gebhart/patrepeval huggingface dataset:
Kinetic model of sugar diffusion from sugar beet tissue treated by pulsed electric field (2004)

Abstract Extraction of sugar from sugar beet slices was studied following various pulsed electric field (PEF) treatments (intensities from 300 to 800 V cm −1 and number of pulses varying between 50 and 1000). Slices treated by PEF were immersed in water at ambient temperature at a liquid/solid ratio of 3. A significant increase in extraction yield was observed. This enhancement was due to permeabilisation of the cellular membrane and to the additional quantity of juice appearing on the surface of slices after PEF treatment being extracted rapidly by convection. The optimal conditions of PEF treatment were an intensity of 670 V cm −1 and 250 pulses. The extraction kinetics was studied on the basis of two approaches: Fick's diffusion equation and a two‐exponential kinetic model. The coefficient of diffusion was only slightly influenced by the conditions of PEF treatment. The two‐exponential model successfully described both the rapid and prolonged stages of extraction. By heating the solution at mild temperatures of 30–50 °C, the coefficient of diffusion was increased and the kinetics of extraction was enhanced. The quality of cellular juice obtained after PEF treatment was higher than that of juice obtained after thermal pretreatment at 75 °C. Copyright © 2004 Society of Chemical Industry
<title>SAR image construction from periodically gapped phase-history data</title> (2002)

It is known that high-resolution synthetic aperture radar (SAR) imaging can be cast as a spectral analysis problem, and consequently a number of sophisticated spectral estimation methods have been applied to SAR imaging. These method include the classical Capon method and the closely related Amplitude and Phase Estimation (APES) algorithm. In this paper, we show how Capon and APES can be extended to deal with spectral analysis of periodically gapped (PG) data, i.e. data where samples are missing in a periodic fashion. This problem is highly relevant for SAR imaging with angular diversity since in that case the measured phase-history data matrix contains missing columns. Our extension of Capon and APES is based on a transform that maps a one-dimensional (1D) periodically gapped time-series into a uniformly sampled two-dimensional (2D) data set. We show that the stationarity properties of the 1D signal are left unchanged by the transformation, and as a result the conventional 2D Capon and APES methods can be applied to the transformed data. An associated inverse transform is used to extract the 1D spectral estimate from the 2D one. The new method is computationally and conceptually non-intricate and it does not involve any interpolation of the missing data. Despite its striking simplicity, numerical results indicate that the new method can be a promising tool for SAR imaging with angular diversity as well as for time-series analysis. In SAR applications, the new method may be particularly suitable for accurate imaging of a small region of interest.
<title>Multiplexed optical fiber Fabry-Perot sensors for strain metrology</title> (1999)

The authors demonstrate that several optical fiber Fabry-Perot sensors can be multiplexed in series for axial strain monitoring at each individual sensor. White light interferometry was employed using the laser-referenced Michelson interferometer of a standard Fourier transform spectrometer as a receiving (interrogating) interferometer. The primary aim was to demonstrate that at least six fiber Fabry-Perot transducer interferometers (sensors) can be multiplexed in series provided that each sensor has a unique optical cavity length within the multiplex. The resulting differing optical path differences at each fiber Fabry-Perot sensor give rise to sharp correlation features (side-bursts) at unique positions in the time domain as observed in the interferogram. An optical cavity length change due to an axial strain perturbation is observed as a change in the position in the time-domain of the side-burst feature associated with the fiber Fabry-Perot sensor. This paper demonstrates that multiplexed strain metrology in the quasi-static regime using fiber Fabry-Perot sensors is possible with a measurement range of typically 0 to 4000 microstrain and a strain resolution of better than 10 microstrain.
ETR/ITER systems code (1988)

