gebhart/patrepeval huggingface dataset:
Ligand-dependent interaction of nuclear receptors with potential transcriptional intermediary factors (mediators) (1996)

The activity of the ligand-inducible activation function 2 (AF-2) contained in the ligand binding domain (LBD) of nuclear receptors (NRs) is thought to be mediated by transcriptional intermediary factors (TIFs). We have recently reported the isolation and characterization of two novel mouse proteins, designated TIF1 and mSUG1, that interact in a ligand-dependent fashion with the LBD (region E) of several NRs in vivo as well as in vitro. Remarkably, these interactions require the conserved core motif of the AF-2 activating domain (AF-2 AD) and can be blocked by AF-2 antagonists. TIF1 and mSUG1 might therefore represent TIFs/mediators for the ligand-dependent AF-2 of NRs. By comparing the interaction properties of these two putative TIFs with different NRs including the oestrogen (ER), thyroid hormone (TR), vitamin D3 (VDR), retinoic acid (RAR alpha) and retinoid X (RXR) receptors, we demonstrate that: (i) RXR alpha efficiently interacts with TIF1, but not with mSUG1, whereas TR alpha interacts much more efficiently with mSUG1 than with TIF1, and RAR alpha, VDR and ER efficiently interact with both TIF1 and mSUG1; (ii) the amphipathic alpha helix core of AF-2 AD is differentially involved in the interactions of RAR alpha with TIF1 and mSUG1; and (iii) the AF-2 AD cores of RAR alpha and ER are similarly involved in their interaction with TIF1, but not with mSUG1. Thus the interaction interfaces between the various NRs and either TIF1 or mSUG1 may vary depending on the nature of both the receptor and the putative mediator of its AF-2 function. We discuss the possible roles of TIF1 and mSUG1 as mediators of the transcriptional activity of the AF-2 of NRs.
Opportunities and Challenges for Compact Fusion Energy (2015)

AbstractThe realization of power from Magnetic Confinement Fusion is presently following a plan that will span several decades. The mainstream route is via ITER, combined with, or followed by, materials development on a Fusion Neutron Science Facility, then a DEMO reactor, which, as presently visualised, is considerably larger than ITER. We consider smaller-scale alternatives and developments which may make more rapid progress towards the much needed goal of economic, safe, clean fusion power, but still based on the tokamak.
Structure–Activity Relationship Studies of the Tricyclic Indoline Resistance-Modifying Agent (2014)

Previously we discovered a tricyclic indoline, N-[2-(6-bromo-4-methylidene-2,3,4,4a,9,9a-hexahydro-1H-carbazol-4a-yl)ethyl]-4-chlorobenzene-1-sulfonamide (1, Of1), from bioinspired synthesis of a highly diverse polycyclic indoline alkaloid library, that selectively resensitizes methicillin-resistant Staphylococcus aureus strains to β-lactam antibiotics. Herein, we report a thorough structure-activity relationship investigation of 1, which identified regions of 1 that tolerate modifications without compromising activity and afforded the discovery of a more potent analogue with reduced mammalian toxicity.
Ground reaction force control at each foot: A momentum-based humanoid balance controller for non-level and non-stationary ground (2010)

We present a novel momentum-based method for maintaining balance of humanoid robots. By controlling the desired ground reaction force (GRF) and center of pressure (CoP) at each support foot, our method can naturally deal with non-level and non-stationary ground at each foot-ground contact, as well as different frictional properties. We do not make use of the net GRF and CoP which may be difficult or impossible to compute for non-level grounds. Our method minimizes the ankle torques during double support. We show the effectiveness of this new balance control method by simulating various experiments with a humanoid robot including maintaining balance when two feet are on separate moving supports with different inclinations and velocities.
RPNet: A Representation Learning-Based Star Identification Algorithm (2019)

