gebhart/patrepeval huggingface dataset:
Synthesis and size classification of metal oxide nanoparticles for biomedical applications (2004)

Magnetic nanoparticles are considered for biomedical applications, such as the medium in magnetic resonance imaging, hyperthermia, drug delivery, and for the purification or classification of DNA or virus. The performance of magnetic nanoparticles in biomedical application such as hyperthermia depends very much on the magnetic properties, size and size distribution. We briefly described the basic idea behind their use in drug delivery, magnetic separation and hyperthermia and discussed the prerequisite properties magnetic particles for biomedical applications. Finally reported the synthesis and classification scheme to prepare magnetite (Fe<sub>3</sub>O<sub>4</sub>) nanoparticles with narrow size distribution for magnetic fluid hyperthermia.
Perioperative haemostasis and coagulation management in cardiac surgery: a European survey (2007)

Background and objectivesDuring the last decade many aspects of haemostasis and coagulation management greatly changed in cardiac surgery. On one side, new anti-platelet agents entered the market and became more and more widely used; on the other one, point-of-care monitoring tools are nowadays available for perioperative use. The present survey is aimed to investigate the perioperative haemostasis and coagulation management in European Cardiac Surgery Institutions.MethodsA questionnaire exploring different aspects of perioperative haemostasis and coagulation management was sent to 320 Cardiac Surgery Institutions in Europe.Results82 Institutions replied to the survey. Due to the poor quality of the data collection, 9 Institutions were excluded. A pool of 73 questionnaires coming from 24 different Countries was analyzed. Non-routine coagulation tests (antithrombin activity) are done in 34% of the Institutions before the operation and in 23% after the operation. Point-of-care tests are applied as a preoperative routine in 9.9% of the Institutions (thromboelastography, 5.7%; PFA-100, 1.4%; others, 2.8%) and in selected patients in 50% of the Institutions. Postoperative point-of-care test are applied in 17.9% of the Institutions (thromboelastography, 2.7%; PFA-100, 1.4%; others, 13.8%). Allogeneic blood products use widely differs among Institution: packed red cells are used in 47.5% of the patients (range 8%–90%), fresh frozen plasma in 29% (2%–100%) and platelets in 12.4% (0%–50%).ConclusionsPerioperative haemostasis and coagulation management is widely different among European Institutions. Point-of-care coagulation and platelet function tests are gaining a significant role. Transfusional policy appears strongly Institution-dependent.
Enzymatic fuel cells : from fundamentals to applications (2014)

"Covering the fundamentals of enzymatic fuel cells as well as their design, optimization, integration, and future trends, Enzymatic Fuel Cells provides practical applications of enzymatic fuel cells, including their use in biomedical applications and as power supplies for small portable power devices. Blending introductory reading with a concise scheme of illustration and a special emphasis on methodology of fabrication and testing of enzymatic fuel cells, the book is ideally suited for environmental and chemical engineers, wastewater industry professionals, electrochemists, biologists, and students"--
Assessing Regression Quality (2008)

This chapter contains sections titled: Methods to Assess Regression Quality Application of Regression Concepts Problems
Hole Concentration Reduction in CuI by Zn Substitution and its Mechanism: Toward Device Applications (2022)

Copper iodide (CuI) is a promising p-type transparent semiconductor with excellent carrier mobility. However, the high hole concentration in conventionally fabricated CuI including the single crystal hinders its applicability to the channel layer of thin-film transistors. We found that Zn substitution into Cu<sup>+</sup> sites can effectively reduce the hole concentration. Experimental and computational examinations showed that the dominant mechanism involved the formation of a defect pair, the Zn-substituted Cu site (Zn<sub>Cu</sub>) and Cu vacancy (V<sub>Cu</sub>), and the simultaneous suppression of V<sub>Cu</sub> arising from the stabilization of Cu<sup>+</sup> in the Zn-substituted CuI lattice, rather than hole compensation by the electrons generated from Zn<sup>2+</sup> substitution into Cu<sup>+</sup> sites. Our results show that the hole concentration of Zn-substituted CuI is tunable in the range of 10<sup>14</sup>-10<sup>18</sup> cm<sup>-3</sup>, making it suitable for thin-film transistors and hole transport layers in OLEDs.
Selection of optimised ligands by fluorescence-activated bead sorting (2023)

