gebhart/patrepeval huggingface dataset:
Irisin Protects Heart Against Ischemia-Reperfusion Injury Through a SOD2-Dependent Mitochondria Mechanism (2018)

Irisin, a muscle-origin protein derived from the extracellular domain of the fibronectin domain-containing 5 protein (FNDC5), has been shown to modulate mitochondria welfare through paracrine action. Here, we test the hypothesis that irisin contributes to cardioprotection after myocardial infarction by preserving mitochondrial function in cardiomyocytes. Animal model studies show that intravenous administration of exogenous irisin produces dose-dependent protection against ischemia/reperfusion (I/R)-induced injury to the heart as reflected by the improvement of left ventricular ejection fraction and the reduction in serum level of cTnI (n = 15, P < 0.05). I/R-induced apoptosis of cardiomyocytes is reduced after irisin treatment. The irisin-mediated protection has, at least in part, an effect on mitochondrial function because administration of irisin increases irisin staining in the mitochondria of the infarct area. Irisin also reduces I/R-induced oxidative stress as determined by mitochondrial membrane potential evaluation and superoxide FLASH event recording (n = 4, P < 0.05). The interaction between irisin and superoxide dismutase2 (SOD2) plays a key role in the protective process because irisin treatment increases SOD activity (n = 10, P < 0.05) and restores the mitochondria localization of SOD2 in cardiomyocytes (n = 5, P < 0.05). These results demonstrate that irisin plays a protective role against I/R injury to the heart. Targeting the action of irisin in mitochondria presents a novel therapeutic intervention for myocardial infarction.
Stapled endosome disrupting alginate particles for cytosolic delivery of cations (2015)

Divalent cations, the most prevalent minerals in the body, are responsible for a wide variety of cellular functions including signaling, proliferation, differentiation and cell death, and therefore their transmembrane transportation is tightly regulated. Despite the importance of divalent cations in cell activity, there are currently no intracellular delivery methods for divalent cations or modulation of intracellular levels of minerals. Here, we describe endosome disrupting alginate nanoparticles termed Alginoketals, which can deliver divalent cations to the cytosol of the cells. Alginoketals are generated by crosslinking alginic acid with endosome disrupting ketals, and using divalent cations as the stapling or binding agent. We show that Alginoketals were able to deliver copper (II) in the cytosol of the cancer cells thereby disrupting copper homeostasis and inducing cell death via accumulation of hydrogen peroxide. Alginoketal-copper (II)-based particles act as superoxide dismutase mimics and are the first class of divalent cation delivery vehicles, with potential application in cancer therapy, regenerative medicine and drug delivery.
Synthesis and <i>In Vitro</i> Antibacterial Activity of Novel 3‐Azabicyclo[3.3.0]octanyl Oxazolidinones (2012)

We synthesized a series of oxazolidinone-type antibacterials in which morpholine C-ring of linezolid has been modified by substituted 3-azabicyclo[3.3.0]octanyl rings. Acetamide or 1,2,3-triazole heterocycle was used as C-5 side chain of oxazolidinone. The resulting series of compounds was then screened in vitro against panel of susceptible and resistant Gram-positive, Gram-negative bacteria, and Mycobacterium tuberculosis (Mtb). Several analogs in this series exhibited potent in vitro antibacterial activity comparable or superior to linezolid against the tested bacteria. Compounds 10a, 10b, 11a, and 15a displayed highly potent activity against M. tuberculosis. Selected compound 10b showed good human microsomal stability and CYP-profile, and showed low activity against hERG channel.
Domain Ontology Induction Using Word Embeddings (2016)

Ontology, the shared formal conceptualization of domain information, has been shown to have multiple applications in modeling, processing and understanding natural language text. In this work, we use distributed word vectors out of various recent language models from Deep Learning for semi-automated domain ontology creation for closed domains. We cover all major aspects of Domain Ontology Induction or Learning like concept identification, attribute identification, taxonomical and non-taxonomical relationship identification using the distributed word vectors. Preliminary results show that simple clustering based methods using distributed word vectors from these language models outperforms methods using models like LSI in ontology learning for closed domains.
Multifunctional Forceps for Use in Endoscopic Surgery—Initial Design, Prototype, and Testing (2011)

