gebhart/patrepeval huggingface dataset:
Finite difference magnetoelastic simulator (2021)

We describe an extension of the micromagnetic finite difference simulation software MuMax3 to solve elasto-magneto-dynamical problems. The new module allows for numerical simulations of magnetization and displacement dynamics in magnetostrictive materials and structures, including both direct and inverse magnetostriction. The theoretical background is introduced, and the implementation of the extension is discussed. The magnetoelastic extension of MuMax3 is freely available under the GNU General Public License v3.
COMBINED EFFECTS OF SUBCOOLING AND SURFACE ORIENTATION ON POOL BOILING OF HFE-7100 FROM A SIMULATED ELECTRONIC CHIP (2003)

Abstract The effects of orientation and subcooling on pool boiling of the HFE-7100 dielectric liquid near atmospheric pressure (0.085 MPa) from a 10 × 10 mm smooth copper surface are investigated experimentally. Results are obtained for inclination angles θ = 0° (upward-facing), 30°, 60°, 90°, 120°, 150°, and 180° (downward-facing) and liquid subcoolings ΔTsub = 0, 10, 20, and 30 K. Increasing θ decreases the saturation nucleate boiling heat flux at high surface superheats (ΔTsat > 20 K), but increases it only slightly at lower surface superheats. The critical heat flux (CHF) decreases slowly with increasing θ from 0° to 90°, and then deceases faster with increasing θ to 180°. CHF increases linearly with increased subcooling, but the rate increases from 0.016 K−1 at 0° to 0.048 K−1 at 180°. At θ = 0° and ΔTsub = 30 K, CHF is ∼ 36 W/cm2 and 24.45 W/cm2 for saturation boiling, while at θ = 180° CHF = 10.85 W/cm2 at ΔTsub = 30 K and only 4.30 W/cm2 at saturation. The developed correlation for CHF of HFE-7100, as a function of θ and ΔTsub, is within ±10% of the present data. The recorded still photographs of the boiling surface in the experiments illustrate the effects of liquid subcooling and surface orientation at different nucleate boiling heat fluxes and surface superheats on vapor bubble accumulation and/or induced mixing at the surface.
ADAM10 Inhibition of Human CD30 Shedding Increases Specificity of Targeted ImmunotherapyIn vitro (2007)

CD30 is a transmembrane protein selectively overexpressed on many human lymphoma cells and therefore an interesting target for antibody-based immunotherapy. However, binding of therapeutic antibodies stimulates a juxtamembrane cleavage of CD30 leading to a loss of target antigen and an enhanced release of the soluble ectodomain of CD30 (sCD30). Here, we show that sCD30 binds to CD30 ligand (CD153)-expressing non-target cells. Because antibodies bind to sCD30, this results in unwanted antibody binding to these cells via sCD30 bridging. To overcome shedding-dependent damage of normal cells in CD30-specific immunotherapy, we analyzed the mechanism involved in the release. Shedding of CD30 can be enhanced by protein kinase C (PKC) activation, implicating the disintegrin metalloproteinase ADAM17 but not free cytoplasmic calcium. However, antibody-induced CD30 shedding is calcium dependent and PKC independent. This shedding involved the related metalloproteinase ADAM10 as shown by the use of the preferential ADAM10 inhibitor GI254023X and by an ADAM10-deficient cell line generated from embryonically lethal ADAM10(-/-) mouse. In coculture experiments, the antibody-induced transfer of sCD30 from the human Hodgkin's lymphoma cell line L540 to the CD30-negative but CD153-expressing human mast cell line HMC-1 was inhibited by GI254023X. These findings suggest that selective metalloproteinase inhibitors blocking antibody-induced shedding of target antigens could be of therapeutic value to increase the specificity and reduce side effects of immunotherapy with monoclonal antibodies.
A Practical Synthesis of the Major 3‐Hydroxy‐2‐pyrrolidinone Metabolite of a Potent CDK2/Cyclin A Inhibitor. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
CD105 Is a Surface Marker for Receptor-Targeted Gene Transfer into Human Long-Term Repopulating Hematopoietic Stem Cells (2014)

