gebhart/patrepeval huggingface dataset:
Policies: Giving Users Control over Calls. (2003)

Abstract. Features provide extensions to a basic service, but in new systems users require much greater flexibility oriented towards their needs. Traditional features do not easily allow for this. We propose policies as the features of the future. Policies can be defined by the end-user, and allow for the use of rich context information when controlling calls. This paper discusses an architecture to allow for policy definition and call control by policies and describes the operation of a system based on this architecture. One aspect is policy definition, the APPEL policy description language that serves this purpose. An important aspect of the architecture is integral feature interaction handling. It is in this last aspect that we foresee a role for agents, and hope that this paper will stimulate some collaboration between the two mostly distinct research areas of feature interaction and agent technologies. 1
Effective color correction via chromaticity adjustment and least square approximation (2013)

According to the observation that an image under the canonical light has a nearly neutral chromaticity distribution, an efficient three-step color correction approach is proposed: First, a preliminary color-corrected image is generated by linearly shifting the chromaticity distribution of an input image towards the neutral point. Then, a least square approximation formulation is presented to derive the illuminant color from the preliminary color-corrected image. Finally, based on the derived illuminant color and the Von Kries model, a refined color-corrected image can be obtained. From the experimental results on the widely-used SFU image dataset, the proposed approach could achieve comparable or even better performances against other well-known methods. In addition, several web images are examined to further demonstrate the effectiveness of our approach.
Modified Basis Pursuit Denoising(modified-BPDN) for noisy compressive sensing with partially known support (2010)

In this work, we study the problem of reconstructing a sparse signal from a limited number of linear `incoherent' noisy measurements, when a part of its support is known. The known part of the support may be available from prior knowledge or from the previous time instant (in applications requiring recursive reconstruction of a time sequence of sparse signals, e.g. dynamic MRI). We study a modification of Basis Pursuit Denoising (BPDN) and bound its reconstruction error. A key feature of our work is that the bounds that we obtain are computable. Hence, we are able to use Monte Carlo to study their average behavior as the size of the unknown support increases. We also demonstrate that when the unknown support size is small, modified-BPDN bounds are much tighter than those for BPDN, and hold under much weaker sufficient conditions (require fewer measurements).
Protecting the beneficial functionality of lipoproteins by 1-Fe, a corrole-based catalytic antioxidant (2010)

Functionally defective HDL emerges as a main risk factor in cardiovascular diseases, on top of imbalanced serum lipoprotein ratios. We now show that 1-Fe, an iron(III) corrole catalytic antioxidant, spontaneously forms tightly-bound conjugates with LDL (secondarily) and HDL (primarily) of human serum. This is demonstrated by HPLC separation of serum/1-Fe mixtures and analysis of the corrole-containing fractions by UV-vis and circular dichroism spectroscopy. The LDL/1-Fe and HDL/1-Fe conjugates are resistant to functionality damaging events induced by oxidizing (copper salts) and nitrating species (peroxynitrite), as realized by heavily reduced formation of conjugated dienes, hydroperoxides, aldehydes, and nitrotyrosine. What is more, even already oxidized LDL becomes less atherogenic upon conjugation. Treatment with 1-Fe preserves the cardioprotective properties of HDL (cholesterol efflux, reduction of intracellular oxidative-stress, and inhibition of apoptosis), which are otherwise damaged under conditions of oxidative-stress. The novelty of 1-Fe relies in the unique bipolarity of the corrole macrocycle (responsible for its general affinity for lipoproteins), the affinity of the corrole-chelated iron(III) center to two histidine residues from (a particular subclass of) HDL-associated proteins, and the excellent catalytic activity regarding the decomposition of the most toxic naturally-occurring species/molecules.
Photosensitivity and Imaging Characteristics of Ion-Implanted PLZT Ceramics (1985)

