gebhart/patrepeval huggingface dataset:
Load line emulation based maximum power point tracking (2008)

This work is concerned with maximum power point tracking in photovoltaic systems. Under the suggested method, tracking of the maximum power point is accomplished partially by a linear control loop that emulates a nearly matched load line and partially by the fine tuning of this load line employing an iterative process that resembles conventional MPPT methods. This way, excellent tracking is achieved both in steady state and in transient situations.
Using Deception to Hide Things from Hackers: Processes, Principles, and Techniques (2006)

Deception offers one means of hiding things from an adversary. This paper introduces a model for understanding, comparing, and developing methods of deceptive hiding. The model characterizes deceptive hiding in terms of how it defeats the underlying processes that an adversary uses to discover the hidden thing. An adversary’s process of discovery can take three forms: direct observation (sensing and recognizing), investigation (evidence collection and hypothesis formation), and learning from other people or agents. Deceptive hiding works by defeating one or more elements of these processes. The model is applied to computer security, and it is also applicable to other domains.
Extending the Language of DNA Molecular Recognition by Polyamides:  Unexpected Influence of Imidazole and Pyrrole Arrangement on Binding Affinity and Specificity (2004)

Pyrrole (Py) and imidazole (Im) polyamides can be designed to target specific DNA sequences. The effect that the pyrrole and imidazole arrangement, plus DNA sequence, have on sequence specificity and binding affinity has been investigated using DNA melting (DeltaT(M)), circular dichroism (CD), and surface plasmon resonance (SPR) studies. SPR results obtained from a complete set of triheterocyclic polyamides show a dramatic difference in the affinity of f-ImPyIm for its cognate DNA (K(eq) = 1.9 x 10(8) M(-1)) and f-PyPyIm for its cognate DNA (K(eq) = 5.9 x 10(5) M(-1)), which could not have been anticipated prior to characterization of these compounds. Moreover, f-ImPyIm has a 10-fold greater affinity for CGCG than distamycin A has for its cognate, AATT. To understand this difference, the triamide dimers are divided into two structural groupings: central and terminal pairings. The four possible central pairings show decreasing selectivity and affinity for their respective cognate sequences: -ImPy > -PyPy- >> -PyIm- approximately -ImIm-. These results extend the language of current design motifs for polyamide sequence recognition to include the use of "words" for recognizing two adjacent base pairs, rather than "letters" for binding to single base pairs. Thus, polyamides designed to target Watson-Crick base pairs should utilize the strength of -ImPy- and -PyPy- central pairings. The f/Im and f/Py terminal groups yielded no advantage for their respective C/G or T/A base pairs. The exception is with the -ImPy- central pairing, for which f/Im has a 10-fold greater affinity for C/G than f/Py has for T/A.
Making use of population information in evolutionary artificial neural networks (1998)

This paper is concerned with the simultaneous evolution of artificial neural network (ANN) architectures and weights. The current practice in evolving ANN's is to choose the best ANN in the last generation as the final result. This paper proposes a different approach to form the final result by combining all the individuals in the last generation in order to make best use of all the information contained in the whole population. This approach regards a population of ANN's as an ensemble and uses a combination method to integrate them. Although there has been some work on integrating ANN modules, little has been done in evolutionary learning to make best use of its population information. Four linear combination methods have been investigated in this paper to illustrate our ideas. Three real-world data sets have been used in our experimental studies, which show that the recursive least-square (RLS) algorithm always produces an integrated system that outperforms the best individual. The results confirm that a population contains more information than a single individual. Evolutionary learning should exploit such information to improve generalization of learned systems.
Voxel-Based 6-DOF Haptic Rendering Improvements (2006)

An approach is presented for realizing an order-of-magnitude improvement in spatial accuracy for voxel-based 6-DOF haptics. It trades constant-time performance for greater spatial accuracy. This helps to make 6-DOF haptics applicable to extraordinarily complex real-world task simulations, which often admit no other known solution short of physical mockup. A reduction of haptic fidelity is tactically incurred but simultaneously mitigated by augmenting standard voxel-sampling methodology with distance fields, temporal coherence, and culling of redundant polyhedral surface interactions. This is applied to large-scale haptic scenarios involving multiple moving objects and to collaborative virtual environments.
Nonpeptide angiotensin II receptor antagonists. Synthesis and biological activity of benzimidazolecarboxylic acids (1993)

