gebhart/patrepeval huggingface dataset:
Macrophage M1/M2 Polarization Dynamically Adapts to Changes in Cytokine Microenvironments in Cryptococcus neoformans Infection (2013)

The outcome of cryptococcal pneumonia correlates with local macrophage polarization status, as M1 and M2 polarization marks protective and nonprotective responses, respectively. Overall, pulmonary macrophage polarization status changes over time during a cryptococcal infection. This could have been caused by repolarization of individual macrophages or by a replacement of M2-polarized cells by new M1-polarized cells. To explore the ability of macrophages to change between polarization states, we conducted a series of experiments using in vitro macrophages. Coculture of macrophages with Cryptococcus neoformans resulted in development of a weak M1-like phenotype, with modestly increased inducible nitric oxide synthase (iNOS) but lacking interleukin 6 (IL-6) induction. The C. neoformans-induced M1-like polarization state was plastic, as macrophages stimulated first with C. neoformans and then with gamma interferon (IFN-γ) or IL-4 expressed mRNA polarization patterns similar to those stimulated with cytokines alone. To further evaluate macrophage polarization plasticity, cytokine stimulatory conditions were established which fully polarized macrophages. IFN-γ and IL-4 stimulation differentially induced complete M1 and M2 polarization, defined by differential expression of marker mRNA panels, surface marker expression, and tumor necrosis factor alpha (TNF-α) protein production. Switching IFN-γ- to IL-4-stimulating conditions, and vice versa, resulted in uniform changes in profiles of polarization marker genes consistent with the most recent cytokine environment. Furthermore, the ability of sequentially stimulated macrophages to inhibit C. neoformans reflected the most recent polarizing condition, independent of previous polarization. Collectively, these data indicate that M1/M2 macrophage polarization phenotypes are highly plastic to external signals, and interventions which therapeutically repolarize macrophages could be beneficial for treatment of cryptococcosis.
Tumescent Technique Chronicles (1995)

1 In private practice. Address correspondence and reprint requests to: Jeffrey A. Klein, MD, 30280 Rancho Viejo Road, San Juan Capistrano, CA 92675.
Electronic structure and photoexcited-carrier dynamics in nanometer-size CdSe clusters (1990)

We use transient optical hole burning and photoluminescence to investigate the static and dynamic electronic properties of 32-\AA{} CdSe quantum dots. We observe a number of discrete electronic transitions, resolve LO-phonon progressions, and obtain homogeneous linewidths and electron--LO-phonon couplings. We find that the band-gap luminescence is not from the exciton state, but from a surface trapped state. Rapid (\ensuremath{\sim}160 fs) trapping into these surface states results in long-lived (\ensuremath{\sim}10--100 ns) bleach and induced-absorption features in pump-probe experiments.
Multiple-center-of-projection images (1998)

In image-based rendering, images acquired from a scene are used to represent the scene itself. A number of reference images are required to fully represent even the simplest scene. This leads to a number of problems during image acquisition and subsequent reconstruction. We present the multiple-center-of-projection image, a single image acquired from multiple locations, which solves many of the problems of working with multiple range images.
Private Session Initiation Protocol (SIP) Proxy-to-Proxy Extensions for Supporting the PacketCable Distributed Call Signaling Architecture (2003)

In order to deploy a residential telephone service at very large scale across different domains, it is necessary for trusted elements owned by different service providers to exchange trusted information that conveys customer-specific information and expectations about the parties involved in the call. This document describes private extensions to the Session Initiation Protocol (SIP) (RFC3261) for supporting the exchange of customer information and billing information between trusted entities in the PacketCable Distributed Call Signaling Architecture. These extensions provide mechanisms for access network coordination to prevent theft of service, customer originated trace of harassing calls, support for operator services and emergency services, and support for various other regulatory issues. The use of the extensions is only applicable within closed administrative domains, or among federations of administrative domains with previously agreed-upon policies where coordination of charging and other functions is required.
Affinity Purification and Properties of Cathepsin‐E‐Like Acid Proteinase from Rat Spleen (1978)

