gebhart/patrepeval huggingface dataset:
Molecular structure and function of myelin protein P0 in membrane stacking (2018)

Abstract Compact myelin forms the basis of nerve insulation essential for higher vertebrates. Dozens of myelin membrane bilayers undergo tight stacking, and in the peripheral nervous system, this is partially enabled by myelin protein zero (P0). Consisting of an immunoglobulin (Ig)-like extracellular domain, a single transmembrane helix, and a cytoplasmic extension (P0ct), P0 harbours an important task in ensuring the integrity of compact myelin in the extracellular compartment, referred to as the intraperiod line. Several disease mutations resulting in peripheral neuropathies have been identified for P0, reflecting its physiological importance, but the arrangement of P0 within the myelin ultrastructure remains obscure. We performed a biophysical characterization of recombinant P0ct. P0ct contributes to the binding affinity between apposed cytoplasmic myelin membrane leaflets, which not only results in fluidity changes of the bilayers themselves, but also potentially involves the rearrangement of the Ig-like domains in a manner that stabilizes the intraperiod line. Transmission electron cryomicroscopy of native full-length P0 showed that P0 stacks lipid membranes by forming antiparallel dimers between the extracellular Ig-like domains. The zipper-like arrangement of the P0 extracellular domains between two membranes explains the double structure of the myelin intraperiod line. Our results contribute to the understanding of PNS myelin, the role of P0 therein, and the underlying molecular foundation of compact myelin stability in health and disease.
Data supporting "The Role of Photon Recycling in Perovskite Light-Emitting Diodes" (2019)

Data underlying each of the graphical figures in the associated publication regarding photon recycling in perovskite LEDs. These include: Figure 1: absorption and emissions spectra; PLE spectra; intensity dependence of luminescence. Figure 2: spatial PL intensity, and PL spectra at various positions. Figure 3: Output of optical model.
Lysophospholipid G Protein-coupled Receptors (2004)

The many biological responses documented for lysophospholipids that include lysophosphatidic acid and sphingosine 1-phosphate can be mechanistically attributed to signaling through specific G protein-coupled receptors. At least nine receptors have now been identified, and the total number is likely to be larger. In this brief review, we note cogent features of lysophospholipid receptors, including the current nomenclature, signaling properties, development of agonists and antagonists, and physiological functions.
Electrically driven photonic crystal nanocavity lasers, LEDs, and modulators (2012)

A fabrication procedure for electrically pumping photonic crystal membrane devices using a lateral p-i-n junction has been developed and is described in this work. The lateral junction is optimized to efficiently inject current into a photonic crystal nanocavity. We have demonstrated electrically pumped lasing by using the lateral junction to pump a quantum dot photonic crystal nanocavity laser. Continuous wave lasing is observed at temperatures up to 150K, and a threshold of 181nA at 50K is demonstrated - the lowest threshold ever demonstrated in an electrically pumped laser. At room temperature we find that our devices do not lase, but behave as single-mode light-emitting diodes (LEDs). When directly modulated, we find that our LEDs have an ultrafast electrical response up to 10 GHz corresponding to less than 1 fJ/bit energy operation. In addition, we have demonstrated electrical pumping of photonic crystal nanobeam LEDs, and have built fiber taper coupled electro-optic modulators in the same lateral junction platform.
Biochemical and structural characterization of recombinant copper‐metallothionein from Saccharomyces cerevisiae (1999)

Methods were developed for large-scale purification of recombinant Cu-metallothionein (Cu-MT) for structural investigations and the determination of Cu-binding stoichiometry. Cu-MT of Saccharomyces cerevisiae overexpressed in Escherichia coli was purified using a procedure based on ion exchange and gel filtration chromatography followed by reversed-phase HPLC. The purified protein was fully characterized by electrophoresis, amino acid analysis, atomic absorption spectroscopy and elemental analysis, and was shown to contain 10 +/- 2 Cu(I) per molecule of protein. Small angle X-ray scattering measurements yielded a radius of gyration of 1.2 nm for the recombinant protein, indicating a more extended structure in solution than that derived from the recent NMR data [Peterson, C.W., Narula, S.S. & Armitage, I.A. (1996) FEBS Lett. 379, 85-93].
Sex differences in neurotransmitter levels in different brain regions after acute and chronic morphine treatment in mice (2023)

