gebhart/patrepeval huggingface dataset:
MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands (2023)

Affinity ranking of structurally diverse small-molecule ligands is a challenging problem with important applications in structure-based drug discovery. Absolute binding free energy methods can model diverse ligands, but the high computational cost of the current methods limits application to data sets with few ligands. We recently developed MELD-Bracket, a Molecular Dynamics method for efficient affinity ranking of ligands [ <i>JCTC</i> 2022, 18 (1), 374-379]. It utilizes a Bayesian framework to guide sampling to relevant regions of phase space, and it couples this with a bracket-like competition on a pool of ligands. Here we find that 6-competitor MELD-Bracket can rank dozens of diverse ligands that have low structural similarity and different net charges. We benchmark it on four protein systems─PTB1B, Tyk2, BACE, and JAK3─having varied modes of interactions. We also validated 8-competitor and 12-competitor protocols. The MELD-Bracket protocols presented here may have the appropriate balance of accuracy and computational efficiency to be suitable for ranking diverse ligands from typical drug discovery campaigns.
Toward Coherent Control of Single Yb3+ Ions in a Nanophotonic Cavity (2019)

We report on detection and coherent optical driving of single Yb3+ ions coupled to a nanophotonic resonator fabricated in the YVO4 host crystal and outline a path toward control of single 171Yb3+ spins.
Automated Multi-Objective Design Optimization of PM AC Machines Using Computationally Efficient FEA and Differential Evolution (2013)

The design optimization methods described in this paper are employing an ultrafast computationally efficient finite element analysis technique. A minimum number of magnetostatic solutions are used for the analysis, which makes possible the study of thousands of candidate motor designs with typical PC-workstation computational resources. A multi-objective differential evolution algorithm that considers a large number of independent stator and rotor geometric variables and performance criteria, such as average and ripple torque, losses, and efficiency, is used. The optimization method is demonstrated on different permanent magnet (PM) ac synchronous motors in the kilowatt and megawatt power ranges. For the low-power PM ac machine study, a nine-slot six-pole topology is considered. For the high-power PM ac machines, four case studies were carried out with the following: fractional-slot embedded surface PM (SPM), fractional-slot interior PM (IPM), integer-slot SPM, and integer-slot IPM, respectively. Four motor topologies are systematically compared based on optimal Pareto sets. The design optimization of IPM motors includes an additional search for an optimum operating torque angle corresponding to the maximum-torque-per-ampere condition.
Radio channel characterization at 5.85 GHz for wireless M2M communication of industrial robots (2016)

The fourth industrial revolution, also referred to as Industrie 4.0, has triggered a number of research projects to improve communication systems for industrial environments. Wireless technologies for mission-critical machine-to-machine communication are expected to enable very efficient and highly flexible production processes. It is especially challenging for wireless interfaces to fulfill the required end-to-end latency and the reliability constraints of the automation industry. In order to design novel PHY and MAC schemes for ultra low delay, ultra reliable and deterministic transmission of data, e.g., through optimized pulse shaping, we study the indoor radio propagation in a representative factory automation cell where industrial robots are to be controlled. We performed channel measurements using a broadband channel sounder at 5.85 GHz carrier frequency. During the measurements, the robots were in motion and executed a typical pick-and-place process. From the recorded data we evaluate the channel characteristics and calculate relevant delay statistics. We distinguish two measurement series that differ in the scattering environment and present the derived parameters. Finally, we discuss the impact of our results on the design of new 5G waveforms for industrial radio systems.
Distinguishing dispersion from distributed scattering in S2fiber mode analysis (2013)

