gebhart/patrepeval huggingface dataset:
Cloning, mapping, and characterization of activated leukocyte-cell adhesion molecule (ALCAM), a CD6 ligand. (1995)

Antibody-blocking studies have demonstrated the role of CD6 in thymocyte-thymic epithelial (TE) cell adhesion. Here we report that CD6 expressed by COS cells mediates adhesion to TE cells and that this interaction is specifically blocked with an anti-CD6 monoclonal antibody (mAb) or with a mAb (J4-81) that recognized a TE cell antigen. We isolated and expressed a cDNA clone encoding this antigen and show that COS cells transfected with this cDNA bind a CD6 immunoglobulin fusion protein (CD6-Rg). This antigen, which we named ALCAM (activated leukocyte-cell adhesion molecule) because of its expression on activated leukocytes, appears to be the human homologue of the chicken neural adhesion molecule BEN/SC-1/DM-GRASP. The gene was mapped to human chromosome 3q13.1-q13.2 by fluorescence in situ hybridization of cDNA probes to metaphase chromosomes. We prepared an ALCAM-Rg fusion protein and showed that it binds to COS cell transfectants expressing CD6, demonstrating that ALCAM is a CD6 ligand. The observations that ALCAM is also expressed by activated leukocytes and that both ALCAM and CD6 are expressed in the brain suggest that ALCAM-CD6 interactions may play a role in the binding of T and B cells to activated leukocytes, as well as in interactions between cells of the nervous system.
Logic synthesis for engineering change (1999)

During the process of very large scale integration design, specifications are often changed. To preserve as large a portion of the engineering effort as possible, it is desirable that such changes will not lead to a very different design. In this work, we consider logic synthesis algorithms for handling engineering changes. To solve it, we propose a combination of multiple-error diagnosis and logic minimization techniques. Given a new specification and an existing synthesized network, our algorithms first identify the candidate signals in the network, and then synthesize the candidate functions. The synthesis step utilizes the existing network as much as possible so that the new specification can be realized with minimal changes.
The three sorCS genes are differentially expressed and regulated by synaptic activity (2004)

We have isolated the murine sorCS3 gene, a new member of the family of receptors containing a Vps10p-domain. Receptors of this family facilitate rapid endocytosis and are thought to be involved in intracellular sorting. SorCS3 and the highly homologous sorCS1 and sorCS2 genes were expressed in a combinatorial, mostly non-overlapping pattern in both the developing and mature central nervous system. During development, distribution and abundancy of their transcripts was regulated. Moreover, their expression was differentially influenced by neuronal activity in the hippocampus of adult mice. Although kainic acid-induced seizures had no effect on sorCS2 mRNA levels, they dramatically increased the expression of sorCS1 and sorCS3. The activity-dependent induction of sorCS1 expression required de novo protein synthesis, whereas that of sorCS3 did not. Our results imply that the three sorCS genes have diverse, but partly overlapping functions in the developing and mature central nervous system.
Intravenous, intralesional and endolymphatic administration of lymphokines in human cancer. (1986)

Starting in 1976 we have given two types of lymphokine preparation to 78 individual patients with cancer with no evidence of long-term toxicity. Lymphokine from the 1788 lymphoblastoid line (1788-LK) was given intravenously and intralesionally to 39 of these patients and buffy coat interleukin (BC-IL) to 40 of the patients. On intravenous injection both preparations produced pyrexia and other acute phase changes but with an earlier time course after BC-IL. Feelings of well-being were volunteered and the patients often remained in a steady clinical state for a long time when previously their condition had been deteriorating. Histological studies after intralesional injection into recurrent breast nodules (1788-LK and BC-IL) and prostate (1788-LK) showed an inflammatory cell infiltrate and tumour cell necrosis. Endolymphatic infusion of BC-IL in 23 patients with malignant melanoma was followed by clinical, radiological and histological evidence of lymph node activation. 10 of these patients had had excision of poor prognosis primary tumour only and during the follow-up period (5-17 months) none had a recurrence. Our experience suggests that administration of lymphokines has a place in the total management of cancer patients.
Properties of Ilmenite Water-Based Drilling Fluids for HPHT Applications (2013)

