gebhart/patrepeval huggingface dataset:
Link Prediction in Social Networks Using Computationally Efficient Topological Features (2011)

Online social networking sites have become increasingly popular over the last few years. As a result, new interdisciplinary research directions have emerged in which social network analysis methods are applied to networks containing hundreds millions of users. Unfortunately, links between individuals may be missing due to imperfect acquirement processes or because they are not yet reflected in the online network (i.e., friends in real world did not form a virtual connection.) Existing link prediction techniques lack the scalability required for full application on a continuously growing social network which may be adding everyday users with thousands of connections. The primary bottleneck in link prediction techniques is extracting structural features required for classifying links. In this paper we propose a set of simple, easy-to-compute structural features that can be analyzed to identify missing links. We show that a machine learning classifier trained using the proposed simple structural features can successfully identify missing links even when applied to a hard problem of classifying links between individuals who have at least one common friend. A new friends measure that we developed is shown to be a good predictor for missing links and an evaluation experiment was performed on five large social networks datasets: Face book, Flickr, You Tube, Academia and The Marker. Our methods can provide social network site operators with the capability of helping users to find known, offline contacts and to discover new friends online. They may also be used for exposing hidden links in an online social network.
The Random Cluster Model for Robust Geometric Fitting (2014)

Random hypothesis generation is central to robust geometric model fitting in computer vision. The predominant technique is to randomly sample minimal subsets of the data, and hypothesize the geometric models from the selected subsets. While taking minimal subsets increases the chance of successively "hitting" inliers in a sample, hypotheses fitted on minimal subsets may be severely biased due to the influence of measurement noise, even if the minimal subsets contain purely inliers. In this paper we propose Random Cluster Models, a technique used to simulate coupled spin systems, to conduct hypothesis generation using subsets larger than minimal. We show how large clusters of data from genuine instances of the model can be efficiently harvested to produce accurate hypotheses that are less affected by the vagaries of fitting on minimal subsets. A second aspect of the problem is the optimization of the set of structures that best fit the data. We show how our novel hypothesis sampler can be integrated seamlessly with graph cuts under a simple annealing framework to optimize the fitting efficiently. Unlike previous methods that conduct hypothesis sampling and fitting optimization in two disjoint stages, our algorithm performs the two subtasks alternatingly and in a mutually reinforcing manner. Experimental results show clear improvements in overall efficiency.
Novel Characterization of Lymphatic Valve Formation during Corneal Inflammation (2011)

Lymphatic research has progressed rapidly in recent years. Though lymphatic dysfunction has been found in a wide array of disorders from transplant rejection to cancer metastasis, to date, there is still little effective treatment for lymphatic diseases. The cornea offers an optimal site for lymphatic research due to its accessible location, transparent nature, and lymphatic-free but inducible features. However, it still remains unknown whether lymphatic valves exist in newly formed lymphatic vessels in the cornea, and how this relates to an inflammatory response. In this study, we provide the first evidence showing that lymphatic valves were formed in mouse cornea during suture-induced inflammation with the up-regulation of integrin alpha 9. The number of corneal valves increased with the progression of inflammatory lymphangiogenesis. Moreover, we have detected lymphatic valves at various developmental stages, from incomplete to more developed ones. In addition to defining the average diameter of lymphatic vessels equipped with lymphatic valves, we also report that lymphatic valves were more often located near the branching points. Taken together, these novel findings not only provide new insights into corneal lymphatic formation and maturation, but also identify a new model for future investigation on lymphatic valve formation and possibly therapeutic intervention.
PULSE: Self-Supervised Photo Upsampling via Latent Space Exploration of Generative Models (2020)

