gebhart/patrepeval huggingface dataset:
Incremental semi-supervised subspace learning for image retrieval (2004)

Subspace learning techniques are widespread in pattern recognition research. They include Principal Component Analysis (PCA), Locality Preserving Projection (LPP), etc. These techniques are generally unsupervised which allows them to model data in the absence of labels or categories. In relevance feedback driven image retrieval system, the user provided information can be used to better describe the intrinsic semantic relationships between images. In this paper, we propose a semi-supervised subspace learning algorithm which incrementally learns an adaptive subspace by preserving the semantic structure of the image space, based on user interactions in a relevance feedback driven query-by-example system. Our algorithm is capable of accumulating knowledge from users, which could result in new feature representations for images in the database so that the system's future retrieval performance can be enhanced. Experiments on a large collection of images have shown the effectiveness and efficiency of our proposed algorithm.
Purification of a malonyltransferase from Streptomyces coelicolor A3(2) and analysis of its genetic determinant (1995)

Streptomyces coelicolor A3(2) synthesizes each half molecule of the dimeric polyketide antibiotic actinorhodin (Act) from one acetyl and seven malonyl building units, catalyzed by the Act polyketide synthase (PKS). The synthesis is analogous to fatty acid biosynthesis, and there is evident structural similarity between PKSs of Streptomyces spp. and fatty acid synthases (FASs). Each system should depend on a malonyl coenzyme A:acyl carrier protein malonyltransferase, which charges the FAS or PKS with the malonyl units for carbon chain extension. We have purified the Act acyl carrier protein-dependent malonyltransferase from stationary-phase, Act-producing cultures and have determined the N-terminal amino acid sequence and cloned the structural gene. The deduced amino acid sequence resembles those of known malonyltransferases of FASs and PKSs. The gene lies some 2.8 Mb from the rest of the act cluster, adjacent to an open reading frame whose gene product resembles ketoacylsynthase III of Escherichia coli FAS. The malonyltransferase was expressed equally as well during vegetative growth (when other components of the act PKS were not expressed) as in the stationary phase, suggesting that the malonyltransferase may be shared between the FAS and PKS of S. coelicolor. Disruption of the operon containing the malonyltransferase gene proved to be impossible, supporting the idea that the malonyltransferase plays an essential role in fatty acid biosynthesis.
Regulation of Pancreatic β Cell Mass by Neuronal Signals from the Liver (2008)

Metabolic regulation in mammals requires communication between multiple organs and tissues. The rise in the incidence of obesity and associated metabolic disorders, including type 2 diabetes, has renewed interest in interorgan communication. We used mouse models to explore the mechanism whereby obesity enhances pancreatic beta cell mass, pathophysiological compensation for insulin resistance. We found that hepatic activation of extracellular regulated kinase (ERK) signaling induced pancreatic beta cell proliferation through a neuronal-mediated relay of metabolic signals. This metabolic relay from the liver to the pancreas is involved in obesity-induced islet expansion. In mouse models of insulin-deficient diabetes, liver-selective activation of ERK signaling increased beta cell mass and normalized serum glucose levels. Thus, interorgan metabolic relay systems may serve as valuable targets in regenerative treatments for diabetes.
Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response (2005)

Horizontal gene transfer contributes to the evolution of bacterial species. Mobile genetic elements play an important role in horizontal gene transfer, and characterization of the regulation of these elements should provide insight into conditions that influence bacterial evolution. We characterized a mobile genetic element, ICEBs1, in the Gram-positive bacterium Bacillus subtilis and found that it is a functional integrative and conjugative element (ICE) capable of transferring to Bacillus and Listeria species. We identified two conditions that promote ICEBs1 transfer: conditions that induce the global DNA damage response and crowding by potential recipients that lack ICEBs1. Transfer of ICEBs1 into cells that already contain the element is inhibited by an intercellular signaling peptide encoded by ICEBs1. The dual regulation of ICEBs1 allows for passive propagation in the host cell until either the potential mating partners lacking ICEBs1 are present or the host cell is in distress.
The ability of frequency doubling technology (FDT) perimetry to predict the onset of glaucomatous visual field loss for standard automated perimetry (SAP) (2002)

