gebhart/patrepeval huggingface dataset:
Quantitative detection of periodontopathic bacteria in atherosclerotic plaques from coronary arteries (2009)

Oral pathogens, including periodontopathic bacteria, are thought to be aetiological factors in the development of cardiovascular disease. In this study, the presence of Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum-periodonticum-simiae group, Porphyromonas gingivalis, Prevotella intermedia, Prevotella nigrescens and Tannerella forsythia in atheromatous plaques from coronary arteries was determined by real-time PCR. Forty-four patients displaying cardiovascular disease were submitted to periodontal examination and endarterectomy of coronary arteries. Approximately 60-100 mg atherosclerotic tissue was removed surgically and DNA was obtained. Quantitative detection of periodontopathic bacteria was performed using universal and species-specific TaqMan probe/primer sets. Total bacterial and periodontopathic bacterial DNA were found in 94.9 and 92.3 %, respectively, of the atheromatous plaques from periodontitis patients, and in 80.0 and 20.0 %, respectively, of atherosclerotic tissues from periodontally healthy subjects. All periodontal bacteria except for the F. nucleatum-periodonticum-simiae group were detected, and their DNA represented 47.3 % of the total bacterial DNA obtained from periodontitis patients. Porphyromonas gingivalis, A. actinomycetemcomitans and Prevotella intermedia were detected most often. The presence of two or more periodontal species could be observed in 64.1 % of the samples. In addition, even in samples in which a single periodontal species was detected, additional unidentified microbial DNA could be observed. The significant number of periodontopathic bacterial DNA species in atherosclerotic tissue samples from patients with periodontitis suggests that the presence of these micro-organisms in coronary lesions is not coincidental and that they may in fact contribute to the development of vascular diseases.
The effects of UV-B irradiation on the corneal endothelium (1987)

Rabbit eyes, in vivo and in vitro, were exposed to UV-B irradiation at 300 nm, from a mercury arc lamp with an 11 nm bandpass filter. Radiant exposure ranged from 0.1 J/cm2 to 0.5 J/cm2. In vivo, swelling of the cornea resulted over a 12 to 40 hr period, the extent and duration being directly related to exposure. Recovery of normal thickness was complete within four days. Corneas removed at 18 hr after exposure recovered normal thickness during a five hour perfusion period, except for those most heavily exposed. When removed at 42 hr post exposure all corneas thinned to almost normal thickness. SEM showed the endothelial cells of exposed eyes to have either exaggerated villi on the surface and a disorganized mosaic or, after higher exposures, to be devoid of villi and have loose, flap like cell borders and large "blebs." After exposure of isolated corneas mounted for perfusion, swelling again ensued and similar changes were observed in the appearance of the cells, except that "blebs" were not found. No significant changes were observed in the metabolic components ATP, ascorbate and glutathione, nor was there any indication of lipid peroxidation. At higher in vivo exposures, the aqueous humor did show a decrease in ascorbate concentration and an increase in protein content, which probably result from a breakdown of the blood-aqueous barrier. UV-B irradiation may cause or promote changes in the endothelium associated with aging, but the one time radiant exposures of the magnitude used in this study, appear to have no severe or permanently toxic effects.
Role of the Electrophilic Lipid Peroxidation Product 4-Hydroxynonenal in the Development and Maintenance of Obesity in Mice (2008)

