gebhart/patrepeval huggingface dataset:
Adaptation of Salmonella enterica Serovar Senftenberg to Linalool and Its Association with Antibiotic Resistance and Environmental Persistence (2017)

A clinical isolate of <i>Salmonella enterica</i> serovar Senftenberg, isolated from an outbreak linked to the herb <i>Ocimum basilicum</i> L. (basil), has been shown to be resistant to basil oil and to the terpene alcohol linalool. To better understand how human pathogens might develop resistance to linalool and to investigate the association of this resistance with resistance to different antimicrobial agents, selective pressure was applied to the wild-type strain by sequential exposure to increasing concentrations of linalool. The results demonstrated that <i>S</i> Senftenberg adapted to linalool with a MIC increment of at least 8-fold, which also resulted in better resistance to basil oil and better survival on harvested basil leaves. Adaptation to linalool was shown to confer cross protection against the antibiotics trimethoprim, sulfamethoxazole, piperacillin, chloramphenicol, and tetracycline, increasing their MICs by 2- to 32-fold. The improved resistance was shown to correlate with multiple phenotypes that included changes in membrane fatty acid composition, induced efflux, reduced influx, controlled motility, and the ability to form larger aggregates in the presence of linalool. The adaptation to linalool obtained <i>in vitro</i> did not affect survival on the basil phyllosphere <i>in planta</i> and even diminished survival in soil, suggesting that development of extreme resistance to linalool may be accompanied by a loss of fitness. Altogether, this report notes the concern regarding the ability of human pathogens to develop resistance to commercial essential oils, a resistance that is also associated with cross-resistance to antibiotics and may endanger public health.<b>IMPORTANCE</b> Greater consumer awareness and concern regarding synthetic chemical additives have led producers to control microbial spoilage and hazards by the use of natural preservatives, such as plant essential oils with antimicrobial activity. This report establishes, however, that these compounds may provoke the emergence of resistant human pathogens. Herein, we demonstrate the acquisition of resistance to basil oil by <i>Salmonella</i> Senftenberg. Exposure to linalool, a component of basil oil, resulted in adaptation to the basil oil mixture, as well as cross protection against several antibiotics and better survival on harvested basil leaves. Collectively, this work highlights the hazard to public health while using plant essential oils without sufficient knowledge about their influence on pathogens at subinhibitory concentrations.
A Method for non-destructive microwave focusing for deep brain and tissue stimulation (2022)

In the paper, we present a numerical method for focusing microwave power within biological tissue. The data from the simulations in the paper are included herein.
Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site (2021)

&lt;p&gt;Organophosphorus (OP) compounds are among the most toxic of chemical substances and widely used as insecticides, pesticides, and chemical warfare agents. The most important enzyme inhibited by OP compounds is acetylcholinesterase (AChe). Inactivation of AChe function results in the accumulation of neurotransmitter, leading to death due to serious respiratory disorders. Organophosphorus hydrolase (OPH), also called phosphotriesterase, is a homo-dimeric metalloenzyme that can hydrolyze various OP agents in the circulatory system, resulting in products that are generally of reduced toxicity. The best OPH substrate found to date is the insecticide diethyl p-nitrophenyl phosphate (paraoxon). Most structural and kinetic studies assume that the binding orientation of paraoxon is identical to that of diethyl 4-methylbenzylphosphonate, which is the only substrate analog co-crystallized with OPH. In the current work, we used a combined docking and molecular dynamics (MD) approach to predict the likely binding mode of paraoxon in the OPH active site. We identified a potential binding mode of paraoxon that does not match the binding mode of diethyl 4-methylbenzylphosphonate. Then, we used the predicted binding mode to run MD simulations on the wild type (WT) OPH complexed with paraoxon, and OPH mutants complexed with paraoxon. Additionally, we identified 3 hot-spot residues (D253, H254, and I255) involved in the stability of the OPH active site. To further assess these predictions, we then experimentally assayed single and double mutants involving these residues (D253E, H254S, I255S, D253E-H254R and D253E-I255G) for hydrolytic activity against paraoxon. Computational structural analysis of protein-substrate dynamics shows different hydrogen bonding profiles for mutants involving D253 (D253E, D253E-H254R, and D253E-I255G) compared to WT OPH. Additionally, the binding free energy calculations and the experimental kinetics (particularly, &lt;i&gt;k&lt;/i&gt;&lt;sub&gt;cat&lt;/sub&gt; and &lt;i&gt;K&lt;sub&gt;M&lt;/sub&gt;&lt;/i&gt;) of the reactions between each OPH mutant and paraoxon show that mutated forms D253E, D253E-H254R, and D253E-I255G exhibit enhanced activity over WT OPH. Interestingly, our experimental results show that the activity of the double mutant D253E-H254R increased by 19-fold compared to WT OPH.&lt;/p&gt;
Effect of Ketoconazole and Rifampicin on the Pharmacokinetics of Ranitidine in Healthy Human Volunteers: A Possible Role of P-Glycoprotein (2006)

