gebhart/patrepeval huggingface dataset:
Self‐Propelled Soft Protein Microtubes with a Pt Nanoparticle Interior Surface (2016)

Human serum albumin (HSA) microtubes with an interior surface composed of Pt nanoparticles (PtNPs) are self-propelled in aqueous H<sub>2</sub> O<sub>2</sub> medium. They can capture cyanine dye and Escherichia coli (E. coli) efficiently. Microtubes were prepared by wet templating synthesis by using a track-etched polycarbonate (PC) membrane with alternate filtrations of aqueous HSA, poly-l-arginine (PLA), and citrate-PtNPs. Subsequent dissolution of the PC template yielded uniform hollow cylinders made of (PLA/HSA)<sub>8</sub> PLA/PtNP stacking layers (1.16±0.02 μm outer diameter, ca. 23 μm length). In aqueous H<sub>2</sub> O<sub>2</sub> media, the soft protein microtubes are self-propelled by jetting O<sub>2</sub> bubbles from the open-end terminus. The effects of H<sub>2</sub> O<sub>2</sub> and surfactant concentrations on the velocity were investigated. The swimming microtube captured cyanine dye in the HSA component of the wall. Addition of an intermediate γ-Fe<sub>3</sub> O<sub>4</sub> layer allowed manipulation of the direction of movement of the tubule by using a magnetic field. Because the exterior surface is positively charged, the bubble-propelled microtubes adsorbed E. coli with high efficiency. The removal ratio of E. coli by a single treatment reached 99 %.
Nondestructive characterization of laser powder bed fusion parts with neutron Bragg edge imaging (2021)

Laser powder bed fusion is an efficient technique for additive manufacturing of metallic materials. The quality of the material produced depends on the optimization of a large range of build parameters and the complex thermo-mechanical build process is prone to inducing detrimental material features such as porosity and residual stresses negatively affecting fatigue resistance and lifetime. Here we apply neutron Bragg edge radiography in a parametric study on printing 316L steel. The parameters concerned are the laser scanning speed and strategy as well as the optional use of support structures. Analyses of the full field single shot wavelength-resolved Bragg edge radiography data enables to characterize local density inhomogeneities, as well as cracks, based on the long wavelength tail of the spectrum and variations of the stress field but also textural features based on the Bragg edge pattern. It is found that in the performed study not only respective differences in the residual stresses due to parameter variation are manifesting but also systematic irregularities due to machine imperfections (e.g. issues with the powder coater) are observed in the printed samples. The study supports the use of the parallel scanning strategy without supports and with the lower utilized scanning speed.
Strategies for realizing photonic crystal fiber bandpass filters (2008)

Numerical design strategies are presented to achieve efficient broad or narrow band-pass filters based on index-guiding, solid-core, and single-mode photonic crystal fibers (PCFs). The filtering characteristics have been verified through BPM solver. By scaling the pitch constant, the bandpass window can be shifted accordingly. The fiber design constitutes a fluorine-doped central core, enlarged air-holes surrounding the down-doped core, and small air-holes in the cladding. The proposed bandpass filter is based on controlling the leakage losses, so one can tune filter characteristics simply by changing its length. From numerical simulations we show that for large values of air-hole diameter in the first ring, the bandpass window is narrow, while for low doping concentration and small sized air-holes in the first ring, bandpass window is very broad. We also simulate how the hole-size and number of rings in the PCF cladding affects the device characteristics. We find that a 5-cm long PCF with down-doped core and eleven rings of air-holes can result in approximately 440 nm 3-dB bandwidth with more than 90% of transmission. The longer device has reduced transmission and smaller 3-dB bandwidth. Tolerance analysis has also been performed to check the impact of fiber tolerances on the performance of the PCF bandpass filter. It has been observed that the decrement in cladding hole-diameter by 1% reduces the transmission to 21% from its peak value of 93%, however +/-1% tolerance in the inner hole-diameter degrades the transmission to 75% from its peak.
Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles (2010)

