gebhart/patrepeval huggingface dataset:
Phosphorylation of eukaryotic initiation factor-2α promotes the extracellular survival of obligate intracellular parasite <i>Toxoplasma gondii</i> (2010)

While seeking a new host cell, obligate intracellular parasites, such as the protozoan Toxoplasma gondii, must be able to endure the stress of an extracellular environment. The mechanisms Toxoplasma use to remain viable while deprived of a host cell are not understood. We have previously shown that phosphorylation of Toxoplasma eukaryotic initiation factor-2α (TgIF2α) is a conserved response to stress. Here we report the characterization of Toxoplasma harboring a point mutation (S71A) in TgIF2α that prevents phosphorylation. Results show that TgIF2α phosphorylation is critical for parasite viability because the TgIF2α-S71A mutants are ill-equipped to cope with life outside the host cell. The TgIF2α-S71A mutants also showed a significant delay in producing acute toxoplasmosis in vivo. We conclude that the phosphorylation of TgIF2α plays a crucial role during the lytic cycle by ameliorating the stress of the extracellular environment while the parasite searches for a new host cell.
Imaging performance of a dedicated radiation transparent RF coil on a 1.0 Tesla inline MRI-linac (2018)

This work describes the first imaging studies on a 1.0 Tesla inline MRI-Linac using a dedicated transmit/receive RF body coil that has been designed to be completely radio transparent and provide optimum imaging performance over a large patient opening. A series of experiments was performed on the MRI-Linac to investigate the performance and imaging characteristics of a new dedicated volumetric RF coil: (1) numerical electromagnetic simulations were used to measure transmit efficiency in two patient positions; (2) image quality metrics of signal-to-noise ratio (SNR), ghosting and uniformity were assessed in a large diameter phantom with no radiation beam; (3) radiation induced effects were investigated in both the raw data (k-space) and image sequences acquired with simultaneous irradiation; (4) radiation dose was measured with and without image acquisition; (5) RF heating was studied using an MR-compatible fluoroptic thermometer and; (6) the in vivo image quality and versatility of the coil was demonstrated in normal healthy subjects for both supine and standing positions. Daily phantom measurements demonstrated excellent imaging performance with stable SNR over a period of 3 months (42.6 ± 0.9). Simultaneous irradiation produced no statistical change in image quality (p > 0.74) and no interference in raw data for a 20 × 20 cm radiation field. The coil was found to be efficient over large volumes and negligible RF heating was observed. Volunteer scans acquired in both supine and standing positions provided artefact free images with good anatomical visualisation. The first completely radio transparent RF coil for use on a 1.0 Tesla MRI-Linac has been described. There is no impact on either the imaging or dosimetry performance with a simultaneous radiation beam. The open design enables imaging and radiotherapy guidance in a variety of positons.
Abstract 1983: A cell-permeable Stat3 SH2 domain mimetic inhibitor of Stat3 activation inhibits growth of human breast tumor xenografts (2011)

Abstract Human tumors harbor multiple molecular aberrations that have become the driving force for uncontrolled cell proliferation and survival, and other tumor-associated processes. Constitutive activation of the Signal Transducer and Activator of Transcription (Stat) 3 protein is a frequent occurrence in many human cancers, including breast cancer. Given the role of aberrant Stat3 activity in human tumors, small-molecule Stat3 inhibitors would be useful novel therapeutics and tools for probing Stat3-mediated tumor processes. We herein report that a 28-mer peptide, SPI, composed of the amino acid residues 588-615 of the Stat3 SH2 domain, replicates Stat3 biochemical properties and functions as a Stat3 inhibitor. Studies show SPI and Stat3 (or Stat3 SH2 domain) both bind with similar affinities to known Stat3-binding phosphotyrosine (pY) peptide motifs, including the epidermal growth factor receptor (EGFR) peptides, pY1068EGFR and pY1086EGFR, and the high-affinity, interleukin-6 receptor (IL-6R)/gp130-derived peptide, GpYLPQTV-NH2. Consequently, SPI potently and selectively inhibits Stat3 SH2 domain:pY interactions and disrupts the binding of Stat3 to the IL-6R/gp130 peptide, GpYLPQTV-NH2. Fluorescence imaging studies show SPI is cell membrane-permeable. Treatment with SPI of malignant cells that harbor aberrant Stat3 activity resulted in the selective inhibition of constitutive Stat3 phosphorylation, and of Stat3 DNA-binding and transcriptional activities. By contrast, similar treatments have little or no effects on the induction of the Stat1, Stat5, and Erk1/2MAPK pathways in malignant cells or in EGF-stimulated fibroblasts. In contrast to normal cells, human breast, pancreatic, prostate, and non-small cell lung cancer cells harboring constitutively-active Stat3 are highly sensitive to SPI and undergo extensive morphology changes, concomitant with the loss of viability and apoptosis. Significantly, treatment with SPI or its inverse sequence version strongly inhibited the growth of human breast tumor xenografts in mice, which is associated with the down-regulation of the expression of the known Stat3-regulated genes, Cyclin D1, Bcl-xL and Survivin. Our study identifies SPI as a novel molecular probe for interrogating Stat3 signaling and that functions as a selective Stat3 inhibitor, which induces antitumor response in vivo. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1983. doi:10.1158/1538-7445.AM2011-1983
Antiangiogenic Activity and in Silico Cereblon Binding Analysis of Novel Thalidomide Analogs (2020)

