gebhart/patrepeval huggingface dataset:
In vivo cytotoxicity of ovarian cancer cells through tumor-selective expression of the BAX gene. (1999)

The BAX proapoptotic protein is capable of inducing cell death either directly, through its effects on mitochondrial function, or indirectly, by lowering the apoptotic threshold in response to certain chemotherapy agents. In this study, we tested the hypothesis that selective expression of BAX in human ovarian cancer through adenoviral gene transfer might represent a novel approach to eradicating tumor cells in vivo. Two constructs were prepared using replication-deficient adenoviral vectors containing either the cDNA for beta-galactosidase (Ad.DF3.betaGAL) or hemagglutinin (HA)-tagged BAX (Ad.DF3.BAX) under the control of the DF3 promoter. The DF3 promoter was used to confer tumor-specific gene expression in view of its restricted pattern of expression in the majority of human ovarian cancers and its limited expression in normal peritoneal mesothelial cells. In vitro infection of up to seven different epithelial cancer cell lines with Ad.DF3.betaGAL or Ad.DF3.BAX resulted in expression of either beta-galactosidase activity or HA-BAX protein, respectively, which was highly correlated with DF3 levels. Furthermore, infection with Ad.DF3.BAX was capable of highly selective cytotoxicity of DF3-positive ovarian cancer clonogenic cells in vitro. The effect of i.p. administration of Ad.DF3.BAX was also assessed in nude mice inoculated with the DF3-positive 36M2 human ovarian cancer cell line. Expression of either beta-galactosidase activity (after Ad.DF3.betaGAL treatment) or HA-BAX transcripts (after Ad.DF3.BAX treatment) was restricted to tumor tissue in vivo. Importantly, administration of Ad.DF3.BAX on days 2 and 3 after tumor inoculation was capable of eradicating >99% of tumor implants. These results demonstrate the feasibility of tumor selective expression of a proapoptotic protein such as BAX through adenoviral gene transfer.
Hypervalent (tert-Butylperoxy)iodanes Generate Iodine-Centered Radicals at Room Temperature in Solution:  Oxidation and Deprotection of Benzyl and Allyl Ethers, and Evidence for Generation of α-Oxy Carbon Radicals (1996)

1-(tert-Butylperoxy)-1,2-benziodoxol-3(1H)-one (1a) oxidizes benzyl and allyl ethers to the esters at room temperature in benzene or cyclohexane in the presence of alkali metal carbonates. Since this reaction is compatible with other protecting groups such as MOM, THP, and TBDMS ethers, and acetoxy groups, and because esters are readily hydrolyzed under basic conditions, this new method provides a convenient and effective alternative to the usual reductive deprotection. Oxidation with 1a occurs readily with C−H bonds activated by both enthalpic effects (benzylic, allylic, and propargylic C−H bonds) and/or polar effects (α-oxy C−H bonds), generating α-oxy carbon-centered radicals, which can be detected by nitroxyl radical trapping. Measurement of the relative rates of oxidation for a series of ring-substituted benzyl n-butyl ethers 2d and 2p−s indicated that electron-releasing groups such as p-MeO and p-Me groups increase the rate of oxidation, and Hammett correlation of the relative rate factors with the σ+ constants of substituents afforded the reaction constant ρ+ = −0.30. The large value of the isotope effect obtained for the oxidation of benzyl n-butyl ether 2d (kH/kD = 12−14) indicates that the rate-determining step of the reactions probably involves a high degree of benzylic C−H bond breaking. The effects of molecular dioxygen were examined, and the mechanism involving the intermediacy of the tert-butylperoxy acetal 5 and/or the hydroperoxy acetal 32 is proposed. Particularly noteworthy is the finding that (tert-butylperoxy)iodane 1a can generate the tert-butylperoxy radical and the iodine-centered radical 33a, even at room temperature in solution, via homolytic bond cleavage of the hypervalent iodine(III)−peroxy bond.
Determination of gastric emptying in nonobese diabetic mice (2007)