In the interests of practicalities and cost, these results suggest that single samples can generate reliable data, but only after careful compensation for technical bias in the experiment. We recommend that investigators appreciate the propensity for such variation in the design stages of a microarray experiment and that the use of suitable correction methods become routine during the statistical analysis of the data.
100-GHz integrated photoreceiver using optical-to-radio converter and enhancement mode PHEMT amplifier driven by photonic power supply (2017)

We present a 100-GHz integrated photoreceiver using an optical-to-radio converter and an enhancement-mode PHEMT amplifier driven by all optical resources without an external electric power supply. Technology for the simultaneous generation of radio and power was developed using a zero-bias operational uni-travelling carrier (UTC) high-speed photodetector. To improve the optical-to-electrical conversion efficiency, a 110-GHz enhancement-mode InP-PHEMT amplifier was also newly developed, which operates using an internal electric power supply in an optical-to-radio converter. Using a hybrid integration based on all optical resources, a +5.5 dBm RF output at 97 GHz was successfully achieved through the optical-to-radio conversion process. Herein, the two key devices and the integrated photoreceiver are discussed.
Improving performance of fully scalable, flexible transparent conductive films made from carbon nanotubes and ethylene-vinyl acetate (2022)

We report process improvements for the fabrication of single-walled carbon nanotube ethylene-vinyl acetate transparent conductive films. CNT:EVA films demonstrate high resilience against folding and can replace the external dopant in a spiro-OMeTAD based hole selective contact of n-i-p perovskite solar cells achieving a steady-state efficiency of 16.3%. The adapted process is fully scalable, and compared to previous reports (Mazzotta et al., 2018) lowers the material cost dramatically and improves DC to optical conductivity ratio by two orders of magnitude to σdc/σop=3.6 for pristine and σdc/σop=15 for chemically doped films. We analyse the microstructure of our films via small angle neutron scattering and find a positive correlation between the long range packing density of the CNT:EVA films and the σdc/σop performance. Increasing monomer ratio and chain length of the EVA polymer improves resilience against bending strain, whereas no significant effect on the CNT wrapping and electrical conductivity of resulting films is found.
Airway management in laryngotracheal injuries from blunt neck trauma in children (2015)

Pediatric laryngotracheal injuries from blunt neck trauma are extremely rare, but can be potentially catastrophic. Early diagnosis and skillful airway management is critical in avoiding significant morbidity and mortality associated with these cases. We present a case of a patient who suffered a complete tracheal transection and cervical spine fracture following a clothesline injury to the anterior neck. A review of the mechanisms of injury, clinical presentation, initial airway management, and anesthetic considerations in laryngotracheal injuries from blunt neck trauma in children are presented.
Regulation of growth and metabolism (2014)

mTOR is the target of the immunosuppressive drug rapamycin and the central component of a nutrientand hormone-sensitive signaling pathway that regulates cell growth and proliferation. We now appreciate that this pathway becomes deregulated in many human cancers and has an important role in the control of metabolism and aging. We have identified two distinct mTOR-containing proteins complexes, one of which regulates growth through S6K and another that regulates cell survival through Akt. These complexes, mTORC1 and mTORC2, define both rapamycin-sensitive and insensitive branches of the mTOR pathway. I will discuss new results from our lab on the regulation and functions of the mTORC1 and mTORC2 pathways.
Nipah virus budding is ESCRT-dependent. (2016)

