bluuebunny/crossref_metadata_2025_split huggingface dataset:
NUMERICAL METHODS FOR WAVE SCATTERING PHENOMENA BY MEANS OF DIFFERENT BOUNDARY INTEGRAL FORMULATIONS
Authors: NOLTE BODO , SCHÄFER INGO , EHRLICH JAN , OCHMANN MARTIN , BURGSCHWEIGER RALF , MARBURG STEFFEN 
Published: July 2008

Different numerical approaches for the physical phenomena of scattering waves from an obstacle are presented. They are based on different integral formulations. Fluid structure interaction effects are numerically treatable as well. We use the Boundary Element Method (BEM) in different approaches because the inherently satisfied Sommerfeld radiation condition makes sure that no reflecting waves from boundaries at infinity occur. One of the biggest disadvantages of numerical methods like BEM is the fact that they have difficulties with handling the high frequency range. For the high frequency range approximations like the Kirchhoff–Helmholtz integral equation have to be used. With varying assumptions of the reflecting behavior of the structure different approaches for the higher frequency range are obtained, where the explicit solving of a system of equations is not necessary. Another high frequency approach is the plane wave approximation which is compared with the Kirchhoff approach of the first kind. Additionally a modified Kirchhoff approach is introduced. Because the incident pressure on the scatterer's surface is known the integral is evaluated analytically on triangular patches. The discretization is no longer frequency dependent and the size of the patches only depends on the curvature of the structure. Large planar parts can be discretized with one element only. This leads to a substantial advantage in terms of calculation time over the traditional Kirchhoff approach. Like the traditional approach this procedure is valid under the assumption of high frequency or far field conditions.
Application of molar element ratio analysis of lag talus composite samples to the exploration for iron oxide–copper–gold mineralization: Mantoverde area, northern Chile
Authors: Benavides Jorge , Kyser T. Kurtis , Clark Alan H. , Stanley Clifford , Oates Christopher 
Published: July 2008

A molar element ratio analysis based on whole-rock, multi-element geochemical data for regional lag talus composite samples is evaluated as an exploratory method for iron oxide–copper–gold mineralization (IOCG) in hyperarid settings. This study is focused in the now hyperarid Mantoverde area, III Región of northern Chile (latitude 26°01′ to 26°53′S), and comprises the Andean Coastal Cordillera and Central Valley. The area contains numerous structurally controlled iron oxide-Cu-(Au) prospects and deposits hosted by calc-alkaline volcanic and plutonic rocks of Jurassic–Cretaceous age. Comparison with data for outcrop samples indicates that lag talus composite samples reflect the composition of bedrock in terms of major and selected trace elements. As with outcrop samples, zirconium is the most conserved element in the talus samples, and is therefore used as common denominator in different molar ratios.
A molar element ratio analysis using geochemical data from talus composite samples indicates that rocks associated with mineralization have been K-enriched and Na-depleted. Consequently, gradients in the K/Al and Na/Al molar ratios are useful targeting parameters. Similarly, a lithogeochemical alteration index, recently defined by the authors, quantifies the degree of hydrothermal alteration of host rocks and can be used to both target potential anomalous sectors (strongly altered rocks) and delimit barren areas. It is evident that lag talus composite samples constitute a reliable and effective sampling medium in regional exploration programmes for IOCG deposits in hyperarid settings.
An energy characterization platform for memory devices and energy-aware data compression for multilevel-cell flash memory
Authors: Joo Yongsoo , Cho Youngjin , Shin Donghwa , Park Jaehyun , Chang Naehyuck 
Published: July 2008

