gebhart/patrepeval huggingface dataset:
Structural Requirements for the Ectodomain Cleavage of Human Cell Surface Macrophage Colony-stimulating Factor (1996)

One form of human macrophage colony-stimulating factor (CSF-1(256), M-CSFalpha) is a member of a restricted set of cell surface transmembrane proteins, which is selected to undergo proteolytic ectodomain cleavage. To determine the substrate requirements for this cleavage, we have constructed a series of mutations in the cytoplasmic tail, transmembrane domain, and juxtamembrane region of CSF-1(256) and stably expressed the mutated genes in NIH 3T3 cells. Our results demonstrate that membrane association of the CSF-1 precursor is required for cleavage of its growth factor ectodomain and furthermore that the juxtamembrane region Pro161-Gln162-Leu163-Gln164-Glu165 (PQLQE) (residues 161-165 of the ectodomain) is an essential determinant of cell surface CSF-1(256) cleavage and that the cleavage site is partially sequence-specific. Furthermore, a mechanism of steric hindrance, which likely involves interference with protease accessibility, is postulated to explain the observed decreases in the cleavage efficiency in certain CSF-1 mutants. Finally, our results strongly suggest that the CSF-1 ectodomain is cleaved at or very near the cell surface by a membrane-associated proteolytic system.
Vaccination with dendritic cell/tumor fusion cells results in cellular and humoral antitumor immune responses in patients with multiple myeloma (2010)

We have developed a tumor vaccine in which patient-derived myeloma cells are chemically fused with autologous dendritic cells (DCs) such that a broad spectrum of myeloma-associated antigens are presented in the context of DC-mediated costimulation. We have completed a phase 1 study in which patients with multiple myeloma underwent serial vaccination with the DC/multiple myeloma fusions in conjunction with granulocyte-macrophage colony-stimulating factor. DCs were generated from adherent mononuclear cells cultured with granulocyte-macrophage colony-stimulating factor, interleukin-4, and tumor necrosis factor-α and fused with myeloma cells obtained from marrow aspirates. Vaccine generation was successful in 17 of 18 patients. Successive cohorts were treated with 1 × 10(6), 2 × 10(6), and 4 × 10(6) fusion cells, respectively, with 10 patients treated at the highest dose level. Vaccination was well tolerated, without evidence of dose-limiting toxicity. Vaccination resulted in the expansion of circulating CD4 and CD8 lymphocytes reactive with autologous myeloma cells in 11 of 15 evaluable patients. Humoral responses were documented by SEREX (Serologic Analysis of Recombinant cDNA Expression Libraries) analysis. A majority of patients with advanced disease demonstrated disease stabilization, with 3 patients showing ongoing stable disease at 12, 25, and 41 months, respectively. Vaccination with DC/multiple myeloma fusions was feasible and well tolerated and resulted in antitumor immune responses and disease stabilization in a majority of patients.
Glutathione Depletion in Rats Impairs T-Cell and Macrophage Immune Function (1993)

Critical illness is associated with both immunosuppression and glutathione deficiency. We determined if in vivo depletion of glutathione would adversely affect immune status. Rats with normal glutathione levels and those with glutathione stores depleted by diethyl maleate underwent analysis of splenocyte function and mesenteric lymph node lymphocyte function. Lymphocytes of the spleen and mesenteric lymph nodes were tested for concanavalin A proliferative response and interleukin 2 production. Tumor necrosis factor and interleukin 6 secretion by splenic adherent cells was also measured. Glutathione-depleted animals had significantly decreased lymphocyte proliferation and decreased production of tumor necrosis factor and interleukin 6 but unaltered interleukin 2 production. These findings indicate that in vivo glutathione deficiency impairs macrophage and T-cell function. Because glutathione depletion may occur in sepsis, trauma, and shock, treatments that help maintain glutathione levels may enhance immunocompetence and thus improve the ability of patients to recover from critical illness.
Requirement for delivery of signals by physical interaction and soluble factors from accessory cells in the induction of receptor-mediated T cell proliferation. Effectiveness of IFN-gamma modulation of accessory cells for physical interaction with T cells. (1989)

