gebhart/patrepeval huggingface dataset:
High level knowledge sources in usable speech recognition systems (1989)

The authors detail an integrated system which combines natural language processing with speech understanding in the context of a problem solving dialogue. The MINDS system uses a variety of pragmatic knowledge sources to dynamically generate expectations of what a user is likely to say.
Human angiostatin inhibits murine hemangioendothelioma tumor growth in vivo. (1997)

Angiostatin inhibits angiogenesis and metastatic tumor growth; however, its usefulness in treating primary nonmetastasizing tumors is less well understood. We now report the effectiveness of human angiostatin administration in a mouse hemangioendothelioma model. Human angiostatin was administered to mice with s.c. hemangioendothelioma and associated disseminated intravascular coagulopathy (Kasabach-Merritt syndrome). Angiostatin significantly reduced tumor volume in comparison to nontreated controls, increased survival, and prevented the profound thrombocytopenia and anemia of Kasabach-Merritt syndrome. Apoptosis of tumor cells was induced by angiostatin, but tumor cell proliferation was not inhibited. These data suggest angiostatin as a novel treatment for nonmetastasizing vascular tumors and for Kasabach-Merritt syndrome.
Atomic-resolution measurements with a new tunable diode laser-based interferometer (2004)

We develop a new implementation of a Michelson interferometer designed to make measurements with an uncertainty of less than 20 pm. This new method uses a tunable diode laser as the light source, with the diode laser wavelength continuously tuned to fix the number of fringes in the measured optical path. The diode laser frequency is measured by beating against a reference laser. High-speed, accurate frequency measurements of the beat frequency signal enables the diode laser wavelength to be measured with nominally 20-pm accuracy for the measurements described. The new interferometer design is lightweight and is mounted directly on an ultra-high vacuum scanning tunneling microscope capable of atomic resolution. We report the simultaneous acquisition of an atomic resolution image, while the relative lateral displacement of the tip along the sample distance is measured with the new tunable diode laser Michelson interferometer. © 2004 Society of Photo-Optical Instrumentation Engineers.
Interleukin-11 therapy selectively downregulates type I cytokine proinflammatory pathways in psoriasis lesions (1999)

Psoriasis is a chronic inflammatory skin disease in which epidermal hyperplasia results from skin infiltration by type I T lymphocytes and release of associated cytokines. A multifunctional cytokine, rhIL-11, modulates macrophage and type I T-lymphocyte function in cell culture and shows anti-inflammatory activity in animal models. We are testing subcutaneous delivery of rhIL-11 to patients with psoriasis in a phase 1 open-label dose-escalation clinical trial. Tissue was obtained from lesional and uninvolved skin before and during treatment with rhIL-11 and was examined by histology/immunohistochemistry and quantitative RT-PCR. Expression of over 35 genes was examined in all patients, and multiple genetic markers of psoriasis were identified. Expression of numerous proinflammatory genes was elevated in psoriatic tissue compared with nonlesional skin. Seven of 12 patients responded well to rhIL-11 treatment. Amelioration of disease by rhIL-11, as shown by reduced keratinocyte proliferation and cutaneous inflammation, was associated with decreased expression of products of disease-related genes, including K16, iNOS, IFN-gamma, IL-8, IL-12, TNF-alpha, IL-1beta, and CD8, and with increased expression of endogenous IL-11. We believe that this is the first study in humans to indicate that type I cytokines can be selectively suppressed by an exogenous immune-modifying therapy. The study highlights the utility of pharmacogenomic monitoring to track patient responsiveness and to elucidate anti-inflammatory mechanisms.
MutantEscherichia coliHeat-Labile Toxin B Subunit That Separates Toxoid-Mediated Signaling and Immunomodulatory Action from Trafficking and Delivery Functions (2003)

