gebhart/patrepeval huggingface dataset:
Mean value coordinates for arbitrary planar polygons (2006)

Barycentric coordinates for triangles are commonly used in computer graphics, geometric modeling, and other computational sciences because they provide a convenient way to linearly interpolate the data that is given at the corners of a triangle. The concept of barycentric coordinates can also be extended in several ways to convex polygons with more than three vertices, but most of these constructions break down when used in the nonconvex setting. Mean value coordinates offer a choice that is not limited to convex configurations, and we show that they are in fact well-defined for arbitrary planar polygons without self-intersections. Besides their many other important properties, these coordinate functions are smooth and allow an efficient and robust implementation. They are particularly useful for interpolating data that is given at the vertices of the polygons and we present several examples of their application to common problems in computer graphics and geometric modeling.
Kinetic studies on the reaction of compound II of myeloperoxidase with ascorbic acid. Role of ascorbic acid in myeloperoxidase function. (1990)

Ascorbic acid is known to stimulate leukocyte functions. In a recent publication it was suggested that the role of ascorbic acid is to reduce compound II of myeloperoxidase back to the native enzyme (Bolscher, B. G. J. M., Zoutberg, G. R., Cuperus, R. A., and Wever, R. (1984) Biochim. Biophys. Acta 784, 189-191). In this paper we report rapid spectral scan and transient state kinetic results on the reaction of three myeloperoxidase compounds II, namely, human neutrophil myeloperoxidase, canine myeloperoxidase, and bovine spleen heme protein with ascorbate. We show by rapid scan spectra that compound II does not pass through any other intermediate when ascorbic acid reduces it back to native form. We also show that the reactions of all three compounds II involve a simple binding interaction before enzyme reduction with an apparent dissociation constant of 6.3 +/- 0.9 x 10(-4) to 2.0 +/- 0.3 x 10(-3)M and a first-order rate constant for reduction of 12.6 +/- 0.6 to 18.8 +/- 1.3 s-1. The optimum pH is 4.5, and at this pH the activation energy for the reaction is 13.2 kJ mol-1. Results of this work lend further evidence that the spleen green heme protein is very similar if not identical to leukocyte myeloperoxidase based on a comparison of spectral scans, pH-rate profiles, and kinetic parameters. We demonstrate that chloride cannot reduce compound II whereas iodide reduces compound II to native enzyme at a rate comparable to that of ascorbate. This explains why ascorbate accelerates chlorination but inhibits iodination. Formation of compound II is a dead end for the generation of hypochlorous acid; ascorbate regenerates more native enzyme to enhance the chlorination reaction namely: myeloperoxidase + peroxide----compound I followed by compound I + chloride----HOCl. On the other hand, ascorbate is a competitor with iodide for both compounds I and II and so inhibits iodination.
Use of beta-1,3-glucan-specific antibody to study the cyst wall of Pneumocystis carinii and effects of pneumocandin B0 analog L-733,560 (1994)

A new class of promising antipneumocystis agents, cyclic lipopeptide pneumocandin analogs, has been shown to effectively prevent Pneumocystis carinii cyst development in murine models. These compounds are believed to inhibit the biosynthesis of beta-1,3-glucan, a major constituent of the cell walls of various pathogenic fungi. However, all evidence of the presence of this polymer in P. carinii cysts is based on indirect methods. To address this, highly specific rabbit polyclonal antiserum was raised against a laminariheptaose-human transferrin hapten conjugate. This antiserum was used to demonstrate the presence of beta-1,3-glucan in alkaline extracts of P. carinii-infected rat lung tissue and to quantitate the degree of infection in this tissue as laminarin equivalents. The antiserum was also used to localize beta-1,3-glucan in P. carinii-infected rat lung tissue at the transmission electron microscopic level by immunogold labeling. High concentrations of beta-1,3-glucan were present in the electron-lucent layer of the P. carinii cyst wall, but beta-1,3-glucan was absent from intracystic bodies and trophozoites. Ultrastructural evaluation of lung tissue from P. carinii-infected rats treated with the pneumocandin analog L-733,560 demonstrated that the few cysts which remained are deformed, lack the translucent layer of the cyst wall, and contain minimal amounts of beta-1,3-glucan.
Application of ice-air jet blasting in treatment of sensitive surfaces (2007)

