gebhart/patrepeval huggingface dataset:
Supramolecular Approaches to Second-Order Nonlinear Optical Materials. Self-Assembly and Microstructural Characterization of Intrinsically Acentric [(Aminophenyl)azo]pyridinium Superlattices (1996)

This paper describes the synthesis and characterization of self-assembled second-order nonlinear optical multilayer materials containing the high-hyperpolarizability [(aminophenyl)azo]pyridinium chromophore. The chromophoric multilayers are assembled on clean glass or single-crystal silicon substrates via the following iterative reaction sequence: (1) treatment with 4-ClCH2C6H4SiCl3, 3-BrC3H6SiCl3, or 3-IC3H6SiCl3 to afford a self-assembled coupling layer; (2) quaternization of 4-[[4-[N,N-bis(hydroxylethyl)amino]phenyl]azo]pyridine in a “topotactic” fashion to generate an [(aminophenyl)azo]pyridinium chromophore layer; (3) cross-linking with octachlorotrisiloxane to afford a capping layer (which also regenerates surface hydroxyl groups for subsequent layer deposition). The new chromophore precursor 4-[[4-[N,N-bis(hydroxylethyl)-amino]phenyl]azo]pyridine was synthesized by diazotization of 4-aminopyridine followed by coupling with N-phenyldiethanolamine and has been characterized by elemental analysis, mass spectrometry, and infrared, UV−vis, and NMR spectroscopies. The chromophoric multilayers have been characterized by X-ray photoelectron and transmission optical spectroscopies, spectroscopic ellipsometry, X-ray reflectivity, advancing contact angle measurements, and polarized second harmonic generation (SHG). The excellent structural regularity of the chromophoric multilayers is indicated by the linear dependence of the [(aminophenyl)azo]pyridinium chromophore longitudinal HOMO → LUMO charge-transfer excitation absorbance at 572 nm and the ellipsometry- and X-ray reflectivity-derived multilayer thicknesses on the number of assembled trilayers, while the uniform polar order of the stacked chromophoric multilayers is evidenced by the quadratic dependence of the second harmonic generation intensities on the number of trilayers. The [(aminophenyl)azo]pyridinium multilayers are photochemically stable, have very high structural regularities, and exhibit a second-order nonlinear optical susceptibility (χ(2)) of ∼3.6 × 10-7 esu (∼150 pm/V) at a fundamental wavelength of 1064 nm. Finally, atomic force microscopy reveals that the surfaces of the self-assembled multilayers are very smooth (root mean square roughness = 12 Å for a 10 trilayer sample), undoubtedly reflecting the high three-dimensional structural regularities of the individual layers.
The Potential of Medicinal Plants as Treatments for Infections Caused by Aspergillus spp. (2022)

Aspergillus spp. are saprophytic fungi that contribute to the recycling of carbon and nitrogen in nature, surviving and proliferating on organic debris. They can be pathogenic in humans, especially in immunocompromised individuals and those with pre-existing lung diseases. Skin infections, hypersensitive reactions, chronic pulmonary infections and several acute life-endangering infections manifest as a sign of the prevalence of the fungus in the human body. The conglomerate of these diseases caused by Aspergillus spp. is referred to as aspergillosis. The underexplored territory of using medicinal plants as potential treatments, particularly for aspergillosis, warrants a larger scope of research as it brings many possibilities for a better understanding of the disease and the improvement of pre-existing treatments and, in addition, possible invention of new drugs. This chapter discusses various types of aspergillosis, the mode of action, conventional treatments and their side effects, and research into medicinal plants as a potential alternative treatment of the fungus disease.
Overview of the Sixth Social Media Mining for Health Applications (#SMM4H) Shared Tasks at NAACL 2021 (2021)

Arjun Magge, Ari Klein, Antonio Miranda-Escalada, Mohammed Ali Al-Garadi, Ilseyar Alimova, Zulfat Miftahutdinov, Eulalia Farre, Salvador Lima López, Ivan Flores, Karen O’Connor, Davy Weissenbacher, Elena Tutubalina, Abeed Sarker, Juan Banda, Martin Krallinger, Graciela Gonzalez-Hernandez. Proceedings of the Sixth Social Media Mining for Health (#SMM4H) Workshop and Shared Task. 2021.
Return of the Runtimes (2017)

