gebhart/patrepeval huggingface dataset:
Tumor-Targeted Human T Cells Expressing CD28-Based Chimeric Antigen Receptors Circumvent CTLA-4 Inhibition (2015)

Adoptive T cell therapy represents a promising treatment for cancer. Human T cells engineered to express a chimeric antigen receptor (CAR) recognize and kill tumor cells in a MHC-unrestricted manner and persist in vivo when the CAR includes a CD28 costimulatory domain. However, the intensity of the CAR-mediated CD28 activation signal and its regulation by the CTLA-4 checkpoint are unknown. We investigated whether T cells expressing an anti-CD19, CD3 zeta and CD28-based CAR (19-28z) displayed the same proliferation and anti-tumor abilities than T cells expressing a CD3 zeta-based CAR (19z1) costimulated through the CD80/CD28, ligand/receptor pathway. Repeated in vitro antigen-specific stimulations indicated that 19-28z+ T cells secreted higher levels of Th1 cytokines and showed enhanced proliferation compared to those of 19z1+ or 19z1-CD80+ T cells. In an aggressive pre-B cell leukemia model, mice treated with 19-28z+ T cells had 10-fold reduced tumor progression compared to those treated with 19z1+ or 19z1-CD80+ T cells. shRNA-mediated CTLA-4 down-regulation in 19z1-CD80+ T cells significantly increased their in vivo expansion and anti-tumor properties, but had no effect in 19-28z+ T cells. Our results establish that CTLA-4 down-regulation may benefit human adoptive T cell therapy and demonstrate that CAR design can elude negative checkpoints to better sustain T cell function.
Fibrodysplasia Ossificans Progressiva in a Maine Coon Cat with Prominent Ossification in Dorsal Muscle (2009)

A one-year and six-month-old female Maine Coon cat presented with skin problems and paravertebral induration with a history of seven months. Survey radiographs and computed tomography revealed prominent calcifications in both sides of cervical, thoracic and lumbar vertebrae and soft tissue in femoral regions, below knee regions and in brachial regions. Histopathological findings from muscle biopsy samples showed connective tissue proliferation around adjacent skeletal muscle, cartilage formation and endochondral ossification. On the basis of these findings, this feline patient was diagnosed with fibrodysplasia ossificans progressiva (FOP). The most prominent signs observed in this FOP case were significant calcifications of dorsal muscle and presentation of cutaneous signs at the early stage.
Topological and mutational analysis of KpsM, the hydrophobic component of the ABC‐transporter involved in the export of polysialic acid in Escherichia coli K1 (1994)

The 17 kb kps gene cluster of Escherichia coli K1, which encodes the information required for synthesis, assembly and translocation of the polysialic acid capsule of E. coli K1, is divided into three functional regions. Region 3 contains two genes, kpsM and kpsT, essential for the transport of capsule polymer across the cytoplasmic membrane. The hydrophobicity profile of KpsM suggests that it is an integral membrane protein while KpsT contains a consensus ATP-binding site. KpsM and KpsT belong to the ATP-binding cassette (ABC) superfamily of membrane transporters. In this study, we investigate the topology of KpsM within the cytoplasmic membrane using beta-lactamase fusions and alkaline phosphatase sandwich fusions. Our analysis provides evidence for a model of KpsM having six membrane-spanning regions, with the N- and C-terminal domains facing the cytoplasm, and a short domain within the third periplasmic loop, which we refer to as the SV-SVI linker localizing in the membrane. Protease digestion studies are consistent with regions of KpsM exposed to the periplasmic space. In vivo cross-linking studies provide support for dimerization of KpsM within the cytoplasmic membrane. Linker-insertion and site-directed mutagenesis define the N-terminus, the first cytoplasmic loop, and the SV-SVI linker as regions that are important for the function of KpsM in K1 polymer transport.
Activation of Glycogen Synthase Kinase 3β Promotes the Intermolecular Association of Tau (2007)

