gebhart/patrepeval huggingface dataset:
Robust Model Predictive Control (1987)

Concepts of model predictive control are extended to uncertain linear systems. An on-line optimizing control scheme is developed which has as its objective the minimization of the worst-case tracking error for a family of linear plants. For uncertainty descriptions which provide impulse response models as affine functions of uncertain parameters, it is shown that the required minimax optimization can be recast as a linear program. Situations which lead to such an uncertainty description are discussed. An example is presented to demonstrate the properties of the proposed control scheme.
Aqueous polymer two‐phase systems: Effective tools for plasma membrane proteomics (2006)

Plasma membranes (PMs) are of particular importance for all living cells. They form a selectively permeable barrier to the environment. Many essential tasks of PMs are carried out by their proteinaceous components, including molecular transport, cell-cell interactions, and signal transduction. Due to the key role of these proteins for cellular function, they take center-stage in basic and applied research. A major problem towards in-depth identification and characterization of PM proteins by modern proteomic approaches is their low abundance and immense heterogeneity in different cells. Highly selective and efficient purification protocols are hence essential to any PM proteome analysis. An effective tool for preparative isolation of PMs is partitioning in aqueous polymer two-phase systems. In two-phase systems, membranes are separated according to differences in surface properties rather than size and density. Despite their rare application to the fractionation of animal tissues and cells, they represent an attractive alternative to conventional fractionation protocols. Here, we review the principles of partitioning using aqueous polymer two-phase systems and compare aqueous polymer two-phase systems with other methods currently used for the isolation of PMs.
Elastic wave equation traveltime and waveform inversion of crosswell data (1997)

Abstract A method is presented for reconstructing P- and S-velocity distributions from elastic traveltimes and waveforms. The input data consist of crosswell hydrophone records generated by a piezoelectric borehole source. Borehole effects are partially accounted for by using a low-frequency Green's function to simulate the pressure generated in the fluid-filled receiver well. The tube waves in the borehole are ignored, on the assumption that they can be removed from the field data by median filtering. In addition, the source-radiation pattern is partially taken into account by inverting for the equivalent stress components acting on the earth at the source location. The elastic wave equation traveltime and waveform inversion (WTW) method is applied to both synthetic crosswell data and the McElroy field crosswell data. As predicted by theory, results show that elastic WTW tomograms provide a sharper interface image than delineated in the traveltime tomograms. The spatial resolution of the McElroy traveltime tomogram is about 20 m compared to about 3 m and 1.5 m, respectively, for the associated P- and S-velocity WTW tomograms. From these tomograms, detailed porosity maps of the interwell geology are constructed. There is a very good correlation between the P-velocity tomograms and the P-velocity log profiles, and there is a good correlation between the smooth parts of the S-velocity tomogram and the S-velocity logs. Unfortunately, the high-wavenumber parts of the S-velocity tomograms do not correlate well with the high-wavenumber parts of the S-velocity logs. We believe this problem is partly caused by not taking into account attenuation effects in the WTW algorithm.
Measuring Driver Impairments: Sleepiness, Distraction, and Workload (2012)

Snow was falling heavily when Sarah was driving on a slippery road to her cousin's country cottage. It was dark outside, and the visibility was poor. She had planned to arrive before sunset, but the rental service had made a mistake, and it took hours before she got her rental car at the airport. It was past midnight now, and after a long day of traveling, Sarah was starting to get sleepy. Fortunately, there were only 15 km to go, but her eyelids were starting to feel heavy. To stay awake, she put her favorite CD on, turned up the volume, and started to sing along. This seemed to help a little-good-only 10 km to go. This was when Sarah's phone started ringing, and she awkwardly tried to find the mute button for the car stereo while answering the phone. As she looked up again, she barely caught a glimpse of the red brake lights of the car in front of her as she smashed into it.
Optimization of bow-tie antennas for pulse radiation (1994)

Resistively loaded bow-tie antennas are considered as radiators for temporally short, broad-bandwidth pulses. Analysis is by the finite-difference time-domain (FDTD) method. The geometrical details of the antenna and the resistive loading along the antenna are chosen to optimize this antenna for pulse radiation. Theoretical results for the reflected voltage in the coaxial feed line and the time-varying radiated electric field are compared throughout with experimental measurements. The optimized, resistive bow-tie antenna is shown to radiate a pulse that more closely resembles that of the excitation than is radiated by a metallic bow tie of comparable size. Issues involving the use of the FDTD method for modeling fully three-dimensional antennas are also discussed. These issues include the use of a simple feed model and the staircasing of the edges of the antenna.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ultrasensitive reversible chromophore reaction of BODIPY functions as high ratio double turn on probe (2018)

