gebhart/patrepeval huggingface dataset:
Seismic Ground Roll Absorption and Reemission by Sand Dunes (2018)

Abstract Ground roll is a significant source of noise in land seismic data, with crossline scattered ground roll particularly difficult to suppress. This noise arises from surface heterogeneities lateral to the receiver spread, and in desert regions sand dunes are a major contributor. However, the nature of this noise is poorly understood, preventing the design of more effective data acquisition or processing techniques. Here we present numerical simulations demonstrating that a barchan sand dune acts as a resonator, absorbing energy from ground roll and reemitting it over an extensive period of time. We derive and validate a mathematical framework that quantitatively describes the properties of the emitted waves and demonstrate that wave amplitude is estimable from easily measurable bulk properties of the dune. Having identified regions in time, space, and frequency space at which noise will be more significant, we propose reducing dune‐scattered noise through careful survey design and data processing. In particular, we predict that seismic noise will be lower upwind of barchan dunes, and at frequencies far from a resonant frequency 2 c S / H , for dune height H and typical seismic velocity within the dune c S . This work is especially relevant to seismic acquisition in the vicinity of a dune field, where scattered noise appears incoherent and difficulties arise with alternative approaches to noise suppression.
Metanephric adenofibroma: robotic partial nephrectomy of a large Wilms' tumor variant. (2010)

Difficult to differentiate from WT, it is imperative that MAF be recognized and appropriately diagnosed because unlike adult WT, the natural history of MAF is indolent and adjuvant chemo/radiation therapy is rarely necessary. This case reinforces the importance of review of potential WT variants by the NWTSG.
In Vivo Coating of Bacterial Magnetic Nanoparticles by Magnetosome Expression of Spider Silk-Inspired Peptides (2018)

Magnetosomes are natural magnetic nanoparticles with exceptional properties that are synthesized in magnetotactic bacteria by a highly regulated biomineralization process. Their usability in many applications could be further improved by encapsulation in biocompatible polymers. In this study, we explored the production of spider silk-inspired peptides on magnetosomes of the alphaproteobacterium Magnetospirillum gryphiswaldense. Genetic fusion of different silk sequence-like variants to abundant magnetosome membrane proteins enhanced magnetite biomineralization and caused the formation of a proteinaceous capsule, which increased the colloidal stability of isolated particles. Furthermore, we show that spider silk peptides fused to a magnetosome membrane protein can be used as seeds for silk fibril growth on the magnetosome surface. In summary, we demonstrate that the combination of two different biogenic materials generates a genetically encoded hybrid composite with engineerable new properties and enhanced potential for various applications.
<title>Teaching sensor technology and MEMS processing using an in-house educational MPW process</title> (1999)

This paper presents a new innovative way of teaching modern sensor technology and practical MEMS-processing by using an in-house Multi Project Wafer (MPW) process especially developed for education purposes. This process has been used as the base for a project course called Sensor Technology, which includes a substantial laboratory component. In this project, the student actively follows the complete sensor development process from design and fabrication to the evaluation of modern MEMS sensors. The design and CAD work for five different sensor types (each having several different versions) has completed prior to the course but the students are introduced to the tools used for the design and simulation of microstructures. The students themselves perform most of the fabrication steps in the cleanroom and all evaluation of the fabricated sensors. Our new in-house MPW-process allows the students to fabricate five different piezoresistive sensor types for measuring flow (both mechanical and thermal transducers), acceleration (both 1- and 3-axis), pressure and angular velocity using one mask set consisting of only four masks. Each sensor type then is produced in many different versions (size and geometry) giving the students flexibility to choose sensors for specific applications during the sensor evaluation. Successful evaluations of pressure, flow and acceleration sensors fabricated by the students have been carried out. The sensor evaluation part also gives the student experience in practical electrical measurements on real devices. Both the course concept and the unique educational MPW-process will be described in this paper.
Orientational anisotropy in simulated vapor-deposited molecular glasses (2015)

Enhanced kinetic stability of vapor-deposited glasses has been established for a variety of glass organic formers. Several recent reports indicate that vapor-deposited glasses can be orientationally anisotropic. In this work, we present results of extensive molecular simulations that mimic a number of features of the experimental vapor deposition process. The simulations are performed on a generic coarse-grained model and an all-atom representation of N,N'-bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD), a small organic molecule whose vapor-deposited glasses exhibit considerable orientational anisotropy. The coarse-grained model adopted here is found to reproduce several key aspects reported in experiments. In particular, the molecular orientation of vapor-deposited glasses is observed to depend on substrate temperature during deposition. For a fixed deposition rate, the molecular orientation in the glasses changes from isotropic, at the glass transition temperature, Tg, to slightly normal to the substrate at temperatures just below Tg. Well below Tg, molecular orientation becomes predominantly parallel to the substrate. The all-atom model is used to confirm some of the equilibrium structural features of TPD interfaces that arise above the glass transition temperature. We discuss a mechanism based on distinct orientations observed at equilibrium near the surface of the film, which get trapped within the film during the non-equilibrium process of vapor deposition.
CdSe Nanocrystal Based Chem‐/Biosensors (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Low-Temperature, Low-Pressure Chemical Vapor Deposition and Solid Phase Crystallization of Silicon–Germanium Films (2008)

