gebhart/patrepeval huggingface dataset:
HTTP adaptive streaming QoE estimation with ITU-T rec. P. 1203 (2018)

This paper describes an open dataset and software for ITU-T Ree. P.1203. As the first standardized Quality of Experience model for audiovisual HTTP Adaptive Streaming (HAS), it has been extensively trained and validated on over a thousand audiovisual sequences containing HAS-typical effects (such as stalling, coding artifacts, quality switches). Our dataset comprises four of the 30 official subjective databases at a bitstream feature level. The paper also includes subjective results and the model performance. Our software for the standard was made available to the public, too, and it is used for all the analyses presented. Among other previously unpublished details, we show the significant performance improvements of using bitstream-based models over metadata-based ones for video quality analysis, and the robustness of combining classical models with machine-learning-based approaches for estimating user QoE.
Carbon-nanotube based flexible electrodes for retinal recording and stimulation (2013)

A lingering technological bottleneck in the field of neuro-prosthetics is the quality of the stimulating electrodes. Such electrodes should be soft, micron in size and capable of injecting enough charge to evoke localized neuronal activity without causing tissue damage during extended operation (years). Carbon nanotubes have been shown over the past several years as a promising material in this realm. Here we present the use of carbon nanotubes for neuronal applications. Specifically, we show how this exciting material can be applied to fabricate a new flexible neuronal micro electrode device. The device is based entirely on carbon nanotube technology, where both the conducting traces and the stimulating electrodes consist of conducting carbon nanotube films embedded in a polymeric support. The use of carbon nanotubes bestows the electrodes flexibility and excellent electrochemical properties. Recording and stimulation tests with chick retinas were used to demonstrate the suitability of the new device for high-efficacy neuronal stimulation applications. Preliminary in-vivo examination of these surfaces show marked retina-carbon nanotube attachment. Finally, progress towards photo activated carbon nanotube electrodes is described.
On the Mechanism of the Polynucleotide Joining Reaction (1968)

Polynucleotide-joining enzymes (ligases) have been identified in uninfected and phage-infected Escherichia coli (Gellert, 1967; Olivera and Lehman, 1967a; Zimmerman et al., 1967; Gefter et al., 1967; Weiss and Richardson, 1967a; Cozzarelli et al., 1967). Both types of enzyme catalyze the synthesis of a phosphodiester bond between the 3′ hydroxyl and 5′ phosphoryl termini of DNA chains which have been properly aligned in a double-helical structure. Such enzymes are of interest because of their possible involvement in genetic recombination, ‘dark’ repair of ultraviolet-induced lesions, and in DNA synthesis. It has already been demonstrated that the polynucleotide ligase induced by phage T4 is essential for normal T4 DNA replication (Fareed and Richardson, 1967).
Protein Recognition and Denaturation by Self‐Assembling Fragments on a DNA Quadruplex Scaffold (2006)

Gesichtserkennung: Quadruplex-DNA wurde als nichtkovalentes Gerüst genutzt, um für die Proteinerkennung und -denaturierung verantwortliche bindende Gruppen zu projizieren. Der beste Quadruplex senkt die Schmelztemperatur von Cytochrom c um etwa 45 K.
Image Restoration Preprocessing for Low Light Auto-Focusing in Digital Cameras (2007)

The performance of passive auto-focus (AF) systems suffers when operating under low-lighting conditions due to the flatness of the sharpness function. In this paper, an adaptive noise reduction method prior to AF sharpness filter is introduced for the purpose of elevating the suppressed peak in the sharpness function . Experimental results show that the use of adaptive noise reduction preprocessing enables focusing at lower lux levels as compared to non-adaptive noise reduction preprocessing.
Oxidative stress inhibits insulin signal transduction in cultured human vascular smooth muscle cells: a possible contribution to mechanism of insulin resistance (2001)

