gebhart/patrepeval huggingface dataset:
Reverse-engineering human olfactory perception from chemical features of odor molecules (2016)

Abstract Despite 25 years of progress in understanding the molecular mechanisms of olfaction, it is still not possible to predict whether a given molecule will have a perceived odor, or what olfactory percept it will produce. To address this stimulus-percept problem for olfaction, we organized the crowd-sourced DREAM Olfaction Prediction Challenge. Working from a large olfactory psychophysical dataset, teams developed machine learning algorithms to predict sensory attributes of molecules based on their chemoinformatic features. The resulting models predicted odor intensity and pleasantness with high accuracy, and also successfully predicted eight semantic descriptors (“garlic”, “fish”, “sweet”, “fruit”, “burnt”, “spices”, “flower”, “sour”). Regularized linear models performed nearly as well as random-forest-based approaches, with a predictive accuracy that closely approaches a key theoretical limit. The models presented here make it possible to predict the perceptual qualities of virtually any molecule with an impressive degree of accuracy to reverse-engineer the smell of a molecule. One Sentence Summary Results of a crowdsourcing competition show that it is possible to accurately predict and reverse-engineer the smell of a molecule.
Atovaquone and Proguanil Hydrochloride: A Review of Nonclinical Studies (1999)

Nonclinical studies of atovaquone and proguanil hydrochloride supported the clinical development of this combination for treatment and prophylaxis of malaria.
<i>In-vitro</i>detection of artificial caries on vertical dental cavity walls using infrared photothermal radiometry and modulated luminescence (2012)

The main objective of the study was to investigate the ability of frequency-domain photothermal radiometry (PTR) and modulated luminescence (LUM) to detect secondary caries lesions on the walls of restorations (wall lesions). Changes in experimental PTR-LUM signals due to sequential demineralization on entire vertical walls of sectioned tooth samples were investigated. In addition, transverse micro-radiography (TMR) analysis (used as a gold standard) was conducted to measure the degree of demineralization that occurred in each sample. Statistical correlation between TMR results and PTR-LUM signals was determined using Pearson's correlation coefficient. LUM signals were found to be dominated by the scattered component of the incident laser beam. The more clinically relevant cases of localized demineralization and remineralization on vertical walls were also investigated to examine whether PTR-LUM signals are sensitive to demineralization and remineralization of much smaller areas. The overall results demonstrated that PTR-LUM is sensitive to progressive demineralization and remineralization on vertical walls of sectioned tooth samples.
Development of 3D Measurement System using Phase Shift Digital Holography (2013)

In these years, demand for three-dimensional measurement technology is higher. However, in many of the traditional three-dimensional measurement methods, such as the method using phase shift patterns projection, it is difficult to measure shape of specular reflective and transparent objects, because power of reflected light is too high from specular reflective objects or too low from transparent objects, so that information of reflected light cannot be acquired accurately by digital camera. Digital holography has been used for resolving this problem. In traditional digital holography, interference fringe of measure object's light wave and reference light wave is recorded by digital camera. Using Fresnel diffraction principle, phase information of measure object's light wave can be required and shape of measure object can be calculated using interferometry principle. It can be used for reflective and transparent objects measurement, but as the principle of Fresnel diffraction, DC and conjugate components exist in calculated phase information as noises, so accuracy of measurement is lower. Phase shift digital holography is able to remove noises using special devices to change phase of reference light wave, but the devices are high price and the system is complex, so practical application of phase shift digital holography is difficult. In this paper, we propose a new method of phase shift digital holography using light detection principle. Simultaneously, we propose a digital holography reconstruction method using the convolution approach rather than the traditional Fresnel approach. The proposal method realized a compact phase shifting holography system with low price and a high accuracy three-dimensional measurement method. Therefore, we are able to realize the practical applications of digital holography with low price and higher accuracy.
Petrofacies Determination in Unconventional Reservoirs Driven by a Simulation-to-Seismic Process (2015)