The homopentameric B-subunit components of Escherichia coli heat-labile enterotoxin (EtxB) and cholera toxin (CtxB) possess the capacity to enter mammalian cells and to activate cell-signaling events in leukocytes that modulate immune cell function. Both properties have been attributed to the ability of the B subunits to bind to GM1-ganglioside receptors, a ubiquitous glycosphingolipid found in the plasma membrane. Here we describe the properties of EtxB(H57S), a mutant B subunit with a His-->Ser substitution at position 57. The mutant was found to be severely defective in inducing leukocyte signaling, as shown by failure to (i) trigger caspase 3-mediated CD8(+)-T-cell apoptosis, (ii) activate nuclear translocation of NF-kappaB in Jurkat T cells, (iii) induce a potent anti-B-subunit response in mice, or (iv) serve as a mucosal adjuvant. However, its GM1 binding, cellular uptake, and delivery functions remained intact. This was further validated by the finding that EtxB(H57S) was as effective as EtxB in delivering a conjugated model class I epitope into the major histocompatibility complex class I pathway of a dendritic cell line. These observations imply that GM1 binding alone is not sufficient to trigger the signaling events responsible for the potent immunomodulatory properties of EtxB. Moreover, they demonstrate that its signaling properties play no role in EtxB uptake and trafficking. Thus, EtxB(H57S) represents a novel tool for evaluating the complex cellular interactions and signaling events occurring after receptor interaction, as well as offering an alternative means of delivering attached peptides in the absence of the potent immunomodulatory signals induced by wild-type B subunits.
High-resolution x-ray diffraction from multilayered self-assembled Ge dots (1997)

We have studied multilayers of self-assembled Ge-rich dots embedded in silicon grown by molecular-beam epitaxy using high resolution x-ray reciprocal space mapping and reflectivity. The Si spacer thicknesses between the dot arrays were in the range of 10--40 nm, the typical dot size was about 150 nm for the diameter and 7 nm for the height. The measured reciprocal space maps were simulated using statistical kinematical x-ray-diffraction theory, and a good agreement between experimental and simulated data has been achieved. From the measurements, the in-plane strain in the dot lattice was determined. We derived the degree of the vertical correlation of the dot positions (``stacking'') and a lateral ordering of the dots in a square array with main axes parallel to the 〈100〉 directions, with an array lattice constant of about 500 nm.
In Vitro Secreting Profile of Human Mesenchymal Stem Cells (2008)

In addition to their multilineage potential, mesenchymal stem cells (MSCs) also have a wide range of functionality. Not only can MSCs reconstruct a tissue, but they also have the ability to control or cure other cells and can reconstruct a coordinating function. The opportunity to control other cells depends on MSCs being able to secrete factors like cytokines and chemokines. Therefore, we focused on asking, Which factors can be secreted by human MSCs? To answer this question, we analyzed the secreting profile of in vitro-expanded MSCs by using cytokine arrays. The media concentrations of 44 of the 120 analyzed cytokines were significantly increased by MSCs. Conversely, concentrations of 40 cytokines given with the sera were significantly decreased. The data presented here provide an overview about a large range of factors that were secreted by MSCs under cell culture conditions. These data indicate that MSCs demonstrate all previously described functions in cellular interactions without an external stimulus. The MSCs secreted angiogenic, immunosuppressive, anti-apoptotic, and proliferation-stimulating factors.
Human plasma and recombinant factor VII. Characterization of O-glycosylations at serine residues 52 and 60 and effects of site-directed mutagenesis of serine 52 to alanine (1991)

