gebhart/patrepeval huggingface dataset:
Cadzow’s basic algorithm, alternating projections and singular spectrum analysis (2010)

After observing a noisy time series or signal, it is common practice to try to separate the noise from the observed measurements. Singular value decomposition based methods are often used to split the observed signal into a number of components. Components associated with noise may be removed from the signal, and subsequent analyses may be undertaken. This paper will describe two methods commonly used to remove noise from a signal; the so-called singular spectrum analysis, and Cadzow's basic algorithm. Connections between both methods will be drawn, and both will be related to the method of alternating projections, and structured low rank approximation (finding a lower rank approximation of a given matrix with specified structure). A simulation study and example based on real data will highlight and explain the differences between both methods.
Investigation of Passenger Vehicle Rental Rates: Case Study in Virginia (2000)

The rental rates for centralized fleet passenger vehicles that the Virginia Department of Transportation’s (VDOT) Division of Fleet Management charges state agencies were investigated. Similar studies by Virginia’s Joint Legislative and Audit Review Commission were reviewed, Fleet Management data were analyzed, and regression analyses were performed to develop new replacement criteria and more equitable rental rates for customers. The impacts of these suggested rates on the VDOT Fleet Management budget and customers were identified.
Cooperation between Phosphorylation and Acetylation Processes in Transcriptional Control (1999)

We previously reported that the activation of the M promoter of the human choline acetyltransferase (ChAT) gene by butyrate and trapoxin in transfected CHP126 cells is blocked by PD98059, a specific mitogen-activated protein kinase kinase (MEK) inhibitor (E. Espinos and M. J. Weber, Mol. Brain Res. 56:118-124, 1998). We now report that the transcriptional effects of histone deacetylase inhibitors are mediated by an H7-sensitive serine/threonine protein kinase. Activation of the ChAT promoter by butyrate and trapoxin was blocked by 50 microM H7 in both transient- and stable-transfection assays. Overexpression of p300, a coactivator protein endowed with histone acetyltransferase activity, stimulated the ChAT promoter and had a synergistic effect on butyrate treatment. These effects were blocked by H7 and by overexpressed adenovirus E1A 12S protein. Moreover, both H7 and PD98059 suppressed the activation of the Rous sarcoma virus (RSV) and simian virus 40 promoters by butyrate in transfection experiments. Similarly, the induction of the cellular histone H1(0) gene by butyrate in CHP126 cells was blocked by H7 and by PD98059. Previous data (L. Cuisset, L. Tichonicky, P. Jaffray, and M. Delpech, J. Biol. Chem. 272:24148-24153, 1997) showed that the induction of the H1(0) gene by butyrate is blocked by okadaic acid, an inhibitor of protein phosphatases. We now show that the activation of the ChAT and RSV promoters by butyrate in transfected CHP126 cells is also blocked by 200 nM okadaic acid. Western blotting and in vivo metabolic labeling experiments showed that butyrate has a biphasic effect on histone H3 phosphorylation, i.e., depression for up to 16 h followed by stimulation. The data thus strongly suggest that the transcriptional effects of histone deacetylase inhibitors are mediated through the activation of MEK1 and of an H7-sensitive protein kinase in addition to protein phosphatases.
Quantitative Assessment of the Ischemic Brain by Means of Perfusion-Related Parameters Derived From Perfusion CT (2001)

The assessment of cerebral ischemia by means of perfusion parameters derived from perfusion CT provides valuable information to predict tissue outcome. Quantitative analyses of the severity of ischemic lesions should be implemented into the diagnostic management of stroke patients.
Revealing the genetic structure of a trait by sequencing a population under selection (2011)