A tokamak systems code capable of modeling experimental test reactors has been developed and is described in this document. The code, named TETRA (for Tokamak Engineering Test Reactor Analysis), consists of a series of modules, each describing a tokamak system or component, controlled by an optimizer/driver. This code development was a national effort in that the modules were contributed by members of the fusion community and integrated into a code by the Fusion Engineering Design Center. The code has been checked out on the Cray computers at the National Magnetic Fusion Energy Computing Center and has satisfactorily simulated the Tokamak Ignition/Burn Experimental Reactor II (TIBER) design. A feature of this code is the ability to perform optimization studies through the use of a numerical software package, which iterates prescribed variables to satisfy a set of prescribed equations or constraints. This code will be used to perform sensitivity studies for the proposed International Thermonuclear Experimental Reactor (ITER). 22 figs., 29 tabs.
A New Model of Protein Adsorption Kinetics Derived from Simultaneous Measurement of Mass Loading and Changes in Surface Energy (2007)

We describe a novel technology based on changes in the resonant frequency of an acoustically actuated surface and use it to measure temporal changes in the surface energy gamma (N m(-1)) of an elastomeric polymer membrane due to the adsorption of macromolecules from aqueous solution. The resonant elastomeric surface-tension (REST) sensor permits simultaneous determination of mass loading kinetics and gamma(t) for a given adsorption process, thereby providing a multivariable data set from which to build and test models of the kinetics of adsorption at solid-liquid interfaces. The technique is used to measure gamma(t) during the adsorption of either sodium dodecyl sulfate (SDS) or hen egg-white lysozyme (HEWL) onto an acrylic polymer membrane. The adsorption of SDS is reversible and is characterized by a decrease in gamma over a time period that coincides with that required for the mass loading of the membrane. For the adsorption of HEWL labeled with Alexa Fluor 532 dye, gamma continues to change long after the surface concentration of labeled HEWL, measured by using the elastomeric polymer membrane as an optical waveguide, reaches steady state. Gradual but significant changes in gamma(t) are observed as long as the concentration of protein in the bulk solution, c(b), remains nonzero. HEWL remains adsorbed to the membrane when c(b) = 0, but changes in gamma(t) are not observed under this condition, indicating that the interaction of bound protein molecules with those free in solution contribute to the prolonged change in the surface energy. This observation has been used to define a new model for the kinetics of globular protein adsorption to a solid-liquid interface that includes a mechanism by which the molecules in the bulk can facilitate the desorption of a sorbate molecule or change the energetic states of adsorbed molecules and, thus, the overall surface energy. The model is shown to capture the unique features of protein adsorption kinetics, including the relatively fast mass loading, the much more gradual change in surface energy that does not cease until the protein is removed from the bulk, the rapid desorption of an incubation-time-dependent fraction of bound protein when the protein is removed from the bulk, and the fixing of the residual surface concentration and surface energy at constant values once the removal of reversibly bound protein and free protein is complete.
Semitransparent Organic Photovoltaic Cells with Laminated Top Electrode (2008)

We demonstrate semitransparent small molecular weight organic photovoltaic cells using a laminated silver nanowire mesh as a transparent, conductive cathode layer. The lamination process does not damage the underlying solar cell and results in a transparent electrode with low sheet resistance and high optical transmittance without impacting photocurrent collection. The resulting semitransparent phthalocyanine/fullerene organic solar cell has a power conversion efficiency that is 57% of that of a device with a conventional metal cathode due to differences in optical absorption.
1248. Genomic Sequencing and Clinical Data Integration for Next-Generation Infection Prevention (2018)

