gebhart/patrepeval huggingface dataset:
Physical and Functional Interaction between Dorfin and Valosin-containing Protein That Are Colocalized in Ubiquitylated Inclusions in Neurodegenerative Disorders (2004)

Dorfin, a RING-IBR type ubiquitin ligase (E3), can ubiquitylate mutant superoxide dismutase 1, the causative gene of familial amyotrophic lateral sclerosis (ALS). Dorfin is located in ubiquitylated inclusions (UBIs) in various neurodegenerative disorders, such as ALS and Parkinson's disease (PD). Here we report that Valosin-containing protein (VCP) directly binds to Dorfin and that VCP ATPase activity profoundly contributes to the E3 activity of Dorfin. High through-put analysis using mass spectrometry identified VCP as a candidate of Dorfin-associated protein. Glycerol gradient centrifugation analysis showed that endogenous Dorfin consisted of a 400-600-kDa complex and was co-immunoprecipitated with endogenous VCP. In vitro experiments showed that Dorfin interacted directly with VCP through its C-terminal region. These two proteins were colocalized in aggresomes in HEK293 cells and UBIs in the affected neurons of ALS and PD. VCP(K524A), a dominant negative form of VCP, reduced the E3 activity of Dorfin against mutant superoxide dismutase 1, whereas it had no effect on the autoubiquitylation of Parkin. Our results indicate that VCPs functionally regulate Dorfin through direct interaction and that their functional interplay may be related to the process of UBI formation in neurodegenerative disorders, such as ALS or PD.
An In vivo Dual-Reporter System of Cyanobacteria Using Two Railroad-Worm Luciferases with Different Color Emissions (2004)

In vivo genetic reporter systems using luciferase enzymes enable the real-time monitoring of gene expression in living cells. We have challenged concurrent monitoring of two independent promoter activities within the same cells to precisely compare their characteristics in vivo. In this report, we describe a simple dual-reporter system capable of simultaneously monitoring two promoter activities in living cyanobacterial cells. Two railroad-worm luciferases catalyzing the bioluminescent emissions of different colors served as the dual reporters; each emission was successfully separated by interference filters to estimate the individual bioluminescence signals using photomultiplier tubes. Using this system, we clearly demonstrated the difference in the expression profiles between promoters in the same cells.
Chemoselective Oxidation of Sulfides to Sulfoxides Using <i>N</i>-<i>t</i>-Butyl-<i>N</i>-chlorocyanamide (2005)

Abstract A simple, efficient and highly chemoselective method has been developed for the synthesis of sulfoxides from sulfides using N-t-butyl-N-chlorocyanamide as an oxidant in a mixed acetonitrile–water solution with a 1:1 mol ratio of oxidant to sulfides. N-t-butyl-N-chlorocyanamide, a source of positive chlorine, has been used for conversion of the variety of sulfides into their corresponding sulfoxides in quantitative yields.
The Importance of Reaction Conditions on the Chemical Structure of N,O-Acylated Chitosan Derivatives (2019)

The structure of acylated chitosan derivatives strongly determines the properties of obtained products, influencing their hydrodynamic properties and thereby their solubility or self-assembly susceptibility. In the present work, the significance of slight changes in acylation conditions on the structure and properties of the products is discussed. A series of chitosan-acylated derivatives was synthesized by varying reaction conditions in a two-step process. As reaction media, two diluted acid solutions-i.e., acetic acid and hydrochloric acid)-and two coupling systems-i.e., 1-ethyl-3-(3-dimethyl-aminopropyl)-1-carbodiimide hydrochloride (EDC) and <i>N</i>-hydroxysulfosuccinimide (EDC/NHS)-were used. The chemical structure of the derivatives was studied in detail by means of two spectroscopic methods, namely infrared and nuclear magnetic resonance spectroscopy, in order to analyze the preference of the systems towards <i>N</i>- or <i>O</i>-acylation reactions, depending on the synthesis conditions used. The results obtained from advanced <sup>1</sup>H-<sup>13</sup>C HMQC spectra emphasized the challenge of achieving a selective acylation reaction path. Additionally, the study of the molecular weight and solution behavior of the derivatives revealed that even slight changes in their chemical structure have an important influence on their final properties. Therefore, an exact knowledge of the obtained structure of derivatives is essential to achieve reaction reproducibility and to target the application.
A Photovoltaic Device Using an Electrolyte Containing Photosynthetic Reaction Centers (2010)

