gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Nonflow Zinc/Halogen Storage Cell Made of Thin Film Composite. (1989)

Abstract Semi‐solid zinc halide cells in the form of thin laminated composites are developed and shown to deliver hundreds of discharge/charge cycles with high efficiency and without changes in the performance.
Purification of Human α2 -Plasmin Inhibitor Using Monoclonal Antibody Column Chromatography (1989)

alpha 2-Plasmin inhibitor (alpha 2PI) was purified directly from human plasma by using a monoclonal antibody affinity column, which recognizes the reactive site of alpha 2PI. alpha 2PI was eluted from the column under mild conditions with 50% v/v ethyleneglycol containing 0.05% Tween 80 in phosphate-buffered saline, pH 7.4. The yield was around 50% and the specific activity of the purified protein was the same as that of the best product of preparation conventionally purified alpha 2PI.
Abstract 2156: Targeting polo-like kinase 1 with novel inhibitors of the polo-box domain. (2013)

Abstract Polo-like Kinase 1 (PLK1) is a central player in cell cycle regulation and mitotic progression. Observations that PLK1 is over-expressed in many cancer types have led to efforts to target this protein therapeutically. Several ATP-binding site inhibitors of PLK1 have advanced to clinical trials, but these compounds inhibit at least three of the four known mammalian PLKs to varying degrees. This is problematic because, for example, PLK3 acts as a tumor suppressor and has opposing functions to PLK1. Moreover, a recent study identified a single point mutation near the ATP binding site that renders PLK1 resistant to several structurally unrelated ATP-based inhibitors, while retaining kinase activity. The Polo-box domain (PBD) of each PLK is a phospho-peptide binding motif that determines substrate recognition and subcellular localization. Our approach is to target the PBD of PLK1 to achieve desired PLK1 selectivity and improve efficacy. We recently reported a structure-activity relationship for a series of fragment-ligated inhibitory peptides (FLIPs) designed to be selective for the PBD of PLK1 (Mol. Cancer Ther., 2012, 11, 1683-1692). Our most potent compound in that class possessed a binding affinity to the PLK1 PBD (IC50 value of 8.6 μM), and insignificant levels of PLK3 binding up to 600 μM, which represents at least a 100-fold selectivity. The compound was able to induce cellular phenotypes consistent with a PLK1 knockdown, including aberrant mitoses and induction of apoptosis. Here, we report the development of new FLIP analogues with improved potency in binding to the PLK1 PBD. Specifically, we have designed, synthesized, and tested new benzoic acid capping groups to exploit a hydrophobic cleft in the PBD binding site. This newer generation of compounds possess binding affinities to the PLK1 PBD with IC50 values below 1 μM. Studies are in progress to determine PLK1 selectivity and activity in cells. Future studies will explore the ability of PBD-targeted compounds to circumvent resistance to ATP-based compounds. Citation Format: Merissa Baxter, Sandra Craig, Campbell McInnes, Michael D. Wyatt. Targeting polo-like kinase 1 with novel inhibitors of the polo-box domain. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2156. doi:10.1158/1538-7445.AM2013-2156
Gypsum bioconversion to sulfur: a two-step microbiological process (1983)

The isolation, cultivation, and process applications of a sulfate-reducing bacterial strain are described. The organism is an obligate anaerobe, gram-negative species capable of propagation in an inorganic medium with acetate as the sole preformed carbon source; gaseous products of metabolism are hydrogen sulfide and carbon dioxide. The strain is here referred to as a Desulfobacter sp. In the context of gypsum control and removal, this organism appears suitable for the first step of a two-step bioconversion process wherein sulfate ultimately is converted to elemental sulfur. The second organism is Chlorobium limicola f. sp. thiosulfatophilum, a photosynthetic green sulfur bacterium which converts the hydrogen sulfide and carbon dioxide produced by Desulfobacter to free sulfur, biomass, and soluble organic acids which are suitable metabolites for the support of growth of Desulfobacter. Preliminary data are presented for the rate of sulfate reduction, which can reach levels of 1.58 mmol liter hr when cultures are operated in a chemostat mode. Initial results suggest that batch cultures of Chlorobium will continue conversion of H2S to S after cell division has ceased. Net free sulfur production was reduced by the appearance of increasing levels of thiosulfate and sulfate, possibly because of altered metabolic pathways during senescencemore » of the culture or because of nutritional limitations. 14 references, 3 figures.« less
Extraordinary THz transmission in ring apertures (2011)

