gebhart/patrepeval huggingface dataset:
A novel anti‐inflammatory role for secretory phospholipase A 2 in immune complex‐mediated arthritis (2010)

Phospholipase A2 (PLA2) catalyses the release of arachidonic acid for generation of lipid mediators of inflammation and is crucial in diverse inflammatory processes. The functions of the secretory PLA2 enzymes (sPLA2), numbering nine members in humans, are poorly understood, though they have been shown to participate in lipid mediator generation and the associated inflammation. To further understand the roles of sPLA2 in disease, we quantified the expression of these enzymes in the synovial fluid in rheumatoid arthritis and used gene-deleted mice to examine their contribution in a mouse model of autoimmune erosive inflammatory arthritis. Contrary to expectation, we find that the group V sPLA2 isoform plays a novel anti-inflammatory role that opposes the pro-inflammatory activity of group IIA sPLA2. Mechanistically, group V sPLA2 counter-regulation includes promotion of immune complex clearance by regulating cysteinyl leukotriene synthesis. These observations identify a novel anti-inflammatory function for a PLA2 and identify group V sPLA2 as a potential biotherapeutic for treatment of immune-complex-mediated inflammation.
Increasing the Versatility of Digitizations through Post-Camera Flat-Fielding (2015)

Capturing images of paintings is a challenging field where the photographer must struggle between the balance of evenly illuminating the painting and using extreme lighting angles to enhance the painting's physical attributes. Flat-fielding is a scientific technique that has the ability to preserve the enhanced physical attributes of the painting while also providing uniform illumination across the scene. When the flat-fielding is done in post-camera processing, the non-flat-fielded image is preserved and can be used in conjunction with the flat-fielded image to illustrate the varying degrees between directional lighting, typical of a gallery environments, and the uniform illumination often seen in archiving studios.
NIPEP-IBD; A SYNTHETIC PEPTIDE TARGETING NOVEL MOLECULE, INTEGRIN BETA 1, TO RESTITUTE INTESTINAL EPITHELIAL CELLS FOR INFLAMMATORY BOWEL DISEASE (IBD) TREATMENT (2022)

Abstract Under Inflammatory bowel disease (IBD), impaired intestinal barrier from lumen is highly associated with ongoing IBD symptoms and it also contributes as a precursor for IBD. Current IBD therapeutics lack on mucosal regeneration, which the unmet needs could be the next first in class therapeutics for IBD. Here, we propose NIPEP-IBD, a synthetically modified peptide that promotes adhesion, migration, and differentiation of intestinal epithelial cells via interaction of integrin beta 1. From NIBEC’s specialized peptide discovery platform screening, specifically sequenced peptide has been selected for regenerative functional peptide, termed NIPEP-IBD. NIPEP-IBD selectively targeted and bound to integrin beta 1 protein, and its interaction was also verified in vitro, using immunoprecipitation and immunofluorescence assays on epithelial cells. Consequently, NIPEP-IBD increased integrin beta 1 expression, followed by phosphorylated FAK and RhoA proteins. As FAK-RhoA signaling pathway is known to modulate cytoskeletal rearrangement and maturation of epithelial cells, tight junction markers and rapid wound closure of epithelial cells was accelerated by NIPEP-IBD induction. The effect of NIPEP-IBD was further analyzed in vivo IBD model. DSS-induced colitis mouse model was used to analyze therapeutic effect of NIPEP-IBD in each IP and PO administration, and impaired mucosa layer by DSS was recovered by NIPEP-IBD, verified with H&amp;E staining. Moreover, NIPEP-IBD treated mice showed reduced immune cell infiltration in colon tissue and reduced pro-inflammatory cytokines in plasma. In vivo fluorescence imaging system was further used to track distribution of NIPEP-IBD, and NIPEP-IBD specifically binds to impaired epithelium, co-localized with integrin beta 1 protein. The following GLP toxicity studies, ADME studies, and PK studies demonstrated that safety of NIPEP-IBD was verified as a therapeutic agent. Therefore, NIPEP-IBD is a safe and effective therapeutic peptide on IBD patients by restituting epithelial layer of colon and maintain its remission.
The subtype 2 of angiotensin II receptors and pressure‐natriuresis in adult rat kidneys (1999)

