gebhart/patrepeval huggingface dataset:
The extracellular domain of the c-erbB-2 oncoprotein is released from tumor cells by proteolytic cleavage. (1993)

A molecule that is immunologically related to the c-erbB-2 oncogene product (p185HER2/neu) was detected in the conditioned culture medium from neu-overexpressing tumor cell lines and in sera of advanced-stage breast carcinoma patients. Using a sensitive (in the range of 0.5 ng ml-1) double-determinant radioimmunoassay (DDIRMA) with two monoclonal antibodies (MAbs) directed against the neu extracellular domain (ECD), soluble oncoproteins were detected in supernatants from several neu-positive tumor cell lines, independent of the levels of membrane p185HER2 expression. The molecule detected did not react with a MAb directed against an intracytoplasmic epitope of the p185HER2. Western blot analysis of the concentrated supernatant revealed a protein of approximately 110 kDa molecular mass, which closely matches the predicted size of the glycosylated p185HER2 ECD. Immunoprecipitation of culture supernatant from cell surface-radioiodinated cells confirmed the 110 kDa molecular mass of the glycosylated shed protein, which migrated to 86 kDa after deglycosylation. Proteolytic cleavage of the p185HER2 molecule was demonstrated in release assays carried out with protease inhibitors. The combined use of leupeptin and EDTA completely inhibited release of the molecule. Analysis of sera from breast carcinoma patients and healthy donors by DDIRMA revealed the presence of soluble neu in 15% of pathologic sera but none of the normal sera. A good correlation was found between neu-overexpression in the primary tumor and the soluble marker in serum of patients with advanced disease; sera of early-stage patients were always negative, independent of neu-overexpression in the tumor. These results suggest the usefulness of soluble neu as an indicator of tumor aggressiveness but not as a diagnostic marker of breast cancer.
Fast, Minimum Storage Ray-Triangle Intersection (1997)

Abstract We present a clean algorithm for determining whether a ray intersects a triangle. The algorithm translates the origin of the ray and then changes the base to yield a vector (t u v) T , where t is the distance to the plane in which the triangle lies and (u, v) represents the coordinates inside the triangle. One advantage of this method is that the plane equation need not be computed on the fly nor be stored, which can amount to significant memory savings for triangle meshes. As we found our method to be comparable in speed to previous methods, we believe it is the fastest ray-triangle intersection routine for triangles that do not have precomputed plane equations.
Cytomorphometry of uveal melanoma. Comparison of fine needle aspiration biopsy samples with histologic sections. (1991)

A number of approaches are being investigated to increase the prognostic accuracy for uveal melanoma patients; the standard deviation of nucleolar area measurements and the DNA content appear to correlate better with survival than do classic histologic parameters. The utility of performing cytomorphometric measurements on fine needle aspiration (FNA) biopsy samples was prospectively analyzed for 24 eyes containing uveal melanomas that were examined with both 25-gauge FNA biopsy and standard histologic techniques. "Masked" analysis of the cellular composition of the 24 cases showed the presence or absence of epithelioid cells to be accurately predicted on the FNA samples in all cases. Image analysis cytomorphometric measurements of nucleolar area showed marked variability (with r less than 0.4) when FNA and histologic samples from the same case were compared. The relationship between these measurements was affected by cell type, sampling, specimen processing and investigator experience.
Isolation of High Avidity Melanoma-Reactive CTL from Heterogeneous Populations Using Peptide-MHC Tetramers (1999)