A unique acid proteinase different from cathepsin D was purified from rat spleen by a method involving precipitation at pH 3.5, affinity chromatography on pepstatin–Sepharose 4B and concanavalin A–Sepharose 4B, chromatography on Sephadex G‐100 and DEAE‐Sephacel, and isoelectric focusing. A purification of 4200‐fold over the homogenate was achieved and the yield was 11%. The purified enzyme appeared to be homogeneous on electrophoresis in polyacrylamide gels. The isoelectric point of the enzyme was determined to be 4.1–4.4. The enzyme hydrolyzed hemoglobin with a pH optimum of about 3.1. The molecular weight of the enzyme was estimated to be about 90000 by gel filtration on Sephadex G‐100. In sodium dodecylsulfate polyacrylamide gel electrophoresis, the purified enzyme showed a single protein band corresponding to a molecular weight of about 45000. The hydrolysis of bovine hemoglobin by the enzyme was much higher than that of serum albumin. Various synthetic and natural inhibitors of the enzyme were tested. The enzyme was inhibited by Zn 2+ , Fe 3+ , Pb 2+ , cyanide, p ‐chloromercuribenzoate, iodoacetic acid and pepstatin, whereas 2‐mercaptoethanol, phenylmethyl‐sulfonyl fluoride and leupeptin showed no effect.
Bioconversion of Xylan to Triglycerides by Oil-Rich Yeasts (1984)

A series of lipid-accumulating yeasts was examined for their potential to saccharify xylan and accumulate triglyceride. Of the genera tested, including Candida, Cryptococcus, Lipomyces, Rhodosporidium, Rhodotorula, and Trichosporon, only Cryptococcus and Trichosporon isolates saccharified xylan. All of the strains could assimilate xylose and accumuate triglyceride under nitrogen-limiting conditions. Strains of Cryptococcus albidus were found to be especially useful for a one-step saccharification of xylan coupled to triglyceride synthesis. Cryptococcus terricolus, a strain constitutive for lipid accumulation, lacked extracellular xylanase, but did assimilate xylose and xylobiose and was able to continuously convert xylan to triglyceride if the culture medium was supplemented with xylanase.
Discovery of 5-[5-Fluoro-2-oxo-1,2- dihydroindol-(3Z)-ylidenemethyl]-2,4- dimethyl-1H-pyrrole-3-carboxylic Acid (2-Diethylaminoethyl)amide, a Novel Tyrosine Kinase Inhibitor Targeting Vascular Endothelial and Platelet-Derived Growth Factor Receptor Tyrosine Kinase (2003)

To improve the antitumor properties and optimize the pharmaceutical properties including solubility and protein binding of indolin-2-ones, a number of different basic and weakly basic analogues were designed and synthesized. 5-[5-Fluoro-2-oxo-1,2-dihydroindol-(3Z)-ylidenemethyl]-2,4-dimethyl-1H-pyrrole-3-carboxylic acid (2-diethylaminoethyl)amide (12b or SU11248) has been found to show the best overall profile in terms of potency for the VEGF-R2 and PDGF-Rbeta tyrosine kinase at biochemical and cellular levels, solubility, protein binding, and bioavailability. 12b is currently in phase I clinical trials for the treatment of cancers.
Host Cell Entry of Powdery Mildew Is Correlated with Endosomal Transport of Antagonistically Acting VvPEN1 and VvMLO to the Papilla (2013)

Challenge by a nonadapted powdery mildew fungal pathogen leads to the formation of a local cell-wall apposition (papilla) beneath the point of attempted penetration. Several plasma membrane (PM) proteins with opposing roles in powdery mildew infection, including Arabidopsis thaliana PENETRATION1 (PEN1) and barley (Hordeum vulgare) MILDEW RESISTANCE LOCUS O (MLO), are localized to the site of powdery mildew attack. PEN1 contributes to penetration resistance to nonadapted powdery mildews, whereas MLO is a susceptibility factor required by adapted powdery mildew pathogens for host cell entry. Our previous studies have demonstrated that the vesicle and endosomal trafficking inhibitors, brefeldin A and wortmannin, have opposite effects on the penetration rates of adapted and nonadapted powdery mildews on grapevine. These findings prompted us to study the pathogen-induced intracellular trafficking of grapevine variants of MLO and PEN1. We first identified grapevine (Vitis vinifera) VvPEN1 and VvMLO orthologs that rescue Arabidopsis Atpen1 and Atmlo2 mlo6 mlo12 null mutants, respectively. By using endomembrane trafficking inhibitors in combination with fluorescence microscopy, we demonstrate that VvMLO3/VvMLO4 and VvPEN1 are co-trafficked together from the PM to the site of powdery mildew challenge. This focal accumulation of VvMLO3/VvMLO4 and VvPEN1 to the site of attack seems to be required for their opposing functions during powdery mildew attack, because their subcellular localization is correlated with the outcome of attempted powdery mildew penetration.
Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions (2007)