Memory devices often consume more energy than microprocessors in current portable embedded systems, but their energy consumption changes significantly with the type of transaction, data values, and access timing, as well as depending on the total number of transactions. These variabilities mean that an innovative tool and framework are required to characterize modern memory devices running in embedded system architectures.
We introduce an energy measurement and characterization platform for memory devices, and demonstrate an application to multilevel-cell (MLC) flash memories, in which we discover significant value-dependent programming energy variations. We introduce an energy-aware data compression method that minimizes the flash programming energy, rather than the size of the compressed data, which is formulated as an entropy coding with unequal bit-pattern costs. Deploying a probabilistic approach, we derive energy-optimal bit-pattern probabilities and expected values of the bit-pattern costs which are applicable to the large amounts of compressed data typically found in multimedia applications. Then we develop an energy-optimal prefix coding that uses integer linear programming, and construct a prefix-code table. From a consideration of Pareto-optimal energy consumption, we can make tradeoffs between data size and programming energy, such as a 41% energy savings for a 52% area overhead.
PuzzledDelightful graph theory
Authors: Winkler Peter 
Published: July 2008

Welcome to the new puzzle column. Each column will present three puzzles. The first two will have known (and usually elegant) solutions that will appear in the next issue of Communications. The third will be an open problem; good luck with that one.
Readers are encouraged to submit prospective puzzles for future columns to puzzled@cacm.acm.org.
We start with three delightful graph-theoretic puzzles. Here we go.
Homologa efectiva y sucesiones espectrales (abstract only)
Authors: Ibáñez Ana Romero Ibáñez 
Published: July 2008

Effective homology and spectral sequences are two different techniques of Algebraic Topology which can be used for the computation of homology and homotopy groups. In this work we try to relate both methods, showing that the effective homology method can also be used to produce algorithms computing some spectral sequences. In the thesis we focus our attention on two particular situations: spectral sequences associated with filtered complexes and the Bousfield-Kan spectral sequence.
The first part of the memoir is devoted to spectral sequences of filtered complexes, which under some good conditions converge to the homology groups of the initial complex. Making use of the effective homology method, we have developed several algorithms computing the different components of these spectral sequences: groups and differential maps in every stage, convergence level and filtration of the homology groups induced by the initial filtration. These algorithms have been implemented as a new module for the Kenzo system, a program of Symbolic Computation in Algebraic Topology, and can be used to determine two classical examples of spectral sequences, those of Serre and Eilenberg-Moore.
Other spectral sequences are not defined by means of filtered complexes. This is the case of the Bousfield-Kan spectral sequence, related with the computation of homotopy groups, which is studied in the second part of the thesis. Our algorithms for the computation of spectral sequences of filtered complexes cannot be applied, but the effective homology method can be useful again to develop a constructive version of the Bousfield-Kan spectral sequence. As a first necessary step, our main result is an algorithm computing the effective homology of the free simplicial Abelian group RX generated by a 1-reduced simplicial set X. This algorithm allows the construction of the levels 1 and 2 of the spectral sequence; for the computation of the higher "pages", we present a sketch of a new algorithm which is not finished yet. Furthermore, we include a proof of the convergence of the spectral sequence.
Computational complexity of numerical solutions of initial value problems for differential algebraic equations (abstract only)
Authors: Ilie Silvana 
Published: July 2008

We investigate the cost of solving initial value problems for differential algebraic equations depending on the number of digits of accuracy requested. A recent result showed that the cost of solving initial value problems (IVP) for ordinary differential equations (ODE) is polynomial in the number of digits of accuracy. This improves on the classical result of information-based complexity, which predicts exponential cost. The new theory is based on more realistic assumptions.
The algorithm analyzed in this thesis is based on a previously published Taylor series method for solving a general class of differential algebraic equations. We consider DAE of constant index to which the method applies. The DAE is allowed to be of arbitrary index, fully implicit and have derivatives of order higher than one.
Similarly, by considering a realistic model, we show that the cost of computing the solution of IVP for DAE with the algorithm adopted and by using automatic differentiation is polynomial in the number of digits of accuracy. We also show that non-adaptation is more expensive than adaptation, giving thus a theoretical justification of the success of adaptivity in practice.
A particular case frequently arising in practical applications, the index-1 DAE, is treated separately, in more depth. On the other hand, an analysis of the higher-index DAE is significantly more complicated and applies to a wider class of problems. In both cases, continuous output is also given.
These results apply to many important problems arising in practice. We present an interesting theoretical application to polynomial system solving.
On the functional decomposition of multivariate laurent polynomials (abstract only)
Authors: Watt Stephen M. 
Published: July 2008