The public cloud is moving to a Platform-as-a-Service model where services such as data management, machine learning or image classification are provided by the cloud operator while applications are written in high-level languages and leverage these services.
Sounds recorded in the presence of sei whale, Balaenoptera borealis (1991)

Opportunistic recordings were made on 12 days during the months of August and September in 1986–1989 between Browns and Baccari Banks on the Nova Scotian shelf. Sei whales, Balaenoptera borealis, were seen in the recording area on 16 of the 32 recording sessions. Subsequent signal analysis revealed that a distinctive sound type was recorded on all of the 16 recording sessions when sei whales were seen and on six sessions when no sei whales were seen. On some recordings two to three different sources (based on sound quality and received levels) are apparent. All these sounds share the same basic characteristics. The signal consists of two phrases, each lasting about 0.5–0.8 s, with an inter-phrase interval of 0.4–1 s, and restricted to the 1.5–3.5 kHz band. Each phrase is composed of a series of 10–20 FM sweeps lasting approximately 30–40 ms/sweep. These signals are similar to the few sei whale sounds reported by Thompson et al. [in Behavior of Marine Animals, Vol. 3, Cetaceans, edited by H. E. Winn and B. L. Olla (1979)]. These sounds are distinctly different from those for all other cetaceans known to frequent these waters.
Shaping clonal hematopoiesis (2020)

In this issue of Blood, Eskelund et al characterize clonal hematopoiesis in serial samples from persons with mantle cell lymphoma (MCL) undergoing frontline treatment, providing evidence that treatment plays an important role in the development of clonal hematopoiesis.(1)
Adaptive de-blending of dithered simultaneous sources (2021)

In marine seismic data acquisition, de-blending multiple simultaneous sources is a challenging, undetermined problem and sparsity constraints are often used to derive a stable solution. In this article, we discuss the impact of additional adaptive constraints. In particular, we investigate conformity to a) direct wave modelling, b) ghost modelling and c) variations of signal-to-noise ratio. We find that these additional constraints improve convergence significantly. We demonstrate the performance of the proposed approach on a narrow-azimuth marine streamer survey acquired with triple-source simultaneous shooting and natural dithers. The proposed approach addresses the key de-blending challenges for this dataset which are protecting aliased steeply dipping events and avoiding signal damage.
Education program at the Massachusetts Institute of Technology research reactor for pre-college science teachers (1989)

A Pre-College Science Teacher (PCST) Seminar program has been in place at the Massachusetts Institute of Technology (MIT) Nuclear Reactor Laboratory for 4 yr. The purpose of the PCST program is to educate teachers in nuclear technology and to show teachers, and through them the community, the types of activities performed at research reactors. This paper describes the background, content, and results of the MIT PCST program.
Recent advances in liver-directed gene transfer vectors. (2004)

Liver gene therapy has a long way to go and efficient and innocuous liver-directed gene transfer vectors are therefore urgently required.
Prolonged release of pentazocine from multiple O/W/O emulsions (1989)

AbstractMultiple O/W/O emulsions containing pentazocine were prepared and tested in vitro and in vivo. The effect of two different concentrations of three additives, viz. sodium chloride, glucose and glycerol, location of the drug either in one or any two phases of the O/W/O emulsions and pH of the receptor fluid on in vitro release characteristics of the drug was studied. All the parameters influenced the drug release. Multiple O/W/O emulsions gave higher extent of drug release than the simple O/W emulsions. The results of in vivo studies in mice showed prolonged tissue levels of pentazocine from the multiple O/W/O emulsions in comparison to aqueous drug solution and simple O/W emulsion.
CYTOMEGALOVIRUS DISEASE IS ASSOCIATED WITH INCREASED COST AND HOSPITAL LENGTH OF STAY AMONG ORTHOTOPIC LIVER TRANSPLANT RECIPIENTS1 (1997)

