gebhart/patrepeval huggingface dataset:
Adaptive architectures for control of uncertain dynamical systems with actuator and unmodeled dynamics (2019)

Summary In adaptive control of uncertain dynamical systems, it is well known that the presence of actuator and/or unmodeled dynamics in feedback loops can yield to unstable closed‐loop system trajectories. Motivated by this standpoint, this paper focuses on the analysis and synthesis of multiple adaptive architectures for control of uncertain dynamical systems with both actuator and unmodeled dynamics. Specifically, we first analyze model reference adaptive control architectures with standard, hedging‐based, and expanded reference models for this class of uncertain dynamical systems and develop sufficient stability conditions. We then synthesize a robustifying term for the latter architecture and analytically show that this term can allow for a relaxed sufficient stability condition. The proposed theoretical treatments involve Lyapunov stability theory, linear matrix inequalities, and matrix mathematics. Finally, we compare the resulting sufficient stability conditions of the considered adaptive control architectures on a benchmark mechanical system subject to actuator and unmodeled dynamics.
The process of designing and developing spliceostatin class of splicing inhibitors as payloads for antibody drug conjugates (2015)

The natural product FR901464 (1), spliceostatin C (2) and thailanstatin (3), are ultrapotent inhibitors of eukaryotic RNA splicing, via binding to the SF3b subunit of the U2 snRNA subcomplex, an essential component of the spliceosome. Manipulation of the biosynthetic genes that control production of these analogs in the bacteria have allowed us to generate sufficient material for a medicinal chemistry approach to evaluating this mechanistic class as potential payloads for antibody drug conjugates (ADCs). This oral presentation will detail some successful ways to leverage spliceostatin analogs to generate potent and efficacious ADCs for the treatment of cancer.
Fast Sparse Superposition Codes Have Near Exponential Error Probability for <formula formulatype="inline"><tex Notation="TeX">$R&lt;{\cal C}$</tex></formula> (2013)

For the additive white Gaussian noise channel with average codeword power constraint, sparse superposition codes are developed. These codes are based on the statistical high-dimensional regression framework. In a previous paper, we investigated decoding using the optimal maximum-likelihood decoding scheme. Here, a fast decoding algorithm, called the adaptive successive decoder, is developed. For any rate R less than the capacity C, communication is shown to be reliable with nearly exponentially small error probability. Specifically, for blocklength n, it is shown that the error probability is exponentially small in n/logn.
2nd generation anti-HIV designer T cells cure HIV-infected cultures and preferentially survive versus 1st generation designer T cells (52.19) (2010)

Abstract Immunotherapies that have the potential to eradicate reservoirs of HIV infected cells may be useful to suppress or cure HIV/AIDS. T cells expressing chimeric immune receptors (CIR) through gene modification (designer T cells) can be redirected to kill HIV-infected cells. Previously, an anti-HIV CIR, CD4ζ (1st generation), was created to kill HIV+ cells. However, the adoptive transfer of autologous CD4ζ T cells failed to control the viral infection in clinical trials. We created a 2nd generation CIR for enhanced potency by providing co-stimulatory signal (CD4CD28ζ). Our data show that both 1st and 2nd generation CIRs expressed well on retrovirally transduced human T cells and kill HIV+ targets with high efficiency, whereas CD28 in the CIR confers a distinct advantage in the expansion potential and cytokine IL2 secretion. Interestingly, our preliminary data show that all 1st generation designer T cells died in 7 days when co-cultured with HIV+ cells, whereas 2nd generation designer T cells survived with cure of the infected cultures. This stunning result shows dramatic benefit in the new 2nd generation CIR versus the 1st generation that was used in human clinical trials. We are presently exploring whether this cell death in the 1st generation designer T cells is due to heightened sensitivity to AICD and/or due to HIV infection. Either way, these data show a striking benefit to our new 2nd generation designer T cells as a promising therapy for HIV/AIDS.
Synthesis of the (Dialkylamino)borate, [Ph<sub>2</sub>B(CH<sub>2</sub>NMe<sub>2</sub>)<sub>2</sub>]<sup>-</sup>, Affords Access to N-Chelated Rhodium(I) Zwitterions (2002)