Hematopoietic stem cells (HSCs) are an important target cell population for gene therapy since they can reconstitute the entire hematopoietic system. HSC-enriched cell populations can be recognized based on cell surface marker expression, such as CD34, which is broadly expressed on immature and partially differentiated cells. In mice, co-expression of CD34 and CD105 was previously shown to be relatively more specific for the most immature, long-term repopulating HSCs. Here, we evaluated whether CD105, which is expressed on 30%-80% of CD34(+) cells, is a marker also for human long-term repopulating HSCs. Therefore, we tracked the mature progeny of CD34(+) cells transduced with the CD105-targeted lentiviral vector CD105-LV in xenotolerant mice. Transduction was blocked with soluble CD105 protein confirming specificity. Importantly, CD105-LV transduced human CD34(+) cells engrafted in NOD-scid IL2Rγ(-/-) mice with up to 20% reporter gene-positive cells detected long term in all human hematopoietic lineages in bone marrow (BM), spleen, and blood. In addition, competitive repopulation experiments in mice showed a superior engraftment of CD105-LV transduced CD34(+) cells in BM and spleen compared with cells transduced with a conventional nontargeted lentiviral vector. Thus, human CD34(+)/CD105(+) cells are enriched for early HSCs with high repopulating capacity. Targeting this cell population with CD105-LV offers a novel gene transfer strategy to reach high engraftment rates of transduced cells and highlights the applicability of receptor-targeted vectors to trace cell subsets offering an alternative to prospective isolation by surface markers.
Enhancement of human cancer cell migration and invasion by anaphylatoxin C5a viaaberrantly expressed C5a-receptor. (2012)

e21084 Background: Accumulated evidence has revealed implications of chemokines and their receptors in the pathophysiology of cancer. Anaphylatoxin C5a, a fragment of the complement 5th component (C5), is a potent chemokine for leukocytes that express the C5a receptor (C5aR). Recent reports indicate production of C5a by proteases of various origins, besides a by-product of activation of the complement system, and expression of C5aR in non-myeloid cells, suggesting an involvement of C5a in these cell biology. However, little is known about roles of C5aR in human cancer. Aim of our study was to investigate the expression and the role of C5aR on cancer cells in proliferation and invasion. Methods: Surgically resected cancer tissues and cancer cell lines were investigated C5aR expression. The effect of C5a on cancer cell proliferation, cell shape and invasion activity were examined in vitro and in vivo. Results: By immunohistochemical analysis, C5aR was strongly expressed in human cholangiocarcinoma samples. Using RT-PCR, immunoblotting and flow cytometric analysis human cholangiocarcinoma cell line MEC but not HuCCT1 were found to express C5aR. Incubation of both cancer cells with C5a did not increase these cells, indicating no mitogenic effect of C5a on these cells. Interestingly, C5a stimulated invasion of MEC and C5aR-transgenic HuCCT1 when examined by Matrigel invasion assay, which was suppressed by anti C5aR antibody. F-actin staining and human MMPs array revealed that C5a induced actin polymerization and MMPs production, respectively, in MEC and C5aR-transgenic HuCCT1. In contrast, these C5a effects were not seen in HuCCT1. Conclusions: These results illustrate a novel activity of C5a-C5aR axis that promotes cancer cell invasion through cytoskeletal rearrangement and MMP release. Thus, targeting this signaling pathway may provide a useful therapeutic option for cancer treatment.
Material Properties of a Highly Anteverted Vitamin E-Stabilized Polyethylene Liner After Sixteen Months In Vivo (2014)

Beecher, Benjamin MD; Huddleston, James MD; Rowell, Shannon BS; Goodman, Stuart MD, PhD; Malchau, Henrik MD, PhD; Kwon, Young-Min MD, PhD; Muratoglu, Orhun K. PhD Author Information
Reprogramming cell fate with a genome-scale library of artificial transcription factors (2016)

