gebhart/patrepeval huggingface dataset:
Fluorescent ligands to investigate GPCR binding properties and oligomerization (2013)

Fluorescent ligands for GPCRs (G-protein-coupled receptors) have been synthesized for a long time but their use was usually restricted to receptor localization in the cell by fluorescent imaging microscopy. During the last two decades, the emergence of new fluorescence-based strategies and the concomitant development of fluorescent measurement apparatus have dramatically widened the use of fluorescent ligands. Among the various strategies, TR (time-resolved)-FRET (fluorescence resonance energy transfer) approaches exhibit an interesting potential to study GPCR interactions with various partners. We have derived various sets of ligands that target different GPCRs with fluorophores, which are compatible with TR-FRET strategies. Fluorescent ligands labelled either with a fluorescent donor (such as europium or terbium cryptate) or with a fluorescent acceptor (such as fluorescein, dy647 or Alexa Fluor® 647), for example, kept high affinities for their cognate receptors. These ligands turn out to be interesting tools to develop FRET-based binding assays. We also used these fluorescent ligands to analyse GPCR oligomerization by measuring FRET between ligands bound to receptor dimers. In contrast with FRET strategies, on the basis of receptor labelling, the ligand-based approach we developed is fully compatible with the study of wild-type receptors and therefore with receptors expressed in native tissues. Therefore, by using fluorescent analogues of oxytocin, we demonstrated the existence of oxytocin receptor dimers in the mammary gland of lactating rats.
Microbial synthesis of a branched-chain ester platform from organic waste carboxylates (2016)

Processing of lignocellulosic biomass or organic wastes produces a plethora of chemicals such as short, linear carboxylic acids, known as carboxylates, derived from anaerobic digestion. While these carboxylates have low values and are inhibitory to microbes during fermentation, they can be biologically upgraded to high-value products. In this study, we expanded our general framework for biological upgrading of carboxylates to branched-chain esters by using three highly active alcohol acyltransferases (AATs) for alcohol and acyl CoA condensation and modulating the alcohol moiety from ethanol to isobutanol in the modular chassis cell. With this framework, we demonstrated the production of an ester library comprised of 16 out of all 18 potential esters, including acetate, propionate, butanoate, pentanoate, and hexanoate esters, from the 5 linear, saturated C<sub>2</sub>-C<sub>6</sub> carboxylic acids. Among these esters, 5 new branched-chain esters, including isobutyl acetate, isobutyl propionate, isobutyl butyrate, isobutyl pentanoate, and isobutyl hexanoate were synthesized <i>in vivo</i>. During 24 h <i>in situ</i> fermentation and extraction, one of the engineered strains, EcDL208 harnessing the SAAT of <i>Fragaria ananassa</i> produced ~63 mg/L of a mixture of butyl and isobutyl butyrates from glucose and butyrate co-fermentation and ~127 mg/L of a mixture of isobutyl and pentyl pentanoates from glucose and pentanoate co-fermentation, with high specificity. These butyrate and pentanoate esters are potential drop-in liquid fuels. This study provides better understanding of functional roles of AATs for microbial biosynthesis of branched-chain esters and expands the potential use of these esters as drop-in biofuels beyond their conventional flavor, fragrance, and solvent applications.
Enantiospecific Total Synthesis of (−)-Anhydromacrosalhine-methine and Partial Synthesis of the Antiamoebic Bisindole Alkaloid (−)-Macrocarpamine1 (1998)

An enantiospecific total synthesis of (−)-anhydromacrosalhine-methine (7a) was completed from d-(+)-tryptophan via the asymmetric Pictet−Spengler reaction. In addition, a partial synthesis of (−)-anhydromacrosalhine-methine (7a) was carried out from the natural product (+)-ajmaline (10). The coupling reaction of plant-derived (+)-pleiocarpamine (8) with synthetic diene 7a provided the antiamoebic bisindole alkaloid (−)-macrocarpamine (1) in 75% yield. This sequence serves as the first example of the action of a nucleophile at [at C(2)] on a protonated form [C(3)] of pleiocarpamine 8 in the Alstonia series to provide a bisindole alkaloid.
Solid–liquid separation of an effluent produced by a fixed media biofilm reactor (2017)

