gebhart/patrepeval huggingface dataset:
The Optimal Antigen Response of Chimeric Antigen Receptors Harboring the CD3ζ Transmembrane Domain Is Dependent upon Incorporation of the Receptor into the Endogenous TCR/CD3 Complex (2010)

Chimeric Ag receptors (CARs) expressed in T cells permit the redirected lysis of tumor cells in an MHC-unrestricted manner. In the Jurkat T cell model system, expression of a carcinoembryonic Ag-specific CD3zeta CAR (MFEzeta) resulted in an increased sensitivity of the transduced Jurkat cell to generate cytokines when stimulated through the endogenous TCR complex. This effect was driven through two key characteristics of the MFEzeta CAR: 1) receptor dimerization and 2) the interaction of the CAR with the endogenous TCR complex. Mutations of the CAR transmembrane domain that abrogated these interactions resulted in a reduced functional capacity of the MFEzeta CAR to respond to carcinoembryonic Ag protein Ag. Taken together, these results indicate that CARs containing the CD3zeta transmembrane domain can form a complex with the endogenous TCR that may be beneficial for optimal T cell activation. This observation has potential implications for the future design of CARs for cancer therapy.
Solution structure of hyaluronic acid oligomers by experimental and theoretical NMR, and molecular dynamics simulation (2001)

The conformational properties of hyaluronic acid (HA) oligomers in aqueous solution were investigated by combining high-resolution NMR experimental results, theoretical simulation of NMR two-dimensional (2D) spectra by Complete Relaxation Matrix Analysis (CORMA), and molecular dynamics calculations. New experimental findings recorded for the tetra- and hexasaccharides enabled the stiffness of the HA and its viscoelastic properties to be interpreted. In particular, rotating frame nuclear Overhauser effect spectroscopy spectra provided new information about the arrangement of the glycosidic linkage. From (13)C NMR relaxation the rotational correlation time (tau(c)) were determined. The tau(c) were employed in the calculation of geometrical constraints, by using the MARDIGRAS algorithm. Restrained simulated annealing and 1 ns of unrestrained molecular dynamic simulations were performed on the hexasaccharide in a box of 1215 water molecules. The beta(1 --> 3) and beta(1 --> 4) glycosidic links were found to be rigid. The lack of rotational degree of freedom is due to direct and/or water-mediated interresidue hydrogen bonding. Both single or tandem water bridges were found between carboxylate group and N-acetil group. The carboxylate group of glucuronic acid is not involved in a direct link with the amide group of N-acetyl glucosamine and this facilitated bonding between the residue and the water molecules.
Binding of CDK9 to TRAF2. (1998)

CDK9 has been recently shown to have increased kinase activity in differentiated cells in culture and a differentiated tissue-specific expression in the developing mouse. In order to identify factors that contribute to CDK9's differentiation-specific function, we screened a mouse embryonic library in the yeast two-hybrid system and found a tumor necrosis factor signal transducer, TRAF2, to be an interacting protein. CDK9 interacts with a conserved domain in the TRAF-C region of TRAF2, a motif that is known to bind other kinases involved in TRAF-mediated signaling. Endogenous interaction between the two proteins appears to be specific to differentiated tissue. TRAF2-mediated signaling may incorporate additional kinases to signal cell survival in myotubes, a cell type that is severely affected in TRAF2 knockout mice.
Diffractive Bifocal Lens Designs (1993)

Modifying the number, width, depth, and shape of the echelettes in a diffractive bifocal lens will influence the image intensity and quality within the zero, first, and higher order images. By appropriately varying these parameters optimal bifocal lens designs may be achieved.
How Many Species Are There on Earth? (1988)

This article surveys current answers to the factual question posed in the title and reviews the kinds of information that are needed to make these answers more precise. Various factors affecting diversity are also reviewed. These include the structure of food webs, the relative abundance of species, the number of species and of individuals in different categories of body size, along with other determinants of the commonness and rarity of organisms.
Rigid-Motion Scattering for Texture Classification (2014)

