bluuebunny/crossref_metadata_2025_split huggingface dataset:
2D ISING MODEL WITH COMPETING INTERACTIONS AND ITS APPLICATION TO CLUSTERS AND ARRAYS OF π-RINGS, GRAPHENE AND ADIABATIC QUANTUM COMPUTING
Authors: O'HARE ANTHONY , KUSMARTSEV F. V. , KUGEL K. I. 
Published: September 2009

We study the two-dimensional Ising model with competing nearest-neighbour and diagonal interactions and investigate the phase diagram of this model. We show that the ground state at low temperatures is ordered either as stripes or as the Néel antiferromagnet. However, we also demonstrate that the energy of defects and dislocations in the lattice is close to the ground state of the system. Therefore, many locally stable (or metastable) states associated with local energy minima separated by energy barriers may appear forming a glass-like state. We discuss the results in connection with two physically different systems. First, we deal with planar clusters of loops including a Josephson π-junction (a π-rings). Each π-ring carries a persistent current and behaves as a classical orbital moment. The type of particular state associated with the orientation of orbital moments in the cluster depends on the interaction between these orbital moments and can be easily controlled, i.e. by a bias current or by other means. Second, we apply the model to the analysis of the structure of the newly discovered two-dimensional form of carbon, graphene. Carbon atoms in graphene form a planar honeycomb lattice. Actually, the graphene plane is not ideal but corrugated. The displacement of carbon atoms up and down from the plane can be also described in terms of Ising spins, the interaction of which determines the complicated shape of the corrugated graphene plane. The obtained results may be verified in experiments and are also applicable to adiabatic quantum computing where the states are switched adiabatically with the slow change of coupling constant.
Blockade of a Chemokine, CCL2, Reduces Chronic Colitis-Associated Carcinogenesis in Mice
Authors: Popivanova Boryana Konstantinova , Kostadinova Feodora Ivanova , Furuichi Kengo , Shamekh Mohamed M. , Kondo Toshikazu , Wada Takashi , Egashira Kensuke , Mukaida Naofumi 
Published: September 2009

Abstract
Accumulating evidence indicates the crucial contribution of chronic inflammation to various types of carcinogenesis, including colon carcinoma associated with ulcerative colitis and asbestosis-induced malignant mesothelioma. Ulcerative colitis–associated colon carcinogenesis can be recapitulated in mice by azoxymethane administration followed by repetitive dextran sulfate sodium ingestion. In the course of this carcinogenesis process, the expression of a macrophage-tropic chemokine, CCL2, was enhanced together with intracolonic massive infiltration of macrophages, which were a major source of cyclooxygenase (COX)-2, a crucial mediator of colon carcinogenesis. Mice deficient in CCL2-specific receptor, CCR2, exhibited less macrophage infiltration and lower tumor numbers with attenuated COX-2 expression. Moreover, CCL2 antagonists decreased intracolonic macrophage infiltration and COX-2 expression, attenuated neovascularization, and eventually reduced the numbers and size of colon tumors, even when given after multiple colon tumors have developed. These observations identify CCL2 as a crucial mediator of the initiation and progression of chronic colitis–associated colon carcinogenesis and suggest that targeting CCL2 may be useful in treating colon cancers, particularly those associated with chronic inflammation. [Cancer Res 2009;69(19):7884–92]
Binding between heparin and the integrin VLA-4
Authors: Schlesinger Martin , Simonis Dirk , Schmitz Patrick , Fritzsche Juliane , Bendas Gerd 
Published: September 2009

