gebhart/patrepeval huggingface dataset:
Cellular zinc and redox buffering capacity of metallothionein/thionein in health and disease. (2007)

Zinc is involved in virtually all aspects of cellular and molecular biology as a catalytic, structural, and regulatory cofactor in over 1000 proteins. Zinc binding to proteins requires an adequate supply of zinc and intact molecular mechanisms for redistributing zinc ions to make them available at the right time and location. Several dozen gene products participate in this process, in which interactions between zinc and sulfur donors determine the mobility of zinc and establish coupling between cellular redox state and zinc availability. Specifically, the redox properties of metallothionein and its apoprotein thionein are critical for buffering zinc ions and for controlling fluctuations in the range of picomolar concentrations of "free" zinc ions in cellular signaling. Metallothionein and other proteins with sulfur coordination environments are sensitive to redox perturbations and can render cells susceptible to injury when oxidative stress compromises the cellular redox and zinc buffering capacity in chronic diseases. The implications of these fundamental principles for zinc metabolism in type 2 diabetes are briefly discussed.
Super-polynomial quantum speed-ups for boolean evaluation trees with hidden structure (2012)

We give a quantum algorithm for evaluating a class of boolean formulas (such as NAND trees and 3-majority trees) on a restricted set of inputs. Due to the structure of the allowed inputs, our algorithm can evaluate a depth n tree using O(n2+logω) queries, where ω is independent of n and depends only on the type of subformulas within the tree. We also prove a classical lower bound of nΩ(log log n) queries, thus showing a (small) super-polynomial speed-up.
Optical bistability in a silicon nitride waveguide grating (2016)

Using the Fourier Modal Method for gratings with Kerr media [J. Opt. Soc. Am. B 31, 2371 (2014)] we demonstrate that low energy Optical Bistability for normally incident light field can be observed by strong nonlinear light-matter interactions in a Silicon Nitride waveguide-grating with 2-D periodicity. Finite divergence of the incident light beam has been taken into account in our numerical study and the gratings are designed to observe bistable behavior in direct transmitted light inside the optical telecommunication C-band (1520 nm-1570 nm). The waveguide grating structures are fabricated from PECVD synthesized Silicon Nitride thin film on top of quartz with standard electron beam lithography and reactive ion etching techniques. We aim to demonstrate this phenomenon experimentally using a tunable narrow line-width pulsed laser. Our resonant nanostructures may find applications in free space all-optical information processing and all-optical switching.
Table S3 from Single and Dual Targeting of Mutant EGFR with an Allosteric Inhibitor (2023)

&lt;p&gt;Pharmacokinetic properties of JBJ-02-112-05 and JBJ-04-125-02.&lt;/p&gt;
An intuitive muscle-computer interface using ultrasound sensing and Markovian state transitions (2018)

In recent work regarding gesture recognition and muscle computer interfaces, ultrasound-based sensing strategies have been demonstrated as a viable alternative to the pervasive surface electromyography (sEMG) modality. However, in order to facilitate switching between available gestures, both sEMG and ultrasound-based strategies have traditionally relied on unintuitive control mechanisms. The most common among these are: requiring the users to return to rest as an intermediary state between motions; mode switching through co-contraction or other ad-hoc user input; and switching based on muscle activations that are functionally unrelated to the desired motion. The unintuitive nature of such control has historically led to increased user frustration, and is often cited a major reason for device abandonment in the prosthetic control setting. In this work, we propose using an approach inspired by Hidden Markov Models (HMMs) with a novel continuous gesture recognition mechanism, for ultrasound-based sensing. We empirically calculate the average classification accuracy of our novel method during non-transitionary periods to be 99%. We then demonstrate that including predictions made during transition periods reduces this value to 69% Finally, by encoding the temporal dependency of the system within a Hidden Markov Model framework, we show that we can reduce the error caused by the instability of predictions during transitions, measured as the normalized Levenshtein distance from the true ordering, by approximately 98.8%.
BEHAVIORAL SIMULATION AND SYNTHESIS ENVIRONMENT FOR CONTINUOUS-TIME SINGLE-LOOP SINGLE-BIT BASEBAND DELTA-SIGMA ANALOG-TO-DIGITAL MODULATORS (2006)

