julilili42/papers huggingface dataset:
Chronobiological Background to Cathemerality: Circadian Rhythms in Eulemur fulvus albifrons (Prosimii) and Aotus azarai boliviensis (Anthropoidea)
2006-01-19

Cathemeral activity, in which the animals’ motor activity is almost evenly distributed throughout the dark and the light portion of the day, has been described in various lemur genera (Eulemur, Hapalemur) and in the owl monkey Aotus azarai of the Argentinean Chaco. Proximate and ultimate factors responsible for this behaviour are still being debated. However, the chronobiological background of the behaviour has largely been ignored. We studied E. fulvus albifrons and A. a. boliviensis under controlled laboratory conditions to assess whether their activity rhythm is endogenously regulated by a circadian timing system that obeys general rules found in other mammals, or whether there are characteristic differences. To this end, we carried out long-term activity recordings on individuals of both subspecies kept under constant light and various light-dark cycles (LDs) using a PC-controlled electro-acoustic device in combination with telemetric body temperature measurements. Both subspecies developed free-running circadian activity and body temperature rhythms with periods deviating from 24 h in constant light, and LDs turned out to be the most efficient Zeitgeber synchronizing this endogenous rhythmicity to the external 24-hour day. The luminosity prevailing during the dark time of the LD had a decisive effect on levels of activity in the lemurs and induced strong masking effects on their circadian activity pattern. The results indicate that, from a chronobiological viewpoint, both species should be considered as dark active primates. Their diel activity rhythm is regulated by a normally responding circadian timing system and strong activity inhibiting or enhancing direct effects of light intensity. Thus, hypotheses on proximate and/or ultimate factors of cathemerality in primates must also consider its circadian background.
Local configurations on surfaces of icosahedral quasicrystals
2006-01-19

Abstract\\n The surfaces of icosahedral quasicrystals of an F-phase, orthogonal to a fivefold symmetry axis have a terrace-like appearance. On highly resolved images of these terraces one observes different local configurations. We search for possible corresponding configurations in the bulk model of atomic positions &lt;i&gt;M&lt;/i&gt; based on the icosahedral tiling &lt;i&gt;T&lt;/i&gt;&lt;sup&gt;*(2F)&lt;/sup&gt;.
Efficient Synthesis of Isobenzofuran‐1(3H)‐ones (Phthalides) and Selected Biological Evaluations.
2006-01-19

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access the actual ChemInform Abstract, please click on HTML or PDF.
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
2006-01-20

Abstract Motivation: Functional annotation of unknown proteins is a major goal in proteomics. A key annotation is the prediction of a protein's subcellular localization. Numerous prediction techniques have been developed, typically focusing on a single underlying biological aspect or predicting a subset of all possible localizations. An important step is taken towards emulating the protein sorting process by capturing and bringing together biologically relevant information, and addressing the clear need to improve prediction accuracy and localization coverage. Results: Here we present a novel SVM-based approach for predicting subcellular localization, which integrates N-terminal targeting sequences, amino acid composition and protein sequence motifs. We show how this approach improves the prediction based on N-terminal targeting sequences, by comparing our method TargetLoc against existing methods. Furthermore, MultiLoc performs considerably better than comparable methods predicting all major eukaryotic subcellular localizations, and shows better or comparable results to methods that are specialized on fewer localizations or for one organism. Availability: Contact: hoeglund@informatik.uni-tuebingen.de
High-Resolution Magnetic Resonance Angiography of the Renal Arteries Using Parallel Imaging Acquisition Techniques at 3.0 T
2006-01-20

CEMRA at 3.0 T is advantageous in terms of better SNR and T1 weighting; therefore, measurement time can be reduced and spatial resolution can be increased without corruption of signal yield. Consequently, high-field MRA may be preferred for the evaluation of renal vascular anatomy in potential kidney donors or for the detection of renal artery stenosis.
Data Reduction, Exact, and Heuristic Algorithms for Clique Cover
2006-01-21