One approach to understanding the genetic basis of traits is to study their pattern of inheritance among offspring of phenotypically different parents. Previously, such analysis has been limited by low mapping resolution, high labor costs, and large sample size requirements for detecting modest effects. Here, we present a novel approach to map trait loci using artificial selection. First, we generated populations of 10-100 million haploid and diploid segregants by crossing two budding yeast strains of different heat tolerance for up to 12 generations. We then subjected these large segregant pools to heat stress for up to 12 d, enriching for beneficial alleles. Finally, we sequenced total DNA from the pools before and during selection to measure the changes in parental allele frequency. We mapped 21 intervals with significant changes in genetic background in response to selection, which is several times more than found with traditional linkage methods. Nine of these regions contained two or fewer genes, yielding much higher resolution than previous genomic linkage studies. Multiple members of the RAS/cAMP signaling pathway were implicated, along with genes previously not annotated with heat stress response function. Surprisingly, at most selected loci, allele frequencies stopped changing before the end of the selection experiment, but alleles did not become fixed. Furthermore, we were able to detect the same set of trait loci in a population of diploid individuals with similar power and resolution, and observed primarily additive effects, similar to what is seen for complex trait genetics in other diploid organisms such as humans.
Understanding and Optimizing Asynchronous Low-Precision Stochastic Gradient Descent (2017)

Stochastic gradient descent (SGD) is one of the most popular numerical algorithms used in machine learning and other domains. Since this is likely to continue for the foreseeable future, it is important to study techniques that can make it run fast on parallel hardware. In this paper, we provide the first analysis of a technique called Buckwild! that uses both asynchronous execution and low-precision computation. We introduce the DMGC model, the first conceptualization of the parameter space that exists when implementing low-precision SGD, and show that it provides a way to both classify these algorithms and model their performance. We leverage this insight to propose and analyze techniques to improve the speed of low-precision SGD. First, we propose software optimizations that can increase throughput on existing CPUs by up to 11×. Second, we propose architectural changes, including a new cache technique we call an obstinate cache, that increase throughput beyond the limits of current-generation hardware. We also implement and analyze low-precision SGD on the FPGA, which is a promising alternative to the CPU for future SGD systems.
Enabling network programmability in LTE/EPC architecture using OpenFlow (2014)

Nowadays, mobile operators face the challenge to sustain the future data tsunami. In fact, today's increasing data and control traffic generated by new kinds of network usage puts strain on mobile operators', without creating any corresponding equivalent revenue. In our previous work, we analyzed the 3GPP LTE/EPC architecture and showed that a redesign of this architecture is needed to suit future network usages and to provide new revenue generating services. Moreover, we proposed a new control plane based on the OpenFlow (OF) protocol for the LTE/EPC architecture that enables flexibility and programmability aspects. In this paper, we are interested in the programmability aspect. We show how the data plane can be easily configured thanks to OF. In addition, we evaluate the signaling load of our proposed architecture and compare it to that of 3GPP LTE/EPC architecture. The preliminary findings suggest that managing the data plane with OF has little impact on the signaling load while the network programmability is improved.
Electricity market design for the prosumer era (2016)

Prosumers are agents that both consume and produce energy. With the growth in small and medium-sized agents using solar photovoltaic panels, smart meters, vehicle-to-grid electric automobiles, home batteries and other ‘smart’ devices, prosuming offers the potential for consumers and vehicle owners to re-evaluate their energy practices. As the number of prosumers increases, the electric utility sector of today is likely to undergo significant changes over the coming decades, offering possibilities for greening of the system, but also bringing many unknowns and risks that need to be identified and managed. To develop strategies for the future, policymakers and planners need knowledge of how prosumers could be integrated effectively and efficiently into competitive electricity markets. Here we identify and discuss three promising potential prosumer markets related to prosumer grid integration, peer-to-peer models and prosumer community groups. We also caution against optimism by laying out a series of caveats and complexities. Small-scale renewable energy systems and smart technologies are enabling energy consumers to become producers and service providers as well. This Perspective explores this ‘prosumption’ phenomenon, highlighting three promising prosumer market models and the challenges for future implementation.
Sensing and 3D Mapping of Soil Compaction (2008)