The aims of this study were to determine the effect of ketoconazole and rifampicin on the oral pharmacokinetics of ranitidine in human volunteers and to investigate the role of P-glycoprotein (P-gp) using in vitro systems. A randomized, placebo controlled crossover oral pharmacokinetic study was conducted in 12 healthy male human volunteers and in vitro (everted sac) and in situ (intestinal loop) studies were conducted in rats to study the role of P-gp. There was a statistically significant (p < 0.05) difference observed in the pharmacokinetic parameters C(max), AUC and MRT after pretreatment with rifampicin (600 mg orally once per day for 7 days). The C(max), AUC(0-infinity), and MRT were decreased by 53%, 52%, and 18%, respectively. Ketoconazole treatment (200 mg orally once per day for 5 days) increased the C(max), AUC(0-infinity) and T1/2 by 78%, 74%, and 56%, respectively, whereas T(max) was decreased by 31%. No statistically significant differences were observed in renal clearance (CLR) of ranitidine after treatment with either ketoconazole or rifampicin. Presence of ketoconazole significantly reduced the mean cumulative efflux concentrations (serosal to mucosal) of ranitidine to 35%, 41% and 55% in the duodenal, jejunum and ileal regions of the everted sacs, respectively, whereas, the mean cumulative efflux concentrations of ranitidine were increased by 14%, 36% and 25% in duodenal, jejunal and ileal regions of the rat small intestine, respectively, after pretreatment with rifampicin. The presence of ketoconazole improved the absorption of ranitidine significantly by increasing the percentage of total dose disappearing from the loops of duodenum, jejunum and ileum of rat small intestine by 82%, 84% and 85%, respectively. In contrast, treatment with rifampicin decreased the absorption of ranitidine by decreasing the percentage of total dose disappearing in duodenal, jejunal and ileal regions of the intestinal loops by 40%, 39% and 25%, respectively. Ranitidine was shown to be a P-gp substrate in vivo in human volunteers and it was found that oral bioavailability of ranitidine was influenced at the intestinal absorption phase.
Occupational asthma and allergy in the detergent industry: new developments (2002)

This review highlights the latest developments in the control of enzyme-induced occupational asthma and allergy (rhinitis and conjunctivitis) in the detergent industry. The industry has developed guidelines for the safe handling of enzymes in order to reduce the risk of occupational allergy and asthma. Those manufacturing facilities that follow all of the guidelines enjoy very low or no cases of asthma and allergy among workers exposed to enzymes. The key to the success of the management of enzyme-induced allergy and asthma is prospective surveillance for the development of enzyme-specific IgE antibody before the onset of allergic symptoms. This allows for continuing interventions to reduce exposures, so as to minimize or eliminate those associated with symptoms. Workers with IgE to enzymes can still continue to work in the industry symptom-free for their entire career. This indicates that exposures needed to induce sensitization are different and probably lower than exposures needed to elicit enzyme allergic symptoms. The experience of the detergent enzyme industry in controlling occupational allergens can be applied to other industries. The detergent enzyme story can be viewed as a model for the control of type 1 protein allergens in the workplace.
The application of perturbation methods to nonlinear problems in flight mechanics (1976)