A rigid-motion scattering computes adaptive invariants along translations and rotations, with a deep convolutional network. Convolutions are calculated on the rigid-motion group, with wavelets defined on the translation and rotation variables. It preserves joint rotation and translation information, while providing global invariants at any desired scale. Texture classification is studied, through the characterization of stationary processes from a single realization. State-of-the-art results are obtained on multiple texture data bases, with important rotation and scaling variabilities.
Antioxidant and anticholinesterase constituents of Salvia poculata (2009)

Two triterpenoids, namely 2\alpha,3\alpha-dihydroxy-24-nor- 4(23),12-oleanadien-28-oic acid (1) and ursolic acid (2); 4 flavonoids, namely 5-hydroxy-7,4'-dimethoxyflavone (3), cirsimaritin (4), eupatilin (5), and salvigenin (6); a diterpenoid, namely sclareol (7); and a steroid, namely \beta-sitosterol (8), were isolated from the aerial parts of Salvia poculata Nab., a Turkish endemic Salvia species. Total phenolic and flavonoid contents of the crude extract were determined as pyrocatechol and quercetin equivalents, respectively. The antioxidant activity of the crude extract and the isolated compounds (2-8) was established using \beta-carotene bleaching, superoxide anion radical, and ABTS cation radical scavenging activity. In addition, the anticholinesterase activity of the crude extract and the isolated compounds (2-8) against the enzymes acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) was determined. The phytochemistry and antioxidant and anticholinesterase activities of S. poculata were investigated for the first time in this study. The crude extract of S. poculata exhibited a significant antioxidant effect as well as butyrylcholinesterase inhibitory activity. Ursolic acid (2) and cirsimaritin (4) possessed high butyrylcholinesterase inhibitory activity.
RNA amplification with transcript sequencing (RAWTS) (1988)

Journal Article RNA amplification with transcript sequencing (RAWTS) Get access Gobinda Sarkar, Gobinda Sarkar Department of Biochemistry and Molecular Biology, Mayo Clinic/FoundationRochester, MN 55905, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Steve S. Sommer Steve S. Sommer Department of Biochemistry and Molecular Biology, Mayo Clinic/FoundationRochester, MN 55905, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 11, 10 June 1988, Page 5197, https://doi.org/10.1093/nar/16.11.5197 Published: 10 June 1988 Article history Accepted: 28 April 1988 Published: 10 June 1988
STRUCTURES AND FUNCTIONS OF MULTILIGAND LIPOPROTEIN RECEPTORS: Macrophage Scavenger Receptors and LDL Receptor-Related Protein (LRP) (1994)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
ANIMALS Animal Protection: Provide for Protection of Farm Animal and Research Facilities (1990)

The Act creates a new article that provides for misdemeanor and felony offenses for destruction or damage to animals or property of an animal research facility. The Act also imposes penalties and provides for recovery of damages, punitive damages, court costs, and attorney's fees.
Biological Basis of Bone Formation, Remodeling, and Repair—Part II: Extracellular Matrix (2008)

The bony biochemical environment is a complex system that permits and promotes cellular functions that lead to matrix production and ossification. In Part I of this review, we discussed the important actions of signaling molecules, including hormones, cytokines, and growth factors. Here, we review other constituents of the extracellular matrix, including minerals, fibrinous and nonfibrinous proteins, and enzymes such as the matrix metalloproteinases. We conclude with a discussion of the role of biochemical modulation in endogenous and exogenous tissue engineering.
Learning Two-View Correspondences and Geometry Using Order-Aware Network (2019)

Establishing correspondences between two images requires both local and global spatial context. Given putative correspondences of feature points in two views, in this paper, we propose Order-Aware Network, which infers the probabilities of correspondences being inliers and regresses the relative pose encoded by the essential matrix. Specifically, this proposed network is built hierarchically and comprises three novel operations. First, to capture the local context of sparse correspondences, the network clusters unordered input correspondences by learning a soft assignment matrix. These clusters are in a canonical order and invariant to input permutations. Next, the clusters are spatially correlated to form the global context of correspondences. After that, the context-encoded clusters are recovered back to the original size through a proposed upsampling operator. We intensively experiment on both outdoor and indoor datasets. The accuracy of the two-view geometry and correspondences are significantly improved over the state-of-the-arts. Code will be available at https://github.com/zjhthu/OANet.git.
Comparison of the three aspartokinase isozymes in Bacillus subtilis Marburg and 168 (1990)