Soil compaction is an important physical limiting factor for the root growth and plant emergence and is one of the major causes for reduced crop yield worldwide. The objective of this study was to generate 2D/3D soil compaction maps for different depth layers of the soil. To do so, a soil penetrometer was designed, which was mounted on the three-point hitch of an agricultural tractor, consisting of a mechanical system, data acquisition system (DAS), and 2D/3D imaging and analysis software. The system was successfully tested in field conditions, measuring soil penetration resistances as a function of depth from 0 to 40 cm at 1 cm intervals. The software allows user to either tabulate the measured quantities or generate maps as soon as data collection has been terminated. The system may also incorporate GPS data to create geo-referenced soil maps. The software enables the user to graph penetration resistances at a specified coordinate. Alternately, soil compaction maps could be generated using data collected from multiple coordinates. The data could be automatically stratified to determine soil compaction distribution at different layers of 5, 10,.…, 40 cm depths. It was concluded that the system tested in this study could be used to assess the soil compaction at topsoil and the randomly distributed hardpan formations just below the common tillage depths, enabling visualization of spatial variability through the imaging software.
AccD6, a Key Carboxyltransferase Essential for Mycolic Acid Synthesis in Mycobacterium tuberculosis, Is Dispensable in a Nonpathogenic Strain (2011)

Acetyl coenzyme A carboxylase (ACC) is a key enzyme providing a substrate for mycolic acid biosynthesis. Although in vitro studies have demonstrated that the protein encoded by accD6 (Rv2247) may be a functional carboxyltransferase subunit of ACC in Mycobacterium tuberculosis, the in vivo function and regulation of accD6 in slow- and fast-growing mycobacteria remain elusive. Here, directed mutagenesis demonstrated that although accD6 is essential for M. tuberculosis, it can be deleted in Mycobacterium smegmatis without affecting its cell envelope integrity. Moreover, we showed that although it is part of the type II fatty acid synthase operon, the accD6 gene of M. tuberculosis, but not that of M. smegmatis, possesses its own additional promoter (P(acc)). The expression level of accD6(Mtb) placed only under the control of P(acc) is 10-fold lower than that in wild-type M. tuberculosis but is sufficient to sustain cell viability. Importantly, this limited expression level affects growth, mycolic acid content, and cell morphology. These results provide the first in vivo evidence for AccD6 as a key player in the mycolate biosynthesis of M. tuberculosis, implicating AccD6 as the essential ACC subunit in pathogenic mycobacteria and an excellent target for new antitubercular compounds. Our findings also highlight important differences in the mechanism of acetyl carboxylation between pathogenic and nonpathogenic mycobacterial species.
Roll‐to‐Roll Manufacturing (2018)

Roll-to-roll (R2R) manufacturing is an important manufacturing technology platform widely used for a host of applications and product categories, spanning many industries. There are two main reasons for the attractiveness and widespread use of R2R processes throughout many segments of the economy. First, such processes can readily accommodate high-volume, high-throughput operations, thus making them well suited for mass production of 2D film-type products. Second, R2R processes are highly cost effective by virtue of their high throughput and because all process steps in such operations are co-located in a single site and often conducted by a single production machine and fewer operators, unlike batch operations in which all or most process steps are performed independently from one another. The cost and overall layout of R2R operations are often dictated by health, safety, environmental, and regulatory considerations. Two elements of R2R operations that are particularly susceptible to environmental challenges are solvent coating and drying steps and some chemical vapor deposition steps involving hazardous gases or plasma.
Skeletal muscle GLUT-4 and postexercise muscle glycogen storage in humans (1996)

The purpose of this study was to examine the relationship between skeletal muscle GLUT-4 protein and postexercise glycogen storage in human subjects fed adequate carbohydrate. Eleven men completed 2 h of cycling, and a biopsy of the vastus lateralis was performed immediately after exercise cessation for the determination of muscle GLUT-4 protein and glycogen concentrations, glycogen synthase activity, and citrate synthase activity. The subjects ingested meals providing 2.0 g carbohydrate/kg body weight at 0, 2, and 4 h postexercise, and a second biopsy was performed 6 h postexercise. Muscle glycogen concentration increased significantly during the 6-h recovery period (glycogen immediately postexercise, 27.2 +/- 5.4 mmol/kg wet weight; glycogen storage, 52.4 +/- 2.9 mmol x kg wet weight-1 x 6 h-1; P<0.05). Glycogen storage during recovery was directly related to GLUT-4 protein (2.20 +/- 0.33 arbitrary standard units; r = 0.63; P<0.05) and inversely related to glycogen immediately postexercise (r = -0.70; P < 0.05). A direct correlation existed between glycogen storage during recovery and the activity of the I form of glycogen synthase (r = 0.60; P < 0.05). These results suggest that muscle GLUT-4 protein concentration, as well as factors relating to glucose disposal, may affect postexercise glycogen storage in humans fed adequate carbohydrate.
Direct Evidence for Increased Hydroxyl Radicals Originating From Superoxide in the Failing Myocardium (2000)