The performance of bio-photovoltaic devices with a monolayer of the immobilized photosynthetic reaction center (RC) is generally low because of weak light absorption and poor charge transfer between the RC and the electrode. In this paper, a new bio-photovoltaic device is described in which the RC is dissolved in the electrolyte of an electrochemical cell. The charges generated by the illuminated RC are transferred to electrodes via mediators. The difference between the reaction rates of two types of mediator at the electrode surfaces determines the direction of the photocurrent in the device. Experimental results show that the magnitude of the photocurrent is proportional to the incident light intensity, and the current increases nonlinearly with an increase in the RC concentration in the electrolyte. With further optimization this approach should lead to devices with improved light absorption.
Tetrapropyl-tetraphenyl-diindenoperylene derivative as a green absorber for high-voltage stable organic solar cells (2011)

We present small molecule organic solar cells (SMOSC) based on flat heterojunctions (FHJ) of the alternative green donor 2,3,10,11-tetrapropyl-1,4,9,12-tetraphenyl-diindeno[1,2,3-cd:1',2',3'-lm]perylene (P4-Ph4-DIP) and the fullerene ${\mathrm{C}}_{60}$. P4-Ph4-DIP absorbs in the green spectral range and thus fills the spectral gap that standard absorber materials (zinc or copper phthalocyanine for red and ${\mathrm{C}}_{60}$ for blue absorption) leave, thus allowing broad coverage of the sun spectrum, which is of major interest for tandem devices. The materials properties of P4-Ph4-DIP are studied, and SMOSC are characterized by current voltage, external quantum efficiency, and aging measurements. The solar cells display very high fill factors FF $>$ 76% and open circuit voltages ${V}_{\mathrm{OC}}$ of close to 1 V. Mismatch-corrected efficiencies of up to 1.9% are obtained. Aging measurements show that ${\mathrm{C}}_{60}$ in conjunction with P4-Ph4-DIP yields extremely stable devices. We observe $\ensuremath{\approx}$ 88% of the initial efficiency after 2500 h illumination at 999 mW/cm${}^{2}$ illumination intensity, with no observable change in short-circuit current density. Furthermore, we also show that a systematic variation of donor thickness in FHJ can be combined with transfer matrix formalism-based optical simulations and the continuity equation for excitons to reliably determine the exciton diffusion length ${L}_{\mathrm{D}}$. A value of 9 $\ifmmode\pm\else\textpm\fi{}$ 1 nm is found for P4-Ph4-DIP.
Anisotropy detection by tomography and polarization analysis in a 3D three-component VSP (2001)

Vertical Seismic Profiles (VSP) allow borehole information (e.g. well logs and geological ties) to be extended to the surrounding space. Well logs span only one dimension i.e. depth along the well itself, but with a very high resolution. Conversely, conventional surface seismic data provides information with a lower resolution, but with a much wider 2D or 3D extent. Matching of events in the VSP and the surface seismic increases the physical and geological consistency of the Earth model we can build in depth. Depth is the natural dimension for VSP data, while surface seismic provides a reflectivity image of the Earth in the time domain. The velocity of seismic waves connects the two worlds. Seismic tomography estimates a 2D or 3D velocity field by jointly inverting different wave types, i.e. diret, reflected and refracted arrivals. It provides a macro-model for the velocity field that is consistent with the resolution of the available signal, without assuming simple shapes for the interfaces or smooth velocities. Thus, it can bridge both the gap between the time and depth domains, and also between data with different resolution scales: almost 100 m for seismic waves, and about 1 m for sonic logs.
Nirmatrelvir Resistant SARS-CoV-2 Variants with High Fitness in Vitro (2022)