The present work examined the effects of the subtype 2 of angiotensin II (AT2) receptors on the pressure-natriuresis using a new peptide agonist, and the possible involvement of cyclic guanosine 3', 5' monophosphate (cyclic GMP) in these effects. In adult anaesthetized rats (Inactin, 100 mg kg(-1), i.p.) deprived of endogenous angiotensin II by angiotensin converting enzyme inhibition (quinapril, 10 mg kg(-1), i.v.), T2-(Ang II 4-8)2 (TA), a highly specific AT2 receptor agonist (5, 10 and 30 microg kg(-1) min(-1), i.v.) or its solvent was infused in four groups. Renal functions were studied at renal perfusion pressures (RPP) of 90, 110 and 130 mmHg and urinary cyclic GMP excretion when RPP was at 130 mmHg. The effects of TA (10 microg kg(-1) min(-1)) were reassessed in animals pretreated with PD 123319 (PD, 50 microg kg(-1) min(-1), i.v.), an AT2 receptor antagonist and the action of the same dose of PD alone was also determined. Increases in RPP from 90 to 130 mmHg did not change renal blood flow (RBF) but induced 8 and 15 fold increases in urinary flow and sodium excretion respectively. The 5 microg kg(-1) min(-1) dose of TA was devoid of action. The 10 and 30 microg kg(-1) min(-1) doses did not alter total RBF and glomerular filtration rate, but blunted pressure-diuresis and natriuresis relationships. These effects were abolished by PD. TA decreased urinary cyclic GMP excretion. After pretreatment with PD, this decrease was reversed to an increase which was also observed in animals receiving PD alone. In conclusion, renal AT2 receptors oppose the sodium and water excretion induced by acute increases in blood pressure and this action cannot be directly explained by changes in cyclic GMP.
Flavor Analysis of rin/+ and Other Tomato hybrids and Inbreds Using Sensory and Chemical Methods (1998)

Consumer dissatisfaction with commercial tomato ( Lycopersicon esculentum Mill.) eating quality is well-known. An array of tomato cultivars were tested for overall flavor by experienced or trained taste panels over several seasons. Fruit were also analyzed for aromatic volatiles, soluble solids (SS), and titratable acidity (TA). `Solar Set' was the most consistent cultivar for overall flavor, always ranking in the most preferred statistical group. Cultivars that were bred for increased firmness, either by crossing firm lines (ultrafirms) or that were heterozygous for the ripening inhibitor ( rin ) gene, tended to rank low in overall flavor and sweetness. Comparisons made included ultrafirm lines, rin/+ hybrids with one to three backcrosses to the high-flavored parent of `Solar Set' (Fla. 7060), Fla. 7060, and `Solar Set' with two rin backcrosses. Experienced panel ratings were highest for Fla 7060 followed by the rin/+ hybrids (in descending order of backcrosses to Fla. 7060), followed by the ultrafirm lines. SS and TA were highest in one ultrafirm (SS = 9.1, TA = 0.68) and lowest in one of the rin/+ hybrids (SS = 6.3, TA = 0.37) while the rest of the samples showed intermediate values. Analysis of flavor volatiles showed Fla. 7060 to be generally higher in most volatiles compared to the ultrafims and two of the rin/+ hybrids. Significant differences were found for methanol, ethanol, 1-penten-3-one, hexanal, trans-2-hexanal, trans -2-heptenal, cis-3-hexenol, 2+3-methylbutanol, 6-methyl-5-hepten-2-one, 2-isobutylthiazole, and geranylacetone.
Sep]ration-Free Super-Resolution from Compressed Measurements is Possible: an Orthonormal Atomic Norm Minimization Approach (2018)

We consider the problem of recovering the superposition of R distinct complex exponential functions from compressed non-uniform time-domain samples. Total Variation (TV) minimization or atomic norm minimization was proposed in the literature to recover the R frequencies or the missing data. However, in order for TV minimization and atomic norm minimization to recover the missing data or the frequencies, the underlying R frequencies are required to be well-separated, even when the measurements are noiseless. This paper shows that the Hankel matrix recovery approach can super-resolve the R complex exponentials and their frequencies from compressed nonuniform measurements, regardless of how close their frequencies are to each other. We propose a new concept of orthonormal atomic norm minimization (OANM), and demonstrate that the success of Hankel matrix recovery in separation-free super-resolution comes from the fact that the nuclear norm of a Hankel matrix is an orthonormal atomic norm. More specifically, we show that, in traditional atomic norm minimization, the underlying parameter values must be well separated to achieve successful signal recovery, if the atoms are changing continuously with respect to the continuously-valued parameter. In contrast, for the OANM, it is possible the OANM is successful even though the original atoms can be arbitrarily close.
Isolation of chick tenascin variants and fragments (1991)

