gebhart/patrepeval huggingface dataset:
Preliminary report for analysis of genome wide mutations from four ciprofloxacin resistant B. anthracis Sterne isolates generated by Illumina, 454 sequencing and microarrays for DHS (2011)

The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. As the result of a different DHS project, we have selected for and isolated a large number of ciprofloxacin resistant B. anthracis Sterne isolates. These isolates vary in the concentrations of ciprofloxacin that they can tolerate, suggesting multiple mutations in the samples. In collaboration with University of Houston, Eureka Genomics and Oak Ridge National Laboratory, we analyzed the ciprofloxacin resistant B. anthracis Sterne isolates by microarray hybridization, Illumina and Roche 454 sequencing to understand the error rates and sensitivity of the different methods. The report provides an assessment of the results and a complete set of all protocols used and all data generated along with information to interpret the protocols and data sets.
Practical operation range improvement of Voltage-Sourced Converter based STATCOM (2012)

Voltage-Sourced Converter (VSC) based STATCOM is used for voltage regulation in transmission and distribution systems. In order to lower the STATCOM losses and total system loss, switching devices in “angle controlled” STATCOM are fired once with the line frequency (50/60 Hz). Despite the superior features on voltage waveform quality and efficiency, the practical angle controlled STATCOMs suffer from the over current and possible saturation of the interfacing transformers caused by negative sequence generated by system faults and disturbances. In this paper, the current control scheme and Instantaneous Phase-Locked Loop (IPLL) for an “angle controlled” STATCOM are presented. From power electronic point of view, IPLL prevents over-current in the VSC under system faults and bus voltage distortions. The current control can further improve STATCOM operation with higher percentages of negative sequence voltage. In addition to improved system performance under fault, the system can be installed with regular transformers, not custom-designed or over-rated transformers. RTDS (Real Time Digital Simulator) results verify the applicability of the proposed IPLL based control methods.
Multidetector computed tomography for characterization of calcium deposits in reperfused myocardial infarction (2009)

64-slice MDCT has the potential to demonstrate the progression and regression of calcium deposits, interstitial edema, and infarction. The presence of calcium deposits was transient and associated with reperfused recent infarction. The extent of calcium deposits was positively correlated with infarction size and negatively with global left-ventricular function.
Specifying Functional Requirements and QoS Parameters for IoT Systems (2017)

The Internet of Things (IoT) has emerged as a new paradigm aimed at providing systems for monitoring and controlling of physical entities. As with other application domains, the ultimate goal of an IoT system is to address the requirements elicited from its various stakeholders. However, the specification of requirements for IoT systems is a non-trivial task. First, there is a reasonable potential for conflicts across stakeholders' requirements. Second, regarding the multi-layered architecture of IoT, the specification of requirements of lower layers may influence on the requirements specification regarding upper layers. Without support for conceiving a precise requirements model serving as the basis for the IoT system design, there is a considerable risk that the stakeholders' concerns will not be addressed properly. The objective of this study is to investigate how multiple stakeholders' requirements can be precisely specified in a requirements model, considering conflicts and influences. In this sense, we propose a modeling language, named as IoT-RML, which provide means for conceiving requirements models for IoT systems.
Evaluation of a multiplexed oligonucleotide ligation assay for SARS-CoV-2 variant identification (2023)

This multiplexed oligonucleotide ligation assays demonstrated accurate SARS-CoV-2 variant typing compared to whole genome sequencing. Such an approach has the potential to provide improved turnaround compared to sequencing and more detailed mutation coverage than RT-qPCR.
Tissue factor cytoplasmic domain exacerbates post-infarct left ventricular remodeling via orchestrating cardiac inflammation and angiogenesis (2021)

