gebhart/patrepeval huggingface dataset:
A Method for Identifying Small-Molecule Aggregators Using Photonic Crystal Biosensor Microplates (2009)

Small molecules identified through high-throughput screens are an essential element in pharmaceutical discovery programs. It is now recognized that a substantial fraction of small molecules exhibit aggregating behavior leading to false positive results in many screening assays, typically due to nonspecific attachment to target proteins. Therefore, the ability to efficiently identify compounds within a screening library that aggregate can streamline the screening process by eliminating unsuitable molecules from further consideration. In this work, we show that photonic crystal (PC) optical biosensor microplate technology can be used to identify and quantify small-molecule aggregation. A group of aggregators and nonaggregators were tested using the PC technology, and measurements were compared with those gathered by three alternative methods: dynamic light scattering (DLS), an α-chymotrypsin colorimetric assay, and scanning electron microscopy (SEM). The PC biosensor measurements of aggregation were confirmed by visual observation using SEM, and were in general agreement with the α-chymotrypsin assay. DLS measurements, in contrast, demonstrated inconsistent readings for many compounds that are found to form aggregates in shapes, very different from the classical spherical particles assumed in DLS modeling. As a label-free detection method, the PC biosensor aggregation assay is simple to implement and provides a quantitative direct measurement of the mass density of material adsorbed to the transducer surface, whereas the microplate-based sensor format enables compatibility with high-throughput automated liquid-handling methods used in pharmaceutical screening.
6,7‐Dihydrocyclopenta‐1,3‐Dioxin‐5(4 H )‐One (2003)

Abstract (R,R)‐N,N′‐bis(3,5‐di‐tert‐butylsalicylidene)‐1,2‐cyclohexanediamino manganese(III) chloride, a highly enantioselective epoxidation catalyst product: 6,7‐Dihydrocyclopenta‐1,3‐Dioxin‐5(4H)‐One
Norepinephrine transporter occupancy by nortriptyline in patients with depression: a positron emission tomography study with (S,S)-[18F]FMeNER-D2 (2013)

Norepinephrine transporter (NET) plays important roles in the treatment of various neuropsychiatric disorders, such as depression and attention deficit hyperactivity disorder (ADHD). Nortriptyline is a NET-selective tricyclic antidepressant (TCAs) that has been widely used for the treatment of depression. Previous positron emission tomography (PET) studies have reported over 80% serotonin transporter occupancy with clinical doses of selective serotonin reuptake inhibitors (SSRIs), but there has been no report of NET occupancy in patients treated with relatively NET-selective antidepressants. In the present study, we used PET and (S,S)-[18¹⁸F]FMeNER-D₂ to investigate NET occupancies in the thalamus in 10 patients with major depressive disorder taking various doses of nortriptyline, who were considered to be responders to the treatment. Reference data for the calculation of occupancy were derived from age-matched healthy controls. The result showed approximately 50-70% NET occupancies in the brain as a result of the administration of 75-200 mg/d of nortriptyline. The estimated effective dose (ED₅₀) and concentration (EC₅₀) required to induce 50% occupancy was 65.9 mg/d and 79.8 ng/ml, respectively. Furthermore, as the minimum therapeutic level of plasma nortriptyline for the treatment of depression has been reported to be 70 ng/ml, our data indicate that this plasma nortriptyline concentration corresponds to approximately 50% NET occupancy measured with PET, suggesting that more than 50% of central NET occupancy would be appropriate for the nortriptyline treatment of patients with depression.
Enhancement of $f_{\mathrm {max}}$ to 910 GHz by Adopting Asymmetric Gate Recess and Double-Side-Doped Structure in 75-nm-Gate InAlAs/InGaAs HEMTs (2016)

A high maximum frequency of oscillation (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> ) of 910 GHz was achieved at InAlAs/InGaAs highelectron mobility transistors (HEMTs) with a relatively long gate length (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> ) of 75 nm by adopting an asymmetric gate recess and a double-side-doped structure. The f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> improved significantly by extending the drain-side gate recess length (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">RD</sub> ) to 250 nm; meanwhile, the source-side gate-recess length (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">RS</sub> ) was kept to 70 nm. The improvement in fmax was due to a decrease in the drain output conductance (g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> ) and drain-to-gate capacitance (CGD) after the extension of L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">RD</sub> . gd was further suppressedby applying a double-side-doped structure to the InP-based HEMTs. A reduction in g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> resulted in a drastic improvement in f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> even though L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> was a longer value.
GENO-02INTEGRATED ANALYSIS OF MOLECULAR SUBTYPES IN GLIOBLASTOMA MULTIFORME (2015)

