gebhart/patrepeval huggingface dataset:
An Amine-Reactive Phenazine Ethosulfate (arPES)—A Novel Redox Probe for Electrochemical Aptamer-Based Sensor (2022)

Electrochemical aptamer-based biosensors (E-ABs) are attractive candidates for use in biomarker detection systems due to their sensitivity, rapid response, and design flexibility. There are only several redox probes that were employed previously for this application, and a combination of redox probes affords some advantages in target detection. Thus, it would be advantageous to study new redox probes in an E-AB system. In this study, we report the use of amine-reactive phenazine ethosulfate (arPES) for E-AB through its conjugation to the terminus of thrombin-binding aptamer. The constructed E-AB can detect thrombin by square-wave voltammetry (SWV), showing peak current at −0.15 V vs. Ag/AgCl at pH 7, which differs from redox probes used previously for E-ABs. We also compared the characteristics of PES as a redox probe for E-AB to methylene blue (MB), which is widely used. arPES showed stable signal at physiological pH. Moreover, the pH profile of arPES modified thrombin-binding aptamer revealed the potential application of arPES for a simultaneous multianalyte detection system. This could be achieved using different aptamers with several redox probes in tandem that harbor various electrochemical peak potentials. Our findings present a great opportunity to improve the current standard of biological fluid monitoring using E-AB.
3-D Statistical Indoor Channel Model for Millimeter-Wave and Sub-Terahertz Bands (2020)

Millimeter-wave (mmWave) and Terahertz (THz) will be used in the sixth-generation (6G) wireless systems, especially for indoor scenarios. This paper presents an indoor three-dimensional (3-D) statistical channel model for mmWave and sub-THz frequencies, which is developed from extensive channel propagation measurements conducted in an office building at 28 GHz and 140 GHz in 2014 and 2019. Over 15,000 power delay profiles (PDPs) were recorded to study channel statistics such as the number of time clusters, cluster delays, and cluster powers. All the parameters required in the channel generation procedure are derived from empirical measurement data for 28 GHz and 140 GHz line-of-sight (LOS) and non-line-of-sight (NLOS) scenarios. The channel model is validated by showing that the simulated root mean square (RMS) delay spread and RMS angular spread yield good agreements with measured values. An indoor channel simulation software is built upon the popular NYUSIM outdoor channel simulator, which can generate realistic channel impulse response, PDP, and power angular spectrum.
US Imaging of Tumor Angiogenesis with Microbubbles Targeted to Vascular Endothelial Growth Factor Receptor Type 2 in Mice (2008)

US imaging with contrast microbubbles targeted to VEGFR2 allows noninvasive visualization of VEGFR2 expression in tumor vessels in mice.
Active learning approaches to analysis of thin-film printed sensors for determining nitrate levels in soil (2023)

In order to train a learning-based prediction model, large datasets are typically required. One of the major restrictions of machine learning applications using customized databases is the cost of human labor. In the previous papers [3, 4, 5], it is demonstrated through experiments that the correlation between thin-film nitrate sensor performance and surface texture exists. In the previous papers, several methods for extracting texture features from sensor images are explored, repeated cross-validation and a hyperparameter auto-tuning method are performed, and several machine learning models are built to improve prediction accuracy. In this paper, a new way to achieve the same accuracy with a much smaller dataset of labels by using an active learning structure is presented.
Molecular population genetics of structural variants of esterase 6 in Drosophila melanogaster (1989)

Several lines of evidence indicate that natural selection operates between the major EST6-F and EST6-S allozymes of Drosophila melanogaster. In particular, consistent latitudinal clines and seasonal variation in their relative frequencies strongly suggest that they are not selectively equivalent in field populations. Several laboratory studies have found frequency-dependent fitness differences among the Est6-F and Est6-S genotypes. Moreover, the purified EST6-F and EST6-S allozymes differ in biochemical properties and the physiology of the enzyme, as a major component of the seminal fluid, suggests that these differences could affect reproductive aspects of fitness. However, molecular analyses reveal high levels of variation in the EST6 protein both within and between the EST6-F and EST6-S allozymes. Limited thermostability and more sensitive electrophoretic analyses reveal at least 17 variants of the two allozymes and sequence comparisons among 13 isolates of the Est6 gene reveal 16 nucleotide polymorphisms that would lead to amino acid differences. Two closely linked amino acid differences are strongly associated with the major difference between EST6-F and EST6-S; either or both of these are likely to cause the observed biochemical differences between EST6-F and EST6-S and may be the primary targets for the selection between these allozymes. The functional and adaptive significance of the other amino acid polymorphisms is unclear, although the data suggest that the EST6-8 haplotype within EST6-S has both arisen and proliferated relatively recently.
ChemInform Abstract: NICKEL(II), COBALT(II), AND IRON(II) LACUNAR COMPLEXES HAVING VERY SMALL CAVITIES: SYNTHESES, PROPERTIES, AND REACTIONS WITH DIOXYGEN (1984)