Abstract Introduction The coagulation protein tissue factor (TF) regulates inflammation and angiogenesis via its cytoplasmic domain in infection, cancer and diabetes. While TF is highly abundant in the heart and implicated in cardiac injuries and dysfunction, the contribution of its cytoplasmic domain in cardiac pathology remains unclear. Purpose We aimed to investigate the contribution of the cytoplasmic domain of TF to post-infarct myocardial injury and adverse left ventricular (LV) remodeling. Methods and results Myocardial infarction was induced by permanent occlusion of the left anterior descending coronary artery. Male mice with C57BL/Jax background were used for the study. Compared with wild-type mice, mice lacking the TF cytoplasmic domain (TFΔCT) had a higher survival rate (90.5% versus 70%, p=0.0298) during a 28-day follow-up after myocardial infarction. Among surviving mice, TFΔCT mice had better cardiac function and less LV remodeling (ESV: 114.5±13.1mL for WT, 67.06±10.8mL for TFΔCT, p&amp;lt;0.001; EDV: 146.6±12.4mL for WT, 99.97±11.71mL for TFΔCT, p&amp;lt;0.001) than wild-type mice. Bone marrow chimerism indicated that deletion of the TF cytoplasmic domain in either bone marrow-derived cells or cardiac resident cells could alleviate post-infarct cardiac dysfunction. Speckle-tracking strain analysis revealed that the overall improvement of post-infarct cardiac performance in TFΔCT mice was attributed to reduced myocardial deformation in the peri-infarct region (strain-%: 11.14±0.97 for WT, 15.34±1.10 for TFΔCT, p=0.007; strain rate-/s: 3.89±0.26 for WT, 5.18±0.21 for TFΔCT, p=0.0005). Histological analysis demonstrated that TFΔCT hearts had in the infarct area greater proliferation of endothelial cells and myofibroblasts accompanied with better scar formation. Compared with wild-type hearts, infarcted TFΔCT hearts showed less infiltration of proinflammatory cells with concomitant lower expression of protease-activated receptor-1 (PAR1)-Rac1 axis. Furthermore, infarcted TFΔCT hearts presented markedly higher peri-infarct vessel density associated with enhanced endothelial cell proliferation and higher expression of PAR2 and PAR2-associated pro-angiogenic pathway factors. Conclusions Our findings demonstrate that the TF cytoplasmic domain exacerbates post-infarct cardiac injury and adverse LV remodeling via differential regulation of inflammation and angiogenesis. Targeted inhibition of the TF cytoplasmic domain-mediated intracellular signaling may ameliorate post-infarct LV remodeling without perturbing coagulation. Funding Acknowledgement Type of funding sources: Public Institution(s). Main funding source(s): National University Health System of Singapore
A new spectrally sharpened sensor basis to predict color naming, unique hues, and hue cancellation (2012)

When light is reflected off a surface, there is a linear relation between the three human photoreceptor responses to the incoming light and the three photoreceptor responses to the reflected light. Different colored surfaces have different linear relations. Recently, Philipona and O'Regan (2006) showed that when this relation is singular in a mathematical sense, then the surface is perceived as having a highly nameable color. Furthermore, white light reflected by that surface is perceived as corresponding precisely to one of the four psychophysically measured unique hues. However, Philipona and O'Regan's approach seems unrelated to classical psychophysical models of color constancy. In this paper we make this link. We begin by transforming cone sensors to spectrally sharpened counterparts. In sharp color space, illumination change can be modeled by simple von Kries type scalings of response values within each of the spectrally sharpened response channels. In this space, Philipona and O'Regan's linear relation is captured by a simple Land-type color designator defined by dividing reflected light by incident light. This link between Philipona and O'Regan's theory and Land's notion of color designator gives the model biological plausibility. We then show that Philipona and O'Regan's singular surfaces are surfaces which are very close to activating only one or only two of such newly defined spectrally sharpened sensors, instead of the usual three. Closeness to zero is quantified in a new simplified measure of singularity which is also shown to relate to the chromaticness of colors. As in Philipona and O'Regan's original work, our new theory accounts for a large variety of psychophysical color data.
Effective ice model for under-ice propagation using the fluid-fluid parabolic equation (2013)