Application of water ice particles for precision cleaning was investigated experimentally. Several setups for ice particle generation and blasting were constructed. It was suggested that an efficient technology for formation of particles, in the range of 0.32.0 mm, involves ice crushing during water solidification. Freezing of water mist in a nitrogen bath constitutes the efficient technique to generate particles in the range of 1525 microns. It was shown that ice-air jet containing larger particles is suitable for precision decontamination of metal, plastic, electronic and electromechanical parts, while the micron size particles are appropriate for processing of substrates in biomedical and food industries.
Altered Low Frequency Oscillations of Cortical Vessels in Patients with Cerebrovascular Occlusive Disease – A NIRS Study (2013)

Analysis of cerebral autoregulation by measuring spontaneous oscillations in the low frequency spectrum of cerebral cortical vessels might be a useful tool for assessing risk and investigating different treatment strategies in carotid artery disease and stroke. Near infrared spectroscopy (NIRS) is a non-invasive optical method to investigate regional changes in oxygenated (oxyHb) and deoxygenated hemoglobin (deoxyHb) in the outermost layers of the cerebral cortex. In the present study we examined oxyHb low frequency oscillations, believed to reflect cortical cerebral autoregulation, in 16 patients with both symptomatic carotid occlusive disease and cerebral hypoperfusion in comparison to healthy controls. Each hemisphere was examined with two NIRS channels using a 3 cm source detector distance. Arterial blood pressure (ABP) was measured via a finger plethysmograph. Using transfer function analysis ABP-oxyHb phase shift and gain as well as inter-hemispheric phase shift and amplitude ratio were assessed. We found that inter-hemispheric amplitude ratio was significantly altered in hypoperfusion patients compared to healthy controls (P = 0.010), because of relatively lower amplitude on the hypoperfusion side. The inter-hemispheric phase shift showed a trend (P = 0.061) toward increased phase shift in hypoperfusion patients compared to controls. We found no statistical difference between hemispheres in hypoperfusion patients for phase shift or gain values. There were no differences between the hypoperfusion side and controls for phase shift or gain values. These preliminary results suggest an impairment of autoregulation in hypoperfusion patients at the cortical level detected by NIRS.
Ca2+/calmodulin-dependent protein kinase II: identification of threonine-286 as the autophosphorylation site in the alpha subunit associated with the generation of Ca2+-independent activity. (1988)

Autophosphorylation of Ca2+/calmodulin-dependent protein kinase II converts the enzyme to a Ca2+-independent form. The time course for this conversion correlates with the autophosphorylation of a threonine residue located within a thermolytic phosphopeptide common to the alpha and beta/beta' subunits. In the present study, this site was identified in the alpha subunit. After autophosphorylation under conditions that produced near-maximal Ca2+-independent activity, the alpha and beta/beta' subunits were separated by NaDodSO4/PAGE, and the alpha subunit was cleaved with cyanogen bromide. The major phosphopeptide (CB-1), containing phosphothreonine as the only radiolabeled amino acid, was purified by reverse-phase high performance liquid chromatography and subjected to automated gas-phase Edman degradation. The sequence obtained, Xaa-Arg-Gln-Glu-Thr-Val-Asp-Xaa-Leu-Lys-Lys-Phe-Asn-Ala-Arg-Arg-Lys-Leu, represented the NH2-terminal 18 residues (residues 282-299) of a 26-amino acid cyanogen bromide peptide predicted from the deduced primary structure of the alpha subunit and contained a consensus sequence for Ca2+/calmodulin-dependent kinase II phosphorylation that included Thr-286. The sequences obtained for two phosphopeptides derived from secondary chymotryptic digestion of CB-1 confirmed that Thr-286 was the phosphorylated residue.
1α,25(OH)2D3 Exerts Cytostatic Effects on Murine Osteosarcoma Cells and Enhances the Cytocidal Effects of Anticancer Drugs (1989)

