gebhart/patrepeval huggingface dataset:
Intracellular accumulation and immunological responses of lipid modified magnetic iron nanoparticles in mouse antigen processing cells (2017)

Understanding the effects of magnetic iron nanoparticles (MINPs) on the immune response is vitally important for biomedical applications such as cancer therapy, disease diagnosis and novel cancer imaging. In this study, lipid modified MINPs were designed and prepared by introducing the neutral lipid DSPE-PEG or the zwitterionic lipid DSPE-PCB into hydrophobic MINPs through hydrophobic interaction (L-MINPs and ZL-MINPs, respectively). The effect of L-MINPs and ZL-MINPs on the intracellular accumulation and immune responses of three kinds of antigen processing cells was examined. The results indicated that the high cellular uptake efficiency of surface coated MINPs was strongly related to the nature of the coating lipid, with the zwitterionic lipid being more effective than PEGylated ones. Besides, the results from flow cytometry (FCM), confocal laser scanning microscopy (CLSM) and Prussian blue staining demonstrated a time- and concentration-dependent MINP internalization. The uptake of zwitterionic lipid modified MINPs (ZL-MINPs) induced very low cytotoxicity and a strong mixed Th1/Th2 type immune response. L-MINPs could induce a strong increase in pro-inflammatory cytokines with a slight secretion of Th2 cytokines. Besides, no IL-10 was observed in both groups, indicating that MINPs with lipid modification were absence of immunosuppression. In conclusion, this study addresses an important implication of the lipid type and Fe concentration on the immune stimulation of cells and supports the potential for further development of biomedical applications.
Incorporation of Zn in GaAs during organometallic vapor phase epitaxy growth compared to equilibrium (1995)

The zinc concentration measured after organometallic vapor phase epitaxy (OMVPE) growth on (100)-oriented GaAs at 700 °C has been compared to the zinc concentration measured after in-diffusion under near-equilibrium conditions. During diffusion, the concentration of Zn 20 nm below the surface was found to vary with P1/2Zn, as expected for bulk solid–vapor equilibrium. During growth, the concentration of Zn varied linearly with PZn up to a maximum value which was found to correspond to the solubility limit set by second phase formation, e.g., growth of Zn3As2. Although large differences were observed between the results of the two experiments when using nominally identical ambient conditions, all of the results are consistent with a thermodynamic model in which the Fermi level at the surface is pinned approximately 200 meV below the intrinsic Fermi level. Typical OMVPE growth conditions appear to give a bulk zinc concentration which is supersaturated relative to the ambient partial pressures used, and to enhance the diffusion of Zn into the substrate.
Image reconstruction from a small number of projections (2008)

Image reconstruction from projections suffers from an inherent difficulty: there are different images that have identical projections in any finite number of directions. However, by identifying the type of image that is likely to occur in an application area, one can design algorithms that may be efficacious in that area even when the number of projections is small. One such approach uses total variation minimization. We report on an algorithm based on this approach, and show that sometimes it produces medically-desirable reconstructions in computerized tomography (CT) even from a small number of projections. However, we also demonstrate that such a reconstruction is not guaranteed to provide the medically-relevant information: when data are collected by an actually CT scanner for a small number projections, the noise in such data may very well result in a tumor in the brain not being visible in the reconstruction.
Learning Informative Representations of Biomedical Relations with Latent\n Variable Models (2020)

Extracting biomedical relations from large corpora of scientific documents is\na challenging natural language processing task. Existing approaches usually\nfocus on identifying a relation either in a single sentence (mention-level) or\nacross an entire corpus (pair-level). In both cases, recent methods have\nachieved strong results by learning a point estimate to represent the relation;\nthis is then used as the input to a relation classifier. However, the relation\nexpressed in text between a pair of biomedical entities is often more complex\nthan can be captured by a point estimate. To address this issue, we propose a\nlatent variable model with an arbitrarily flexible distribution to represent\nthe relation between an entity pair. Additionally, our model provides a unified\narchitecture for both mention-level and pair-level relation extraction. We\ndemonstrate that our model achieves results competitive with strong baselines\nfor both tasks while having fewer parameters and being significantly faster to\ntrain. We make our code publicly available.\n
Signaling Pathways Involved in Human Vascular Smooth Muscle Cell Proliferation and Matrix Metalloproteinase-2 Expression Induced by Leptin (2005)