An approach is presented to permit efficient computation of the waterborne acoustic field in the presence of sea ice. The range-dependent wide-angle parabolic equation (PE) is used to model the acoustic field with a hard, lower-density layer (ice) placed above the ocean and seafloor. The ice layer is characterized by its thickness, compressional speed, density, and attenuation. Acoustic loss due to sea ice is primarily driven by conversion to shear waves, and in this model the effect will be approximated by attenuation within the ice layer. Rough interface scattering at the air-ice and ice-water interfaces will be handled by generating range-dependent realizations from a data-derived ice thickness model. An inversion for ice parameters is conducted using the work of Jin et al. [J. Acoust. Soc. Am. 96(5)] and by matching the transmission loss of Diachok [J. Acoust. Soc. Am. 59(5)]. Model-data comparisons between this three-layer PE and measurements the taken in the Fram Strait in 2010 and in the Canada Basin in 2011 will be presented.
Bayesian dropout approximation in deep learning neural networks: analysis of self-aligned quadruple patterning (2020)

Predictive modeling of the pitch-walk variance from multistep coupled processes, such as SAQP using experimental metrology observables, has the potential to give both deep understanding and a control mechanism for pitch-walk variance. In this study, with the Bayesian dropout approximation, a methodology using Bayesian inference via use of stochastic neural networks was employed to both model and predict the SAQP pitch-walk variance distribution. Bayesian neural networks were implemented as variational ensembles of networks with hidden layers, where the neural net training uses conventional dropout, while the forward solves employ a dropout Bayesian vector methodology previously developed by Gal and Ghahramani.<sup>1, 2</sup> An important distinction here is that the forward propagations effectively sample the network to make a prediction, resulting in a distribution of outputs achieving the best model, not just a single expectation value. A complete dataset of fin module OCD metrology measurements per chip at top mandrel, bottom mandrel, and final fin reveal were used. Since the measured dataset was limited to small number chip locations, data augmentation with the highly efficient method of the volume of simplex was used to generate 30K samples. The synthetic data and the experimental data were used for neural network calibration and validation, respectively.
Particle Cleaning of EUV Reticles (2009)

Due to absorption of EUV light, EUV reticles are not likely to have pellicles for particulate contamination protection, thus even nanosize particles on the reticle could result in fatal defects in every printed die. Consequently, measures must be taken to detect and remove particles above a certain critical size that are deposited on the reticle in the course of its use. In this paper we first present the very stringent requirements that a cleaning technique must satisfy in order to be employed for EUV reticle cleaning. The main challenges consist in the capability of removing very small particles (sub-100 nm), in principle of any type (organic/inorganic) and without damage to the reticle. We then focus on two of the techniques that we are investigating, laser shockwave cleaning (LSC) and high voltage cleaning (HVC). Both of them are dry techniques, which is a necessary requirement in view of their potential integration in the lithography tool. We finally present cleaning and damage tests results, including cleaning of 40-nm polystyrene-latex (PSL) spheres on large areas.
Color Homography (2016)

We show the surprising result that colors across a change in viewing condition (changing light color, shading and camera) are related by a homography. Our homography color correction application delivers improved color fidelity compared with the linear least-square.
MR Imaging of Spatial Extent of Microvascular Injury in Reperfused Ischemically Injured Rat Myocardium: Value of Blood Pool Ultrasmall Superparamagnetic Particles of Iron Oxide (2002)

Clariscan has potential for estimating the spatial extent of microvascular injury in ischemically injured myocardium and may be useful as a marker of microvascular injury after thrombolytic therapy.
A 0.18 μm BiCMOS technology featuring 120/100 GHz (f/sub T//f/sub max/) HBT and ASIC-compatible CMOS using copper interconnect (2002)