The primary aim of single-image super-resolution is to construct a high-resolution (HR) image from a corresponding low-resolution (LR) input. In previous approaches, which have generally been supervised, the training objective typically measures a pixel-wise average distance between the super-resolved (SR) and HR images. Optimizing such metrics often leads to blurring, especially in high variance (detailed) regions. We propose an alternative formulation of the super-resolution problem based on creating realistic SR images that downscale correctly. We present a novel super-resolution algorithm addressing this problem, PULSE (Photo Upsampling via Latent Space Exploration), which generates high-resolution, realistic images at resolutions previously unseen in the literature. It accomplishes this in an entirely self-supervised fashion and is not confined to a specific degradation operator used during training, unlike previous methods (which require training on databases of LR-HR image pairs for supervised learning). Instead of starting with the LR image and slowly adding detail, PULSE traverses the high-resolution natural image manifold, searching for images that downscale to the original LR image. This is formalized through the “downscaling loss,” which guides exploration through the latent space of a generative model. By leveraging properties of high-dimensional Gaussians, we restrict the search space to guarantee that our outputs are realistic. PULSE thereby generates super-resolved images that both are realistic and downscale correctly. We show extensive experimental results demonstrating the efficacy of our approach in the domain of face super-resolution (also known as face hallucination). Our method outperforms state-of-the-art methods in perceptual quality at higher resolutions and scale factors than previously possible.
QSAR Accelerated Discovery of Potent Ice Recrystallization Inhibitors (2016)

Ice recrystallization is the main contributor to cell damage and death during the cryopreservation of cells and tissues. Over the past five years, many small carbohydrate-based molecules were identified as ice recrystallization inhibitors and several were shown to reduce cryoinjury during the cryopreservation of red blood cells (RBCs) and hematopoietic stems cells (HSCs). Unfortunately, clear structure-activity relationships have not been identified impeding the rational design of future compounds possessing ice recrystallization inhibition (IRI) activity. A set of 124 previously synthesized compounds with known IRI activities were used to calibrate 3D-QSAR classification models using GRid INdependent Descriptors (GRIND) derived from DFT level quantum mechanical calculations. Partial least squares (PLS) model was calibrated with 70% of the data set which successfully identified 80% of the IRI active compounds with a precision of 0.8. This model exhibited good performance in screening the remaining 30% of the data set with 70% of active additives successfully recovered with a precision of ~0.7 and specificity of 0.8. The model was further applied to screen a new library of aryl-alditol molecules which were then experimentally synthesized and tested with a success rate of 82%. Presented is the first computer-aided high-throughput experimental screening for novel IRI active compounds.
Curcumin Induces Glutathione Biosynthesis and Inhibits NF-κB Activation and Interleukin-8 Release in Alveolar Epithelial Cells: Mechanism of Free Radical Scavenging Activity (2004)

Oxidants and tumor necrosis factor-alpha (TNF-alpha) activate transcription factors such as nuclear factor-kappaB (NF-kappaB), which is involved in the transcription of proinflammatory mediators, including interleukin-8 (IL-8). Curcumin (diferuloylmethane) is a naturally occurring flavonoid present in the spice turmeric, which has a long traditional use as a chemotherapeutic agent for many diseases. We hypothesize that curcumin may possess both antioxidant and antiinflammatory properties by increasing the glutathione levels and inhibiting oxidant- and cytokine-induced NF-kappaB activation and IL-8 release from cultured alveolar epithelial cells (A549). Treatment of A549 cells with hydrogen peroxide (H2O2; 100 microM) and TNF-alpha (10 ng/ml) significantly increased NF-kappaB and activator protein-1 (AP-1) activation, as well as IL-8 release. Curcumin inhibited both H2O2- and TNF-alpha-mediated activation of NF-kappaB and AP-1, and IL-8 release. Furthermore, an increased level of GSH and glutamylcysteine ligase catalytic subunit mRNA expression was observed in curcumin-treated cells as compared with untreated cells. Curcumin interacted directly with superoxide anion (O2*-) and hydroxyl radical (*OH) as shown by electron paramagnetic resonance, quenching the interaction of the radicals with the spin trap, Tempone-H. This suggests that curcumin has multiple properties: as an oxygen radical scavenger, antioxidant through modulation of glutathione levels, and antiinflammatory agent through inhibition of IL-8 release in lung cells.
Phase-locking swallows in coupled oscillators with delayed feedback (2010)

