gebhart/patrepeval huggingface dataset:
Real Time Differentiation of G-Protein Coupled Receptor (GPCR) Agonist and Antagonist by Two Photon Fluorescence Laser Microscopy (2004)

Receptor-based signaling mechanisms are the primary source of cellular regulation. The superfamily of G protein-coupled receptors (GPCR) is the largest and most ubiquitous of the receptor-mediated processes. Desensitization of G-protein-coupled receptors is a fundamental mechanism regulating the cellular response to agonists. We have recently studied the agonist and antagonist of the human melanocortin receptors (hMC1, hMC3, hMC4, and hMC5 receptors), the human delta opioid receptor, and the human gluacagon receptor with the help of synthetic fluorescent labeled ligands and fluorescent protein-labeled beta-arrestin-receptors that shed new insight on cellular signaling and rapid screening of drugs in real time. It was demonstrated that stimulation of these receptors by the cognate agonist triggers the rapid internalization of ligand-receptor complexes, while the interaction of the receptor with antagonists does not follow this pathway. Furthermore, receptor internalization is dependent upon beta-arrestin, which has been shown to be responsible for the rapid desensitization of cAMP-signaling processes.
Description and initial evaluation of a Xenopus metamorphosis assay for detection of thyroid system-disrupting activities of environmental compounds (2005)

A need is recognized for the development and evaluation of bioassays for detection of thyroid system-disrupting compounds. The issue of testing for thyroid disruption can be addressed by exploiting amphibian metamorphosis as a biological model. In the present study, a test protocol for a Xenopus metamorphosis assay (XEMA) was developed and its interlaboratory transferability was evaluated in an informal ring test with six laboratories participating. In the XEMA test, exposure of Xenopus laevis tadpoles was initiated at stages 48 to 50 and continued for 28 d. Development and growth of tadpoles were assessed by means of developmental stage and whole body length determinations, respectively. For initial test protocol evaluation, thyroxine (T4), and propylthiouracil (PTU) were used as positive controls for thyroid system-modulating activity, and ethylenethiourea (ETU) was used as a test compound. Exposure of tadpoles to 1 microg/L T4 produced a significant acceleration of metamorphosis whereas PTU concentrations of 75 and 100 mg/L completely inhibited metamorphosis. Five different ETU concentrations (5, 10, 25, 50, and 100 mg/L) were tested and a concentration-dependent inhibition of metamorphosis was observed. None of the compounds affected tadpole survival, and only PTU caused a slight retardation in tadpole growth. This study demonstrates that the XEMA test provides a sensitive, robust, and practical testing approach for detection of compounds with both agonistic and antagonistic effects on the thyroid system in Xenopus tadpoles.
Electrically Driven Optical Modulator with a Strongly Coupled Quantum Dot (2009)

The frequency of a quantum-dot strongly coupled to a photonic-crystal cavity was electrically controlled. Electro-optic modulation (150MHz) of a coherently coupled probe laser is demonstrated. Operation at 10GHz and 1fJ/bit are achievable with this device.
LEGAN: Disentangled Manipulation of Directional Lighting and Facial Expressions whilst Leveraging Human Perceptual Judgements (2021)

Building facial analysis systems that generalize to extreme variations in lighting and facial expressions is a challenging problem that can potentially be alleviated using natural-looking synthetic data. Towards that, we propose LEGAN, a novel synthesis framework that leverages perceptual quality judgments for jointly manipulating lighting and expressions in face images, without requiring paired training data. LEGAN disentangles the lighting and expression subspaces and performs transformations in the feature space before upscaling to the desired output image. The fidelity of the synthetic image is further refined by integrating a perceptual quality estimation model, trained with face images rendered using multiple synthesis methods and their crowd-sourced naturalness ratings, into the LEGAN framework as an auxiliary discriminator. Using objective metrics like FID and LPIPS, LEGAN is shown to generate higher quality face images when compared with popular GAN models like StarGAN and StarGAN-v2 for lighting and expression synthesis. We also conduct a perceptual study using images synthesized by LEGAN and other GAN models and show the correlation between our quality estimation and visual fidelity. Finally, we demonstrate the effectiveness of LEGAN as training data augmenter for expression recognition and face verification tasks.
Nanoscale Mixing of Soft Solids (2011)

