gebhart/patrepeval huggingface dataset:
Multistep Simulation-Optimization Modeling Approach for Partitioning Water Distribution System into District Meter Areas (2018)

This paper presents an integrated solution approach for solving the challenge of partitioning a large water-distribution system into district meter areas (DMAs). The solution method is formulated to employ graph algorithms to generate DMA partitions, and apply a high performance genetic algorithm optimizer to optimize DMA partitions, boundary links, system interventions including parallel pipes, replacement pipes, and tank capacities. The solutions are interactively evaluated and fine-tuned by using well-developed modeling software to adjust the boundary link status and place pressure reduction valves (PRVs). Finally, the PRV settings are optimized to reduce the nodal pressures to meet the maximum allowable pressures inside DMAs. The approach has been applied to the Battle of Water Networks DMAs (BWNDMA). Good solutions have been obtained for the case study. In particular, water-balance analysis is carried out to identify which water-supply source is going to supply which DMA region according to the available amount of water that is allowed to be extracted. Link status and settings are adjusted accordingly to optimize the system performance. Throughout the solution process engineering judgment has been employed, together with the simulation and optimization models, to obtain the optimized solutions while meeting the constraints.
Progress on the Design of the Polarized Medium-energy Electron Ion Collider at JLab (2015)

The Medium-energy Electron Ion Collider (MEIC) at JLab is designed to provide high luminosity and high polarization needed to reach new frontiers in the exploration of nuclear structure. The luminosity, exceeding 1033 cm⁻²s^{−1} in a broad range of the center-of-mass (CM) energy and maximum luminosity above 1034 cm⁻²s^{−1}, is achieved by high-rate collisions of short small-emittance low-charge bunches made possible by high-energy electron cooling of the ion beam and synchrotron radiation damping of the electron beam. The polarization of light ion species (p, d, 3He) can be easily preserved and manipulated due to the unique figure-8 shape of the collider rings. A fully consistent set of parameters have been developed considering the balance of machine performance, required technical development and cost. This paper reports recent progress on the MEIC accelerator design including electron and ion complexes, integrated interaction region design, figure-8-ring-based electron and ion polarization schemes, RF/SRF systems and ERL-based high-energy electron cooling. Luminosity performance is also presented for the MEIC baseline design.
Analysis of the dust evolution in the circumstellar disks of T Tauri stars (2006)

Aims.We present a compositional analysis of spectra of 32 young stellar objects (YSOs). Our sample consists of 5 intermediate-mass stars and 27 low-mass stars. Although some previous studies give reasons for the similarity between the dust in circumstellar disks of T Tauri stars and Herbig Ae/Be stars, a quantitative comparison has been lacking so far. Therefore, we include a discussion of the results of the m spectroscopic survey of van Boekel et al. (2005, A&A, 437, 189), who focus on Herbig Ae/Be stars, the higher mass counterparts of T Tauri stars, and draw comparisons to this and other studies.
Mechanisms of Resistance to Mitogen-Activated Protein Kinase Pathway Inhibition in BRAF-Mutant Melanoma (2012)

Anticancer drug resistance remains a crucial impediment to the care of many patients with cancer. Although the exact mechanisms of resistance may differ for each therapy, common mechanisms of resistance predominate, including drug inactivation or modification, mutation of the target protein, reduced drug accumulation, or bypass of target inhibition. With the discovery and use of targeted therapies (such as small-molecule kinase inhibitors), resistance has received renewed attention-especially in light of the dramatic responses that may emerge from such therapeutics in particular genetic or molecular contexts. Recently, the mitogen-activated protein kinase (MAPK) pathway has become exemplary in this regard, since it is activated in many different cancers. Drugs targeting RAF and MAPK kinase (MEK) are currently in clinical trials for the treatment of several types of cancer. Vemurafenib, a selective RAF kinase inhibitor recently approved for the treatment of BRAF(V600E) melanoma, shows strong efficacy initially; however, the development of resistance is nearly ubiquitous. In vitro testing and analysis of patient samples have uncovered several mechanisms of resistance to RAF inhibition. Surprisingly, mutations in the drug-binding pocket have not thus far been observed; however, other alterations at the level of RAF, as well as downstream activation of MEK and bypass of MEK/extracellular signal-regulated kinase (ERK) signaling altogether, confer resistance to vemurafenib. Looking forward, combined RAF and MEK inhibitor treatments may improve efficacy-yet we must anticipate mechanisms of resistance to this combination as well. Therefore, understanding and/or determining the mechanism of resistance are paramount to effective cancer treatment.
A MEMS-based correlation radiometer (2004)

