gebhart/patrepeval huggingface dataset:
Faster and Better: A Machine Learning Approach to Corner Detection (2008)

The repeatability and efficiency of a corner detector determines how likely it is to be useful in a real-world application. The repeatability is important because the same scene viewed from different positions should yield features which correspond to the same real-world 3D locations. The efficiency is important because this determines whether the detector combined with further processing can operate at frame rate. Three advances are described in this paper. First, we present a new heuristic for feature detection and, using machine learning, we derive a feature detector from this which can fully process live PAL video using less than 5 percent of the available processing time. By comparison, most other detectors cannot even operate at frame rate (Harris detector 115 percent, SIFT 195 percent). Second, we generalize the detector, allowing it to be optimized for repeatability, with little loss of efficiency. Third, we carry out a rigorous comparison of corner detectors based on the above repeatability criterion applied to 3D scenes. We show that, despite being principally constructed for speed, on these stringent tests, our heuristic detector significantly outperforms existing feature detectors. Finally, the comparison demonstrates that using machine learning produces significant improvements in repeatability, yielding a detector that is both very fast and of very high quality.
Linkage and mutational analysis of familial Alzheimer disease kindreds for the APP gene region. (1992)

A large number of familial Alzheimer disease (FAD) kindreds were examined to determine whether mutations in the amyloid precursor protein (APP) gene could be responsible for the disease. Previous studies have identified three mutations at APP codon 717 which are pathogenic for Alzheimer disease (AD). Samples from affected subjects were examined for mutations in exons 16 and 17 of the APP gene. A combination of direct sequencing and single-strand conformational polymorphism analysis was used. Sporadic AD and normal controls were also examined by the same methods. Five sequence variants were identified. One variant at APP codon 693 resulted in a Glu-->Gly change. This is the same codon as the hereditary cerebral hemorrhage with amyloidosis-Dutch type Glu-->Gln mutation. Another single-base change at APP codon 708 did not alter the amino acid encoded at this site. Two point mutations and a 6-bp deletion were identified in the intronic sequences surrounding exon 17. None of the variants could be unambiguously determined to be responsible for FAD. The larger families were also analyzed by testing for linkage of FAD to a highly polymorphic short tandem repeat marker (D21S210) that is tightly linked to APP. Highly negative LOD scores were obtained for the family groups tested, and linkage was formally excluded beyond theta = .10 for the Volga German kindreds, theta = .20 for early-onset non-Volga Germans, and theta = .10 for late-onset families. LOD scores for linkage of FAD to markers centromeric to APP (D21S1/S11, D21S13, and D21S215) were also negative in the three family groups. These studies show that APP mutations account for AD in only a small fraction of FAD kindreds.
Cloning and functional expression of a rat brain corticotropin releasing factor (CRF) receptor. (1993)

Corticotropin releasing factor (CRF), a key neuroregulator of the hypothalamic-pituitary-adrenal cortical axis, also displays a broad range of effects on the endocrine, central nervous and immune systems. Having recently characterized the human pituitary CRF receptor by expression cloning of cDNA from a human Cushing's corticotropic adenoma, we report here the structure of the cDNA for a rat brain CRF receptor (rCRF-R) which was cloned by hybridization from a rat brain cDNA library. The sequence of the rCRF-R encodes a 415 amino acid protein comprising seven membrane spanning domains. The rCRF-R is 97% identical at the amino acid level to the human pituitary tumor CRF receptor, differing by only 12 amino acids. When expressed in COSM6 cells, the rCRF-R binds CRF with high affinity (Kd = 1.7 (0.8-3.8)nM). The receptor transduces a CRF stimulated accumulation of intracellular cAMP which is inhibited by the CRF antagonist, alpha helCRF(9-41). These results suggest that the brain expresses a CRF receptor similar to that in the pituitary.
High dose inhaled atrial natriuretic peptide is a bronchodilator in asthmatic subjects (1994)