Determining whether a univariate polynomial may be written as the functional composition of two others of lower degree is a question that has been studied since at least the work of Ritt [1]. Algorithms by Barton and Zippel [2] and then by Kozen and Landau [3] have been incorporated in many computer algebra systems. Generalizations have been studied for functional decomposition of rational functions [4], algebraic functions [5], multivariate polynomials [6] and univariate Laurent polynomials [7].
We explore the functional decomposition problem for multivariate Laurent polynomials, considering the case f = g o h where g is univariate and h may be multivariate. We present an algorithm to find such a decomposition if it exists.
The algorithm proceeds as follows: First, a variable weighting is chosen to make the weighted degree zero term in f constant. The positive degree and negative degree parts of h are then reconstructed separately, in a manner similar to that of Kozen and Landau, but by treating the homogeneous collections of terms by grade rather than individual monomials. Then terms of the univariate polynomial g are reconstructed degree by degree using a generic univariate projection of h.
Reduced Atherosclerotic Lesions in P2Y1/Apolipoprotein E Double-Knockout Mice
Authors: Hechler Béatrice , Freund Monique , Ravanat Catherine , Magnenat Stéphanie , Cazenave Jean-Pierre , Gachet Christian 
Published: July 2008

Background—The P2Y1receptor plays a key role in arterial thrombosis and is widely expressed in many cell types involved in atherosclerosis. The aim of this study was to evaluate its potential involvement in the development of atherosclerotic lesions.Methods and Results—Apolipoprotein E–deficient (ApoE−/−) andP2Y1−/−/ApoE−/−mice were maintained on regular chow for 17 or 30 weeks before analysis of atherosclerotic lesions. At 17 weeks, lesions in the aortic sinus and entire aorta were smaller inP2Y1−/−/ApoE−/−compared with those inApoE−/−animals. At 30 weeks, the aortic sinus lesions inP2Y1−/−/ApoE−/−mice were still diminished in size and displayed reduced inflammation, reflected by decreased macrophage infiltration and diminished VCAM-1 immunostaining, compared with those inApoE−/−mice. They also had a lower smooth muscle cell content. Unexpectedly, bone marrow transplantation showed that the absence of the P2Y1receptor in blood cells only led to no significant modification of the lesion compared with controlApoE−/−reconstituted animals. Conversely, the absence of the P2Y1receptor except in blood cells resulted in a reduction in lesion size similar to that in controlP2Y1−/−/ApoE−/−reconstituted mice, pointing to a role of non–hematopoietic-derived P2Y1receptors, most likely the endothelial or smooth muscle cell P2Y1receptors. In addition, although this was not statistically significant, plasma cholesterol levels were consistently decreased inP2Y1−/−animals, suggesting that a modification of lipid metabolism could be responsible for the observed phenotype.Conclusion—The P2Y1receptor contributes to atherosclerosis, primarily through its role in non–hematopoietic-derived cells.
MT1-MMP collagenolytic activity is regulated through association with tetraspanin CD151 in primary endothelial cells
Authors: Yañez-Mó María , Barreiro Olga , Gonzalo Pilar , Batista Alicia , Megías Diego , Genís Laura , Sachs Norman , Sala-Valdés Mónica , Alonso Miguel A. , Montoya María C. , Sonnenberg Arnoud , Arroyo Alicia G. , Sánchez-Madrid Francisco 
Published: July 2008