We describe the development of a MEMS-based correlation radiometer for remote detection of chemical species. The radiometer utilizes a new type of MEMS programmable diffraction grating called the Polychromator. The Polychromator contains an array of 1024 electrostatically actuated reflective beams that are 10 microns wide by 1 cm long, and have a vertical travel of approximately 2 - 4 microns. The Polychromator grating is used to replace the reference cell of conventional correlation radiometry. Appropriate programming of the deflection profile of the grating array enables the production of any spectral transfer function desired for the correlation measurement. Advantages of this approach to correlation radiometry include the ability to detect multiple chemical species with a compact instrument, the ability to optimize the reference spectra to eliminate chemical interferences, and the ability to produce reference spectra for hazardous and transient species.
Unsupervised Heart Sound Decomposition and State Estimation with Generative Oscillation Models (2021)

This paper proposes a new generative probabilistic model for phonocardiograms (PCGs) that can simultaneously capture oscillatory factors and state transitions in cardiac cycles. Conventionally, PCGs have been modeled in two main aspects. One is a state space model that represents recurrent and frequently appearing state transitions. Another is a factor model that expresses the PCG as a non-stationary signal consisting of multiple oscillations. To model these perspectives in a unified framework, we combine an oscillation decomposition with a state space model. The proposed model can decompose the PCG into cardiac state dependent oscillations by reflecting the mechanism of cardiac sounds generation in an unsupervised manner. In the experiments, our model achieved better accuracy in the state estimation task compared to the empirical mode decomposition method. In addition, our model detected S2 onsets more accurately than the supervised segmentation method when distributions among PCG signals were different.
MOS-Based Multiuser Multiapplication Cross-Layer Optimization for Mobile Multimedia Communication (2007)

We propose a cross-layer optimization strategy that jointly optimizes the application layer, the data-link layer, and the physical layer of a wireless protocol stack using an application-oriented objective function. The cross-layer optimization framework provides efficient allocation of wireless network resources across multiple types of applications run by different users to maximize network resource usage and user perceived quality of service. We define a novel optimization scheme based on the mean opinion score (MOS) as the unifying metric over different application classes. Our experiments, applied to scenarios where users simultaneously run three types of applications, namely voice communication, streaming video and file download, confirm that MOS-based optimization leads to significant improvement in terms of user perceived quality when compared to conventional throughput-based optimization.
Characterization testing of dual junction GaInP/sub 2//GaAs/Ge solar cell assemblies (2002)

The first commercial communications satellite with dual junction solar arrays was launched in August of 1997. The satellite is an HS 601HP series spacecraft built by Hughes Space and Communications Company (HSC). The solar cell assemblies consist of large area gallium-indium-phosphide on gallium-arsenide on germanium (GaInP/sub 2//GaAs/Ge) solar cells with active GaInP/sub 2/ and GaAs junctions. The cells were developed by Spectrolab Inc. for the HS 601HP and HS 702 spacecraft product lines under a research and development contract from HSC. A comprehensive characterization program was performed on the GaInP/sub 2//GaAs/Ge solar cell assemblies used on the HSC arrays. The results provided a complete database enabling the design of the solar array, and demonstrated that the GaInP/sub 2//GaAs/Ge cells meet the spacecraft requirements at end-of-life.
Magnetic and electric compound action signals in human sural nerve (2003)

Magnetic and electric compound action signals (CASs) of the human sural nerve were recorded just before a nerve biopsy was carried out. CASs contain information on action potential propagation between stimulus and recording site. Evaluation of fiber diameter distributions (FDDs) computed from measured CAS and FDDs derived from nerve histology could indicate a local nerve pathology that might not be detected from nerve histology alone. Preliminary electrophysiological data and results of the automated analysis of nerve histology are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
<em>In Vivo</em> Investigation of Antimicrobial Blue Light Therapy for Multidrug-resistant <em>Acinetobacter baumannii</em> Burn Infections Using Bioluminescence Imaging (2017)

Burn infections continue to be an important cause of morbidity and mortality. The increasing emergence of multidrug-resistant (MDR) bacteria has led to the frequent failure of traditional antibiotic treatments. Alternative therapeutics are urgently needed to tackle MDR bacteria. An innovative non-antibiotic approach, antimicrobial blue light (aBL), has shown promising effectiveness against MDR infections. The mechanism of action of aBL is not yet well understood. It is commonly hypothesized that naturally occurring endogenous photosensitizing chromophores in bacteria (e.g., iron-free porphyrins, flavins, etc.) are excited by aBL, which in turn produces cytotoxic reactive oxygen species (ROS) through a photochemical process. Unlike another light-based antimicrobial approach, antimicrobial photodynamic therapy (aPDT), aBL therapy does not require the involvement of an exogenous photosensitizer. All it needs to take effect is the irradiation of blue light; therefore, it is simple and inexpensive. The aBL receptors are the endogenous cellular photosensitizers in bacteria, rather than the DNA. Thus, aBL is believed to be much less genotoxic to host cells than ultraviolet-C (UVC) irradiation, which directly causes DNA damage in host cells. In this paper, we present a protocol to assess the effectiveness of aBL therapy for MDR Acinetobacter baumannii infections in a mouse model of burn injury. By using an engineered bioluminescent strain, we were able to noninvasively monitor the extent of infection in real time in living animals. This technique is also an effective tool for monitoring the spatial distribution of infections in animals.
Figure S1-S5 from Activating an Adaptive Immune Response with a Telomerase-Mediated Telomere Targeting Therapeutic in Hepatocellular Carcinoma (2023)