Atrial natriuretic peptide (ANP) has been shown to be an effective bronchodilator when given intravenously, but its efficacy by inhalation has not been assessed. In the first part of the current study, six asthmatic subjects, mean (SEM) forced expiratory volume in one second (FEV1) 2.09 (0.30) l, received 0.1 and 1 mg atrial natriuretic peptide by inhalation, and in the second study five subjects, FEV1 1.92 (0.40) l, received 5 mg ANP by inhalation. ANP was given in a placebo-controlled, double blind, randomized manner, with measurement of FEV1 over the following 60 min. Nebulized salbutamol was given at 60 min as a measure of the maximal bronchodilator response attainable by conventional therapy. No significant bronchodilator effect was seen following the 0.1 or 1 mg inhalation, although the latter produced a minimal transient elevation in peripheral atrial natriuretic peptide plasma levels. A bronchodilator effect was seen with the 5 mg dose, which produced delta FEV1 0.42 (0.09) l compared to 0.93 (0.13) l subsequently produced by salbutamol. This effect peaked at 5 min and was no different from placebo from 10 min onwards. We conclude that atrial natriuretic peptide may produce significant bronchodilation when given by inhalation in high doses, and speculate that substances which generate cyclic guanosine monophosphate (cGMP) in airway smooth muscle warrant further investigation as potential bronchodilatory agents.
Characterization of a functional (pro)renin receptor in rat brain neurons (2008)

(Pro)renin receptor (PRR), the newest member of the renin-angiotensin system (RAS), is turning out to be an important player in the regulation of the cardiovascular system. It plays a pivotal role in activation of the local RAS and stimulates signalling pathways involved in proliferative and hypertrophic mechanisms. However, the role of PRR in the brain remains unknown. Thus, our objective in this study was to determine whether a functional PRR is present in neurons within the brain. Neuronal co-cultures from the hypothalamus and brainstem areas of neonatal rat brain express PRR mRNA. Immunoreactivity for PRR was primarily localized on the neuronal cell soma and in discrete areas in the neurites. Treatment of neurons with renin, in the presence of 2 microm losartan, caused a time- and dose-dependent stimulation of phosphorylation of extracellular signal related kinase ERK1 (p44) and ERK2 (p42) isoforms of mitogen-activated protein kinase. Optimal stimulation of fourfold was observed within 2 min with 20 nm renin. Electrophysiological recordings showed that treatment of the neurons with renin, in the presence of 2 microm losartan, resulted in a steady and stable decrease in action potential frequency. A 46% decrease in action potential frequency was observed within 5 min of treatment and was attenuated by co-incubation with a PRR blocking peptide. These observations demonstrate that the PRR is present in neurons within the brain and that its activation by renin initiates the MAP kinase signalling pathway and inhibition of neuronal activity.
Transgenic Tobacco Plants Expressing a Coat Protein Gene of Tobacco Mosaic Virus Are Resistant to Some Other Tobamoviruses (1990)

Transgenic tobacco plants expressing the coat protein (CP) gene of tobacco mosaic virus were tested for resistance against infection by five other tobamoviruses sharing 45-82% homology in CP amino acid sequence with the CP of tobacco mosaic virus. The transgenic plants (CP+) showed significant delays in systemic disease development after inoculation with tomato mosaic virus or tobacco mild green mosaic virus compared to the control (CP-) plants, but showed no resistance against infection by ribgrass mosaic virus. On a transgenic local lesion host, the CP+ plants showed greatly reduced numbers of necrotic lesions compared to the CP- plants after inoculation with tomato mosaic virus, pepper mild mottle virus, tobacco mild green mosaic virus, and Odontoglossum ringspot virus but not ribgrass mosaic virus. The implications of these results are discussed in relation to the possible mechanism(s) of CP-mediated protection.
Complement component 3 binding to Haemophilus influenzae type b in the presence of anticapsular and anti-outer membrane antibodies (1992)

Antibodies directed against the capsular polysaccharide (polyribosyl ribitol phosphate [PRP]) or the outer membrane proteins (OMP) of Haemophilus influenzae type b (Hib) promote bactericidal activity, complement 3 (C3) binding, and ingestion by phagocytic cells. To assess the relative contribution of anti-OMP to host defense against Hib, we compared the opsonic activities of anti-PRP and anti-OMP as reflected by the amounts of C3 bound to the bacterial surface. Immunoglobulin G (IgG) fractions containing either anti-PRP or anti-OMP were incubated with Hib in the presence of a C5-deficient complement source. C3, total IgG, and IgG subclasses bound to the bacteria were quantified by enzyme-linked immunosorbent assay. The maximum amount of C3 which could be bound to Hib was greater in the presence of anti-PRP than in the presence of anti-OMP. Also, except at low IgG concentrations, the rate of increase in bound C3 as a function of increasing IgG concentration was greater for anti-PRP than for anti-OMP. Hib-bound anti-OMP consisted primarily of IgG1 and IgG3, whereas bound anti-PRP was primarily IgG1 and IgG2. Thus, the potential for C3 binding to Hib is greater in the presence of anti-PRP than in the presence of anti-OMP, probably because of the larger number of binding sites available to the former. Nonetheless, OMP appear to provide important targets for opsonic antibody and would be logical components of a PRP-conjugate vaccine or may be efficacious as vaccines against nontypeable H. influenzae.
ANDROGEN AND ESTROGEN RECEPTORS IN SPLENIC T LYMPHOCYTES: EFFECTS OF FLUTAMIDE AND TRAUMA-HEMORRHAGE (2000)

