gebhart/patrepeval huggingface dataset:
Layered Semi-Markov road generation for driving simulations (2011)

Driving simulators offer several advantages in driver behavioral research, including low cost, repeatable experiments, and the ability to simulate scenarios that would be too dangerous for real cars. An effective simulation must elicit the same responses from drivers as a real car. Several factors contribute to this realism including a good physics engine, a realistic environment, and expected behavior from simulated traffic and drivers. In this paper, we present a novel method of generating a wide variety of realistic roads called Layered Semi-Markov Model. These roads are tested on five drivers with a driver distraction detection experiment. The results of this experiment matched the expected behavior and subjective feedback showed a favorable response.
Overcoming regulatory T‐cell suppression by a lyophilized preparation of Streptococcus pyogenes (2013)

Cancer vaccines have yet to yield clinical benefit, despite the measurable induction of humoral and cellular immune responses. As immunosuppression by CD4(+) CD25(+) regulatory T (Treg) cells has been linked to the failure of cancer immunotherapy, blocking suppression is therefore critical for successful clinical strategies. Here, we addressed whether a lyophilized preparation of Streptococcus pyogenes (OK-432), which stimulates Toll-like receptors, could overcome Treg-cell suppression of CD4(+) T-cell responses in vitro and in vivo. OK-432 significantly enhanced in vitro proliferation of CD4(+) effector T cells by blocking Treg-cell suppression and this blocking effect depended on IL-12 derived from antigen-presenting cells. Direct administration of OK-432 into tumor-associated exudate fluids resulted in a reduction of the frequency and suppressive function of CD4(+) CD25(+) Foxp3(+) Treg cells. Furthermore, when OK-432 was used as an adjuvant of vaccination with HER2 and NY-ESO-1 for esophageal cancer patients, NY-ESO-1-specific CD4(+) T-cell precursors were activated, and NY-ESO-1-specific CD4(+) T cells were detected within the effector/memory T-cell population. CD4(+) T-cell clones from these patients had high-affinity TCRs and recognized naturally processed NY-ESO-1 protein presented by dendritic cells. OK-432 therefore inhibits Treg-cell function and contributes to the activation of high-avidity tumor antigen-specific naive T-cell precursors.
Modulation of the phosphate‐starvation response in Escherichia coli by genetic manipulation of the polyphosphate pathways (1996)

The effect of intracellular polyphosphate on the phosphate-starvation response in Escherichia coli was studied by genetically manipulating the intracellular polyphosphate levels and by performing phosphate shifts on the genetically engineered strains. Strains that produced large quantities of polyphosphate and were able to degrade it induced the phosphate-starvation response to a lesser extent than wild-type strains, whereas strains that were unable to degrade a large intracellular polyphosphate pool induced the phosphate-starvation response to a greater extent than wild-type strains. These results have important implications for expression of heterologous genes under control of the phoA promoter. © 1996 John Wiley & Sons, Inc.
An Updated Unified Pharmacophore Model of the Benzodiazepine Binding Site on &#947;-Aminobutyric Acida Receptors: Correlation with Comparative Models (2007)

A successful unified pharmacophore/receptor model which has guided the synthesis of subtype selective compounds is reviewed in light of recent developments both in ligand synthesis and structural studies of the binding site itself. The evaluation of experimental data in combination with a comparative model of the alpha1beta2gamma2 GABA(A) receptor leads to an orientation of the pharmacophore model within the Bz BS. Results not only are important for the rational design of selective ligands, but also for the identification and evaluation of possible roles which specific residues may have within the benzodiazepine binding pocket.
ChemInform Abstract: Synthesis of (‐)‐ and (+)‐Frontalin. (1987)

Abstract The phenyl menthyl glyoxalate (I) reacts with the Grignard reagent (II) to yield the adduct (III), together with the reduction product (IV).
The PI3 kinase/mTOR blocker NVP-BEZ235 overrides resistance against irreversible ErbB inhibitors in breast cancer cells (2010)

