gebhart/patrepeval huggingface dataset:
Optical properties of nondegenerate ground-state polymers: Three dioxythiophene-based conjugated polymers (2003)

We report the optical properties of three dioxythiophene-based conjugated polymers: poly(3,4-ethylenedioxythiophene) poly(3,4-propylenedioxythiophene), and poly(3,4-(2,2-dimethylpropylenedioxy)thiophene). Films of ca. 200 nm thickness of these polymers were prepared on indium-tin-oxide coated glass substrates using a potentiostatic electropolymerization method. The reflectance and transmittance of the samples were measured over a broad energy range from the midinfrared through the ultraviolet. To extract the optical constants of the polymers, we modeled all of the layers of this multilayer thin-film structure using a Drude-Lorentz model. From the parameters obtained, we compute the optical constants, such as absorption coefficient and frequency-dependent conductivity. These functions yield information about the electronic structure of the neutral and doped polymers, which show evidence for polaron states at low doping and bipolarons at the maximum doping level. We observed doping-dependent changes in the electronic structure of these polymers as well as doping-induced infrared-active vibrational modes.
Dynamic Diffusion Maps-based Path Planning for Real-time Collision Avoidance of Mobile Robots (2018)

Given a route to a destination, a mobile robot still needs to locally plan a path to avoid collisions in continuously changing environment, e.g., a hall with pedestrians and moving obstacles. In this paper, diffusion maps are applied to find a local path for reaching a goal and avoiding collisions simultaneously. The proposed path planning algorithm plans a local path by utilizing a receding horizon approach, and therefore the algorithm repeats planning at every sample time. With this approach, mobile robots do not have to carry a prior map all the time because updated environment information is used for planning at every sample time. Extensive simulation is performed in different scenarios and demonstrates a good performance in collision avoidance.
Measurement-efficient optical wavemeters (2004)

We describe a method for efficiently determining the wavelength of a monochromatic source and provide an experimental proof-of-concept. The photomeasurement efficiency for a wavemeter can be written as eta(N,q) = (1 + logqN)/m, where N is the number of spectral channels, q is the number of distinguishable output levels per photodetector, and m is the actual number of photomeasurements made. An implementation is developed that achieves a theoretical efficiency of eta(N,q) = 1. The proof-of-concept experiment achieves efficiencies eta = O(1), where the deviation from theory is attributable to well-known optical effects and should be correctable in future versions.
Securing Ultra-High-Bandwidth Science DMZ Networks with Coordinated Situational Awareness (2017)

The Science DMZ (SDMZ) is a special purpose network infrastructure that is engineered to cater to the ultra-high bandwidth needs of the scientific and high performance computing (HPC) communities. These networks are isolated from stateful security devices such as firewalls and deep packet inspection (DPI) engines to allow HPC data transfer nodes (DTNs) to efficiently transfer petabytes of data without associated bandwidth and performance bottlenecks. This paper presents our ongoing effort toward the development of more fine-grained data flow access control policies to manage SDMZ networks that service large-scale experiments with varying data sensitivity levels and privacy constraints.
Multiple roles of ATP and adenosine in somatosensory processing: Therapeutic implications (1996)

A number of lines of evidence support roles for adenosine and adenosine 5′-triphosphate (ATP) in the transmission and modulation of somatosensory information in the dorsal horn of the spinal cord. Adenosine and ATP have also been demonstrated to have nociceptive (pain-related) and antinociceptive actions in the periphery. Thus, adenosine and ATP have multiple functions in somatosensory processing, which are dependent upon the site and on the relative activation of P1 and P2 purinoceptor subtypes on neurons and non-neuronal cells. The multiple roles provide a rich number of potential therapeutic targets for producing analgesia in a number of clinical pain states. However, because of the multiple and potentially contrasting pro- and anti-nociceptive roles of adenosine and ATP, pharmacological targeting of specific sites and purinoceptor subtypes will be necessary to achieve maximum effectiveness while minimizing side effects. Drug Dev. Res. 39:279–288, 1996. © 1997 Wiley-Liss, Inc.
Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development (2015)

We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarters of the CLL cases had little to no genetic subclonal evolution. However, we identified significant recurrent DNA methylation changes during progression at 4752 CpGs enriched for regions near Polycomb 2 repressive complex (PRC2) targets. Progression-associated CpGs near the PRC2 targets undergo methylation changes in the same direction during disease progression as during normal development from naive to memory B cells. Our study shows that CLL progression does not typically occur via subclonal evolution, but that certain CpG sites undergo recurrent methylation changes. Our results suggest CLL progression may involve developmental processes shared in common with the generation of normal memory B cells.
A2AR Adenosine Signaling Suppresses Natural Killer Cell Maturation in the Tumor Microenvironment (2017)

