gebhart/patrepeval huggingface dataset:
Fluorescent energy transfer nucleic acid probes : designs and protocols (2006)

Although fluorescent probes and assays, which use energy transfer (ET) for monitoring DNA reactions, have multiplied in recent years, until now there have been no manuals summarizing the many different protocols and probe designs. Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols is the first publication to provide such a collection. In the volume, hands-on experts-often the original developers of the technique-comprehensively describe a variety of fluorescent probes and devices that use ET, including molecular beacons, molecular break lights, TaqMan probes, LUX™ primers, Invader assay, aptazymes, DNAzymes, molecular machines, biosensors, and logic gates for molecular-scale computation. Merging work on nanotechnology and fluorescent probes, the authors assemble the first comprehensive treatment of all the key DNA- and RNA-based ET probes and present strategies for their optimized custom design. They discuss both fluorescence resonance energy transfer (FRET)-based and non-FRET-based constructs, and provide a complete set of techniques to monitor DNA and RNA reactions, such as hybridization, amplification, cleavage, folding, and associations with proteins, other molecules, and metal ions. Detailed protocols are provided for distance determination in protein-DNA complexes and the detection of topological DNA alterations, mutations, and single-nucleotide polymorphisms. The protocols follow the successful Methods in Molecular Biology™ series format, each offering an outline of the principles behind the technique, step-by-step detailed instructions, and comprehensive troubleshooting. Exhaustive and state-of-the-art, Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols is an invaluable resource for both novice and experienced researchers who wish to use the latest developments in fluorescent probes in any field of molecular biology
Properties of randomly distributed sparse acoustic sensors for ground vehicle tracking and localization (2006)

In order to resolve multiple closely spaced sources moving in a tight formation using unattended acoustic sensors, the array aperture must be extended using a sparse array geometry. Traditional sparse array algorithms rely on the spatial invariance property often leading to inaccurate Direction of Arrival (DOA) estimates due to the large side-lobes present in the power spectrum. Many problems of traditional sparse arrays can be alleviated by forming a sparse array using randomly distributed single microphones. The power spectrum of a random sparse array will almost always exhibit low side-lobes, thus increasing the ability of the beamforming algorithm to accurately separate and localize sources. This paper examines the robustness of randomly distributed sparse array beamforming in situations where the exact sensor location is unknown and benchmark its performance with that of traditional baseline sparse arrays. A realistic acoustic propagation model is also used to study fading effects as a function of range and its influence on the beamforming process for various sparse array configurations.
Retracted Article: Equilibrium and kinetic studies on adsorptive removal of malachite green by the citrate-stabilized magnetite nanoparticles (2014)

Citrate-stabilized iron oxide nanoparticles can be used for the efficient removal of malachite green.
Gaseous breakdown studies using a modified image converter streak camera (1981)

The temporal and spatial information of gaseous breakdowns occurring from the nanosecond to millisecond time scales are important to the basic understanding and applications of gaseous discharges. A streak camera is an ideal tool for acquiring both time- and space-dependent data simultaneously. However, there are several problems associated with using a conventional streak camera for gaseous breakdown studies. Modifications have been made specifically to solve these problems, while the features of the original streak camera are preserved. A signal overlapping problem has been eliminated by extending the dead time to 70 ms. Streak camera response times have been minimized by adjusting the bias voltages. One streak range has been extended to 7 ms to cover the entire event of a gaseous discharge. The modifications and experimental evaluation of the modified streak camera will be presented.
Study on the recognition of templates and their analogues on molecularly imprinted polymer using computational and conformational analysis approaches (2004)

A simplified computational model was proposed to simulate the synthesis of molecularly imprinted polymers (MIP), removal of template and recognition of the template and its analogues by MIP. The MIPs with nicotinamide and iso-nicotinamide as templates were prepared using methacrylic acid as functional monomer. Based on our computational model, the interaction energies between the monomer and the template or its analogues were calculated, which were well correlated with the retention factors and imprinting factors obtained on HPLC columns packed with the corresponding MIP particles. The imprinting effects of the template and its analogues were also investigated from the viewpoint of conformational analysis. The computational data were successfully used to predict the chromatographic behaviour of some chemicals in separation on HPLC columns. We believe that the computational method will find application in designing monomers for MIP synthesis and in studying recognition of templates and their analogues on MIP.
2.5D system integration: a design driven system implementation schema (2004)

