gebhart/patrepeval huggingface dataset:
Optical modulation of transgene expression in retinal pigment epithelium (2013)

Over a million people in US alone are visually impaired due to the neovascular form of age-related macular degeneration (AMD). The current treatment is monthly intravitreal injections of a protein which inhibits Vascular Endothelial Growth Factor, thereby slowing progression of the disease. The immense financial and logistical burden of millions of intravitreal injections signifies an urgent need to develop more long-lasting and cost-effective treatments for this and other retinal diseases. Viral transfection of ocular cells allows creation of a “biofactory” that secretes therapeutic proteins. This technique has been proven successful in non-human primates, and is now being evaluated in clinical trials for wet AMD. However, there is a critical need to down-regulate gene expression in the case of total resolution of retinal condition, or if patient has adverse reaction to the trans-gene products. The site for genetic therapy of AMD and many other retinal diseases is the retinal pigment epithelium (RPE). We developed and tested in pigmented rabbits, an optical method to down-regulate transgene expression in RPE following vector delivery, without retinal damage. Microsecond exposures produced by a rapidly scanning laser vaporize melanosomes and destroy a predetermined fraction of the RPE cells selectively. RPE continuity is restored within days by migration and proliferation of adjacent RPE, but since the transgene is not integrated into the nucleus it is not replicated. Thus, the decrease in transgene expression can be precisely determined by the laser pattern density and further reduced by repeated treatment without affecting retinal structure and function.
A “2-omega” technique for measuring anisotropy of thermal conductivity (2012)

A popular method of measuring the thermal conductivity of thin films and substrates, the "3-omega" method, is modified to yield a new technique for measuring the anisotropy in thermal transport in bulk materials. The validity of the proposed technique is established by measuring the thermal conductivity of strontium titanate, which is expected to be isotropic because of its cubic unit cell. The technique is then applied to rutile TiO(2). The analysis of experimental results on (100) and (001) TiO(2) reveals that the anisotropy is a function of the crystalline quality, as quantified by the effective thermal conductivity obtained through conventional "3-omega" measurements. The advantages of the proposed technique are similar to those of the standard "3-omega" method, namely the simplicity of sample preparation and measurement, and negligible errors due to radiation because of the small volume of material being heated. For anisotropy determination, the proposed technique has the additional advantage that a single sample is sufficient to determine both components of the thermal conductivity, namely the values in and perpendicular to the plane of cleavage. This is significant for materials in which there is a large variation in the crystalline quality from sample to sample. For such materials, it is unreliable to use two different samples, one for measuring the thermal conductivity in each direction. Experimental data are analyzed using a 3D Fourier-series based method developed in this work. The proposed method determines each component of the thermal conductivity with an estimated accuracy of about 10%.
PON Resilience (2014)

Passive Optical Networks are being applied to a wider set of applications, including those that are outage sensitive. Protection or resilience techniques address this need. This paper reviews these techniques, focusing on active research areas.
Multimode modeling of digital modulation in nearly single-mode semiconductor lasers (2016)

We present multimode modeling of the digitalmodulation characteristics of nearly single-mode semiconductor lasers. The model takes into account the mechanisms of spectral suppression of modal gain; namely, symmetric and asymmetric gain suppressions. The digital modulation performance of the laser is quantitatively examined in terms of the turn-on jitter, on-off ratio and a Q-factor. We study the effect of the modulation parameters on the modulation characteristics of the laser. We also clarify the effect of the asymmetric gain suppression on the modulated signals of the oscillating modes. In addition, we examine the validity of modeling the digital modulation of the laser via a single-mode rate equation model. We show that the modulation characteristics improve with an increase in the bias and/or modulation current or with a decrease in the bit rate due to reduction in the bit-pattern effect. The asymmetric gain suppression does not affect the characteristics of the total laser signal, however it enhances the modulation of the nearest modes on the long-wavelength side of the gain spectrum.
<title>Biologically inspired hexapedal robot using field-effect electroactive elastomer artificial muscles</title> (2001)