Insulin resistance is underlain in multiple risk factor syndrome of cardiovascular diseases. Regarding the mechanism of insulin resistance, genetic factors, aging and obesity are supposed to be main causes. It is just recently reported that oxidative stress induces insulin resistance in adipose tissue. In order to reveal the influence of oxidative stress on insulin signal transduction in vascular smooth muscle cells (VSMC), we investigated insulin-mediated VSMC growth and expression of insulin receptor substrate-1 (IRS-1) under long exposure of H2O2. Cultured human aortic VSMC were incubated with or without insulin 1000μU/ml and H2O2 (10nM-1μM) for 48 hours. VSMC growth was evaluated by 3H-thymidine uptake. IRS-1 expression was analyzed by Western blotting. The effect of probucol(1μM) was tested as an antioxidant drug. Insulin promoted VSMC growth (57.8% vs. control, p<0.05), but long time exposure of 10nM and 100nM H2O2 significantly suppressed this insulin-mediated VSMC growth (34.1%, 52.9% vs. insulin, p<0.01, respectively). 10μM H2O2 induced cell death. Probucol prevented inhibition of insulin mediated-VSMC growth by 10nM H2O2 (40.3%, 17.6% vs. insulin+H2O2, p<0.01, p<0.05, respectively). Furthermore, IRS-1 expression was inhibited by 10nM and 100nM H2O2 by 69.2%, 84.6% (p<0.01), and probucol significantly recovered this inhibition by 10nM H2O2 by 14.0% (p<0.05). In summary, long term exposure of oxidative stress such as H2O2 would be inhibiting IRS-1 expression and insulin signal transduction in VSMC. Probucol attenuated these inhibition by oxidative stress. Thus, oxidative stress, which is elevating in hypertensive and diabetes patients, might be one possible mechanism of progression of insulin resistance or accelerating insulin resistance in those patients. Antioxidant drug such as probucol might be useful for prevention and therapy for oxidative stress-induced insulin resistance.
Real-time imaging system for a small OpenPET prototype (2010)

The “OpenPET” geometry has potential for real-time tracking of targeted tumors and in situ visualization of dose distribution in radiation therapy. For the real-time imaging system, we are intending to use one-pass list-mode dynamic row-action maximum likelihood algorithm (DRAMA) and implement it using general-purpose computation on graphics processing unit techniques. However, it is difficult to consistently reconstruct in real-time because the amount of list-mode data acquired in PET scan can be large depending on the activity and reconstruction speed depends on the amount of the list-mode data. In this study, we developed a system to control the data used in the reconstruction step keeping quantitative performance. In the proposed system, data transfer control system limits the event count to be used in the reconstruction step according to the reconstruction speed, and the reconstructed images are properly intensified by using ratio of the used count to the total count. We implemented the system on a small OpenPET prototype system and evaluated the performance in terms of the real-time tracking ability by displaying reconstructed images in which the intensity was compensated. The intensity of the displayed image was properly correlated with the original count rate and a frame rate of 2 frames per second was achieved without significant delay.
Suppression of autophagy by extracellular vesicles promotes myofibroblast differentiation in COPD pathogenesis (2015)