We investigate a 3D die-stacking based VLSI integration strategy, socalled 2.5D integration, which can potentially overcome many problems stumbling the development of monolithic system-on-chip (SoC). Here, we review available fabrication technologies and testing solutions for the new integration strategy. We also propose a design driven system implementation schema for this new integration strategy. A layout synthesis framework is under development by us to analyze typical "what if" questions and resolve major physical attributes for a 2.5D system according to the design specification and constraints.
Enantioselective trimethylsilylcyanation of some aldehydes catalyzed by chiral Schiff base-titanium alkoxide complexes (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnantioselective trimethylsilylcyanation of some aldehydes catalyzed by chiral Schiff base-titanium alkoxide complexesMasahiko Hayashi, Yasunori Miyamoto, Tetsuya Inoue, and Nobuki OguniCite this: J. Org. Chem. 1993, 58, 6, 1515–1522Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/jo00058a037https://doi.org/10.1021/jo00058a037research-articleACS PublicationsRequest reuse permissionsArticle Views1532Altmetric-Citations201LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Trajectory planning in a dynamic workspace: a 'state-time space' approach (1998)

This paper addresses trajectory planning in a dynamic workspace, i.e. motion planning for a robot subject to dynamic constraints and moving in a workspace with moving obstacles. First the novel concept of state-time space is introduced, i.e. the state space of the robot augmented of the time dimension. Like configuration space which is a tool to formulate path-planning problems, state-time space is a tool to formulate trajectory planning in dynamic workspace problems. It permits us to study the different aspects of dynamic trajectory planning, i.e. moving obstacles and dynamic constraints, in a unified way. Then this new concept is applied to the case of a car-like robot subject to dynamic constraints and moving along a given path on a dynamic planar workspace. A near-time-optimal approach that searches the solution trajectory over a restricted set of canonical trajectories is presented. These canonical trajectories are defined as having discrete and piecewise constant acceleration. Under these assumptions, it is possible to transform the problem of finding the time-optimal canonical trajectory to finding the shortest path in a directed graph embedded in the state-time space.
Architecture and CAD for speed and area optimization of FPGAs (1998)

The chronic administration of estradiol induces a high incidence (80-100%) of renal tumors in male Syrian hamsters. As part of our examination of a mechanism of carcinogenesis by free radicals generated during redox cycling of catecholestrogen metabolites, we assayed levels of 8-hydroxy-2'-deoxyguanosine (8-OHdGua), a marker product of hydroxy radical interaction with DNA, in livers and kidneys of hamsters treated with estradiol. Injections of 50 and 100 mg/kg estradiol doubled renal 8-OHdGua levels over controls [10.0 +/- 0.1 (SD) and 5.4 +/- 0.4 8-OHdGua/10(5) dGua, respectively] and raised hepatic 8-OHdGua levels almost 4-fold over control values, respectively. These changes were observed in kidney 4 h and in liver 1 or 2 h after treatment of hamsters with estradiol. Estradiol implants administered to hamsters for 3 days raised renal levels of 8-OHdGua by 50% over control values. Six days after 17 beta-estradiol implantation, 8-OHdGua levels returned to near-normal values. Liver DNA was not affected by estradiol implants. These data support a mechanism of estrogen-induced carcinogenesis by free radicals generated via redox cycling of catecholestrogen metabolites.
Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses (2008)

The combinatorial nature of genetic recombination can potentially provide organisms with immediate access to many more positions in sequence space than can be reached by mutation alone. Recombination features particularly prominently in the evolution of a diverse range of viruses. Despite rapid progress having been made in the characterization of discrete recombination events for many species, little is currently known about either gross patterns of recombination across related virus families or the underlying processes that determine genome-wide recombination breakpoint distributions observable in nature. It has been hypothesized that the networks of coevolved molecular interactions that define the epistatic architectures of virus genomes might be damaged by recombination and therefore that selection strongly influences observable recombination patterns. For recombinants to thrive in nature, it is probably important that the portions of their genomes that they have inherited from different parents work well together. Here we describe a comparative analysis of recombination breakpoint distributions within the genomes of diverse single-stranded DNA (ssDNA) virus families. We show that whereas nonrandom breakpoint distributions in ssDNA virus genomes are partially attributable to mechanistic aspects of the recombination process, there is also a significant tendency for recombination breakpoints to fall either outside or on the peripheries of genes. In particular, we found significantly fewer recombination breakpoints within structural protein genes than within other gene types. Collectively, these results imply that natural selection acting against viruses expressing recombinant proteins is a major determinant of nonrandom recombination breakpoint distributions observable in most ssDNA virus families.
Photorealistic Facial Expression Synthesis by the Conditional Difference Adversarial Autoencoder (2017)