The levels of two aspartokinase isozymes, a lysine-sensitive enzyme and an aspartokinase that is inhibited synergistically by lysine plus threonine, differ strikingly in different strains of Bacillus subtilis. In derivatives of B. subtilis 168 growing in minimal medium, the predominant isozyme is the lysine-sensitive aspartokinase. In B. subtilis ATCC 6051, the Marburg strain, the level of the lysine-sensitive aspartokinase is much lower during growth in minimal medium, and the major aspartokinase activity is the lysine-plus-threonine-sensitive isozyme. Molecular cloning and nucleotide sequence determination of the genes for the lysine-sensitive isozymes from the two B. subtilis strains and their upstream control regions showed these genes to be identical. Evidence that the lysine-sensitive aspartokinase, referred to as aspartokinase II, is distinct from the threonine-plus-lysine-sensitive aspartokinase comes from the observation that disruption of the aspartokinase II gene by recombinational insertion had no effect on the latter. Mutants were obtained from the aspartokinase II-negative strain that also lacked the threonine-plus-lysine-sensitive aspartokinase, which will be referred to as aspartokinase III. Aspartokinase II could be selectively restored to these mutants by transformation with plasmids carrying the aspartokinase II gene. Study of the growth properties of the various mutant strains showed that the loss of either aspartokinase II or aspartokinase III had no effect on growth in minimal medium but that the loss of both enzymes interfered with growth unless the medium was supplemented with the three major end products of the aspartate pathway. It appears, therefore, that aspartokinase I alone cannot provide adequate supplies of precursors for the synthesis of lysine, threonine, and methionine by exponentially growing cells.
Inhibition of cellular senescence by developmentally regulated FGF receptors in mesenchymal stem cells (2011)

Bone-derived mesenchymal stem cells (MSCs) are important cells for use in cell therapy, tissue engineering, and regenerative medicine, but also to study bone development, homeostasis, and repair. However, little is known about their developmental ontology and in vivo identity. Because fibroblast growth factors (FGFs) play key roles in bone development and their receptors are developmentally regulated in bones, we hypothesized that MSCs should express FGF receptors (FGFRs), reflecting their developmental origin and potential. We show here that FGFR1/2 are expressed by rare mesenchymal progenitors in putative MSC niches in vivo, including the perichondrium, periosteum, and trabecular marrow. FGFR1⁺ cells often appeared as pericytes. These cells display a characteristic MSC phenotype in vitro when expanded with FGF-2, which appears to maintain MSC stemness by inhibiting cellular senescence through a PI3K/AKT-MDM2 pathway and by promoting proliferation. FGFRs may therefore be involved in MSC self-renewal. In summary, FGFR1/2 are developmentally regulated markers of MSCs in vivo and in vitro and are important in maintaining MSC stemness.
Attachment of Carbohydrate to the Variable Region of Myeloma Immunoglobulin Light Chains (1970)

Approximately 15 per cent of the light chains from homogeneous immunoglobulins in patients with multiple myeloma contain an oligosaccharide group. Five human myeloma light chains that contained carbohydrate were studied. The sequence Asn-[unk]-Ser/Thr was at the site of carbohydrate attachment in all light chains. The carbohydrate group was attached to the asparagine residue of this triplet sequence which in all five light chains was located in the variable region. The occasional occurrence of carbohydrate in myeloma light chains is seen as the consequence of a variable region mutation creating an Asn-[unk]-Ser/Thr sequence to which carbohydrate is attached by an enzyme capable of recognizing the characteristic triplet sequence.
One sense per collocation (1993)

Previous work [Gale, Church and Yarowsky, 1992] showed that with high probability a polysemous word has one sense per discourse. In this paper we show that for certain definitions of collocation, a polysemous word exhibits essentially only one sense per collocation. We test this empirical hypothesis for several definitions of sense and collocation, and discover that it holds with 90--99% accuracy for binary ambiguities. We utilize this property in a disambiguation algorithm that achieves precision of 92% using combined models of very local context.
Human peripheral blood CD4 T cell-engrafted non-obese diabetic-scid IL2rγnull H2-Ab1 tm1GruTg (human leucocyte antigen D-related 4) mice: a mouse model of human allogeneic graft-versus-host disease (2011)