AbstractMT1-MMP plays a key role in endothelial function, as underscored by the angiogenic defects found in MT1-MMP deficient mice. We have studied the molecular interactions that underlie the functional regulation of MT1-MMP. At lateral endothelial cell junctions, MT1-MMP colocalizes with tetraspanin CD151 (Tspan 24) and its associated partner α3β1 integrin. Biochemical and FRET analyses show that MT1-MMP, through its hemopexin domain, associates tightly with CD151, thus forming α3β1 integrin/CD151/MT1-MMP ternary complexes. siRNA knockdown of HUVEC CD151 expression enhanced MT1-MMP-mediated activation of MMP2, and the same activation was seen in ex vivo lung endothelial cells isolated from CD151-deficient mice. However, analysis of collagen degradation in these experimental models revealed a diminished MT1-MMP enzymatic activity in confined areas around the cell periphery. CD151 knockdown affected both MT1-MMP subcellular localization and its inclusion into detergent-resistant membrane domains, and prevented biochemical association of the metalloproteinase with the integrin α3β1. These data provide evidence for a novel regulatory role of tetraspanin microdomains on the collagenolytic activity of MT1-MMP and indicate that CD151 is a key regulator of MT1-MMP in endothelial homeostasis.
Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project
Authors: Flockerzi Aline , Ruggieri Alessia , Frank Oliver , Sauter Marlies , Maldener Esther , Kopper Bernd , Wullich Bernd , Seifarth Wolfgang , Müller-Lantzsch Nikolaus , Leib-Mösch Christine , Meese Eckart , Mayer Jens 
Published: July 2008

Abstract

Background
A significant proportion of the human genome is comprised of human endogenous retroviruses (HERVs). HERV transcripts are found in every human tissue. Expression of proviruses of the HERV-K(HML-2) family has been associated with development of human tumors, in particular germ cell tumors (GCT). Very little is known about transcriptional activity of individual HML-2 loci in human tissues, though.

Results
By employing private nucleotide differences between loci, we assigned ~1500 HML-2 cDNAs to individual HML-2 loci, identifying, in total, 23 transcriptionally active HML-2 proviruses. Several loci are active in various human tissue types. Transcription levels of some HML-2 loci appear higher than those of other loci. Several HML-2 Rec-encoding loci are expressed in GCT and non-GCT tissues. A provirus on chromosome 22q11.21 appears strongly upregulated in pathologic GCT tissues and may explain high HML-2 Gag protein levels in GCTs. Presence of Gag and Env antibodies in GCT patients is not correlated with activation of individual loci. HML-2 proviruses previously reported capable of forming an infectious HML-2 variant are transcriptionally active in germ cell tissue. Our study furthermore shows that Expressed Sequence Tag (EST) data are insufficient to describe transcriptional activity of HML-2 and other HERV loci in tissues of interest.

Conclusion
Our, to date, largest-scale study reveals in greater detail expression patterns of individual HML-2 loci in human tissues of clinical interest. Moreover, large-scale, specialized studies are indicated to better comprehend transcriptional activity and regulation of HERVs. We thus emphasize the need for a specialized HERV Transcriptome Project.
The frequency of CD127low expressing CD4+CD25high T regulatory cells is inversely correlated with human T lymphotrophic virus type-1 (HTLV-1) proviral load in HTLV-1-infection and HTLV-1-associated myelopathy/tropical spastic paraparesis
Authors: Michaëlsson Jakob , Barbosa Hugo Marcelo R , Jordan Kimberley A , Chapman Joan M , Brunialti Milena KC , Neto Walter Kleine , Nukui Youko , Sabino Ester C , Chieia Marco Antonio , Oliveira Acary Souza Bulle , Nixon Douglas F , Kallas Esper G 
Published: July 2008