Photorealistic facial expression synthesis from single face image can be widely applied to face recognition, data augmentation for emotion recognition or entertainment. This problem is challenging, in part due to a paucity of labeled facial expression data, making it difficult for algorithms to disambiguate changes due to identity and changes due to expression. In this paper, we propose the conditional difference adversarial autoencoder, CDAAE, for facial expression synthesis. The CDAAE takes a facial image of a previously unseen person and generates an image of that human face with a target emotion or facial action unit label. The CDAAE adds a feedforward path to an autoencoder structure connecting low level features at the encoder to features at the corresponding level at the decoder. It handles the problem of disambiguating changes due to identity and changes due to facial expression by learning to generate the difference between low-level features of images of the same person but with different facial expressions. The CDAAE structure can be used to generate novel expressions by combining and interpolating between facial expressions/action units within the training set. Our experimental results demonstrate that the CDAAE can preserve identity information when generating facial expression for unseen subjects more faithfully than previous approaches. This is especially advantageous when training with small databases.
An electrochromic supercapacitor and its hybrid derivatives: quantifiably determining their electrical energy storage by an optical measurement (2015)

Quantifiably determining the electrical energy storage of solid-state supercapacitors is fulfilled by integrating electrochromic tungsten oxide electrodes.
Factor-specific modulation of CREB-binding protein acetyltransferase activity (1999)

CREB-binding proteins (CBP) and p300 are essential transcriptional coactivators for a large number of regulated DNA-binding transcription factors, including CREB, nuclear receptors, and STATs. CBP and p300 function in part by mediating the assembly of multiprotein complexes that contain additional cofactors such as p300/CBP interacting protein (p/CIP), a member of the p160/SRC family of coactivators, and the p300/CBP associated factor p/CAF. In addition to serving as molecular scaffolds, CBP and p300 each possess intrinsic acetyltransferase activities that are required for their function as coactivators. Here we report that the adenovirus E1A protein inhibits the acetyltransferase activity of CBP on binding to the C/H3 domain, whereas binding of CREB, or a CREB/E1A fusion protein to the KIX domain, fails to inhibit CBP acetyltransferase activity. Surprisingly, p/CIP can either inhibit or stimulate CBP acetyltransferase activity depending on the specific substrate evaluated and the functional domains present in the p/CIP protein. While the CBP interaction domain of p/CIP inhibits acetylation of histones H3, H4, or high mobility group by CBP, it enhances acetylation of other substrates, such as Pit-1. These observations suggest that the acetyltransferase activities of CBP/p300 and p/CAF can be differentially modulated by factors binding to distinct regions of CBP/p300. Because these interactions are likely to result in differential effects on the coactivator functions of CBP/p300 for different classes of transcription factors, regulation of CBP/p300 acetyltransferase activity may represent a mechanism for integration of diverse signaling pathways.
Scalable Distributed Last-Level TLBs Using Low-Latency Interconnects (2018)

Recent studies have shown the potential of last-level TLBs shared by multiple cores in tackling memory translation performance challenges posed by "big data" workloads. A key stumbling block hindering their effectiveness, however, is their high access time. We present a design methodology to reduce these high access times so as to realize high-performance and scalable shared L2 TLBs. As a first step, we study the benefits of replacing monolithic shared TLBs with a distributed set of small TLB slices. While this approach does reduce TLB lookup latency, it increases interconnect delays in accessing remote slices. Therefore, as a second step, we devise a lightweight single-cycle interconnect among the TLB slices by tailoring wires and switches to the unique communication characteristics of memory translation requests and responses. Our approach, which we dub NOCSTAR (NOCs for scalable TLB architecture), combines the high hit rates of shared TLBs with low access times of private L2 TLBs, enabling significant system performance benefits.
Recent advances in lineage differentiation from stem cells: hurdles and opportunities? (2018)

Pluripotent stem cells have the property of long-term self-renewal and the potential to give rise to descendants of the three germ layers and hence all mature cells in the human body. Therefore, they hold the promise of offering insight not only into human development but also for human disease modeling and regenerative medicine. However, the generation of mature differentiated cells that closely resemble their <i>in vivo</i> counterparts remains challenging. Recent advances in single-cell transcriptomics and computational modeling of gene regulatory networks are revealing a better understanding of lineage commitment and are driving modern genome editing approaches. Additional modification of the chemical microenvironment, as well as the use of bioengineering tools to recreate the cellular, extracellular matrix, and physical characteristics of the niche wherein progenitors and mature cells reside, is now being used to further improve the maturation and functionality of stem cell progeny.
Application of ferroelectric materials for improving output power of energy harvesters (2018)

In terms of advances in technology, especially electronic devices for human use, there are needs for miniaturization, low power, and flexibility. However, there are problems that can be caused by these changes in terms of battery life and size. In order to compensate for these problems, research on energy harvesting using environmental energy (mechanical energy, thermal energy, solar energy etc.) has attracted attention. Ferroelectric materials which have switchable dipole moment are promising for energy harvesting fields because of its special properties such as strong dipole moment, piezoelectricity, pyroelectricity. The strong dipole moment in ferroelectric materials can increase internal potential and output power of energy harvesters. In this review, we will provide an overview of the recent research on various energy harvesting fields using ferroelectrics. A brief introduction to energy harvesting and the properties of the ferroelectric material are described, and applications to energy harvesters to improve output power are described as well.
Ergodic Spectrum Management (2020)