Purpose: To evaluate the ability of Frequency Doubling Technology (FDT) to predict the development of glaucomatous Standard Automated Perimetry (SAP) deficits in glaucoma suspects (converters). Methods: FDT perimetry was conducted using a custom display system (Quadravision) that consisted of four high resolution (1280 × 1600 pixels) 21 inch monochrome monitors combined with front surface mirrors to cover the central 30 degrees radius of the visual field. A 24-2 stimulus presentation pattern (6 degree grid bracketing the horizontal and vertical meridians), consisting of 54 locations throughout the central 24 degrees radius, was employed for FDT testing. The targets were 4 degree diameter squares, which displayed 0.5 cycle/degree sinusoidal gratings undergoing 18 Hz counterphase flicker. Background luminance was 50 cd/m2. Thresholds were obtained by means of a Modified Binary Staircase (MOBS) procedure. SAP visual fields were obtained with the Humphrey Field Analyzer II (Model 750), using a 24-2 stimulus display, the standard background luminance (10 cd/m2), the standard stimulus size (III) and a Full Threshold procedure. 119 eyes of 89 glaucoma suspects (with normal SAP visual fields at baseline) were evaluated with FDT and SAP annually over a four year time period. Results: Results of a multivariate analysis (CART) revealed that the Pattern Standard Deviation (PSD) index for FDT at baseline was able to predict the development of SAP deficits four years later. 13 out of 19 SAP converters and 84 out of 100 SAP non-converters were correctly identified using the baseline FDT PSD alone (area under ROC = 0.74). The efficacy of additional FDT parameters will also be presented. Conclusions: FDT perimetry appears to detect glaucomatous visual field losses prior to SAP in most instances. In addition, FDT visual field abnormalities seem to be predictive of the future development of glaucomatous visual field loss for SAP.
Zirconium and Titanium Diamine Bis(phenolate) Catalysts for α-Olefin Polymerization:  From Atactic Oligo(1-hexene) to Ultrahigh-Molecular-Weight Isotactic Poly(1-hexene) (2004)

Aiming at higher activities of group IV diamine bis(phenolate) catalysts in olefin polymerization, ligands containing electron-withdrawing groups have been introduced. The dibenzyl Zr complexes of these ligands lead to highly active 1-hexene catalysts upon activation yielding, however, low-molecular-weight atactic poly(1-hexene). In contrast, the corresponding titanium complexes are highly active and lead to ultrahigh-molecular-weight poly(1-hexene) of different isotacticities, dictated by the size of the phenolate substituents.
Linker mutagenesis in the gene of an outer membrane protein of escherichia coli, LamB (1984)

In order to identify sequences involved in the localization of LamB, an outer membrane protein from E coli K12, mutagenesis by linker insertion has been performed on a lamB gene copy carried on a plasmid devised for this purpose. An analysis of the first set of 16 clones constructed by this technique shows that, in these clones, the lamB protein is altered either by frameshift mutations leading to abnormal COOH terminal (usually premature termination) or by in-phase deletions or small insertions. Except for two in-phase linker insertions, which only slightly changed the behavior of the protein, the modified proteins are either toxic to cell growth or unstable. In all cases examined so far, the modified proteins were in the outer membrane. We suggest that toxicity is due to incorrect folding, which leads to disruption of the outer membrane. The nature of the genetic alterations leads to the hypothesis that the first 183 amino acids of the LamB mature protein contain, together with the signal sequence, all the instructions needed for proper localization.
Glucoamylase structural, functional, and evolutionary relationships (1997)