Abstract Nach bekannten Methoden werden durch Reaktion von [3,11‐Bis‐(1‐methoxyethyliden)‐2,12‐dimethyl‐1,5,9,13‐tetraazacyclohexadeca‐1,4,9,12‐tetraen]‐nickel(II)‐hexafluorophosphat mit N,N′‐Dimethylpropan‐1,3‐diamin in Acetonitril bzw. durch Reaktion des Ligand‐Hexafluorophosphat‐Salzes mit Co(II)‐acetat bzw. Dichloro‐bis‐[pyridin]‐eisen(ll) die neuen Komplexe (I) dargestellt und ihre elektrochemischen Eigenschaften untersucht.
ChemInform Abstract: Circular Dichroism of Carbohydrate‐Molybdate Complexes (1995)

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.
Development of a Two-Step Route to 3-PBC and βCCt, Two Agents Active against Alcohol Self-Administration in Rodent and Primate Models (2011)

To gain access to 3-propoxy-β-carboline hydrochloride (3-PBC·HCl) (1·HCl) and β-carboline-3-carboxylate-tert-butyl ester (βCCt) (2), potential clinical agents active against alcohol self-administration, a two-step route was developed. This process involves a palladium-catalyzed Buchwald-Hartwig coupling and an intramolecular Heck reaction. This two-step route provides rapid access to multigram quantities of 3-PBC (1) and βCCt (2), as well as analogues for studies of alcohol self-administration. The overall yield of 3-PBC (1) was improved from 8% to 50% by this route.
XML Document Clustering Using Common XPath (2005)

XML is becoming a common way of storing data. The elements and their arrangement in the document’s hierarchy not only describe the document structure but also imply the data’s semantic meaning, and hence provide valuable information to develop tools for manipulating XML documents. In this paper, we pursue a data mining approach to the problem of XML document clustering. We introduce a novel XML structural representation called common XPath (CXP), which encodes the frequently occurring elements with the hierarchical information, and propose to take the CXPs mined to form the feature vectors for XML document clustering. In other words, data mining acts as a feature extractor in the clustering process. Based on this idea, we devise a path-based XML document clustering algorithm called PBClustering which groups the documents according to their CXPs, i.e. their frequent structures. Encouraging simulation results are observed and reported.
Joint Object Reference Digital Interferometer (JORDI): A Single Spatial Light Modulator Based Design (2014)

The joint object reference digital interferometer (JORDI) is a single-channel apparatus for recording coherent holograms. Normally, two spatial light modulators (SLMs) are required for its realization. Presented here is a new design that uses only a single SLM.
Evaluation Techniques for Automatic Semantic Extraction: Comparing Syntactic and Window Based Approaches (1993)

As large on-line corpora become more prewlent, a number of attempts have been made to automatically extract thesaurus-like relations directly from text using knowledge poor methods. In the absence of any specific application, comparing the results of these attempts is difficult. Here we propose an ewluation method using gold standards, i.e., pre-existing hand-compiled resources, as a means of comparing extraction techniques. Using this ewluation method, we compare two semantic extraction techniques which produce similar word lists, one using syntactic context of words , and the&amp;apos;other using windows of heuristiclly tagged words. The two techniques are very similar except that in one case selective natural language processing, a partial syntactic analysis, is performed. On a 4 megabyte corpus, syntactic contexts produce significantly better results against the gold standards for the most characteristic words in the corpus, while windows produce better results for rare words.
High speed modulation of hybrid silicon evanescent lasers (2009)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text D. Dai, A. Fang, and J. E. Bowers, "High speed modulation of hybrid silicon evanescent lasers," in Advances in Optical Sciences Congress, OSA Technical Digest (CD) (Optica Publishing Group, 2009), paper IMC1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Development of an Intracellular Screen for New Compounds Able To Inhibit Mycobacterium tuberculosis Growth in Human Macrophages (2015)