Using a combination of techniques we developed, we infected zebrafish embryos using pseudotyped retroviruses and mapped the genomic locations of the proviral integrations in the F(1) offspring of the infected fish. From F(1) fish, we obtained 2,045 sequences representing 933 unique retroviral integrations. A total of 599 were mappable to the current genomic assembly (Zv6), and 233 of the integrations landed within genes. By inbreeding fish carrying proviral integrations in 25 different genes, we were able to demonstrate that in approximately 50% of the gene "hits," the mRNA transcript levels were reduced by >/=70%, with the highest probability for mutation occurring if the integration was in an exon or first intron. Based on these data, the mutagenic frequency for the retrovirus is nearly one in five integrations. In addition, a strong mutagenic effect is seen when murine leukemia virus integrates specifically in the first intron of genes but not in other introns. Three of 19 gene inactivation events had embryonic defects. Using the strategy we outlined, it is possible to identify 1 mutagenic event for every 30 sequencing reactions done on the F(1) fish. This is a 20- to 30-fold increase in efficiency when compared with the current resequencing approach [targeting induced local lesions in genomes (TILLING)] used in zebrafish for identifying mutations in genes. Combining this increase in efficiency with cryopreservation of sperm samples from the F(1) fish, it is now possible to create a stable resource that contains mutations in every known zebrafish gene.
Altered Selectivity of Parathyroid Hormone (PTH) and PTH-Related Protein (PTHrP) for Distinct Conformations of the PTH/PTHrP Receptor (2007)

PTH and PTHrP use the same G protein-coupled receptor, the PTH/PTHrP receptor (PTHR), to mediate their distinct biological actions. The extent to which the mechanisms by which the two ligands bind to the PTHR differ is unclear. We examined this question using several pharmacological and biophysical approaches. Kinetic dissociation and equilibrium binding assays revealed that the binding of [(125)I]PTHrP(1-36) to the PTHR was more sensitive to GTPgammaS (added to functionally uncouple PTHR-G protein complexes) than was the binding of [(125)I]PTH(1-34) ( approximately 75% maximal inhibition vs. approximately 20%). Fluorescence resonance energy transfer-based kinetic analyses revealed that PTHrP(1-36) bound to the PTHR more slowly and dissociated from it more rapidly than did PTH(1-34). The cAMP signaling response capacity of PTHrP(1-36) in cells decayed more rapidly than did that of PTH(1-34) (t(1/2) = approximately 1 vs. approximately 2 h). Divergent residue 5 in the ligand, Ile in PTH and His in PTHrP, was identified as a key determinant of the altered receptor-interaction responses exhibited by the two peptides. We conclude that whereas PTH and PTHrP bind similarly to the G protein-coupled PTHR conformation (RG), PTH has a greater capacity to bind to the G protein-uncoupled conformation (R(0)) and, hence, can produce cumulatively greater signaling responses (via R(0)-->RG isomerization) than can PTHrP. Such conformational selectivity may relate to the distinct modes by which PTH and PTHrP act biologically, endocrine vs. paracrine, and may help explain reported differences in the effects that the ligands have on calcium and bone metabolism when administered to humans.
<title>Physics of photopolymer-liquid crystal composite holographic gratings</title> (1996)