Abstract It is well-understood that hydraulic rock types categorize flow unit regimes in porous media such that modeling of these regimes according to hydraulic conductivity is possible in a reservoir simulator. This hydraulic characterization is necessary in reservoir simulation to spatially dictate multiphase flow behavior throughout the modeled reservoir. The spatial delineation of these multiphase data then relies on a singular relationship between petrophysical properties, which can be used to assign the multiphase properties to the simulation grid; the properties and requisite relationship of choice are between absolute permeability and porosity. This paper illustrates that a simulation-to-seismic modeling approach can be used to reconcile large-scale flow disparities in the dynamic reservoir model, resultant of diminished spatial constraints during the creation of the static petrophysical model with seismic attribute array data. The results demonstrate that the assignment of multiphase hydraulic descriptions to petrofacies have considerable control on simulated rates and produced volumes. The examination of selected simulation scenarios leads to the conclusion that petrofacies, when derived considering petrophysical cutoffs and hydraulic rock types, provide an alternative to incorporating depositional facies constraints during the modeling of select shale reservoirs, wherein the understanding of a regionalized modeling constraint is limited. Additionally, it is shown that geologic facies are not flow units while they are considered regionalized variables. The uncertainty associated with unconstrained petrofacies is then recognized as broad; but, it is accepted that this modeled petrophysical system allows for the described petrofacies to be used as a proxy for hydraulic conductivity in the absence of a facies-based spatial constraint. A novel approach is introduced in this work to construct petrofacies from log curves and core data to relate hydraulic rock types and petrophysical properties to the simulation grid using a methodology that honors the available seismic. The mathematical formulation used to describe petrofacies can be modest or elaborate; however, they differ from geologic facies, which can be described as regionalized variables. Unlike geologic facies, petrofacies do not adhere to interpretable geometries and thus might not be considered as regionalized variables or functionally modeled with deterministic or stochastic algorithms.
<title>Tomographic image reconstruction and rendering with texture-mapping hardware</title> (1994)

The image reconstruction problem, also known as the inverse Radon transform, for x-ray computed tomography (CT) is found in numerous applications in medicine and industry. The most common algorithm used in these cases is filtered backprojection (FBP), which, while a simple procedure, is time-consuming for large images on any type of computational engine. Specially-designed, dedicated parallel processors are commonly used in medical CT scanners, whose results are then passed to graphics workstation for rendering and analysis. However, a fast direct FBP algorithm can be implemented on modern texture-mapping hardware in current high-end workstation platforms. This is done by casting the FBP algorithm as an image warping operation with summing. Texture-mapping hardware, such as that on the Silicon Graphics Reality Engine (TM), shows around 600 times speedup of backprojection over a CPU-based implementation (a 100 Mhz R4400 in this case). This technique has the further advantages of flexibility and rapid programming. In addition, the same hardware can be used for both image reconstruction and for volumetric rendering. The techniques can also be used to accelerate iterative reconstruction algorithms. The hardware architecture also allows more complex operations than straight-ray backprojection if they are required, including fan-beam, cone-beam, and curved ray paths, with little or no speed penalties.
Structured Memory based Deep Model to Detect as well as Characterize Novel Inputs (2018)

While deep learning has pushed the boundaries in various machine learning tasks, the current models are still far away from replicating many functions that a normal human brain can do. Explicit memorization based deep architecture have been recently proposed with the objective to understand and predict better. In this work, we design a system that involves a primary learner and an adjacent representational memory bank which is organized using a comparative learner. This spatially forked deep architecture with a structured memory can simultaneously predict and reason about the nature of an input, which may even belong to a category never seen in the training data, by relating it with the memorized past representations at the higher layers. Characterizing images of unseen object classes in both synthetic and real world datasets is used as an example to showcase the operational success of the proposed framework.
Adaptive control of multiple beam satellite transponders (2002)