Tau is hyperphosphorylated and undergoes proteolysis in Alzheimer disease brain. Caspase-cleaved tau efficiently forms fibrillary structures in vitro and in situ. Glycogen synthase kinase 3beta (GSK3beta) phosphorylates tau and induces the aggregation of caspase-cleaved tau in situ. Given the hypothesis that increased association of tau precedes the formation of fibrillar structures, we generated a cell model to quantitate the extent of tau association in situ using fluorescence resonance energy transfer (FRET) microscopy. The cyan and yellow fluorescent proteins were attached to full-length (T4) and caspase-cleaved (T4C3) tau at either the N or C termini, and a pair of cyan and yellow fluorescent protein-tagged tau were co-transfected into human embryonic kidney cells. The FRET efficiency was examined in the presence of a constitutively active or a kinase-dead GSK3beta. Active GSK3beta significantly increased FRET efficiency with both T4 and T4C3, indicating that GSK3beta activation resulted in an increase in the self-association of both T4 and T4C3, but interestingly only T4 is efficiently phosphorylated by GSK3beta. There was no significant difference in FRET efficiency between T4 and T4C3, although only T4C3 in the presence of active GSK3beta leads to the formation of Sarkosyl-insoluble inclusions. These FRET studies demonstrate that GSK3beta facilitates the association of T4 and T4C3, and the presence of caspase-cleaved tau is necessary for the evolution of tau oligomers into Sarkosyl-insoluble inclusions even though it is not extensively phosphorylated. These data imply that increased association of tau should not be regarded as a direct indicator of the formation of insoluble tau aggregates.
Identification of species-specific and cross-reactive epitopes in human polyomavirus capsids using monoclonal antibodies (2009)

The human antibody response to polyomavirus capsid proteins is not well characterized. Recombinant BK virus (BKV), JC virus (JCV) and simian virus 40 (SV40) virus-like particles (VLP) were produced in a baculovirus system, and mouse monoclonal antibodies (mAbs) to these proteins were generated using standard methods. Nine of 12 BKV mAbs showed neutralizing activity. The non-neutralizing antibodies also bound BKV pseudocapsids in an ELISA binding assay. Most antibodies recognized conformational species-specific epitopes, but several exceptions were found: (i) BKV mAb BK-F11 cross-reacted with a linear buried epitope common to both JCV and SV40 pseudocapsids, (ii) two of six JCV antibodies (JC-6.7 and JC-7.9) and two of 13 SV40 antibodies (VP1-H2 and VP1-I2) recognized linear buried epitopes common to all three viruses and (iii) SV40 antibody VP1-E5 recognized a linear surface epitope on JCV pseudocapsids.
Multi-level partition of unity implicits (2005)

We present a new shape representation, the multi-level partition of unity implicit surface, that allows us to construct surface models from very large sets of points. There are three key ingredients to our approach: 1) piecewise quadratic functions that capture the local shape of the surface, 2) weighting functions (the partitions of unity) that blend together these local shape functions, and 3) an octree subdivision method that adapts to variations in the complexity of the local shape.Our approach gives us considerable flexibility in the choice of local shape functions, and in particular we can accurately represent sharp features such as edges and corners by selecting appropriate shape functions. An error-controlled subdivision leads to an adaptive approximation whose time and memory consumption depends on the required accuracy. Due to the separation of local approximation and local blending, the representation is not global and can be created and evaluated rapidly. Because our surfaces are described using implicit functions, operations such as shape blending, offsets, deformations and CSG are simple to perform.
Draft social policy and procedures (revised) (1999)

The report is the environmental assessment for the Rajasthan State Power Sector Restructuring Project, and addresses potential adverse effects on the environment as a result of the project. Adverse environmental impacts, and mitigating measures follow. Transmission lines, and substations will not disturb natural habitats, for those will be installed within 100 km of any wild life protection area, and, though lines pass through agricultural land, cultivation is permitted under the towers, and conductors, posing no threat to the surroundings. Soil erosion during construction will be controlled through the installation of retaining walls, and stone pitching, and, vegetation propagation will be ensured as needed. However, there is the potential for electromagnetic frequency (EMF) radiation, noise disturbances, and electric interference along transmission lines, therefore minimum transmission line clearance distances will address EMF effects, in accordance with the Electricity Act. Furthermore, the potential of electrocution hazard exist, thus the Rajasthan State Electricity Board will restrict public access, by fencing substations in accordance with the Electricity Act. The second volume, Social Policy and Procedures, address displaced populations losing land, who will be compensated as per the Land Acquisition Act, through rehabilitation grants to ensure replacement values.
Mitogen-Activated Protein Kinase Activation Is Involved in Platelet-Derived Growth Factor-Directed Migration by Vascular Smooth Muscle Cells (1997)