For the past few decades, research and design of CAD tools have focused on developing a set of tools that will guarantee designers first-pass fabrication success.There have been many variations of digital design "suites" that make this claim.With the increase in integrated circuit complexity and the drive for systems-on-a-chip (SoC), companies and universities are now focusing their efforts on creating design tools addressing the analog and RF domains.System-level design is one of the most important and challenging elements in the mixed-signal design process.Currently, many system designs are approached from a bottom-up perspective where components are designed individually and then assembled at the system-level.Concepts such as analog and digital interfacing, defining component specifications, and system verification are typically lacking or are addressed too late.Rapid modeling and component-level trade-offs are important in the design of systems.Many of these integration issues can be addressed early in the design phase by having the capability to predict and model component-level effects.In order to address these issues of system design and synthesis, four primary tools have been developed.These tools include (1) a continuous-time delta-sigma system modeler and designer, (2) a circuit sizer, (3) a performance analysis system, and (4) a parameterized module layout generator.Various analog synthesis flows have been developed using these tools.The first goal of this thesis is to provide the design community with a behavioral environment that will model and aid in the creation of continuous-time single-loop single-bit baseband deltasigma analog-to-digital modulators using MATLAB R and Simulink R .The second goal is to use the designs from the delta-sigma toolbox to produce component-level specifications derived from system-level requirements.In this thesis, the developed tools were used in a synthesis loop to design, implement, and verify two continuous-time delta-sigma modulators and their respective components.A third order modulator was designed with 1 MHz instantaneous bandwidth and a sampling rate of 64 MSps using the top-down design methodology.The modulator performed with an SNR of 60 dB and ENOB of 9.7 bits.A fourth order modulator with a sample rate of 50 MSps was designed with a bandwidth of 390 kHz, and the bottom-up design methodology was used.This design performed with an SNR of 74.2 dB and ENOB of 12.0 bits.I extend my gratitude to Dr. Hal Carter and Dr. Wen-Ben Jone for their valuable suggestions
Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism (2009)

Recent studies have documented various roles of adrenal corticosteroid signaling in cardiac physiology and pathophysiology. It is known that glucocorticoids and aldosterone are able to bind glucocorticoid receptor (GR) and mineralocorticoid receptor, and these ligand-receptor interactions are redundant. It, therefore, has been impossible to delineate how these nuclear receptors couple with corticosteroid ligands and differentially regulate gene expression for operation of their distinct functions in the heart. Here, to particularly define the role of GR in cardiac muscle cells, we applied a ligand-based approach involving the GR-specific agonist cortivazol (CVZ) and the GR antagonist RU-486 and performed microarray analysis using rat neonatal cardiomyocytes. We indicated that glucocorticoids appear to be a major determinant of GR-mediated gene expression when compared with aldosterone. Moreover, expression profiles of these genes highlighted numerous roles of glucocorticoids in various aspects of cardiac physiology. At first, we identified that glucocorticoids, via GR, induce mRNA and protein expression of a transcription factor Kruppel-like factor 15 and its downstream target genes, including branched-chain aminotransferase 2, a key enzyme for amino acid catabolism in the muscle. CVZ treatment or overexpression of KLF15 decreased cellular branched-chain amino acid concentrations and introduction of small-interfering RNA against KLF15 cancelled these CVZ actions in cardiomyocytes. Second, glucocorticoid-GR signaling promoted gene expression of the enzymes involved in the prostaglandin biosynthesis, including cyclooxygenase-2 and phospholipase A2 in cardiomyocytes. Together, we may conclude that GR signaling should have distinct roles for maintenance of cardiac function, for example, in amino acid catabolism and prostaglandin biosynthesis in the heart.
Least-squares Generalized Interferometric Multiple Imaging (2016)