SummaryHeparin possesses antimetastatic effects that were related to various molecular mechanisms beyond anticoagulant activities. The ability of heparin to interfere with the function of adhesion receptors in the metastatic course appears as a promising therapeutic approach. This refers to numerous findings that heparin attenuates metastasis in a selectin-dependent manner. We recently demonstrated that heparin interferes with the integrin VLA-4 on murine melanoma cells binding to VCAM-1. To confirm this activity and to obtain further insight into molecular recognition of heparin by VLA-4, we investigated the inhibition of VLA-4 mediated binding of human melanoma MV3 cells to immobilized VCAM-1 by different heparins. The size of heparin has an important impact on inhibition. Unfractionated heparin (UFH) and tinzaparin, a low-molecular-weight heparin (LMWH) representing a mean of about 18– 20 monomers, displayed high inhibitory activity. Fractionating tinzaparin to 14– 18 monomers reduced inhibition slightly, while the pentasaccharide fondaparinux was without effects. To confirm molecular recognition of tinzaparin by VLA-4,a surface acoustic wave-biosensor was applied. A VLA-4 containing membrane preparation of MV3 cells was immobilised at the sensors to allow for detection of kinetic binding constants of tinzaparin compared to VCAM-1. Tinzaparin binds to VLA-4 with affinity in the low micromolar range (4.61× 10−6 M), which clearly indicates specific molecular recognition. Furthermore, tinzaparin displays a nearly identical koff compared toVCAM-1 (5.13× 10−3 s-1 versus 3.44× 10–3 s-1) which is evident for interference with the ligand binding. The data provide evidence for a direct confirmation of heparin binding to VLA-4 and thus, contribute to understand the antimetastatic activity of heparin.
The Tainted Heparin Story: An Update
Authors: Guerrini Marco , Shriver Zachary , Bisio Antonella , Naggi Annamaria , Casu Benito , Sasisekharan Ram , Torri Giangiacomo 
Published: September 2009

SummaryRecently, certain batches of heparin have been associated with an acute, rapid onset of serious side-effects indicative of allergictype reactions.These reports generated significant concern regarding the possible presence of a dangerous contaminant within heparin and highlighted the need to re-assess the purity criteria of heparin preparations for clinical use. Given the nature of the array of all possible contaminants, traditional screening tests cannot safely differentiate between contaminated and uncontaminated heparin preparations. Monoand bi-dimensional NMR spectroscopy are powerful techniques that are able to detect and quantify a wide variety of potential sulfated polysaccharide contaminants. As such, these techniques are powerful tools for the analysis and assessment of heparin preparations.
Structural features of low-molecular-weight heparins affecting their affinity to antithrombin
Authors: Bisio Antonella , Vecchietti Davide , Citterio Laura , Guerrini Marco , Raman Rahul , Bertini Sabrina , Eisele Giorgio , Naggi Annamaria , Sasisekharan Ram , Torri Giangiacomo 
Published: September 2009

SummaryAs part of a more extensive investigation on structural features of different low-molecular-weight heparins (LMWHs) that can affect their biological activities, Enoxaparin,Tinzaparin and Dalteparin were characterised with regards to the distribution of different chain length oligosaccharides as determined by size-exclusion (SE) chromatography, as well as their structure as defined by 2D-NMR spectra (HSQC). The three LMWHs were also fractionated into high affinity (HA) and no affinity (NA) pools with regards to their ability to bind antithrombin (AT).The HA fractions were further subfractionated and characterised. For the parent LMWHs and selected fractions,molecular weight parameters were measured using a SE chromatographic system with a triple detector (TDA) to obtain absolute molecular weights. The SE chromatograms clearly indicate that Enoxaparin is consistently richer in shorter oligosaccharides than Tinzaparin and Dalteparin. Besides providing the content of terminal groups and individual glucosamine and uronic acid residues with different sulfate substituents, the HSQC-NMR spectra permitted us to evaluate and correlate the content of the pentasaccharide, AT-binding sequence A-G-A*-I-A (AT-bs) through quantification of signals of the disaccharide sequence G-A*.Whereas the percent content of HA species is approximately the same for the three LMWHs, substantial differences were observed for the chain distribution of AT-bs as a function of length, with the AT-bs being preferentially contained in the longest chains of each LMWH. The above information will be useful in establishing structure-activity relationships currently under way. This study is therefore critical for establishing correlations between structural features of LMWHs and their AT-mediated anticoagulant activity.
Expression of thrombin-activatable fibrinolysis inhibitor (TAFI) is up-regulated by increase in intracellular cyclic AMP levels in cultured HepG2 cells
Authors: Kojima Yuka , Masuda Yutaka , Takada Kimihiko , Sugimoto Katsuyoshi , Ikeda Tomohiro , Ishii Hidemi 
Published: September 2009