The endogenous sex steroids, testosterone and beta-estradiol, play a major role in inflammatory processes. They regulate several cytokine genes by interaction with their intracellular receptors that are, essentially, transcription factors. Because T-lymphocyte functions are altered following trauma-hemorrhage in male mice, we investigated whether (i) receptors for androgen (AR) and estrogen (ER) are present in splenic T lymphocytes, (ii) receptor expressions are altered following trauma-hemorrhage, and (iii) pretreatment of male mice with the AR antagonist, flutamide, alters receptor expressions and IL-6 release. Analysis of nuclear extracts indicated the presence of AR and ER in splenic T lymphocytes. No difference in receptor expressions between males and females or following trauma-hemorrhage was observed. Pretreatment of males with flutamide, however, led to increased ER expression in T lymphocytes of sham and trauma-hemorrhaged animals. This suggested that flutamide is capable of inducing the expression of another receptor belonging to a different gonadal steroid. Because response elements for AR and ER are present in the promoter region of the IL-6 gene, release of IL-6 and expression of signal transducer and activator of transcription 3 (STAT3) were analyzed as functional parameters in splenic T lymphocytes. Trauma-hemorrhage decreased IL-6 release by T lymphocytes and the release was restored to sham levels with flutamide pre-treatment. Similarly, STAT3 expression was decreased in T lymphocytes following trauma-hemorrhage and the expression was restored by flutamide pre-treatment. These data collectively demonstrate the importance of gonadal steroids in the regulation of splenic T-lymphocyte functions.
A novel strategy for the identification of toxinlike structures in spider venom (2005)

We compared two different approaches to sequence information analysis from the expressed sequence tag (EST) library constructed for the venom glands of the spider Agelena orientalis. Some results were more illustrative and reliable by the contig analysis technique, whereas our novel method, with specific structural markers introduced for protein structure detection, allowed us to overcome some limitations of the contig analysis. A novel technique was suggested for the identification in data banks of the spider's ion channel inhibitor toxins using primary structure features common to all spiders. Analysis of about 150 polypeptides made it possible to introduce 3 primary structure motifs for spider toxins: the Principal Structural Motif (PSM), which postulates the existence of 6 amino acid residues between the first and second cysteine residue and the Cys-Cys sequence at a distance of 5-10 amino acid residues from the second cysteine; the Extra Structural Motif (ESM), which postulates the existence of a pair of CXC fragments in the C-region; and the Processing Quadruplet Motif (PQM), which specifies the Arg residue at position -1 and Glu residues at positions -2, -3, and/or -4 in the precursor sequences just before the postprocessing site. In the processed data bank we found 48 toxinlike structures with ion channel inhibitor motifs. These include agelenin earlier isolated from Agelena opulenta and 25 more homologous sequences, 15 homologs of mu-agatoxin 2 from the spider Agelenopsis aperta, 3 structures with low homology to omega-agatoxin-IIIA, and 4 new structures. Also we showed that toxinlike structures exceed two thirds of the overall database sequences.
Ruthenium‐Catalyzed Regioselective Deuteration of Alcohols at the β‐Carbon Position with Deuterium Oxide (2011)

