gebhart/patrepeval huggingface dataset:
Insights into the UDP-sugar selectivities of human UDP-glycosyltransferases (UGT): a molecular modeling perspective (2015)

Enzymes of the human uridine diphosphate (UDP)-glycosyltransferase (UGT) superfamily typically catalyze the covalent addition of a sugar from UDP-sugar cofactors to relatively small lipophilic compounds. The sugar conjugates are often biologically less active with improved water-solubility, facilitating more effective elimination from the body. Experimental data indicate that UGT proteins exhibit differing selectivities toward various UDP-sugars. Although, three-dimensional (3D) structures of UGT proteins are required to provide insights into the UDP-sugar selectivities observed for the various UGT proteins, there are currently, no experimental structures available for human UGTs bound to UDP-sugar(s). Thus, the absence of 3D structures poses a major challenge for analyzing UDP-sugar selectivity at an atomic level. In this commentary, we highlight the application of comparative homology modeling for understanding the UDP-sugar selectivities of UGT proteins. Homology models of the C-terminal (CT) domain indicate a highly conserved structural fold across the UGT family with backbone root mean-squared deviations (rmsds) between 0.066 and 0.079 Å with respect to the UGT2B7-CT X-ray crystal structure. The models show that four residues in the terminal portion of the CT signature sequence play an important role in UDP-sugar selectivity. The N-terminal domain is less likely to be associated with UDP-sugar selectivity, although, a conserved residue, Arg-259 (UGT2B7 numbering) in the UGT 1 and 2 families may influence UDP-sugar selectivity. Overall, the models demonstrate excellent agreement with experimental observations in predicting the key residues that influence the selectivity of UDP-sugar binding.
Desolvation‐Triggered Versatile Transfer‐Printing of Pure BN Films with Thermal–Optical Dual Functionality (2020)

Although hexagonal boron nitride (BN) nanostructures have recently received significant attention due to their unique physical and chemical properties, their applications have been limited by a lack of processability and poor film quality. In this study, a versatile method to transfer-print high-quality BN films composed of densely stacked BN nanosheets based on a desolvation-induced adhesion switching (DIAS) mechanism is developed. It is shown that edge functionalization of BN sheets and rational selection of membrane surface energy combined with systematic control of solvation and desolvation status enable extensive tunability of interfacial interactions at BN-BN, BN-membrane, and BN-substrate boundaries. Therefore, without incorporating any additives in the BN film and applying any surface treatment on target substrates, DIAS achieves a near 100% transfer yield of pure BN films on diverse substrates, including substrates containing significant surface irregularities. The printed BNs demonstrate high optical transparency (>90%) and excellent thermal conductivity (>167 W m<sup>-1</sup> K<sup>-1</sup>) for few-micrometer-thick films due to their dense and well-ordered microstructures. In addition to outstanding heat dissipation capability, substantial optical enhancement effects are confirmed for light-emitting, photoluminescent, and photovoltaic devices, demonstrating their remarkable promise for next-generation optoelectronic device platforms.
Operating room fire safety. (2011)

Operating room fires are a rare but preventable danger in modern healthcare operating rooms. Optimal outcomes depend on all operating room personnel being familiar with their roles in fire prevention and fire management. Despite the recommendations of major safety institutes, this familiarity is not the current practice in many healthcare facilities. Members of the anesthesiology and the surgery departments are commonly not actively involved in fire safety programs, fire drills, and fire simulations that could lead to potential delays in prevention and management of intraoperative fires.
EverCrypt: A Fast, Verified, Cross-Platform Cryptographic Provider (2020)