The lipid peroxidation product 4-hydroxynonenal (4-HNE) is a signaling mediator with wide-ranging biological effects. In this paper, we report that disruption of mGsta4, a gene encoding the 4-HNE-conjugating enzyme mGSTA4-4, causes increased 4-HNE tissue levels and is accompanied by age-dependent development of obesity which precedes the onset of insulin resistance in 129/sv mice. In contrast, mGsta4 null animals in the C57BL/6 genetic background have normal 4-HNE levels and remain lean, indicating a role of 4-HNE in triggering or maintaining obesity. In mGsta4 null 129/sv mice, the expression of the acetyl-CoA carboxylase (ACC) transcript is enhanced several-fold with a concomitant increase in the tissue level of malonyl-CoA. Also, mitochondrial aconitase is partially inhibited, and tissue citrate levels are increased. Accumulation of citrate could lead to allosteric activation of ACC, further augmenting malonyl-CoA levels. Aconitase may be inhibited by 4-HNE or by peroxynitrite generated by macrophages which are enriched in white adipose tissue of middle-aged mGsta4 null 129/sv mice and, upon lipopolysaccharide stimulation, produce more reactive oxygen species and nitric oxide than macrophages from wild-type mice. Excessive malonyl-CoA synthesized by the more abundant and/or allosterically activated ACC in mGsta4 null mice leads to fat accumulation by the well-known mechanisms of promoting fatty acid synthesis and inhibiting fatty acid beta-oxidation. Our findings complement the recent report that obesity causes both a loss of mGSTA4-4 and an increase in the level of 4-HNE [Grimsrud, P. A., et al. (2007) Mol. Cell. Proteomics 6, 624-637]. The two reciprocal processes are likely to establish a positive feedback loop that would promote and perpetuate the obese state.
Solution structure of .omega.-conotoxin GVIA using 2-D NMR spectroscopy and relaxation matrix analysis (1993)

We report here the solution structure of omega-conotoxin GVIA, a peptide antagonist of the N-type neuronal voltage-sensitive calcium channel. The structure was determined using two-dimensional NMR in combination with distance geometry and restrained molecular dynamics. The full relaxation matrix analysis program MARDIGRAS was used to generate maximum and minimum distance restraints from the crosspeak intensities in NOESY spectra. The 187 restraints obtained were used in conjunction with 23 angle restraints from vicinal coupling constants as input for the structure calculations. The backbones of the best 21 structures match with an average pairwise RMSD of 0.58 A. The structures contain a short segment of triple-stranded beta-sheet involving residues 6-8, 18-21, and 24-27, making this the smallest published peptide structure to contain a triple-stranded beta-sheet. Conotoxins have been shown to be effective neuroprotective agents in animal models of brain ischemia. Our results should aid in the design of novel nonpeptide compounds with potential therapeutic utility.
Edge-preserving smoothing and applications (2002)

In this article, we introduce a noise-reduction method, edge-preserving smoothing (EPS), that we have successfully applied as a preprocessing step before running algorithms to detect sharp edges in seismic data. These edges often correspond to important geologic features (e.g., faults, fractures, and channels).
Acute and Chronic Nicotinic Interactions with Dopamine Systems and Working Memory Performancea (1995)

Nicotine has been found to improve memory performance in a variety of tests in rats, monkeys, and humans. Interactions of nicotinic systems with dopamine (DA) systems may be important for this effect. We conducted a series of studies of nicotinic agonist and antagonist interactions with DA systems using rats in a win-shift working memory task in the radial-arm maze. The working memory deficit caused by the nicotinic antagonist mecamylamine was potentiated by the D1/D2 DA antagonist haloperidol and the specific D2 antagonist raclopride. In contrast, the mecamylamine-induced deficit was reversed by co-administration of the D2/D3 agonist quinpirole. Nicotine also has significant interactions with dopamine drugs with regard to working memory performance in the radial-arm maze. The DA agonist pergolide did not by itself improve radial-arm maze memory performance, but when given together with nicotine it produced an elevated dose-dependent increase in choice accuracy. The D1 agonist SKF 38393 significantly impaired radial-arm maze choice accuracy. Nicotine was effective in reversing this deficit. When given together with nicotine, the D2/D3 agonist quinpirole improved RAM choice accuracy relative to either drug alone. Acute local infusion of mecamylamine to the midbrain DA nuclei effectively impairs working memory function in the radial-arm maze. In contrast to acute nicotinic manipulations, considerably less evidence exists that the effects of chronic nicotine administration are influenced by DA systems. This may be an example of the different neural substrates that underlie the memory improvement caused by acute and chronic nicotine.
Practical Block-Wise Neural Network Architecture Generation (2018)