We demonstrated extraordinary THz transmission through ring apertures on a metal film. Transmission of 60% was obtained with an aperture-to-area ratio of only 1.4%. We show that the high transmission can be suppressed by over 18 dB with a thin layer of free carriers in the silicon substrate underneath the metal film. This result suggests that CMOS-compatible terahertz switch can be built by controlling the carrier density near the aperture.
Error-resilient video coding for wireless video telephony applications (2012)

In this paper, we present an error resilient video coding scheme for wireless video telephony applications that uses feedback to limit error propagation. In conventional feedback-based error resilient schemes, error propagation can significantly degrade visual quality when feedback delay is in the order of a few seconds. We propose a coding structure based on multiple description coding that mitigates error propagation during feedback delay, and uses feedback to adapt its coding structure to effectively limit error propagation. We demonstrate the effectiveness of our approach at different error rates when compared to conventional coding schemes that use feedback.
Parallel discovery of multiple chemotypes antagonizing p53/mdm2/mdmx (2007)

A266 We describe a general and new fragment-based approach, which can be used for the efficient and rapid discovery of multiple chemotypes of hit compounds. This approach is based on the identification of an important fragment using existent structures from the pdb and from literature. The fragment is used as a starting material to produce virtual compound libraries leaned on a database of >500 different multi component reaction (MCR) scaffolds. These compound libraries are docked/modeled into the published pdb structure of interest, with the constraint of sterical fixation of the fragment as apparent from the structural information. The ranking list is manually inspected for consistency. The selected “best” compounds are picked and rapidly synthesized in the wet-lab using convergent MCR chemistry and thereafter screened for activity. We will demonstrate the new technique for the protein protein interaction p53/mdm2, where we have been able to rapidly discover several unprecedented antagonist classes which are “drug-like” and straight-forward to optimize using MCR chemistry. Moreover, we where able to discover a dual-action p53/mdm2/mdm4 scaffold. All our hits have been structurally confirmed by NMR spectroscopy with labeled mdm2/mdmx. This approach has several potential advantages over other fragment-based approaches. In principle it is not dependant on expensive techniques (nmr, x-ray). It smoothly passages from a fragment into several new “drug-like” scaffolds without using often artificial linker chemistry. It potentially enhances successful advancement of a project towards clinical translation due to the progression and preclinical optimization of several chemotypes in parallel.
Analysis of parallel beam gyroscope (2003)

A parallel beam structure has many significant features, as follows: (i) the tip moves in parallel at the end; (ii) this structure converts a small displacement into a large strain; and (iii) when piling up this structure, each unit doesn't interfere with the other units. We used this structure for a piezoelectric vibrating gyroscope (angular rate sensor), and detected angular rate using this gyroscope. In the paper, we analyze features of the parallel beam structure by the finite element method. We show that the resonance frequency of the drive unit and sensor unit can be easily adjusted by changing the mass at the tip. From this result, this structure suits the gyroscope.
Auto-vectorization through code generation for stream processing applications (2009)

We describe language- and code generation-based approaches to providing access to architecture-specific vectorization support for high-performance data stream processing applications. We provide an experimental performance evaluation of several stream operators, contrasting our code generation approach with the native auto-vectorization support available in the GNU gcc and Intel icc compilers.
Effects of Methylecgonidine on acetylcholine-induced bronchoconstriction and indicators of lung injury in guinea pigs (1995)