Resistance against first and second generation (irreversible) ErbB inhibitors is an unsolved problem in clinical oncology. The purpose of this study was to examine the effects of the irreversible ErbB inhibitors pelitinib and canertinib on growth of breast and ovarian cancer cells. Although in vitro growth-inhibitory effects of both drugs exceeded by far the effects of all reversible ErbB blockers tested (lapatinib, erlotinib, and gefitinib), complete growth inhibition was usually not reached. To define the mechanism of resistance, we examined downstream signaling pathways in drug-exposed cells by Western blot analysis. Although ErbB phosphorylation was reduced by pelitinib and canertinib, activation of the AKT/mTOR pathway remained essentially unaltered in drug-resistant cells. Correspondingly, transfection of tumor cells with constitutively activated AKT was found to promote resistance against all ErbB inhibitors tested, whereas dominant negative AKT reinstalled sensitivity in drug-resistant cells. In a next step, we applied PI3K/AKT/mTOR blockers including the dual PI3K/mTOR kinase inhibitor NVP-BEZ235. These agents were found to cooperate with pelitinib and canertinib in producing in vitro growth inhibition in cancer cells resistant against ErbB-targeting drugs. In conclusion, our data show that ErbB drug-refractory activation of the PI3K/AKT/mTOR pathway plays a crucial role in resistance against classical and second-generation irreversible ErbB inhibitors, and NVP-BEZ235 can override this form of resistance against pelitinib and canertinib.
Structural basis for the recognition of complex-type N-glycans by Endoglycosidase S (2018)

Endoglycosidase S (EndoS) is a bacterial endo-β-N-acetylglucosaminidase that specifically catalyzes the hydrolysis of the β-1,4 linkage between the first two N-acetylglucosamine residues of the biantennary complex-type N-linked glycans of IgG Fc regions. It is used for the chemoenzymatic synthesis of homogeneously glycosylated antibodies with improved therapeutic properties, but the molecular basis for its substrate specificity is unknown. Here, we report the crystal structure of the full-length EndoS in complex with its oligosaccharide G2 product. The glycoside hydrolase domain contains two well-defined asymmetric grooves that accommodate the complex-type N-linked glycan antennae near the active site. Several loops shape the glycan binding site, thereby governing the strict substrate specificity of EndoS. Comparing the arrangement of these loops within EndoS and related endoglycosidases, reveals distinct-binding site architectures that correlate with the respective glycan specificities, providing a basis for the bioengineering of endoglycosidases to tailor the chemoenzymatic synthesis of monoclonal antibodies.
Data from <i>In vivo</i> Evaluation of Mucoadhesive Nanoparticulate Docetaxel for Intravesical Treatment of Non–Muscle-Invasive Bladder Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The present work describes the development and &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; evaluation of a mucoadhesive nanoparticulate docetaxel (DTX) formulation for intravesical bladder cancer therapy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Mucoadhesive formulations based on hyperbranched polyglycerols (HPG), hydrophobically derivatized with C&lt;sub&gt;8&lt;/sub&gt;/C&lt;sub&gt;10&lt;/sub&gt; alkyl chains in the core and modified with methoxy-polyethylene glycol (MePEG) and amine groups in the shell (HPG-C&lt;sub&gt;8/10&lt;/sub&gt;-MePEG-NH&lt;sub&gt;2&lt;/sub&gt;) were synthesized and DTX was loaded into these by a solvent evaporation method. Both low-grade (RT4, MGHU3) and high-grade (UMUC3) human urothelial carcinoma cell lines were treated with various concentrations of DTX formulations &lt;i&gt;in vitro&lt;/i&gt;. KU7 cells that stably express firefly luciferase (KU7-luc) were inoculated in female nude mice by intravesical instillation and quantified using bioluminescence imaging. Mice with established KU7-luc tumors were given a single intravesical instillation with PBS, Taxotere (DTX from Sanofi-aventis), and DTX-loaded HPG-C&lt;sub&gt;8/10&lt;/sub&gt;-MePEG and/or HPG-C&lt;sub&gt;8/10&lt;/sub&gt;-MePEG-NH&lt;sub&gt;2&lt;/sub&gt;. Drug uptake was conducted using LC/MS-MS (liquid chromatography/tandem mass spectrometry) and tumor microenvironment and uptake of rhodamine labeled HPGs was assessed.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt;&lt;i&gt;In vitro&lt;/i&gt;, all DTX formulations potently inhibited bladder cancer proliferation. However, &lt;i&gt;in vivo&lt;/i&gt;, DTX-loaded HPG-C&lt;sub&gt;8/10&lt;/sub&gt;-MePEG-NH&lt;sub&gt;2&lt;/sub&gt; (mucoadhesive DTX) was the most effective formulation to inhibit tumor growth in an orthotopic model of bladder cancer. Furthermore, mucoadhesive DTX significantly increased drug uptake in mouse bladder tissues. In addition, rhodamine labeled HPG-C&lt;sub&gt;8/10&lt;/sub&gt;-MePEG-NH&lt;sub&gt;2&lt;/sub&gt; showed enhanced uptake of these nanoparticles in bladder tumor tissues.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our data show promising &lt;i&gt;in vivo&lt;/i&gt; antitumor efficacy and provide preclinical proof of principle for the intravesical application of mucoadhesive nanoparticulate DTX formulation in the treatment of bladder cancer. &lt;i&gt;Clin Cancer Res; 17(9); 2788–98. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Type‐I HTLV antibody in urban and rural Ghana, West Africa (1984)