A series of 2-substituted-1-[(biphenyl-4-yl)methyl]-1H-benzimidazole-7- carboxylic acids was prepared from the key intermediate 3-amino-2-[[(biphenyl-4- yl)methyl]amino]benzoate (6a-c) in order to clarify the structure-activity relationships of various analogues of 2-butyl-1-[[2'-(1H-tetrazol-5-yl)biphenyl-4-yl]methyl]-1H-ben zimidazole- 7-carboxylic acid (CV-11194), a potent and long acting angiotensin II (AII) receptor antagonist. The AII antagonistic activity of the benzimidazoles was investigated by in vitro assays, which included an AII receptor binding assay and AII-induced vasocontraction assay, as well as by in vivo assays such as an AII-induced pressor response in rats. Most of the benzimidazoles showed high affinity for the AII receptor (IC50 value, 10(-6)-10(-7) M) and inhibited the AII-induced pressor response at 1 or 3 mg/kg po, and the effects were more potent than those of CV-11194 and DuP 753. The structure-activity relationship studies on the binding affinity and the inhibition of AII-induced pressor response suggested that straight chains of a certain length (e.g., ethoxy groups, ethyl groups) were the best as substituents at the 2-position and that their steric factors, lipophilicity, and electronic effects affected the potency of the AII antagonistic action. Both a carboxyl group at the 7-position and a tetrazole ring at the 2'-position were particularly important for potent and orally active AII antagonistic activity and a long-acting hypotensive effect. The representative compound, 2-ethoxy-1-[[2'-(1H-tetrazol-5-yl)biphenyl-4-yl]methyl]-1H- benzimidazole-7-carboxylic acid (26b, CV-11974), inhibited the specific binding of [125I]AII to bovine adrenal cortical membrane with an IC50 value of 1.1 x 10(-7) M. The AII-induced contraction of rabbit aortic strips was antagonized by CV-11974 (IC50 value, 3.0 x 10(-10) M). Oral administration of CV-11974 to conscious normotensive rats at 1 mg/kg resulted in long-lasting inhibition of the AII-induced pressor response. CV-11974 at 0.1-1 mg/kg iv reduced blood pressure dose-dependently in spontaneously hypertensive rats.
Random classification noise defeats all convex potential boosters (2008)

A broad class of boosting algorithms can be interpreted as performing coordinate-wise gradient descent to minimize some potential function of the margins of a data set. This class includes AdaBoost, LogitBoost, and other widely used and well-studied boosters. In this paper we show that for a broad class of convex potential functions, any such boosting algorithm is highly susceptible to random classification noise. We do this by showing that for any such booster and any nonzero random classification noise rate η, there is a simple data set of examples which is efficiently learnable by such a booster if there is no noise, but which cannot be learned to accuracy better than 1/2 if there is random classification noise at rate η. This negative result is in contrast with known branching program based boosters which do not fall into the convex potential function framework and which can provably learn to high accuracy in the presence of random classification noise.
Mode conversion coefficients in optical fibers (1975)

A simple method has been devised for the experimental determination of mode conversion coefficients in multimode fibers and involves only the observation of the far-field output as the angle of incidence of a collimated input beam is changed. The normalized mode coupling coefficient in a liquid-core fiber is D = 3 x 10(-6) rad(2) m(-1) and increases by as much as a factor of 10 when transverse pressure is applied. Values some 2 orders of magnitude larger are found in glass-core fibers. There is good agreement between the theory presented and experiment.
Reversible methylation of promoter-bound STAT3 by histone-modifying enzymes (2010)

