gebhart/patrepeval huggingface dataset:
A nested dissection approach to modeling transport in nanodevices: Algorithms and applications (2013)

SUMMARY Modeling nanoscale devices quantum mechanically is a computationally challenging problem where new methods to solve the underlying equations are in a dire need. In this paper, we present an approach to calculate the charge density in nanoscale devices, within the context of the nonequilibrium Green's function approach. Our approach exploits recent advances in using an established graph partitioning approach. The developed method has the capability to handle open boundary conditions that are represented by full self‐energy matrices required for realistic modeling of nanoscale devices. Our method to calculate the electron density has a reduced complexity compared with the established recursive Green's function approach. As an example, we apply our algorithm to a quantum well superlattice and a carbon nanotube, which are represented by a continuum and tight binding Hamiltonian, respectively, and demonstrate significant speedup over the recursive method. Copyright © 2013 John Wiley & Sons, Ltd.
DNA Polymerases α and δ Are Immunologically and Structurally Distinct (1989)

The relationship between DNA polymerases alpha and delta are evaluated immunologically by monoclonal antibody specifically against DNA polymerase alpha and murine polyclonal antiserum against calf thymus DNA polymerase delta. DNA polymerases alpha and delta are found to be immunologically distinct. The structural relationship between the proliferating cell nuclear antigen (PCNA)-dependent calf DNA polymerase delta and DNA polymerase alpha from human and calf was analyzed by two-dimensional tryptic peptide mapping of the catalytic polypeptides. The results demonstrate that the catalytic polypeptides of the PCNA-dependent calf polymerase delta and DNA polymerase alpha are distinct, unrelated, and do not share any common structural determinants. The immunological and structural relationship between a recently identified PCNA-independent form of DNA polymerase delta from HeLa cells was also assessed. This PCNA-independent human polymerase delta was found to be immunologically unrelated to human polymerase alpha but to share some immunological and structural determinants with the PCNA-dependent calf thymus polymerase delta.
Enzymatic synthesis of arginine-based cationic surfactants (1999)

A novel enzymatic approach for the synthesis of arginine N-alkyl amide and ester derivatives is reported. Papain deposited onto solid support materials was used as catalyst for the amide and ester bond formation between Z-Arg-OMe and various long-chain alkyl amines and alcohols (H2N-Cn2, HO-Cn; n = 8–16) in organic media. Changes in enzymatic activity and product yield were studied for the following variables: organic solvent, aqueous buffer content, support for the enzyme deposition, presence of additives, enzyme loading, substrate concentration, and reaction temperature. The best yields (81–89%) of arginine N-alkyl amide derivatives were obtained at 25°C in acetonitrile with an aqueous buffer content ranging from 0 to 1% (v/v) depending on the substrate concentration. The synthesis of arginine alkyl ester derivatives was carried out in solvent-free systems at 50 or 65°C depending on the fatty alcohol chain length. In this case, product yields ranging from 86 to 89% were obtained with a molar ratio Z-Arg-OMe/fatty alcohol of 0.01. Papain deposited onto polyamide gave, in all cases, both the highest enzymatic activities and yields. Under the best reaction conditions the syntheses were scaled up to the production of 2 g of final product. The overall yields, which include reaction, Nα-benzyloxycarbonyl group (Z) deprotection and purification, varied from 53 to 77% of pure (99.9% by HPLC) product. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 63: 333–343, 1999.
Inversion of large-support ill-posed linear operators using a piecewise Gaussian MRF (1998)