We introduce a new spectrogram approach for analyzing spatially- and spectrally-resolved interferometry (S<sup>2</sup>) data that overcomes the previously overlooked ambiguity between dispersion and distributed scattering. Traditionally, S<sup>2</sup> yields a one-dimensional spectrum of inter-modal group delays between higher-order-modes (HOMs) and the dominant fundamental mode. According to this interpretation, inter-modal group delay broadening is considered to be a location signature of HOM scattering; for example, a narrow peak in the spectrum is interpreted to be a discrete scattering event whereas a broad feature is interpreted to be distributed scattering along the fiber. Since the inter-modal dispersion is high for weakly guided HOMs, discrete scattering events will also manifest as broadened features. For the first time, we demonstrate a spectrogram approach to S<sup>2</sup> analysis in which the spectral interference data is analyzed over small staggered wavelength windows and the inter-modal group delay is plotted as a function of wavelength. In this new two-dimensional map the wavelength dependence of the inter-modal group delay produces an inclination of streaks traversing the spectrogram. This new perspective resolves the ambiguity as to whether group delay broadening is caused by fiber dispersion or distributed scattering that is inherent to the previous one-dimensional S<sup>2</sup> mapping. The spectrogram is a more accurate map of mode conversion along the fiber length and is essential for evaluating high power fibers and devices. Results for standard telecom single mode fiber and a large-mode-area fiber are presented.
Channel occupancy time distribution in a cellular radio system (1987)

The distribution of the channel occupancy time in a cellular radio system is studied, namely, the distribution of the time spent by customers on one frequency channel within a given cell. Two approaches are used. The first one relies on a computer simulation allowing a general model for mobiles behavior. The second is analytical, and assume a simplified system where mobiles keep constant directions. The results of both methods are compared with a fitted exponential distribution, and excellent agreements are found for most practical situations. In addition, a simple expression giving the average number of handoffs for a random customer is obtained. The results derived in this paper provide useful and simple tools to analyze cellular systems.
Controlling the confinement of fullerene C60 molecules using a saddle shape Ni(ii) macrocycle (2008)

A saddle-shaped Ni-macrocycle bearing flexible benzyl arms, Ni(TBTAA), 1, has been prepared and structurally authenticated in the solid state as a toluene adduct, with the toluene residing in the extended cavity of the macrocycle, close to two of benzylic substituents. The Ni-macrocycle forms a crystalline inclusion complex with fullerene C60, {C60∩(1)2}·(toluene)5, 2, which has each fullerene encapsulated by two macrocycles involving π⋯π interactions to the phenyl lined face of the macrocycles, as well as CH⋯π from the benzyl groups and toluene molecules closing up the fullerene surface. The CH⋯π for the benzyl groups effectively increases the steric demands of the macrocycle over the surface of the fullerene, circumventing any fullerene⋯fullerene interactions. The nature of the interactions in the fullerene complex has been probed using Hirshfeld surface analysis.
Bone morphogenetic proteins and the synovial joints (2004)

Bone morphogenetic proteins (BMPs) are involved in a broad array of morphogenetic processes. These span from the specification of the dorso-ventral body axis to patterning, organogenesis and differentiation of most tissues. Nevertheless, the initial discovery of BMPs as protein preparations that induced ectopically and in vivo a cascade of endochondral bone formation in rats, has strongly stimulated the study of their role in the development of the skeleton and in patterning of the synovial joints [1-3]. Additionally, with their remarkable cartilage and bone morphogenetic activity, BMPs represent an attractive therapeutic option for skeletal and joint disorders. Indeed, growing scientific evidence supports the concept that tissue repair and regeneration recapitulates to a certain extent the process of tissue formation during embryonic development. Recent advances in unraveling the molecular basis of developmental processes support BMP signaling as potential targets in reparative approaches in joint diseases.
Enzyme Fuel Cell for Cellulolytic Sugar Conversion Employing FAD Glucose Dehydrogenase and Carbon Cloth Electrode Based on Direct Electron Transfer Principle~!2010-01-09~!2010-02-04~!2010-05-17~! (2010)