Due to its antiangiogenic and anti-immunomodulatory activity, thalidomide continues to be of clinical interest despite its teratogenic actions, and efforts to synthesize safer, clinically active thalidomide analogs are continually underway. In this study, a cohort of 27 chemically diverse thalidomide analogs was evaluated for antiangiogenic activity in an ex vivo rat aorta ring assay. The protein cereblon has been identified as the target for thalidomide, and in silico pharmacophore analysis and molecular docking with a crystal structure of human cereblon were used to investigate the cereblon binding abilities of the thalidomide analogs. The results suggest that not all antiangiogenic thalidomide analogs can bind cereblon, and multiple targets and mechanisms of action may be involved.
High‐Yield Synthesis of Uniform Star Polymers—Is Controlled Radical Polymerization Always Needed? (2009)

Abstract Star formation : A novel and easy method is reported for the synthesis of well‐defined star polymers with high star yield by applying conventional radical copolymerization of linear macromonomer and divinyl cross‐linkers in a homogeneous solution (see figure). magnified image
Signal Processing based on Stable radix-2 DCT Algorithms having Orthogonal Factors (2015)

This paper presents stable, radix-2, completely recursive discrete cosine transformation algorithms DCT-I and DCT-III solely based on DCT-I, DCT-II, DCT-III, and DCT-IV having sparse and orthogonal factors. Error bounds for computing the completely recursive DCT-I, DCT-II, DCT-III, and DCT-IV algorithms having sparse and orthogonal factors are addressed. Image compression results are presented based on the recursive 2D DCT-II and DCT-IV algorithms for image size $512 \times 512$ pixels with transfer block sizes $8 \times 8$, $16 \times 16$, and $32 \times 32$ with $93.75\%$ absence of coefficients in each transfer block. Finally signal flow graphs are demonstrated based on the completely recursive DCT-I, DCT-II, DCT-III, and DCT-IV algorithms having orthogonal factors.
T cell multideterminant regions in the human immunodeficiency virus envelope: toward overcoming the problem of major histocompatibility complex restriction (1989)

Helper T cell determinants should be an important component of an anti-human immunodeficiency virus (HIV) vaccine aimed at either antibody or cytotoxic T cell immunity. However, model protein studies have raised concern about the usefulness of any single determinant, because a given determinant is likely to be seen by only a small subset of major histocompatibility complex (MHC) types within the population. Here, we use 44 peptides, including ones predicted and not predicted on the basis of amphipathicity to be potential T cell sites, to locate T cell antigenic determinants recognized by mice of four MHC haplotypes immunized with the whole gp 160 envelope protein. Although the preselection of peptides necessitates caution in a statistical analysis, alpha-amphipathic peptides predominated among sites eliciting the strongest response. Although we have not tested the entire sequence, we have identified six multideterminant regions, in which overlapping peptides are recognized by mice of either three or all four MHC types. Four of the six regions have sequences relatively conserved among HIV-1 isolates. The existence of such multideterminant regions recognized by multiple MHC haplotypes suggests the possibility that use of peptides longer than a minimal determinant and containing several overlapping determinants may be a possible approach to circumvent the serious problem of MHC restriction in peptide vaccines aimed at eliciting T cell immunity.
Adaptive Control of Dynamical Systems with Unstructured Uncertainty and Unmodeled Dynamics (2019)