Abstract The oral protease inhibitor nirmatrelvir is expected to play a pivotal role for prevention of severe cases of coronavirus disease 2019 (COVID-19). To facilitate monitoring of potentially emerging resistance, we studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) escape from nirmatrelvir. Resistant variants selected in cell culture harbored different combinations of substitutions in the SARS-CoV-2 main protease (Mpro). Reverse genetic studies in a homologous infectious cell culture system revealed up to 80-fold resistance conferred by the combination of substitutions L50F and E166V. Resistant variants had high fitness increasing the likelihood of occurrence and spread of resistance. Molecular dynamics simulations revealed that E166V and L50F+E166V weakened nirmatrelvir-Mpro binding. The SARS-CoV-2 polymerase inhibitor remdesivir retained activity against nirmatrelvir resistant variants and combination of remdesivir and nirmatrelvir enhanced treatment efficacy compared to individual compounds. These findings have implications for monitoring and ensuring treatment programs with high efficacy against SARS-CoV-2 and potentially emerging coronaviruses.
From Chiral <i>ortho</i>-Benzoquinone Monoketals to Nonracemic Indolinocodeines through Diels–Alder and Cope Reactions (2012)

The S-dienol (-)-4 containing 10 carbons and one oxygen of the final product was prepared in 98.6% ee and 39% yield from cyclohexan-1,3-dione. It was attached to the aromatic ring as a monoether of catechol S-(-)-6 and subsequently subjected to oxidative ketalization in methanol. The allylated phenanthrofuran obtained was selectively oxidized at the terminal double bond. The fifth ring was completed by a "one-pot" amidation-cyclization process promoted by palladium acetate. The final homochiral indolinocodeine (-)-31 was obtained in 16 steps and 3.6% overall yield from cyclohexan-1,3-dione.
Hierarchical routing with QoS (2012)

We present our simulation-based design of hierarchical routing systems using the following state parameters to support quality of service (QoS): delay, hop count, and available bandwidth. Without revealing its internal structure, a cluster in a hierarchical system can advertise to other clusters its
Improvement of Reactivity of Carbon Iron Ore Composite with Biomass Char for Blast Furnace (2009)

Enhancement of reactivity of the burden in the blast furnace can decrease the reducing agent of blast furnace. Besides high reactivity coke, the carbon iron ore composite is considered to be a typical high reactivity burden that can control the thermal reserve zone temperature. Since the reactivity of biomass char is much higher than that of coke, the use of carbon iron ore composite with biomass char will be favorable for decreasing the reducing agent. In the present study the reaction and reducing behavior of the carbon iron ore composite with biomass char were investigated. The gasification rate of biomass char was measured in CO2 atmosphere, and the reaction rate equation of that was derived. The microscopic structure change of biomass during carbonization was experimentally analyzed. According to the experimental results, the reduction of the composite begins at about 550°C in an inert gas atmosphere, and it is much lower than the composite with coke. Analysis of the reaction of carbon iron ore composite was carried out with the reaction model of the carbon iron ore composite based on a lumped system, in which the reaction rate of biomass char and iron ore were installed. The reaction model shows that the biomass char can improve the reduction behavior of the carbon iron ore composite especially in the lower temperature region. Moreover, the influence of gas atmosphere and the optimum structure of the composite were investigated by the model calculation to estimate the optimum condition of the composite in the blast furnace.
Gas chromatography of volatiles from breath and urine (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGas chromatography of volatiles from breath and urineRoy. Teranishi, T. R. Mon, Arthur B. Robinson, Paul. Cary, and Linus. PaulingCite this: Anal. Chem. 1972, 44, 1, 18–20Publication Date (Print):January 1, 1972Publication History Published online1 May 2002Published inissue 1 January 1972https://pubs.acs.org/doi/10.1021/ac60309a012https://doi.org/10.1021/ac60309a012research-articleACS PublicationsRequest reuse permissionsArticle Views468Altmetric-Citations100LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Down-regulation of PLCγ2–β-catenin pathway promotes activation and expansion of myeloid-derived suppressor cells in cancer (2013)