The chemistry of aptamers is largely limited to natural nucleotides, and although modifications of nucleic acids can enhance target aptamer affinity, there has not yet been a technology for selecting the right modifications in the right locations out of the vast number of possibilities, because enzymatic amplification does not transmit sequence-specific modification information. Here we show the first method for the selection of specific nucleoside modifications that increase aptamer binding efficacy, using the oncoprotein EGFR as a model target. Using fluorescence-activated bead sorting (FABS), we have successfully selected optimized aptamers from a library of >65 000 variations. Hits were identified by tandem mass spectrometry and validated by using an EGFR binding assay and computational docking studies. Our results provide proof of concept for this novel strategy for the selection of chemically optimised aptamers and offer a new method for rapidly synthesising and screening large aptamer libraries to accelerate diagnostic and drug discovery.
Envelope-specific antibodies and antibody-derived molecules for treating and curing HIV infection (2020)

HIV-1 is a retrovirus that integrates into host chromatin and can remain transcriptionally quiescent in a pool of immune cells. This characteristic enables HIV-1 to evade both host immune responses and antiretroviral drugs, leading to persistent infection. Upon reactivation of proviral gene expression, HIV-1 envelope (HIV-1 Env) glycoproteins are expressed on the cell surface, transforming latently infected cells into targets for HIV-1 Env-specific monoclonal antibodies (mAbs), which can engage immune effector cells to kill productively infected CD4+ T cells and thus limit the spread of progeny virus. Recent innovations in antibody engineering have resulted in novel immunotherapeutics such as bispecific dual-affinity re-targeting (DART) molecules and other bi- and trispecific antibody designs that can recognize HIV-1 Env and recruit cytotoxic effector cells to kill CD4+ T cells latently infected with HIV‑1. Here, we review these immunotherapies, which are designed with the goal of curing HIV-1 infection.
Manuscript: New GHG Methodology to Quantify Sewer Methane (2018)

the Intergovernmental Panel on Climate Change (IPCC) has identified that wastewater in closed, underground sewers in the developed world are not a significant methane (CH4) source (IPCC 2006). Other greenhouse gas (GHG) protocols have followed IPCC's lead and have ignored sewer CH4. This simplification has been contradicted by research (Guisasola, 2008; Foley, 2009; Guisasola, 2009; Gutierrez, 2009; van Voorthuizen, 2011; Willis, 2012; and Liu, 2014) where significant CH4 emissions have been repeatedly detected from both pressure mains and gravity sewers. The Water Research Foundation's (WRF, formerly WE&RF and WERF) Conveyance Asset Prediction System (CAPS) project (WERF Project #U5R12) developed a methodology for estimating collection-system methane (CH4) on a sewershed-wide basis. The method uses hydraulic-model output at average flows, actual sewage temperatures and actual flow rates as input. A Knowledge Development Forum (a workshop that is not for CEU credit) entitled “Sewer-Methane GHG-Methodology Standardization” will be held on Saturday at WEFTEC-2018 in New Orleans. The forum objective is to drive toward WEF-industry consensus on a new greenhouse gas (GHG) accounting methodology for adoption by ICLEI, the California Air Resource Board (CARB), IPCC, and other protocols. This paper summarizes the method and provides specific guidance on its use for estimating sewer-CH4 generation.
Investigation of Phase Mixing in Amorphous Solid Dispersions of AMG 517 in HPMC-AS Using DSC, Solid-State NMR, and Solution Calorimetry (2015)