Artificial transcription factors (ATFs) are precision-tailored molecules designed to bind DNA and regulate transcription in a preprogrammed manner. Libraries of ATFs enable the high-throughput screening of gene networks that trigger cell fate decisions or phenotypic changes. We developed a genome-scale library of ATFs that display an engineered interaction domain (ID) to enable cooperative assembly and synergistic gene expression at targeted sites. We used this ATF library to screen for key regulators of the pluripotency network and discovered three combinations of ATFs capable of inducing pluripotency without exogenous expression of Oct4 (POU domain, class 5, TF 1). Cognate site identification, global transcriptional profiling, and identification of ATF binding sites reveal that the ATFs do not directly target Oct4; instead, they target distinct nodes that converge to stimulate the endogenous pluripotency network. This forward genetic approach enables cell type conversions without a priori knowledge of potential key regulators and reveals unanticipated gene network dynamics that drive cell fate choices.
Arundic Acid (ONO-2506) Ameliorates Delayed Ischemic Brain Damage by Preventing Astrocytic Overproduction of S100B (2005)

After focal cerebral ischemia, the infarct volume increases rapidly within acute infarct expansion (initial 12 to 24 h) and continues slowly during delayed infarct expansion (25 to 168 h). While acute infarct expansion represents progressive necrosis within the ischemic core, delayed infarct expansion starts as disseminated apoptotic cell death in a narrow rim surrounding the infarct border, which gradually coalesces to form a larger infarct. Discovery of a distinct correlation between reactive astrogliosis along the infarct border and delayed infarct expansion in the rodent ischemia model led us to investigate the possible causal relationship between the two events. Specifically, the calcium binding protein S100B exerts detrimental effects on cell survival through activation of various intracellular signaling pathways, resulting in altered protein expression. Arundic acid [(R)-(-)-2-propyloctanoic acid, ONO-2506] is a novel agent that inhibits S100B synthesis in cultured astrocytes. In the rodent ischemia model, this agent was shown to inhibit both the astrocytic overexpression of S100B and the subsequent activation of signaling pathways in the peri-infarct area. Concurrently, delayed infarct expansion was prevented, and neurologic deficits were promptly ameliorated. The results of subsequent studies suggest that the efficacy of arundic acid is mediated by restoring the activity of astroglial glutamate transporters via enhanced genetic expression.
Investigational CYP51 Inhibitors VT-1161 and VT-1129 Show Strong Activity In Vitro Against Candida krusei (2016)

Background. Candida krusei is the fifth most common Candida species recovered from clinical specimens in the United States and worldwide. At Duke University Hospital it was responsible for 4 % (96/2560) of blood stream infections between 1992 and 2013, and has increased to 6%-10% over the past decade (2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013). C. krusei is intrinsically resistant to fluconazole, and the emergence of voriconazole resistance following exposure to fluconazole is a pressing concern. VT-1161 and VT-1129 represent a new generation of fungal CYP51 inhibitors, and are both highly selective and potent against Candida species, including azole-and echinocandinresistant isolates. In Phase 1 and 2 clinical trials, VT-1161 has achieved plasma concentrations of up to 10 g/mL with an excellent safety profile. Preclinical data for VT-1129 predict similar safety and PK profiles.
Tracking chondrocytes and assessing their proliferation with PKH26: Effects on secretion of proteoglycan 4 (PRG4) (2006)

Distinguishing between implanted and host-derived cells, as well as between distinct cell phenotypes, would be useful in assessing the mechanisms of cell-based repair of cartilage. The fluorescent tracker dye, PKH26, was previously applied to several cell types to assess proliferation in vitro and to track cells in vivo. The objectives of this study were to assess the utility of PKH26 for tracking chondrocytes from superficial and middle zones and their proliferation, and determine the effects of PKH26 on chondrocyte functions, in particular, proliferation and secretion of Proteoglycan 4 (PRG4). PKH26-labeled and unlabeled superficial and middle zone chondrocytes were plated in either low- or high-density monolayer culture and analyzed for retention of PKH26 by flow cytometry and fluorescence microscopy at days 0 and 7. Cell suspensions and conditioned media were analyzed for DNA and secretion of PRG4, respectively. Flow cytometric histograms were deconvolved so that the number of cells in each doubling generation contributing to the final cell population could be estimated. Chondrocytes were consistently and intensely labeled with PKH26 through 7 cycles of division. At day 7 of culture, >97% of superficial zone cells seeded at low or high density could be distinguished as fluorescent, as could middle zone cells seeded at high density. Retention of cell fluorescence after PKH26 labeling and lack of adverse effects on cell proliferation and synthesis of PRG4 suggest that PKH26 can be useful in determining the fate and function of implanted chondrocytes in vivo, as well as monitoring proliferation in vitro.
Maintained Hematologic and Organ Responses Following Risk Adapted Stem Cell Transplant (SCT) in Systemic Light-Chain Amyloidosis (AL) Using Bortezomib and Dexamethasone as Consolidation Therapy (2012)

