gebhart/patrepeval huggingface dataset:
Prolonging Survival of Corneal Transplantation by Selective Sphingosine-1-Phosphate Receptor 1 Agonist (2014)

Corneal transplantation is the most used therapy for eye disorders. Although the cornea is somewhat an immune privileged organ, immune rejection is still the major problem that reduces the success rate. Therefore, effective chemical drugs that regulate immunoreactions are needed to improve the outcome of corneal transplantations. Here, a sphingosine-1-phosphate receptor 1 (S1P1) selective agonist was systematically evaluated in mouse allogeneic corneal transplantation and compared with the commonly used immunosuppressive agents. Compared with CsA and the non-selective sphingosine 1-phosphate (S1P) receptor agonist FTY720, the S1P1 selective agonist can prolong the survival corneal transplantation for more than 30 days with a low immune response. More importantly, the optimal dose of the S1P1 selective agonist was much less than non-selective S1P receptor agonist FTY720, which would reduce the dose-dependent toxicity in drug application. Then we analyzed the mechanisms of the selected S1P1 selective agonist on the immunosuppression. The results shown that the S1P1 selective agonist could regulate the distribution of the immune cells with less CD4+ T cells and enhanced Treg cells in the allograft, moreover the expression of anti-inflammatory cytokines TGF-β1 and IL-10 unregulated which can reduce the immunoreactions. These findings suggest that S1P1 selective agonist may be a more appropriate immunosuppressive compound to effectively prolong mouse allogeneic corneal grafts survival.
Free energy determinants of tertiary structure and the evaluation of protein models (2000)

We develop a protocol for estimating the free energy difference between different conformations of the same polypeptide chain. The conformational free energy evaluation combines the CHARMM force field with a continuum treatment of the solvent. In almost all cases studied, experimentally determined structures are predicted to be more stable than misfolded "decoys." This is due in part to the fact that the Coulomb energy of the native protein is consistently lower than that of the decoys. The solvation free energy generally favors the decoys, although the total electrostatic free energy (sum of Coulomb and solvation terms) favors the native structure. The behavior of the solvation free energy is somewhat counterintuitive and, surprisingly, is not correlated with differences in the burial of polar area between native structures and decoys. Rather. the effect is due to a more favorable charge distribution in the native protein, which, as is discussed, will tend to decrease its interaction with the solvent. Our results thus suggest, in keeping with a number of recent studies, that electrostatic interactions may play an important role in determining the native topology of a folded protein. On this basis, a simplified scoring function is derived that combines a Coulomb term with a hydrophobic contact term. This function performs as well as the more complete free energy evaluation in distinguishing the native structure from misfolded decoys. Its computational efficiency suggests that it can be used in protein structure prediction applications, and that it provides a physically well-defined alternative to statistically derived scoring functions.
A Bayesian approach to subvoxel tissue classification in NMR microscopic images of trabecular bone (1994)

NMR microscopy is currently being used as an investigational tool for the evaluation of micromorphometric parameters of trabecular bone as a possible means to assess its strength. Since, typically, the image voxel size is not significantly smaller than individual trabecular elements, partial volume blurring can be a major complication for accurate tissue classification. In this paper, a Bayesian segmentation technique is reported that achieves improved subvoxel tissue classification. Each voxel is subdivided either into eight subvoxels twice the original resolution, or up to four subvoxels along the transaxial direction and the subvoxels optimally classified as volume blurring, the likelihood for the number of marrow subvoxels in each voxel can be computed on the basis of its measured signal. To resolve the ambiguity of the location of the marrow subvoxels, a Gibbs distribution is introduced to model the interaction between the subvoxels. Neighboring subvoxel pairs with the same tissue label are encouraged, and pairs with distinct labels are penalized. The segmentation is achieved by maximizing the a posteriori probability of the label image using the block ICM (iterative conditional mode) algorithm. The potential of the proposed technique is demonstrated in real and synthetic NMR microscopic images.
Automatic QRS detection during body surface mapping of ventricular tachycardia (1992)