Immunogenic peptides of human tumor Ag have been used to generate antigen-specific CTL. However, the vast majority of these peptide-specific CTL clones are of low avidity and are peptide, but not tumor, reactive. Peptide-MHC tetramers have been shown to bind specific TCRs with sufficient affinity to be useful reagents for flow cytometry. In this paper we demonstrate that peptide-MHC tetramers can also be used to selectively identify high avidity tumor-reactive CTL and enrich, from a heterogeneous population, the subpopulation of peptide-reactive T cells that can lyse tumor targets. The melanoma proteins, MART-1 and gp100, were used to induce potentially tumor-reactive T cells, and the intensity of T cell staining by TCR binding of specific peptide-MHC tetramers was assessed. A range of fluorescence intensity was detected, and the magnitude of tetramer binding was correlated with T cell avidity. The population of peptide-reactive T cells was phenotypically similar with regard to expression of TCR and adhesion molecules, suggesting that this differential avidity for tumor cells reflected differential affinity of the TCR for its peptide-MHC ligand. Sorting, cloning, and expansion of tetramerhigh CTL from a heterogeneous population of peptide-stimulated PBMCs enabled rapid selection of high avidity tumor-reactive CTL clones, which retained their functional and tetramerhigh phenotype on re-expansion. These results demonstrate that the avidity of a T cell for its tumor target is due to the specific affinity of the TCR for its peptide-MHC ligand, that this interaction can be described using peptide-MHC tetramers and used to isolate high avidity tumor-reactive CTL.
Length and thickness dependence of longitudinal flexural resonance frequency shifts of a piezoelectric microcantilever sensor due to Young’s modulus change (2008)

For piezoelectric microcantilever sensors (PEMSs) whose resonance frequency shift during detection is due to Young’s modulus change in the piezoelectric layer, we showed that their detection longitudinal flexural resonance frequency shift, Δf, is inversely proportional to the square of the PEMS length, L2; their relative resonance frequency shift, Δf/f, inversely proportional to the PEMS thickness, t; and their mass detection sensitivity, Δf/Δm, inversely proportional to wL3 where w is the width. The resonance frequency shift caused by Young’s modulus change in the piezoelectric layer is more than 300 times larger than would be expected from the mass change.
Induction of protective cytotoxic T cells to murine cytomegalovirus by using a nonapeptide and a human-compatible adjuvant (Montanide ISA 720) (1995)

The use of synthetic peptides representing cytotoxic T-cell (CTL) epitopes for human vaccination requires the identification of a suitable adjuvant formulation. A single immunization with Montanide ISA720/tetanus toxoid/YPHFMPTNL protected mice against murine cytomegalovirus and induced epitope-specific CTL. Such formulations will find application in peptide-based CTL anti-viral vaccines.
Bioactive surface for neural electrodes: Decreasing astrocyte proliferation via transforming growth factor‐β1 (2007)

Implantation of deep-brain recording devices is a traumatic event, which inevitably elicits reactive gliosis. The ensuing glial scar encapsulating the implanted device impedes the long-term functional recording capability of the microelectrode. In this work, a bioactive surface is prepared by conjugation of transforming growth factor-beta one (TGF-beta1) and laminin to dextran, which is in turn conjugated to a biomaterial substrate. Poly-L-lysine coated surfaces are treated with oxidized dextran, and the dextran is re-oxidized with sodium metaperiodate to generate hemiacetal structures to which TGF-beta1 and laminin are covalently bound. Covalent conjugation of the ligand is confirmed by enzyme-linked immunosorbent assay. A primary cell line of astrocytes is incubated on a surface conjugated with laminin and TGF-beta1 and a surface only conjugated with laminin. Proliferation on the laminin plus TGF-beta1 surface is 57% less (p < 0.002) than the control surface (laminin alone). The results demonstrate that conjugated TGF-beta1 retains its efficacy toward astrocyte proliferation and represents a potential strategy for reducing glial scar formation in vivo.
View-based interpretation of real-time optical flow for gesture recognition (2002)

The authors have developed a real-time, view-based gesture recognition system. Optical flow is estimated and segmented into motion blobs. Gestures are recognized using a rule-based technique based on characteristics of the motion blobs such as relative motion and size. Parameters of the gesture (e.g., frequency) are then estimated using context specific techniques. The system has been applied to create an interactive environment for children.
The Neurospora mitochondrial tyrosyl-tRNA synthetase is sufficient for group I intron splicing in vitro and uses the carboxy-terminal tRNA-binding domain along with other regions. (1991)