Risk-adapted MEL dosing has improved the safety but may also compromise the efficacy of SCT for pts with AL. We report results of a phase II trial using bortezomib and dexamethasone (BD) as consolidation following risk-adapted SCT for pts with AL. Newly diagnosed pts with AL involving ≤ 2 organs were assigned MEL 100, 140 or 200mg/m2 with SCT, based on age, renal function and cardiac involvement. Response was assessed at 2-3, 12, and 24 mos post-SCT. Pts with persistent clonal plasma cell disease at 2-3 mos post-SCT received consolidation with BD for up to 6 cycles. Organ response and overall survival (OS) were assessed at 12 and 24 mos post-SCT. 41 pts with kidney (71%), heart (46%), liver/GI (12%) and peripheral nervous system (12%) disease were enrolled; 44% had 2 organ-involvement. One pt was ineligible; 1 is within 100 days of SCT. Four pts with advanced cardiac AL died within 100 days of SCT, resulting in 10% (4/40) TRM. With median follow-up 39 mos, OS at 12 mos post-SCT was 88%. In pts with heart involvement OS was 74% and 58% at 12 and 24 mos respectively, versus 100% at both time points in those without cardiac AL (P = 0003). Increased BNP and troponin were associated with worse OS, HR 1.3 (P = 0.0001) and HR 3.9 (P = 0.0003), respectively. Post-SCT, the hematologic RR was 54% with 28% pts achieving CR. For persistent clonal disease, 65% (22/34) received BD. Among all pts evaluable at 12 mos post-SCT, the hematologic RR was 96% (26/27) with 67% CR; 1 pt progressed. At 24 mos post-SCT the RR was 84% (16/19) including 50% who maintained CR; 3 more pts progressed. Of pts who received BD, 89% had an improved hematologic response; all responded after 1 cycle. Organ responses evolved over time and were seen in 56% and 88% of pts at 12 and 24 mos post-SCT, respectively. In pts with renal AL, 45% (9/20) achieved an organ response at 12 mos which increased to 92% (12/13) by 24 mos. No pt had worsening organ function. In newly diagnosed AL pts, BD following risk-adapted SCT is effective for eradicating persistent clonal disease. Hematologic responses are rapid resulting in high overall and unprecedented CR rates. Organ function improves in the majority of patients, over time. Cardiac disease is associated with inferior OS and cardiac biomarkers are useful for assigning risk. Relapses occur after completion of therapy and a maintenance regimen following post-SCT consolidation is worthy of further study.
Ultrastructural and immunocytochemical changes in retinal pigment epithelium, retinal glia, and fibroblasts in vitreous culture. (1990)

Retinal pigment epithelial (RPE) cells, retinal glial, and fibroblasts, three cell types believed to play a role in the pathogenesis of epiretinal membrane formation, were maintained in vitreous culture to determine the influence of vitreous on their ultrastructure and expression of cytokeratin, glial fibrillary acidic protein (GFAP), vimentin, and glutamine synthetase (GS). Using a highly sensitive, preembedding technique for the immunolocalization of these antigens at the ultrastructural level, most RPE cells were found to lose cytokeratin and vimentin within 1 day after seeding on irradiated vitreous. The percentage of keratin-positive cells then increased with time in culture. If the vitreous was placed on RPE cells cultured in monolayer instead of placing the cells on the vitreous, keratin and vimentin were expressed these intermediate filament proteins diminished with time. Glutamine synthetase was found in RPE cells grown in monolayer with or without a vitreous overlay, but not in RPE cells grown on the surface of vitreous. Retinal glial grown on vitreous showed a time-dependent decrease in the number of cells expressing GFAP and a corresponding increase in cells expressing vimentin or GS. Some fibroblasts in vitreous culture expressed vimentin but not the other antigens evaluated. A substantial number of cells in each culture did not stain positively for cytokeratin, GFAP, vimentin, or GS. All three cell types showed phenotypic diversity at the ultrastructural level with each cell type being capable of assuming the same morphologic appearance under certain conditions. These results demonstrate the phenotypic plasticity of RPE cells, retinal glia, and fibroblasts when grown in contact with vitreous and provide further evidence that neither ultrastructure, intermediate filament protein expression, nor the presence of GS is sufficient to determine the cell type of origin of cells in epiretinal membranes.
Minimal Intestinal Epithelial Cell Toxicity in Response to Short- and Long-Term Food-Relevant Inorganic Nanoparticle Exposure (2013)

