gebhart/patrepeval huggingface dataset:
Generation of yield-embedded Pareto-front for simultaneous optimization of yield and performances (2010)

As the variations of shrunk processes increasing at rapid rate, the performances of analog/mixed-signal chips remarkably fluctuate. It is necessary to take the yield as a design objective in design optimization. This paper presents a novel method to generate yield-embedded Pareto-front to simultaneously optimize both the yield and performances. Unlike the traditional approaches which generate the yield-aware Pareto-front to optimize performances for the fixed yield, this work embeds the yield as an objective of the optimization and evolutionarily optimizes both yield and performances by the so-called yield-embedded NSGA. The experiments demonstrate the gradual evolutions and global searching for the better performances and higher yields under PVT variations. The generation accelerated by parallel computations gains 4.8x speedup with 80% efficiency.
Enabling Fog Computing for Industrial Automation Through Time-Sensitive Networking (TSN) (2018)

In this article, we advocate for the use of IEEE 802.1 Time-Sensitive Networking (TSN) as deterministic transport for the network layer of fog computing in industrial automation. We give an overview of the relevant TSN protocol services and motivate the use of TSN. We propose a configuration agent architecture based on IEEE 802.1Qcc and OPC Unified Architecture (OPC UA), capable of performing runtime network configuration. We briefly present the configuration challenges for scheduled networks (considering a subset of TSN mechanisms), and illustrate one problem: the configuration of schedule tables of such networks for hard real-time control applications. We propose a list scheduling-based heuristic to solve this problem. Our evaluation and comparison to previous work demonstrate the feasibility of reconfiguring the scheduled network at runtime for industrial applications within the fog.
FIR prefiltering improves Prony's method (1991)

Prony's method, a technique for determining the parameters of sinusoidal signals, is known to be very sensitive to measurement errors in the observed signal samples. The authors present two prefiltering methods that improve the performance of Prony's method. The simple prefiltering operation reduces the effects of noise in the data without violating the fundamental property of Prony's method. In the first method, the prefilter is synthesized using prior knowledge regarding the approximate regions in the frequency domain where the signals are known to lie. In the second method, no prior knowledge is necessary. The prefilter is iteratively computed from the data samples themselves. Simulation results are given. Connections to other linear prediction methods are also indicated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Cloud-based malware detection for evolving data streams (2008)

Data stream classification for intrusion detection poses at least three major challenges. First, these data streams are typically infinite-length, making traditional multipass learning algorithms inapplicable. Second, they exhibit significant concept-drift as attackers react and adapt to defenses. Third, for data streams that do not have any fixed feature set, such as text streams, an additional feature extraction and selection task must be performed. If the number of candidate features is too large, then traditional feature extraction techniques fail. In order to address the first two challenges, this article proposes a multipartition, multichunk ensemble classifier in which a collection of v classifiers is trained from r consecutive data chunks using v -fold partitioning of the data, yielding an ensemble of such classifiers. This multipartition, multichunk ensemble technique significantly reduces classification error compared to existing single-partition, single-chunk ensemble approaches, wherein a single data chunk is used to train each classifier. To address the third challenge, a feature extraction and selection technique is proposed for data streams that do not have any fixed feature set. The technique's scalability is demonstrated through an implementation for the Hadoop MapReduce cloud computing architecture. Both theoretical and empirical evidence demonstrate its effectiveness over other state-of-the-art stream classification techniques on synthetic data, real botnet traffic, and malicious executables.
Extending Amdahl's law in the multicore era (2009)

research-article Share on Extending Amdahl's law in the multicore era Authors: Erlin Yao Institute of Computing Technology, Chinese Academy of Sciences Institute of Computing Technology, Chinese Academy of SciencesView Profile , Yungang Bao Institute of Computing Technology, Chinese Academy of Sciences Institute of Computing Technology, Chinese Academy of SciencesView Profile , Guangming Tan Institute of Computing Technology, Chinese Academy of Sciences Institute of Computing Technology, Chinese Academy of SciencesView Profile , Mingyu Chen Institute of Computing Technology, Chinese Academy of Sciences Institute of Computing Technology, Chinese Academy of SciencesView Profile Authors Info & Claims ACM SIGMETRICS Performance Evaluation ReviewVolume 37Issue 2September 2009pp 24–26https://doi.org/10.1145/1639562.1639571Published:16 October 2009Publication History 22citation654DownloadsMetricsTotal Citations22Total Downloads654Last 12 Months30Last 6 weeks13 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Characteristics of n-octyl <i>β</i>-<scp>d</scp>-thioglucopyranoside, a new non-ionic detergent useful for membrane biochemistry (1984)

n-Octyl beta-D-thioglucopyranoside, a new non-ionic detergent, was synthesized. Properties, and applicability to membrane proteins, of this detergent were investigated. The detergent was easily removed by dialysis. The solubilizing power of this detergent for Escherichia coli membrane proteins was similar to that of n-octyl beta-D-glucopyranoside, which has been widely used in membrane biochemistry. No inactivation of proteins was observed after the solubilization. n-Octyl beta-D-thioglucopyranoside was superior to n-octyl beta-D-glucopyranoside in that it was much more stable and could be synthesized at much lower cost.
Does negation really matter (2010)

