gebhart/patrepeval huggingface dataset:
Generic image classification using visual knowledge on the web (2003)

In this paper, we describe a generic image classification system with an automatic knowledge acquisition mechanism from the World-Wide Web. Due to the recent spread of digital imaging devices, the demand for image recognition of various kinds of real world scenes becomes greater. For realizing it, visual knowledge on various kinds of scenes is required. Then, we propose gathering visual knowledge on real world scenes for generic image classification from the World-Wide Web. Our system gathers a large number of images from the Web automatically and makes use of them as training images for generic image classification. It consists of three modules, which are an image-gathering module, an image-learning module and an image classification module. The image-gathering module gathers images related to given class keywords from the Web automatically. The learning module extracts image features from gathered images and associates them with each class. The image classification module classifies an unknown image into one of the classes corresponding to the class keywords by using the association between image features and classes. In the experiments, we achieved a classification rate 44.6% for generic images by using images gathered from the World-Wide Web automatically as training images.
Rough metal and dielectric layers make an even better hyperbolic metamaterial absorber (2014)

We numerically investigate the influence of roughness in layer thicknesses on the properties of hyperbolic metamaterials (HMMs). We show that random spatial variation of dielectric and metal layer thicknesses, similar to what occurs during actual structure fabrication, leads to dramatic absorption increase compared to an ideal, smooth-layer HMM; the absorption increases more strongly when roughness is induced throughout the HMM rather than in its surface layer only. Hence, we have found that moderate surface roughness does not deteriorate the HMM functionality, at least in absorption-related applications, thus eliminating the challenge of ultrasmooth metal layer fabrication. More severe roughness can also prove useful in the design of inexpensive HMM-based broadband absorbers.
Finite-difference calculation of travel times (1988)

The travel times of the first arriving seismic waves through any velocity structure can be rapidly computed on a two- or three-dimensional numerical grid by finite-difference extrapolation from point to point. Wavefronts, rather than the traditional rays, are tracked. Head waves are properly treated and shadow zones are filled by the appropriate diffractions. Differences of less than 0.03 per cent are found between the results of this technique and raytracing for a complex, two-dimensional model. This scheme is useful for the windowing of finite-difference calculations to increase computing speed, and promises to aid in earthquake location, tomographic inversion, and Kirchhoff migration in structures that have strong lateral velocity gradients.
Characterization of C 1 -Metabolizing Prokaryotic Communities in Methane Seep Habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by Analyzing pmoA , mmoX , mxaF , mcrA , and 16S rRNA Genes (2004)

Samples from three submerged sites (MC, a core obtained in the methane seep area; MR, a reference core obtained at a distance from the methane seep; and HC, a gas-bubbling carbonate sample) at the Kuroshima Knoll in the southern Ryuku arc were analyzed to gain insight into the organisms present and the processes involved in this oxic-anoxic methane seep environment. 16S rRNA gene analyses by quantitative real-time PCR and clone library sequencing revealed that the MC core sediments contained abundant archaea (approximately 34% of the total prokaryotes), including both mesophilic methanogens related to the genus Methanolobus and ANME-2 members of the Methanosarcinales, as well as members of the delta-Proteobacteria, suggesting that both anaerobic methane oxidation and methanogenesis occurred at this site. In addition, several functional genes connected with methane metabolism were analyzed by quantitative competitive-PCR, including the genes encoding particulate methane monooxygenase (pmoA), soluble methane monooxygenase (mmoX), methanol dehydrogenese (mxaF), and methyl coenzyme M reductase (mcrA). In the MC core sediments, the most abundant gene was mcrA (2.5 x 10(6) copies/g [wet weight]), while the pmoA gene of the type I methanotrophs (5.9 x 10(6) copies/g [wet weight]) was most abundant at the surface of the MC core. These results indicate that there is a very complex environment in which methane production, anaerobic methane oxidation, and aerobic methane oxidation all occur in close proximity. The HC carbonate site was rich in gamma-Proteobacteria and had a high copy number of mxaF (7.1 x 10(6) copies/g [wet weight]) and a much lower copy number of the pmoA gene (3.2 x 10(2) copies/g [wet weight]). The mmoX gene was never detected. In contrast, the reference core contained familiar sequences of marine sedimentary archaeal and bacterial groups but not groups specific to C1 metabolism. Geochemical characterization of the amounts and isotopic composition of pore water methane and sulfate strongly supported the notion that in this zone both aerobic methane oxidation and anaerobic methane oxidation, as well as methanogenesis, occur.
Genome-Based Metabolic Engineering of Mannheimia succiniciproducens for Succinic Acid Production (2006)