Low-pressure chemical vapor deposition of silicon–germanium and its SPC below are investigated. The effects of precursor ratio [ ], pressure, and temperature are examined with the goals of film composition tunability and high deposition rates. is found to be a better source gas than DCS because the decomposition rate of is faster than that of DCS during the deposition process. In the system, the binary deposition mechanism is well explained by the "enhancement" model. The deposition temperature and chamber pressure affect the conversion factor, enabling independent tuning of the film composition and deposition rate. Amorphous and films are obtained at 350 and by adjusting the deposition conditions while keeping the deposition rates high. Compositional effects of the SiGe films on the SPC are also investigated.
Widely-tunable transmitters and photonic integrated circuits (2005)

Widely-tunable lasers and single-chip transmitters, in which such lasers are integrated with modulators and semiconductor-optical-amplifiers, have recently become the core of practical modules that are gaining wide-spread use in new wavelength-division-multiplexed systems. More-photonic advanced ICs have been demonstrated for use it advanced communication and sensor system
Eprenetapopt (APR-246) and Azacitidine in TP53-Mutant Myelodysplastic Syndromes (2021)

Combination treatment with eprenetapopt and azacitidine is well-tolerated yielding high rates of clinical response and molecular remissions in patients with <i>TP53</i>-mutant MDS and oligoblastic AML.
Effect of temperature on Ti and TiN films deposited on a BN substrate (1998)

Nitrides (such as BN and TiN) are widely used in various industrial applications because of their excellent wear and corrosion resistance and their thermal and electronic properties. The structural and chemical features formed during plasma vapor deposition of Ti/TiN on BN substrates have been studied using synchrotron radiation near edge absorption spectroscopy (NEXAFS). Various phases of interest have been formed with different annealing temperatures. Diffusion of the nitridation and the interference from oxidation (e.g., TiO2) and boride formation are of particular concern. X-ray photoelectron spectroscopy and secondary ion mass spectroscopy measurements complement our NEXAFS data. Phase formation and chemical bonding between the coating and the substrate are shown to be determining factors for the microhardness.
FCS = Fluorescence Correlation Spectroscopy TIR-FCS = Total Internal Reflection FCS (2006)

Abstract We present the development and application of a dual-color setup that can be used for confocal fluorescence correlation spectroscopy (FCS), total internal reflection FCS (TIR-FCS) as well as dual color imaging.As exemplary application we performed preliminary measure-ments for DNA-Sequencing with a novel surface chemistry. Motivation • Single molecule detection of chemical kinetics A(red)+B(blue) AB• Monitoring biological processes (eg molecular binding essays)• in vivo observations of dynamics of molecular motors Application functionalized surfaceLinker to surfacecircularized singleDNA strandconfined excitation anddetection Volumecompleted DNA strandEnzymefree Nucleotides DNA Sequencing • improved surface chemistry• bind single DNA strand to surface• labeling nucleotides• observation in confocal volume Figure 4: DNA Sequencing methodFigure 5: Image of dual colored spots afterseveral minutes of nucleotide-incorporation Outlook • Advanced concepts for further confined sampling volumes• Higher concentrations of labeled molecules• More colors or/and lifetime seperation• More biological systems
A Reflective Approach to Providing Flexibility in Application Distribution (2010)

Current middleware systems suffer from drawbacks. Often one is forced to make decisions early in the design process about which classes may participate in inter-machine communication. Further, application level and middleware specific semantics cannot be separated forcing an unnatural design. The RAFDA project proposes to adress these deficiencies by creating an adaptive, reflective framework that enables the transformation of non-distributed applications into isomorphic applications whose distribution architecture is flexible. This paper describes the code transformation techniques that have been developed as part of the project. The system enables the distribution of a program according to a flexible configuration without user intervention. Proxy objects can then be substituted, permitting cross-address space communication. The distributed program can adapt to its environment by dynamically altering its distribution boundaries.
Genomic Analysis of wig-1 Pathways (2012)

Antisense oligonucleotides can effectively reduce wig-1 levels in mouse liver and brain, which results in specific changes in gene expression for pathways relevant to both the nervous system and cancer.
Insights into heparin‐induced thrombocytopenia (1992)

