gebhart/patrepeval huggingface dataset:
Expression of Sox3 throughout the developing central nervous system is dependent on the combined action of discrete, evolutionarily conserved regulatory elements (2003)

SOX3 is one of the earliest neural markers in vertebrates and is thought to play a role in specifying neuronal fate. To investigate the regulation of Sox3 expression we identified cis-regulatory regions in the Sox3 promoter that direct tissue-specific heterologous marker gene expression in transgenic mice. Our results show that an 8.3 kb fragment, comprising 3 kb upstream and 3 kb downstream of the Sox3 transcriptional unit, is sufficient in a lacZ reporter construct to reproduce most aspects of Sox3 expression during CNS development from headfold to midgestation stages. The apparently uniform expression of Sox3 in the neural tube depends, however, on the combined action of distinct regulatory modules within this 8.3 kb region. Each of these gives expression in a subdomain of the complete expression pattern. These are restricted along both the rostral-caudal and dorso-ventral axes and can be quite specific, one element giving expression largely confined to V2 interneuron precursors. We also find that at least some of the regulatory sequences are able to drive expression of the transgene in the CNS Xenopus laevis embryos in a manner that reflects the endogenous Sox3 expression pattern. These results imply that the underlying mechanism regulating early CNS patterning is conserved, despite several substantial differences in neurogenesis between mammals and amphibians.
<title>Pulse shortening in high-power backward wave oscillators</title> (1996)

Pulse shortening is a phenomenon common to all high-power microwave devices. Whereas in electron beam driven sources the electron beam propagation in the device may be for several microseconds or more, the microwave pulse duration is typically no greater than approximately 100 ns. Specific reasons for pulse shortening may vary among devices, but all explanation of the phenomenon put forth involve the introduction of plasma into the interaction region near the walls and/or the degradation of the beam quality. To gain a better understanding of pulse shortening in high power backward wave oscillators (BWO's), an investigation is being conducted at the University of New Mexico (UNM) on the UNM Long-Pulse BWO Experiment. Recent experiments have involved monitoring the beam current in the slow-wave structure (SWS) at different radii as a function of time. The current waveforms are correlated with the time histories of microwave pulses measured in separate experiments. The results reveal the appearance of electrons between SWS ripples at times corresponding to when the microwave signal peaks. A drop in the main beam current is observed shortly thereafter. Coatings of TiO<SUB>2</SUB> and Cr have been placed on the inner surface of the SWS in an effort to suppress electron emission. Initial results with the TiO<SUB>2</SUB> coatings have shown a measurable increase in microwave pulse width.
Inhibition of integrin-linked kinase (ILK) suppresses activation of protein kinase B/Akt and induces cell cycle arrest and apoptosis of PTEN-mutant prostate cancer cells (2000)

PTEN is a tumor suppressor gene located on chromosome 10q23 that encodes a protein and phospholipid phosphatase. Somatic mutations of PTEN are found in a number of human malignancies, and loss of expression, or mutational inactivation of PTEN, leads to the constitutive activation of protein kinase B (PKB)/Akt via enhanced phosphorylation of Thr-308 and Ser-473. We recently have demonstrated that the integrin-linked kinase (ILK) can phosphorylate PKB/Akt on Ser-473 in a phosphoinositide phospholipid-dependent manner. We now demonstrate that the activity of ILK is constitutively elevated in a serum- and anchorage-independent manner in PTEN-mutant cells, and transfection of wild-type (WT) PTEN into these cells inhibits ILK activity. Transfection of a kinase-deficient, dominant-negative form of ILK or exposure to a small molecule ILK inhibitor suppresses the constitutive phosphorylation of PKB/Akt on Ser-473, but not on Thr-308, in the PTEN-mutant prostate carcinoma cell lines PC-3 and LNCaP. Transfection of dominant-negative ILK and WT PTEN into these cells also results in the inhibition of PKB/Akt kinase activity. Furthermore, dominant-negative ILK or WT PTEN induces G(1) phase cycle arrest and enhanced apoptosis. Together, these data demonstrate a critical role for ILK in PTEN-dependent cell cycle regulation and survival and indicate that inhibition of ILK may be of significant value in PTEN-mutant tumor therapy.
Macrocyclic G-Quadruplex Ligands (2010)

G-quadruplex stabilizing compounds have recently received increased interest due to their potential application as anticancer therapeutics. A significant number of structurally diverse G-quadruplex ligands have been developed. Some of the most potent and selective ligands currently known are macrocyclic structures which have been modeled after the natural product telomestatin or from porphyrin-based ligands discovered in the late 1990s. These two structural classes of G-quadruplex ligands are reviewed here with special attention to selectivity and structure-activity relationships, and with focus on the recent developments.
Investigation of Numerical Diffusion in Aerodynamic Flow Simulations with Physics Informed Neural Networks (2021)