Animal studies on diabetic gastroparesis are limited by inability to follow gastric emptying changes in the same mouse. The study aim was to validate a nonlethal gastric emptying method in nonobese diabetic (NOD) LtJ mice, a model of type 1 diabetes, and study sequential changes with age and early diabetic status. The reliability and responsiveness of a [(13)C]octanoic acid breath test in NOD LtJ mice was tested, and the test was used to measure solid gastric emptying in NOD LtJ mice and nonobese diabetes resistant (NOR) LtJ mice. The (13)C breath test produced results similar to postmortem recovery of a meal. Bethanechol accelerated gastric emptying [control: 92 +/- 9 min; bethanechol: 53 +/- 3 min, mean half emptying time (T(1/2)) +/- SE], and atropine slowed gastric emptying (control: 92 +/- 9 min; atropine: 184 +/- 31 min, mean T(1/2) +/- SE). Normal gastric emptying (T(1/2)) in nondiabetic NOD LtJ mice (8-12 wk) was 91 +/- 2 min. Aging had differing effects on gastric emptying in NOD LtJ and NOR LtJ mice. Onset of diabetes was accompanied by accelerated gastric emptying during weeks 1-2 of diabetes. Gastric emptying returned to normal by weeks 3-5 with no delay. The [(13)C]octanoic acid breath test accurately measures gastric emptying in NOD LtJ mice, is useful to study the time course of changes in gastric emptying in diabetic NOD LtJ mice, and is able to detect acceleration in gastric emptying early in diabetes. Opposing changes in gastric emptying between NOD LtJ and NOR LtJ mice suggest that NOR LtJ mice are not good controls for the study of gastric emptying in NOD LtJ mice.
Enhanced photovoltaic efficiency in polymer-fullerene composites by thermally controlled interdiffusion (2004)

The interface between polymer and fullerene in organic photovoltaic devices is improved by thermally induced interdiffusion. Starting from a bilayer of 2-methoxy-5-(2’-ethylhexyloxy)-1,4-phenylenevinylene copolymer (MEH-PPV) and the Buckminsterfullerene (C<sub>60</sub>) devices are heated in the vicinity of the glass transition temperature creating a gradient bulk-heterojunction. Interdiffused devices show photoluminescence quenching with concomitant improvements in photocurrents. Variation of the polymer layer thickness shows an increase in photocurrents with decreasing layer thickness within the examined thickness regime as transport of the separated charges out of the device is improved. The interdiffusion was observed <i>in situ</i> by monitoring the photocurrents during the heating step. Cross-sectional transmission electron microscopy reveals C<sub>60</sub> clusters of up to 30 nm in diameter in the interdiffused devices. The clustering of the fullerene molecules puts a significant constraint on the interdiffusion process.
Exploratory Visualization Involving Incremental, Approximate Database Queries and Uncertainty (2012)

Large datasets can mean slow queries, for which users must wait. Incremental visualization systems can give faster results at a cost of accuracy. This article asked analysts to use one and report on their results. Their feedback provides suggestions for alternative visualizations to represent a query still in progress.
Mutation analysis and loss of heterozygosity of PEDF in central nervous system primitive neuroectodermal tumors (1997)

Deletion of 17p is the most frequent abnormality observed in central nervous system (CNS) primitive neuroectodermal tumors (PNETs), implicating the presence of a tumor suppressor gene which maps to 17p. The gene for pigment epithelium-derived factor (PEDF) has been cloned and mapped to 17p13. PEDF belongs to the serine protease inhibitor (SERPIN) gene family. The PEDF protein has neurotrophic and neuronal-survival activities and is expressed in the CNS. Twenty tumor and matched normal DNA samples from patients with PNETs were screened by single-strand conformation polymorphism (SSCP) analysis to determine loss of heterozygosity (LOH) and to identify potential mutations within the 8 exons of the PEDF gene. Ten of the 20 tumors demonstrated LOH, consistent with the deletion status of 17p determined by cytogenetic or fluorescence in situ hybridization studies. SSCP analysis of the genomic DNA from the 10 cases with LOH demonstrated several polymorphisms in exons 4 and 7, but no mutations. Our results are consistent with a loss of alleles on 17p in 50% of CNS PNETs, but do not suggest that PEDF is a candidate for the PNET suppressor gene in 17p13. Int. J. Cancer 72:277–282, 1997. © 1997 Wiley-Liss, Inc.
Kunitz domain inhibitors of tissue factor-factor VIIa. II. Potent and specific inhibitors by competitive phage selection. (1994)