To cover the edges of a graph with a minimum number of cliques is an NP-complete problem with many applications. The state-of-the-art solving algorithm is a polynomial-time heuristic from the 1970's. We present an improvement of this heuristic. Our main contribution, however, is the development of efficient and effective polynomial-time data reduction rules that, combined with a search tree algorithm, allow for exact problem solutions in competitive time. This is confirmed by experiments with real-world and synthetic data. Moreover, we prove the fixed-parameter tractability of covering edges by cliques.
Max-tolerance graphs as intersection graphs: cliques, cycles, and recognition
2006-01-22

Max-tolerance graphs can be regarded as generalized interval graphs, where two intervals Ii and Ij only induce an edge in the corresponding graph iff they overlap for an amount of at least max{ti, tj} where ti is an individual tolerance parameter associated to each interval Ii. A new geometric characterization of max-tolerance graphs as intersection graphs of isosceles right triangles, shortly called semi-squares, leverages the solution of various graph-theoretic problems in connection with max-tolerance graphs. First, we solve the maximal and maximum cliques problem. It arises naturally in DNA sequence analysis where the maximal cliques might be interpreted as functional domains carrying biologically meaningful information. We prove an upper bound of O(n3) for the number of maximal cliques in max-tolerance graphs and give an efficient O(n3) algorithm for their computation. In the same vein, the semi-square representation yields a simple proof for the fact that this bound is asymptotically tight, i.e., a class of max-tolerance graphs is presented where the instances have Ω(n3) maximal cliques. Additionally, we answer an open question posed in [8] by showing that max-tolerance graphs do not contain complements of cycles Cn for n > 9. By exploiting the new representation more deeply, we can go even further and prove that the recognition problem for max-tolerance graphs is NP-hard.
Convolution quadrature time discretization of fractional diffusion-wave equations
2006-01-23

We propose and study a numerical method for time discretization of linear and semilinear integro-partial differential equations that are intermediate between diffusion and wave equations, or are subdiffusive. The method uses convolution quadrature based on the second-order backward differentiation formula. Second-order error bounds of the time discretization and regularity estimates for the solution are shown in a unified way under weak assumptions on the data in a Banach space framework. Numerical experiments illustrate the theoretical results.
Investigation of coupled hydraulic–geomechanical processes at the KTB site: pressure‐dependent characteristics of a long‐term pump test and elastic interpretation using a geomechanical facies model
2006-01-23

Abstract The German Continental Deep Drilling Program comprising a pilot borehole down to 4000 m and a main borehole down to 9101 m in southeast Germany (KTB) is continuing to provide a unique opportunity for the identification of important factors and processes in deep‐seated fluid and energy transfer. In situ stress conditions significantly impact flow, transport and exchange characteristics of fracture networks that dominate the permeability of crystalline reservoir rocks. In this paper, several scales of information are combined to present a fully three‐dimensional hydraulic finite element model of the principal KTB fault zones, and linked to a geomechanical model describing the alteration of the hydraulic parameters with stress changes caused by fluid extraction. The concept of geomechanical facies is introduced to define and characterize architectural elements in the subsurface system. Evaluation of a long‐term pump test in the KTB pilot hole, June 2002–July 2003, coupled with a geomechanical model gives an insight into some of the elastic and nonelastic processes controlling hydraulic transport in the basement rocks. Trends in the decline of the permeability and the degree of storage in the system could only partially be explained by elastic processes, clearly indicating the importance of nonelastic processes. A number of inelastic processes are suggested as areas for further research.
GROUND-STATE BARYON MASSES IN THE PERTURBATIVE CHIRAL QUARK MODEL
2006-01-23

The mass differences of the flavor octet and decuplet ground-state baryons are studied in the perturbative chiral quark model. We present a way to understand the nontrivial spin- and flavor-dependent mass differences, whereby both pseudoscalar mesons and gluons play a significant role.
Surviving glioblastoma for more than 5 years: The patient's perspective
2006-01-24

The authors performed a comprehensive analysis of the functional outcome of 10 patients who had survived 5 years from a diagnosis of glioblastoma. Neurologic deficits were mild in most patients, but neuropsychological testing demonstrated cognitive deficits in all patients. Depression and anxiety were common. Although most patients thought that their social functioning and work ability were impaired, little reduction in overall quality of life was perceived.
Model-independent study of the Dirac structure of the nucleon-nucleon interaction
2006-01-24