This paper presents a 3.0 mm diameter multifunctional endoscopic forceps design for use in minimally invasive flexible endoscopic surgical procedures. Multifunctional capabilities including grasping, spreading, and cauterizing tissue are demonstrated experimentally and compared to commercially available forceps. Models of the proposed design predict considerable improvements in opening range (140%) and force application (87%) for both grasping and spreading when compared to currently used endoscopic forceps. Several of the tool’s design characteristics promote fail-safe malfunctions, including locking before catastrophic failure and a decreased likelihood in detached parts. Initial benchtop testing shows good agreement between prototype performance and model prediction. Frictional losses experienced during testing were found to depend on load orientation.
METHODS FOR TRACING AND FORECASTING CONGESTED TRAFFIC PATTERNS (2001)

The two recent models ASDA' and FOTO' for the online automatic tracing and prediction of congested traffic flow patterns on highways are considered. The model ASDA (Automatische Staudynamikanalyse: Automatic Tracing of Moving Traffic Jams) (Kerner, et al.) is devoted to the automatic tracing and prediction of the propagation of moving traffic jams The model FOTD (Forecasting of Traffic Objects) (Kerner, Aleksic and Rehbom) is devoted to the tracing and prediction of the patterns of synchronized traffic flow'. The methods ASDA and FOTO are explained with a short theoretical background which is based on the three-phase-traffic-the-ory by Kerner.
Root-Surface Caries in Rats and Humans: Inhibition by a Non-Antimicrobial Property of Tetracyclines (1998)

The incidence of root caries has been found to increase as the population ages and as edentulism becomes less prevalent due to improved dental awareness and care, and as exposure of roots due to gingival recession has also increased in the elderly. The mechanism of root caries is thought to be mediated by both bacterial and mammalian proteases produced by plaque and the periodontal tissues, respectively. In the current study, a rat model of periodontal disease was used in which gnotobiotic rats were infected intra-orally with a periodontal pathogen (P. gingivalis). Infecting the rats with P. gingivalis increased the collagenase activity in the gingival tissue in association with severe alveolar bone loss. Treating P. gingivalis-infected rats with doxycycline or CMT-1 prevented the destruction of the periodontium by MMPs, thus preventing exposure of roots to subgingival bacterial plaque and host tissue collagenases and the subsequent development of root caries. In addition, a low-dose doxycycline (LDD, 20 mg bid, non-antimicrobial dose) for 3 months was used in humans predisposed to increased root caries as the result of heavy use of smokeless (chewing) tobacco, causing gingival recession, subgingival plaque accumulation with Gram-negative bacteria, increased gingival crevicular fluid flow (GCF), and elevated GCF collagenase. Daily administration of LDD in smokeless tobacco patients reduced the GCF collagenase and prevented the further development of root caries.
Photometric Mesh Optimization for Video-Aligned 3D Object Reconstruction (2019)

In this paper, we address the problem of 3D object mesh reconstruction from RGB videos. Our approach combines the best of multi-view geometric and data-driven methods for 3D reconstruction by optimizing object meshes for multi-view photometric consistency while constraining mesh deformations with a shape prior. We pose this as a piecewise image alignment problem for each mesh face projection. Our approach allows us to update shape parameters from the photometric error without any depth or mask information. Moreover, we show how to avoid a degeneracy of zero photometric gradients via rasterizing from a virtual viewpoint. We demonstrate 3D object mesh reconstruction results from both synthetic and real-world videos with our photometric mesh optimization, which is unachievable with either naïve mesh generation networks or traditional pipelines of surface reconstruction without heavy manual post-processing.
Medium‐pressure UV for oocyst inactivation (1999)