Active-site inhibitors of the human tissue factor-Factor VIIa complex (TF.FVIIa) that are both potent and specific have been selected from Alzheimer's amyloid beta-protein precursor inhibitor (APPI) Kunitz domain libraries using a strategy termed competitive phage selection. Phage display Libraries I-III, previously sorted by direct selection, were sorted by competitive selection against immobilized TF.FVIIa in which increasing amounts of Factor XIa (FXIa) were added to the selection buffer to remove phage with high affinity for FXIa. The most striking difference in the selected Kunitz domain sequences was at the P4' position where Lys was highly preferred instead of Leu which was found here by direct selection (Dennis, M. S., and Lazarus, R. A. (1994) J. Biol. Chem. 269, 22129-22136). In addition, both Lys and Arg were selected in the P1 position as opposed to Arg alone. A new library (Library IV) was constructed which contained all previously observed amino acids at 9 positions in the primary and secondary binding loops of APPI. Comparable results were obtained by sorting Library IV against immobilized TF.FVIIa in the presence of either FXIa alone or FXIa, plasma kallikrein, and plasmin. The Kunitz domains obtained by either competitive selection strategy potently inhibited TF.FVIIa, with Ki* values ranging from about 2 to 20 nM; the Ki* values were generally > 1 microM for FXIa and plasma kallikrein and ranged from 4 to 200 nM for plasmin. Variants selective for TF.FVIIa were assayed for free FVIIa and FXa inhibitory activity and characterized in coagulation assays. A rationale for the selection of Lys at both the P4' and P1 positions based upon comparison of sequences and structures of relevant serine proteases and inhibitors is presented.
Mutational analysis of the herpes simplex virus virion host shutoff protein: evidence that vhs functions in the absence of other viral proteins (1995)

Herpes simplex virus (HSV) virions contain one or more factors that trigger rapid shutoff of host protein synthesis and accelerated decay of cellular and viral mRNAs in infected cells. HSV isolates bearing mutations at the virion host shutoff (vhs) locus (gene UL41) are defective for both processes, indicating that the vhs protein is required; however, it is not clear whether the role of vhs in shutoff is direct or indirect and if other virion components are also necessary. We therefore used a transient-cotransfection assay to determine if the vhs protein displays activity in the absence of other viral gene products. We found that a vhs expression vector strongly suppressed expression of a cotransfected lacZ reporter gene and that this effect was eliminated by the vhs1 point mutation that abolishes virion-induced host shutoff during HSV infection. Further evidence for the biological relevance of the transfection assay came from the demonstration that five vhs in-frame linker insertion mutations yielded concordant results when assayed in cotransfected cells and following transfer into the viral genome: three mutations eliminated activity in both assays, while two had no effect. On the basis of these results, we conclude that the vhs protein can trigger host shutoff in the absence of other HSV proteins. The cotransfection assay was used to rapidly assess the activities of a panel of linker insertion mutants spanning the vhs polypeptide. All mutations that mapped to regions conserved among the vhs homologs of alphaherpesvirus inactivated function; in contrast, four of five mutations that mapped to regions that are absent from several vhs homologs had no effect. These results further support the biological relevance of the transfection assay and begin to delineate functional domains of the vhs polypeptide.
Significance of chemokines and activated platelets in patients with diabetes (2000)

Levels of platelet-derived microparticles (PMPs), platelet activation markers (P-selectin expressed on, or annexin V binding to, platelets (plt:P-selectin or plt:annexin V, respectively)), chemokines (IL-8, monocyte chemotactic peptide-1 (MCP-1), and regulated on activation normally T-cell expressed and secreted (RANTES)), and soluble P- and E-selectins were compared in peripheral blood from diabetic and control patients in order to develop a better understanding of their potential contribution to diabetic vascular complications. Significant increases were found for PMPs, plt:P-selectin, MCP-1, RANTES and soluble P- and E-selectins in diabetic individuals, whereas IL-8 levels were similar. Furthermore, after ticlopidine treatment, most of these factors receded to baseline levels observed in non-diabetic patients. Our findings indicate that ticlopidine might be able to prevent or reduce vascular complications in diabetic patients.
Long-term clinical and radiological results of the Lord total hip prosthesis (1996)

We enrolled 98 patients (107 hips) with a mean age of 47 years (SD 8.6) into a prospective study of the Madreporic Lord THR; 34 hips had primary and 73 secondary osteoarthritis. After ten years, the survival rate using revision as the endpoint for failure was 70% (+/-9) for the cup and 98% (+/-0.3) for the stem. The combined clinical and radiological survival rates were 46% (+/-11) and 81% (+/-10), respectively. Osteoporosis due to stress-shielding was observed in the proximal femur. Hips with radiologically dense bone postoperatively showed the most pronounced bone loss. We recommend continued radiological follow-up of patients with this type of implant to allow revision to be performed before there is severe bony destruction of the pelvis.
Determination of time-resolved fluorescence emission spectra and anisotropies of a fluorophore-protein complex using frequency-domain phase-modulation fluorometry. (1984)