A convenient method for regioselective H/D exchange between D(2)O and alcohols at the β-carbon position using the catalytic system [(p-cymene)RuCl(2)]/ethanolamine/KOH is described. This method is applicable for deuteration of both primary and secondary alcohols. The H/D exchange reactions proceed through an oxidation/modification/reduction reaction sequence. Alcohols are first temporarily oxidized to carbonyl compounds by the hydrogen transfer catalyst. The carbonyl compounds then undergo deuteration at the carbon adjacent to the carbonyl group by keto-enol tautomerization in the presence of D(2)O and a catalytic amount of base. The deuterated carbonyl compounds are then reduced to produce deuterated alcohols. In support of the reaction mechanism, a well-defined bimetallic ruthenium complex was isolated from the reaction of [{(p-cymene)RuCl(2)}(2)] with ethanolamine. The activity of this complex is similar to that of [{(p-cymene)RuCl(2)}(2)]/ethanolamine.
Optimizing pentose utilization in yeast: the need for novel tools and approaches (2010)

Hexose and pentose cofermentation is regarded as one of the chief obstacles impeding economical conversion of lignocellulosic biomass to biofuels. Over time, successful application of traditional metabolic engineering strategy has produced yeast strains capable of utilizing the pentose sugars (especially xylose and arabinose) as sole carbon sources, yet major difficulties still remain for engineering simultaneous, exogenous sugar metabolism. Beyond catabolic pathways, the focus must shift towards non-traditional aspects of cellular engineering such as host molecular transport capability, catabolite sensing and stress response mechanisms. This review highlights the need for an approach termed 'panmetabolic engineering', a new paradigm for integrating new carbon sources into host metabolic pathways. This approach will concurrently optimize the interdependent processes of transport and metabolism using novel combinatorial techniques and global cellular engineering. As a result, panmetabolic engineering is a whole pathway approach emphasizing better pathways, reduced glucose-induced repression and increased product tolerance. In this paper, recent publications are reviewed in light of this approach and their potential to expand metabolic engineering tools. Collectively, traditional approaches and panmetabolic engineering enable the reprogramming of extant biological complexity and incorporation of exogenous carbon catabolism.
The clinical manipulation of angiogenesis: pathology, side-effects, surprises, and opportunities with novel human therapies (2000)

The rst phase of angiogenesis research has provided knowledge of the basic pathobiology of angiogenesis and its manipulation in models, mouse, and man. The rst line of therapeutic substances has been devised and is now in clinical trials. New lessons are being learned from clinical observations. Unexpected side-effects are being noted, particularly affecting the nervous system. Other side-effects may be anticipated from a sound knowledge of clinical pathology and recognition of the commonality of angiogenesis to multiple disease mechanisms, but these may be tolerable or avoidable. Angiogenesis researchers await further feedback and ideas from the clinic to stimulate the next phase of basic and applied research.
Template recognition of protein‐imprinted polymer surfaces (2000)

Synthetic materials capable of specifically recognizing proteins are important in separations, biosensors, and biomaterials. In this study, polysaccharide-like surfaces with tailored protein-binding nanocavities were prepared by a novel templating approach based on radiofrequency plasma deposition of thin films. The template-imprinted proteins included albumin, immunoglobulin, fibrinogen, lysozyme, ribonuclease A, α-lactalbumin, and glutamine synthetase. Transmission electron microscopy showed that nanometer-sized “pits” in the shape of imprinted protein were formed on the surfaces of template-imprinted polymer films. Electron spectroscopy for chemical analysis and time-of-flight secondary ion mass spectrometry indicated the saccharide covering of imprint surfaces and the removal of template proteins. 125I-labeled protein adsorption from single solutions showed a similar amount of protein was adsorbed to its own imprint as to the imprint of another protein. However, more protein remained on the former surface than on the latter following elution with the detergents Tween 20 or sodium dodecyl sulfate. Competitive adsorption of a binary protein mixture showed a highly preferential adsorption of template protein to the corresponding imprint. This template recognition diminished as the number of protein-imprinted pits decreased. Structurally unstable proteins such as α-lactalbumin exhibited weaker template recognition that “robust” proteins such as lysozyme. The hypothesis that protein recognition is due to complementarity between the protein and its imprinted nanopit was supported by protein turnover experiments that showed template protein adsorbed to its own imprint was less readily displaced by a nontemplate protein. © 2000 John Wiley & Sons, Inc. J Biomed Mater Res, 49, 1–11, 2000.
Identification of new genes associated with melanoma (2011)