Abstract Barite is the most common weighting material for drilling fluids, which contain several heavy components including lead, cadmium, mercury, and arsenic. Some of these heavy materials can discharge into the sea, which is not allowed especially in the case of oil-based drilling fluid. The supply of barite is geographically limited, with high transportation costs. To overcome the high cost, shortage, and common problems of barite, an alternative weighting material, ilmenite (5 µm), is introduced which is heavier than barite and more stable at high temperature. Also, the micronized ilmenite was introduced to overcome the ECD challenges in some drilling operations at reasonable cost. Extensive lab work was done in order to:optimize the rheological properties of the drilling fluid,determine the optimum pH that gives stable dispersion,assess the thermal stability,optimize the filtration parameters (filtrate volume and filter cake thickness), andcharacterize the ilmenite-based filter cake. Zeta potential results showed that ilmenite was stable when mixed with water at a pH above 7 and it was dispersed and stable when mixed with the drilling fluid components. Drilling fluids have a density range from 100 to 120 pcf and a plastic viscosity of 28–32 cp. The optimized water-based drilling fluid formula had a small filtrate volume (12 cm3) and thin filter cake (0.2 in.) under dynamic conditions. SEM analysis showed that ilmenite filter cake was heterogeneous and contained ilmenite particles in the layer closer to the rock surface. The kem-seal plus had a big effect to control the rheological properties of the drilling fluid at 350°F. This study will provide a complete evaluation of the drilling fluids with ilmenite as a weighting material and will help drilling engineers to better design drilling fluids for HPHT wells.
Alpha particles initiate biological production of superoxide anions and hydrogen peroxide in human cells. (1997)

The mechanism(s) by which high-linear energy transfer a particles, like those emitted by inhaled radon and radon daughters, cause lung cancer has not been elucidated. Conceivably, DNA damage that is induced by a particles may be mediated by the metabolic generation of reactive oxygen species (ROS), in addition to direct a particle-DNA interactions and hydroxyl radical-DNA interactions. Using normal human lung fibroblasts, we investigated the hypothesis that densely ionizing alpha particles may induce the intracellular generation of superoxide (O2.-) and hydrogen peroxide (H2O2). Ethidium bromide and 2',7'-dichlorofluorescein, fluorescent products of the membrane-permeable dyes hydroethidine and 2',7'-dichlorofluorescin diacetate, respectively, were used to monitor the intracellular production of O2.- and H2O2, respectively, by flow cytometry. Compared to sham-irradiated cells, fibroblasts that were exposed to alpha particles (0.4-19 cGy) had significant increases in intracellular O2.- production, along with concomitant increases in H2O2 production. Further analyses suggest that the plasma membrane-bound NADPH-oxidase is primarily responsible for this increased intracellular generation of ROS and that the ROS response does not require direct nuclear or cellular "hits" by the a particles. In this latter regard, we additionally report that unirradiated cells also show the ROS response when they are incubated with serum-containing culture medium that has been exposed to a particles or when they are incubated with supernatants from a-irradiated cells. Our overall results support the possibility that a particles, at least in part, may mediate their DNA-damaging effects indirectly via a ROS-related mechanism.
Coupling Selectivity with Sensitivity in an Integrated Chemosensor Framework:  Design of a Hg2+-Responsive Probe, Operating above 500 nm (2003)

For the highly selective and sensitive sensing of Hg2+ in water, a new design concept was realized where the selectivity of the probe's binding site is amplified by electronic properties of the chromophore. The molecular architecture of this phenoxazinone-type sensor molecule combines two potential coordination sites via an amino-keto conjugative backbone. These structural prerequisites allow only the most preferred mercuric ion to bind to the dithia dioxa monoaza crown unit, while other heavy, transition, and main group metal ions as well as protons are trapped at the keto group, inducing opposite spectral effects due to interaction with either the donor (Hg2+) or the acceptor group (other cations) of the probe. Besides these advantageous features, the probe operates well within the visible range of the spectrum and displays rather intense molar absorptivities as well as fluorescence quantum yields.
mTOR-Dependent Synapse Formation Underlies the Rapid Antidepressant Effects of NMDA Antagonists (2010)