The fumarate salt of methylecgonidine (MEG; anhydroecgonine methylester), a pyrolysis product of cocaine, has previously been shown to antagonize contractions of guinea pig isolated trachea induced by acetylcholine (ACh) and other spasmogenics. We determined the effects of MEG fumarate on ACh-induced bronchoconstriction in vivo. Specific airway conductance (SGaw) was measured in guinea pigs receiving 30-300 mg/kg s.c. MEG fumarate and exposed one hour later to nebulized ACh (0.2-3.2%; by inhalation). MEG fumarate did not induce any changes in SGaw; neither did it antagonize dose-dependent decreases in SGaw induced by ACh. However, tremors, salivation, startle and increased numbers of fecal boli were observed after MEG administration. Thus, unlike antagonism of ACh-induced contractions of guinea pig isolated trachea observed in vitro, MEG fumarate does not antagonize ACh-induced bronchoconstriction in vivo, even at doses which induced changes in grossly-observable behavior. Inhalation of a condensation aerosol of MEG base induced lung damage as evidenced by the presence of blood and higher levels of protein and lactate dehydrogenase in the lung lavage fluid of MEG-treated animals than of control animals. Aerosols of MEG fumarate, on the other hand, did not induce lung damage when inhaled. These results extend previous observations that MEG base may contribute to detrimental pulmonary effects of crack smoking.
<title>Surface-mediated alignment of liquid crystals with polarized light (Invited Paper)</title> (1992)

Liquid crystals are utilized in many display applications. The use of liquid crystals in electro- optic phase devices, spatial light modulators and laser optics is becoming increasingly more common. Critical to most of these applications is the uniform macroscopic alignment of the liquid crystals. We have discovered a new process of controlling the local macroscopic alignment of liquid crystal molecules using polarized light. This discovery gives an additional degree of freedom in controlling liquid crystal alignment. In addition, complex devices (i.e., binary phase devices) that would be difficult to achieve using conventional alignment techniques (i.e., buffing, deposition, etc.) may be readily attainable using optical techniques. The optically induced alignment described in this paper possesses memory, write-rewrite capability, and high spatial resolution on the order of micrometers or less.
Investigation of Mode Interaction in Optical Microresonators for Kerr Frequency Comb Generation (2014)

Mode interaction in silicon nitride micro-resonators is investigated. We provide clear experimental evidence of mode interaction between two families of transverse modes and demonstrate a link between such interactions and initiation of comb generation in resonators with normal dispersion.
Physics-guided probabilistic modeling of extreme precipitation under climate change (2020)

Earth System Models (ESMs) are the state of the art for projecting the effects of climate change. However, longstanding uncertainties in their ability to simulate regional and local precipitation extremes and related processes inhibit decision making. Existing state-of-the art approaches for uncertainty quantification use Bayesian methods to weight ESMs based on a balance of historical skills and future consensus. Here we propose an empirical Bayesian model that extends an existing skill and consensus based weighting framework and examine the hypothesis that nontrivial, physics-guided measures of ESM skill can help produce reliable probabilistic characterization of climate extremes. Specifically, the model leverages knowledge of physical relationships between temperature, atmospheric moisture capacity, and extreme precipitation intensity to iteratively weight and combine ESMs and estimate probability distributions of return levels. Out-of-sample validation suggests that the proposed Bayesian method, which incorporates physics-guidance, has the potential to derive reliable precipitation projections, although caveats remain and the gain is not uniform across all cases.
Co-Designing Multi-Packet Reception, Network Coding, and MAC Using a Simple Predictive Model (2011)

We design a cross-layer approach to optimize the joint use of multi-packet reception and network coding, in order to relieve congestion. We construct a model for the behavior of the 802.11 MAC and apply it to several key canonical topology components and their extensions to any number of nodes. The results obtained from this model match the available experimental results, which are for routing and opportunistic network coding, with fidelity. Using this model, we show that fairness allocation by the MAC can seriously impact performance; hence, we devise a new MAC that not only substantially improves throughput relative to the current 802.11 MAC, but also provides fairness to flows of information rather than to nodes. We show that the proper combination of network coding, multi-packet reception, and our new MAC protocol achieves super-additive throughput gains of up to 6.3 times that of routing alone with the use of the standard 802.11 MAC. Finally, we extend the model to analyze the asymptotic behavior of our new MAC as the number of nodes increases.
Human Immunodeficiency Virus Reverse Transcriptase T Helper Epitopes Identified in Mice and Humans: Correlation with a Cytotoxic T Cell Epitope (1991)