We analyzed the mechanism by which accessory cells support the induction of the proliferation of human peripheral blood T cells by a monoclonal anti-CD3 antibody, OKT3. Cross-linking of T cell receptor/CD3 complex by anti-CD3 coupled to latex beads and the addition of IL-1 are not enough to induce the IL-2 production and proliferation of T cells extensively depleted of accessory cells, while the addition of both the culture supernatant of macrophages or a monoblastic cell line, U937 cells, and the paraformaldehyde-fixed macrophages or U937 cells which had been precultured with interferon-gamma before fixation into the culture of the T cells with anti-CD3-latex did induce the T cell proliferation. Lack of the addition of either one of these did not induce the response. These results indicate that the signal(s) delivered by soluble factors released from the accessory cells and that delivered by the physical interaction between accessory cells and T cells are both required for the induction of IL 2 production and proliferation of T cells by anti-CD3-latex. Importantly, the macrophages or U937 cells had to be cultured with Con A-stimulated lymphocyte culture supernatant or IFN-gamma prior to fixation with paraformaldehyde, suggesting that a molecule(s) inducible on accessory cells surface by IFN-gamma or other lymphokine is necessary for the effective accessory cell-T cell interaction to induce the T cell response. It was further revealed that the activity of the culture supernatant of accessory cells may be mediated synergistically by IL 1 and a certain other factor(s) and was actually shown to be replaced by the combined addition of rIL-1 and rIL-6 but not by rIL-1 alone. The experimental system described here will be very useful for dissecting the accessory functions for T cell activation.
On the dispersion of love waves in a continuously Stratified layered earth (1977)

Love wave dispersion equation in a continuously heterogeneous layered-flat-earth has been stable studied. Different types of plausible variation of Plastic parameters in each of the layers have been considered and the corresponding displacements have been obtained. Thomson Harkell Matrix method has been employed to derive the dispersion equation of SH surface waves in such a layered earth.
Isolation and characterization of anti-Salmonella lactic acid bacteria from the porcine gastrointestinal tract (2004)

The data demonstrate that some porcine intestinal LAB isolates may offer potential as probiotics for the reduction of Salmonella carriage in pigs.
LabVIEW 2009 Student Edition (2006)

For courses in Measurement and Instrumentation, Electrical Engineering lab, and Physics and Chemistry lab. This revised printing has been updated to include new LabVIEW 8.2 Student Edition. National Instruments' LabVIEW is the defacto industry standard for test, measurement, and automation software solutions. With the Student Edition of LabVIEW, students can design graphical programming solutions to their classroom problems and laboratory experiments with software that delivers the graphical programming capabilites of the LabVIEW professional version. . The Student Edition is also compatible with all National Instruments data acquisition and instrument control hardware. Note: The LabVIEW Student Edition is available to students, faculty, and staff for personal educational use only. It is not intended for research, institutional, or commercial use. For more information about these licensing options, please visit the National Instruments website at (http:www.ni.com/academic/)
Frequency Trimming of Aluminum Nitride Microresonators Using Rapid Thermal Annealing (2013)

To transition aluminum nitride (AlN) microresonator filters into a manufacturable technology, accurate control of the resonator frequency across a wafer is required. This paper describes a postfabrication rapid thermal anneal approach to trim resonator frequency over 27000 ppm with an accuracy of 500 ppm. Measurements made on 22.4 MHz resonators indicate that the effect of annealing on the resonators saturates in 5 min and upshift the resonator frequency super linearly with temperature. We replicate the frequency trimming effect on hermetically sealed wafer level packaged devices to reduce the across-wafer frequency distribution from 22000 to 4000 ppm. We confirm that this postannealing technique is permanent by temperature cycling the resonators from 50°C to 125°C. This technique provides a method to trim AlN microresonator frequency overcoming effects such as thin film variations, which are inherent to microsystems fabrication.
Intraspecific Variation in Small-Subunit rRNA Sequences in GenBank: Why Single Sequences May Not Adequately Represent Prokaryotic Taxa (1995)