The adaptive control of multiple beam transponders is proposed to more effectively use satellite resources. This adaptive control provides a means to configure coverage areas, allocate bandwidth, and maintain power control in response to demands for satellite services. A simple example illustrates the features of this concept.
User-to-User Delegation in a Federated Identity Environment (2011)

Abstract- Delegation protocols over the Web are mostly used for user-to-machine and machine-to-machine delegations. As more organizations operate in a federated identity environment, user-to-user delegation also becomes a required functionality. User-to-machine or machine-to-machine delegation methods cannot directly apply to user-to-user delegation because human cannot effectively process protocol messages. This paper proposes a new method that allows user-to-user delegations in a federated identity environment. The identity provider (IdP) acts as the delegation authority that manages delegations. Service providers (SPs) in the same environment can use this delegation service, instead of managing delegations individually. The service includes delegation assignment, invocation, and revocation. The method allows service providers to exercise access controls and to decide if the delegator has the right to delegate and if the delegatee should be authorized to perform the requested services. This method is applicable to any access control models.
Abstract 287: Erythropoietin Enables Mitochondria to Preserve Oxidative Phosphorylation Under Conditions of Calcium Overload and Oxidative Stress (2011)

Introduction: We previously reported in rats that a single bolus dose of erythropoietin (Epo) given at the start of CPR enhanced, within minutes, the efficacy of chest compression. The effect was attributed to attenuation of reductions in left ventricular distensibility; an effect previously linked to preservation of mitochondrial bioenergetic function. Hypothesis: We now investigated whether Epo could enable mitochondria to maintain oxidative phosphorylation under conditions of calcium overload and oxidative stress, which are central to injury caused by ischemia and reperfusion. Methods: Mitochondria were isolated from the left ventricle of hearts harvested from groups of rats (n=3) that received during spontaneous circulation no Epo or received Epo (5,000 U/kg) in bolus dose into the right atrium at 60, 240, and 480 seconds before harvest. Separate aliquots of mitochondria were subjected to incremental concentrations of calcium (1.5, 12.5, and 25 µM free calcium) or tert-butyl hydroperoxide (250 and 5000 µM). Phosphate:oxygen (P:O) ratios were then measured in a respiration chamber (MT 200, Mitocell, Strathkelvin Instruments). Results: Epo, in a time dependent manner, prevented reductions in P:O ratios observed when mitochondria were exposed to incremental concentrations of calcium or tert-butyl hydroperoxide (Table). Conclusions: Preservation of left ventricular myocardial distensibility could partly result from a favorable effect of Epo enabling mitochondria to resist injury caused by calcium overload and oxidative stress, and within a response time sufficiently rapid to favorably impact cardiac resuscitation.
A novel, site-specific, aromatic hydroxylation by mutants of Pseudomonas testosteroni (1979)

G. O. Daumy, A. S. McColl and G. C. Andrews, J. Chem. Soc., Chem. Commun., 1979, 1073a DOI: 10.1039/C3979001073A
Respiration‐induced B<sub>0</sub>field fluctuation compensation in balanced SSFP: Real‐time approach for transition‐band SSFP fMRI (2006)

In functional MRI (fMRI) the resonance frequency shift induced from respiration is a major source of physiological noise. In transition-band SSFP fMRI the respiration-induced resonance offset not only increases noise interference, it also shifts the activation band. This leads to a reduction in the contrast-to-noise ratio (CNR) and the potential for varying contrast levels during the experiment. A novel real-time method that compensates for the respiration-induced resonance offset frequency is presented. This method utilizes free induction decay (FID) phase information to measure the resonance offset. For compensation, one can update the resonant frequency in real time by changing the transmit RF pulse and receiver phases to track the measured offset. The results show decreased signal power in the respiration frequency band and increased numbers of activated voxels with higher Z-scores compared to uncompensated experiments.
RabGEF1 regulates stem cell factor/c-Kit-mediated signaling events and biological responses in mast cells (2006)

