gebhart/patrepeval huggingface dataset:
Adhesion of Mussel Foot Protein-3 to TiO2 Surfaces: the Effect of pH (2013)

The underwater adhesion of marine mussels relies on mussel foot proteins (mfps) rich in the catecholic amino acid 3,4-dihydroxyphenylalanine (Dopa). As a side chain, Dopa is capable of strong bidentate interactions with a variety of surfaces, including many minerals and metal oxides. Titanium is among the most widely used medical implant material and quickly forms a TiO2 passivation layer under physiological conditions. Understanding the binding mechanism of Dopa to TiO2 surfaces is therefore of considerable theoretical and practical interest. Using a surface forces apparatus, we explored the force-distance profiles and adhesion energies of mussel foot protein 3 (mfp-3) to TiO2 surfaces at three different pHs (pH 3, 5.5 and 7.5). At pH 3, mfp-3 showed the strongest adhesion force on TiO2, with an adhesion energy of ∼-7.0 mJ/m(2). Increasing the pH gives rise to two opposing effects: (1) increased oxidation of Dopa, thus, decreasing availability for the Dopa-mediated adhesion, and (2) increased bidentate Dopa-Ti coordination, leading to the further stabilization of the Dopa group and, thus, an increase in adhesion force. Both effects were reflected in the resonance-enhanced Raman spectra obtained at the three deposition pHs. The two competing effects give rise to a higher adhesion force of mfp-3 on the TiO2 surface at pH 7.5 than at pH 5.5. Our results suggest that Dopa-containing proteins and synthetic polymers have great potential as coating materials for medical implant materials, particularly if redox activity can be controlled.
RTRB-07PRECLINICAL EVALUATION OF IRRADIATION THROUGH TUMOR TREATING FIELDS (TTFIELDS) CERAMIC TRANSDUCER ARRAYS (2015)

TTFields are an effective anticancer modality delivered via continuous, noninvasive application of low intensity, intermediate frequency, alternating electric fields. TTFields are delivered using insulated ceramic transducer arrays that are placed directly on the scalp in the region surrounding a tumor. Preclinical data suggest that the combination of TTFields with irradiation is most effective when TTFields are applied immediately after exposure to irradiation therapy. In practice, this could be accomplished by leaving the transducer arrays attached to the patients' during radiation therapy. Initial investigations using an ion chamber connected to a unidos dosemeter demonstrated that the TTFields transducer arrays absorb only a small fraction of the irradiation energy but lead to a dramatic increase in the energy directly below the ceramic arrays. This could potentially abolish the skin sparing effect. The purpose of this study was to evaluate the impact of direct irradiation through the TTFields ceramic transducer arrays on rat skin. Insulated ceramic transducers with hydrogel identical to those used for TTFields application in glioblastoma patients were placed on a rat's head. No additional adverse events were observed when single irradiation doses of 2-15 Gy were applied to the rat head through the transducers. In order to further test potential damage in conditions similar to clinical practice, rats were irradiated with 2 Gy, five times a week for two weeks through ceramic arrays placed on the rat's dorsal skin. Skin screening revealed that irradiation through the ceramic arrays did not lead to adverse reactions. These results should be further validated through clinical testings.
Development of CO 2 laser excited by 2.45-GHz microwave discharge (1990)

A new technique to excite a CO<sub>2</sub> laser by 2.45GHz microwave discharge is developed. Microwave plasma produced by the technique is so stable and homogeneous that any additional means to effectuate laser action such as fast circulation of laser gas and external magnetic field are not necessary. Utilizing the technique, a compact diffusion cooled CO<sub>2</sub> laser with 40cm active length is constructed. A magnetron available for microwave ovens is used as the power source of the laser. Average output power of 116W and maximum conversion efficiency of 18% in CW mode, peak output power of 1.2kW in pulse mode are obtained. Output beam with good focusibility is extracted by applying an unstable-waveguide hybrid resonator.
(Invited) Perspectives on the Impact of Interfacial Interactions and Ion/Electron Transport for Robust Energy Storage Solutions (2022)