We propose a method for the reconstruction of signals and images observed partially through a linear operator with a large support (e.g., a Fourier transform on a sparse set). This inverse problem is ill-posed and we resolve it by incorporating the prior information that the reconstructed objects are composed of smooth regions separated by sharp transitions. This feature is modeled by a piecewise Gaussian (PG) Markov random field (MRF), known also as the weak-string in one dimension and the weak-membrane in two dimensions. The reconstruction is defined as the maximum a posteriori estimate. The prerequisite for the use of such a prior is the success of the optimization stage. The posterior energy corresponding to a PG MRF is generally multimodal and its minimization is particularly problematic. In this context, general forms of simulated annealing rapidly become intractable when the observation operator extends over a large support. In this paper, global optimization is dealt with by extending the graduated nonconvexity (GNC) algorithm to ill-posed linear inverse problems. GNC has been pioneered by Blake and Zisserman in the field of image segmentation. The resulting algorithm is mathematically suboptimal but it is seen to be very efficient in practice. We show that the original GNC does not correctly apply to ill-posed problems. Our extension is based on a proper theoretical analysis, which provides further insight into the GNC. The performance of the proposed algorithm is corroborated by a synthetic example in the area of diffraction tomography.
Expression of the E-cadherin/β-catenin/tcf-4 Pathway in Gastric Diseases with Relation to Helicobacter pylori Infection: Clinical and Pathological Implications (2014)

The expression of E-cadherin and β-catenin progressively decreases during the process of GC tumorigenesis, while overexpression of TCF4 occurs. H. pylori infection is associated with a significant increase in the expression of E-cadherin and β-catenin in the cytoplasm and nucleus in GC patients, especially those with the intestinal type.
Compensation methods for head motion detected during PET imaging (1996)

The authors describe two methods to correct for motion artifacts in head images obtained by positron emission tomography (PET). The methods are based on six-dimensional motion data of the head that have to be acquired simultaneously during scanning. The data are supposed to represent the rotational and translational deviations of the head as a function of time, with respect to the initial head position. The first compensation method is a rebinning procedure by which the lines of response are geometrically transformed according to the current values of the motion data, assuming a cylindrical scanner geometry. An approximation of the rebinning transformations by use of large look-up tables, having the potential of on-line event processing, is presented. The second method comprises post-processing of the reconstructed images by unconstrained or constrained deconvolution of the image or image segments with kernels that are generated from the motion data. The authors use motion data that were acquired with a volunteer in supine position, immobilized by a thermoplastic head holder, to demonstrate the effects of the compensation methods. Preliminary results obtained with test data indicate that the methods have the potential to improve the resolution of PET images in cases where significant head motion has occurred, provided that the head position and orientation can be accurately measured.
Imaging in Neovascular Age-Related Macular Degeneration (2011)

Imaging plays an essential role in the diagnosis and treatment of age-related macular degeneration (AMD). This review describes the imaging modalities most commonly employed by ophthalmologists caring for patients with neovascular AMD. Imaging modalities discussed include fluorescein angiography, optical coherence tomography, indocyanine green angiography, and fundus autofluorescence.
Studies on the masking of unpleasant taste of beclamide: microencapsulation and tabletting (1990)

Beclamide was microencapsulated in order to mask the taste, by a simple coacervation method using gelatin. Anhydrated sodium sulphate was used as coacervating agent. Glutaraldehyde, glutaraldehyde:isopropanol (8 : 32) and formaldehyde:isopropanol (8 : 32) were used as hardening agents. The optimum microencapsulation conditions were: 44 g water, 9 g beclamide and 47 g sodium sulphate as components at a temperature of 40 + 0.5 degrees C with glutaraldehyde (25 per cent w/v) as hardening agent. The dissolution rate of beclamide from prepared microcapsules was determined by a rotating basket and the dissolution kinetics were investigated according to the zero-order, Hixson-Crowell and Higuchi equations. The dissolution pattern of beclamide was first-order kinetic. Release rate constants, t50%, t90% and AUC values were calculated. All these values were discussed for differently obtained microcapsules. Beclamide was formulated in conventional, chewable and effervescent tablet forms. Physical tests were applied to all tablets. The paddle method was used as an in vitro dissolution test method for evaluation of conventional tablets.
An Inter-Classes Obfuscation Method for Java Program (2008)