BACKGROUND: The Cancer Genome Atlas (TCGA) project previously identified genetic changes in the DNA sequence and copy number, DNA methylation, and gene expression of glioblastoma multiforme (GBM) tumors, leading to an enthused effort to compile and characterize changes in the genome, transcriptome, and proteome of human GBM tumors, so that aberrantly functioning molecular pathways and tumor subtypes could be identified. METHODS: Agilent GeneSpring and Mass Profiler Professional (MPP) software was used to perform integrated multi-omics analysis of mRNA expression, miRNA expression, protein expression, and copy number aberration associated with GBM. Additionally, analysis was performed on an independent discovery proteomics study of GBM and control (brain fragments from epilepsy surgery) patients measured using a label-free proteomics approach. RESULTS: Correlation analysis performed between mRNA and miRNA datasets from TCGA identified potential candidate miRNAs regulating the known Proneural signature genes OLIG2, NKX2-2, and SOX11. It also highlighted the molecular events leading to suppression of p53 in Proneural tumor signaling. Sample-sample correlation and PCA analysis on patient specimens resulted in clear separation between control and tumor samples. In addition, the tumor samples were segregated into two to three subgroups, suggesting that different TCGA subtypes may be present. Indeed, combined analysis of mRNA expression data from TCGA study and proteomics data from the label-free study identified a core subset of 54 GBM subtype signatures, clearly differentiating the known subtypes in the larger TCGA cohort. CONCLUSION: Our observation suggests that GBM tumor heterogeneity may be best characterized by both mRNA and protein abundance of the signature genes, opening a possibility for follow-up studies with potential diagnostic and clinical significance.
Acomparisonof perceptually-based metrics for objective evaluation of geometryprocessing (2010)

International audience
Deep Complex-Valued Convolutional-Recurrent Networks for Single Source DOA Estimation (2022)

Despite having conceptual and practical advantages, Complex-Valued Neural Networkss (CVNNs) have been much less explored for audio signal processing tasks than their real-valued counterparts. We investigate the use of a complex-valued Convolutional Recurrent Neural Network (CRNN) for Direction-of-Arrival (DOA) estimation of a single sound source on an enclosed room. By training and testing our model with recordings from the DCASE 2019 dataset, we show our architecture compares favourably to a real-valued CRNN counter-part both in terms of estimation error as well as speed of convergence. We also show visualizations of the complex-valued feature representations learned by our method and provide interpretations for them.
MP45-08 PHOSPHODIESTERASE TYPE 5 INHIBITOR (PDE5I) USE AFTER RADICAL PROSTATECTOMY (RP) IS NOT ASSOCIATED WITH INCREASED RISK OF BIOCHEMICAL RECURRENCE RISK (BCR) (2020)

INTRODUCTION AND OBJECTIVE: The data on the association between PDE5i utilization and BCR after RP and PDE5i is mixed. We aimed to provide a better risk assessment based on exposure data. METHODS: Patients completed a PDE5i exposure survey serially after RP in a prospective, quality of life study evaluating men post-RP. PDE5i exposure scores: 0-never, 1-sometimes, 2-regularly, 3-daily. Men who had data on PDE5i use at 3m, 6m, 9m, and 12m in the first year following RP were included in the analysis, thus PDE5i exposure score is the mean of the surveys and ranged from 0-3. The tested predictors of BCR were: age, preoperative PSA, Gleason score (G), surgical margin status (SMS), seminal vesicle involvement (SVI), extra capsular extension (ECE), and lymph node involvement (LNI). Prostate cancer risk categorization was deemed high if: Gleason 8+, LNI+, SMS+ or SVI+. Correlation coefficients and Chi-square was used for univariate analysis and time-to-event (Cox Proportional Hazards) analysis was used for multivariable analysis. RESULTS: Mean age of 647 men was 60.5±7 years. 106 men (16%) had BCR. PDE5i groups are summarized in Figure 1. On univariate analysis, race (black vs white), PSA, and diabetes were associated with BCR (p=0.03 to <0.01). PDE5i score as a continuous variable was not significant (HR 0.96, 95% CI: 0.70-1.33, p=0.82). The highest use PDE5i group (mean score = 2.01 – 3) was not significantly different from the never used group (mean score = 0) (HR 0.95, 95% CI 0.2 – 4.42). On multivariable analysis, race, baseline PSA, and diabetes were associated with BCR (HR 1.55, 1.04, 2.12, respectively). PDE5i dose score was again not a significant predictor of BCR (HR: 0.98, 95% CI: 0.70-1.36). CONCLUSIONS: Using a PDE5i exposure score, PDE5i use is not a risk factor for BCR in RP patients.Source of Funding: None
Self-Assembled Monolayers on Gold Generated from Alkanethiols with the Structure RNHCOCH2SH (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelf-Assembled Monolayers on Gold Generated from Alkanethiols with the Structure RNHCOCH2SHSuk-Wah Tam-Chang, Hans A. Biebuyck, George M. Whitesides, Nooh Jeon, and Ralph G. NuzzoCite this: Langmuir 1995, 11, 11, 4371–4382Publication Date (Print):November 1, 1995Publication History Published online1 May 2002Published inissue 1 November 1995https://pubs.acs.org/doi/10.1021/la00011a033https://doi.org/10.1021/la00011a033research-articleACS PublicationsRequest reuse permissionsArticle Views1656Altmetric-Citations201LEARN 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
ChemInform Abstract: INDOLIZIDINE ALKALOID SYNTHESIS. PREPARATION OF THE PHARAOH ANT TRAIL PHEROMONE AND GEPHYROTOXIN 223 STEREOISOMERS (1980)