A novel star identification network (RPNet) based on representation learning is proposed in this paper. Unlike other pattern-based stars identification algorithms, the RPNet does not require the creation of an elaborate pattern, nor does it need to search among patterns. Instead, a star pattern generator (SPG) in the RPNet helps in finding the best pattern that can distinguish different stars clearly. A star pattern classifier (SPC) in the RPNet is utilized to recognize the pattern generated before. The simulations show that the RPNet is extremely robust toward star position noise, star magnitude noise, and false stars. The performance on simulation images outperforms almost all other pattern-based stars identification algorithms. On average, it achieves an identification rate of 99.23% in simulated star images. The identification rate on real star images is higher than 98%. Moreover, the algorithm achieves this performance with lesser memory and faster speed compared to polygon algorithms.
Efficient compression of non-manifold polygonal meshes (1999)

We present a method for compressing non-manifold polygonal meshes, i.e. polygonal meshes with singularities, which occur very frequently in the real-world. Most efficient polygonal compression methods currently available are restricted to a manifold mesh: they require a conversion process, and fail to retrieve the original model connectivity after decompression. The present method works by converting the original model to a manifold model, encoding the manifold model using an existing mesh compression technique, and clustering, or stitching together during the decompression process vertices that were duplicated earlier to faithfully recover the original connectivity. This paper focuses on efficiently encoding and decoding the stitching information. By separating connectivity from geometry and properties, the method avoids encoding vertices (and properties bound to vertices) multiple times; thus a reduction of the size of the bit-stream of about 10% is obtained compared with encoding the model as a manifold.
Development of a low profile acoustical door for use on racks and cabinets for the information technology industry (2005)

This paper presents the design of 19 inch rack acoustical doors balancing acoustical attenuation, airflow impedance and distribution in a short depth by combining air foil technology with acoustic baffle design. Design optimization was done utilizing fluid flow analytical modeling and verified with a air flow bench and an acoustical rack door test fixture. Higher heat loads in rack mounted computer equipment drive higher cooling requirements. In order to provide air cooling solutions, higher volumetric air flow is required resulting in higher acoustical noise levels. These noise levels can result in noise levels that are unacceptable to the customer. Acoustical doors lower noise levels but are prone to high flow impedance, uneven flow distribution and large physical depth. High impedances require higher air moving device speeds to offset the lost volumetric air flow. This decreases the effective acoustical attenuation. Various rack modules have different inlet and outlet air flow locations making the distribution of the air from the door (front) or into the door(rear) important. Solutions to these problems usually require large depths in order to provide blockage of line of site and gradual air flow lines to keep impedance low and provide even distribution of the air.
A rational framework for evaluating the next generation of vaccines against Mycobacterium avium subspecies paratuberculosis (2014)

Since the early 1980s, several investigations have focused on developing a vaccine against Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease in cattle and sheep. These studies used whole-cell inactivated vaccines that have proven useful in limiting disease progression, but have not prevented infection. In contrast, modified live vaccines that invoke a Th1 type immune response, may improve protection against infection. Spurred by recent advances in the ability to create defined knockouts in MAP, several independent laboratories have developed modified live vaccine candidates by transpositional mutation of virulence and metabolic genes in MAP. In order to accelerate the process of identification and comparative evaluation of the most promising modified live MAP vaccine candidates, members of a multi-institutional USDA-funded research consortium, the Johne's disease integrated program (JDIP), met to establish a standardized testing platform using agreed upon protocols. A total of 22 candidates vaccine strains developed in five independent laboratories in the United States and New Zealand voluntarily entered into a double blind stage gated trial pipeline. In Phase I, the survival characteristics of each candidate were determined in bovine macrophages. Attenuated strains moved to Phase II, where tissue colonization of C57/BL6 mice were evaluated in a challenge model. In Phase III, five promising candidates from Phase I and II were evaluated for their ability to reduce fecal shedding, tissue colonization and pathology in a baby goat challenge model. Formation of a multi-institutional consortium for vaccine strain evaluation has revealed insights for the implementation of vaccine trials for Johne's disease and other animal pathogens. We conclude by suggesting the best way forward based on this 3-phase trial experience and challenge the rationale for use of a macrophage-to-mouse-to native host pipeline for MAP vaccine development.
Process for production of hydrocarbon liquid from oil shale. [850/sup 0/ to 1250/sup 0/F] (1977)