Intimate phase mixing between the drug and the polymer is considered a prerequisite to achieve good physical stability for amorphous solid dispersions. In this article, spray dried amorphous dispersions (ASDs) of AMG 517 and HPMC-as were studied by differential scanning calorimetry (DSC), solid-state NMR (SSNMR), and solution calorimetry. DSC analysis showed a weakly asymmetric (ΔTg ≈ 13.5) system with a single glass transition for blends of different compositions indicating phase mixing. The Tg-composition data was modeled using the BKCV equation to accommodate the observed negative deviation from ideality. Proton spin-lattice relaxation times in the laboratory and rotating frames ((1)H T1 and T1ρ), as measured by SSNMR, were consistent with the observation that the components of the dispersion were in intimate contact over a 10-20 nm length scale. Based on the heat of mixing calculated from solution calorimetry and the entropy of mixing calculated from the Flory-Huggins theory, the free energy of mixing was calculated. The free energy of mixing was found to be positive for all ASDs, indicating that the drug and polymer are thermodynamically predisposed to phase separation at 25 °C. This suggests that miscibility measured by DSC and SSNMR is achieved kinetically as the result of intimate mixing between drug and polymer during the spray drying process. This kinetic phase mixing is responsible for the physical stability of the ASD.
Regulation of immunoglobulin transcription rates and mRNA processing in proliferating normal B lymphocytes by activators of protein kinase C. (1987)

Immunoglobulin gene expression in normal splenic B lymphocytes stimulated with lipopolysaccharide was selectively down-regulated by anti-IgM antibodies and a protein-kinase C-activating phorbol ester, phorbol 12,13-dibutyrate. This control was concomitant with a decreased rate of transcription of the IgM gene while "polymerase pausing" was induced in the IgD gene. The suppression was resistant to treatment with cycloheximide, indicating that it was not caused by a labile repressor protein. The down-regulation of immunoglobulin gene expression affected only the secretory form of immunoglobulin, while the mRNA levels for the membrane-bound form of immunoglobulin remained unaltered. We conclude that the mechanisms controlling immunoglobulin gene expression in untransformed B lymphocytes differ from those operating in tumors derived from the same cell lineage.
The polyphenol epigallocatechin-3-gallate affects lipid rafts to block activation of the c-Met receptor in prostate cancer cells (2010)

The HGF/c-Met pathway is an important regulator of signaling pathways responsible for invasion and metastasis of most human cancers, including prostate cancer. Exposure of DU145 prostate tumor cells to HGF stimulates the PI3-kinase and MAPK pathways, leading to increased scattering, motility, and invasion, which was prevented by the addition of EGCG. EGCG acted at the level of preventing phosphorylation of tyrosines 1234/1235 in the kinase domain of the c-Met receptor without effecting dimerization. HGF-induced changes were independent of the formation of reactive oxygen species, suggesting that EGCG functioned independent of its antioxidant ability. ECG, another tea polyphenol, was as effective as EGCG, while EGC and EC were less effective. EGCG added up to 4 h after the addition of HGF still blocked cell scattering and reduced the HGF-induced phosphorylation of c-Met, Akt, and Erk, suggesting that EGCG could act both by preventing activation of c-Met by HGF and by attenuating the activity of pathways already induced by HGF. HGF did not activate the MAPK and PI3-K pathways in cells treated with methyl-beta-cyclodextrin (mCD) to remove cholesterol. Furthermore, subcellular fractionation approaches demonstrated that only phosphorylated c-Met accumulated in Triton X-100 membrane insoluble fractions, supporting a role for lipid rafts in regulating c-Met signaling. Finally, EGCG treatment inhibited DiIC16 incorporation into membrane lipid ordered domains, and cholesterol partially inhibited the EGCG effects on signaling. Together, these results suggest that green tea polyphenols with the R1 galloyl group prevent activation of the c-Met receptor by altering the structure or function of lipid rafts.
Effects of Dasatinib on Src Kinase Activity and Downstream Intracellular Signaling in Primitive Chronic Myelogenous Leukemia Hematopoietic Cells (2008)

