gebhart/patrepeval huggingface dataset:
Coupling of Titania Inverse Opals to Nanocrystalline Titania Layers in Dye-Sensitized Solar Cells (2008)

We report a quantitative comparison of the photoaction spectra, short circuit current densities, and power conversion efficiencies of dye-sensitized solar cells (DSSCs) that contain bilayers of nanocrystalline TiO2 (nc-TiO2) and titania inverse opal photonic crystals (PCs). Cells were fabricated with PC/nc-TiO2 and nc-TiO2/PC bilayer films on glass/tin oxide anode of the cell, as well as in a split configuration in which the nc-TiO2 and PC layers were deposited on the anode and cathode sides of the cell, respectively. Incident photon current efficiencies at single wavelengths and current-voltage curves in white light were obtained with both cathode and anode side illumination. The results obtained support a model proposed by Miguez and co-workers, in which coupling of the low refractive index PC layer to the higher index nc-TiO2 layer creates a standing wave in the nc-TiO2 layer, enhancing the response of the DSSC in the red region of the spectrum. This enhancement is very sensitive to the degree of physical contact between the two layers. A gap on the order of 200 nm thick, created by a polymer templating technique, is sufficient to decouple the two layers optically. The coupling of the nc-TiO2 and PC layers across the gap could be improved slightly by treatment with TiCl4 vapor. In the bilayer configuration, there is an enhancement in the IPCE across the visible spectrum, which is primarily caused by defect scattering in the PC layer. There is also an increase of 20-50 mV in the open circuit photovoltage of the cell. With anode side illumination, the addition of a PC layer to the nc-TiO2 layer increased the efficiency of DSSCs from 6.5 to 8.3% at a constant N719 dye loading of 155-160 nmol/cm2.
Binding of Oligoarginine to Membrane Lipids and Heparan Sulfate:  Structural and Thermodynamic Characterization of a Cell-Penetrating Peptide (2005)

Cell-penetrating peptides (CPPs) comprise a group of arginine-rich oligopeptides that are able to deliver exogenous cargo into cells. A first step in the internalization of CPPs is their binding to the cell surface, a reaction likely to involve membrane phospholipids and/or heparan sulfate proteoglycans (HSPGs). The present work characterizes the interaction of R(9), one of the most efficient CPPs, with either heparan sulfate (HS) or lipid vesicles composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG). Isothermal titration calorimetry shows that R(9) binds to HS with high affinity. Assuming that HS has n independent and equivalent binding sites for R(9), we find an association constant of 3.1 x 10(6) M(-1) at 28 degrees C. At this temperature, the reaction enthalpy is DeltaH(degrees)pep = - 5.5 kcal/mol and approximately 7 R(9) molecules bind per HS chain, which is equivalent to approximately 0.95 cationic/anionic charge ratio. Delta decreases in magnitude upon an increase in temperature, and the reaction becomes entropy-driven at higher temperatures (>or=37 degrees C). The positive heat-capacity change entailed by this reaction (DeltaC(degrees)P = +167 cal mol(-1) K(-1)) indicates the loss of polar residues on R(9)-HS binding, suggesting that hydrophobic forces play no major role on binding. Calorimetric analysis of the interaction of R(9) with POPC/POPG (75:25) vesicles reveals an association constant of 8.2 x 10(4) M(-1) at 28 degrees C. Using a surface partition equilibrium model to correct for electrostatic effects, we find an intrinsic partition constant of approximately 900 M(-1), a value that is also confirmed by electrophoretic mobility measurements. This corresponds to an electrostatic contribution of approximately 33% to the total free energy of binding. Deuterium nuclear magnetic resonance (NMR) shows no change in the headgroup conformation of POPC and POPG, suggesting that binding takes place at some distance from the plane of the polar groups. (31)P NMR indicates that the lipid bilayer remains intact upon R(9) binding. The fact that R(9) binds with greater affinity to HS than to anionic lipid vesicles makes the former molecule a more likely target in binding this CPP to the cell surface.
Physical change in cytoplasmic messenger ribonucleoproteins in cells treated with inhibitors of mRNA transcription. (1984)

