gebhart/patrepeval huggingface dataset:
Digital Image Reconstruction: Deblurring and Denoising (2005)

▪ Abstract Digital image reconstruction is a robust means by which the underlying images hidden in blurry and noisy data can be revealed. The main challenge is sensitivity to measurement noise in the input data, which can be magnified strongly, resulting in large artifacts in the reconstructed image. The cure is to restrict the permitted images. This review summarizes image reconstruction methods in current use. Progressively more sophisticated image restrictions have been developed, including (a) filtering the input data, (b) regularization by global penalty functions, and (c) spatially adaptive methods that impose a variable degree of restriction across the image. The most reliable reconstruction is the most conservative one, which seeks the simplest underlying image consistent with the input data. Simplicity is context-dependent, but for most imaging applications, the simplest reconstructed image is the smoothest one. Imposing the maximum, spatially adaptive smoothing permitted by the data results in the best image reconstruction.
Large-Scale Clinical Systems. Impact of Large-Scale Systems on Clinical Practice: Assessing the Effectiveness of a Computerized Pharmacy System (1990)

Somatic mutation signatures are an informative facet of cancer aetiology, however they are rarely useful for predicting patient outcome. The aim of this study is to evaluate the utility of a panel of 142 mutation-signature-associated metrics (P142) for predicting cancer progression in patients from a 'TCGA PanCancer Atlas' cohort. The P142 metrics are comprised of AID/APOBEC and ADAR deaminase associated SNVs analyzed for codon context, strand bias, and transitions/transversions. TCGA tumor-normal mutation data was obtained for 10,437 patients, representing 31 of the most prevalent forms of cancer. Stratified random sampling was used to split patients into training, tuning and validation cohorts for each cancer type. Cancer specific machine learning (XGBoost) models were built using the output from the P142 panel to predict patient Progression Free Survival (PFS) status as either "High PFS" or "Low PFS". Predictive performance of each model was evaluated using the validation cohort. Models accurately predicted PFS status for several cancer types, including adrenocortical carcinoma, glioma, mesothelioma, and sarcoma. In conclusion, the P142 panel of metrics successfully predicted cancer progression status in patients with some, but not all cancer types analyzed. These results pave the way for future studies on cancer progression associated signatures.
Copper(II) complexes of diastereoisomeric methionylmethionines in aqueous solution. Favoring of the amide-deprotonated complex in the L,L-dipeptide without sulfur coordination (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCopper(II) complexes of diastereoisomeric methionylmethionines in aqueous solution. Favoring of the amide-deprotonated complex in the L,L-dipeptide without sulfur coordinationRaffaele P. Bonomo, Giuseppe Maccarrone, Enrico Rizzarelli, and Maurizio VidaliCite this: Inorg. Chem. 1987, 26, 17, 2893–2897Publication Date (Print):August 1, 1987Publication History Published online1 May 2002Published inissue 1 August 1987https://pubs.acs.org/doi/10.1021/ic00264a036https://doi.org/10.1021/ic00264a036research-articleACS PublicationsRequest reuse permissionsArticle Views62Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Antioxidant Effects of Oral Ang-(1-7) Restore Insulin Pathway and RAS Components Ameliorating Cardiometabolic Disturbances in Rats (2019)

In prevention studies of metabolic syndrome (MetS), Ang-(1-7) has shown to improve the insulin signaling. We evaluated the HP<i>β</i>CD/Ang-(1-7) treatment on lipid metabolism, renin-angiotensin system (RAS) components, oxidative stress, and insulin pathway in the liver and gastrocnemius muscle and hepatic steatosis in rats with established MetS. After 7 weeks of high-fat (FAT) or control (CT) diets, rats were treated with cyclodextrin (HP<i>β</i>CD) or HP<i>β</i>CD/Ang-(1-7) in the last 6 weeks. FAT-HP<i>β</i>CD/empty rats showed increased adiposity index and body mass, gene expression of ACE/ANG II/AT1R axis, and oxidative stress. These results were accompanied by imbalances in the insulin pathway, worsening of liver function, hyperglycemia, and dyslipidemia. Oral HP<i>β</i>CD/Ang-(1-7) treatment decreased <i>ACE</i> and <i>AT1R</i>, increased <i>ACE2</i> gene expression in the liver, and restored thiobarbituric acid reactive substances (TBARS), catalase (CAT), superoxide dismutase (SOD), insulin receptor substrate (<i>Irs-1</i>), glucose transporter type 4 (<i>GLUT4</i>), and serine/threonine kinase 2 (<i>AKT-2</i>) gene expression in the liver and gastrocnemius muscle improving hepatic function, cholesterol levels, and hyperglycemia in MetS rats. Overall, HP<i>β</i>CD/Ang-(1-7) treatment restored the RAS components, oxidative stress, and insulin signaling in the liver and gastrocnemius muscle contributing to the establishment of blood glucose and lipid homeostasis in MetS rats.
Eliminating glutaraldehyde from crosslinked collagen films using supercritical CO2 (2017)