We explore the role negation and speculation identification plays in the multi-label document-level classification of medical reports for diseases. We identify the polarity of assertions made on noun phrases which reference diseases in the medical reports. We experiment with two machine learning classifiers: one based upon Lucene and the other based upon BoosTexter. We find the performance of these systems on document-level classification of medical reports for diseases fails to show improvement when their input is enhanced by the polarity of assertions made on noun phrases. We conclude that due to the nature of our machine
Proteomic analysis of acrylamide gel separated proteins immobilized on polyvinylidene difluoride membranes following proteolytic digestion in the presence of 80% acetonitrile (2003)

Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) combined with mass spectrometry (MS) is a highly accurate and sensitive means of identifying proteins. We have developed a novel method for digesting proteins on polyvinylidene difluoride (PVDF) membranes for subsequent matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS analysis. After Tricine sodium dodecyl sulfate (SDS)-PAGE, separated proteins were electroblotted onto PVDF membranes in a semidry discontinuous buffer system, visualized by staining with Coomassie Blue, excised, digested with trypsin or lysC in 80% acetonitrile, and then analyzed by MALDI-TOF MS. This method has several advantages over in-gel digestion in terms of sample handling, sensitivity, and time. We identified 105 fmol of Bacillus subtilis SecA and 100 approximately 500 fmol of standard proteins. We also analyzed the submembrane protein fraction solubilized by 1% n-dodecyl-beta-D-maltoside from B. subtilis membranes after separation by 2-D PAGE, and identified 116 protein spots. This method can detect proteins at the 10 approximately 50 fmol level by pooling more than ten identical electroblotted protein spots.
Transcatheter coronary artery diagnostic techniques including impedance-catheter and impedance-guidewire measurement of absolute coronary blood flow. (1989)

Interventional cardiology requires precise assessment of coronary anatomy and physiology. Unfortunately, however, important interventional decisions are frequently made on the basis of arteriographic data alone. Increasing evidence suggests that visual interpretation of coronary arteriographic studies is irreproducible, inaccurate, and poorly predictive of coronary physiology. Moreover, arteriography is of little value in assessing endothelial ulceration and mural thrombus, which are important pathophysiologic features of unstable angina and acute myocardial infarction. In response to these limitations, several diagnostic transcatheter techniques have been developed that allow more complete assessment of coronary physiology and function. These include fiberoptic angioscopy, reflection spectroscopy (which can combine automated laser therapy with diagnosis), ultrasonic catheterization, and translesional gradient determination. Doppler catheterization permits the assessment of overall coronary flow reserve with the aid of induced hyperemia, whereas subselective digital radiography allows the evaluation of regional coronary flow reserve. The coronary flow reserve, however, may be falsely lowered immediately after balloon dilation, because of endothelial injury, repeated ischemia, or the administration of vasoactive drugs. To circumvent this problem, we have developed impedance-catheter and impedance-guidewire systems that, by applying impedance technology and the principles of indicator dilution, are capable of measuring absolute coronary blood flow. For a flow indicator, we use 0.5 mL of glucose solution (D5W), which has little effect on intrinsic blood flow. The validity of this approach has been demonstrated in experimental and clinical studies. The impedance guidewire is less obstructive than the catheter system, so it probably will become the method with clinical application.
Thyroid Hormone, Retinoic Acid, and Testosterone Suppress Proliferation and Induce Markers of Differentiation in Cultured Rat Sertoli Cells (2003)

This study uses a high purity cell culture system to extend previous observations of factors controlling the end of the Sertoli cell proliferative phase. Thyroid hormone, retinoic acid, and testosterone were assessed for their ability to halt the proliferative phase and regulate the expression of markers associated with maturation of the Sertoli cell. We show that these hormones share similar suppressive effects on the rate of Sertoli cell division without any apparent additive effects. We demonstrate that these hormones induce the progressive accumulation of cell cycle inhibitors p27Kip1 and p21Cip1 in Sertoli cells, a likely regulatory mechanism controlling the suppression of proliferation. We used real-time RT-PCR to examine the effects of these factors on the expression of mRNA encoding the Id proteins, demonstrating an increase in Id2 and Id3 expression in Sertoli cells treated with thyroid hormone, retinoic acid, or testosterone. Finally, we examined the expression of a number of genes that have been implicated in the Sertoli cell differentiation process. Our results suggest that these hormones can induce aspects of Sertoli cell differentiation in vitro, providing a valuable in vitro model for studying Sertoli cell function.
Field cancerization in the colon: a role for aberrant DNA methylation? (2014)

