gebhart/patrepeval huggingface dataset:
Glutaredoxin Protects Cerebellar Granule Neurons from Dopamine-induced Apoptosis by Dual Activation of the Ras-Phosphoinositide 3-Kinase and Jun N-terminal Kinase Pathways (2001)

Glutaredoxin 2 (Grx2) from Escherichia coli protects cerebellar neurons from dopamine-induced apoptosis via nuclear factor kappa B (NF-kappaB) activation, which is mediated by the expression of redox factor-1 (Ref-1). An analysis of the mechanisms underlying Grx2 protective activity revealed dual activation of signal transduction pathways. Grx2 significantly activated the Ras/phosphoinositide 3-kinase/Akt/NF-kappaB cascade in parallel to the Jun N-terminal kinase (JNK)/AP1 cascade. Dopamine, in comparison, down-regulated both pathways. Treatment of neurons with Ref-1 antisense oligonucleotide reduced the ability of Grx2 to activate Akt and AP-1 but had no effect on the phosphorylation of JNK1/2, suggesting that Akt/NF-kappaB and AP-1 are regulated by Ref-1. Exposure of the neurons to JNK1/2 antisense oligonucleotide in the presence of Grx2 significantly reduced AP-1 and NF-kappaB DNA binding activities and abolished Grx2 protection. These results demonstrate that dual activation of Ras/phosphoinositide 3-kinase and AP-1 cascades, which are mediated by Ref-1, is an essential component of the Grx2 mechanism of action.
Superprism Effect: Physics, Modeling, and Fabrication (2006)

A general, rigorous theory of photonic crystal refraction is developed for both ordinary crystallographic surfaces and quasi-periodic surfaces. A wavelength demultiplexer is designed based on the superprism effect. Fabricated photonic crystals are presented.
JaxPruner: A concise library for sparsity research (2023)

This paper introduces JaxPruner, an open-source JAX-based pruning and sparse training library for machine learning research. JaxPruner aims to accelerate research on sparse neural networks by providing concise implementations of popular pruning and sparse training algorithms with minimal memory and latency overhead. Algorithms implemented in JaxPruner use a common API and work seamlessly with the popular optimization library Optax, which, in turn, enables easy integration with existing JAX based libraries. We demonstrate this ease of integration by providing examples in four different codebases: Scenic, t5x, Dopamine and FedJAX and provide baseline experiments on popular benchmarks.
Modeling of metal-ferroelectric-semiconductor field effect transistor subthreshold current (1994)

Abstract A subthreshold current model for metal-ferroelectric-semiconductor field effect transistor (MFSFET) is derived from a new analytical ferroelectric hysteresis model,1.2 the semiconductor surface model,3 the classical diffusion current model,4 as well as the Maxwell equations. The model predicates the shift of MFSFET subthreshold current between forward sweep and backward sweep of gate bias. The simulation results show the effects of coercive voltage, the remanent polarization, the saturation polarization, and the free interface charge between ferroelectric and semiconductor. The external field effect on the saturation polarization (better known as ferroelectric space charge effect) is also modeled. The conventional method to evaluate the interface trapped charge for metal-oxide-semiconductor system is also proposed for MFS system based on the ideal subthreshold current model and its experimental data.
Transactions letters - Combining long-term and low-rate short-term channel state information over correlated mimo channels (2008)

A simple structure to exploit both long-term and partial short-term channel state information at the transmitter (CSIT) over a family of correlated multiple-antenna channels is proposed. Partial short-term CSIT in the form of a weighting matrix is combined with a unitary transformation based on the long-term channel statistics. The heavily quantized feedback link is directly optimized to maximize the expected achievable rate under different power constraints, using vector quantization and convex optimization techniques on a sample channel distribution. Robustness against errors in the feedback link is also pursued with tools in channel optimized vector quantization. Simulations indicate the benefits of the proposed scheme.
[Generation of functional organs from pluripotent stem cells]. (2015)