&lt;p&gt;&lt;b&gt;(A)&lt;/b&gt; Wild-type (WT) and dominant-negative (DN) Vps4A-inducible 293 cells were infected with &lt;i&gt;Gaussia&lt;/i&gt; luciferase-expressing NiV at a multiplicity of infection (MOI) of 2. Cells were induced with doxycycline (dox) post-infection, and viral titers in the supernatant were determined at the indicated time points. Error bars represent standard deviations for 3 replicates. Induction of DN Vps4A significantly inhibits the release of NiV at 24 hours post-infection (hpi). ***, p&lt;0.001, two-way ANOVA followed by Bonferroni posttests. &lt;b&gt;(B)&lt;/b&gt; Induction of WT or DN Vps4A did not affect &lt;i&gt;Gaussia&lt;/i&gt; luciferase (Gluc) production, indicating unimpaired virus protein production. ns, not significant, two-way ANOVA followed by Bonferroni posttests. &lt;b&gt;(C)&lt;/b&gt; Vps4A-inducible 293 cells were infected with wild-type NiV at MOI 2, and Vps4A (WT vs. DN) was induced (+Dox) or not (-Dox) immediately after infection as in Fig 1A. At 24 hpi, cell lysates (CL) were collected, and virions were ultracentrifuged through 20% sucrose and resuspended in Laemmli SDS sample buffer for Western analysis. The 0 hpi time point represents the last wash after removal of the inoculum to determine the background level of residual virus. Induction of DN Vps4A clearly resulted in less virions (NiV) released into the supernatant.]&lt;/p&gt;
Exploiting the interactions of aromatic units for folding and assembly in aqueous environments (2016)

A variety of non-covalent interactions (including hydrogen bonding, ionic interactions, metal coordination and desolvation/solvation) have been utilized to organize oligomers into well-defined structures. Herein is described a survey of aromatic foldamers that capitalize on electrostatic complementarity of substituted aromatic units to drive folding and assembly in aqueous environments. A brief description of recent advances in the understanding of aromatic interactions is provided, followed by examples of foldamers that exploit interactions between aromatic units to drive their assembly in predictable fashion. The history of our aromatic foldamers is traced from the first structure designed to fold into a pleated structure in an aqueous environment to a heteroduplex system more related to nucleic acids. Taken together, the results demonstrate that electrostatic complementarity of aromatic units provides a versatile framework for driving predictable folding and assembly in aqueous environments.
ARE THE CAUSES OF ILIOPSOAS-RELATED GROIN PAIN IN TOTAL HIP ARTHROPLASTY AND HIP RESURFACING ARTHROPLASTY EQUIVALENT? A CASE-CONTROLLED INVESTIGATION USING A VALIDATED SIMULATION (2023)

Iliopsoas tendonitis occurs in up to 30% of patients after hip resurfacing arthroplasty (HRA) and is a common reason for revision. The primary purpose of this study was to validate our novel computational model for quantifying iliopsoas impingement in HRA patients using a case-controlled investigation. Secondary purpose was to compare these results with previously measured THA patients. We conducted a retrospective search in an experienced surgeon's database for HRA patients with iliopsoas tendonitis, confirmed via the active hip flexion test in supine, and control patients without iliopsoas tendonitis, resulting in two cohorts of 12 patients. The CT scans were segmented, landmarked, and used to simulate the iliopsoas impingement in supine and standing pelvic positions. Three discrete impingement values were output for each pelvic position, and the mean and maximum of these values were reported. Cup prominence was measured using a novel, nearest-neighbour algorithm. The mean cup prominence for the symptomatic cohort was 10.7mm and 5.1mm for the asymptomatic cohort (p &lt;&lt; 0.01). The average standing mean impingement for the symptomatic cohort was 0.1mm and 0.0mm for the asymptomatic cohort (p &lt;&lt; 0.01). The average standing maximum impingement for the symptomatic cohort was 0.2mm and 0.0mm for the asymptomatic cohort (p &lt;&lt; 0.01). Impingement significantly predicted the probability of pain in logistic regression models and the simulation had a sensitivity of 92%, specificity of 91%, and an AUC ROC curve of 0.95. Using a case-controlled investigation, we demonstrated that our novel simulation could detect iliopsoas impingement and differentiate between the symptomatic and asymptomatic cohorts. Interestingly, the HRA patients demonstrated less impingement than the THA patients, despite greater cup prominence. In conclusion, this tool has the potential to be used preoperatively, to guide decisions about optimal cup placement, and postoperatively, to assist in the diagnosis of iliopsoas tendonitis.
Structure of the Monophosphoryl Lipid A Moiety Obtained from the Lipopolysaccharide of Chlamydia trachomatis (1997)

