gebhart/patrepeval huggingface dataset:
Recombinant tumor necrosis factor and interleukin 1 enhance slow-wave sleep (1987)

The cytokines interleukin 1 (IL 1) and interferon (IFN) are immune response modifiers that are also pyrogenic and somnogenic. Tumor necrosis factor (TNF) (cachectin) is another pyrogenic monocyte product whose production can be elicited by somnogenic agents such as endotoxin. Human recombinant TNF (rTNF), therefore, was assayed for somnogenic activity. Intravenous (iv) or intracerebroventricular (ICV) injections of rTNF enhanced slow-wave sleep (SWS) and electroencephalographic slow-wave (0.5-4.0 Hz) activity. Recombinant TNF also suppressed rapid-eye-movement sleep (REM) and induced biphasic fevers whether given by intravenous or ICV injection. Responses to rTNF were compared with those elicited by human recombinant beta-IL 1 (rIL 1). Sleep responses elicited by rIL 1 were similar to those previously reported for native IL 1 and to those elicited by rTNF. However, unlike rTNF, rIL 1 induced monophasic fevers. Animal behavior and brain temperature changes that occur during the transition from one arousal state to another remained undisturbed after either rTNF or rIL 1 treatment. The fact that TNF and IL 1 as well as other immunoactive substances, e.g., IFN, muramyl peptides, and endotoxin, enhance SWS suggests that SWS is linked to the immune response. We conclude that TNF, in addition to IL 1 and IFN, is an endogenous somnogen.
Effect of low pH and heparin on the structure of acidic fibroblast growth factor (1994)

Changes in the fluorescence of the single tryptophan of acidic fibroblast growth factor have been used to monitor the effect of low pH on the conformation of the molecule, and the consequences of heparin binding and high ionic strength under such conditions. These studies demonstrate that the conformation of the protein changes reversibly below pH 5, and that heparin, depending on the conditions, may either prevent that change or induce a new irreversible modification of the structure, which runs parallel to the partial inactivation of the protein. It is also demonstrated that secondary heparin-binding sites appear at low pH, which favor the formation of precipitates at some protein/heparin ratios. Precipitation and inactivation of fibroblast growth factor at low pH may hinder its wound-healing activity, since acidification seems frequent in wounds.
Hybridization of Frenkel and Wannier-Mott excitons in an optical microcavity (2006)

We demonstrate strong-coupling and exciton hybridization in an organic-inorganic microcavity containing InGaP QWs and the small molecular weight organic tetraphenylporphyrin. The hybrid excited state is found to persist up to temperatures of 100 K.
Unexpected properties of polymeric DNA-nanocomplexes synthesized in picoliter droplets (2011)

Nucleic acids have emerged as a promising class of drugs but require a safe and efficient delivery system to realize their full therapeutic potential. While non-viral vectors may be safer than viral vectors, the need to improve their delivery efficiencies has provided the impetus to control the structural and chemical properties of DNA nanocomplexes. We have previously shown uniform size distribution of gene-loaded nanocomplexes synthesized in picoliter droplets. This study demonstrated that these homogeneous nanocomplexes reduced cytotoxicity significantly while the therapeutic efficacy was not compromised, which will help pave the way of applying gene as a “drug”.
Enhanced Detection of Low-Abundance Host Cell Protein Impurities in High-Purity Monoclonal Antibodies Down to 1 ppm Using Ion Mobility Mass Spectrometry Coupled with Multidimensional Liquid Chromatography (2015)