We reported in previous papers that both the near-UV and the visible photosensitivities of ferroelectric-phase PLZT (lead lanthanum zirconate titanate) ceramics are increased by as much as four orders of magnitude by ion implantation or a combination of thermal diffusion of Al and ion implantation. New results are presented here on high-energy (1 MeV) implants of Al and Ni and coimplants of Al+Ne and Ni+Ne, and these results are compared with earlier 500 keV implants of Al and Cr and coimplants of Al+Ne and Cr+Ne as surface modification techniques for increasing the visible photosensitivity of PLZT. The important role of grain size in determining optimum contrast and resolution of stored optical information is described in terms of new experimental results.
Reply (1995)

Clinical Pharmacology & Therapeutics (1995) 57, 95–97; doi:
Novel Formulations for Non-Invasive Delivery and Stabilization of Peptides (2013)

We extend to you a warm and sunny Aloha in celebration of the 23 rd American Peptide Symposium and the 6 th International Symposium. The meeting theme, Peptides Across the Pacific, embraced the spirit of the scientific and social program. Peptides Across the Pacific encompassed the important role that peptide science currently plays in so many disciplines and explored the potential impact peptides can make in scientific fields that have yet to realize the utility of these wonderful molecules.
Combining MDL transliteration training with discriminative modeling (2009)

We present a transliteration system that introduces minimum description length training for transliteration and combines it with discriminative modeling. We apply the proposed approach to transliteration from English to 8 non-Latin scripts, with promising results.
The Unsatisfactory ThinPrep Pap Test (2002)

Cervical cytology specimens classified as "unsatisfactory for interpretation" represent a potential source of undetected disease. This prospective study analyzed the potential benefits of a laboratory procedure to reprocess unsatisfactory ThinPrep Pap Tests (Cytyc, Boxborough, MA). All unsatisfactory ThinPrep samples were reprocessed using a glacial acetic acid wash. The study period unsatisfactory rate was compared with that for the previous 12 months. The initial unsatisfactory rate was 1.3% (197/15,154). Of the unsatisfactory ThinPrep samples, 55.8% (110/197) had residual material for reprocessing. After reprocessing, 67.3% (74/110) were reclassified as "satisfactory" or "satisfactory but limited by," and the final unsatisfactory rate was 0.8% (123/15,154), a 62% decrease. Compared with the previous 12-month rate of 0.9% (209/23,730), this was a 12% reduction. Seven (6.4%) of 110 initially classified as unsatisfactory contained an epithelial abnormality (atypical squamous cells of undetermined significance, 3; atypical glandular cells of undetermined significance, 2; low-grade squamous intraepithelial lesion, 1; squamous cell carcinoma, 1) on the reprocessed slide. Reprocessing of unsatisfactory ThinPrep slides yielded additional cellular abnormalities that otherwise would have been undetected. The present study confirms that reprocessing of unsatisfactory ThinPrep slides is a beneficial laboratory procedure.
Processor sharing for cooperative multi-task applications (1992)

by Karen Marie Tracey A processor sharing system allows busy users in a networked environment to take advantage of the processing power of idle machines. Experimental systems have demonstrated the usefulness of the concept, but processor sharing has yet to achieve widespread acceptance. Simplistic sharing policies and programming difficulty are two factors that combine to limit the use and acceptance of processor sharing. Group management, a new approach to processor sharing presented here, addresses these problems. Group management is designed to support processor sharing applications that consist of multiple cooperating tasks. This new approach provides a framework for the development of sophisticated sharing policies that can support a variety of applications with differing execution characteristics. In addition, it provides services to programmers that ease the task of writing programs for, and running programs in, a processor sharing environment. This dissertation introduces group...
The interaction between C5a and sphingosine-1-phosphate in neutrophils for antineutrophil cytoplasmic antibody mediated activation (2014)

S1P triggered by C5a-primed neutrophils could further activate neutrophils. Blocking S1P could attenuate C5a-induced activation of neutrophils by ANCA. The interaction between S1P and C5a plays an important role in neutrophils for ANCA-mediated activation.
Room-temperature manipulation and decoherence of a single spin in diamond (2006)