Bcr-Abl tyrosine kinase inhibitors (TKI) are effective in inducing remissions in chronic myelogenous leukemia (CML) patients but do not eliminate primitive CML hematopoietic cells. There is a need to identify mechanisms that contribute to retention of CML progenitors. Src family tyrosine kinases have been identified as potential mediators of Bcr-Abl-induced leukemogenesis. Dasatinib (BMS-354825) is a potent dual Abl/Src kinase inhibitor approved for clinical use in CML patients. We evaluated Src activity in primitive human CML progenitors from different stages of disease and investigated effects of Dasatinib on Src activity and downstream signaling pathways. P-Src expression was increased in CD34+ cells and CD34+CD38- cells in all phases of CML. Dasatinib showed potent Src inhibitory activity in CML progenitors, inhibiting both Bcr-Abl-dependent and -independent Src activity. In contrast, Imatinib inhibited only Bcr-Abl-dependent Src activity. Dasatinib inhibited P-mitogen-activated protein kinase (MAPK), P-Akt, and P-STAT5 levels in CML progenitors in the absence of growth factors but not in the presence of growth factors. A marked increase in P-MAPK levels seen in the presence of growth factors with Imatinib was much less prominent with Dasatinib. Dasatinib significantly suppressed CML colony-forming cells and long-term culture-initiating cells but did not significantly alter the level of apoptosis-regulating proteins in CML CD34+ cells. Our results indicate that Dasatinib, in addition to potent anti-Bcr-Abl kinase activity, effectively inhibits Src kinase activity and downstream signaling pathways in CML progenitors but does not induce a strong proapoptotic response. These observations argue against a prominent role for Src kinases in persistence of primitive CML cells in TKI-treated patients.
Dynamics of $I = {3 \over 2}$ nuclei in isotropic slow motion, anisotropic and partially ordered phases (2010)

Abstract NMR of quadrupolar nuclei, and, in particular 23 Na in soft tissues has attracted renewed interest due to the importance that sodium plays in physiology. The quadrupolar coupling and relaxation dynamics, including the appearance of the dynamic frequency shift are treated in this article. The equations governing irreducible spherical tensor analysis are derived and discussed. Experiments are shown to demonstrate how parameters such as the correlation time, the instantaneous and the residual quadrupolar couplings can be extracted from the data. Such experiments and procedures are particularly useful in the analysis of 23 Na NMR data from tissues or cell suspensions. © 2010 Wiley Periodicals, Inc. Concepts Magn Reson Part A 36A: 362–387, 2010
Targeted Stimulation of Retinal Ganglion Cells in Epiretinal Prostheses: A Multiscale Computational Study (2020)

Retinal prostheses aim at restoring partial sight to patients that are blind due to retinal degenerative diseases by electrically stimulating the surviving healthy retinal neurons. Ideally, the electrical stimulation of the retina is intended to induce localized, focused, percepts only; however, some epiretinal implant subjects have reported seeing elongated phosphenes in a single electrode stimulation due to the axonal activation of retinal ganglion cells (RGCs). This issue can be addressed by properly devising stimulation waveforms so that the possibility of inducing axonal activation of RGCs is minimized. While strategies to devise electrical stimulation waveforms to achieve a focal RGCs response have been reported in literature, the underlying mechanisms are not well understood. This article intends to address this gap; we developed morphologically and biophysically realistic computational models of two classified RGCs: D1-bistratified and A2-monostratified. Computational results suggest that the sodium channel band (SOCB) is less sensitive to modulations in stimulation parameters than the distal axon (DA), and DA stimulus threshold is less sensitive to physiological differences among RGCs. Therefore, over a range of RGCs distal axon diameters, short-pulse symmetric biphasic waveforms can enhance the stimulation threshold difference between the SOCB and the DA. Appropriately designed waveforms can avoid axonal activation of RGCs, implying a consequential reduction of undesired strikes in the visual field.
Products, Intermediates, Mass Balances, and Reaction Pathways for the Oxidation of Trichloroethylene in Air via Heterogeneous Photocatalysis (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProducts, Intermediates, Mass Balances, and Reaction Pathways for the Oxidation of Trichloroethylene in Air via Heterogeneous PhotocatalysisWilliam A. Jacoby, Mark R. Nimlos, Daniel M. Blake, Richard D. Noble, and Carl A. KovalCite this: Environ. Sci. Technol. 1994, 28, 9, 1661–1668Publication Date (Print):September 1, 1994Publication History Published online1 May 2002Published inissue 1 September 1994https://pubs.acs.org/doi/10.1021/es00058a018https://doi.org/10.1021/es00058a018research-articleACS PublicationsRequest reuse permissionsArticle Views434Altmetric-Citations101LEARN 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
High performance mobile SoC design and technology co-optimization to mitigate high-K metal gate process induced variations (2014)