An experimental study dedicated to the characterization of the settleability of solids produced in immersed fixed media biofilm reactors has been carried out. The influence of operating temperature (0.1 to 16 °C) and surface organic loading rate (OLR) (0.4 to 10 g of soluble carbonaceous BOD<sub>5</sub> per m<sup>2</sup> of media per day) on settleable solids quantities, particle size distributions (PSD) as well as flocs morphology was evaluated. Results have shown that the OLR has no statistically significant influence on the settleability of the suspended solids. However, the operating temperature was identified as a factor that significantly influences the settling potential. The highest operating temperatures (14-16 °C) were related to the worst settling performances. On the other hand, the best settling performances were observed at intermediate operating temperatures (around 10 °C). The latter conditions were also associated with the largest fractions of large particles (>100 μm) in the effluent. Differences in PSD were found to be well correlated with settling performances. Part of the performance results variability which cannot be explained by differences in PSD can potentially be attributed to differences in flocs morphology (compactness).
On the Physics of Towed Streamer Controlled Source Electromagnetics in Shallow Water in the Presence of Transverse Anisotropy (2017)

In recent years, marine controlled source electromagnetics (CSEM) has found increasing use in hydrocarbon exploration due to its ability to detect thin resistive zones beneath the seafloor. It is the purpose of this paper to evaluate the effect of an electrically-thin ocean on the physics of CSEM using the towed streamer in-line configuration through examination of the electric field and the time-averaged energy flow depicted by the real part of the complex Poynting vector, and for an isotropic and transversely anisotropic sedimentary sequence. The observable electric field following excitation by a horizontal electric dipole (HED) source can be understood through the energy flow within the entire structure caused by the competing influences of guided energy flow in the reservoir layer and the air interaction. The influence of transverse anisotropy in a sedimentary sequence is to enhance the effect of guided energy flow as compared to an isotropic structure, yielding a response that is analogous to that in deeper water for an isotropic medium. Presentation Date: Tuesday, September 26, 2017 Start Time: 9:20 AM Location: 362A Presentation Type: ORAL
Water and propylene carbonate as storage and switching media in pulsed power systems (2004)

The electrical characteristics of two polar liquids, water and propylene carbonate, under high electric stress have been studied. The liquids were placed between a hemispherical electrode of 1.7mm diameter and a plane electrode with gap distances of 200 /spl mu/m and 400 /spl mu/n. A voltage pulse of 200 ns duration was applied by means of a Blumlein pulse generator. The increase in current with voltage was recorded up to the breakdown voltage, including the transition phase to breakdown. Schlieren diagnostics, with a temporal resolution of 2 ns, was used to study the changes in the index of refraction of water when it was used as the switch medium, both before and during breakdown. The results of our measurements showed that the electrodes determine, to a large extent, the hold-off voltage. By polishing the stainless steel electrodes, the breakdown strength was increased from 1 MV/cm to 2.2 MV/cm for propylene carbonate as dielectric. Similar increases were found for water as dielectric between polished electrodes. The rate of current rise after breakdown was measured as 4.5-10/sup 11/ A/s for distilled water, a value which is comparable to that measured in gas switches. The Schlieren photographs showed that, depending on the polarity, the breakdown is preceded by the treeing of streamers into the gap.
Hematopoiesis in the embryonic mouse spleen. II. Alterations after phenylhydrazine administration to the mothers (1975)

The effect of phenylhydrazine (PHZ) on the hematopoietic events in the embryonic spleen of C57Bl/6J mice was examined by light and electron microscopy. Following PHZ in injections to the mothers, the embryonic spleen revealed a marked increase in erythroid precursors, with a shift to mature cells. This phenomenon was part of a more generalized stimulation of erythorpoiesis, expressed by a shift to mature red cell precursors in the embryonic livers and an increase in the percentage of non-nucleated cells in the embryonic peripheral blood. Concomitantly stimulation of phagocytosis in the spleen of embryos in the early gestational days and increased vascularity were observed, and a later effect of granulocytopoietic stimulation. The effect on erythropoiesis in the embryonic spleen might be a sequence of erythropoietin stimulation, either in the mothers or the fetuses, due to anemia and hypoxia following PHZ injections.
Abstract 814: Truncated HBx-dependent silencing of growth arrest-specific 2 promotes hepatocarcinogenesis through inhibition of p53-mediated apoptosis (2015)