Convolutional neural networks have gained a remarkable success in computer vision. However, most usable network architectures are hand-crafted and usually require expertise and elaborate design. In this paper, we provide a block-wise network generation pipeline called BlockQNN which automatically builds high-performance networks using the Q-Learning paradigm with epsilon-greedy exploration strategy. The optimal network block is constructed by the learning agent which is trained sequentially to choose component layers. We stack the block to construct the whole auto-generated network. To accelerate the generation process, we also propose a distributed asynchronous framework and an early stop strategy. The block-wise generation brings unique advantages: (1) it performs competitive results in comparison to the hand-crafted state-of-the-art networks on image classification, additionally, the best network generated by BlockQNN achieves 3.54% top-1 error rate on CIFAR-10 which beats all existing auto-generate networks. (2) in the meanwhile, it offers tremendous reduction of the search space in designing networks which only spends 3 days with 32 GPUs, and (3) moreover, it has strong generalizability that the network built on CIFAR also performs well on a larger-scale ImageNet dataset.
Shallow parsing with conditional random fields (2003)

Conditional random fields for sequence labeling offer advantages over both generative models like HMMs and classifiers applied at each sequence position. Among sequence labeling tasks in language processing, shallow parsing has received much attention, with the development of standard evaluation datasets and extensive comparison among methods. We show here how to train a conditional random field to achieve performance as good as any reported base noun-phrase chunking method on the CoNLL task, and better than any reported single model. Improved training methods based on modern optimization algorithms were critical in achieving these results. We present extensive comparisons between models and training methods that confirm and strengthen previous results on shallow parsing and training methods for maximum-entropy models.
Changing trends in anti-coagulant therapies. Are heparins and oral anti-coagulants challenged? (2008)

The conventional management of thrombotic and cardiovascular disorders is based on the use of heparin, oral anticoagulants and aspirin. Despite progress in the sciences, these drugs still remain a challenge and mystery. The development of low molecular weight heparins (LMWHS) and the synthesis of heparinomimetics represent a refined use of heparin. Additional drugs will continue to develop. However, none of these drugs will ever match the polypharmacology of heparin. Aspirin still remains the leading drug in the management of thrombotic and cardiovascular disorders. The newer antiplatelet drugs such as adenosine diphosphate receptor inhibitors, GPIIb/IIIa inhibitors and other specific inhibitors have limited effects and have been tested in patients who have already been treated with aspirin. Warfarin provides a convenient and affordable approach in the long-term outpatient management of thrombotic disorders. The optimized use of these drugs still remains the approach of choice to manage thrombotic disorders. The new anticoagulant targets, such as tissue factor, individual clotting factors, recombinant forms of serpins (antithrombin, heparin co-factor II and tissue factor pathway inhibitors), recombinant activated protein C, thrombomodulin and site specific serine proteases inhibitors complexes have also been developed. There is a major thrust on the development of orally bioavailable anti-Xa and IIa agents, which are slated to replace oral anticoagulants. Both the anti-factor Xa and anti-IIa agents have been developed for oral use and have provided impressive clinical results. However, safety concerns related to liver enzyme elevations and thrombosis rebound have been reported with their use. For these reasons, the US Food and Drug Administration did not approve the orally active antithrombin agent Ximelagatran for several indications. The synthetic pentasaccharide (Fondaparinux) has undergone clinical development. Unexpectedly, Fondaparinux also produced major bleeding problems at minimal dosages. Fondaparinux represents only one of the multiple pharmacologic effects of heparins. Thus, its therapeutic index will be proportionately narrower. The newer antiplatelet drugs have added a new dimension in the management of thrombotic disorders. The favorable clinical outcomes with aspirin and clopidogrel have validated COX-1 and P2Y12 receptors as targets for new drug development. Prasugrel, a novel thienopyridine, Cangrelor and AZD 6140 represent newer P2Y12 antagonists. Cangrelor and AZD 6140 are direct inhibitors, whereas Prasugrel requires metabolic activation. While clinically effective, recent results have prompted a closure of a clinical trial with Prasugrel due to bleeding. The newer anticoagulant and antiplatelet drugs are attractive, however, none of these are expected to replace the conventional drugs in polytherapeutic approaches. Heparins, warfarin and aspirin will continue to play a major role in the management of thrombotic and cardiovascular disorders for years to come.
Pulmonary arteriovenous malformations: techniques and long-term outcome of embolotherapy. (1988)