A QRS detection algorithm has been developed for use in body surface mapping of ventricular tachycardia. To detect the QRS complexes the algorithm uses three computed signals: the sum of the absolute value of all leads, the sum of the absolute value of the differences of consecutive samples in all leads and, the second order derivative of the first mentioned.
Investigation of the N-BP Binding at FPPS by Combined Computational Approaches (2015)

Nitrogen-containing bisphosphonates (N-BPs) are important drugs widely used in a variety of bone resorption diseases. These compounds target the farnesyl pyrophosphate synthase (FPPS), a key enzyme of the mevalonate pathway involved in several pathologies. The inhibition of FPPS is a promising pharmacological approach and the development of structure-based methods for the prediction of the enzyme-inhibitor binding energy, can provide a guide for the rational design of new N-BPs. In this study multiple docking and post-docking strategies were applied to develop an effective computational workflow able to correctly predict the binding geometry and energy of a diverse set of known N-BPs. Preliminarily, we identified a model structure of the target allowing to predict the binding pose for all studied ligands and improving the estimation of the target-ligand interaction energies. A significant correlation between calculated and experimental binding affinities was found by dividing the whole group of N-BPs inhibitors into two subsets according to the structure's size, suggesting that the contributions to the binding energy are differently weighted in the two groups and that the FPPS inhibition mechanism may be based on ligand dimensions. The obtained quantitative models can be further exploited for either screening or optimization studies of newly designed N-BPs.
Open Domain Question Answering via Semantic Enrichment (2015)

Most recent question answering (QA) systems query large-scale knowledge bases (KBs) to answer a question, after parsing and transforming natural language questions to KBs-executable forms (e.g., logical forms). As a well-known fact, KBs are far from complete, so that information required to answer questions may not always exist in KBs. In this paper, we develop a new QA system that mines answers directly from the Web, and meanwhile employs KBs as a significant auxiliary to further boost the QA performance. Specifically, to the best of our knowledge, we make the first attempt to link answer candidates to entities in Freebase, during answer candidate generation. Several remarkable advantages follow: (1) Redundancy among answer candidates is automatically reduced. (2) The types of an answer candidate can be effortlessly determined by those of its corresponding entity in Freebase. (3) Capitalizing on the rich information about entities in Freebase, we can develop semantic features for each answer candidate after linking them to Freebase. Particularly, we construct answer-type related features with two novel probabilistic models, which directly evaluate the appropriateness of an answer candidate's types under a given question. Overall, such semantic features turn out to play significant roles in determining the true answers from the large answer candidate pool. The experimental results show that across two testing datasets, our QA system achieves an 18%~54% improvement under F_1 metric, compared with various existing QA systems.
Underwater Color Restoration Using U-Net Denoising Autoencoder (2019)

Visual inspection of underwater structures by vehicles, e.g. remotely operated vehicles (ROVs), plays an important role in scientific, military, and commercial sectors. However, the automatic extraction of information using software tools is hindered by the characteristics of water which degrade the quality of captured videos. As a contribution for restoring the color of underwater images, Underwater Denoising Autoencoder (UDAE) model is developed using a denoising autoencoder with U-Net architecture. The proposed network takes into consideration the accuracy and the computation cost to enable realtime implementation on underwater visual tasks using end-to-end autoencoder network. Underwater vehicles perception is improved by reconstructing captured frames; hence obtaining better performance in underwater tasks. Related learning methods use generative adversarial networks (GANs) to generate color corrected underwater images, and to our knowledge this paper is the first to deal with a single autoencoder capable of producing same or better results. Moreover, image pairs are constructed for training the proposed network, where it is hard to obtain such dataset from underwater scenery. At the end, the proposed model is compared to a state-of-the-art method.
Web Site–Based Destination Images: A Comparison of Macau and Hong Kong (2011)