We recently reported that RabGEF1 is a negative regulator of high-affinity Fc receptor for IgE (Fc epsilonRI)-dependent mast cell activation and that mice lacking RabGEF1 develop severe skin inflammation and increased numbers of dermal mast cells. To better understand how RabGEF1 can regulate signaling events and biological responses in mast cells, we examined the responses of bone marrow-derived cultured mast cells (BMCMCs) from wild-type (+/+) and Rabgef1 knockout (-/-) mice after stimulation with the c-Kit ligand, stem cell factor (SCF), an important regulator of mast cell development, survival, proliferation, and activation. We found that RabGEF1-deficient mast cells exhibited enhanced and prolonged activation of Ras and extracellular regulated kinase, and significantly elevated IL-6 secretion, after stimulation with SCF. SCF-induced activation of c-Jun N-terminal kinase was increased in Rabgef1-/- BMCMCs, but without corresponding significant increases in SCF-induced migration or adhesion. SCF-mediated activation of the survival-enhancing kinase, Akt, also was increased in Rabgef1-/- BMCMCs, and these cells had a survival advantage over their +/+ counterparts in vitro. Despite enhanced Ras activation in the absence of RabGEF1, SCF-induced proliferation was lower in Rabgef1-/- BMCMCs compared with their +/+ counterparts. Finally, we found that c-Kit internalization was delayed in the absence of RabGEF1, probably reflecting a positive role for RabGEF1 in the regulation of endocytic events, and that infection of Rabgef1-/- BMCMCs with a wild-type RabGEF1 lentiviral construct normalized c-Kit internalization to the levels seen in +/+ BMCMCs. Thus, RabGEF1 plays a critical role in the regulation of SCF/c-Kit-mediated signaling events and biological responses in mast cells.
Combustion of calcium treated coals (1984)

The combustion of calcium-exchanged coals was studied in laminar flow and fluid bed reactors under strongly fuel-lean conditions. The purpose of the study was to understand the nature of release and capture of sulfur oxides in the presence of finely dispersed calcium oxide and explore the effectiveness of calcium-exchange pretreatment for sulfur emission control in coal combustion. The experimental variables were residence time, oxygen concentration, furnace temperature and amount of calcium-additive. The two coals used in this study were PSOC 623, a Texas lignite, and PSOC 680, an Indiana high volatile B bituminous. Analysis of the experimental data indicated that sulfur capture increased as residence time or oxygen concentration increased. The results also showed that sulfur capture was approximately proportional to the Ca/S ratio of the coals. 8 references, 10 figures, 5 tables.
High CRI phosphor blends for near-UV LED lamps (2004)

Currently, the highest color rendering index (CRI) value obtained in commercially available LED devices is around 90. This falls short of the CRI values typical for incandescent lamps (defined at 100). Similarly, the commercially available LEDs for higher color temperature have CRI values of 65-85, well below the theoretical maximum of 100. New phosphor blends are proposed for use with LED chips emitting in the 350-450 nm range. The application of such blends can afford CRI values greater than 95, over the entire range of color temperatures of interest for general illumination (2500K - 8000K). In some cases, the CRI values approach the theoretical maximum of 100. LED based lamps with a steady state performance of 23 LPW and 25 lumens per chip at 3000K, with a general CRI (Ra) of 97 and a mean CRI (R1-R14) of 96 are demonstrated.
Superconductor analog to digital converter for sigint applications (2008)