Succinic acid is a four-carbon dicarboxylic acid produced as one of the fermentation products of anaerobic metabolism. Based on the complete genome sequence of a capnophilic succinic acid-producing rumen bacterium, Mannheimia succiniciproducens, gene knockout studies were carried out to understand its anaerobic fermentative metabolism and consequently to develop a metabolically engineered strain capable of producing succinic acid without by-product formation. Among three different CO2-fixing metabolic reactions catalyzed by phosphoenolpyruvate (PEP) carboxykinase, PEP carboxylase, and malic enzyme, PEP carboxykinase was the most important for the anaerobic growth of M. succiniciproducens and succinic acid production. Oxaloacetate formed by carboxylation of PEP was found to be converted to succinic acid by three sequential reactions catalyzed by malate dehydrogenase, fumarase, and fumarate reductase. Major metabolic pathways leading to by-product formation were successfully removed by disrupting the ldhA, pflB, pta, and ackA genes. This metabolically engineered LPK7 strain was able to produce 13.4 g/liter of succinic acid from 20 g/liter glucose with little or no formation of acetic, formic, and lactic acids, resulting in a succinic acid yield of 0.97 mol succinic acid per mol glucose. Fed-batch culture of M. succiniciproducens LPK7 with intermittent glucose feeding allowed the production of 52.4 g/liter of succinic acid, with a succinic acid yield of 1.16 mol succinic acid per mol glucose and a succinic acid productivity of 1.8 g/liter/h, which should be useful for industrial production of succinic acid.
Construction of a defective adenovirus vector expressing the pseudorabies virus glycoprotein gp50 and its use as a live vaccine (1990)

The gene encoding the pseudorabies virus glycoprotein gp50 was cloned at the very left end of the genome of adenovirus type 5 to give a recombinant adenovirus (Ad-gp50) defective for the E1A gene. Ad-gp50 expressed high levels of gp50 in cells which either complemented (293 cells) or did not complement (Vero and HeLa cells) the E1A gene. Surprisingly, over an extended period, higher levels of gp50 were produced in HeLa cells which lack the E1A gene. Rabbits and mice inoculated with Ad-gp50 showed a strong antibody response against gp50. Some of them were protected from a virulent challenge with pseudorabies virus.
Directional crystallization of polyethylene oxide by laser irradiation (1990)

Abstract Polyethylene oxide films have been directionally crystallized in a scanning beam from a tunable CO 2 laser at 10.6 µm. For unidirectional scanning, elongated spherulites were produced below a scan rate of 7 µm/s, whereas parallel fibers resulted after scanning at rates below 0.2 μm/s. Higher speed processing was effected by superposing a rapid reciprocating transverse motion of the sample onto the relatively slow longitudinal scanning by the beam. In this case, spherulites were elongated below a 100 µm/s longitudinal scan rate and nucleation was completely suppressed below 25 µm/s.
U.S.-Russian experts NATO collaborative research grant exchange visit meeting on excess Pu ceramics formulations and characterizations (1998)

This document contains the agenda and meeting notes. Topics of discussion included US Pu disposition ceramics activities, Russian experience and proposals in Pu ceramics, and development of possible Russian ceramic proposals or collaborations.
Inhibition of mast cell-mediated cytotoxicity by IFN- alpha/beta and - gamma . (1990)

