gebhart/patrepeval huggingface dataset:
A Survey on Keyword and Key Phrase Extraction with Deep Learning (2019)

With the technological developments, a large amount of data has been produced. Tera bytes of data previously recorded by manpower were digitized with the use of personal computers. As a result, rapidly growing data stacks were formed, making it difficult to find information among these unanticipated data. The need to make sense of this data has made predefined statistical methods more important. It is possible to access the required information from a single document or from the document stacks by means of text mining methods. This problem, which was previously solved mostly by statistical methods or Natural Language Processing (NLP) techniques, has been started to be solved by machine learning algorithms and artificial neural networks. In recent years, deep learning, which is a specialized study area of artificial neural networks, gives better results than the current statistical and NLP methods in many problems and has provided the application of these methods in problems such as machine translation, keyword extraction and summarizing. In this study, deep learning methods used in the extraction of keywords and key phrases are examined.
Measurement and simulation based effective bandwidth estimation (2005)

Effective bandwidth represents the resource demand for network traffic to achieve its QoS goal. However, so far, the estimation of the effective bandwidth for modern Internet traffic has been difficult and inaccurate. We present a novel scheme using measurement and simulation techniques to estimate the effective bandwidth. The advantages of the scheme lie in its accuracy, its applicability to various traffic environments, and its efficiency. We describe the simulation procedure, the efficient search algorithm to lock the effective bandwidth quickly, the sample size determination algorithm, and the performance judgment policy in the simulation to guarantee the estimation accuracy. We also examine the issue of estimating the effective bandwidth of aggregate traffic from sub-aggregates, and provide an empirical formula to achieve very good accuracy.
Early Wake-Up Decision Algorithm for ONUs in TDM-PONs With Sleep Mode (2016)

Recent IEEE and ITU-T standards for time division multiplexing-passive optical networks (TDM-PONs) with sleep mode recommend that the optical line terminal (OLT) in a TDM-PON should be in charge of invoking the optical network units (ONUs) to move into the sleep state in the absence of frames. It is considered that, upon upstream frame arrival, a sleeping ONU can leave the sleep state, in which an ONU turns off its transmitter or both its transmitter and receiver, immediately, prior to its assigned sleep interval length. In this paper, we refer to this approach as immediate early wake-up (IMEW). According to the standards, the OLT may or may not allow an ONU to trigger an early wake-up function (EWF) upon the upstream frames&#x2019; arrival. If the OLT does not allow the EWF [we refer to this as not support early wake-up (NSEW)], an ONU should stay in the sleep state during its assigned sleep duration and buffer all the upstream frames while it is in this state. In IMEW, the upstream frames experience a small delay, but the ONU&#x2019;s energy consumption increases remarkably. Conversely, in NSEW, an ONU consumes less energy compared to IMEW at the price of increasing the upstream frame delay and the possibility of having its buffer overflow. In this paper, the limitations of IMEW and NSEW have motivated us to propose a novel early wake-up decision (EWuD) algorithm that aims at meeting the upstream frame delay requirement while reducing the ONUs&#x2019; energy consumption as much as possible. The role of the EWuD algorithm is to select an appropriate time for triggering EWF, taking into consideration two factors: 1) buffer overflow probability and 2) delay requirement violation of upstream frames. We evaluate EWuD performances using our TDM-PON OPNET modular-based simulation model under a wide range of scenarios. The findings demonstrate that our proposed EWuD can successfully meet the delay requirements of all upstream frames while reducing the ONUs&#x2019; energy consumption significantly.
Micronutrient dietary supplements--a new fourth approach. (2001)

Currently the three main widely used strategies to control micronutrient deficiencies are food diversification, fortification, and consumption of medicinal supplements. In Tanzania a fourth strategy has been evaluated in school children, and is to be studied in pregnant and lactating women. The dietary supplement comes in the form of a powder used to prepare a fruit flavored drink. Children consumed for six months 25 grams per school day attended, the powder being added to 200 ml of water. The dietary supplement provides between 40 and 100 percent of the RDA of 10 micronutrients, which includes iron, vitamin A and iodine. Unlike medicinal supplements it provides the multiple vitamins and minerals in physiologic, not megadoses. In a well conducted randomized double blind placebo controlled trial, a dietary supplement in the form of a fortified powder fruit drink produced statistically significant differences not only in vitamin A and iron status, but also in the growth of young school age children.
ComboNet: Combined 2D & 3D Architecture for Aorta Segmentation (2020)