Hematopoietic stem cells (HSCs) have played a major role in stem cell biology, providing many conceptual ideas and models. Among them is the concept of the "niche", a special bone-marrow microenvironment that by exchanging cues regulates stem-cell fate. The HSC niche also plays an important role in HSC transplantation. Successful engraftment of donor HSCs depends on myeloablative pretreatment to empty the niche. The concept of the stem-cell niche has now been extended to the generation of organs. We postulated that an empty "organ niche" exists in a developing animal when development of an organ is genetically disabled. This organ niche should be developmentally compensated by blastocyst complementation using wild-type primary stem cells (PSCs). We proved the principle of organogenesis from xenogeneic PSCs in an embryo unable to form a specific organ, demonstrating the generation of functionally normal rat pancreas by injecting rat PSCs into pancreatogenesis-disabled mouse embryos. This principle has held in pigs. When pancreatogenesis-disabled pig embryos underwent complementation with blastomeres from wild-type pig embryos to produce chimeric pigs, the chimeras had normal pancreata and survived to adulthood. Demonstration of the generation of a functional organ from PSCs in pigs is a very important step toward generation of human cells, tissues, and organs from individual patients' own PSCs in large animals.
Biosensing and actuation for microbiorobots (2010)

In this paper, we describe how signaling networks and actuation in bacterial cells and biomolecular networks of bacteria can be used to develop an integrated micro-bio-robotic system. SU8 microstructures blotted with swarmer cells of Serratia Marcescens in a monolayer are propelled by the bacteria in the absence of any environmental stimulus. We call such microstructures with bacteria Micro Bio Robots (MBRs) and the uncontrolled motion in the absence of stimuli self actuation. Our paper has two primary contributions. First, we demonstrate the control of MBRs using self-actuation, DC electric fields and ultra-violet radiation, and develop experimentally validated mathematical model for the MBRs. This model allows us to use self-actuation and electrokinetic actuation to steer the MBR to any position and orientation in a planar micro channel. Second, we describe the development of biosensors for the MBRs. This is done by attaching genetically engineered Escherichia coli cells that are capable of sensing nonmetabolizable lactose analog methyl-β-D-thiogalactoside (TMG). We describe the fabrication process for MBRs and show experimental results demonstrating sensing, actuation and control.
Mechanism of inhibition of human leukocyte elastase by monocyclic .beta.-lactams (1993)

The kinetic and catalytic mechanisms of time-dependent inhibition of human polymorphonuclear leukocyte elastase (HLE) by the monocyclic beta-lactams described by Knight et al. [Knight, W.B., et al. (1992) Biochemistry 31, 8160] are investigated in this work. The dependence of the pseudo-first-order rate constant (k(obs)) on inhibitor concentration was saturable. The individual kinetic constants for the inhibition by L-680,833, [S-(R*,S*)]-4-[(1-(((1-(4- methylphenyl)butyl)amino)carbonyl)-3,3-diethyl-4-oxo-2- azetidinyl)oxy]benzeneacetic acid, and L-683,845, [S-(R*,S*)]-4-[(1-(((1-(5-benzofuranyl)butyl)amino)carbonyl)- 3,3-diethyl-4-oxo-2-azetidinyl)oxy]benzeneacetic acid, at pH 7.5 were k(inact) = 0.08 and 0.06 s-1 and Ki = 0.14 and 0.06 microM, respectively. The relative potency of this class of compounds as measured by k(inact)/Ki is primarily controlled by the Ki, term which ranged from 6 nM to 8 mM, while K(inact) was relatively insensitive to structural changes and varied by only an order of magnitude. Inactivation by the beta-lactams was efficient, requiring only 1.3 and 1.7 equiv of L-680,833 and L-683,845 to inactivate HLE. These values are indicative of some partitioning between turnover of inhibitor and inactivation. The partition ratio ranged as high as 3.5:1 depending upon the structure of the inhibitors, but this ratio was essentially independent of the availability and identity of a leaving group at C-4 of the lactam ring. Inactivation and partitioning liberate the leaving group when present at C-4. p-Hydroxy-m-nitrophenylacetic acid is liberated from this position at a rate similar to that for enzyme inactivation, suggesting kinetic competence of this process. Other products observed during the interaction of L-680,833 with HLE include a substituted urea, a species previously observed during the base-catalyzed decomposition of this class of compounds, and small amounts of products observed during reactivation of beta-lactam-derived HLE-I complexes. Both the pH dependence of k(inact)/Ki for the inactivation of HLE by [S-(R*,S*)]-4-[(1-(((1-(4-methylphenyl)butyl)amino)carbonyl)-3,3-diethyl - 4-oxo-2-azetidinyl)oxyl]benzoic acid and V/K for HLE-catalyzed substrate hydrolysis indicate that a single ionizable group with a pK of approximately 7 must be deprotonated for both processes. This group is likely the active site histidine. The data are consistent with initial formation of a Michaelis complex, acylation of the catalytic serine, and loss of the leaving group at C-4 of the original beta-lactam ring followed by partitioning between regeneration of active enzyme and production of a stable enzyme-inhibitor complex.(ABSTRACT TRUNCATED AT 400 WORDS)
Immersive experimentation in a wave propagation laboratory (2013)