Extracellular adenosine is a key immunosuppressive metabolite that restricts activation of cytotoxic lymphocytes and impairs antitumor immune responses. Here, we show that engagement of A2A adenosine receptor (A2AR) acts as a checkpoint that limits the maturation of natural killer (NK) cells. Both global and NK-cell-specific conditional deletion of A2AR enhanced proportions of terminally mature NK cells at homeostasis, following reconstitution, and in the tumor microenvironment. Notably, A2AR-deficient, terminally mature NK cells retained proliferative capacity and exhibited heightened reconstitution in competitive transfer assays. Moreover, targeting A2AR specifically on NK cells also improved tumor control and delayed tumor initiation. Taken together, our results establish A2AR-mediated adenosine signaling as an intrinsic negative regulator of NK-cell maturation and antitumor immune responses. On the basis of these findings, we propose that administering A2AR antagonists concurrently with NK cell-based therapies may heighten therapeutic benefits by augmenting NK cell-mediated antitumor immunity.<b>Significance:</b> Ablating adenosine signaling is found to promote natural killer cell maturation and antitumor immunity and reduce tumor growth. <i>Cancer Res; 78(4); 1003-16. ©2017 AACR</i>.
Tandem Allylation/1,2-Boronate Rearrangement for the Asymmetric Synthesis of Indolines with Adjacent Quaternary Stereocenters (2018)

A three-component coupling using lithiated indoles, boronate esters and allylic acetates generates chiral indolines with adjacent quaternary stereocenters. Successful stereocontrol required the use of phosphoramidite ligands not previously described for organopalladium chemistry. Mechanistic studies indicate a monodentate PdL intermediate, and a stepwise allylation-aryl/alkyl migration. A protodeborylation strategy was used to install a C-H bond in place of the C-B bond. A photoredox coupling was used to replace C-B bond with a C-C bond in a highly diastereoselective manner. In the specific case of methyl-vinyl ketone, a novel radical-mediated annulation provides polycyclic products with high enantio- and diastereoselectivity.
Reduction of gastrointestinal tract colonization by Klebsiella quasipneumoniae using antimicrobial protein KvarIa (2022)

Mouse GI tract colonization with K. quasipneumoniae can be achieved if natural gut microbiota is suppressed by prior antibiotic treatment. The study demonstrates that GI infection caused by K. quasipneumoniae can be significantly reduced using Eudragit®-protected klebicin KvarIa.
High-frequency high-order parallel resonant converter (1989)

A novel approach to the analysis of design of a high-order high-frequency LCC-type capacitive coupled parallel resonant converter (PRC-LCC) operated in the continuous-conduction mode is presented. The presence of an additional capacitor in series with the inductance of the conventional PRC results in a converter with more desirable control characteristics. It is shown that, at switching frequencies lower than the resonant frequency, the gain of the LCC-type converter is lower than the grain of the conventional PRC. This facilitates the converter design with a lower turn-ratio transformer and therefore allows for a higher operating frequency. The complete state-plane diagram of the LCC-type converter, from which a set of steady-state characteristic curves is plotted, is given. Various design curves for component value selections and device ratings are given. A design example with computer simulation results is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Measurement of the dc Kerr and electrostrictive phase modulation in silica (2001)

We report, to our knowledge, the first polarization-resolved measurement of the frequency dependence of both the electronic and the electrostrictive contributions to the dc Kerr coefficient in silica. At the acoustic resonance the perpendicular polarization phase shift is a factor of 2.3 times greater than in the parallel polarization, confirming the presence of strong electrostriction. We find good agreement between the phase-shift measurements and theoretical models of both the polarization and frequency dependence. The analysis indicates the dc Kerr coefficient χ1111(3)(-ω;ω, 0, 0) to be 1.9×10-22 m2/V2. From these results the electrostrictive contribution to a poled-silica device near the device acoustic resonance is expected to be r33,Es=28 pm/V, over an order of magnitude greater than the electronic Kerr electro-optic coefficient r33,Kerr=0.2 pm/V.
Development and Characterization of a Cocrystal as a Viable Solid Form for an Active Pharmaceutical Ingredient (2013)

