gebhart/patrepeval huggingface dataset:
Relative Contributions of Measles Virus Hemagglutinin- and Fusion Protein-Specific Serum Antibodies to Virus Neutralization (2005)

The relative contribution of measles virus hemagglutinin (H)- or fusion protein (F)-specific antibodies to virus neutralization (VN) has not been demonstrated. We have depleted these specific antibodies from sera collected from young adults, who had been vaccinated during childhood, by prolonged incubation with viable transfected human melanoma cells expressing H or F. Simultaneous depletion of antibodies of both specificities completely abrogated VN activity. Depletion of F-specific antibodies only had a minimal effect, whereas removal of H-specific antibodies resulted in almost complete reduction of VN activity. These results demonstrate that measles virus neutralizing antibodies are mainly directed to the H protein.
Characterization of the Phospholipases of<i>Bacillus cereus</i>and Their Effects on Erythrocytes, Bone, and Kidney Cells (1965)

Slein, Milton W. (Fort Detrick, Frederick, Md.), and Gerald F. Logan, Jr. Characterization of the phospholipases of Bacillus cereus and their effects on erythrocytes, bone, and kidney cells. J. Bacteriol. 90:69-81. 1965.-Culture filtrates of Bacillus cereus contain phospholipases that split phosphoryl choline, phosphoryl ethanolamine, and phosphoryl inositol from the phospholipids phosphatidyl choline (PTC), sphingomyelin, phosphatidyl ethanolamine (PTE), and phosphatidyl inositol (PTI). It is possible that one enzyme catalyzes the degradation of PTE and PTC, but the other phospholipases appear to be separate entities. Some activity on phosphatidyl serine has also been noted. Quantitative paper chromatography has been used for characterizing the phospholipases that are separated on N,N'-diethylaminoethyl cellulose columns. A procedure for the analysis of inositol is included. A sensitive kidney cortex homogenate test is described that depends on the release of alkaline phosphatase for the measurement of phosphatasemia factor (PF) activity associated with the phospholipases. The effects of the phospholipases on erythrocytes, kidney, and bone cells are discussed. Hemolysin activity is inhibited by crude soybean "lecithin," but hemolysis does not seem to be identical with PTE- or PTC-phospholipase activity. PF activity is also inhibited by the "lecithin." Highest PF activity is associated with PTI-phospholipase. The phospholipase fractions differ in their sensitivities to trypsin. Phospholipases with similar properties have been obtained from culture filtrates of B. anthracis.
Osteopontin: It's Role in Regulation of Cell Motility and Nuclear Factor κB-mediated Urokinase Type Plasminogen Activator Expression (2005)

Cancer progression depends on an accumulation of metastasis supporting cell signaling molecules that target signal transduction pathways and ultimately gene expression. Osteopontin (OPN) is one such chemokine like metastasis gene which plays a key signaling event in regulating the oncogenic potential of various cancers by controlling cell motility, invasiveness and tumor growth. We have reported that OPN stimulates tumor growth and nuclear factor kappaB (NFkappaB)-mediated promatrix metalloproteinase-2 (pro-MMP-2) activation through IkappaBalpha/IKK (IkappaBalpha kinase) signaling pathway in melanoma cells. Urokinase type plasminogen activator (uPA), a widely acting serine protease degrades the ECM components and plays a pivotal role in cancer progression. However, the molecular mechanism by which upstream kinases regulate the OPN-induced NFkappaB activation and uPA secretion in human breast cancer cells is not well defined. Here we report that OPN induces the phosphatidylinositol 3'-kinase (PI 3'-kinase) activity and phosphorylation of Akt/PKB (protein kinase B) in highly invasive (MDA-MB-231) and low invasive (MCF-7) breast cancer cells. The OPN-induced Akt phosphorylation was inhibited when cells were transfected with dominant negative mutant of p85 domain of PI 3'-kinase (Deltap85) indicating that PI 3'-kinase is involved in Akt phosphorylation. OPN enhances the interaction between IkappaBalpha kinase (IKK) and phosphorylated Akt. OPN also induces NFkappaB activation through phosphorylation and degradation of IkappaBalpha by inducing the IKK activity. OPN also enhances uPA secretion, cell motility and ECM-invasion. Furthermore, cells transfected with Deltap85 or super-repressor form of IkappaBalpha suppressed the OPN-induced uPA secretion and cell motility. Pretreatment of cells with PI 3'-kinase inhibitors or NFkappaB inhibitory peptide (SN50) reduced the OPN-induced uPA secretion, cell motility and ECM-invasion. Taken together, OPN induces NFkappaB activity and uPA secretion by activating PI 3'-kinase/Akt/IKK-mediated signaling pathways and further demonstrates a functional molecular link between OPN induced PI 3'-kinase dependent Akt phosphorylation and NFkappaB-mediated uPA secretion, and all of these ultimately control the motility and invasiveness of breast cancer cells.
Edge-constrained joint view triangulation for image interpolation (2002)