We show that a nonlinear coupling with delayed feedback between two limit-cycle oscillators can lead to phase-locked, periodically modulated, and chaotic phase synchronization as well as to desynchronization. Parameter regions with stable phase-locked states attain the well-known form of the swallows or shrimps found and studied for nonlinear maps. We demonstrate that the swallow regions can be accompanied by a different bifurcation scenario where the periodic orbits of the phase-locked states undergo a torus bifurcation instead of a previously reported period-doubling bifurcation. This property has an impact on the spatial organization of the swallows in the parameter space. The swallow regions contribute to the synchronization domain of the considered system, and we analytically approximate the parameter synchronization threshold.
Effects of Melatonin and Haloperidol Given via Vortex Vein on the Intraocular Pressure (1993)

Melatonin injected into the vortex vein of a rabbit eye produced an increase in intraocular pressure (IOP) which lasted for up to 5 h. Injection of haloperidol caused a decrease in IOP; this effect was totally reversed by melatonin. It is probable that these effects are caused by physiological antagonisms. Injection of the mu opiate agonist (D-ala2-n-methyl-ph2-gly5-ol) enkephalin caused a decrease in the IOP of artificially ventilated rabbits and a decrease in melatonin levels in iris, iris root-ciliary body, and retina of the rabbit eye. Melatonin levels did not decrease after anesthesia with rompunketamine. It is probable that the decrease in melatonin levels is specific to certain classes of opioids, and endogenous opioids may play a role in the regulation of ocular melatonin levels and hence IOP.
ChemInform Abstract: Design and Synthesis of 2‐Cyano‐3,12‐dioxoolean‐1,9‐dien‐28‐oic Acid, a Novel and Highly Active Inhibitor of Nitric Oxide Production in Mouse Macrophages. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
DomainFlow (2013)

A scalable network with high bisection bandwidth and high availability requires efficient use of the multiple paths between pairs of end hosts. OpenFlow is an innovative technology and enables fine-grained, flow level control of Ethernet switching. However, the flow table structure defined by OpenFlow is not hardware friendly and the scalability is limited by the switch device. OpenFlow is also not sufficient for fast multipath failover. To overcome these limitations, we propose DomainFlow in which the network is split into sections and exact matches are used where possible to enable practical flow management using OpenFlow for commodity switches. We applied a prototype of DomainFlow to multipath flow management in the Virtual eXtensible LAN (VXLAN) overlay network environment. The total number of flow entries was reduced to 1/128 using currently available commodity switches, which was not possible before.
Joint Millimeter-Wave Fronthaul and OFDMA Resource Allocation in Ultra-Dense CRAN (2017)

Ultra-dense (UD) wireless networks and cloud radio access networks (CRAN) are two promising network architectures for the emerging fifth-generation wireless communication systems. By jointly employing them, a new appealing network solution is proposed in this paper, termed UD-CRAN. In a UD-CRAN, millimeter-wave (mmWave) wireless fronthaul is preferred for information exchange between the central processor and the distributed remote radio heads (RRHs), due to its lower cost and higher flexibility in deployment, compared with fixed optical links. This motivates our study in this paper on the downlink transmission in a mmWave fronthaul enabled, orthogonal frequency division multiple access (OFDMA)-based UD-CRAN. In particular, the fronthaul is shared among the RRHs via time division multiple access (TDMA), while the RRHs jointly transmit to the users on orthogonal frequency sub-channels using OFDMA. The joint resource allocation over the TDMA-based mmWave fronthaul and OFDMA-based wireless transmission is investigated to maximize the weighted sum rate of all users. Although the problem is non-convex, we propose a Lagrange duality-based solution, which can be efficiently computed with good accuracy. To further reduce the complexity, we also propose a greedy search-based heuristic, which achieves close to optimal performance under practical setups. Finally, we show the significant throughput gains of the proposed joint resource allocation approach compared with other benchmark schemes by simulations.
Anti-Apical-Membrane-Antigen-1 Antibody Is More Effective than Anti-42-Kilodalton-Merozoite-Surface-Protein-1 Antibody in Inhibiting <i>Plasmodium falciparum</i> Growth, as Determined by the In Vitro Growth Inhibition Assay (2009)