Factor VII is a multidomain, vitamin K-dependent plasma glycoprotein that participates in the extrinsic pathway of blood coagulation. Earlier studies demonstrated a novel disaccharide (Xyl-Glc) or trisaccharide (Xyl2-Glc) O-glycosidically linked to serine 52 in human plasma factor VII (Nishimura, H., Kawabata, S., Kisiel, W., Hase, S., Ikenaka, T., Shimonishi, Y., and Iwanaga, S. (1989) J. Biol. Chem. 264, 20320-20325). In the present study, human plasma and recombinant factor VII were isolated and subjected to enzymatic fragmentation. Peptides comprising residues 48-62 of the first epidermal growth factor-like domain of each factor VII preparation were isolated for comparative analysis. Using a combined strategy of amino acid sequencing, carbohydrate and amino acid composition analysis, and mass spectrometry, three different glycan structures consisting of either glucose, glucose-xylose, or glucose-(xylose)2 were detected O-glycosidically linked to serine 52 in plasma and recombinant factor VII. Approximately equal amounts of the three glycan structures were observed in plasma factor VII, whereas in recombinant factor VII the glucose and the glucose-(xylose)2 structures predominated. In addition to the O-linked glycan structures observed at serine 52, a single fucose was found to be covalently linked at serine 60 in both human plasma and recombinant factor VII. Carbohydrate and mass spectrometry analyses indicated that the fucosylation of serine 60 was virtually quantitative. Metabolic labeling studies using [14C]fucose confirmed the presence of O-linked fucose at serine 60. In order to assess whether the carbohydrate moiety at serine 52 contributes to the biological activity of factor VII, we have constructed a site-specific mutant of recombinant factor VII in which serine 52 has been replaced with an alanine residue. Mutant factor VIIa exhibited approximately 60% of the coagulant activity of wild-type factor VIIa in a clotting assay. The amidolytic activity of mutant factor VIIa was indistinguishable from that observed for recombinant wild-type factor VIIa. In addition, the ability of mutant factor VIIa in complex with either purified relipidated tissue factor apoprotein or tissue factor on the surface of a human bladder carcinoma cell line (J82) to activate either factor X or factor IX was virtually identical to that observed for wild-type factor VIIa. These results indicate that the carbohydrate moiety O-glycosidically linked to serine 52 does not appear to be involved either in the interaction of factor VIIa with tissue factor, or the expression of its proteolytic activity toward factor X or factor IX following complex formation with tissue factor.(ABSTRACT TRUNCATED AT 400 WORDS)
3-Methyl-2-butenal: An Enzymatic Degradation Product of the Cytokinin, N6-(Δ2-Isopentenyl)adenine (1975)

An enzyme preparation from immature corn kernels catalyzed cleavage of N-6-(delta-2-isopentenyl)adenine to give the aldehyde, 3-methyl-2-butenal, as the major side-chain derived product. This product, in the form of the semicarbazone, was identical with an authentic product by several criteria: chromatographic behavior, mass and ultraviolet spectra.
Identification and Functional Analysis of Human Tom22 for Protein Import into Mitochondria (2000)

Mitochondria have a receptor complex in the outer membrane which recognizes and translocates mitochondrial proteins synthesized in the cytosol. We report here the identification and functional analysis of human Tom22 (hTom22). hTom22 has an N-terminal negatively charged region exposed to the cytosol, a putative transmembrane region, and a C-terminal intermembrane space region with little negative charge. Tom22 forms a complex with Tom20, and its cytosolic domain functions as an import receptor as in fungi. An import inhibition assay, using pre-ornithine transcarbamylase (pOTC) derivatives and a series of hTom22 deletion mutants, showed that the C-terminal segment of the cytosolic domain is important for presequence binding, whereas the N-terminal domain is important for binding to the mature portion of pOTC. No evidence for pOTC interaction with the Tom22 intermembrane space domain was obtained. Binding studies revealed that the presequence is critical for pOTC binding to Tom20, whereas both the presequence and mature portion are important for binding to Tom22. A cell-free immunoprecipitation assay indicated that an internal segment of the Tom22 cytosolic domain is important for interaction with Tom20.
The Role of veA in Aspergillus flavus Infection of Peanut, Corn and Cotton (2009)

The aflatoxin-producing fungus Aspergillus flavus is a causal agent of preharvest contamination of food commodities such as oil seed crops worldwide. Peanut, corn and cottonseed are among the oil seeds that are susceptible to aflatoxin contamination during invasion of these crops by A. flavus. Contamination of agricultural commodities with aflatoxins can result in serious economic hardships to producers and adverse health impacts in both humans and domestic animals. It is therefore of great importance to determine ways to control A. flavus dissemination, survival and toxin formation. In this study we demonstrate the role of the veA regulatory gene in the contamination of peanut, corn and cotton by A. flavus. Virulence of A. flavus on peanut and corn seeds was reduced in the absence of the veA gene product. Generation of air-borne asexual spores was reduced and production of aflatoxin and sclerotia in peanut seeds, viable or non-viable, or in viable corn seed was completely blocked when infected with the A. flavus veA mutant (� veA). In planta inoculation of cotton bolls also showed that conidiation was decreased in bolls inoculated with theveA strain and spread of theveA strain to seed in locules adjacent to the inoculated locule was less than observed with the wild-type veA strain. As observed in peanut and corn, no aflatoxin was produced in seed harvested from cotton bolls inoculated with theveA strain while aflatoxin was present in seed from wild-type veA inoculated bolls.
Reduction of enterotoxic activity of Escherichia coli heat-stable enterotoxin by substitution for an asparagine residue (1988)

