gebhart/patrepeval huggingface dataset:
Adaptive inverse model control of pressure based ventilation (2001)

For the control of critical care ventilators, the problem of tracking a desired pressure trajectory within a patient connecting circuit is solved using indirect adaptive control. This control uses an inverse model of patient lung mechanics and the ventilator connecting circuit. Online estimates of physical parameters are provided using standard recursive least squares with forgetting factor. The indirect method achieves robust performance over a wide range of patient conditions, and also since physical estimates of respiratory parameters are available, they can be applied to diagnostics and/or additional control measures for ventilation. This control method has been applied to NPB 840 ventilator hardware in the loop using the real time simulation software, VisSim. Experimental results on mechanical test lungs show a large improvement in uniform tracking by the adaptive controller over classical PID control methods currently used throughout the ventilator industry.
Resilient virtual optical network provisioning over software-defined optical networks (2016)

Resiliency of the virtualization layer in software-defined optical networks is key for ondemand high-bandwidth services. We propose a resilient virtualization solution that can relax the reliability of physical optical nodes while providing highly-available services.
Abstract 3845: A novel selectivity determinant informs the development of next-generation stapled peptide inhibitors of anti-apoptotic BFL-1/A1 (2016)

Abstract The development of selective inhibitors for the individual anti-apoptotic BCL-2 family proteins implicated in oncogenesis and chemoresistance remains a formidable but pressing challenge. Precisely tailored compounds would serve as ideal molecular probes and targeted therapies to respectively study and treat human cancers driven by discrete apoptotic blockades. The remarkable potential of this strategy is exemplified by ABT-199, a potent and selective small molecule BCL-2 inhibitor that is proving effective at reactivating apoptosis in BCL-2-dependent cancers. The BCL-2 protein homologue, BFL-1/A1, has emerged as a resistance factor in a series of human cancers, including melanoma, leukemia, and lymphoma, but remains undrugged. To identify binding and specificity determinants for targeting BFL-1/A1, we screened a library of hydrocarbon-stapled BH3 domain helices and identified a subclass of compounds that engage BFL-1/A1 with exquisite selectivity in vitro and in situ. The mechanistic basis for this specificity revealed a unique topographic feature of the BFL-1/A1 binding groove. Leveraging this natural BFL-1/A1 selectivity factor, we designed next-generation stapled peptide inhibitors that block BFL-1/A1's capacity to both bind BH3 domains and suppress BAX-mediated membrane poration. Our studies inform a new pharmacologic strategy for potent and selective inhibition of anti-apoptotic BFL-1/A1 in human cancer. Citation Format: Annissa J. Huhn, Rachel M. Guerra, Gregory H. Bird, Loren D. Walensky. A novel selectivity determinant informs the development of next-generation stapled peptide inhibitors of anti-apoptotic BFL-1/A1. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3845.
New 4-(heteroanilido)piperidines, structurally related to the pure opioidagonist fentanyl, with agonist and/or antagonist properties (1989)

A research program based on certain heterocyclic modifications (12-50) of the fentanyl (1) molecule has generated a novel class of opioids. In the mouse hot-plate test, these compounds were weaker analgesics than 1. Two types of antagonists were observed in morphine-treated rabbits: those (e.g., 28) that reversed both respiratory depression and analgesia and those (e.g. 32) that selectively reversed respiratory depression. Evaluation of in vitro binding affinities to rat brain opioid receptors was inconclusive for a common locus of action for the agonist as well as the antagonist component. Further pharmacological evaluation of 32, N-(2-pyrazinyl)-N-(1-phenethyl-4-piperidinyl)-2-furamide, in the rat showed it to be a potent analgesic (ED50 = 0.07 mg/kg, tail-flick test) with little cardiovascular and respiratory depression when compared to fentanyl.
A novel tyrosine kinase inhibitor restores chondrocyte differentiation and promotes bone growth in a gain-of-function Fgfr3 mouse model (2011)