Superconductor analog-to-digital converters (ADC) offer high sensitivity and large dynamic range. We report recent advances in the low-pass phase-modulation-demodulation (PMD) oversampled analog-to-digital converter (ADC). The oversampled data from the PMD front-end are passed along with sampling clock to an on-chip digital filter. In the past, the maximum frequency of operation of such chips were limited by that of the digital decimation filter (DDF) to about 30 GHz. Recently, we have designed a chip that allows the PMD front-end to be clocked twice as fast as the DDF, resulting in sampling rates of 46.08 GHz and 29.44 GHz for chips with critical current densities of 4.5 and 1 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> respectively. We have also designed a new PMD front-end, with a quarter-rate quantizer (QRQ) that allows 18-20 dB extension of dynamic range. We are also pursuing a subranging ADC design with two PMD front-ends connected with fluxon amplifier and subtractor circuitry that promises a dynamic range extension by 25-30 dB. We report signal-to-noise ratio and spur-free dynamic range measurement results for various ADC chips, and project performance for future improvements.
Comparative clinical evaluation of the Yale Multigrasp Hand (2016)

While the functionality of myoelectric prosthetic hands continues to increase, body-powered terminal devices continue to be preferred by upper-limb amputees. Until now, the ability to achieve various grasp types in an anthropomorphic hand has been exclusive to myoelectric hands. The Yale Multigrasp Prosthetic Hand, a novel anthropomorphic multi-grasp body-powered terminal device, was designed and tested for use as an upper-limb prosthesis. The functionality of the Yale Multigrasp Prosthetic Hand was evaluated through benchtop testing and a twelve-subject able-body study. One unilateral trans-radial amputee and one bilateral trans-radial amputee performed evaluation studies to determine the level of dexterity achieved with the hand. Results show comparable performance to current commercially available terminal devices on both the Box and Blocks and Southampton Hand Assessment Protocol.
2,4,6-Trisubstituted Pyrimidines as a New Class of Selective Adenosine A<sub>1</sub> Receptor Antagonists (2004)

Adenosine receptor antagonists usually possess a bi- or tricyclic heteroaromatic structure at their core with varying substitution patterns to achieve selectivity and/or greater affinity. Taking into account molecular modeling results from a series of potent adenosine A1 receptor antagonists, a pharmacophore was derived from which we show that a monocyclic core can be equally effective. To achieve a compound that may act at the CNS we propose imposing a restriction related to its polar surface area (PSA). In consequence, we have synthesized two novel series of pyrimidines, possessing good potency at the adenosine A1 receptor and desirable PSA values. In particular, compound 30 (LUF 5735) displays excellent A1 affinity (Ki = 4 nM) and selectivity (< or =50% displacement of 1 muM concentrations of the radioligand at the other three adenosine receptors) and has a PSA value of 53 A2.
Femtosecond laser polishing of germanium [Invited] (2019)

Freeform optics can reduce the cost, weight, and size of advanced imaging systems, but it is challenging to manufacture the complex rotationally asymmetric surfaces to optical tolerances. To address the need for disruptive, high-precision sub-aperture forming and finishing techniques for freeform optics, we investigate an alternative, non-contact polishing methodology using femtosecond lasers, combining modeling, experiments, and demonstrations. Femtosecond-laser-based polishing of germanium was investigated using an experimentally-validated two-temperature model of laser/germanium interaction to guide the understanding and selection of laser parameters to achieve near-nonthermal ablation for polishing and figuring. For the first time to our knowledge, model-guided femtosecond laser polishing of germanium was successfully demonstrated, achieving precision material removal while maintaining single-digit nanometer optical surface quality. The demonstrated femtosecond-laser-based polishing technique lays the foundation for semiconductor optics polishing/fabrication using femtosecond lasers and opens a viable path for high-precision, complex sub-aperture optical polishing tasks on various materials.
Preparation of a Bispecific F(ab') <sub>2</sub> Targeted to the Human IL-2 Receptor (1995)

The heterodimer-forming leucine zippers Fos and Jun can efficiently mediate the formation of bispecific F(ab')2 when they are fused separately to two different Fab' fragments. This recombinant method can be used in conjunction with the humanization process to yield humanized bispecific F(ab')2. The potential immunogenicity of the leucine zippers can be eliminated by their removal using pepsin digestion. This method has been scaled up to produce hundreds of milligrams of a bispecific F(ab')2 that targets two subunits of the human IL-2 receptor.