We present an overview of the physics of holographic grating formation and electro-optical switching in a unique polymer-dispersed liquid crystal material. Anisotropic counter-diffusion of liquid crystal (LC) molecules and monomers during holographic recording appears to produce conditions favorable for distorting phase-separated sub-micrometer LC droplets into prolate ellipsoids with major axes along the grating vector. A simple shaped-droplet mechanical model yields results in good agreement with optical diffraction data for polarization properties and switching fields as well as response and relaxation times, as long as droplets can be assumed to be positive uniaxial domains. Normal surface anchoring of LC molecules is likely in these systems, based on NMR data, and this tends to strongly influence the effective refractive index and birefringence of the droplets.
Efficient Adeno‐Associated Virus‐Mediated Gene Expression in Human Placenta‐Derived Mesenchymal Cells (2003)

Mesenchymal cells from various sources are pluripotent and are attractive sources for cell transplantation. In this study, we analyzed recombinant adeno-associated virus (rAAV)-mediated gene expression in human placenta-derived mesenchymal cells (hPDMCs), which reside in placental villi. After transduction of AV-CAG-EGFP, a rAAV expressing enhanced green fluorescence protein (EGFP), hPDMCs showed much higher level of EGFP expression than human umbilical vein endothelial cells or rat aortic smooth muscle cells. The number of EGFP-positive hPDMCs infected by AV-CAG-EGFP alone did not increase significantly by coinfection of adenovirus, which enhanced expression level of the rAAV vector. Moreover, flow cytometric analysis showed discrete positive fraction of EGFP-expressing hPDMCs, which is about 15-20% of the cells infected with AV-CAG-EGFP. Therefore, some cell population in hPDMCs might be highly susceptible to rAAV-mediated gene transduction. In addition, stable EGFP expressions were observed in about 1% of hPDMCs infected with AV-CAG-EGFP at 4 weeks post-infection. Collectively, hPDMCs have characters favorable for rAAV-mediated gene expression.
V2X Meets NOMA: Non-Orthogonal Multiple Access for 5G-Enabled Vehicular Networks (2017)

Benefiting from widely deployed infrastructure, the LTE network has recently been considered as a promising candidate to support vehicle-to-everything (V2X) services. However, with a massive number of devices accessing the V2X network in the future, the conventional OFDM-based LTE network faces congestion issues due to its low efficiency of orthogonal access, resulting in significant access delay and posing a great challenge especially to safety-critical applications. The non-orthogonal multiple access (NOMA) technique has been well recognized as an effective solution for the future 5G cellular networks to provide broadband communications and massive connectivity. In this article, we investigate the applicability of NOMA in supporting cellular V2X services to achieve low latency and high reliability. Starting with a basic V2X unicast system, a novel NOMAbased scheme is proposed to tackle the technical hurdles in designing high spectrally efficient scheduling and resource allocation schemes in the ultra-dense topology. We then extend it to a more general V2X broadcasting system. Other NOMA-based extended V2X applications and some open issues are also discussed.
Interleukin‐10 differentially regulates B7‐1 (CD80) and B7‐2 (CD86) expression on human peripheral blood dendritic cells (1995)

Abstract Most of the immunosuppressive effects of interleukin‐10 (IL‐10) are related to functional inhibition of antigen‐presenting cells (APC). Herein, we investigate the influence of recombinant (r)IL‐10 on human dendritic cells (DC) purified from peripheral blood of healthy volunteers. First, we found that rIL‐10 inhibited in a dose‐dependent manner the proliferative responses as well as the production of IL‐2 and interferon‐γ (IFN‐γ) in mixed lymphocyte reaction (MLR) between purified T cells and DC. This rIL‐10 effect could be attributed to a direct effect on DC, as DC preincubated with rIL‐10 were found to be deficient in the induction of alloreactive T cells even when anti‐IL‐10 neutralizing mAb was added at the time of MLR. Flow cytometric analysis indicated that rIL‐10 did not modify the expression of ICAM‐1 (CD54) and B7‐1 (CD80), but decreased HLA‐DR and B7‐2 (CD86) expression at the DC surface. We conclude that the inhibitory effect of rIL‐10 on primary alloreactive T cell responses involves down‐regulation of class II MHC and B7‐2 expression at the DC surface.
Molecular Docking and 3D-QSAR CoMFA Studies on Indole Inhibitors of GIIA Secreted Phospholipase A2 (2010)