&lt;p&gt;Supplementary Data&lt;/p&gt;
Streptopeptolin, a Cyanopeptolin-Type Peptide from Streptomyces olivochromogenes (2018)

Cyanopeptolin-type peptides are cyclic depsipeptides that commonly have 3-amino-6-hydroxy-2-piperidone (Ahp) unit in the molecules. So far, cyanopeptolin-type peptides have been isolated as protease inhibitors from a wide variety of cyanobacteria. In the course of screening for new peptides, a new peptide streptopeptolin, which had the similar structure to cyanopeptolin, was isolated from the extract of <i>Streptomyces olivochromogenes</i> NBRC 3561. Streptopeptolin is the first cyanopeptolin-type peptide isolated from actinobacteria. The structure of streptopeptolin was determined by the analysis of electrospray ionization mass spectrometry and NMR to be cyclic depsipeptide containing unusual amino acids, Ahp, and <i>N</i>-methyl tyrosine. As a result of protease inhibition test, streptopeptolin showed inhibitory activity against chymotrypsin. The whole genome sequence data of <i>S. olivochromogenes</i> revealed the biosynthetic gene cluster for streptopeptolin, which encoded a nonribosomal peptide synthetase. We proposed a biosynthetic pathway of streptopeptolin based on bioinformatics analysis.
Integrity Analysis of Electrically Actuated Resonators With Delayed Feedback Controller (2011)

In this work, we investigate the stability and integrity of parallel-plate microelectromechanical systems resonators using a delayed feedback controller. Two case studies are investigated: a capacitive sensor made of cantilever beams with a proof mass at their tip and a clamped-clamped microbeam. Dover-cliff integrity curves and basin-of-attraction analysis are used for the stability assessment of the frequency response of the resonators for several scenarios of positive and negative gain in the controller. It is found that in the case of a positive gain, a velocity or a displacement feedback controller can be used to effectively enhance the stability of the resonators. This is confirmed by an increase in the area of the basin of attraction of the resonator and in shifting the Dover-cliff curve to higher values. On the other hand, it is shown that a negative gain can significantly weaken the stability and integrity of the resonators. This can be of useful use in MEMS for actuation applications, such as in the case of capacitive switches, to lower the activation voltage of these devices and to ensure their trigger under all initial conditions.
Roughness, Holes, and Bumps (2009)

This review of the literature found that most people are aware of extreme cases of roughness, such as the potholes and severe bumps, and that the effect of these surface irregularities on safety is widely recognized. The hazard of a washboard road where a driver can lose control of a vehicle at inappropriate speeds is readily understood. The transition of a roadway from a smooth surface to a rough one, however, may give a driver difficulty in controlling the vehicle and can be more subtle in its influence on safety. By violating driver expectancy, a road that is differentially rough may be less safe than a uniformly rough road.
zHyperLink: Low-latency I/O for Db2 on IBM Z and DS8880 storage (2018)

zHyperLink is a new low-latency I/O capability for storage area networks (SANs). When using zHyperLink, the IBM z14 processor, along with the DS8880 Storage System (IBM's latest enterprise-class storage for mainframe attachment), delivers up to a 90% reduction in storage I/O service times compared with fiber channel transport technology. zHyperLink I/O service times eliminate the need for an operating system task switch for most read I/O operations, fundamentally improving application response times and changing system scaling behavior. Initial use of zHyperLink on IBM Z, IBM DS8880 storage, and z/OS accelerates the Db2 for z/OS relational database transaction processing information management system hierarchal database and reduces the elapsed time for Virtual Storage Access Method applications. These improvements occur without any application changes. In this paper, we explain the strategic importance of a low-latency I/O capability for the SAN and describe the z14 architecture, hardware, firmware, and software implementation concepts and the preliminary performance results for Db2.
Computing the exit-time for a finite-range symmetric jump process (2015)

Abstract This paper investigates the exit-time for a broad class of symmetric finite-range jump processes via the corresponding master equation, a nonlocal diffusion equation suitably constrained. In direct analogy to the classical diffusion equation with a homogeneous Dirichlet boundary condition, the nonlocal diffusion equation is augmented with a homogeneous volume-constraint. The volume-constrained master equation provides an efficient alternative over Monte Carlo simulation for computing an important statistic of the process. Several numerical examples are given.
LovG: The Thioesterase Required for Dihydromonacolin L Release and Lovastatin Nonaketide Synthase Turnover in Lovastatin Biosynthesis (2013)