Migration of vascular smooth muscle cells (VSMCs) is a crucial response to vascular injury resulting in neointima formation and atherosclerosis. Platelet-derived growth factor (PDGF-BB) functions as a potent chemoattractant for VSMCs and enhances these pathologies in the vasculature. However, little is known about the intracellular pathways that mediate VSMC migration. In the present study, we investigated the role of mitogen-activated protein kinase (MAPK) activation in this function, since PDGF-BB as well as other growth factors activate this pathway. Using an in-gel kinase assay, we observed that PD 98059 an inhibitor of MEK that activates MAP kinase, inhibited PDGF-BB-induced activation of ERK-1 and ERK-2 in cultured rat aortic smooth muscle cells in a concentration-dependent manner. In contrast, PDGF-mediated activation of intracellular calcium release was not affected by PD 98059. The chemotactic response of both rat aortic smooth muscle cells (RASMCs) and human umbilical vein smooth muscle cells (HUSMCs) toward PDGF-BB (10 ng/mL) was significantly reduced by PD 98059 (10 mumol/L) to 41.7 +/- 7.1% in RASMCs (P < .01) and to 47.2 +/- 5.3% in HUSMCs (P < .01). Similar inhibition was seen at 30 mumol/L, less at 1 mumol/L. To further confirm the specificity of these results implicating the MAPK pathway, an antisense oligodeoxynucleotide (ODN) directed against the initiation translation site of rat ERK-1 and ERK-2 mRNA was used to suppress MAP kinase synthesis and function in rat VSMCs. Liposomal transfection with 0.4 mumol/L antisense ODN reduced ERK-1 and ERK-2 protein by 65% (P < .01) after 48 hours. The chemotactic response to PDGF-BB (10 ng/mL) was reduced by 75% (P < .01) in rat VSMCs transfected with the same antisense ODN concentration. Sense and scrambled control ODNs (0.4 mumol/L) did not affect ERK-1 and ERK-2 protein concentrations or chemotaxis of VSMCs induced by PDGF-BB. These experiments provide the first evidence that activation of MAPK is a critical event in PDGF-mediated signal transduction regulating VSMC migration.
Antigen CD34+ marrow cells engraft lethally irradiated baboons. (1988)

The CD34 antigen is present on 1-4% of human marrow cells including virtually all hematopoietic progenitors detected by in vitro assays. Since the anti-CD34 monoclonal antibody 12-8 reacts with a similar marrow population in baboons, it was possible to test whether this antigen is expressed by stem cells responsible for hematopoietic reconstitution in vivo. CD34+ cells were enriched from marrows of five baboons using avidin-biotin immunoadsorption. After lethal irradiation, the five animals were given 15-27 X 10(6) autologous marrow cells (3.2-4.4 X 10(6) cells/kg) containing 65-91% CD34+ cells. All animals achieved granulocyte counts greater than 1,000/mm3 and platelet counts greater than 20 X 10(3)/mm3 by 13-24 d posttransplant and subsequently developed normal peripheral blood counts. Two additional animals received 184 and 285 X 10(6) marrow cells/kg depleted of CD34+ cells. One animal died at day 29 without engraftment, while the other had pancytopenia for greater than 100 d posttransplant. The data suggest that stem cells responsible for hematopoietic reconstitution are CD34+.
ADAMTS-1 Is an Active Metalloproteinase Associated with the Extracellular Matrix (1999)

Cellular disintegrin and metalloproteinases (ADAMs) are a family of genes with a sequence similar to the snake venom metalloproteinases and disintegrins. ADAMTS-1 is a unique ADAM family protein with respect to the presence of thrombospondin type I motifs and the capacity to bind to the extracellular matrix. Because ADAMTS-1 has a potential zinc-binding motif in the metalloproteinase domain, we examined in this study whether ADAMTS-1 is an active metalloproteinase by means of the proteinase trapping mechanism of alpha2-macroglobulin. We found that the soluble type of ADAMTS-1 protein is able to form a covalent-binding complex with alpha2-macroglobulin. Furthermore, the point mutation within the zinc-binding motif of ADAMTS-1 protein eliminates its capacity to bind to alpha2-macroglobulin. These data demonstrate that the metalloproteinase domain of ADAMTS-1 is catalytically active. In addition, we showed that the removal of the pro-domain from the ADAMTS-1 precursor is impaired in the furin-deficient cell line, LoVo, and that the processing ability of the cells is restored by the co-expression of the furin cDNA. These data provide evidence that the ADAMTS-1 precursor is processed in vivo by furin endopeptidase in the secretory pathway. Consequently, ADAMTS-1 is an active metalloprotease that is associated with the extracellular matrix. This study strongly suggests that ADAMTS-1 may play a role in the inflammatory process through its protease activity.
Recombinant CD40 ligand exerts potent biologic effects on T cells. (1994)