The prevalence of antibodies against the newly described human T-cell lymphoma virus, type I (HTLV-I) in two communities in Ghana, West Africa, is described. There was no difference by community (urban, 3.6% and rural, 4.0%). Prevalence increased with age, being 5.9% among persons greater than 10 years old, but did not differ by sex. There was no difference when data were analysed by housing status or crowding. Non-confirmed reactions in the assay system were frequent and correlated with both prevalence and titer of antibody against malaria. Possible explanations include vector-borne transmission like that of malaria, but the relationship is more probably due to a polyclonal stimulation of B cells, enhancing the potential for detecting reactivity in the assay. Because assay systems vary and because most laboratories do not routinely use a confirmation assay, results presented by different groups must be interpreted cautiously.
Origins of stereoselectivity in radical additions: reactions of alkenes and radicals bearing oxazolidine and thiazolidine amide groups (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrigins of stereoselectivity in radical additions: reactions of alkenes and radicals bearing oxazolidine and thiazolidine amide groupsNed A. Porter, Ian J. Rosenstein, Robert A. Breyer, John D. Bruhnke, Wen Xue Wu, and Andrew T. McPhailCite this: J. Am. Chem. Soc. 1992, 114, 20, 7664–7676Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/ja00046a010https://doi.org/10.1021/ja00046a010research-articleACS PublicationsRequest reuse permissionsArticle Views1280Altmetric-Citations65LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
A Prospective, Case-control Study of Tobacco Dependence in Thromboangiitis Obliterans (Buerger’s Disease) (2006)

Thromboangiitis obliterans (TAO) is often cited as an extreme phenotype of vasculopathy and tobacco dependence. Although tobacco exposure is essential to progression of arterial ischemia in TAO, expert opinion differs regarding the degree of tobacco dependence in this population. The authors designed a prospective, case-control study to test the hypothesis that subjects with TAO have a greater degree of tobacco dependence than control subjects with coronary atherosclerosis (coronary artery disease [CAD]) do. Subjects with TAO (n = 218, confirmed by angiography, biopsy, or noninvasive arterial testing) or CAD (n = 343, diagnosed by coronary angiography) were mailed a standardized questionnaire regarding tobacco use, to which 103 and 273 responded, respectively. The degree of tobacco dependence in each group was ascertained by several methods, including the Fagerström Test for Nicotine Dependence Questionnaire. The TAO group was younger at index date (year of first diagnosis for TAO patients, year of percutaneous transluminal coronary angioplasty [PTCA] for CAD patients) (TAO 37.6+/-9.0 vs CAD 43.3+/-4.9 yr, p < 0.0001), but the groups did not differ in age at first tobacco exposure (TAO 16.7+/-3.1 vs CAD 17.3+/-4.2 yr, p = 0.67), current tobacco use at time of survey (TAO 54% vs CAD 46%, p = 0.17), or Fagerström score (TAO 4.7+/-2.3 vs CAD 5.1+/-2.3, p = 0.24). Kaplan-Meier curves showed no significant difference in time to topping tobacco use after first diagnosis (p = 0.076). TAO subjects smoked fewer cigarettes per day than CAD subjects (TAO 22.3+/-10.7 vs CAD 27.7+/-15.3 cigarettes/day, p = 0.003). Among current smokers (n = 170), TAO subjects also smoked fewer cigarettes/day (20.2+/-8.2 vs 24.6+/-12.7, p = 0.03), and were more likely to have made a serious attempt to stop (97% vs 90%, p = 0.03). In contrast to case reports of extreme tobacco dependence in the TAO population, the degree of tobacco dependence in subjects with TAO is similar to that in subjects with CAD.
Real-time 1550 um retromodulated video link (2004)