Neurospora mitochondrial tyrosyl-tRNA synthetase (mt tyrRS), which is encoded by nuclear gene cyt-18, functions in splicing of group I introns in mitochondria. Here, we overproduced functional cyt-18 protein in Escherichia coli and purified it to near homogeneity. The purified protein has splicing and tyrRS activities similar to those of cyt-18 protein isolated from mitochondria and is by itself sufficient to splice the mitochondrial large rRNA intron in vitro. Structure-function relationships in the cyt-18 protein were analyzed by in vitro mutagenesis. We confirmed that a small amino-terminal domain not found in bacterial tyrRSs is required for splicing activity, but not tyrRS activity. Two linker insertion mutations, which disrupt the predicted ATP-binding site, completely inhibit tyrRS activity but leave substantial splicing activity. Finally, deletions or linker insertion mutations in the putative carboxy-terminal tRNA-binding domain inhibit both tyrRS and splicing activities, although some have differential effects on the two activities. Our results show that the normal catalytic activity of the cyt-18 protein is not required for splicing and are consistent with the hypothesis that the protein functions by binding to the precursor RNA and facilitating formation of the correct RNA structure. Regions required for splicing are distributed throughout the cyt-18 protein and overlap, but are not identical to, regions required for tyrRS activity. The finding that the putative carboxy-terminal tRNA-binding domain is required for both tyrRS and splicing activities suggests that the mechanism for binding the intron has similarities to the mechanism for binding tRNA(Tyr).
Nitrogen-15 NMR spectroscopy of hydrogen-bonding interactions in the active site of serine proteases: evidence for a moving histidine mechanism (1986)

Nitrogen-15 NMR spectroscopy has been used to study the hydrogen-bonding interactions involving the histidyl residue in the catalytic triad of alpha-lytic protease in the resting enzyme and in the transition-state or tetrahedral intermediate analogue complexes formed with phenylmethanesulfonyl fluoride and diisopropyl fluorophosphate. The 15N shifts indicate that a strong hydrogen bond links the active site histidine and serine residues in the resting enzyme in solution. This result is at odds with interpretations of the X-ray diffraction data of alpha-lytic protease and of other serine proteases, which indicate that the serine and histidine residues are too far apart and not properly aligned for the formation of a hydrogen bond. In addition, the nitrogen-15 shifts demonstrate that protonation of the histidine imidazole ring at low pH in the transition-state or tetrahedral intermediate analogue complexes formed with phenylmethanesulfonyl fluoride and diisopropyl fluorophosphate triggers the disruption of the aspartate-histidine hydrogen bond. These results suggest a catalytic mechanism involving directed movement of the imidazole ring of the active site histidyl residue.
Murine c-fms cDNA: cloning, sequence analysis and retroviral expression. (1988)

We have isolated and sequenced a cDNA clone coding for the murine c-fms gene. The 3677 nucleotide cDNA clone codes for a protein of 976 amino acids, which has 76% and 75% homology to the v-fms and human proteins, respectively. The predicted membrane protein, c-fms, has an amino terminal signal sequence and external, transmembrane and cytoplasmic domains. The homology between murine c-fms and v-fms or human c-fms is the strongest (90%-95%) in the cytoplasmic domain and weakest (59%-63%) in the external domain. The c-fms clone was inserted into a retroviral vector containing a neomycin resistance gene and cell lines resistant to G418 were isolated. These cell lines expressed protein which was immunoprecipitated by anti-c-fms antibodies and of the same size as murine c-fms. These cells were also found to specifically bind human CSF-1.
Synthesis and processing of silicon nanocrystallites using a pulsed laser ablation supersonic expansion method (1994)