A BiCMOS technology is presented that integrates a high performance NPN (f/sub T/=120 GHz and f/sub max/=100 GHz), ASIC compatible 0.11 /spl mu/m L/sub eff/ CMOS, and a full suite of passive elements. Significant HBT performance enhancement compared to previously published results has been achieved through further collector and base profile optimization guided by process and device simulations. Base transit time reduction was achieved by simultaneously increasing the Ge ramp and by limiting the base diffusion with the addition of carbon doping to SiGe epitaxial base. This paper describes IBM's next generation SiGe BiCMOS production technology targeted at the communications market.
Screening for Cancer Genetic Syndromes With a Simple Risk-Assessment Tool in a Community-Based Open-Access Colonoscopy Practice (2016)

Gunaratnam, Naresh T MD; Akce, Mehmet MD; Al Natour, Riad MD; Bartley, Angela N MD; Fioritto, Ann F BS; Hanson, Kristen MS, CGC; Ladabaum, Uri MD, MS Author Information
Gentlemen Capitalists: British Imperialism, in South East Asia, 1770–1890. By Anthony Webster. International Library of Historical Studies, vol. 9. London: Tauris Academic Studies, 1998. vi, 282 pp. $59.50 (cloth). (2001)

Book Review| August 01 2001 Gentlemen Capitalists: British Imperialism, in South East Asia, 1770–1890 Gentlemen Capitalists: British Imperialism, in South East Asia, 1770–1890. By Anthony Webster. International Library of Historical Studies, vol. 9. London: Tauris Academic Studies, 1998. vi, 282 pp. $59.50 (cloth). Kenneth R. Hall Kenneth R. Hall Ball State University Search for other works by this author on: This Site Google Journal of Asian Studies (2001) 60 (3): 928–929. https://doi.org/10.2307/2700178 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Permissions Cite Icon Cite Search Site Citation Kenneth R. Hall; Gentlemen Capitalists: British Imperialism, in South East Asia, 1770–1890. Journal of Asian Studies 1 August 2001; 60 (3): 928–929. doi: https://doi.org/10.2307/2700178 Download citation file: Zotero Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search Books & JournalsAll JournalsJournal of Asian Studies Search Advanced Search Copyright © The Association for Asian Studies, Inc. 20012001 Article PDF first page preview Close Modal You do not currently have access to this content.
Effect of tank size on kLa and mixing time in aerated stirred reactors with non‐newtonian fluids (2011)

Abstract The most important scale‐up parameters of aerated bioreactors are investigated in 42 and 340 L vessels, with water and various xanthan gum and carboxymethyl cellulose solutions. The study focuses mainly on mass transfer ( k L a ) measurements under various operating conditions. The relevance of existing correlations is discussed. The traditional viscosity‐contribution approach appears unable to predict the changes in k L a during scale‐up and an alternative formulation is proposed. The effect of rheology on power consumption and mixing time is in fair agreement with works published on this topic.
The OME Framework for genome-scale systems biology (2014)