Analytical-techniques are developed for deriving approximate&#13;\nsolutions to a class of problems that arise in nonlinear flight&#13;\nmechanics typically when an aeroplane is flying close to a stability&#13;\nboundary. The techniques are based on pertoz-bation methods and the&#13;\nmethod of multiple scales is used to correct for_nonuriformities&#13;\notherwise present in the asymptotic expai!,. 3ions. Applications are&#13;\nmainly concerned with the lateral dynamics of slender aircraft flying&#13;\nat high incidence. Approximations are derived for both linear and&#13;\nnonlinear lateral motions that serve to illustrate the importance of&#13;\nparticular parameters in the problem. For the linear theory the&#13;\napproximations are achieved by reducing the fourth order system to two.&#13;\nweakly coupled second order systems. The nonlinear theory is mainly&#13;\nconcerned with the effect of aerodynamic nonlinearity on the lateral&#13;\noscillation when the latter has marginal stability or instability, as&#13;\npredicted by the linear theory.&#13;\nThe analytic approximations are extended for use in the problem&#13;\nof estimating damping moments on aircraft in oscillatory motion. For&#13;\nthis purpose approximations are constructed for the logarithmic&#13;\ndecrement of a nonlinear oscillation that can be used to fit experimental&#13;\nmeasurements. Some thoughtis given to-the issue of memory effects in the&#13;\nrepresentation of aerodynamic forces and moments.
Editorial (2000)

Die endotracheale Intubation ist nach wie vor die häufigste Methode, die Atemwege im Rahmen einer Allgemeinanaesthesie zu sichern. In den meisten Fällen wird vor der Intubation die Narkose mit einem Hypnotikum, einem Opioid und einem Muskelrelaxans eingeleitet. Ein wesentliches Zielkriterium ist hierbei, ausreichende Intubationsbedingungen zu erzeugen, die alle durch Anästhetika beeinflußt werden. Dabei müssen direkte und indirekte Wirkungen unterschieden werden. Gute Intubationsbedingungen erzeugen Muskelrelaxantien primär über eine tiefe neuromuskuläre Blockade. Hypnotika über ihren zentralen Angriffspunkt im Sinne der Narkosetiefe und Opiate über die vegetative Dämpfung nach dem Intubationsstimulus. Neuere Studien haben jedoch gezeigt, daß die einzelnen Substanzen über ihre spezifischen Wirkprinzipien hinaus, die Intubationsbedingungen beeinflussen können. So vertiefen Hypnotika die neuromuskuläre Blockade über ihre Wirkung auf die neuromuskuläre Transmission. Andererseits können kardiozirkulatorische Effekte der Hypnotika und Opioide die Verteilung der Muskelrelaxantien hin zu ihrem Wirkort beeinträchtigen. Neben solchen Wechselwirkungen - also pharmakodynamischen und pharmokokinetischen Einflüssen der Substanzen auf die Intubationsbedindungen - ist das sogenannte „timing” der einzelnen Substanzen von Bedeutung. Um die Intubationsbedingungen zu optimieren, muß die maximale Wirkintensität der Substanz-Kombinationen zum Zeitpunkt der Laryngoskopie und Plazierung des endotrachealen Tubus ihr Maximum erreicht haben. Besondere Bedeutung erlangt die Optimierung des Zeitablaufs bei Patienten mit Aspirationsgefahr. Die allgemein anerkannte Forderung, daß zwischen Verlust der Schutzreflexe und endotrachealer Intubation ein Zeitraum von weniger als einer Minute vergehen darf, erfordert Substanzen mit entsprechend schnellem Wirkeintritt, aber auch ein klinisches Vorgehen, das die unterschiedlichen Anschlagzeiten berücksichtigt.
A Compact and Low Power Two-Axis Scanning Laser Rangerfinder for Mobile Robots (2000)

In this paper we present a prototype two-axis scanning laser rangefinder, or LIDAR, intended for use on small mobile robots.
Pharmacokinetic and metabolic parameters of tianeptine in healthy volunteers and in populations with risk factors. (1988)