Assessing the state of mixing on the molecular scale in soft solids is challenging. Concentrated solutions of micelles formed by self-assembly of polystyrene-block-poly(ethylene-alt-propylene) (PS-PEP) diblock copolymers in squalane (C(30)H(62)) adopt a body-centered cubic (bcc) lattice, with glassy PS cores. Utilizing small-angle neutron scattering (SANS) and isotopic labeling ((1)H and (2)H (D) polystyrene blocks) in a contrast-matching solvent (a mixture of squalane and perdeuterated squalane), we demonstrate quantitatively the remarkable fact that a commercial mixer can create completely random mixtures of micelles with either normal, PS(H), or deuterium-labeled, PS(D), cores on a well-defined bcc lattice. The resulting SANS intensity is quantitatively modeled by the form factor of a single spherical core. These results demonstrate both the possibility of achieving complete nanoscale mixing in a soft solid and the use of SANS to quantify the randomness.
A New Endoluminal Platform Facilitating Endoscopic Removal of Large and Flat Colonic Lesions (2012)

Purpose: Endoscopic removal of large and flat colonic polyps is technically difficult, often requires special endoscopic techniques and currently only performed in highly specialized tertiary centers by a limited group of physicians with advanced endoscopic skills. There is a need for technology facilitating an excision of difficult colonic polyps. AIM: To evaluate on a live porcine model a newly developed endoscopic device facilitating colonoscopic removal of large and flat colonic lesions. Methods: All experiments were performed under general anesthesia with endotracheal intubation on 50-100-kg domestic pigs. LumenR retractor system consists of an expandable and dynamically-controlled intra-luminal chamber, mounted on a flexible overtube, and two associated articulating instrument guides. The system is front-loaded over the colonoscope and introduced into the colon. When the target area is reached, the retractor system is advanced forward and deployed creating an expanded, optimally reconfigured and stable operating field around the target lesion. Then endoscopic removal of the lesion is performed using commercially available endoscopic instruments (forceps, injection needles, snares, clips, etc.) through the biopsy channel of the colonoscope with assistance of two articulating instrument guides of the LumenR retractor system. Results: After successful completion of 20 benchmark studies on isolated colons, we performed 6 animal experiments. Delivery and deployment of the LumenR retractor system was achieved in all animals, creating a stable and optimally reconfigured operating space around the target lesion. This space was sufficient to perform all necessary colonoscopic manipulations. Delivery of endoscopic accessories through the LumenR articulating instrument guides added 2 extra “arms” for various manipulations (grasping, pulling, pushing, etc), creating an effect of triangulation closely resembling laparoscopic procedures. Endoscopic mucosal resection and submucosal dissection of simulated target lesions were successfully performed in all animals. Conclusion: LumenR retractor system allows creation of a stable and optimally reconfigured operating space inside the colon with delivery of additional endoscopic instruments in triangulating fashion. The position of the colonoscope, endoscopic instruments and the target tissue in relation to each other were markedly optimized for performing even technically difficult endoscopic procedures. This novel endoscopic platform has a potential to improve and simplify endoscopic removal of large and flat colonic lesions. Disclosure: Dr. Kantsevoy is consultant for LumenR, LLC. Mr. John To is an engineer for LumenR, LLC. Dr. Piskun is inventor for LumenR, LLC.
ChemInform Abstract: Asymmetric Epoxidation of Fluorinated Allylic Alcohols. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Extended Packaging through Addition of Readable Information to the Printing (2009)

Packaging is the interface between your product and your customer. To enhance the customer experience, the packaging should provide brand identification and allow the user to readily obtain information that is customized to their interests. Variable data printing (VDP) provides the label converter with the tools to highlight important brand and product related information, either directly or through interpretation of tacitly designed marks on the label. If branding concerns preclude the implementation of specific information-bearing marks (e.g. barcodes and/or security deterrents), the branding information itself can be made variable without impacting the perceived aesthetics of the package design. This is possible because VDP allows each label's layout1&#x2014;not just content&#x2014;to be unique. Several layout variances can be added to the packaging in a semi-covert manner; that is, they are not noticed until they are known to be present. These include variances in the size, x- or y-position, metameric pairs, placement over the background, and rotation of non-rectangular elements. The VDP layout differences from a template encode information. Variability humans are particular sensitive to&#x2014;text kerning, misalignment, absolute color differences&#x2014;are poor candidates for the layout VDP. Our work illustrates how to put in place an overall VDP layout system.
Mechanism of the molecular mobility of water in the temperature range 298–359 K (2009)

