gebhart/patrepeval huggingface dataset:
A Taxonomy of Visual Cluster Separation Factors (2012)

Abstract We provide two contributions, a taxonomy of visual cluster separation factors in scatterplots, and an in‐depth qualitative evaluation of two recently proposed and validated separation measures. We initially intended to use these measures to provide guidance for the use of dimension reduction (DR) techniques and visual encoding (VE) choices, but found that they failed to produce reliable results. To understand why, we conducted a systematic qualitative data study covering a broad collection of 75 real and synthetic high‐dimensional datasets, four DR techniques, and three scatterplot‐based visual encodings. Two authors visually inspected over 800 plots to determine whether or not the measures created plausible results. We found that they failed in over half the cases overall, and in over two‐thirds of the cases involving real datasets. Using open and axial coding of failure reasons and separability characteristics, we generated a taxonomy of visual cluster separability factors. We iteratively refined its explanatory clarity and power by mapping the studied datasets and success and failure ranges of the measures onto the factor axes. Our taxonomy has four categories, ordered by their ability to influence successors: Scale, Point Distance, Shape, and Position. Each category is split into Within‐Cluster factors such as density, curvature, isotropy, and clumpiness, and Between‐Cluster factors that arise from the variance of these properties, culminating in the overarching factor of class separation. The resulting taxonomy can be used to guide the design and the evaluation of cluster separation measures.
AN AUTOMATED APPROACH TO EXTRACTING RIVER BANK LOCATIONS FROM AERIAL IMAGERY USING IMAGE TEXTURE (2013)

A fundamental challenge in river analysis and modelling is the lack of readily available and reliable information on river bank geometry. Traditional survey methods are expensive and time consuming and often difficult to execute in many river systems because of hazardous terrain or lack of access. However, as high quality aerial and satellite imagery becomes available for more of the globe, it is increasingly possible to extract these bank locations directly from imagery. The most direct method of doing this involves manually designating edges based on visual criterion. This, however, is often prohibitively time consuming and labour intensive, and the quality is dependent on the individual doing the task. This paper describes a quick and fully automated method for locating water surface and river banks in high resolution aerial imagery without recourse to any multispectral information, by segmenting based on the local entropy of the image. This method is demonstrated on imagery of several rivers and its advantages and limitations are discussed. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
Observation of Nonlinear Dissipation in Piezoresistive Diamond Nanomechanical Resonators by Heterodyne Down-Mixing (2013)

We report the observation of nonlinear dissipation in diamond nanomechanical resonators measured by an ultrasensitive heterodyne down-mixing piezoresistive detection technique. The combination of a hybrid structure as well as symmetry breaking clamps enables sensitive piezoresistive detection of multiple orthogonal modes in a diamond resonator over a wide frequency and temperature range. Using this detection method, we observe the transition from purely linear dissipation at room temperature to strongly nonlinear dissipation at cryogenic temperatures. At high drive powers and below liquid nitrogen temperatures, the resonant structure dynamics follows the Pol-Duffing equation of motion. Instead of using the broadening of the full width at half-maximum, we propose a nonlinear dissipation backbone curve as a method to characterize the strength of nonlinear dissipation in devices with a nonlinear spring constant.
Fracture friendly optical proximity correction (2005)

Optical Proximity Correction (OPC) improves image fidelity by adding and subtracting small enhancement shapes from the original pattern data. Although the presence of these small shapes improves the final wafer image quality, it causes an increase in total figure count, longer fracture processing time, and the introduction of sliver figures. These undesirable artifacts can have a negative impact on the mask write time and mask image quality. In this paper we outline alternative OPC treatments which reduce the additional figures produced, and make the layout configurations friendlier to the subsequent mask fabrication phase. These include the alignment of neighboring small shapes during the OPC operation, and the preservation of jog alignment during the biasing phase. Illustrations of example pattern data, and improvement results in terms of figure counts are described.
ChemInform Abstract: Monodentate Non‐C2‐symmetric Chiral N‐Heterocyclic Carbene Complexes for Enantioselective Synthesis. Cu‐Catalyzed Conjugate Additions of Aryl‐ and Alkenylsilylfluorides to Cyclic Enones. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Immediate IPTV channel leave by explicit user tracking in PON (2007)

In this paper, we propose a novel IPTV channel leave mechanism for Passive Optical Network (PON). By explicit user tracking and automatic differentiation of IGMP v2 and v3 users, the proposed mechanism can realize immediate channel leave in both Optical Line Terminal (OLT) and Optical Network Unit (ONU) while avoiding removing the channel which still has users. Simulation results show that the proposed mechanism can significantly save the bandwidth consumption during "channel surf" by users, compared to the standard IGMP timeout mechanism.
A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data (2011)

