gebhart/patrepeval huggingface dataset:
Biochemical and Functional Analyses of the Human Toll-like Receptor 3 Ectodomain (2007)

The structure of the human Toll-like receptor 3 (TLR3) ectodomain (ECD) was recently solved by x-ray crystallography, leading to a number of models concerning TLR3 function (Choe, J., Kelker, M. S., and Wilson, I. A. (2005) Science 309, 581-585; Bell, J. K., Botos, I., Hall, P. R., Askins, J., Shiloach, J., Segal, D. M., and Davies, D. R. (2005) Proc. Natl. Acad. Sci. U. S. A. 102, 10976-10980) The structure revealed four pairs of cysteines that are putatively involved in disulfide bond formation, several residues that are predicted to be involved in dimerization between ECD subunits, and surfaces that could bind to poly(I:C). In addition, there are two loops that protrude from the central solenoid structure of the protein. We examined the recombinant TLR3 ECD for disulfide bond formation, poly(I:C) binding, and protein-protein interaction. We also made over 80 mutations in the residues that could affect these features in the full-length TLR3 and examined their effects in TLR3-mediated NF-kappaB activation. A number of mutations that affected TLR3 activity also affected the ability to act as dominant negative inhibitors of wild type TLR3. Loss of putative RNA binding did not necessarily affect dominant negative activity. All of the results support a model where a dimer of TLR3 is the form that binds RNA and activates signal transduction.
Technology Transfer Opportunities: Automated Ground-Water Monitoring, A Proven Technology (1998)

Introduction The U.S. Geological Survey (USGS) has developed and tested an automated ground-water monitoring system that measures and records values of selected water-quality properties and constituents using protocols approved for manual sampling. Prototypes using the automated process have demonstrated the ability to increase the quantity and quality of data collected and have shown the potential for reducing labor and material costs for ground-water quality data collection. Automated ground-water monitoring systems can be used to monitor known or potential contaminant sites, such as near landfills, underground storage tanks, or other facilities where potential contaminants are stored, to serve as early warning systems monitoring ground-water quality near public water-supply wells, and for ground-water quality research.
Deterministic replay of distributed Java applications (2002)

Execution behavior of a Java application can be nondeterministic due to concurrent threads of execution, thread scheduling, and variable network delays. This nondeterminism in Java makes the understanding and debugging of multi-threaded distributed Java applications a difficult and a laborious process. It is well accepted that providing deterministic replay of application execution is a key step towards programmer productivity and program under-standing. Towards this goal, we developed a replay framework based on logical thread schedules and logical intervals. An application of this framework was previously published in the context of a system called Deja Vu that provides deterministic replay of multi-threaded Java programs on a single Java Virtual Machine (JVM). In contrast, this paper focuses on distributed Deja Vu that provides deterministic replay of distributed Java applications running on multiple JVMs. We describe the issues and present the design, implementation and preliminary performance results of distributed Deja Vu that supports both multi-threaded and distributed Java applications.
Abstract B84: Novel and selective inhibitors of histone deacetylases (HDAC) 1 and 2 significantly enhance the activity of the DNA methyltransferase inhibitor azacitidine in acute myeloid leukemia (AML) (2015)