A process for producing hydrocarbon liquids in preference to gases from oil shale is described. The shale is introduced at the top of a reaction chamber which includes an upper oil shale preheat zone having a temperature not more than about 950/sup 0/F, a hydroretort reaction zone at a temperature of about 850/sup 0/ to about 1250/sup 0/F, and a lower hydrogen preheat zone to recover heat from spent shale. Solids from the shale are passed downwardly through the chamber so that the shale, and particularly the oil therein, is gradually heated to the reaction temperature over a relatively extended period of at least ten minutes so as to inhibit the formation of a carbon residue. A hydrogen-rich gas, containing hydrogen in excess of stoichiometric amounts needed for the hydroretorting of the oil in the shale, is passed upwardly in the reaction chamber and countercurrent to the shale solids passing downwardly therethrough. A hydroretorting reaction is promoted in the reaction chamber between the oil or organic material in the shale and the hydrogen so as to produce predominately distillable hydrocarbon liquids and a low proportion of low molecular weight paraffinic hydrocarbon gases. The process can be controlled to maximize productionmore » of aliphatic and alicyclic hydrocarbon liquids which may be utilized for wide variety of purposes including gasification for the production of synthetic pipeline-quality gas from oil shale. 12 claims, 1 figure.« less
Expression of thyrotropin-releasing hormone receptor 2 (TRH-R2) in the central nervous system of rats (2000)

The distribution of the recently discovered thyrotropin-releasing hormone (TRH) receptor subtype TRH-R2 was studied in rat brain, pituitary, and spinal cord by in situ hybridization histochemistry and compared with the distribution patterns of the other elements of TRH signaling, namely TRH, TRH-R1, and the TRH-degrading ectoenzyme (TRH-DE). In contrast to the very restricted mRNA expression of TRH-R1 in the central nervous system, TRH-R2 mRNA was widely distributed with highest transcript levels throughout the thalamus, in the cerebral and cerebellar cortex, medial habenulae, medial geniculate nucleus, pontine nuclei, and throughout the reticular formation. In accordance with the well-known endocrine function of TRH, TRH-R1 is found predominantly expressed in hypothalamic regions. Expression of TRH-R1 in various brainstem nuclei and spinal cord motoneurons seems to be associated with the described effects of TRH on the vegetative and autonomic system as well as on the somatomotor system. Furthermore, the fully complementary expression of both receptor subtypes, even in regions where transcripts for both receptors were found (e.g., medial septum, lateral hypothalamus superior colliculi, substantia nigra, etc.), indicates that in discrete neuroanatomical pathways the two receptors serve highly specific functions for the transmission of TRH signals. Together with TRH-DE, the putative terminator of TRH actions that shows in various, but not all, brain areas, an overlapping mRNA distribution pattern with both receptors, the distribution of TRH-R2 mRNA seems to provide the anatomical basis for the described effects of TRH on higher cognitive functions as well as its effect on arousal, locomotor activity, and pain perception.
Optical and electrical properties of two-dimensional palladium diselenide (2019)