A total of 284 differentially expressed genes was detected in PM compared with MN and 189 genes in MM compared with PM affecting common cancer pathways such as MAPK-, Wnt- and Notch-signalling. Using principal component analysis, the samples could be grouped according to their histological entity. We identified a panel of novel melanoma-associated markers: frizzled-related protein, an antagonist of Wnt; tranducin-like enhancer of split 1, a transcription factor partner of TCF/LEF-1; CNTN1, an activator of Notch signalling; two Serpin peptidase inhibitors, Serpin B3/B4 and the TGF-β family member GDF15, the latter with association to MAPK-signalling.
Natural Signal Classification by Neural Cliques and Phase-Locked Attractors (2006)

Cortical neural networks are responsible for identification, recognition and classification of natural signals mediated by various sensory channels. These tasks are still too complex to be accomplished by state-of-the-art engineering systems. There is, therefore, a great deal of interest in the development of suitable biologically-motivated architectures which are based on a realistic model of generic neural ensembles. We present a computational architecture for classification of natural signals, such as physiological signals,based on the emergence of instant neural cliques and phase-locked attractors in liquid architectures. The emergence of instant neural cliques enables mapping of complex classes of signals onto specific spatio-temporal firing patterns. The convergence of neural cliques onto attractors, along phase-locked pathways, reveals a new type dynamic behavior of neural ensembles, which lends itself to simple discrete-output computational systems.
Isoform-Specific Effect of Apolipoprotein E on Cell Survival and β-Amyloid-Induced Toxicity in Rat Hippocampal Pyramidal Neuronal Cultures (1998)

Although the genetic link between the ε4 allele of apolipoprotein E (apoE) and Alzheimer’s disease is well established, the isoform-specific activity of apoE underlying this correlation remains unclear. To determine whether apoE influences the neurotoxic actions of β-amyloid (Aβ), we examined the effect of native preparations of apoE3 and E4 on Aβ-induced toxicity in primary cultures of rat hippocampal pyramidal neurons. The source of apoE was conditioned medium from HEK-293 cells stably transfected with human apoE3 or E4 cDNA. ApoE4 (10 μg/ml) alone was toxic to the cultures, whereas apoE3 had no effect. ApoE3 treatment prevented the toxicity induced by 10 μ m Aβ(1–40) or Aβ(25–35). The apoE3 protective effect appears to be specific to Aβ-induced toxicity, because apoE3 did not protect against the cytotoxicity produced by NMDA or staurosporine, nor did apoE3 affect the increase in intracellular calcium induced by either NMDA or KCl. ApoE3 had no effect on the toxicity produced by Aβ in the presence of receptor-associated protein, an inhibitor of apoE receptors, particularly the LDL-receptor-related protein. Interaction with apoE receptors may not mediate the toxic actions of apoE4, because receptor-associated protein did not affect apoE4-induced neurotoxicity. Consistent with our previous biochemical experiments, analysis of the culture medium revealed that SDS-stable apoE3:Aβ complex is present in greater abundance than apoE4:Aβ complex. Thus, the protection from Aβ-induced neurotoxicity afforded by apoE3 treatment may result from clearance of the peptide by apoE3:Aβ complex formation and uptake by apoE receptors.
A novel approach to glioma gene therapy: down-regulation of the vascular endothelial growth factor in glioma cells using ribozymes. (1998)

Glioblastoma multiforme is one of the most highly vascularized solid neoplasms, therefore treatments that target neovascularization process would be of great clinical importance. Studies of glioblastoma angiogenesis have revealed that expression of the vascular endothelial growth factor (VEGF) is up-regulated in these tumors. Previous reports have shown that down-regulation of VEGF correlates with modification in the glioma growth. To examine this phenomenon further, in this study we constructed two hammerhead ribozymes (RZI and RZII) to target the 5' common region of VEGF mRNA. Both ribozymes exhibited site-specific cleavage to a 318-nucleotide VEGF transcript and showed a high digestion efficiency in vitro (65-95%). After the transfection of glioma cells with two expression vectors carrying the ribozyme sequence, Northern blot analyses detected high levels of ribozyme expression. Treatment of the glioma cells with the ribozymes resulted in a reduction in VEGF mRNA in six of eight clones. Furthermore, the anti-VEGF effect was confirmed at protein level. Thus, enzyme-linked immunoabsorbent analyses (ELISA) showed a >70% reduction in the VEGF165 expression level. These results indicate that hammerhead ribozymes may be useful in down-regulating VEGF expression and suggest that anti-VEGF strategies may be used to potentiate other gene therapies targeting tumor suppressor genes.