In vivo studies indicate the infectivity of treated Cryptosporidium parvum oocysts more reliably than do in vitro assays. Inactivation of Cryptosporidium parvum oocysts in finished drinking water by medium‐pressure ultraviolet (UV) light was investigated at bench scale using a collimated beam apparatus and at demonstration scale using a UV reactor. Oocyst viability was assessed in vitro (using 4',6‐diamidino‐2‐phenylindole with propidium iodide and maximized in vitro excystation) and in vivo (using neonatal mouse infectivity assays). In vivo bench‐scale studies showed > 4‐log inactivation at UV dosages as low as 41 mJ cm –2 , although in vitro surrogate assays showed little or no inactivation at this or higher UV dosages. The in vitro assays, which indicate oocyst viability, grossly overestimated the UV dosages required to prevent oocyst infection in susceptible hosts. Results of demonstration studies, carried out under the Environmental Technology Verification program of the National Sanitation Foundation and the US Environmental Protection Agency, agreed with the bench‐scale results and showed that a UV dosage as low as 19 mJ cm –2 provided 3.9‐log inactivation of Cryptosporidium oocysts.
<title>High Pressure Reinjection CO<formula><inf><roman>2</roman></inf></formula> Oscillator</title> (1980)

The design and performance of a uv preionized CO2 oscillator capable of 10 atm operation is described. When used as a reinjection oscillator this device is capable of subnanosecond pulses of CO2 radiation with powers in excess of 1 GW.
Efficient transcoding of JPEG2000 images (2003)

One of the key properties of the JPEG2000 standard is that it is possible to parse a JPEG2000 bit-stream to extract a lower resolution and/or quality image without having to perform dequantization and requantization. This property is especially useful given the variety of devices with vastly differing bandwidth and display capabilities that can now access the Internet. It is anticipated that a high-resolution JPEG2000-compressed image stored at an image server will be accessed by a variety of clients with differing needs for resolution and image quality. To satisfy the needs of these heterogeneous clients, it is essential that the server have the ability to transcode a JPEG2000 image in an efficient manner with very little loss in image quality. In this paper, we present a number of methods for transcoding a JPEG2000 image and evaluate each with respect to computational complexity and the quality of the transcoded image.
Improved current-mode control with single-cycle load transient (2016)

Non-linear single-cycle load transient improvement structures are proposed for current-mode controlled converters. Two popular variable-frequency current-mode controls are Constant On-Time (COT) and Ramp Pulse Modulation (RPM) due to their fast transient response. However, conventional COT and RPM both need multiple steps to increase the inductor current during load step-up transient. The fastest transient response is a single-cycle response. In this paper, two methods are proposed to achieve single-cycle load transient for current-mode control by improving the present control structures. For both methods of improvement, the operation mechanism of the control remains unchanged during steady-state. The proposed improvements can be used for RPM and COT in single-phase and multiphase.
The effects of porcine somatotropin and dietary lysine on growth performance and carcass characteristics of finishing swine. (1990)

Seventy-two finishing pigs (initial weight = 57.6 kg) were utilized to determine the effects of porcine somatotropin (pST) and dietary lysine level on growth performance and carcass characteristics. Pigs were injected daily with 4 mg pST in the extensor muscle of the neck and fed either a pelleted corn-sesame meal diet (.6% lysine, 17.8% CP) or diets containing .8, 1.0, 1.2 or 1.4% lysine provided by additions of L-lysine.HCl. All diets were formulated to contain at least twice the required amounts of other amino acids. Control pigs received a placebo injection and the .6%-lysine diet. Increasing levels of dietary lysine resulted in increased ADG and improved feed conversion (quadratic, P less than .01) for pST-treated pigs. The calculated daily lysine intake was 16.6, 13.6, 19.6, 25.1, 29.6 and 33.6 g for the control and pST-treated pigs fed .6, .8, 1.0, 1.2 and 1.4% lysine, respectively, over the entire experiment. Breakpoint analysis indicated that cumulative ADG and feed conversion were optimized at 1.19 and 1.22% lysine, respectively. Longissimus muscle area and trimmed ham and loin weights increased as dietary lysine was increased among pST-treated pigs (quadratic, P less than .01). Breakpoint analysis indicated that 1.11% lysine maximized longissimus muscle area, whereas trimmed ham and loin weights were maximized at .91 and .98% lysine, respectively. Adjusted backfat thickness was not affected by dietary lysine, but pST-treated pigs had less backfat (P less than .05) than control pigs did. Percentage moisture of the longissimus muscle increased (linear, P less than .05), as did percentage CP (quadratic, P less than .05), whereas fat content decreased (linear, P less than .05) as lysine level increased. Similar trends in composition were observed for muscles of the ham (semimembranosus, semitendinosus, and biceps femoris). Shear-force values from the longissimus and semimembranosus were lowest for control pigs, but they increased as dietary lysine level increased among pST-treated pigs. Sensory panel evaluations indicated that juiciness and tenderness decreased (linear, P less than .05) as dietary lysine level increased. Plasma urea concentrations decreased linearly (P less than .01) on d 28 as lysine level increased, whereas plasma lysine and insulin were increased (quadratic, P less than .01). Plasma glucose and free fatty acid concentrations on d 28 tended to increase (quadratic, P less than .10) with increasing dietary lysine level.(ABSTRACT TRUNCATED AT 400 WORDS)
Production of porous metal oxides (2005)