Small, autonomous mobile robots are needed for applications such as reconnaissance over difficult terrain or internal inspection of large industrial systems. Previous work in experimental biology and with legged robots has revealed the advantages of using leg actuators with inherent compliance for robust, autonomous locomotion over uneven terrain. Recently developed field-effect electroactive elastomer artificial muscle actuators offer such compliance as well as attractive performance parameters such as force/weight and efficiency, so we developed a small (670 g) six-legged robot, FLEX, using AM actuators. Electrically, AM actuators are a capacitive, high-impedance load similar to piezoelectrics, which makes them difficult to rive optimally with conventional circuitry. Still, we were able to devise a modular, microprocessor-based control system capable of driving 12 muscles with up to 5,000 V, operating form an on- board battery. The artificial muscle actuators had excellent compliance and peak performance, but suffered from poor uniformity and degradation over time. FLEX is the first robot of its kind. While there is room for improvement in some of the robot systems such as actuators and their drivers, this work has validated the idea of using artificial muscle actuators in biologically inspired walking robots.
Super-condenser enables labelfree nanoscopy. (2019)

Labelfree nanoscopy encompasses optical imaging with resolution in the 100 nm range using visible wavelengths. Here, we present a labelfree nanoscopy method that combines coherent imaging techniques with waveguide microscopy to realize a super-condenser featuring maximally inclined coherent darkfield illumination with artificially stretched wave vectors due to large refractive indices of the employed Si3N4 waveguide material. We produce the required coherent plane wave illumination for Fourier ptychography over imaging areas 400 μm2 in size via adiabatically tapered single-mode waveguides and tackle the overlap constraints of the Fourier ptychography phase retrieval algorithm two-fold: firstly, the directionality of the illumination wave vector is changed sequentially via a multiplexed input structure of the waveguide chip layout and secondly, the wave vector modulus is shortend via step-wise increases of the illumination light wavelength over the visible spectrum. We test the method in simulations and in experiments and provide details on the underlying image formation theory as well as the reconstruction algorithm. While the generated Fourier ptychography reconstructions are found to be prone to image artefacts, an alternative coherent imaging method, rotating coherent scattering microscopy (ROCS), is found to be more robust against artefacts but with less achievable resolution.
Water Relations of Seed Development and Germination in Muskmelon (Cucumis meloL.) (1989)

The germinability, vigour, and desiccation tolerance of muskmelon (Cucumis melo L. cv. Top Mark) seeds was studied in relation to changes in seed water content during development within the fleshy fruit. Seed water content (fresh weight basis) declined from 91% to 42% between 10 d and 35 d after anthesis (DAA) (when maximum dry weight was attained), then declined more slowly to a minimum of 35% at 50 DAA before increasing again to 43% at 65 DAA. Fresh intact seeds were first germinable at 25 to 30 DAA and attained maximum germination percentages at 45 DAA. Between 15 and 35 DAA, cotyledons, hypocotyls, radicles and epicotyls of isolated embryos (testa and perisperm envelope removed) sequentially developed the ability to grow when incubated on water. Dehydration to water contents less that those attained within the fleshy fruit is not a requirement for development of germination capacity of muskmelon seeds. Seeds became tolerant of rapid desiccation after 25 DAA, and drying of immature seeds (25 to 40 DAA) increased their germination percentages upon subsequent imbibition. Washing, drying, or washing followed by drying increased seedling vigour (root length) as compared to fresh seeds, which had very poor vigour. Water absorption isotherms were constructed to test whether changes in water-binding components were correlated with the development of desiccation tolerance. Isotherms for seeds older than 25 DAA fit well to the D'Arcy/Watt model, which postulates the existence of high-affinity, low-affinity and multi-molecular water-binding sites. Desiccation-intolerant seeds younger than 25 DAA lacked the component of the absorption isotherm characteristic of the high-affinity water-binding sites which have been hypothesized to confer desiccation tolerance. However, we were unable to determine whether the absence of high-affinity binding characteristics was specifically related to desiccation intolerance or was artifactual due to the loss of volatiles when immature seed samples were dried at high temperatures.
Optofluidics: A Flat Lens with Tunable Phase Gradient by Using Random Access Reconfigurable Metamaterial (Adv. Mater. 32/2015) (2015)