Over the past decade, conversion-type anodes have been viewed as an attractive alternative for use in the next-generation of high capacity battery materials. However, many technological limitations exist in the stability and long-term reliability of these anodes for the commercialization of these electrodes. Here, we explore the complex interfacial interactions between the components of composite electrodes along with the impact of the chemical/electrochemical environment on performance. Fundamental insight into the factors that influence ion and electron transport within the composite systems are expected to help elucidate the key physical and chemical properties needed for the development of high-capacity materials for battery applications.
Study of the effect of Sn grain boundaries on IMC morphology in solid state inter-diffusion soldering (2019)

This paper reports on 3D phase field simulations of IMC growth in Co/Sn and Cu/Sn solder systems. In agreement with experimental micrographs, we obtain uniform growth of the CoSn<sub>3</sub> phase in Co/Sn solder joints and a non-uniform wavy morphology for the Cu<sub>6</sub>Sn<sub>5</sub> phase in Cu/Sn solder joints. Furthermore, simulations were performed to obtain an insight in the impact of Sn grain size, grain boundary versus bulk diffusion, IMC/Sn interface mobility and Sn grain boundary mobility on IMC morphology and growth kinetics. It is found that grain boundary diffusion in the IMC or Sn phase have a limited impact on the IMC evolution. A wavy IMC morphology is obtained in the simulations when the grain boundary mobility in the Sn phase is relatively large compared to the interface mobility for the IMC/Sn interface, while a uniform IMC morphology is obtained when the Sn grain boundary and IMC/Sn interface mobilities are comparable. For the wavy IMC morphology, a clear effect of the Sn grain size is observed, while for uniform IMC growth, the effect of the Sn grain size is negligible.
Abstract 819: Targeted sequencing to detect somatic mutations, translocations and copy-number variation in human tumors simultaneously. (2013)

Abstract The ability to harness the power of next generation sequencing for characterizing the cancer genome would be extremely valuable to the cancer research community and ultimately improve diagnosis and individualized therapy. We present a targeted approach using massively parallel sequencing to simultaneously detect mutations, translocations and copy-number variations in archived clinical tumor specimen. Targeted sequencing was achieved by designing RNA baits to capture the exons of 504 genes with relevance to cancer. The bait set was augmented with specific intronic sequences to detect translocations often involved in cancer. The overall performance of the hybrid capture was improved by optimizing the tiling strategy of the baits. These improvements significantly shifted fragments with low or no-coverage closer to the overall mean, resulting in a more uniform coverage distribution. To validate the targeted gene panel we sequenced tumor samples harboring mutations, translocations and copy-number alterations that were previously identified by clinically approved assays. All the known alterations were confirmed with additional potentially actionable mutations. The ultimate goal of the targeted panel is to screen cancer patients quickly and economically allowing simultaneous detection of all common genomic alterations in the cancer genome. Citation Format: Paul Van Hummelen, Matthew Ducar, Robert T. Jones, Alina Raza, Ashwini Sunkavalli, Megan Hanna, Adri Mills, Ravali Adusumilli, Prateek Kumar, Laura Schubert, Marc Breneiser, Anna C. Cooley, Elizabeth Garcia, Lynette M. Scholl, Neal I. Lindeman, Nikhil Wagle, Levi Garraway, Kristian Cibulskis, Scott L. Carter, Michael Lawrence, Gad Getz, Matthew L. Meyerson, William C. Hahn, Laura E. MacConaill. Targeted sequencing to detect somatic mutations, translocations and copy-number variation in human tumors simultaneously. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 819. doi:10.1158/1538-7445.AM2013-819
Subchannel Allocation in Relay-Enhanced OFDMA Downlink with Imperfect Feedback (2009)

This paper studies the resource allocation for orthogonal frequency division multiple access (OFDMA) in a fixed amplify-and-forward (AF) relay link. We express closed-form average capacity results for the system when frequency allocation is based on limited and imperfect feedback information and multiple antennae are assumed at the relay node (RN) and the user equipment (UE). Feedback strategies based on the best-M method and resource block (RB)-wise one bit quantization are analyzed and compared. Capacity expressions are presented for space-time block coding (STBC) and transmit antenna selection (AS) schemes. The capacity results with imperfect feedback path are of particular interest. The results illustrate that promising tradeoff between the system performance, feedback overhead, and robustness against feedback errors can be achieved by using AS and limited feedback in frequency allocation.
Supplementary Table 5 from <i>HOXB13</i> G84E Mutation in Finland: Population-Based Analysis of Prostate, Breast, and Colorectal Cancer Risk (2023)