Heparin-induced thrombocytopenia (HIT) is characterized by the presence of an antibody which can activate platelets in the presence of heparin. The in vitro Ca2+ mobilization induced by purified IgG from patients with HIT was evaluated to elucidate the platelet activation mechanism in this syndrome. HIT-IgG induced platelet activation in a heparin-dependent manner. This activation was inhibited by high viscosity, consistent with a previously documented cell-cell-mediated mechanism. We found that F(ab')2 fragments from an anti-GPIIb/IIIa monoclonal antibody in some cases, and dextran sulphate or salmon sperm DNA in all cases, could substitute for heparin, suggesting that heparin exposes a neo-antigen on the platelet surface rather than serving as the primary antigen in the process. Furthermore, heparin, dextran sulphate and salmon sperm DNA all augmented the platelet activation induced by aggregated IgG, suggesting an additional charge shielding effect. These data suggest the following mechanism for platelet activation in HIT: heparin binds to the platelet surface, exposing a neoantigen which elicits an antibody response in some patients. Antibody binding in the presence of heparin leads to platelet activation through Fc receptor mediated platelet-platelet interaction, a process augmented by the charge shielding effect of heparin.
The influence of the EUV spectrum on plasma induced by EUV radiation in argon and hydrogen gas (2015)

Plasmas induced by EUV radiation are scarcely investigated, although they are unique since they are created without any discharge. These plasmas are also of interest from an applicational point of view, since they are related to the lifetime of optics in EUV lithography tools. In order to assess this impact, it is essential to characterize and understand EUV-induced plasma. In this contribution the influence of the background gas (argon and hydrogen) in the lithography tool and the spectrum of the illumination source on the electron density of EUVinduced plasma is investigated using microwave cavity resonance spectroscopy.
Mathematical Modeling of Extracellular Electron Transfer in Biofilms (2015)

Due to their complexity, electrochemically active biofilms must be studied with a multidisciplinary mindset, bringing together ideas and techniques from multiple fields. Mathematical modeling is a powerful tool that can provide a unifying framework for theories and data from the disparate and multidisciplinary fields of biofilm research. In this chapter, our goal was to develop a model capable of simulating two simultaneous electron transfer mechanisms in electrochemically active biofilms and demonstrate the practical implementation of this model using a MATLAB® client connection to run finite element method software Comsol Multiphysics®. Evidence in the literature suggests that some biofilms, particularly Shewanella oneidensis, produce the requisite components for multiple extracellular electron transfer mechanisms. In this study, a generic model is presented that incorporates diffusion- and conduction-based mechanisms and allows electrochemically active biofilms to utilize both mechanisms simultaneously. The model was applied to S. oneidensis and Geobacter sulfurreducens biofilms using experimentally generated data found in the literature. Our simulation results show that (1) biofilms having both mechanisms available, especially if they can interact, may have a metabolic advantage over biofilms that can use only a single mechanism; (2) the thickness of G. sulfurreducens biofilms is likely not limited by conductivity; (3) accurate intrabiofilm diffusion coefficient values are critical for current generation predictions; and (4) the local biofilm potential and redox potential are two distinct parameters and cannot be assumed to have identical values. Finally, we determined that simulated cyclic and squarewave voltammetry based on our model are currently not capable of determining the specific percentages of extracellular electron transfer mechanisms in a biofilm. This chapter shows how mathematical modeling can be used as a unifying tool for investigating electrochemically active biofilms and electron transfer mechanisms.
Time-resolved lasing dynamics for plasmonic system with gain (Presentation Recording) (2015)

To study the light-matter interaction between plasmonic systems and gain media, numerous theoretical and numerical methods have been proposed. Among them, because of its accurate treatment of the quantum property of gain media, the time domain (TD) multi-physics approach is viewed as the most powerful method, especially for analysis of transient dynamics. Even though the finite difference, finite-volume and finite element TD methods can be readily coupled to a multi-level atomic system through auxiliary differential equations, for each of them however there is limited information on accurate TD kinetic parameters fitted with experimental measurements. In this work, we develop a multi-physics time domain model to inspect our most recent lasing experiment with a silver nanohole array. We use a classical finite difference time-domain (FDTD) model coupled to the rate equations of a 4-level gain system. To retrieve kinetic energy parameters for accurate modeling, we first fit 1-D simulations with pump-probe experiments studying Rhodamine-101 (R-101) dye embedded in epoxy on an indium tin oxide silica substrate. The retrieved parameters are then fed into a 3-D model to study the lasing behavior of the R-101-coated nanohole array. The simulated emission intensity shows a clear lasing effect, which is in good agreement with the experimental measurements. By tracing the population inversion and polarization dynamics, the amplification and lasing regimes inside the nanohole cavity can be clearly distinguished. With the help of our systematic approach, we can further improve understanding of the time-resolved physics of active plasmonic nanostructures with gain.
Shugoshin ensures maintenance of the spindle assembly checkpoint response and efficient spindle disassembly (2021)