Deducing the structure of neural circuits is one of the central problems of modern neuroscience. Recently-introduced calcium fluorescent imaging methods permit experimentalists to observe network activity in large populations of neurons, but these techniques provide only indirect observations of neural spike trains, with limited time resolution and signal quality. In this work we present a Bayesian approach for inferring neural circuitry given this type of imaging data. We model the network activity in terms of a collection of coupled hidden Markov chains, with each chain corresponding to a single neuron in the network and the coupling between the chains reflecting the network’s connectivity matrix. We derive a Monte Carlo Expectation–Maximization algorithm for fitting the model parameters; to obtain the sufficient statistics in a computationally-efficient manner, we introduce a specialized blockwise-Gibbs algorithm for sampling from the joint activity of all observed neurons given the observed fluorescence data. We perform large-scale simulations of randomly connected neuronal networks with biophysically realistic parameters and find that the proposed methods can accurately infer the connectivity in these networks given reasonable experimental and computational constraints. In addition, the estimation accuracy may be improved significantly by incorporating prior knowledge about the sparseness of connectivity in the network, via standard L1 penalization methods.
Group-velocity-matched cascaded quadratic nonlinearities of femtosecond pulses in periodically poled MgO:LiNbO_3 (2003)

Large nonlinear phase shifts were generated with femtosecond pulses at 1560 nm through cascaded quadratic interactions in periodically poled MgO-doped LiNbO3. The off-diagonal component of the nonlinear coefficient was utilized for simultaneous quasi phase matching and group-velocity matching. The effective nonlinear refractive index was varied from -2.9 x 10(-14) to +3.3 x 10(-14) cm2/W by tuning the phase-mismatch conditions.
Caenorhabditis elegans Inositol 5-Phosphatase Homolog Negatively Regulates Inositol 1,4,5-Triphosphate Signaling in Ovulation (2002)

Ovulation in Caenorhabditis elegans requires inositol 1,4,5-triphosphate (IP(3)) signaling activated by the epidermal growth factor (EGF)-receptor homolog LET-23. We generated a deletion mutant of a type I 5-phosphatase, ipp-5, and found a novel ovulation phenotype whereby the spermatheca hyperextends to engulf two oocytes per ovulation cycle. The temporal and spatial expression of IPP-5 is consistent with its proposed inhibition of IP(3) signaling in the adult spermatheca. ipp-5 acts downstream of let-23, and interacts with let-23-mediated IP(3) signaling pathway genes. We infer that IPP-5 negatively regulates IP(3) signaling to ensure proper spermathecal contraction.
Uncatalyzed Preparation of α‐Amino Phosphonates under Solvent‐Free Conditions (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
A Tissue-Engineered Conduit for Peripheral Nerve Repair (1998)

A tubular nerve guidance conduit possessing the macroarchitecture of a polyfascicular peripheral nerve was created. The establishment of resident Schwann cells onto poly-L-lactic acid and polylactic-co-glycolic acid surfaces was demonstrated, and the feasibility of in vivo regeneration through the conduit was shown. It is hypothesized that these tissue-engineered devices, composed of widely used biocompatible, biodegradable polymer materials and adherent Schwann cells, will be useful in promoting both more robust and more precisely directed peripheral nerve regeneration.
Supplementary Figure 4 from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC (2023)

&lt;p&gt;Supplementary Figure 4 - PDF file 103K, Pharmacokinetic analysis of CO-1686 in nu/nu mice&lt;/p&gt;
Nausea, Vomiting and Diarrhea: An Unusual Presentation of Multiple Sclerosis (1997)

The case of a young woman who presented with nausea, vomiting and diarrhea is outlined; the etiology turned out to be a first attack of multiple sclerosis. Plausible mechanisms are discussed.
Withdrawal: Identification of tumor antigens among the HLA peptidomes of glioblastoma tumors and plasma. (2019)

The original version of this article was withdrawn by the authors. An error was discovered in the creation of the protein database file that was used for searching, which led to some incorrect associations between peptides and proteins. A corrected version of the manuscript has been supplied which contains the very similar peptide identifications as the original, but the resulting number of proteins in various categories has now changed, and as a result some of the figures and supplementary files have changed also. The underlying conclusions of this study, however, remain unaltered.
NFV Service Federation: enabling Multi-Provider eHealth Emergency Services (2020)

