gebhart/patrepeval huggingface dataset:
Lamb-wave delay lines with interdigital electrodes (1973)

Propagation characteristics and the equivalent circuit model of delay lines using Lamb waves excited by interdigital transducers on unpolarized PZT ceramic plates have been studied. Dispersive characteristics of phase velocities of Lamb waves excited by the interdigital transducers are in good agreement with the numerical solution from the dispersive equation of phase velocities developed by Worlton. When the product of frequency times plate thickness is below 1.3×106 Hz mm, the zeroth symmetric Lamb wave is strongly excited. The Lamb waves are excited most effectively when the half-period of interdigital electrode is equal to the wavelength of the Lamb wave. Also, the values of the attenuation coefficient and the reflection coefficient from the edge of the specimen are given. It is shown that the generation of symmetrical-mode Lamb waves by our transducer is equivalently represented by a thickness mode transducer of half-wavelength inserted perpendicular to the plate.
A New Covariance Estimate for Bayesian Classifiers in Biometric Recognition (2004)

In many biometric pattern-recognition problems, the number of training examples per class is limited, and consequently the sample group covariance matrices often used in parametric and nonparametric Bayesian classifiers are poorly estimated or singular. Thus, a considerable amount of effort has been devoted to the design of other covariance estimators, for use in limited-sample and high-dimensional classification problems. In this paper, a new covariance estimate, called the maximum entropy covariance selection (MECS) method, is proposed. It is based on combining covariance matrices under the principle of maximum uncertainty. In order to evaluate the MECS effectiveness in biometric problems, experiments on face, facial expression, and fingerprint classification were carried out and compared with popular covariance estimates, including the regularized discriminant analysis and leave-one-out covariance for the parametric classifier, and the Van Ness and Toeplitz covariance estimates for the nonparametric classifier. The results show that, in image recognition applications whenever the sample group covariance matrices are poorly estimated or ill posed, the MECS method is faster and usually more accurate than the aforementioned approaches in both parametric and nonparametric Bayesian classifiers.
Modulation of the effects of alveolar macrophages on lung fibroblast collagen production rate. (1987)

Alveolar macrophages (AM) may function as effector cells that can either stimulate or inhibit lung fibroblast collagen production. However, conditions that determine the predominant effect of AM on fibroblasts are not well understood. To delineate factors that modulate the effects of AM on lung fibroblasts, we studied the interaction of AM products and fibroblasts in vitro. The AM were obtained by bronchoalveolar lavage of hamsters with bleomycin-induced pulmonary fibrosis. Conditioned medium (CM) from the AM cultures was incubated in varying amounts with lung fibroblast (IMR-90) cultures. After metabolic labeling with [3H]proline, fibroblast collagen production based on procollagen-specific radioactivity was determined (Anal Biochem 1984; 140:478). Macrophage CM in concentrations greater than 5% suppressed collagen production, an event attributed to the macrophage-derived suppressive factor that we have previously characterized (J Clin Invest 1983; 72:2082). Macrophages were also determined to produce PGE2 in culture (500 pg/10(6) cells). Authentic PGE2 at concentrations found in CM was found to suppress fibroblast collagen production, indicating that AM-derived PGE2 contributes to the suppressive activity in CM. To examine possible stimulatory factors in CM, the fibroblasts were preincubated with indomethacin. This approach was based on our previous observation that AM-derived suppressive factor increases endogenous fibroblast PGE2 and that its activity can be blocked by indomethacin. Macrophage CM in a concentration of 20% did not suppress the collagen production of indomethacin-treated fibroblasts. However, CM concentrations of 5 and 10% increased collagen production (173 and 143% of control values, respectively), indicating the presence of stimulatory factor(s) in macrophage-conditioned medium.(ABSTRACT TRUNCATED AT 250 WORDS)
Structural requirements of bitter taste receptor activation (2010)