Image-based-interpolation creates smooth and photo-realistic views between two view points. The concept of joint view triangulation (JVT) has been proven to be an efficient multi-view representation to handle visibility issue. However, the existing JVT built only on a regular sampling grid, often produces undesirable artifacts for artificial objects. To tackle these problems, a new edge-constrained joint view triangulation is developed in this paper to integrate contour points and artificial rectilinear objects as triangulation constraints. Also a super-sampling technique is introduced to refine visible boundaries. The new algorithm is successfully demonstrated on many real image pairs.
Sophisticated Architecture is Required for the Sinoatrial Node to Perform Its Normal Pacemaker Function (2003)

The heart's pacemaker, the sinoatrial node, does not consist of a group of uniform sinoatrial node cells embedded in atrial muscle. Instead, it is a heterogeneous tissue with multiple cell types and a complex structure. Evidence suggests that from the periphery to the center of the sinoatrial node, there is a gradient in action potential shape, pacemaking, ionic current densities, connexin expression, Ca2+ handling, myofilament density, and cell size. This complexity may be necessary for the sinoatrial node to pacemake under diverse conditions, drive the more hyperpolarized atrial muscle, and resist proarrhythmic perturbations.
Laser damage in triglycine sulfate: Experimental results and thermal analysis (1973)

An investigation of the effects of 10.6-μm laser radiation on triglycine-sulfate (TGS) crystals determined that the primary irreversible damage mechanisms in TGS pyroelectric detectors are cracking and thermal decomposition (charring). Irradiation thresholds for cracking and charring were determined for TGS crystals of typical detector dimensions as a function of laser power density and irradiation time. These energy density thresholds exhibit two distinct regions of behavior: For short irradiation times E0 is independent of τ while for long times E0 varies as τ1/2. The thresholds are given empirically by E0 (crack) = [0.65 + 22(τ)1/2] J/cm2 and E0(char) = [4.0 + 34 (τ)1/2] J/cm2. A theoretical model describing thermally induced damage in irradiated crystals is presented. The energy density damage thresholds obtained from this model are compared to the experimental results. These results on material damage are used to predict damage thresholds in operating TGS detectors. These predictions are in good agreement with experimentally determined detector thresholds.
Proximal Deep Structured Models (2016)

Many problems in real-world applications involve predicting continuous-valued random variables that are statistically related. In this paper, we propose a powerful deep structured model that is able to learn complex non-linear functions which encode the dependencies between continuous output variables. We show that inference in our model using proximal methods can be efficiently solved as a feed-foward pass of a special type of deep recurrent neural network. We demonstrate the effectiveness of our approach in the tasks of image denoising, depth refinement and optical flow estimation.
Stochastic Variance-Reduced Policy Gradient (2018)

In this paper, we propose a novel reinforcement- learning algorithm consisting in a stochastic variance-reduced version of policy gradient for solving Markov Decision Processes (MDPs). Stochastic variance-reduced gradient (SVRG) methods have proven to be very successful in supervised learning. However, their adaptation to policy gradient is not straightforward and needs to account for I) a non-concave objective func- tion; II) approximations in the full gradient com- putation; and III) a non-stationary sampling pro- cess. The result is SVRPG, a stochastic variance- reduced policy gradient algorithm that leverages on importance weights to preserve the unbiased- ness of the gradient estimate. Under standard as- sumptions on the MDP, we provide convergence guarantees for SVRPG with a convergence rate that is linear under increasing batch sizes. Finally, we suggest practical variants of SVRPG, and we empirically evaluate them on continuous MDPs.
Quality comparison of automatic3D city house modelling methodsfrom laser data (2007)

