gebhart/patrepeval huggingface dataset:
Tandem SH2 domains of ZAP-70 bind to T cell antigen receptor zeta and CD3 epsilon from activated Jurkat T cells. (1993)

A proximal and critical biochemical event upon T cell antigen receptor (TCR) stimulation is the activation of a protein tyrosine kinase (PTK) pathway. ZAP-70, a PTK of the p72syk family, associates with phosphorylated TCR subunits upon TCR stimulation. Here we report that the tandem SH2 domains of ZAP-70, expressed as a fusion protein, bind to tyrosine-phosphorylated CD3 epsilon and TCR zeta from activated Jurkat T cell lysates. The single N- and C-terminal SH2 domains of ZAP-70, expressed separately, do not bind these TCR subunits. In comparison to fusion proteins containing SH2 domains from other proteins, the tandem SH2 domains of ZAP-70 demonstrate a remarkably restricted repertoire of protein binding, binding only TCR zeta and CD3 epsilon. ZAP-70 is also recovered in the binding assay, but this is likely to be a consequence of its interaction with multiple SH2 binding sites on the zeta-zeta and CD3 epsilon-containing dimers.
Weak anion and cation exchange mixed‐bed microcolumn for protein separation (2010)

Abstract To separate proteins with a wide distribution of p I s under the conditions compatible to online tryptic digestion (with preferable pH=8.0), weak anion and cation exchange chromatography (WAX/WCX) mixed‐bed microcolumn has been developed. With a mixture of five proteins with p I s ranging from 4.2 to 11.4, the effect of WAX/WCX ratio on the separation performance was investigated, and an optimum packing ratio of 1:1 w/w was obtained. Moreover, the undesirable hydrophobic interaction between the proteins and the stationary phase was suppressed with 10% ACN v/v added in the mobile phases. Under the optimized conditions compatible to tryptic digestion, basic and acidic proteins were resolved simultaneously, with RSDs of relative retention time on six columns less than 6%, indicating the good resolution and packing reproducibility. Furthermore, one RPLC fraction of proteins extracted from rat middle brain and the whole protein mixture extracted from rat liver were analyzed, respectively. The results demonstrated better separation performance on WAX/WCX microcolumns than that on both weak anion exchange chromatography and weak cation exchange chromatography at pH ∼8. We anticipate that WAX/WCX microcolumns are promising for the integration of protein separation and tryptic digestion aiming at high‐throughput proteome study.
Characterization of Bispecific T-cell Engager (BiTE®) Antibodies with a High-Capacity T-cell Dependent Cellular Cytotoxicity (TDCC) Assay (2014)

The Bispecific T-cell Engager (BiTE) antibody modality is a clinically validated immunotherapeutic approach for targeting tumors. Using T-cell dependent cellular cytotoxicity (TDCC) assays, we measure the percentage of specific cytotoxicity induced when a BiTE molecule engages T-cells, redirects T-cell mediated cytolysis, and ultimately kills target cells. We establish a novel luminescence-based TDCC assay quantified by measuring cell viability via constitutive expression of luciferase. The luciferase-based TDCC assay performance is valid and comparable to an adenosine triphosphate (ATP)-based detection method. We demonstrate that the luciferase-based TDCC assay is an efficient homogeneous assay format that is amenable to both suspension and adherent target cells. The luciferase-based TDCC assay eliminates the need for plate-washing protocols, allowing for higher-throughput screening of BiTE antibodies and better data quality. Assay capacity is also improved by performing serial dilutions of BiTE antibodies in 384-well format with an automated liquid handler. We describe here a robust, homogeneous TDCC assay platform with capacity for in vitro assessment of BiTE antibody potency and efficacy using multiple tumor cell lines and T-cell donors.
Potassium Superoxide as an Alternative Reagent for Winterfeldt Oxidation of β-Carbolines (2002)

Potassium superoxide was examined as an alternative oxidation reagent for the Winterfeldt reaction. KO(2) was found to be superior to the original Winterfeldt protocol for base-sensitive substrates. [reaction--see text]
Molecular characterization of the Aedes aegypti odorant receptor gene family (2007)