Experimental and clinical studies have suggested an increased production of reactive oxygen species (ROS) in the failing myocardium. The present study aimed to obtain direct evidence for increased ROS and to determine the contribution of superoxide anion (*O(2)(-)), H(2)O(2), and hydroxy radical (*OH) in failing myocardial tissue. Heart failure was produced in adult mongrel dogs by rapid ventricular pacing at 240 bpm for 4 weeks. To assess the production of ROS directly, freeze-clamped myocardial tissue homogenates were reacted with the nitroxide radical, 4-hydroxy-2,2,6, 6,-tetramethyl-piperidine-N-oxyl, and its spin signals were detected by electron spin resonance spectroscopy. The rate of electron spin resonance signal decay, proportional to *OH level, was significantly increased in heart failure, which was inhibited by the addition of dimethylthiourea (*OH scavenger) into the reaction mixture. Increased *OH in the failing heart was abolished to the same extent in the presence of desferrioxamine (iron chelator), catalase (H(2)O(2) scavenger), and 4,5-dihydroxy-1,3-benzene disulfonic acid (Tiron; LaMotte) (*O(2)(-) scavenger), indicating that *OH originated from H(2)O(2) and *O(2)(-). Further, *O(2)(-) produced in normal myocardium in the presence of antimycin A (mitochondrial complex III inhibitor) could reproduce the increase of H(2)O(2) and *OH seen in the failing tissue. There was a significant positive relation between myocardial ROS level and left ventricular contractile dysfunction. In conclusion, in the failing myocardium, *OH was produced as a reactive product of *O(2)(-) and H(2)O(2), which might play an important role in left ventricular failure.
A review of supervised machine learning algorithms (2016)

Supervised machine learning is the construction of algorithms that are able to produce general patterns and hypotheses by using externally supplied instances to predict the fate of future instances. Supervised machine learning classification algorithms aim at categorizing data from prior information. Classification is carried out very frequently in data science problems. Various successful techniques have been proposed to solve such problems viz. Rule-based techniques, Logic-based techniques, Instance-based techniques, stochastic techniques. This paper discusses the efficacy of supervised machine learning algorithms in terms of the accuracy, speed of learning, complexity and risk of over fitting measures. The main objective of this paper is to provide a general comparison with state of art machine learning algorithms.
Adaptive Feedback Compression for Joint Transmission Coordinated Multi-Point (2013)

In this paper, we study adaptive feedback compression of explicit multi-cell channel state information (CSI) for joint transmission coordinated multi-point (JT CoMP) in future mobile networks. The scheme comprises of three steps: First, the strongest cells are clustered using a network-defined threshold. Next, the strongest taps are selected using a threshold related to noise and out-of-cluster interference. Finally, adaptive quantization is applied so that the channel mean square error (MSE) remains sufficiently small. We show that the number of quantization bits grows linearly with the signal to noise ratio (SNR) in dB, as required by information theory. Results indicate that explicit CSI from all relevant cells around a terminal can be provided using fw kbits per reporting interval in 20 MHz bandwidth. The scheme is implemented and tested in real time.
The ARIES-CS Compact Stellarator Fusion Power Plant (2008)