Colorectal cancer is the third most common cancer worldwide and arises secondary to the progressive accumulation of genetic and epigenetic alterations in normal colon cells, which results in a polyp-to-cancer progression sequence. It is known that individuals with a personal history of colon adenomas or cancer are at increased risk for metachronous colon neoplasms. One explanation for this increased risk could be field cancerization, which is a phenomenon in which the histologically normal tissue in an organ is primed to undergo transformation. Epigenetic alterations appear to be promising markers for field cancerization. In this review, we discuss field cancerization in the colon and the data supporting the use of methylated DNA as a biomarker for this phenomenon.
Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis (1996)

Sequence heterogeneities in 16S rRNA genes from individual strains of Paenibacillus polymyxa were detected by sequence-dependent separation of PCR products by temperature gradient gel electrophoresis (TGGE). A fragment of the 16S rRNA genes, comprising variable regions V6 to V8, was used as a target sequence for amplifications. PCR products from P. polymyxa (type strain) emerged as a well-defined pattern of bands in the gradient gel. Six plasmids with different inserts, individually demonstrating the migration characteristics of single bands of the pattern, were obtained by cloning the PCR products. Their sequences were analyzed as a representative sample of the total heterogeneity. An amount of 10 variant nucleotide positions in the fragment of 347 bp was observed, with all substitutions conserving the relevant secondary structures of the V6 and V8 regions in the RNA molecules. Hybridizations with specifically designed probes demonstrated different chromosomal locations of the respective rRNA genes. Amplifications of reverse-transcribed rRNA from ribosome preparations, as well as whole-cell hybridizations, revealed a predominant representation of particular sequences in ribosomes of exponentially growing laboratory cultures. Different strains of P. polymyxa showed not only remarkably differing patterns of PCR products in TGGE analysis but also discriminative whole-cell labeling with the designed oligonucleotide probes, indicating the different representation of individual sequences in active ribosomes. Our results demonstrate the usefulness of TGGE for the structural analysis of heterogeneous rRNA genes together with their expression, stress problems of the generation of meaningful data for 16S rRNA sequences and probe designs, and might have consequences for evolutionary concepts.
The Possible Role of Antioxidant Vitamin C in Alzheimer’s Disease Treatment and Prevention (2013)

Oxidative stress is suggested to play a major role in the pathogenesis of Alzheimer's disease (AD). Among the antioxidants, vitamin C has been regarded as the most important one in neural tissue. It also decreases β-amyloid generation and acetylcholinesterase activity and prevents endothelial dysfunction by regulating nitric oxide, a newly discovered factor in the pathogenesis and progression of AD. However, clinical trials using antioxidants, including vitamin C, in patients with AD yielded equivocal results. The current article discusses the relevance of vitamin C in the cellular and molecular pathogenesis of AD and explores its therapeutic potential against this neurodegenerative disorder.
Towards <scp>HBV</scp> curative therapies (2018)

Tremendous progress has been made over the last 2 decades to discover and develop approaches to control hepatitis B virus (HBV) infections and to prevent the development of hepatocellular carcinoma using various interferons and small molecules as antiviral agents. However, none of these agents have significant impact on eliminating HBV from infected cells. Currently the emphasis is on silencing or eliminating cccDNA, which could lead to a cure for HBV. Various approaches are being developed including the development of capsid effectors, CRISPR/Cas9, TALENS, siRNA, entry and secretion inhibitors, as well as immunological approaches. It is very likely that a combination of these modalities will need to be employed to successfully eliminate HBV or prevent virus rebound on discontinuation of therapy. In the next 5 years clinical data will emerge which will provide insight on the safety and feasibility of these approaches and if they can be applied to eradicate HBV infections globally. In this review, we summarize current treatments and we highlight and examine recent therapeutic strategies that are currently being evaluated at the preclinical and clinical stage.
Targeted delivery of doxorubicin to the rat brain at therapeutic levels using MRI‐guided focused ultrasound (2007)