To correlate structural features with glucoamylase properties, a structure-based multisequence alignment was constructed using information from catalytic and starch-binding domain models. The catalytic domain is composed of three hydrophobic folding units, the most labile and least hydrophobic of them being missing in the most stable glucoamylase. The role of O-glycosylation in stabilizing the most hydrophobic folding unit, the only one where thermostabilizing mutations with unchanged activity have been made, is described. Differences in both length and composition of interhelical loops are correlated with stability and selectivity characteristics. Two new glucoamylase subfamilies are defined by using homology criteria. Protein parsimony analysis suggests an ancient bacterial origin for the glucoamylase gene. Increases in length of the belt surrounding the active site, degree of O-glycosylation, and length of the linker probably correspond to evolutionary steps that increase stability and secretion levels of Aspergillus-related glucoamylases.
Notch Subunit Heterodimerization and Prevention of Ligand-Independent Proteolytic Activation Depend, Respectively, on a Novel Domain and the LNR Repeats (2004)

Notch proteins are transmembrane receptors that participate in a highly conserved signaling pathway that regulates morphogenesis in metazoans. Newly synthesized Notch receptors are proteolytically cleaved during transit to the cell surface, creating heterodimeric mature receptors comprising noncovalently associated extracellular (N(EC)) and transmembrane (N) subunits. Ligand binding activates Notch by inducing two successive proteolytic cleavages, catalyzed by metalloproteases and gamma-secretase, respectively, that permit the intracellular portion of N to translocate to the nucleus and activate transcription of target genes. Prior work has shown that the presence of N(EC) prevents ligand-independent activation of N, but the mechanisms involved are poorly understood. Here, we define the roles of two regions at the C-terminal end of N(EC) that participate in maintaining the integrity of resting Notch receptors through distinct mechanisms. The first region, a hydrophobic, previously uncharacterized portion of N(EC), is sufficient to form stable complexes with the extracellular portion of N. The second region, consisting of the three Lin12/Notch repeats, is not needed for heterodimerization but acts to protect N from ligand-independent cleavage by metalloproteases. Together, these two contiguous regions of N(EC) impose crucial restraints that prevent premature Notch receptor activation.
Homogeneous Biocatalysis in both Fluorous Biphasic and Supercritical Carbon Dioxide Systems (2007)

Einfach einfacher: Cytochrom c und α-Chymotrypsin (CMT) können in fluorigen Solventien oder überkritischem CO2 mithilfe perfluorierter anionischer Tenside (Krytox 157 FSL, KDP 4606) solubilisiert werden (hydrophobic ion pairing). An einem Modellsystem für die homogene fluorige Zweiphasen-Biokatalyse mit dem CMT-KDP-Komplex in Hexan/Perfluormethylcyclohexan wird die Vereinfachung von Produktabtrennung und Biokatalysator-Recycling gezeigt. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2007/z701488_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Pro‐ versus Anti‐inflammatory Cytokine Profile in Patients with Severe Sepsis: A Marker for Prognosis and Future Therapeutic Options (2000)

Serum concentrations of the proinflammatory cytokines tumor necrosis factor-alpha (TNF-alpha), interleukin (IL)-1beta, and IL-6, and the anti-inflammatory cytokine Il-10, and IL-1 receptor antagonists (IL-1ra) and soluble TNF receptors (sTNFRs) were measured in 65 patients with severe sepsis. All patients were evaluated clinically and microbiologically and were followed up for clinical outcome. Levels of both pro- and anti-inflammatory cytokines were significantly elevated in patients with sepsis. Elevated serum IL-10 and TNF-alpha levels and a high IL-10 to TNF-alpha ratio were associated with death, whereas higher levels of TNF-alpha, IL-6, IL-1ra, and sTNFR were detected in patients with an early hemodynamic deterioration. Interleukin-10 and IL-10:TNF-alpha ratio remained higher in nonsurvivors, whereas IL-10 paralleled the sepsis score. Although both the inflammatory and anti-inflammatory response is profoundly augmented in patients with severe sepsis, the sustained overproduction of the anti-inflammatory cytokine IL-10 is the main predictor of severity and fatal outcome.
Global featureless estimation of radial distortions (2008)