The extracellular-matrix glycoprotein, tenascin, consists of disulfide-linked subunits of 190, 200 and 230 kDa (the three splicing variants reported in chicken) and usually exists as a six-armed structure under the electron microscope. We used monoclonal antibodies to isolate and characterize different splicing variants and proteolytic fragments obtained from the native protein. Purified monomeric tenascin has a native molecular mass of 216 kDa and is structured as single arms. Tenascin fragments obtained by pepsin digestion bind to monoclonal antibody (mAb) TnM1 which is directed against epidermal-growth-factor-like repeats in the N-terminal half of all subunits. These fragments represent the thin proximal part of the tenascin arms and they are still partially linked to dimers and trimers via disulfide bridges. Using mAb Tn68, that reacts with a fibronectin-type-III repeat towards the C-terminus, a tenascin fragment, generated by treatment with pronase, can be isolated. Ultrastructurally, this fragment looks like the thicker distal part of the tenascin arms. Only the 230-kDa variant of tenascin gives rise to this distal fragment after cleavage within the alternatively spliced fibronectin-type-III repeats. Native tenascin and all fragments containing the distal part of its arms bind to heparin-agarose, whereas the proximal fragments do not. Oligomeric and monomeric tenascin inhibit fibronectin-mediated fibroblast spreading with comparable efficiency when added to the culture medium, while the proximal fragment has no effect. The distal fragment as well as reduced and alkylated tenascin are active in this assay, but only at higher molar concentrations when compared to the native protein.
ChemInform Abstract: Trifluoroethyl Phenyl Iodonium Triflate (IV): Modified Preparation and N‐Trifluoroethylation of Amino Alcohols. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
374 PRODUCTION OF TRANSGENIC CLONED PIGLETS BY USING PORCINE FETAL FIBROBLASTS OVEREXPRESSING ENDOTHELIAL NITRIC OXIDE SYNTHASE (2005)

Vascular function, vascular structure, and homeostasis are thought to be regulated in part by endothelial nitric oxide synthase (eNOS). In addition, eNOS plays an important role in modulating metabolism of skeletal and cardiac muscle in health and disease. The pig is an optimal model for human diseases because of the large number of important similarities between the genomic, metabolism, and cardiovascular systems of pigs and humans. The main goal of this study was to produce pigs that carry an endogenous eNOS gene driven by a Tie-2 promoter and tagged with a V5 His tag so that a better understanding of cardiovascular regulation by eNOS can be gained. Nuclear transfer was conducted to create these animals, and the effects of two different oocyte activation treatments and two different culture systems were examined. Mature oocytes were purchased from BoMed, Inc. (Maidson, WI, USA) and enucleated by micromanipulation. Donor cells were injected into the perivitelline space and electrically fused to the recipient oocyte. Treatment 1 consisted of electrical fusion/activation in 1 mM calcium in mannitol; Treatment 2 consisted of electrical fusion in 0.1 mM calcium in mannitol, followed by chemical activation in 200 µM thimerosal for 10 min followed by 8 mM DTT for 30 min. The fusion rate (71% vs. 82%) was lower ( P &amp;lt; 0.0001) in Treatment 2 than in Treatment 1. For those oocytes that fused, the cleavage rates (5.9% vs. 0.4%) at 14-18 h were higher ( P &amp;lt; 0.0001) for Treatment 2. Fused oocytes were cultured for 12-18 h in 5% O2, 5% CO2, 90% N2 (low oxygen) or 5% CO2 in air (normal oxygen), and were then surgically transferred to the oviducts of gilts that exhibited estrus on the day of fusion or the day of transfer. In February four cloned transgenic piglets were born (birth weights were 495, 595, 965, and 685 g). Two were from Treatment 1 and low oxygen, and the other two were from Treatment 2 and normal oxygen, and all are currently healthy. PCR, RT-PCR, and Western blotting analysis confirmed that the pigs were transgenic, made message, and made the fusion protein. Immunohistochemistry confirmed that the fusion protein localized in the endothelial cells of the placental vasculature from the conceptuses as did the endogenous eNOS. In addition to the transgenic males, four wild-type females were born (birth weights were 585 (this one died on Day 4) 445, 930, and 585 g). All four were from Treatment 2 and low oxygen, and three are healthy. In conclusion, viable piglets were produced from both Treatments 1 and 2, as well as in both high and low oxygen conditions. Thus, both activation conditions and culture systems are compatible with development to term. These pigs will serve as the founders for a colony of miniature pigs that will help to elucidate the function of eNOS in regulating muscle metabolism and the cardiorespiratory system. This work was funded by a grant from the NIH RR18276 and Food for the 21st Century.
Investigation of photoreaction mechanism of photosensitive glass by femtosecond laser (2005)