Toxicity of commercial nanoparticles of titania, silica, and zinc oxides is being investigated in this in vitro study. Particles of these compositions are found in many food items, and thus this study is directed toward particle behavior in simulated digestion media and their interaction with intestinal epithelial cell line C2BBe1, a clone of Caco-2 cells, originally isolated from a human colon cancer. Even though the primary particle size of all three particles was below 50 nm, the particles appeared as aggregates in culture media with a negatively charged surface. In the presence of pepsin (pH 2), the charge on the titania became positive, and silica was almost neutral and aggregated extensively, whereas ZnO dissolved. For silica and titania, treatment with simulated intestinal digestive solution led to a strongly negatively charged surface and particle sizes approaching values similar to those in media. On the basis of infrared spectroscopy, we concluded that the surface of silica and titania was covered with bile salts/proteins after this treatment. Transmission electron microscopy indicated that the C2BBe1 cells internalized all three particles. Toxicity assays included investigation of necrosis, apoptosis, membrane damage, and mitochondrial activity. Titania and SiO₂ particles suspended in media at loading levels of 10 μg/cm² exhibited no toxicity. With ZnO at the same loading level, mild toxicity was observed based only on the LDH assay and decrease of mitochondrial activity and not necrosis or apoptosis. Titania particles exposed to the simulated digestion media exhibited mild toxicity based on decrease of mitochondrial activity, likely due to transport of toxic bile salts via adsorption on the particle surface.
Frailty and Access to Kidney Transplantation (2019)

Frailty is associated with lower chance of listing and lower rate of transplant, and is a potentially modifiable risk factor.
Quantification of Tissue Oxygenation Using an Intensity-Based Wearable Device and Machine Learning Approaches (2021)

We report a lightweight, cost-efficient wearable device to measure phosphorescence of an oxygen-sensing dye, leading to an estimation of pO 2 through fit-based and machine learning approaches.
High Momentum Jet Flames at Elevated Pressure, E: Quantification of Droplet Size Distribution and Transport (2020)

Abstract The present work investigates a model combustor that approximates a full-scale segment of a high momentum jet stabilised combustion concept with the objective to broaden fuel flexibility limits. The rig features optical access for detailed laser based diagnostics. The current experiments are conducted at a pressure of 8 bar, constant jet velocity and adiabatic flame temperature. Three different injection systems are used to inject oil and oil / water blends. Droplet size distributions and turbulent droplet transport are quantified by means of phase Doppler interferometry. The injection system has a noticeable impact on the droplet size distribution. Water addition affects the fuel placement in radial direction significantly with distinct droplet transport into the reaction zone. The jet core and droplet transport is maintained as far as 7 x/d axial downstream from the nozzle exit. The shear layer shows a turbulent intensity of 12% of the main jet bulk velocity that drives the radial droplet transport into the recirculation zone. Mass flow and number density estimations illustrate the spatial distribution of the liquid loading in the combustion chamber. The present findings are complementary to the work in part A–D, support the development of fuel and load flexible high momentum jets based combustion concepts and the development and validation of numerical models.
Multicritical phenomena and microphase ordering in random block copolymers melts (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMulticritical phenomena and microphase ordering in random block copolymers meltsGlenn H. Fredrickson, Scott T. Milner, and Ludwik LeiblerCite this: Macromolecules 1992, 25, 23, 6341–6354Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://pubs.acs.org/doi/10.1021/ma00049a034https://doi.org/10.1021/ma00049a034research-articleACS PublicationsRequest reuse permissionsArticle Views1014Altmetric-Citations200LEARN 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
Supplemental File 1 from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks (2023)

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