Although IFN enhance the cytotoxic activity of NK cells, K cells, and monocytes, IFN-alpha/beta and IFN-gamma did not stimulate the cytotoxic activity of rat peritoneal mast cells (PMC), but had an inhibitory effect. Preincubation for 2 h with 100 and 200 U/ml of IFN-gamma and IFN-alpha/beta, respectively, inhibited PMC cytotoxicity against WEHI-164 target cells. Lower concentrations of IFN-gamma (12.5 U/ml) and IFN-alpha/beta (25 U/ml) inhibited cytotoxicity of PMC after 8 h preincubation. The inhibitory effect of IFN was concentration and time dependent. In contrast to cytotoxicity, the release of histamine by PMC was not stimulated by the target cells WEHI-164 and there was no correlation between histamine release and cytotoxic activity of PMC. Specific antibody to subclasses of IFN prevented the inhibition of PMC cytotoxic activity, but preincubation with antibodies to the alternate subclass of IFN did not affect the observed inhibition. Moreover, the presence of both subclasses of IFN showed an additive inhibition of PMC cytotoxicity. The cytotoxic activity of PMC can be completely inhibited by the addition of anti-TNF during the assay. At high concentrations (400 U/ml), IFN inhibited the release of TNF from PMC. In the presence of RNA or protein synthesis inhibitors, IFN did not inhibit cytotoxicity of PMC further. We postulate that IFN may alter gene expression in mast cells in a manner that down-regulates their functions.
Molecular pathology of the cell cycle in human cancer cells (1993)

Recent evidence from molecular biology studies of the cell cycle machinery suggests that, apart from oncogenes and tumor suppressor genes, the genes encoding the key cell cycle regulatory proteins could serve as additional targets for oncogenic mutations involved in the multistep process of carcinogenesis. In an attempt to identify such potential cancer-associated aberrations of the cell cycle regulators, the expression of cdc2 and cdk2 kinases, as well as cyclins A, B1 and D1, was analyzed by immunoblotting in a panel of more than 40 human cancer cell lines derived from 17 different tumor types. The expression of cdc2, cdk2, cyclin B1 and cyclin A polypeptides was detectable in all lines examined, and moderate variation in protein level does not provide evidence for any obvious abnormalities in the cancer cell lines studied. The application of a series of novel monoclonal antibodies (Mab) to human cdc2 revealed the existence of an intriguing protein, designated p37, immunologically and structurally related to cdc2, which is strongly and selectively expressed in about 50% of the cancer cell lines. In contrast to cyclin A, which has also been implicated in tumorigenesis, we found pronounced variation in abundance of the cyclin D1 protein. Our data suggest that dysregulation of cyclin D1 (a candidate bcl-1, PRAD1 oncogene) can be involved in the pathogenesis of some additional tumor types (e.g., sarcomas and neuroblastomas) besides those reported for amplification and/or mRNA overexpression of this oncogene.(ABSTRACT TRUNCATED AT 250 WORDS)
Posttraumatic Stress Disorder and Risk of Dementia Among US Veterans (2010)

In a predominantly male veteran cohort, those diagnosed as having PTSD were at a nearly 2-fold-higher risk of developing dementia compared with those without PTSD. Mechanisms linking these important disorders need to be identified with the hope of finding ways to reduce the increased risk of dementia associated with PTSD.
Endoscopic Ultrasound–Guided Fine Needle Aspiration Biopsy of Patients With Suspected Pancreatic Cancer: Diagnostic Accuracy and Acute and 30-Day Complications (2003)

EUS-FNA is highly accurate in identifying patients with suspected pancreatic cancer, especially when other modalities have failed. Major complications after EUS-FNA are rare, and minor complications are similar to those reported for upper endoscopy. It seems that follow-up at 1 wk might capture all of the adverse events related to EUS-FNA.
Potent, Novel in Vitro Inhibitors of thePseudomonasaeruginosaDeacetylase LpxC (2002)

Deacetylation of uridyldiphospho-3-O-(R-hydroxydecanoyl)-N-acetylglucosamine by LpxC is the first committed step in the Pseudomonas aeruginosa biosynthetic pathway to lipid A; homologous enzymes are found widely among Gram-negative bacteria. As an essential enzyme for which no inhibitors have yet been reported, the P. aeruginosa LpxC represents a highly attractive target for a novel antibacterial drug. We synthesized several focused small-molecule libraries, each composed of a variable aromatic ring, one of four heterocyclic/spacer moieties, and a hydroxamic acid and evaluated the LpxC inhibition of these compounds against purified P. aeruginosa enzyme. To ensure that the in vitro assay would be as physiologically relevant as possible, we synthesized a tritiated form of the specific P. aeruginosa glycolipid substrate and measured directly the enzymatically released acetate. Several of our novel compounds, predominantly those having fluorinated substituents on the aromatic ring and an oxazoline as the heterocyclic moiety, demonstrated in vitro IC(50) values less than 1 microM. We now report the synthesis and in vitro evaluation of these P. aeruginosa LpxC inhibitors.
<title>Fractal approach to low-rate video coding</title> (1993)