Summary Imaging internal multiples properly has the potential to enhance the quality of the migrated images since they may illuminate subsurface zones that are poorly illuminated by single-scattering energy, such as vertical and nearly vertical faults, and salt flanks. The generalized interferometric multiple imaging procedure aims to migrate internally multiply-scattered energy. Imaging first-order internal multiples using this procedure is composed of a data extrapolation based datuming step, an interferometric cross-correlation datuming step followed by a zero-lag cross-correlation imaging condition with the forward extrapolated datumed data. However, this procedure yields migrated images that suffers from low spatial resolution, and migration artifacts due to the datuming steps based on cross-correlation, cross-talk noise, and band-limited nature of the source wavelet. We propose a least-squares generalized interferometric multiple imaging procedure, in which we replace the first two datuming steps by least-squares datuming ones. The proposed framework would suppress the cross-talk noise and migration artifacts, and deconvolve the source wavelet. Therefore, it would enhance the resolution of the subsurface reflectivity distribution illuminated by first-order internal multiples. Application to two synthetic datasets improved the illumination of subsurface scatterers and the high-resolution delineation of a vertical fault plane using first-order internal multiples.
Reactive magnetron sputter deposited CN<i>x</i>: Effects of N2 pressure and growth temperature on film composition, bonding, and microstructure (1996)

The effects of growth processes on the chemical bond structure, microstructure, and mechanical properties of carbon–nitride (CNx) thin films, deposited by reactive magnetron sputtering in a pure N2 discharge, are reported. The film deposition rate RD increases with increasing N2 pressure PN2 while N/C ratios remain constant. The maximum N concentration was ∼35 at. %. RD was found to be dependent upon the film growth temperature Ts. For a given PN2, RD decreased slightly as Ts was increased from 100 to 600 °C. The variations in RD with both PN2 and Ts can be explained by ion-induced desorption of cyano radicals CNx from both the target and growth surfaces during deposition. X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy (FTIR) analyses showed that N atoms in films grown at Ts≳350 °C with low nitrogen partial pressures PN2, ∼2.5 mTorr, were bound to C atoms through hybridized sp2 and sp3 configurations. For low Ts=100 °C and higher PN2, 10 mTorr, triple-bonded C≡N was detected by FTIR. Two types of microstructures were observed by high-resolution transmission electron microscopy, depending on Ts: an amorphous phase, containing crystalline clusters for films deposited at Ts=100 °C, while a turbostraticlike or fullerenelike phase was observed for films deposited at Ts≳200 °C CNx films deposited a higher Ts and lower PN2 were found to have higher hardness and elastic modulus.
Human NK cells display major phenotypic and functional changes over the life span (2010)

Aging is generally associated with an increased predisposition to infectious diseases and cancers, related in part to the development of immune senescence, a process that affects all cell compartments of the immune system. Although many studies have investigated the effects of age on natural killer (NK) cells, their conclusions remain controversial because the diverse health status of study subjects resulted in discordant findings. To clarify this situation, we conducted the first extensive phenotypic and functional analysis of NK cells from healthy subjects, comparing NK cells derived from newborn (cord blood), middle-aged (18-60 years), old (60-80 years), and very old (80-100 years) subjects. We found that NK cells in cord blood displayed specific features associated with immaturity, including poor expression of KIR and LIR-1/ILT-2 and high expression of both NKG2A and IFN-gamma. NK cells from older subjects, on the other hand, preserved their major phenotypic and functional characteristics, but with their mature features accentuated. These include a profound decline of the CD56(bright) subset, a specific increase in LIR-1/ILT-2, and a perfect recovering of NK-cell function following IL2-activation in very old subjects. We conclude that the preservation of NK cell features until very advanced age may contribute to longevity and successful aging.
Received Power Based Unmanned Aerial Vehicles (UAVs) Jamming Detection and Nodes Classification Using Machine Learning (2023)