The effects of 1 alpha,25-dihydroxyvitamin D3 (1 alpha,25-(OH)2D3), 1 alpha-hydroxyvitamin D3 (1 alpha(OH)D3), and dexamethasone on colony formation of Dunn osteosarcoma cells (TA 102 cells) were investigated. Concentrations of 1 alpha,25(OH)2D3, 1 alpha(OH)D3, and dexamethasone at which they exerted 50% reduction of the total area of TA 102 colony formation were 9 X 10(-9) M, 9 X 10(-8) M, and 5 X 10(-6) M, respectively. Effects of anticancer drugs on TA 102 cells were also investigated and concentrations needed for 50% growth inhibition (50% inhibitory concentration values) of cis-platinum, mitomycin C (MMC), methotrexate (MTX), and Adriamycin (ADR) against TA 102 cells were calculated to be 0.07 microgram/ml, 0.0008 microgram/ml, 0.0008 microgram/ml, and 0.0005 microgram/ml, respectively. The simultaneous treatment of TA 102 cells with 10(-8) M of 1 alpha,25(OH)2D3 and anticancer drugs significantly enhanced the respective inhibitory effects on colony formation. In this treatment, the IC50 value of MMC was calculated to be 6.4 X 10(-6) micrograms/ml, which was 1/160 of the expected IC50 value of MMC (8 X 10(-4) micrograms/ml). Similar synergistic effects were observed when the cells were treated with 1 alpha,25(OH)2D3 and low concentrations of cis-platinum, MTX, or ADR.
Scalable Sketch-Based Image Retrieval Using Color Gradient Features (2015)

We present a scalable system for sketch-based image retrieval (SBIR), extending the state of the art Gradient Field HoG (GF-HoG) retrieval framework through two technical contributions. First, we extend GF-HoG to enable color-shape retrieval and comprehensively evaluate several early-and late-fusion approaches for integrating the modality of color, considering both the accuracy and speed of sketch retrieval. Second, we propose an efficient inverse-index representation for GF-HoG that delivers scalable search with interactive query times over millions of images. A mobile app demo accompanies this paper (Android).
Self-organization of a sound source localization robot by perceptual cycle (2004)

We have built a system that can acquire the ability for sound source localisation by self-organization through repetition of motion and sensing. The learning model consists of two modules - a visual estimation module and an auditory estimation module of neural networks. The visual estimation module learns by direct inverse modeling and the auditory estimation module uses the output from the visual estimation module in learning. We conducted an experiment using a robot and a sound source to investigate the validity of the proposed module. The experimental results demonstrate that sound source localization ability can be acquired without supervision.
Protection Against Mucoid Pseudomonas aeruginosa in Rodent Models of Endobronchial Infections (1990)

Chronic endobronchial infection with mucoid Pseudomonas aeruginosa accounts for much of the morbidity and mortality in patients with cystic fibrosis (CF). Reduced morbidity is observed when infection is absent. Clinical investigations have implicated opsonizing antibody specific for the mucoid exopolysaccharide (MEP) surrounding these bacteria as a potential immunologic protective mechanism, whereas nonopsonizing antibody to MEP is not protective. Mice and rats immunized with doses of MEP that elicited opsonizing antibody had reduced levels of infection compared with nonimmune controls after intratracheal challenge with mucoid P. aeruginosa enmeshed in agar beads. Doses of MEP that elicited nonopsonizing antibody were not protective. Parallel experiments in which passive transfer of polyclonal and monoclonal opsonizing and nonopsonizing antibody were used yielded similar results. These data indicate that MEP-specific opsonizing antibody can protect against chronic P. aeruginosa infection in this model of disease.
Coot: model-building tools for molecular graphics (2004)

CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.
Nonadhesive Liquid Embolic Agent for Cerebral Arteriovenous Malformations: Preliminary Histopathological Studies in Swine Rete Mirabile (1998)

Embolyx E, an occlusive and nonadhesive embolic agent, is capable of producing permanent occlusion of swine RMB with the development of mild intra- and perivascular inflammatory changes and no clinical complications. The slow endovascular delivery of DMSO produces no untoward angiographic, pathological, or clinical changes. A fast injection of DMSO causes endothelial necrosis and severe inflammatory response in the arterial wall. This embolic material seems to have appropriate biochemical, anatomic, and histopathological characteristics to be used in the treatment of cerebral arteriovenous malformations or vascular cranial base tumors.
CD8+T lymphocytes infiltrating breast cancer (2012)

Lymphocytic infiltration is often seen in breast cancer and has been suggested as a marker of host anti-tumor response but its importance in prognosis remains controversial. Our recent study demonstrated an association between tumor-infiltrating CD8(+) T lymphocytes in invasive breast cancer and better prognosis.
Physician Incentives in Health Maintenance Organizations (2004)