Relativistic and non-relativistic modern nucleon-nucleon potentials are mapped on a relativistic operator basis using projection techniques. This allows to compare the various potentials at the level of covariant amplitudes were a remarkable agreement is found. In nuclear matter large scalar and vector mean fields of several hundred MeV magnitude are generated at tree level. This is found to be a model independent feature of the nucleon-nucleon interaction.
Data and Graph Mining in Chemical Space for ADME and Activity Data Sets
2006-01-25

Abstract We present a classification method, which is based on a coordinate‐free chemical space. Thus, it does not depend on descriptor values commonly used by coordinate‐based chemical space methods. In our method the molecular similarity of chemical structures is evaluated by a generalized maximum common graph isomorphism, which supports the usage of numerical physicochemical atom property labels in addition to discrete‐atom‐type labels. The Maximum Common Substructure (MCS) algorithm applies the Highest Scoring Common Substructure (HSCS) ranking of Sheridan and co‐workers, which penalizes discontinuous fragments. For all compared classification algorithms used in this work we analyze their usefulness based on two objectives. First, we are interested in highly accurate and general hypotheses and second, the interpretation ability is highly important to increase our structural knowledge for the ADME data sets and the activity data set investigated in this work.
Docetaxel, estramustine and prednisone for hormone-refractory prostate cancer: a single-center experience.
2006-01-25

Although the patients included in the present study had advanced disease, responses were promising and toxicity was tolerable. These preliminary data support the findings of recently published studies and suggest that docetaxel-based chemotherapy is going to play an important role as a regimen for patients with HRPC.
Occlusion-driven scene sorting for efficient culling
2006-01-25

Image space occlusion culling is a powerful approach to reduce the rendering load of large polygonal models. However, occlusion culling is not for free; it trades overhead costs with the rendering costs of the possibly occluded geometry. Meanwhile, occlusion queries based on image space occlusion culling are supported on modern graphics hardware. However, a significant consumption of fillrate bandwidth and latency costs are associated with these queries.In this paper, we propose new techniques to reduce redundant occlusion queries. Our approach uses several "Occupancy Maps" to organize scene traversal. The respective information is accumulated efficiently by hardware-supported asynchronous occlusion queries. To avoid redundant requests, we arrange these multiple occlusion queries according to the information of the Occupancy Maps. Our presented technique is conservative and benefits from a partial depth order of the geometry.
Volumetric high dynamic range windowing for better data representation
2006-01-25

Volume data is usually generated by measuring devices (eg. CT scanners, MRI scanners), mathematical functions (eg., Marschner/Lobb function), or by simulations. While all these sources typically generate 12 bit integer or floating point representations, commonly used displays are only capable of handling 8 bit gray or color levels. In a typical medical scenario, a 3D scanner will generate a 12 bit dataset, from which a subrange of the active full accuracy data range of 0 up to 4096 voxel values will be downsampled to an 8 bit per-voxel accuracy. This downsampling is usually achieved by a linear mapping operation and by clipping of value ranges left and right of the chosen subrange.In this paper, we propose a novel windowing operation that is based on methods from high dynamic range image mapping. With this method, the contrast of mapped 8 bit volume datasets is significantly enhanced, in particular if the imaging modality allows for a high tissue differentiation (eg., MRI). Thus, it also allows better and easier segmentation and classification. We demonstrate the improved contrast with different error metrics and a perception-driven image difference to indicate differences between three different high dynamic range operators.
Determinants of AQP6 trafficking to intracellular sites versus the plasma membrane in transfected mammalian cells
2006-01-26