The enormous dynamic range of proteinaceous species present in protein biotherapeutics poses a significant challenge for current mass spectrometry (MS)-based methods to detect low-abundance HCP impurities. Previously, an HCP assay based on two-dimensional chromatographic separation (high pH/low pH) coupled to high-resolution quadrupole time-of-flight (QTOF) mass spectrometry and developed in the author's laboratory has been shown to achieve a detection limit of about 50 ppm (parts per milion) for the identification and quantification of HCPs present in monoclonal antibodies following Protein A purification.1 To improve the HCP detection limit we have explored the utility of several new analytical techniques for HCP analysis and thereby developed an improved liquid chromatography-mass spectrometry (LC-MS) methodology for enhanced detection of HCPs. The new method includes (1) the use of a new charge-surface-modified (CSH) C18 stationary phase to mitigate the challenges of column saturation, peak tailing, and distortion that are commonly observed in the HCP analysis; (2) the incorporation of traveling-wave ion mobility (TWIM) separation of coeluting peptide precursors, and (3) the improvement of fragmentation efficiency of low-abundance HCP peptides by correlating the collision energy used for precursor fragmentation with their mobility drift time. As a result of these improvements, the detection limit of the new methodology was greatly improved, and HCPs present at a concentration as low as 1 ppm (1 ng HCP/mg mAb) were successfully identified and quantified. The newly developed method was applied to analyze two high-purity mAbs (NIST mAb and Infliximab) expressed in a murine cell line. For both samples, low-abundance HCPs (down to 1 ppm) were confidently identified, and the identities of the HCPs were further confirmed by targeted MS/MS experiments. In addition, the performance of the assay was evaluated by an interlaboratory study in which three independent laboratories performed the same HCP assay on the mAb sample. The reproducibility of this assay is also discussed.
Efficient Hilbert transform-based alternative to Tofts physiological models for representing MRI dynamic contrast-enhanced images in computer-aided diagnosis of prostate cancer (2015)

In computer-aided diagnosis (CAD) systems for prostate cancer, dynamic contrast enhanced (DCE) magnetic resonance imaging is useful for distinguishing cancerous and benign tissue. The Tofts physiological model is a commonly used representation of the DCE image data, but the parameters require extensive computation. Hence, we developed an alternative representation based on the Hilbert transform of the DCE images. The time maximum of the Hilbert transform, a binary metric of early enhancement, and a pre-DCE value was assigned to each voxel and appended to a standard feature set derived from T2-weighted images and apparent diffusion coefficient maps. A cohort of 40 patients was used for training the classifier, and 20 patients were used for testing. The AUC was calculated by pooling the voxel-wise prediction values and comparing with the ground truth. The resulting AUC of 0.92 (95% CI [0.87 0.97]) is not significantly different from an AUC calculated using Tofts physiological models of 0.92 (95% CI [0.87 0.97]), as validated by a Wilcoxon signed rank test on each patient’s AUC (p = 0.19). The time required for calculation and feature extraction is 11.39 seconds (95% CI [10.95 11.82]) per patient using the Hilbert-based feature set, two orders of magnitude faster than the 1319 seconds (95% CI [1233 1404]) required for the Tofts parameter-based feature set (p&lt;0.001). Hence, the features proposed herein appear useful for CAD systems integrated into clinical workflows where efficiency is important.
Embroidery and Cloth Fiber Workflows on Disney’s ”Encanto” (2022)

Walt Disney Animation Studios’ ”Encanto” tells the tale of an extraordinary family, the Madrigals, who live in the hidden mountains of Colombia. The garments are an important aspect of the characters’ design and express their individual personalities. Accurate cloth looks have been difficult to achieve with our traditional look development workflow. We present the techniques utilized to create the varied and complex fiber-level cloth features in the film. In order to produce the desired level of geometric detail, we developed a new workflow that procedurally models each cloth fiber in Houdini and then binds the resulting curves to the clothing geometry via Disney’s XGen. We also extended our embroidery workflow to support a wide variety of embroidery types and styles which are exemplified by Mirabel’s outfit and include needle paint, knot, and rope stitching.
Investigation and control of the uniformity of drug nanoparticles directly deposited on the particulate surfaces of excipient by PLD (2007)

Pulsed laser deposition (PLD) of drug nanoparticles for pharmaceutical preparation was investigated. Indomethacin (IM) was preliminary mixed with magnesium stearate (StMg) to prepare a target for PLD. By using the composite targets, the percentage of deposited nanoparticles in the collected powder increased compared to when only IM was ablated. The percentage of IM nanoparticles was the highest when IM and StMg were mixed at 1:1 ratio. Nanoparticles of the composite target were deposited on the micron sized particulate excipient, i.e., SiO2, potato starch, and lactose. The excipient powders were mixed by rotation. Their surface coverage was evaluated by FE-SEM observation and diffuse reflectance (DR) UV-Vis spectroscopy. The surface coverage was estimated to be around 50 % for 20 min deposition time. Simple rotation of the excipient powders was found to be one of the effective methods for uniform deposition of nanoparticles.
Maximum likelihood dosage estimation for Bayesian transmission tomography (2002)