We report on room-temperature coherent manipulation of the spin of a single nitrogen-vacancy center in diamond and a study of its coherence as a function of magnetic field. We use magnetic resonance to induce Rabi nutations and apply a Hahn spin echo to remove the effect of low-frequency dephasing. A sharp rise in the decoherence rate is observed at magnetic fields where the nitrogen-vacancy center spin couples resonantly to substitutional nitrogen spins via the magnetic dipolar coupling. Finally, we find evidence that away from these energy resonances spin flips of nitrogen electrons are the main source of decoherence.
Cellular distribution of neurotensin receptors in rat brain: Immunohistochemical study using an antipeptide antibody against the cloned high affinity receptor (1996)

Receptors for the neuropeptide, neurotensin, were localized by immunohistochemistry in the rat brain by using an antibody raised against a sequence of the third intracellular loop of the cloned high affinity receptor. Selective receptor immunostaining was observed throughout the brain and brainstem. This immunostaining was totally prevented by preadsorbing the antibody with the immunogenic peptide. The regional distribution of the immunoreactivity conformed for the most part to that of [3H]- or [125I]-neurotensin binding sites previously identified by autoradiography. Thus, the highest levels of immunostaining were observed in the islands of Calleja, diagonal band of Broca, magnocellular preoptic nucleus, pre- and parasubiculum, suprachiasmatic nucleus, anterodorsal nucleus of the thalamus, substantia nigra, ventral tegmental area, pontine nuclei and dorsal motor nucleus of the vagus, all of which had previously been documented to contain high densities of neurotensin binding sites. There were, however, a number of regions reportedly endowed with neurotensin binding sites, including the central amygdaloid nucleus, periaqueductal gray, outer layer of the superior colliculus and dorsal tegmental nucleus, which showed no or divergent patterns of immunostaining, suggesting that they might be expressing a molecularly distinct form of the receptor. At the cellular level, neurotensin receptor immunoreactivity was predominantly associated with perikarya and dendrites in some regions (e.g., in the basal forebrain, ventral midbrain, pons and rostral medulla) and with axons and axon terminals in others (e.g., in the lateral septum, bed nucleus of the stria terminalis, neostriatum, paraventricular nucleus of the thalamus and nucleus of the solitary tract). These data indicate that neurotensin may act both post- and presynaptically in the central nervous system and confirm that some of its effects are exerted on projection neurons. There were also areas, such as the cerebral cortex, nucleus accumbens and para- and periventricular nucleus of the hypothalamus, which contained both immunoreactive perikarya/dendrites and axon terminals, consistent with either a joint association of the receptor with afferent and efferent elements or its presence on interneurons. Taken together, these results also suggest that the neurotensin high affinity receptor protein is associated with a neuronal population that is more extensive than originally surmised from in situ hybridization studies.
Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth (2015)

H3K9 methylation directs heterochromatin formation by recruiting multiple heterochromatin protein 1 (HP1)-containing complexes that deacetylate histones and methylate cytosine bases in DNA. In Neurospora crassa, a single H3K9 methyltransferase complex, called the DIM-5,-7,-9, CUL4, DDB1 Complex (DCDC), is required for normal growth and development. DCDC-deficient mutants are hypersensitive to the genotoxic agent methyl methanesulfonate (MMS), but the molecular basis of genotoxic stress is unclear. We found that both the MMS sensitivity and growth phenotypes of DCDC-deficient strains are suppressed by mutation of embryonic ectoderm development or Su-(var)3-9; E(z); Trithorax (set)-7, encoding components of the H3K27 methyltransferase Polycomb repressive complex-2 (PRC2). Trimethylated histone H3K27 (H3K27me3) undergoes genome-wide redistribution to constitutive heterochromatin in DCDC- or HP1-deficient mutants, and introduction of an H3K27 missense mutation is sufficient to rescue phenotypes of DCDC-deficient strains. Accumulation of H3K27me3 in heterochromatin does not compensate for silencing; rather, strains deficient for both DCDC and PRC2 exhibit synthetic sensitivity to the topoisomerase I inhibitor Camptothecin and accumulate γH2A at heterochromatin. Together, these data suggest that PRC2 modulates the response to genotoxic stress.
Comparative Transcriptome Analysis of Four Prymnesiophyte Algae (2014)

Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG) database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists.
Compression of Dense and Regular Point Clouds (2006)

Abstract We present a simple technique for single‐rate compression of point clouds sampled from a surface, based on a spanning tree of the points. Unlike previous methods, we predict future vertices using both a linear predictor, which uses the previous edge as a predictor for the current edge, and lateral predictors that rotate the previous edge 90° left or right about an estimated normal . By careful construction of the spanning tree and choice of prediction rules, our method improves upon existing compression rates when applied to regularly sampled point sets, such as those produced by laser range scanning or uniform tesselation of higher‐order surfaces. For less regular sets of points, the compression rate is still generally within 1.5 bits per point of other compression algorithms .
Chlorhexidine Preserves Dentin Bond <i>in vitro</i> (2007)

Loss of hybrid layer integrity compromises resin-dentin bond stability. Matrix metalloproteinases (MMPs) may be partially responsible for hybrid layer degradation. Since chlorhexidine inhibits MMPs, we hypothesized that chlorhexidine would decelerate the loss of resin-dentin bonds. Class I preparations in extracted third molars were sectioned into two halves. One half was customarily restored (etch-and-rinse adhesive/resin composite), and the other was treated with 2% chlorhexidine after being acid-etched before restoration. Specimens were stored in artificial saliva with/without protease inhibitors. Microtensile bond strengths and failure mode distribution under SEM were analyzed immediately after specimens' preparation and 6 months later. With chlorhexidine, significantly better preservation of bond strength was observed after 6 months; protease inhibitors in the storage medium had no effect. Failure analysis showed significantly less failure in the hybrid layer with chlorhexidine, compared with controls after 6 months. In conclusion, this in vitro study suggests that chlorhexidine might be useful for the preservation of dentin bond strength.
COUNCIL ROLL (2012)

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Redox Regulation of Cell Growth and Cell Death (2003)

Oxidative stress evokes various cellular events, including activation of transcription factors, apoptosis, and cell cycle arrest. Accumulating evidence shows that reduction/oxidation (redox) plays an important role in the regulation of apoptosis and cell cycle arrest elicited by oxidative stress. Cellular redox is controlled by the thioredoxin (TRX) and glutathione (GSH) systems. TRX and GSH systems regulate cell growth and cell death by the activation of transcription factors, the sensitivity of cells to cytokines and growth factors, and the components of the apoptosis pathways. This brief review describes the current knowledge on the redox regulation of cell growth and apoptosis.
Structure-Function Studies of Two Novel UDP-GlcNAc C6 Dehydratases/C4 Reductases (2002)