A phosphoric acid cocrystal of a drug substance candidate at Boehringer Ingelheim was identified from the standard salt form screen and was characterized and shown to have desirable physicochemical properties, stability characteristics, and improved solubility and bioavailability compared to those of the free form. The cocrystal structure was determined by single-crystal X-ray structure analysis and resolved hydrogen-bonding interactions between chains of phosphoric acid molecules and chains of molecules of the free base. Comparison of the key physicochemical properties and biopharmaceutical properties of the cocrystal against a salt form demonstrated the advantage of the cocrystal over the sulfate salt with its superior stability characteristics. The cocrystal was developed as a robust drug substance form for further development and scale-up. The crystallization of the cocrystal form from organic solutions exhibited a strong relationship between water content in the crystallization system and the crystallization kinetics. The effect on the kinetics was used for effective particle size control for the cocrystals, important for optimizing the surface area, dissolution rate, and thus, bioavailability of the drug substance.
Polymake: an approach to modular software design in computational geometry (2001)

polymake is a software package designed for the study of the combinato rics and the geometry of convex polytopes and polyhedra. It offers access to a wide variety of algorithms and tools within a common framework. As a key design feature it allows to incorporate the functionality of a great variety of other software packages in a modular way. polymake is open source software; it is freely available on the Internet at \url{http://www.math.tu-berlin.de/diskregeom/polymake/}. AMS Subject Classification (2000): 52-04 (52Bxx)
Intensive Care Unit Admission Parameters Improve the Accuracy of Operative Mortality Predictive Models in Cardiac Surgery (2010)

A double-stage assessment of operative mortality risk provides a higher accuracy of the prediction. Elevated blood lactates and tachycardia reflect a condition of inadequate cardiac output. Their inclusion in the assessment of the severity of the clinical conditions after cardiac surgery may offer a useful tool to introduce more sophisticated hemodynamic monitoring techniques. Comparison between the predicted operative mortality risk before and after the operation may offer an assessment of the operative performance.
A Wideband Sliding Correlator based Channel Sounder in 65 nm CMOS: An Evaluation Board Design (2020)

Wide swaths of bandwidth at millimeter-wave (mm- Wave) and Terahertz (THz) frequencies stimulate diverse applications in wireless sensing, imaging, position location, cloud computing, and much more. These emerging applications motivate wireless communications hardware to operate with multi- Gigahertz (GHz) bandwidth, at nominal costs, minimal size, and power consumption. Channel sounding system implementations currently used to study and measure wireless channels utilize numerous commercially available components from multiple manufacturers that result in a complex and large assembly with many costly and fragile cable interconnections between the constituents and commonly achieve a system bandwidth under one GHz. This paper presents an evaluation board (EVB) design that features a sliding correlator based channel sounder with 2 GHz null-to-null RF bandwidth in a single monolithic integrated circuit (IC) fabricated in 65 nm CMOS technology. The EVB landscape provides necessary peripherals for signal interfacing, amplification, buffering, and enables integration into both the transmitter and receiver of a channel sounding system, thereby reducing complexity, size, and cost through integrated design. The channel sounder IC on the EVB is the world's first to report gigabit-per-second baseband operation using low-cost CMOS technology, allowing the global research community to now have an inexpensive and compact channel sounder system with nanosecond time resolution capability for the detection of multipath signals in a wireless channel.
Design of Co∕Pd multilayer system with antiferromagnetic-to-ferromagnetic phase transition (2008)

Among the known magnetic material systems, most are either purely antiferromagnetic or purely ferromagnetic at temperatures up to their critical temperature. There are only very few examples of materials that undergo a temperature dependent phase transition from an antiferromagnetic to a ferromagnetic phase or vice versa, and of these, only the chemically ordered alloy FeRh exhibits this transition near room temperature. Here we present a perpendicular anisotropy multilayer structure that by careful tuning of the constituent layers and their coupling mimics the magnetic behavior of FeRh, yet allows great flexibility in tuning its magnetic properties over a wide temperature range.
Throughput scaling in random wireless networks (2006)

Abstract — We propose and analyze two models of networks in which pairs of nodes communicate over a shared wireless medium. We are interested in the maximum total aggregate traffic flow that is possible through the network. Our first model differs substantially from most existing models in that the channel connections in our network are entirely random: we assume that, rather than being governed by geometry and a decay law, the strength of the connections between nodes is drawn independently from a common distribution. The next model is more general and works at two scales. At a local scale, characterized by nodes being within a distance r from each other, connections are drawn independently from some distribution, but at a global scale, characterized by nodes being further apart from each other than a distance r, channel connections are governed by a Rayleigh distribution, with the power satisfying a distance-based decay law. For both models we show that an appropriate distribution for the channel strengths and other parameters can give a throughput that scales almost linearly in the number of nodes of the network. This is a significant improvement over the square-root scaling that has been shown in several previous works. I.
Processing body sensor data streams for continuous physiological monitoring (2010)

With the recent advancement in the wearable sensor technology, various body sensor network systems are being incorporated in the garments to monitor continuous physiological as well as motor behavior of an individual. The raw physiological time series data coming from on-body sensors requires a thorough analysis for extraction of meaningful information. In addition, extracted information need to be presented/recommended to monitoring personnel/self to derive the high-level interpretation of the physiological state without having domain knowledge.In this paper, we propose a knowledge management system that extracts and conveys the information of the physiological states using individualized factor analysis model. The factor analysis based on the quantitative features extracted from the raw data streams provides the hidden knowledge components in the form of latent factors. We tested this system on the raw electromyogram signals from the hand muscles collected during the continuous monitoring of repetitive hand movements, where the hidden information in the form of intensity level of the activity and the muscle fatigue was extracted from the time and frequency domain features.
Insight into the Mechanism of Hydrogenation of Amino Acids to Amino Alcohols Catalyzed by a Heterogeneous MoOx‐Modified Rh Catalyst (2014)

