gebhart/patrepeval huggingface dataset:
Pharmacological Inhibition of the ClpXP Protease Increases Bacterial Susceptibility to Host Cathelicidin Antimicrobial Peptides and Cell Envelope-Active Antibiotics (2012)

The ClpXP protease is a critical bacterial intracellular protease that regulates protein turnover in many bacterial species. Here we identified a pharmacological inhibitor of the ClpXP protease, F2, and evaluated its action in Bacillus anthracis and Staphylococcus aureus. We found that F2 exhibited synergistic antimicrobial activity with cathelicidin antimicrobial peptides and antibiotics that target the cell well and/or cell membrane, such as penicillin and daptomycin, in B. anthracis and drug-resistant strains of S. aureus. ClpXP inhibition represents a novel therapeutic strategy to simultaneously sensitize pathogenic bacteria to host defenses and pharmaceutical antibiotics.
Inhibitory Effects of Phyllanthus amarus and Its Major Lignans on Human Microsomal Cytochrome P450 Activities: Evidence for CYP3A4 Mechanism-Based Inhibition (2010)

Phyllanthus amarus has long been used as a herbal medicine in several countries. Phytochemicals in herbal medicine may interact with cytochromes P450 (CYP) and thus raise the potential of herb-drug interactions; therefore, the inhibitory effects of P. amarus and its major phytochemicals phyllanthin and hypophyllanthin on CYP isoforms were determined using human liver microsomes and selective substrates. Both ethanolic and aqueous extracts of P. amarus inhibited CYP1A2, CYP2D6, CYP2E1 and CYP3A4 in a dose-dependent manner. Compared to known CYP3A inhibitors, the IC(50) values of the ethanolic and aqueous extracts on testosterone 6β-hydroxylation were higher than that of ketoconazole but were lower than those of erythromycin and clarithromycin. Both extracts were weak inhibitors of CYP1A2, CYP2D6 and CYP2E1. In addition, phyllanthin and hypophyllanthin were potent mechanism-based inhibitors of CYP3A4 with K(I) values of 1.75 ± 1.20 µM and 2.24 ± 1.84 µM and k(inact) values of 0.18 ± 0.05 min(-1) and 0.15 ± 0.06 min(-1), respectively. The k(inact)/K(I) ratios of these lignans were higher than those reported for some therapeutic drugs that act as mechanism-based inhibitors of CYP3A4. These results suggest that co-administration of P. amarus with drugs that are metabolized by CYP3A4 may potentially result in herb-drug interactions.
Energy harvesting analysis for Moball, A self-propelled mobile sensor platform capable of long duration operation in harsh terrains (2014)

This paper considers the design and optimization of an autonomous electromechanical control and energy scavenging system for the wind-propelled Moball, a spherical mobile sensor platform concept [1, 2]. This mechanism converts mechanical motion to electrical energy, and the same mechanism can function as an actuator to self-generate motion. Simulations of a simplified model on flat ground show that a 2m diameter Moball operating in typical Arctic conditions can generate 1. 8-2.7W of power continuously while being wind-propelled. We also demonstrate a simple motion control algorithm, showing that self-propulsion in windless conditions requires 1-1.5W. Hence, using this mechanism, a Moball can self-generate sufficient energy for long duration missions involving self-propulsion, sensing, and communication in harsh, cold, windy climates (e.g., Polar regions on Earth, or the surface of Titan or Mars) where solar energy may be limited. Simulations with key design parameters are also used to draw general conclusions regarding optimal design for energy recovery. The addition of springs inside the generating mechanism greatly increases the range of wind speeds over which Moball can harvest energy.
Wideband array antenna concept (2005)