One of the key challenges in developing 5G/6G is to offer improved vertical service support providing enlarged service flexibility, coverage and connectivity while enhancing the business relations among different stakeholders. To address this challenge, Network Service Federation (NSF) is a required feature to enable the deployment and the management of vertical services that may span multiple provider domains owned by different operators and/or service providers. In this demonstration, we show our proposed NSF solution to dynamically deploy an eHealth network service across multiple provider domains at different locations.
A Call for Clinical Studies (2014)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTA Call for Clinical StudiesWarren C. W. ChanCite this: ACS Nano 2014, 8, 5, 4055–4057Publication Date (Web):May 27, 2014Publication History Published online27 May 2014Published inissue 27 May 2014https://pubs.acs.org/doi/10.1021/nn5026466https://doi.org/10.1021/nn5026466editorialACS PublicationsCopyright © 2014 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1195Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (2 MB) Get e-AlertscloseSUBJECTS:Bioengineering and biotechnology,Nanomedicine,Nanoscience,Nanotechnology,Pharmaceutics Get e-Alerts
A bidirectional coherent acoustic communication system for underwater vehicles (2002)

An acoustic modem for bidirectional communication with an unmanned underwater vehicle has been developed and installed on the Florida Atlantic University Ocean Explorer. The modem is used to test and demonstrate two-way phase-coherent communications between surface platforms and AUVs. However, in addition to serving as a testbed for investigating specific issues associated with high-rate vehicle communications, the modem has been used in actual practice to transmit vehicle status information, CTD data and compressed images to observers on the surface in near real-time. The system includes both medium frequency (2-4 kHz) and high frequency (20-30 kHz) transmission capability for short and medium range data uplink, as well as a towed array for reception at the medium frequency (MF) and a small vertical array for use at the high frequency (HF). The communication system has been tested in Florida, New England and the Bahamas where ranges of 2 km at HF and 4 km at MF have been achieved at burst rates of 6700 bps and 1670 bps respectively in water depths of 10-30 m.
Data from Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models (2023)

&lt;div&gt;Abstract&lt;p&gt;Patient-derived xenograft (PDX) and circulating tumor cell–derived explant (CDX) models are powerful methods for the study of human disease. In cancer research, these methods have been applied to multiple questions, including the study of metastatic progression, genetic evolution, and therapeutic drug responses. As PDX and CDX models can recapitulate the highly heterogeneous characteristics of a patient tumor, as well as their response to chemotherapy, there is considerable interest in combining them with next-generation sequencing to monitor the genomic, transcriptional, and epigenetic changes that accompany oncogenesis. When used for this purpose, their reliability is highly dependent on being able to accurately distinguish between sequencing reads that originate from the host, and those that arise from the xenograft itself. Here, we demonstrate that failure to correctly identify contaminating host reads when analyzing DNA- and RNA-sequencing (DNA-Seq and RNA-Seq) data from PDX and CDX models is a major confounding factor that can lead to incorrect mutation calls and a failure to identify canonical mutation signatures associated with tumorigenicity. In addition, a highly sensitive algorithm and open source software tool for identifying and removing contaminating host sequences is described. Importantly, when applied to PDX and CDX models of melanoma, these data demonstrate its utility as a sensitive and selective tool for the correction of PDX- and CDX-derived whole-exome and RNA-Seq data.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Implications:&lt;/b&gt; This study describes a sensitive method to identify contaminating host reads in xenograft and explant DNA- and RNA-Seq data and is applicable to other forms of deep sequencing. &lt;i&gt;Mol Cancer Res; 15(8); 1012–6. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Dehydration Field Tests on Draugen (1998)

Abstract Tests were carried out to investigate the potential of new Zeta Dynamics internals for the optimisation of the water handling capacity of the Draugen primary separators. To this end these new internals were installed in the Draugen test separator and an assessment was made of its separation performance before as well as after the installation. Since the production at Draugen is still practically dry, the advent of water production was simulated by flowing heated seawater through the separator. The tests were carried out on the wellstream of one of the horizontal platform wells, and water was injected upstream of the choke valve using the high mixing intensity in the valve to disperse the water in the crude. The tests consisted of varying the crude and water flow, and measuring the distribution of water and oil upstream, inside and downstream of the separator, via sampling and radiological techniques. It could be concluded that the modification of the separator internals has not led to an obvious breakthrough in separation performance. The new internals improve the flow distribution, as claimed by the vendor. This appears from the sharper interfaces in the tests after the modification, and from the reduced spread in the residence time distributions. However, the new inlet internal has a negative effect on the phase distribution of the incoming feed. This appears from the increasing mixing of gas, crude and water in the separator with increasing flowrate, this despite the simultaneously decreasing stability of the crude/water dispersion and the existing gas/liquid stratification at the inlet. It can be conjectured that the originally installed Shell 'Schoepentoeter' inlet gives less resistance to the flow and may even favour coalescence and preseparation due to centrifugal acceleration. The test results show that the size of the water droplets at the inlet is correlated with the water concentration and the pressure drop over the choke valve. However, the correlation is different from the one established from laboratory experiments, which is probably due to the different degree of premixing in both cases. The density profiles in the separator give evidence for the presence of a dispersion band, varying in size with process conditions. The predictions of separation efficiency as a function of flow rate and feed droplet size according to the SRTCA dispersion band expansion model (ref. SPE 38816) are in agreement with the test results. Finally the future dehydration capacity of the Draugen installation was estimated by combining the validated separation efficiency correlations with calculations of the droplet size expected at the prevailing operating conditions. P. 121
Preparation and Faraday effect of EuS microcrystal-embedded oxide thin films (2001)