Bayesian reconstruction and restoration methods require the choice of parameters related to variance in both stochastic image models and observed data. In practice these parameters, or their ratio, is often chosen heuristically. The authors present a method for joint maximum-likelihood (ML) estimation of these two parameters in transmission tomography, with emphasis on the X-ray//spl gamma/-ray dosage parameter. The estimation algorithm employs the expectation-maximization method, with the unobserved image as the complete data. The ML parameter estimator is shown to yield values which are practical for tomographic reconstruction, both with synthetic phantoms and real data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Effect of an Active Substrate on Nanoparticle‐Enhanced Fluorescence (2008)

Proximity of fluorescent molecules to noble metal nanoparticles leads to a strong enhancement of the fluorescent intensity during irradiation with light, a consequence of resonant coupling to localized particle plasmons. In this communication we show that the substrate can have a profound effect on this simple picture, not merely shifting the resonance, but actively reshaping the local fields, and resulting in even larger enhancements.
Stream processing performance for Blue Gene/P supercomputer (2008)

Stream processing systems are designed to support applications that use real time data. Examples of streaming applications include security agencies processing data from communications media, battlefield management systems for military operations, consumer fraud detection based on online transactions, and automated trading based on financial market data. Many stream processing applications are faced with the challenge of increasingly large volumes of data and the requirement to deliver low-latency responses predicated by analysis of that data. In this paper, we assess the applicability of the Blue Gene architecture for stream computing applications. This work is part of a larger effort to demonstrate the efficacy of using a Blue Gene for streaming applications. Blue Gene supercomputers provide a high-bandwidth low-latency network connecting a set of I/O and compute nodes. We examine Blue Genepsilas suitability for stream computing applications by assessing its messaging capability for typical stream computing messaging workloads. In particular, this paper presents results from micro-benchmarks we used to evaluate the raw performance of Blue Gene/P (Blue Gene/P) supercomputer under loads produced by high volumes of streaming data. We measure the performance of data streams that originate outside the supercomputer, are directed through the I/O nodes to the compute nodes and then terminate outside. Our performance experiments demonstrate that the Blue Gene/P hardware delivers low-latency and high-throughput capability in a manner usable by streaming applications.
Abstract 1106: Co-administration of the iRGD tumor-penetrating peptide improves the tumor immunostimulatory effects of low-dose IL-2 (2019)

Abstract Background: Recombinant IL-2 at high doses is an effective immunotherapy treatment for various types of solid tumors. However, its clinical utility has been limited by serious mechanism-based side-effects. The clinical-stage iRGD peptide specifically targets tumors and, via activation of the ‘CendR’ trans-tissue transport pathway, increases tumor penetration and accumulation of various types of co-administered drugs. By selectively increasing the drug delivery into tumors, but not to normal tissues, iRGD potentiates the pharmacological activity of various anti-cancer agents within tumor tissue, while reducing their toxicities. In this study we investigate whether co-administration of iRGD with low-dose IL-2 can improve the tumor immune microenvironment by increasing in the ratios of tumor-killing effector CD8 cells vs. the immunosuppressive T-regulatory cells. Methods: Subcutaneous breast tumors (4T1) were generated in immunocompetent mice. Mice were treated with either vehicle control, iRGD, IL-2, or IL-2 + iRGD for 5 days. Tumors were preserved for immunohistochemistry (IHC) or enzymatically digested for fluorescence activated cell sorting (FACS) 16 hours after the last dosing. The FACS and IHC panels were designed to detect the percentage of total T cells, CD4 and CD8 T cells, and Treg cells. Results: Low doses of IL-2 alone were found to increase Tregs within the tumor but had no effect in CD4 or CD8 effector T cells, compared to vehicle treatment. However, when Low dose IL-2 was co-administered with iRGD, we observed a significantly lower percentage of T regs and an increase in CD4 effector T cells. More importantly the ratio of CD8 / Treg cells was increased by at least 10-fold, compared to low dose IL-2 alone. Conclusions: The combination treatment with iRGD and low doses of IL-2 is capable of favorably altering the tumor immune microenvironment such that immunosuppressive T reg cells were reduced, while there was an increase in the effector CD4 and CD8 T-cell populations. The tumor-selective IL-2 pharmacology benefit obtained with iRGD co-administration may provide new options for the use of the well-validated IL-2 in solid tumor patients, including a strategy to overcome the primary resistance to PD-1 blockade. Citation Format: Harri Jarvelainen, Gregory P. Botta, Tatiana Hurtado De Mendoza, Erkki Ruoslahti. Co-administration of the iRGD tumor-penetrating peptide improves the tumor immunostimulatory effects of low-dose IL-2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1106.
Fast and multiplexed superresolution imaging with DNA-PAINT-ERS (2020)