Collagen has received considerable attention as a biomaterial for tissue engineering because of its low immunogenicity, controllable biodegradation, and ability to influence cell growth and proliferation. Frequently, collagen scaffolds require crosslinking to improve mechanical strength, requiring agents like glutaraldehyde that have high residual cytotoxicity. A novel method for extracting residual glutaraldehyde from crosslinked collagen films with supercritical carbon dioxide (CO<sub>2</sub> ) is presented. CO<sub>2</sub> is a nontoxic, nonflammable substance that is relatively inert and can be used to process biomaterials at mild pressures and physiologic temperatures. In this work, it was first determined that type I collagen is chemically compatible with both liquid and supercritical CO<sub>2</sub> . Treated collagen showed minimal changes in physicochemical properties as determined by differential scanning calorimetry, gel electrophoresis, and circular dichroism. CO<sub>2</sub> was subsequently used to extract residual glutaraldehyde from crosslinked collagen films. Glutaraldehyde concentration was reduced by over 95%, from over 20 ppm before treatment to about 1 ppm, in only 1 h. CO<sub>2</sub> treatment caused negligible alteration of thermal stability but did significantly increase film stiffness and tensile strength. However, these changes were minor compared to heat-based removal of glutaraldehyde. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 86-94, 2018.
An Efficient Hardware Design for Accelerating Sparse CNNs With NAS-Based Models (2021)

Deep convolutional neural networks (CNNs) have achieved remarkable performance at the cost of huge computation. As the CNN models become more complex and deeper, compressing CNNs to sparse by pruning the redundant connection in the networks has emerged as an attractive approach to reduce the amount of computation and memory requirement. On the other hand, FPGAs have been demonstrated to be an effective hardware platform to accelerate CNN inference. However, most existing FPGA accelerators focus on dense CNN models, which are inefficient when executing sparse models as most of the arithmetic operations involve addition and multiplication with zero operands. In this work, we propose an accelerator with software–hardware co-design for sparse CNNs on FPGAs. To efficiently deal with the irregular connections in the sparse convolutional layers, we propose a weight-oriented dataflow that exploits element–matrix multiplication as the key operation. Each weight is processed individually, which yields low decoding overhead. Then, we design an FPGA accelerator that features a tile look-up table (TLUT) and a channel multiplexer (CMUX). The TLUT is designed to match the index between sparse weights and input pixels. Using TLUT, the runtime decoding overhead is mitigated by using an efficient indexing operation. Moreover, we propose a weight layout to enable efficient on-chip memory access without conflicts. To cooperate with the weight layout, a CMUX is inserted to locate the address. Finally, we build a neural architecture search (NAS) engine that leverages the reconfigurability of FPGAs to generate an efficient CNN model and choose the optimal hardware design parameters. The experiments demonstrate that our accelerator can achieve 223.4-309.0 GOP/s for the modern CNNs on Xilinx ZCU102, which provides a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2.4\times $ </tex-math></inline-formula> – <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$12.9\times $ </tex-math></inline-formula> speedup over previous dense CNN accelerators on FPGAs. Our FPGA-aware NAS approach shows <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2\times $ </tex-math></inline-formula> speedup over MobileNetV2 with 1.5% accuracy loss.
Effect of SiGe Layer Thickness in Starting Substrate on Electrical Properties of Ultrathin Body Ge-on-Insulator pMOSFET Fabricated by Ge Condensation (2017)