Murine and human CD40 ligand (CD40L) were recently cloned, expressed, and shown to possess potent activity on human and murine B cells, including stimulation of proliferation and Ig secretion in the presence of cytokines. In addition to its action on B lymphocytes, this report demonstrates that CD40L induced both CD4+ and CD8+ T cells isolated from murine lymphoid tissues to proliferate in the presence of submitogenic dosages of Con A, PHA, CD3 mAb, and TCR-alpha beta mAb. The presence of CD40L during suboptimal TCR stimulation resulted in increased expression of the activation Ags IL-2R alpha and CD69 and increased IL-2 production. Taken together, these results show that CD40L is a potent activator of murine T cells and suggest that CD40L is involved in the regulation of T cell function mediated through T:T cell interaction.
Spatial Epigenome Sequencing at Tissue Scale and Cellular Level (2021)

Abstract Spatial biology is emerging as a new frontier of biomedical research in development and disease, but currently limited to transcriptome and a panel of proteins. Here we present spatial epigenome profiling for three histone modifications (H3K27me3, H3K4me3, H3K27ac) via next-generation sequencing by combining in-tissue CUT&amp;Tag chemistry and microfluidic deterministic barcoding. Spatial chromatin states in mouse embryos or olfactory bulbs revealed tissue type-specific epigenetic regulations, in concordance with ENCODE reference data, but providing spatially resolved genome-wide profiles at tissue scale. Using fluorescence imaging to identify the tissue pixels (20μm) each containing one nucleus allowed us to extract single-cell epigenomes in situ. Spatial chromatin state profiling in tissue may enable unprecedented opportunities to study epigenetic regulation, cell function and fate decision in normal physiology and pathogenesis.
Mesoscale Transcranial Spontaneous Activity Mapping in GCaMP3 Transgenic Mice Reveals Extensive Reciprocal Connections between Areas of Somatomotor Cortex (2014)

Transgenic mice expressing genetically encoded activity indicators are an attractive means of mapping mesoscopic regional functional cortical connectivity given widespread stable and cell-specific expression compatible with chronic recordings. Cortical functional connectivity was evaluated using wide-field imaging in lightly anesthetized Emx1-creXRosa26-GCaMP3 mice expressing calcium sensor in cortical neurons. Challenges exist because green fluorescence signals overlap with endogenous activity-dependent autofluorescence and are affected by changes in blood volume and oxygenation. Under the conditions used for imaging and analysis (0.1-1 Hz frequency band), autofluorescence and hemodynamic effects contributed 3% and 8% of the SD of spontaneous activity-dependent GCaMP3 fluorescence when signals were recorded through intact bone. To evaluate the accuracy and sensitivity of this approach, the topology of functional connections between somatomotor cortex (primary S1 and secondary S2 somatosensory, and primary motor cortex M1) was estimated. During sequences of spontaneous activity, calcium signals recorded at each location of area S1 were correlated with activity in contralateral area S1, ipsilateral area S2, and bilateral areas M1. Reciprocal results were observed when "seed pixels" were placed in S2 and M1. Coactivation of areas implies functional connections but could also be attributed to both regions receiving common upstream drive. These apparent connections revealed during spontaneous activity coactivation by GCaMP3 were confirmed by intracortical microstimulation but were more difficult to detect using intrinsic signals from reflected red light. We anticipate GCAMP wide-field imaging will enable longitudinal studies during plasticity paradigms or after models of CNS disease, such as stroke, where the weighting within these connectivity maps may be altered.
Cloning and Characterization of Two Human Polyspecific Organic Cation Transporters (1997)

Previously we cloned a polyspecific transporter from rat (rOCT1) that is expressed in renal proximal tubules and hepatocytes and mediates electrogenic uptake of organic cations with different molecular structures. Recently a homologous transporter from rat kidney (rOCT2) was cloned but not characterized in detail. We report cloning and characterization of two homologous transporters from man (hOCT1 and hOCT2) displaying approximately 80% amino acid identity to rOCT1 and rOCT2, respectively. Northern blots showed that hOCT1 is mainly transcribed in liver, while hOCT2 is found in kidney. Using in situ hybridization and immunohistochemistry, expression of hOCT2 was mainly detected in the distal tubule where the transporter is localized at the luminal membrane. After expression in Xenopus laevis oocytes, hOCT1 and hOCT2 mediate tracer influx of N-1-methylnicotinamide (NMN), tetraethylammonium (TEA), and 1-methyl-4-phenylpyridinium (MPP). For cation transport by hOCT2 apparent K(m) and K(i) values were determined in tracer flux measurements. In addition, electrical measurements were performed with voltage-clamped oocytes. Similar to rOCT1, cation transport by hOCT2 was pH independent, electrogenic, and polyspecific; however, the cation specificity was different. In voltage-clamped hOCT2-expressing oocytes, inward currents were induced by superfusion with MPP, TEA, choline, quinine, d-tubocurarine, pancuronium, and cyanine863. Cation transport in distal tubules is indicated for the first time. Here hOCT2 mediates the first step in cation reabsorption. hOCT1 may participate in hepatic excretion of organic cations.
TERMINAL PHOSPHATE LABELED NUCLEOTIDES: SYNTHESIS, APPLICATIONS, AND LINKER EFFECT ON INCORPORATION BY DNA POLYMERASES (2005)