Managed care organizations rely on incentives that encourage physicians to limit medical expenditures, but little is known about how physicians respond to these incentives. We address this issue by analyzing the physician incentive contracts in use at a health maintenance organization. By combining knowledge of the incentive contracts with internal company records, we examine how medical expenditures vary with the intensity of the incentive to cut costs. Our investigation leads us to a novel explanation for high‐powered group incentives: such incentives can improve efficiency in the allocation of resources when the allocation process is based on the professional judgment of multiple agents. Our empirical work indicates that medical expenditures at the HMO are 5 percent lower than they would have been in the absence of incentives.
Unsupervised Models for Named Entity Classification (1999)

This paper discusses the use of unlabeled examples for the problem of named entity classification. A large number of rules is needed for coverage of the domain, suggesting that a fairly large number of labeled examples should be required to train a classifier. However, we show that the use of unlabeled data can reduce the requirements for supervision to just 7 simple &amp;quot;seed&amp;quot; rules. The approach gains leverage from natural redundancy in the data: for many named-entity instances both the spelling of the name and the context in which it appears are sufficient to determine its type. We present two algorithms. The first method uses a similar algorithm to that of (Yarowsky 95), with modifications motivated by (Blum and Mitchell 98). The second algorithm extends ideas from boosting algorithms, designed for supervised learning tasks, to the framework suggested by (Blum and Mitchell 98). 1 Introduction Many statistical or machine-learning approaches for natural language problems require a rel...
Essential contribution of caspase 3/CPP32 to apoptosis and its associated nuclear changes (1998)

Caspases are fundamental components of the mammalian apoptotic machinery, but the precise contribution of individual caspases is controversial. CPP32 (caspase 3) is a prototypical caspase that becomes activated during apoptosis. In this study, we took a comprehensive approach to examining the role of CPP32 in apoptosis using mice, embryonic stem (ES) cells, and mouse embryonic fibroblasts (MEFs) deficient for CPP32. CPP32(ex3-/-) mice have reduced viability and, consistent with an earlier report, display defective neuronal apoptosis and neurological defects. Inactivation of CPP32 dramatically reduces apoptosis in diverse settings, including activation-induced cell death (AICD) of peripheral T cells, as well as chemotherapy-induced apoptosis of oncogenically transformed CPP32(-/-) MEFs. As well, the requirement for CPP32 can be remarkably stimulus-dependent: In ES cells, CPP32 is necessary for efficient apoptosis following UV- but not gamma-irradiation. Conversely, the same stimulus can show a tissue-specific dependence on CPP32: Hence, TNFalpha treatment induces normal levels of apoptosis in CPP32 deficient thymocytes, but defective apoptosis in oncogenically transformed MEFs. Finally, in some settings, CPP32 is required for certain apoptotic events but not others: Select CPP32(ex3-/-) cell types undergoing cell death are incapable of chromatin condensation and DNA degradation, but display other hallmarks of apoptosis. Together, these results indicate that CPP32 is an essential component in apoptotic events that is remarkably system- and stimulus-dependent. Consequently, drugs that inhibit CPP32 may preferentially disrupt specific forms of cell death.
Acetic Acid Production from Fructose by Clostridium formicoaceticum Immobilized in a Fibrous-Bed Bioreactor (1998)

The fermentation kinetics of acetic acid production from fructose by Clostridium formicoaceticum was studied at pH 7.6 and 37 degreesC. Recycle batch, fed-batch, and continuous fermentations using immobilized cells in a fibrous-bed bioreactor were studied for their potential application in producing acetic acid from fructose, a fermentable sugar commonly found in corn steep liquor and many other food processing wastes. For the immobilized cell fermentation, acetic acid yield from fructose was approximately 1.0 g/g, with a final acetate concentration of approximately 78 g/L and the overall reactor productivity (based on the fibrous bed bioreactor volume) of approximately 0.95 g/(L.h) in the fed-batch fermentation. For a similar fed-batch fermentation with free cells, acetic acid yield was approximately 0.9 g/g, the highest final acetate concentration was approximately 46 g/L, and the overall productivity was approximately 0.12 g/(L.h). In the continuous fermentation with immobilized cells, the reactor productivity decreased from 3.2 to 1. 3 g/(L.h) as retention time increased from 16 to 72 h to reach 100% conversion. Compared to free-cell fermentations, the superior performance of the fibrous-bed bioreactor can be attributed to the high density (>30 g/L) of viable cells immobilized in the fibrous bed. The fermentation product, acetic acid, was found to be a noncompetitive inhibitor to the cells. However, the immobilized cells had a higher maximum production rate (pmax) and a higher value for the inhibition rate constant (Kp) than those for the free cells, suggesting that the immobilized cells in the fibrous-bed bioreactor were less sensitive to acetic acid inhibition than the free cells. This improvement in kinetic behaviors for immobilized cells confirms that the fibrous-bed bioreactor can be used as an effective tool for adapting and screening for acetate-tolerant strains.
A Single-Vector, Single-Injection Trivalent Filovirus Vaccine: Proof of Concept Study in Outbred Guinea Pigs (2015)