Background information . Most AQPs (aquaporins) function at the plasma membrane, however AQP6 is exclusively localized to membranes of intracellular vesicles in acid‐secreting type‐A intercalated cells of renal collecting ducts. The intracellular distribution indicates that AQP6 has a function distinct from trans‐epithelial water movement. Results . We show by mutational analyses and immunofluorescence that the N‐terminus of AQP6 is a determinant for its intracellular localization. Presence or absence at the plasma membrane of AQP6 constructs was confirmed by electrophysiological methods. Addition of a GFP (green fluorescent protein) or a HA (haemagglutinin) epitope tag (GFP—AQP6 or HA—AQP6) to the N‐terminus of AQP6, directed AQP6 to the plasma membranes of transfected Madin—Darby canine kidney cells. In contrast, addition of a GFP tag to the C‐terminus (AQP6–GFP) caused the protein to remain intracellular, similar to untagged wild‐type AQP6. Replacement of the N‐terminus of AQP6 by that of AQP1 also directed AQP6 to the plasma membranes, whereas the N‐terminus of AQP6 retained AQP1 in cytosolic sites. Conclusion . Our results suggest that the N‐terminus of AQP6 is critical for trafficking of the protein to the intracellular sites. Moreover, our studies provide an approach for future identification of proteins involved in vesicle sorting in the acid‐secreting type‐A intercalated cells.
Disk eccentricity and embedded planets
2006-01-27

\\n \\n Context.\\n \\n \\nAims.We investigate the response of an accretion disk to the\\npresence of a perturbing protoplanet embedded in the disk through time\\ndependent hydrodynamical simulations.\\n \\nMethods.The disk is treated as a two-dimensional viscous fluid and the planet\\nis kept on a fixed orbit. We run a set of simulations\\nvarying the planet mass, and the viscosity and temperature of the\\ndisk. All runs are followed until they reach a quasi-equilibrium\\nstate.\\n \\nResults.We find that for planetary masses above a certain minimum mass,\\nalready for a viscosity of , the disk\\nmakes a transition from a nearly circular state into an\\neccentric state. Increasing the planetary mass leads to a\\nsaturation of disk eccentricity with a maximum value of around 0.25.\\nThe transition to the eccentric state is driven by the excitation of\\nan spiral wave at the outer 1:3 Lindblad resonance. The effect\\noccurs only if the planetary mass is large enough to clear a\\nsufficiently wide and deep gap to reduce the damping effect of the\\nouter 1:2 Lindblad resonance. An increase in viscosity or\\ntemperature in the disk, which both tend to close the gap, have an\\nadverse influence on the disk eccentricity.\\n \\nConclusions.In the eccentric state the mass accretion\\nrate onto the planet is greatly enhanced, an effect that may ease the\\nformation of massive planets beyond about 5 MJup that are\\notherwise difficult to reach.\\n
Long term variability of Cygnus X-1
2006-01-27

Continuing the observational campaign initiated by our group, we present the long term spectral evolution of the Galactic black hole candidate Cygnus X-1 in the X-rays and at 15 GHz. We present ∼200 pointed observations taken between early 1999 and late 2004 with the Rossi X-ray&#13;\\nTiming Explorer and the Ryle radio telescope. The X-ray spectra are remarkably well described by a simple broken power law spectrum with an exponential cutoff. Physically motivated Comptonization models, e.g., by Titarchuk (1994, ApJ, 434, 570, compTT) and by Coppi (1999, in High Energy Processes in Accreting Black Holes, ed. J. Poutanen, &amp; R. Svensson (San Francisco: ASP), ASP Conf. Ser., 161, 375, eqpair), can reproduce this simplicity; however, the success of the phenomenological broken power law models cautions against “overparameterizing” the more physical models. Broken power law models reveal a significant linear correlation between the photon index of the lower energy&#13;\\npower law and the hardening of the power law at ∼10 keV. This phenomenological soft/hard power law correlation is partly attributable to correlations of broad band continuum components, rather than being dominated by the weak hardness/reflection fraction correlation present in the Comptonization model. Specifically, the Comptonization models show that the bolometric flux of a soft excess (e.g., disk component) is strongly correlated with the compactness ratio of the Comptonizing medium, with L disk&#13;\\n∝( h / s ) −0.19 . Over the course of our campaign, Cyg X-1 transited several times into the soft state, and exhibited a large number of “failed state transitions”. The fraction of the time spent in such low radio emission/soft X-ray spectral states has increased from ∼10% in 1996–2000 to ∼34% since early 2000. We find that radio flares&#13;\\ntypically occur during state transitions and failed state transitions (at h / s ∼ 3), and that there is a strong correlation between the 10–50 keV X-ray flux and the radio luminosity of the source. We demonstrate that rather than there being distinctly separated states, in contrast to the timing properties the spectrum of Cyg X-1 shows variations between extremes of properties, with clear cut examples of spectra at every intermediate point in the observed spectral correlations.&#13;\\n
The sepiapterin reductase gene region reveals association in the PARK3 locus: analysis of familial and sporadic Parkinson’s disease in European populations
2006-01-27