EuS microcrystal-embedded SiO2, Al2O3, and TiO2 thin films have been prepared by using rf sputtering method. X-ray diffraction analysis indicates that EuS microcrystal is precipitated as a single phase in Al2O3 and TiO2 films while precipitation of EuS is not detected in SiO2 film. Faraday effect attributable to the 4f7–4f65d transition of Eu2+ in EuS microcrystalline phase is observed in Al2O3 and TiO2 films. In particular, Faraday rotation angle observed for EuS-embedded TiO2 film is large; for instance, the magnitude of Verdet constant for as-deposited TiO2 film prepared without heating of substrate during the sputtering is 0.15 deg/cm Oe at wavelength of 700 nm. This value is larger by two orders of magnitude than those of Eu2+- or Tb3+-containing oxide glasses which show the largest Faraday rotation angle among rare-earth-containing glasses, and is comparable to the value for EuSe single crystal.
A novel TaqMan real-time PCR assay to estimate ex vivo human immunodeficiency virus type 1 fitness in the era of multi-target (pol and env) antiretroviral therapy (2003)

Despite numerous studies on human immunodeficiency virus type 1 (HIV-1) fitness, many key conceptual and technical questions are still unsolved. For example, the proper system to determine virus fitness of HIV-1 is still unknown. In this study, an assay was developed to estimate HIV-1 fitness based on growth competition experiments and TaqMan real-time PCR. This novel technique was compared with several methods (i.e. virus growth kinetics, growth competition/heteroduplex-tracking analysis and single-cycle replication capacity assay) in order to analyse the impact of various genomic regions and overall genetic background on virus fitness. HIV-1 primary isolates and three different sets of recombinant viruses [i.e. recombinant clones carrying protease (PR), reverse transcriptase (RT) or the 3' end of Gag, PR and RT (3'Gag/PR/RT), sequences amplified by PCR from the same primary isolates)] were evaluated. Here, it is demonstrated that, in spite of intrinsic differences, both growth competition/TaqMan and single-cycle replication assays detected a significant reduction in HIV-1 fitness as a consequence of drug-resistant mutations in pol. However, this new assay, based on HIV-1 isolates, may be useful to quantify replicative fitness in viruses from patients treated simultaneously with antiretroviral drugs targeting different genomic regions of HIV-1 (e.g. pol and env).
Person Re-identification in the Wild (2017)

This paper presents a novel large-scale dataset and comprehensive baselines for end-to-end pedestrian detection and person recognition in raw video frames. Our baselines address three issues: the performance of various combinations of detectors and recognizers, mechanisms for pedestrian detection to help improve overall re-identification (re-ID) accuracy and assessing the effectiveness of different detectors for re-ID. We make three distinct contributions. First, a new dataset, PRW, is introduced to evaluate Person Re-identification in the Wild, using videos acquired through six synchronized cameras. It contains 932 identities and 11,816 frames in which pedestrians are annotated with their bounding box positions and identities. Extensive benchmarking results are presented on this dataset. Second, we show that pedestrian detection aids re-ID through two simple yet effective improvements: a cascaded fine-tuning strategy that trains a detection model first and then the classification model, and a Confidence Weighted Similarity (CWS) metric that incorporates detection scores into similarity measurement. Third, we derive insights in evaluating detector performance for the particular scenario of accurate person re-ID.
Effects of disorder on magnetic vortex gyration (2011)

A vortex gyrating in a magnetic disk has two regimes of motion in the presence of disorder. At large gyration amplitudes, the vortex core moves quasi-freely through the disorder potential. As the amplitude decreases, the core can become pinned at a particular point in the potential and precess with a significantly increased frequency. In the pinned regime, the amplitude of the gyration decreases more rapidly than it does at larger precession amplitudes in the quasi-free regime. In part, this decreased decay time is due to an increase in the effective damping constant and in part due to geometric distortion of the vortex. A simple model with a single pinning potential illustrates these two contributions.
Carotid Body Denervation Markedly Improves Survival in Rats With Hypertensive Heart Failure (2017)

CBD attenuated the progression of hypertension and worsening of heart failure possibly through sympathoinhibition, and markedly improved survival in a rat model of hypertensive heart failure.