An important question in taste research is how 25 receptors of the human TAS2R family detect thousands of structurally diverse compounds. An answer to this question may arise from the observation that TAS2Rs in general are broadly tuned to interact with numerous substances. Ultimately, interaction with chemically diverse agonists requires architectures of binding pockets tailored to combine flexibility with selectivity. The present study determines the structure of hTAS2R binding pockets. We focused on a subfamily of closely related hTAS2Rs exhibiting pronounced amino acid sequence identities but unique agonist activation spectra. The generation of chimeric and mutant receptors followed by calcium imaging analyses identified receptor regions and amino acid residues critical for activation of hTAS2R46, -R43, and -R31. We found that the carboxyl-terminal regions of the investigated receptors are crucial for agonist selectivity. Intriguingly, exchanging two residues located in transmembrane domain seven between hTAS2R46, activated by strychnine, and hTAS2R31, activated by aristolochic acid, was sufficient to invert agonist selectivity. Further mutagenesis revealed additional positions involved in agonist interaction. The transfer of functionally relevant amino acids identified in hTAS2R46 to the corresponding positions of hTAS2R43 and -R31 resulted in pharmacological properties indistinguishable from the parental hTAS2R46. In silico modeling of hTAS2R46 allowed us to visualize the putative mode of interaction between agonists and hTAS2Rs. Detailed structure-function analyses of hTAS2Rs may ultimately pave the way for the development of specific antagonists urgently needed for more sophisticated analyses of human bitter taste perception.
Coefficients of combining concept classes in a collection (1988)

This report considers combining information to improve retrieval. The vector space model has been extended so different classes of data are associated with distinct concept types and their respective subvectors. Two collections with multiple concept types are described, ISI-1460 and CACM-3204. Experiments indicate that regression methods can help predict relevance, given query-document similarity values for each concept type. After sampling and transformation of data, the coefficient of determination for the best model was .48 (.66) for ISI (CACM). Average precision for the two collections was 11% (31%) better for probabilistic feedback with all types versus with terms only. These findings may be of particular interest to designers of document retrieval or hypertext systems since the role of links is shown to be especially beneficial.
Addition of Difluorocarbene to 4‘,5‘-Unsaturated Nucleosides:  Synthesis and Deoxygenation Reactions of Difluorospirocyclopropane Nucleosides1 (2006)

Synthetic routes to 4'-(2,2-difluorospirocyclopropane) analogues of adenosine, cytidine, and uridine are described. Treatment of 2',3'-O-isopropylidene-4',5'-unsaturated compounds derived from adenosine and uridine with difluorocarbene (generated from PhHgCF3 and NaI) gave diastereomeric mixtures of the 2,2-difluorospirocyclopropane adducts. Stereoselectivity resulting from hindrance by the isopropylidene group favored addition at the beta face. Removal of base and sugar protecting groups gave new difluorospirocyclopropane nucleoside analogues. The protected uridine analogue was converted into its cytidine counterpart via a 4-(1,2,4-triazol-1-yl) intermediate. Stannyl radical-mediated deoxygenation of the 3'-O-TBS-2'-thionocarbamate derivatives gave the 2'-deoxy products of direct hydrogen transfer. In contrast, identical treatment of the 2'-O-TBS-3'-thionocarbamate isomers resulted in opening of the vicinal difluorocyclopropane ring upon generation of a C3' radical followed by homoallylic hydrogen transfer to give 4'-(1,1-difluoroethyl)-3',4'-unsaturated nucleoside derivatives. Structural aspects and biological effect considerations are discussed.
Downregulation of Cu/Zn superoxide dismutase leads to cell death via the nitric oxide-peroxynitrite pathway (1996)