Abstract AML is a heterogeneous group of hematopoietic stem cell disorders characterized by defects in myeloid differentiation and increased proliferation of neoplastic hematopoietic precursor cells. There is a great need for novel approaches to treat AML due to limited improvements in the treatment of patients over the past several decades. Aberrant epigenetic regulation plays an important role in the pathogenesis of AML, and the DNA methyltransferase inhibitor azacitidine is approved for the treatment of myelodysplastic (MDS), which frequently progresses to AML, and is commonly used in AML patients. Numerous clinical studies are ongoing to investigate the benefit of combining azacitidine with other investigational agents in AML. HDAC inhibitors are promising agents for the treatment of AML. Selective HDAC inhibitors are predicted to reduce combination drug toxicity and other side effects observed with pan-HDAC inhibitors, while still enabling therapeutic benefits. In this work, we demonstrate that potent and selective inhibitors of HDAC1/2 are highly efficacious both as single agents and in combination with azacitidine in preclinical models of AML, including established AML cell lines and bone marrow samples freshly derived from AML patients. Combination treatment in vivo demonstrated good tolerability, and ongoing efficacy studies in AML xenograft models will be discussed. At the molecular level, gene expression profiling and DNA methylation mapping were performed on MV4-11 cells treated with an HDAC1/2 inhibitor, azacitidine, or the combination. Molecular signatures were analyzed by GSEA. Significantly more genes and signatures were upregulated than downregulated by the single agent and combination treatments, consistent with the transcription activation mechanism of these compounds. Signatures and genes involved in myeloid cell differentiation, apoptosis and cell cycle arrest were identified as potential mediators of the combinatorial effects of HDAC1/2 inhibition with azacitidine. Together, these findings support the clinical evaluation of selective HDAC1/2 inhibitors in combination with azacitidine in AML and potentially MDS patients. Citation Format: Chengyin Min, Steven N. Quayle, Pengyu Huang, Jeffrey R. Shearstone, Simon S. Jones, Min Yang. Novel and selective inhibitors of histone deacetylases (HDAC) 1 and 2 significantly enhance the activity of the DNA methyltransferase inhibitor azacitidine in acute myeloid leukemia (AML). [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B84.
Fretting Fatigue Modeling and Repair Evaluation for Generator Rotors (2003)

Generator Rotor Tooth Cracks have been recently observed on some long service generator rotors. The purpose of this paper is to document the root cause analysis as well as a repair methodology that was developed in support of one of these cracked units. The paper discusses the development of a finite element model to understand the operating modes and failure mechanisms that caused the initiation of these cracks. The results of the analysis agreed very well with field observations on cracked units and with some limited repair options that have been successfully used in the past. An experimental fretting fatigue testing program is currently underway to substantiate and extend the results reported in this paper.
Visual servoing for automatic and uncalibrated needle placement for percutaneous procedures (2000)

This paper presents a new approach to image-based guidance of a needle or surgical tool during percutaneous procedures. The method is based on visual servoing. It requires no prior calibration or registration. The technique provides highly precise 3D-alignment of the tool with respect to an anatomic target. By taking advantage of projective geometry and projective invariants, this can be achieved in a fixed number (12) of iterations. In addition the approach estimates the required insertion depth. Experiments include automatic 3D alignment and insertion of a needle held by a medical robot into a pig kidney under X-ray fluoroscopy.
A New Continuum Robot With Crossed Elastic Strips: Extensible Sections With Only One Actuator per Section (2015)

We propose a new kind of continuum robot based on crossed elastic strips. The actuator-specified location of the crossover point controls the lengths of the sections, enabling a wider range of configurations than would be possible with traditional fixed-section-length robots. Push-pull actuation of the crossed strips controls the curvature of the sections. We provide a model that describes the resulting configurations in terms of tangent circular arcs of varying lengths. Experiments with a prototype yield tip positions that agree with model predictions with an average error of 4.6% of the robot’s length.
A Layered-Steered Space-Time Coded system with optimal power allocation (2010)

Layered Steered Space-Time Codes (LSSTC) is a recently proposed multiple-input multiple-output (MIMO) system that combines the benefits of vertical Bell Labs space-time (VBLAST) scheme, space-time block codes (STBC) and beamforming. We suggest a new downlink scheme employing LSSTC with optimal power allocation, by assuming that the user feeds the BS with the average SNR per VBLAST layer through the uplink feedback channel. The motivation behind proposing such a system is to enhance the error performance by assigning power to the layers in an optimum manner. We refer to the system proposed as the optimum power allocation LSSTC (OPA-LSSTC). We will show that the OPA-LSSTC can provide about a 3 dB gain compared to the equal power allocation case.
Impaired physiological responses to chronic hypoxia in mice partially deficient for hypoxia-inducible factor 1α (1999)