Model reference adaptive control of dynamical systems with unstructured system uncertainties and unmodeled dynamics is considered in this paper. Specifically, a stability tradeoff for this class of dynamical systems is shown first. With the goal of relaxing the resulting stability tradeoff, adaptive robustifying terms are designed next. The key aspect of the proposed relaxation procedure is that the proposed terms guarantee closed-loop system stability even with respect to significant system uncertainties, subject to unmodeled dynamics satisfying a condition. An illustrative numerical example is further given to demonstrate our theoretical findings.
Multiport optical fibre switch using a new hexagonal prism design (1985)

The optical fibre switching function required to substitute one spare transmitter for any one of eight other active laser transmitters that may be failing is implemented in a single switching device using a new prism design that permits the exchange of optical signals between parallel beams.
Thermally Programmable pH Buffers (2012)

Many reactions in both chemistry and biology rely on the ability to precisely control and fix the solution concentrations of either protons or hydroxide ions. In this report, we describe the behavior of thermally programmable pH buffer systems based on the copolymerization of varying amounts of acrylic acid (AA) groups into N-isopropylacrylamide polymers. Because the copolymers undergo phase transitions upon heating and cooling, the local environment around the AA groups can be reversibly switched between hydrophobic and hydrophilic states affecting the ionization behavior of the acids. Results show that moderate temperature variations can be used to change the solution pH by two units. However, results also indicate that the nature of the transition and its impact on the pH values are highly dependent on the AA content and the degree of neutralization.
Design and Synthesis of Brefeldin A Sulfide Derivatives as Prodrug Candidates with Enhanced Aqueous Solubilities (1998)

The addition of a variety of thiols to the alpha,beta-unsaturated lactone functionality present in brefeldin A has been carried out, and the resulting sulfides have been oxidized to the corresponding sulfoxides. These sulfoxides have the potential to undergo syn elimination to regenerate brefeldin A. The sulfoxides were more active than the sulfides as cytotoxic agents in a variety of human cancer cell cultures with the activities of the sulfoxides approaching that of brefeldin A itself. The cytotoxicities of the sulfoxides may be due to their conversion back to brefeldin A. The kinetics of sulfoxide elimination to form brefeldin A were studied in four cases, and the results indicate that substantial amounts of brefeldin A are likely to be generated during the cytotoxicity assays of the sulfoxide derivatives. Since the oxidation of sulfides to sulfoxides is a common metabolic reaction, the sulfides derived from brefeldin A can be considered as potential brefeldin A prodrugs. Several of the sulfide derivatives were determined to have enhanced aqueous solubilities relative to brefeldin A itself. A number of brefeldin A succinates, glutarates, oxidation products, and sulfone derivatives were also prepared and evaluated for cytotoxicity in cancer cell cultures. Some of the more active brefeldin A derivatives were tested in an in vivo animal model in which hollow fibers containing cancer cell cultures were implanted subcutaneously (SC) and intraperitoneally (IP), and the compounds were administered IP. Greater cytotoxic activity was observed at the SC site than at the IP site for the majority of these compounds, an observation which is consistent with the hypothesis that they are acting as brefeldin A prodrugs in vivo.
Design, Fabrication and Mechancial Characterization of Vertical Micro Contact Probe (2006)

In this paper, the new vertical micro contact probe for the testing of circuits in chips is designed, and then the mechanical behavior is characterized. Vertical micro contact probes are used for circuit inspection tool 'probe card' which has irregular area arrays and narrow pitch electrode pads. The new micro contact probes are designed to fulfill the requirements of 100 mum electrode pitch, minimum 20 mum over drive and minimum 20 mN force to break the surface native oxide layer. Zigzag spring shaped vertical probes are designed, and fabricated with Ni-Co alloy by electroplating method. Mechanical characterizations of micro contact probes are performed by compression tester. Finally, these experiment results are compared with simulation results and the error sources are analyzed.
Design of smart window based on electrochromic polymers: new derivatives of 3,4-alkylenedioxythiophene (2004)

