gebhart/patrepeval huggingface dataset:
Angiogenic Role of MMP‐2/9 Expressed on the Cell Surface of Early Endothelial Progenitor Cells/Myeloid Angiogenic Cells (2015)

Since the introduction of angiogenic cell therapy using early endothelial progenitor cells (EPCs), myeloid angiogenic cells (MACs) have been expected to be useful in treating ischemic diseases. In order to elucidate the angiogenic properties of MACs/EPCs, we clarified the characteristics of MACs as compared to M2 macrophages (Mϕs). Comparison of the gene expression profiles of MACs and late EPCs revealed that MACs expressed greater amounts of metalloproteinase (MMP)-9. It should be noted that the profile of MMP-2/9 expression on the cell surface of MACs was similar to that of M2 Mϕs, and that cell surface MMP-2/9 might be an active form based on molecular size. In addition, the invasion of MACs was prohibited not only by MMP-2/9 inhibitor, but also by the hyaluronidase treatment that caused the down-regulation of MMP-9 on the cell surface of MACs and inhibited their invasion activity. These results indicate that cell surface MMP-2/9 plays an important role in the high invasion ability of MACs. The conditioned medium of both MACs and M2 Mϕs stimulated tube formation of endothelial cells in vitro. MACs caused an increase in vessel formation in in vivo models through the production of IL-8. We propose that the role of MACs with cell surfaces expressing MMP-2/9 is rapidly invading ischemic tissue.
Blending Multiple Nitrogen Dioxide Data Sources for Neighborhood Estimates of Long-Term Exposure for Health Research (2017)

Exposure to traffic related nitrogen dioxide (NO<sub>2</sub>) air pollution is associated with adverse health outcomes. Average pollutant concentrations for fixed monitoring sites are often used to estimate exposures for health studies, however these can be imprecise due to difficulty and cost of spatial modeling at the resolution of neighborhoods (e.g., a scale of tens of meters) rather than at a coarse scale (around several kilometers). The objective of this study was to derive improved estimates of neighborhood NO<sub>2</sub> concentrations by blending measurements with modeled predictions in Sydney, Australia (a low pollution environment). We implemented the Bayesian maximum entropy approach to blend data with uncertainty defined using informative priors. We compiled NO<sub>2</sub> data from fixed-site monitors, chemical transport models, and satellite-based land use regression models to estimate neighborhood annual average NO<sub>2</sub>. The spatial model produced a posterior probability density function of estimated annual average concentrations that spanned an order of magnitude from 3 to 35 ppb. Validation using independent data showed improvement, with root mean squared error improvement of 6% compared with the land use regression model and 16% over the chemical transport model. These estimates will be used in studies of health effects and should minimize misclassification bias.
(±)-N-(3-Hydroxy-1,2-diphenylpropyl)-4-methylbenzenesulfonamide (2008)

In the title compound, C(22)H(23)NO(3)S, the relative stereochemistry of the two stereogenic centres is anti with respect to the H atoms. The mol-ecular packing of the crystal shows a double-strand arrangement, consisting of one strand of (S*,S*) enanti-omers and one strand of (R*,R*) enanti-omers. Both strands lie parallel to each other along the a axis. Each strand is made up of dimers in which the mol-ecules are connected to each other via an inter-molecular O-H⋯O hydrogen bond between the hydroxyl groups and an O-H⋯π inter-action with the aromatic ring. These units are then connected to neighbouring dimers via N-H⋯O hydrogen bonds and C-H⋯O interactions. Intramolecular C-H⋯O interactions are also observed.
The Anorexia Nervosa Genetics Initiative: Overview and Methods (2017)