The rapid antidepressant response after ketamine administration in treatment-resistant depressed patients suggests a possible new approach for treating mood disorders compared to the weeks or months required for standard medications. However, the mechanisms underlying this action of ketamine [a glutamate N-methyl-D-aspartic acid (NMDA) receptor antagonist] have not been identified. We observed that ketamine rapidly activated the mammalian target of rapamycin (mTOR) pathway, leading to increased synaptic signaling proteins and increased number and function of new spine synapses in the prefrontal cortex of rats. Moreover, blockade of mTOR signaling completely blocked ketamine induction of synaptogenesis and behavioral responses in models of depression. Our results demonstrate that these effects of ketamine are opposite to the synaptic deficits that result from exposure to stress and could contribute to the fast antidepressant actions of ketamine.
Loudspeaker Array Processing For Personal Sound Zone Reproduction. (2014)

Sound zone reproduction facilitates listeners wishing to consume personal audio content within the same acoustic enclosure by filtering loudspeaker signals to create constructive and destructive interference in different spatial regions. Published solutions to the sound zone problem are derived from areas such as sound field synthesis and beamforming. The first contribution of this thesis is a comparative study of multi-point approaches. A new metric of planarity is adopted to analyse the spatial distribution of energy in the target zone, and the well-established metrics of acoustic contrast and control effort are also used. Simulations and experimental results demonstrate the advantages and disadvantages of the approaches. Energy cancellation produces good acoustic contrast but allows very little control over the target sound field; synthesis-derived approaches precisely control the target sound field but produce less contrast. Motivated by the limitations of the existing optimization methods, the central contribution of this thesis is a proposed optimization cost function ‘planarity control’, which maximizes the acoustic contrast between the zones while controlling sound field planarity by projecting the target zone energy into a spatial domain. Planarity control is shown to achieve good contrast and high target zone planarity over a large frequency range. The method also has potential for reproducing stereophonic material in the context of sound zones. The remaining contributions consider two further practical concerns. First, judicious choice of the regularization parameter is shown to have a significant effect on the contrast, effort and robustness. Second, attention is given to the problem of optimally positioning the loudspeakers via a numerical framework and objective function. The simulation and experimental results presented in this thesis represent a significant addition to the literature and will influence the future choices of control methods, regularization and loudspeaker placement for personal audio. Future systems may incorporate 3D rendering and listener tracking.
Computer Control of Microscopes Using µManager (2010)

With the advent of digital cameras and motorization of mechanical components, computer control of microscopes has become increasingly important. Software for microscope image acquisition should not only be easy to use, but also enable and encourage novel approaches. The open-source software package µManager aims to fulfill those goals. This unit provides step-by-step protocols describing how to get started working with µManager, as well as some starting points for advanced use of the software.
Discovering Underlying Plans Based on Distributed Representations of Actions (2016)

Plan recognition aims to discover target plans (i.e., sequences of actions) behind observed actions, with history plan libraries or domain models in hand. Previous approaches either discover plans by maximally matching observed actions to plan libraries, assuming target plans are from plan libraries, or infer plans by executing domain models to best explain the observed actions, assuming complete domain models are available. In real world applications, however, target plans are often not from plan libraries and complete domain models are often not available, since building complete sets of plans and complete domain models are often difficult or expensive. In this paper we view plan libraries as corpora and learn vector representations of actions using the corpora; we then discover target plans based on the vector representations. Our approach is capable of discovering underlying plans that are not from plan libraries, without requiring domain models provided. We empirically demonstrate the effectiveness of our approach by comparing its performance to traditional plan recognition approaches in three planning domains.
Common Requirements for Melanocortin-4 Receptor Selectivity of Structurally Unrelated Melanocortin Agonist and Endogenous Antagonist, Agouti Protein (2001)