SummaryThrombin-activatable fibrinolysis inhibitor (TAFI), a carboxypeptidase B-like proenzyme, is predominantly biosynthesised in the liver and released into circulating plasma. Activated TAFI has a role in maintaining the balance between blood coagulation and fibrinolysis. We investigated the regulation of TAFI expression in cultured human hepatoma HepG2 cells. Stimulation of the cells with forskolin and dibutyryl cyclic AMP (DBcAMP) increased TAFI antigen levels in the cells in parallel with TAFI mRNA levels and antigen release from the cells into the conditioned medium. The elevated TAFI expression was abolished by pretreatment of the cells with KT5720, a protein kinase A (PKA) inhibitor. The promoter activity of the TAFI gene and the half-life of the TAFI transcript in DBcAMP-stimulated HepG2 cells increased to 1.5-fold and 2.0-fold, respectively, of those in the control cells. The increased promoter activity and the prolonged half-life were abolished by pretreatment of the cells with KT5720.These results suggest that an increase in intracellular cAMP levels upregulates TAFI expression in the cells in accompaniment with an elevation of TAFI mRNA levels, and that the elevated mRNA levels are derived from both transcriptional and post-transcriptional regulations of the TAFI gene mediated by activation of the AMP/PKA signaling pathway.
Activated partial thromboplastin time monitoring in patients receiving unfractionated heparin for venous thromboembolism in relation to clinical outcomes
Authors: Laor Arie , Bitterman Haim , Vardi Moshe 
Published: September 2009

SummaryVenous thromboembolism (VTE) is a prevalent and serious condition, which requires anticoagulation treatment for prolonged time duration. The use of unfractionated heparin administered intravenously or subcutaneously for acute management of VTE has been studied with favourable clinical results. Most physicians use activated partial thromboplastin time to monitor the treatment effect, in an effort to obtain better efficacy with less bleeding complications. Recent data however does not support this practice. We set to explore the medical literature for the correlation between the level of anticoagulation and the clinical outcomes. Randomised controlled trials comparing subcutaneous unfractionated heparin to any other treatment modality in patients with venous thromboembolism were obtained and a meta-analysis was performed. Seventeen reports from 15 randomised controlled trials were included. Of these, eleven included anticoagulation measurements. Seven and six trials were included in our analysis for subcutaneous and intravenous modes of administration, respectively. No correlation between the anticoagulation level and the major clinical outcomes were found, except for the initial anticoagulation measurement and the total mortality at three months, but not to death related to treatment or disease progression. In conclusion, weight-adjusted subcutaneous unfractionated heparin without anticoagulation monitoring may be feasible for patients with acute venous thromboembolism. No differences exist between intravenous and subcutaneous modes of administration with regards to the correlation between anticoagulant measures and the clinical outcomes. More research is needed to substantiate this observation.
A Case Study: The Indirect Aerosol Effects of Mineral Dust on Warm Clouds
Authors: Li R. , Min Q-L. , Harrison L. C. 
Published: September 2009

Abstract
The indirect aerosol effect (Twomey effect) is studied during a Saharan dust-transport event that presented an unusually favorable combination of a dust-loading gradient across clouds with warm cloud-top temperatures. Standard retrievals from the Moderate Resolution Imaging Spectroradiometer (MODIS), the Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E), and the Clouds and the Earth’s Radiant Energy System (CERES) provide cloud-top temperature (a surrogate for height), liquid water path (LWP), classification of precipitation regime, and radiation flux. The authors correlate a retrieved mean effective droplet radius (re) versus the number concentration of cloud condensation nuclei (NCCN), using the regressed slope d lnre/d lnNCCN as the estimator of the aerosol indirect effect (AIE). Results demonstrate statistically significant AIE for only some of the segregated cloud classes. For nonprecipitating clouds (the most direct test of Twomey effect), the estimated AIE is effectively −0.07 over all wider temperature bands and is statistically significant from 1.1 to 1.9 σ. Further classification by LWP strengthens both the AIE (for all LWP &gt; 150 g m−2) to approximately −0.16, and substantially increases the statistical significance, to better than 5σ.
Shortwave radiation forcing of dust aerosols is also estimated directly from satellite measurements. The direct shortwave (SW) radiation effect of Saharan dusts at solar zenith angle 21.6° is 53.48 ± 8.56 W m−2 per unit aerosol optical depth, with a correlation coefficient of 0.92. The indirect SW forcing of Saharan dust is 29.88 ± 2.42 W m−2 per unit AOD for clouds with LWP of 100 g m−2.
On the Variability of the Global Net Radiative Energy Balance of the Nonequilibrium Earth
Authors: Harries John E. , Belotti Claudio 
Published: September 2009