Abstract Background Typical Infection Prevention to detect pathogen transmission in hospitals has relied on observation of (1) uncommon pathogen phenotypes or (2) greater than expected number of pathogen phenotypes in a given timeframe and/or location. Genome sequencing of targeted organisms in conjunction with routine patient geo-temporal information and antibiotic susceptibility data holds promise in identifying transmissions with greater sensitivity and specificity, saving time and effort in reviewing for transmission events. Methods In an on-going genomic sequencing surveillance effort in a tertiary care hospital, drug-resistant clinical isolates from the “ESKAPE” pathogens were routinely sequenced in 2017. In parallel, potential clusters were identified for 2017 through conventional Infection Prevention approaches. Groups identified by their genetic distances along with visualizations on antimicrobial susceptibilities, and patient location histories and dates were displayed in an interactive interface, Philips IntelliSpace Epidemiology (PIE), and reviewed by Infection Prevention. Results Among 656 patients, 1,239 drug-resistant ESKAPE samples were sequenced. Thirty-eight genetically related groups involving 196 patients were identified. Groups ranged in size from two to 44 patients, primarily consisting of VRE and MRSA. Notably, a review of the 38 groups identified 20 groups where the information at hand suggested a concern for transmission. 16 of the 20 were not previously identified by Infection Prevention. Using PIE to review all 38 groups identified from 1 year’s worth of data required 3 hours of time by an Infection Prevention professional, averaging less than 5 minutes per cluster, less than 1 minute per patient, and 11 minutes of review time per actionable opportunity. By conventional means, approximately 23 hours would have been required to review the genomic groups without the aid of the PIE tool. Conclusion The use of PIE’s genomic-defined groups, along with the integrated clinical data platform, allows for a greater ability, certainty, and speed to detect clusters of organisms representing transmission in the hospital setting. Applied prospectively, PIE can detect transmissions sooner than by conventional means for potential patient safety gains and cost savings. Disclosures D. Chen, Philips: Scientific Advisor, Consulting fee. M. Fortunato-Habib, Philips Healthcare: Collaborator and Employee, Salary. A. Hoss, Philips: Employee, Salary. R. Kolde, Philips: Employee, Salary. A. Dhand, Merck: Speaker’s Bureau, Speaker honorarium. Astellas: Scientific Advisor, Consulting fee. R. Sussner, Philips: Scientific Advisor, Consulting fee. J. Carmona, Philips Healthcare: Employee, Salary. B. Gross, Philips Healthcare: Employee, Investigator, Research Contractor, Scientific Advisor and Shareholder, Salary. J. Fallon, Philips Healthcare: Investigator, Research support.
Interleukin-12 Promotes Gamma Interferon-Dependent Neutrophil Recruitment in the Lung and Improves Protection against Respiratory Streptococcus pneumoniae Infection (2007)

The ability of exogenous interleukin-12 (IL-12) to elicit protective innate immune responses against the extracellular pathogen Streptococcus pneumoniae was tested by infecting BALB/c mice intranasally (i.n.) with S. pneumoniae after i.n. administration of IL-12. It was found that administration of IL-12 resulted in lower bacterial burdens in the infected mice and significantly improved survival rates. All IL-12-treated mice contained higher levels of pulmonary gamma interferon (IFN-gamma) after infection and significantly more neutrophils than infected mice not treated with IL-12. IFN-gamma was found to be essential for IL-12-induced resistance and for neutrophil influx into the lungs, and the observed changes correlated with increased levels of the IL-8 homologue keratinocyte-derived chemokine (KC). In addition, in vitro tumor necrosis factor alpha (TNF-alpha) production by alveolar macrophages stimulated with heat-killed pneumococci was enhanced by IFN-gamma, and TNF-alpha in turn could enhance production of KC by lung cells. Finally, IL-12-induced protection was dependent upon the presence of neutrophils and the KC receptor CXCR2. Taken together, the results indicate that exogenous IL-12 can improve innate defense in the lung against S. pneumoniae by inducing IFN-gamma production, which in turn enhances chemokine expression, and promotes pulmonary neutrophil recruitment into the infected lung. The findings show that IL-12 and IFN-gamma can mediate a protective effect against respiratory infection caused by extracellular bacterial pathogens.
Experimental superposition of time directions (2022)

Experimental dataset for "Experimental superposition of time directions"
LL18-ML-3rdGenScint-PD3Jg_PM Answers (2018)