Background: Parkinson’s disease is a genetically complex disease with mixed mode of inheritance. Recently, a haplotype across the sepiapterin reductase (SPR) gene, which is located in the PARK3 linkage region, was shown to modulate age of onset of Parkinson’s disease in sibships from North America. Objective: To make a thorough assessment of the SPR gene region in sporadic Parkinson’s disease. Methods: A linkage study in 122 European sibship families with five microsatellite and 17 single nucleotide polymorphism (SNP) markers in and around the SPR gene region, and an association analysis in 340 sporadic cases of Parkinson’s disease and 680 control subjects from Germany with 40 SNPs. Linkage was evaluated by non-parametric linkage scores and genotypic or haplotype association was tested by regression analysis, assuming different risk effect models. Results: Significant LOD scores between 2 and 3 were obtained at the two SPR-flanking markers D2S2110 and D2S1394 and seven SNP markers around the SPR gene. We found the previously reported promoter SNP rs1876487 also significantly associated with age of onset in our sib pair families (p-value 0.02). One strong linkage disequilibrium (LD) block of 45 kb including the entire SPR gene was observed. Within this LD block all 14 inter-correlated SNPs were significantly associated with Parkinson’s disease affection status (p-value 0.004). Conclusions: DNA polymorphisms in a highly intercorrelated LD block, which includes the SPR gene, appear to be associated with both sporadic and familial Parkinson’s disease. This confirms a previous study showing that SPR potentially modulates the onset of or risk for Parkinson’s disease.
An ASM Based SystemC Simulation Semantics
2006-01-27

We present a formal definition of the event based SystemC V2.0 simulation semantics by means of distributed Abstract State Machines (ASMs). Our definition provides a rigorous and concise, but yet readable, definition of the SystemC specific operations and their interaction with the simulation scheduler that covers channel updates, notify, notify_delayed, wait, and next_trigger operations. We present the semantics in the form of rules by means of distributed ASMs reflecting the lines of the SystemC V2.0 Standard Manuals and reference implementation. The semantics introduced is defined to complement the language reference manual with aprecise definition reflecting an abstract model of the SystemC reference implementation, which can be used for advanced applications and for investigating interoperabilities with other languages.
Fluorescence Spectroscopy in Turbid Media and Tissues
2006-01-28

Most organic and inorganic materials on Earth are strongly light scattering and many of them are fluorescent. Examples are found in the fields of biology, mineralogy, technology, or chemistry (plant and animal tissue, minerals, pigments, papers and printing products, polymer blends, optically brightened products, microdisperse adsorption systems, stationary chromatographic phases, and so on). Quantitative fluorimetry of such systems starts with the absorption of light that is strongly modified by the physical process of multiple scattering and by possible chemical interactions of the absorbers with the scattering environment. The absorption in scattering media is usually investigated with the methods of regular and diffuse reflectance or transmittance spectroscopy, the photometric laws of which are well understood under large area of irradiation and to some extent also under spot irradiation. The photophysical and photochemical processes following absorption can be investigated nowadays very sensitively by fluorimetric methods, but compared to transparent systems it is still a significant problem to quantify the spectral, temporal, and spatial distribution of the emitted light fluxes correctly. The following chapter presents some of the recent theoretical and experimental developments in fluorescence spectroscopy of turbid media, mixing review and original results and concentrating especially on the limit of dominant scattering, i.e., low absorptivity and high probability of multiple scattering. This limit is the most interesting one since fluorimetry is a powerful method especially in trace analysis and not in highly concentrated systems, and the case of low scattering can easily be extrapolated from the more general results of the high scattering limit.