We previously showed that the downregulation of Cu/Zn superoxide dismutase (SOD1) activity in PC12 cells by exposure to an appropriate antisense oligonucleotide causes their apoptotic death. In this report, we used this model to examine the pathways by which SOD1 downregulation leads to death and to compare these pathways with those responsible for death caused by withdrawal of trophic support. To improve delivery of the SOD1 antisense oligonucleotide, we coupled it to a carrier "vector" peptide homologous to the third helix of the Drosophila Antennapedia homeodomain. This caused not only efficient cellular uptake even in the presence of serum, but also inhibition of SOD1 activity and promotion of apoptosis at 100-fold lower concentrations of oligonucleotide. Death induced by SOD1 downregulation appeared to require the reaction of superoxide with nitric oxide (NO) to form peroxynitrite. In support of this, inhibitors of NO synthase, the enzyme responsible for NO synthesis, blocked death in our experiments, whereas NO generators and donors accelerated cell death. N-Acetylcysteine and chlorophenylthiol cAMP, which rescue PC12 cells and neurons from the withdrawal of nerve growth factor and other forms of trophic support, did not protect PC12 cells from SOD1 downregulation. In contrast, overexpression of bcl-2, which also rescues these cells form loss of trophic support, was equally effective in saving the cells in the SOD1 downregulation paradigm. Taken together with past findings, such observations suggest that SOD1 downregulation and withdrawal of trophic support trigger apoptosis via distinct initial mechanisms but may utilize a common final pathway to bring about death. Our findings may be relevant to the causes and potential amelioration of neuronal degenerative disorders caused by impaired regulation of cellular levels of NO and superoxide.
Programmable dispersion compensation and pulse shaping in a 26-fs chirped-pulse amplifier (1998)

We have constructed a 26-fs chirped-pulse amplifier that incorporates a programmable liquid-crystal spatial light modulator in the pulse stretcher. The modulator serves a dual purpose. First, we apply frequency-dependent phase shifts to compensate for cubic, quartic, and nonlinear phase dispersion in the amplifier, which results in a reduction in pulse duration from 32 to 26 fs, in agreement with the transform limit of the amplified pulse spectrum. Second, we are able to produce high-fidelity compressed amplified shaped pulses by applying phase masks directly within the stretcher. Shaped pulse energies of greater than 1 mJ are routinely obtained.
Collagen-binding integrin α1β1 regulates intestinal inflammation in experimental colitis (2002)

Central to inflammatory responses are the integrin-mediated adhesive interactions of cells with their ECM-rich environment. We investigated the role of the collagen-binding integrin 1 1 in intestinal inflammation using the mouse model of colitis induced by dextran sodium sulfate (DSS). mAb's directed against murine 1 were found to significantly attenuate inflammation and injury in DSS-treated wild-type mice; similar protection was seen in mice deficient for 1 1 integrin. Blockade or loss of 1 1 was also associated with decreased mucosal inflammatory cell infiltrate and cytokine production. Importantly, we demonstrated that development and 1 -mediated inhibition of DSS-induced colitis occurred independently of lymphocytes (Rag-2 -/-mice), and identified the monocyte as a key 1 1 -expressing cell type involved in the development of colitis in this model. In response to DSS, both 1 deficiency and anti- 1 mAb treatment significantly reduced monocyte accumulation and activation within the lamina propria. In summary, the data demonstrate that engagement of leukocyte-associated 1 1 receptors with ECM plays a pivotal role in mediating intestinal inflammation via promotion of monocyte movement and/or activation within the inflamed interstitium. Therapeutic strategies designed to disrupt such interactions may prove beneficial in treating intestinal inflammation.
Synergy in Efficacy of Fungal Entomopathogens and Permethrin against West African Insecticide-Resistant Anopheles gambiae Mosquitoes (2010)

Combining fungi and permethrin induced a higher impact on mosquito survival than the use of these control agents alone. The observed synergism in efficacy shows the potential for integrated fungus-insecticide control measures to dramatically reduce malaria transmission and enable control at more moderate levels of coverage even in areas where insecticide resistance has rendered pyrethroids essentially ineffective.
NKG2D function protects the host from tumor initiation (2005)

The activation NKG2D receptor has been shown to play an important role in the control of experimental tumor growth and metastases expressing ligands for NKG2D; however, a function for this recognition pathway in host protection from de novo tumorigenesis has never been demonstrated. We show that neutralization of NKG2D enhances the sensitivity of wild-type (WT) C57BL/6 and BALB/c mice to methylcholanthrene (MCA)-induced fibrosarcoma. The importance of the NKG2D pathway was additionally illustrated in mice deficient for either IFN-gamma or tumor necrosis factor-related apoptosis-inducing ligand, whereas mice depleted of natural killer cells, T cells, or deficient for perforin did not display any detectable NKG2D phenotype. Furthermore, IL-12 therapy preventing MCA-induced sarcoma formation was also largely dependent on the NKG2D pathway. Although NKG2D ligand expression was variable or absent on sarcomas emerging in WT mice, sarcomas derived from perforin-deficient mice were Rae-1(+) and immunogenic when transferred into WT syngeneic mice. These findings suggest an important early role for the NKG2D in controlling and shaping tumor formation.
Identification of a new JNK inhibitor targeting the JNK-JIP interaction site (2008)