Activating germline fibroblast growth factor receptor 3 (FGFR3) mutations cause achondroplasia (ACH), the most common form of human dwarfism and a spectrum of skeletal dysplasias. FGFR3 is a tyrosine kinase receptor and constitutive FGFR3 activation impairs endochondral ossification and triggers severe disorganization of the cartilage with shortening of long bones. To decipher the role of FGFR3 in endochondral ossification, we analyzed the impact of a novel tyrosine kinase inhibitor (TKI), A31, on both human and mouse mutant FGFR3-expressing cells and on the skeleton of Fgfr3(Y367C/+) dwarf mice. We found that A31 inhibited constitutive FGFR3 phosphorylation and restored the size of embryonic dwarf femurs using an ex vivo culture system. The increase in length of the treated mutant femurs was 2.6 times more than for the wild-type. Premature cell cycle exit and defective chondrocyte differentiation were observed in the Fgfr3(Y367C/+) growth plate. A31 restored normal expression of cell cycle regulators (proliferating cell nuclear antigen, KI67, cyclin D1 and p57) and allowed pre-hypertrophic chondrocytes to properly differentiate into hypertrophic chondocytes. Our data reveal a specific role for FGFR3 in the cell cycle and chondrocyte differentiation and support the development of TKIs for the treatment of FGFR3-related chondrodysplasias.
Gap solitons and optical switching in axially uniform photonic crystal fibers (2004)

Through detailed computational experiments, and an analytical model, we describe the first axially uniform Kerr-nonlinear system that supports the existence of gap solitons.
High-Temperature Superconducting Homopolar Inductor Alternator for Marine Applications (2008)

This paper describes a high power density high-temperature superconducting (HTS) electric machine topology that is scalable for marine propulsion and power generation. The design, currently being pursued for airborne applications, is based on homopolar inductor alternator (HIA) technology, which is new within HTS applications. The basic machine design configuration of the HTS HIA is based on a stationary HTS field excitation coil, a solid rotor, and an advanced but conventional stator comprising liquid-cooled air-gap armature winding and an advanced iron core. High power density is obtained by the enhanced magneto-motive force capability of the HTS coil, the increased airgap flux density and armature current loading, and the high tip velocity of the rotor. Preliminary scaled up designs look attractive for three marine applications: propulsion drive, primary ship power generation, and power generation modules. The generators are driven directly by the turbines without the additional complexity of a clutch and gear system. A conceptual design study of a 36-MW 3600-r/min generator, a 4-MW 7000-r/min auxiliary generator, and a 36-MW 120-r/min and 4-MW 132-r/min propulsion motor are summarized.
White organic light emitting devices for general illumination (2003)

Organic light emitting devices (OLEDs) are potentially an efficient, general illumination, light source. We examine the different physical processes within the OLED and how each contributes to the light generation efficacy. We combine optical models of light transport, and experimental measurements to produce a map of a practical light source.
Potent Macrocyclic Inhibitors of the Hepatitis C Virus NS3 Protease Incorporating Cyclopentane and Cyclopentene Derived Scaffolds (2006)

Potent Macrocyclic Inhibitors of the Hepatitis C Virus NS3 Protease Incorporating Cyclopentane and Cyclopentene Derived Scaffolds
SRK, the stigma-specific S locus receptor kinase of Brassica, is targeted to the plasma membrane in transgenic tobacco. (1996)

The S locus receptor kinase (SRK) gene is one of two S locus genes required for the self-incompatibility response in Brassica. We have identified the product of the SRK6 gene in B. oleracea stigmas and have shown that it has characteristics of an integral membrane protein. When expressed in transgenic tobacco, SRK6 is glycosylated and targeted to the plasma membrane. These results provide definitive biochemical evidence for the existence in plants of a plasma membrane-localized transmembrane protein kinase with a known cell-cell recognition function. The timing of SRK expression in stigmas follows a time course similar to that previously described for another S locus-linked gene, the S locus glycoprotein (SLG) gene, and correlates with the ability of stigmas to mount a self-incompatibility response. Based on SRK6 promoter studies, the site of gene expression overlaps with that of SLG and exhibits predominant expression in the stigmatic papillar cells. Although reporter gene studies indicated that the SRK promoter was active in pollen, SRK protein was not detected in pollen, suggesting that SRK functions as a cell surface receptor exclusively in the papillar cells of the stigma.
Dynamics and Control of Spacecraft With a Generalized Model of Variable Speed Control Moment Gyroscopes (2015)