This paper presents a unique wideband array concept that includes a wideband array aperture incorporating radiating elements of different sizes and inter-element spacings. The array is a fully-filled aperture consisting of a core region surrounded by several layers of radiating elements which increase in size. By proper selection of the core region and the number of layers, one can form a beam with specified beamwidth over a five to one frequency range. The proposed concept considerably reduces the cost and complexity by decreasing the effective number of radiating elements and the corresponding receive or transmit modules. Numerical simulation results, ignoring the mutual coupling effects, are presented for array patterns at several frequencies to prove the concept. A possible beamforming concept is also included. Additional work is planned to prove the viability of the concept by taking the mutual coupling into account.
Approaches and Resources for Prediction of the Effects of Non-Synonymous Single Nucleotide Polymorphism on Protein Function and Interactions (2008)

Almost all (99.9%) nucleotide bases are exactly the same in all people, however, the remaining 0.1% account for about 1.4 million locations where single-base DNA differences/polymorphisms (SNPs) occur in humans. Some of these SNPs, called non-synonymous SNPs (nsSNPs), result in a change of the amino acid sequences of the corresponding proteins affecting protein functions and interactions. This review summarizes the plausible mechanisms that nsSNPs may affect the normal cellular function. It outlines the approaches that have been developed in the past to predict the effects caused by nsSNPs with special emphasis on the methods that use structural information. The review provides systematic information on the available resources for predicting the effects of nsSNPs and includes a comprehensive list of existing SNP databases and their features. While nsSNPs resulting in amino acid substitution in the core of a protein may affect protein stability irreversibly, the effect of an nsSNP resulting to a mutation at the surface of a protein or at the interface of protein-protein complexes, could, in principle be, subject of drug therapy. The importance of understanding the effects caused by nsSNP mutations at the protein-protein and protein-DNA interfaces is outlined.
Collection of breath for hydrogen estimation. (1981)

The breath hydrogen test is used in gastroenterological investigation, particularly for sugar malabsorption, transit time, and the investigation of small-bowel bacterial overgrowth. Several methods of collecting breath from infants and children for hydrogen assay have been described. Four such techniques (postnasal catheter, nasal prong, Rahn-Otis end-tidal sampler, and modification of a party toy--the 'Wiggins's blowout') were compared with breath collection using the Haldane-Priestley tube. Multiple sampling of breath from 3 adults was performed after initial lactulose loads to increase breath hydrogen excretion. The variability between the different assay techniques was less than the inherent variability of repeated breath hydrogen assays using the same technique. Each technique is therefore adequate for breath hydrogen collection; we recommend the Rahn-Otis end-tidal sampler in young infants and children, and the Haldane-Priestley tube in older children, since these were most acceptable to the children and their parents.
A framework for inverse planning of beam-on times for 3D small animal radiotherapy using interactive multi-objective optimisation (2015)

Advances in precision small animal radiotherapy hardware enable the delivery of increasingly complicated dose distributions on the millimeter scale. Manual creation and evaluation of treatment plans becomes difficult or even infeasible with an increasing number of degrees of freedom for dose delivery and available image data. The goal of this work is to develop an optimisation model that determines beam-on times for a given beam configuration, and to assess the feasibility and benefits of an automated treatment planning system for small animal radiotherapy. The developed model determines a Pareto optimal solution using operator-defined weights for a multiple-objective treatment planning problem. An interactive approach allows the planner to navigate towards, and to select the Pareto optimal treatment plan that yields the most preferred trade-off of the conflicting objectives. This model was evaluated using four small animal cases based on cone-beam computed tomography images. Resulting treatment plan quality was compared to the quality of manually optimised treatment plans using dose-volume histograms and metrics. Results show that the developed framework is well capable of optimising beam-on times for 3D dose distributions and offers several advantages over manual treatment plan optimisation. For all cases but the simple flank tumour case, a similar amount of time was needed for manual and automated beam-on time optimisation. In this time frame, manual optimisation generates a single treatment plan, while the inverse planning system yields a set of Pareto optimal solutions which provides quantitative insight on the sensitivity of conflicting objectives. Treatment planning automation decreases the dependence on operator experience and allows for the use of class solutions for similar treatment scenarios. This can shorten the time required for treatment planning and therefore increase animal throughput. In addition, this can improve treatment standardisation and comparability of research data within studies and among different institutes.
Smart Contract-Based Car Insurance Policies (2018)