3D segmentation with deep learning if trained with full resolution is the ideal way of achieving the best accuracy. Unlike in 2D, 3D segmentation generally does not have sparse outliers, prevents leakage to surrounding soft tissues, at the very least it is generally more consistent than 2D segmentation. However, GPU memory is generally the bottleneck for such an application. Thus, most of the 3D segmentation applications handle sub-sampled input instead of full resolution, which comes with the cost of losing precision at the boundary. In order to maintain precision at the boundary and prevent sparse outliers and leakage, we designed ComboNet. ComboNet is designed in an end to end fashion with three sub-network structures. The first two are parallel: 2D UNet with full resolution and 3D UNet with four times sub-sampled input. The last stage is the concatenation of 2D and 3D outputs along with a full-resolution input image which is followed by two convolution layers either with 2D or 3D convolutions. With ComboNet we have achieved $92.1\%$ dice accuracy for aorta segmentation. With Combonet, we have observed up to $2.3\%$ improvement of dice accuracy as opposed to 2D UNet with the full-resolution input image.
Monte Carlo Simulations of Absolute Binding Free Energy of Targeted Nanocarriers to Cell Surfaces (2010)

We have developed a computational methodology based on Metropolis Monte Carlo (MC) and the weighted histogram analysis method (WHAM) to calculate the absolute binding free energy between functionalized nanocarriers (NC) and endothelial cell (EC) surfaces. The binding affinities are then calculated according to the free energy landscapes. The predictions quantitatively agree with the analogous measurements of specific antibody coated NCs (100 nm in diameter) to intracellular adhesion molecule-1 (ICAM-1) expressing EC surface in in vitro cell culture experiments. We then systematically explore the effects from a broad range of experimentally tunable parameters including the antibody surface coverage σs of NC, glycocalyx in both in vivo and in vitro conditions, shear flow and NC size. The simulation results agree remarkably well with experimental data in all scenarios. Of particular biological significance, our model predicts a threshold σs value below which the NC binding affinities reduce drastically and drop lower than that of single anti-ICAM-1 molecule to ICAM-1; our results reveal that this is due to a change in the multivalency (or number of bonds formed per NC). The trend and threshold values are exactly recovered by the in vivo measurements of the endothelium targeting of NCs in the pulmonary vascular in mice [Liu et al. PNAS 107: 16530-16535 (2010)]. Increasing the shear flow rate enhances the NC binding affinities till a threshold value is reached; this quantitatively agrees with existing experiments and a novel mechanism is revealed based on our model results. On this basis, our computational protocol represents a quantitative and predictive approach for model driven design and optimization of functionalized nanocarriers in targeted vascular drug delivery.This work is supported by NIH Grants: R01-EB006818 (D.M.E.), R01-HL087036 (V.R.M.), and NSF Grant: CBET-0853389 (R.R.).
Multichannel THz line detection by a microlens array excited photoconductive antenna array (2008)

We present multichannel THz ultrashort pulse detection by a photoconductive antenna array consisting of 16 photoconductive antennas. The efficient excitation of the photoconductive antennas has been realized by a microlens array which creates 16 single spots from the exciting fs-laser beam. The detected THz signal/noise ratio has been improved by an order of magnitude in comparison to an excitation by a line focus.
Technical implementations of light sheet microscopy (2018)