Porous complex oxides are produced by reacting metal oxide precursors in the presence of a pore-forming material to provide pore sizes in the range of 7-250 nm, followed by removal of the pore-forming material under conditions preserving the structure and compn. of the formed oxides. The pore-forming material are carbon black particles having a particle size of 10-100 nm. The carbon particles are removed from the formed oxide by heating at 100-300°. A surfactant can be added to the reaction mixt. [on SciFinder(R)]
Method for Structural Determination of Lipid-Derived Radicals (2020)

Diversified oxidized-lipid molecules are responsible for inflammation and cell death, including ferroptosis. Lipid radicals are the source of these oxidized lipids, which are the initial key molecules in the lipid peroxidation chain reaction. However, owing to their extremely high reactivity and short half-life, an established detection technique is not available. Here, we propose a high-performance liquid chromatography fluorometry and high-resolution tandem mass spectrometry system combined with a fluorescent probe as a structural analysis method for lipid-derived radicals. We detected 132 lipid-derived radicals, including 111 new species, from five polyunsaturated fatty acids. In addition, a database was constructed for which the initial fatty acid could be determined using the radical structure. Further, 12 endogenous lipid-derived radicals were identified in carcinogen-induced liver cancer mouse models. Therefore, this method and its corresponding database will provide novel insights into mechanisms underlying the lipid peroxidation, including the associated inflammation and ferroptosis.
Selective Blockade of Glycoprotein VI Clustering on Collagen Helices (2006)

Platelet activation by collagen relies on the interaction of the receptor glycoprotein VI (GPVI) with collagen helices. We have previously generated two recombinant single chain human antibodies (scFvs) to human GPVI. The first, 10B12, binds to the collagen-binding site on the apical surface between the two immunoglobulin-like domains (D1D2) of the receptor and so directly inhibits GPVI function. The second, 1C3, binds D1D2 independently of 10B12 and has been shown to have a more subtle effect on platelet responses to collagen. Here we have shown that 1C3 potentiates the effect of 10B12 on platelet aggregation induced by collagen and cross-linked collagen-related peptide (CRP-XL). We investigated this by measuring the effect of both scFvs on the binding of D1D2 to immobilized collagen and CRP. As expected, 10B12 completely inhibited binding of GPVI to each ligand in a dose-dependent manner. However, 1C3 inhibited only a proportion of GPVI binding to its ligands, implying that it interferes with another aspect of ligand recognition by GPVI. To further understand the mode of inhibition, we used a unique set of CRPs in which the content of critical glycine-proline-hydroxyproline (GPO) triplets was varied in relation to an "inert" scaffold sequence of GPP motifs. We observed that a stepwise increase in D1D2 binding with (GPO)(2) content was blocked by 1C3. Together these results indicate that 1C3 inhibits clustering of the immunoglobulin-like domains of GPVI on collagen/CRPs, a conclusion that is supported by mapping the 1C3 epitope to the region including isoleucine 148 in D2.
Biochemical Characterization of an <scp>l</scp> -Xylulose Reductase from <i>Neurospora crassa</i> (2007)

An l-xylulose reductase identified from the genome sequence of the filamentous fungus Neurospora crassa was heterologously expressed in Escherichia coli as a His(6) tag fusion protein, purified, and characterized. The enzyme may be used in the production of xylitol from the major pentose components of hemicellulosic waste, d-xylose and l-arabinose.
SLOPE: Shrinkage of Local Overlapping Patches Estimator for Lensless Compressive Imaging (2016)