We report the first time-resolved fluorescence emission spectra and time-resolved fluorescence anisotropies obtained using frequency-domain fluorescence spectroscopy. We examined the fluorophore p-2-toluidinyl-6-naphthalenesulfonic acid (TNS) in viscous solvents and bound to the heme site of apomyoglobin using multifrequency phase fluorometers. Fluorescence phase shift and modulation data were obtained at modulation frequencies ranging from 1 to 200 MHz. For time-resolved emission spectra, the impulse response for the decay of intensity at each emission wavelength was obtained from the frequency response of the sample at the same emission wavelength. The decays have negative pre-exponential factors, consistent with a time-dependent spectral shift to longer wavelengths. These multiexponential decays were used to construct the time-resolved emission spectra, which were found to be in good agreement with earlier spectra obtained from time-domain measurements. Additionally, time-resolved anisotropies were obtained from the frequency-dependent phase angle differences between the parallel and perpendicularly polarized components of the emission. The rotational correlation times of TNS bound to apomyoglobin are consistent with those expected for this probe rigidly bound to the protein. TNS in propylene glycol also displayed a single exponential decay of anisotropy. These results, in conjunction with the previous successful resolution of multiexponential decays of fluorescence intensity (Lakowicz, J. R., Gratton, E., Laczko, G., Cherek, H., and Limkeman, M. (1984) Biophys. J., in press; Gratton, E., Lakowicz, J. R., Maliwal, B. P., Cherek, H., Laczko, G., and Limkeman, M. (1984) Biophys. J., in press) demonstrate that frequency-domain measurements provide information which is, at a minimum, equivalent to that obtainable from time-domain measurements.
Compromised anti-tumor responses in tumor necrosis factor-α knockout mice (2000)

The response of lymphokine-activated killer (LAK) and natural killer (NK) cells from mice lacking tumor necrosis factor-alpha (TNF-alpha-/- mice) was impaired in cytotoxicity assays against various tumor cell targets. Furthermore, allogeneic cytotoxic T lymphocyte (CTL) responses were also impaired as compared to TNF-alpha+/+ littermates (control mice). Cytotoxicity was restored both upon in vitro incubation of TNF-alpha-/- lymphocytes with recombinant TNF-alpha (rTNF-alpha) or upon in vivo treatment of TNF-alpha-/- mice with rTNF-alpha. Using combinations of monoclonal antibodies we were able to show that TNF-alpha-/- effector lymphocytes exhibit both perforin- and Fas ligand-based cytotoxicity. Furthermore, upon in vivo administration of rTNF-alpha these effectors, in addition to perforin and Fas ligand, are also armed with TNF-alpha cytotoxic molecules, thus resembling to the cytotoxic effectors from control mice. In a tumor model, immunized TNF-alpha-/- mice failed to reject the syngeneic fibrosarcoma MC57X, but did so when injected with rTNF-alpha. In vivo administration of anti-TNF-alpha mAb neutralized the effect of rTNF-alpha supporting the growth of MC57X cells. Our data provide novel evidence for TNF-alpha as an essential factor in (i) controlling cytotoxicity in vitro and in vivo and (ii) promoting tumor rejection in vivo.
TLR4 Engagement during TLR3-Induced Proinflammatory Signaling in Dendritic Cells Promotes IL-10–Mediated Suppression of Antitumor Immunity (2011)

Toll-like receptor (TLR) agonists are promising adjuvants for immune therapy of cancer, but their potential efficacy as single or combinatorial agents has yet to be fully evaluated. Here, we report that among all TLR agonists tested, dendritic cells (DC) stimulated with the TLR3 agonist polyI:C displayed the strongest activity in stimulating proinflammatory responses and the production of melanoma antigen-specific CD8(+) T cells. Simultaneous treatment with TLR7/8 agonists further improved these responses, but the inclusion of bacterial lipopolysaccharide (LPS), a TLR4 agonist, suppressed proinflammatory cytokine production. This inhibition was contingent upon rapid induction of the suppressive cytokine interleukin (IL)-10 by LPS, leading to dysregulated immune responses and it could be reversed by signal transducers and activators of transcription 3 knockdown, p38 blockade or antibodies to IL-10 and its receptor. Our findings show how certain TLR agonist combinations can enhance or limit DC responses associated with antitumor immunity, through their relative ability to induce IL-10 pathways that are immune suppressive.
Molecular Characterization and Expression of a Phytase Gene from the Thermophilic Fungus Thermomyces lanuginosus (1998)