The project has two major technical objectives: a) Development of plastic scintillators with ultra-fast decays for fast neutron detection and imaging with: Light Output (LO) on the level of best commercial plastics (e.g. EJ-200), and Scintillation decay times <1 ns; b) Development of 6Li-loaded organic scintillators for simultaneous detection of fast and thermal neutrons discriminated from gammaray background with the goal is to achieve large gamma-neutron Pulse Shape Discrimination Figures of Merit (PSD FOM) ~4.5 in crystals and ~3.5 in plastics at the light output range of the thermal capture.
Regulatory network of acid resistance genes in Escherichia coli (2003)

Overexpression of the response regulator EvgA confers an acid-resistant phenotype to exponentially growing Escherichia coli. This acid resistance is partially abolished by deletion of ydeP, yhiE or ydeO, genes induced by EvgA overexpression. Microarray analysis identified two classes of operons (genes). The first class contains seven operons induced by EvgA overexpression in the absence of ydeO, an AraC/XylS regulator gene. The second class contains 12 operons induced by YdeO overexpression. Operons in the second class were induced by EvgA overexpression only in the presence of ydeO. EvgA is likely to directly upregulate operons in the first class, and indirectly upregulate operons in the second class via YdeO. Analysis using the motif-finding program alignace identified an 18 bp inverted repeat motif in six upstream regions of all seven operons directly regulated by EvgA. Gel mobility shift assays showed the specific binding of EvgA to the six sequences. Introduction of mutations into the inverted repeats upstream of ydeP and b1500-ydeO resulted in reduction in EvgA-induced ydeP and ydeO expression and acid resistance. These results suggest that EvgA binds to the inverted repeats and upregulates the downstream genes. Overexpression of YdeP, YdeO and YhiE conferred acid resistance to exponentially growing cells, whereas GadX overexpression did not. Microarray analysis also identified several GadX-activated genes. Several genes induced by overexpression of YdeO and GadX overlapped; however, yhiE was induced only by YdeO. The acid resistance induced by YdeO overexpression was abolished by deletion of yhiE, gadC, slp-yhiF, hdeA or hdeD, genes induced by YdeO overexpression, suggesting that several genes orchestrate YdeO-induced acid resistance. We propose a model of the regulatory network of the acid resistance genes.
Phase behavior of colloidal superballs: Shape interpolation from spheres to cubes (2010)

The phase behavior of hard superballs is examined using molecular dynamics within a deformable periodic simulation box. A superball's interior is defined by the inequality |x|(2q)+|y|(2q)+|z|(2q)≤1 , which provides a versatile family of convex particles (q≥0.5) with cubelike and octahedronlike shapes as well as concave particles (q<0.5) with octahedronlike shapes. Here, we consider the convex case with a deformation parameter q between the sphere point (q=1) and the cube (q=∞). We find that the asphericity plays a significant role in the extent of cubatic ordering of both the liquid and crystal phases. Calculation of the first few virial coefficients shows that superballs that are visually similar to cubes can have low-density equations of state closer to spheres than to cubes. Dense liquids of superballs display cubatic orientational order that extends over several particle lengths only for large q. Along the ordered, high-density equation of state, superballs with 1<q<3 exhibit clear evidence of a phase transition from a crystal state to a state with reduced long-ranged orientational order upon the reduction of density. For q≥3 , long-ranged orientational order persists until the melting transition. The width of the apparent coexistence region between the liquid and ordered, high-density phase decreases with q up to q=4.0. The structures of the high-density phases are examined using certain order parameters, distribution functions, and orientational correlation functions. We also find that a fixed simulation cell induces artificial phase transitions that are out of equilibrium. Current fabrication techniques allow for the synthesis of colloidal superballs and thus the phase behavior of such systems can be investigated experimentally.
Rational Design of a Humanized Glucagon‐Like Peptide‐1 Receptor Agonist Antibody (2014)