Today there are different methods to automatically generate 3D models from laser data, whichgive varying results. The two methods used in this study are, a fully automatic methoddeveloped by the Swedish Defence Research Agency, FOI, and a semiautomatic methodwithin the program Terra Scan which is developed by Terrasolid, a Finnish company.The report describes the way these methods have been implemented, and it evaluates theoutput quality of each model set created from specified criteria.In order to be able to verify the quality, a statistical model was created with the purpose ofusing it for other situations as well in the future.The modelling methods gave different results and both had their strengths and theirweaknesses, which makes them applicable for different tasks. The strength in FOI’s method isthat it could recreate even more advanced buildings and still get a good visual impression, e.g.Stockholm’s central station.One advantage with the method used in Terra Scan is that it has good capabilities and tools toedit the models, which makes it possible to vary the quality depending on the purpose.In order to generate the best result this method is not supposed to be used in an automaticway.
Using Ultrasonic Hand Tracking to Augment Motion Analysis Based Recognition of Manipulative Gestures (2005)

The paper demonstrates how ultrasonic hand tracking can be used to improve the performance of a wearable, accelerometer and gyroscope based activity recognition system. Specifically we target the recognition of manipulative gestures of the type found in assembly and maintenance tasks. We discuss how relevant information can be extracted from the ultrasonic signal despite problems with low sampling rate, occlusions and reflections that occur in this type of application. We then introduce several methods of fusing the ultrasound and motion sensor information. We evaluate our methods on an experimental data set that contains 21 different actions performed repeatedly by three different subjects during simulated bike repair. Due to the complexity of the recognition tasks with many similar and vaguely defined actions and person independent training both the ultrasound and motion sensors perform poorly on their own. However with our fusion methods recognition rates well over 90% can be achieved for most activities. In extreme case recognition rates go up from just over 50% for separate classifications to nearly 89% with our fusion methods.
Intraretinal xenografts of differentiated human retinoblastoma cells integrate with the host retina (1992)

We report on the successful use of chemically modified Y79 human retinoblastoma cells for intraretinal xenografting into damaged adult mammalian eyes. Y79 cells were exposed in vitro to retinoic acid/butyrate to induce differentiation. Using a multisite transplantation method, the suspension was injected into the subretinal space of Fischer 344 rats. The survival, integration, and differentiation potential of these cells was studied, following their return to the intraocular milieu from which the progenitor cells originated. The grafted cells survived and differentiated into immature photoreceptor elements in the subretinal and intraretinal locations, as multiple clusters of rosette-forming cells intimately attached to the host neuroretina. The differentiation process included development of synaptic connectivity of the ribbon type with the surrounding neuropil. No signs of renewed cell division were found within grafts performed on 42 rat eyes, and there was no indication of cell-mediated host reaction against the transplants. This study indicates that tumorigenicity can be suppressed in mitotically arrested Y79 cells, and that these cells are capable of undergoing differentiation in vivo. This provides evidence of the remarkable differentiation properties of human retinoblastomas while indicating that Y79 cells may ultimately be able to substitute for fetal cells in experimental retinal transplantation.
Natural Gas Hydrates in the Alaskan Arctic (1988)

Summary The occurrence of in-situ natural gas hydrates in the arctic North Slope of Alaska is governed by several thermodynamic and geologic parameters, such as mean annual surface temperature, geothermal gradients above and below the base of the permafrost, pore-fluid salinity, permafrost base depth and temperature, subsurface pressure, and composition. Accurate knowledge of these parameters is necessary to determine the depths and thicknesses of zones of potential hydrate occurrences. The role of the parameters Is discussed in this paper. To determine the hydrate-stability zone, a nomogram has been developed and has been used for several Alaskan wells. For further delineation of gas hydrates, the neutron-transit-time crossplots have served as a valuable tool. To quantify gas hydrate deposits in terms of thickness, porosity, and saturation; use of neutron- and sonic-porosity-correction factors and Pickett crossplots is recommended.
Identification and Functional Characterization of Human Soluble Epoxide Hydrolase Genetic Polymorphisms (2000)