Software is a valuable form of data, representing significant intellectual property, and reverse engineering of software code by competitors may reveal important technological secrets. This problem becomes more serious when facing with the platform independent language - Java byte code. We introduce an inter-classes software obfuscation technique which extracts the codes of some methods in user-defined classes and embeds them into some other object's methods in the object pool. Since all objects in the object pool are upcast to their common base type, which object's method will really execute can only be ascertained at runtime. Thus, drastically obscured the program flow. Combined with some enhanced mechanisms, this technique can even resist to dynamic analysis to a certain extent. Experimental result shows that there is little influence to the execution efficiency.
Performance bounds for antenna selection in MIMO systems (2004)

This paper discusses antenna sub-set selection in multiple-input multiple-output wireless systems. The antennas are selected so as to maximize the channel capacity. We present a near-optimal selection algorithm that enables tractable statistical analysis of the selection gain. We show that with antenna selection the capacity is statistically lower bounded by the capacity of the set of parallel independent SIMO channels each with selection diversity. We leverage this result to prove the equivalence in diversity order between the full system (all receive antennas) and the system with antenna selection. Simulations validating analysis and illustrating algorithm performance are also presented.
Somatostatin-28 regulates GLP-1 secretion via somatostatin receptor subtype 5 in rat intestinal cultures (2002)

Five somatostatin receptors (SSTRs) bind somatostatin-14 (S-14) and somatostatin-28 (S-28), but SSTR5 has the highest affinity for S-28. To determine whether S-28 acting through SSTR5 mediates inhibition of glucagon-like peptide-1 (GLP-1), fetal rat intestinal cell cultures were treated with somatostatin analogs with relatively high specificity for SSTRs 2-5. S-28 dose-dependently inhibited GLP-1 secretion stimulated by gastrin-releasing peptide more potently than S-14 (EC(50) 0.01 vs. 5.8 nM). GLP-1 secretion was inhibited by an SSTR5 analog, BIM-23268, more potently than S-14 and nearly as effectively as S-28. The SSTR5 analog L-372,588 also suppressed GLP-1 secretion equivalent to S-28, but a structurally similar peptide, L-362,855 (Tyr to Phe at position 7), was ineffective. An SSTR2-selective analog was less effective than S-28, and an SSTR3 analog was inactive. Separate treatment with GLP-1-(7-36)-NH(2) increased S-28 and S-14 secretion by three- and fivefold; BIM-23268 abolished S-28 without altering S-14, whereas the SSTR2 analog was inactive. The results indicate that somatostatin regulation of GLP-1 secretion occurs via S-28 through activation of SSTR5. GLP-1-stimulated S-28 secretion is also autoregulated by SSTR5 activation, suggesting a feedback loop between GLP-1 and S-28 modulated by SSTR5.
Shape‐constrained flock animation (2008)

Abstract We propose a novel shape‐constrained flock animation system for interactively controlling flock navigation in virtual environments. This system is capable of making the spatial distribution of a flock meet static or deforming shape constraints while performing flock simulation. Such a capability can find many applications in the entertainment industry. Given a 3D constraining shape, our system first draws a set of uniform sample points through a 3D surface mosaicing process or a stratified point sampling strategy. Once correspondences between flock members and sample points have been established, points on the target shape are used as homing destinations to guide flock migration. Under a global path control scheme, an effective fuzzy control logic, which dynamically adjusts steering forces and control forces, has been developed to create visually pleasing shape‐constrained flock animations. Copyright © 2008 John Wiley & Sons, Ltd.
An automated technique for the quantitative assessment of 3D-MRSI data from patients with glioma (2001)

Although proton magnetic resonance spectroscopic imaging (1H-MRSI) has been shown to be effective for localizing tumor in patients with gliomas, it is not a routinely used clinical tool. This is due, in part, to the lack of a standardized, objective method for analyzing spectra. We present an automated technique for a) selecting a population of voxels from each patient that have the spectral features of normal brain regions, and b) using the selected voxels as internal controls for quantifying the probability of abnormality at each voxel location. The technique was demonstrated on a phantom, 14 normal volunteers, and 30 patients with histologically proven tumor. In addition, we demonstrated the usefulness of the method for monitoring patients in serial studies from two glioma patients with progressive disease.
Genetic Algorithms for Combinatorial Optimization: The Assemble Line Balancing Problem (1994)