Abstract Background: Genetic factors contribute to anorexia nervosa (AN); and the first genome-wide significant locus has been identified. We describe methods and procedures for the Anorexia Nervosa Genetics Initiative (ANGI), an international collaboration designed to rapidly recruit 13000 individuals with AN as well as ancestrally matched controls. We present sample characteristics and the utility of an online eating disorder diagnostic questionnaire suitable for large-scale genetic and population research. Methods: ANGI recruited from the United States (US), Australia/New Zealand (ANZ), Sweden (SE), and Denmark (DK). Recruitment was via national registers (SE, DK); treatment centers (US, ANZ, SE, DK); and social and traditional media (US, ANZ, SE). All cases had a lifetime AN diagnosis based on DSM-IV or ICD-10 criteria (excluding amenorrhea). Recruited controls had no lifetime history of disordered eating behaviors. To assess the positive and negative predictive validity of the online eating disorder questionnaire (ED100K-v1), 109 women also completed the Structured Clinical Interview for DSM-IV (SCID), Module H. Results: Blood samples and clinical information were collected from 13,364 individuals with lifetime AN and from controls. Online diagnostic phenotyping was effective and efficient; the validity of the questionnaire was acceptable. Conclusions: Our multipronged recruitment approach was highly effective for rapid recruitment and can be used as a model for efforts by other groups. High online presence of individuals with AN rendered the Internet/social media a remarkably effective recruitment tool in some countries. ANGI has substantially augmented Psychiatric Genomics Consortium AN sample collection. ANGI is a registered clinical trial: clinicaltrials.gov NCT01916538 ; https://clinicaltrials.gov/ct2/show/NCT01916538?cond=Anorexia+Nervosa&amp;draw=1&amp;rank=3 .
Clinical Implementation of Prostate Image Guided Radiation Therapy: A Prospective Study to Define the Optimal Field of Interest and Image Registration Technique Using Automated X-Ray Volumetric Imaging Software (2008)

Alignment of the CBCT with the reference CT is called image registration (IR). The parameters for utilizing the automated Elekta XVI IR software for IGRT of the prostate still remain to be defined. In this study, we compare several automated XVI IR parameters to manual registration to identify the optimal automated IR technique for the prostate gland. 280 prostate IRs were conducted as follows: 210 automated, and 70 manual IR were performed using 70 CBCT scans of seven patients. The three arms of the automated registrations were: (i) extended FOI/Bone + grey scale (double IR); (ii) limited FOI/GS (single IR); and (iii) extended FOI/GS (single IR). Automated IRs were compared to manual IRs; x, y, z shifts, failures, and errors recorded for off-line analysis. Based on the most successful parameters, a departmental protocol was developed and 432 automated IR were performed (on 20 patients) for analysis. Automated IR were classified as: Successful, failed, error, or unregistered. In arm 1, the rate of successful, failed, error, and unregistered IR were 52.8%, 1.5%, 8.6%, 37.1%, respectively, arm 2: 90% successful, 10% failed, arm 3: 100% successful. Using the arm 3 parameters for the 432 automated IRs, the incidence of unregistered scans was 0%, rescanning was required in 1% of treatments, and the time for performing the auto IR was < 5.5 minutes. We found that extended FOI + single (GS) IR results in shifts comparable to manual IR using automated XVI software. We experienced multiple unsuccessful registrations with the other methods. We conclude that when utilizing the Elekta XVI automated IR software, the extended FOI/single IR results in successful registrations most often. In addition, it is currently effectively used in our clinical practice.
Frequency-diverse microwave imaging using planar Mills-Cross cavity apertures (2016)

We demonstrate a frequency diverse, multistatic microwave imaging system based on a set of transmit and receive, radiating, planar cavity apertures. The cavities consist of double-sided, copper-clad circuit boards, with a series of circular radiating irises patterned into the upper conducting plate. The iris arrangement is such that for any given transmitting and receiving aperture pair, a Mills-Cross pattern is formed from the overlapped patterns. The Mills-Cross distribution provides optimum coverage of the imaging scene in the spatial Fourier domain (k-space). The Mills-Cross configuration of the apertures produces measurement modes that are diverse and consistent with the computational imaging approach used for frequency-diverse apertures, yet significantly minimizes the redundancy of information received from the scene. We present a detailed analysis of the Mills-Cross aperture design, with numerical simulations that predict the performance of the apertures as part of an imaging system. Images reconstructed using fabricated apertures are presented, confirming the anticipated performance.
Increasing GPU Translation Reach by Leveraging Under-Utilized On-Chip Resources (2021)