Here we describe the development and validation of an intracellular high-throughput screening assay for finding new antituberculosis compounds active in human macrophages. The assay consists of a luciferase-based primary identification assay, followed by a green fluorescent protein-based secondary profiling assay. Standard tuberculosis drugs and 158 previously recognized active antimycobacterial compounds were used to evaluate assay robustness. Data show that the assay developed is a short and valuable tool for the discovery of new antimycobacterial compounds.
Development of a PET probe detecting tumors, which are responsive to gefitinib treatment (2016)

1089 Objectives Gefinitib is a molecularly target drug approved by FDA for the treatment of patients with metastatic non-small cell lung cancer (NSCLC), whose tumors have epidermal growth factor receptor (EGFR) exon 19 deletions or L858R mutations. However, within one year after the onset of the treatment, more than 90% of the NSCLC patients show drug resistance caused by second EGFR mutations (For example, T790M). Therefore, to detect the second EGFR mutation is very important in the therapeutic process of NSCLC. However, the only way to detect the mutation directly is invasive biopsy test and the development of noninvasively detected methodology has been desired. Our research target is to develop a PET tracer, which can detect the second EGFR mutations. Methods Five thienopyrimidine derivatives (FTPs1~5) were designed and synthesized as candidate compounds. Utilizing Promega ADP-Glo kinase assay kit, inhibitory activities of these compounds against wild type EGFR(WT), single mutated EGFR(L858R), EGFR(T790M), and double mutated EGFR(DM L858R/T790M) were evaluated. Next, using compounds radiolabeled by fluorine-18, in vivo imaging study was performed using mice bearing human NSCLC of NCI-H3255 and NCI-H1975. Results FTPs1~5 were synthesized by conventional organic chemical method. All synthesized compounds were confirmed based on the 1H NMR measurements. IC50 value (EGFR tyrosine kinase inhibition) of Gefitinib against EGFR(WT), EGFR(L858R), EGFR(T790M) and EGFR(L858R/T790M) was 0.020, 0.021, 0.868 and 7.11 μM, respectively. FTPs1~5 showed weak inhibitory activity against EGFR(T790M) and EGFR(L858R/T790M), and the IC50 values were over 10 μM, indicating FTPs1~5 could not bind to the EGFR with T790M mutation. FTPs2 and 4 kept inhibitory activity against EGFR(WT) and EGFR(L858R), and those IC50 (0.009 - 0.04 μM) were slightly lower or comparable to that of Gefitinib.
Then, FTP2 showing the lowest IC50 value of 0.009 μM against EGFR(L858R) among FTPs1~5 was radiolabeled by fluorine-18, and i.v. injected to mice bearing human NSCLC of NCI-H3255 (EGFR(L858R)), NCI-H1975 (EGFR(L858R/T790M)), and PET images were acquired at 3 h post-injection. The following ex vivo study indicated accumulation of [18F]FTP2 at NCI-H3255 and NCI-H1975 were 2.4 and 1.0 %ID/g, respectively, and those signal intensity ratio against muscle was 6.0 and 2.0. Conclusions The results in the present study suggest that [18F]FTP2 can detect NSCLC, which can be subjected to the EGFR targeted molecular therapy.
Revealing the interface nature of ZDDP tribofilm by X-ray photoelectron spectroscopy and atom probe tomography (2020)