The Raman spectra of liquid water in the region of O-H stretching vibrations were obtained in the temperature range 298–359 K. The Raman spectra were decomposed into the components using the XPSPEAK-4.1 program, and their temperature dependence was evaluated. The number of bifurcate hydrogen bonds and the percentage of rotational conformers containing bifurcate bonds were shown to increase with temperature. The defect mechanism of the molecular mobility of water on the hydrogen bond network in the temperature range 298–359 K was proposed.
Airborne UXO detection and classification from a UAS (2021)

Land-based electromagnetic induction (EMI) sensors have performed very well at unexploded ordnance detection and classification over the last two decades. These sensors have incorporated multiple transmitters and/or multiple receivers in order to acquire sufficient data for inversion and classification. However, these sensors are typically cart based or towed behind vehicles and are too heavy and bulky to incorporate onto an unmanned aerial system (UAS). We have recently developed an advanced EMI instrument light enough to be mounted on a UAS. This system is meant to detect ordinance to a depth of 2 m and therefore incorporates a large 1.6 m diameter transmitter as well as three 75 cm transmitters. The system also has three receivers incorporated into the hoop structure (green squares, see figure below). We used lightweight plastic tubing to house the transmitter coils as well as lightweight electronics to control the data acquisition pathway. These electronics include a small stick computer, a raspberry pi, a custom-built four channel transmitter and receiver amplifiers, and a Picoscope 4824. Together the entire payload weighs about 9 pounds and is mounted on a turbo ACE infinity nine UAS. We present initial results from tests in the backyard near and over New Hampshire.
Evaluation of bacterial presence on lead X-ray aprons utilised in the operating room via IBIS and standard culture methods (2019)

Lead X-ray aprons worn in the operating room harbour bacteria. Disinfecting before use may prevent the introduction of virulent organisms to patients. Our proposed method of sanitising with a disinfectant wipe is quick and effective.
Enrichment of an Endosulfan-Degrading Mixed Bacterial Culture (2000)

An endosulfan-degrading mixed bacterial culture was enriched from soil with a history of endosulfan exposure. Enrichment was obtained by using the insecticide as the sole source of sulfur. Chemical hydrolysis was minimized by using strongly buffered culture medium (pH 6.6), and the detergent Tween 80 was included to emulsify the insecticide, thereby increasing the amount of endosulfan in contact with the bacteria. No growth occurred in control cultures in the absence of endosulfan. Degradation of the insecticide occurred concomitant with bacterial growth. The compound was both oxidized and hydrolyzed. The oxidation reaction favored the alpha isomer and produced endosulfate, a terminal pathway product. Hydrolysis involved a novel intermediate, tentatively identified as endosulfan monoaldehyde on the basis of gas chromatography-mass spectrometry and chemical derivatization results. The accumulation and decline of metabolites suggest that the parent compound was hydrolyzed to the putative monoaldehyde, thereby releasing the sulfite moiety required for growth. The monoaldehyde was then oxidized to endosulfan hydroxyether and further metabolized to (a) polar product(s). The cytochrome P450 inhibitor, piperonyl butoxide, did not prevent endosulfan oxidation or the formation of other metabolites. These results suggest that this mixed culture is worth investigating as a source of endosulfan-hydrolyzing enzymes for use in enzymatic bioremediation of endosulfan residues.
Discovery and Chemical Development of Grazoprevir: An HCV NS3/4a Protease Inhibitor for the Treatment of the Hepatitis C Virus Infection (2020)

