gebhart/patrepeval huggingface dataset:
Cefoxitin resistance by a chromosomal cephalosporinase in Escherichia coli. (1980)

Cefoxitin resistance, an unique property found in clinical isolates of Escherichia coli was investigated. Cefoxitin resistant strains, 255 and GN206, produced cephalosporinase constitutively. The cephalosporinase was located in the periplasm, and its production was considered to be mediated by chromosomal gene(s). Cephalosporinase-less mutants from both strains were susceptible to cefoxitin as well as other β-lactam antibiotics, suggesting that the cephalosporinase was responsible for the resistance to β-lactam antibiotics including cefoxitin. The cephalosporinases from the E. coli strains were partially purified and their enzymological properties were compared with those of cephalosporinases of Citrobacter freundii and Proteus morganii. Although the cephalosporinases of E. coli, as well as other cephalosporinases, showed little activity for cefoxitin-hydrolysis, the E. coli cephalosporinases exhibited a significantly higher affinity for cefoxitin than other cephalosporinases. It was assumed that the E. coli enzyme located around the targets of cefoxitin protected the targets from the antibiotic by its high affinity for the antibiotic.
In Vitro Anti-Inflammatory and Regenerative Effects of Autologous Conditioned Serum from Dogs with Osteoarthritis (2022)

Osteoarthritis (OA) is mostly incurable and non-regenerative with long-term complications. Autologous conditioned serum (ACS), which is enriched in Interleukin 1 receptor antagonists (IL-1RA) and growth factors, could be an alternative treatment to accelerate the positive therapeutic effects. ACS is proposed to alleviate inflammation by blocking IL-1 receptors. However, to date, there is no report focusing on the cell-mediated anti-inflammation and regenerative effect caused by ACS, especially the ACS from patients. Therefore, this study aims to investigate the therapeutic potential of ACS generated from dogs with spontaneous OA, focusing on its promising anti-inflammatory and regenerative properties in vitro compared to the matched plasma. We found that ACS prepared from ten OA dogs contained significant concentrations of IL-1RA, vascular endothelial growth factor, and transforming growth factor beta, which are key cytokines in anti-inflammation and angiogenesis. Furthermore, we found that ACS suppressed T cell activity by reducing proliferation of effector T cells and simultaneously expanding numbers of immune suppressive FOXP3<sup>+</sup> T cells. Lastly, we showed that ACS enhanced the proliferation of osteocytes and fibroblasts and promoted extracellular matrix gene expression in primary chondrocyte culture. Therefore, these studies indicate that ACS prepared from dogs with OA is active as an immunomodulatory and regenerative strategy for use in OA management.
CASSIOPEIA D4.3 - case study 3 report: hub connectivity-driven variable aircraft speeds (2013)

This document reports on how the CASSIOPEIA agent-based model has been developed, through a case study, to explore the use of dynamic cost indexing on flights arriving at a major European hub airport. A scenario that simulated many flights using dynamic cost indexing to recover delay to a residual of 10 minutes resulted in a considerable average cost saving achieved per flight.
Detection of Nematophagous Fungi from Heterodera schachtii Females Using a Baiting Experiment with Soils Cropped to Brassica Species from California’s Central Coast (2020)

Until the early 1990s, cyst nematodes were abundant pathogens in fields where hosts of Heterodera spp. were frequent members of crop rotations along California’s Central Coast. To mitigate damage caused by Heterodera schachtii and H. cruciferae, the soil fumigant 1,3-dichloropropene (1,3-D) was used by more than 43% of surveyed broccoli growers. Over the last few decades, use of 1,3-D and other nematicides has dramatically diminished, suggesting a decline in nematode disease pressure. The goal of this study was to examine the hypothesis that increased population densities of nematophagous fungi contribute to the low populations of Heterodera spp. in fields frequently cropped to their hosts. In 2016, soil samples were collected from 152 Brassica fields with a broad geographical distribution, from Santa Barbara County to Santa Cruz County. The average number of Heterodera cysts per 250 cm 3 of soil ranged from 0.5 to 27.5, with 62% of the soils harboring no detectable cyst nematodes and only a few samples reaching a potentially damaging threshold level. A baiting experiment with H. schachtii and cabbage was performed in a greenhouse to detect nematophagous fungi associated with nematode females as their posterior end emerged and became exposed to the soil’s rhizosphere. An Illumina-based sequence analysis of these H. schachtii females identified several known nematophagous fungi, including members of the Hyalorbilia oviparasitica clade, Pochonia chlamydosporia, certain Fusarium spp., and others. These soils clearly harbor a diverse population of hyperparasitic fungi that could be biologically suppressing cyst nematodes below a damaging threshold. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Process monitoring on drilling fiber-reinforced plastics and aluminum stacks using acoustic emissions (2018)