Over a 10-year period, 276 pulmonary arteriovenous malformations (PAVMs) were occluded with balloon embolotherapy in 76 patients, 67 (88%) of whom had hereditary hemorrhagic telangiectasia. Eleven patients (14%) were discovered by means of family screening with measurement of arterial blood gases and chest radiography. Epistaxis, dyspnea, hemoptysis, and hemothorax occurred in 79%, 71%, 13%, and 9% of patients, respectively. Clinical histories of strokes and transient ischemic attacks were present in 18% and 37% of patients, respectively. Computed tomographic scans of 59 patients showed stroke in 36%. Sixty-five percent of PAVMs were located in the lower lobes, which correlated with the finding of more pronounced hypoxemia in the upright position. After embolotherapy, symptomatic hypoxemia was corrected, and serial values have remained constant for 5 years. Complications were minimal, and no patient required surgery. Balloon embolotherapy is effective long-term therapy for PAVMs, and family screening should be pursued because of the possibility of a higher frequency of paradoxical embolization (stroke) than previously recognized.
Functional Alterations in Alzheimerʼs Disease (1993)

In Alzheimer's disease, the relationship between structural alterations such as neurofibrillary tangles and senile plaques and neuronal function is unknown. Cytochrome oxidase, the terminal enzyme of the electron transport, is a marker of neuronal functional activity. Its activity is diminished in experimentally deafferented neurons. Based on evidence that the molecular layer of the dentate gyrus is deafferented in the brains of individuals with Alzheimer's disease, we hypothesized that cytochrome oxidase activity would be diminished in this region secondary to reduced glutamatergic input. Using cytochrome oxidase histochemistry, we found a change in the distribution of cytochrome oxidase in the molecular layer of the dentate gyrus and a decrease in activity in both the dentate gyrus and hippocampal subfields in Alzheimer's disease. In contrast, we found relatively little structural pathology in the dentate gyrus, CA4, and CA3 in these individuals. These results suggest that neurons that remain structurally intact in Alzheimer's disease may nonetheless undergo changes in metabolic function as neural systems fail.
Quality Control and Protein Folding in the Secretory Pathway (2003)

The biosynthesis of secretory and membrane proteins in the endoplasmic reticulum (ER) yields mostly properly folded and assembled structures with full biological activity. Such fidelity is maintained by quality control (QC) mechanisms that avoid the production of nonnative structures. QC relies on chaperone systems in the ER that monitor and assist in the folding process. When folding promotion is not sufficient, proteins are retained in the ER and eventually retranslocated to the cytosol for degradation by the ubiquitin proteasome pathway. Retention of proteins that fail QC can sometimes occur beyond the ER, and degradation can take place in lysosomes. Several diseases are associated with proteins that do not pass QC, fail to be degraded efficiently, and accumulate as aggregates. In other cases, pathology arises from the downregulation of mutated but potentially functional proteins that are retained and degraded by the QC system.
Identification of Immunodominant Antigens during Infection with Mycobacterium tuberculosis (1992)