An enzyme fuel cell employing a carbon cloth electrode and bacterial FAD dependent glucose dehydrogenase (FADGDH) based on the direct electron transfer principle was constructed, and its scalability and cellulolytic sugar conversion were investigated. FADGDH was immobilized on the carbon cloth electrode together with carbon paste to form a multi-module type enzyme fuel cell by combining platinum-supported carbon immobilized carbon cloth as the cathode. The enzyme fuel cell was stable for more than 7 days of continuous operation. The 3 3 module (18 cm 2 ) enzyme fuel cell generated 68 W (3.8 W/cm 2 ) using glucose as the substrate, which was almost 9 times that of a single-module enzyme fuel cell. Thanks to the substrate specificity of bacterial FADGDH, cellulolytic sugars were revealed to be a good substrate for the enzyme fuel cell with cellobiose (9.3 W/cm 2 ), cellotriose (9.2 W/cm 2 ), or cellotetraose (6.3 W/cm 2 ). These results demonstrated that together with the feasibility of using carbon cloth as the electrode material, FADGDH as the anode catalyst will become the norm in electrochemical biomass applications in the future.
Upconversion photoluminescence in poly(ladder-type-pentaphenylene) doped with metal (II)-octaethyl porphyrins (2005)

We report on the optimization of the upconversion photoluminescence in films of conjugated polymers doped with platinum porphyrin. The upconversion emission was observed to take place at pump intensities as low as 0.5kW∕cm2. Comparison between the photoluminescence integral intensity of polyfluorene and ladder-type pentaphenylene polymer shows a five-fold increase of the efficiency of the upconversion process for the latter. The higher upconversion efficiency can be partially attributed to the reduced reabsorption of the photoluminescence in the case of the ladder-type pentaphenylene matrix.
Chemical oxygen-iodine laser for decommissioning and dismantlement of nuclear facilities. (2000)

Conceptual designs of a Chemical Oxygen-Iodine Laser (COIL) facility for decommissioning and dismantlement (D&D) of nuclear facility is proposed. The requisite output power and beam quality was determined based on our preliminary experiments of nonmetal material processing. Assuming the laser power of 30kW it is derived that the begun quality of M2=36 is required to cut a biological shield wall (1000mm thickness) of a nuclear power plant at a cutting speed of 10mm/min. Then the requisite specification of an optical fiber to deliver the laser is calculated. The mass flow and heat balance of proposed facility is calculated based on our recent COIL studies. With the high-pressure subsonic mode, the vacuum pump size is minimized compared to the supersonic operation. Finally, the size of facility is estimated assuming two-hour continuous operation. It is revealed that such a system can be packed in five railway containers (6058mm×2438mm×2438mm).
Ultrasensitive Single Extracellular Vesicle Detection Using High Throughput Droplet Digital Enzyme-Linked Immunosorbent Assay (2022)

Extracellular vesicles (EVs) have attracted enormous attention for their diagnostic and therapeutic potential. However, it has proven challenging to achieve the sensitivity to detect individual nanoscale EVs, the specificity to distinguish EV subpopulations, and a sufficient throughput to study EVs among an enormous background. To address this fundamental challenge, we developed a droplet-based optofluidic platform to quantify specific individual EV subpopulations at high throughput. The key innovation of our platform is parallelization of droplet generation, processing, and analysis to achieve a throughput (∼20 million droplets/min) more than 100× greater than typical microfluidics. We demonstrate that the improvement in throughput enables EV quantification at a limit of detection = 9EVs/μL, a >100× improvement over gold standard methods. Additionally, we demonstrate the clinical potential of this system by detecting human EVs in complex media. Building on this work, we expect this technology will allow accurate quantification of rare EV subpopulations for broad biomedical applications.
Coatings for Automotive Planetary Gearsets (2003)

The operating environment in typical automotive planetary gearsets leads to harsh tribological conditions. Relatively low operating speeds combined with low viscosity lubricants hinder the formation of protective oil films. As power density increases, gear surface fatigue (pitting) limits gear life and the life of the transmission as a whole. Coatings have been found to be effective in extending pitting fatigue life of gears. The authors have tested a number of different coatings over the last ten years. Some of them increased gear life by fifteen times in bench tests. The most successful coatings have been hard, ceramic coatings such as B4C and Diamond-Like Carbon (DLC) that smooth the mating surface and improve the lubrication conditions in the contact. Recently CrN, a widely available and affordable coating, has been studied and found to be a good alternative to other coatings.
Competing populations and decision making (2014)