Cytomegalovirus (CMV) is a cause of considerable morbidity and mortality among orthotopic liver transplant (OLT) recipients. To study the impact of CMV on cost and hospital length of stay in this population, we undertook an analysis of a cohort of OLT recipients from four transplant centers in Boston who participated in a CMV prophylaxis trial. First posttransplant year hospital length of stay (including the hospital stay after transplantation and readmissions within 1 year after transplantation) was available for all 141 patients included in the study. In a multiple linear regression model bacteremia (P=0.0001), CMV disease (P=0.0007), abdominal reexploration (excluding retransplantation) (P=0.0070), recipient age < or = 16 years (P=0.0352), and the number of units of blood products (red blood cells, platelets, or fresh frozen plasma) administered during transplantation (P=0.0523) were shown to be independently associated with longer first posttransplant year hospital length of stay. Cost data for in-hospital care for the year beginning with admission for liver transplantation were available for 66 OLT recipients. Using a multiple linear regression model, development of CMV disease (P=0.0001), the number of units of blood products administered during transplantation (P=0.0001), bacteremia (P=0.0002), decreased pretransplant renal function (estimated by creatinine clearance) (P=0.0109), and need for retransplantation (P=0.0619) were shown to be independently associated with higher cost. These data strongly suggest that CMV disease has a direct impact on cost and hospital length of stay in liver transplantation.
Spatial watermark for image content authentication (2002)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
Red blood cell antibodies in pregnancy and their clinical consequences: synergistic effects of multiple specificities (2009)

Anti-D was the single most frequent and harmful specificity closely followed by anti-K. Combinations of antibody specificities were more harmful than single specificities, and a potentially synergistic effect should be considered.
Identification and functional analysis of a phytoene desaturase gene from the extremely radioresistant bacterium Deinococcus radiodurans (2007)

The phytoene-related desaturases are the key enzymes in the carotenoid biosynthetic pathway. The gene encoding phytoene desaturase in the deinoxanthin synthesis pathway of Deinococcus radiodurans was identified and characterized. Two putative phytoene desaturase homologues (DR0861 and DR0810) were identified by analysis of conserved amino acid regions, and the former displayed the highest identity (68 %) with phytoene desaturase of the cyanobacterium Gloeobacter violaceus. DR0861 gene knockout and dinucleotide-binding motif deletion resulted in the arrest of lycopene synthesis and the accumulation of phytoene. The colourless DR0861 knockout mutant became more sensitive to acute ionizing radiation and oxygen stress. Complementation of the mutant with a heterologous or homologous gene restored its pigment and resistance. The desaturase activity of DR0861 (crtI) was further confirmed by the assay of enzyme activity in vitro and heterologous expression in Escherichia coli containing crtE and crtB genes (responsible for phytoene synthesis) from Erwinia uredovora. In addition, the amount of lycopene synthesis in E. coli resulting from the expression of crtI from D. radiodurans was determined, and this had significant dose-dependent effects on the survival rate of E. coli exposed to hydrogen peroxide and ionizing radiation.
4 Thermotolerance, Thermoresistance, and Thermosensitization (1990)

I. INTRODUCTION When organisms or cells in culture are exposed to temperatures that are outside their normal growth range, the response to that change is modulated by many environmental factors. These include parameters such as availability of nutrients, including glucose and oxygen, and the pH of the old and the new milieu, to name two of the more important ones. Our concern in this chapter is, however, with an intrinsic determinant that also influences responses to temperature changes, namely, the thermal history of the organism. The importance of thermal history has been known for a considerable time, particularly to plant pathologists (Alexandrov 1977) and, for that matter, to farmers and gardeners. These know from experience that if a plant is to be moved from a cold to a warm environment, the probability of its survival is vastly enhanced if the move is not made in one step, but gradually. In other words, if the plant is given a chance to adapt to small changes in temperature, it acquires additional thermal resistance. This acquired characteristic increases the temperature range of survival. In the last few years, it has been shown that the same considerations apply not only to plants, but also to bacteria, mammalian cells, and even complex organisms such as rodents. Humans survive fevers; these reach temperatures that kill un-adapted cells in vitro. Human cells in vivo must, therefore, also develop temporary heat resistance. The molecular basis of this adaptive process has, until recently, been totally unknown. We now have...
Identification of conserved antigens for early serodiagnosis of relapsing fever Borrelia (2009)