The attitude dynamics model for a spacecraft with a variable speed control moment gyroscope (VSCMG) is derived using the principles of variational mechanics. The resulting dynamics model is obtained in the framework of geometric mechanics, relaxing some of the assumptions made in prior literature on control moment gyroscopes (CMGs). These assumptions include symmetry of the rotor and gimbal structure, and no offset between the centers of mass of the gimbal and the rotor. The dynamics equations show the complex nonlinear coupling between the internal degrees-of-freedom associated with the VSCMG and the spacecraft base body's rotational degrees-of-freedom. This dynamics model is then further generalized to include the effects of multiple VSCMGs placed in the spacecraft base body, and sufficient conditions for nonsingular VSCMG configurations are obtained. General ideas on control of the angular momentum of the spacecraft using changes in the momentum variables of a finite number of VSCMGs are provided. A control scheme using a finite number of VSCMGs for attitude stabilization maneuvers in the absence of external torques and when the total angular momentum of the spacecraft is zero is presented. The dynamics model of the spacecraft with a finite number of VSCMGs is then simplified under the assumptions that there is no offset between the centers of mass of the rotor and gimbal, and the rotor is axisymmetric. As an example, the case of three VSCMGs with axisymmetric rotors, placed in a tetrahedron configuration inside the spacecraft, is considered. The control scheme is then numerically implemented using a geometric variational integrator (GVI). Numerical simulation results with zero and nonzero rotor offset between centers of mass of gimbal and rotor are presented.
Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution (2011)

Directed evolution is a valuable technique to improve enzyme activity in the absence of a priori structural knowledge, which can be typically enhanced via structure-guided strategies. In this study, a combination of both whole-gene error-prone polymerase chain reaction and site-saturation mutagenesis enabled the rapid identification of mutations that improved RmlA activity toward non-native substrates. These mutations have been shown to improve activities over 10-fold for several targeted substrates, including non-native pyrimidine- and purine-based NTPs as well as non-native D- and L-sugars (both α- and β-isomers). This study highlights the first broadly applicable high throughput sugar-1-phosphate nucleotidyltransferase screen and the first proof of concept for the directed evolution of this enzyme class toward the identification of uniquely permissive RmlA variants.
Accelerated Adsorption with Activated Carbon Fiber (1995)

Abstract The properties of a new type of polyamphoteric activated carbon fiber (ACF) were investigated theoretically and experimentally. Results are compared with those from granular activated carbon (GAC) and ion-exchange resin (IER) materials. The adsorption rate of ACF was found to be two orders of magnitude higher than that of the GAC and one order of magnitude higher than that of the IER.
Inheritance of Three Stearic Acid Mutants of Soybean<sup>1</sup> (1985)

Three mutant lines of soybean [ Glycine max (L.) Merrill] were identified that had three‐ to six‐fold increases in stearic acid content in the seed oil compared with their parents. Our objective was to determine the inheritance of high stearic acid in the three mutants. Reciprocal crosses were made between each mutant and its parent and among the three mutants. Fatty acid analysis of the seed oil of the parents and the F 1 , F 2 , and F 3 generations indicated that high stearic acid in the mutants was controlled by a single locus. The Fas allele for low stearic acid in each parent was partially dominant to the allele for high stearic acid in the mutant derived from it. Crosses among the mutants indicated that each possessed a different allele at the same locus. The allele fas a , in the mutant A6, and fas 6 , in the mutant FA41545, were not dominant to each other. Both fas a and fas b were completely dominant to thefas allele in the mutant A81‐606085. None of the segregates from the mutant ✕ mutant crosses had a stearic acid content outside the range of the parents. Maternal and cytoplasmic effects were not important in the control of stearic acid content in these mutants.
Lexical Image Processing (2008)