T lymphocytes isolated from mice infected with Mycobacterium tuberculosis response vigorously to proteins secreted by the bacilli and these antigens may be of importance in the generation of protective immunity against the disease. In this study, short-term culture filtrate (ST-CF), which constitutes a complex mixture of secreted proteins, was fractionated by a modified preparative SDS-PAGE technique. The ability of each fraction to be recognized by T cells isolated from infected mice was evaluated by quantifying proliferation and IFN-gamma production in cell cultures. Two molecular mass regions 4-11 and 26-35 kDa were found to possess marked stimulatory properties. Four potent single antigens were mapped within the stimulatory regions. These purified antigens stimulated T cells isolated from mice at the height of a tuberculous infection to produce large amounts of IFN-gamma. Two of these stimulatory antigens belonged to the antigen 85 complex.
Large-scale Comparative Sentiment Analysis of News Articles (2009)

Online media offers great possibilities to retrieve more news items than ever. In contrast to these technical developments, human capabilities to read all these news items have not increased likewise. To bridge this gap, this poster presents a visual analytics tool for conducting semi-automatic sentiment analysis of large news feeds. The tool retrieves and analyzes the news of two categories (Terrorist Attack and Natural Disasters) and news which belong to both categories of the Europe Media Monitor (EMM) with respect to positive and negative opinion words. While this happens automatically, the more demanding news analysis of finding trends, spotting peculiarities and putting events into context is left to the human expert.
Interleukin‐1, Interleukin‐2, Interleukin‐4, Interleukin‐6, Tumor Necrosis Factor α, and Interferon‐γ Levels in Sera from Patients With Scleroderma (1992)

IL-2, IL-4, and IL-6 may be among the cytokines that contribute to the disease process in scleroderma patients. To our knowledge, this is the first report of elevated serum IL-4 levels in human disease.
Analysis of recommendation algorithms for e-commerce (2000)

Article Free Access Share on Analysis of recommendation algorithms for e-commerce Authors: Badrul Sarwar GroupLens Research Group / Army HPC Research Center, Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN GroupLens Research Group / Army HPC Research Center, Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MNView Profile , George Karypis GroupLens Research Group / Army HPC Research Center, Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN GroupLens Research Group / Army HPC Research Center, Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MNView Profile , Joseph Konstan GroupLens Research Group / Army HPC Research Center, Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN GroupLens Research Group / Army HPC Research Center, Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MNView Profile , John Riedl GroupLens Research Group / Army HPC Research Center, Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN GroupLens Research Group / Army HPC Research Center, Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MNView Profile Authors Info & Claims EC '00: Proceedings of the 2nd ACM conference on Electronic commerceOctober 2000 Pages 158–167https://doi.org/10.1145/352871.352887Published:17 October 2000Publication History 1,115citation13,063DownloadsMetricsTotal Citations1,115Total Downloads13,063Last 12 Months2,132Last 6 weeks300 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Nutritional and Chemical Composition and Antiviral Activity of Cultivated Seaweed Sargassum naozhouense Tseng et Lu (2012)

Sargassum naozhouense is a brown seaweed used in folk medicine and applied for thousands of years in Zhanjiang, Guangdong province, China. This study is the first time to investigate its chemical composition and antiviral activity. On the dry weight basis, this seaweed was constituted of ca. 35.18% ash, 11.20% protein, 1.06% lipid and 47.73% total carbohydrate, and the main carbohydrate was water-soluble polysaccharide. The protein analysis indicated the presence of essential amino acids, which accounted for 36.35% of the protein. The most abundant fatty acids were C14:0, C16:0, C18:1 and C20:4. The ash fraction analysis indicated that essential minerals and trace elements, such as Fe, Zn and Cu, were present in the seaweed. IR analysis revealed that polysaccharides from cultivated S. naozhouense may be alginates and fucoidan. The polysaccharides possessed strong antiviral activity against HSV-1 in vitro with EC(50) of 8.92 μg/mL. These results demonstrated cultivated S. naozhouense has a potential for its use in functional foods and antiviral new drugs.