Abstract
Recent observations and model studies of the earth’s radiative energy balance have focused attention on the earth’s top of atmosphere (TOA) energy balance. This is the balance between the shortwave energy absorbed by the earth, which is represented by a spatially and temporally averaged absorbed flux , and the emitted longwave energy, which is represented by the corresponding averaged emitted flux . The TOA average net flux FN is defined as the difference between the two over the averaged area and time, which may be a local, regional, or global average. A global nonzero net flux represents a measure of imbalance between the energy being absorbed and emitted by the earth for the time interval in question. It is of interest to ask what the natural variability of the net flux might be and whether, during times of climate change, signals of important climate change processes might be detected against this natural background variation; examples of these signals include evidence of ocean heat storage, the effects of El Niño, and the radiative effects of volcanic eruptions. In this paper, the authors review the significance of the net flux, survey the observational evidence from a range of satellite instruments over several decades, and analyze some of the most recent observations from the Clouds and the Earth’s Radiant Energy System (CERES) program to determine what signals and what natural variability might be expected in the TOA net flux. Based on this analysis, the use of broadband radiation measurements for global climate change studies can be assessed.
Structural evolution during the dehydration of gypsum materials
Authors: Jacques S. D. M. , González-Saborido A. , Leynaud O. , Bensted J. , Tyrer M. , Greaves R. I. W. , Barnes P. 
Published: September 2009

AbstractThe dehydration of pure and waste gypsums has been examined using in situ synchrotron angledispersive X-ray diffraction. Pure gypsum was studied under a number of defined environments; various industrial waste gypsums were also studied under a common standard environment. It is found that the dehydration of gypsum to anhydrite proceeds via the hemihydrate and γ-anhydrite phases and the interplay and behaviour of these phases has been determined by full structural ‘Rietveld’ refinement. In the study of the pure gypsum system, the hemihydrate structure is shown to be preserved as water is lost. A ‘zero-water hemihydrate’ is observed before refinement in the higher symmetry γ-anhydrite cell is possible. The waste gypsum materials studied showed significant differences in the temperatures at which key transformation events occurred; these observations raise implications concerning the re-use of by-product gypsum materials. Finally, high temperature data are re-examined in the search for a variation of the anhydrite structure.
Necdin restricts proliferation of hematopoietic stem cells during hematopoietic regeneration
Authors: Kubota Yasushi , Osawa Masatake , Jakt Lars Martin , Yoshikawa Kazuaki , Nishikawa Shin-Ichi 
Published: September 2009

Abstract
Hematopoietic stem cell (HSC) proliferation is tightly regulated by a poorly understood complex of positive and negative cell-cycle regulatory mechanisms. Necdin (Ndn) is an evolutionally conserved multifunctional protein that has been implicated in cell-cycle regulation of neuronal cells. Here, we provide evidence that necdin plays an important role in restricting excessive HSC proliferation during hematopoietic regeneration. We identify Ndn as being preferentially expressed in the HSC population on the basis of gene expression profiling and demonstrate that mice deficient in Ndn show accelerated recovery of the hematopoietic system after myelosuppressive injury, whereas no overt abnormality is seen in steady-state hematopoiesis. In parallel, after myelosuppression, Ndn-deficient mice exhibit an enhanced number of proliferating HSCs. Based on these findings, we propose that necdin functions in a negative feedback loop that prevents excessive proliferation of HSCs during hematopoietic regeneration. These data suggest that the inhibition of necdin after clinical myelosuppressive treatment (eg, chemotherapy, HSC transplantation) may provide therapeutic benefits by accelerating hematologic recovery.
Anti-proliferative activity of silver nanoparticles
Authors: AshaRani PV , Hande M Prakash , Valiyaveettil Suresh 
Published: September 2009

Abstract

Background
Nanoparticles possess exceptional physical and chemical properties which led to rapid commercialisation. Silver nanoparticles (Ag-np) are among the most commercialised nanoparticles due to their antimicrobial potential. Ag-np based cosmetics, therapeutic agents and household products are in wide use, which raised a public concern regarding their safety associated with human and environmental use. No safety regulations are in practice for the use of these nanomaterials. The interactions of nanomaterials with cells, uptake mechanisms, distribution, excretion, toxicological endpoints and mechanism of action remain unanswered.