AbstractBackgroundCD4+CD25highregulatory T (TReg) cells modulate antigen-specific T cell responses, and can suppress anti-viral immunity. In HTLV-1 infection, a selective decrease in the function of TRegcell mediated HTLV-1-tax inhibition of FOXP3 expression has been described. The purpose of this study was to assess the frequency and phenotype of TRegcells in HTLV-1 asymptomatic carriers and in HTLV-1-associated neurological disease (HAM/TSP) patients, and to correlate with measures of T cell activation.ResultsWe were able to confirm that HTLV-I drives activation, spontaneous IFNγ production, and proliferation of CD4+ T cells. We also observed a significantly lower proportion of CTLA-4+TRegcells (CD4+CD25highT cells) in subjects with HAM/TSP patients compared to healthy controls. Ki-67 expression was negatively correlated to the frequency of CTLA-4+TRegcells in HAM/TSP only, although Ki-67 expression was inversely correlated with the percentage of CD127lowTRegcells in healthy control subjects. Finally, the proportion of CD127lowTRegcells correlated inversely with HTLV-1 proviral load.ConclusionTaken together, the results suggest that TRegcells may be subverted in HAM/TSP patients, which could explain the marked cellular activation, spontaneous cytokine production, and proliferation of CD4+T cells, in particular those expressing the CD25highCD127lowphenotype. TRegcells represent a potential target for therapeutic intervention for patients with HTLV-1-related neurological diseases.
Spx mediates oxidative stress regulation of the methionine sulfoxide reductases operon in Bacillus subtilis
Authors: You CongHui , Sekowska Agnieszka , Francetic Olivera , Martin-Verstraete Isabelle , Wang YiPing , Danchin Antoine 
Published: July 2008

AbstractBackgroundAll aerobically grown living cells are exposed to oxidative damage by reactive oxygen species (ROS). A major damage by ROS to proteins is caused by covalent modifications of methionine residues giving methionine sulfoxide (Met-SO). Methionine sulfoxide reductases are enzymes able to regenerate methionine and restore protein function after oxidative damage.ResultsWe characterized the methionine sulfoxide reductase genesmsrAandmsrBinBacillus subtilis, forming an operon transcribed from a single sigma A-dependent promoter. ThemsrABoperon was specifically induced by oxidative stress caused by paraquat (PQ) but not by H2O2. Spx, a global oxidative stress regulator inB. subtilis, is primarily responsible for this PQ-specific induction ofmsrABexpression. In support of this finding, anspxdeletion mutant is extremely sensitive to PQ, and increased expression ofmsrAwas identified in aclpXmutant in which Spx accumulated. However, the Spx effect was also visible under conditions where the protein did not accumulate (PQ treatment), suggesting a specific molecular effect at the level of the Spx protein. Indeed, the CXXC motif of Spx was found essential for its function in the PQ-specific induction ofmsrABexpression. PQ caused a modification of Spx requiring at least one of the cysteines of the CXXC motif of Spx. The PQ modified form of Spx showed a dynamic changein vivo.ConclusionThe Spx mediated PQ-specific regulation pathway of themsrABoperon inB. subtilisis reported. Our results suggest that PQ induced the expression ofmsrABpartially through an oxidation on Spx via modification of its CXXC motif.
Creatine kinase B deficient neurons exhibit an increased fraction of motile mitochondria
Authors: Kuiper Jan WP , Oerlemans Frank TJJ , Fransen Jack AM , Wieringa Bé 
Published: July 2008

Abstract

Background
Neurons require an elaborate system of intracellular transport to distribute cargo throughout axonal and dendritic projections. Active anterograde and retrograde transport of mitochondria serves in local energy distribution, but at the same time also requires input of ATP. Here we studied whether brain-type creatine kinase (CK-B), a key enzyme for high-energy phosphoryl transfer between ATP and CrP in brain, has an intermediary role in the reciprocal coordination between mitochondrial motility and energy distribution. Therefore, we analysed the impact of brain-type creatine kinase (CK-B) deficiency on transport activity and velocity of mitochondria in primary murine neurons and made a comparison to the fate of amyloid precursor protein (APP) cargo in these cells, using live cell imaging.

Results
Comparison of average and maximum transport velocities and global transport activity showed that CK-B deficiency had no effect on speed of movement of mitochondria or APP cargo, but that the fraction of motile mitochondria was significantly increased by 36% in neurons derived from CK-B knockout mice. The percentage of motile APP vesicles was not altered.

Conclusion
CK-B activity does not directly couple to motor protein activity but cells without the enzyme increase the number of motile mitochondria, possibly as an adaptational strategy aimed to enhance mitochondrial distribution versatility in order to compensate for loss of efficiency in the cellular network for ATP distribution.