Human soluble epoxide hydrolase (sEH), an enzyme directing the functional disposition of a variety of endogenous and xenobiotic-derived chemical epoxides, was characterized at the genomic level for interindividual variation capable of impacting function. RNA was isolated from 25 human liver samples and used to generate full-length copies of soluble epoxide hydrolase cDNA. The resulting cDNAs were polymerase chain reaction amplified, sequenced, and eight variant loci were identified. The coding region contained five silent single nucleotide polymorphisms (SNPs) and two variant loci resulting in altered protein sequence. An amino acid substitution was identified at residue 287 in exon 8, where the more common arginine was replaced by glutamine. A second variant locus was identified in exon 13 where an arginine residue was inserted following serine 402 resulting in the sequence, arginine 403-404, instead of the more common, arginine 403. This amino acid insertion was confirmed by analyzing genomic DNA from individuals harboring the polymorphic allele. Slot blot hybridization analyses of the liver samples indicated that sEH mRNA steady-state expression varied approximately 10-fold. Transient transfection experiments with CHO and COS-7 cells were used to demonstrate that the two new alleles possess catalytic activity using trans-stilbene oxide as a model substrate. Although the activity of the glutamine 287 variant was similar to the sEH wild type allele, proteins containing the arginine insertion exhibited strikingly lower activity. Allelic forms of human sEH, with markedly different enzymatic profiles, may have important physiological implications with respect to the disposition of epoxides formed from the oxidation of fatty acids, such as arachidonic acid-derived intermediates, as well in the regulation of toxicity due to xenobiotic epoxide exposures.
Second-order resonant Raman spectra of single-walled carbon nanotubes (2000)

An analysis of the second-order resonant Raman spectra of single-walled carbon nanotubes using different laser energies in the range 1.58--2.71 eV is presented. Major emphasis is given to the overtones and combination modes associated with the two dominant features of the first-order spectra, the radial breathing mode and the tangential mode. Both of these modes, as well as their second-order counterparts, are associated with resonant enhancement phenomena arising from electron-phonon coupling to the unique one-dimensional density of electronic states for the single-wall carbon nanotubes.
Analysis of shortest-path routing algorithms in a dynamic network environment (1992)

In a dynamic network environment under heavy traffic load, shortest-path routing algorithms, particularly those that attempt to adapt to traffic changes, frequently exhibit oscillatory behaviors and cause performance degradation. In this paper we first examine the problems from the perspective of control theory and decision making, and then analyze the behaviors of the shortest-path routing algorithms in details.
Phytochelatins in Cadmium-Sensitive and Cadmium-Tolerant Silene vulgaris (Chain Length Distribution and Sulfide Incorporation) (1994)

In response to a range of Cd concentrations, the root tips of Cd-tolerant plants of Silene vulgaris exhibit a lower rate of PC production accompanied by a lower rate of longer chain PC synthesis than those of Cd-sensitive plants. At the same Cd exposure level, stable PC-Cd complexes are more rapidly formed in the roots of Cd-sensitive plants than in those of tolerant plants. At an equal PC concentration in the roots, the PC composition and the amount of sulfide incorporated per unit of PC-thiol is the same in both populations. Although these compounds might play some role in mechanisms that contribute to Cd detoxification, the ability to produce these compounds in greater amounts is not, itself, the mechanism that produces increased Cd tolerance in tolerant S. vulgaris plants.
Use of heme reporters for studies of cytochrome biosynthesis and heme transport (1996)