Computational Fluid Dynamics (CFD) simulations are used for many air flow simulations including road vehicle aerodynamics. Numerical diffusion occurs when local flow direction is not aligned with the mesh lines and when there is a non-zero gradient of the dependent variable in the direction normal to the streamline direction. It has been observed that typical numerical discretization schemes for the Navier-Stokes equations such as first order upwinding produce very accurate solutions without numerical diffusion when the mesh is aligned with the streamline directions. On the other hand, numerical diffusion is maximized when the streamline direction is at an angle of 45° relative to the mesh line. The amount of numerical diffusion can be reduced by mesh refinements such as aligning mesh lines along the local flow direction or by introducing higher order numerical schemes which may introduce potential numerical instability or additional computational cost. Couple test cases of a simple steady-state incompressible and inviscid air flow convection problem were used to investigate whether numerical diffusion occurs when using Physics Informed Neural Networks (PINNs) that rely on automatic differentiation as opposed to numerical techniques used in traditional Computational Fluid Dynamics (CFD) solvers. Numerical diffusion was not observed when PINNs were used to solve the Partial Differential Equation (PDE) for the simple convection problem irrespective of flow angle. The PINN correctly simulated the streamwise upwinding, which has great potential to improve the accuracy of Navier-Stokes solvers.
Ca 2+ release-activated Ca 2+ Channel Inhibitors (2014)

Ca(2+) release-activated Ca(2+) (CRAC) channels are becoming important targets for therapeutic intervention in several areas of disease, including immunology, allergy and cancer. In parallel to the progression towards reliable methods for measuring CRAC currents and their inhibition, patents have been generated by several companies. In this Patent Review, an analysis of the patents in the CRAC channel inhibition filed is presented. A discussion of the biological methods used in the patents is included. The general interest in this area is growing fast with almost 80% of the patents issued after 2010.
Zinc oxide (ZnO) hybrid metasurfaces exhibiting broadly tunable topological properties (2022)

Extreme light confinement observed in periodic photonic structures, such as the vortex singularities in momentum (<i>k</i>) space, has been associated with their topological nature. Consequently, by exploiting and tuning their topological properties, optical metasurfaces have been demonstrated as an attractive platform for active photonics. However, given the fact that most active media under external excitations can only provide limited refractive index change, the potential advancements offered by the topological character of active metasurfaces have remained mostly unexplored. Zinc oxide (ZnO), which has recently exhibited optically-induced extraordinarily large permittivity modulations at visible and near-infrared frequencies, is an excellent active material for dynamic metasurfaces exhibiting strong tuning. This work demonstrates that a hybrid metasurface consisting of an array of ZnO nanodisks on a silver backplane displays broadly tunable topological properties. In particular, by performing <i>k</i>-space scattering simulations using measured pump-fluence-dependent material properties of ZnO, we study in detail the light reflection from the hybrid metasurface. Our results validate that the large <i>k</i>-space topology tuning of the metasurface can result in enormously strong polarization manipulation of near-infrared light in the vicinity of the topological features. The observed polarization switching effect is highly sensitive to the polarization and wavelength of an incident wave, owing to the symmetry and dispersion characteristics of the proposed system. Our study indicates that leveraging a combination of the extraordinary material properties and the <i>k</i>-space topology, hybrid metasurfaces based on ZnO may open new avenues for creating all-optical switchable metadevices.
Time-Resolved Structural Evolution of Additive-Processed Bulk Heterojunction Solar Cells (2012)

Solution deposition using high-boiling-point additives such as octanedithiol (ODT) provides a simple and widely used fabrication option for improving the power conversion efficiencies of solar cells composed of narrow-band-gap conjugated polymer donor/fullerene acceptor blends. Previous examination of the resulting device active layers has shown that the use of additives influences the degree of phase segregation within the bulk heterojunction (BHJ) blend and also improves ordering within the polymeric domains. In this work, in situ grazing-incidence wide-angle X-ray scattering as a function of time was used to explore the dynamics of the BHJ evolution. These studies showed that a small percentage of ODT in chlorobenzene (CB) induced the nucleation of polymeric crystallites within 2 min of deposition, increased the orientational order of specific polymorphs, and promoted further crystallite nucleation over a period longer than 40 min after casting. Similar structural changes did not occur when the same BHJ blend was cast from pure CB.
56.3: Electrowetting Light Valves with Greater than 80% Transmission, Unlimited View Angle, and Video Response (2005)

Abstract Greater than 80% transmission has been demonstrated for electrowetting light valves (ELVs). The ELV pixel structure consists of a backlit oil/water‐on‐dielectric electrowetting cell. Recent improvements in pixel design and oil formulation now allow for lower voltage and higher contrast operation. The ELVs are also video rate capable and unlimited in view angle.
Selectively Micro-Patternable Fibers via In-Fiber Photolithography (2020)