This paper reports the synthesis of the first bis(amino)borate ligand, [Ph(2)B(CH(2)NMe(2))(2)](-), an anionic equivalent of tertiary diamines. Anionic [Ph(2)B(CH(2)NMe(2))(2)] is an excellent bidentate ligand auxiliary and is used to prepare a series of N-chelated, zwitterionic rhodium(I) complexes.
A study of design and production process for hand exoskeleton device to be fitted on to individual patients (2016)

In the authors' earlier study, we presented a hand exoskeleton device using layered spring blades. The advantages of the presented mechanism are compact, lightweight and high adaptability to various objects thanks to the compliant structure. In this paper, we considered the design and production process of the hand exoskeleton device to be fitted on to individual patients.
Gramicidin A Mutants with Antibiotic Activity against Both Gram‐Positive and Gram‐Negative Bacteria (2016)

Antimicrobial peptides (AMPs) have shown potential as alternatives to traditional antibiotics for fighting infections caused by antibiotic-resistant bacteria. One promising example of this is gramicidin A (gA). In its wild-type sequence, gA is active by permeating the plasma membrane of Gram-positive bacteria. However, gA is toxic to human red blood cells at similar concentrations to those required for it to exert its antimicrobial effects. Installing cationic side chains into gA has been shown to lower its hemolytic activity while maintaining the antimicrobial potency. In this study, we present the synthesis and the antibiotic activity of a new series of gA mutants that display cationic side chains. Specifically, by synthesizing alkylated lysine derivatives through reductive amination, we were able to create a broad selection of structures with varied activities towards Staphylococcus aureus and methicillin-resistant S. aureus (MRSA). Importantly, some of the new mutants were observed to have an unprecedented activity towards important Gram-negative pathogens, including Escherichia coli, Klebsiella pneumoniae and Psuedomonas aeruginosa.
Mechanistic considerations of the pyrolytic formation of metal boride thin films by chemical vapor deposition from borane precursors (1995)

The formation of metal boride thin films by CVD is an area of potentially significant technological consequence. Interest in these materials is primarily due to their breadth of unique physical properties and to their wide structural diversity. Recently, we have explored the use of a number of boron-containing CVC precursors to prepare a wide variety of both pure metal and metal boride thin film materials. The highly efficient formation of polycrystalline transition metal and lanthanide metal boride thin films from borane precursors has now been well demonstrated through this CVD chemistry. The fundamentally important chemical processes and reactions in the CVD of boranes in forming metal boride films has, however, remained mostly a mystery. In order to rationally design new precursors and tailor the deposited solid state materials, an understanding of these fundamental processes is critical. In our recent work, which will be reported here, we have begun detailed mechanistic studies into the CVD of metal borides. These reactions have been found to occur both in the gas phase and on the surface of the reactor. A variety of studies have provided valuable insights into these complexes chemical reactions including labeling, thermal, product distribution, surface analysis, kinetic and other investigations.
Transverse Relaxation-Optimized Spectroscopy (TROSY) for NMR Studies of Aromatic Spin Systems in <sup>13</sup>C-Labeled Proteins (1998)

Transverse relaxation-optimized spectroscopy (TROSY) yields greatly improved sensitivity for multidimensional NMR experiments with aromatic spin systems in proteins. TROSY makes use of the fact that due to the large anisotropy of the 13C chemical shift tensor, the transverse relaxation of one component of the 13C doublet in aromatic 13C−1H moieties is reduced by interference of dipole−dipole (DD) coupling and chemical shift anisotropy (CSA) relaxation. The full advantage of TROSY for studies of aromatic spin systems is obtained at presently available resonance frequencies from 500 to 800 MHz. Since the 13C chemical shifts are recorded using a constant-time evolution period, the TROSY improvement in signal-to-noise relative to corresponding conventional NMR experiments increases with increasing molecular size and can be further significantly enhanced by combined use of the 1H and 13C steady-state magnetizations.With selective observation of the slowly relaxing component of the 13C doublets in experiments recorded without 1H decoupling during the 13C chemical shift evolution period, a 4−10-fold sensitivity gain for individual aromatic 13C−1H correlation peaks was achieved for the uniformly 13C-labeled 18 kDa protein cyclophilin A. A new 3D ct-TROSY-HCCH-COSY experiment is presented, which correlates the resonances of 13C nuclei with those of covalently bound 13C−1H groups and can be applied for complete identification of aromatic spin systems. In this scheme the chemical shift evolution of neighboring aromatic 13C spins are recorded in two indirectly detected spectral dimensions, so that the additional third dimension is obtained without increase of the number of delays.
Transmission of eight 20-Gb/s channels over 232 km of conventional single-mode fiber (1995)