Following its tyrosine phosphorylation, STAT3 is methylated on K140 by the histone methyl transferase SET9 and demethylated by LSD1 when it is bound to a subset of the promoters that it activates. Methylation of K140 is a negative regulatory event, because its blockade greatly increases the steady-state amount of activated STAT3 and the expression of many (i.e., SOCS3) but not all (i.e., CD14) STAT3 target genes. Biological relevance is shown by the observation that overexpression of SOCS3 when K140 cannot be methylated blocks the ability of cells to activate STAT3 in response to IL-6. K140 methylation does not occur with mutants of STAT3 that do not enter nuclei or bind to DNA. Following treatment with IL-6, events at the SOCS3 promoter occur in an ordered sequence, as shown by chromatin immunoprecipitations. Y705-phosphoryl-STAT3 binds first and S727 is then phosphorylated, followed by the coincident binding of SET9 and dimethylation of K140, and lastly by the binding of LSD1. We conclude that the lysine methylation of promoter-bound STAT3 leads to biologically important down-regulation of the dependent responses and that SET9, which is known to help provide an activating methylation mark to H3K4, is recruited to the newly activated SOCS3 promoter by STAT3.
European Origin of Bradyrhizobium Populations Infecting Lupins and Serradella in Soils of Western Australia and South Africa (2005)

We applied a multilocus phylogenetic approach to elucidate the origin of serradella and lupin Bradyrhizobium strains that persist in soils of Western Australia and South Africa. The selected strains belonged to different randomly amplified polymorphic DNA (RAPD)-PCR clusters that were distinct from RAPD clusters of applied inoculant strains. Phylogenetic analyses were performed with nodulation genes (nodA, nodZ, nolL, noeI), housekeeping genes (dnaK, recA, glnII, atpD), and 16S-23S rRNA intergenic transcribed spacer sequences. Housekeeping gene phylogenies revealed that all serradella and Lupinus cosentinii isolates from Western Australia and three of five South African narrow-leaf lupin strains were intermingled with the strains of Bradyrhizobium canariense, forming a well supported branch on each of the trees. All nodA gene sequences of the lupin and serradella bradyrhizobia formed a single branch, referred to as clade II, together with the sequences of other lupin and serradella strains. Similar patterns were detected in nodZ and nolL trees. In contrast, nodA sequences of the strains isolated from native Australian legumes formed either a new branch called clade IV or belonged to clade I or III, whereas their nonsymbiotic genes grouped outside the B. canariense branch. These data suggest that the lupin and serradella strains, including the strains from uncultivated L. cosentinii plants, are descendants of strains that most likely were brought from Europe accidentally with lupin and serradella seeds. The observed dominance of B. canariense strains may be related to this species' adaptation to acid soils common in Western Australia and South Africa and, presumably, to their intrinsic ability to compete for nodulation of lupins and serradella.
Src Regulates Constitutive Internalization and Rapid Resensitization of a Cholecystokinin 2 Receptor Splice Variant (2005)

The third intracellular loop domain of G protein-coupled receptors regulates their desensitization, internalization, and resensitization. Colorectal and pancreatic cancers, but not the nonmalignant tissue, express a splice variant of the cholecystokinin 2 receptor (CCK2R) called CCK(2i4sv)R that, because of intron 4 retention, contains an additional 69 amino acids within its third intracellular loop domain. This structural alteration is associated with agonist-independent activation of Src kinase (Olszewska-Pazdrak, B., Townsend, C. M., Jr., and Hellmich, M. R. (2004) J. Biol. Chem. 279, 40400-40404). The purpose of the study was to determine the roles of intron 4 retention and Src kinase on CCK(2i4sv)R desensitization, internalization, and resensitization. Gastrin1-17 (G17) binds to both CCK2R and CCK(2i4sv)R and induces intracellular Ca2+ ([Ca2+]i) increases. Agonist-induced increases in [Ca2+]i were used to assess receptor activity. Src kinase activity was inhibited by transducing cells with a retrovirus containing a dominant-negative mutant Src (A430V). The subcellular location of enhanced green fluorescent protein-tagged receptors was monitored using laser scanning confocal microscopy. Both receptor variants desensitized at the same rate; however, CCK(2i4sv)R resensitized five times faster than CCK2R. Without agonist, 80% of CCK(2i4sv)R is located in an intracellular compartment. In contrast, 80% of CCK2R was located on the plasma membrane. Treatment with inverse agonist (YM022) or expression of dominant-negative Src blocked the constitutive internalization of CCK(2i4sv)R, resulting in its accumulation on the plasma membrane. Expression of dominant-negative Src slowed the rate of CCK(2i4sv)R resensitization. Inhibition of Src did not affect G17-induced internalization of either receptor variant. Constitutive internalization of CCK(2i4sv)R increases its rate of resensitization by creating an intracellular pool of receptors that can rapidly recycle back to the plasma membrane.
A case for high performance computing with virtual machines (2006)