Accumulating evidence suggests that high concentrations of leptin observed in obesity and diabetes may contribute to their adverse effects on cardiovascular health. Metformin monotherapy is associated with reduced macrovascular complications in overweight patients with type 2 diabetes. It is uncertain whether such improvement in the cardiovascular outcome is related to specific vasculoprotective effects of this drug. In the present study, we determined the effect of leptin on human aortic smooth muscle cell (HASMC) proliferation and matrix metalloproteinase (MMP)-2 expression, the signaling pathways mediating these effects, and the modulatory effect of metformin on these parameters. Incubation of HASMCs with leptin enhanced the proliferation and MMP-2 expression in these cells and increased the generation of intracellular reactive oxygen species (ROS). These effects were abolished by vitamin E. Inhibition of NAD(P)H oxidase and protein kinase C (PKC) suppressed the effect of leptin on ROS production. In HASMCs, leptin induced PKC, extracellular signal-regulated kinase (ERK)1/2, and nuclear factor-kappaB (NF-kappaB) activation and inhibition of these signaling pathways abrogated HASMC proliferation and MMP-2 expression induced by this hormone. Treatment of HASMCs with metformin decreased leptin-induced ROS production and activation of PKC, ERK1/2, and NF-kappaB. Metformin also inhibited the effect of leptin on HASMC proliferation and MMP-2 expression. Overall, these results demonstrate that leptin induced HASMC proliferation and MMP-2 expression through a PKC-dependent activation of NAD(P)H oxidase with subsequent activation of the ERK1/2/NF-kappaB pathways and that therapeutic metformin concentrations effectively inhibit these biological effects. These results suggest a new mechanism by which metformin may improve cardiovascular outcome in patients with diabetes.
A Self-Cooled Liquid Breeder Blanket for a Laser IFE Power Plant with Magnetic Intervention (2007)

A possible way to address the issue of dry wall survival in a Laser IFE chamber is to use magnetic diversion in order to steer away the ions from the chamber wall (representing ˜25-30% of the yield energy). A cusp magnetic field is imposed on to the chamber; the ions from the micro-explosion are trapped within the magnetic field and are directed to more readily accessible and replaceable dump regions at the equator and poles. A large fraction of the magnetic energy can be dissipated in the chamber walls if an electrically resistive structural material is used. An advanced blanket based on a self-cooled liquid breeder (e.g.Pb-17Li or flibe) and SiCf/SiC structure has been proposed for this purpose and a scoping design study performed as part of the High Average Power Laser program effort.This paper summarizes the results of this scoping study, and highlights the advantages of such a concept as well as the key issues that need to be addressed by R&D.
[Lysine overproduction mutations in the yeast Saccharomyces cerevisiae and its transfection into industrial Yeast strains ]. (2001)

Yeast mutants resistant to a toxic lysine analog, thialysine were obtained by a method described in the literature. A strain excreting the maximum amount of lysine (0.45 g/l) was selected from these mutants. The intracellular content of lysine was also increased by 30%. The genetic nature of lysine overproduction was studied in this strain. An increase in the amount of excreted lysine was shown to be determined by at least two genes, one of which carries a mutation of thialysine resistance manifesting the pleiotropic effect of lysine overproduction (Th1R) and the other is involved in the regulation of lysine production (PRL). Linkage groups of these genes were determined: the first gene was mapped to the IV chromosome and the second, to the XV chromosome. Both genetic characters were introduced into industrial baker's yeast strains via a series of backcrosses. The stabilization of the genome in the newly derived strains was confirmed by electrokaryotyping.
Predicting teachers’ formative assessment practices: Teacher personal and contextual factors (2022)