As a demonstration of the upgradeability of conventional single-mode fiber systems, we demonstrate the transmission of eight 20-Gb/s channels over 232 km of nondispersion-shifted fiber using dispersion-compensating fiber with negative dispersion-slope. All channels were received without discernible transmission penalties. Due to fiber nonlinearity, differences were observed in system performance depending on the arrangement of the fibers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Wear Properties and Life Prediction of Frictional Materials for Ultrasonic Motors (1995)

The characteristics and life of an ultrasonic motor are strongly related to the frictional material used on the sliding surface, because the motor is driven by frictional force and its life is limited to that of the frictional material. Hence wear evaluation of the frictional material is necessary for life prediction of the ultrasonic motor. In this experiment, the wear of carbon-fiber-reinforced plastics (CFRP) used as frictional material in ultrasonic motors is evaluated. The specific wear rate is derived from a simple wear test and is applied to estimate the wear of the CFRP used in the ultrasonic motor. The life of the ultrasonic motor, as well as that of frictional material, can be estimated using the equation derived from the experiment.
A model predictive control strategy for supply chain management in semiconductor manufacturing under uncertainty (2004)

Model predictive control (MPC) is presented as a tactical decision module for supply chain management in semiconductor manufacturing. A representative problem which includes distinguishing features of semiconductor manufacturing supply chains, such as material reconfiguration and stochastic product splits, is examined. Fluid analogies are used to model the supply chain dynamics, with stochasticity and nonlinearity occurring on the throughput time, yield and customer demand. Given inventory targets and capacity limits, MPC using linear time invariant models can make the system outputs track the targets and improve customer service levels. The flexibility provided by the choice of tuning parameters in MPC to achieve better performance and robustness in semiconductor manufacturing supply chain management is demonstrated.
Liquid fuel conversion using gliding discharge in Tornado for direct use in solid oxide fuel cells (2008)

Conversion of liquid hydrocarbon fuels to produce synthesis gas using non-equilibrium gliding discharges is performed using a reverse vortex flow ("tornado") reactor. Part of the integrated system is plasma reformer, which utilizes syngas (CO + H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) for direct use in a solid oxide fuel cell for onboard conversion liquid fuels into electricity. This integrated system can be an advance power generator that can be used in remote areas where only hydrocarbon fuel sources are available and have potential military applications.
Nuclear Magnetic Resonance (NMR) Cylindrical Blood Flowmeter (1980)

In vitro tests were performed to evaluate a single-sideband crossedcoil cylindrical NMR flowmeter, for the noninvasive measurement of arterial flow rates through a cross-section of human limbs. The output signals from the NMR flowmeter, a Doppler ultrasound velocimeter, and an electromagnetic (EM) flowmeter were comparable. The frequency response showed an upper frequency 3db roll-off point of 2.1 Hz (126 pulses per minute). The relationship between the NMR peak-to-peak output voltage and pak-flow was linear in the range of physiological flow. Calibration in the linear region was essentially independent of tube positioning and tube cross section. The instrument detected flow bidirectionally, but gave a 2 times greater output voltage in the preferential direction. The NMR flowmeter is appropriate to estimate average flow rates with the human subject at rest. This NMR flowmeter is a contactless instrument, and flows can be measured unimpaired by clothing, bandages or cast.
A comprehensive security architecture for dynamic, web service based virtual organizations for businesses (2006)