The Escherichia coli heat-stable enterotoxins (STs) are small peptide toxins consisting of 18 (STp) or 19 (STh) amino acids. STp and STh share biologically active sequences which reside in the C-terminal 13 amino acid residues, but the role of each amino acid in the active sequences is not clear. We substituted in vivo Asp, Tyr, His, Gln, Lys, and Arg for the Asn residue at position 11 of STp by oligonucleotide-directed site-specific mutagenesis and examined the biological activities of the resulting mutants. All mutant STs reacted with both monoclonal and polyclonal antibodies, demonstrating that the amino acid substitutions at position 11 did not cause a significant change in the conformation of STp. However, the substitutions invariably caused a significant decrease in enterotoxic activities. The most remarkable decrease was observed with Asn-11----Lys-11 and Asn-11----Arg-11 mutations; that is, enterotoxic activity could not be detected in the culture supernatant of either of these mutant strains. These results indicate that Asn-11 of STp plays an essential role in the enterotoxic activity. The amide group and the length of side chain of Asn-11 seem to be especially important for enterotoxic activity.
A Microanalytical Device for the Assessment of Coagulation Parameters in Whole Blood (1998)

The following describes the development of a disposable cartridge for use at the patient side to perform traditional coagulation assays on fresh whole blood samples. The cartridge provides a means by which a blood sample can be metered and quantitatively mixed with reagents which activate the coagulation cascade. Clot formation is subsequently detected using a microfabricated sensor also housed within the cartridge. The functional features of the cartridge and sensor are described and climcal results are presented.
Transgenic mice with mu and kappa genes encoding antiphosphorylcholine antibodies. (1986)

Transgenic mice were produced that carried in their germlines rearranged kappa and/or mu genes with V kappa and VH regions from the myeloma MOPC-167 kappa and H genes, which encode anti-PC antibody. The mu genes contain either a complete gene, including the membrane terminus (mu genes), or genes in which this terminus is deleted and only the secreted terminus remains (mu delta mem genes). The mu gene without membrane terminus is expressed at as high a level as the mu gene with the complete 3' end, suggesting that this terminus is not required for chromatin activation of the mu locus or for stability of the mRNA. The transgenes are expressed only in lymphoid organs. In contrast to our previous studies with MOPC-21 kappa transgenic mice, the mu transgene is transcribed in T lymphocytes as well as B lymphocytes. Thymocytes from mu and kappa mu transgenic mice display elevated levels of M-167 mu RNA and do not show elevated levels of kappa RNA, even though higher than normal levels of M-167 kappa RNA are detected in the spleen of these mice. Approximately 60% of thymocytes of mu transgenic mice produce cytoplasmic mu protein. However, despite a large amount of mu RNA of the membrane form, mu protein cannot be detected on the surface of T cells, perhaps because it cannot associate with T cell receptor alpha or beta chains. Mice with the complete mu transgene produce not only the mu transgenic mRNA but also considerably increased amounts of kappa RNA encoded by endogenous MOPC-167 like kappa genes. This suggests that B cells are selected by antigen (PC) if they coexpress the mu transgene and appropriate anti-PC endogenous kappa genes. Mice with the mu delta mem gene, however, do not express detectable levels of the endogenous MOPC-167 kappa mRNA. Like the complete mu transgene, the M-167 kappa transgene also causes amplification of endogenous MOPC-167 related immunoglobulins; mice with the kappa transgene have increased amounts of endogenous MOPC-167-like mu or alpha or gamma in the spleen, all of the secreted form. Implications for the regulation of immunoglobulin gene expression and B cell triggering are discussed.
Dendritic spines of rat cerebellar Purkinje cells: serial electron microscopy with reference to their biophysical characteristics (1988)