A number of terminal phosphate-labeled nucleotides with three or more phosphates and with varied length linkers attached between the terminal phosphate and the dye have been synthesized. These nucleotides have been tested as substrates for different DNA and RNA polymerases. We have also explored their utility in DNA sequencing, SNP analysis, nucleic acid amplification, quantitative PCR, and other biochemical assays.
Proportions of circulating T cells with a regulatory cell phenotype increase with HIV-associated immune activation and remain high on antiretroviral therapy (2007)

Proportions of circulating T cells with a regulatory cell phenotype increase with HIV-associated immune activation and remain high after 1 year on ART.
Morphology of Ultrathin Supported Diblock Copolymer Films:  Theory and Experiment (2000)

An analysis of the morphological behavior of substrate-supported diblock copolymer films for thicknesses t below the equilibrium period L0 of the copolymer is presented. Substrate-supported films generally exhibit dissimilar interactions between the copolymer block components and the free and substrate surfaces. Accordingly, in this study, self-consistent-field calculations that incorporate asymmetric surface energetics were used to assess equilibrium film morphologies. Phase diagrams were constructed as a function of film thickness, surface interaction energies, the segmental interaction, and the chain length. In conjunction, experiments were conducted on a series of polystyrene-b-poly(n-alkyl methacrylate) copolymer films supported by silicon substrates. These employed a novel atomic force microscopy technique that allowed for the precise tracking of morphology as a function of film thickness. Comparison of the experimental results and calculations revealed several common trends. In particular, hybrid morphologies, incorporating both surface-parallel and surface-perpendicular elements, were observed both experimentally and through the calculations for the thickness regime, t ∼ 0.5L0. The stability of such structures was found to be closely linked to the symmetry of the surface energetics.
An exo-α-sialidase from bifidobacteria involved in the degradation of sialyloligosaccharides in human milk and intestinal glycoconjugates (2010)

Bifidobacteria are health-promoting enteric commensals that are assumed to proliferate predominantly in the intestines of breast-fed infants by assimilating human milk oligosaccharides (HMOs) that are frequently fucosylated and/or sialylated. We previously identified two different α-l-fucosidases in Bifidobacterium bifidum and showed that the strain furnishes an extracellular degradation pathway for fucosylated HMOs. However, the catabolism of sialylated HMOs by bifidobacteria has remained unresolved. Here we describe the identification and characterization of an exo-α-sialidase in bifidobacteria. By expression cloning, we isolated a novel exo-α-sialidase gene (siabb2) from B. bifidum JCM1254, which encodes a protein (SiaBb2) consisting of 835-amino-acid residues with a predicted molecular mass of 87 kDa. SiaBb2 possesses an N-terminal signal sequence, a sialidase catalytic domain classified into the glycoside hydrolase family 33 (GH33) and a C-terminal transmembrane region, indicating that the mature SiaBb2 is an extracellular membrane-anchored enzyme. The recombinant enzyme expressed in Escherichia coli showed the highest activity in an acidic pH range from 4.0 to 5.0, and at 50 °C. Notably, 80% activity remained after 30 min incubation at 80 °C, indicating that the enzyme is highly thermostable. SiaBb2 liberated sialic acids from sialyloligosaccharides, gangliosides, glycoproteins and colominic acid; however, the linkage preference of the enzyme was remarkably biased toward the α2,3-linkage rather than α2,6- and α2,8-linkages. Expression of siabb2 in B. longum 105-A, which has no endogenous exo-α-sialidase, enabled this strain to degrade sialyloligosaccharides present in human milk. Our results suggest that SiaBb2 plays a crucial role in bifidobacterial catabolism of sialylated HMOs.