Apical membrane antigen 1 (AMA1) and the 42-kDa merozoite surface protein 1 (MSP1(42)) are leading malaria vaccine candidates. Several preclinical and clinical trials have been conducted, and an in vitro parasite growth inhibition assay has been used to evaluate the biological activities of the resulting antibodies. In a U.S. phase 1 trial with AMA1-C1/Alhydrogel plus CPG 7909, the vaccination elicited anti-AMA1 immunoglobulin G (IgG) which showed up to 96% inhibition. However, antibodies induced by MSP1(42)-C1/Alhydrogel plus CPG 7909 vaccine showed less than 32% inhibition in vitro. To determine whether anti-MSP1(42) IgG had less growth-inhibitory activity than anti-AMA1 IgG in vitro, the amounts of IgG that produced 50% inhibition of parasite growth (Ab(50)) were compared for rabbit and human antibodies. The Ab(50)s of rabbit and human anti-MSP1(42) IgGs were significantly higher (0.21 and 0.62 mg/ml, respectively) than those of anti-AMA1 IgGs (0.07 and 0.10 mg/ml, respectively) against 3D7 parasites. Ab(50) data against FVO parasites also demonstrated significant differences. We further investigated the Ab(50)s of mouse and monkey anti-AMA1 IgGs and showed that there were significant differences between the species (mouse, 0.28 mg/ml, and monkey, 0.14 mg/ml, against 3D7 parasites). Although it is unknown whether growth-inhibitory activity in vitro reflects protective immunity in vivo, this study showed that the Ab(50) varies with both antigen and species. Our data provide a benchmark for antibody levels for future AMA1- or MSP1(42)-based vaccine development efforts in preclinical and clinical trials.
Proteasome Inhibition Is Partially Effective in Attenuating Pre-Existing Immunity against Recombinant Adeno-Associated Viral Vectors (2012)

Pre-existing immunity against adeno-associated virus (AAV) remains a major challenge facing the clinical use of systemic administration of recombinant AAV vectors for the treatment of genetic and acquired diseases using gene therapy. In this study, we evaluated the potential of bortezomib (marketed under trade name Velcade) to abrogate a pre-existing immunity to AAV in mice, thereby allowing subsequent transduction by a recombinant AAV vector of the same serotype. We demonstrate that bortezomib efficiently reduces AAV-specific IgG titres and moderates the cytotoxic T cell response in mice that have a pre-existing immunity to AAV2/8. Significant depletion of AAV2/8-specific IgG-producing plasma cells in secondary lymphoid organs and bone marrow was observed. However, this inhibition of the immune response by bortezomib was insufficient to allow subsequent re-infection with a recombinant AAV vector of a similar serotype. We show that this shortcoming is probably due to the combination of residual antibody levels and the inability of bortezomib to completely deplete the memory B cells that are re-activated in response to a repeated infection with a recombinant AAV vector. Taken together, the results of this study argue for the use of immunosuppressive therapies that target both plasma and memory B cells for the efficient elimination of pre-existing immunity against AAV2/8 vectors.
Comparative Pharmacological Properties among Calcium Channel Blockers: T-Channel versus L-Channel Blockade (1998)