Borrelia hermsii is a blood-borne pathogen transmitted by the argasid tick Ornithodoros hermsi. Since spirochaete clearance in mice is associated with an IgM-mediated response, an immunoproteomic analysis was used to identify proteins reactive with IgM. We report that IgM from both mice and human patients infected with B. hermsii not only reacted with the previously identified variable membrane proteins but also identified candidate antigens including heat-shock proteins, an adhesin protein, ABC transporter proteins, flagellar proteins, housekeeping proteins, an immune evasion protein, and proteins with unknown function. Furthermore, IgM reactivity to recombinant glycerophosphodiester phosphodiesterase was detected during early spirochaete infection and prior to a detectable IgG response. Lastly, a conserved hypothetical protein was produced in Escherichia coli and tested with immune serum against B. hermsii and Borrelia recurrentis. These results identify a much larger set of immunoreactive proteins, and could help in the early serodiagnosis of this tick-borne infection.
CNTF receptor subunit α as a marker for glioma tumor-initiating cells and tumor grade (2012)

These data indicate that CNTFRα plays a role in the formation or maintenance of tumor-initiating cells in gliomas, is a marker that correlates with histological grade, may underlie treatment resistance in some cases, and is a potential therapeutic target.
Classification of Cytochrome P450 Activities Using Machine Learning Methods (2009)

The cytochrome P(450) (CYP) system plays an integral part in the metabolism of drugs and other xenobiotics. Knowledge of the structural features required for interaction with any of the different isoforms of the CYP system is therefore immensely valuable in early drug discovery. In this paper, we focus on three major isoforms (CYP 1A2, CYP 2D6, and CYP 3A4) and present a data set of 335 structurally diverse drug compounds classified for their interaction (as substrate, inhibitor, or any interaction) with these isoforms. We also present machine learning models using a variety of commonly used methods (k-nearest neighbors, decision tree induction using the CHAID and CRT algorithms, random forests, artificial neural networks, and support vector machines using the radial basis function (RBF) and homogeneous polynomials as kernel functions). We discuss the physicochemical features relevant for each end point and compare it to similar studies. Many of these models perform exceptionally well, even with 10-fold cross-validation, yielding corrected classification rates of 81.7 to 91.9% for CYP 1A2, 89.2 to 92.9% for CYP 2D6, and 87.4 to 89.9% for CYP3A4. Our models help in understanding the structural requirements for CYP interactions and can serve as sensitive tools in virtual screenings and lead optimization for toxicological profiles in drug discovery.
The effect of air pollution on the transcriptomics of the immune response to respiratory infection (2021)

Combustion related particulate matter air pollution (PM) is associated with an increased risk of respiratory infections in adults. The exact mechanism underlying this association has not been determined. We hypothesized that increased concentrations of combustion related PM would result in dysregulation of the innate immune system. This epidemiological study includes 111 adult patients hospitalized with respiratory infections who underwent transcriptional analysis of their peripheral blood. We examined the association between gene expression at the time of hospitalization and ambient measurements of particulate air pollutants in the 28 days prior to hospitalization. For each pollutant and time lag, gene-specific linear models adjusting for infection type were fit using LIMMA (Linear Models For Microarray Data), and pathway/gene set analyses were performed using the CAMERA (Correlation Adjusted Mean Rank) program. Comparing patients with viral and/or bacterial infection, the expression patterns associated with air pollution exposure differed. Adjusting for the type of infection, increased concentrations of Delta-C (a marker of biomass smoke) and other PM were associated with upregulation of iron homeostasis and protein folding. Increased concentrations of black carbon (BC) were associated with upregulation of viral related gene pathways and downregulation of pathways related to antigen presentation. The pollutant/pathway associations differed by lag time and by type of infection. This study suggests that the effect of air pollution on the pathogenesis of respiratory infection may be pollutant, timing, and infection specific.
LSC 2013 abstract - Increased expression of bitter taste receptors on peripheral blood leukocytes from children with severe asthma compared to healthy controls (2013)

