gebhart/patrepeval huggingface dataset:
Infection Prophylaxis Update (2006)

The use of prophylactic antibiotics in surgery has been debated for numerous years. Although their indications have been elucidated in the general surgery literature, their role in plastic surgery has yet to be clearly defined. Although the incidence of surgical site infections in clean, elective plastic surgery procedures has been reported to be as low as 1.1%, the use of antibiotics has surged over the past 20 years. Much of the increased use has been attributed to common surgical practice and fear of legal ramifications rather than empirically based data. In contrast, there remain numerous physicians who argue against routine antibiotic use in plastic surgery. This article summarizes the recent literature on infection prophylaxis and advises physicians to consider relative risks and benefits when deciding which patients should receive prophylactic antibiotics.
Identification of <i>N</i>-{<i>cis</i>-3-[Methyl(7<i>H</i>-pyrrolo[2,3-<i>d</i>]pyrimidin-4-yl)amino]cyclobutyl}propane-1-sulfonamide (PF-04965842): A Selective JAK1 Clinical Candidate for the Treatment of Autoimmune Diseases (2018)

Janus kinases (JAKs) are intracellular tyrosine kinases that mediate the signaling of numerous cytokines and growth factors involved in the regulation of immunity, inflammation, and hematopoiesis. As JAK1 pairs with JAK2, JAK3, and TYK2, a JAK1-selective inhibitor would be expected to inhibit many cytokines involved in inflammation and immune function while avoiding inhibition of the JAK2 homodimer regulating erythropoietin and thrombopoietin signaling. Our efforts began with tofacitinib, an oral JAK inhibitor approved for the treatment of rheumatoid arthritis. Through modification of the 3-aminopiperidine linker in tofacitinib, we discovered highly selective JAK1 inhibitors with nanomolar potency in a human whole blood assay. Improvements in JAK1 potency and selectivity were achieved via structural modifications suggested by X-ray crystallographic analysis. After demonstrating efficacy in a rat adjuvant-induced arthritis (rAIA) model, PF-04965842 (25) was nominated as a clinical candidate for the treatment of JAK1-mediated autoimmune diseases.
Link protein interactions with hyaluronate and proteoglycans. Characterization of two distinct domains in bovine cartilage link proteins. (1987)

Hyaluronic acid-binding region and trypsin-link protein were prepared from bovine nasal cartilage proteoglycan complex after trypsin digestion. Binary complexes were reformed between trypsin-link protein and hyaluronic acid-binding region or hyaluronate. Upon trypsin treatment of these complexes, two fragments deriving from trypsin-link protein were characterized. One of them, of 20 kDa, corresponds in fact to a 140-amino acid long fragment and bears the glycosylated site of trypsin-link protein; it appears to be involved in proteoglycan/link protein interaction. The other, of 22 kDa, corresponds to the 200 C-terminal amino acids of trypsin-link protein; it appears to be involved in the binding of link protein with hyaluronic acid. A structural model of bovine trypsin-like protein depicting two distinct domains involved in hyaluronate and proteoglycan subunit interactions is proposed.
Evolution of diverse antiviral CD8<sup>+</sup> T cell populations after murine cytomegalovirus infection (2005)

Cytomegalovirus (CMV) is a major human pathogen normally controlled by cellular immune responses. The infection can be modeled in the mouse using murine CMV (MCMV). During the latent phase of infection, two different patterns of CD8(+) T cell responses have been observed: some specificities show increasing frequencies over time ("memory inflation"), while others, which are present acutely, are barely detectable at later time points. This distinction is independent of initial immunodominance. We analyzed the extent to which such responses differ functionally and tracked both their population distribution and their evolution over time. We observed two clear patterns of memory development that diverged early after infection. Acutely, CD8(+) T cells directed against all epitopes showed similar activation, phenotype and distribution. Thereafter, one set of responses ("inflationary") increased in frequency over time, was found in high numbers in non-lymphoid organs and was associated with an activated (CD28(low) CD27(low)CD122(low)) phenotype. In contrast, CD8(+) T cells responses specific for other MCMV epitopes ("non-inflationary") showed a slow reversion to a classical "central" memory phenotype without enrichment in non-lymphoid organs. A simple model to describe the equilibrium state in MCMV is presented, which may point to previously unexplored antiviral populations present after human CMV infection.
Characterization of a binding protein for leukemia inhibitory factor localized in extracellular matrix (1993)