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1991 Volvo Award in experimental studies. Cauda equina syndrome: neurologic recovery following immediate, early, or late decompression. (1991)

An animal model of cauda equina syndrome was developed. Neurologic recovery was analyzed following immediate, early, and delayed decompression. Five experimental groups, each containing six dogs, were studied. Compression of the cauda equina was performed in all 30 dogs following an L6-7 laminectomy. The cauda equina was constricted by 75% in each group. The first group was constricted and immediately decompressed. The remaining groups were constricted for 1 hour, 6 hours, 24 hours, and 1 week, respectively, before being decompressed. Somatosensory evoked potentials were performed before and after surgery, before and immediately after decompression, and 6 weeks following decompression. Daily neurologic exams using the Tarlov grading scale were performed. At 6 weeks postdecompression, all dogs were killed, and the neural elements analyzed histologically. Following compression, all 30 dogs had significant lower extremity weakness, tail paralysis, and urinary incontinence. All dogs recovered significant motor function 6 weeks following decompression. The dogs with immediate decompression generally recovered neurologic function within 2-5 days. The dogs receiving 1-hour and 6-hour compression recovered within 5-7 days. The dogs receiving 24-hour compression remained paraparetic 5-7 days, with bladder dysfunction for 7-10 days and tail dysfunction persisting for 4 weeks. The dogs with compression for 1 week were paraparetic (Tarlov Grade 2 or 3) and incontinent during the duration of cauda equina compression. They recovered to walking by 1 week and Tarlov Grade 5 with bladder and tail control at the time of euthanasia. Immediately after compression, all five groups demonstrated at least 50% deterioration of the posterior tibial nerve evoked potential amplitudes.(ABSTRACT TRUNCATED AT 250 WORDS)
Phase I dose-escalation study of tumor necrosis factor-alpha and concomitant radiation therapy. (2006)

The maximal tolerated dose of tumor necrosis factor-alpha when given with radiotherapy is at least 150 microg/m2 and a dose-limiting toxicity was not observed. Future studies will show whether responses to treatment are increased over those expected with radiation alone. Tumor localization of tumor necrosis factor-alpha by gene therapy combined with radiation therapy may eliminate the systemic toxicity we observed.
Controlling the Regiospecific Oxidation of Aromatics via Active Site Engineering of Toluene para-Monooxygenase of Ralstonia pickettii PKO1 (2004)

A primary goal of protein engineering is to control catalytic activity. Here we show that through mutagenesis of three active site residues, the catalytic activity of a multicomponent monooxygenase is altered so that it hydroxylates all three positions of toluene as well as both positions of naphthalene. Hence, for the first time, an enzyme has been engineered so that its regiospecific oxidation of a substrate can be controlled. Through the A107G mutation in the alpha-subunit of toluene para-monooxygenase, a variant was formed that hydroxylated toluene primarily at the ortho-position while converting naphthalene to 1-naphthol. Conversely, the A107T variant produced >98% p-cresol and p-nitrophenol from toluene and nitrobenzene, respectively, as well as produced 2-naphthol from naphthalene. The mutation I100S/G103S produced a toluene para-monooxygenase variant that formed 75% m-cresol from toluene and 100% m-nitrophenol from nitrobenzene; thus, for the first time a true meta-hydroxylating toluene monooxygenase was created.
A novel polylocus method for linkage analysis using the lod‐score or affected sib‐pair method (1993)

Abstract A novel approach to combining data from multiple linked loci is proposed that can provide substantial increases in power over normal two‐point linkage analysis or sib‐pair analysis, with a substantial saving in computing time over traditional multipoint methods. © 1993 Wiley‐Liss, Inc.
Utility of rapid prototyping in Complex DORV: does it alter management decisions? (2016)