Purpose To decrease wear and friction, zinc dialkyldithiophosphate (ZDDP) has been used in engine oil for several decades, but the mechanism of the tribofilm formation is still unclear. The purpose of this study is to characterize the chemical details of the tribofilm by using high-resolution approaching. Design/methodology/approach An ISO VG 100 mineral oil mixed with ZDDP was used in sliding tests on cylindrical roller bearings. Tribofilm formation was observed after 2 h of the sliding test. X-ray photoelectron spectroscopy (XPS) and atom probe tomography (APT) were used for chemical analysis of the tribofilm. Findings The results show that the ZDDP tribofilm consists of the common ZDDP elements along with iron oxides. A considerable amount of zinc and a small amount of sulfur were observed. In particular, an oxide interlayer with sulfur enrichment was revealed by APT between the tribofilm and the steel substrate. The depth profile of the chemical composition was obtained, and a tribofilm of approximately 40 nm thickness was identified by XPS. Originality/value A sulfur enrichment at the interface is observed by APT, which is beneath an oxygen enrichment. The clear evidence of the S interlayer confirms the hard and soft acids and bases principle. Peer review The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-01-2020-0035/
The effect of the core on the thermotropic behavior of three‐arm star poly[11‐(4′‐cyanophenyl‐4′′‐phenoxy)undecyl acrylate]s synthesized by atom transfer radical polymerization (2008)

Abstract “Three‐arm star” poly[11‐(4′‐cyanophenyl‐4′′‐phenoxy)undecyl acrylate]s were synthesized by atom transfer radical polymerization (ATRP) of 11‐(4′‐cyanophenyl‐4′′‐phenoxy)undecyl acrylate using two new trifunctional initiators: 1,3,5‐tri‐ (methyl 2‐bromopropionate)benzene and 2,4,6‐tri[4′‐methyl(2′′‐bromopropionate)phenoxymethyl]mesitylene. The polymers synthesized with 1,3,5‐tri(methyl 2‐bromopropionate)benzene (series II) contained 14–127 repeat units according to gel permeation chromatography relative to linear polystyrene (GPC PSt ) and 13–271 repeat units according to GPC with a light scattering detector (GPC LS ). Those synthesized with 2,4,6‐tri[4′‐methyl(2′′‐bromopropionate)phenoxymethyl]mesitylene (series III) contained 14–87 repeat units according to GPC PSt and 10–120 repeat units according to GPC LS . The absolute molecular weight, size, and shape of both series of polymers were characterized by light scattering in CH 2 Cl 2 , and their thermotropic behavior was analyzed using differential scanning calorimetry; both types of properties were compared to those of the other architectures, especially the corresponding three‐arm star poly[11‐(4′‐cyanophenyl‐4′′‐phenoxy)undecyl acrylate]s synthesized previously using 1,3,5‐trisbromomethylmesitylene as the initiator. The size and shape of the three‐arm star polymers in CH 2 Cl 2 are similar, although the isotropization temperature in the solid state decreases and the breadth of the isotropization transition increases with increasing size and flexibility of the trifunctional core. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4363–4382, 2008
The frequency of B cells secreting antibodies against donor MHC antigens in rats rejecting renal allografts (1990)

Abstract. We have estimated the frequency of B cells secreting antibodies against donor MHC antigens in rats rejecting histoincompatible renal allografts. In a major plus minor antigen-incompatible DA-to-WF combination on day 4 post-transplantation, reverse protein A plaque assay demonstrated that in the graft the frequency of lymphoid cells secreting Ig was 1:850. A major locus-incompatible and minor locus-compatible, congeneic LBN-to-Lewis strain combination was then applied to estimate the specificity of the secreted antibody. The lymphoid inflammatory cells were fused with mouse myeloma cells, cultured under limiting dilution conditions, and assayed by ELISA to donor and irrelevant strain spleen cells. Among cells infiltrating the graft, the fusion frequency was 1:172 103 the frequency of Ig-producing hybrids 1:400 103 (i. e., this assay was approximately three log orders less sensitive than the reverse pA assay). The frequency of hybridomas secreting specific antibodies against donor MHC antigens was 1:720 103 (i. e., every second hybridoma deriving from inflammatory population produced specific Ig). In addition, there was at least one obviously polyspecific population of hybridomas, detectable only in the spleen and reactive with all rat strains tested with a frequency of 1:700 103. The inflammatory cells were also cultured directly under limiting dilution conditions, and the frequency of Ig-secreting cells was determined by ELISA. The frequency of inflammatory lymphocytes secreting detectable amounts of immunoglobulin in the supernatant was 1:14 103 in the graft (i. e., this assay was approximately one log order less sensitive than the reverse protein A plaque assay). Donor-strain reactive cells were not detected in the spleen or blood of nontransplanted Lewis (recipient) rats, nor were they detected in the blood of the transplant recipient. Our results show that B cells secreting antibodies against graft donor MHC antigens are present in the graft-infiltrating cells' inflammatory population. In the inflammatory population only approximately 1:850 of the inflammatory cells are engaged in Ig secretion, and at most 1:2 of these produce specific antibody to graft donor MHC antigens. This finding suggests that a nonspecific (polyclonal) Ig-producing population is also present in situ. These results are also concordant with the reported low frequency of specific T cells of both cytotoxic and helper type at the site of inflammation and emphasize the importance of nonspecific inflammatory (“delayed hypersensitivity”) mechanisms in acute allograft rejection.
Longitudinal and Cross-Sectional Analysis of Cytotoxic T Lymphocyte (CTL) Responses and their Relationship to Vertical HIV Transmission (1998)