Past studies identified isolated factors influencing teachers' formative assessment practices (FAP) but did not show a comprehensive model of it. Hence, this study systematically creates and tests a theoretical model of FAP by determining whether personal or contextual factors are linked to teachers' FAP. We collected longitudinal data from 296 Hong Kong primary and secondary teachers through two waves of the survey. The results of a multivariate outcome, multilevel analysis showed that personal (teacher rank, years of teaching experience, and self-efficacy) and contextual factors (school support, total number of teachers in a school, and teaching grade) significantly impact teachers’ FAP.
The Cell Line Secretome, a Suitable Tool for Investigating Proteins Released in Vivo by Tumors: Application to the Study of p53-Modulated Proteins Secreted in Lung Cancer Cells (2009)

Malignant processes such as metastasis, invasion, or angiogenesis are tightly dependent on the composition of the extracellular medium, which is itself affected by the release of proteins by the tumor cells. p53, a major tumor suppressor protein very frequently mutated and/or inactivated in cancer cells, is known to modulate the release of proteins by the tumor cells; however, while p53-modulated intracellular proteins have been extensively studied, little is known concerning their extracellular counterparts. Here, we characterized the p53-dependent secretome of a lung tumor model in vitro (H358 human nonsmall cell lung adenocarcinoma cell line with a homozygous deletion of p53) and demonstrate that the modulation of exported proteins can also be detected in vivo in the plasma of tumor-bearing mice. We used a clone of H358, stably transfected with a tetracycline-inducible wild-type p53-expressing vector. With the use of iTRAQ labeling and LC-MALDI-MS/MS analysis, we identified 909 proteins released in vitro by the cells, among which 91 are p53-modulated. Three proteins (GDF-15, FGF-19, and VEGF) were also investigated in H358/TetOn/p53 xenograft mice. The ELISA dosage on total tumor protein extracts confirmed the influence of p53 on the release of these proteins in vivo. Moreover, the GDF-15 concentration was measured in the plasma and its p53-dependent modulation was confirmed. To our knowledge, this is the first report establishing that the in vitro cell line secretome is reliable and reflects the extracellular release of proteins from tumor cells in vivo and could be used to identify putative tumor markers.
OmniSpect: An Open MATLAB-Based Tool for Visualization and Analysis of Matrix-Assisted Laser Desorption/Ionization and Desorption Electrospray Ionization Mass Spectrometry Images (2013)

We present omniSpect, an open source web- and MATLAB-based software tool for both desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) that performs computationally intensive functions on a remote server. These functions include converting data from a variety of file formats into a common format easily manipulated in MATLAB, transforming time-series mass spectra into mass spectrometry images based on a probe spatial raster path, and multivariate analysis. OmniSpect provides an extensible suite of tools to meet the computational requirements needed for visualizing open and proprietary format MSI data.
Membrane Permeating Macrocycles: Design Guidelines from Machine Learning (2022)

The ability to predict cell-permeable candidate molecules has great potential to assist drug discovery projects. Large molecules that lie beyond the Rule of Five (bRo5) are increasingly important as drug candidates and tool molecules for chemical biology. However, such large molecules usually do not cross cell membranes and cannot access intracellular targets or be developed as orally bioavailable drugs. Here, we describe a random forest (RF) machine learning model for the prediction of passive membrane permeation rates developed using a set of over 1000 bRo5 macrocyclic compounds. The model is based on easily calculated chemical features/descriptors as independent variables. Our random forest (RF) model substantially outperforms a multiple linear regression model based on the same features and achieves better performance metrics than previously reported models using the same underlying data. These features include: (1) polar surface area in water, (2) the octanol-water partitioning coefficient, (3) the number of hydrogen-bond donors, (4) the sum of the topological distances between nitrogen atoms, (5) the sum of the topological distances between nitrogen and oxygen atoms, and (6) the multiple molecular path count of order 2. The last three features represent molecular flexibility, the ability of the molecule to adopt different conformations in the aqueous and membrane interior phases, and the molecular "chameleonicity." Guided by the model, we propose design guidelines for membrane-permeating macrocycles. It is anticipated that this model will be useful in guiding the design of large, bioactive molecules for medicinal chemistry and chemical biology applications.
An Evaluation of Image Feature Detectors Based on Spatial Density and Temporal Robustness in Microsurgical Image Processing (2019)