In order to meet the lightweight demands in aviation industry, more and more multi-material composites are processed in aircrafts’ structural parts. A common connection to join these stack materials to other parts of the components is to use rivets. For that type of connection it is necessary to drill precise holes in the stack material. Due to the fact of the multi-layer design with different material properties and therefore a different machinability of the components, high demands on tool performance and process stability are set. When drilling carbon fiber reinforced plastics (CFRP), flaws, such as delamination and fringes as well as a poor bore hole quality, have to be avoided regarding the demands of the manufactured workpiece. In contrast, when processing the metal layer, there is a demand of burr-free holes after the machining process. This leads to high challenges in optimizing the drilling process and the tool geometry in order to accomplish long and reliable tool service times when processing generally expensive aircraft components. In order to monitor the drilling process of CFRP-aluminum stacks, this work shows the application of acoustic emission (AE) measurement technology to investigate the cutting mechanisms and enable a prediction for bore hole quality. For this purpose, the spectrum of the acoustic emission of the cutting process is examined for the various stages when cutting the different layers of the stack. Here, varying cutting mechanisms in regard to chip, burr formation and jamming of chips are observed and discussed. In wear-out tests the tool service times, the development of tool wear and the generated workpiece quality are recorded and the applicability of AE for process control is shown. Afterwards, suitable approaches are introduced in order to relate the tool wear state to the burr height by tracking the acoustic emission.
Effect of network topology on the ordering dynamics of voter models (2005)

We introduce and study the reverse voter model, a dynamics for spin variables similar to the well‐known voter dynamics. The difference is in the way neighbors influence each other: once a node is selected and one among its neighbors chosen, the neighbor is made equal to the selected node, while in the usual voter dynamics the update goes in the opposite direction. The reverse voter dynamics is studied analytically, showing that on networks with degree distribution decaying as k−v, the time to reach consensus is linear in the system size N for all v > 2. The consensus time for link‐update voter dynamics is computed as well. We verify the results numerically on a class of uncorrelated scale‐free graphs.
A Hybrid Markov and LSTM Model for Indoor Location Prediction (2019)

Accurate and robust indoor location prediction plays an important role in indoor location services. Markov chains (MCs) have been widely adopted for location prediction due to their strong interpretability. However, multi-order Markov chains ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula> -MCs) are not suitable for predicting long sequences due to problems of dimensionality. This study proposes a hybrid Markov model for location prediction that integrates a long short-term memory model (LSTM); this hybrid model is referred to as the Markov-LSTM. First, a multi-step Markov transition matrix is defined to decompose the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula> -MC into multiple first-order MCs. The LSTM is then introduced to combine multiple first-order MCs to improve prediction performance. Extensive experiments are conducted using real indoor Wi-Fi positioning datasets collected in a shopping mall. The results show that the Markov-LSTM model significantly outperforms five existing baseline methods in terms of its predictive performance.
α-Halogenohydrazides: useful starting material for the synthesis of hydrazinoazapeptides and azauracils (1999)

An efficient method for the synthesis of pseudodipeptides, which combines an aza glycine residue with various hydrazinoacid moieties by simple substitution of the halogen of α-halohydrazides, is described. Some of these hydrazinoazapeptides lead to hydrazones by oxidation or to azaaminouracils by cyclization.Key words: hydrazinohydrazides, hydrazones, hydrazinoazapeptides, azaaminouracils, pseudopeptides.
Multiple time scale flight control using re-configurable sliding modes (2002)