Calcium antagonists are potent vasodilators and are widely used in the treatment of hypertension and angina pectoris. The currently available compounds belong to three classes: (1) dihydropyridines (e.g. nifedipine, amlodipine and felodipine), (2) phenylalkylamines (e.g. verapamil) and (3) benzothiazepines (e.g. diltiazem). The three classes differ in their pharmacological profile and safety. For example, verapamil and diltiazem lower heart rate, while dihydropyridines increase it or leave it unchanged. With most of the latter compounds, a marked activation of the sympathetic nervous system has been noted. Most compounds exhibit negative inotropic effects, particularly the first-generation molecules, which is disadvantageous in patients with impaired left-ventricular function. The most common side effects of these drugs are flushing, headache and edema. With verapamil, constipation may represent a problem in certain patients. Hence, in spite of a large number of calcium antagonists available, there remains a need for new compounds with enhanced efficacy and improved tolerability. A new compound should lack any negative inotropism, avoid any increase in sympathetic outflow or heart rate and exhibit a high degree of vascular selectivity. Furthermore, a low incidence of side effects, particularly ankle edema and optimal pharmacokinetics allowing once-daily dosing would be desirable. Mibefradil is a new calcium antagonist with promising pharmacological and clinical properties. The compound has a high bioavailability, lacks negative inotropic effects at therapeutic concentrations, does not exhibit reflex tachycardia during vasodilation and actually slightly decreases heart rate. It is a potent direct vasodilator efficacious in hypertension and chronic angina pectoris, elicits endothelium-dependent relaxations and facilitates the effects of nitric oxide in vascular smooth muscle. The drug is a particularly efficacious vasodilator in intramyocardial coronary arteries which may be important for its anti-ischemic effects and the lack of steal in the coronary circulation. Furthermore, mibefradil has antiproliferative properties in human vascular smooth muscle cells in culture. As a unique property, mibefradil blocks T-type calcium channels and hence represents a new class of calcium channel blockers. In patients with hypertension, mibefradil has a high efficacy in controlling blood pressure. The drug does not cause constipation and has a low incidence of ankle edema. A large trial is under way to further delineate the properties of this new calcium antagonist in patients with heart failure.
Development and Implementation of a Web-Enabled 3D Consultation Tool for Breast Augmentation Surgery Based on 3D-Image Reconstruction of 2D Pictures (2012)

We tested our tool for 3D, Web-based, patient-specific consultation in the clinical scenario of breast augmentation. This example shows that the current state of development allows for creation of responsive and effective Web-based, 3D medical tools, even with highly complex and time-consuming computation, by off-loading them to a dedicated high-performance data center. The efficient combination of advanced technologies, based on analysis and understanding of human anatomy and physiology, will allow the development of further Web-based reconstruction and predictive interfaces at different scales of the human body. The consultation tool presented herein exemplifies the potential of combining advancements in the core areas of computer science and biomedical engineering with the evolving areas of Web technologies. We are confident that future developments based on a multidisciplinary approach will further pave the way toward personalized Web-enabled medicine.
Nonlocality of Kohn-Sham Exchange-Correlation Fields in Dielectrics (1997)

The theory of the macroscopic field appearing in the Kohn-Sham exchange-correlation potential for dielectric materials, as introduced by Gonze, Ghosez, and Godby [Phys. Rev. Lett. 78, 294 (1997)], is reexamined. It is shown that this Kohn-Sham field cannot be determined from a knowledge of the local state of the material (local crystal potential, electric field, and polarization) alone. Instead, it has an intrinsically nonlocal dependence on the global electrostatic configuration. For example, it vanishes in simple transverse configurations of a polarized dielectric, but not in longitudinal ones.
A 68-ns 4-Mbit CMOS EPROM with high-noise-immunity design (1990)

In a VLSI memory, noise generated by its own operation is a serious problem. The noise disturbs data sensing, especially in EPROMs which have a single-ended sensing scheme. To develop high-density and high-speed EPROMs, it is necessary to solve the noise problems. Incorrect EPROM functions due to the noise are discussed. High-noise-immunity circuit techniques for stable data sensing and high-speed access time are proposed. These are divided bit-line layout, reference line with dummy bit lines, and a chip-enable transition detector. Using these circuit techniques and 0.8- mu m n-well CMOS technology, a 512 K*8-b CMOS EPROM was developed. A 68-ns access time was achieved. The die size is 5.62 mm*15.30 mm, and it is assembled in a 600-mil cerdip package.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Modular Synthesis of Phenanthridine Derivatives by Oxidative Cyclization of 2‐Isocyanobiphenyls with Organoboron Reagents (2012)

Where HAS you been? A manganese-mediated annulation of 2-isocyanobiaryls with organoboronic acids is developed for the synthesis of a broad range of phenanthridine derivatives. Mechanistic studies indicate that the reaction proceeds by the intramolecular homolytic aromatic substitution (HAS) of an imidoyl radical intermediate.