Exposure of intact cells to UV light brings about cross-linking of polyadenylated mRNA to a set of cytoplasmic proteins which are in direct contact with the mRNA in vivo. Substantial amounts of an additional protein of molecular weight 38,000 (38K) become cross-linked to the mRNA when cells are treated with inhibitors of mRNA synthesis (actinomycin D, camptothecin, and 5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole) or after infection with vesicular stomatitis virus. Cordycepin, which inhibits polyadenylation but not mRNA synthesis, has no such effect. Inhibitors of protein synthesis and of rRNA synthesis are also without effect on 38K cross-linking to mRNA. The onset of the effect of inhibitors of mRNA synthesis on the UV cross-linkable interaction between mRNA and 38K is rapid and reaches a maximal level in less than 60 min, and it is completely and rapidly reversible. In cells treated with actinomycin D, the amount of 38K which becomes cross-linked to mRNA is proportional to the extent of inhibition of mRNA synthesis. The association of 38K with mRNA during transcriptional arrest does not require protein synthesis because simultaneous treatment with the protein synthesis inhibitor emetine does not interfere with it. The effectors which promote the interaction of 38K with mRNA do not affect the proteins which are in contact with polyadenylated heterogeneous nuclear RNA and do not markedly affect protein synthesis in the cell. The 38K protein can be isolated with the polyribosomal polyadenylated fraction from which it was purified, and monoclonal antibodies against it were prepared. Immunofluorescence microscopy shows mostly cytoplasmic and some nuclear staining. These observations demonstrate that commonly used inhibitors of transcription affect the physical state of messenger ribonucleoproteins in vivo.
mTOR Kinase Inhibition Causes Feedback-Dependent Biphasic Regulation of AKT Signaling (2011)

The results of this study show the adaptive capabilities of oncogenic signaling networks, as AKT signaling becomes reactivated through a feedback-induced AKT species phosphorylated on T308 but lacking S473. The addition of RTK inhibitors can prevent this reactivation of AKT signaling and cause profound cell death and tumor regression in vivo, highlighting the possible need for combinatorial approaches to block feedback-regulated pathways.
Gendered Spaces of Terror and Assault: The Testimonio of REMHI and the Commission for Historical Clarification in Guatemala (2000)

On 25 February 1999, Guatemalans received the much anticipated report of the United Nations-sponsored Commission for Historical Clarification (CEH), Memory of Silence, which detailed wartime atrocities and decades-long American support of the Guatemalan army. This document followed the earlier release of the Catholic church's own REMHI report (Recuperation of Historical Memory Inter-diocesan Project), Guatemala: never again . Using the recently released reports and databases of the CEH and REMHI, we explore the significant use of testimonio as a tool of shared witnessing, collective remembrance, and individual recollection of the special brutality directed against Maya women. Through testimonio, the outcomes of visible and invisible terror and violence in Guatemala are articulated as personal, social and geographic spaces of terror, all of which are gendered and racialised. With the civil war officially over, Maya women of Guatemala see the spaces of terror diminish. Given debates over testimonio, however, the grounds for assault and denial remain fertile.
Disulfide Bonds and the Quaternary Structure of Factor VIII/von Willebrand Factor (1978)