The synthesis, characterization and polymerization of two new electrochromic (EC) monomers based on 3, 4-alkylenedioxythiophene are reported. One is 3, 4-bis-(2, 2, 2-trifluoro-ethoxy)-thiophene which contains electron withdrawing group. Another is 6, 6-dimethy-6, 7-dihydro-5H-4, 8-dioxa-2-thia-6-sila-azulene which contains an electron donating group. Primary experiment results show that the new monomers have potential to form EC materials with new colors after polymerization. Color mixing of two EC polymers with blue and red color was studied. The principle of subtractive color mixing for achieving new color EC materials is also demonstrated.
The Immunoglobulin D-binding Part of the Outer Membrane Protein MID from Moraxella catarrhalis Comprises 238 Amino Acids and a Tetrameric Structure (2002)

Moraxella catarrhalis IgD-binding protein (MID), a 200-kDa outer membrane protein comprising 2,139 amino acids, has recently been isolated and shown to display a unique and specific affinity for human IgD. To identify the IgD-binding region, MID was digested with proteases. In addition, a series of truncated fragments of MID were manufactured and expressed in Escherichia coli followed by analysis for IgD binding in Western and dot blots. The smallest fragment with essentially preserved IgD binding was comprised of 238 amino acid residues (MID(962-1200)). Shorter recombinant proteins gradually lost IgD-binding capacity, and the shortest IgD-binding fragment comprising 157 amino acids (MID(985-1142)) displayed a 1,000-fold reduced IgD binding compared with the full-length molecule. The truncated MID(962-1200) was efficiently attracted to a standard IgD serum and to purified myeloma IgD(kappa) and IgD(lambda) sera but not to IgG, IgM, or IgA myeloma sera. Furthermore, the fragment specifically bound to peripheral blood B lymphocytes, and the binding was inhibited by preincubation with anti-IgD-Fab polyclonal antibodies. Results obtained by introducing five amino acids randomly into MID(962-1200) using transposons suggested that alpha-helix structures were important for IgD binding. Ultracentrifugation experiments and gel electrophoresis revealed that native MID(962-1200) was a tetramer. Interestingly, tetrameric MID(962-1200) attracted IgD more than 20-fold more efficiently than the monomeric form. Thus, a tetrameric structure of MID(962-1200) is crucial for optimal IgD-binding capacity.
A Novel Smad7 Genetic Variant Mapping on the Genomic Region Targeted by Mongersen Is Associated with Crohn’s Disease (2020)

This is the first study to show an association between <i>Smad7</i> rs144204026 SNP and CD patients. Data indicate that such a variant does not negatively influence the in vitro inhibitory effect of Smad7 AS on Smad7.
Design of an one-cycle decompression hardware for performance increase in embedded systems (2002)

Code compression is known as an effective technique to reduce instruction memory size on an embedded system. However, code compression can also be very effective in increasing processor-to-memory bandwidth and hence provide increased system performance. In this paper we describe our design and design methodology of the first running prototype of a one-cycle code decompression unit that decompresses compressed instructions on-the-fly. We describe in detail the architecture that enables decompression of multiple instructions in one cycle and we present the design methodologies and tools used. The stand-alone decompression unit does not require any modifications on the processor core. We observed up to 63% performance increase with 25% in average over a wide variety of applications running on the hardware prototype under various system configurations.
Variational Bayesian Symbol Detection for Massive MIMO Systems with Symbol-Dependent Transmit Impairments (2019)

In this paper, we propose a variational Bayesian inference approach for a low-complexity symbol detection for massive MIMO systems with symbol- dependent transmit-side impairments. This study is motivated by observations that realworld communication transceivers are often affected by the hardware impairments, such as non-linearities of power amplifiers, I/Q imbalance, phase drifts due to non-ideal oscillators, and carrier frequency offsets. Particularly, symbol-dependent perturbations are fully accounted into the designed hierarchical signal model as unknown model parameters. The developed variational Bayesian symbol detector is able to learn the unknown perturbations in an iterative fashion. Numerical evaluation confirms the effectiveness of the proposed approach.
Diffraction-based femtosecond pulse shaping with a two-dimensional spatial light modulator (2005)