The activity of melanocortin receptors (MCR) is regulated by melanocortin peptide agonists and by the endogenous antagonists, Agouti protein and AgRP (Agouti-related protein). To understand how the selectivity for these structurally unrelated agonists and antagonist is achieved, chimeric and mutants MC3R and MC4R were expressed in cell lines and pharmacologically analyzed. A region containing the third extracellular loop, EC3, of MC4R was essential for selective Agouti protein antagonism. In addition, this part of MC4R, when introduced in MC3R, conferred Agouti protein antagonism. Further mutational analysis of this region of MC4R demonstrated that Tyr<sup>268</sup> was required for the selective interaction with Agouti protein, because a profound loss of the ability of Agouti protein to inhibit <sup>125</sup>I-labeled [Nle<sup>4</sup>,d-Phe<sup>7</sup>]α-melanocyte-stimulating hormone (MSH) binding was observed by the single mutation of Tyr<sup>268</sup> to Ile. This same residue conferred selectivity for the MC4R selective agonist, [d-Tyr<sup>4</sup>]MT-II, whereas it inhibited interaction with the MC3R-selective agonist, [Nle<sup>4</sup>]Lys-γ<sub>2</sub>-MSH. Conversely, mutation of Ile<sup>265</sup> in MC3 (the corresponding residue of Tyr<sup>268</sup>) to Tyr displayed a gain of affinity for [d-Tyr<sup>4</sup>]MT-II, but not for Agouti protein, and a loss of affinity for [Nle<sup>4</sup>]Lys-γ<sub>2</sub>-MSH as compared with wild-type MC3R. This single amino acid mutation thus confers the selectivity of MC3R toward a pharmacological profile like that observed for MC4R agonists but not for the antagonist, Agouti protein. Thus, selectivity for structurally unrelated ligands with opposite activities is achieved in a similar manner for MC4R but not for MC3R.
Critical Role for CD8 in Binding of MHC Tetramers to TCR: CD8 Antibodies Block Specific Binding of Human Tumor- Specific MHC-Peptide Tetramers to TCR (2001)

There are conflicting opinions about the role that the T cell coreceptors CD4 and CD8 play in TCR binding and activation. Recent evidence from transgenic mouse models suggests that CD8 plays a critical role in TCR binding and activation by peptide-MHC complex multimers (tetramers). Here we show with a human CTL clone specific for a tumor-associated MHC-peptide complex that the binding of tetramers to the TCR on these cells is completely blocked by anti-human CD8 Abs. Moreover, the staining of CTLs with specific MHC-peptide tetramers simultaneously with anti-CD8 Abs was completely blocked with three different anti-CD8 Abs. This blockage was mediated by anti-CD8 Abs but not anti-CD3 Abs and was dose dependent. The blocking effect of the anti-CD8 Abs was attributable to directly inhibiting tetramer binding and was not attributable to Ab-mediated TCR-CD8 internalization and down-regulation. Our results have important implications in TCR binding to MHC-peptide tetramers. MHC-peptide tetramers are widely used today in combination with anti-CD8 Abs for the phenotypic analysis of T cell populations and in the study of T cell responses under various pathological conditions such as infectious diseases and cancer. Our results indicate that also in the human system CD8 plays a critical role in the interaction of MHC-peptide multimers with TCR.
Development of Sensitive Immunoassays for Free and Total Human Glandular Kallikrein 2 (2004)

The wide variation in the free-to-total hK2 ratio suggests that hK2 in blood plasma is not consistently in the free, noncomplexed form in patients with prostate cancer. The new assay is sufficiently sensitive to be used to study the diagnostic accuracies of free and total hK2 for prostate cancer.
Alkylating agents: in vitro studies of cross-resistance patterns in human cell lines. (1986)