Multimaterial fibers engineered to integrate glasses, metals, semiconductors, and composites found applications in ubiquitous sensing, biomedicine, and robotics. The longitudinal symmetry typical of fibers, however, limits the density of functional interfaces with fiber-based devices. Here, thermal drawing and photolithography are combined to produce a scalable method for deterministically breaking axial symmetry within multimaterial fibers. Our approach harnesses a two-step polymerization in thiol-epoxy and thiol-ene photopolymer networks to create a photoresist compatible with high-throughput thermal drawing in atmospheric conditions. This, in turn, delivers meters of fiber that can be patterned along the length increasing the density of functional points. This approach may advance applications of fiber-based devices in distributed sensors, large area optoelectronic devices, and smart textiles.
Twin Polymerization at Spherical Hard Templates: An Approach to Size‐Adjustable Carbon Hollow Spheres with Micro‐ or Mesoporous Shells (2013)

Kitset hollow spheres: The combination of twin polymerization with hard templates makes hollow carbon spheres (HCSs) with tailored properties easily accessible. The thickness and pore texture of the HCS shells and also the diameter of the spherical cavity can be varied. The application potential of synthesized HCS is substantiated by an excellent cycling stability of lithium-sulfur batteries.
Study of ecotoxicity of silver nanoparticles using algae (2016)

Silver nanoparticles have been prepared and tested for their ecotoxicity using Chlorella vulgaris Beijer. algae as a hydrobiotic test organism and a photometric method of control. The toxicity was supposed to originate from Ag+ ions released into the aqueous solution. Also, the toxicity of the stabilizing agent was found to be comparable to that of silver nanoparticles.
Profile Control of Donor Ions by Sn Co-implantation in Germanium (2018)

We studied N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> /P junction formation in germanium by various ion species systematically. We evaluated the effect of co-implantation of C, Al and Sn in detail. It should be emphasized that the trade-off relationship between Rs and Xj can be overcome by Sn co-implantation, although a slight increase in Rs value was observed. Diffusion of phosphorus can be controlled by Sn co-implantation technique. We also evaluated the residual defects and stress generation of Sn co-implantation.
444 DEVELOPMENT OF NEW DRUGS FOR CHAGAS DISEASE. (2006)

<h3></h3> Chagas disease results from infection with the protozoan pathogen <i>Trypanosoma cruzi</i> (<i>T. cruzi</i>). The disease is endemic in South and Central America with &gt; 16 million people chronically infected and ≈14,000 deaths per year. Current treatment options are inadequate to cure this infection; thus, research is needed to discover better chemotherapeutics. We have an ongoing project making inhibitors to a key enzyme involved in sterol biosynthesis of <i>T. cruzi</i>, sterol 14-demethylase (Tc14DM). This enzyme, the target of azole antifungal drugs, is a well established antimicrobial target. We hypothesize that new compounds can be synthesized with optimal anti-<i>T. cruzi</i> activity, and these will be sufficiently active to cure animals (and humans) with chronic <i>T. cruzi</i> infection. We have discovered two new chemical classes that bind the Tc14DM and that have potent activity against <i>T. cruzi</i> cultures with ED<sub>50</sub> values in the 1-10 nM range. The active compounds are a series of disubstituted imidazoles and another series derived from the cancer drug tipifarnib. We have shown the disubstituted imidazoles dramatically suppress <i>T. cruzi</i> parasitemia in the mouse model of Chagas disease. Working in collaboration with chemists at Yale University and University of Washington, we are working to optimize these lead compounds for pharmacological properties and efficacy against <i>T. cruzi</i>.
An Assessment of the Lolium perenne (Perennial Ryegrass) Seedborne Microbiome across Cultivars, Time, and Biogeography: Implications for Microbiome Breeding (2021)

Research into the bacterial component of the seed microbiome has been intensifying, with the aim of understanding its structure and potential for exploitation. We previously studied the intergenerational seed microbiome of one cultivar of perennial ryegrass with and without one strain of the commercially deployed fungal endophyte <i>Epichloë festucae</i> var. <i>lolii</i>. The work described here expands on our previous study by exploring the bacterial seed microbiome of different commercial cultivar/<i>Epichloë festucae</i> var. <i>lolii</i> combinations in collections of single seeds from the harvest year 2016. In this dataset, a cultivar effect could be seen between the seed microbiomes from cultivars Alto and Trojan. The bacterial component of the seed microbiome from pooled seeds from a single cultivar/<i>E</i>. <i>festucae</i> var. <i>lolii</i> combination harvested from 13 seed production farms around Canterbury in the year 2018 was also studied. This dataset allows the effect of different production locations on the bacterial seed microbiome to be examined. By comparing the two sets of data, bacteria from the genera <i>Pantoea</i>, <i>Pseudomonas</i>, <i>Duganella</i>, <i>Massilia</i>, and an unknown Enterobacteriaceae were observed to be in common. This core bacterial microbiome was stable over time but could be affected by supplemental taxa derived from the growth environment of the parental plant; differing microbiomes were seen between different seed production farms. By comparison to a collection of bacterial isolates, we demonstrated that many of the members of the core microbiome were culturable. This allows for the possibility of exploiting these microbes in the future.
Conceptual design of a whole body PET machine (1988)