Abstract Aus dem Pyrrolin‐urethan (Ia) erhält man mit Lithiumdiisopropylamid (LDA) und Butyllithium das Substitutionsprodukt (Ib), das analog weiter zu (II) substituiert wird.
The emergence of revolutionary China, 1949-1965 (1987)

This is the first of the two final volumes of The Cambridge History of China, which describe the efforts of the People's Republic of China to grapple with the problems of adaptation to modern times. Volume 14 deals with the achievements of the economic and human disasters of the new regime's first sixteen years (1949-65). Part I chronicles the attempt to adapt the Soviet model of development to China, and Part II covers the subsequent efforts of China's leaders to find native solutions that would provide more rapid and appropriate answers to China's problems. Each of the two parts of the volume analyzes the key issues and developments in the spheres of politics, economics, culture, education, and foreign relations. The contributors, all leading scholars of the period, show the interrelation of Chinese actions in all these spheres, and the describe how, gradually, events led to the Cultural Revolution launched by Mao Tse-tung in 1966.
Azide-resistant mutants inAcinetobacter calcoaceticusA2 are defective in protein secretion (1994)

Azide, an inhibitor of ATPase, and a specific inhibitor of protein export was used in order to select for protein secretion mutants in Acinetobacter calcoaceticus A2. Two such mutants were isolated that were azide-resistant and defective in the general protein transport system. The mutation also conferred additional phenotypic changes, including an inability to grow on minimal media or at 40 degrees C. The existence of protein secretion mutants with a selectable phenotype may be useful for the genetic study of protein export.
Optimum Family of Spectrum-Shaping Functions for PAPR Reduction of DFT-Spread OFDM Signals (2006)

The required power back-off in the uplink of the Evolved UTRA cellular system is considered in this paper. It is shown that the discrete prolate spheroidal window is optimum for the reduction of the peak-to-average ratio by spectrum shaping. It is also useful for reducing the cubic metric. Measures for power back-off and results for required average power are presented for different spectrum shaping functions. It is shown that spectrum shaping with the optimum functions reduces the required power back-off with small increase in the required average power for pi /2-shifted BPSK and low to intermediate data rates.
Molecular structure, morphology, and antioxidant consumption in medium density polyethylene pipes in hot‐water applications (1992)

Abstract Changes in polymer structure and antioxidant concentration have been systematically studied as functions of temperature, hoop stress, exposure time, and location in pipe wall on pressure tested pipes of medium density polyethylene. The pressure tests have been performed with water as the internal medium and air as the external medium at temperatures in the range 80 to 105°. Infrared spectroscopy shows that oxidation is initiated at the inner wall surface just prior to the onset of the so‐called stage III fracture. X‐ray diffraction and size exclusion chromatography show that oxidation involves only the amorphous phase and results in a significant molar mass reduction. The near‐inner‐wall material exhibits a 10% reduction in mass average molar mass before the onset of stage III fracture and thereafter a more dramatic decrease. Oxidation induction time measurements by differential scanning calorimetry show that the antioxidant concentration is almost twice as high in the center of the wall as in the near‐inner‐wall and outer‐wall material of the unexposed pipe, that the loss of antioxidant is anomalously rapid at the beginning of the high temperature exposure, and that the antioxidant concentration profile gradually becomes more skewed towards the outer wall on prolonged exposure. The data presented in this paper are used in a parallel paper for modeling purposes.
Development of a Novel SPR Assay to Study CXCR4–Ligand Interactions (2020)