Fluorescence-based microscopy is among the most successful methods in biological studies. It played a critical role in the visualization of subcellular structures and in the analysis of complex cellular processes, and it is nowadays commonly employed in genetic and drug screenings. Among the fluorescence-based microscopy techniques, light sheet fluorescence microscopy (LSFM) has shown a quite interesting set of benefits. The technique combines the speed of epi-fluorescence acquisition with the optical sectioning capability typical of confocal microscopes. Its unique configuration allows the excitation of only a thin plane of the sample, thus fast, high resolution imaging deep inside tissues is nowadays achievable. The low peak intensity with which the sample is illuminated diminishes phototoxic effects and decreases photobleaching of fluorophores, ensuring data collection for days with minimal adverse consequences on the sample. It is no surprise that LSFM applications have raised in just few years and the technique has been applied to study a wide variety of samples, from whole organism, to tissues, to cell clusters, and single cells. As a consequence, in recent years numerous set-ups have been developed, each one optimized for the type of sample in use and the requirements of the question at hand. Hereby, we aim to review the most advanced LSFM implementations to assist new LSFM users in the choice of the LSFM set-up that suits their needs best. We also focus on new commercial microscopes and "do-it-yourself" strategies; likewise we review recent designs that allow a swift integration of LSFM on existing microscopes.
Discovery and characterization of the feline miRNAome (2017)

The domestic cat is an important human companion animal that can also serve as a relevant model for ~250 genetic diseases, many metabolic and degenerative conditions, and forms of cancer that are analogous to human disorders. MicroRNAs (miRNAs) play a crucial role in many biological processes and their dysregulation has a significant impact on important cellular pathways and is linked to a variety of diseases. While many species already have a well-defined and characterized miRNAome, miRNAs have not been carefully studied in cats. As a result, there are no feline miRNAs present in the reference miRNA databases, diminishing the usefulness of medical research on spontaneous disease in cats for applicability to both feline and human disease. This study was undertaken to define and characterize the cat miRNAome in normal feline tissues. High-throughput sequencing was performed on 12 different normal cat tissues. 271 candidate feline miRNA precursors, encoding a total of 475 mature sequences, were identified, including several novel cat-specific miRNAs. Several analyses were performed to characterize the discovered miRNAs, including tissue distribution of the precursors and mature sequences, genomic distribution of miRNA genes and identification of clusters, and isomiR characterization. Many of the miRNAs were regulated in a tissue/organ-specific manner.
An overview of the biphasic dehydration of sugars to 5-hydroxymethylfurfural and furfural: a rational selection of solvents using COSMO-RS and selection guides (2020)

A wide overview of the biphasic production of 5-hydroxymethylfurfural and furfural from lignocellulosic sugars is presented together with a screening of solvents following a methodology based on COSMO-RS and section guides.
Variability of N-Terminal Probrain Natriuretic Peptide in Stable Chronic Heart Failure and Its Relation to Changes in Clinical Variables (2009)

Although other reported studies have revealed variations in the range of 80%, in this prespecified stable heart-failure population variation of NT-proBNP at 14-day, 1-month, 2-month, and 3-month follow-up was lower and was not related to renal function or weight. In view of the low index of individuality we observed, within-person variation is quite low compared to between-person variation. Consideration of these facts is important for the interpretation of clinical trials and the use of NT-proBNP in monitoring patients with heart failure.
Proteoglycan 4: From Mere Lubricant to Regulator of Tissue Homeostasis and Inflammation (2018)

Proteoglycan 4 (PRG4), first identified in synovial fluid, is an extracellular matrix structural protein in the joint implicated in reducing shear at the cartilage surface as well as controlling adhesion-dependent synovial growth and regulating bulk protein deposition onto the cartilage. However, recent evidence suggests that it can bind to and effect downstream signaling of a number of cell surface receptors implicated in regulating the inflammatory response. Therefore, we pose the hypothesis: Does PRG4 regulate the inflammatory response and maintain tissue homeostasis? Based on these novel findings implicating PRG4 as an inflammatory signaling molecule, we will present and discuss several hypotheses regarding potential mechanisms by which PRG4 may be able to regulate inflammation. If future studies can demonstrate that PRG4 is a potent inflammatory mediator, this will change current paradigms in the musculoskeletal and ophthalmological fields regarding the how the inflammatory microenvironment is regulated in these tissues and potentially others.
The influence of covalent immobilization conditions on antibody accessibility on nanoparticles (2017)