ABSTRACT Background and Purpose Pain management is a major health burden. Pain results from the integration of the nociceptive message and neuronal communication relying on neurotransmitters such as glutamate, γ-aminobutyric acid (GABA), dopamine, noradrenaline and serotonin in brain regions including the periaqueductal gray (PAG), the nucleus accumbens (Nac), the caudate-putamen (Cpu) and the amygdala. Morphine remains the gold standard painkiller for severe pain via the activation of the mu opioid receptors. However, among side effects, morphine chronic treatment lead to antinociceptive tolerance. As antinociceptive tolerance might be linked to neurotransmission dysregulation, we have compared various neurotransmitter concentrations in acute vs chronic morphine conditions in the amygdala, PAG, Cpu, and the Nac of male and female mice. Experimental approach Sex differences in morphine antinociception and tolerance were assessed using the tail-immersion test. The behavioural effects of acute and chronic morphine treatments, as well as sex differences in the levels of dopamine, serotonin, noradrenaline, glutamate and GABA in the amygdala, PAG, Cpu, and the Nac were determined by an absolute quantification LC-MS/MS approach using the isotopic dilution method. Key results This study indicates, as previously reported, that female mice are less sensitive to morphine and develop morphine antinociceptive tolerance earlier than males (ED50 of 5.5±0.24 days vs 1.54±0.11 days, respectively). However, the rate at which the tolerance developed did not differ between both sex. We have found major differences in dopamine, serotonin, noradrenaline, glutamate and GABA levels between female and male mice in the amygdala, PAG, Cpu, and the Nac. Finally, no major effect of anti-nociceptive tolerance induced by chronic morphine was observed compared to acute administration of morphine. Conclusion Neurotransmitter differences are attributable mainly to sex differences in pain-related CNS regions. However, the impacts of morphine anti-nociceptive tolerance on dopamine, serotonin, noradrenaline, glutamate and GABA contents appeared to be limited.
An ADMM-based approach for multi-class recursive parameter estimation (2021)

Due to the increasing popularity of cloud-based architectures, it is of paramount importance to understand how to benefit from shared information for solving collaborative estimation problems and exploit the additional computational resources available. Meanwhile, it is crucial to devise solutions that allow connected devices to retain private data and to carry out the desired tasks on their own, when disconnected from the cloud.In this paper, we present a cloud-aided iterative solution for multi-class parameter estimation for a set of mass-produced devices. The method exploits the similarity between systems operating under comparable conditions and their connection to the cloud, while allowing devices to retain and process raw data privately. The effectiveness of the strategy is assessed on a numerical example, showing its potential.
GNSS Spoof Detection using Independent Range Information (2016)