Abstract The clinical application of chemotherapy to brain tumors has been severely limited because antitumor agents are typically unable to penetrate an intact blood‐brain barrier (BBB). Although doxorubicin (DOX) has been named as a strong candidate for chemotherapy of the central nervous system (CNS), the BBB often prevents cytotoxic levels from being achieved. In this study, we demonstrate a noninvasive method for the targeted delivery of DOX through the BBB, such that drug levels shown to be therapeutic in human tumors are achieved in the normal rat brain. Using MRI‐guided focused ultrasound with preformed microbubbles (Optison) to locally disrupt the BBB and systemic administration of DOX, we achieved DOX concentrations of 886 ± 327 ng/g tissue in the brain with minimal tissue effects. Tissue DOX concentrations of up to 5,366 ± 659 ng/g tissue were achieved with higher Optison doses, but with more significant tissue damage. In contrast, DOX accumulation in nontargeted contralateral brain tissue remained significantly lower for all paired samples ( p < 0.001). These results suggest that targeted delivery by focused ultrasound may render DOX chemotherapy a viable treatment option against CNS tumors, despite previous accessibility limitations. In addition, MRI signal enhancement in the sonicated region correlated strongly with tissue DOX concentration ( r = 0.87), suggesting that contrast‐enhanced MRI could perhaps indicate drug penetration during image‐guided interventions. Our technique using MRI‐guided focused ultrasound to achieve therapeutic levels of DOX in the brain offers a large step forward in the use of chemotherapy to treat patients with CNS malignancies. © 2007 Wiley‐Liss, Inc.
A Survey of Recent Prefetching Techniques for Processor Caches (2016)

As the trends of process scaling make memory systems an even more crucial bottleneck, the importance of latency hiding techniques such as prefetching grows further. However, naively using prefetching can harm performance and energy efficiency and, hence, several factors and parameters need to be taken into account to fully realize its potential. In this article, we survey several recent techniques that aim to improve the implementation and effectiveness of prefetching. We characterize the techniques on several parameters to highlight their similarities and differences. The aim of this survey is to provide insights to researchers into working of prefetching techniques and spark interesting future work for improving the performance advantages of prefetching even further.
Clean image synthesis and target numerical marching for optical imaging with backscattering light (2011)

Scanning backscattering imaging and independent component analysis (ICA) are used to probe targets hidden in the subsurface of a turbid medium. A new correction procedure is proposed and used to synthesize a "clean" image of a homogeneous host medium numerically from a set of raster-scanned "dirty" backscattering images of the medium with embedded targets. The independent intensity distributions on the surface of the medium corresponding to individual targets are then unmixed using ICA of the difference between the set of dirty images and the clean image. The target positions are localized by a novel analytical method, which marches the target to the surface of the turbid medium until a match with the retrieved independent component is accomplished. The unknown surface property of the turbid medium is automatically accounted for by this method. Employing clean image synthesis and target numerical marching, three-dimensional (3D) localization of objects embedded inside a turbid medium using independent component analysis in a backscattering geometry is demonstrated for the first time, using as an example, imaging a small piece of cancerous prostate tissue embedded in a host consisting of normal prostate tissue.
Effect of Charge Carrier Lipid on Skin Penetration, Retention, and Hair Growth of Topically Applied Finasteride-Containing Liposomes (2011)

The aim of this study was to investigate the effect of charge carrier lipid on the skin penetration, retention, and hair growth of topically applied finasteride-containing liposomes. Finasteride-containing liposomes were prepared by traditional thin film hydration method using Phospholipon<TEX>$^{(R)}$</TEX> 85 G and cholesterol with or without charge carrier lipid (1,2 dimyristoyl-sn-glycero-3-phosphate or 1,2-dioleoyl-trimethylammonium-propane for anionic and cationic charge, respectively). Freshly prepared finasteride-containing liposome suspension was applied on the hairless mouse skin, and skin penetration and retention were measured using Keshary-Chien diffusion cell. Non-liposomal formulation (ethanol 10% solution containing 0.5 mg/ml of FNS) was also used as a control. The amount of finasteride in the diffusion cell and mouse skin was measured by HPLC. The hair growth was evaluated using depilated male C57BL/6N mice. Mean particle size of all finasteride-containing liposomes was less than a micron, and polydispersity index revealed size homogeneity. Skin penetration and retention studies showed that significantly less amount of finasteride was penetrated when applied as anionic liposome while more amount of the drug was retained. Specifically, in liposome prepared with 10% anionic charge carrier lipid, penetration was 12.99 <TEX>${\mu}g/cm^2$</TEX> while retention was 79.23 <TEX>${\mu}g/cm^2$</TEX> after 24 h of application. In hair growth study, finasteride-containing anionic liposomes showed moderate efficacy, but the efficacy was not found when applied as cationic liposomes. In conclusion, topical application of finasteride using anionic liposome formulation appears to be useful option for the treatment of androgenetic alopecia to avoid systemic side effects of the drug.