An integrated study of compact stellarator power plants, ARIES-CS, has been conducted to explore attractive compact stellarator configurations and to define key research and development (R&D) areas. The large size and mass predicted by earlier stellarator power plant studies had led to cost projections much higher than those of the advanced tokamak power plant. As such, the first major goal of the ARIES-CS research was to investigate if stellarator power plants can be made to be comparable in size to advanced tokamak variants while maintaining desirable stellarator properties. As stellarator fusion core components would have complex shapes and geometry, the second major goal of the ARIES-CS study was to understand and quantify, as much as possible, the impact of the complex shape and geometry of fusion core components. This paper focuses on the directions we pursued to optimize the compact stellarator as a fusion power plant, summarizes the major findings from the study, highlights the key design aspects and constraints associated with a compact stellarator, and identifies the major issues to help guide future R&D.
Dynamic finite-state vector quantization of digital images (1994)

A vector quantization (VQ) scheme with finite memory called dynamic finite-state vector quantization (DFSVQ) is presented. The encoder consists of a large codebook, so called super-codebook, where for each input vector a fixed number of its codevectors are chosen to generate a much smaller codebook (sub-codebook). This sub-codebook represents the best matching codevectors that could be found in the super-codebook for encoding the current input vector. The choice for the codevectors in the sub-codebook is based on the information obtained from the previously encoded blocks where directional conditional block probability (histogram) matrices are used in the selection of the codevectors. The index of the best matching codevector in the sub-codebook is transmitted to the receiver. An adaptive DFSVQ scheme is also proposed in which, when encoding an input vector, first the sub-codebook is searched for a matching codevector to satisfy a pre-specified waveform distortion. If such a codevector is not found in tile current sub-codebook then the whole super-codebook is checked for a better match. If a better match is found then a signaling flag along with the corresponding index of the codevector is transmitted to the receiver. Both the DFSVQ encoder and its adaptive version are implemented. Experimental results for several monochrome images with a super-codebook size of 256 or 512 and different sub-codebook sizes are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Stable Hyponitrite-Bridged Iron Porphyrin Complex (2009)

The coupling of two nitric oxide (NO) molecules in heme active sites is an important contributor to the conversion of NO to nitrous oxide (N(2)O) by heme-containing enzymes. Several formulations for the presumed heme-Fe{N(2)O(2)}(n-) intermediates have been proposed previously, however, no crystal structures of heme-Fe{N(2)O(2)}(n-) systems have been reported to date. We report the first isolation and characterization of a stable bimetallic hyponitrite iron porphyrin, [(OEP)Fe](2)(mu-N(2)O(2)), prepared from the reaction of [(OEP)Fe](2)(mu-O) with hyponitrous acid. Density functional theoretical calculations were performed on the model compound [(porphine)Fe](2)(mu-N(2)O(2)) to characterize its electronic structure and properties.
Heredity and prostate cancer: A study of World War II veteran twins (1997)

BACKGROUND Increased risk of prostate cancer among men with a family history of the disease has been observed in several epidemiological studies, and family studies have identified hereditary prostate cancer characterized by early onset and autosomal dominant inheritance. METHODS In this study, we examine prostate cancer heritability among twins in the NAS-NRC Twin Registry, with cases ascertained from a number of sources: recent telephone interviews, Medicare and Department of Veterans Affairs hospitalizations, previous mail questionnaires, and death certificates. A total of 1,009 prostate cancer cases were identified among the cohort of 31,848 veteran twins born in the years 1917–1927. RESULTS Probandwise concordance for prostate cancer was substantially higher among monozygous twin pairs, 27.1%, than among dizygous twin pairs, 7.1% (P < 0.001). CONCLUSIONS These data suggest that genetic influences account for approximately 57%, and environmental influences for 43%, of the variability in twin liability for prostate cancer. Prostate 33:240–245, 1997. © 1997 Wiley-Liss, Inc.
How to Build a Multimedial Communication/Creation System for Music and Human Motion (1992)

A multimedial communication/creation system, called NUNTIUS, will be presented. The ultimate goal of the multimedial communication is to allow both transmission of data between the medial modalities and autonomous evaluation and utilization of that data. This goal presuppose the existence of two creation stations, one for music and one for choreography.