A high-intensity femtosecond (fs) laser can fabricate complicated three-dimensional microstructures inside photosensitive glass with high spatial resolution. In this work, the mechanism of the photoreaction of the photosensitive glass to the infrared fs laser is investigated. We examine the photoinduced electron excitation process on the basis of the determination of the critical dose and a change of the optical-absorption spectrum after the fs laser irradiation. The photoreaction mechanism is discussed in comparison with the case of an ultraviolet nanosecond laser irradiation. Finally, the successive interband electron excitation through defect levels by multiphoton absorption is proposed.
Drilling with Induced Vibrations Improves ROP and Mitigates Stick/Slip in Vertical and Directional Wells (2014)

Abstract For years drillers have been taught to mitigate all vibrations in the drillstring while drilling to maximize Rate of Penetration (ROP), limit bit damage, and extend bit life. While limiting lateral vibrations and stick/slip are proven ways to improve performance and maintain directional control, in recent years it has been conclusively proven in the field that inducing axial agitation with specialized downhole tools can significantly improve lateral reach. Currently, however, the benefits of downhole oscillation tools have not been thoroughly studied for other performance gains, such as improved ROP in non-directional wells. An extensive research study, including lab and field testing, found that a low-frequency, benign axial vibration can increase the ROP significantly in all well types. Initial laboratory experiments were performed by inducing axial vibrations into the drilling process on a small scale drill bit in hard rock. Dramatic improvements in ROP and drilling efficiency were observed, with the added benefits of improved bit life and an unexpected reduction in stick/slip. This lab experiment was later tested in the field by utilizing a proven downhole oscillation tool in an active Bottom Hole Assembly (BHA) to create the effect that was simulated in the lab. The field tests showed the same results as the lab tests: significant performance gains were observed in several test wells using the downhole oscillation tool as compared to offset data. In addition, this same downhole oscillation tool showed drastically improved directional control when run above a Rotary Steerable System (RSS) tool, and stick/slip was practically eliminated with no negative effect on bit life or BHA reliability. High-speed sensor data collected at the bit during both the lab and field tests will further demonstrate the validity of the theory. Testing for a hard-rock application with roller cone bits is forthcoming, as the data indicates possible performance gains in this environment as well. Overall, the study revealed many benefits, such as improving well placement, reducing Non-Productive Time (NPT) and time to Total Depth (TD) by preventing BHA component damage through beneficial axial vibrations from the downhole oscillation tool. The data indicates that "benign vibration" can drastically improve drilling performance.
Radio-frequency ablation as primary management of well-tolerated sustained monomorphic ventricular tachycardia in patients with structural heart disease and left ventricular ejection fraction over 30% (2014)