Genetic algorithms are one example of the use of a random element within an algorithm for combinatorial optimization. We consider the application of the genetic algorithm to a particular problem, the Assembly Line Balancing Problem. A general description of genetic algorithms is given, and their specialized use on our test-bed problems is discussed. We carry out extensive computational testing to find appropriate values for the various parameters associated with this genetic algorithm. These experiments underscore the importance of the correct choice of a scaling parameter and mutation rate to ensure the good performance of a genetic algorithm. We also describe a parallel implementation of the genetic algorithm and give some comparisons between the parallel and serial implementations. Both versions of the algorithm are shown to be effective in producing good solutions for problems of this type (with appropriately chosen parameters). INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
Characterization of the umu-complementing operon from R391 (1995)

In addition to conferring resistances to antibiotics and heavy metals, certain R factors carry genes involved in mutagenic DNA repair. These plasmid-encoded genes are structurally and functionally related to the chromosomally encoded umuDC genes of Escherichia coli and Salmonella typhimurium. Three such plasmid operons, mucAB, impCAB, and samAB, have been characterized at the molecular level. Recently, we have identified three additional umu-complementing operons from IncJ plasmid R391 and IncL/M plasmids R446b and R471a. We report here the molecular characterization of the R391 umu-complementing operon. The nucleotide sequence of the minimal R plasmid umu-complementing (rum) region revealed an operon of two genes, rumA(R391) and rumB(R391), with an upstream regulatory signal strongly resembling LexA-binding sites. Phylogenetic analysis revealed that the RumAB(R391) proteins are approximately equally diverged in sequence from the chromosomal UmuDC proteins and the other plasmid-encoded Umu-like proteins and represent a new subfamily. Genetic characterization of the rumAB(R391) operon revealed that in recA+ and recA1730 backgrounds, the rumAB(R391) operon was phenotypically indistinguishable from mucAB. In contrast, however, the rumAB(R391) operon gave levels of mutagenesis that were intermediate between those given by mucAB and umuDC in a recA430 strain. The latter phenotype was shown to correlate with the reduced posttranslational processing of the RumA(R391) protein to its mutagenically active form, RumA'(R391). Thus, the rumAB(R391) operon appears to possess characteristics that are reminiscent of both chromosome and plasmid-encoded umu-like operons.
A Monoclonal Antibody Directed against a<i>Candida albicans</i>Cell Wall Mannoprotein Exerts Three Anti-<i>C. albicans</i>Activities (2003)

Antibodies are believed to play a role in the protection against Candida albicans infections by a number of mechanisms, including the inhibition of adhesion or germ tube formation, opsonization, neutralization of virulence-related enzymes, and direct candidacidal activity. Although some of these biological activities have been demonstrated individually in monoclonal antibodies (MAbs), it is not clear if all these anti-C. albicans activities can be displayed by a single antibody. In this report, we characterized a monoclonal antibody raised against the main target of salivary secretory immunoglobulin A in the cell wall of C. albicans, which exerts three anti-C. albicans activities: (i) inhibition of adherence to HEp-2 cells, (ii) inhibition of germination, and (iii) direct candidacidal activity. MAb C7 reacted with a proteinic epitope from a mannoprotein with a molecular mass of >200 kDa predominantly expressed on the C. albicans germ tube cell wall surface as well as with a number of antigens from Candida lusitaniae, Cryptococcus neoformans, Aspergillus fumigatus, and Scedosporium prolificans. MAb C7 caused a 31.1% inhibition in the adhesion of C. albicans to HEp-2 monolayers and a 55.3% inhibition in the adhesion of C. albicans to buccal epithelial cells, produced a 38.5% decrease in the filamentation of C. albicans, and exhibited a potent fungicidal effect against C. albicans, C. lusitaniae, Cryptococcus neoformans, A. fumigatus, and S. prolificans, showing reductions in fungal growth ranging from 34.2 to 88.7%. The fungicidal activity showed by MAb C7 seems to be related to that reported by antibodies mimicking the activity of a killer toxin produced by the yeast Pichia anomala, since one of these MAbs also reacted with the C. albicans mannoprotein with a molecular mass of >200 kDa. Results presented in this study support the concept of a family of microbicidal antibodies that could be useful in the treatment of a wide range of microbial infections when used alone or in combination with current antimicrobial agents.
Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. (1994)