This chapter outlines the discovery and chemical development of the hepatitis C virus NS3/4a protease inhibitor, grazoprevir, approved in combination with the NS5a inhibitor elbasvir as Zepatier® for the treatment of hepatitis C virus (HCV) infection. Highly potent and efficacious HCV NS3/4a protease inhibitors have been a key factor in the recent evolution of all-oral HCV infection therapies. The path to the final manufacturing process of grazoprevir required chemistry evolution with innovative breakthroughs and thorough evaluation of various bond connection strategies. Focusing on problem solving and mechanistic understanding of the chemistry issues, this chapter describes the entire chemical development journey starting from Discovery Chemistry. The development of two generation large-scale syntheses for grazoprevir are discussed in detail. The initial safety concerns and hazardous issues encountered during process scale-up are explained, and the solutions to overcome these issues through staged process evolution and ultimately with new chemical transformation for an ideal process are described. Our chemical development delivers the most effective synthesis of this highly complex molecule with an optimal sequence of bond connection to assemble four building blocks in the final manufacturing process, which has been successfully implemented at factory scale.
Optimizing the parameters of the steam-carbon dioxide conversion of methane by Gibbs energy minimization (2011)

The thermodynamic equilibrium for the steam-carbon dioxide conversion of methane was studied by Gibbs energy minimization. The degree of coke formation, the content of methane and carbon dioxide in the synthesis gas, and the synthesis gas H2/CO ratio were plotted as functions of the molar ratios of CO2/CH4 and H2O/CH4 in the initial mixture at different temperatures and pressures. The regions of the optimum CH4/CO2/H2O molar ratios for steam-carbon dioxide conversion were discovered, with no coke formation taking place in these regions. The optimized CH4/CO2/H2O molar fractions characterized by the minimum content of methane and carbon dioxide in the synthesis gas were found for each region.
Suppression of wear in cyclically loaded polycrystalline silicon MEMS via a thin silicon carbide coating (2011)

The surfaces of a microfabricated polysilicon test structure, designed to measure adhesion forces in MEMS, were modified with a thin (~50 nm) silicon carbide coating to take advantage of the outstanding tribological, electrical, and chemical properties of polycrystalline SiC (polySiC). Adhesion forces in polySiC-coated interfaces as a function of apparent area of contact have been determined quantitatively and compared to those in uncoated polycrystalline silicon (polySi) contacts. A detailed study of changes in physico-chemical surface properties after >;100 billion contact cycles is also presented, highlighting suppression of wear upon SiC coating.
Two-permutation-based hashing with binary mixing (2015)

Abstract We consider the generic design of compression functions based on two n -bit permutations and XOR-based mixing functions. It is known that any such function mapping <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>n</m:mi> <m:mo>+</m:mo> <m:mi>α</m:mi> </m:mrow> </m:math> ${n+\alpha }$ to α bits, with <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mn>1</m:mn> <m:mo>≤</m:mo> <m:mi>α</m:mi> <m:mo>≤</m:mo> <m:mi>n</m:mi> </m:mrow> </m:math> ${1\le \alpha \le n}$ , can achieve at most <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mo>min</m:mo> <m:mo>{</m:mo> <m:msup> <m:mn>2</m:mn> <m:mrow> <m:mi>α</m:mi> <m:mo>/</m:mo> <m:mn>2</m:mn> </m:mrow> </m:msup> <m:mo>,</m:mo> <m:msup> <m:mn>2</m:mn> <m:mrow> <m:mi>n</m:mi> <m:mo>/</m:mo> <m:mn>2</m:mn> <m:mo>-</m:mo> <m:mi>α</m:mi> <m:mo>/</m:mo> <m:mn>4</m:mn> </m:mrow> </m:msup> <m:mo>}</m:mo> </m:mrow> </m:math> ${\min \lbrace 2^{\alpha /2},2^{n/2-\alpha /4}\rbrace }$ collision security. Using techniques similar to Mennink and Preneel [CRYPTO 2012, Lecture Notes in Comput. Sci. 7417, Springer, Heidelberg (2012), 330–347], we show that there is only one equivalence class of these functions achieving optimal collision security, and additionally <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mo>min</m:mo> <m:mo>{</m:mo> <m:msup> <m:mn>2</m:mn> <m:mi>α</m:mi> </m:msup> <m:mo>,</m:mo> <m:msup> <m:mn>2</m:mn> <m:mrow> <m:mi>n</m:mi> <m:mo>/</m:mo> <m:mn>2</m:mn> </m:mrow> </m:msup> <m:mo>}</m:mo> </m:mrow> </m:math> ${\min \lbrace 2^{\alpha },2^{n/2}\rbrace }$ preimage security. The equivalence class compares well with existing functions based on two or three permutations, and is well-suited for wide-pipe hashing.
FUT2Genetic Variants and Reported Respiratory and Gastrointestinal Illnesses During Infancy (2018)