Abstract Hepatocellular carcinoma (HCC) is a worldwide threat to public health, especially in China where chronic hepatitis B virus (HBV) infection is found in 80-90% of all HCCs. The HBV encoded X antigen (HBx) is a trans-regulatory protein involved in the virus-induced hepatocarcinogenesis. Although the carboxyl-terminus truncated HBx, rather than the full-length counterpart, is frequently overexpressed in human HCCs, its functional mechanisms have yet been fully defined. In this study, we investigated the molecular pathogenesis of a naturally-occurring HBx variant which has 35 amino acids deleted at C-terminus (HBxΔ35). By performing genome-wide scanning analysis and PCR validation, we identified growth arrest-specific 2 (GAS2) as a direct target of HBxΔ35 at transcriptional level in human immortalized liver cells. HBxΔ35 was found to bind the promoter region of GAS2 and suppress its expression to promote hepatocellular proliferation and tumorigenicity. Further functional assays showed that overexpression of GAS2 inhibited tumor growth both in vitro and in vivo by inducing p53-dependent apoptosis. Conversely, siRNA-mediated knockdown of GAS2 in hepatocytes attenuated apoptotic response and reduced cell susceptibility to etoposide-induced apoptosis. Notably, GAS2 expression was significantly down-regulated in truncated HBx-expressing HCCs compared with the corresponding normal tissues. In conclusion, our integrated study uncovered a novel viral mechanism in hepatocarcinogenesis, wherein HBxΔ35 ablates p53-driven apoptosis via direct silencing of GAS2, and thereby provides survival advantage for pre-neoplastic hepatocytes to facilitate cancer development. Citation Format: Alfred S. L. Cheng, Ranxu Zhu, Myth T.S. Mok, Wai Kang, Ka-Fai To, Joseph J.Y. Sung, Henry L.Y. Chan. Truncated HBx-dependent silencing of growth arrest-specific 2 promotes hepatocarcinogenesis through inhibition of p53-mediated apoptosis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 814. doi:10.1158/1538-7445.AM2015-814
ChemInform Abstract: PREPARATION AND SYNTHETIC UTILITY OF TERT‐BUTYLDIPHENYLSILYL ETHERS (1976)

Abstract Die Silyl‐ Ätherbindung des beim Behandeln von Methyl‐oz‐D‐Glucopyranosid mit tert.‐Butyldiphenylsilylchlorid entstehenden Äthers (Ia) (primäre Hydroxylgruppen werden bevorzugt vor sekundären silyliert) oder der analog erhältlichen Äther (Ib) ist gegenüber Säuren oder unter den Bedingungen der Hydrogenolyse wesentlich stabiler, als z.B. die 0‐ tert‐Butylv, die O‐Tetrahydropyranyl‐oder die 0‐ tert.‐Butyl‐dimethylsilyl‐Bindung der entsprechenden (Ib).
Front Cover: In Vitro and In Vivo Proteomic Comparison of Human Neural Progenitor Cell‐Induced Photoreceptor Survival (2019)

DOI: 10.1002/pmic.201800213 In article number 1800213, Jones et al. identify mechanisms during human neural progenitor cell (hNPC) treatment of retinal degenerate rodents. Functional organization and anatomical connectivity of retina are highly complex and synchronized like an orchestra. As the retinal degeneration advances, photoreceptors are lost, whereas hNPC treatment slows the progression of degeneration and photoreceptors are preserved, as represented by the photoreceptor notes of the musical staff and corresponding histological staining of retinas. Proteomic analysis of hNPC treated tissue detects decreases in cell death, increases in cell survival, and the NRF2-mediated response as a potential mechanism for photoreceptor preservation.
Human Pose Extraction from Monocular Videos using Constrained Non-Rigid Factorization (2007)

We focus on the problem of automatically extracting the 3D configuration of human poses from 2D image features tracked over a finite interval of time . This problem is highly non-linear in nature and confounds standard regression techniques. Our approach effectively marries a non-rigid factorization algorithm with prior learned statistical models from archival motion capture database. We show that a stand alone non-rigid factorization algorithm is highly unsuitable for this problem. However, when coupled with the learned statistical model in the form of a constrained non- linear programming method, it yields a substantially better solution.
What is the Best Way to Optimally Parameterize the MPC Cost Function for Vehicle Guidance? (2022)