Mutations in the PISTILLATA (PI) gene of Arabidopsis thaliana cause homeotic conversion of petals to sepals and of stamens to carpels. It is thus classed as a B function floral homeotic gene and acts together with the product of the other known B function gene, APETALA3 (AP3). We have cloned PI and determined the time and places of its expression in developing flowers. Surprisingly, the initial patterns of PI and AP3 expression are different. By positive regulatory interactions between PI and AP3, later expression patterns are coincident or nearly coincident. The pattern of PI expression also depends on the activity of the floral development genes APETALA2 and SUPERMAN and on the activity of PI itself. The PI and APETALA3 proteins specifically associate in solution and so may act together in regulating PI and other genes.
B-cell-based therapies for multiple sclerosis (2011)

In the first of two studies reported by Rose and coworkers, patients with relapsing-remitting multiple sclerosis (RRMS) or secondary-progressive multiple sclerosis (SPMS) were initiated on daclizumab with the same dose. A positive effect on relapses was observed. Safety data coming from daclizumab's regulatory-approved indication in renal transplantation suggest that the drug is overall safe and well tolerated. However, safety data from other of-label indications, such as uveitis, seem to confirm safety concerns regarding a mild increase in infection rate as well as skin reactions. Daclizumab is a novel and promising therapy for MS patients now being tested as monotherapy in a large Phase 3 trial using an active comparator arm. Daclizumab's mechanism of action is not fully understood, but an increase in regulatory immune cells has been related to clinical response and is now thought to play a more important role than direct anti-inflammatory effects derived from IL-2 blockade.
3D Endoscopic Optical Coherence Tomography Based on Rapid-Scanning MEMS Mirrors (2009)

The paper reports 3D in vivo endoscopic imaging enabled by integrating rapid-scanning MEMS mirrors into an optical coherence tomography (OCT) imaging probe. The MEMS mirrors have large aperture size, large scan range and low drive voltage. Polarization-sensitive OCT imaging has also been demonstrated.
Static text region detection in video sequences using color and orientation consistencies (2008)

Motion compensated error of the static text in the frame rate conversion (FRC) is most annoying artifact because people cannot read it. In this paper, we present a novel static text region detection algorithm for preventing the motion compensation error in FRC. We use some consistent properties of the static text that the color of the text is spatio-temporally consistent and the orientation of the text boundary is preserved in consecutive frames. We observe whether each pixelpsilas consistency is preserved for several frames, and then we decide it as a static text. Our algorithm can not only perfectly extract the static text region but also easily be implemented in hardware because of its ease.
The <i>Caenorhabditis elegans lin-12</i> gene mediates induction of ventral uterine specialization by the anchor cell (1995)

The anchor cell (AC) of the Caenorhabditis elegans gonad has a critical role in the development of a functional egg-laying system, which is accomplished through cell-cell interactions. Lateral inhibitory lin-12-mediated signaling among two bipotential cells causes one to adopt the ventral uterine precursor (VU) cell fate while the other becomes the AC. The AC then induces formation of vulval tissue. We find that the AC also induces a particular ventral uterine intermediate precursor fate (pi) by a mechanism that is genetically and temporally distinct from vulval induction. This process requires lin-12, but unlike previously described lin-12-mediated decisions, signaling is unidirectional, is between dissimilar cells and does not involve lateral inhibition. The pi fates are necessary for egg laying and appear to produce a distinct specialized cell type. Thus, patterning of the ventral uterus by the AC is crucial to the development of a functional egg-laying system.