Processes in the insurance economy are often cumbersome and expensive because of the inherently opposing interests of insurers and customers. Smart contracts bear a large potential to simplify these processes and thereby reduce costs. In this paper, we present CAIPY, our smart contract-based ecosystem for simple and transparent car insurance. In CAIPY, smart contracts do not replace but support current processes to enable significant cost savings, e.g., by removing the necessity for manual inspection of insurance claims in presence of tamper-resistant car sensors. However, the involved parties can resort to well-established processes at any time, trading off cost efficiency against process reliability. CAIPY thus showcases how smart contracts can support insurers without introducing new risks.
Technical report Automated scoring of micronuclei in binucleated human lymphocytes (1996)

Manual and automatic scoring of micronuclei (MN) in binucleated human lymphocytes (BNC) were compared after irradiation of whole blood samples. The blood samples were irradiated with X-ray doses (1, 2 or 3 Gy) and stained with Giemsa. The preparation technique was optimized in such a way that acceptable conditions (cell density, contrast) were obtained for both scoring procedures. To estimate the quality of automatic micronucleus detection, two researchers who had different experience in scoring MN (6 months and 5 years) analysed the samples independently from each other. Automatic scoring was carried out with a digital image analysis system and the recognition procedure was divided into two parts. The BNC positions were detected with low microscope magnification (100x), and the recognition of micronuclei within the cytoplasm of the classified BNC was carried out at high magnification (630x). A fuzzy logic classification system as well as two different segmentation steps (preclassification and postclassification) made it possible that about 94% of all automatically recognized BNC were classified correctly). On the other hand, the classification system was optimized in such a way that false positive decisions were minimized (95% of automatically recognized micronuclei were classified correctly). Failure to recognize micronuclei (8.5%-25% false negatives) was mainly due to extremely small micronuclei, poor contrast with respect to the cytoplasm, and aggregation of micronuclei especially at higher doses.
Videopot: Indexing-Based Desktop Video Search System (2006)

We present videopot, a desktop video search system designed for digital video files stored on personal computers. The core metric of this system is based on video-indexing technology and an automatic related-term collection framework. Digital files on local disks are crawled, and images of representative scenes are extracted from video files using video-indexing technology. Related terms, used as target information in the video search, are collected from both local files and Web pages using an automatic related-term collection algorithm. These images and terms are then stored in the metadata database. We describe a unique search result interface that helps users distinguish the target video. In the search results interface, the results of the video search are listed at two levels to let users search videos faster. The effectiveness of images on our interface derived from video-indexing is evaluated through a comparison with a conventional file search application
Synthesis and Characterization of Novel Hydroxyalkyl Carbamate and Dihydroxyalkyl Carbamate Terminated Poly(dimethylsiloxane) Oligomers and Their Block Copolymers with Poly(ε-caprolactone) (2006)

Novel hydroxyalkyl carbamate, dihydroxyalkyl carbamate terminated poly(dimethylsiloxane) (PDMS) oligomers, and carbamate-linked block copolymers with poly(ε-caprolactone) (PCL) were designed, synthesized, and characterized using combinatorial and high-throughput experimentation (CHTE). Novel hydroxyalkyl carbamate terminated PDMS oligomers were synthesized by reacting 3-aminopropyl terminated PDMS oligomers with ethylene carbonate (EC); further reaction of these oligomers with ε-caprolactone (ε-CL) resulted in novel carbamate-linked PCL−PDMS−PCL triblock copolymers. Novel dihydroxyalkyl carbamate terminated PDMS oligomers were synthesized by reacting 3-aminopropyl terminated PDMS with glycerine carbonate (GC); further reaction of these oligomers with ε-CL resulted in novel H-type block copolymers of PDMS and PCL. Structural characterization of the synthesized oligomers and block copolymers was carried out with high-throughput FTIR, DSC, and NMR. Molecular weights of the oligomers and block copolymers were characterized using Rapid GPC.
Effects of phosphatidylserine in Alzheimer's disease. (1992)