Chronic hypoxia induces polycythemia, pulmonary hypertension, right ventricular hypertrophy, and weight loss. Hypoxia-inducible factor 1 (HIF-1) activates transcription of genes encoding proteins that mediate adaptive responses to hypoxia, including erythropoietin, vascular endothelial growth factor, and glycolytic enzymes. Expression of the HIF-1alpha subunit increases exponentially as O2 concentration is decreased. Hif1a-/- mouse embryos with complete deficiency of HIF-1alpha due to homozygosity for a null allele at the Hif1a locus die at midgestation, with multiple cardiovascular malformations and mesenchymal cell death. Hif1a+/- heterozygotes develop normally and are indistinguishable from Hif1a+/+ wild-type littermates when maintained under normoxic conditions. In this study, the physiological responses of Hif1a+/- and Hif1a+/+ mice exposed to 10% O2 for one to six weeks were analyzed. Hif1a+/- mice demonstrated significantly delayed development of polycythemia, right ventricular hypertrophy, pulmonary hypertension, and pulmonary vascular remodeling and significantly greater weight loss compared with wild-type littermates. These results indicate that partial HIF-1alpha deficiency has significant effects on multiple systemic responses to chronic hypoxia.
Distributed, Automatic File Description Tuning in Peer-to-Peer File-Sharing Systems (2007)

Peers in peer-to-peer file-sharing systems cannot effectively share their files if they are poorly described. Terms one user employs to describe an instance of a file may not be those that are commonly associated with the file, making this instance difficult to locate. To alleviate this problem, a server can ask its peers for help in improving the description of files they have in common. We consider the design of a fully distributed, automatic system for the exchange of descriptive metadata. Experimental results show that the proposed techniques are effective in improving search accuracy with reasonable cost.
A novel bit and power allocation algorithm for duplex operation of DMT based DSL modems (2003)

DMT-based DSL modems allocate power and information bits for quadrature amplitude modulation of discrete tones in each DMT frame. The algorithms in the literature apply only to modems that operate in the simplex mode. This paper describes an algorithm that is suitable for echo cancelled duplex DMT-modems that use overlapping frequency bands for upstream and downstream transmissions. The algorithm minimizes the weighted sum of the power transmitted by the central office (CO) and the customer premise equipment or the remote terminal (RT) with the objective of reducing crosstalk at the CO. The paper also discusses how the algorithm can be used to determine echo canceller performance requirements.
NK cells specifically TCR-dressed to kill cancer cells (2019)

These results suggest that an NK cell line could be the basis for an off-the-shelf TCR-based cancer immunotherapy solution. FUND: This work was supported by the Research Council of Norway (#254817), South-Eastern Norway Regional Health Authority (#14/00500-79), by OUS-Radiumhospitalet (Gene Therapy program) and the department of Oncology at the University of Lausanne.
Modeling, measurement, and a simple analytic approximation for the return loss of erbium-doped fiber amplifiers (1995)

When fiber-optic systems contain erbium-doped fiber amplifiers (EDFA), reflections are enhanced by the gain of the amplifiers and can degrade system performance. We present a simple approximate analytic expression for the return loss of pumped EDFAs, with and without discrete reflections that applies at both the signal and pump wavelengths. A novel return loss measurement test set is used to verify the validity of this expression for a particular EDFA design. Using a computer simulation, the return loss is computed as a function of EDFA design to assess the range of validity of the approximate expression. The expression serves as an easy way to chain amplifiers and accurately predict the effects of reflections in long systems.
Shear Processing of Wood Chips into Feedstock Particles (2012)