Summary Graft-versus-host disease (GVHD) is a life-threatening complication of human allogeneic haematopoietic stem cell transplantation. Non-obese diabetic (NOD)-scid IL2rγnull (NSG) mice injected with human peripheral blood mononuclear cells (PBMC) engraft at high levels and develop a robust xenogeneic (xeno)-GVHD, which reproduces many aspects of the clinical disease. Here we show that enriched and purified human CD4 T cells engraft readily in NSG mice and mediate xeno-GVHD, although with slower kinetics compared to injection of whole PBMC. Moreover, purified human CD4 T cells engraft but do not induce a GVHD in NSG mice that lack murine MHC class II (NSG-H2-Ab1 tm1Gru, NSG-Ab°), demonstrating the importance of murine major histocompatibility complex (MHC) class II in the CD4-mediated xeno-response. Injection of purified human CD4 T cells from a DR4-negative donor into a newly developed NSG mouse strain that expresses human leucocyte antigen D-related 4 (HLA-DR4) but not murine class II (NSG-Ab° DR4) induces an allogeneic GVHD characterized by weight loss, fur loss, infiltration of human cells in skin, lung and liver and a high level of mortality. The ability of human CD4 T cells to mediate an allo-GVHD in NSG-Ab° DR4 mice suggests that this model will be useful to investigate acute allo-GVHD pathogenesis and to evaluate human specific therapies.
Calibration of radially symmetric distortion based on linearity in the calibrated image (2011)

For calibration of general radially symmetric distortion of omnidirectional cameras such as fish-eye lenses, calibration parameters are usually estimated so that curved lines, which are supposed to be straight in the real-world, are mapped to straight lines in the calibrated image, which is called plumbline principle. Under the principle, the camera with radially symmetric distortion can be calibrated by at least one distorted line in a image, theoretically, and the calibrated image is equivalent to the image taken by an ideal pin-hole camera. In this paper, the method to optimize the calibration parameters by maximizing the sum of the straightness, which is invariant under translation, rotation and magnification (scaling), of distorted lines on calibrated image is proposed. The performance of the proposed method is evaluated by artificial data and a real image.
Heterologous expression of the bifunctional thymidylate synthase-dihydrofolate reductase from Leishmania major (1988)

The bifunctional thymidylate synthase-dihydrofolate reductase (TS-DHFR) of Leishmania major has been cloned and expressed in Escherichia coli and Saccharomyces cerevisiae. The strategy involved placing the entire 1560-bp coding sequence into a parent cloning plasmid that was designed to permit introduction of unique restriction sites at the 5'- and 3'-ends. In this manner, the entire coding sequence could be easily subcloned into a variety of expression vectors. High levels of TS-DHFR gene expression were driven by tac, pL and T7 RNA pol promoters in E. coli, and the GAPDH-ADH-2 promoter in S. cerevisiae. L. major TS-DHFR also complemented TS deficiency in E. coli. In E. coli, the protein accumulated to very high levels, but most was present as inactive inclusion bodies. Nevertheless, substantial amounts were soluble; up to 2% of the soluble protein was catalytically active TS-DHFR. In the yeast systems, essentially all of the bifunctional protein was soluble and catalytically active, and crude extracts contained about 100-fold more enzyme than do extracts from wild-type L. major. The expressed TS-DHFR from yeast and E. coli was purified to homogeneity by methotrexate-Sepharose affinity chromatography. About 8.5 mg of homogeneous, catalytically active protein is obtained from a 1-L culture of yeast, and 1.5 mg was obtained from 1 L of E. coli culture. A 200-L fermentation of the yeast expression system yielded a crude extract containing over 4 g of TS-DHFR.(ABSTRACT TRUNCATED AT 250 WORDS)
Contact line deposits in an evaporating drop (2000)