We present EverCrypt: a comprehensive collection of verified, high-performance cryptographic functionalities available via a carefully designed API. The API provably supports agility (choosing between multiple algorithms for the same functionality) and multiplexing (choosing between multiple implementations of the same algorithm). Through abstraction and zero-cost generic programming, we show how agility can simplify verification without sacrificing performance, and we demonstrate how C and assembly can be composed and verified against shared specifications. We substantiate the effectiveness of these techniques with new verified implementations (including hashes, Curve25519, and AES-GCM) whose performance matches or exceeds the best unverified implementations. We validate the API design with two high-performance verified case studies built atop EverCrypt, resulting in line-rate performance for a secure network protocol and a Merkle-tree library, used in a production blockchain, that supports 2.7 million insertions/sec. Altogether, EverCrypt consists of over 124K verified lines of specs, code, and proofs, and it produces over 29K lines of C and 14K lines of assembly code.
Acute and Long-Term Treatment With Dapagliflozin and Association With Serum Soluble Urokinase Plasminogen Activator Receptor (2022)

<b>Background:</b> Elevated soluble urokinase plasminogen activator receptor (suPAR) is highly associated with increased risk of diabetic complications. Dapagliflozin is a drug inhibiting the sodium-glucose co-transporter 2 in the kidney to decrease blood glucose, while also decreasing risk of kidney disease, heart failure, and death. Therefore, we have investigated suPAR as a monitor for treatment effect with dapagliflozin in diabetes. <b>Methods:</b> suPAR was measured in two double-blinded randomized clinical cross-over trials. The first trial investigated the effect of a single dose dapagliflozin 50 mg or placebo 12 h after intake, in individuals with type 1 diabetes and albuminuria. The second trial investigated the effect of a daily dose dapagliflozin 10 mg or placebo for 12 weeks, in individuals with type 2 diabetes and albuminuria. suPAR was measured in serum samples taken, in the acute trial, after treatment with dapagliflozin and placebo, and in the long-term trial, before and after treatment with dapagliflozin and placebo. Effect of dapagliflozin on suPAR levels were assessed using paired <i>t</i>-test. <b>Results:</b> 15 participants completed the acute trial and 35 completed the long-term trial. Mean difference in suPAR between dapagliflozin and placebo in the acute trial after 12 h was 0.70 ng/ml (95% CI: 0.66; 1.33, <i>p</i> = 0.49). In the long-term trial the mean difference was 0.06 ng/ml (95% CI -0.15; 0.27, <i>p</i> = 0.57). <b>Conclusion:</b> Based on our findings we conclude that suPAR is not a feasible marker to monitor the effect of treatment with dapagliflozin. Thus, a further search of suitable markers must continue.
Resveratrol attenuates hypoxic injury in a primary hepatocyte model of hemorrhagic shock and resuscitation (2014)

Resveratrol prevents cell death in HSR and exerts a protective effect on the mitochondria in a hepatocyte model of hypoxic injury-reoxygenation possibly via Sirt-1 modulation of p53 and NF-κB activity.
Cd–S–Se quantum dot embedded glasses with dual emissions for wide color gamut white LED (2021)

Abstract Cd‐S‐Se quantum dot embedded glasses (QDEGs) with dual‐band emissions of green and red were synthesized by assembling two QDEGs, to obtain a color converter for white LEDs (wLEDs) with a wide color gamut and long‐term stability. Each QDEG, possessing different sizes of QD, was prepared by adjusting heat‐treatment conditions. They were then bonded to each other by an additional heat treatment to fabricate a pattern structured QDEG (pQDEG). The fabrication conditions of the pQDEGs, such as their heat‐treatment condition and thickness, were varied to improve the color gamut. pQDEG‐based WLEDs were demonstrated and their optical properties such as color coordinates, luminous efficiency, and color rendering index (CRI) were monitored. The effect of pQDEG fabrication conditions on the resultant emission spectra and color gamut were discussed.
Polymer Multilayer Films Obtained by Electrochemically Catalyzed Click Chemistry (2009)