A tunable flat lens with a random access reconfigurable metamaterial (RARM) is demonstrated by A.-Q. Liu, N. I. Zheludev, and co-workers on page 4739. The RARM is realized by using an optofluidic metamaterial where resonant properties of every individual metamolecule can be continuously tuned at will using a microfluidic system, which therefore functions as a metamaterial platform creating optical properties on demand.
Hydrodynamical Study of Combined Effects of an Orifice Plate and a Bluff Body for Flow Measurements (2020)

Abstract The effect of the diameter of an orifice plate when a bluff body is placed upstream of it is numerically studied. A circular cylinder used as a bluff body usually generates a wake of vortices known as Von Karman vortices. It was found in this study that it depends on the opening of an orifice plate behind the bluff body there is a transition from the classical Von Karman system of vortices to a pulsation type of flow. The numerical calculation performed by a Lattice Boltzmann approach reveal the nature of the vortices each time that the diameter of the orifice is changed as well as the frequencies related to the shedding of the vortices behind the obstacles.
IL-37 exerts therapeutic effects in experimental autoimmune encephalomyelitis through the receptor complex IL-1R5/IL-1R8 (2020)

<b>Background:</b> Interleukin 37 (IL-37), a member of IL-1 family, broadly suppresses inflammation in many pathological conditions by acting as a dual-function cytokine in that IL-37 signals via the extracellular receptor complex IL1-R5/IL-1R8, but it can also translocate to the nucleus. However, whether IL-37 exerts beneficial actions in neuroinflammatory diseases, such as multiple sclerosis, remains to be elucidated. Thus, the goals of the present study were to evaluate the therapeutic effects of IL-37 in a mouse model of multiple sclerosis, and if so, whether this is mediated via the extracellular receptor complex IL-1R5/IL-1R8. <b>Methods:</b> We used a murine model of MS, the experimental autoimmune encephalomyelitis (EAE). We induced EAE in three different single and double transgenic mice (hIL-37tg, IL-1R8 KO, hIL-37tg-IL-1R8 KO) and wild type littermates. We also induced EAE in C57Bl/6 mice and treated them with various forms of recombinant human IL-37 protein. Functional and histological techniques were used to assess locomotor deficits and demyelination. Luminex and flow cytometry analysis were done to assess the protein levels of pro-inflammatory cytokines and different immune cell populations, respectively. qPCRs were done to assess the expression of IL-37, IL-1R5 and IL-1R8 in the spinal cord of EAE, and in blood peripheral mononuclear cells and brain tissue samples of MS patients. <b>Results:</b> We demonstrate that IL-37 reduces inflammation and protects against neurological deficits and myelin loss in EAE mice by acting via IL1-R5/IL1-R8. We also reveal that administration of recombinant human IL-37 exerts therapeutic actions in EAE mice. We finally show that IL-37 transcripts are not up-regulated in peripheral blood mononuclear cells and in brain lesions of MS patients, despite the IL-1R5/IL-1R8 receptor complex is expressed. <b>Conclusions:</b> This study presents novel data indicating that IL-37 exerts therapeutic effects in EAE by acting through the extracellular receptor complex IL-1R5/IL-1R8, and that this protective physiological mechanism is defective in MS individuals. IL-37 may therefore represent a novel therapeutic avenue for the treatment of MS with great promising potential.
A Review of Technology Push Product Development Models and Processes (2004)

There are many models of product development processes. The two most common classes of development are market pull (MP) and technology push (TP). TP product development differs from MP in that the development begins with a specified technology rather than a specified customer. Because TP development is generally considered more difficult and challenging, most of the product development research has focused on MP development and many researchers and practitioners favor MP development over TP development. However, successful TP development has been shown to be a source of innovation that cannot be realized through MP development and is still performed by many companies. This paper review lays the necessary foundation for building better TP models by first examining the evolution of TP models, and then reviewing deficiencies that have been attributed to MP models when they are used to accomplish TP product development. This paper also amalgamates the success factors of successfully developed TP products, and then groups them into categories that can be used to further investigate how comprehensive existing and proposed TP models are.Copyright © 2004 by ASME
Optimal subspace techniques for DOA estimation (2001)