Solids dispersed in a drying drop will migrate to the edge of the drop and form a solid ring. This phenomenon produces ringlike stains and occurs for a wide range of surfaces, solvents, and solutes. Here we show that the migration is caused by an outward flow within the drop that is driven by the loss of solvent by evaporation and geometrical constraint that the drop maintain an equilibrium droplet shape with a fixed boundary. We describe a theory that predicts the flow velocity, the rate of growth of the ring, and the distribution of solute within the drop. These predictions are compared with our experimental results.
Detection and enumeration of periodontopathogenic bacteria in subgingival biofilm of pregnant women (2012)

The aim of this study was to use the fluorescence in situ hybridization (FISH) technique to test the hypothesis of qualitative and quantitative differences of 8 periodontopathogens between pregnant and non-pregnant women. This cross-sectional study included 20 pregnant women in their second trimester of pregnancy and 20 non-pregnant women. Probing depth, bleeding on probing, clinical attachment level, and presence of calculus were recorded. Subgingival plaque samples were collected and the FISH technique identified the presence and numbers of Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Campylobacter rectus, Porphyromonas gingivalis, Treponema denticola, Fusobacterium nucleatum, Prevotella intermedia and Prevotella nigrescens. The Mann-Whitney U-test was applied to compare the data between the two groups. The mean age, ethnicity, marital status, education, and economic level in both groups were similar. The clinical parameters showed no significant differences between pregnant and non-pregnant women. The numbers of subgingival periodontopathogens were not found to be significantly different between groups, despite the higher mean counts of P. intermedia in pregnant women. Colonization patterns of the different bacteria most commonly associated with periodontal disease were not different in the subgingival plaque of pregnant and non-pregnant women.
SUPERCRITICAL WATER TREATMENT OF BIOMASS FOR ENERGY AND MATERIAL RECOVERY (2005)

ABSTRACT Supercritical water liquefaction and gasification is reviewed with the introduction of some recent findings by the authors. Supercritical water gasification is suitable for recovery of energy from wet biomass while supercritical water liquefaction opens the door to effective treatment of biomass species in terms of material recovery. Cellulose, one of the main components of biomass, is completely dissolved in supercritical water. Once dissolved, reaction of cellulose can take place swiftly by hydrolysis and pyrolysis. The hydrolysis reaction, otherwise slower than pyrolysis due to the mass transfer limitation, is faster than decomposition in supercritical water, and a possibility of efficient glucose recovery has been shown. Once dissolved, super saturation is kept when the solution is cooled down, and swift hydrolysis by enzyme is also possible. Lignin can be also converted into specialty chemicals by using supercritical cresol/water mixture as a solvent. Dissolution of cellulose also enables efficient gasification of biomass. Complete gasification of biomass has been realized with production of combustible gas including hydrogen, carbon monoxide, and methane. Keywords: supercritical waterbiomasscelluloseligninliquefactiongasificationchemicals
Novel eicosanoid and docosanoid mediators: resolvins, docosatrienes, and neuroprotectins (2005)

In view of the many beneficial actions attributed to omega-3 dietary supplementation, identification of novel potent mediators from omega-3 that are both anti-inflammatory and protective may have wide implications.
Detecting Stress During Real-World Driving Tasks Using Physiological Sensors (2005)

This paper presents methods for collecting and analyzing physiological data during real-world driving tasks to determine a driver's relative stress level. Electrocardiogram, electromyogram, skin conductance, and respiration were recorded continuously while drivers followed a set route through open roads in the greater Boston area. Data from 24 drives of at least 50-min duration were collected for analysis. The data were analyzed in two ways. Analysis I used features from 5-min intervals of data during the rest, highway, and city driving conditions to distinguish three levels of driver stress with an accuracy of over 97% across multiple drivers and driving days. Analysis II compared continuous features, calculated at 1-s intervals throughout the entire drive, with a metric of observable stressors created by independent coders from videotapes. The results show that for most drivers studied, skin conductivity and heart rate metrics are most closely correlated with driver stress level. These findings indicate that physiological signals can provide a metric of driver stress in future cars capable of physiological monitoring. Such a metric could be used to help manage noncritical in-vehicle information systems and could also provide a continuous measure of how different road and traffic conditions affect drivers.