A whole-body positron-emission tomography (PET) machine based on a novel type of large-area sodium iodide (NaI) detector is being designed. Monte Carlo computer simulations have been used to compare some of the performance parameters of a tomograph based on the detectors to similar parameters of conventional small-crystal machines. Three different prototypes have been constructed, and many tests have been performed, including measurements of transverse spatial resolution, depth-of-interaction resolution, energy resolution, time resolution, and high-counting-rate capabilities. The simulation and measurement results are presented and discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Using geostatistics to aid in reservoir characterization (1995)

Proper characterization of reservoir heterogeneities is a well recognized requirement to accurately predict reservoir performance. Given the large investment requirements, long development schedules, and the often uncertain economic outlook, sound decision making requires reasonable estimates of how much, and when, oil will be produced. It is no longer sufficient to estimate total oil in place and apply an ad-hoc recovery factor to determine reserves. Average values for properties such as porosity, fluid saturations, and thickness can be used to establish the total amount of fluids in place. However, averages are less reliable once volumetrics have been estimated; predicting fluid movement within a reservoir is more difficult because flow is greatly influenced by extreme high and low values not well characterized by average quantities. As a result, the general trend in the oil industry has been to underpredict the variability and overpredict the continuity of reservoir properties, which usually results in optimistic predictions of reservoir performance.
Digital Solutions to Diagnose and Manage Postbariatric Hypoglycemia (2022)

Postbariatric hypoglycemia (PBH) is an increasingly recognized late metabolic complication of bariatric surgery, characterized by low blood glucose levels 1-3 h after a meal, particularly if the meal contains rapid-acting carbohydrates. PBH can often be effectively managed through appropriate nutritional measures, which remain the cornerstone treatment today. However, their implementation in daily life continues to challenge both patients and health care providers. Emerging digital technologies may allow for more informed and improved decision-making through better access to relevant data to manage glucose levels in PBH. Examples include applications for automated food analysis from meal images, digital receipts of purchased food items or integrated platforms allowing the connection of continuously measured glucose with food and other health-related data. The resulting multi-dimensional data can be processed with artificial intelligence systems to develop prediction algorithms and decision support systems with the aim of improving glucose control, safety, and quality of life of PBH patients. Digital innovations, however, face trade-offs between user burden vs. amount and quality of data. Further challenges to their development are regulatory non-compliance regarding data ownership of the platforms acquiring the required data, as well as user privacy concerns and compliance with regulatory requirements. Through navigating these trade-offs, digital solutions could significantly contribute to improving the management of PBH.
Mitral Isthmus Ablation with and Without Temporary Spot Occlusion of the Coronary Sinus: A Randomized Clinical Comparison of Acute Outcomes (2012)

Temporary spot occlusion of CS is safe and significantly reduces the requirement of epicardial ablation to achieve MI block. It does not improve overall procedural success rate and procedural duration. Tissue cooling by CS blood flow is just one of the several challenges in MI ablation.
Channel modeling for hybrid magneto-optical recording (2000)

A physical channel model of readback signals from a hybrid MO recording using magnetic flux detection is presented. The system performance has been investigated using the proposed model, together with the comparison of channel characteristics in the longitudinal, near field and hybrid architectures. Preliminary iterative decoding results with this channel model are also presented.
Solar Fuels: The Rational Design of a Single‐Component Photocatalyst for Gas‐Phase CO2 Reduction Using Both UV and Visible Light (Adv. Sci. 1/2014) (2014)

Advances towards the vision of the “solar fuels refinery” of the future are portrayed in the cover art, based on article 1400013 by G. A. Ozin and co-workers. In the article, the attributes of hydroxide groups and oxygen vacancies are identified for non-stoichiometric indium oxide photocatalytic nanoparticles in the light-assisted, gas-phase conversion of carbon dioxide to carbon monoxide. The ultimate goal of this work is to facilitate an energy transition from today's unsustainable “fossil fuel economy” to a new and sustainable “carbon dioxide economy”. The cover was designed by Chenxin Qian