We consider the problem of image registration in the case of a radial deformation around an unknown center. We propose a novel approach for the estimation of the radial distortion parameters, which is applicable for camera calibration and image correction. The parameters of the deformation consist of the center of distortion (which is not necessarily the center of the image) and the parameters of the distortion function. We propose a closed form explicit solution that performs well for a wide family of radial distortion models and reduces the non linear problem to that of testing a small number of hypotheses. In most distortion estimation methods, some features like points, corners or lines are extracted from the distorted image. In contrast to the feature based methods, our proposed solution uses all of the information in the distorted image which is reasonable considering the fact that the distortion impacts the entire image. Successful experiments of parameter estimation with real and synthetic images with and without noise are presented in this paper.
The strobilurin fungicides (2002)

Strobilurins are one of the most important classes of agricultural fungicide. Their invention was inspired by a group of fungicidally active natural products. The outstanding benefits they deliver are currently being utilised in a wide range of crops throughout the world. First launched in 1996, the strobilurins now include the world's biggest selling fungicide, azoxystrobin. By 2002 there will be six strobilurin active ingredients commercially available for agricultural use. This review describes in detail the properties of these active ingredients--their synthesis, biochemical mode of action, biokinetics, fungicidal activity, yield and quality benefits, resistance risk and human and environmental safety. It also describes the clear technical differences that exist between these active ingredients, particularly in the areas of fungicidal activity and biokinetics.
Behavioral Neurobiology of Alcohol Addiction: Recent Advances and Challenges (2002)

Addictive behavior associated with alcoholism is characterized by compulsive preoccupation with obtaining alcohol, loss of control over consumption, and development of tolerance and dependence, as well as impaired social and occupational functioning. Like other addictive disorders, alcoholism is characterized by chronic vulnerability to relapse after cessation of drinking. To understand the factors that compel some individuals to drink excessively, alcohol research has focused on the identification of brain mechanisms that support the reinforcing actions of alcohol and the progression of changes in neural function induced by chronic ethanol consumption that lead to the development of dependence. More recently, increasing attention has been directed toward the understanding of neurobiological and environmental factors in susceptibility to relapse.
Periurethral Injection of Autologous Fat for the Treatment of Sphincteric Incontinence (1994)

A total of 15 women with stress incontinence and 6 men with post-prostatectomy sphincteric incontinence underwent periurethral injection of autologous fat while under local anesthesia. The fat was harvested from the abdominal wall by liposuction. Preoperative evaluation consisted of a micturition diary, questionnaire, semiquantitative pad test, cystoscopy and urodynamics. Sequential injections were performed at 1 to 3-month intervals. Results were assessed by subjective patient scores, pad tests and clinical evaluation performed at intervals. Followup was 12 to 30 months (mean 18). Only 1 man and none of the women with urethral hypermobility had lasting improvement. Of the 15 women 12 had intrinsic sphincteric deficiency (type 3 stress incontinence) and they were our most successful group. Of the 12 women 10 (83%) were improved (mean score of 8.8-7 before injection compared to 1.87 after injection) at 1 month following the initial injection. Of the 9 patients who continued with the treatment 7 (78%) noticed lasting improvement objectively and subjectively after 1 to 4 injections (mean 2.4). We believe that this technique shows sufficient promise as an alternative therapy for sphincteric incontinence to warrant continued clinical investigation.
Disulfide exchange folding of insulin-like growth factor I (1992)

The disulfide exchange folding properties of insulin-like growth factor I (IGF-I) have been analyzed in a redox buffer containing reduced (10 mM) and oxidized (1 mM) glutathione. Under these conditions, the 3 disulfide bridges of the 70 amino acid peptide were not quantitatively formed. Instead, five major forms of IGF-I were detected, and these components were concluded to be in equilibrium as their relative amounts were similar starting from either reduced, native, or a mismatched variant of IGF-I containing two non-native disulfides. The different components in the mixtures were trapped by thiol alkylation using vinylpyridine and subsequently isolated by reverse-phase HPLC. The purified variants were further characterized using plasma desorption mass spectrometry and peptide mapping. Two of the five different forms were identified as native and mismatched IGF-I. One form was a variant with only one disulfide bond, and the other two major components had two disulfides formed. In a separate experiment, early refolding intermediates were trapped by pyridylethylation after only 90 s of refolding in the glutathione buffer, starting from reduced IGF-I. The intermediates were identical to the components observed at equilibrium, but at different relative concentrations. On the basis of the disulfide bond patterns of the different components in the equilibrium mixtures, we conclude that the disulfide between cysteines-47 and -52 in IGF-I is an unfavorable high-energy bond that may exist in the native molecule in a strained configuration.
CD38 as a therapeutic target. (2007)