The phyA gene encoding an extracellular phytase from the thermophilic fungus Thermomyces lanuginosus was cloned and heterologously expressed, and the recombinant gene product was biochemically characterized. The phyA gene encodes a primary translation product (PhyA) of 475 amino acids (aa) which includes a putative signal peptide (23 aa) and propeptide (10 aa). The deduced amino acid sequence of PhyA has limited sequence identity (ca. 47%) with Aspergillus niger phytase. The phyA gene was inserted into an expression vector under transcriptional control of the Fusarium oxysporum trypsin gene promoter and used to transform a Fusarium venenatum recipient strain. The secreted recombinant phytase protein was enzymatically active between pHs 3 and 7.5, with a specific activity of 110 micromol of inorganic phosphate released per min per mg of protein at pH 6 and 37 degrees C. The Thermomyces phytase retained activity at assay temperatures up to 75 degrees C and demonstrated superior catalytic efficiency to any known fungal phytase at 65 degrees C (the temperature optimum). Comparison of this new Thermomyces catalyst with the well-known Aspergillus niger phytase reveals other favorable properties for the enzyme derived from the thermophilic gene donor, including catalytic activity over an expanded pH range.
Frequency, Specificity, and Sites of Expansion of CD8+ T Cells during Primary Pulmonary Influenza Virus Infection (2005)

We have used intracellular cytokine staining and MHC class I tetramer binding in conjunction with granzyme B protease expression and in vivo BrdU uptake to characterize the primary murine CD8(+) T cell response to pulmonary influenza virus infection. We have observed that the majority (>90%) of the CD8(+) T cell response to the A/Japan/305/57 virus in the lung at the peak of the response (days 9-11) is directed to four epitopes (three dominant and one subdominant). Using induction of granzyme B as a surrogate to identify specific activated CD8(+) T cells, we found that an unexpectedly large fraction ( approximately 70%) of lung-infiltrating CD8(+) T cells expressed granzyme B on day 6 of infection when estimates by MHC tetramer/intracellular cytokine staining yielded substantially lower frequencies ( approximately 30%). In addition, by using intranasal administration of BrdU during infection, we obtained evidence for proliferative expansion of activated CD8(+) T cells in the infected lung early (days 5-7) in the primary response. These results suggest that the frequency and number of specific CTL present in the lung early in infection may be underestimated by standard detection methods, and primary CD8(+) T cell expansion may occur in both secondary lymphoid organs and the infected lung.
Globally optimal stitching of tiled 3D microscopic image acquisitions (2009)

The implementation of this method is available as an ImageJ plugin distributed as a part of the Fiji project (Fiji is just ImageJ: http://pacific.mpi-cbg.de/).
Enrichment of polyunsaturated fatty acids withGeotrichum candidum lipase (1994)

Abstract Three lipases, isolated previously in our laboratory, each with different fatty acid and positional specificities, and a known lipase from Candida cylindracea were screened for concentrating docosahexaenoic (DHA) and eicosapentaenoic (EPA) acids in glycerides. Geotrichum candidum lipase was found to be suitable for their concentration in glycerides. Tuna oil was treated at 30°C with this lipase for 16 h, and 33.5% hydrolysis resulted in the production of glycerides containing 48.7% of DHA and EPA. The hydrolysis was not increased despite adding further lipase, so the glycerides were extracted, and the reaction was repeated. The second hydrolysis produced glycerides containing 57.5% of DHA and EPA in a 54.5% yield, with recovery of 81.5% of initial DHA and EPA. Of the total glycerides, 85.5% were triglycerides. These results showed that G. candidum lipase was effective in producing glycerides that contained a high concentration of polyunsaturated fatty acids in good yield.
Is oncofetal fibronectin a trophoblast glue for human implantation? (1991)

Using an antibody probe specific for the class of fibronectins that contain the oncofetal domain, it was shown that oncofetal fibronectin (onfFN) is present wherever trophoblasts make contact with extraplacental extracellular matrix (ECM). In normal human implantation sites, onfFN was localized to a highly specific region-the ECM connecting extravilous trophoblasts and trophoblastic cell columns to the uterine decidua. This same zone of onfFN was present in an analogous location in extrauterine gestations. Like these in vivo extravillous trophoblasts, isolated cytotrophoblasts in primary culture synthesized and secreted onfFN as they underwent differentiation. Furthermore, when cocultured with an ECM gel, cytotrophoblast aggregates deposited onfFN at cell-ECM contact sites, resembling early implanting trophoblasts in vivo. In the presence of cyclic AMP agonists, onfFN synthesis was inhibited markedly. It is concluded from these results that onfFN is a trophoblast protein that, under cAMP regulation, could mediate implantation and placental-uterine attachment throughout gestation.