Human Factor VIII/von Willebrand factor, purified by calcium citrate-cellulose chromatography and 4% agarose gel filtration was subjected to sodium dodecyl sulfate gel electrophoresis on gels containing 2% acrylamide and 0.5% agarose. We find a series of multimers of which the apparent molecular weight of the higher members was congruent with5 million. The higher multimers were isolated by 2% agarose gel filtration. Treatment of the high molecular weight multimers with 2-mercaptoethanol at concentrations of 0.005-0.5% in the presence of 1% dodecyl sulfate resulted in a shift to lower molecular weight multimers. Between mercaptoethanol concentrations of 0.01 and 0.5%, the predominant species was the dimer of the basic subunit. Mercaptoethanol concentrations >0.5% were required to reduce the interchain disulfide bonds of the dimer. An artificial multimeric series was prepared by cross-linking von Willebrand factor subunits with dimethylsuberimidate. Comparison of the multimers produced by reduction with the multimers produced by cross-linking, demonstrated the absence of odd-numbered multimers from the reduced series. Thus, the protomeric unit appears to be the dimer. High molecular weight multimers had both ristocetin cofactor activity and Factor VIII procoagulant activity. Reduction of the protein in the absence of denaturing agents, caused a gradual shift to lower molecular weight species and a concomitant loss of von Willebrand factor activity. In contrast, Factor VIII activity was unchanged by reduction. These studies suggest that the moieties having von Willebrand factor activity and those having Factor VIII activities are covalently linked by disulfide bonds.
Potent Inhibition of NFAT Activation and T Cell Cytokine Production by Novel Low Molecular Weight Pyrazole Compounds (2001)

NFAT (nuclear factor of activated T cell) proteins are expressed in most immune system cells and regulate the transcription of cytokine genes critical for the immune response. The activity of NFAT proteins is tightly regulated by the Ca(2+)/calmodulin-dependent protein phosphatase 2B/calcineurin (CaN). Dephosphorylation of NFAT by CaN is required for NFAT nuclear localization. Current immunosuppressive drugs such as cyclosporin A and FK506 block CaN activity thus inhibiting nuclear translocation of NFAT and consequent cytokine gene transcription. The inhibition of CaN in cells outside of the immune system may contribute to the toxicities associated with cyclosporin A therapy. In a search for safer immunosuppressive drugs, we identified a series of 3,5-bistrifluoromethyl pyrazole (BTP) derivatives that block Th1 and Th2 cytokine gene transcription. The BTP compounds block the activation-dependent nuclear localization of NFAT as determined by electrophoretic mobility shift assays. Confocal microscopy of cells expressing fluorescent-tagged NFAT confirmed that the BTP compounds block calcium-induced movement of NFAT from the cytosol to the nucleus. Inhibition of NFAT was selective because the BTP compounds did not affect the activation of NF-kappaB and AP-1 transcription factors. Treatment of intact T cells with the BTP compounds prior to calcium ionophore-induced activation of CaN caused NFAT to remain in a highly phosphorylated state. However, the BTP compounds did not directly inhibit the dephosphorylation of NFAT by CaN in vitro, nor did the drugs block the dephosphorylation of other CaN substrates including the type II regulatory subunit of protein kinase A and the transcription factor Elk-1. The data suggest that the BTP compounds cause NFAT to be maintained in the cytosol in a phosphorylated state and block the nuclear import of NFAT and, hence, NFAT-dependent cytokine gene transcription by a mechanism other than direct inhibition of CaN phosphatase activity. The novel inhibitors described herein will be useful in better defining the cellular regulation of NFAT activation and may lead to identification of new therapeutic targets for the treatment of autoimmune disease and transplant rejection.
A constitutively activated chimeric cytokine receptor confers factor- independent growth in hematopoietic cell lines (1996)