We report the covalent layer-by-layer construction of polyelectrolyte multilayer (PEM) films by using an efficient electrochemically triggered Sharpless click reaction. The click reaction is catalyzed by Cu(I) which is generated in situ from Cu(II) (originating from the dissolution of CuSO(4)) at the electrode constituting the substrate of the film. The film buildup can be controlled by the application of a mild potential inducing the reduction of Cu(II) to Cu(I) in the absence of any reducing agent or any ligand. The experiments were carried out in an electrochemical quartz crystal microbalance cell which allows both to apply a controlled potential on a gold electrode and to follow the mass deposited on the electrode through the quartz crystal microbalance. Poly(acrylic acid) (PAA) modified with either alkyne (PAA(Alk)) or azide (PAA(Az)) functions grafted onto the PAA backbone through ethylene glycol arms were used to build the PEM films. Construction takes place on gold electrodes whose potentials are more negative than a critical value, which lies between -70 and -150 mV vs Ag/AgCl (KCl sat.) reference electrode. The film thickness increment per bilayer appears independent of the applied voltage as long as it is more negative than the critical potential, but it depends upon Cu(II) and polyelectrolyte concentrations in solution and upon the reduction time of Cu(II) during each deposition step. An increase of any of these latter parameters leads to an increase of the mass deposited per layer. For given buildup conditions, the construction levels off after a given number of deposition steps which increases with the Cu(II) concentration and/or the Cu(II) reduction time. A model based on the diffusion of Cu(II) and Cu(I) ions through the film and the dynamics of the polyelectrolyte anchoring on the film, during the reduction period of Cu(II), is proposed to explain the major buildup features.
Wogonin and related natural flavones are inhibitors of CDK9 that induce apoptosis in cancer cells by transcriptional suppression of Mcl-1 (2011)

The wogonin-containing herb Scutellaria baicalensis has successfully been used for curing various diseases in traditional Chinese medicine. Wogonin has been shown to induce apoptosis in different cancer cells and to suppress growth of human cancer xenografts in vivo. However, its direct targets remain unknown. In this study, we demonstrate for the first time that wogonin and structurally related natural flavones, for example, apigenin, chrysin and luteolin, are inhibitors of cyclin-dependent kinase 9 (CDK9) and block phosphorylation of the carboxy-terminal domain of RNA polymerase II at Ser(2). This effect leads to reduced RNA synthesis and subsequently rapid downregulation of the short-lived anti-apoptotic protein myeloid cell leukemia 1 (Mcl-1) resulting in apoptosis induction in cancer cells. We show that genetic inhibition of Mcl-1 or CDK9 expression by siRNA is sufficient to mimic flavone-induced apoptosis. Pull-down and in silico docking studies demonstrate that wogonin directly binds to CDK9, presumably to the ATP-binding pocket. In contrast, wogonin does not inhibit CDK2, CDK4 and CDK6 at doses that inhibit CDK9 activity. Furthermore, we show that wogonin preferentially inhibits CDK9 in malignant compared with normal lymphocytes. Thus, our study reveals a new mechanism of anti-cancer action of natural flavones and supports CDK9 as a therapeutic target in oncology.
Structural second-order nonlinearity in plasmonic metamaterials (2018)

Nonlinear processes are at the core of many optical technologies whose further development require optimized materials suitable for nanoscale integration. Here we demonstrate the emergence of a strong bulk second-order nonlinear response in a plasmonic nanorod composite comprised of centrosymmetric materials. We develop an effective-medium description of the underlying physics, compare its predictions to the experimental results, and analyze the limits of its applicability. We demonstrate strong tunable generation of the p-polarized second-harmonic light in response to either s-orp-polarized excitation. High second-harmonic enhancement is observed for fundamental frequencies in the epsilon-near-zero spectral range. The work demonstrates emergence of structurally tunable nonlinear optical response in plasmonic composites and presents a new nonlinear optical platform suitable for integrated nonlinear photonics.
Microscopic Models for Engineering of Optoelectronic Devices (invited). (2020)

Abstract not provided.
Information-Based Color Feature Representation for Image Classification (2007)