In this paper we propose a security architecture for Virtual Organizations for businesses. The Virtual Organizations we consider are based on web servicetechnology, and are dynamic, i.e. their membership may change frequently throughout its lifetime. The security architecture advances over previous approaches with a new approach for distributed administration based on policy generation which allows local security administrators to remain in complete control over the policies deployed. We show the advantages of our architecture in the case of member replacement.
ELECTRICAL RESISTANCE TOMOGRAPHY (2000)

This report covers the electrical resistance tomography (ERT) work performed at the Hanford Reservation, 200 East Area Vadose test (Sisson and Lu) site during the period March 23 through May 5, 2001. The purposes of the ERT work were to: (1) compare and contrast the development of the highly concentrated sodium thio-sulfate plume (FY01 work) with the fresh river water plume observed during FY00; (2) use the resistance images to infer the dynamics of the plume during two or three of the sodium thiosulfate releases and during the water ''chaser'' release; (3) determine the influence of the site's steel casings on the capability to construct reliable ERT images; (4) determine if the steel casings at the site can be used as long electrodes to provide useful images of at least one release; and (5) develop quantitative estimates of the noise in the data and its effect on reconstructed images.
Improving cold storage and processing traits in potato through targeted gene knockout (2015)

Cold storage of potato tubers is commonly used to reduce sprouting and extend postharvest shelf life. However, cold temperature stimulates the accumulation of reducing sugars in potato tubers. Upon high-temperature processing, these reducing sugars react with free amino acids, resulting in brown, bitter-tasting products and elevated levels of acrylamide--a potential carcinogen. To minimize the accumulation of reducing sugars, RNA interference (RNAi) technology was used to silence the vacuolar invertase gene (VInv), which encodes a protein that breaks down sucrose to glucose and fructose. Because RNAi often results in incomplete gene silencing and requires the plant to be transgenic, here we used transcription activator-like effector nucleases (TALENs) to knockout VInv within the commercial potato variety, Ranger Russet. We isolated 18 plants containing mutations in at least one VInv allele, and five of these plants had mutations in all VInv alleles. Tubers from full VInv-knockout plants had undetectable levels of reducing sugars, and processed chips contained reduced levels of acrylamide and were lightly coloured. Furthermore, seven of the 18 modified plant lines appeared to contain no TALEN DNA insertions in the potato genome. These results provide a framework for using TALENs to quickly improve traits in commercially relevant autotetraploid potato lines.
Comparison of intracytoplasmic sperm injection for inbred and hybrid mice (2001)

We compared the results of intracytoplasmic sperm injection (ICSI) that leads to full term development of hybrid (B6C3F1 and B6D2F1) and inbred (C57BL/6) mouse embryos. Although fertilization and pre-implantation development of C57BL/6 eggs were similar to those of F1 hybrid eggs, post-implantation development of the embryos from C57BL/6 females was significantly poorer than those of the eggs from hybrid females. Reciprocal crosses of C57BL/6 and B6C3F1 gametes revealed that the low rate of post-implantation development of C57BL/6 embryos was due to oocyte factor(s), rather than the sperm factor.
A Systematic Approach for Model-Based Aircraft Engine Performance Estimation (2009)

A requirement for effective aircraft engine performance estimation is the ability to account for engine degradation, generally described in terms of unmeasurable health parameters such as efficiencies and flow capacities related to each major engine module. This paper presents a linear point design methodology for minimizing the degradation-induced error in model-based aircraft engine performance estimation applications. The technique specifically focuses on the underdetermined estimation problem, where there are more unknown health parameters than available sensor measurements. A condition for Kalman filter-based estimation is that the number of health parameters estimated cannot exceed the number of sensed measurements. In this paper, the estimated health parameter vector will be replaced by a reduced order tuner vector whose dimension is equivalent to the sensed measurement vector. The reduced order tuner vector is systematically selected to minimize the theoretical mean squared estimation error of a maximum a posteriori estimator formulation. This paper derives theoretical estimation errors at steady-state operating conditions, and presents the tuner selection routine applied to minimize these values. Results from the application of the technique to an aircraft engine simulation are presented and compared to the estimation accuracy achieved through conventional maximum a posteriori and Kalman filter estimation approaches. Maximum a posteriori estimation results demonstrate that reduced order tuning parameter vectors can be found that approximate the accuracy of estimating all health parameters directly. Kalman filter estimation results based on the same reduced order tuning parameter vectors demonstrate that significantly improved estimation accuracy can be achieved over the conventional approach of selecting a subset of health parameters to serve as the tuner vector. However, additional development is necessary to fully extend the methodology to Kalman filter-based estimation applications.
Penicillin‐Derived Inhibitors that Simultaneously Target both Metallo‐ and Serine‐β‐lactamases (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Developmental expression of the mitochondrial pyruvate dehydrogenase complex in pea (<i>Pisum sativum</i>) seedlings (2001)