2017 International Conference on Solid State Devices and Materials,Effect of SiGe Layer Thickness in Starting Substrate on Electrical Properties of Ultrathin Body Ge-on-Insulator pMOSFET Fabricated by Ge Condensation
Calcineurin is required for male sex pheromone biosynthesis and female acceptance (2018)

Lepidoptera sex pheromone biosynthesis is regulated by pheromone biosynthesis activating neuropeptide (PBAN). PBAN regulates not only female sex pheromone biosynthesis but also male sex pheromone biosynthesis. Previous research has confirmed that PBAN regulates sex pheromone biosynthesis using Ca<sup>2+</sup> as a secondary messenger in all examined species to date. However, the downstream signal of Ca<sup>2+</sup> has remained elusive. In the present study, calcineurin A (CNA), a downstream signal of Ca<sup>2+</sup> , was discovered in Helicoverpa armigera male hairpencil and named HaCNA. Sequence analysis demonstrated that the open reading frame of HaCNA contains 1488 nucleotides encoding 495 amino acid residues. A homology search revealed that HaCNA shares a high amino acid identity with the CNA of other insects. Developmental and spatial expression analyses revealed that the mRNA levels of HaCNA peaked at 24 h after emergence and that HaCNA expression was ubiquitous in all examined tissues. Activity analysis revealed that PBAN activates HaCNA, and a Ca<sup>2+</sup> inhibitor, Lacl<sub>3</sub> , attenuated the effect of PBAN by decreasing HaCNA activity. Pharmacological inhibitor and RNA interference-mediated knockdown assays revealed that both activity inhibition and decreased mRNA levels of HaCNA led to a significant decrease in the production of the male sex pheromone components [octadecanol and (Z)-11 hexadecanol)] and in the efficacy of female mating acceptance. Our results demonstrate that HaCNA acts as downstream signal of PBAN/Ca<sup>2+</sup> and plays an important role in PBAN-induced male sex pheromone biosynthesis and female mating acceptance.
Influence of High Hydrostatic Pressure on the Processes of Recrystallization of a Copper and Aging of a Cu-Be Alloy (1981)

In order to study the influence of hydrostatic pressure on the processes of recrystallization and aging of metallic materials, isothermal heat treatments have been done on a cold rolled OFHC copper and a Cu-Be alloy under 0.1 MPa and 800 MPa, and change in hardness with the holding time has been discussed. The results obtained are as follows:(1) No evident qualitative difference in structure due to pressure was observed in the OFHC copper after the primary recrystallization.(2) The change in hardness during the primary recrystallization was delayed by applying high hydrostatic pressure, and the time necessary for obtaining a given value of hardness under 800 MPa was about 2.9 times as large as the time under 0.1 MPa. This value is close to 2.5 calculated by assuming that the activation volume of self-diffusion of copper is about 0.7 \Bar{V} (\Bar{V} is the molar volume of copper).(3) As for the Cu-Be alloy, the increase in hardness was also delayed under high hydrostatic pressure. The time required for coming up to a certain hardness number under 800 MPa was about 2 times as large as the time under 0.1 MPa. Also in this case, a similar value of about 2.2 was calculated by assuming that the activation volume of diffusion of Be atom in copper is 0.55\Bar{V}Cu+0.15\Bar{V}Be (\Bar{V}Cu and \Bar{V}Be are the molar volumes of copper and beryllium, respectively).
Fabrication, characterization and index profile modeling of high-damage resistance Zn-diffused waveguides in congruent and MgO:lithium niobate (1992)

A study of the fabrication and optical properties of planar waveguides fabricated in MgO:LiNbO/sub 3/ and LiNbO/sub 3/ substrates by diffusion of a ZnO film is presented. Transmission electron microscopy was used to show that using ZnO instead of metallic zinc as a source, and maintaining the ZnO film thickness below a prescribed value, greatly reduces second phase precipitation and produces usable waveguides. Dopant and refractive index profiles were characterized by electron microprobe analysis and interference microscopy, respectively. The dependence of the Zn diffusion coefficient on temperature and the dependence of the refractive-index change on Zn concentration are inferred from these measurements. A simple model is also reported which predicts the index profile of the waveguide given the film thickness, diffusion time and temperature. The validity of the model is demonstrated by comparison between calculated profiles and profiles measured by prism coupling and IWKB analysis.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Graphene-Based Membranes for Molecular Separation (2015)