For the image classification task, the color histogram is widely used as an important color feature indicating the content of the image. However, the high-resolution color histograms are usually of high dimension and contain much redundant information which does not relate to the image content, while the low-resolution histograms cannot provide adequate discriminative information for image classification. In this paper, a new color feature representation is proposed which not only takes the correlation among neighbouring components of the conventional color histogram into account but removes the redundant information as well. A high-resolution, uniform quantized color histogram is first obtained from the image. Then the redundant bins are removed and some neighbouring bins are combined together to generate a new feature component to maximize the discriminative ability. The mutual information is adopted to evaluate the discriminative power of a specific feature set and an iterative algorithm is performed to derive the histogram quantization and their corresponding feature generation. To illustrate the effectiveness of the proposed feature representation, an application of detecting adult images, i.e., image classification between erotic and benign images, is carried out. Two widely used classification techniques, SVM and Adaboost, are employed as the classifier. Experimental results show the superior performance of our color representation compared with the conventional color histogram in image classification.
<i>In vitro</i>activity of rifabutin against 293 contemporary carbapenem-resistant<i>Acinetobacter baumannii</i>clinical isolates and characterization of rifabutin mode of action and resistance mechanisms (2020)

Abstract Background Rifabutin, an oral drug approved to treat Mycobacterium avium infections, demonstrated potent activity against Acinetobacter baumannii in nutrient-limited medium enabled by rifabutin cellular uptake through the siderophore receptor FhuE. Objectives To determine rifabutin in vitro activity and resistance mechanisms in a large panel of A. baumannii isolates. Methods Two hundred and ninety-three carbapenem-resistant A. baumannii clinical isolates collected from Europe, the USA and Asia during 2017–19 were used for MIC determination. Sequencing/genotyping of fhuE, rpoB and arr-2 genes in isolates with elevated rifabutin MIC combined with genetic engineering and gene expression quantification was used to characterize rifabutin’s mode of action and resistance mechanisms. Results Rifabutin showed excellent activity on the strain panel, with an MIC50/90 of 0.008/1 mg/L, and was superior to all other antibiotics tested, including colistin, tigecycline and cefiderocol (MIC90 of 8 mg/L). Rifabutin remained active on resistant subpopulations, including strains resistant to the siderophore–drug conjugate cefiderocol (MIC90 of 2 mg/L, n = 23). At least two independent resistance mechanisms were required to abolish rifabutin activity, which is in line with the dose-dependent mutational resistance frequency reaching 10−9 at rifabutin concentrations at or above 2 mg/L. Conclusions This study demonstrated the potent activity of rifabutin against carbapenem-resistant A. baumannii. We propose that FhuE-mediated active uptake of rifabutin enables activity against rifampicin-resistant isolates. To achieve clinically meaningful strain coverage and to avoid rapid resistance development, rifabutin concentrations ≥2 mg/L are required, something rifabutin oral formulations cannot deliver.
Isolation of<i>Sarcocystis</i><i>speeri</i>Dubey and Lindsay, 1999 Parasite from the South American Opossum (<i>Didelphis albiventris</i>) from Argentina (2000)

Sarcocystis sporocysts from the intestines of 2 opossums (Didelphis albiventris) from Argentina were fed to gamma-interferon knockout (KO) and nude mice. Protozoal schizonts were seen in brain, liver, spleen, and adrenal glands of mice examined 33-64 days after feeding sporocysts. Sarcocysts were seen in skeletal muscles of KO mice 34-71 days after feeding sporocysts. Schizonts and sarcocysts were structurally similar to Sarcocystis speeri Dubey and Lindsay, 1999 seen in mice fed sporocysts from the North American opossum Didelphis virginiana from the United States.
The Effective Duration of Antimicrobial Activity of Mafenide Acetate After Reconstitution (2018)

Mafenide acetate is an effective but costly antimicrobial solution used for burn wounds. The package insert instructs the user to discard unused solution within 48 hours of opening. The purpose of this study is to evaluate the antimicrobial activity of mafenide acetate beyond 48 hours after reconstitution, to possibly reduce cost by eliminating product waste. Staphylococcus aureus and Pseudomonas aeruginosa isolates were used to seed Mueller-Hinton agar plates. Filter paper disks were then saturated with 5% mafenide acetate at 0, 2, 7, 14, 30, and 60 days after reconstitution. Disks were then placed on the seeded agar plates and incubated. After incubation, the zone of inhibition around each plate was measured. A zone of inhibition of 2 mm or greater was indicative of susceptibility. Mafenide acetate remained efficacious, with a zone of inhibition of >2 mm to both organisms at 0, 2, 7, 14, 30, and 60 days after mafenide acetate reconstitution. This in vitro study demonstrates that the antimicrobial activity of mafenide acetate remains present for at least 60 days after reconstitution. Unused mafenide may not need to be discarded at 48 hours after opening. Reducing wasted product has the potential to translate into cost savings.
Detection of Lead in Soil with Excimer Laser Fragmentation Fluorescence Spectroscopy (2005)