T cell immunity may be critical to development of a vaccine for human immunodeficiency virus (HIV-1). T helper epitopes were identified in three predominantly conserved regions in the HIV-1 reverse transcriptase by using reverse transcriptase-immunized mice of five major histocompatibility complex haplotypes. One peptide (residues 38-52) that stimulated H-2k T cells also contained an epitope recognized by cytotoxic T cells from the same mice and from HIV-infected patients. Such concordance between helper and cytotoxic T lymphocyte epitopes, observed in four cases, may be important in vaccine development. Peptide 36-52 was recognized by interleukin-2-producing peripheral blood T cells from 9 of 17 HIV-seropositive humans studied, of multiple human leukocyte antigen-DR and -DQ types. The broad recognition of this peptide by both helper and cytotoxic T cells substantiates its potential importance in a vaccine.
Optimizing surface coils and the self-shielded gradiometer (2003)

A computational method for optimizing both single- and two-layer surface coils is presented that is relatively easy to implement in practice using either a variational approach or through standard numerical matrix diagonalization techniques. The technique is applied, in particular, to develop a self-shielded gradiometer that is relatively immune to radiofrequency (rf) interference from distant sources with a minimal compromise to its ability to sense rf from nearby sources, properties necessary for nuclear quadrupole resonance detection of buried land mines. Results of the optimization procedure are evaluated using finite-element numerical techniques and measurements on prototype coils for a number of configurations. These results show that practical coils can be constructed that approximate the theoretically optimized coils quite well. In addition, the trade off between the surface coil sensitivity and noise immunity is presented for the self-shielded gradiometer configuration.
Semantic Resizing of Charts Through Generalization:A Case Study with\n Line Charts (2021)

Inspired by cartographic generalization principles, we present a\ngeneralization technique for rendering line charts at different sizes,\npreserving the important semantics of the data at that display size. The\nalgorithm automatically determines the generalization operators to be applied\nat that size based on spatial density, distance, and the semantic importance of\nthe various visualization elements in the line chart. A qualitative evaluation\nof the prototype that implemented the algorithm indicates that the generalized\nline charts pre-served the general data shape, while minimizing visual clutter.\nWe identify future opportunities where generalization can be extended and\napplied to other chart types and visual analysis authoring tools.\n
Cirrhotic Human Liver Extracellular Matrix 3D Scaffolds Promote Smad-Dependent TGF-β1 Epithelial Mesenchymal Transition (2019)

An altered liver microenvironment characterized by a dysregulated extracellular matrix (ECM) supports the development and progression of hepatocellular carcinoma (HCC). The development of experimental platforms able to reproduce these physio-pathological conditions is essential in order to identify and validate new therapeutic targets for HCC. The aim of this work was to validate a new in vitro model based on engineering three-dimensional (3D) healthy and cirrhotic human liver scaffolds with HCC cells recreating the micro-environmental features favoring HCC. Healthy and cirrhotic human livers ECM scaffolds were developed using a high shear stress oscillation-decellularization procedure. The scaffolds bio-physical/bio-chemical properties were analyzed by qualitative and quantitative approaches. Cirrhotic 3D scaffolds were characterized by biomechanical properties and microarchitecture typical of the native cirrhotic tissue. Proteomic analysis was employed on decellularized 3D scaffolds and showed specific enriched proteins in cirrhotic ECM in comparison to healthy ECM proteins. Cell repopulation of cirrhotic scaffolds highlighted a unique up-regulation in genes related to epithelial to mesenchymal transition (EMT) and TGFβ signaling. This was also supported by the presence and release of higher concentration of endogenous TGFβ1 in cirrhotic scaffolds in comparison to healthy scaffolds. Fibronectin secretion was significantly upregulated in cells grown in cirrhotic scaffolds in comparison to cells engrafted in healthy scaffolds. TGFβ1 induced the phosphorylation of canonical proteins Smad2/3, which was ECM scaffold-dependent. Important, TGFβ1-induced phosphorylation of Smad2/3 was significantly reduced and ECM scaffold-independent when pre/simultaneously treated with the TGFβ-R1 kinase inhibitor Galunisertib. In conclusion, the inherent features of cirrhotic human liver ECM micro-environment were dissected and characterized for the first time as key pro-carcinogenic components in HCC development.
Dual modification of Alzheimer’s disease PHF-tau protein by lysine methylation and ubiquitylation: a mass spectrometry approach (2011)