Automated docking allowing a "protein-based" alignment was performed on a set of indole inhibitors of the GIIA secreted phospholipase A(2) (GIIA sPLA(2)). A correlation between the binding scores and the experimental inhibitory activity was observed (r(2) = 0.666, N = 34). All the indole inhibitors were docked in the active site of the GIIA sPLA(2) enzyme, and the best score docking pose of each inhibitor was used for the "protein-based" alignment of the compounds. A three-dimensional quantitative structure-activity relationship (3D-QSAR) model was then established using the comparative molecular field analysis (CoMFA) method. The set of 34 indole inhibitors was divided into two subsets: the training set, composed of 26 compounds, and the test set, consisting of eight compounds. The robustness and the predictive ability of the generated CoMFA model were examined by using the test set. A good correlation (r(2) = 0.997) between predicted and experimental inhibitory activity data allows the validation of the CoMFA model. Finally, the generated CoMFA model was used for the design and evaluation of new compounds. The new designed compounds exert improved predicted inhibitory activity and may be a target for the synthesis of new GIIA sPLA(2) indole inhibitors.
Low-temperature bonding of poly-(methyl methacrylate) microfluidic devices under an ultrasonic field (2008)

High bond strength at low temperature without shape distortion is a major goal in microfluidic device fabrication. In this paper, we present a new easy bonding method for poly-(methyl methacrylate) (PMMA) microdevices at low temperature in an ultrasonic field. The ultrasonic energy spot effect at an interface could lead to a high bond strength up to 30 mJ cm−2 at only 60 °C. This bond strength is tens of times higher than the typical value in the literature (Tsao et al 2007 Lab. Chip. 7 499). The benefit from the low bonding temperature is that no deformation of the channel was evident. Few changes in the substrate surface property were observed. The static water contact angle of the bonded substrates had a small decrease compared to that of the virgin ones. The bonded microchannel devices were not reduced in transparency and smoothness. This method is batch-production oriented because many microdevices could be bonded at one time.
Ferroelectric Properties of Individual Barium Titanate Nanowires Investigated by Scanned Probe Microscopy (2002)

We report scanned probe investigations on the ferroelectric properties of individual single-crystalline barium titanate nanowires. We show that nonvolatile electric polarization can be reproducibly induced and manipulated on these nanowires, thereby demonstrating that nanowires as small as 10 nm in diameter retain ferroelectricity. The coercive field for polarization reversal is determined to be ∼7 kV/cm, and the retention time for the induced polarization exceeds 5 days. These nanowires should provide promising materials for fundamental investigations on nanoscale ferroelectricity, and they may also be useful in nanoscale nonvolatile memory applications.
Correlations of Total Pelvic Spongiosa Volume With Both Anthropometric Parameters and Computed Tomography–Based Skeletal Size Measurements (2006)

Patient-specific dosimetry within the field of molecular radiotherapy continues to pose a challenge owing to the difficulty in predicting marrow toxicity. This study examined the correlation between total pelvic spongiosa volume (TPSV) and independent variables, which include both readily measured or calculated anthropometric parameters (AP), and image-based skeletal measurements requiring computed tomography (CT) images or skeletal radiographs. Fourteen (14) patients (5 male and 9 female) undergoing total hip arthroplasty (THA) were subjected to modified pelvic CT scans. These scans were utilized to estimate TPSV, which was comprised of the volumes of spongiosa within the L5 vertebra, os coxae, sacrum, and both proximal femurs. The APs investigated included total body height (TBH), total body mass (TBM), body mass index (BMI), body surface area (BSA), maximum effective mass (MEM), lean body mass (LBM), and fat-free mass (FFM). Skeletal measurements were also obtained from the CT images of the pelvic region. Correlation coefficients (r) were obtained for TPSV and each set of APs as well as each set of skeletal measurements. Total body height (r = 0. 80) and os coxae height (r = 0.83) had the highest correlation coefficients of all the APS and skeletal measurements, respectively. FFM (r = 0.50), LBM (r = 0.42), TBM (r = 0.11), and BSA (r = 0.11) did not correlate well with TPSV, which accounts for approximately 45% of total spongiosa seen throughout the skeleton at sites associated with active bone marrow. Skeletal height measurements appear to have a much higher correlation with TPSV than either their corresponding skeletal width measurements or parameters that are a function of an individual's TBM.