Strains of Escherichia coli containing mutations in the cydDC genes are defective for synthesis of the heme proteins cytochrome bd and c-type cytochromes. The cydDC genes encode a putative heterodimeric ATP-binding cassette transporter that has been proposed to act as an exporter of heme to the periplasm. To more fully understand the role of this transporter (and other factors) in heme protein biosynthesis, we developed plasmids that produce various heme proteins (e.g., cytochrome b5, cytochrome b562, and hemoglobin) in the periplasm of E. coli. By using these reporters, it was shown that the steady-state levels of polypeptides of heme proteins known to be stable without heme (e.g., cytochrome b5 and hemoglobin apoprotein) are significantly reduced in a cydC mutant. Exogenous addition of hemin to the cydC mutant still resulted in < 10% of wild-type steady-state levels of apohemoglobin in the periplasm. Since the results of heme reporter studies are not consistent with lower heme availability (i.e., heme export) in a cydC mutant, we analyzed other properties of the periplasm in cydC mutants and compared them with those of the periplasm in cydAB (encoding cytochrome bd) mutants and wild-type cells. Our results led us to favor a hypothesis whereby cydDC mutants are defective in the reduction environment within the periplasmic space. Such an imbalance could lead to defects in the synthesis of heme-liganded proteins. The heme reporters were also used to analyze strains of E. coli with a defect in genes encoding homologs of a different ABC transporter (helABC). The helABC genes have previously been shown to be required for the assembly of c-type cytochromes in Rhodobacter capsulatus (R. G. Kranz, J. Bacteriol. 171:456-464, 1989; D. L. Beckman, D. R. Trawick, and R. G. Kranz, Genes Dev. 6:268-283, 1992). This locus was shown to be essential in E. coli for endogenous cytochrome c biogenesis but not cytochrome b562 synthesis. Consistent with these and previous results, it is proposed that the HelABC transporter is specifically involved in heme export for ligation (hel). This class of periplasmic cytochromes is proposed to require heme liganding before undergoing correct folding.
Changing Incidence of Glomerular Disease in Olmsted County, Minnesota (2006)

Membranous nephropathy (MN) is considered the most common cause of nephrotic syndrome in white adults, but recent studies have shown an increasing incidence of focal segmental glomerulosclerosis (FSGS). These studies are difficult to interpret because the majority of cases came from urban tertiary referral centers. For validating these findings in the general population, trends in the incidence of various forms of glomerular disease (glomerulonephritis [GN]) among the residents of Olmsted County, MN were studied. Biopsy data of local patients who had a diagnosis of a nondiabetic glomerular disease from 1974 through 2003 were reviewed. Biopsies were categorized as (1) FSGS, (2) MN, (3) minimal change, (4) lupus nephritis, (5) membranoproliferative GN (MPGN), (6) IgA nephropathy (IgAN), (7) crescentic/necrotizing GN, and (8) other. Time trends in the annual age- and gender-adjusted (2000 US population) incidence rate per 100,000 Olmsted County population were estimated. A total of 195 biopsies were analyzed. Overall, IgAN was present in 22%, FSGS was present in 17%, and MN was present in 10%. Between 1974 to 1983 and 1994 to 2003, the incidence of any type of GN among Olmsted County residents increased more than two-fold (P < 0.001), FSGS by 13-fold (P < 0.001), and IgAN by three-fold (P = 0.002). Increases in MN were nonsignificant (2.5-fold; P = 0.13). Currently (1994 to 2003), the most frequent type of GN is IgAN (25%), followed by FSGS (20%) and MN (11%), with annual incidence rates of 2.1, 1.8, and 1.0 per 100,000/yr, respectively. This study confirms that the incidence of GN is growing overall, particularly for FSGS, which is the leading cause of nephrotic syndrome in white adults.
Initial degradation of deoxyribonucleic acid after injection in mammals. (1965)

The fate of DNA[2][1] in the blood of rabbits and mice, after i.v. and i.p. injection, has been followed by viscosimetry and chemical determination of acid-precipitable DNA. It has been shown that the initial degradation of DNA is due to neutral DNase activity, which sets up a very effective biochemical barrier against exogenous DNA. The change in molecular weight of DNA administered in vivo has been calculated and correlated with the time after which physical properties of DNA are not consistent with biologic activity. This time can be expected to vary from a few sec to about 10 min in animal species with low plasma DNase level, such as man. It can be increased by using DNase-inhibitors like methyl green.

Although it is unlikely that a large amount of highly polymerized DNA could reach cells without previous depolymerization after i.v. administration, our results are compatible with the expression of any infecting or transforming properties of this material.

 [1]: #fn-2