Leukemia Inhibitory Factor (LIF) interacts with two classes of high affinity binding sites on rat UMR cells cultured in monolayer. One class of binding sites was found to be localized in the extracellular matrix (ECM) after removal of cells from the culture dish. The interaction of LIF with ECM-localized binding sites is not dependent upon either glycosylation of LIF or the presence of extracellular glycosyaminoglycans. Chemical cross-linking studies demonstrate that LIF interacts with a 200-kD cell-associated protein and a 140-kD ECM-localized protein. A 140-kD protein could also be specifically precipitated from solubilised metabolically radiolabeled UMR ECM by antibodies directed against LIF by virtue of its ability to form a stable complex with unlabeled LIF. In addition, soluble LIF associated with this ECM-localized protein is biologically active in terms of inhibition of ES cell differentiation. The properties of ECM-localized 140-kD species are very similar to those of the secreted form of the LIF receptor suggesting that the ECM localization of LIF and LIF signal transduction may be closely coupled.
Purification and Some Properties of a Haim-sensitive<i>α</i>-Amylase from Newly Isolated<i>Bacillus</i>sp. No. 195 (1992)

Newly isolated Bacillus sp. No. 195 produced an extracellular alpha-amylase sensitive to Haim which was found to inhibit specifically animal alpha-amylases. The enzyme was purified easily by two steps of starch adsorption and gel filtration using Sephacryl S-200. The purified enzyme, which showed a single band on native-PAGE or SDS-PAGE, had a molecular weight of 60,000 as judged on SDS-PAGE. The optimum pH value for activity and the isoelectric point were around 7.0 and 4.5, respectively. The sensitivity of the amylase to Haim was similar to that of animal amylase rather than bacterial amylase. It was suggested that a Haim-amylase complex might be formed at the molar ratio of 1:1. The amino acid sequence F-S-W similar to the triplet F-E-W highly conserved among alpha-amylases sensitive to proteinaceous inhibitors, such as Hoe 467-A or Haim, was found in the amino-terminal part of the No. 195 amylase.
Eigenmobilities in background electrolytes for capillary zone electrophoresis: IV. Computer program PeakMaster (2004)

We are introducing a computer implementation of the mathematical model of zone electrophoresis (CZE) described in Stedry, M., Jaros, M., Hruska, V., Gas, B., Electrophoresis 2004, 25, 3071-3079 program PeakMaster. The computer model calculates eigenmobilities, which are the eigenvalues of the matrix tied to the linearized continuity equations, and which are responsible for the presence of system eigenzones (system zones, system peaks). The model also calculates other parameters of the background electrolyte (BGE)-pH, conductivity, buffer capacity, ionic strength, etc., and parameters of the separated analytes--effective mobility, transfer ratio, molar conductivity detection response, and relative velocity slope. This allows the assessment of the indirect detection, conductivity detection and peak broadening (peak distortion) due to electromigration dispersion. The computer model requires the input of the BGE composition, the list of analytes to be separated, and the system instrumental configuration. The output parameters of the model are directly comparable with experiments; the model also simulates electropherograms in a user-friendly way. We demonstrate a successful application of PeakMaster for inspection of BGEs having no stationary injection zone.
Floating constraints in lexical choice (1997)

Lexical choice is a computationally complex task, requiring a generation system to consider a potentially large number of mappings between concepts and words. Constraints that aid in determining which word is best come from a wide variety of sources, including syntax, semantics, pragmatics, the lexicon, and the underlying domain. Furthermore, in some situations, different constraints come into play early on, while in others, they apply much later. This makes it difficult to determine a systematic ordering in which to apply constraints. In this paper, we present a general approach to lexical choice that can handle multiple, interacting constraints. We focus on the problem of floating constraints, semantic or pragmatic constraints that float, appearing at a variety of different syntactic ranks, often merged with other semantic constraints. This means that multiple content units can be realized by a single surface element, and conversely, that a single content unit can be realized by a variety of surface elements. Our approach uses the Functional Unification Formalism (FUF) to represent a generation lexicon, allowing for declarative and compositional representation of individual constraints.
A New Power Conversion System for Megawatt PMSG Wind Turbines Using Four-Level Converters and a Simple Control Scheme Based on Two-Step Model Predictive Strategy—Part I: Modeling and Theoretical Analysis (2014)

