , Zhan Ming , Yang Yeyi , Kondeti Vinay K , Kanwar Yashpal S 
Published: July 2011

AbstractTransforming growth factor (TGF)‐β has been shown to play a central role in the development of tubulointerstitial fibrosis, which can be corrected via treatment with paclitaxel. The biology of microRNA (miR) can be modulated by paclitaxel. We hypothesized that paclitaxel may attenuate renal fibrosis in a rat model of remnant kidney disease by inhibiting TGF‐β induced‐miRs. Rats in groups of 12 were subjected to 5/6 nephrectomy and received low‐dose intraperitoneal injection of paclitaxel. Renal functions were assessed at 8 weeks. The TGF‐β signalling cascade and ECM proteins were evaluated by real‐time polymerase chain reaction (TRT–PCR) and immunofluorescence microscopy. Animals with remnant kidneys developed hypertension, which was not relieved with paclitaxel treatment. However, paclitaxel treatment resulted in dampening the proteinuric response, reduction in serum BUN, creatinine levels and urine protein : creatinine ratio and normalization of creatinine clearance. These effects were accompanied by the inhibition of Smad2/3 activation, attenuation of renal fibrosis and normalization of integrin‐linked kinase (ILK), COL(I)A1, COL(IV)A2 and α‐SMA expression. Also, paclitaxel down‐regulated the expression of miR‐192, miR‐217 and miR ‐377, while miR‐15 was up‐regulated in the remnant kidney. In vitro, in tubular epithelial cells (NRK‐52E), paclitaxel also inhibited TGF‐β1‐induced Smad2/3 activation and normalized ILK, COL(I)A1, COL(IV)A2 and α‐SMA expression. Furthermore, ChIP analyses indicated that Taxol suppressed Smad3‐mediated miR‐192 transcriptional activity. Over‐expression of miR‐192 in NRK‐52E mimicked the changes seen in the remnant kidney, while inclusion of miR‐192 inhibitor in the culture medium blocked TGF‐β1‐induced COL(I)A1 and COL(IV)A2 expression, while ILK and α‐SMA were unaffected. These data suggest that low‐dose paclitaxel ameliorates renal fibrosis via modulating miR‐192 pathobiology and TGF‐β/Smad signalling. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Hypoxia‐inhibited dual‐specificity phosphatase‐2 expression in endometriotic cells regulates cyclooxygenase‐2 expression
Authors: Wu Meng‐Hsing , Lin Shih‐Chieh , Hsiao Kuei‐Yang , Tsai Shaw‐Jenq 
Published: July 2011

AbstractEndometriosis is one of the most common gynaecological diseases that significantly reduces the life qualify of affected women and their families. Aberrant expression of cyclooxygenase‐2 (COX‐2), and thus over‐production of prostaglandin E2 (PGE2) has been shown to play critical roles in the development of this disease. However, the mechanism responsible for COX‐2 over‐expression remains obscure. Here, we provide evidence for what we believe is a novel mechanism in regulating COX‐2 expression in endometriotic stromal cells. Dual‐specificity phosphatase‐2 (DUSP2), a nuclear phosphatase that inactivates mitogen‐activated protein kinase (MAPK), is markedly down‐regulated in stromal cells of ectopic endometriotic tissues, which results in prolonged activation of extracellular signal‐regulated kinase (ERK) and p38 MAPK and increased COX‐2 expression. Expression of DUSP2 is inhibited by hypoxia inducible factor‐1α (HIF‐1α) at the transcriptional level. Treatment of normal endometrial stromal cells with hypoxia, or chemicals that cause HIF‐1α accumulation, results in DUSP2 down‐regulation, prolonged ERK phosphorylation and COX‐2 over‐expression. In contrast, forced expression of DUSP2 under hypoxia abolishes HIF‐1α‐induced ERK phosphorylation and COX‐2 expression. Furthermore, suppression of DUSP2 by HIF‐1α in eutopic endometrial stromal cells increases sensitivity of cox‐2 gene to interleukin‐1β stimulation, a phenomenon resembling endometriotic stromal cell characteristics. Taken together, these data suggest that DUSP2 is an important molecule in endometrial physiology and that hypoxia‐inhibited DUSP2 expression is a critical factor for the development of endometriosis. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Mass spectrometric immunoassay for quantitative determination of transthyretin and its variants
Authors: Trenchevska Olgica , Kamcheva Elena , Nedelkov Dobrin 
Published: July 2011