Monophosphoryl lipid A was prepared from the lipopolysaccharide of Chlamydia trachomatis, converted to the methyl ester, and fractionated by reverse-phase high-performance liquid chromatography. The peak fractions were collected and analyzed by mass spectrometry. Matrix-assisted laser desorption/ionization and liquid secondary ion mass spectrometry of the first of two major high-performance liquid chromatographic fractions showed multiple quasi-molecular ions of MNa+ at m/z 1780, 1794, 1808, 1822, and 1836. The positive-ion liquid secondary ion mass spectrometry spectrum also showed a minor series of peaks at m/z 1916, 1930, 1944, 1958, and 1971, consistent with the formation of matrix adducts with 3-nitrobenzyl alcohol. Oxonium ions representing the distal subunit were observed at m/z 1057, 1071, 1085, 1099, and 1113. The second fraction was similarly analyzed and found to contain structural homologs of the first fraction. Based on this study, the major lipid A component of chlamydial lipopolysaccharide is a glucosamine disaccharide that contains five fatty acids and a phosphate in the distal segment. Three fatty acyl groups are in the distal segment, and two are in the reducing end segment. The acyloxyacyl group is located in the distal segment in amide linkage. Two structural series, differing by 14 atomic mass units in the reducing subunit, were observed. Chlamydial lipid A is complex and consists of at least 20 homologous structural components. The relatively low potency of Chlamydia trachomatis lipopolysaccharide in activating lipopolysaccharide-responsive cells might be related to the unusual fatty acid composition of the lipid A moiety.
Resonance Raman Spectroscopy of Met121Glu Azurin (2000)

The resonance Raman spectra for Pseudomonas aeruginosa Met121Glu azurin have been measured at wavelengths throughout the 600-nm absorption band at low and high pH. The spectra of the mutant at pH 3.5 and 7.0 are identical. Analysis of the 600-nm absorption band and resulting resonance Raman excitation profiles under both pH conditions indicates that the excited-state distortions in this mutant are smaller than those in the native protein.
Supplementary Figure Legends 1-10, Methods from Metabolomics Strategy Reveals Subpopulation of Liposarcomas Sensitive to Gemcitabine Treatment (2023)

&lt;p&gt;PDF file - 114K&lt;/p&gt;
Surface Ordering and Finite‐size Effects at the First Order Phase Transition SmA‐SmC in Liquid‐crystalline Free‐standing Films (1993)

Abstract High precision optical reflectivity measurements and optical image analyses are applied to investigate the first order SmA‐SmC* phase transition in free‐standing films. By decreasing the thickness of the films the critical point is observed, where the first order phase transition disappears. A mean‐field theory describing the process of surface ordering in smectic membranes is presented.
Dynamic charge mapping in layered polymer films (2014)

This paper describes a hybrid algorithm for the solution of the drift-diffusion equations for bipolar charge transport in layered polymer films. Dynamic charge mapping is achieved using a source distribution technique for the solution of the Poisson equation and time-integration using a fourth order total variation diminishing Runge-Kutta scheme that satisfies the Courant-Friedrichs-Levy stability criterion. An integral equation formulation allow conducting and insulating boundaries and material interfaces to be represented by equivalent free and bound charge distributions that collectively satisfy all local and far-field boundary conditions. This hybrid technique solves the drift-diffusion equations that simulate charge injection, field-dependent mobility transport, recombination, and trapping/de-trapping in the bulk and at material and physical interfaces. The resulting charge map is the taxonomy of the different charge types and their abundance; presenting a dynamic view of the temporal and spatial distributions. Results are discussed for single-layer and multi-layered samples with physical and material interfaces. Conditions for creation of charge packets and electroluminescence due to recombination are computed and discussed.
Listeria monocytogenes virulence factors are secreted in biologically active Extracellular Vesicles (2017)