Complex ventricular-arterial (VA) relationships in patients with double outlet right ventricle (DORV) make preoperative assessment of potential repair pathways challenging. The relationship of the ventricular septal defect (VSD) to one or both great arteries must be understood and this influences the choice of surgical procedure [1] In neonates and infants with DORV, Computed Tomography (CT) is often performed due to the ability to get high spatial resolution and ECG gated images [2], however it is possible to get the necessary information from Magnetic Resonance (MR) imaging with an added advantage of avoiding exposure to ionizing radiation. Both CT and MR allow image acquisition in three dimensions (3D) but traditional viewing of the anatomy using the multiplanar reformatting is actually done in two dimensions (2D). Volume rendering from either modality may also be performed, but typically only the external vascular anatomy is depicted. We hypothesized that it is possible to accurately define the intracardiac anatomy in infants with DORV using virtual and physical 3D printed (rapid prototyped) models created from either MR or CT and this can both aid in better defining potential VA pathways and may assist in surgical decision making.
Development of a CELestial Infrared Nuller Experiment (CELINE) for broadband nulling and new single-mode fiber testing (2010)

The small angular distance (&lt;100 mas) and the huge flux ratio (10<sup>7</sup>) between an Earth-like exoplanet in the socalled habitable zone and its host star makes it very difficult to direct image such systems. Nulling interferometry consists of a very powerful technique that combines destructively the light from two or more collectors to dim the starlight and to reveal faint companions in its vicinity. We have developed a new nulling experiment based on the fiber nuller principle. This fully symmetric reflective nulling bench aims at testing broadband nulling in both H and K bands as well as characterizing photonic fibers for modal filtering. We present in this paper the design, the development as well as preliminary results of the experiment.
Output power enhancement in AlGaN/GaN heterostructure field-effect transistors with multilevel metallization (2016)

Abstract To improve wafer utilization efficiency and heat dissipation performance, this paper proposes multilevel metallization-structured, lateral-type AlGaN/GaN heterostructure field-effect transistors (HFETs) on a 150 mm Si substrate using photosensitive polyimide (PSPI) as the intermetal dielectric layer. The maximum drain current of the HFETs is 46.3 A, which is 240% higher than that of conventional AlGaN/GaN HFETs with the same die size. Furthermore, the drain current drop of the HFETs under high-bias operation is reduced from 14.07 to 8.09%, as compared to that of conventional HFETs.
AzTEC: A new millimeter-wave camera (2007)

AzTEC is a large-format bolometer array camera developed at the University of Massachusetts, Amherst, and will serve as one of the first facility instruments of the Large Millimeter Telescope (LMT). AzTEC’s detector array is comprised of 144 silicon nitride micromesh bolometers with a bandpass defined through a series of changeable filters and coupling optics. AzTEC was recently commissioned at 1.1 millimeters on the James Clerk Maxwell Telescope (JCMT) and successfully completed its first science-grade observing run in the winter 2005/2006. We experienced excellent performance throughout the run, with a median raw per-pixel sensitivity to point-like sources of 14 mJy √s. We present the instrument design and achieved specifications, as well as the nature of AzTEC data and its format. We also discuss calibration and observing strategies for using the AzTEC instrument.
Hearing the Way Forward: Exploring Ambient Navigational Awareness with Reduced Cognitive Load through Spatial Audio-AR (2023)

Notifications and alerts can both convey critical data needed to make decisions as we go about our day, and at the same time be completely ignored as a result of the overuse of these channels. Auditory notifications can be especially intrusive given their demand for synchronous attention. However, during some activities, such as navigation guidance via GPS, immediate information cues are necessary. In this case audio alerts and instructions are typically implemented as voice commands, but processing language requires significant cognitive resources and attention. In this study we report findings about the feasibility of a novel ambient pedestrian guidance system inspired by neuroscience. Results suggest that it is possible to communicate precise spatial actions without the intrusion of verbal turn-by-turn cues. We also share learnings from our use of low-fidelity prototyping to evaluate the novel audio-AR interaction.
Nickel-Catalyzed Addition of C–C Bonds of Amides to Strained Alkenes: The 1,2-Carboaminocarbonylation Reaction (2022)

C(aryl)-C(═O) bonds of aryl amides can be activated and added across alkenes with the aid of a nickel catalyst. This 1,2-carboaminocarbonylation reaction enables the dicarbofunctionalization of alkenes with an atom economy of 100%.