Abstract : We report an eye-safe, 1550 nm, retromodulated infrared data link which supports real-time color video. The retromodulated link was 2 meters in the lab and supported 3 Mbps and 30 frames per second using wavelet compression. The device consumes about 75-100 mW and is 10 grams, mounted. We will show a video sequence from the test. We will also discuss future plans for the device.
Physics-Informed Gaussian Process Regression for Optical Fiber Communication Systems (2021)

We present a framework for enhancing Gaussian process regression machine learning models with a priori knowledge derived from models of the transmission physics in optical networks. This is done by framing the regression problem as multi-task learning, in which both the measured data and targets derived from a physical model of the system are used to optimise the kernel hyperparameters. We discuss the theoretical assumptions made and the validity of the approach. It is demonstrated that physics-informed Gaussian processes facilitate Bayesian inference with fewer data points than standard Gaussian processes, opening up application areas in which measurements are expensive. The transparency, interpretability and explainability of the proposed technique and the subsequent increased likelihood of adoption by industry are discussed.
Heterologous expression of insect P450 enzymes that metabolize xenobiotics (2020)

Insect cytochrome P450-monooxygenases (P450s) are an enzyme superfamily involved in the oxidative transformation of endogenous and exogenous substrates, including insecticides. They were also shown to determine insecticide selectivity in beneficial arthropods such as bee pollinators, and to detoxify plant secondary metabolites. The recent explosion in numbers of P450s due to increased invertebrate genomes sequenced, allowed researchers to study their functional relevance for xenobiotic metabolism by recombinant expression using different expression systems. Troubleshooting strategies, including different systems and protein modifications typically adapted from mammalian P450s, have been applied to improve the functional expression, with partial success. The aim of this mini review is to critically summarize different strategies recently developed and used to produce recombinant insect P450s for xenobiotic metabolism studies.
Synthesis of Melanin-Like Pigments by Sporothrix schenckii In Vitro and during Mammalian Infection (2003)

Melanin has been implicated in the pathogenesis of several important human fungal pathogens. Existing data suggest that the conidia of the dimorphic fungal pathogen Sporothrix schenckii produce melanin or melanin-like compounds; in this study we aimed to confirm this suggestion and to demonstrate in vitro and in vivo production of melanin by yeast cells. S. schenckii grown on Mycosel agar produced visibly pigmented conidia, although yeast cells grown in brain heart infusion and minimal medium broth appeared to be nonpigmented macroscopically. However, treatment of both conidia and yeast cells with proteolytic enzymes, denaturant, and concentrated hot acid yielded dark particles similar in shape and size to the corresponding propagules, which were stable free radicals consistent with identification as melanins. Melanin particles extracted from S. schenckii yeast cells were used to produce a panel of murine monoclonal antibodies (MAbs) which labeled pigmented conidia, yeast cells, and the isolated particles. Tissue from hamster testicles infected with S. schenckii contained fungal cells that were labeled by melanin-binding MAbs, and digestion of infected hamster tissue yielded dark particles that were also reactive. Additionally, sera from humans with sporotrichosis contained antibodies that bound melanin particles. These findings indicate that S. schenckii conidia and yeast cells can produce melanin or melanin-like compounds in vitro and that yeast cells can synthesize pigment in vivo. Since melanin is an important virulence factor in other pathogenic fungi, this pigment may have a similar role in the pathogenesis of sporotrichosis.
Catalytic aza-Wittig Cyclizations for Heteroaromatic Synthesis (2008)