We studied 51 patients meeting clinical criteria for probable Alzheimer's disease (AD). Patients were treated for 12 weeks with a formulation of bovine cortex phosphatidylserine (BC-PS; 100 mg t.i.d.) or placebo, and those treated with the drug improved on several cognitive measures relative to those administered placebo. Differences between treatment groups were most apparent among patients with less severe cognitive impairment. Results suggest that phosphatidylserine may be a promising candidate for study in the early stages of AD.
Stochastic Nodal Analysis: EnKF and PF applied to petroleum production systems (2017)

A petroleum production system is generally modelled based on the concept of nodal analysis, where the entire system is broken down into discrete elements such as near-well bore, tubing, surface choke and flow line. Operating flow rates and pressures can be estimated with a nodal analysis procedure by calculation of the intersection of performance curves. Input parameters in nodal analysis of production systems are considered deterministic, however, some of these parameters are better represented as distributions. In this report, the ensemble-based data assimilation methods “ensemble Kalman filter” (EnKF) and “particle filter” (PF) are applied to steady-state models of a production system for tuning of uncertain model parameters during the test separator phase. The performance of the EnKF and the PF is tested with the use of twin experiments. The calibrated model parameters of the choke, tubing and the near-well bore elements with EnKF and PF can be used to create an ensemble of performance curves leading to an ensemble of operating flow rates and pressures. The foreseen next step is to use the posterior distributions of model parameters as inputs for soft sensing of flow rates during semi-steady-state production for a single phase oil reservoir, where the oil rate and reservoir pressure are considered as unknown parameters. In the twin experiments as used in this thesis, a total number of three steady-state pressure drop measurements was used to estimate a total of six independent parameters which constitutes an ill-posed problem, resulting in non-unique parameter estimates. It is recommended to alleviate this issue by either reducing the number of parameters or by using multiple separator tests at different flow rates.
Semisynthesis of SY-1 for Investigation of Breast Cancer Stem Cell Selectivity of C-Ring-Modified Salinomycin Analogues (2014)

Salinomycin, a naturally occurring polyether ionophore was recently found to selectively reduce the proportion of CD44(+)/CD24(-) cells, a phenotype associated with breast cancer stem cells. Subsequent studies from our group showed that chemical modification of the allylic C20 hydroxyl of salinomycin, located at the C-ring, can enhance the activity of derivatives against breast cancer cells over 5-fold compared to the native structure. Access to C-ring-modified salinomycin analogues is thus of interest from both a mechanistic and a synthetic perspective. Here, we report efficient strategies for gram scale synthesis of the natural product SY-1 (20-deoxy salinomycin), and a saturated analogue, 18,19-dihydro SY-1, for a comparative in vitro investigation of the biological profiles of these compounds with that of salinomycin. Across several assays, the deoxygenated structures required higher concentrations to elicit similar cellular responses to that of salinomycin. Similarly to salinomycin, SY-1 or 18,19-dihydro SY-1 treatment was found to reduce the proportion of CD44(+)/CD24(-) cells with essentially complete selectivity up to ∼IC25. Importantly, the proportion of CD44(+)/CD24(-) cells showed a pronounced U-shaped dose response curve for salinomycin and its derivatives, but not for paclitaxel. The concentration for maximum response in this assay followed differences in IC50 for salinomycin and its analogues, which emphasizes the importance of taking concentration dependence into account when comparing effects on the CD44(+)/CD24(-) phenotype. Small differences in the global conformation within the triad of compounds investigated together with differences in activity across assays emphasize the importance of substitution at C20 for the activity of salinomycin and its derivatives.
Oxydation des aldéhydes par le chlorite de sodium (1990)

Le chlorite de sodium est un reactif tres efficace d'oxydation des aldehydes en acides correspondants. Les reactions se font a temperature ambiante dans une solution dichloromethane-acide acetique pour tous les aldehydes, excepte pour les salicyladehydes. Nous montrons que ceux-ci peuvent etre oxydes dans une solution DMSO-methanolate de sodium. Les rendements en acide sont bons, meme pour les aldehydes aromatiques possedant des groupements electro-donneurs
Computational modeling of cardiovascular response to orthostatic stress (2002)