Current color image encoding and processing generally considers the color value of a pixel based on a quantized set of coordinates in an n-dimensional color space. While this approach is useful and practical for numerous reasons, it is informative to consider how these representations and processing techniques might make use of the highest level cognitive description of color, the color name or color category. This paper proposes how a lexical or name-based representation of an image might be generated. Color naming algorithms based on classical logic, prototype theory and fuzzy logic are presented and compared. This paper also describes specific applications of this lexical quantization such as morpholexical analysis, lexical harmony and non-photorealistic rendering.
Neutralization of the infectivity of sporozoites of Plasmodium knowlesi by antibodies to a synthetic peptide. (1984)

Antibodies against a synthetic peptide representing the repetitive epitope of the circumsporozoite protein (CS) of Plasmodium knowlesi have properties similar to those of antibodies against the native protein. Either antibody reacts with the synthetic peptide, cross-links the CS protein on the membrane of the parasite giving the CSP reaction, and neutralizes the infectivity of sporozoites. The synthetic peptide and sporozoite extracts were equally effective when used in an immunoradiometric assay as antigens to detect antibodies to CS proteins. It is likely that the corresponding synthetic repeats from the human malaria parasites could be used to measure levels of anti-sporozoite antibodies in endemic areas, or to evaluate the humoral response to anti-sporozoite vaccines. The authors are grateful to Dr. Robert Gwadz, NIH, for supplying Anopheles mosquitoes and P. knowlesi sporozoites used in this study.
High thrust-to-power ratio micro-cathode arc thruster (2016)

The Micro-Cathode Arc Thruster (μCAT) is an electric propulsion device that ablates solid cathode material, through an electrical vacuum arc discharge, to create plasma and ultimately produce thrust in the μN to mN range. About 90% of the arc discharge current is conducted by electrons, which go toward heating the anode and contribute very little to thrust, with only the remaining 10% going toward thrust in the form of ion current. A preliminary set of experiments were conducted to show that, at the same power level, thrust may increase by utilizing an ablative anode. It was shown that ablative anode particles were found on a collection plate, compared to no particles from a non-ablative anode, while another experiment showed an increase in ion-to-arc current by approximately 40% at low frequencies compared to the non-ablative anode. Utilizing anode ablation leads to an increase in thrust-to-power ratio in the case of the μCAT.
The plastid DNA of the malaria parasite <i>Plasmodium falciparum</i> is replicated by two mechanisms (2002)

In common with other apicomplexan parasites, Plasmodium falciparum, a causative organism of human malaria, harbours a residual plastid derived from an ancient secondary endosymbiotic acquisition of an alga. The function of the 35 kb plastid genome is unknown, but its evolutionary origin and genetic content make it a likely target for chemotherapy. Pulsed field gel electrophoresis and ionizing radiation have shown that essentially all the plastid DNA comprises covalently closed circular monomers, together with a tiny minority of linear 35 kb molecules. Using two-dimensional gels and electron microscopy, two replication mechanisms have been revealed. One, sensitive to the topoisomerase inhibitor ciprofloxacin, appears to initiate at twin D-loops located in a large inverted repeat carrying duplicated rRNA and tRNA genes, whereas the second, less drug sensitive, probably involves rolling circles that initiate outside the inverted repeat.
Reversible and Irreversible Chemisorption in Nonporous‐Crystalline Hybrids (2013)