In sporadic Alzheimer's disease (AD), neurofibrillary lesion formation is preceded by extensive post-translational modification of the microtubule associated protein tau. To identify the modification signature associated with tau lesion formation at single amino acid resolution, immunopurified paired helical filaments were isolated from AD brain and subjected to nanoflow liquid chromatography-tandem mass spectrometry analysis. The resulting spectra identified monomethylation of lysine residues as a new tau modification. The methyl-lysine was distributed among seven residues located in the projection and microtubule binding repeat regions of tau protein, with one site, K254, being a substrate for a competing lysine modification, ubiquitylation. To characterize methyl lysine content in intact tissue, hippocampal sections prepared from post mortem late-stage AD cases were subjected to double-label confocal fluorescence microscopy using anti-tau and anti-methyl lysine antibodies. Anti-methyl lysine immunoreactivity colocalized with 78 ± 13% of neurofibrillary tangles in these specimens. Together these data provide the first evidence that tau in neurofibrillary lesions is post-translationally modified by lysine methylation.
Monocyte chemotactic protein-4: tissue-specific expression and signaling through CC chemokine receptor-2 (1997)

Chemokines constitute a family of low-molecular-weight proteins that attract or activate a variety of cell types, including leukocytes, endothelial cells, and fibroblasts. An electronic search of the GenBank Expressed Sequence Tags database uncovered a partial cDNA sequence with homology to the chemokine monocyte chemotactic protein-1 (MCP-1). Isolation of the full-length clone revealed that it encodes the chemokine MCP-4, an eosinophil chemoattractant recently described by Uguccioni et al. [J. Exp. Med. 183, 2379-2384]. Recombinant MCP-4 was expressed in mammalian cells and purified by heparin-Sepharose chromatography. Sequencing the amino terminus of this protein corroborated the reported sequence of recombinant MCP-4 produced in insect cells. As shown by calcium flux assays, MCP-4 activated the cloned G protein-coupled receptor CCR-2, which also recognizes MCP-1 and MCP-3. Northern hybridization indicated that MCP-4 is constitutively expressed at high levels in the small intestine, colon, and lung. This expression profile is consistent with its role as a chemoattractant for eosinophils, which can be rapidly mobilized to the lung or intestine in response to invading pathogens. In marked contrast to MCP-1, MCP-4 was not induced in cell lines treated with pro-inflammatory stimuli such as lipopolysaccharide or tumor necrosis factor alpha.
CCA retention and its effects on the bonding performance of decommissioned treated wood: a preliminary study (2009)

Chromated copper arsenate (CCA) continues to be widely used as a wood preservative for industrial uses in the u.s. Disposal of treated wood is a potential long-terDl environmental liability. Current practices for disposing of decommissioned preservative-treated wood include landfilling and incineration, which are increasingly impractical due to environmental impacts. To date, however, research has not yielded commercially successful methods of recycling spent treated wood Novel approaches are needed for the recycling of large quantities of decommissioned treated wood products. Engineering quality decommissioned preservative-treated wood for value-added, structural, industrial products will extend the service life of treated wood and would be a practical solution to the current disposal problems of treated wood. However, the bonding of decommissioned preservative-treated wood with synthetic resins for engineered products has not been investigated adequately. The objectives of this preliminary study were to (1) investigate CCA retention across and along decommissioned utility poles, (2) evaluate the effects of two surface preparation methods on improving bonding strength between treated wood, and (3) evaluate the effect of CCA retention on bonding strength of decommissioned treated wood. Results showed that CCA retention decreased from the outside to the inside and from the top to the bottom of the decommissioned poles of this study. CCA interfered with the bonding of treated wood after treatment with both priming and incising.