Virtual machine (VM) technologies are experiencing a resurgence in both industry and research communities. VMs offer many desirable features such as security, ease of management, OS customization, performance isolation, check-pointing, and migration, which can be very beneficial to the performance and the manageability of high performance computing (HPC) applications. However, very few HPC applications are currently running in a virtualized environment due to the performance overhead of virtualization. Further, using VMs for HPC also introduces additional challenges such as management and distribution of OS images.In this paper we present a case for HPC with virtual machines by introducing a framework which addresses the performance and management overhead associated with VM-based computing. Two key ideas in our design are: Virtual Machine Monitor (VMM) bypass I/O and scalable VM image management. VMM-bypass I/O achieves high communication performance for VMs by exploiting the OS-bypass feature of modern high speed interconnects such as Infini-Band. Scalable VM image management significantly reduces the overhead of distributing and managing VMs in large scale clusters. Our current implementation is based on the Xen VM environment and InfiniBand. However, many of our ideas are readily applicable to other VM environments and high speed interconnects.We carry out detailed analysis on the performance and management overhead of our VM-based HPC framework. Our evaluation shows that HPC applications can achieve almost the same performance as those running in a native, non-virtualized environment. Therefore, our approach holds promise to bring the benefits of VMs to HPC applications with very little degradation in performance.
Myocardial perfusion imaging with PET (2013)

PET-myocardial perfusion imaging (MPI) allows accurate measurement of myocardial perfusion, absolute myocardial blood flow and function at stress and rest in a single study session performed in approximately 30 min. Various PET tracers are available for MPI, and rubidium-82 or nitrogen-13-ammonia is most commonly used. In addition, a new fluorine-18-based PET-MPI tracer is currently being evaluated. Relative quantification of PET perfusion images shows very high diagnostic accuracy for detection of obstructive coronary artery disease. Dynamic myocardial blood flow analysis has demonstrated additional prognostic value beyond relative perfusion imaging. Patient radiation dose can be reduced and image quality can be improved with latest advances in PET/CT equipment. Simultaneous assessment of both anatomy and perfusion by hybrid PET/CT can result in improved diagnostic accuracy. Compared with SPECT-MPI, PET-MPI provides higher diagnostic accuracy, using lower radiation doses during a shorter examination time period for the detection of coronary artery disease.
Adhesion Molecule Mechanisms Mediating Monocyte Migration Through Synovial Fibroblast and Endothelium Barriers: Role for CD11/CD18, Very Late Antigen-4 (CD49d/CD29), Very Late Antigen-5 (CD49e/CD29), and Vascular Cell Adhesion Molecule-1 (CD106) (1998)

Monocytes migrate through vascular endothelium, and then in connective tissue. As a model of this process, we investigated adhesion molecules involved in monocyte migration through HUVEC and a barrier of human synovial fibroblasts (HSF). Minimal spontaneous monocyte migration (6-7%) occurred through either cell barrier, but this increased markedly (27-35% of added monocytes) when a C5a chemotactic gradient was present. Migration across unstimulated HUVEC was partially inhibited (40%) by mAb to CD18 (beta2 integrin) and completely blocked by anti-CD18 plus anti-alpha4 (CD49d; very late Ag-4 (VLA-4)) mAbs. In contrast, migration across HSF induced by C5a or monocyte chemoattractant protein-1 was not inhibited by mAb to CD18 and was only partially inhibited (33%) in combination with anti-alpha4 mAb. The CD18- and VLA-4-independent migration across HSF was completely inhibited by mAb to alpha5 of VLA-5. The inhibitory effect of mAbs to VLA-4 and VLA-5 was on the monocyte and required blockade of CD11/CD18 to be observed. In contrast to HSF, no role for VLA-5 in monocyte transendothelial migration was detected. Both HSF and IL-1-stimulated HUVEC expressed vascular cell adhesion molecule-1 (VCAM-1). However, VLA-4-mediated monocyte migration across HSF was only partially dependent on VCAM-1, in contrast to transendothelial migration, which was completely blocked by anti-VCAM-1 mAbs. In conclusion, unlike transendothelial migration, for which VLA-4 is the alternative mechanism to CD11/CD18 on monocytes, both VLA-4 and VLA-5 can mediate monocyte migration through fibroblast barriers. In addition to VCAM-1, other ligand(s) on HSF are also involved in the VLA-4-mediated migration.
Historical Perspective of the Development of Thrombin Inhibitors (2002)