The CD38 molecule is well represented on cell surfaces in many cases of a variety of lymphoid tumors, notably multiple myeloma, AIDS-associated lymphomas, and post-transplant lymphoproliferations. As such, this molecule is a promising target for antibody therapy. After early disappointments, improved anti-CD38 antibodies of strong cytolytic potential have been described by 3 groups. First, a human IgG monoclonal anti-CD38 antibody raised in mice transgenic for human Ig has been found to induce potent complement and cellular cytotoxicities against both myeloma cell lines and fresh harvests from myeloma marrow and leukemic blood. This antibody also exhibits the singular property of inhibiting the CD38 cyclase activity. Second, a series of CD38-specific human antibodies, with high affinities and high ADCC activities against cell lines and primary cultures of myeloma, has been selected from a unique phage-display library. Finally, to enhance specificity for myeloma cells, bispecific domain antibodies targeting both CD38 and CD138 have been developed. As they lack any Fc module, these constructs rely on cytotoxicity for delivering a toxin to tumor cells. The list of candidate CD38-bearing neoplasms as targets for these antibody constructs can now be expanded to include acute promyelocytic leukemia, and possibly other myeloid leukemias, in which surface CD38 can be induced by retinoid treatment. One caveat here is that evidence has been produced to suggest that CD38 promotes pulmonary manifestations of the hazardous retinoic acid syndrome.
Cloning, overexpression, and genomic mapping of the 14-kDa subunit of human replication protein A. (1993)

Replication protein A (RPA) is a three-subunit protein that plays a central role in eukaryotic DNA replication, recombination, and repair. We have previously reported the cloning and bacterial expression of the 70- and 32-kDa subunits of human RPA (hRPA). We have now cloned the 14-kDa subunit (hRPA3) from a HeLa cell cDNA library. The hRPA3 cDNA is a 692-base pair sequence that contains an open reading frame encoding a protein of 121 amino acids with a calculated molecular mass of 13.6 kDa. The deduced amino acid sequence shows only limited similarity to the small subunit of yeast RPA and is unrelated to any other protein in the current data banks. A recombinant protein containing a short histidine tag at the NH2 terminus has been purified in good yield from Escherichia coli by metal-chelate affinity chromatography. Antibodies prepared against recombinant hRPA3 recognize the native protein and inhibit SV40 DNA replication in vitro. We have localized the genes for the 70-, 32-, and 14-kDa subunits to chromosomes 17, 1, and 7, respectively, using polymerase chain reaction amplification of genomic DNA from rodent-human hybrid cell lines. Since RPA appears to be involved in several fundamental cellular processes, the physical mapping of the RPA genes may be useful in identifying possible human genetic defects associated with RPA deficiency or dysfunction.
Signal detection using the radial basis function coupled map lattice (2000)

Conventional detection methods used in current marine radar systems do not perform efficiently in detecting small targets embedded in a clutter environment. Based on a recent observation that sea clutter, radar echoes from a sea surface, is chaotic rather than random, we propose using a spatial temporal predictor to reconstruct the chaotic dynamic of sea clutter because electromagnetic wave scattering is a spatial temporal phenomenon which is physically modeled by partial differential equations. The spatial temporal predictor used here is called radial basis function coupled map lattice (RBF-CML) which uses a linear combiner to fuse either measurements in different spatial domains for an RBF prediction or predictions from several RBF nets operated on different spatial regions. Using real-life radar data, it is shown that the RBF-CML is an effective method to reconstruct the sea clutter dynamic. The RBF-CML predictor is then applied to detect small targets in sea clutter using the constant false alarm rate (CFAR) principle. The spatial temporal approach is shown, both theoretically and experimentally, to be superior to a conventional CFAR detector.