Abstract Optical image processing is part of many applications used for brain surgeries. Microscope camera, or patient movement, like brain-movement through the pulse or a change in the liquor, can cause the image processing to fail. One option to compensate movement is feature detection and spatial allocation. This allocation is based on image features. The frame wise matched features are used to calculate the transformation matrix. The goal of this project was to evaluate different feature detectors based on spatial density and temporal robustness to reveal the most appropriate feature. The feature detectors included corner-, and blob-detectors and were applied on nine videos. These videos were taken during brain surgery with surgical microscopes and include the RGB channels. The evaluation showed that each detector detected up to 10 features for nine frames. The feature detector KAZE resulted in being the best feature detector in both density and robustness.
Internal Nanoparticle Structure of Temperature-Responsive Self-Assembled PNIPAM-b-PEG-b-PNIPAM Triblock Copolymers in Aqueous Solutions: NMR, SANS, and Light Scattering Studies (2016)

In this study, we report detailed information on the internal structure of PNIPAM-b-PEG-b-PNIPAM nanoparticles formed from self-assembly in aqueous solutions upon increase in temperature. NMR spectroscopy, light scattering, and small-angle neutron scattering (SANS) were used to monitor different stages of nanoparticle formation as a function of temperature, providing insight into the fundamental processes involved. The presence of PEG in a copolymer structure significantly affects the formation of nanoparticles, making their transition to occur over a broader temperature range. The crucial parameter that controls the transition is the ratio of PEG/PNIPAM. For pure PNIPAM, the transition is sharp; the higher the PEG/PNIPAM ratio results in a broader transition. This behavior is explained by different mechanisms of PNIPAM block incorporation during nanoparticle formation at different PEG/PNIPAM ratios. Contrast variation experiments using SANS show that the structure of nanoparticles above cloud point temperatures for PNIPAM-b-PEG-b-PNIPAM copolymers is drastically different from the structure of PNIPAM mesoglobules. In contrast with pure PNIPAM mesoglobules, where solidlike particles and chain network with a mesh size of 1-3 nm are present, nanoparticles formed from PNIPAM-b-PEG-b-PNIPAM copolymers have nonuniform structure with "frozen" areas interconnected by single chains in Gaussian conformation. SANS data with deuterated "invisible" PEG blocks imply that PEG is uniformly distributed inside of a nanoparticle. It is kinetically flexible PEG blocks which affect the nanoparticle formation by prevention of PNIPAM microphase separation.
Autoimmune arthritis induces paired immunoglobulin‐like receptor B expression on CD4+ T cells from SKG mice (2017)

The chronic, destructive autoimmune arthritis in SKG mice, which closely resembles human rheumatoid arthritis, is the result of self-reactive T cells escaping thymic deletion. Since the inhibitory receptor LIR-1 is up-regulated on auto-reactive T cells in human rheumatoid arthritis, the role of its murine ortholog PIR-B was investigated. Peripheral CD4<sup>+</sup> T cells from SKG mice were found to frequently express PIR-B, and this population produces more frequently IL-17 upon in vitro stimulation compared to PIR-B<sup>-</sup> cells. A much larger fraction of PIR-B<sup>+</sup> T cells, however, was found to secret no IL-17, but IFN-γ. With regards to the clinical course of the disease, high frequencies of PIR-B<sup>+</sup> CD4<sup>+</sup> T cells were found to be associated with a milder course of arthritis, suggesting that the net effect of PIR-B expression is suppression of autoreactive T cells. Our results indicate that overexpression of PIR-B on IL-17-producing SKG CD4<sup>+</sup> T cells might represent an effective counter-regulatory mechanism against the destructive potential of those cells. More importantly, a major population of PIR-B<sup>+</sup> T cells in SKG mice appears to play an inhibitory role by way of their IFN-γ production, since high frequencies of those cells ameliorate the disease.
Effects of Storage Time and Temperature After Blood Sampling from Turkeys on Plasma Concentrations of Potassium, Sodium, and Chloride (2006)