The purposes of this study were to identify and compare the image representations of Macau and Hong Kong as they are communicated on the Web. The research approach for this study collected the textual data on Macau and Hong Kong. Semantic network analysis and content analysis methods were applied to identify the image categories each city projects on the Web. t-Tests were also conducted to compare the Macau and Hong Kong image categories. The results suggest that Macau could likely transform to a mega-gaming hub with casino strips, themed properties, and entertainment complexes, a transformation that is not expected to shake the superior position of Hong Kong as a shopping paradise and conference center.
Image Deblurring Using Smartphone Inertial Sensors (2016)

Removing image blur caused by camera shake is an ill-posed problem, as both the latent image and the point spread function (PSF) are unknown. A recent approach to address this problem is to record camera motion through inertial sensors, i.e., gyroscopes and accelerometers, and then reconstruct spatially-variant PSFs from these readings. While this approach has been effective for highquality inertial sensors, it has been infeasible for the inertial sensors in smartphones, which are of relatively low quality and present a number of challenging issues, including varying sensor parameters, high sensor noise, and calibration error. In this paper, we identify the issues that plague smartphone inertial sensors and propose a solution that successfully utilizes the sensor readings for image deblurring. With both the sensor data and the image itself, the proposed method is able to accurately estimate the sensor parameters online and also the spatially-variant PSFs for enhanced deblurring performance. The effectiveness of this technique is demonstrated in experiments on a popular mobile phone. With this approach, the quality of image deblurring can be appreciably raised on the most common of imaging devices.
An Ultra-Wide Band Umbilical Cord for Cognitive Radio Systems (2006)

This paper describes how cognitive radio (CR) could benefit from software-defined radio (SDR) compatible ultra-wide band (UWB) systems. It introduces the notion of umbilical cord that can keep a CR device connected to its surrounding world, thanks to sensing and low speed over-the-air reconfiguration (OTAR) means provided by low-data rate (LDR) systems, and to fast OTAR downloading facilities based on high-data rate (HDR) hot spots. A particular UWB architecture supporting SDR-compatible technological constraints is proposed as candidate to realize this promising combination of capabilities
Mathematical modelling of calcium wave propagation in mammalian airway epithelium: evidence for regenerative ATP release (2009)

Airway epithelium has been shown to exhibit intracellular calcium waves after mechanical stimulation. Two classes of mechanism have been proposed to explain calcium wave propagation: diffusion through gap junctions of the intracellular messenger inositol 1,4,5-trisphosphate (IP3), and diffusion of paracrine extracellular messengers such as ATP. We have used single cell recordings of airway epithelium to parameterize a model of an airway epithelial cell. This was then incorporated into a spatial model of a cell culture where both mechanisms for calcium wave propagation are possible. It is shown that a decreasing return on the radius of Ca2+ wave propagation is achieved as the amount of ATP released from the stimulated cell increases. It is therefore shown that for a Ca2+ wave to propagate large distances, a significant fraction of the intracellular ATP pool would be required to be released. Further to this, the radial distribution of maximal calcium response from the stimulated cell does not produce the same flat profile of maximal calcium response seen in experiential studies. This suggests that an additional mechanism is important in Ca2+ wave propagation, such as regenerative release of ATP from cells downstream of the stimulated cell.
Distributed quantum sensing using continuous-variable multipartite entanglement (2018)

Distributed quantum sensing uses quantum correlations between multiple sensors to enhance the measurement of unknown parameters beyond the limits of unentangled systems. We describe a sensing scheme that uses continuous-variable multipartite entanglement to enhance distributed sensing of field-quadrature displacement. By dividing a squeezed-vacuum state between multiple homodyne-sensor nodes using a lossless beam-splitter array, we obtain a root-mean-square (rms) estimation error that scales inversely with the number of nodes (Heisenberg scaling), whereas the rms error of a distributed sensor that does not exploit entanglement is inversely proportional to the square root of the number of nodes (standard quantum limit scaling). Our sensor's scaling advantage is destroyed by loss, but it nevertheless retains an rms-error advantage in settings in which there is moderate loss. Our distributed sensing scheme can be used to calibrate continuous-variable quantum key distribution networks, to perform multiple-sensor cold-atom temperature measurements, and to do distributed interferometric phase sensing.
Removal of humic acid foulant from ultrafiltration membrane surface using photocatalytic oxidation process (2005)