Shugoshin proteins are evolutionarily conserved across eukaryotes, with some species-specific cellular functions, ensuring the fidelity of chromosome segregation. They act as adaptors at various subcellular locales to mediate several protein-protein interactions in a spatio-temporal manner. Here, we characterize shugoshin (Sgo1) in the human fungal pathogen Candida albicans. We observe that Sgo1 retains its centromeric localization and performs its conserved functions of regulating the sister chromatid biorientation, centromeric condensin localization, and maintenance of chromosomal passenger complex (CPC). We identify novel roles of Sgo1 as a spindle assembly checkpoint (SAC) component with functions in maintaining a prolonged SAC response by retaining Mad2 and Bub1 at the kinetochores in response to improper kinetochore-microtubule attachments. Strikingly, we discover the in vivo localization of Sgo1 along the length of the mitotic spindle. Our results indicate that Sgo1 performs a hitherto unknown function of facilitating timely disassembly of the mitotic spindle in C. albicans. To summarize, this study unravels a unique functional adaptation of shugoshin in maintaining genomic stability.
Revisiting the role of acids and hydrogen bond acceptors in enamine formation (2020)

A systematic investigation into the effects of acids and hydrogen bond acceptors on the reaction rates and equilibria of enamine formation is reported. Acids can accelerate the reaction but do not change the reaction equilibria. In comparison, hydrogen bond acceptors facilitate the enamine formation via their strong hydrogen bonding interaction with the water generated in the reaction.
Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion (2020)

The hand of molecular mimicry in shaping SARS-CoV-2 evolution and immune evasion remains to be deciphered. We identify 33 distinct 8-mer/9-mer peptides that are identical between SARS-CoV-2 and human proteomes, along similar extents of viral mimicry observed in other viruses. Interestingly, 20 novel peptides have not been observed in any previous human coronavirus (HCoV) strains. Four of the total mimicked 8-mers/9-mers map onto HLA-B*40:01, HLA-B*40:02, and HLA-B*35:01 binding peptides from human PAM, ANXA7, PGD, and ALOX5AP proteins. This mimicry of multiple human proteins by SARS-CoV-2 is made salient by the targeted genes being focally expressed in arteries, lungs, esophagus, pancreas, and macrophages. Further, HLA-A*03 restricted 8-mer peptides are shared broadly by human and coronaviridae helicases with primary expression of the mimicked human proteins in the neurons and immune cells. This study presents the first comprehensive scan of peptide mimicry by SARS-CoV-2 of the human proteome and motivates follow-up research into its immunological consequences.
Fatigue Life and Its stress Ratio Dependence of Short Carbon Fiber-Reinforced Polyamide Composites (2016)

The static and fatigue behaviors of discontinuous carbon fiber-reinforced polyamide (DCF/PA) composite have been examined. Static tension and compression tests are first performed at different temperatures (RT, 70°C and 130°C) to quantify the temperature dependence of basic mechanical properties of the composite. Then, constant amplitude fatigue tests are carried out for different stress ratios (0.1, χ, -1, and 10) at different temperatures (RT, 70°C and 130°C), respectively. The fatigue test results demonstrate that the S-N relationship of the discontinuous fiber composite significantly depends on stress ratio, and the fatigue degradation occurs most rapidly at the critical stress ratio in line with the observations made thus far for continuous fiber composites. Finally, the anisomorphic constant fatigue life diagram approach developed for continuous carbon fiber composites is applied to the DCF/PA composite, and it is proved that this method can successfully be used to predict the fatigue life of the discontinuous carbon fiber composite at different stress ratios.
Efficient coupling between free electrons and the supermode of a silicon slot waveguide (2023)

Laser light can modulate the kinetic energy spectrum of free electrons and induce extremely high acceleration gradients, which are instrumental to electron microscopy and electron acceleration, respectively. We present a design scheme for a silicon photonic slot waveguide which hosts a supermode to interact with free electrons. The efficiency of this interaction relies on the coupling strength per photon along the interaction length. We predict an optimum value of 0.4266, resulting in the maximum energy gain of 28.27 keV for an optical pulse energy of only 0.22 nJ and duration 1 ps. The acceleration gradient is 1.05 GeV/m, which is lower than the maximum imposed by the damage threshold of Si waveguides. Our scheme shows how the coupling efficiency and energy gain can be maximized without maximizing the acceleration gradient. It highlights the potential of silicon photonics technology in hosting electron-photon interactions with direct applications in free-electron acceleration, radiation sources, and quantum information science.
The case for broader computer architecture education (2004)

Most introductory computer architecture courses -- at both the graduate and undergraduate level -- are primarily courses on CPU architecture. They tend to cover instruction set architecture, processor microarchitecture, and perhaps caches. While this is all useful content, our students would be better served by an introductory course that paints a more complete picture of computer architecture and one that better places computer architecture in context with the related fields of digital design and compilers.