The high-affinity receptor for granulocyte-macrophage colony-stimulating factor (GMR) comprises at least 2 distinct subunits, alpha and beta common (beta c), whereas the normal erythropoietin receptor (nEpoR) comprises only one known subunit. An arginine to cysteine (R129C) mutation of the extracytoplasmic domain of the murine EpoR leads to Epo-independent growth in transduced cells (cEpoR). To investigate the proliferative functions of the cytoplasmic regions of each GMR subunit separately and the potential of the R129C EpoR mutation to induce factor-independent growth through heterologous receptor regions, we constructed four hybrid receptors: the extracellular region of either murine nEpoR or cEpoR linked to the transmembrane and cytoplasmic regions of either the human GMR alpha or beta c subunit (nE alpha, nE beta, cE alpha, and cE beta). We then expressed them in an interleukin-3-dependent murine cell line, Ba/F3. Expression of nE beta led to Epo-dependent growth, whereas expression of cE beta conferred factor-independent growth. Surprisingly, expression of cE alpha also resulted in factor-independent cell growth, whereas nE alpha did not respond to Epo. Furthermore, the functional hybrid receptors showed Epo-dependent (nE beta) or constitutive (cE alpha and cE beta) tyrosine phosphorylation of the cytoplasmic kinases JAK1 and JAK2. We reasoned that the proliferative signal of cE alpha was transduced either through the alpha tail itself or through an accessory protein such as the endogenous murine beta common subunit (mu beta c). To distinguish these possibilities, the chimeric receptor cE alpha was expressed in the interleukin-2-dependent murine cell line, CTLL-2, that does not express mu beta c. cE alpha did not induce cell growth in CTLL-2; however, when mu beta c was coexpressed with cE alpha in CTLL-2, factor-independent growth was reconstituted. In conclusion, the cytoplasmic domain of the GMR alpha subunit requires a beta chain for transduction of a proliferative signal. Furthermore, the R129C EpoR mutation can constitutively activate heterologous receptors to mediate factor-independent proliferation.
Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination (2007)

Relationships among amino acids determine stability and function and are also constrained by evolutionary history. We develop a probabilistic hypergraph model of residue relationships that generalizes traditional pairwise contact potentials to account for the statistics of multi-residue interactions. Using this model, we detected non-random associations in protein families and in the protein database. We also use this model in optimizing site-directed recombination experiments to preserve significant interactions and thereby increase the frequency of generating useful recombinants. We formulate the optimization as a sequentially-constrained hypergraph partitioning problem; the quality of recombinant libraries with respect to a set of breakpoints is characterized by the total perturbation to edge weights. We prove this problem to be NP-hard in general, but develop exact and heuristic polynomial-time algorithms for a number of important cases. Application to the beta-lactamase family demonstrates the utility of our algorithms in planning site-directed recombination.
Generation of arbitrarily focused images by using multiple differently focused images (1998)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
Reversal of a novel multidrug resistance mechanism in human colon carcinoma cells by fumitremorgin C. (1998)

We selected a human colon carcinoma cell line in increasing concentrations of mitoxantrone to obtain a resistant subline, S1-M1-3.2, with the following characteristics: profound resistance to mitoxantrone; significant cross-resistance to doxorubicin, bisantrene, and topotecan; and very low levels of resistance to Taxol, vinblastine, colchicine, and camptothecin. This multidrug resistance (MDR) phenotype, which was not reversed by verapamil or another potent P-glycoprotein (Pgp) inhibitor, CL 329,753, was dependent, in part, upon an energy-dependent drug efflux mechanism. Pgp and the multidrug resistance protein (MRP) were not elevated in the resistant cells relative to the drug-sensitive parent, suggesting that resistance was mediated by a novel pathway of drug transport. A cell-based screen with S1-M1-3.2 cells was used to identify agents capable of circumventing this non-Pgp, non-MRP MDR. One of the active agents identified was a mycotoxin, fumitremorgin C. This molecule was extremely effective in reversing resistance to mitoxantrone, doxorubicin, and topotecan in multidrug-selected cell lines showing this novel phenotype. Reversal of resistance was associated with an increase in drug accumulation. The compound did not reverse drug resistance in cells with elevated expression of Pgp or MRP. We suggest that fumitremorgin C is a highly selective chemosensitizing agent for the resistance pathway we have identified and can be used as a specific pharmacological probe to distinguish between the diverse resistance mechanisms that occur in the MDR cell.
Technetium-99m labeling of murine monoclonal antibody fragments. (1986)