Two-dimensional (2D) noble-metal dichalcogenides exhibit exceptionally strong thickness-dependent bandgaps, which can be leveraged in a wide variety of device applications. A detailed study of their optical (e.g., optical bandgaps) and electrical properties (e.g., mobilities) is important in determining potential future applications of these materials. In this work, we perform detailed optical and electrical characterization of 2D PdSe2 nanoflakes mechanically exfoliated from a single-crystalline source. Layer-dependent bandgap analysis from optical absorption results indicates that this material is an indirect semiconductor with bandgaps of approximately 1.37 and 0.50 eV for the monolayer and bulk, respectively. Spectral photoresponse measurements further confirm these bandgap values. Moreover, temperature-dependent electrical measurements of a 6.8-nm-thick PdSe2 flake-based transistor show effective electron mobilities of 130 and 520 cm2 V−1 s−1 at 300 K and 77 K, respectively. Finally, we demonstrate that PdSe2 can be utilized for short-wave infrared photodetectors. A room-temperature specific detectivity (D*) of 1.8 × 1010 cm Hz1/2 W−1 at 1 μm with a band edge at 1.94 μm is achieved on a 6.8-nm-thick PdSe2 flake-based photodetector.
ERK Mutations Confer Resistance to Mitogen-Activated Protein Kinase Pathway Inhibitors (2014)

The use of targeted therapeutics directed against BRAF(V600)-mutant metastatic melanoma improves progression-free survival in many patients; however, acquired drug resistance remains a major medical challenge. By far, the most common clinical resistance mechanism involves reactivation of the MAPK (RAF/MEK/ERK) pathway by a variety of mechanisms. Thus, targeting ERK itself has emerged as an attractive therapeutic concept, and several ERK inhibitors have entered clinical trials. We sought to preemptively determine mutations in ERK1/2 that confer resistance to either ERK inhibitors or combined RAF/MEK inhibition in BRAF(V600)-mutant melanoma. Using a random mutagenesis screen, we identified multiple point mutations in ERK1 (MAPK3) and ERK2 (MAPK1) that could confer resistance to ERK or RAF/MEK inhibitors. ERK inhibitor-resistant alleles were sensitive to RAF/MEK inhibitors and vice versa, suggesting that the future development of alternating RAF/MEK and ERK inhibitor regimens might help circumvent resistance to these agents.
Method for making low-resistivity contacts to high <i>T</i> <i>c</i> superconductors (1988)

A method for making low-resistivity contacts to high Tc superconductors has been developed, which has achieved contact surface resistivities less than 10 μΩ cm2 at 76 K and does not require sample heating above ∼150 °C. This is an upper limit for the contact resistivity obtained at high current densities up to 102–103 A/cm2 across the contact interface. At lower measuring current densities the contact resistivities were lower and the voltage-current curve was nonlinear, having a superconducting transition character. On cooling from 295 to 76 K, the contact resistivity decreased several times, in contrast to indium solder contacts where the resistivity increased on cooling. The contacts showed consistently low resistivity and little degradation when exposed to dry air over a four-month period and when repeatedly cycled between room temperature and 76 K. The contacts are formed by sputter depositing a layer of a noble metal−silver and gold were used−on a clean superconductor surface to protect the surface and serve as a contact pad. External connections to the contact pads have been made using both solder and wire-bonding techniques.
Scanning slit delivery system (1989)

We describe the structure and function of a delivery system designed for use with an argon fluoride excimer laser for corneal surgery. The basic principle of the delivery system is to shape the laser beam with a slit mask to a defined configuration. The image of the slit is moved across the cornea in a mathematically defined pattern to ablate a given amount of tissue, creating a new anterior radius of curvature for the cornea. The location of the beam on the cornea is determined by a rotating dove prism and a translating spherical lens, each of which is controlled by computer-regulated servomotors. The system is versatile and can be used for laser myopic or hyperopic keratomileusis, for correction of astigmatism by surface ablation, for creation of radial or transverse linear cuts, for excision of corneal buttons, and for uniform lamellar corneal smoothing procedures. The delivery system is currently used in the laboratory for the ablation of nonhuman primate corneas.
Testing clock distribution circuits using an analytic signal method (2002)