The olfactory-driven blood-feeding behaviour of female Aedes aegypti mosquitoes is the primary transmission mechanism by which the arboviruses causing dengue and yellow fevers affect over 40 million individuals worldwide. Bioinformatics analysis has been used to identify 131 putative odourant receptors from the A. aegypti genome that are likely to function in chemosensory perception in this mosquito. Comparison with the Anopheles gambiae olfactory subgenome demonstrates significant divergence of the odourant receptors that reflects a high degree of evolutionary activity potentially resulting from their critical roles during the mosquito life cycle. Expression analyses in the larval and adult olfactory chemosensory organs reveal that the ratio of odourant receptors to antennal glomeruli is not necessarily one to one in mosquitoes.
Azabicycloalkanes as analgetics. II. An improved synthesis of 1-phenyl-6-azabicyclo(3,2,1)octane derivatives. (1976)

An improved synthesis of 6, 7endo-dimethyl-1-(3-hydroxyphenyl)-6-azabicyclo [3, 2, 1]-octane (10c), a new analgetic agent with a low addiction liability, is described. Grignard reaction of 3-ethoxy-2-cyclohexen-1-one (1) with m-methoxyphenylmagnesium bromide gave the α, β-unsaturated ketone (2b). Hydrocyanation of the latter followed by methanolysis yielded the keto ester (5b). The bicyclic lactam (8b), a key intermediate in the original synthesis was obtained by reductive amination of 5b with methylamine. As a result of this sequence of reactions, 10c could be obtained in 7 steps from 1 in 42% overall yield. By an application of this new method, a number of 1-phenyl-6-azabicyclo [3, 2, 1] octane derivatives with various substituents on benzene ring (10d-k), nitrogen (31), and C8 (39-46) have been prepared for pharmacological evaluation.
Redox regulation of the genes for cobinamide biosynthesis in Salmonella typhimurium (1989)

Transcription of the cobinamide biosynthetic genes (the CobI operon) was induced under three different physiological conditions: anaerobiosis (anaerobic respiration or fermentation), aerobic respiration at low oxygen levels, and aerobic respiration with a partial block of the electron transport chain. After a shift to inducing conditions, there was a time lag of approximately 50 min before the onset of CobI induction. Under conditions of anaerobic respiration, the level of CobI transcription was dependent on the nature of both the electron donor (carbon and energy source) and the acceptor. Cells grown with electron acceptors with a lower midpoint potential showed higher CobI expression levels. The highest level of CobI transcription observed was obtained with glycerol as the carbon source and fumarate as the electron acceptor. The high induction seen with glycerol was reduced by mutational blocks in the glycerol catabolic pathway, suggesting that glycerol does not serve as a gratuitous inducer but must be metabolized to stimulate CobI transcription. In the presence of oxygen, CobI operon expression was induced 6- to 20-fold by the following: inhibition of cytochrome o oxidase with cyanide, mutational blockage of ubiquinone biosynthesis, and starvation of mutant cells for heme. We suggest that the CobI operon is induced in response to a reducing environment within the cell and not by the absence of oxygen per se.
Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two-dimensional electrophoresis gels (2000)

Progress in the field of proteomics is dependent upon an ability to visualise close to an entire protein complement via a given array technology. These efforts have previously centred upon two-dimensional gel electrophoresis in association with immobilised pH gradients in the first dimension. However, limitations in this technology, including the inability to separate hydrophobic, basic, and low copy number proteins have hindered the analysis of complete proteomes. The challenge is now to overcome these limitations through access to new technology and improvements in existing methodologies. Proteomics can no longer be equated with a single two-dimensional electrophoresis gel. Greater information can be obtained using targeted biological approaches based upon sample prefractionation into specific cellular compartments to determine protein location, while novel immobilised pH gradients spanning single pH units can be used to display poorly abundant proteins due to their increased resolving power and loading capacity. In this study, we show the effectiveness of a combined use of two differential subproteomes (as defined by relative solubilities, cellular location and narrow-range immobilised pH gradients) to increase the resolution of proteins contained on two-dimensional gels. We also present new results confirming that this method is capable of displaying up to a further 45% of a given microbial proteome. Subproteomics, utilising up to 40 two-dimensional gels per sample will become a powerful tool for near-to-total proteome analysis in the postgenome era. Furthermore, this new approach can direct biological focus towards molecules of specific interest within complex cells and thus simplify efforts in discovery-based proteome research.
Targeting of T lymphocytes to Neu/HER2-expressing cells using chimeric single chain Fv receptors. (1993)