Model predictive control (MPC) is a promising approach for the lateral and longitudinal control of autonomous vehicles. However, the parameterization of the MPC with respect to high-level requirements such as passenger comfort as well as lateral and longitudinal tracking is a challenging task. Numerous tuning parameters as well as conflicting requirements need to be considered. This contribution formulates the MPC tuning task as a multi-objective optimization problem. Solving it is challenging for two reasons: First, MPC-parameterizations are evaluated on an computationally expensive simulation environment. As a result, the used optimization algorithm needs to be as sampleefficient as possible. Second, for some poor parameterizations the simulation cannot be completed and therefore useful objective function values are not available (learning with crash constraints). In this contribution, we compare the sample efficiency of multi-objective particle swarm optimization (MOPSO), a genetic algorithm (NSGA-II) and multiple versions of Bayesian optimization (BO). We extend BO, by introducing an adaptive batch size to limit the computational overhead and by a method on how to deal with crash constraints. Results show, that BO works best for a small budget, NSGA-II is best for medium budgets and for large budgets none of the evaluated optimizers is superior to random search. Both proposed BO extensions are shown to be beneficial.
Solar cell preparation in thin silicon membranes (2002)

Solar cells prepared in a thin (/spl ap/30 /spl mu/m) crystalline silicon membrane with a supporting frame allow an evaluation of the potential of c-Si thin film cells on cheap substrates. At the same time, lightweight and more radiation-hard solar cells may have direct applications in space. This paper studies the fabrication process of solar cells in /spl ap/30 /spl mu/m thick p-Si epitaxial layers, incorporating a p/sup ++/-Si etch-stop/back-surface field layer, using KOH etching. Wax, rubber and silicon nitride were tested as masking materials during the etching. It was found that both wax and silicon nitride could be used as materials for the masking of supporting frames for solar cell thinning up to 30 /spl mu/m. However, silicon nitride does not reliably protect the frontside structure.
Method for genetic identification of unknown organisms (2023)

A method of rapid, genome and proteome based identification of unknown pathogenic or non-pathogenic organisms in a complex sample. The entire sample is analyzed by creating millions of emulsion encapsulated microdroplets, each containing a single pathogenic or non-pathogenic organism sized particle and appropriate reagents for amplification. Following amplification, the amplified product is analyzed.
Energy conservation and interference mitigation: From decoupling property to win-win strategy (2010)

This paper studies the problem of conserving the energy of mobile terminals in a multi-cell TDMA networks supporting bursty real-time sessions. The associated optimization problem involves joint scheduling, rate control, and power control. To tackle the complexity, we propose a decomposition method that decouples the overall problem into two sub-problems: intra-cell energy optimization and inter-cell interference control. This decomposition results in a “win-win” situation: it reduces the energy consumptions and inter-cell interference at the same time. Simulations show that our decomposition method can achieve an energy reduction of more than 70% compared to the simplistic maximum transmit power policy. It can achieve an energy reduction of more than 50% compared to the case where only intra-cell energy optimal transmission is performed. We also derive an interesting decoupling property assuming that the interference power stays constant over a TDMA frame: if the idle power consumption of mobile terminals is no less than their circuit power consumption during transmission, or when both are negligible, then the energy-optimal transmission rates of the mobile terminals are independent of the inter-cell interference power level.
Compound Specific Stable Isotope Signatures of Chemical Threat Agents: Incapacitants (2022)

In year 2 of this project (2017), our group focused on determining the causes of isotopic signatures in fentanyl. In order to better predict isotopic signatures in fentanyl, we analyzed the nitrogen isotope compositions of two key intermediates of fentanyl, NPP and ANPP. In addition, we analyzed additional fentanyl products produced using the Valdez route, along with five other alternative fentanyl routes. A new, more sensitive GC-C-IRMS method has been developed, which allows for compound specific isotope analysis of Chemical Attribution Signatures (CAS) in fentanyl.
Properties of holographic associative memory prepared by the polarization encoding process (1988)