G protein-coupled receptors (GPCRs) are involved in a plethora of different diseases. Consequently, these proteins are considered as an important class of drug targets. Measuring detailed kinetic information on these types of proteins has been challenging. Surface plasmon resonance (SPR) can provide this information, however, the use of SPR on GPCRs remains a complex issue. Here, we report an SPR assay to investigate the interactions between the full-length chemokine receptor CXCR4 and nanobody-Fc (Nb-Fc) ligands. Nb-Fcs consist of two monovalent VHH domains fused with an Fc domain of a human IgG molecule. The CXCR4 protein used in this assay was produced with a C-terminal 10x-histidine tag and was immobilized on a nitrilotriacetic acid chip. In order to verify the sensitivity and effectiveness of this assay, the results were compared to data obtained from cellular assays as well as from another SPR assay using CXCR4 virus-like particles (VLPs). CXCR4 remained intact and stable for at least 12 h, and the kinetic results correlated well with both the cellular assays and the VLP SPR assay results. Apart from determining the binding kinetics of Nb-Fc with CXCR4, our results contributed to understanding CXCR4 interaction dynamics. In conclusion, this assay provides a viable experimental platform that has high potential to be expanded for studying other molecules as well as other histidine-tagged GPCRs.
Tumor necrosis factor activates human endothelial cells through the p55 tumor necrosis factor receptor but the p75 receptor contributes to activation at low tumor necrosis factor concentration. (1993)

Tumor necrosis factor-alpha (TNF-alpha) interacts with two distinct membrane receptor proteins, p55 and p75, which are variably expressed on different cell types. We have examined the function of p55 and p75 on human endothelial cells (EC). Both receptor types are detected on cultured EC by FACS analysis. A mutagenized recombinant human TNF (R32W-TNF), which binds selectively to p55, is equipotent with human recombinant wild-type TNF (wt-TNF) in upregulating several different leukocyte adhesion molecules as well as class I major histocompatibility complex molecules. R32W-TNF also fully desensitizes EC to wt-TNF, as assessed by inhibition of re-induction of endothelial leukocyte adhesion molecule-1 (ELAM-1). At low wt-TNF concentrations, induction of ELAM-1 is partly inhibited by blocking monoclonal antibodies to either p55 or p75 and to a greater extent by a combination of both monoclonal antibodies. In contrast, ELAM-1 induction by R32W-TNF is only inhibited by anti-p55. We conclude that both TNF receptors (p55 and p75) can contribute to TNF-induced activation of EC, but that signaling through p55 is sufficient.
Combined microbial/chemical synthesis of (+)-(R)-methyloxirane having high enantiomeric excess (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCombined microbial/chemical synthesis of (+)-(R)-methyloxirane having high enantiomeric excessEthan S. Simon, George M. Whitesides, Douglas C. Cameron, David J. Weitz, and Charles L. CooneyCite this: J. Org. Chem. 1987, 52, 18, 4042–4044Publication Date (Print):September 1, 1987Publication History Published online1 May 2002Published inissue 1 September 1987https://pubs.acs.org/doi/10.1021/jo00227a018https://doi.org/10.1021/jo00227a018research-articleACS PublicationsRequest reuse permissionsArticle Views208Altmetric-Citations16LEARN 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
Affective Audio-Visual Words and Latent Topic Driving Model for Realizing Movie Affective Scene Classification (2010)

This paper presents a novel method for movie affective scene classification that outputs the emotion (in the form of labels) that the scene is likely to arouse in viewers. Since the affective preferences of users play an important role in movie selection, affective scene classification has the potential to develop more attractive user-centric movie search and browsing applications. Two main issues in designing movie affective scene classification are considered. One is “how to extract features that are strongly related to the viewer's emotions”, and the other is “how to map the extracted features to the emotion categories”. For the former, we propose a method to extract emotion-category-specific audio-visual features named affective audio-visual words (AAVWs). For the latter issue, we propose a classification model named latent topic driving model (LTDM). Assuming that viewers' emotions are dynamically changed by the movie scene sequences, LTDM models emotions as Markovian dynamic systems driven by the sequential stimuli of the movie content. Experiments on 206 movie scenes extracted from 24 movie titles and the corresponding labels of eight emotion categories given by 16 subjects show that our method outperforms conventional approaches in terms of the subject agreement rate.
Identification of linker molecules suited for deposition and study of Mn12 single molecule magnets on Au surfaces (2008)

The authors report on a scanning tunneling microscopy/spectroscopy investigation of the possibility to influence the assembly of monolayers of Mn12 single molecule magnets on a functionalized Au(111) surface by using flexible linker molecules. The results corroborate the general suitability of the deposition via ligand exchange reaction but, on the other hand, reveal the need for a compromise between conductivity and flexibility of the linker molecules. The results are discussed with respect to previous attempts [A. Naitabdi et al., Adv. Mater. (Weinheim, Ger.) 17, 1612 (2005)] to deposit ordered monolayers of Mn12 molecules on Au(111).