The life sciences are undergoing continuous and accelerating integration with computational and engineering sciences. The biology that many in the field have been trained on may be hardly recognizable in ten to twenty years. One of the major drivers for this transformation is the blistering pace of advancements in DNA sequencing and synthesis. These advances have resulted in unprecedented amounts of new data, information, and knowledge. Many software tools have been developed to deal with aspects of this transformation and each is sorely needed. However, few of these tools have been forced to deal with the full complexity of genome-scale models along with high throughput genome-scale data. This particular situation represents a unique challenge, as it is simultaneously necessary to deal with the vast breadth of genome-scale models and the dizzying depth of high-throughput datasets. It has been observed time and again that as the pace of data generation continues to accelerate, the pace of analysis significantly lags behind. It is also evident that, given the plethora of databases and software efforts, it is still a significant challenge to work with genome-scale metabolic models, let alone next-generation whole cell models. We work at the forefront of model creation and systems scale data generation. The OME Framework was borne out of a practical need to enable genome-scale modeling and data analysis under a unified framework to drive the next generation of genome-scale biological models. Here we present the OME Framework. It exists as a set of Python classes. However, we want to emphasize the importance of the underlying design as an addition to the discussions on specifications of a digital cell. A great deal of work and valuable progress has been made by a number of communities towards interchange formats and implementations designed to achieve similar goals. While many software tools exist for handling genome-scale metabolic models or for genome-scale data analysis, no implementations exist that explicitly handle data and models concurrently. The OME Framework structures data in a connected loop with models and the components those models are composed of. This results in the first full, practical implementation of a framework that can enable genome-scale design-build-test. Over the coming years many more software packages will be developed and tools will necessarily change. However, we hope that the underlying designs shared here can help to inform the design of future software.
Spontaneous Ionization of a Hydrogen Atom in an Electric Field. I (1971)

The time-independent Schrödinger equation expressed in parabolic coordinates for a hydrogen atom in an electric field was numerically integrated for the state n = 5, n1 = 3, n2 = 0, and m = 1 to obtain the resonance energy Er and the rate of ionization τ−1 for field intensities ranging from 8 × 105 to 11 × 105 V/cm. It is found that near the resonance energy, τ−1 varies quadratically with (E − Er)2 in accordance with the well known Weisskopf–Wigner treatment of metastable states. When E is nearly equal to Er, the wavefunction has a node at the outer turning point—no explanation is offered. At the very high field intensities considered, there was considerable difference between Er
Developmental Expression of 2489 Gene Clusters During Pig Embryogenesis: An Expressed Sequence Tag Project1 (2004)

Identification of mRNAs that are present at early stages of embryogenesis is critical for a better understanding of development. To this end, cDNA libraries were constructed from germinal vesicle-stage oocytes, in vivo-produced four-cell- and blastocyst-stage embryos, and from in vitro-produced four-cell- and blastocyst-stage embryos. Randomly picked clones (10 848) were sequenced from the 3' end and those of sufficient quality (8066, 74%) were clustered into groups of sequence similarity (>95% identity), resulting in 2489 clusters. The sequence of the longest representative expressed sequence tag (EST) of each cluster was compared with GenBank and TIGR. Scores below 200 were considered unique, and 1114 (44.8%) did not have a match in either database. Sequencing from the 5' end yielded 12 of 37 useful annotations, suggesting that one third of the 1114 might be identifiable, still leaving over 700 unique ESTs. Virtual Northerns compared between the stages identified numerous genes where expression appears to change from the germinal vesicle oocyte to the four-cell stage, from the four-cell to blastocyst stage, and between in vitro- and in vivo-derived four-cell- and blastocyst-stage embryos. This is the first large-scale sequencing project on early pig embryogenesis and has resulted in the discovery of a large number of genes as well as possible stage-specific expression. Because many of these ESTs appear to not be in the public databases, their addition will be useful for transcriptional profiling experiments conducted on early pig embryos.
Matrix-Lifting SDP for Decoding in Multiple Antenna Systems (2007)

Recently, a lot of quasi-maximum likelihood decoding methods have been introduced to solve the decoding problem in multiple antenna systems. The general method proposed in [1] has a near optimal performance for M-ary QAM or PSK constellation. The advantage of this algorithm is that it can be implemented for any constellation with an arbitrary binary labeling, say Gray labeling. However, it is more complex compared to some other methods that special-ized their algorithm for a limited scenario (also with degraded performance). In this paper, we introduce a new general algorithm based on matrix-lifting Semi-Definite Programming (SDP). The new relaxation introduces a small degradation in the performance; however, the reduction in the complexity is prohibitively large. The number of variables is decreased from O(N 2 K 2) to O((N + K) 2). Moreover, it can be implemented for any constellation and labeling method.