Abstract DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) facilitates multiplexing in superresolution microscopy but is practically limited by slow imaging speed. To address this issue, we propose the additions of ethylene carbonate (EC) to the imaging buffer, sequence repeats to the docking strand, and a spacer between the docking strand and the affinity agent. Collectively termed DNA-PAINT-ERS (E = EC, R = Repeating sequence, and S = Spacer), these strategies can be easily integrated into current DNA-PAINT workflows for both accelerated imaging speed and improved image quality through optimized DNA hybridization kinetics and efficiency. We demonstrate the general applicability of DNA-PAINT-ERS for fast, multiplexed superresolution imaging using previously validated oligonucleotide constructs with slight modifications.
Clarus Quality Checking Algorithm Documentation Report (2010)

With funding and support from the USDOT RITA IntelliDrive(SM) initiative and direction from the FHWA Road Weather Management Program, NCAR enhanced QCh algorithms that are a part of the current Clarus System. Moreover, NCAR developed new QCh algorithms to extend the capabilities of the current Clarus System. This document highlights the current status of all the QCh algorithms in the Clarus System.\n
TIMP3 is a CLOCK‐dependent diurnal gene that inhibits the expression of UVB‐induced inflammatory cytokines in human keratinocytes (2017)

As the outermost physical barrier of an organism, the skin is diurnally exposed to UV radiation (UVR). Recent studies have revealed that the skin exhibits a circadian rhythm in various functions, and this oscillation is disturbed and reset via a strong environmental cue, the UVR. However, a molecular link between circadian perturbation by UVR and UVR-induced cellular responses has not been investigated. We identified tissue inhibitor of metalloproteinase ( TIMP)- 3 as a novel circadian locomotor output cycles kaput (CLOCK)-dependent diurnal gene by using a CLOCK-knockdown strategy in human keratinocytes. Among dozens of identified transcripts down-regulated by CLOCK knockdown, TIMP3 displayed a rhythmic expression in a CLOCK-dependent manner, in which the expression of matrix metalloproteinase (MMP)-1 and inflammatory cytokines, such as TNF-α, chemokine (C-X-C motif) ligand (CXCL)-1, and IL-8, were inversely regulated. Upon UVB exposure, the expression of CLOCK and TIMP3 was down-regulated, which led to an up-regulation of secretion of MMP1 and TNF-α proteins and in the transcription of CXCL1 and IL-8 via CCAAT-enhancer binding protein (C/EBP)-α. UVB-induced TNF-α secretion increased further or decreased by knockdown or overexpression of TIMP3, respectively, as well as by CLOCK. As a novel CLOCK-dependent diurnal gene, TIMP3 inhibits the expression of inflammatory cytokines that are up-regulated by UV irradiation in human keratinocytes. Thus, our work suggests a molecular link between circadian perturbation by UVR and UVR-induced inflammation.-Park, S., Kim, K., Bae, I.-H., Lee, S. H., Jung, J., Lee, T. R., Cho, E.-G. TIMP3 is a CLOCK-dependent diurnal gene that inhibits the expression of UVB-induced inflammatory cytokines in human keratinocytes.
Chiral porphyrazine near-IR optical imaging agent exhibiting preferential tumor accumulation (2009)