The experimental results indicated that without the TiO2 particles and PCO treatment, the permeate flux of ultrafiltration (UF) membrane declined to 40% of the initial permeate flux after 8 hours filtration. Feeding the humic acid solution with TiO2 particles dosage of 1 g/L with calcium ions into UF membrane, after the same filtration time and PCO reaction at 120 minutes, the permeate flux was increased to about 90% of the initial permeate flux. At longer PCO reaction times, a better water quality of UF permeate was observed. It has been found that with the coexistence of calcium ions in humic acid solution, the smaller molecular fragments of humic acid (HA) generated by PCO reaction may be transferred to the surface of TiO2 by means of adsorption. The humic acid adsorption by TiO2 in the presence of Ca2+ is also pH dependent. The adsorption rates were 21.0, 14.9 and 10.8 ppmTOC/gTiO2 for pH value of 4, 7 and 10 respectively. The combination of effects of PCO mineralization of humic acid into CO2 and adsorption of humic acid by TiO2 through the forming of HA-Ca(2+)-TiO2 aggregate particles were responsible for the removal of humic acid foulant from UF membrane surface.
A 3W 55% PAE CMOS PA with Closed-Loop 20:1 VSWR Protection (2007)

A 0.25 μm 2V CMOS PA for GSM applications delivers 3W output power with 55% PAE. A closed-loop mismatch protection method is implemented that enables the PA to sustain a 20:1 load VSWR at full power. The circuit enables faster protection lock-in by reducing the number of low-frequency poles in the loop response.
Antimicrobial Activities of Pseudomonads against Plant Pathogenic Organisms and Efficacy of Pseudomonas aeruginosa ATCC7700 against Bacterial Wilt of Tomato. (1997)

Numerous strains of pseudomonads formed growth inhibition zones around their colonies which had been placed on lawns of phytopathogenic bacteria and fungi used as indicators. The antimicrobial activity spectra against the indicator bacteria and fungi varied greatly with the species and strain of the pseudomonads, suggesting that various antimicrobial substances participated in the antagonism. Strain ATCC7700 of Pseudomonas aeruginosa was highly antagonistic in vitro to various plant pathogenic bacteria and fungi, especially to Ralstonia solanacearum. Treating of tomato roots with P. aeruginosa at the time of transplanting in R. solanacearum-infested soil increased the percentage of seedling survival. Soaking the root systems of tomato seedlings in a bacterial suspension of ca. 1010 cfu/ml resulted in the highest suppressiveness. Pretreating tomato roots with killed cells of P. aeruginosa also gave protection, suggesting that mechanisms other than antibiotic production, such as induced resistance and infection sites competition were involved in suppression of the disease.
Remote optical detection of biomass burning using a potassium emission signature (2002)

A remotely detectable signature for biomass burning that is specific to flaming combustion is found in the strong emission lines of potassium (K) at 766.5 nm and 769.9 nm. Ground level spectra of a test fire illustrate the high contrast signal provided by K emission. Image data collected at high altitude using the Airborne Visible Infrared Imaging Spectrometer (AVIRIS) sensor and analysed for K emission vividly displays the fire fronts of a 1995 fire in Brazil. Sensors for K emission can use silicon detector technology for advantages in high sensitivity, low cost, wide area coverage and fine spatial resolution.
Nonlinear interaction of ultrasound with an unbounded rough interface (2006)