Physical laboratory-based seismic modelling allows wave propagation to be studied in realistic media which may be beyond current computer modeling capability. A wave propagation laboratory is presented which fully links a physical wave propagation experiment to a numerical simulation in real time. The laboratory has applications for acoustic and elastic wave propagation and allows broadband signals interacting with targets on a laboratory scale to be studied. Applications include studying nonlinear effects or wave propagation in media where the physics of wave propagation is not well understood.
Reactive Power Capability and Voltage Control with Wind Turbines (2012)

To keep the voltage within certain ranges is important for the stability and quality of electrical power systems. Decentralised power systems contribute to an increasing share in power generation and can offer additional benefits to secure a safe operation of the grid. The provision of reactive power by decentralised generation systems allows to influence the electrical power system with regard to power flow and voltage regulation. The quality and benefit of a voltage regulation depends on the dynamic range of reactive power provision and the underlying control structure. Although the generation of active power depends on the wind conditions and is therefore fluctuating, modern decentralised feeding systems, especially wind turbines with dynamic reactive power capabilities, are already able to substantial contribute to power system stability and voltage stability in particular; independent from the wind. Further developments in wind turbine dynamics in combination with new control concepts and communication systems, will contribute to secure a safe electrical energy supply under a steady increasing share of renewable energy.
The Palmar Locking Compression Plate is Biomechanically Comparable to the Dorsal PI Plate for Dorsally Comminuted, Intraarticular Wrist Fractures (2007)

A clinically appropriate fracture model and testing regimen were used to test the null hypothesis that a palmarly applied locking plate was inferior to a dorsally applied Pi plate in the stabilisation of dorsally comminuted intraarticular wrist fractures. Sixteen standardised fractures of Synbone models of the radius were stabilised using either a palmar locking compression T plate (the experimental group) ( n = 8) or a dorsally applied Pi plate (the control group) ( n = 8). The constructs were tested on an Instron materials testing machine. Deformation was monitored during 500 loading cycles to 200 N. The mean permanent deformation and stiffness favoured the palmar locking compression T plate over the dorsal Pi plate ( P = 0.036). However, the absolute difference was only 0.5 mm. Such a small difference is unlikely to be clinically detectable and, therefore, we conclude that there is no clinically significant difference between the two types of fixation.
A study on motion analysis in load control type treadmill using wearable sensor system (2019)

The purpose of this study is dynamic motion analysis of load control treadmill using inertial sensor and ground reaction force. The wearable sensor system based on inertial sensor outputs angular velocity and acceleration. The posture information is estimated by the sensor fusion using the Extended Kalman filter. The treadmill installs the force plates, and the load control system using propulsion force is installed. The hip, knee and ankle joint torque are calculated by the inertial sensor outputs, the posture information and the force plate output using the Newton-Euler method. The gait measurement experiment was conducted by using the treadmill and the wearable sensor system. The analysis results indicated the difference of joint torque by change of target load in the treadmill. Furthermore, the joint torque including the effect of inclination is calculated, the characteristics gait motion in the load control type treadmill was considered approaching the inclination and the actual road condition.
Serologic profile of a cohort of pigs and antibody response to an autogenous vaccine for Actinobacillus suis (2001)