A chiral porphyrazine (pz), H(2)[pz(trans-A(2)B(2))] (247), has been prepared that exhibits preferential in vivo accumulation in the cells of tumors. Pz 247 exhibits near-infrared (NIR) emission with lambda > 700 nm in the required wavelength range for maximum tissue penetration. When MDA-MB-231 breast tumor cells are treated with 247, the agent shows strong intracellular fluorescence with an emission maximum, 704 nm, which indicates that it localizes within a hydrophobic microenvironment. Pz 247 is shown to associate with the lipophilic core of LDL and undergo cellular entry primarily through receptor-mediated endocytosis accumulating in lysosomes. Preliminary in vivo studies show that 247 exhibits preferential accumulation and retention in the cells of MDA-MB-231 tumors subcutaneously implanted in mice, thereby enabling NIR optical imaging with excellent contrast between tumor and surrounding tissue. The intensity of fluorescence from 247 within the tumor increases over time up to 48 h after injection presumably due to the sequestration of circulating 247/LDL complex by the tumor tissue. As the need for cholesterol, and thus LDL, is elevated in highly proliferative tumor cells over nontumorigenic cells, 247 has potential application for all such tumors.
Calibration of the Circle-plus-Arc Trajectory (2006)

In this paper, a novel calibration method for C-arm cone-beam (CB) scanners is presented which allows the calibration of the circle-plus-arc trajectory. The circle-plus-arc trajectory has been investigated recently for exact image reconstruction and is especially well suited for C-arm systems. The main idea is the separation of the trajectory into two segments (circle segment and arc segment) which are calibrated independently. For each trajectory segment, a calibration phantom is placed in an optimal way. The calibration results are then combined by computing the transformation the phantom experienced inbetween the independent runs. This combination can be done in a postprocessing step by using the singular value decomposition (SVD). The method works for any calibration procedure in which the phantom has a favored orientation with respect to a trajectory segment. Results are presented for both, simulated as well as real data acquired with a Siemens AXIOM Artis C-arm system.
Phase-separation of wetting fluids using nanoporous alumina membranes and micro-glass capillaries (2014)

Phase separation in two-phase microfluidic exchangers is a promising strategy for reducing the required pumping power. Past research has focused on using hydrophobic nanoporous structures in order to extract water vapor and retain liquid within the vapor-cooling device. This study focuses on characterizing the bursting pressure, the maximum Laplace pressure for liquid containment, of nanoporous alumina membranes and micro-glass capillaries. The pore size diameters of the alumina membranes have a nominal diameter of 170 nm that can produce a pressure drop of 1.5 kPa for wetting dielectric liquids. In order to contain higher Laplace pressures, the pore geometry for 'pinning' of the fluid at the liquid-vapor interface needs to be optimized. Single glass micro-glass capillaries were used in order to study the 'pinning effect' of wetting fluids for various micro-capillary diameters. The glass capillary diameters ranged from 250–840 µm with measured Laplace pressures up to ∼0.9 kPa. Experimental results agreed well with an analytical model that calculates the Laplace pressure as a function of pore geometry.
Solvent‐Free One‐Step Photochemical Hydroxylation of Benzene Derivatives by the Singlet Excited State of 2,3‐Dichloro‐5,6‐dicyano‐p‐benzoquinone Acting as a Super Oxidant (2014)

Photoinduced hydroxylation of neat deaerated benzene to phenol occurred under visible-light irradiation of 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ), which acts as a super photooxidant in the presence of water. Photocatalytic solvent-free hydroxylation of benzene derivatives with electron-withdrawing substituents such as benzonitrile, nitrobenzene, and trifluoromethylbenzene used as neat solvents has been achieved for the first time by using DDQ as a super photooxidant to yield the corresponding phenol derivatives and 2,3-dichloro-5,6-dicyanohydroquinone (DDQH2 ) in the presence of water under deaerated conditions. In the presence of dioxygen and tert-butyl nitrite, the photocatalytic hydroxylation of neat benzene occurred with DDQ as a photocatalyst to produce phenol. The photocatalytic reactions are initiated by oxidation of benzene derivatives with the singlet and triplet excited states of DDQ to form the corresponding radical cations, which associate with benzene derivatives to produce the dimer radical cations, which were detected by the femto- and nanosecond laser flash photolysis measurements to clarify the photocatalytic reaction mechanisms. Radical cations of benzene derivatives react with water to yield the OH-adduct radicals. On the other hand, DDQ(.) (-) produced by the photoinduced electron transfer from benzene derivatives reacts with the OH-adduct radicals to yield the corresponding phenol derivatives and DDQH2 . DDQ is recovered by the reaction of DDQH2 with tert-butyl nitrite when DDQ acts as a photocatalyst for the hydroxylation of benzene derivatives by dioxygen.