The filoviruses, Marburg marburgvirus (MARV), Zaire ebolavirus (ZEBOV), and Sudan ebolavirus (SEBOV), cause severe and often fatal hemorrhagic fever in humans and nonhuman primates (NHPs). Monovalent recombinant vesicular stomatitis virus (rVSV)-based vaccine vectors, which encode a filovirus glycoprotein (GP) in place of the VSV glycoprotein, have shown 100% efficacy against homologous filovirus challenge in rodent and NHP studies. Here, we examined the utility of a single-vector, single-injection trivalent rVSV vector expressing MARV, ZEBOV, and SEBOV GPs to protect against MARV-, ZEBOV-, and SEBOV-induced disease in outbred Hartley guinea pigs where we observed protection from effects of all 3 filoviruses.
Non-Specific dsRNA-Mediated Antiviral Response in the Honey Bee (2013)

Honey bees are essential pollinators of numerous agricultural crops. Since 2006, honey bee populations have suffered considerable annual losses that are partially attributed to Colony Collapse Disorder (CCD). CCD is an unexplained phenomenon that correlates with elevated incidence of pathogens, including RNA viruses. Honey bees are eusocial insects that live in colonies of genetically related individuals that work in concert to gather and store nutrients. Their social organization provides numerous benefits, but also facilitates pathogen transmission between individuals. To investigate honey bee antiviral defense mechanisms, we developed an RNA virus infection model and discovered that administration of dsRNA, regardless of sequence, reduced virus infection. Our results suggest that dsRNA, a viral pathogen associated molecular pattern (PAMP), triggers an antiviral response that controls virus infection in honey bees.
Studies with Endothelin-3 and Endothelin-1 on Rat Blood Pressure and Isolated Tissues (1989)

In an anesthetized rat, endothelin-1 (ET-1) causes a rapid, transient fall in blood pressure followed by a large, sustained rise. Rat endothelin-3 (ET-3) differs from porcine endothelin-1 (ET-1) by six amino acids and is 20 times less potent at contracting rat aortic strips. The comparative effects of ET-3 and ET-1 on blood pressure were studied in anesthetized rats in which the arterial blood pressure was continually monitored. Dose-response curves for the contraction of rat stomach strips, guinea pig ileum, and guinea pig trachea were also constructed. In the anesthetized rat, ET-3 was slightly (but not significantly) less potent than ET-1 at producing the transient blood pressure fall but was three times less potent at causing the subsequent rise. The two peptides were equipotent at contracting rat stomach strips but ET-3 was 10 times less potent at contracting the guinea pig ileum. Rat ET-3 was less potent at contracting the guinea pig trachea and had a lower maximal effect. These results suggest the existence of multiple receptor subtypes for ET.
Quantification of Bacterial Groups within Human Fecal Flora by Oligonucleotide Probe Hybridization (2000)

To investigate the population structure of the predominant phylogenetic groups within the human adult fecal microbiota, a new oligonucleotide probe designated S-G-Clept-1240-a-A-18 was designed, validated, and used with a set of five 16S rRNA-targeted oligonucleotide probes. Application of the six probes to fecal samples from 27 human adults showed additivity of 70% of the total 16S rRNA detected by the bacterial domain probe. The Bacteroides group-specific probe accounted for 37% +/- 16% of the total rRNA, while the enteric group probe accounted for less than 1%. Clostridium leptum subgroup and Clostridium coccoides group-specific probes accounted for 16% +/- 7% and 14% +/- 6%, respectively, while Bifidobacterium and Lactobacillus groups made up less than 2%.