Results
Normal human lung fibroblasts (IMR-90) and human glioblastoma cells (U251) were exposed to different doses of Ag-nps in vitro. Uptake of Ag-nps occurred mainly through endocytosis (clathrin mediated process and macropinocytosis), accompanied by a time dependent increase in exocytosis rate. The electron micrographs revealed a uniform intracellular distribution of Ag-np both in cytoplasm and nucleus. Ag-np treated cells exhibited chromosome instability and mitotic arrest in human cells. There was efficient recovery from arrest in normal human fibroblasts whereas the cancer cells ceased to proliferate. Toxicity of Ag-np is mediated through intracellular calcium (Ca2+) transients along with significant alterations in cell morphology and spreading and surface ruffling. Down regulation of major actin binding protein, filamin was observed after Ag-np exposure. Ag-np induced stress resulted in the up regulation of metallothionein and heme oxygenase -1 genes.

Conclusion
Here, we demonstrate that uptake of Ag-np occurs mainly through clathrin mediated endocytosis and macropinocytosis. Our results suggest that cancer cells are susceptible to damage with lack of recovery from Ag-np-induced stress. Ag-np is found to be acting through intracellular calcium transients and chromosomal aberrations, either directly or through activation of catabolic enzymes. The signalling cascades are believed to play key roles in cytoskeleton deformations and ultimately to inhibit cell proliferation.
Live cell imaging with protein domains capable of recognizing phosphatidylinositol 4,5-bisphosphate; a comparative study
Authors: Szentpetery Zsofia , Balla Andras , Kim Yeun Ju , Lemmon Mark A , Balla Tamas 
Published: September 2009

Abstract

Background
Phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P
2] is a critically important regulatory phospholipid found in the plasma membrane of all eukaryotic cells. In addition to being a precursor of important second messengers, PtdIns(4,5)P
2 also regulates ion channels and transporters and serves the endocytic machinery by recruiting clathrin adaptor proteins. Visualization of the localization and dynamic changes in PtdIns(4,5)P
2 levels in living cells is critical to understanding the biology of PtdIns(4,5)P
2. This has been mostly achieved with the use of the pleckstrin homology (PH) domain of PLCδ1 fused to GFP. Here we report on a comparative analysis of several recently-described yeast PH domains as well as the mammalian Tubby domain to evaluate their usefulness as PtdIns(4,5)P
2 imaging tools.

Results
All of the yeast PH domains that have been previously shown to bind PtdIns(4,5)P
2 showed plasma membrane localization but only a subset responded to manipulations of plasma membrane PtdIns(4,5)P
2. None of these domains showed any advantage over the PLCδ1PH-GFP reporter and were compromised either in their expression levels, nuclear localization or by causing peculiar membrane structures. In contrast, the Tubby domain showed high membrane localization consistent with PtdIns(4,5)P
2 binding and displayed no affinity for the soluble headgroup, Ins(1,4,5)P3. Detailed comparison of the Tubby and PLCδ1PH domains showed that the Tubby domain has a higher affinity for membrane PtdIns(4,5)P
2 and therefore displays a lower sensitivity to report on changes of this lipid during phospholipase C activation.

Conclusion
These results showed that both the PLCδ1PH-GFP and the GFP-Tubby domain are useful reporters of PtdIns(4,5)P
2 changes in the plasma membrane, with distinct advantages and disadvantages. While the PLCδ1PH-GFP is a more sensitive reporter, its Ins(1,4,5)P3 binding may compromise its accuracy to measure PtdIns(4,5)P
2changes. The Tubby domain is more accurate to report on PtdIns(4,5)P
2 but its higher affinity and lower sensitivity may limit its utility when phospholipase C activation is only moderate. These studies also demonstrated that similar changes in PtdIns(4,5)P
2 levels in the plasma membrane can differentially regulate multiple effectors if they display different affinities to PtdIns(4,5)P
2.