Abstract Bovine antibody BLV1H12 possesses a unique “stalk–knob” architecture in its ultralong heavy chain CDR3, allowing substitutions of the “knob” domain with protein agonists to generate functional antibody chimeras. We have generated a humanized glucagon‐like peptide‐1 (GLP‐1) receptor agonist antibody by first introducing a coiled‐coil “stalk” into CDR3H of the antibody herceptin. Exendin‐4 (Ex‐4), a GLP‐1 receptor agonist, was then fused to the engineered stalk with flexible linkers, and a Factor Xa cleavage site was inserted immediately in front of Ex‐4 to allow release of the N‐terminus of the fused peptide. The resulting clipped herceptin–Ex‐4 fusion protein is more potent in vitro in activating GLP‐1 receptors than the Ex‐4 peptide. The clipped herceptin–Ex‐4 has an extended plasma half‐life of approximately four days and sustained control of blood glucose levels for more than a week in mice. This work provides a novel approach to the development of human or humanized agonist antibodies as therapeutics.
Supplementary Figures S1-S4 from Ubiquitin Proteasome System Stress Underlies Synergistic Killing of Ovarian Cancer Cells by Bortezomib and a Novel HDAC6 Inhibitor (2023)

Supplementary Figures S1-S4 from Ubiquitin Proteasome System Stress Underlies Synergistic Killing of Ovarian Cancer Cells by Bortezomib and a Novel HDAC6 Inhibitor
A carbohydrate approach for the formal total synthesis of (−)-aspergillide C (2014)

An enantioselective formal total synthesis of aspergillide C is accomplished using commercially available tri-O-acetyl-D-galactal employing a Ferrier-type C-glycosylation, utilizing a Trost hydrosilylation and protodesilylation as key reactions.
Improved accuracy of myocardial blood flow quantification by first pass perfusion MR when corrected for steady state T1 relaxation (2013)

Quantification of myocardial blood flow (MBF) on first-pass dynamic contrast enhanced (DCE ) MR perfusion imaging has been performed by several different methods. However MBF estimates are dependent on the analysis model used, as the absolute concentration of the contrast agent during first pass is not known. To improve the accuracy of the MBF estimates calibration is required. We propose a novel approach for the quantification of MBF based on patient-specific calibration using steady state T1 relaxation values (1) (figure 1).
Increased Nitrogenase Activity in Solar‐Driven Biohybrids Containing Non‐photosynthetic Bacteria and Conducting Polymers (2023)

A conductive polymer-based photosynthetic biohybrid is constructed to enhance biological nitrogen fixation by increasing nitrogenase activity in the non-photosynthetic bacterium Azotobacter Chroococcum (A. Chroococcum). The light-harvesting cationic poly(fluorene-alt-phenylene) (PFP) electrostatically binds to the surface of the bacteria and possesses satisfactory conductivity to facilitate electron transfer to the bacterium, promoting the nitrogen fixation pathway through redox proteins on the surface of the bacteria when under illumination. Therefore, the nitrogenase activity, hydrogen, NH<sub>4</sub> <sup>+</sup> -N and L-amino acids production are increased by 260 %, 37 %, 44 %, and 47 %, respectively. The expression levels of nifD and nifK encoding molybdenum-iron (MoFe) protein and relevant nitrogen-fixing proteins are up-regulated. These photoactive conductive polymer-bacteria biohybrids provide a new method for improving the biological nitrogen fixation capability of non-photosynthetic nitrogen-fixing bacteria.
Clear Cell Renal Cell Carcinoma: Multiphasic Multidetector CT Imaging Features Help Predict Genetic Karyotypes (2011)

The genetic makeup of ccRCCs affects their imaging features at multidetector CT examinations. Multidetector CT imaging characteristics may help suggest differences at the cytogenetic level among ccRCCs.
A heuristic particle swarm optimization (2007)

A heuristic version of the particle swarm optimization (PSO) is introduced in this paper. In this new method called "The heuristic particle swarm optimization(HPSO)", we use heuristics to choose the next particle to update its velocity and position. By using heuristics , the convergence rate to local minimum is faster. To avoid premature convergence of the swarm, the particles are re-initialized with random velocity when moving too close to the global best position. The combination of heuristics and re-initialization mechanism make HPSO outperform the basic PSO and recent versions of PSO.