The objective of this study is to develop a model of the cardiovascular system capable of simulating the short-term (< or = 5 min) transient and steady-state hemodynamic responses to head-up tilt and lower body negative pressure. The model consists of a closed-loop lumped-parameter representation of the circulation connected to set-point models of the arterial and cardiopulmonary baroreflexes. Model parameters are largely based on literature values. Model verification was performed by comparing the simulation output under baseline conditions and at different levels of orthostatic stress to sets of population-averaged hemodynamic data reported in the literature. On the basis of experimental evidence, we adjusted some model parameters to simulate experimental data. Orthostatic stress simulations are not statistically different from experimental data (two-sided test of significance with Bonferroni adjustment for multiple comparisons). Transient response characteristics of heart rate to tilt also compare well with reported data. A case study is presented on how the model is intended to be used in the future to investigate the effects of post-spaceflight orthostatic intolerance.
A New Multi-Path Routing Methodology Based on Logit Type Assignment (2009)

We present a new multi-path routing methodology called MLB-routing based on multinomial logit model, which is well known as the random utility theory. The key concept of the study is to incorporate multiple paths from same origin to destination, and distribute packets followed by the multinomial logit type probability. Since MLB-routing is pure multi-path routing, it reduce the severe convergence to same links and increases the bandwidth utilization in the network. Compared to the existing multi-path routing schemes that select pre-determined alternate paths, the proposed method can dynamically distribute packets to every possible paths and thus is more efficient than them. Furthermore, it should be mentioned that this methodology could be implemented as both link-state protocol and distance-vector protocol. Therefore, it has enough affinity for present Internet mechanism. Using simulations, we have also shown that this methodology produces more efficient use of network and causes significant improvements in end-to-end delays and jitter times.
Terahertz absorption and dispersion of fluorine-doped single-walled carbon nanotube (2005)

We present experimental and theoretical results on the absorption and dispersion of a single-walled carbon nanotube (SWNT) with and without fluorine (F) doping in the frequency range of 0.2–3THz. Under the doping conditions, the power absorption, index of refraction, and the real and imaginary parts of the conductivity are decreased compared to those for pure SWNTs because the charge transfer to the F2 molecule will be increased. Our measurement of pure SWNT agrees well with the Maxwell-Garnett and Drude models. However, the F-doped SWNT requires adding a Lorentz oscillator term for good agreement between theory and measurement.
A Comprehensive Solution for Deterministic Replay Debugging of SoftPLC Applications (2011)

Deterministic replay debugging is an approach to finding bugs in deployed software. It records an application run in the field so that it can deterministically be replayed offline in a development system for debugging purposes. To enable deterministic replay debugging, it is necessary to record all external influences and sources of nondeterminism in the original program run. From that trace log and from a known initial state, the program can be replayed deterministically without requiring any connection to the original environment. In this paper, we present a solution for deterministic replay debugging of hard real-time multitasking SoftPLC applications written in the IEC 61131-3 languages. By taking advantage of the special properties of these programs and by careful engineering, our technique allows recording a SoftPLC application run in the field with minimal overhead and obeying real-time constraints. In later phases, which are offline, the original program run is reconstructed from the minimal information recorded so it can be replayed for debugging. In comparison to previous work, our solution has several advantages: Instead of recording task scheduling information, it reconstructs the task interleaving based on data dependencies, thereby significantly simplifying the recording phase. Additionally, it incorporates a technique for periodically capturing the complete internal state of the system, which can later be used as a starting point for replay. We present the conceptual basis of our approach, a tool chain which provides deterministic replay debugging to the user as a set of fully automated tools, and an evaluation as well as an industrial case study for validating the approach.
Peripheral corticotropin releasing hormone mediates post-inflammatory visceral hypersensitivity in rats (2008)

These results suggest that increased peripheral CRH mediates the enhanced visceral nociception in rats recovered from experimental colitis.