&lt;p&gt;PDF file - 43K, Table shows 30 amino acids having the lowest relative solvent accessibilities. The first column indicates the predicted class for the amino acid denoted by the letters B (buried) and E (exposed). Second Column shows the amino acid while in third column the amino acid position is indicated. Fourth column shows the predicted value of relative solvent accessibility (RSA). Fifth column shows the z-fit score of for the RSA prediction which represents the reliability of the RSA prediction. G84 and its proximate amino acids residues are highlighted in red.&lt;/p&gt;
Behavioral effects of cannabinoids show differential sensitivity to cannabinoid receptor blockade and tolerance development (2004)

This study compared the potency and efficacy of the cannabinoids delta-tetrahydrocannabinol (delta-THC), HU-210, WIN 55,212-2 and CP 55,940 in suppressing food-reinforced operant behavior, increasing reaction latency in a hot-plate test and inducing hypothermia, and tested whether these behavioral effects induced by CP 55,940 showed differential sensitivity to the cannabinoid CB1 receptor antagonist SR141716A, and to tolerance development. After acute i.p. administration to rats, operant behavior was more potently affected than reaction latency and body temperature, but the order of potency of the different drugs was similar across the tests: HU-210<CP 55,940<WIN 55,212-2=delta-THC. SR141716A blocked the hypothermic and analgesic effects more potently/efficiently than the response-rate suppressive effect of CP 55,940. After repeated administration of CP 55,940, the extent and speed of tolerance development was most pronounced in the hypothermia test, and least pronounced in the operant test. It is concluded that the more the behavioral effect induced by a cannabinoid receptor agonist is situated at the left-hand side of the dose-spectrum, the more the effect is resistant to blockade by a cannabinoid receptor antagonist and to the development of tolerance. The possible consequence of this observation for the therapeutic use of cannabinoids is discussed.
Champagne: Whole-genome phylogenomic character matrix method places Myomorpha basal in Rodentia (2019)

We present Champagne, a whole-genome method for generating cha racter m atrices for p hylogenomic a nalysis using large g e n omic e vents that, by rigorously picking orthologous genes and locating large, virtually homoplasy-free insertion and deletion events, delivers a character matrix that outperforms existing morphological and nucleotide-based matrices on both established phylogenies, and difficult-to-resolve nodes in the mammalian tree. Champagne harbors distinct theoretical advantages, and can easily be run on any clade of related species, of the many currently being sequenced. Champagne considerably improves the retention index in the parsimony analysis of a number of widely established topologies, observes incomplete lineage sorting (ILS) at the root of Paenungulata, finds little evidence for human-chimp-gorilla ILS, and most surprisingly, offers convincing evidence for a reconsideration of squirrel’s position in the rodent tree.
Double‐diffusive natural convection in a porous medium under constant heat and mass fluxes (1999)

Double-diffusive natural convection in a rectangular fluid-saturated porous medium has been studied analytically and numerically. The analysis reveals that there is a range of buoyancy ratios N in which one obtains two types of solutions or oscillating convection. In the case of 0.4 < N < 1.0, there exist two analytical solutions when Rc = 100 and Le = 30. In that case, two solutions, temperature-dominated and concentration-dominated solutions, are calculated when the aspect ratio is small. It is found that the oscillation is due to a temporal formation of a two-roll flow pattern in the cavity when the aspect ratio is sufficiently large. The oscillation of time-dependent Nusselt number and flow patterns are shown. © 1999 Scripta Technica, Heat Trans Asian Res, 28(4): 255–265, 1999
Mutation of Rv2887 , a marR -Like Gene, Confers Mycobacterium tuberculosis Resistance to an Imidazopyridine-Based Agent (2015)