Extracellular vesicles (EVs), such as exosomes and microvesicles, encapsulate proteins and microRNAs (miRNAs) as new modulators of both intercellular crosstalk and disease pathogenesis. The composition of EVs is modified by various triggers to maintain physiological homeostasis. In response to cigarette smoke exposure, the lungs develop emphysema, myofibroblast accumulation and airway remodelling, which contribute to chronic obstructive pulmonary disease (COPD). However, the lung disease pathogenesis through modified EVs in stress physiology is not understood. Here, we investigated an EV-mediated intercellular communication mechanism between primary human bronchial epithelial cells (HBECs) and lung fibroblasts (LFs) and discovered that cigarette smoke extract (CSE)-induced HBEC-derived EVs promote myofibroblast differentiation in LFs. Thorough evaluations of the modified EVs and COPD lung samples showed that cigarette smoke induced relative upregulation of cellular and EV miR-210 expression of bronchial epithelial cells. Using co-culture assays, we showed that HBEC-derived EV miR-210 promotes myofibroblast differentiation in LFs. Surprisingly, we found that miR-210 directly regulates autophagy processes via targeting ATG7, and expression levels of miR-210 are inversely correlated with ATG7 expression in LFs. Importantly, autophagy induction was significantly decreased in LFs from COPD patients, and silencing ATG7 in LFs led to myofibroblast differentiation. These findings demonstrate that CSE triggers the modification of EV components and identify bronchial epithelial cell-derived miR-210 as a paracrine autophagy mediator of myofibroblast differentiation that has potential as a therapeutic target for COPD. Our findings show that stressor exposure changes EV compositions as emerging factors, potentially controlling pathological disorders such as airway remodelling in COPD.
Data from Near-Infrared Dye-Labeled Anti-Prostate Stem Cell Antigen Minibody Enables Real-Time Fluorescence Imaging and Targeted Surgery in Translational Mouse Models (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;The inability to intraoperatively distinguish primary tumor, as well as lymphatic spread, increases the probability of positive surgical margins, tumor recurrence, and surgical toxicity. The goal of this study was to develop a tumor-specific optical probe for real-time fluorescence-guided surgery.&lt;/p&gt;Experimental Design:&lt;p&gt;A humanized antibody fragment against PSCA (A11 minibody, A11 Mb) was conjugated with a near-infrared fluorophore, IRDye800CW. The integrity and binding of the probe to PSCA were confirmed by gel electrophoresis, size-exclusion chromatography, and flow cytometry, respectively. The ability of the probe to detect tumor-infiltrated lymph nodes and metastatic lesions was evaluated in 2 xenograft models, as well as in transgenic mice expressing human PSCA (hPSCA). An invasive intramuscular model was utilized to evaluate the efficacy of the A11 Mb-IRDye800CW-guided surgery.&lt;/p&gt;Results:&lt;p&gt;A11 Mb was successfully conjugated with IRDye800CW and retained specific binding to PSCA. &lt;i&gt;In vivo&lt;/i&gt; imaging showed maximal signal-to-background ratios at 48 hours. The A11 Mb-IRDye800CW specifically detected PSCA-positive primary tumors, tumor-infiltrated lymph nodes, and distant metastases with high contrast. Fluorescence guidance facilitated more complete tumor resection, reduced tumor recurrence, and improved overall survival, compared with conventional white light surgery. The probe successfully identified primary orthotopic tumors and metastatic lesions in hPSCA transgenic mice.&lt;/p&gt;Conclusions:&lt;p&gt;Real-time fluorescence image–guided surgery with A11 Mb-IRDye800CW enabled detection of lymph node metastases and positive surgical margins, facilitated more complete tumor removal, and improved survival, compared with white light surgery. These results may be translatable into clinical practice to improve surgical and patient outcomes.&lt;/p&gt;&lt;/div&gt;
Longitudinal Changes in Quantitative Spinal Cord MRI in Multiple Sclerosis Patients: Results of a 5-year Study (S47.001) (2018)

To assess quantitative spinal cord(SC)-MRI measures over 5 years, and characterize the relationship between changes in quantitative SC-MRI with clinical disability.
THE MICRO-PHOTOLUMINESCENCE OF A SINGLE V-GROOVE GaAs/AlGaAs QUANTUM WIRE (2000)

The micro-photoluminescence(μ-PL) scan has been performed on a single V-groove GaAs/AlGaAs quantum wire in the direction perpendicular to the wire.The variatio n of μ-PL spectra from various quantum structures with different spatial positi ons has been observed.In the region of quantum wire (QWR) the PL spectra contain the peaks from QWR,necking quantum well (NQWL) and vertical quantum well (VQWL) ,while in the area about 1μm and farther away from the QWR the PL spectra show the peaks from side-wall quantum well (SQWL) and top quantum well (TQWL).All the scanned PL spectra have been fitted by Gauss line shape.The asymmetric PL peaks of QWR and SQWL were decomposed into two components which were ascribed to the optical transitions between the electron ground state in the conduction band and the heavy hole and the light hole ground states in the valence band.The variati on of PL intensity from luminescent components with the spatial positions direct ly demonstrates the origin of the photoluminescence relating to different quantu m structures,and reflects the carrier transfer from SQWL to QWR,resulting in th e PL quenching of SQWL.
Analysis of Empirical Bayesian Methods for Neuroelectromagnetic Source Localization (2007)

The ill-posed nature of the MEG/EEG source localization problem requires the incorporation of prior assumptions when choosing an appropriate solution out of an infinite set of candidates. Bayesian methods are useful in this capacity because they allow these assumptions to be explicitly quantified. Recently, a number of empirical Bayesian approaches have been proposed that attempt a form of model selection by using the data to guide the search for an appropriate prior. While seemingly quite different in many respects, we apply a unifying framework based on automatic relevance determination (ARD) that elucidates various attributes of these methods and suggests directions for improvement. We also derive theoretical properties of this methodology related to convergence, local minima, and localization bias and explore connections with established algorithms.
Supplementary Table S2 from CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions (2023)