Small-subunit rRNA (SSU rRNA) sequencing is a powerful tool to detect, identify, and classify prokaryotic organisms, and there is currently an explosion of SSU rRNA sequencing in the microbiology community. We report unexpectedly high levels of intraspecific variation (within and between strains) of prokaryote SSU rRNA sequences deposited in GenBank. A total of 82% of the prokaryote species with two published SSU rRNA sequences had more variable positions than a 0.1% random sequencing error would predict, and 48% of these sequence pairs had more variable positions than predicted by a 1.0% random sequencing error. Other sources of sequence variability must account for some of this intraspecific variation. Given these results, phylogenetic studies and biodiversity estimates obtained by using prokaryotic SSU rRNA sequences cannot proceed under the assumption that rRNA sequences of single operons from single isolates adequately represent their taxa. Sequencing SSU rRNA molecules from multiple operons and multiple isolates is highly recommended to obtain meaningful phylogenetic hypotheses, as is careful attention to accurate strain identification.
A 20-MHz sixth-order BiCMOS parasitic-insensitive continuous-time filter and second-order equalizer optimized for disk-drive read channels (1993)

A fast parasitic-insensitive continuous-time filter and equalizer integrated circuit that uses an active integrator is described. Circuit techniques for excess-phase cancellation and for setting the corner-frequency of the filter and equalizer are also described. These techniques result in a filter and equalizer chip with performance independent of process, supply, and temperature without employing phase-lock loops. The 20-MHz sixth-order Bessel filter and second-order equalizer operate from 5 V and generate only 0.24% (-52 dB) of total harmonic distortion when processing 2-V/sub pp/ differential output signals. The device is optimized to limit high-frequency noise and to amplitude equalize the data pulses in hard disk read-channel systems. The device supports data rates of up to 36 Mb/s and is built in a 1.5- mu m, 4-GHz BiCMOS technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antegrade intramedullary fixation of humeral shaft fractures by Rush pins (2011)

Most humeral shaft fractures (>90%) heal with nonsurgical management, which is practiced by the use of hanging cast, but it is most effective only in spiral or oblique fracture pattern. During this immobilization period, the patients must remain upright or semi-upright at all times, even while sleeping, with the cast in a dependent position for effectiveness. It causes suffering to most patients. Intramedullary flexible nailing used for displaced transverse humeral shaft fracture was advocated decades ago. Now, we try to use Rush pins to fulfill the theory of “filling-up” and “3-point” fixation. Nine patients (five men and four women) underwent this closed reduction and internal fixation with Rush pin procedure between July 2007 and June 2009. Their average age was 43.2 years (range, 19–68 years). The union status was checked by radiologic and physical examinations. The shoulder function was evaluated by Oxford Shoulder Questionnaire. The surgery was performed with an incision on lateral cortex of humeral surgical neck. The size and number of Rush pins were decided according to the inner diameter and length of the humeral shaft. The Rush pins were prebent before insertion. The whole procedure of pin insertion was carried out under C-arm guidance. None of these patients had radial nerve injury or pin migration. Two complications were noted, one with proximal hook prominence and the other one with nonunion of fracture because of overdistraction. Otherwise, all the other patients regained pretraumatic shoulder range of motion, union of fracture, and were satisfied with the shoulder function and clinical result. Although it is technique demanding, it has the benefits of avoiding damaging rotator cuff and exposing radial nerve, saving operating time, minimizing soft tissue dissection, and being cost-effective. Furthermore, patients had a better life quality during the period of immobilization because of fracture.
The complete primary structure of human matrix metalloproteinase-3. Identity with stromelysin. (1988)

We have determined the complete primary structure for human matrix metalloproteinase-3 (MMP-3), which has 477 residues including a 17-residue signal peptide. The result indicates that MMP-3 is identical with stromelysin (Whitham, S. E., Murphy, G., Angel, P., Rahmsdorf, H.-J., Smith, B. J., Lyons, A., Harris, T. J. R., Reynolds, J. J., Herrlich, P., and Docherty, A. J. P. (1986) Biochem. J. 240, 913-916). A striking result is that MMP-3 and collagenase are 54% identical in sequence, suggesting a common origin for the evolution of the two proteinases. We also show that in human synovial fibroblast cultures human recombinant interleukin-1 beta rapidly induces high levels of MMP-3 mRNA and, conversely, that retinoic acid or dexamethasone can suppress the MMP-3 mRNA levels. Similar results were obtained for human synovial collagenase mRNA. The data suggest that MMP-3 and collagenase expression are coordinately modulated in synovial fibroblast cultures.
KRAS mutation confers resistance to antibody‐dependent cellular cytotoxicity of cetuximab against human colorectal cancer cells (2013)