The alkylating agents represent one of the most important classes of antitumor agents and play a major role in combination with other agents in the curative chemotherapy of selected human cancers. By repeatedly exposing cells to escalating doses of an alkylating agent, we have developed four human tumor cell lines which are relatively stably resistant to the drug with which the culture was treated. The response of these cell lines to a variety of alkylating agents was compared to the response of the parent cell lines to the same drug. The Raji/HN2 line was 7-fold resistant to nitrogen mustard and about 3-fold resistant to 4-hydroxyperoxycyclophosphamide, but it was not resistant to N,N'-bis(2-chloroethyl)-N-nitrosourea (BCNU), melphalan (MEL), busulfan, trimethyleneiminethiophosphoramide, 4-hydroperoxyifosfamide, or cisplatin [cis-diamminedichloroplatinum(II)] (CDDP). The Raji/BCNU line was 5.3-fold resistant to BCNU and 4-fold resistant to both MEL and CDDP. The Raji/CP line was 7-fold resistant to CDDP and 3-fold resistant to both nitrogen mustard and BCNU, but it was not resistant to busulfan, trimethyleneiminethiophosphoramide, or 4-hydroperoxyifosfamide. The SCC-25/CP line, which was 12-fold resistant to CDDP, was 5-fold resistant to MEL and 3-fold resistant to 4-hydroxyperoxycyclophosphamide. The SCC-25/CP line was almost 24-fold resistant to methotrexate after 30-min treatment and about 7-fold resistant to methotrexate after continuous treatment. None of the other cell lines was resistant to methotrexate. The survival of SCC-25 and SCC-25/CP cells exposed to several antineoplastic agents was examined over several logs of survival. The SCC-25/CP cells are highly resistant to CDDP; the ratio of the slopes of the survival curves (SCC-25/CP to SCC-25) of the two lines was 43. At survivals of 1%, resistance to MEL and BCNU became evident in the SCC-25/CP line. At survivals of 0.1%, resistance to mitomycin C and, to a lesser degree, to Adriamycin and vincristine was evident. It is more difficult to produce resistance to alkylating agents, even with extended selection pressure, than to other antineoplastic drugs such as antimetabolites and natural products. We found no evidence of pleiotropic resistance in any alkylating agent-resistant cell line. Our results suggest that a judicious choice of alkylating agents given in sequential or concurrent combination may be a rational treatment strategy with potential applications in the clinic.
Pretreatment of adult bone marrow mesenchymal stem cells with cardiomyogenic growth factors and repair of the chronically infarcted myocardium (2006)

The in vivo cardiac differentiation and functional effects of unmodified adult bone marrow mesenchymal stem cells (MSCs) after myocardial infarction (MI) is controversial. We postulated that ex vivo pretreatment of autologous MSCs using cardiomyogenic growth factors will lead to cardiomyogenic specification and will result in superior biological and functional effects on cardiac regeneration of chronically infarcted myocardium. We used a chronic dog MI model generated by ligation of the coronary artery (n = 30). Autologous dog bone marrow MSCs were isolated, culture expanded, and specified into a cardiac lineage by adding growth factors, including basic FGF, IGF-1, and bone morphogenetic protein-2. Dogs underwent cell injection >8 wk after the infarction and were randomized into two groups. Group A dogs (n = 20) received MSCs specified with growth factors (147 +/- 96 x 10(6)), and group B (n = 10) received unmodified MSCs (168 +/- 24 x 10(6)). After the growth factor treatment, MSCs stained positive for the early muscle and cardiac markers desmin, antimyocyte enhancer factor-2, and Nkx2-5. In group A dogs, prespecified MSCs colocalized with troponin I and cardiac myosin. At 12 wk, group A dogs showed a significantly larger increase in regional wall thickening of the infarcted territory (from 22 +/- 8 to 32 +/- 6% in group A; P < 0.05 vs. baseline and group B, and from 19 +/- 7 to 21 +/- 7% in group B, respectively) and a decrease in the wall motion score index (from 1.60 +/- 0.05 to 1.35 +/- 0.03 in group A; P < 0.05 vs. baseline and group B, and from 1.58 +/- 0.07 vs. 1.56 +/- 0.08 in group B, respectively). The biological ex vivo cardiomyogenic specification of adult MSCs before their transplantation is feasible and appears to improve their in vivo cardiac differentiation as well as the functional recovery in a dog model of the chronically infarcted myocardium.
Nanoscale Morphology of High-Performance Polymer Solar Cells (2005)

Transmission electron microscopy and electron diffraction are used to study the changes in morphology of composite films of poly(3-hexylthiophene) (P3HT) and a methanofullerene derivative (PCBM) in bulk heterojunction solar cells. Thermal annealing produces and stabilizes a nanoscale interpenetrating network with crystalline order for both components. P3HT forms long, thin conducting nanowires in a rather homogeneous, nanocrystalline PCBM film. Both the improved crystalline nature of films and increased but controlled demixing between the two constitutes therein after annealing explains the considerable increase of the power conversion efficiency observed in these devices.