A new compressive sensing inversion framework is developed via exploiting the sparsity of local overlapping patches, with the lensless compressive imaging as an exemplar application. This novel framework is formulated to an iteratively two-step process, with the first step projecting the measurements to the data level and the second step aiming to denoise the results obtained in the first step. Under the structure of the sensing matrix used in the hardware, we prove that the proposed algorithm enjoys the anytime property; the algorithm produces a sequence of solutions that monotonically converge to the true signal (thus, anytime). The performance of the proposed algorithm is verified by the real measurements captured by the compressive sensing camera, i.e., the lensless camera, while the algorithm can also be used in other compressive sensing hardware setups. The algorithm is further enhanced by investigating the group sparsity of similar patches in order to improve the performance. Experiments demonstrate that encouraging results are obtained by measuring about 10% (of the image pixels) compressive measurements on both simulation and real data sets.
Stress-Induced Chloroplast Degradation in <i>Arabidopsis</i> Is Regulated via a Process Independent of Autophagy and Senescence-Associated Vacuoles (2014)

Two well-known pathways for the degradation of chloroplast proteins are via autophagy and senescence-associated vacuoles. Here, we describe a third pathway that was activated by senescence- and abiotic stress-induced expression of Arabidopsis thaliana CV (for chloroplast vesiculation). After targeting to the chloroplast, CV destabilized the chloroplast, inducing the formation of vesicles. CV-containing vesicles carrying stromal proteins, envelope membrane proteins, and thylakoid membrane proteins were released from the chloroplasts and mobilized to the vacuole for proteolysis. Overexpression of CV caused chloroplast degradation and premature leaf senescence, whereas silencing CV delayed chloroplast turnover and senescence induced by abiotic stress. Transgenic CV-silenced plants displayed enhanced tolerance to drought, salinity, and oxidative stress. Immunoprecipitation and bimolecular fluorescence complementation assays demonstrated that CV interacted with photosystem II subunit PsbO1 in vivo through a C-terminal domain that is highly conserved in the plant kingdom. Collectively, our work indicated that CV plays a crucial role in stress-induced chloroplast disruption and mediates a third pathway for chloroplast degradation. From a biotechnological perspective, silencing of CV offers a suitable strategy for the generation of transgenic crops with increased tolerance to abiotic stress.
Superspace crystal symmetry of thermoelectric misfit cobalt oxides and predicted structural models (2007)

Single crystals of thermoelectric misfit lamellar cobalt oxide phases in the Bi-Ca-Co-O and I-Bi-Ca-Co-O systems were synthesized. They are characterized by aperiodic structures involving two partially independent sublattices: a CdI(2)-type pseudohexagonal CoO(2) layer and a rocksalt-type BiCaO(2) slab allowing the intercalation of iodine. The crystal symmetry of these structures is discussed using the four-dimensional superspace formalism. The superspace Laue classes of the iodine-free and the intercalated compounds are P2/m(0delta(1/2)) (a(1) = 4.901, b(1) = 4.730, b(2) = 2.80, c(1) = 14.66 A, beta = 93.49 degrees ) and A2/m(0delta1) (a'1 = 4.903, b'1 = 4.742, c'1 = 36.51 A, beta = 87.30 degrees ), respectively. A comparison is given with the related Bi-Sr-Co-O misfit compounds. The present structures are compatible with the presence of an intrinsic modulation with a wavelength matching the misfit aperiodicity in the b direction. Preliminary partial structure refinements confirm the layer stacking of the structure and the intercalation of I between the Bi-O layers for the second phase. A comparison with other cobalt oxide phases, as well as symmetry and metric considerations allow us to predict average structures for these new phases and to describe the common structural features assumed for all these lamellar misfit cobalt oxides.
NKG2A inhibits TH2 cell effector function in vitro (2007)

We show that signalling through NKG2A suppresses TH2 effector function. This may provide a means to modulate Th1/Th2 balance in diseases where Th2 cytokines predominate.