Background: Bitter taste receptor (TAS2R) signalling may be a novel pathway involved in asthma pathogenesis. TAS2R agonists are potent bronchodilators in human and animal models (Deshpande et al. Nature 2010; Pulkkinen et al. Am J Physiol Lung Cell Mol Physiol 2012) and transcriptome analysis has revealed that several TAS2R genes are differentially expressed in white blood cells from children with severe asthma (Orsmark-Pietras ATS 2011 A6375). Our aim was to examine by RT-PCR whether TAS2R expression of 11 different TAS2R genes differed between children with severe asthma and healthy controls. Methods: Blood leukocytes were isolated and RNA was extracted from 19 children with diagnosed severe problematic asthma and 18 healthy controls. Subject characteristics were previously described (Konradsen et al. Pediatr Allergy Immuol 2011). RT-PCR was performed using primers for 11 different human TAS2Rs, and the endogenous control GAPDH. Results: Expression of most TAS2Rs was greater in children with severe asthma and these differences reached statistical significance for TAS2R13, TAS2R14 and TAS2R19 (fig 1). Conclusion: Along with previous observations of TAS2R agonists having bronchodilatory effects, the current observations support the notion that bitter taste signalling may represent a novel mechanism in asthma pathogenesis.
Nanofilament Silicon for Matrix-Free Laser Desorption/Ionization Mass Spectrometry (2011)

Mass spectrometry (MS) provides quantitative information toward accurate mass identification of unknown molecules and has become a powerful and widely used technique for bioanalysis. In this chapter, we describe the fabrication and MS analysis steps for a high sensitivity matrix-free laser desorption/ionization mass spectrometry (LDI-MS) target substrate termed nanofilament silicon (nSi). Unlike other nanostructured porous silicon surfaces, nSi possesses an open pore morphology with associated benefits including efficient transport of sample into the nanopores and effective removal of solvent from the surface. The utility of nSi targets for LDI-MS analysis lies primarily in the analysis of small molecules, which are typically less than 5,000 Da with a detection sensitivity in the attomole range.
Tarihi Colmar’ın Kentsel Konfigürasyonu İçinde Herzog & De Meuron’un Musée Unterlinden Yapısı ve Aldo Rossi’nin Şehir Teorisiyle Olan İlişkisi (2021)

The aim of this paper is to investigate the Musee Unterlinden project of Herzog & De Meuron in France / Colmar as a modern architecture within a historical context and to analyze Herzog & De Meuron’s design methodology from the perspective of Aldo Rossi`s city theory. Thus Aldo Rossi was for Herzog & De Meuron one of the two most influential urban theoreticians in the postmodern time. The research methodology bases on the exertion to understand the intention of the architects, by analysing their documentation including papers and various presentations of the project in German and English. A comparison of Musee Unterlinden with other museum projects enriches the understanding of Herzog & De Meuron’s design process. The scope of the analysis reaches from the scale of urban design to relevant materials and details. Finally, the concept of the project has been analysed with Aldo Rossi`s terminology and thoughts. As a result, this paper addresses not only the urban configuration concept of the Unterlinden project but also the abstraction of monumental typologies and volumes in Aldo Rossi`s city theory. Herzog & De Meuron integrates the history of the city, its morphology and material after an experimental and artistic transformation into the contemporary image of the city. Herzog & De Meuron does not only renew architecture and its production but also the city with its own artefacts.
ChemInform Abstract: Stereoselective Synthesis of the Brassinolide Side Chain by the Use of a 5‐exo‐α‐Silyl Radical Cyclization‐Protiodesilylation Sequence. (1996)

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.
High resolution DF architectures using a robust symmetric number system encoding (2002)

A direction finding architecture that implements an innovative number system encoding of phase samples, the robust symmetric number system (RSNS), is described. The RSNS possesses Gray code properties and provides significant advantages over conventional phase scanning methods and other symmetric number system encoding techniques. The design equations for a RSNS array are presented. Simulation results for a prototype RSNS array are shown, and its performance compared to previously published results for other number system encoded direction finding architectures.
Investigation of dopant profiles in erbium doped optical fibres by ion microprobe and fluorescence confocal microscopy (2006)

Dopant profiles in erbium doped optical fibres acquired by the application of fluorescence intensity based confocal microscopy technique and the employment of a nanoscale-secondary ion mass spectrometry (NanoSIMS) system are presented and compared.