This paper presents a machine-learning method for detecting jamming UAVs and classifying nodes during jamming attacks on Wireless Sensor Networks (WSNs). Jamming is a type of Denial of Service (DoS) attack and intentional interference where a malicious node transmits a high-power signal to increase noise on the receiver side to disrupt the communication channel and reduce performance significantly. To defend and prevent such attacks, the first step is to detect them. The current detection approaches use centralized techniques to detect jamming, where each node collects information and forwards it to the base station. As a result, overhead and communication costs increased. In this work, we present a jamming attack and classify nodes into different categories based on their location to the jammer by employing a single node observer. As a result, we introduced a machine learning model that uses distance ratios and power received as features to detect such attacks. Furthermore, we considered several types of jammers transmitting at different power levels to evaluate the proposed metrics using MATLAB. With a detection accuracy of 99.7% for the k-nearest neighbors (KNN) algorithm and average testing accuracy of 99.9%, the presented solution is capable of efficiently and accurately detecting jamming attacks in wireless sensor networks.
Development and Characterization of Membrane and Catalyst Materials for the Cucl(aq)/HC(aq) Electrolytic Cell (2015)

Recent developments in membrane and electrocatalyst characterization techniques for materials used in the CuCl(aq)/HCl(aq) electrolytic cell have significantly increased the amount of experimental data available in literature. Rotating disc electrode (RDE) and membrane conductivity cells capable of operating in highly concentrated HCl(aq) were developed to characterize the material performance of key MEA materials for this electrolytic cell. Specifically, exchange current density and transfer coefficient values for platinum and carbon as the electrocatalyst material for the anode reaction of this electrolytic cell were quantified in highly concentrated HCl(aq) 1 . Additionally, conductivity and permeability parameters of hot-pressed Nafion 117 were characterized for applications in highly concentrated HCl(aq) and CuCl(aq) solutions 2 . Though these fundamental properties are now available, there remained a need for a simple model to connect these properties appropriately to overall cell performance. While equilibrium thermodynamics of this electrolytic cell was carefully studied 3 , the cell electrode kinetics and transport in the membrane have not been modeled yet. Principles of non-equilibrium thermodynamics have the potential to incorporate membrane transport properties and electrochemical kinetic data together into a simple but useful model of this electrolytic cell. The use of linear phenomenological equations with phenomenological coefficients can be used to model the effects of permeability and conductivity on the ohmic resistance of the electrolytic cell. In addition to linear non-equilibrium processes, non-linear nonequilibrium thermodynamic expressions of the electrochemical reactions can be used to model the effects of electrocatalyst properties on the overall cell performance. As a result, suitable electrocatalysts and membrane materials were identified and their effects on the electrolytic cell performance were quantified in the form of a non-equilibrium thermodynamic model. References: 1. D. M. Hall, E. G. LaRow, R. S. Schatz, J. R. Beck, and S. N. Lvov, J. Electrochem. Soc. , 162 , F108–F114 (2015). 2. R. Schatz, S. Kim, S. Khurana, M. Fedkin, and S. N. Lvov, ECS Trans. , 50 , 153–164 (2013). 3. D. M. Hall, N.N. Akinfiev, E. G. LaRow, R. S. Schatz, and S. N. Lvov, Electrochim. Acta , 143 , 70-82 (2014).
AN EPIDEMIOLOGICAL ANALYSIS OF FACTORS INFLUENCING THE INCREASE IN <i>TAENIA OVIS</i> PREVALENCE DURING THE NEW ZEALAND <i>ECHINOCOCCUS GRANULOSUS</i> CONTROL PROGRAM (1977)