Chromophore reactions with changes to conjugation degree, especially those between the conjugated and unconjugated state, will bring a large spectral variation. To realize such a process, a meso-naked BODIPY (MNBOD) with two electron-withdrawing groups around the core is designed and synthesized. The resulting system is extremely sensitive to bases. The red, highly fluorescent solution readily becomes colorless and non-fluorescent after base addition; however, the color and fluorescence can be totally and instantly restored by addition of acid or formaldehyde. Analyses show that two identical MNBODs are connected by a C-C single bond (sp<sup>3</sup>) at the meso-position through a radical reaction that results in an unconjugated, colorless dimer complexed with bases. When the bases are consumed, the dimer immediately dissociates into the red, highly fluorescent, conjugated MNBOD monomer. With 260 nm spectral change and over 120,000 turn-on ratio, this chromophore-reaction can be utilized as a sensitive reaction-based dual-signal probe.
Microfluidic logic gates and timers (2007)

We use surface tension-based passive pumping and fluidic resistance to create a number of microfluidic analogs to electronic circuit components. Three classes of components are demonstrated: (1) OR/AND, NOR/NAND, and XNOR digital microfluidic logic gates; (2) programmable, autonomous timers; and (3) slow, perfusive flow rheostats. The components can be implemented with standard pipettes and provide a means of non-electronic and autonomous preprogrammed control with potential utility in cell studies and high throughput screening applications.
Teardrop Reflector-Assisted Unidirectional Hybrid Silicon Microring Lasers (2012)

We study directional bistability in hybrid silicon microring lasers and demonstrate a unidirectional laser. Unidirectional emission is achieved by integrating a passive reflector that feeds laser emission back into the laser cavity to introduce an extra unidirectional gain. We show that the length of the passive reflector is a critical parameter in determining the lasing behavior.
Rapid and accurate estimation of blood saturation, melanin content, and epidermis thickness from spectral diffuse reflectance (2010)

We present a method to determine chromophore concentrations, blood saturation, and epidermal thickness of human skin from diffuse reflectance spectra. Human skin was approximated as a plane-parallel slab of variable thickness supported by a semi-infinite layer corresponding to the epidermis and dermis, respectively. The absorption coefficient was modeled as a function of melanin content for the epidermis and blood content and oxygen saturation for the dermis. The scattering coefficient and refractive index of each layer were found in the literature. Diffuse reflectance spectra between 490 and 620 nm were generated using Monte Carlo simulations for a wide range of melanosome volume fraction, epidermal thickness, blood volume, and oxygen saturation. Then, an inverse method was developed to retrieve these physiologically meaningful parameters from the simulated diffuse reflectance spectra of skin. A previously developed accurate and efficient semiempirical model for diffuse reflectance of two layered media was used instead of time-consuming Monte Carlo simulations. All parameters could be estimated with relative root-mean-squared error of less than 5% for (i) melanosome volume fraction ranging from 1% to 8%, (ii) epidermal thickness from 20 to 150 mum, (iii) oxygen saturation from 25% to 100%, (iv) blood volume from 1.2% to 10%, and (v) tissue scattering coefficient typical of human skin in the visible part of the spectrum. A similar approach could be extended to other two-layer absorbing and scattering systems.
Successful Treatment of a Nine-Year Case of Complex Regional Pain Syndrome Type-I (Reflex Sympathetic Dystrophy) With Intravenous Ketamine-Infusion Therapy in a Warfarin-Anticoagulated Adult Female Patient (2002)

Editor's Comment: This report of a single case study is presented in unusual detail because of the exceptional promise of the technique described, and the importance of further study. Complex Regional Pain Syndrome challenges our most informed and skillful interventions. The field is replete with reports of promising “cures” that fail to be replicated. We hope that this report will stimulate further studies of this intervention in carefully constructed studies of a larger series, with randomization, before conclusions can be drawn. 

Complex Regional Pain Syndrome (CRPS) is a painful and debilitating neuropathic pain disorder. CRPS is classified into two types [1]. Both types appear to occur after a traumatic event. With type-I, which is more common, no or only minor nerve damage may be detectable [2]. With type-II, however, clearly detectable nerve damage is usually evident [2].

Patients with CRPS frequently experience a devastating degree of never-ending burning pain that is life-altering [3]. The quality and intensity of the pain experienced in CRPS, in addition to the functional impairment that may ensue, often times threatens the very existence and reason to live for many individuals with this disorder. Conventional therapies are often only palliative; this is particularly true with patients who have suffered from CRPS, or whose underlying pathology remains undetected or untreated, for prolonged periods of time.