Kissing bonds are one type of the defects in friction stir welds (FSWs), and often difficult to detect using linear ultrasound. Under the insonification of intensive ultrasound, they may show nonlinear behavior. This nonlinearity has been exploited to detect such deficient bonds. A kissing bond can be treated as an imperfect interface between rough surfaces in contact (an imperfect rough interface). Motivated by the practical problem, a theoretical model has been developed for calculating the nonlinear interaction of ultrasound with an imperfect planar rough interface. The model is established based on elastodynamic theory. It is a first-order differential equation governing the ultrasonic response of the interface (interface opening displacement). The model can be used for various planar interfaces like smooth interfaces, rough interfaces with either linear or nonlinear relation between contact force and interface opening, and rough interfaces with a hysteretic response to ultrasonic load. Analytical solutions are available for smooth interfaces, rough interfaces with linear relation between contact force and interface opening, and rough interfaces with piece-wise linear bistability (causing hysteresis). The model is applied to the prediction of experimental data from a single interface formed by compressing two copper cylinders together. The results show that the proposed model for rough surfaces may give a better prediction than Richardson's theory that is built for smooth interfaces and may give overestimation for rough interfaces.
Improving Federated Learning Personalization via Model Agnostic Meta Learning (2019)

Federated Learning (FL) refers to learning a high quality global model based on decentralized data storage, without ever copying the raw data. A natural scenario arises with data created on mobile phones by the activity of their users. Given the typical data heterogeneity in such situations, it is natural to ask how can the global model be personalized for every such device, individually. In this work, we point out that the setting of Model Agnostic Meta Learning (MAML), where one optimizes for a fast, gradient-based, few-shot adaptation to a heterogeneous distribution of tasks, has a number of similarities with the objective of personalization for FL. We present FL as a natural source of practical applications for MAML algorithms, and make the following observations. 1) The popular FL algorithm, Federated Averaging, can be interpreted as a meta learning algorithm. 2) Careful fine-tuning can yield a global model with higher accuracy, which is at the same time easier to personalize. However, solely optimizing for the global model accuracy yields a weaker personalization result. 3) A model trained using a standard datacenter optimization method is much harder to personalize, compared to one trained using Federated Averaging, supporting the first claim. These results raise new questions for FL, MAML, and broader ML research.
Protein A-Activated rat Splenic Lymphocyte Proliferation Involves Tyrosine Kinase-Phospholipase C-Protein Kinase C Pathway (2000)

Protein A (PA) of Staphylococcus aureus was long been known for its affinity towards the Fc domain of immunoglobulin G. It is now well established that PA is a potent biological response modifier showing simultaneously antitumor, antitoxic, and anticarcinogenic properties. This bacterial protein was also observed to stimulate production of cytokines. But the molecular mechanism(s) of immunocyte activation by PA still remained essentially unknown. In this report, we demonstrate a hitherto undescribed role of PA as a signal inducer in rat splenic lymphocytes. Our studies describe that PA induces transition of G0/G1 to S and G2/M phases of cell cycle, thus ultimately stimulating splenic lymphocyte proliferation. It has also been revealed that PA binds to rat splenic lymphocytes in a dose dependent manner and stimulates proliferation via tyrosine kinase-phospholipase C (PLC)-Ca2+-dependent protein kinase C (PKC) pathway. These observations will be of valid help in correlating the immunostimulatory activities of PA with the molecular mechanism(s) of its action.
GloMoSim: A Scalable Network Simulation Environment (2002)

Large-scale hybrid networks that include wireless, wired, and satellite based communications are becoming common in both military and commercial situations. This paper describes a scalable simulation environment called GloMoSim (for Global Mobile Information System Simulator) that effectively utilizes parallel execution to reduce the simulation time of detailed high-fidelity models of large communication networks. The paper also presents a set of case studies that evaluate the performance of large wireless networks with thousands of nodes and compares the impact of different lower layer protocols on the performance of typical applications. 1. Introduction High-level design problems for the digital communication infrastructure in the military and commercial environment, are extremely challenging in a number of dimensions: the scale is large, network traffic is a mix of voice, data, and imagery; connectivity can change dynamically in unpredictable ways, and the quality of service requi...