The accessibility of particle-coupled antibodies is important for many analytical applications, but comprehensive data on parameters controlling the accessibility are scarce. Here we report on the site-specific accessibility of monoclonal antibodies, immobilized on magnetic nanoparticles (500 nm) by the widely used covalent EDC coupling method, with the variation of four key coupling parameters (surface activation and immobilization pH, crosslinker and antibody concentration ratios). By developing quantitative radio-labelled assays, the number of immobilized antibodies, the Fab domain accessibility (in a sandwich immunoassay), and the Fc domain accessibility (in a Protein G assay) were determined. For sub-monolayer surface coverage, the observed numbers of accessible Fab and Fc domains are equal and scale linearly with the antibody density. For above monolayer coverage, the fractions of accessible Fab and Fc domains decrease, in an unequal manner. The results show that the antibody accessibility is primarily determined by the antibody surface density, rather than by chemical reactivity or the charge state, and that crowded conditions affect Fab and Fc accessibility in an unequal manner.
In situevaluation of the genotoxic potential of the river Nile: I. Micronucleus and nuclear lesion tests of erythrocytes ofOreochromis niloticus niloticus(Linnaeus, 1758) andClarias gariepinus(Burchell, 1822) (2011)

This study aimed to investigate the genotoxic potential of chemicals present along the course of the river Nile using frequencies of micronuclei (MN) and nuclear lesions (NL) in erythrocytes of Nile tilapia Oreochromis niloticus niloticus and African catfish Clarias gariepinus, as biomarkers. Results showed that most of the physicochemical parameters detected and heavy metal concentrations were significantly higher in the water collected from the estuaries of the river Nile compared to other sites of the upper Nile. The frequencies of MN and NL in peripheral blood erythrocytes of Nile tilapia and African catfish were significantly higher in estuary sites in Damietta and Rosetta compared to upper sites. The lowest level of genotoxicity was observed at two sites (Aswan and Kena), considered to be less contaminated. Our results suggested that higher frequencies of MN and NL determined at Damietta and Rosetta sites may be indicative of damage produced by pollutants in these areas. The most remarkable result was that MN and NL frequencies appear to be strongly related to water quality at different sites examined, indicating that MN frequencies may serve as a reliable biomarker for testing genotoxicity in situ. The positive correlation between MN and NL induction suggested that NL may be a useful complementary assay for genotoxicity analyses when fish are used as experimental animals. It was also found that seasonal variations in MN and NL frequencies might contribute to a better understanding of genotoxic responses in the field. The use of fish as indicator organisms for monitoring the presence of genotoxic-inducing contaminants in the environment seemed justified because the effects of exposure to a “complex mixture” such as river water were obtained. Nile tilapia appears to be a more suitable bioindicator species than African catfish in studying genotoxic chemical pollution in the river Nile attributed to a higher sensitivity.
Multifunctional Free-Standing Single-Walled Carbon Nanotube Films (2011)

We report a simple and rapid method to prepare multifunctional free-standing single-walled carbon nanotube (SWCNT) films with variable thicknesses ranging from a submonolayer to a few micrometers having outstanding properties for a broad range of exceptionally performing devices. We have fabricated state-of-the-art key components from the same single component multifunctional SWCNT material for several high-impact application areas: high efficiency nanoparticle filters with a figure of merit of 147 Pa(-1), transparent and conductive electrodes with a sheet resistance of 84 Ω/◻ and a transmittance of 90%, electrochemical sensors with extremely low detection limits below 100 nM, and polymer-free saturable absorbers for ultrafast femtosecond lasers. Furthermore, the films are demonstrated as the main components in gas flowmeters, gas heaters, and transparent thermoacoustic loudspeakers.
Digital still cameras (1999)