The early diagnosis and treatment of CRPS is essential to the amelioration of this disorder [3]. Multidisciplinary approaches to pain relief, now strongly encouraged, include the concomitant administration of physical therapy, exercise, and behavior modification. The mainstays of therapy include the administration of anticonvulsants, antidepressants, narcotics, sympathetic blocks, and topical anesthetics. The early use of implantable spinal cord stimulators has also been advocated [4]. Despite conventional treatment strategies, many CRPS patients continue to suffer from a …
Wearable brain cap with contactless electroencephalogram measurement for brain-computer interface applications (2009)

Many brain computer interfaces (BCI) are based on feature selection from electroencephalogram (EEG) signals. To acquire these signals, a set of electrodes is used, most of the times attached to a brain cap. Several brain cap designs have been presented, as well many different electrodes. So far, all the brain caps are difficult and uncomfortable to wear. Moreover, the electrodes, wet or dry, are also difficult to place. Despite the huge potential that a BCI offers, for disabled and healthy people, new brain caps are required to overcome these two main problems. In this work, a wearable brain cap is presented with the ability to measure the required EEG signals without requiring any electrical contact with the head. The wearable cap is obtained using a flexible polymeric material, with new integrated contactless electrodes. The electrodes may be obtained using a new electroactive gel, which is used to read the EEG signals.
Enantioselective Addition ofa Trifluoromethyl Anion to Aryl Ketones and Aldehydes (2003)

The identification and development of a catalyst for the enantioselective nucleophilic addition of a trifluoromethyl anion to a ketone is described. An easily prepared cinchonine-derived catalyst was used in amounts as low as 4 mol% to afford enantiomeric excess as high as 92%.
Nash equilibria in competitive societies, with applications to facility location, traffic routing and auctions (2003)

We consider the following class of problems. The value of an outcome to a society is measured via a submodular utility function (submodularity has a natural economic interpretation: decreasing marginal utility). Decisions, however, are controlled by non-cooperative agents who seek to maximise their own private utility. We present, under basic assumptions, guarantees on the social performance of Nash equilibria. For submodular utility functions, any Nash equilibrium gives an expected social utility within a factor 2 of optimal, subject to a function-dependent additive term. For non-decreasing, submodular utility functions, any Nash equilibrium gives an expected social utility within a factor 1+/spl delta/ of optimal, where 0/spl les//spl delta//spl les/1 is a number based upon discrete curvature of the function. A condition under which all sets of social and private utility functions induce pure strategy Nash equilibria is presented. The case in which agents themselves make use of approximation algorithms in decision making is discussed and performance guarantees given. Finally we present specific problems that fall into our framework. These include competitive versions of the facility location problem and k-median problem, a maximisation version of the traffic routing problem studied by Roughgarden and Tardos (2000), and multiple-item auctions.
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation (2020)

Numerous somatic mutations occurring in the epidermal growth factor receptor (EGFR) family (ErbB) of receptor tyrosine kinases (RTK) have been reported from cancer patients, although relatively few have been tested and shown to cause functional changes in ErbBs. The ErbB receptors are dimerized and activated upon ligand binding, and dynamic conformational changes of the receptors are inherent for induction of downstream signaling. For two mutations shown experimentally to alter EGFR function, A702V and the Δ<sup>746</sup>ELREA<sup>750</sup> deletion mutation, we illustrate in the following protocol how molecular dynamics (MD) simulations can probe the (1) conformational stability of the mutant tyrosine kinase structure in comparison with wild-type EGFR; (2) structural consequences and conformational transitions and their relationship to observed functional changes; (3) effects of mutations on the strength of binding ATP as well as for binding between the kinase domains in the activated asymmetric dimer; and (4) effects of the mutations on key interactions within the EGFR binding site associated with the activated enzyme. The protocol provides a detailed step-by-step procedure as well as guidance that can be more generally useful for investigation of protein structures using MD simulations as a means to probe structural dynamics and the relationship to biological function.
Optimizing disjunctive queries with expensive predicates (1994)

In this work, we propose and assess a technique called bypass processing for optimizing the evaluation of disjunctive queries with expensive predicates. The technique is particularly useful for optimizing selection predicates that contain terms whose evaluation costs vary tremendously; e.g., the evaluation of a nested subquery or the invocation of a user-defined function in an object-oriented or extended relational model may be orders of magnitude more expensive than an attribute access (and comparison). The idea of bypass processing consists of avoiding the evaluation of such expensive terms whenever the outcome of the entire selection predicate can already be induced by testing other, less expensive terms. In order to validate the viability of bypass evaluation, we extend a previously developed optimizer architecture and incorporate three alternative optimization algorithms for generating bypass processing plans.
The use of statistical MUNE in a multicenter clinical trial (2004)