ABSTRACT Outer membrane vesicles produced by Gram-negative bacteria have been studied for half a century but the possibility that Gram-positive bacteria secreted extracellular vesicles (EVs) was not pursued due to the assumption that the thick peptidoglycan cell wall would prevent their release to the environment. However, following discovery in fungi, which also have cell walls, EVs have now been described for a variety of Gram-positive bacteria. EVs purified from Gram-positive bacteriaare implicated in virulence, toxin release and transference to host cells, eliciting immune responses, and spread of antibiotic resistance. Listeria monocytogenes is a Gram-positive bacterium that is the etiological agent of listeriosis. Here we report that L. monocytogenes produces EVs with diameter ranging from 20-200 nm, containing the pore-forming toxin listeriolysin O(LLO) and phosphatidylinositol-specific phospholipase C (PI-PLC). Using simultaneous m etabolite, p rotein, and l ipid e xtraction (MPLEx) multi-omics we characterized protein, lipid and metabolite composition of bacterial cells and secreted EVs and found that EVs carry the majority of listerial virulence proteins. Cell-free EV preparations were toxic to the murine macrophage cell line J774.16, in a LLO-dependent manner, evidencing EV biological activity. The deletion of plcA increased EV toxicity, suggesting PI-PLC can restrain LLO activity. Using immunogold electron microscopy we detect LLO localization at several organelles within infected human epithelial cells and with high-resolution fluorescence imaging we show that dynamic lipid structures are released from L. monocytogenes that colocalize with LLO during infection. Our findings demonstrate that L. monocytogenes utilize EVs for toxin release and implicate these structures in mammalian cytotoxicity.
Synthesis, Pharmacological Evaluation, and Structure−Activity Relationship and Quantitative Structure−Activity Relationship Studies on Novel Derivatives of 2,4-Diamino-6,7-dimethoxyquinazoline α1-Adrenoceptor Antagonists (1999)

A new series of novel piperazine and non-piperazine derivatives of 2, 4-diamino-6,7-dimethoxyquinazoline was synthesized and evaluated for binding affinity toward alpha1-adrenergic and other G-protein-coupled aminergic receptors. The alpha1-adrenoceptor (AR) subtype selectivity was also investigated for the most interesting compounds. Only compound 16 showed moderate selectivity toward the alpha1b-AR subtype. Selected compounds were tested in vivo in a dog model indicating activity on blood pressure and on the lower urinary tract. Compound 10 showed in vivo potency close to that of prazosin. Powerful interpretative and predictive theoretical QSAR models have been obtained. The theoretical descriptors employed in the rationalization of the alpha1-adrenergic binding affinity depict the key features for receptor binding which can be summarized in an electrostatic interaction between the protonated amine function and a primary nucleophilic site of the receptor, complemented by short-range attractive (polar and dispersive) and repulsive (steric) intermolecular interactions. Moreover, on predictive grounds, the ad hoc derived size and shape QSAR model developed in a previous paper (Rastelli, G.; et al. J. Mol. Struct. 1991, 251, 307-318) proved to be successful in predicting nanomolar alpha1-adrenergic binding affinity for compound 28.
Study of undoped channel FinFETs in active rail clamp ESD networks (2008)

In this paper we investigate state-of-the-art undoped channel FinFETs and FinDiodes with an emphasis on I/O and ESD applicability. Utilizing electrical characterization data, 3D TCAD, and a compact model, we demonstrate that FinFETs and FinDiodes exhibit a very appealing combination of high breakdown voltage and low Ioff for I/O and ESD protection circuit applications.
A 3D Skin Melanoma Spheroid-Based Model to Assess Tumor-Immune Cell Interactions (2020)

Three-dimensional (3D) tumor spheroids have the potential to bridge the gap between two-dimensional (2D) monolayer tumor cell cultures and solid tumors with which they share a significant degree of similarity. However, the progression of solid tumors is often influenced by the dynamic and reciprocal interactions between tumor and immune cells. Here we present a 3D tumor spheroid-based model that might shed new light on understanding the mechanisms of tumor and immune cell interactions. The model first utilizes the hanging drop assay, which serves as one of the simplest methods for generating 3D spheroids and requires no specialized equipment. Next, pre-established spheroids can be co-cultured either directly or indirectly with an immune cell population of interest. Using skin melanoma, we provide a detailed description of the model, which might hold a significant importance for the development of successful therapeutic strategies.