JNK is a stress-activated protein kinase that modulates pathways implicated in a variety of disease states. JNK-interacting protein-1 (JIP1) is a scaffolding protein that enhances JNK signaling by creating a proximity effect between JNK and upstream kinases. A minimal peptide region derived from JIP1 is able to inhibit JNK activity both in vitro and in cell. We report here a series of small molecules JIP1 mimics that function as substrate competitive inhibitors of JNK. One such compound, BI-78D3, dose-dependently inhibits the phosphorylation of JNK substrates both in vitro and in cell. In animal studies, BI-78D3 not only blocks JNK dependent Con A-induced liver damage but also restores insulin sensitivity in mouse models of type 2 diabetes. Our findings open the way for the development of protein kinase inhibitors targeting substrate specific docking sites, rather than the highly conserved ATP binding sites. In view of its favorable inhibition profile, selectivity, and ability to function in the cellular milieu and in vivo, BI-78D3 represents not only a JNK inhibitor, but also a promising stepping stone toward the development of an innovative class of therapeutics.
Molecular characterization and protein analysis of the cap region, which is essential for encapsulation in Bacillus anthracis (1989)

By using genetic complementation tests with various in vitro-constructed mutants with mutations in the cap region (which is essential for encapsulation in Bacillus anthracis), we identified three cistrons, capB, capC, and capA, in this order of arrangement. Minicell analysis revealed that these cistrons produce proteins of 44, 16, and 46 kilodaltons, respectively. The complete nucleotide sequence of 3,244 base pairs covering the whole cap region was determined and revealed the existence of the three open reading frames of capB (397 amino acid residues; molecular weight, 44,872), capC (149 amino acid residues; molecular weight, 16,522), and capA (411 amino acid residues; molecular weight, 46,420) arranged in the order predicted by complementation tests. These three cistrons were all transcribed in the same direction from promoters unique to each cistron. Judging from the predicted amino acid sequence of the three proteins and from their localization and their sensitivity to various physicochemical treatments, they appeared to be membrane-associated enzymes mediating the polymerization of D-glutamic acid via the membrane. Capsular peptides immunologically identical to that of B. anthracis were found in B. subtilis, B. megaterium, and B. licheniformis, but no sequence homologous to the cap region was found in any of these bacilli other than B. anthracis. Using strains of B. anthracis with or without insertional inactivation of the cap region, we found that the capsule of B. anthracis conferred strong resistance to phagocytosis upon the bacterial host.
Construction and Characterization of an agr Deletion Mutant of Staphylococcus epidermidis (2000)

The physiological significance of the accessory gene regulator (agr) system of Staphylococcus epidermidis was investigated by construction of an agr deletion mutant via allelic replacement with a spectinomycin resistance cassette. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis showed that the protein pattern was strongly altered in the mutant; the amounts of most surface proteins were higher, whereas the amounts of most exoproteins were lower. The agr system of S. epidermidis thus appears to have an important impact on growth phase-dependent protein synthesis as has been shown for Staphylococcus aureus. The activity of the exoenzymes lipase and protease, assumed to be involved in staphylococcal pathogenicity, was investigated by agar diffusion assays and SDS-PAGE activity staining. A general reduction of these enzyme activities in the agr mutant was found. The difference in overall lipase activity was small, but zymographic analysis suggested a clear defect in lipase processing in the agr mutant.
Acid production in glycolysis-impaired tumors provides new insights into tumor metabolism. (2002)

These results are consistent with the paradigm that tumor metabolism is determined mainly by substrate availability and not by the metabolic demand of tumor cells per se. In particular, it appears that the local glucose and oxygen availabilities each independently affect tumor acidity. These findings have significant implications for cancer treatment.
Acid Mucopolysaccharides in the Liver of Pekin Duck with Amyloidosis (1969)