Global Navigation Satellite Systems (GNSS) are well known to be accurate providers of position information across the globe; as such, they are commonly used to locate and navigate craft in various transportation modes. Because of high signal availabilities, capable receivers, and well-populated satellite constellations, GNSS users typically believe that the position information provided by their GNSS receiver is perfectly accurate. More sophisticated users look beyond accuracy and are also concerned with the integrity of the GNSS information; for example, RAIM algorithms were developed to ensure users that the provided position information is resistant to several possible satellite failure modes. Advances in electronics technology have enabled the creation of malicious RF interference of GNSS signals. Inexpensive jamming devices overpower or distort the GNSS receiver’s input so as to completely deny the GNSS user of PNT information. While a serious concern when we expect PNT information to be available at all times, current generation GNSS receivers warn the user when PNT is unavailable; some of the more sophisticated receiver designs can also battle jamming. A second threat to GNSS integrity is spoofing, the creation of counterfeit GNSS signals. This type of attack is considered more dangerous than a jamming attack since an erroneous PNT solution is often worse than no solution at all. A variety of approaches have been proposed in the literature to recognize spoofing and can vary widely based upon the assumed capabilities and a priori knowledge of the spoofer. Some of these are based on characteristics of the RF signal alone (e.g. vestigial peaks in the correlator outputs) or employ multiple antennae (e.g. beamforming) or multiple receivers (looking for consistent data). Another spoof detection method is to compare the GNSS measurement to data from a sensor of a different type that cannot be spoofed; for example, several prior efforts have considered IMU data. This paper considers the use of range measurements (range only, no bearing) to detect spoofing. Range might be measured using RF signals (e.g. DME for avionics) although other modalities could be effective (e.g. a calibrated barometric altimeter). Assuming that the data set consists of a GNSS measurement and ranges to one or more fixed sites, this paper develops the binary hypothesis test between spoofing and no spoofing. The unknown positions naturally lead to a generalized likelihood approach. We initially focus on the simplest case of one range measurement and a simple Gaussian model for the GNSS position measurement; this scenario allows for a simple closed form solution from which we can examine the characteristics of the test (it is similar to RAIM) and to observe the interaction between the relative accuracy of the sensors (GNSS and range) on the form of the hypothesis test and its resulting performance at detecting spoofing. We then generalize the results to multiple ranges and correlated statistics.
Difficult removal of exposed peripheral nerve stimulator leads: a report of 2 cases (2021)

Thorough patient education, early postimplantation assessment, and extended routine follow-up are necessary to decrease lead-associated complications. If migration does occur, the potential impact of scar tissue on removal should be considered.
Solar Cycle Influences Seen in Ground-Based Geocoronal Hydrogen Measurements (2006)

Long term observations of geocoronal hydrogen offer potential to contribute to our understanding of vertical coupling processes affecting hydrogen-containing species. For example, models predict a 40-75% increase in exospheric hydrogen associated with a doubling of tropospheric concentrations of carbon dioxide and methane [Roble, AGU meeting, Spring 2005; Roble and Dickinson, 1989; Ehhalt, 1986]. Understanding the influence of the solar cycle on the upper atmosphere is required to isolate signatures of natural variability from those due to human-caused change. Mid-latitude ground-based Fabry-Perot Interferometer observations of geocoronal hydrogen fluorescence emissions by Wisconsin observers now span more than two decades and include observations taken near Madison, Wisconsin, as well as more recent observations from the Kitt Peak Observatory, near Tucson, Arizona. Observations of thermospheric exospheric Balmer-alpha column emissions by the Wisconsin H- Alpha Mapper (WHAM) Fabry-Perot (Kitt Peak, Arizona) show a statistically significant solar cycle variation over solar cycle 23 with intensities at midrange shadow altitudes approximately 45% higher during solar maximum compared with solar minimum conditions. The higher signal-to-noise WHAM observations corroborate suggestions of a solar cycle trend in observations of Balmer-alpha emissions from Wisconsin over solar cycle 22. Geocoronal hydrogen column emissions are a function of both the vertical density structure and the incoming solar UV radiation, both of which change over the course of the solar cycle. Multiple scattering of solar Lyman line radiation below the Earth's shadow complicates the analysis of the observations requiring the use of detailed data/forward modeling comparisons to retrieve geophysical information such as the hydrogen column abundance from the observations [Bishop, 1999; Bishop et al., 2004]. We will discuss our previous solar minimum observations and plans for observations during the upcoming solar minimum period, including the challenges and strategies associated with comparing data taken with different, but similarly designed, instruments at different mid-latitude observatories. We will also discuss work in progress on parameter definitions in the forward modeling technique, tested in terms of sensitivity under differing observing applications (e.g., lone station measurements versus coincident measurements acquired by several independent instruments).
Simulation-based verification for high-level synthesis (1991)