Following oral administration in the fasting healthy subject, the mean maximum concentration of tianeptine is 334 +/- 79 ng/ml. Absorption of tianeptine from the tablet form is rapid and complete. Maximum plasma concentration is obtained by the first hour following administration (0.94 +/- 0.47 h). Absolute bioavailability is 99 +/- 29%. Tianeptine is thus rapidly and completely absorbed in the tablet form and is not subject to first-pass effect. Distribution of tianeptine in the body is characterized by the following: its rapidity, the mean distribution half-life being about 0.7 h; its limited extent, the apparent volume of distribution being about 0.8 L/kg (0.77 +/- 0.31 L/kg); and protein binding, which averages 93.8 +/- 2.4%. Elimination of tianeptine is characterized by a short mean half-life of 2 h 30 min (2.5 +/- 1.1 h) and by renal excretion of 0.4 ml/min (0.4 +/- 0.4 ml/min). Tianeptine is extensively metabolized. Major metabolites are analogs of tianeptine with a C5 and C3 lateral chain and a N-demethylated derivative. Studies have shown negligible influence on pharmacokinetic parameters of chronic alcoholism even in case of hepatic cirrhosis. In renal failure, and in the elderly, studies have revealed a 1-h prolongation of elimination half-life which suggests that the dosage should be limited to two tablets per day in such cases.
À‐trous wavelet transform‐based hybrid image fusion for face recognition using region classifiers (2018)

Abstract This paper presents a new hybrid fusion framework based on thermal and visible face images. Fusion of information is done here in two phases, first at the pixel level and then at the decision level. For the pixel level fusion process, à‐trous wavelet transform is applied on both the thermal and visible face images. In decision level fusion, 34 region classifiers, each concentrating on a specified region of the face image, are tested individually for their ability to identify a person from the face image. The region classifiers, which contribute significantly in recognizing the face image, are considered for decision level fusion using majority voting. All experiments have been conducted on the UGC‐JU face database and IRIS benchmark face database. The maximum recognition rate is about 97.22% for both the databases whereas decisions of 17 region classifiers among 34 are considered. Experimental results and comparative study show that the proposed fusion method provides a framework for recognition of face images in uncontrolled environments such as variations in illumination conditions, pose, and facial expressions.
The Effect of Histopathologic Analysis and Tissue Cultures on Inpatient Management of Cellulitis: a Randomized Control Trial (2022)

Abstract Background . In the absence of a gold-standard diagnostic modality for cellulitis, sterile inflammatory disorders may be misdiagnosed as cellulitis. Objective. To determine the utility of skin biopsy and tissue culture for the diagnosis and management of patients admitted with a diagnosis of cellulitis. Design . Pilot, single-blind parallel group randomized controlled clinical trial evaluating length of stay and antibiotic use in 56 patients with a primary diagnosis of cellulitis. Skin biopsy and tissue culture results were only reported in the intervention group. Corollary analysis of adipose tissue inflammation and structural changes in cellulitis. Results . Hospital length of stay showed the greatest opportunity for further study as a primary outcome (intervention: 4, IQR (2-6) vs control: 5 IQR (3-8) days; p = 0.124). In the corollary study, there were differentially expressed genes related to inflammation ( CD74 ), macrophage characterization ( CD14, MCP1, CD36) and extracellular matrix proteins ( VEGFA, FGF1, FGFR1/3, TIMP1, COL12A1 ) in the adipose tissue of chronic cellulitis patients. Limitations . Limited number of participants. Conclusion . The study demonstrated that hospital length of stay and anti-pseudomonal antibiotic de-escalation are endpoints worth further study. The corollary study demonstrated multiple inflammatory and structural genes that are upregulated in this disease process.
Lightning-Induced Voltages on Overhead Distribution Lines: Theoretical and Experimental Investigation of Related Problems and their Impact on Power Quality (2004)

Recent power quality studies have been focused on the source-identification of voltage disturbances at distribution network busses. This paper describes a method aimed at correlating indirect-lightning events with power systems relay operations, associated with voltage dips. The proposed method, based on the coordinated use of the Italian lightning location system CESI-SIRF, the Italian monitoring system of protection manoeuvres CESI-SAM, and the availability of an advanced simulation tool for the accurate simulation of lightning-induced voltages on complex power networks, namely the LIOV-EMTP code, is applied to the real case of an Italian distribution system.&#13;\nThe LIOV-EMTP code is also employed along with a statistical procedure based on the Monte Carlo method to carry out a statistical analysis aimed at assessing the lightning performance of a typical Italian distribution line.
The Effect of β-Hydroxy-β-Methylbutyrate on Growth, Mortality, and Carcass Qualities of Broiler Chickens (1994)