Cetuximab is a chimeric IgG1 monoclonal antibody (mAb) that targets the extracellular domain of epidermal growth factor receptor (EGFR). Oncogenic KRAS mutations in tumors have been shown to be a negative predictor of the response of colorectal cancer (CRC) to cetuximab treatment. Cetuximab exerts its therapeutic effects through several mechanisms including antibody-dependent cellular cytotoxicity (ADCC). However, the influence of KRAS mutations on cetuximab-mediated ADCC is not fully understood. Here, we investigated cetuximab-mediated ADCC in two pairs of isogenic CRC cells with or without a KRAS mutation. Peripheral blood mononuclear cells (PBMCs) from healthy volunteers and NK92, a natural killer (NK) cell line that exogenously expresses FcγRIIIa (CD16a), were used as effector cells. In an ADCC assay, perforin-dependent target cell lysis was not affected by the KRAS mutation status. On the other hand, perforin-independent ADCC was observed only in CRC cells with wild-type KRAS, but not in cells with mutant KRAS. Neutralizing experiments revealed that the Fas-Fas ligand (FasL) interaction was responsible for the induction of apoptosis and perforin-independent ADCC. Furthermore, the presence of effector cells clearly enhanced the growth-inhibitory effect of cetuximab only in CRC cells with wild-type KRAS, but not in those with mutant KRAS. These findings suggest that ADCC is an important mode of action of cetuximab and that KRAS mutation impairs the therapeutic effect exerted by cetuximab-mediated ADCC.
Getting Help With Linux (1998)

So you've heard a lot about the power of Linux and you're eager to try it out for yourself. But where do you start?
Four assay methods for glycated hemoglobin compared as screening tests for diabetes mellitus: the Islington Diabetes Survey. (1988)

We assessed the utility of four methods of glycated hemoglobin assay (agar gel electrophoresis with Schiff base, agar gel electrophoresis with prior removal of Schiff base, boronate affinity chromatography, and isoelectric focusing) as screening tests for diabetes mellitus, studying 223 subjects undergoing an oral glucose-tolerance test after fasting and 2 h after ingestion of 75 g of glucose. Assessment of glucose tolerance status according to the 1980 World Health Organization diagnostic criteria indicated that 13 subjects (5.8%) had diabetes, 48 (21.5%) had impaired glucose tolerance, and nine (4.0%) could not be classified (six of these because of missing values). Use of receiver-operating characteristic curves to compare the assays as screening tests showed the affinity chromatography assay to be superior. Assays for glycated hemoglobin after fasting had better precision than post-glucose-load assays as screening tests, and test characteristics of glycated hemoglobin assays on fasting subjects were similar to those of the blood-glucose estimation after fasting. We conclude that measurement of glycated hemoglobin may be a useful screening test for diabetes, and that such measurement of stable glycated hemoglobin is as accurate as measurement of fasting blood-glucose in screening for diabetes. For this use, we found methods that measure stable glycated hemoglobin superior to that measuring both stable and labile Schiff-base fractions.
Characterization of α‐adrenoceptors in the vasculature of the canine nasal mucosa (1986)

alpha-Adrenoceptors present in the vasculature of the nasal mucosa in beta-adrenoceptor blocked dogs have been characterized pharmacologically using selective alpha 1- and alpha 2-adrenoceptor agonists and antagonists. In pentobarbitone-anaesthetized dogs, intra-arterial (i.a.) administration of the selective alpha 1-agonists cirazoline and phenylephrine, the selective alpha 2-agonist UK-14,304 and the mixed alpha 1/alpha 2-agonists adrenaline, noradrenaline and oxymetazoline produced dose-related nasal vasoconstrictor responses (as measured by decreases in nasal cavity pressure). The rank order of agonist potency was adrenaline greater than oxymetazoline = UK-14,304 greater than noradrenaline greater than cirazoline greater than phenylephrine. The nasal response to cirazoline was inhibited by the selective alpha 1-adrenoceptor antagonist prazosin but not by the new, potent selective alpha 2-adrenoceptor antagonist RX811059. In contrast, UK-14,304 was inhibited only by RX811059. Either prazosin or RX811059 reduced the effect of the mixed agonist adrenaline. In spinal dogs, the noradrenaline-evoked fall in nasal cavity pressure was reduced by either prazosin or RX811059. Prazosin attenuated markedly the nasal vasoconstrictor response to electrical stimulation of postganglionic fibres emerging from the superior cervical ganglion (SNS) whereas RX811059 was ineffective. Administration of the neuronal re-uptake inhibitor cocaine potentiated the effect of i.a. noradrenaline but reduced marginally the maximal response to SNS. After cocaine, RX811059 enhanced the effect of SNS and attenuated the response to noradrenaline. Prazosin reduced effectively the responses to both SNS and noradrenaline after cocaine. Pretreatment with the alpha 2-agonist UK-14,304 did not affect the response to noradrenaline in the nasal cavity but evoked a persistent (up to 2 h) reduction in the response to SNS. RX811059 antagonized the inhibitory effect of UK-14,304. These results demonstrate that both postjunctional alpha 1- and alpha 2-adrenoceptors mediating vasoconstriction are present in the canine nasal mucosa. In addition, sympathetic neurones innervating the nasal mucosa are characterized by a very efficient re-uptake process and contain prejunctional alpha 2-adrenoceptors.
OverSim: A Flexible Overlay Network Simulation Framework (2007)