&lt;p&gt;Annotations for the sgRNA libraries containing sequences, target gene information, Zscore and RNAseq data for each cell line screened.&lt;/p&gt;
PEGylated recombinant Aplysia punctata ink toxin depletes arginine and lysine and inhibits growth of tumor xenografts (2023)

Abstract In recent years, a novel treatment method for cancer emerged, which is based on the starvation of tumors of amino acids like arginine. The deprivation of arginine in serum is based on enzymatic degradation and can be realized by arginine deaminases like the L-amino acid oxidase found in the ink toxin of the sea hare Aplysia punctata . Previously isolated from the ink, the L-amino acids oxidase was described to oxidate the essential amino acid L-lysine and L-arginine to their corresponding deaminated alpha-keto acids. Here, we present the recombinant production and functionalization of amino acid oxidase Aplysia Punctata ink toxin (APIT). PEGylated APIT (APIT-PEG) increased the blood circulation time. APIT-PEG treatment of patient-derived xenografted mice shows a significant dose dependent reduction of tumor growth over time mediated by amino acid starvation of the tumor. Treatment of mice with APIT-PEG which lead to deprivation of arginine was well tolerated.
GarNet++: Improving Fast and Accurate Static 3D Cloth Draping by Curvature Loss (2020)

In this paper, we tackle the problem of static 3D cloth draping on virtual human bodies. We introduce a two-stream deep network model that produces a visually plausible draping of a template cloth on virtual 3D bodies by extracting features from both the body and garment shapes. Our network learns to mimic a physics-based simulation (PBS) method while requiring two orders of magnitude less computation time. To train the network, we introduce loss terms inspired by PBS to produce plausible results and make the model collision-aware. To increase the details of the draped garment, we introduce two loss functions that penalize the difference between the curvature of the predicted cloth and PBS. Particularly, we study the impact of mean curvature normal and a novel detail-preserving loss both qualitatively and quantitatively. Our new curvature loss computes the local covariance matrices of the 3D points, and compares the Rayleigh quotients of the prediction and PBS. This leads to more details while performing favorably or comparably against the loss that considers mean curvature normal vectors in the 3D triangulated meshes. We validate our framework on four garment types for various body shapes and poses. Finally, we achieve superior performance against a recently proposed data-driven method.
Pulsatility does not alter the response to a physiological increment in glucagon in the conscious dog (1994)

The present study was designed to investigate if pulsatile hyperglucagonemia of physiological magnitude has greater efficacy in stimulating hepatic glucose production than constant glucagon. Paired studies were performed in conscious dogs. After insulin and glucagon were clamped at basal concentrations for 2 h, glucagon was elevated for 4 h with either a continuous infusion or pulses having physiological frequency and amplitude. With continuous infusion, plasma glucagon concentrations increased from 56 +/- 7 to 194 +/- 27 ng/l. With pulsatile infusion, glucagon concentrations started at 53 +/- 6 ng/l and then oscillated between 157 +/- 15 and 253 +/- 28 ng/l. Plasma insulin concentrations remained constant at basal levels. Glucose production was determined using a time-varying two-compartment model for glucose kinetics and deconvolution. After 15 min, glucose production had risen from 13.6 +/- 1.1 to 53.8 +/- 3.9 mumol.kg-1.min-1 with continuous infusion and from 12.9 +/- 0.6 to 50.6 +/- 2.9 mumol.kg-1.min-1 with pulsatile infusion. After 4 h, the production had fallen to 16.1 +/- 1.2 and 17.1 +/- 0.7 mumol.kg-1.min-1. In the present animal model with insulin held constant, no difference was noted between the response to continuous or pulsatile glucagon infusion.
Monoclonal antibodies against human T cell leukemia-lymphoma virus (HTLV) p24 internal core protein. Use as diagnostic probes and cellular localization of HTLV. (1984)