Cell surface molecules essential for the transformed phenotype or growth of malignant cells are attractive targets for anticancer immunotherapy. Antibodies specific to Neu/HER2, a human adenocarcinoma-associated growth factor receptor, were demonstrated to have tumor-inhibitory capacity. Yet, the inefficient accessibility of antibodies to solid tumors limits their clinical use. To redirect effector lymphocytes to adenocarcinomas, we constructed and functionally expressed in T cells chimeric single chain receptor genes incorporating both the Ag-binding domain of anti-Neu/HER2 antibodies and the zeta-signal-transducing subunit of the TCR/CD3 complex or the gamma-signal-transducing subunit of the Ig Fc receptor complex. Surface expression of the anti-Neu/HER2 chimeric genes in cytotoxic T cell hybridomas endowed them with specific Neu/HER2 recognition enabling their activation for IL-2 production and lysis of transformed cells overexpressing Neu/HER2. These chimeric genes hold promise for the immunotherapy of cancer.
Hematopoietic development of embryonic stem cells in vitro: cytokine and receptor gene expression. (1991)

A novel system to study early hematopoietic development is described. This report documents the in vitro capacity of murine embryonic stem (ES) cells to differentiate into hematopoietic precursors of most, if not all, of the colony-forming cells found in normal bone marrow. This system is used to correlate the genetic expression of cytokines, their receptors, the beta-globins, and the hematopoietic cell surface markers throughout the time course of ES cell differentiation with the hematopoietic development that occurs in these cultures. Our results indicate that there is a strong transcriptional activation, in a well-defined temporal order, of most of these genes including erythropoietin (Epo), CSF-1, IL-4, beta-globins, as well as the receptors for Epo, CSF-1, and IL-4. IL-3 and GM-CSF were not expressed during the first 24 days of ES cell differentiation. In contrast, the Steel (Sl) factor (SLF) was expressed early and underwent substantial up-regulation during this differentiation, and its receptor, c-kit, was expressed relatively constantly throughout the culture period. Our results are consistent with the conclusion that SLF, Epo, IL-4, and IL-6 are important during the early stages of ES cell differentiation and hematopoietic development. Furthermore, these results argue strongly that IL-3 and GM-CSF are not critical to early hematopoiesis. This system offers a unique in vitro model for studying hematopoietic development at the earliest possible stages.
Polymeric waveguide design of a 2D display system (2006)

Many small scale image display systems, such as head mounted displays (HMDs), beam light from an optical fiber onto deflectable mirrors or rotating polygonal mirrors to produce an image on an image plane. This approach has many size limitations. For instance, light beams of less than 3 millimeters are impractical for displays using mirrors, because mirror scanners and grating deflectors must be significantly larger than the light beam diameter to avoid beam clipping or adding diffraction. Reducing the diameter of a conventional display device reduces the possible number of pixels, and thus reduces the resolution and/or field of view (FOV) of the device. Our proposed HMD system focus on reducing the hardware while maintaining a high resolution by utilizing a microfabricated 2D optical scanner combined with a field-programmable gate array (FPGA) controller for display.
Signaling Through PI3K/Akt Mediates Stretch and PDGF-BB-Dependent DNA Synthesis in Bladder Smooth Muscle Cells (2003)

We conclude that distinct stimuli, such as mechanical stretch and PDGF-BB, promote DNA synthesis in bladder SMC through shared downstream signaling pathways. Furthermore, phenotypically similar cells from the bladder and heart show comparable pathway activation in response to stretch. These findings suggest that similar molecular mechanisms underlie the altered growth responses of the bladder and heart to mechanical overload. This study also provides the first report of Akt activation in bladder SMC and suggests that Akt, consistent with its pivotal role in cardiac hypertrophy, may also be a key regulator of remodeling in the SMC compartment of the bladder exposed to hypertrophic/hyperplastic stimuli in vivo.
Marginal Distributions in Evolutionary Algorithms (1999)