The verification problem is described, and a way to verify a high-level synthesis system automatically is presented. The system, called Satya, maps an algorithmic description to a logic circuit description and compares descriptions to detect semantic errors and identify the cause of those errors. Satya has been used to verify the Bridge synthesis system, which accepts a subset of C as input, but the simulation-based approach underlying Satya is suitable for verifying synthesis systems that use other high-level languages, such as VHDL. The verification results are discussed, and some of the problems that arise in debugging and regression testing are considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Induction of endogenous interleukin 1 alpha limits to one cycle the proliferative response to FGF (2015)

We found that transient FGF stimulation of various cell types results in the novel phenomenon termed “FGF memory” – a sustained blockage of efficient proliferative response to FGF, PDGF or EGF. FGF memory establishment requires HDAC activity, indicating its epigenetic character. FGF treatment stimulates the proinflammatory NFkappaB signaling, which is also critical for FGF memory formation. The search of potential FGF‐induced mediators of FGF memory revealed that FGF induces a sustained expression of the inflammatory cytokine IL1alpha, and this induction is abolished by HDAC inhibitors. Similarly to FGF pretreatment, transient cell treatment with recombinant IL1alphainhibits the proliferative response to further FGF stimulation. However, cells pretreated with FGF or IL1alpha exhibit an enhanced restructuring of actin cytoskeleton and migration in response to FGF. IL1alpha‐prestimulated cells respond to FGF treatment by ERK1/2 phosphorylation and expression of cyclin D1, but not of cyclin A. Both IRAP, a specific inhibitor of IL1 receptor, and neutralizing anti‐IL1alphaantibodies prevent the formation of FGF memory and rescue an efficient proliferative response to FGF restimulation. Thus, FGF memory is mediated by the endogenous IL1alpha. It may play a role in the limitation of proliferative response to tissue damage and prevention of wound‐induced hyperplasia.
Configuration Policy Extraction for Parameter Settings in Cloud Infrastructure Using UML/OCL Verification (2013)

To manage cloud computing infrastructures consisting of many servers having a massive number of configuration parameters is quite burdensome for administrators of infrastructures. While some policy-based management approaches have been proposed to maintain the system configuration, it is quite difficult for administrators to define proper configuration policies for parameter settings in large-scale cloud computing infrastructure. To solve this problem, we developed a method of extracting parameter configuration policies from the configuration information of the existing infrastructure using UML/OCL verification. In this method, first we identify the scopes of management from the hierarchical topology of the cloud infrastructure. Next, we execute verifications of two types of OCL constraints (regarding parameter configuration patterns) for the configuration of the infrastructure, while changing the range of the scopes we focus on. By determining whether or not these constraints can be satisfied with some scopes, we extract policies that represent patterns satisfied between parameter settings of servers deployed in a certain range of the scope. Then, we demonstrate that we can derive configuration policies for all of parameters of servers in an actual cloud service infrastructure through a case study.
Coupling of low-energy electrons in the optimally dopedBi2Sr2CaCu2O8+δsuperconductor to an optical phonon mode (2009)

Laser-based photoemission with photons of energy 6 eV is used to examine the fine details of the very low-energy electron dispersion and associated dynamics in the nodal region of optimally doped Bi2212. A ``kink'' in the dispersion in the immediate vicinity of the Fermi energy is associated with scattering from an optical phonon previously identified in Raman studies. The identification of this phonon as the appropriate mode is confirmed by comparing the scattering rates observed experimentally with the results of calculated scattering rates based on the properties of the phonon mode.
Risk factors of aseptic bone resorption: a study after autologous bone flap reinsertion due to decompressive craniotomy (2013)

In patients undergoing bone flap reinsertion after craniotomy, aseptic bone necrosis is an underestimated problem during long-term follow-up. Especially in younger patients with an expected good neurological recovery and a fragmented bone flap, an initial allograft should be considered because of an increased risk for aseptic bone flap necrosis.
A High-Speed 390GHz BPOOK Transmitter in 28nm CMOS (2020)