This paper presents a method for fast encoding and decoding of image sequences based on fractal coding theory and the hybrid coding concept. The DPCM-loop accounts for statistical dependencies of natural image sequences in temporal direction. Those regions of the original image where the prediction, i.e., motion estimation, and compensation fails are encoded using an advanced fractal coding scheme which originally was developed for encoding of still images. Similar to conditional replenishment coders, not regions of the residual image itself but of the original image are encoded. The introduction of a fractal coding scheme instead of the commonly used DCT turns out to be advantageous especially at very low bit rates (8 - 64 kbit/s). In order to increase reconstruction quality, encoding speed and compression ratio, some additional features such as hierarchical codebook search and multilevel block segmentation, are proposed.
Biochemical characterization of different genotypes of Paenibacillus larvae subsp. larvae, a honey bee bacterial pathogen (2004)

Paenibacillus larvae subsp. larvae (P. l. larvae) is the aetiological agent of American foulbrood (AFB), the most virulent bacterial disease of honey bee brood worldwide. In many countries AFB is a notifiable disease since it is highly contagious, in most cases incurable and able to kill affected colonies. Genotyping of field isolates of P. l. larvae revealed at least four genotypes (AB, Ab, ab and alpha B) present in Germany which are genotypically different from the reference strain DSM 7030. Therefore, based on these data, five different genotypes of P. l. larvae are now identified with genotype AB standing out with a characteristic brown-orange and circled two-coloured colony morphology. Analysing the metabolic profiles of three German genotypes (AB, Ab and ab) as well as of the reference strain using the Biolog system, a characteristic biochemical fingerprint could be obtained for each strain. Cluster analysis showed that while genotypes Ab, ab and the reference strain DSM 7030 are rather similar, genotype AB is clearly different from the others. Analysis of all isolates for plasmid DNA revealed two different plasmids present only in isolates belonging to genotype AB. Therefore, genotype AB is remarkable in all aspects analysed so far. Future analysis will show whether or not these differences will expand to differences in virulence.
Receptors linked to inhibition of adenylate cyclase: additional signaling mechanisms (1988)

Many hormones and neurotransmitters attenuate cyclic AMP (cAMP) accumulation in intact cells by virtue of their ability to inhibit adenylate cyclase activity via the GTP-binding protein denoted as Gi. Nonetheless, a number of physiological findings suggest that attenuation of cAMP production is not sufficient to serve as the only signal for eliciting the diverse physiological effects provoked by these various receptor populations. Additional biochemical and electrophysiological changes are known to occur after occupancy of receptors linked to inhibition of adenylate cyclase, including acceleration of Na+/H+ exchange, activation of K+ conductances, and inhibition of voltage-sensitive Ca2+ channels. This review summarizes the current understanding of how these receptors are coupled to their multiple potential effector mechanisms and offers some speculation about the possible interplay between the biochemical and electrophysiological sequels of receptor occupancy. It is hoped that future studies will establish which constellation of possible signaling mechanisms actually brings about changes in metabolic, secretory, or contractile events in different target cells.
The Effect of Adding Exenatide to a Thiazolidinedione in Suboptimally Controlled Type 2 Diabetes (2007)

Exenatide therapy improved glycemic control, reduced body weight, and caused gastrointestinal symptoms more than placebo in patients with type 2 diabetes that was suboptimally controlled with TZD therapy. ClinicalTrials.gov registration number: NCT00099320. For more information on exenatide click here.
Dynamic synthesis of a macrocycle containing a porphyrin and an electron donor (2005)

New macrocycles incorporating a porphyrin and a [small pi] electron-rich aromatic were prepared from a dynamic disulfide library. The outcome could be influenced by use of templates.
Ubiquitination of endogenous calmodulin in rabbit tissue extracts (1991)