A dual time scale aircraft flight control problem is addressed via sliding mode control theory. Actuator dynamics, deflection limits and rate limits are addressed via sliding mode controller re-configuration. The designed re-configurable sliding mode controller achieves a robust, high accuracy tracking performance to mission angles (such as attack, sideslip and roll angles) in an outer loop before and after damage to an aircraft. Angular rate commands are robustly tracked in an inner loop. The developed re-configurable control strategy is based on a continuous sliding mode controller with a boundary layer re-configuration. Online explicit damage identification is not required. A re-configurable sliding mode controller is designed for an F-16 jet fighter with a nonlinear flight dynamics model. Computer simulations demonstrate high accuracy tracking performance. Actuator's deflection and deflection rate do not saturate.
Effects of dextran-induced hyperviscosity on regional blood flow and hemodynamics in dogs (1989)

In 10 pentobarbitalized dogs, plasma viscosity (Ep) was raised fourfold while apparent blood viscosity (Ea) increased about twofold by two steps of exchange transfusion of 200 ml of plasma with plasma containing high molecular weight dextran (mol wt 500,000, 20% wt/vol). Elevation of Ea was primarily caused by an increase of Ep but not red cell aggregation. As Ea increased, regional blood flow (by 15-microns microspheres) remained constant in most organs but reduced in the small intestine, spleen, and thyroid gland. Vascular hindrance (Z), which reflects the state of vascular geometry, was calculated as flow resistance per Ea. Among various organs, a reduction in Z was noted in the heart, liver, pancreas, kidney, brain, and adrenal gland. In myocardium, there was a progressive reduction of the endocardial-to-epicardial flow ratio, indicating a less profound vasodilation in endocardium than epicardium. These results indicate that dextran-induced hyperviscosity leads to a compensatory vasodilation in several vital organs thus serving to maintain blood flow and nutrient transport.
Aging associated altered response to intracellular bacterial infections and its implication on the host (2020)

Abstract The effects of senescence and aging on geriatric diseases has been well explored but how these influence infections in the elderly have been scarcely addressed. Here, we show that several innate immune responses are elevated in senescent cells and old mice, allowing them to promptly respond to bacterial infections. We have identified higher levels of iNOS as a crucial host response and show that p38 MAPK in senescent cells acts as a negative regulator of iNOS transcription. In old mice, however the ability to impede bacterial proliferation does not correlate with increased survival as elevated immune responses persist unabated eventually affecting the host. The use of anti-inflammatory drugs that could consequently be recommended also decreases iNOS disarming the host of a critical innate immune response. Overall, our study highlights that infection associated mortality in the elderly is not merely an outcome of pathogen load but is also influenced by the host’s ability to resolve inflammation induced damage. Summary statement Using cellular models and old mice we demonstrate the effect of aging on host response to bacterial infections. Aged systems mount a more effective anti-bacterial innate immune response but its persistence results in mortality of the host.
Uber das Eingeweidefett ("Ister") des Herings (1956)

Über das Eingeweidefett (“Ister”) des Herings Get access A. Wulff A. Wulff Hamburg Search for other works by this author on: Oxford Academic Google Scholar ICES Journal of Marine Science, Volume 21, Issue 2, April 1956, Pages 171–174, https://doi.org/10.1093/icesjms/21.2.171 Published: 01 April 1956
<em>In vivo</em> Imaging of the Mouse Spinal Cord Using Two-photon Microscopy (2012)