F(ab')2 fragments of several murine monoclonal antibodies have been labeled with 99mTc by a direct, pretinning method. The fragments were incubated with stannous ions overnight to split disulfide groups--a process which converts dimeric F(ab')2 to monomeric fragments. The pretinned fragments were then either directly labeled with 99mTc, frozen for subsequent labeling, or lyophilized to make kits for 99mTc-labeling at some later date. The 99mTc-labeled fragments were shown to be stable against transchelation when challenged with ethylenediaminetetraacetic acid, retained immunoreactivity, and were capable of binding to human tumor xenografts in nude mice.
THE EFFECT ON THE KIDNEY OF BILATERAL SPLANCHNICECTOMY IN PATIENTS WITH HYPERTENSION (1937)

15 yrs.
Loopy Belief Propagation for Bipartite Maximum Weight b-Matching (2007)

We formulate the weighted b-matching objective function as a probability distribution function and prove that belief propagation (BP) on its graphical model converges to the optimum. Standard BP on our graphical model cannot be computed in polynomial time, but we introduce an algebraic method to circumvent the combinatorial message updates. Empirically, the resulting algorithm is on average faster than popular combinatorial implementations, while still scaling at the same asymptotic rate of O(bn 3). Furthermore, the algorithm shows promising performance in machine learning applications. 1
Smart Fridges with Multimedia Capability for Better Nutrition and Health (2008)

Due to the development of computer technology and the wide use of the Internet, intelligent appliances with multimedia capability have been emerging into our daily life. Kitchen is one of the places where such intelligent appliances have been used. Since modern life style is driving people spending less time on cooking healthy food at home, an enjoyable and healthy life style can be assisted with an intelligent kitchenware such as a smart fridge. In this paper we introduce a novel application for a smart fridge with intelligent multimedia capability. It is designed for managing items stored in it and advising its users with cooking methods depending on what kind of food is stored. It can also perform other functions such as dietary control, nutrition monitoring, eating habit analysis, etc. We are confident that such a smart fridge will be an important component in future smart homes.
Developing a Visual Code-dependency Analysis Tool for the Visual Studio IDE: Research Meets Practice in Showing Containment in an Interactive Diagramming Tool. (2012)

The Microsoft Visual Studio IDE includes various tools for diagrammatic code understanding. I am currently involved in the final stages of preparing the next major version (11) for release later this year. In particular, I am working on a visual dependency analyzer that enables developers to dynamically build up a diagram from a particular piece of code or functionality. In designing and developing this product we have explored a number of methods for showing containment of various code elements to different types of grouping. Such a grouping⎯for example, members within types, types within namespaces, and so on⎯is fundamental to organizing object-oriented software, but is also the ticket to scalability of diagrams representing code. That is, grouping at various levels provides degrees of abstraction that can be applied to reduce the complexity of the visualization.
Modulation of Growth Factor Action (1997)

Peptide growth factors are involved in fundamental cellular processes relevant for cardiovascular physiology and pathology, namely, atherogenesis and angiogenesis. The modulation of growth factor-related signals represents a novel strategy for the treatment of cardiac and vascular disease. Experimental modulation of growth factor action has already provided a better understanding of cardiovascular biology and pathophysiology. In turn, the development of specific and powerful molecular tools is setting the stage for the exploration of their clinical potentials. Current strategies include the use of recombinant proteins, specific inhibitors of protein-protein interactions, tyrosine kinase inhibitors, the generation and application of dominant-negative molecules, the development of antisense strategies, and a variety of different gene transfer approaches. Parallel avenues of research are heading toward the same goal, the specific suppression of potent pathogenic stimuli that induce and promote atherogenesis or the augmentation of beneficial ones such as induction of therapeutic angiogenesis. The successful application of one of these strategies seems to be in reach and will certainly be a milestone in molecular medicine.