In comparison with traditional chemical separation processes, membrane separation is much simpler and more efficient. An ideal membrane for molecular separation should be as thin as possible to maximize its solvent flux, be mechanically robust to prevent it from fracture, and have well-defined pore sizes to guarantee its selectivity. Graphene is an excellent platform for developing size-selective membranes because of its atomic thickness, high mechanical strength, and chemical inertness. In this Perspective, we review the recent advancements on the fabrication of nanoporous graphene membranes and graphene oxide membranes (GOMs) for molecular separation. The methods of fabricating these membranes are summarized, and the mechanisms of molecular separation based on these two types of graphene membranes are compared. The challenges of synthesizing and transferring large-area nanoporous graphene membranes and engineering the performances of GOMs are discussed.
Preparation and Properties of a Selenium-containing Catalytic Antibody as Type I Deiodinase Mimic (2001)

Conversion of thyroxine (T4) to 3,5,3'-triiodothyronine is an essential first step in controlling thyroid hormone action. Type I deiodinase (DI) can catalyze the conversion to produce the bulk of serum 3,5,3'-triiodothyronine. Acting as a mimic of DI, a selenium-containing catalytic antibody (Se-4C5) prepared by converting the serine residues of monoclonal antibody 4C5 raised against T4 into selenocysteines, can catalyze the deiodination of T4 with dithiothreitol (DTT) as cosubstrate. The mimic enzyme Se-4C5 exhibited a much greater deiodinase activity than model compound ebselen and another selenium-containing antibody Se-Hp4 against GSH. The coupling of selenocysteine with the combining pocket of antibody 4C5 endowed Se-4C5 with enzymatic activity. To probe the catalytic mechanism of the catalytic antibody, detailed kinetic studies were carried out in this paper. Investigations into the deiodinative reaction revealed the relationship between the initial velocity and substrate concentration. The characteristic parallel Dalziel plots demonstrated that Se-4C5-catalyzed reaction mechanism was ping-pong one, involving at least one covalent enzyme intermediate. The kinetic properties of the catalytic antibody were similar to those of DI, with Km values for T4 and DTT of approximately 0.8 microm and 1.8 mm, respectively, and a Vm value of 270 pmol per mg of protein per min. The activity could be sensitively inhibited by 6-propyl-2-thiouracil (PTU) with a K(i) value of approximately 120 microm at 2.0 microm T4 concentration. The PTU inhibition was progressively alleviated with the increasing concentration of added DTT, revealing that PTU was a competitive inhibitor for DTT.
Cationic Liposomes Are a Strong Adjuvant for a DNA Vaccine of Human Immunodeficiency Virus Type 1 (1997)

Liposomes have been widely used to enhance the immune response. In the present investigation, we studied their in vivo immunomodulation of an HIV-1-specific DNA vaccine candidate (pCMV160/REV) constructed with the cytomegalovirus (CMV) promoter-conjugated HIV-1 env and rev DNA plasmids. By immunizing with pCMV160/REV and cationic liposomes through various routes (intramuscular, intraperitoneal, subcutaneous, intradermal, and intranasal), we induced higher levels of both antibody production and delayed-type hypersensitivity (DTH) than by using DNA vaccine alone. The HIV-1-specific cytotoxic T lymphocyte (CTL) activity was observed to be stronger on immunization with the DNA vaccine and cationic liposome combination. The intramuscular, intraperitoneal, and intranasal inoculation routes were more effective in inducing strong DTH and antibody responses than the subcutaneous and intradermal routes. Taken together, these results suggest that cationic liposomes can be highly effective when used with DNA vaccines and administered by various routes.
Rapid ‘multi-directed’ cholinergic transmission at central synapses (2020)