Many GPU applications issue irregular memory accesses to a very large memory footprint. We confirm observations from prior work that these irregular access patterns are severely bottlenecked by insufficient Translation Lookaside Buffer (TLB) reach, resulting in expensive page table walks. In this work, we investigate mechanisms to improve TLB reach without increasing the page size or the size of the TLB itself. Our work is based around the observation that a GPU’s instruction cache (I-cache) and Local Data Share (LDS) scratchpad memory are under-utilized in many applications, including those that suffer from poor TLB reach. We leverage this to opportunistically utilize idle capacity and port bandwidth from the GPU’s I-cache and LDS structures for address translations. We explore various potential architectural designs for each structure to optimize performance and minimize complexity. Both structures are organized as a victim cache between the L1 and L2 TLBs to boost translation reach. We find that our designs can increase performance on average by 30.1% without impacting the performance of applications that do not require additional reach.
RNA Cleavage Properties of Nucleobase-Specific RNase MC1 and Cusativin Are Determined by the Dinucleotide-Binding Interactions in the Enzyme-Active Site (2022)

Knowledge of the cleavage specificity of ribonucleases is critical for their application in RNA modification mapping or RNA-protein binding studies. Here, we detail the cleavage specificity and efficiency of ribonuclease MC1 and cusativin using a customized RNA sequence that contained all dinucleotide combinations and homopolymer sequences. The sequencing of the oligonucleotide digestion products by a semi-quantitative liquid chromatography coupled with mass spectrometry (LC-MS) analysis documented as little as 0.5-1% cleavage levels for a given dinucleotide sequence combination. While RNase MC1 efficiently cleaved the [A/U/C]pU dinucleotide bond, no cleavage was observed for the GpU bond. Similarly, cusativin efficiently cleaved Cp[U/A/G] dinucleotide combinations along with UpA and [A/U]pU, suggesting a broader specificity of dinucleotide preferences. The molecular interactions between the substrate and active site as determined by the dinucleotide docking studies of protein models offered additional evidence and support for the observed substrate specificity. Targeted alteration of the key amino acid residues in the nucleotide-binding site confirms the utility of this <i>in silico</i> approach for the identification of key interactions. Taken together, the use of bioanalytical and computational approaches, involving LC-MS and ligand docking of tertiary structural models, can form a powerful combination to help explain the RNA cleavage behavior of RNases.
Investigation on the Cathodic Protection Effect of Low Pressure Cold Sprayed AlZn Coating in Seawater via Numerical Simulation (2017)

Cold spray can deposit a composite coating simply by spraying mechanically-mixed Al and Zn powders, while no quantitative data has been reported on the anti-corrosion performance of different composite cold-sprayed coatings. In the present work, the finite element method was used to estimate the cathodic protection effect by simulating the potential distribution on a damaged cold-sprayed AlZn coating on Q235 steel. The results indicate that AlZn coating can only provide a limiting cathodic protection for substrate, because it can only polarize a very narrow zone negative to −0.78 V (vs. SCE, saturated calomel electrode). The remaining area of the steel substrate still has a very high residual corrosion rate. Computational methods can be used to predict the corrosion rate of AlZn coating, and the simulation results were validated by the results of a weight loss experiment.
Cellulose Reinforcement of Phenol Formaldehyde: Characterization and Chemometric Elucidation (2013)