We confirmed that FUT2 G alleles are associated with a higher risk of infant gastrointestinal illnesses and identified novel associations with respiratory illnesses. FUT2 locus variants need consideration in future studies of gastrointestinal and respiratory illnesses among infants.
New algorithms for the dual of the convex cost network flow problem with application to computer vision (2007)

Motivated by various applications to computer vision, we consider an integer convex optimization problem which is the dual of the convex cost network flow problem. In this&#13;\npaper, we first propose a new primal algorithm for computing an optimal solution of the problem. Our primal algorithm iteratively updates primal variables by solving associated&#13;\nminimum cut problems. The main contribution in this paper is to provide a tight bound for the number of the iterations. We show that the time complexity of the primal algorithm is K ¢ T(n;m) where K is the range of primal variables and T(n;m) is the time needed to compute a minimum cut in a graph with n nodes and m edges.&#13;\nWe then propose a primal-dual algorithm for the dual of the convex cost network flow problem. The primal-dual algorithm can be seen as a refined version of the primal algorithm by maintaining dual variables (flow) in addition to primal variables. Although its time complexity is the same as that for the primal algorithm, we can expect a better performance&#13;\npractically.&#13;\nWe finally consider an application to a computer vision problem called the panoramic stitching problem. We apply several implementations of our primal-dual algorithm to some&#13;\ninstances of the panoramic stitching problem and test their practical performance. &#13;\nWe also show that our primal algorithm as well as the proofs can be applied to the L\\-convex function minimization problem which is a more general problem than the dual of the convex cost network flow problem.
Recent Advances and Future Challenges in 2.5D/3D Heterogeneous Integration (2022)

In this presentation, we will review the recent advances in chiplet-based commercial products and prototypes [2,3,4,5]. Most chiplet usage has been confined to integrating die designed by the same organization applied to building chips for the same product types. The right approach should be able to reduce portfolio costs, scale innovation and improve time to solution [1]. It is important to manage the associated trade-offs, such as thermal, power, I/O escapes, assembly, test, etc. We will conclude the talk by presenting the future 2.xD/3D integration opportunities becoming available [6].
Is Universal Next-Generation Sequencing Testing of Patients With Advanced Cancer Ready for Prime Time?—Reply (2021)

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Temperature dependence of localized exciton transitions in AlGaN ternary alloy epitaxial layers (2008)

The optical properties of Ga-rich AlxGa1−xN (x=0.019, 0.038, 0.057, 0.077, and 0.092) ternary alloy epitaxial layers have been studied by means of temperature-dependent photoluminescence (PL) and time-resolved PL spectroscopy. The luminescence intensity of excitons in five epitaxial layers indicated a thermal quenching process with two activation energies. The two quenching activation energies were attributed to the delocalization of excitons and thermal dissociation of excitons. Anomalous temperature dependence of the PL peak energy was also observed in the epitaxial layers, which enabled the evaluation of the localization energy of the excitons. The localization energy increased as the 1.7th power of the PL linewidth, which reflected a broadening of the density of localized exciton states. In addition, the luminescence decay of the localized excitons for the five epitaxial layers became longer with decreasing emission energy. These observations suggest that the decay of excitons is caused not only by radiative recombination, but also by transfer to lower energy states.
Efficient, Uniform, and Large Area Microwave Magnetic Coupling to NV Centers in Diamond Using Double Split-Ring Resonators (2014)

We report on the development and utilization of a double split-ring microwave resonator for uniform and efficient coupling of microwave magnetic field into nitrogen-vacancy (NV) centers in a diamond over a mm(2) area. Uniformity and magnitude of delivered microwave field were measured using the Rabi nutation experiment on arrays of diamond nanowires with ensemble NV centers. An average Rabi nutation frequency of 15.65 MHz was measured over an area of 0.95 × 1.2 mm, for an input microwave power of 0.5 W. By mapping the Rabi nutation frequency to the magnetic field, the average value of the magnetic field over the aforementioned area and input microwave power was 5.59 G with a standard division of 0.24 G.