In this paper, the description of two gene pool recombination operators is described. Both operators are based on the estimation of the distribution of the parents and its use to generate new individuals. The Univariate Marginal Distribution Algorithm (UMDA) uses simple univariate distributions. It is a perfect algorithm for linear problems. The Bivariate Marginal Distribution Algorithm (BMDA) is an extension of UMDA. In BMDA, the most important pair dependencies are taken into account. The dependencies are measured by the Pearson&amp;apos;s chi-square statistics. The structure of a problem is being discovered during an optimization. BMDA works well for linear problems as well as for problems with interacting genes. 1 Introduction Evolutionary algorithms work over populations of strings. The main schema of evolutionary algorithms is simple. The initial population is generated randomly. From the current population, a set of high quality individuals is selected first. The better the indi...
Porphyrinic Dyads and Triads Assembled around Iridium(III) Bis-terpyridine:  Photoinduced Electron Transfer Processes (2001)

Multicomponent arrays based on a central iridium(III) bis-terpyridine complex (Ir) used as assembling metal and free-base, zinc(II) or gold(III) tetraaryl-porphyrins (PH(2), PZn, PAu) have been designed to generate intramolecular photoinduced charge separation. The rigid dyads PH(2)-Ir, PZn-Ir, PAu-Ir, and the rigid and linear triads PH(2)-Ir-PAu, PZn-Ir-PAu, as well as the individual components Ir, PH(2), PZn, PAu have been synthesized and characterized by various techniques including electrochemistry. Their photophysical properties either in acetonitrile or in dichloromethane and toluene have been determined by steady-state and time-resolved methods. In acetonitrile, excitation of the triad PH(2)-Ir-PAu leads to a charge separation with an efficiency of 0.5 and a resulting charge-separated (CS) state with a lifetime of 3.5 ns. A low-lying triplet localized on PH(2) and the presence of the heavy Ir(III) ion offer the CS state an alternative deactivation path through the triplet state. The behavior of the triad PZn-Ir-PAu in dichloromethane is rather different from that of PH(2)-Ir-PAu in acetonitrile since the primary electron transfer to yield PZn(+)()-Ir(-)-PAu is not followed by a secondary electron transfer. In this solvent, both unfavorable thermodynamic and electronic parameters contribute to the inefficiency of the second electron-transfer reaction. In contrast, in toluene solutions, the triad PZn-Ir-PAu attains a CS state with a unitary yield and a lifetime of 450 ns. These differences can be understood in terms of ground-state charge-transfer interactions as well as different stabilization of the intermediate and final CS states by solvent.
Lymphotoxin: stimulation and regulation of colony-stimulating factors in fibroblasts (1989)

Abstract Colony-stimulating factors (CSFs) are pivotal for proliferation and function of hematopoietic cells. We found that lymphotoxin, a product of activated lymphocytes, stimulates accumulation of granulocyte- macrophage (GM)-CSF and macrophage (M)-CSF proteins and mRNAs in fibroblasts. An increase in GM- and M-CSF mRNA levels occurred within 2 hours after addition of 1,000 U/mL lymphotoxin and levels plateaued over the next 24 hours. Tumor necrosis factor alpha (TNF alpha) was about five times more potent than lymphotoxin at low concentrations, and was nearly 1.5 to to 2 times more potent at maximally stimulating concentrations of the cytokines. Stimulation by lymphotoxin did not require either new protein synthesis or protein kinase-C stimulation. Stability studies of GM- and M-CSF transcripts in fibroblasts showed that M-CSF mRNA was five times more stable (half-life [t 1/2], 100 minutes) than GM-CSF mRNA (t 1/2, 20 minutes). Stability of these mRNAs was unchanged after stimulation of the cells with lymphotoxin. In addition, exposure of cells to 12-O-tetradecanoylphorbol 13-acetate did not alter stability of M-CSF mRNA but markedly prolonged the stability of GM-CSF mRNA. This is consistent with data showing that the AT-rich consensus region in the 3′ untranslated region of many transiently expressed cytokines including GM-CSF but not M-CSF, play a major role in their mRNA stability. Our results suggest that activated lymphocytes can affect hematopoietic cell function and growth by stimulating production of CSFs by mesenchymal cells.
Phase 1/2 open-label, multiple ascending dose trial of AGEN2034, an anti-PD-1 monoclonal antibody, in advanced solid malignancies: Results of dose escalation. (2018)