Ergodic Spectrum Management (ESM)'s basic features are introduced as a cloud-based management of wireless connectivity that targets improvement of internet-user's quality of experience. Ergodic Spectrum Management (or ESM) learns and exploits near-ergodicity, or time-consistency, to improve a communication-link connection's stable and efficient use in time, space, and frequency; while using consumer quality of experience as the target metric. ESM methods can also improve existing radio resource management, particularly advancing unlicensed spectrum-use efficiency to levels at or exceeding those associated with licensed spectra, as shown herein. ESM's use of learned probability distributions' dimensional (time, space, and frequency) consistencies enables latency-insensitive remote-cloud-based resource management to be applied to wireless multi-user transmission. ESM methods are developed for 3 increasingly more effective stages that correspondingly increasingly rely on data collection and functional-profile (policy) guidance of physical-layer design choices. ESM application to either and both of existing and future unlicensed- and licensed-spectra networks is suggested as a means to improve overall wireless performance. Examples and field data are provided to show the potential of very large improvements in wireless system connectivity, throughput, and quality of experience.
Bacterial Origin of a Chloroplast Intron: Conserved Self-Splicing Group I Introns in Cyanobacteria (1990)

A self-splicing group I intron has been found in the gene for a leucine transfer RNA in two species of Anabaena, a filamentous nitrogen-fixing cyanobacterium. The intron is similar to one that is found at the identical position in the same transfer RNA gene of chloroplasts of land plants. Because cyanobacteria were the progenitors of chloroplasts, it is likely that group I introns predated the endosymbiotic association of these eubacteria with eukaryotic cells.
Motor neuropathies and serum IgM binding to NS6S heparin disaccharide or GM1 ganglioside (2010)

IgM binding to NS6S disaccharide is associated with motor neuropathy syndromes and occurs with similar frequency to IgM binding to GM1. Testing for IgM binding to NS6S in addition to GM1 increases the frequency of finding IgM autoantibodies in motor neuropathies from 43% to 64%. High titres of serum IgM binding to GM1, tested with covalent ELISA methodology, have 93% specificity for motor neuropathy syndromes. High titres of serum IgM binding to NS6S have specificity for immune motor neuropathies compared with ALS and CIDP.
Crystal Structure of Hemoglobin Protease, a Heme Binding Autotransporter Protein from Pathogenic Escherichia coli (2005)

The acquisition of iron is essential for the survival of pathogenic bacteria, which have consequently evolved a wide variety of uptake systems to extract iron and heme from host proteins such as hemoglobin. Hemoglobin protease (Hbp) was discovered as a factor involved in the symbiosis of pathogenic Escherichia coli and Bacteroides fragilis, which cause intra-abdominal abscesses. Released from E. coli, this serine protease autotransporter degrades hemoglobin and delivers heme to both bacterial species. The crystal structure of the complete passenger domain of Hbp (110 kDa) is presented, which is the first structure from this class of serine proteases and the largest parallel beta-helical structure yet solved.
ChemInform Abstract: ORGANOBORON COMPOUNDS. CCCVII. CHELATE COMPOUNDS OF BORON FROM AMIDINES AND ALDEHYDES (1976)

Abstract Fügt man zu dem Diphenylborsäure‐n‐butylester (I) nacheinander verdünntes Alkali, einen Aldehyd (II) und salzsaures Acetamidin (III), dann entsteht ein Niederschlag des Chelats (IV).
Tunable Terahertz Absorber Based on Bulk-Dirac-Semimetal Metasurface (2018)

We propose a tunable terahertz (THz) absorber design that utilizes a bulk Dirac semimetal (BDS)-based metasurface. The absorber consists of a BDS film with a periodic ring slot, dielectric layer, and fully reflective gold mirror. Simulations indicate that localized surface plasmon resonance is excited within certain regions close to the ring slot, leading to dipolar plasmon resonance of periodic arrays along the polarization direction, thereby producing resonant absorption. The BDS conductivity scales linearly with the Fermi level that can be tuned by bias application, enhancing the electromagnetic-field concentration and shrinking the effective current path, thereby blue-shifting the operating frequency within an ultrawideband. The thickness of the proposed design is significantly less than the resonant wavelength; therefore, the design yields an ultrathin metasurface absorber. This paper may lead to the investigations of the tunable metasurface device based on the BDS.