We have used serial electron microscopy and 3-dimensional reconstructions of dendritic spines from Purkinje spiny branchlets of normal adult rats to evaluate 2 questions about the relationship of spine geometry to synaptic efficacy. First, do relationships between spine geometry and other anatomical indicators of synaptic activity suggest that spine size and shape might be associated with synaptic efficacy? Reconstructed spines were graphically edited into head and neck compartments; the area of the postsynaptic density (PSD) was measured; the volume of spine smooth endoplasmic reticulum (SER) was computed; and all of the vesicles in the axonal varicosities were counted. Spine head volume and the volume of SER contained in the head are well correlated with the area of the PSD and the number of vesicles in the presynaptic axonal varicosity. Spine neck diameter does not fluctuate with PSD area, head volume, or the vesicle number. These results suggest that the dimensions of the spine head, but not of the spine neck, are likely to reflect differences in synaptic efficacy. Second, does the geometry of cerebellar spine necks reduce the transfer of synaptic charge to the recipient dendrite from the theoretical maximum that could be transferred if the synapse were on a dendritic shaft? Comparison of volume to surface area showed that the spine heads are approximately spherical and the necks are approximately cylindrical. Application of results from a biophysical model that assumed these geometrical shapes for spines (Wilson, 1984) showed that the cerebellar spine necks are unlikely to reduce transfer of synaptic charge by more than 5-20% even if their SER were to completely block passage of current through the portion of the neck that it occupies. We suggest that the constricted spine neck diameter might serve to isolate metabolic events in the vicinity of activated synapses by reducing diffusion to neighboring synapses, without significantly influencing the transfer of synaptic charge to the postsynaptic dendrite.
Total biosynthesis: in vitro reconstitution of polyketide and nonribosomal peptide pathways (2008)

This review surveys efforts to reconstitute key steps in polyketide and nonribosomal peptide biosynthetic pathways with purified enzymes and substrates; 344 references are cited.
Possible involvement of the M2 anti‐inflammatory macrophage phenotype in growth of human gliomas (2008)

Within tumours, many non-neoplastic cells such as fibroblasts, endothelial cells, and macrophages assist tumour growth by producing various growth factors and pro-angiogenic cytokines. Various tumour-derived molecules drive tumour-associated macrophages towards an anti-inflammatory phenotype (M2) and thus promoting tumour growth. Here we investigated microglia/macrophage differentiation in glioma tissues by means of immunostaining of paraffin-embedded glioma samples. The number of microglia/macrophages with positive staining for CD163 and CD204, which are believed to be markers for M2 macrophages, was correlated with the histological grade of the gliomas. The ratio of M2 macrophages in the tumour-associated microglia/macrophages was also associated with the histological grade. Culture supernatant from the glioma cell line can stimulate macrophages to develop into the M2 phenotype in vitro. Macrophage colony-stimulating factor (M-CSF), which strongly induces M2 polarization of macrophages, was significantly correlated with histological malignancy and with the proportion of M2 microglia/macrophages in vivo. In addition, the proportion of M2 microglia/macrophages and M-CSF expression in tumour cells correlated well with proliferation of glioblastoma cells. These results suggest that tumour-derived M-CSF induces a shift of microglia/macrophages towards the M2 phenotype, which influences tumour growth. Evaluation of the proportion of M2 microglia/macrophages and M-CSF expression in tumour tissue would be useful for assessment of microglia/macrophage proliferative activity and the prognosis of patients with gliomas.
Cutting Edge: Inhibition of T Cell Activation by TIM-2 (2006)

T cell Ig and mucin domain protein 2 (TIM-2) has been shown to regulate T cell activation in vitro and T cell-mediated disease in vivo. However, it is still not clear whether TIM-2 acts mainly to augment T cell function or to inhibit it. We have directly examined the function of TIM-2 in murine and human T cell lines. Our results indicate that expression of TIM-2 significantly impairs the induction of NFAT and AP-1 transcriptional reporters by not only TCR ligation but also by the pharmacological stimuli PMA and ionomycin. This does not appear to be due to a general effect on cell viability, and the block in NFAT activation can be bypassed by expression of activated alleles of Ras or calcineurin, or MEK kinase, in the case of AP-1. Thus, our data are consistent with a model whereby TIM-2 inhibits T cell activation.