3086 Background: Agenus AGEN2034 is a fully-human IgG4 monoclonal antibody antagonist targeting Programmed Cell Death Protein-1 (PD-1). The objective was to assess safety, MTD, pharmacokinetic (PK) and pharmacodynamics (PD) characteristics of AGEN2034 in patients (pts) with advanced, refractory malignancies. Analyses of PD-1 receptor occupancy on circulating CD8+ and CD4+ effector memory T lymphocytes was completed. Methods: Thirty pts were enrolled in escalating dose cohorts of 1, 3, and 10 mg/kg. AGEN2034 is administered intravenously Q2W for up to 2 years with cohorts evaluating q3wk dosing at 6 and 10 mg/kg are underway. Results: Ten subjects were enrolled at each dose level. Median age was 58 years (range 23–77) with ECOG 0–1. No DLTs were observed. Immune-related adverse events consistent with this drug class were observed of pneumonitis, colitis, diarrhea, rash and pruritus. 21 of 30 pts had treatment-related adverse events (TRAEs). 13 subjects (43%) discontinued (d/c) due to disease progression and 2 pts d/c due to TRAEs of hepatitis (n = 1) and pneumonitis (n = 1). In 25 evaluable heavily pre-treated pts, three partial responses (two confirmed) were noted in patients with cervical, ovarian and breast cancers in 1mg/kg and 3mg/kg cohorts. At the time of data cut-off, 13 patients had stable disease, including 5 of 5 with ovarian cancer. AGEN2034 demonstrates a dose-proportional Cmax of 19.6 µg/mL at 1 mg/kg and 73.6 µg/mL at 3 mg/kg in 12 patient samples analyzed in the first two cohorts. Average PD-1 receptor occupancy on circulating CD8+ and CD4+ effector memory T lymphocytes (n = 18) demonstrated > 59% saturation at all dose levels at day 15. Conclusions: AGEN2034 is a pharmacologically active, well-tolerated PD-1 antagonist antibody, demonstrating early signals of clinical activity in cervical and ovarian cancers. PK and RO results are comparable to commercial PD-1 antagonists. A phase 2 expansion in pts with relapsed/refractory cervical cancer is underway. Clinical trial information: NCT03104699.
Rapamycin differentially inhibits S6Ks and 4E-BP1 to mediate cell-type-specific repression of mRNA translation (2008)

The mammalian translational initiation machinery is a tightly controlled system that is composed of eukaryotic initiation factors, and which controls the recruitment of ribosomes to mediate cap-dependent translation. Accordingly, the mTORC1 complex functionally controls this cap-dependent translation machinery through the phosphorylation of its downstream substrates 4E-BPs and S6Ks. It is generally accepted that rapamycin, a specific inhibitor of mTORC1, is a potent translational repressor. Here we report the unexpected discovery that rapamycin's ability to regulate cap-dependent translation varies significantly among cell types. We show that this effect is mechanistically caused by rapamycin's differential effect on 4E-BP1 versus S6Ks. While rapamycin potently inhibits S6K activity throughout the duration of treatment, 4E-BP1 recovers in phosphorylation within 6 h despite initial inhibition (1-3 h). This reemerged 4E-BP1 phosphorylation is rapamycin-resistant but still requires mTOR, Raptor, and mTORC1's activity. Therefore, these results explain how cap-dependent translation can be maintained in the presence of rapamycin. In addition, we have also defined the condition by which rapamycin can control cap-dependent translation in various cell types. Finally, we show that mTOR catalytic inhibitors are effective inhibitors of the rapamycin-resistant phenotype.
Functionalization of Carbon Nanotubes by Free Radicals (2003)

Free radicals generated by decomposition of benzoyl peroxide in the presence of alkyl iodides have been used to derivatize small-diameter single-wall carbon nanotubes (HiPco tubes). The degree of functionalization, estimated by thermal gravimetric analysis, is as high as 1 in approximately 5 carbons in the nanotube framework. The derivatized nanotubes exhibits remarkably improved solubility in organic solvents. The attached groups can be removed by heating in an atmosphere of argon. Derivatization was also accomplished by treating SWNTs with various sulfoxides employing Fenton's reagent. [reaction: see text]
Ca2+-transport inhibition by the antitumor agents adriamycin and daunomycin. (1977)

The antitumor agents adriamycin and daunomycin inhibit Ca2+-transport in mitochondria from Ehrlich ascites carcinoma cells as well as in a biphasic model system. The experimental results indicate that both antibiotics interact with phospholipids. The significance of these observations in the pharmacological behavior of these anticancer compounds is discussed.