Actinobacillus suis is a commensal opportunistic pathogen in swine. However, in recent years, an increasing prevalence of clinical signs associated with A. suis has been observed in high health status herds in North America. The objectives of the study were to assess the kinetics of antibodies to A. suis in pigs from a herd showing clinical signs of A. suis infection and, to evaluate the antibody response in gilts following vaccination with an autogenous vaccine. An enzyme-linked immunosorbent assay (ELISA) using a saline extract of boiled-formalinized whole cells of a field strain as the coating antigen was standardized. This ELISA was used as a tool for monitoring, in a comparative way, the variations in A. suis antibody levels. The herd selected for the serologic profile was negative for Actinobacillus pleuropneumoniae infection and showed clinical signs of A. suis infection in 16 to 19-week-old pigs. A cohort of 20 pigs was blood sampled at 5, 8, 12, and 16 weeks of age. The lowest level of serum antibodies was observed between weeks 8 and 12, this probably corresponding to a decrease in maternal immunity. A marked increase in the antibody response was seen at 16-week of age, at the approximate time of onset of A. suis clinical signs in the herd. The evaluation of serum antibody responses to an autogenous vaccine revealed that the humoral immunity of gilts further increased following vaccination although the level of antibodies was already high prior to vaccination. The magnitude of the response to vaccination was higher when the level of antibodies was low prior to the first injection. The ELISA test seems to detect antibodies against the O-chain LPS.
The chemistry and biology of aflatoxin B1: from mutational spectrometry to carcinogenesis (2001)

Dietary exposure to aflatoxin B(1) (AFB(1)) is associated with an increased incidence of hepatocellular carcinoma (HCC), especially in populations in which exposure to hepatitis B virus (HBV) is a common occurrence. Most HCC samples from people living where HBV is prevalent have one striking mutational hotspot: a GC-->TA transversion at the third position of codon 249 of the p53 gene. In this review, the chemical reaction of an electrophilic derivative of aflatoxin with specific DNA sequences is examined, along with the types of mutations caused by AFB(1) and the sequence context dependence of those mutations. An attempt is made to assign the source of these mutations to specific chemical forms of AFB(1)-DNA damage. In addition, epidemiological and experimental data are examined regarding the synergistic effects of AFB(1) and HBV on HCC formation and the predominance of one hotspot GC-->TA transversion in the p53 gene of affected individuals.
Mechanisms of tricuspid valve regurgitation in hypoplastic left heart syndrome: a case-matched echocardiographic–surgical comparison study (2012)

Important structural abnormalities are common in patients with HLHS and TV insufficiency, some readily identified by 2-D echocardiography. However, there are significant discrepancies between echocardiographic and surgical findings. Echocardiographic assessment is sensitive to detect leaflet motion abnormalities, but not leaflet structural abnormalities. Both echocardiographers and surgeons should be aware of these limitations when planning surgical interventions.
ChemInform Abstract: Studies on Organosilicon Chemistry. Part 137. Highly Stereoselective Intramolecular Addition of a Hydroxyl Group to Vinylsilanes via 1,2‐Silyl Migration. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Detection of hot electrons originating from an upper valley at ∼1.7eV above the Γ valley in wurtzite GaN using electron emission spectroscopy (2023)

Using electron emission spectroscopy, measurement and analysis were conducted on the energy distribution of vacuum emitted electrons from electrically driven InGaN/GaN green (peak wavelengths $\ensuremath{\lambda}\ensuremath{\approx}515\phantom{\rule{0.16em}{0ex}}\mathrm{nm}$) light-emitting diodes (LEDs) with and without a prewell superlattice (SL). We report on the detection of a high-energy upper valley at $\ensuremath{\sim}1.7\phantom{\rule{0.16em}{0ex}}\mathrm{eV}$ above the $\mathrm{\ensuremath{\Gamma}}$ valley from samples with no prewell SL. We propose that these upper valley electrons originate predominantly from trap-assisted Auger recombination (TAAR) in green LEDs, as the intensity of these peaks is found to have quadratic dependence on the carrier density $n$ [see Espenlaub et al., J. Appl. Phys. 126, 184502 (2019)]. The high-energy upper valley peak was not observed in the sample with a prewell SL which is attributed to gettering by the prewell SL of still unidentified impurities that act as TAAR centers.
Integrated Modular Motor Drives Based on Multiphase Axial-flux PM Machines with Fractional-slot Concentrated Windings (2021)