Despite improved device performance over traditional Poly-SiON technology, high-K metal gate flow introduces additional device variations not previously seen in Poly-SiON process, especially impacting large dimensional (WxL) devices for matching critical applications. For the first time, we report a comprehensive analysis of device variations introduced from metal gate process, GDIM and GGIM, and their sensitivity to circuit layout. Design optimization and verification mechanisms are developed to mitigate metal gate process induced variations in analog matching circuits. After co-optimization, DAC Vt mismatch is reduced by 2.1X and ADC comparator speed is improved by 23.5% in the analog blocks of an advanced mobile SoC currently in production.
Surfactant modifies the lymphoproliferative activity of macrophages in hypersensitivity pneumonitis (1997)

Alveolar macrophages (AM) from normal individuals suppress mitogen-induced peripheral blood mononuclear cell (PBMC) proliferation, whereas cells from patients with hypersensitivity pneumonitis (HP) enhance PBMC. Because surfactant components can interfere with AM functions, we tested the effect of Survanta (a modified bovine surfactant) and surfactant fractions isolated from bronchoalveolar lavage of normal subjects and HP patients on AM-induced lymphoproliferation. Surfactant fractions were isolated from bronchoalveolar lavage fluids by differential centrifugation into total aggregates (TA) and large aggregates (LA). Surfactant preparations (200 micrograms/ml) from 10 normal subjects (N) or 12 HP patients or of Survanta were added to AM-PBMC cocultures stimulated with phytohemagglutinin (PHA) at 1:1 and 2:1 ratios. Results, expressed as percent of PHA-induced PBMC proliferation cocultures without surfactant, show that normal surfactant and Survanta decrease mitogen-induced proliferation of cells to a larger extent than surfactant from HP patients. For AM-to-PBMC ratios of 1:1, the results were as follows: N TA 10.58 +/- 2.75% (mean +/- SE), N LA 12.96 +/- 2.78%, HP TA 43.09 +/- 7.81%, HP LA 61.64 +/- 7.77%, and Survanta 16.70 +/- 2.95%. Similar data were obtained in 2:1 cocultures. Because surfactant components interact with AM, alterations of surfactant composition in lymphocytic diseases, mainly in the LA fraction, may account for the lack of suppressive activity in AM of HP patients and the observed alveolitis.
Media composition affects the survival of desiccated mammalian cells (2003)

Efforts to improve the tolerance of mammalian cells to desiccation have focused on the role that sugars have in protecting cells from lethal injury. The objective of this study was to examine the effect that the composition of intra- and extracellular trehalose solutions has on the survival of dried 3T3 fibroblasts. Trehalose was introduced into 3T3 fibroblasts using a genetically-engineered mutant of the pore-forming /spl alpha/-hemolysin from Staphylococcus aureus. Cells were dried using natural convection at ambient temperatures. Plasma membrane integrity and the ability to grow and divide in culture were used to assess cell survival. We found that the post-rehydration membrane integrity was a function of the residual moisture content of the cells following drying. Adjusting the initial osmolality of the intra- and extracellular sugar solutions to be isotonic by reducing the concentration of buffer resulted in a significant improvement in the membrane integrity and growth of dried cells. In an isotonic solution of 0.2 M trehalose, approximately 80% of cells survived drying. Understanding the biological response to desiccation will be critical in developing effective strategies for the drying of mammalian cells.
Gas and Hydrocarbon Vapor Permeation in Poly(1-trimethylsilyl-1-propyne)/Poly(1-phenyl-1- propyne) Blends (1996)

Permeation properties of phase-separated blends prepared from glassy poly(1-trimethylsilyl-1-propyne) (PTMSP) and poly(1-phenyl-1-propyne) (PPP) were determined as a function of blend composition with pure hydrogen, nitrogen, oxygen, carbon dioxide, and butane. Blend permeabilities decrease significantly with increasing PPP concentration and suggest the occurrence of a phase inversion at low PPP content (5 to 20 wt%). Based on TEM analysis high-aspect-ratio (extended) PPP ellipsoidal dispersions are found in a PTMSP matrix, indicating that the phase inversion is closely related to dispersed-phase connectivity in the blends.