The tools of synthetic chemistry allow us to fine-tune the reactivity of molecules at a level of precision not yet accessible with inorganic solids. We have investigated hybrids that couple molecules to the superior thermal and mechanical properties of solids. Herein we present, to the best of our knowledge, the first demonstration of reactivity between hybrid perovskites and substrates. Reaction with iodine vapor results in a remarkable expansion of these materials (up to 36 % in volume) where new covalent CI bonds are formed with retention of crystallinity. These hybrids also show unusual examples of reversible chemisorption. Here, solid-state interactions extend the lifetime of molecules that cannot be isolated in solution. We have tuned the half-lives of the iodinated structures from 3 h to 3 days. These nonporous hybrids drive substrate capture and controlled release through chemical reactivity. We illustrate the strengths of the hybrid by considering radioactive iodine capture.
Reprogramming cell fate with artificial transcription factors (2018)

Transcription factors (TFs) reprogram cell states by exerting control over gene regulatory networks and the epigenetic landscape of a cell. Artificial transcription factors (ATFs) are designer regulatory proteins comprised of modular units that can be customized to overcome challenges faced by natural TFs in establishing and maintaining desired cell states. Decades of research on DNA-binding proteins and synthetic molecules has provided a molecular toolkit for ATF design and the construction of genome-scale libraries of ATFs capable of phenotypic manipulation and reprogramming of cell states. Here, we compare the unique strengths and limitations of different ATF platforms, highlight the advantages of cooperative assembly, and present the potential of ATF libraries in revealing gene regulatory networks that govern cell fate choices.
Mutation of a putative protein degradation gene LITAF/SIMPLE in Charcot-Marie-Tooth disease 1C (2003)

Mutations in LITAF may account for a significant proportion of CMT1 patients with previously unknown molecular diagnosis and may define a new mechanism of peripheral nerve perturbation leading to demyelinating neuropathy.
Glycation pattern of peptides condensed with maltose, lactose and glucose determined by ultraviolet matrix‐assisted laser desorption/ionization tandem mass spectrometry (2010)

Protein glycation is the non-enzymatic condensation of sugars with proteins. Although commonly occurring in both the therapeutic and food/beverage industries, protein glycation has not been the focus of many proteomic investigations. This study aims to establish a reliable mass spectrometric method for screening large tandem mass spectrometric (MSMS) datasets for protein glycation with glucose, lactose and maltose. Control experiments using a standard peptide containing a single glycation site led to the discovery of characteristic neutral loss fragmentation patterns in MSMS analysis for glucose, lactose and maltose condensed with peptides. Valid in both tandem time-of-flight (TOFTOF) and quadrupole ion trap time-of-flight matrix-assisted laser desorption/ionization (QIT TOF MALDI) mass spectrometers, these neutral loss signatures were then applied to elucidation of modified peptides from a complex human serum albumin (HSA) digest glycated with each of the proposed sugars. Screening of these large datasets was made possible by specifically designed software solutions that enable the input of detailed user-defined post-translational modifications that are not included in the universally available databases such as Unimod.
Real-time multiple sound source localization using a circular microphone array based on single-source confidence measures (2012)

We propose a novel real-time adaptative localization approach for multiple sources using a circular array, in order to suppress the localization ambiguities faced with linear arrays, and assuming a weak sound source sparsity which is derived from blind source separation methods. Our proposed method performs very well both in simulations and in real conditions at 50% real-time.
Vacuum-Arc Evaporator of Metals with an Extended Planar Cathode (1998)

A Vacuum arc evaporator with an extended planar cathode is described. The cathode is 30 mm thick by 120 mm wide by 750 mm long. The directed motion of the cathode spot occurs under the action of a transverse magnetic field generated by the arc discharge current traversing the cathode towards one of its current leads. The spot position is controlled by the system including a cathode spot position sensor and an electronic magnetic-field control unit. The system provides the programmed control over the zone of cathode spot drift along the cathode. This allows coating deposition onto the substrate with a prescribed thickness distribution in the coordinate parallel to longitudinal axis of the evaporator. The principle of operation of the evaporator imposes no restrictions on the cathode length.