The integrated motor drive (IMD) concept with possible modularization has attracted much attention in a broad spectrum of applications ranging from low-power general-purpose industrial drives to high-power electric propulsion. This paper presents the feasibility study and performance evaluation of using common axial-flux permanent-magnet (AFPM) machines with fractional-slot concentrated windings in IMDs, with the same diameter and a minimum increase in its axial length. Different winding configurations are compared in terms of the torque/power capability and fault tolerance without changing the winding current rating. The possibility of further torque improvement is discussed from the perspective of making full use of the air-gap field harmonics produced by PMs. An AFPM machine available in the lab has been dissembled and used to build the proof-of-concept design, to show the feasibility of the proposed design and benefits of the IMD.
Morphology and structure of the metal–organic framework ZIF-8 during crystallisation measured by a new technique: dynamic angle-resolved second-harmonic scattering (AD-SHS) (2019)

Morphology and structure of a metal-organic framework measured during crystallization measured by a new technique: Dynamic Angle Resolved Second-Harmonic Scattering (AD-SHS).
Recursive Model-based Water-layer Demultiple (2015)

Summary In addition to other subsurface reflections, water-layer related multiples (WLRMs) involve at least one water-layer reflection between the free surface and the water bottom. In shallow water environments, WLRMs typically dominate other classes of multiple, and achieving effective attenuation of WLRMs is of significant interest. When combined with an appropriate adaptive subtraction, Model-based Water-layer Demultiple (MWD) has been found to be highly effective in attenuating WLRMs. In this paper we demonstrate a limitation of the conventional implementation of MWD, and propose an extension to the method to account for this limitation. This extension alleviates the dependence of a successful demultiple result on the adaptive subtraction. We demonstrate the effectiveness of our approach on simple 1D synthetics, and real-world 3D seismic data from towed-streamer acquisition in the North Sea.
Antigenic Profile of Avian H5N1 Viruses in Asia from 2002 to 2007 (2007)

Antigenic profiles of post-2002 H5N1 viruses representing major genetic clades and various geographic sources were investigated using a panel of 17 monoclonal antibodies raised from five H5N1 strains. Four antigenic groups from seven clades of H5N1 virus were distinguished and characterized based on their cross-reactivity to the monoclonal antibodies in hemagglutination inhibition and cell-based neutralization assays. Genetic polymorphisms associated with the variation of antigenicity of H5N1 strains were identified and further verified in antigenic analysis with recombinant H5N1 viruses carrying specific mutations in the hemagglutinin protein. Modification of some of these genetic variations produced marked improvement to the immunogenicity and cross-reactivity of H5N1 strains in assays utilizing monoclonal antibodies and ferret antisera raised against clade 1 and 2 H5N1 viruses, suggesting that these sites represent antigenically significant amino acids. These results provide a comprehensive antigenic profile for H5N1 virus strains circulating in recent years and will facilitate the recognition of emerging antigenic variants of H5N1 virus and aid in the selection of vaccine strains.
A Single Nucleotide Change in the Mouse Genome Accelerates Breast Cancer Progression (2010)

In the growth factor receptor gene FGFR4 the presence of the common single nucleotide polymorphism Arg388 has been associated with progression of various types of cancer including breast cancer. However, a causative relationship is not readily assigned due to genetic heterogeneity in different patient cohorts. To address this issue, we compared the effects of this allele on malignant progression in the WAP-TGFalpha transgenic mouse model of breast cancer. A knock-in strain was generated to introduce an analogous Arg385 allele into the murine FGFR4 gene. Mouse embryonic fibroblasts derived from this strain displayed accelerated cell transformation, with transformed cells exhibiting greater motility and invasive behavior. In the in vivo context of TGFalpha-induced mammary carcinogenesis, tumor development and progression was significantly advanced in tumor mass, size, and onset of pulmonary metastases. Our findings definitively identify the FGFR4 Arg388 allele as a functional prognostic marker for breast cancer progression.
Plasma deposited multipactor coating for high power, sapphire, RF windows (2014)

This program developed a multipactor coating process for single crystal, sapphire, vacuum windows for high power RF transmission. The process replaces sputtered coatings, which are not tightly bonded to the crystal surface. The process creates molecular bonds between the AlO crystal surface and the TiN coating. The process was used to build a sapphire, RF window that was successfully tested to 45 MW.