Hydrogenation of amino acids to amino alcohols is a promising utilization of natural amino acids. We found that MoOx -modified Rh/SiO2 (Rh-MoOx /SiO2 ) is an efficient heterogeneous catalyst for the reaction at low temperature (323 K) and the addition of a small amount of MoOx drastically increases the activity and selectivity. Here, we report the catalytic potential of Rh-MoOx /SiO2 and the results of kinetic and spectroscopic studies to elucidate the reaction mechanism of Rh-MoOx /SiO2 catalyzed hydrogenation of amino acids to amino alcohols. Rh-MoOx /SiO2 is superior to previously reported catalysts in terms of activity and substrate scope. This reaction proceeds by direct formation of an aldehyde intermediate from the carboxylic acid moiety, which is different from the reported reaction mechanism. This mechanism can be attributed to the reactive hydride species and substrate adsorption caused by MoOx modification of Rh metal, which results in high activity, selectivity, and enantioselectivity.
First-principles study on the electronic, optical and thermodynamic properties of ABO3 (A = La,Sr, B = Fe,Co) perovskites (2017)

The electronic, optical and thermodynamic properties of ABO<sub>3</sub> (A = La,Sr, B = Fe,Co) perovskites are investigated using first-principles calculations.
ChemInform Abstract: BEWEIS FUER DEN VERLAUF DER 1,2‐VERSCHIEBUNG IN STEREOCHEMISCH NICHT STARREN MONOHAPTOCYCLOPENTADIENYLMETALLVERBINDUNGEN (1970)

Abstract Aus den PMR‐Spektren der Verbindungen (I) bei tiefer Temperatur und den Kopplungskonstanten ergibt sich, daß die Umlagerung des Monohaptoringes durch eine 1,2‐Verschiebung erfolgt.
Protein Phosphatase 1α Interacts with Venezuelan Equine Encephalitis Virus Capsid Protein and Regulates Viral Replication through Modulation of Capsid Phosphorylation (2018)

Protein phosphatase 1 (PP1) is a serine/threonine phosphatase which has been implicated in the regulation of a number of viruses, including HIV-1, Ebolavirus, and Rift Valley fever virus. Catalytic subunits of PP1 (PP1α, PP1β, and PP1γ) interact with a host of regulatory subunits and target a wide variety of cellular substrates through a combination of short binding motifs, including an RVxF motif present in the majority of PP1 regulatory subunits. Targeting the RVxF-interacting site on PP1 with the small molecule 1E7-03 inhibits HIV-1, Ebolavirus, and Rift Valley fever virus replication. In this study, we determined the effect of PP1 on Venezuelan equine encephalitis virus (VEEV) replication. Treatment of VEEV-infected cells with 1E7-03 decreased viral replication by more than 2 logs (50% effective concentration [EC<sub>50</sub>] = 0.6 μM). 1E7-03 treatment reduced viral titers starting at 8 h postinfection. Viral replication was also decreased after treatment with PP1α-targeting small interfering RNA (siRNA). Confocal microscopy demonstrated that PP1α shuttles toward the cytosol during infection with VEEV and that PP1α colocalizes with VEEV capsid. Coimmunoprecipitation experiments confirmed VEEV capsid interaction with PP1α. Furthermore, immunoprecipitation and mass spectrometry data showed that VEEV capsid is phosphorylated and that phosphorylation is moderated by PP1α. Finally, less viral RNA is associated with capsid after treatment with 1E7-03. Coupled with data showing that 1E7-03 inhibits several alphaviruses, this study indicates that inhibition of the PP1α RVxF binding pocket is a promising therapeutic target and provides novel evidence that PP1α modulation of VEEV capsid phosphorylation influences viral replication.<b>IMPORTANCE</b> Venezuelan equine encephalitis virus (VEEV) causes moderate flu-like symptoms and can lead to severe encephalitic disease and potentially death. There are currently no FDA-approved therapeutics or vaccines for human use, and understanding the molecular underpinning of host-virus interactions can aid in the rational design of intervention strategies. The significance of our research is in identifying the interaction between protein phosphatase 1 (PP1) and the viral capsid protein. This interaction is important for viral replication, as inhibition of PP1 results in decrease viral replication. Inhibition of PP1 also inhibited multiple biomedically important alphaviruses, indicating that PP1 may be a potential therapeutic target for alphavirus-induced disease.