Drug resistance is a major problem in Mycobacterium tuberculosis control, and it is critical to identify novel drug targets and new antimycobacterial compounds. We have previously identified an imidazo[1,2-a]pyridine-4-carbonitrile-based agent, MP-III-71, with strong activity against M. tuberculosis. In this study, we evaluated mechanisms of resistance to MP-III-71. We derived three independent M. tuberculosis mutants resistant to MP-III-71 and conducted whole-genome sequencing of these mutants. Loss-of-function mutations in Rv2887 were common to all three MP-III-71-resistant mutants, and we confirmed the role of Rv2887 as a gene required for MP-III-71 susceptibility using complementation. The Rv2887 protein was previously unannotated, but domain and homology analyses suggested it to be a transcriptional regulator in the MarR (multiple antibiotic resistance repressor) family, a group of proteins first identified in Escherichia coli to negatively regulate efflux pumps and other mechanisms of multidrug resistance. We found that two efflux pump inhibitors, verapamil and chlorpromazine, potentiate the action of MP-III-71 and that mutation of Rv2887 abrogates their activity. We also used transcriptome sequencing (RNA-seq) to identify genes which are differentially expressed in the presence and absence of a functional Rv2887 protein. We found that genes involved in benzoquinone and menaquinone biosynthesis were repressed by functional Rv2887. Thus, inactivating mutations of Rv2887, encoding a putative MarR-like transcriptional regulator, confer resistance to MP-III-71, an effective antimycobacterial compound that shows no cross-resistance to existing antituberculosis drugs. The mechanism of resistance of M. tuberculosis Rv2887 mutants may involve efflux pump upregulation and also drug methylation.
Anionic Polymerization of 4-Methacryloyloxy-TEMPO Using an MMA-Capped Initiator (2014)

Anionic polymerization of 4-methacryloyloxy-TEMPO (TEMPO = 2,2,6,6-tetramethylpiperidin-1-oxyl) was successfully carried out using methyl methacrylate-capped 1,1-diphenylhexyllithium (DPHLi/MMA), of which nucleophilicity is moderate enough to suppress the side reaction between the nitroxide radical of TEMPO moiety and the carbanion of DPHLi, to yield the radical polymer with well-controlled molecular weight, narrow polydispersity index (PDI < 1.10), high yield (>95%), and almost 1.0 radicals per monomer unit.
Subtypes of Relapsing-Remitting Multiple Sclerosis Identified by Network Analysis (2022)

ABSTRACT The objective of this study was to use network analysis to identify subtypes of relapsing-remitting multiple sclerosis subjects based on their cumulative signs and symptoms. We reviewed the electronic medical records of 120 subjects with relapsing-remitting multiple sclerosis and recorded signs and symptoms. Signs and symptoms were mapped to a neuroontology and then collapsed into 16 superclasses by subsumption and normalized. Bipartite (subject-feature) and unipartite (subject-subject) network graphs were created using Gephi. Degree and weighted degree were calculated for each node. Graphs were partitioned into communities using the modularity score. Feature maps were used to visualize differences in features by the community. Network analysis of the unipartite graph yielded a higher modularity score (0.49) than the bipartite graph (0.247). Network analysis can partition multiple sclerosis subjects into communities based on signs and symptoms. Communities of subjects with predominant motor, sensory, pain, fatigue, cognitive, behavior, and fatigue features were found. Larger datasets and additional partitioning algorithms are needed to confirm these results and elucidate their clinical significance.
Five Ws, one H and many tweets (2013)

Widespread using of microblogs leads to have tremendous user generated data available which may characterize the social behavior and relationship of users. Beside the chance to extract some valuable information from the huge amount of data, there are a lot of non-trivial, task specific issue have to be solved to get real value. Detecting and characterizing events, defining users and their relationships, concluding on the reasons are all important questions, have to be understood well, to get a clear picture on the social network behavior of users and to answer WHO, WHEN, WHERE, WHAT, WHY and HOW questions.
Strategies for characterization of fractured rock using cross-borehole electrical tomography (2013)