We report the preparation of nanometer sized crystallites of silicon by a pulsed laser ablation supersonic expansion technique. High resolution transmission electron microscopy is used to verify that particles with diameter in the range of ∼3 nm and greater are produced. Glancing angle x-ray diffraction results confirm that the particles formed have the silicon diamond cubic crystal structure. Visible photoluminescence emission from self-supporting thin films of agglomerated nanocrystallites is observed under excitation with ultraviolet light.
A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays (2004)

Using nanogram quantities on total RNA, the usage of dIVT protocol identified differentially expressed genes and functional categories consistent with those detected by the IVT protocol. There was a loss in sensitivity of about 10% when detecting differentially expressed genes using the dIVT protocol. However, the lower amount of RNA required for this protocol, as compared to the IVT protocol, renders this methodology a highly desirable one for biological systems where sample amounts are limiting.
C-C Chemokine Receptor 2 Inhibitor Improves Diet-Induced Development of Insulin Resistance and Hepatic Steatosis in Mice (2010)

Propagermanium treatment slightly decreased body weight gain and visceral fat accumulation in diet-induced obese (DIO) mice. Further, propagermanium suppressed macrophage accumulation and shifted adipose tissue macrophage polarization from the pro-inflammatory (M1) state to anti-inflammatory (M2) state in DIO mice. Expressions of TNF-alpha and MCP-1 mRNA in adipose tissue were reduced by propagermanium treatment, indicating that propagermanim suppressed inflammation in adipose tissue. Propagermanium treatment also ameliorated glucose tolerance, insulin sensitivity, and decreased hepatic triglyceride in DIO mice. Thus, propagermanium improved diet-induced obesity and related metabolic disorders, such as insulin resistance and hepatic steatosis by suppressing inflammation in adipose tissue. Our data indicate that inhibition of CCR2 could improve diet-induced metabolic disorders, and that propagermanium may be a beneficial drug for the treatment of metabolic syndrome.
Membrane Chromatography: Preparation and Applications to Protein Separation (1999)

As a result of the convective flow of solutes through porous membranes, membrane chromatography has a higher capture efficiency and a higher productivity than column chromatography and shows most promising industrial applications for the recovery, isolation, and purification of proteins and enzymes. This paper presents a comprehensive review of the methods for preparation of adsorptive membranes (such as surface modification, in situ copolymerization, direct formation from hydrophilic materials, and functionalized particulate-entrapped membranes) and deals particularly with novel macroporous chitin and chitosan membranes for protein separations developed by the authors.
Oncostatin M and leukemia inhibitory factor trigger overlapping and different signals through partially shared receptor complexes. (1994)

Leukemia inhibitory factor (LIF) and oncostatin M (OSM) both bind to the same receptor with high affinity and thus mediate an overlapping spectrum of biological activities, the signal transduction mechanisms for which are unclear. We show that mitogen-activated protein kinases are involved in both the LIF and OSM signal transduction pathways. However, we found that OSM is a much more potent inducer of both mitogen-activated protein kinase activity and biological response, both of which correlate with the expression of a second OSM receptor that does not bind LIF. In addition, different patterns of tyrosine-phosphorylated proteins were stimulated by OSM and LIF. We therefore suggest that the two receptors for OSM can be coupled to different signal transduction events.
Generating extracellular amyloid aggregates using E. coli cells (2012)

Diverse proteins are known to be capable of forming amyloid aggregates, self-seeding fibrillar assemblies that may be biologically functional or pathological. Well-known examples include neurodegenerative disease-associated proteins that misfold as amyloid, fungal prion proteins that can transition to a self-propagating amyloid form and certain bacterial proteins that fold as amyloid at the cell surface and promote biofilm formation. To further explore the diversity of amyloidogenic proteins, generally applicable methods for identifying them are critical. Here we describe a cell-based method for generating amyloid aggregates that relies on the natural ability of Escherichia coli cells to elaborate amyloid fibrils at the cell surface. We use several different yeast prion proteins and the human huntingtin protein to show that protein secretion via this specialized export pathway promotes acquisition of the amyloid fold specifically for proteins that have an inherent amyloid-forming propensity. Furthermore, our findings establish the potential of this E. coli-based system to facilitate the implementation of high-throughput screens for identifying amyloidogenic proteins and modulators of amyloid aggregation.
HIV-induced apoptosis requires the CD4 receptor cytoplasmic tail and is accelerated by interaction of CD4 with p56lck. (1996)