Micro sized crystalline cellu lose was uniformly dispersed at loadings of 0, 3, 6, and 10% (by weight) in phenol formaldehyde (PF) and tested for thermal properties and shear strength. The application of cellulose into the PF matrix is considered beneficial because an increase in composite strength will allow for the reduction of petroleu m based PF utilized while simultaneously lowering overall formaldehyde concentrations. Characterization studies found this system to exh ibit cure temperatures in a very narro w temperature range regardless of cellulose loading which would assist in process changes during manufacturing; however, viscosity increases with cellulose loading was significant and could be a limit ing factor.The heat of react ion and nonlinear behavior in lap shear strength with cellulose loading suggests an interaction between cellulose and PF poly mer which appeared optimized at 3% cellu lose. Finally, utilizing novel chemo metric techniques, we were able to partition out the variation in FTIR spectra attributable to a) bulk PF cure and b) cellu lose to PF interaction.
Conditioning-specific membrane changes of rabbit hippocampal neurons measured in vitro. (1986)

Intracellular recordings were made from hippocampal CA1 pyramidal neurons within brain slices of nictitating membrane conditioned, pseudoconditioned, and naive adult male albino rabbits. All neurons included (26 conditioned, 26 pseudoconditioned, and 28 naive) had stable penetration and at least 60 mV action potential amplitudes. Mean input resistances were approximately equal to 60 mu omega for the three groups. A marked reduction in the afterhyperpolarization (AHP) following an impulse was apparent for conditioned (x = -0.98 mV) as compared to the pseudoconditioned (x = -1.7 mV) and naive (x = -2.0 mV) neurons. The AHP has been attributed previously to activation of a Ca2+-dependent outward K+ current. The distribution of AHP amplitudes for the conditioned group included a new lower range of values for which there was little overlap with the other groups. The conditioning-specific reduction of AHP may be due to reduction of ICa2+-K+ as shown previously for conditioned Hermissenda neurons. This conditioning-induced biophysical alteration of the CA1 pyramidal cell must be stored by mechanisms intrinsic to the hippocampal slice and cannot be explained as a consequence of changes of presynaptic input arising elsewhere in the brain. Our experiments demonstrate the feasibility of analyzing cellular mechanisms of associative learning in mammalian brain with the in vitro brain slice technique.
Towards Optimal Force Distribution for Walking Excavators (2015)

This paper presents the successful implementation of force control strategies on a 12 ton walking excavator to optimize the ground reaction force distribution for better stability, less terrain damage and to reduce the operation complexity. Using cleverly arrange standard industrial valve components to separately control in- and out-flow of the hydraulic cylinders, we achieve accurate and fast joint torque control purely based on pressure feedback. On the full system level, we realize an automated force distribution to adjust the center of pressure and to level out the cabin of the machine. While the operator has still full control over the excavator, this assistance system guarantees permanent ground contact and ideal force distribution among the all four wheels independent of the level of the terrain. The proposed method significantly improves operability of the walking excavator in rough terrain.
09102 Abstracts Collection – Perspectives Workshop: Naming and Addressing in a Future Internet (2011)

From 01.03. to 04.03.2009, the Perspectives Workshop 09102 ``Perspectives Workshop: Naming and Addressing in a Future Internet '' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Gut microbiota mediated the protective effects of tuna oil on collagen-induced arthritis in mice (2021)

Rheumatoid arthritis is emerging as a chronic autoimmune disease worldwide. In this study, the beneficial effects of tuna oil (TO) on collagen-induced arthritis (CIA) mice were investigated. Dietary administration of TO relieved arthritis severity and joint bone erosion, and ameliorated systemic inflammation. Furthermore, TO treatments regulated the phosphorylation of nuclear factor-kappa B (NF-κB) and Wnt1/β-catenin signaling pathways in the joint, enhanced osteoblastogenesis biomarkers and suppressed osteoclastogenesis biomarkers, and subsequently re-balanced bone remodeling. Moreover, the impaired intestinal epithelial barrier was repaired after TO treatments, along with gut microbiota modulation. By employing fecal microbiota transplantation, we clarified that the beneficial effects of TO in CIA alleviation were mediated by the modulated gut microbiota. These results indicated that gut microbiota mediated the protective effects of tuna oil on collagen-induced arthritis in mice.
Efficient CNN Building Blocks for Encrypted Data (2021)