Two subfamilies of UDP-GlcNAc C6 dehydratases were recently identified. FlaA1, a short soluble protein that exhibits a typical SYK catalytic triad, characterizes one of these subfamilies, and WbpM, a large membrane protein that harbors an altered SMK triad that was not predicted to sustain activity, represents the other subfamily. This study focuses on investigating the structure and function of these C6 dehydratases and the role of the altered triad as well as additional amino acid residues involved in catalysis. The significant activity retained by the FlaA1 Y141M triad mutant and the low activity of the WbpM M438Y mutant indicated that the methionine residue was involved in catalysis. A Glu(589) residue, which is conserved only within the large homologues, was shown to be essential for activity in WbpM. Introduction of this residue in FlaA1 enhanced the activity of the corresponding V266E mutant. Hence, this glutamate residue might be responsible for the retention of catalytic efficiency in the large homologues despite alteration of their catalytic triad. Mutations of residues specific for the short homologues (Asp(70), Asp(149)-Lys(150), Cys(103)) abolished the activity of FlaA1. Among them, C103M prevented dimerization but did not significantly affect the secondary structure. The fact that we could identify subfamily-specific residues that are essential for catalysis suggested an independent evolution for each subfamily of C6 dehydratases. Finally, the loss of activity of the FlaA1 G20A mutant provided evidence that a cofactor is involved in catalysis, and kinetic study of the FlaA1 H86A mutant revealed that this conserved histidine is involved in substrate binding. None of the mutations investigated altered the substrate, product, and function specificity of these enzymes.
Deafferentation of the septo‐hippocampal pathway in rats as a model of the metabolic events in Alzheimer's disease (2001)

Changes in the metabolic activity within the brain of patients suffering from Alzheimer's disease (AD) were investigated and compared with biochemical alterations in the hippocampus induced by fimbria/fornix transection in the rat. The deafferentation of the hippocampus results in a degeneration of cholinergic septo-hippocampal terminals accompanied by a persistent decrease of choline acetyltransferase (ChAT) and acetylcholine esterase (AChE) activities similar to the cholinergic malfunction in AD. In the animal model the [3H]-cytochalasin B binding to the glucose transporters was elevated up to the day 7 after surgery as was the activity of the phosphofructokinase (PFK) on day 3. A reactive astrogliosis could be evidenced by the upregulation of glial fibrillary acidic protein (GFAP). An increase of the PFK activity was also found in AD being accompanied by enhanced level of GFAP as well. A higher concentration of mRNA for all three isoenzymes of PFK was shown by reverse transcription (RT)-real time polymerase chain reaction (PCR) amplification. However, the pattern of PFK isoenzyme proteins and mRNAs did neither change in diseased human nor in the lesioned rat brain. The activities of the mitochondrial enzymes pyruvate dehydrogenase complex (PDHC) and cytochrome c oxidase (CO) were diminished in the lesioned rat hippocampus on day 7 as well as in AD brain. Subcellular fractionation showed that the activity of these enzymes was affected in the synaptosomal as well as in the extrasynaptosomal mitochondria indicating a loss of neuronal input and also a vulnerability of intrinsic hippocampal neurons and/or non-neuronal cells. The recovery of the mitochondrial enzyme activity in the animal model at later post lesion intervals may be the result of compensatory responses of surviving cells or of sprouting of other non-affected inputs. It is concluded that common metabolic mechanisms may underlie the concurrent degenerative and repair processes in the denervated hippocampus and the diseased Alzheimer brain.
Cation exchange chromatography provides effective retrovirus clearance for antibody purification processes (2011)

Abstract One measure taken to ensure safety of biotherapeutics produced in mammalian cells is to demonstrate the clearance of potential viral contaminants by downstream purification processes. This paper provides evidence that cation exchange chromatography (CEX), a widely used polishing step for monoclonal antibody (mAb) production, can effectively and reproducibly remove xMuLV, a retrovirus used as a model of non‐infectious retrovirus‐like particles found in Chinese hamster ovary cells. The dominant mechanism for xMuLV clearance by the strong cation exchanger, Fractogel SO , is by retention of the virus via adsorption instead of inactivation. Experimental data defining the design space for effective xMuLV removal by Fractogel SO with respect to operational pH, elution ionic strength, loading, and load/equilibration buffer ionic strength are provided. Additionally, xMuLV is able to bind to other CEX resins, such as Fractogel COO − and SP Sepharose Fast Flow, suggesting that this phenomenon is not restricted to one type of CEX resin. Taken together, the data indicate that CEX chromatography can be a robust and reproducible removal step for the model retrovirus xMuLV. Biotechnol. Bioeng. 2012;109: 157–165. © 2011 Wiley Periodicals, Inc.