A new power conversion system is explored in this paper aiming wind turbines rated at the megawatt level. The proposed configuration consists of a medium-voltage, permanent magnet synchronous generator connected to a low-cost three-phase diode bridge rectifier, a dc-dc four-level boost converter as the intermediate stage, and a four-level diode-clamped inverter on the grid-side. The dc-link capacitor voltages are balanced by the boost converter, and thus the control complexity for the grid-tied inverter is greatly simplified. To control the boost converter and grid-tied inverter, a simple method based on a two-step model predictive strategy is presented. In the first part of this paper, the continuous- and discrete-time modeling of the proposed power conversion system is analyzed. The control objectives such as maximum power point tracking, dc-link capacitor voltages balancing, regulation of net dc-bus voltage, reactive power generation, lower switching frequency operation, and common-mode voltage minimization are considered in the design of controller.
Glycogen Synthase Kinase-3β Participates in Nuclear Factor κB–Mediated Gene Transcription and Cell Survival in Pancreatic Cancer Cells (2005)

Recent studies using glycogen synthase kinase-3beta (GSK-3beta)-deficient mouse embryonic fibroblasts suggest that GSK-3beta positively regulates nuclear factor kappaB (NFkappaB)-mediated gene transcription. Because NFkappaB is suggested to participate in cell proliferation and survival pathways in pancreatic cancer, we investigated the role of GSK-3beta in regulating these cellular processes. Herein, we show that pancreatic cancer cells contain a pool of active GSK-3beta and that pharmacologic inhibition of GSK-3 kinase activity using small molecule inhibitors or genetic depletion of GSK-3beta by RNA interference leads to decreased cancer cell proliferation and survival. Mechanistically, we show that GSK-3beta influences NFkappaB-mediated gene transcription at a point distal to the Ikappa kinase complex, as only ectopic expression of the NFkappaB subunits p65/p50, but not an Ikappa kinase beta constitutively active mutant, could rescue the decreased cellular proliferation and survival associated with GSK-3beta inhibition. Taken together, our results simultaneously identify a previously unrecognized role for GSK-3beta in cancer cell survival and proliferation and suggest GSK-3beta as a potential therapeutic target in the treatment of pancreatic cancer.
Predicting 30-day all-cause readmissions from hospital inpatient discharge data (2016)

Inpatient hospital readmissions for potentially avoidable conditions are problematic and costly. In this paper, we build machine learning models using variables widely available in health claims data to predict patients' 30-day readmission risks at the time of discharge. These models show high predictive power on a U.S. nationwide readmission database. They are also capable of providing interpretable risk factors globally at the population level and locally associated with each single discharge. In addition, we propose a model-agnostic approach to provide confidence for each prediction. Altogether, using models with high predictive power, interpretable risk factors and prediction confidence may enable health care systems to accurately target high-risk patients and prevent recurrent readmissions by accurately anticipating the probability of readmission at the point of care.
An Improved Maximum Power Point Tracking Controller for PV Systems Using Artificial Neural Network (2012)

This paper presents an improved maximum power point tracking (MPPT) controller for PV systems. An Artificial Neural Network and the classical PO the response of the proposed MPPT controller is faster than the classical P&O algorithm. Moreover, the average tracking efficiency of the developed algorithm was 95.51% as compared to 85.99% of the classical P&O algorithm. Such developed controller increases the conversion efficiency of a PV system. Streszczenie. W artykule zaprezentowano ulepszony uklad śledzenia maksymalnej mocy w systemie fotowoltaicznym. Zastosowano siec neuronową i klasyczny algorytm P&O. Siec neuronowa w sprzezeniu zwrotnym ma cztery wejścia: promieniowanie sloneczne, temperatura otoczenia i wspolczynniki temperaturowe ISC i Voc. Wyjściem jest optymalne napiecie systemu. (Ulepszona metoda śledzenia maksymalnej mocy systemu fotowoltaicznego z wykorzystaniem sieci neuronowej)
Inverse modelling of in situ soil water dynamics: investigating the effect of different prior distributions of the soil hydraulic parameters (2011)