The roles of the CD4 receptor and the src kinase p56lck were examined in the process of HIV-induced apoptosis of CD4+ T lymphocytes. The presence of the CD4 cytoplasmic tail was found to be essential in delivering an apoptotic signal, and interaction of CD4 with p56lck potentiated HIV-induced apoptosis. Apoptosis, but not HIV replication, was abrogated by deleting the NH2-terminal intracytoplasmic tail of CD4, or by mutating the two critical cysteines in this tail that are responsible for CD4-p56lck interaction. Introduction of p56lck in C8166-45 or MT-2 cells, CD4+ T cell lines deficient for this protein, greatly increased HIV-induced apoptosis and syncytium formation. The ability of p56lck to deliver an apoptotic signal did not depend on its kinase function, since a kinase-deficient mutant was as effective as its normal counterpart in inducing apoptosis, suggesting that p56lck may act as an adapter to anchor other proteins to transduce the death signal.
Correction of Anemia — Payoffs and Problems (2006)

Anemia develops in most patients with chronic kidney disease, historically often requiring transfusion, with obvious risks. With the advent of recombinant erythropoietin in the late 1980s, it became possible to treat anemia without transfusion, ushering in a new era. It soon became clear that additional considerations were important, such as ensuring adequate iron stores, providing sufficient folate and vitamin B12, and identifying other conditions affecting the hemoglobin level. How best to administer erythropoietin — as well as how best to produce it, given cases of pure red-cell aplasia related to production and administration — were also identified as . . .
Effects of ß-glucans on the immune system (2007)

ß-Glucans are naturally occurring polysaccharides. These glucose polymers are constituents of the cell wall of certain pathogenic bacteria and fungi. The healing and immunostimulating properties of mushrooms have been known for thousands of years in the Eastern countries. These mushrooms contain biologically active polysaccharides that mostly belong to group of ß-glucans. These substances increase host immune defense by activating complement system, enhancing macrophages and natural killer cell function. The induction of cellular responses by mushroom and other ß-glucans is likely to involve their specific interaction with several cell surface receptors, as complement receptor 3 (CR3; CD11b/CD18), lactosylceramide, selected scavenger receptors, and dectin-1 (ßGR). ß-Glucans also show anticarcinogenic activity. They can prevent oncogenesis due to the protective effect against potent genotoxic carcinogens. As immunostimulating agent, which acts through the activation of macrophages and NK cell cytotoxicity, ß-glucan can inhibit tumor growth in promotion stage too. Antiangiogenesis can be one of the pathways through which ß-glucans can reduce tumor proliferation, prevent tumor metastasis. ß-Glucan as adjuvant to cancer chemotherapy and radiotherapy demonstrated the positive role in the restoration of hematopiesis following by bone marrow injury. Immunotherapy using monoclonal antibodies is a novel strategy of cancer treatment. These antibodies activate complement system and opsonize tumor cells with iC3b fragment. In contrast to microorganisms, tumor cells, as well as other host cells, lack ß-glucan as a surface component and cannot trigger complement receptor 3-dependent cellular cytotoxicity and initiate tumor-killing activity. This mechanism could be induced in the presence of ß-glucans.
Light widgets (2002)

This paper describes a system for ubiquitous interaction that does not require users to carry any physical devices. In this system, the environment is instrumented with camera/processor combinations that watch users while protecting their privacy. Any visible surface can be turned into an interactive widget triggered by skin-colored objects. Light widgets are tied to the XWeb cross-modal interaction platform to empower them with interactive feedback.