We have an objective to convert cellulosic biomass raw materials into small particles that are optimized for biochemical and/or thermochemical conversion to liquid transportation fuels. As a side effort, we are interested in producing feedstocks for composite bioproducts, solid biofuels, and other uses. Wood chips that have a typical length of 50mm are a common raw material. This experiment seeks to evaluate the change in particle sieve analysis, geometric mean dimension, and particle shape as wood chips are processed through one or more rotary shear configurations as well as to determine the incremental specific energy consumption. Wood chips processed by two passes through a 4.8mm cutter set changed the geometric mean dimension from 26.4mm to 5.6mm at a total cost of less 30MJ/odt. Additional combinations are discussed.
Wearable brain imager/BMI technology for structural, vascular and functional extraction (2016)

Portable, low power, low-cost, flexible wearable Brain Machine Interfaces (BMIs) for real time brain imaging, with far higher potential spatial resolution than EEG, are being designed and prototyped using new chip architectures. Preliminary depth-indexed readings of real-time vascular and probable neural activity in the brain have been demonstrated using arrays of ultra-high dynamic range (160dB DANL) 1cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> Ultra Wide Band (UWB) pulser/antenna/sampler assemblies. These ICs generate 5-300ps pulses and detect the resulting reflections from brain tissue boundaries. They cancel out 1/f noise, and are sensitive enough to detect energy reflected from deep tissues, as well as the signal transmitted through even the longest dimensions of the head, and display vascular pulsation and, for the first time, rudimentary indications of functional brain activity.
A Small Molecule Inhibitor of the β-Catenin-TCF4 Interaction Suppresses Colorectal Cancer Growth In Vitro and In Vivo (2017)

Colorectal cancer is associated with aberrant activation of the Wnt pathway. β-Catenin plays essential roles in the Wnt pathway by interacting with T-cell factor 4 (TCF4) to transcribe oncogenes. We synthesized a small molecule, referred to as HI-B1, and evaluated signaling changes and biological consequences induced by the compound. HI-B1 inhibited β-catenin/TCF4 luciferase activity and preferentially caused apoptosis of cancer cells in which the survival is dependent on β-catenin. The formation of the β-catenin/TCF4 complex was disrupted by HI-B1 due to the direct interaction of HI-B1 with β-catenin. Colon cancer patient-derived xenograft (PDX) studies showed that a tumor with higher levels of β-catenin expression was more sensitive to HI-B1 treatment, compared to a tumor with lower expression levels of β-catenin. The different sensitivities of PDX tumors to HI-B1 were dependent on the β-catenin expression level and potentially could be further exploited for biomarker development and therapeutic applications against colon cancer.
Context Aware Road-user Importance Estimation (iCARE) (2019)

Road-users are a critical part of decision-making for both self-driving cars and driver assistance systems. Some road-users, however, are more important for decision-making than others because of their respective intentions, ego vehicle's intention and their effects on each other. In this paper, we propose a novel architecture for road-user importance estimation which takes advantage of the local and global context of the scene. For local context, the model exploits the appearance of the road users (which captures orientation, intention, etc.) and their location relative to ego-vehicle. The global context in our model is defined based on the feature map of the convolutional layer of the module which predicts the future path of the ego-vehicle and contains rich global information of the scene (e.g., infrastructure, road lanes, etc.), as well as the ego vehicle's intention information. Moreover, this paper introduces a new data set of real-world driving, concentrated around inter-sections and includes annotations of important road users. Systematic evaluations of our proposed method against several baselines show promising results.
The Introduction and Expression of Foreign Genes in Plants (1987)

(1987). The Introduction and Expression of Foreign Genes in Plants. Biotechnology and Genetic Engineering Reviews: Vol. 5, No. 1, pp. 81-106.
Engraftment of human iPS cells and allogeneic porcine cells into pigs with inactivated <i>RAG2</i> and accompanying severe combined immunodeficiency (2014)