The first examples of heterocycle synthesis by iminophosphorane formation/intramolecular aza-Wittig cyclizations that are catalytic in the organophosphorus component are reported. The reaction has been demonstrated in the synthesis of both azine (phenanthridine) and azole (benzoxazole) heterocycles. Catalyst loadings down to 1 mol % have been used with little or no loss in reaction efficiency. The intimate involvement of the phosphine oxide in the catalytic cycle has been verified by in situ infrared spectroscopy.
Syphilis (2006)

Abstract Syphilis is a sexually transmitted disease caused by the bacterium Treponema pallidum subspecies pallidum . It is usually classified as having an infectious phase, primary and secondary lesions, and the now less common noninfectious late stages. Diseases transmitted by nonsexual skin‐to‐skin contact (usually during childhood or adolescence) are caused by the closely related organisms T. pallidum subsp. pertenue (which causes yaws), T. pallidum subsp. endemicum (endemic syphilis) and T. carateum (pinta).
The Costs of Confidentiality in Virtualized FPGAs (2019)

Some modern datacenters are augmenting their compute infrastructure by deploying field-programmable gate arrays (FPGAs) to provide users with specialized accelerators that offer superior compute capability, increased energy efficiency, lower latency, and more programming flexibility than CPUs. However, the higher programming flexibility of FPGAs also gives more capabilities to malicious users to remotely sniff data from other applications running on the same FPGA. This has created a challenge for efficient utilization of FPGAs in datacenters: FPGAs in datacenters are currently not shared between users due to potential security risks. In this paper, we propose different techniques to defeat data-sniffing attacks in datacenter FPGAs by encrypting/decrypting the user application's data. We describe techniques that are appropriate to different trust levels and rigorously evaluate the costs of these data confidentiality techniques in current virtualized FPGAs. In addition, for each trust level, we propose an architectural change to the FPGA to mitigate the costs of providing data confidentiality. We also investigate the role of interconnect in these architectural changes and demonstrate that more efficient security features can be implemented together with the interconnect if the FPGAs use a hard network on chip.
Case Study in Hebrew Character Searching (2011)

Searching for a letter or a word in historical documents is a practical challenge due to the various degradations present in such documents and the wide variance of handwriting. Searching in historical Hebrew documents is somewhat harder because of high similarities among Hebrew characters. In order to determine the features and their combinations appropriate for recognizing Hebrew script, we study a range of known features using a Dynamic Time Warping algorithm. In addition we describe a novel meth od for feature-based searching, which uses a number of models for the same character. This method is based on our original DTW algorithm that can match fragments of several models of the same character to match a query character. Consequently, we are not limited to any particular model of the character set. Application of this method leads to a significant improvement, even when using a small set of models.
A fuzzy logic controller with reconfigurable, cascadable architecture (2003)

A general-purpose fuzzy logic inference engine for real-time control applications has been designed and fabricated in a 1- mu m, 3.3-V, DLM CMOS technology. Up to 102 rules are processed in parallel with a single 688 K transistor device. Features include a dynamically reconfigurable and cascadable architecture, a TTL-compatible host interface, laser programmed redundancy, a special mode for testability, RAM rule storage, and on-chip fuzzification and defuzzification.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison between standard and chain-type FRAM architectures (2001)

Abstract A standard 1T/1C and chain-type ferroelectric memory architecture are presented. The standard memory cell consists of a transistor connected in series to a ferroelectric capacitor while the chain-type cell connects these elements in parallel. Based on the different memory cells, two different arrays have been designed, simulated, and integrated on a single test chip in a 0.35μm process (not presented in this work). They are compared in regard to area, performance, and reliability. It is shown that chain FRAM has the potential to be superior to standard FRAM concerning area because of its innovative cell configuration which reduces the average number of lines per row from two to almost one and therefore removing the connectivity drawback required for bipolar polarization of ferroelectric materials compared to unipolar dielectric polarization. However, this obviously comes at the cost of limited performance and increased design complexity.