In vivo imaging using two-photon microscopy in mice that have been genetically engineered to express fluorescent proteins in specific cell types has significantly broadened our knowledge of physiological and pathological processes in numerous tissues in vivo. In studies of the central nervous system (CNS), there has been a broad application of in vivo imaging in the brain, which has produced a plethora of novel and often unexpected findings about the behavior of cells such as neurons, astrocytes, microglia, under physiological or pathological conditions. However, mostly technical complications have limited the implementation of in vivo imaging in studies of the living mouse spinal cord. In particular, the anatomical proximity of the spinal cord to the lungs and heart generates significant movement artifact that makes imaging the living spinal cord a challenging task. We developed a novel method that overcomes the inherent limitations of spinal cord imaging by stabilizing the spinal column, reducing respiratory-induced movements and thereby facilitating the use of two-photon microscopy to image the mouse spinal cord in vivo. This is achieved by combining a customized spinal stabilization device with a method of deep anesthesia, resulting in a significant reduction of respiratory-induced movements. This video protocol shows how to expose a small area of the living spinal cord that can be maintained under stable physiological conditions over extended periods of time by keeping tissue injury and bleeding to a minimum. Representative raw images acquired in vivo detail in high resolution the close relationship between microglia and the vasculature. A timelapse sequence shows the dynamic behavior of microglial processes in the living mouse spinal cord. Moreover, a continuous scan of the same z-frame demonstrates the outstanding stability that this method can achieve to generate stacks of images and/or timelapse movies that do not require image alignment post-acquisition. Finally, we show how this method can be used to revisit and reimage the same area of the spinal cord at later timepoints, allowing for longitudinal studies of ongoing physiological or pathological processes in vivo.
Structure‐property relationships of chlorinated polyethylenes (1972)

Abstract This experimental study of suspension‐chlorinated linear polyethylenes (CPE), (degree of chlorination 25 to 48% Cl), covers dynamic mechancial behavior at 3.5 and 110 Hz in the temperature range − 100 to 120°C. The semicrystalline samples, with a maximum degree of crystallinity of 25%, showed the main relaxations α and β. The effect of thermal treatment was examined. In the amorphous specimens, in addition to the Tg relaxation, other low temperature damping peaks were observed. The mechancial spectra indicate structure heterogeneity and increasing stiffness with increasing chlorine substitution. For the most prominent β relaxation, the apparent activation energy was determined from the frequency shift of tan δ and E″ maxima. The effect of structure, crystallinity and frequency on Young's moduli are also discussed. For the amorphous γ ray‐Crosslinked elastomeric samples the photoelastic properties were examined at near equilibrium conditions between 30° and 80°C at various degrees of crosslinking. The polarizability anisotropy of the optical link and the Mooney‐Rivlin elasticity constants were determined and an attempt was made to relate the result to the specimens' structure. A compatibility study was also made for a 42% Cl, CPE/high cis polybutadiene polyblend. The damping mechanical spectra indicate a noninteracting system whose Young's moduli can be correlated with those of the pure components using a phenomenological model proposed by Takayanagi.
Chemical Mutagenesis of Vaccinia DNA Topoisomerase Lysine 167 Provides Insights to the Catalysis of DNA Transesterification (2013)

Vaccinia DNA topoisomerase IB (TopIB) relaxes supercoils by forming and resealing a covalent DNA-(3'-phosphotyrosyl(274))-enzyme intermediate. Conserved active site side chains promote the attack of Tyr274 on the scissile phosphodiester via transition state stabilization and general acid catalysis. Two essential side chains, Lys167 and Arg130, act in concert to protonate and expel the 5'-O leaving group. Here we gained new insights to catalysis through chemical mutagenesis of Lys167. Changing Lys167 to cysteine crippled the DNA cleavage and religation transesterification steps (k(cl) = 4.3 × 10(-4) s(-1); k(rel) = 9 × 10(-4) s(-1)). The transesterification activities of the K167C enzyme were revived by in vitro alkylation with 2-bromoethylamine (k(cl) = 0.031 s(-1); k(rel) ≥ 0.4 s(-1)) and 3-bromopropylamine (k(cl) = 0.013 s(-1); k(rel) = 0.22 s(-1)), which convert the cysteines to γ-thialysine and γ-thiahomolysine, respectively. These chemically installed lysine analogues were more effective than a genetically programmed arginine 167 substitution characterized previously. The modest differences in the transesterification rates of the 2-bromoethylamine- and 3-bromopropylamine-treated enzymes highlight that TopIB is tolerant of a longer homolysine side chain for assembly of the active site and formation of the transition state.
A new method for the generation of patterned protein films by encapsulation in arrays of thermally evaporated lipids (2001)