There was an 8-fold increase in the national prevalence of Taenia ovis in dogs during the first decade of the New Zealand hydatid disease control program. The temporal patterns in the prevalence of T. ovis were similar in both rural working dogs and urban pet dogs, with the highest prevalence found in the sheep farming areas. The dramatic increase in the prevalence of T. ovis was a reflection of the change in source of food for many working dogs, from the traditional raw viscera to carcase meat of sheep, a change necessitated by hydatid disease control. Other factors influencing the rise in prevalence of T. ovis in rural dogs were investigated using stepwise multiple regression techniques. The results of the regression analyses suggested that the rate of increase in the prevalence of T. ovis was influenced by 4 major factors: Taenia hydatigena variables (initial prevalence and rate of progress in control), an ethnic variable (Maori proportion in local population), canine variables (numbers of dogs per farm and per owner), and animal husbandry variables (pasture type, sheep density and numbers of sheep per farm). The results were discussed in the light of present knowledge of the epidemiology and immunology of the taeniid cestodes.
Investigation of surface cooling by droplet evaporation with IR thermography (2007)

In the present work infrared thermography is used to analyze the cooling effect of a hot solid surface induced by liquid droplets. In particular water droplets are released onto a BaF2 disk heated by radiation from above; the interface temperature is measured from below by means of an AVIO TVS500 infrared camera, carrying a micro-bolometric FPA sensor which operates in the long wave spectral range. The study is focused on the non-intrusive technique used to measure the transient temperature at the interface between impinging droplets and hot surface; experimental data are reported and compared with theoretical results.
Hybrid silencer by using micro-perforated plate with side-branch cavities (2012)

A plate silencer consists of an expansion chamber with two side-branch cavities covered by light but extremely stiff plates. It works effectively with wide stopband from low-to-medium frequencies only if the plate is extremely stiff, to ensure a strong reflection of acoustic wave to the upstream in the duct. However, a plate with slightly weak bending stiffness will result in non-uniform transmission loss (TL) spectra with narrowed stopband. In this study, a hybrid silencer is proposed by introducing micro-perforations into the plate to elicit the sound absorption in order to compensate for the deficiency in the passband caused by the insufficient sound reflection in certain frequency range due to plate with weaker stiffness. A theoretical model, capable of dealing with the strong coupling between the vibrating micro-perforated plate and sound fields inside the cavity and the duct, is developed. Through a proper balancing between the sound absorption and reflection, the proposed hybrid plate silencer with moderately stiff plates is shown to outperform the typical plate silencer with very stiff plate. Whilst releasing the harsh requirement on the bending stiffness of the plate, the proposed hybrid silencer provides a more flattened and uniform TL and a widened stopband by about 30%.
Atomic Scale Characterization on <scp>III‐V</scp> Based Heterostructure Nanowire Interfaces (2016)

Quasi‐one‐dimensional III‐V semiconducting nanowires attract enormous attention owing to their physical properties such as tunable direct bandgap, high surface to volume ratio, high carrier mobility, tunable structures. Hence they have potential application in next generation electronics, sensors, photonics and photovoltaics. Understanding the details such as, atomic scale structure, local chemical stoichiometry and defects in a sub nanometer scale are inevitable when nanowires are intended for devices. A systematic interfacial investigation on molecular beam epitaxy grown III‐V based nanowires such as InAs, GaAs, [1] in general and in particular, heterostructure nanowires of axially grown Ga x In 1_x As‐InAs and InAs‐InAsSb will be presented. [2] In this work, atomic scale structural interfaces and interfacial chemical composition are analyzed using advanced aberration corrected transmission electron microscopy. Atomic resolution high angle annular dark field scanning transmission electron microscopy (HAADF‐STEM) and high resolution energy dispersive x‐ray spectroscopy techniques are predominatly used for characterizing the grown nanowires. Our work demonstrates on tailoring the growth, periodicities and the stoichiometry of III‐V nanowire heterostructure containing single/multiple electronic barriers involving In,Ga,As and Sb. We aim to provide understanding on the growth of dissimilar interfaces in heterostructure nanowire (see fig 1). In the InAs‐InAsSb heterostructure wires, [1] our work demonstrates the quality of the misfit strained interface in terms of structural abruptness and chemical homogeneity.