Previously we were able to show that purified calmodulins from vertebrates, plants (spinach) and the mold Neurospora crassa can be covalently conjugated to ubiquitin in a Ca 2+ ‐dependent manner. It was therefore pertinent to answer the question if a tissue extract contains all the components necessary for the endogenous synthesis of ubiquityl calmodulin (uCaM). Therefore [ 125 I]ubiquitin, ATP/Mg 2+ and Ca 2+ were added to tissue extracts enriched by a single ion exchange step. In such extracts of red blood cells, skeletel muscle and testis a novel ubiquitin conjugate of 27–29 kDa is formed. This novel band could be identified as ubiquityl‐calmodulin by the following methods: (i) identical R 1 ‐value of novel conjugate and standard uCaM in SDS‐PAGE; (ii) Ca 2+ ‐dependent conjugate formation; (iii) Ca 2+ ‐dependent adsorption to fluphenazine‐Sepharose; (iv) Ca 2+ ‐dependent mobility change of the novel conjugate during SDS‐PAGE; and (v) inhibition of conjugate band formation by phosphorylate kinase. These experiments clearly demonstrate that ubiquityl calmodulin can be endogenously generated in enriched cellular extracts and strongly indicate that this reaction is of importance in vivo.
Adherence of staphylococci to intravascular catheters (1989)

Adherence of seven strains of Staphylococcus epidermidis and three strains of S. aureus to three types of intravascular catheters was assessed by ATP bioluminescence, by culture after ultrasonication and by scanning electronmicroscopy. The catheter materials studied were silicone elastomer, thermoplastic polyurethane and polyurethane coated with Hydromer, a coating which absorbs water and provides a hydrophilic sheath around the catheter. The adherence assays were performed in phosphate-buffered saline on a rotary shaker at 37 degrees C, with the catheters precoated with serum and uncoated, and the results were correlated with bacterial hydrophobicity. There was wide strain-to-strain variation in bacterial adherence; S. aureus and slime-producing S. epidermidis strains adhered better than did non-slime-producing strains. Overall, there was less bacterial adherence to Hydromer-coated catheters than to polyurethane and silicone catheters but it was unrelated to bacterial hydrophobicity. Serum coating of catheters resulted in marked reduction of bacterial adherence.
Improved modeling of side‐chains in proteins with rotamer‐based methods: A flexible rotamer model (1999)

Side-chain modeling has a widespread application in many current methods for protein tertiary structure determination, prediction, and design. Of the existing side-chain modeling methods, rotamer-based methods are the fastest and most efficient. Classically, a rotamer is conceived as a single, rigid conformation of an amino acid side-chain. Here, we present a flexible rotamer model in which a rotamer is a continuous ensemble of conformations that cluster around the classic rigid rotamer. We have developed a thermodynamically based method for calculating effective energies for the flexible rotamer. These energies have a one-to-one correspondence with the potential energies of the rigid rotamer. Therefore, the flexible rotamer model is completely general and may be used with any rotamer-based method in substitution of the rigid rotamer model. We have compared the performance of the flexible and rigid rotamer models with one side-chain modeling method in particular (the self-consistent mean field theory method) on a set of 20 high quality crystallographic protein structures. For the flexible rotamer model, we obtained average predictions of 85.8% for χ 1, 76.5% for χ 1+2 and 1.34 Å for root-mean-square deviation (RMSD); the corresponding values for core residues were 93.0%, 87.7% and 0.70 Å, respectively. These values represent improvements of 7.3% for χ 1, 8.1% for χ 1+2 and 0.23 Å for RMSD over the predictions obtained with the rigid rotamer model under otherwise identical conditions; the corresponding improvements for core residues were 6.9%, 10.5% and 0.43 Å, respectively. We found that the predictions obtained with the flexible rotamer model were also significantly better than those obtained for the same set of proteins with another state-of-the-art side-chain placement method in the literature, especially for core residues. The flexible rotamer model represents a considerable improvement over the classic rigid rotamer model. It can, therefore, be used with considerable advantage in all rotamer-based methods commonly applied to protein tertiary structure determination, prediction, and design and also in predictions of free energies in mutational studies. Proteins 1999;37:530–543. ©1999 Wiley-Liss, Inc.