Progress in molecular biology has stimulated interest in the structure and function of thrombin. It has improved our understanding of its central role in thrombogenesis and has clarified the molecular events of inhibitor binding. This development has resulted in the production of recombinant hirudins and hirudin analogues. It has also allowed the molecular design of synthetic antithrombins, and encouraged the development of these products for clinical use. All pharmacological aspects speak in favor of the use of direct thrombin inhibitors as antithrombotic agents, especially in the potential indications where thrombin plays a crucial pathogenetic role. If their apparent advantages compared with heparin can be definitely demonstrated, the direct thrombin inhibitors may become the drug of choice for certain indications.
A Nonparametric Approach to Bottom-Up Visual Saliency (2007)

This paper addresses the bottom-up influence of local image information on human eye movements.Most existing computational models use a set of biologically plausible linear filters, e.g., Gabor or Difference-of-Gaussians filters as a front-end, the outputs of which are nonlinearly combined into a real number that indicates visual saliency.Unfortunately, this requires many design parameters such as the number, type, and size of the front-end filters, as well as the choice of nonlinearities, weighting and normalization schemes etc., for which biological plausibility cannot always be justified.As a result, these parameters have to be chosen in a more or less ad hoc way.Here, we propose to learn a visual saliency model directly from human eye movement data.The model is rather simplistic and essentially parameter-free, and therefore contrasts recent developments in the field that usually aim at higher prediction rates at the cost of additional parameters and increasing model complexity.Experimental results show that-despite the lack of any biological prior knowledge-our model performs comparably to existing approaches, and in fact learns image features that resemble findings from several previous studies.In particular, its maximally excitatory stimuli have center-surround structure, similar to receptive fields in the early human visual system.
Structure-function relationships of heparin species (1978)

We have fractionated porcine heparin species of low molecular weight, with an average specific anticoagulant activity of 96 units/mg by affinity chromotography. Highly active and relatively inactive preparations of similar size were obtained with specific anticoagulant activities of 360 and 4 units/mg, respectively. The highly active heparin fraction possesses 1.1 additional residues of glucuronic acid and 1.5 fewer residues of N-sulfated glucosamine per molecule compared to the relatively inactive species. This decrease in N-sulfated glucosamine appears to be secondary to a corresponding increase in N-acetylated glucosamine. This form also contains a tetrasaccharide sequence with a N-sulfated glucosamine at its reducing end as well as equivalent amounts of glucuronic acid and iduronic acid. Furthermore, the internal glucosamine residue of this sequence appears to be N-acetylated. Sufficient amounts of this tetrasaccharide sequence are present within the highly active preparation such that each molecule may be endowed with this structure. The relatively inactive product contains a significantly decreased quantity of this tetrasaccharide sequence such that only [unk]20% of these molecules may possess this structure. The mean distance between nonsulfated uronic acid residues of the highly active species is smaller than that separating similar residues of the relatively inactive product. In addition, a larger number of the nonsulfated uronic acid residues of the highly active material appears either to be present in a restricted region of the molecule separated only by glucosamine residues or to be located at penultimate positions within the polysaccharide chain.
Comparative Genomic Hybridization for Molecular Cytogenetic Analysis of Solid Tumors (1992)

Comparative genomic hybridization produces a map of DNA sequence copy number as a function of chromosomal location throughout the entire genome. Differentially labeled test DNA and normal reference DNA are hybridized simultaneously to normal chromosome spreads. The hybridization is detected with two different fluorochromes. Regions of gain or loss of DNA sequences, such as deletions, duplications, or amplifications, are seen as changes in the ratio of the intensities of the two fluorochromes along the target chromosomes. Analysis of tumor cell lines and primary bladder tumors identified 16 different regions of amplification, many in loci not previously known to be amplified.