This paper presents a 390GHz transmitter in 28nm bulk CMOS employing the spectrally efficient binary-phase on-off keying (BPOOK) modulation. A novel switch-based modulator is proposed, enabling high-speed OOK, BPSK and BPOOK modulation at 130GHz. The modulated signal is amplified by a three-stage power amplifier and converted to 390GHz by a frequency tripler. The transmitter achieves an output power of -5.4dBm at 390GHz with a power consumption of 114mW. A maximum data rate of 28Gb/s is achieved with BPOOK and 18Gb/s with OOK and BPSK modulation.
Microwave plasma nitridation of silicon dioxide on strained Si (1998)

Growth of ultrathin (&amp;lt;100 Å) nitrided SiO2 on strained Si using microwave O2/N2O/NH3 plasma is reported. X-ray photoelectron spectroscopy results indicate a nitrogen-rich layer at the strained Si/SiO2 interface. The electrical properties of the nitrided oxides have been characterized using a metal–insulator–semiconductor structure. N2O plasma treatment of O2/NH3 nitrided SiO2 results in a lower insulator charge density (1.2×1011 cm−2) and a higher breakdown voltage.
Low-temperature wafer bonding using sub-micron gold particles for wafer-level MEMS packaging (2012)

Low-temperature wafer bonding using sub-μm gold particles together with wafer-level pattern transfer method has been developed. Sub-μm Au particle patterns were successfully transferred at 150°C and wafer bonding was performed at 200°C. Surface compliant performance was demonstrated by compression deformation measurement.
Propagation of ultra-wide-band electromagnetic pulses through dispersive media (1995)

We develop an efficient method for the analysis of ultra-wide-band (UWB) electromagnetic pulses (e.g., double-exponential pulse) propagating through a waveguide or cold plasma (i.e., the ionosphere). First we show that the inverse Fourier-transform representations for the electric and magnetic fields satisfy second order, nonhomogeneous, ordinary, differential equations. These differential equations are solved analytically, thereby yielding closed-form expressions involving incomplete Lipschitz-Hankel integrals (ILHIs). The ILHIs are computed using efficient convergent and asymptotic series expansions. We demonstrate the usefulness of the ILHI expressions by comparing them with the fast Fourier-transform technique (FFT). Because of the long tails associated with UWB pulses, a large number of sample points are required in the FFT, to avoid aliasing errors. In contrast, the ILHI expressions provide accurate and efficient numerical results, regardless of the number of points computed. An asymptotic series representation for the ILHIs is also employed, to obtain a relatively simple, late-time approximation for the transient fields. This approximate late-time expression is shown to accurately model the waveform over a large portion of its time history.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
MUSIC: Mutation-based SQL Injection Vulnerability Checking (2008)

SQL injection is one of the most prominent vulnerabilities for web-based applications. Exploitation of SQL injection vulnerabilities (SQLIV) through successful attacks might result in severe consequences such as authentication bypassing, leaking of private information etc. Therefore, testing an application for SQLIV is an important step for ensuring its quality. However, it is challenging as the sources of SQLIV vary widely, which include the lack of effective input filters in applications, insecure coding by programmers, inappropriate usage of APIs for manipulating databases etc. Moreover, existing testing approaches do not address the issue of generating adequate test data sets that can detect SQLIV. In this work, we present a mutation-based testing approach for SQLIV testing. We propose nine mutation operators that inject SQLIV in application source code. The operators result in mutants, which can be killed only with test data containing SQL injection attacks. By this approach, we force the generation of an adequate test data set containing effective test cases capable of revealing SQLIV. We implement a MUtation-based SQL Injection vulnerabilities Checking (testing) tool (MUSIC) that automatically generates mutants for the applications written in Java Server Pages (JSP) and performs mutation analysis. We validate the proposed operators with five open source web-based applications written in JSP. We show that the proposed operators are effective for testing SQLIV.
An integrated speech and natural language dialog system : using dialog knowledge in speech recognition (2018)

Computer Science Department