Myeloid-derived suppressor cells (MDSCs) favor tumor promotion, mainly by suppressing antitumor T cell responses in many cancers. Although the mechanism of T cell inhibition is established, the pathways leading to MDSC accumulation in bone marrow and secondary lymphoid organs of tumor-bearing hosts remain unclear. We demonstrate that down-regulation of PLCγ2 signaling in MDSCs is responsible for their aberrant expansion during tumor progression. PLCγ2(-/-) MDSCs show stronger immune-suppressive activity against CD8(+) T cells than WT MDSCs and potently promote tumor growth when adoptively transferred into WT mice. Mechanistically, PLCγ2(-/-) MDSCs display reduced β-catenin levels, and restoration of β-catenin expression decreases their expansion and tumor growth. Consistent with a negative role for β-catenin in MDSCs, its deletion in the myeloid population leads to MDSC accumulation and supports tumor progression, whereas expression of β-catenin constitutively active reduces MDSC numbers and protects from tumor growth. Further emphasizing the clinical relevance of these findings, MDSCs isolated from pancreatic cancer patients show reduced p-PLCγ2 and β-catenin levels compared with healthy controls, similar to tumor-bearing mice. Thus, for the first time, we demonstrate that down-regulation of PLCγ2-β-catenin pathway occurs in mice and humans and leads to MDSC-mediated tumor expansion, raising concerns about the efficacy of systemic β-catenin blockade as anti-cancer therapy.
Imaging and Analysis Platform for Automatic Phenotyping and Trait Ranking of Plant Root Systems (2010)

The ability to nondestructively image and automatically phenotype complex root systems, like those of rice (Oryza sativa), is fundamental to identifying genes underlying root system architecture (RSA). Although root systems are central to plant fitness, identifying genes responsible for RSA remains an underexplored opportunity for crop improvement. Here we describe a nondestructive imaging and analysis system for automated phenotyping and trait ranking of RSA. Using this system, we image rice roots from 12 genotypes. We automatically estimate RSA traits previously identified as important to plant function. In addition, we expand the suite of features examined for RSA to include traits that more comprehensively describe monocot RSA but that are difficult to measure with traditional methods. Using 16 automatically acquired phenotypic traits for 2,297 images from 118 individuals, we observe (1) wide variation in phenotypes among the genotypes surveyed; and (2) greater intergenotype variance of RSA features than variance within a genotype. RSA trait values are integrated into a computational pipeline that utilizes supervised learning methods to determine which traits best separate two genotypes, and then ranks the traits according to their contribution to each pairwise comparison. This trait-ranking step identifies candidate traits for subsequent quantitative trait loci analysis and demonstrates that depth and average radius are key contributors to differences in rice RSA within our set of genotypes. Our results suggest a strong genetic component underlying rice RSA. This work enables the automatic phenotyping of RSA of individuals within mapping populations, providing an integrative framework for quantitative trait loci analysis of RSA.
Towards privacy-preserving recognition of human activities (2015)

A smart room of the future is expected to facilitate intelligent interaction with its occupants while respecting their privacy. Although standard video cameras can be used to learn where the occupants are and what they do, they raise privacy concerns. While this can be mitigated by severely reducing camera resolution, it will also impact the utility of the camera network. This work investigates and quantifies the tradeoff between camera resolution and action recognition accuracy. Rather than building a physical testbed to carry out this study, we use a graphics engine to simulate a room with 5 cameras, and to animate avatars using skeletal movements of real users captured by a Kinect v2 camera. We study resolutions from 100×100 pixels down to 1×1 using a state-of-the-art action recognition method at higher resolutions and we propose a new approach at ultra-low resolutions. In extensive simulations, we conclude that on a dataset of 12 individuals performing 4 actions our algorithm applied to single-pixel data performs very close to the state-of-the-art method applied to 100×100 data, suggesting that reliable action recognition can be achieved without compromising occupant's identity.
Toward an OpenSocial Life Science Gateway (2008)