There is an increasing need to characterize fractured rock systems and to monitor the movement of fluids in these systems. Fractured rock aquifers are increasingly exploited for water resources, and are subject to contamination from industrial activities at the Earth's surface. Deep rock repositories of hazardous waste must be carefully characterized in terms of fracture transport characteristics. More recently, there has been a surge in technologies designed to increase permeability of shale reservoirs by creating fractures to promote fluid removal. However, fractured rock systems present unique challenges for characterization and monitoring technologies. Fracturing typically generates highly heterogeneous and anisotropic systems, making the evaluation of the distribution of physical properties from sparse subsurface measurements particularly problematic. Geophysical imaging technologies are increasingly applied in an effort to overcome the limitations of sparsely located direct observations of subsurface properties. However, the application of geophysical technologies to fractured rock systems presents challenges for imaging as appropriate regularization model constraints for complex, heterogeneous systems are hard to define without additional subsurface information.
Impacts of Crosslinking and Degassing on the Conductivity, Dielectric Loss, and Morphology of Low-Density Polyethylene and Crosslinked Polyethylene (2021)

Crosslinked polyethylene (XLPE) is a key material used for power cable insulation due to its electrical properties and structure. Here, it was shown that the technique of broadband dielectric spectroscopy can be used to analyze both by extracting the temperature coefficient of capacitance (TCC), dielectric loss, and AC conductivity. TCC for low-density polyethylene (LDPE) can be directly compared to its linear thermal expansion coefficient and used as a tool to compare different types of polyethylene. Degassing, a thermal treatment to remove volatile species and increase crystallinity, can be used to control TCC magnitude. In general, changes in the TCC magnitude are reflective of changes in the crystallinity and byproduct concentrations. Degassing also reduced the dielectric loss for both due to morphological changes and byproduct removal. However, it only reduces conductivity at elevated temperatures such as 90 °C for XLPE. Other processing parameters, as well as excessive byproduct concentrations, were also seen to influence TCC, dielectric loss, and conductivity.
Stabilization of electrostatic MEMS resonators using a delayed feedback controller (2010)

We present a study for the stabilization of a MEMS resonator actuated with DC and AC voltages using a delayed feedback controller. We show that the delayed feedback controller, with a careful selection of its parameters, can be used to stabilize an originally unstable resonator operating in the dynamic pull-in frequency band. Also, the controller is shown to enhance the stability of the resonator near pull-in, where it experiences a strong fractal behavior. In both cases, the controller shows superior performance in rejecting disturbances. Experimental and theoretical results are presented to demonstrate the capability of the feedback controller to stabilize the performance of a capacitive resonator. Good agreement between simulation and experiment is demonstrated.
Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism (2022)

NCT02059538.
Quasi-vertical tapers for polymer-waveguide-based interboard optical interconnects (2015)

A mode transformer based on the quasi-vertical taper is designed to enable high coupling efficiency for interboard-level optical interconnects involving single-mode polymer waveguides and standard single-mode fibers. A triangular region fabricated above the waveguide is adopted to adiabatically transform the mode from the fiber into the polymer waveguide. The effects of the geometrical parameters of the taper, including width, height, tip width, etc., on the coupling efficiency are numerically investigated. Based on this, a quasi-vertical taper for the polymer rib waveguide system is designed, fabricated, and characterized. Coupling losses of 1.79±0.30 and 2.23±0.31  dB per coupler for the quasi-TM and quasi-TE mode, respectively, are measured across the optical communication C and L bands (1535 to 1610 nm). Low-cost packaging, leading to widespread utilization of polymeric photonic devices, is envisioned for optical interconnect applications.
Electroptic Polymer Linear Modulators Based on Multiple-Domain Y-Fed Directional Coupler (2010)

We developed an analytical method to optimize the design of Y-fed direction couplers at large modulation depth from 10% to 50%. Simulation results indicate that three and four-domain devices can obtain 45 dB higher distortion suppression than two-domain devices, which can potentially achieve 120 dB spurious free dynamic range. We also experimentally demonstrated that the two-domain electrooptic modulator obtained 94 dB distortion suppression at 20% modulation depth, which is 47 dB higher than a conventional Mach-Zehnder modulator.