Experiments were conducted to determine whether the leucine catabolite beta-hydroxy-beta-methylbutyrate (HMB) could influence protein metabolism in broilers. In Experiment 1, HMB was fed at either .01 or .05% of the diet. beta-Hydroxy-beta-methylbutyrate did not improve feed conversion or BW gain; however, broilers fed HMB at .01% in a diet formulated to meet NRC (1984) recommendations had no mortality (P < .03) from 0 to 21 d of age. In Experiment 2, HMB fed at .003, .01, .03, and .09% of the diet had no significant affect on growth or carcass yield of the broilers when compared with control-fed broilers. In Experiment 3, HMB fed at .001, .003, and .01% of the diet had no effect on broiler growth. In Experiment 4, HMB was fed at .01% of the diet in combination with an antibiotic and coccidiostat (GP). Use of GP increased (P < .01) BW, feed conversion, and carcass yield when compared with the control broilers. In Experiment 5, HMB was fed at .1% of the diet, and effects of sex and GP were examined. beta-Hydroxy-beta-methylbutyrate decreased (P < .01) mortality by 72% in the male broilers. In a combined analysis, HMB fed at .01% of the diet (Experiments 1, 2, and 3) increased breast yield (P < .05) and reduced mortality by 56% (P < .04) from 0 to 21 d of age. In a combined analysis, HMB fed at .003% of the diet (Experiments 2 and 3) increased 42-d BW (P < .02) and hot (P < .04) and chilled (P < .05) carcass yields. In conclusion, across all HMB dosages mortality of male broilers was decreased from 6.37 to 4.39% (-31%, P < .04) by feeding HMB, with the pattern of death suggesting that HMB decreased the incidence of sudden death syndrome in these broilers.
Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State (2018)

Abstract The origin of substrate preference in promiscuous enzymes was investigated by enzyme isotope labelling of the alcohol dehydrogenase from Geobacillus stearothermophilus (BsADH). At physiological temperature, protein dynamic coupling to the reaction coordinate was insignificant. However, the extent of dynamic coupling was highly substrate‐dependent at lower temperatures. For benzyl alcohol, an enzyme isotope effect larger than unity was observed, whereas the enzyme isotope effect was close to unity for isopropanol. Frequency motion analysis on the transition states revealed that residues surrounding the active site undergo substantial displacement during catalysis for sterically bulky alcohols. BsADH prefers smaller substrates, which cause less protein friction along the reaction coordinate and reduced frequencies of dynamic recrossing. This hypothesis allows a prediction of the trend of enzyme isotope effects for a wide variety of substrates.
A method for modeling multiscale geomechanical effects in the stimulated rock volume (2020)

I have developed a workflow to efficiently simulate geomechanical effects in the stimulated rock volume (SRV) by including regional geologic structures such as faults and folds as well as high-resolution-oriented mechanical stratigraphy. The motivation is that the local model used for hydraulic fracture analysis should include macroscale 3D geomechanical effects derived from regional tectonic and seismic data. A practical computational strategy is developed to link multiple 3D geomechanical models derived at different scales and their associated stress effects. I apply the workflow to a synthetic reservoir problem composed of a tectonic-scale structural framework model with three embedded mechanical stratigraphic models representing three stimulated vertical wells. I first combine regional stresses solved with 3D finite-element analysis with perturbation stresses from elastic dislocation modeling using elastic superposition concepts. I then apply the macroscale stress effects as unique boundary conditions to an embedded finite-element submodel, a mesoscale stratigraphic model representing the SRV allowing for resolution of variable stress amplification, and stress rotation in geologic sublayers. Finally, I conduct hydraulic-fracture simulations within the SRV models. The simulated hydraulic fractures are controled by the structural position and mechanical stratigraphy. Closest to the back limb of the main structural anticline, hydraulic fractures tend to be height-restricted, and in some realizations, fractures propagate horizontally. Adjacent to the fold and a fault, where differential stresses are elevated, fracture growth is the most unconstrained in height and length. Results suggest that this multiscale approach can be applied to better predict and understand behaviors related to unconventional reservoir stimulation. The workflow could easily be modified for other operational problems and geologic settings.