This paper presents an application of a new analytic signal method for measuring clock skews in the clock distribution network of microprocessors. The method can measure skews between the master system clock and distributed clocks, between two distributed clocks, or between clocks whose frequencies are related by frequency division. Experimental data using a PowerPC/sup TM/ microprocessor is presented for validation.
Case-Based Reasoning: Predicting Real-Time Drilling Problems and Improving Drilling Performance (2011)

Abstract Over the past decade, oil and gas service companies have implemented real-time operations and remote surveillance centers to reduce the non-productive time (NPT) associated with wellbore integrity and downhole failures. Despite these efforts, NPT remains at around 15 to 35% of the total well cost. Companies seek to reduce NPT with knowledge management systems collecting best practices, knowledge cubes along the wellbore, and lessons learned. On the other hand, drilling activities are inherently data intensive, and as the amount of available data increases, it makes it correspondingly difficult for engineers to interpret the situation in a short period of time. Case-based reasoning (CBR) is a method that can use the real-time drilling data to index and automatically recall the various experiences that are now only available through dedicated knowledge management systems. Using this method, human experience can be collected in a company case base, linked to observed data, and automatically brought forward in real time when it is again relevant. In this paper, we introduce the CBR method and discuss some of the challenges in applying this method to drilling data. The DrillEdge computer system, based on this methodology is introduced, which uses the WITSML standard for drilling data acquisition, integration, and mass storage, making it possible to use in an integrated environment with current real-time operations and remote centers. It will also highlight the importance of a unique user interface to interpret the real-time results during drilling operations. An evaluation of the system was performed in which the system learned to recognize and, subsequently, predict problems when historical data from several land-drilling operations in Latin America were played back as simulations. A rigorous testing routine was applied to evaluate the capability of the CBR system to correctly identify potential risks and provide the user with remedial actions within a specified time-critical window.
New Prodrugs of the Antiprotozoal Drug Pentamidine (2011)

Pentamidine is an effective antimicrobial agent that is approved for the treatment of African trypanosomiasis but suffers from poor oral bioavailability and central nervous system (CNS) penetration. This work deals with the development and systematic characterisation of new prodrugs of pentamidine. For this reason, numerous prodrugs that use different prodrug principles were synthesised and examined in vitro and in vivo. Another objective of the study was the determination of permeability of the different pentamidine prodrugs. While some of the prodrug principles applied in this study are known, such as the conversion of the amidine functions into amidoximes or the O-alkylation of amidoximes with a carboxymethyl residue, others were developed more recently and are described here for the first time. These newly developed methods aim to increase the affinity of the prodrug for the transporters and mediate an active uptake via carrier systems by conjugation of amidoximes with compounds that improve the overall solubility of the prodrug. The different principles chosen resulted in several pentamidine prodrugs with various advantages. The objective of this investigation was the systematic characterisation and evaluation of eight pentamidine prodrugs in order to identify the most appropriate strategy to improve the properties of the parent drug. For this reason, all prodrugs were examined with respect to their solubility, stability, enzymatic activation, distribution, CNS delivery, and oral bioavailability. The results of this work have allowed reliable conclusions to be drawn regarding the best prodrug principle for the antiprotozoal drug pentamidine.
11.1: <i>Invited Paper</i> : Advances in Blue Phosphorescent Organic Light‐Emitting Devices (2006)

Abstract This paper discusses the latest developments towards a commercial blue phosphorescent organic light emitting device (PHOLED™) technology. Progress towards achieving a high efficiency, long‐lived saturated blue PHOLED is discussed. First, a high efficiency (20% EQE, 45 cd/A), light blue (0.17, 0.39) PHOLED is presented. Next, long‐lived blue PHOLEDs having chromaticity co‐ordinates (0.17, 0.38) and (0.16, 0.29) are estimated to degrade to half their initial luminance of 200cd/m 2 after >100,000 hrs and 17,500 hrs, respectively. Finally, results from PHOLEDs designed to increase blue color saturation and lifetime are presented.