AbstractTransthyretin (TTR, or prealbumin) is a tetrameric protein found in plasma and cerebrospinal fluid. Its major role is to transport thyroid hormones (thyroxin‐T4) and retinol (through association with retinol‐binding protein). TTR has been studied extensively due to the great number of point mutations that result in sequence heterogeneity. Many of these variants are associated with pathological conditions that result in extracellular deposition of amyloid fibers in tissues. In this work, we have developed a rapid mass spectrometric immunoassay for determination and quantification of TTR and its variants from human serum and plasma samples. The assay was fully characterized in terms of its precision, linearity and recovery characteristics. The new assay was also compared with a conventional TTR ELISA. Furthermore, we have applied the optimized method to analyze TTR and its modifications in 44 human plasma samples, and in the process optimized a method for TTR proteolytic digestion and identification of point mutations.
Reactome pathway analysis to enrich biological discovery in proteomics data sets
Authors: Haw Robin , Hermjakob Henning , D'Eustachio Peter , Stein Lincoln 
Published: July 2011

AbstractReactome (http://www.reactome.org) is an open‐source, expert‐authored, peer‐reviewed, manually curated database of reactions, pathways and biological processes. We provide an intuitive web‐based user interface to pathway knowledge and a suite of data analysis tools. The Pathway Browser is a Systems Biology Graphical Notation‐like visualization system that supports manual navigation of pathways by zooming, scrolling and event highlighting, and that exploits PSI Common Query Interface web services to overlay pathways with molecular interaction data from the Reactome Functional Interaction Network and interaction databases such as IntAct, ChEMBL and BioGRID. Pathway and expression analysis tools employ web services to provide ID mapping, pathway assignment and over‐representation analysis of user‐supplied data sets. By applying Ensembl Compara to curated human proteins and reactions, Reactome generates pathway inferences for 20 other species. The Species Comparison tool provides a summary of results for each of these species as a table showing numbers of orthologous proteins found by pathway from which users can navigate to inferred details for specific proteins and reactions. Reactome's diverse pathway knowledge and suite of data analysis tools provide a platform for data mining, modeling and analysis of large‐scale proteomics data sets. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 8).
Facile Construction of Nanofibers as a Functional Template for Surface Boron Coordination Reaction
Authors: Xu Xiao‐Ding , Chu Yan‐Feng , Chen Chang‐Sheng , Chen Jing‐Xiao , Cheng Si‐Xue , Zhang Xian‐Zheng , Zhuo Ren‐Xi 
Published: July 2011

AbstractA facile strategy to perform the boron coordination reaction on a template of nanofibers is developed. Peptides with phenylboronic acid tails (peptidyl boronic acids) are designed and prepared as building blocks that can self‐assemble into nanofibers. After the addition of vicinal diol structural motifs to the self‐assembling system, matrix‐assisted laser desorption–ionization time‐of‐flight mass spectrometry indicates that the boron coordination reaction occurs on the template of nanofibers, which results in the increase of the width and roughness of the nanofibers as demonstrated by transmission electron microscopy and atomic force microscopy measurements. Because the surface‐bound vicinal diol structural motifs have an ability to form hydrogen bonds with the peptide segments on the nanofibers, which restrain and disturb the hydrogen‐bonding interaction among the nanofibers, the network structure formed based on the entanglement of nanofibers via hydrogen‐bonding interaction is destroyed, which leads to a gel–sol transition. The novel concept of post‐self‐assembly modification demonstrated here could lead to a new technique for using self‐assembled nanostructures in the emerging fields of nanoscience and nanotechnology.