Signal parameter estimation, and specifically direction of arrival (DOA) estimation for sensor array data is encountered in a number of applications ranging from electronic surveillance to wireless communications. Subspace-based methods have shown to provide computationally as well as statistically efficient algorithms for DOA estimation. Estimator performance is ultimately limited by model disturbances like measurement noise and model errors. Herein, we review a recently proposed framework that allows the derivation of optimal subspace methods, taking both finite sample effects (noise) and model errors into account. We show how this generic estimator reduces to well-known techniques for cases when one disturbance completely dominates the other.
Bication-Mediated Quasi-2D Halide Perovskites for High-Performance Flexible Photodetectors: From Ruddlesden–Popper Type to Dion–Jacobson Type (2020)

Quasi-2D halide perovskites, especially the Ruddlesden-Popper perovskites (RPPs), have attracted great attention because of their promising properties for optoelectronics; however, there are still serious drawbacks, such as inefficient charge transport, poor stability, and unsatisfactory mechanical flexibility, restricting further utilization in advanced technologies. Herein, high-quality quasi-2D halide perovskite thin films are successfully synthesized with the introduction of the unique bication ethylenediammonium (EDA) via a one-step spin-coating method. This bication EDA, with short alkyl chain length, can not only substitute the typically bulky and weakly van der Waals-interacted organic bilayer spacer cations forming the novel Dion-Jacobson phase to enhance the mechanical flexibility of the quasi-2D perovskite (e.g., EDA(MA)<sub><i>n</i>-1</sub>Pb<sub><i>n</i></sub>I<sub>3<i>n</i>+1</sub>; MA = CH<sub>3</sub>NH<sub>3</sub><sup>+</sup>) but also serve as a normal cation to achieve the more intact films (e.g., (<i>i</i>BA)<sub>2</sub>(MA)<sub>3-2<i>x</i></sub>(EDA)<sub><i>x</i></sub>Pb<sub>4</sub>I<sub>13</sub>). When fabricated into photodetectors, these optimized EDA-based perovskites deliver an excellent responsivity of 125 mA/W and a fast response time down to 380 μs under 532 nm irradiation. More importantly, the device with the Dion-Jacobson phase perovskite can be bent down to a radius of 2 mm and processed with 10,000 cycles of the bending test without any noticeable performance degradation because of its superior structure to RPPs. Besides, these films do not exhibit any material deterioration after ambient storage for 30 days. All these performance parameters are already comparable or even better than those of the state-of-the-art RPPs recently reported. This work provides valuable design guidelines of the quasi-2D perovskites to obtain high-performance flexible photodetectors for next-generation optoelectronics.
Accuracy of a semi-automated liver segmentation method using CT scan (2013)

Poster: ECR 2013 / C-2423 / Accuracy of a semi-automated liver segmentation method using CT scan by: G. Chartrand, C. Belanger, A. Gotra, R. Chav, C. Kauffman, J. A. De Guise, A. Tang; Montreal, QC/CA
A reduced-order thermomechanical model and analytical solution for uniaxial shape memory alloy wire actuators (2009)

A lumped shape memory alloy (SMA) model is derived from the thermodynamic model of Chang et al (2006 Contin. Mech. Thermodyn. 18 83–118), using a set of simplifying assumptions, that reduces the system of partial differential equations for an SMA/bias spring actuator to a nonlinear, first-order, ordinary differential equation. Dimensionless state variables and parameters are defined that are useful for characterizing the actuator system and for studying its performance and scaling. A general analytical solution to the nonlinear differential equation governing phase transformation is found in terms of the Lambert function for a piecewise constant Joule heating input and a constant temperature convective environment. The analytical solution provides a useful and convenient tool for assessing the time-dependent, hysteretic response of this simple class of SMA actuators, with which design and optimization studies are performed.
Phosphonium‐metallate, V. Carbonyl(hydrido)(η5‐pentamethylcyclopentadienyl) (trimethyl‐phosphan)eisen(II): Darstellung und Umsetzung mit Trimethyl(methylen)phosphoran (1983)