Abstract Acetylcholine (ACh) is a key neurotransmitter that plays diverse roles in many parts of the central nervous system, including the retina. However, assessing the precise spatiotemporal dynamics of ACh is technically challenging and whether ACh transmits signals via rapid, point-to-point synaptic mechanisms, or broader-scale ‘non-synaptic’ mechanisms has been difficult to ascertain. Here, we examined the properties of cholinergic transmission at individual contacts made between direction-selective starburst amacrine cells and downstream ganglion cells in the retina. Using a combination of electrophysiology, serial block-face electron microscopy, and two-photon ACh imaging, we demonstrate that ACh signaling bears the hallmarks of both non-synaptic and synaptic forms of transmission. ACh co-activates nicotinic ACh receptors located on the intersecting dendrites of pairs of ganglion cells, with equal efficiency (non-synaptic)— and yet retains the ability to generate rapid ‘miniature’ currents (∼1 ms rise times: synaptic). Fast cholinergic signals do not appear to depend on anatomically well-defined synaptic structures. We estimate that ACh spread is limited to ∼1-2 µ m from its sites of release, which may help starbursts drive local direction-selective cholinergic responses in ganglion cell dendrites. Together, our results establish the functional architecture for cholinergic signaling at a central synapse and propose a novel motif whereby single presynaptic sites can co-transmit information to multiple neurons on a millisecond timescale.
STUDIES ON THE ROLE OF THROMBOXANE IN THROMBIN-INDUCED PULMONARY INSUFFICIENCY IN THE RAT (1987)

The pathophysiology of the acute pulmonary damage that may occur in association with sepsis, hemorrhagic shock and microembolism seems to involve the activity of cyclooxygenase derived arachidonate metabolites. In the rat, pulmonary microembolism due to infusion of thrombin together with inhibition of fibrinolysis has been found to induce pulmonary insufficiency with similarities to the clinical adult respiratory distress syndrome. The infusion of thrombin results in systemic hypotension, pulmonary hypertension and platelet aggregation, and subsequently, with a certain dealy in time, to increased pulmonary vascular permeability. The main purposes of this investigation were to study the release of TxA2 and PGI2 following thrcmbin-induced pulmonary microembolizaticn in the rat and to examine the effects of a thromboxane synthetase inhibitor (DazoxibenR) on pulmonary arterial and systemic mean arterial pressure and vascular permeability. During infusion of thrcmbin in rats pulmonary arterial pressure rose from 15 ± 2 to 35 ± 3 rmHg and mean arterial pressure fell from 120 ± 6 to 49 ± 27 mmHg. Plasma thromboxane B2 (TxB2) increased from 0.3 ± 0.004 to 3.6 ± 0.5 ng/ml. Ninety minutes later the lung weight and albunin concentration in the lung were increased (2.21 ± 0.13 g and 22.7 ± 4.7 mg/g) compared with controls (1.12 ± 0.14 g and 8.5 ± 0.9 mg/g). Dazoxiben reduced the elevated pulmonary arterial pressure and the elevated plasma TxB2 concentration following infusion of thrombin. Ninety minutes after infusion of thrcmbin, the in vitro synthesis of TxB2 in lung tissue was increased. Dazoxiben and a specific rabbit anti-rat neutrophil serun reduced this synthesis of TxB in vitro. The lung weight (2.18 ± 0.20 g) and lung albumin concentration (21.4 ± 3.4 mg/g) was not affected by Dazoxiben. The results indicate that TxA2 in an important mediator of the pressure changes in the early phase after infusion of thrombin and that neutrophils are associated with thromboxane formation in the lung tissue. Rats pretreated with the antineutrophil serum had less pulmonary weight (1.69 ± 0.28 g) and the albumin concentration in the edema fluid was decreased (17.3 ± 3.6 mg/g), suggesting that polymorphonuclear leukocytes contributed to the pulmonary dysfunction. Dazoxiben when incubated with thrcmbin in a chromogenic substrate system had a linear, dose-related anti-thrombin effect. At a Dazoxiben concentration of 2.4 mM only a few percent of the thrombin activity remained.
Poly(beta-amino ester)-poly(ethylene glycol) micelles for intracellular therapeutic drug delivery (2016)

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