In this article we demonstrate a versatile method for the generation of patterned protein films by encapsulation in arrays of the lipids, octadecylamine (ODA, cationic), and arachidic acid (AA, anionic). A simple 2 x 2 array of ODA and AA was vacuum deposited on different substrates using appropriate masks. Thereafter, the enzymes pepsin and fungal protease as well as the heme-proteins cytochrome c and hemoglobin were encapsulated in the different elements of the array by sequential immersion (combined with judicious masking) of the array elements in the different protein solutions. The proteins are incorporated into the lipid elements by electrostatic interaction between charged amino acid residues on the protein surface and charged functional groups in the lipid matrix. This procedure leads to spatially distinct regions of the different proteins on one substrate and shows promise for single-chip multianalyte immunoassay/multiplex, high-throughput biosensor and catalysis applications. Fourier transform infrared spectroscopy (FTIR) was used to monitor the incorporation of the proteins in the different elements of the array as well as to ascertain whether intermixing of the proteins in a particular array element had occurred. The heme-protein composite regions were further characterized using UV-VIS spectroscopy.
Seasonality of gestational diabetes mellitus: a South Australian population study (2016)

This study is the first population-based study to demonstrate a seasonal variation for GDM. Several maternal lifestyle and psychosocial factors associated with seasonality and GDM may be influential in the pathophysiologic mechanisms of GDM. Ambient temperature, physical activity, nutrient intake, and vitamin D levels may affect maternal physiology, and fetal and placental development at the cellular level and contribute to the development of GDM. The mechanisms underlying these possible associations are not fully understood and warrant further investigation.
Proteomics Shows New Faces for the Old Penicillin ProducerPenicillium chrysogenum (2012)

Fungi comprise a vast group of microorganisms including the Ascomycota (majority of all described fungi), the Basidiomycota (mushrooms or higher fungi), and the Zygomycota and Chytridiomycota (basal or lower fungi) that produce industrially interesting secondary metabolites, such as β-lactam antibiotics. These compounds are one of the most commonly prescribed drugs world-wide. Since Fleming's initial discovery of Penicillium notatum 80 years ago, the role of Penicillium as an antimicrobial source became patent. After the isolation of Penicillium chrysogenum NRRL 1951 six decades ago, classical mutagenesis and screening programs led to the development of industrial strains with increased productivity (at least three orders of magnitude). The new "omics" era has provided the key to understand the underlying mechanisms of the industrial strain improvement process. The review of different proteomics methods applied to P. chrysogenum has revealed that industrial modification of this microorganism was a consequence of a careful rebalancing of several metabolic pathways. In addition, the secretome analysis of P. chrysogenum has opened the door to new industrial applications for this versatile filamentous fungus.
Spectrum bias, a common unrecognised issue in orthopaedic agreement studies (2015)

Spectrum bias influenced the outcome of this agreement study on treatment plans. An additional CT scan improves the intra-observer agreement on treatment plans for a fracture of the distal radius only when there is therapeutic uncertainty. Reporting and analysing intra-observer agreement based on the surgeon's level of certainty is an appropriate method to minimise spectrum bias. Cite this article: Bone Joint Res 2015;4:190-194.
Electropolishing of stainless steels in a choline chloride based ionic liquid: an electrochemical study with surface characterisation using SEM and atomic force microscopy (2006)

We have studied the anodic dissolution (electropolishing) of various stainless steel alloys in an ionic liquid comprising a 2 : 1 stoichiometric mix of ethylene glycol (EG) and choline chloride. We have used a combination of electrochemical and spectroscopic methods together with in situ liquid probe microscopy. We discuss the role and influence of the surface oxide passivation layer, characterized here by X-ray photoelectron spectroscopy (XPS) and linear sweep voltammetry, on the polishing process. We address the question of dealloying during the polish in order to contribute to our understanding of the viability of the ionic liquid as a replacement industrial electropolishing medium; the current commercial process uses a corrosive mixture of phosphoric and sulfuric acids. Also, we present data from ex situ and in situ liquid AFM studies giving both a qualitative and quantitative insight into the nature and scale of morphological changes at the steel surface during the polishing process.