Wartungsenzym: Es wurde erkannt, dass die rätselhafte Thioesterase LovG die Produktfreisetzung aus der Lovastatin-Nonaketid-Synthase (LNKS oder LovB; siehe Schema) bewirkt. LovG verbessert außerdem den Durchsatz von LovB, indem es fehlerhafte Intermediate hydrolysiert und dadurch weitere katalytische Umsetzungen an LovB ermöglicht. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A randomized controlled trial of two group programs in multiple sclerosis: Long-term (12-month) follow-up effects on fatigue and self-efficacy (P3.351) (2017)

To determine whether multiple sclerosis (MS) participants in Fatigue: Take Control (FTC) experienced decreased fatigue and increased self-efficacy compared to those in MS: Take Control (MSTC), a general MS education program.
Two conformational states of amyloid β-peptide: implications for the pathogenesis of Alzheimer's disease (1995)

Since the discovery of soluble amyloid-beta (sA beta), it became clear that the same amino acid sequence can have both a fibrillar or a soluble state. In this work, we describe the isolation of two different species derived from synthetic A beta(1-40) differing in their conformational and fibrillogenesis properties. The separation was performed taking advantage of the fact that only one species is sedimentable by centrifugation after 2 weeks of incubation at 1 mg/ml. One species is highly amyloidogenic (A beta ac) and has an antiparallel beta-sheet structure and the other one is poorly amyloidogenic (A beta nac) and contains mainly random coil or alpha-helix structure. Chemical changes were not detected in the primary structure of both species and the differences in the physical properties and very likely in biological behaviour are thought to have a conformational basis. We propose that the transformation of the non-amyloidogenic into the amyloidogenic conformation could be the fundamental event in the pathological polymerization of sA beta and in the development of Alzheimer's disease.
Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers (2023)

Interactions between membrane proteins are essential for cell survival but are often poorly understood. Even the biologically functional ratio of components within a multi-subunit membrane complex-the native stoichiometry-is difficult to establish. Here we demonstrate digital nanoreactors that can control interactions between lipid-bound molecular receptors along three key dimensions: stoichiometric, spatial, and temporal. Each nanoreactor is based on a DNA origami ring, which both templates the synthesis of a liposome and provides tethering sites for DNA-based receptors (modelling membrane proteins). Receptors are released into the liposomal membrane using strand displacement and a DNA logic gate measures receptor heterodimer formation. High-efficiency tethering of receptors enables the kinetics of receptors in 1:1 and 2:2 absolute stoichiometries to be observed by bulk fluorescence, which in principle is generalizable to any ratio. Similar single-molecule-in-bulk experiments using DNA-linked membrane proteins could determine native stoichiometry and the kinetics of membrane protein interactions for applications ranging from signalling research to drug discovery.
Optimization of Optical Absorption of Colloids of SiO2@Au and Fe3O4@Au Nanoparticles with Constraints (2016)

We study the optical response of monodisperse colloids of core-shell plasmonic nanoparticles and introduce a computational approach to optimize absorption for photothermal applications that require dilute colloids of non-interacting particles with a prescribed volume fraction. Since the volume fraction is held constant, the particle concentration is size-dependent. Optimization is achieved by comparing the absorption spectra of colloids as a function of particle size and structure. We demonstrate the approach via application to colloids of core-shell SiO<sub>2</sub>@Au and Fe<sub>3</sub>O<sub>4</sub>@Au nanoparticles with particle sizes that range from 5-100 nm and with the incident wavelength varying from 600-1200 nm. The absorption spectra are predicted using Mie theory and the analysis shows that there is a unique mix of parameters (core radius, shell thickness, wavelength) that maximize absorption, independent of the value of volume fraction. We show that lossy Fe<sub>3</sub>O<sub>4</sub> cores produce a much broader absorption peak with much less sensitivity to variations in particle structure and wavelength than lossless SiO<sub>2</sub> cores. This approach can be readily adapted to colloids of nanoparticles with arbitrary materials, shapes and structure using appropriate numerical methods to compute the absorption spectra. As such, it is useful for the rational design of colloids and process variables for a broad range of photothermal applications.
Design Map for Bi-SQUIDs (2017)

We consider and discuss a design map for bi-SQUIDs as devices capable of providing highly linear voltage response to the applied magnetic flux. The response linearity can amount to 90 to 100 dB at the optimally set parameters, the most critically, at the optimally chosen critical current of the third Josephson junction. In this paper, we summarize all our research results into a comprehensive guide for bi-SQUID design, taking into consideration all the device inductances, as well as spread in critical currents and noise impact.