The objectives of this research were to study the effect of several time intervals of turkey blood storage from sampling to centrifugation on plasma K, Na, and Cl concentrations and to study the effect of ambient temperature of turkey blood storage on these same variables. In the first study, 6 consecutive blood samples were obtained from each turkey. The first sample was centrifuged immediately (control), and each of the others was respectively stored for 20, 40, 60, 120, or 360 min at 22 degrees C before centrifugation and plasma harvest. In the second study, 4 consecutive blood samples were obtained from each turkey. The first sample was centrifuged immediately (control), and each of the others was respectively stored at ambient temperatures of 9, 22, and 30 degrees C for 120 min before centrifugation and plasma harvest. Plasma K concentration declines and is significant (P < 0.01) for each of the 20, 40, 60, 120, and 360 min values. Plasma Na concentration increases and Cl decreases were not significant (P < 0.01) until 360 and 120 min, respectively. Significant (P < 0.01) reductions occurred for plasma K concentration for each of the ambient temperature values but were the least at 9 degrees C and greatest when stored at 30 degrees C. Plasma Na concentration decreased (P < 0.01) when stored at 9 degrees C. Though increased (P < 0.01) when stored at 22 and 30 degrees C, the difference was not significant (P < 0.01) between samples stored at either 22 or 30 degrees C. Plasma Cl concentration was decreased (P < 0.01) from control values, but there was no significant difference (P < 0.01) among samples stored at 9, 22, and 30 degrees C. Clot formation and its retraction from serum are unduly delayed after blood is withdrawn from turkeys because birds lack the intrinsic mechanism for blood coagulation. Accordingly, serum is not appropriate for the determination of K concentration in turkeys, and plasma harvested immediately after blood sampling is the fluid of choice for K analysis.
Role of the Norrie Disease Pseudoglioma Gene in Sprouting Angiogenesis during Development of the Retinal Vasculature (2005)

These data provide evidence for a crucial role of Norrin in hyaloid vessel regression and in sprouting angiogenesis during retinal vascular development, especially in the development of the deep retinal capillary networks. They also suggest an early and a late phase of Norrie disease and may provide an explanation for similar phenotypic features of allelic retinal diseases in mice and patients as secondary consequences of pathologic hypoxia.
High Temperature Stability of Ceria-Zirconia Supported Pd Model Catalysts (1998)

&lt;div class="htmlview paragraph"&gt;A series of ceria and ceria-zirconia supported Pd model automotive catalysts were prepared and aged under air or redox conditions at 1050°C for 12 h. The supports were manufactured by different methods and represent a range of compositions. The samples were characterized before and after aging by BET, X-ray diffraction, mercury porosimetry, XPS, H&lt;sub&gt;2&lt;/sub&gt; temperature-programmed reduction, and oxygen storage capacity measurements. Oxygen storage measurements revealed that the behavior of the catalysts varied according to aging conditions and temperature of measurement. Pd/ceria-zirconia catalysts showed higher oxygen storage characteristics after 1050°C aging than Pd/ceria catalysts, and the phase purity of the ceria-zirconia was shown to positively affect the amount of oxygen storage. The initial rates of oxygen release from the model catalysts at 350°C were shown to depend on the preparation conditions of the supports. Sweep tests were carried out on Pd/ceria-zirconia, and showed that high oxygen storage and conversion efficiencies remain after redox aging at 1050°C.&lt;/div&gt;
Expression of the Yeast UBI4 Gene Increases in Response to DNA-Damaging Agents and in Meiosis (1988)

The polyubiquitin gene, UB14, of Saccharomyces cerevisiae is regulated by a variety of environmental stresses and physiological conditions. After exposure of rapidly growing yeast cells to DNA-damaging agents (4-nitroquinoline-1-oxide and N-methyl-N'-nitro-N-nitrosoguanidine), intracellular levels of UB14 transcript increased rapidly. Induction of UB14 transcripts occurred within 30 to 60 min of exposure to 4-nitroquinoline-1-oxide in RAD+, rad52, and rad6 repair-deficient yeast strains. In high-density RAD+ cultures, the effect of alkylating agents on UB14 transcript levels is attenuated, in part because of significant increases in the basal level of this message in untreated cells. We also observed that the levels of UB14 transcripts increased significantly when diploid cells were exposed to sporulation conditions. Maximal levels of UB14 transcripts were reached after 6 to 8 h in sporulation medium. Accumulation of UB14 transcripts occurred in a/alpha diploids that undergo meiosis but not in asporogenous alpha/alpha diploids exposed to the same nutritional conditions.