Pigs with severe combined immunodeficiency (SCID) may provide useful models for regenerative medicine, xenotransplantation, and tumor development and will aid in developing therapies for human SCID patients. Using a reporter-guided transcription activator-like effector nuclease (TALEN) system, we generated targeted modifications of recombination activating gene (RAG) 2 in somatic cells at high efficiency, including some that affected both alleles. Somatic-cell nuclear transfer performed with the mutated cells produced pigs with RAG2 mutations without integrated exogenous DNA. Biallelically modified pigs either lacked a thymus or had one that was underdeveloped. Their splenic white pulp lacked B and T cells. Under a conventional housing environment, the biallelic RAG2 mutants manifested a "failure to thrive" phenotype, with signs of inflammation and apoptosis in the spleen compared with age-matched wild-type animals by the time they were 4 wk of age. Pigs raised in a clean environment were healthier and, following injection of human induced pluripotent stem cells (iPSCs), quickly developed mature teratomas representing all three germ layers. The pigs also tolerated grafts of allogeneic porcine trophoblast stem cells. These SCID pigs should have a variety of uses in transplantation biology.
Process for grinding coal or ores in a liquid medium. [grinding aids] (1978)

A process is described for grinding coal or ores containing metal values comprising carrying out said grinding in a liquid medium and with a grinding aid comprising sulfonated polystyrene or sulfonated polyvinyl toluene or an anionic polyelectrolyte derived therefrom and dispersible in the liquid medium, said grinding aid being present in an amount effective to provide increased grinding efficiency.
A novel coupling technique for end pumping solid-state lasers using 1-cm linear-aperture high-power laser diode bars (1990)

We present a simple and inexpensive optical system that can focus more than 80% of the output power of a laser diode bar with a 1 cm aperture into a spot smaller than 300 µ m in diameter for end pumping of solid-state lasers. The system uses off-the-shelf components and is particularly suitable for three- level laser systems.
Color images visible under UV light (2007)

The present contribution aims at creating color images printed with fluorescent inks that are only visible under UV light. The considered fluorescent inks absorb light in the UV wavelength range and reemit part of it in the visible wavelength range. In contrast to normal color printing which relies on the spectral absorption of light by the inks, at low concentration fluorescent inks behave additively, i.e. their light emission spectra sum up. We first analyze to which extent different fluorescent inks can be superposed. Due to the quenching effect, at high concentrations of the fluorescent molecules, the fluorescent effect diminishes. With an ink-jet printer capable of printing pixels at reduced dot sizes, we reduce the concentration of the individual fluorescent inks and are able to create from the blue, red and greenish-yellow inks the new colorants white and magenta. In order to avoid quenching effects, we propose a color halftoning method relying on diagonally oriented pre-computed screen dots, which are printed side by side. For gamut mapping and color separation, we create a 3D representation of the fluorescent ink gamut in CIELAB space by predicting halftone fluorescent emission spectra according to the spectral Neugebauer model. Thanks to gamut mapping and juxtaposed halftoning, we create color images, which are invisible under daylight and have, under UV light, a high resemblance with the original images.
Determining heterogeneous bottom friction distributions using a numerical wave model (2007)

This paper describes a method for estimating spatially variable bottom roughness lengths ( k b ) in friction‐dominated coastal regions where dense measurements of the significant wave height are available. The method utilizes a numerical wave model to calculate wavefields. The model‐predicted significant wave height is compared to a control simulation with a known k b field, which is a proxy for measured wave heights. The error is used in combination with an influence matrix to successively correct the bottom roughness field. This predictor‐corrector calculation is completed in a series of analysis cycles. The method is demonstrated in an idealized basin with different k b distributions. The test cases simulate swell propagating over a sloping beach. The original k b fields are recovered in a reasonable number of analysis cycles but the method is limited by the influence of bottom friction on the wave height. The inversion is shown to be robust in the presence of errors in the measured wavefield as well as random bathymetry errors. However, the inversion fails if bathymetry errors are large and/or systematic because the friction error is not substantially greater than the error from bathymetry, which is also a key parameter for calculating the wave height. Thus it is important to select parameters and variables that have well‐defined dependencies in the numerical wave model for this procedure to be effective.