Studies on the liver involved with increasing amounts of amyloidosis and control tissues indicate that there is a marked increase in MPS content with severe amyloid infiltration. The increase of MPS was accounted for by increases in heparitin sulfate, chondroitin sulfate B, and somewhat less of chondroitin sulfates A and C. The consistent increase of heparitin sulfate in the liver of the ducks was similar to that observed in amyloidosis in humans and in experimentally induced disease. This remarkable increase of chondroitin sulfate B suggests a link to other vascular diseases and genetic connective tissue defects. The Pekin duck serves as an interesting model to study spontaneously occurring amyloidosis.
Altered expression of beta-adrenergic receptor kinase and beta 1-adrenergic receptors in the failing human heart. (1993)

In addition to other alterations found in failing hearts, the diminished response to beta-receptor agonists appears to involve the combined effects of enhanced expression of beta ARK and reduced expression of beta 1-receptors.
Protein and messenger RNA expression of connexin43 in astrocytomas: implications in brain tumor gene therapy (1996)

The expression of connexin43, the primary gap-junction constituent of glial cells, was evaluated at the messenger RNA and protein levels in different grades of astrocytoma to investigate the relevance of gap junctions in herpes simplex virus-thymidine kinase (HSV-tk)-mediated gene therapy of brain tumors. Transduction of the retroviral-mediated HSV-tk gene into tumor cells with subsequent administration of ganciclovir has recently been used as an experimental therapeutic strategy for treatment of brain tumors. One aspect of this approach is the bystander effect, which augments the efficacy of this therapeutic approach. Glioblastoma cells with minimum levels of connexin43 protein were transfected with a connexin43 complementary DNA. These cells manifested a marked increase in the in vitro bystander effect, supporting the contention that the in vitro bystander effect is a consequence of metabolic cooperation between cells mediated by gap junctions. To assess relative levels of gap-junction protein expression in the relevant tumor type, we examined primary astrocytomas, primary astrocytoma cell cultures, and glioblastoma cell lines. Although most astrocytoma tumor samples expressed connexin43, they differed in the level of expression, with the greatest variation exhibited in high-grade astrocytomas. Primary glioblastoma cell cultures and established glioblastoma cell lines also displayed some variability in connexin43 levels. In aggregate, our results anticipate that glioblastomas will have a varied bystander effect during HSV-tk gene therapy depending on the level of connexin43 expression.
HPatches: A Benchmark and Evaluation of Handcrafted and Learned Local Descriptors (2017)

In this paper, a novel benchmark is introduced for evaluating local image descriptors. We demonstrate limitations of the commonly used datasets and evaluation protocols, that lead to ambiguities and contradictory results in the literature. Furthermore, these benchmarks are nearly saturated due to the recent improvements in local descriptors obtained by learning from large annotated datasets. To address these issues, we introduce a new large dataset suitable for training and testing modern descriptors, together with strictly defined evaluation protocols in several tasks such as matching, retrieval and verification. This allows for more realistic, thus more reliable comparisons in different application scenarios. We evaluate the performance of several state-of-the-art descriptors and analyse their properties. We show that a simple normalisation of traditional hand-crafted descriptors is able to boost their performance to the level of deep learning based descriptors once realistic benchmarks are considered. Additionally we specify a protocol for learning and evaluating using cross validation. We show that when training state-of-the-art descriptors on this dataset, the traditional verification task is almost entirely saturated.
Growth of Core–Shell InP Nanowires for Photovoltaic Application by Selective-Area Metal Organic Vapor Phase Epitaxy (2009)

We report on the formation of core–shell pn junction InP nanowires using a catalyst-free selective-area metalorganic vapor-phase epitaxy (SA-MOVPE) method. A periodically aligned dense core–shell InP nanowire array was fabricated and used in photovoltaic device applications. The device exhibited open-circuit voltage (VOC), short-circuit current (ISC) and fill factor (FF) levels of 0.43 V, 13.72 mA/cm2 and 0.57, respectively, which indicated a solar power conversion efficiency of 3.37% under AM1.5G illumination. This study demonstrates that high quality core–shell structure nanowire fabrication is possible by SA-MOVPE and that the nanowire arrays can be used in integrated nanowire photovoltaic devices.