A new holographic associative memory (HAM) using optical polarization is proposed. Picture elements (pixels) of binary objects are encoded with two mutually perpendicular states of linear polarization, and they are stored in the HAM using a lensless diffuser system. Experimental results of recognizing various inputs are presented. Analytical expressions about the present HAM are derived, and results of computer simulation are also presented.
Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria (2016)

The syntrophic degradation of branched-chain fatty acids (BCFAs) such as 2-methylbutyrate and isobutyrate is an essential step in the production of methane from proteins/amino acids in anaerobic ecosystems. While a few syntrophic BCFA-degrading bacteria have been isolated, their metabolic pathways in BCFA and short-chain fatty acid (SCFA) degradation as well as energy conservation systems remain unclear. In an attempt to identify these pathways, we herein performed comparative genomics of three syntrophic bacteria: 2-methylbutyrate-degrading "Syntrophomonas wolfei subsp. methylbutyratica" strain JCM 14075(T) (=4J5(T)), isobutyrate-degrading Syntrophothermus lipocalidus strain TGB-C1(T), and non-BCFA-metabolizing S. wolfei subsp. wolfei strain Göttingen(T). We demonstrated that 4J5 and TGB-C1 both encode multiple genes/gene clusters involved in β-oxidation, as observed in the Göttingen genome, which has multiple copies of genes associated with butyrate degradation. The 4J5 genome possesses phylogenetically distinct β-oxidation genes, which may be involved in 2-methylbutyrate degradation. In addition, these Syntrophomonadaceae strains harbor various hydrogen/formate generation systems (i.e., electron-bifurcating hydrogenase, formate dehydrogenase, and membrane-bound hydrogenase) and energy-conserving electron transport systems, including electron transfer flavoprotein (ETF)-linked acyl-CoA dehydrogenase, ETF-linked iron-sulfur binding reductase, ETF dehydrogenase (FixABCX), and flavin oxidoreductase-heterodisulfide reductase (Flox-Hdr). Unexpectedly, the TGB-C1 genome encodes a nitrogenase complex, which may function as an alternative H2 generation mechanism. These results suggest that the BCFA-degrading syntrophic strains 4J5 and TGB-C1 possess specific β-oxidation-related enzymes for BCFA oxidation as well as appropriate energy conservation systems to perform thermodynamically unfavorable syntrophic metabolism.
ChemInform Abstract: Imidazo(4,5‐b)quinoxaline Cyanines as Neurokinin Antagonists. (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.
Accelerated cardiac T2 mapping using breath‐hold multiecho fast spin‐echo pulse sequence with k‐t FOCUSS (2011)

Cardiac T(2) mapping is a promising method for quantitative assessment of myocardial edema and iron overload. We have developed a new multiecho fast spin echo (ME-FSE) pulse sequence for breath-hold T(2) mapping with acceptable spatial resolution. We propose to further accelerate this new ME-FSE pulse sequence using k-t focal underdetermined system solver adapted with a framework that uses both compressed sensing and parallel imaging (e.g., sensitivity encoding) to achieve higher spatial resolution. We imaged 12 control subjects in midventricular short-axis planes and compared the accuracy of T(2) measurements obtained using ME-FSE with generalized autocalibrating partially parallel acquisitions and ME-FSE with k-t focal underdetermined system solver. For image reconstruction, we used a bootstrapping two-step approach, where in the first step fast Fourier transform was used as the sparsifying transform and in the final step principal component analysis was used as the sparsifying transform. When compared with T(2) measurements obtained using generalized autocalibrating partially parallel acquisitions, T(2) measurements obtained using k-t focal underdetermined system solver were in excellent agreement (mean difference = 0.04 msec; upper/lower 95% limits of agreement were 2.26/-2.19 msec, respectively). The proposed accelerated ME-FSE pulse sequence with k-t focal underdetermined system solver is a promising investigational method for rapid T(2) measurement of the heart with relatively high spatial resolution (1.7 × 1.7 mm(2) ).
ChemInform Abstract: Amino Acid Derived Thiane Oxide and Dioxide Systems as Disposable Templates: Synthesis of α‐Amino Ketones, anti‐Amino Alcohols and an Amino Cyclopentenone. (1997)

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.