Excimer laser fragmentation fluorescence spectroscopy (ELFFS) is used to monitor lead in soil sample and investigate laser-solid interactions. Pure lead nitrate salt and soil doped with lead nitrate are photolyzed with 193 nm light from an ArF excimer at fluences from 0.4 to 4 J/cm{sup 2}. Lead emission is observed at 357.2, 364.0, 368.3, 373.9 and 405.8 nm. Time-resolved data show the decay time of the lead emission at 405.8 nm grows with increasing fluence, and a plasma is formed above fluences of 2 J/cm{sup 2}, where a strong continuum emission interferes with the analyte signal. Fluences below this threshold allow us to achieve a detection limit of approximately 200 ppm in soil.
Identification of the fibroblast growth factor receptor in human vascular endothelial cells (1988)

The fibroblast growth factor (FGF) receptor of human umbilical vein-derived endothelial (HUE) cells has been identified by affinity labeling. It has an apparent molecular weight of 130,000. It binds both basic and acidic FGF, but not with epidermal growth factor, insulin, or transferrin. The lectin concanavalin-A does not inhibit the binding of 125I-bFGF to HUE cell-surface receptors, whereas it inhibits bFGF binding to BHK-21 cell-surface FGF receptor. This suggests that both types of receptors may differ in their degree of glycosylation. In contrast to other cell types, heparin only slightly inhibits the binding of basic FGF to its receptor. Protamine sulfate, which is anti-angiogenic in vivo, and suramin, a drug used in the therapy of trypanosomiasis and onchocerciasis, also inhibit the binding of basic FGF to the receptor.
A Widely Applicable Method of Resolution of Binaphthyls: Preparation of Enantiomerically Pure 1,1'- Binaphthalene-2,2'-diol, 1,1'-Binaphthalene-2,2'-dithiol, 2'-Mercapto-1,1'-binaphthalen-2-ol, and 1,1'-Binaphthalene-8,8'-diol (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Widely Applicable Method of Resolution of Binaphthyls: Preparation of Enantiomerically Pure 1,1'- Binaphthalene-2,2'-diol, 1,1'-Binaphthalene-2,2'-dithiol, 2'-Mercapto-1,1'-binaphthalen-2-ol, and 1,1'-Binaphthalene-8,8'-diolDavide Fabbri, Giovanna Delogu, and Ottorino De LucchiCite this: J. Org. Chem. 1995, 60, 20, 6599–6601Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/jo00125a057https://doi.org/10.1021/jo00125a057research-articleACS PublicationsRequest reuse permissionsArticle Views548Altmetric-Citations43LEARN 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
Extracellular biosynthesis of gadolinium oxide (Gd<sub>2</sub>O<sub>3</sub>) nanoparticles, their biodistribution and bioconjugation with the chemically modified anticancer drug taxol (2014)

As a part of our programme to develop nanobioconjugates for the treatment of cancer, we first synthesized extracellular, protein-capped, highly stable and well-dispersed gadolinium oxide (Gd2O3) nanoparticles by using thermophilic fungus Humicola sp. The biodistribution of the nanoparticles in rats was checked by radiolabelling with Tc-99m. Finally, these nanoparticles were bioconjugated with the chemically modified anticancer drug taxol with the aim of characterizing the role of this bioconjugate in the treatment of cancer. The biosynthesized Gd2O3 nanoparticles were characterized by UV-vis spectroscopy, transmission electron microscopy (TEM), X-ray diffraction (XRD) and X-ray photoemission spectroscopy (XPS). The Gd2O3-taxol bioconjugate was confirmed by UV-vis spectroscopy and fluorescence microscopy and was purified by using high performance liquid chromatography (HPLC).