To enable the Life Science community to fully use TeraGrid resources for computing and data management, we developed an integrated cyber computational environment named the Open Life Science Gateway. Based on a service-oriented framework, the gateway aggregates a group of bioinformatics applications and data collections into a Web portal. Furthermore, this gateway provides a platform for life science researchers to collaboratively conduct bioinformatics computing, building their communities and sharing data and workflows. In the era of Web 2.0, gadgets such as iGoogle gadgets are becoming increasingly popular for integration and customization of Web contents from different sources. Social networking is also gaining attention because it has created powerful new ways to build virtual communities in a bottom-up manner. Google's OpenSocial framework standardizes the practices of both gadget programming and online social networking, enabling Web developers to write social gadgets that can run in any OpenSocial-compliant container. These new Web technologies can leverage science gateway portals in terms of rich user interface and social network capability, which will promote the adoption of science gateways for advanced education purpose. This paper introduces the Open Life Science Gateway service-oriented framework and describes our efforts to develop OpenSocial gadgets for running bioinformatics analysis tools on the TeraGrid resources. The gadgets can be deployed in OpenSocial containers such as the iGoogle Sandbox and Apache Shindig. With these gadgets, biologists and biology students can easily run their analysis programs and browse outputs through social Web sites.
Evaluation of Modified Portable Digital Camera for Screening of Diabetic Retinopathy (2009)

The modified digital camera is a useful alternative technique to acquire fundus images and provides a tool for screening posterior segment conditions, including diabetic retinopathy in a variety of clinical settings.
Adventitious Viruses Detected in Biopharmaceutical Bulk Harvest Samples over a 10 Year Period. (2016)

While viral safety is a major concern for biologics manufactured using mammalian cells, the numbers of viral contamination events reported in the literature are quite low. During a 10-year period during which biologics derived from a variety of mammalian cell culture processes were evaluated using the in vitro virus screening assay, only reovirus type 2 and Cache Valley virus were detected, and these only in biologics manufactured in Chinese hamster ovary (CHO) cells. From the literature, we know that the murine parvovirus mouse minute virus has also been detected in biologics manufactured using CHO cells. The manifestations of these viral contaminants within the biotech manufacturing processes are discussed, as are the likely sources of the contaminants and some possible approaches for mitigating the risk of future occurrences of these types of contamination.
Enantioselective synthesis of strobamine and its analogues (2010)

2S,5S,8R)-Strobamine (+)-1a was synthesized by adding cinnamoyl cyanide 6a to tropinone 3 lithium enolate generated by treatment of (S,S')-,-dimethyldibenzylamide with butyl lithium in the presence of lithium chloride to give (-)-chalcostrobamine (-)-7a, which yielded a one-to-one mixture of (+)-1a and its C-2 epimer (-)-2a on treatment with 2N sulfuric acid. Compounds (+)-1a and (-)-2a could be separated by column chromatography. (-)-Strobamine (-)-1a and (+)-2a were synthesized by a similar set of reactions using the tropinone 3 lithium enolate generated with butyl lithium in the presence of (R,R')-,'-dimethyldibenzylamide and lithium chloride. (+)-and (-)-p-Methylstrobamine (+)-and (-)-1b and (+)-and (-)-epi-p-methylstrobamine (+)and (-)-2b were synthesized by a similar procedure. The absolute configuration of (+)-epi-pmethylstrobamine (+)-2b was determined by X-ray analysis to have the (2S,5R,8S) configuration.