Four monoclonal antibodies, human T cell leukemia-lymphoma virus (HTLV) 6, 7, 8, and 9, which react with the 24,000 dalton internal core protein of HTLVI, have been developed. These monoclonal antibodies reacted with only HTLV-infected cells and not with a broad spectrum of normal, neoplastic, mitogen-stimulated, or virus-infected cells and tissues. HTLV 6, 7, 8, and 9 identified at least two different antigenic determinants on HTLV p24 that were also recognized by antibodies present in HTLV+ patient sera. Monoclonal antibodies HTLV 6, 7, 8, and 9 reacted in indirect immunofluorescence assays with HTLV p24 localized at the cell surface of 5-d cultures of HTLV-infected T cells and, as well, reacted with T cells infected with HTLVII, a new type of HTLV isolated from a patient (MO) with a T cell variant of hairy cell leukemia. Thus, HTLV 6, 7, 8, and 9 should prove to be useful diagnostic reagents in the identification of HTLV- and HTLVII-infected T cells.
Dynamic Hydrogels: Translating a Protein Conformational Change into Macroscopic Motion (2007)

Die Natur als Vorbild: Ein funktionelles Material in Form eines Hydrogels wurde durch Vernetzen eines künstlichen Calmodulins (das auf die Bindung eines Liganden hin seine Konformation ändert; siehe Bild) mit einem vierarmigen Poly(ethylenglycol) mit endständigen Acrylatgruppen erhalten. Bei Zugabe des Liganden Trifluoperazin schrumpft das Hydrogel um 20 %. Mehrere Schwell- und Schrumpfzyklen waren möglich.
Investigation of the Effective Dose of Agonistic 4-1BB Monoclonal Antibody in a Murine Colon Cancer Metastasis Model (2010)

Purpose: The aim of this study was to find the dose of agonistic 4-1BB monoclonal antibody (㎃b) that results in optimal T cell activation. Methods: Cancer was induced in mice by an intrahepatic parenchymal injection of 1×10? cells of CT26 cells. Cancer-carrying mice (n=84) were divided into seven groups and treated with either rat IgG or agonistic 4-1BB monoclonal antibody (㎃b) (5㎍, 10㎍, 20㎍, 100㎍, 200㎍, or 300㎍). All treatments were administered intraperitoneally on days 7, 9, and 11. Mice from each group were sacrificed on days 14, 28, and 42. Harvested livers were weighed and the numbers of T cells in the splenocytes were analyzed with a FACS Vantage flow cytometer. Results: Liver weights increased when 5㎍ of agonistic 4-1BB ㎃b was administered, but showed no additional weight increase for doses greater than 10㎍. The absolute numbers of CD4＋ and CD8＋ T cells increased in groups treated with low doses of agonistic 4-1BB ㎃b (5㎍, 10㎍, or 20㎍), but did not increase in the groups treated with high doses of ㎃b (100㎍, 200㎍, or 300㎍). The levels of CD4/annexin V and CD8/annexin V increased as the dose increased, and the absolute cell numbers of CD4/annexin V were greater than those of CD8/annexin V. Conclusion: Liver weight, including the cancer mass, failed to increase at agonistic 4-1BB ㎃b doses greater than 10㎍. A high dose (≥100㎍) of agonistic 4-1BB ㎃b resulted in lower counts of absolute T cells. This study suggests that a low dose (20㎍) of agonistic 4-1BB ㎃b can be used for optimal T cell activation in combination with other anti-cancer treatments.
Soluble precursors of 2,3-naphthalocyanine and phthalocyanine for use in thin film transistors (2008)

Soluble precursors of 2,3-naphthalocyanine (Nc) and phthalocyanine (Pc) were prepared and were converted into insoluble semiconducting thin films of Pc and Nc by heating after fabrication via spin-coating.
Molecular characterization H. pylori associated with cytotoxicity and duodenal ulcer (1993)

Helicobacter pylori has been associated with gastritis, peptic ulcer, and gastric adenocarcinoma. We report the nucleotide sequence and expression of an immunodominant antigen of H. pylori and the immune response to the antigen during disease. The antigen, named CagA (cytotoxin-associated gene A), is a hydrophilic, surface-exposed protein of 128 kDa produced by most clinical isolates. The size of the cagA gene and its protein varies in different strains by a mechanism that involves duplication of regions within the gene. Clinical isolates that do not produce the antigen do not have the gene and are unable to produce an active vacuolating cytotoxin. An ELISA to detect the immune response against a recombinant fragment of this protein detects 75.3% of patients with gastroduodenal diseases and 100% of patients with duodenal ulcer (P &amp;lt; 0.0005), suggesting that only bacteria harboring this protein are associated with disease.