Patients with well-tolerated SMVT, SHD, and LVEF > 30% undergoing primary VT ablation without a back-up ICD had a very low rate of arrhythmic death and recurrences were generally non-fatal. These data would support a randomized clinical trial comparing this approach with others incorporating implantation of an ICD as a primary strategy.
Data from Association of Wwox with ErbB4 in Breast Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;i&gt;WWOX&lt;/i&gt;, WW domain-containing oxidoreductase, is a tumor suppressor that is altered in many human cancers, including breast cancer. Wwox interacts with the ErbB4 receptor, reduces nuclear translocation of the cleaved intracellular domain of ErbB4, and inhibits its transactivation function mediated through Yes-associated protein. Here, we assessed the clinical significance of the Wwox-ErbB4 association. We determined Wwox protein expression by immunohistochemistry in a series of 556 breast cancers. Wwox expression was absent in 36% of the cancers, and loss of Wwox expression was associated with unfavorable outcome (&lt;i&gt;P&lt;/i&gt; = 0.02). Membranous location of ErbB4 was associated with favorable survival compared with women whose cancer lacked such ErbB4 expression (&lt;i&gt;P&lt;/i&gt; = 0.02). Wwox expression was strongly associated with membranous ErbB4 localization (&lt;i&gt;P&lt;/i&gt; = 0.0003) and with overall ErbB4 expression (&lt;i&gt;P&lt;/i&gt; = 0.0002). Coexpression of membranous ErbB4 and Wwox was associated with favorable outcome compared with cases with membranous ErbB4 and no Wwox immunoreactivity (&lt;i&gt;P&lt;/i&gt; = 0.002). &lt;i&gt;In vitro&lt;/i&gt;, Wwox associated with the two ErbB4 isoforms, JM-a CYT-1 and JM-a CYT-2, expressed in breast cancer. Moreover, expression of Wwox both &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; led to accumulation of total full-length membrane-associated ErbB4. These results suggest that expression of Wwox is associated with ErbB4 expression and that their coexpression has prognostic significance in breast cancer. [Cancer Res 2007;67(19):9330–6]&lt;/p&gt;&lt;/div&gt;
Desulfurella kamchatkensis sp. nov. and Desulfurella propionica sp. nov., new sulfur-respiring thermophilic bacteria from Kamchatka thermal environments (1998)

Two strains of moderately thermophilic bacteria, which reduce elemental sulfur to hydrogen sulfide, were isolated from volcanic sources in Kamchatka. Strain K-119T was obtained from a thermophilic microbial community associated with Thermothrix thiopara, and strain U-8T was isolated from a cyanobacterial mat inhabiting a sulfide-rich hot spring. Cells of both strains are short Gram-negative rods, motile with one polar flagellum (strain K-119T) or non-motile (strain U-8T). Both strains are obligate anaerobes, have temperature otima of 54-55 degrees C and pH optima of 6.9-7.2. Molecular hydrogen, acetate, fumarate, malate, pyruvate, lactate and long-chain saturated fatty acids served as growth substrates for both species; strain U-8T was also able to grow on propionate. All substrates were oxidized completely, H2S and CO2 being the only metabolic products. Elemental sulfur was obligately required for growth of strain K-119T, whereas strain U-8T was able to grow also with thiosulfate as electron acceptor and on pyruvate without an external electron acceptor. The DNA G + C contents of strains K-119T and U-8T were 31.6 and 32.2 mol%, respectively. Phenotypic features and the results of 16S rRNA sequencing indicate the affiliation of the new isolates to the genus Desulfurella. The DNA-DNA hybridization with Desulfurella acetivorans was 40% for strain K-119T and 55% for strain U-8T; the DNA-DNA hybridization between the new isolates was 32%. Based on the results of morphological, physiological and phylogenetic studies the following two new species are proposed: Desulfurella kamchatkensis sp. nov. with the type strain K-119T (= DSM 10409T) and Desulfurella propionica sp. nov. with the type strain U-8T (= DSM 10410T).
Nonplanar high-k dielectric thickness measurements using CD-SAXS (2009)

Non-planar transistor architectures, such as tri-gates or "FinFETs", have evolved into important solutions to the severe challenges emerging in thermal and power efficiency requirements at the sub-32 nm technology nodes. These architectures strain traditional dimensional metrology solutions due to their complex topology, small dimensions, and number of materials. In this study, measurements of the average dielectric layer thickness are reported for a series of structures that mimic non-planar architectures. The structures are line/space patterns (&asymp; 20 nm linewidth) with a conformal layer of sub-15 nm thick high-k dielectric. Dimensions are measured using a transmission X-ray scattering technique, critical dimension small angle X-ray scattering (CD-SAXS). Our test results indicate that CD-SAXS can provide high precision dimensional data on average CD, pitch, and high-k dielectric layer thickness. CD-SAXS results are compared with analogous data from both top-down scanning electron microscopy and cross-sectional transmission electron microscopy. In addition, we demonstrate the capability of CD-SAXS to quantify a periodic deviation in pitch induced by an imperfection in the phase shift mask.