Machine learning on encrypted data can address the concerns related to privacy and legality of sharing sensitive data with untrustworthy service providers. Fully Homomorphic Encryption (FHE) is a promising technique to enable machine learning and inferencing while providing strict guarantees against information leakage. Since deep convolutional neural networks (CNNs) have become the machine learning tool of choice in several applications, several attempts have been made to harness CNNs to extract insights from encrypted data. However, existing works focus only on ensuring data security and ignore security of model parameters. They also report high level implementations without providing rigorous analysis of the accuracy, security, and speed trade-offs involved in the FHE implementation of generic primitive operators of a CNN such as convolution, non-linear activation, and pooling. In this work, we consider a Machine Learning as a Service (MLaaS) scenario where both input data and model parameters are secured using FHE. Using the CKKS scheme available in the open-source HElib library, we show that operational parameters of the chosen FHE scheme such as the degree of the cyclotomic polynomial, depth limitations of the underlying leveled HE scheme, and the computational precision parameters have a major impact on the design of the machine learning model (especially, the choice of the activation function and pooling method). Our empirical study shows that choice of aforementioned design parameters result in significant trade-offs between accuracy, security level, and computational time. Encrypted inference experiments on the MNIST dataset indicate that other design choices such as ciphertext packing strategy and parallelization using multithreading are also critical in determining the throughput and latency of the inference process.
Anti-Allergic and Anti-Inflammatory Effects and Molecular Mechanisms of Thioredoxin on Respiratory System Diseases (2019)

<b><i>Significance:</i></b> The pathogenesis and progression of allergic inflammation in the respiratory system are closely linked to oxidative stress. Thioredoxin (TRX) is an essential redox balance regulator in organisms and is induced by various oxidative stress factors, including ultraviolet rays, radiation, oxidation, viral infections, ischemia reperfusion, and anticancer agents. <b><i>Recent Advances:</i></b> We demonstrated that systemic administration and transgenic overexpression of TRX is useful in a wide variety of <i>in vivo</i> inflammatory respiratory diseases models, such as viral pneumonia, interstitial lung disease, chronic obstructive pulmonary disease, asthma, acute respiratory distress syndrome, and obstructive sleep apnea syndrome, by removing reactive oxygen species, blocking production of inflammatory cytokines, inhibiting migration and activation of neutrophils and eosinophils, and regulating the cellular redox status. In addition, TRX's anti-inflammatory mechanism is different from the mechanisms associated with anti-inflammatory agents, such as glucocorticoids, which regulate the inflammatory reaction in association with suppressing immune responses. <b><i>Critical Issues:</i></b> Understanding the molecular mechanism of TRX is very helpful for understanding the role of TRX in respiratory diseases. In this review, we show the protective effect of TRX in various respiratory diseases. In addition, we discuss its anti-allergic and anti-inflammatory molecular mechanism in detail. <b><i>Future Directions:</i></b> The application of TRX may be useful for treating respiratory allergic inflammatory disorders. <i>Antioxid. Redox Signal</i>. 32, 785-801.
Influence of Aortocoronary Bypass Surgery on Left Ventricular Performance (1971)

Abstract Quantitative analysis of left ventricular cineangiocardiograms was performed before and after aortocoronary-vein-bypass operations for angina pectoris in 14 selected patients. Eight patients with anatomically successful results had a decrease in left ventricular end-systolic volume, and an increase in ejection fraction and the rate of circumferential fiber shortening at the ventricular equator. In two, improvement in the motion of akinetic regions of the ventricular wall was found. Six other patients had anatomically unsatisfactory results, usually because of occlusion of the graft. Ejection fraction and fiber-shortening rate fell in these, and the end-systolic volume was higher after operation. End-diastolic volume was similar in both groups and was not consistently altered by operation. In patients without severe depression of ventricular performance, ventricular function improved when the operation was technically successful. Deterioration of function accompanied graft occlusion.