Phosphonium Metalates, V. Carbonyl(hydrido)(η 5 ‐pentamethylcyclopentadienyl)(trimethylphosphane)iron(II): Preparation and Reaction with Trimethyl(methylene)phosphorane The iron hydride C 5 Me 5 (CO) 2 FeH ( 2 ) is obtained by the reaction of Na[Fe(CO) 2 C 5 Me 5 ] ( 1 ) with acetic acid. 2 is converted in the presence of trimethylphosphane to C 5 Me 5 (CO)(Me 3 P)FeH ( 3 ), which reacts with the ylide Me 3 P=CH 2 to give C 5 Me 5 (CO)(Me 3 P)FeMe( 4 ) and Me 3 P via the intermediate formation of the phosphonium salt Me 4 P[Fe(CO)(Me 3 P)C 5 Me 5 ] ( 5 ).
INTRAGRAFT IL-15 TRANSCRIPTS ARE INCREASED IN HUMAN RENAL ALLOGRAFT REJECTION1 (1996)

IL-15, a novel growth factor made by a variety of cells, stimulates T cell proliferation in a fashion similar to IL-2. IL-2 transcripts are not routinely found in rejecting human renal allografts at the time of clinically evident rejection. However, T cell proliferation continues as the rejection progresses. We postulated that IL-15 may be actively transcribed during clinical rejection and account, at least in part, for the ongoing T cell expansion. RNA was extracted from renal biopsies and reverse transcribed to cDNA which was used as template for competitive PCR. IL-2 mRNA was detected in just 3 of the 45 biopsy samples. IL-15 transcripts were detected in all renal biopsy specimens and was significantly increased in specimens obtained from rejecting as compared with nonrejecting renal allografts. IL-15 transcription correlates with rejection and may play an important role in T cell mediated rejection.
Proteomic approaches to study ubiquitinomics (2023)

As originally described some 40 years ago, protein ubiquitination was thought to serve primarily as a static mark for protein degradation. In the ensuing years, it has become clear that 'ubiquitination' is a structurally diverse and dynamic post-translational modification and is intricately involved in a myriad of signaling pathways in all eukaryote cells. And like other key pathways in the functional proteome, ubiquitin signaling is often disrupted, sometimes severely so, in human pathophysiology. As a result of its central role in normal physiology and human disease, the ubiquitination field is now represented across the full landscape of biomedical research from fundamental structural and biochemical studies to translational and clinical research. In recent years, mass spectrometry has emerged as a powerful technology for the detection and characterization of protein ubiquitination. Herein we detail qualitative and quantitative proteomic methods using a compare/contrast approach to highlight their strengths and weaknesses.
Monooxygenation by a thermophilic cytochrome P450 via direct electron donation from NADH (2011)

The catalysis of cytochrome P450s requires two-electron donation for the activation of an oxygen molecule. Here, we report the enzymatic catalysis of cytochrome P450, CYP119A2 (P450st), from a thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain 7, with NAD(P)H as an electron donor and no redox partners and the crystallographic analysis of P450st at high resolution. P450st can catalyse styrene epoxidation with either NADH or NADPH as an electron donor. The P450st reaction with NADH exhibited a sequential mechanism. X-ray crystallography at a resolution of 1.94 Å revealed a sufficiently large heme pocket for NAD(P)H binding and a novel contiguous channel from the active site to bulk solvent in the distal heme pocket. The narrow channel may transfer protons or water to the heme pocket even when a bulky compound, such as NAD(P)H, binds in the pocket. In addition, the F/G loop region (Leu151-Glu156), located around the substrate channel, was deleted in the mutant and constructed to improve the accessibility of NAD(P)H to the heme pocket. Kinetic properties of the Δ151-156 mutant were compared with those of the wild-type P450st. The K(m) value of the mutant was about 2 times lower than that of the wild-type. The results indicated that NAD(P)H could provide the electrons for P450st within the heme pocket.
ChemInform Abstract: HYDROBORATION. 61. DIISOPINOCAMPHEYLBORANE OF HIGH OPTICAL PURITY. IMPROVED PREPARATION AND ASYMMETRIC HYDROBORATION OF REPRESENTATIVE CIS‐DISUBSTITUTED ALKENES (1983)

Abstract Das Gleichgewicht zwischen dem als chiralen Reagenz eingesetzten dimeren Borkomplex (III) und den daraus gebildeten Spaltprodukten (I) und (IV) beeinträchtigt die gewünschte asymmetrische Hydroborierung.