Abstract. In situ observations of soil water state variables under natural boundary conditions are often used to estimate the soil hydraulic properties. However, many contributions to the soil hydrological literature have demonstrated that the information content of such data is insufficient to accurately and precisely estimate all the soil hydraulic parameters. In this case study, we explored to which degree prior information about the soil hydraulic parameters can help improve parameter identifiability in inverse modelling of in situ soil water dynamics under natural boundary conditions. We used percentages of sand, silt, and clay as input variables to the ROSETTA pedotransfer function that predicts the parameters in the van Genuchten-Mualem (VGM) model of the soil hydraulic functions. To derive additional information about the correlation structure of the predicted parameters, which is not readily provided by ROSETTA, we employed a Monte Carlo approach. We formulated three prior distributions that incorporate to different extents the prior information about the VGM parameters derived with ROSETTA. The inverse problem was posed in a formal Bayesian framework and solved using Markov chain Monte Carlo (MCMC) simulation with the DiffeRential Evolution Adaptive Metropolis (DREAM) algorithm. Synthetic and real-world soil water content data were used to illustrate the approach. The results of this study demonstrated that prior information about the soil hydraulic parameters significantly improved parameter identifiability and that this approach was effective and robust, even in case of biased prior information. To be effective and robust, however, it was essential to use a prior distribution that incorporates information about parameter correlation.
Human Breathomics Database (2019)

Breathomics is a special branch of metabolomics that quantifies volatile organic compounds (VOCs) from collected exhaled breath samples. Understanding how breath molecules are related to diseases, mechanisms and pathways identified from experimental analytical measurements is challenging due to the lack of an organized resource describing breath molecules, related references and biomedical information embedded in the literature. To provide breath VOCs, related references and biomedical information, we aim to organize a database composed of manually curated information and automatically extracted biomedical information. First, VOCs-related disease information was manually organized from 207 literature linked to 99 VOCs and known Medical Subject Headings (MeSH) terms. Then an automated text mining algorithm was used to extract biomedical information from this literature. In the end, the manually curated information and auto-extracted biomedical information was combined to form a breath molecule database-the Human Breathomics Database (HBDB). We first manually curated and organized disease information including MeSH term from 207 literatures associated with 99 VOCs. Then, an automatic pipeline of text mining approach was used to collect 2766 literatures and extract biomedical information from breath researches. We combined curated information with automatically extracted biomedical information to assemble a breath molecule database, the HBDB. The HBDB is a database that includes references, VOCs and diseases associated with human breathomics. Most of these VOCs were detected in human breath samples or exhaled breath condensate samples. So far, the database contains a total of 913 VOCs in relation to human exhaled breath researches reported in 2766 publications. The HBDB is the most comprehensive HBDB of VOCs in human exhaled breath to date. It is a useful and organized resource for researchers and clinicians to identify and further investigate potential biomarkers from the breath of patients. Database URL: https://hbdb.cmdm.tw.
COMPUTER SKILLS AND WAGES* (1997)

Data from the 1993 Survey of Training and Education show that 52 per cent of males and 60 per cent of females had at some time used a computer. An analysis using earnings functions reveals that computer usage is associated with a wage premium of between 12 and 16 per cent. Experiments show that omission of a variable recording computer usage from a wage equation will result in a bias of between 10 and 15 per cent in the estimated return to a year of schooling and similar distortion to the estimated return to experience.
Maintenance of Mouse Nephron Progenitor Cells in Aggregates with Gamma-Secretase Inhibitor (2015)