Techniques to estimate motor unit number (MUNE) measure the number of functioning motor units in a muscle. In diseases characterized by progressive motor unit loss, such as amyotrophic lateral sclerosis (ALS), MUNE may be useful to monitor disease progression or beneficial response to treatment. As part of a multicenter, placebo-controlled, randomized, double-blind clinical trial testing the efficacy of creatine in patients with ALS, statistical MUNE was measured in 104 patients tested monthly for 6 months. The objective was to determine whether MUNE was a reliable and sensitive outcome measure in the context of a multicenter trial. Formal training and reliability testing was required for all MUNE evaluators. Testing of normal controls showed a high degree of test-retest reliability. All patient data were combined as the experimental treatment showed no efficacy. There was a 23% decline in MUNE over 6 months. The technique as employed in this trial overemphasized the presence of small motor units; this problem was partially addressed by poststudy data monitoring and censuring. Thus, MUNE can be used reliably as an outcome measure in multicenter clinical trials; specific remedies are suggested for the difficulties encountered in this study.
Bioactive Compounds of Colostrum and Its Application (2006)

Colostrum is the initial milk secreted by bovine during parturition and the first few days after birth. Colostrum is a gift of nature used to protect the newborn’s immune system and provides passive immunity against pathogens. The presence of bioactive components such as insulin-like growth factor I and II (IGF-I and IGF-II), lactoferrin, lysozyme, lactoperoxidase, and immunoglobulin make the colostrum active against pathogens such as Escherichia coli, Salmonella typhimurium, Shigella dysenteria, Listeria monocytogens, Streptococcus mutans, Bacillus stearothermophilus, and Bacillus subtilis. It is also active against Herpes simple virus type-I (HSV-I), Human Immuno-deficiency virus-I (HIV-I), and human cytomegalovirus. Lysozyme is an antibacterial and lytic enzyme; whereas lactoperoxidase is a major antibacterial found in colostrum; it is toxic to gram-positive and gram-negative bacteria. Lactoperoxidase inactivates the polio virus, vaccinia, and human immunodeficiency virus type-I in-vitro. Immunoglobulins are considered an important bioactive component in colostrum, and it contains high levels of immunoglobulin G (Ig G). Immunosupplementation with bovine milk antibodies has been shown to provide local protection to the gastrointestinal tract against disease. The restricted technical and hygienic problems, along with the unstable physio-chemical nature of colostrum, has resulted in minimal utilization of colostrum on Industrial scale.
Negative regulation of defense responses in Arabidopsis by two <i>NPR1</i> paralogs (2006)

NPR1 is required for systemic acquired resistance, and there are five NPR1 paralogs in Arabidopsis. Here we report knockout analysis of two of these, NPR3 and NPR4. npr3 single mutants have elevated basal PR-1 expression and the npr3 npr4 double mutant shows even higher expression. The double mutant plants also display enhanced resistance against virulent bacterial and oomycete pathogens. This enhanced disease resistance is partially dependent on NPR1, can be in part complemented by either wild-type NPR3 or NPR4, and is not associated with an elevated level of salicylic acid. NPR3 and NPR4 interact with TGA2, TGA3, TGA5 and TGA6 in yeast two-hybrid assays. Using bimolecular fluorescence complementation analysis, we show that NPR3 interacts with TGA2 in the nucleus of onion epidermal cells and Arabidopsis mesophyll protoplasts. Combined with our previous finding that basal PR-1 levels are also elevated in the tga2 tga5 tga6 triple mutant, we propose that NPR3 and NPR4 negatively regulate PR gene expression and pathogen resistance through their association with TGA2 and its paralogs.
Tissue- and development-specific alternative RNA splicing regulates expression of multiple isoforms of erythroid membrane protein 4.1 (1991)

Protein 4.1, a multifunctional structural protein originally described as an 80-kDa component of the erythroid membrane skeleton, exhibits tissue- and development-specific heterogeneity in molecular weight, subcellular localization, and primary amino acid sequence. Earlier reports suggested that some of this impressive heterogeneity is generated by alternative RNA splicing (Conboy, J. G., Chan, J., Mohandas, N., and Kan, Y. W. (1988) Proc. Natl. Acad. Sci. U. S. A. 85, 9062-9065; Tang, T. K., Leto, T., Marchesi, V. T., and Benz, E. J. (1990) J. Cell Biol. 110, 617-624). We have now completed a systematic analysis of 4.1 mRNA isoforms expressed in erythroid cells, and have generated an "alternative splicing map" which summarizes diagrammatically a multitude of polypeptide isoforms potentially generated by combinatorial splicing of nine alternative exons. Complex 5' splicing events yield mRNA isoforms that may initiate translation at different sites and thus generate elongated or truncated NH2 termini; elongated approximately 135-kDa and prototypical approximately 80-kDa species were detected in both erythrocytes and T-lymphocytes, but in very different ratios. Among the functional domains of 4.1 responsible for interaction with other membrane skeletal elements, four variants of the 10-kDa spectrin-actin-binding region and four variants of the putative 30-kDa glycophorin-binding region are predicted. Developmentally controlled alternative RNA splicing in the spectrin-actin-binding region may help regulate remodeling of membrane architecture and mechanical properties that occur during erythropoiesis.