In order to better understand control of the mitochondrial pyruvate dehydrogenase complex (PDC), total catalytic activity was determined during development of the primary leaves of pea (Pisum sativum L.) seedlings, as well as in each leaf pair of 21-day-old plants. Activity of the PDC in clarified homogenates was highest in the youngest organs and then dropped dramatically as the leaves matured and became photosynthetically competent. As leaves began to senesce, total PDC activity dropped to zero. Steady-state mRNA levels were determined using E1 and E3 cDNA probes. The overall pattern of transcript abundance matched the pattern observed for total PDC activity; transcript levels for E1alpha and E1beta approached zero during senescence. Levels of the E1alpha, E1beta, E2 and E3 subunits of the PDC were analyzed in the same samples, using specific antibodies. Quantitation of the immunoblotting results throughout this developmental series showed a pattern in parallel with that of catalytic activity and mRNA levels, although the relative changes in subunit protein levels were not as extreme as the changes in activity. The exception to the global pattern was that of the E3 subunit: lipoamide dehydrogenase. Expression of this enzyme was highest in mature, fully expanded leaves, which were active in photosynthesis and photorespiration, reflecting the additional role of E3 as a component of glycine decarboxylase.
Abstract 1753: Transcriptomic based Biomarkers Contain Diagnostic and Prognostic Information about Patients with new onset Heart Failure (2007)

INTRODUCTION: One of the clinical dilemmas in cardiology is to accurately diagnose the etiology of patients with new onset heart failure such as to differentiate between potentially reversible myocarditis from idiopathic dilated cardiomyopathy (IDCM). Furthermore, it is difficult to predict the clinical trajectory of patients with IDCM. We hypothesized that the transcriptomic signatures generated from endomyocardial biopsies, obtained from patients at first presentation of heart failure, could serve as novel biomarkers to distinguish between myocarditis and IDCM as well as to predict the prognosis of patients classified as having IDCM. METHODS AND RESULTS: Endomyocardial biopsy samples were collected from 68 patients with new onset heart failure due to IDCM (n=49) and myocarditis (n=19). The average follow-up was 5 years and included information on mortality, need for left ventricular assist device (LVAD), or heart transplant. We used the U133 Plus 2.0 microarray (Affymetrix) and data analysis was performed with Significance Analysis of Microarrays (SAM) and Prediction Analysis of Microarrays (PAM). First, we identified a molecular signature of 39 genes in our training cohort (n=25 IDCM and n=8 myocarditis). When tested in independent patients (myocarditis: n=11; IDCM: n=11), this signature performed with 97% accuracy. Next, we identified a transcriptomic signature of 45 genes in a group of patients with IDCM that delineated between patients classified as having a good prognosis (event free survival > 5 years; n=18) vs a bad prognosis (death or requirement for insertion of LVAD or tx within 2 years of presentation; n=12). We tested this biomarker in independent samples and were able to predict prognosis with 87% accuracy. The transcriptomic biomarker was substantially more accurate in assigning prognosis than the Seattle Heart Failure Score (p=0.011). CONCLUSION: Together these findings illustrate the potential utility of using transcriptomic biomarkers generated from a single endomyocardial biopsy to improve the accuracy of diagnosis and prognosis in patients with new onset heart failure. This creates novel modalities to enhance management and identification of patients at highest risk for complications of heart failure in the short term.