The ARIEL Project for the Prevention of HIV Transmission from Mother to Infant was established to evaluate virologic and immunologic parameters during vertical transmission. To determine the strength and breadth of the cytotoxic T lymphocyte (CTL) response and its correlation with human immunodeficiency virus (HIV) transmission, a cross-sectional study was done of 31 HIV-infected pregnant women, of whom 15 transmitted and 16 did not transmit HIV to their infants. The precursor frequencies of CTL specific for HIV-1 gag, pol, nef, and env from 5 different isolates of the clade B of HIV-1 were determined by limiting dilution analysis. Results showed that variable levels of HIV-specific CTL response were present in HIV-infected pregnant women during and after pregnancy. In addition, CTL precursor frequencies specific for pol and nef were higher during pregnancy in nontransmitters than in transmitters. Thus, CTL responding to different HIV antigens may not be contributing equally to the prevention of vertical transmission.
Synthesis of Cyclic Carbonates from Epoxides and Carbon Dioxide by Using Organocatalysts (2015)

The synthesis of cyclic carbonates through coupling of carbon dioxide with epoxides is 100 % atom economical and is already performed on an industrial scale. Its impact regarding the use of carbon dioxide as a renewable carbon source is expected to grow significantly in the near future, so that the development of efficient catalysts is of high interest in academia and industry. To improve the carbon footprint and sustainability of the cycloaddition reaction, the use of organocatalytic methods is a promising approach. Herein, available metal-free catalysts for the preparation of cyclic carbonates are described and elaborated concerning the overall sustainability of the process. Therefore, the required reaction conditions, as well as the activity of the catalysts and their reusability, are compared and evaluated. In addition to ammonium-, phosphonium-, or imidazolium-based single-component catalysts and their supported analogues, the growing field of research concerning dual catalysts are also discussed in detail.
Author response: Conserved RNA-binding specificity of polycomb repressive complex 2 is achieved by dispersed amino acid patches in EZH2 (2017)

Biochemical and mutagenesis analysis reveal the long-anticipated RNA-binding elements of Polycomb Repressive Complex 2 (PRC2), an important chromatin modifier, allowing construction of separation-of-function mutants of PRC2 defective in RNA binding but retaining histone-modifying activity.
Olsalazine was not better than placebo in maintaining remission in inactive Crohn disease (2002)

Source Citation Mahmud N, Kamm MA, Dupas JL, et al. Olsalazine is not superior to placebo in maintaining remission of inactive Crohn’s colitis and ileocolitis: a double blind, parallel, randomised, multicentre study. Gut. 2001 Oct;49:552-6. 11559654 (All 2002 articles were reviewed for relevancy, and abstracts were last revised in 2008.)
The Liquid Metal IP bridge (2013)

Programmers are increasingly turning to heterogeneous systems to achieve performance. Examples include FPGA-based systems that integrate reconfigurable architectures with conventional processors. However, the burden of managing the coding complexity that is intrinsic to these systems falls entirely on the programmer. This limits the proliferation of these systems as only highly-skilled programmers and FPGA developers can unlock their potential. The goal of the Liquid Metal project at IBM Research is to address the programming complexity attributed to heterogeneous FPGA-based systems. A feature of this work is a vertically integrated development lifecycle that appeals to skilled software developers. A primary enabler for this work is a canonical IP bridge, designed to offer a uniform communication methodology between software and hardware, and that is applicable across a wide range of platforms available off-the-shelf.