A new diffraction-based method is proposed and demonstrated for simultaneous shaping of both the phase and amplitude of femtosecond laser pulses by use of a phase-only two-dimensional spatial light modulator. The method suppresses certain types of temporal replica features ordinarily observed in femtosecond pulse shaping owing to imperfections in modulator devices and allows for multiplexed outputs suitable for use in various applications.
A Continuous Long Running Batch Orchestration Model for Workflow Instance Migration (2010)

Workflow engines which require process instances to run to completion against their creation model are limited in their ability to adapt to model changes. The technique of process instance migration can be used to migrate instances to a new process model, but at any given time only a fraction of instances may be in a state which is compatible with the new model. We propose a continuous batch approach for migration which treats migration itself as a long running problem. The continuous migration approach schedules and orchestrates the evaluation and migration of long running processes over time, controlled by configurable policies while maintaining continuous process availability. We have built a long running process migration simulation to test our approach, looking at both migration success and cost. The simulation confirms the need for a long running migration approach and yields some interesting suggestions for tuning the configuration of the migration system.
Fast and Stable Photochromic Oxazines (2005)

We have designed and synthesized two photochromic compounds incorporating fused indoline and benzooxazine fragments. Variable-temperature 1H NMR spectroscopy demonstrates that their central [1,3]oxazine ring opens thermally with free energy barriers ranging from 14 to 19 kcal mol(-1). The ring-opened species reverts rapidly to the original isomer and can only be detected after chemical trapping. Specifically, the nucleophilic attack of a hydroxide anion to the indolium cation of the ring-opened species prevents re-isomerization. Laser excitation of both compounds induces the opening of the [1,3]oxazine ring in less than 6 ns with quantum yields up to 0.1. The photoinduced ring opening generates a 4-nitrophenolate chromophore, which absorbs strongly at 440 nm. The photogenerated species reverts to the original form with a lifetime of 22 ns for both compounds. Thus, these transformations can be exploited to interconvert the two isomers of each species with nanosecond switching speeds. Furthermore, thousands of switching cycles can be repeated consecutively without any sign of degradation, even in the presence of molecular oxygen. These processes can be reproduced efficiently in poly(methyl methacrylate) matrixes. Under these conditions, the thermal re-isomerization occurs with biexponential kinetics in submillisecond time scales. In principle, the fast isomerization kinetics and excellent fatigue resistance of both compounds offer the opportunity to modulate rapidly and efficiently a variety of molecular and macroscopic properties. Thus, our molecular design can evolve into the realization of a new family of photochromic compounds and materials with promising photoresponsive character.
Comparative study on the preparation and properties of radiation‐grafted polymer electrolyte membranes based on fluoropolymer films (2006)

Abstract In this study the fluoropolymers, poly(ethylene‐ co ‐tetrafluoroethylene) (ETFE) and poly(vinylidene fluoride) (PVDF) films, together with the radiation‐induced crosslinked polytetrafluoroethylene (cPTFE) film were compared on the basis of their preparation and properties of radiation‐grafted polymer electrolyte membranes. The polymer electrolyte membranes were prepared by radiation grafting of styrene into the base films and subsequent sulfonation. The proton conductivity and chemical stability of the three types of membranes with a similar ion exchange capacity (IEC) near 1.0 mmol/g were investigated and are discussed in detail. Although the ETFE‐based polymer electrolyte membrane was relatively more stable, its proton conductivity was lower than those of the PVDF‐ and cPTFE‐based membranes. On the other hand, the cPTFE‐based membrane showed a significantly higher proton conductivity, but its chemical stability was shorter than that of the ETFE‐based membrane. It is considered that the difference in the preparation and properties of the polymer electrolyte membranes was due to the difference in the degree of crystallinity as well as in the chemical structure of the fluoropolymer base films. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 103: 1966–1972, 2007
Synthesis of polyesteramides by new Pd catalyzed carbonylation-polycondensation reaction (2001)

Alternating polyesteramides are prepared by palladium catalyzed carbonylation-polycondensation reactions of aromatic diiodides and aminohydroxy compounds in the presence of an organic base.