Knowledge on how to maintain and expand nephron progenitor cells (NPC) in vitro is important to provide a potentially valuable source for kidney replacement therapies. In our present study, we examined the possibility of optimizing NPC maintenance in the "re-aggregate" system. We found that Six2-expressing (Six2(+))-NPC could be maintained in aggregates reconstituted with dispersed cells from E12.5 mouse embryonic kidneys for at least up to 21 days in culture. The maintenance of Six2(+)-NPC required the presence of ureteric bud cells. The number of Six2(+)-NPC increased by more than 20-fold at day 21, but plateaued after day 14. In an attempt to further sustain NPC proliferation by passage subculture, we found that the new (P1) aggregates reconstituted from the original (P0) aggregates failed to maintain NPC. However, based on the similarity between P1 aggregates and aggregates derived from E15.5 embryonic kidneys, we suspected that the differentiated NPC in P1 aggregates may interfere with NPC maintenance. In support of this notion, we found that preventing NPC differentiation by DAPT, a γ-secretase inhibitor that inhibits Notch signaling pathway, was effective to maintain and expand Six2(+)-NPC in P1 aggregates by up to 65-fold. The Six2(+)-NPC in P1 aggregates retained their potential to epithelialize upon exposure to Wnt signal. In conclusion, we demonstrated in our present study that the "re-aggregation" system can be useful for in vitro maintenance of NPC when combined with γ-secretase inhibitor.
Drugging the microbiome (2020)

Microbiome-modulating therapeutics have the potential to revolutionize medicine. Here, I discuss the challenges and opportunities inherent in creating new microbiome-based drugs.
A Sea Bed Logging (SBL) Calibration Survey over the Troll Gas Field (2004)

E019 A SEA BED LOGGING (SBL) CALIBRATION SURVEY OVER THE TROLL GAS FIELD Introduction 1 Remote resistivity sensing of buried resistive layers in conductive sediments a concept called Sea Bed Logging (SBL - Pat. No. US 6.628.119 B1) has been demonstrated both theoretically by Kong et al. (2002) and Eidesmo et al. (2001) and by calibration surveys over a known oil field offshore Angola (Ellingsrud et al. 2002) and the Ormen Lange gas field offshore Norway (Røsten et al. 2003). These surveys were acquired in deep water areas (> 1000 m) to minimize the background return signal from the air-water
Übersichtsaufsatz / Survey Paper: Struktur und Regelung bei Systemen mit durchlaufenden elastischen Bahnen und Mehrmotoren-Antrieben / Structure and control of systems with continuous moving elastic webs and multi-motor drives (1984)

Article Übersichtsaufsatz / Survey Paper: Struktur und Regelung bei Systemen mit durchlaufenden elastischen Bahnen und Mehrmotoren-Antrieben / Structure and control of systems with continuous moving elastic webs and multi-motor drives was published on December 1, 1984 in the journal at - Automatisierungstechnik (volume 32, issue 1-12).
Scalable min-max multi-objective cyber-security optimisation over probabilistic attack graphs (2019)

We present a framework to efficiently solve a multi-objective optimisation problem for cyber-security defence. Facing an attacker who can mount a multi-stage attack (modelled using attack graphs), the defence problem is to select a portfolio of security controls which minimises the security risk and the (direct and indirect) costs of the portfolio of controls. The main challenges for the optimisation are: (a) the effect of the security controls is in general probabilistic, for example, the effect of staff anti-phishing training; moreover, some controls like taking regular back-ups do not have an attack-preventing effect, but rather, mitigate the losses of a successful attack; (b) each control may affect multiple vulnerabilities; and each vulnerability may be affected by multiple controls; (c) there can be a prohibitively large number of attack paths, each involving exploitation of different vulnerabilities. Our mathematical framework deals with all these problems. In particular, we model the problem as a min-max multi-objective optimisation. Using techniques such as ILP conversion, exact LP relaxation and dualisation, we convert the problem into a very efficient MILP. For instance, it returns the optimal solution for attack graphs with 20,000 nodes in less than four minutes typically.
Patterned glass substrates for enhanced solar energy harvesting in thin film solar cells (2011)

The enhanced photoelectric conversion is demonstrated in nanostructured glass substrates for a-Si thin film solar cell. The nanostructured glass substrates were fabricated using nanosphere lithography and RIE technique. The nanostructure substrates provide antireflective and light scattering characteristics, which enhance the broadband light absorption, especially in near-infrared range. Finally we demonstrate the patterned glass substrates (nipple shape arrays) which are useful in light absorption of a-Si thin film solar cell. Compared to a flat glass substrate cell and Asahi-U glass substrate cell, the power conversion efficiency enhancement achieved 48.4% and 3.1%, the Jsc enhancement achieved 51.6% and 8%.