This paper presents an interpolation method for digital still cameras (DSCs) which is based on color signal correlation. The authors have developed a method of reducing aliasing by increasing the resolution of color signals in DSCs that use a single-plate charge coupled device (CCD) with a primary color filter array. The new method interpolates signals by taking advantage of the fact that color signal variations are similar to one another in a local region of an image. It selects the signal that shows the higher correlation, either in the horizontal or vertical directions, at color signal positions subject to interpolation, thus improving the color resolution. First, the effectiveness of the new method was verified using image simulation. Next, the prototype hardware was fabricated. The prototype is fitted with an original reduced instruction set computer (RISC) built-in dynamic random access memory (DRAM) for processing image signals to provide high-speed camera signal processing. The authors also confirmed that the effectiveness of the new method was also established in actual products.
Sorption, Transport, and Structural Evidence for Enhanced Free Volume in Poly(4-methyl-2-pentyne)/Fumed Silica Nanocomposite Membranes (2002)

In contrast to the performance of traditional filled polymer systems, penetrant permeability coefficients in high-free-volume, glassy poly(4-methyl-2-pentyne) (PMP) increase systematically and substantially with increasing concentration of nonporous, nanoscale fumed silica (FS). For instance, the permeability of PMP containing 40 wt % FS to methane is 2.3 times higher than that of the unfilled polymer. Gas and vapor uptake in the PMP/FS nanocomposites is essentially unaffected by the presence of up to 40 wt % FS, while penetrant diffusion coefficients increase regularly with increasing filler content. This increase in diffusivity is responsible for elevated permeability in the PMP/FS nanocomposites. The addition of FS to PMP augments the permeability of large penetrants more than that of small gases, consistent with a reduction in diffusivity selectivity. Consequently, vapor selectivity in the nanocomposites increases with increasing FS concentration. Activation energies of permeation in PMP decrease with increasing FS content, suggesting that penetrant diffusive jumps require less energy at higher filler concentrations. Positron annihilation lifetime spectroscopy (PALS) reveals that FS subtly increases the free volume in PMP available for molecular transport. The accessible free volume measured by PALS correlates favorably with relative penetrant permeability in the nanocomposites. Transmission electron microscopy confirms that the FS nanoparticles are relatively well dispersed in PMP.
The Human High Affinity Interleukin-2 Receptor (1987)

A novel human interleukin-2 (IL-2) receptor has been identified on the surface of resting and activated human T cells, B cells, and large granular lymphocytes (natural killer cells) by chemical crosslinking of 125I-IL-2. This receptor has an estimated size of 70,000 daltons, lacks reactivity with the anti-Tac antibody, and binds IL-2 with an affinity that is intermediate between the previously recognized high and low affinity forms of the IL-2 receptor. High affinity crosslinking of 125I-IL-2 results in the labeling of both the p70 protein and the Tac antigen, a well-characterized membrane IL-2 receptor, and the crosslinking to both proteins is inhibited by the anti-Tac antibody. Transfection of MLA-144 T cells, which display only intermediate affinity p70 IL-2 receptors (Kd of 0.6–1.2 nM), with the Tac cDNA reconstituted high affinity (Kd of 30–75 pM) IL-2 receptor expression in these cells. IL-2 binding to these reconstituted high affinity receptors was blocked by anti-Tac; however, this antibody did not alter IL-2 binding to the intermediate affinity p70 receptors. Similarly, high affinity IL-2 receptors were reconstituted on the “natural killer-like” YT cells which display 8,000–10,000 p70 receptors and little or no Tac by activation of Tac gene expression with forskolin or IL-1. Together, these data suggest that the high affinity IL-2 receptor corresponds to a membrane receptor complex composed of two different IL-2 binding proteins.
Image Retrieval Based on Anisotropic Scaling and Shearing Invariant Geometric Coherence (2014)

Imposing a spatial coherence constraint on image matching is becoming a necessity for local feature based object retrieval. We tackle the affine invariance problem of the prior spatial coherence model and propose a novel approach for geometrically stable image retrieval. Compared with related studies focusing simply on translation, rotation, and isotropic scaling, our approach can deal with more significant transformations including anisotropic scaling and shearing. Our contribution consists of revisiting the first-order affine adaptation approach and extending its application to represent the geometric coherence of a second-order local feature structure. We comprehensively evaluated our approach using Flickr Logos 32, Holiday, and Oxford Buildings benchmarks. Extensive experimentation and comparisons with state-of-the-art spatial coherence models demonstrate the superiority of our approach in image retrieval tasks.