A fundamental problem in studying peer-to- peer networks is the evaluation of new protocols. This paper presents OverSim, a flexible overlay network simulation framework based on OMNeT++. It was designed to fulfill a number of requirements that have been partially neglected by existing simulation frameworks. OverSim includes several structured and unstructured peer-to-peer protocols like Chord, Kademlia and Gia. These protocol implementations can be used for both simulation as well as real world networks. To facilitate the implementation of additional protocols and to make them more comparable OverSim provides several common functions like a generic lookup mechanism for structured peer-to-peer networks and an RPC interface. Several exchangeable underlay network models allow to simulate complex heterogeneous underlay networks as well as simplified networks for large- scale simulations. We show that with OverSim simulations of overlay networks with up to 100,000 nodes are feasible.
A Novel FLT3 Inhibitor FI-700 Selectively Suppresses the Growth of Leukemia Cells with FLT3 Mutations (2007)

FI-700 is a novel and potent FLT3 inhibitor with promising antileukemia activity.
Ley specific antibody with potent anti-tumor activity is internalized and degraded in lysosomes. (1993)

BR96 is a monoclonal antibody (MAb) that recognizes many human carcinomas and can kill antigen-positive tumor cells in vitro. Using both gold and radiolabeled MAb, the distribution and cellular processing of BR96 during cytolysis has been determined. After a brief (< 3 minutes) MAb treatment, cells in suspension are stained by the nuclear viability dye propidium iodide. Whole MAb and F(ab')2 fragments are equally cytotoxic; monovalent F(ab) fragments, however, have no effect on dye uptake unless cross-linked with goat anti-mouse IgG. The level of toxicity is dependent on both MAb dose and on cell surface receptor density. Cell contact may regulate receptor expression. BR96 receptors are more abundant on cells migrating into the open areas of a scratch wounded confluent culture than on the adjacent contact-inhibited cells. BR96 can also inhibit the anchorage-independent growth of tumor cells in soft agar showing that its effects on propidium iodide staining are not due to transient changes in membrane permeability. Immunogold electron microscopy reveals that, after a 1-minute treatment, BR96 induces significant infolding of the plasma membrane and that internalized MAb is localized to these structures. Immediately thereafter, large cell surface and intracellular vesicles form, mitochondria are swollen, and membrane integrity is lost. Therefore, BR96 seems to cause morphological changes characteristic of necrosis rather than apoptosis. When bound to adherent carcinoma cells, BR96 is distributed uniformly on the apical surface of cells labeled at 4 C and is enriched at points of cell substratum contact. Upon warming of the cells to 37 C, BR96 localizes in small perinuclear clusters and the cell margin is now devoid of label. Immunogold electron microscopy reveals that BR96 undergoes receptor mediated internalization and is localized within the same coated pits, endosomes, and lysosomes as the transferrin receptor. Quantitative studies using iodinated BR96 show that after 6 hours of chase, a maximum of 53% of the radiolabel is located within the intracellular pool. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicates that 84% of this fraction is nondegraded. BR96 probably cycles between the medium and intracellular pools because the remainder of the radiolabel is in the medium as intact MAb. By 24 hours of chase, the intracellular fraction drops to 30%, while the remaining 70% is present in the culture medium, mostly as low molecular weight degradation products.