gebhart/patrepeval huggingface dataset:
A Compact Optical Rubidium Atomic Frequency Standard (2016)

Precision navigation and timing is an important focus in the Air Force Research Laboratory's experimental efforts. The development and testing of an optical frequency standard is suitable for an array of both terrestrial and space based applications. An optical atomic clock based upon a two-photon transition at 778 nm in rubidium, is an ideal candidate to meet the requirements of Global Satellite Navigation System (GNSS), while being a viable option for other applications. Here we demonstrate that a simple architecture, using off-the-shelf components and an external cavity diode laser system that is confined to less than 3 ft2 of breadboard, exhibits a frequency instability of 7 x 10-13/??, for times less than 100 seconds.
Single-chain immunotoxin fusions between anti-tac and Pseudomonas exotoxin: Relative importance of the two toxin disulfide bonds (1993)

Anti-Tac(Fv)-PE40 is a recombinant single-chain immunotoxin in which the variable heavy and light domains of the anti-IL2 receptor antibody, anti-Tac, are connected to each other by a peptide linker and then fused to PE40, a truncated form of Pseudomonas exotoxin (PE). This fusion protein has four disulfide bonds: one in each of the two variables domains, one in domain II (Cys 265-287), and one in domain Ib (Cys 372-379) of PE. To study the importance of the disulfide bonds of the toxin to the activity of single-chain immunotoxins, we constructed mutants in which either the cysteines in the toxin were changed to alanines or the amino acids 365-380 of PE were deleted. We began this study with anti-Tac(Fv)-PE40 and a more active variant, anti-Tac(Fv)-PE40KDEL, in which the carbonyl terminus is changed from REDLK to KDEL. From these proteins we made anti-Tac(Fv)-PE40(4)A and anti-Tac(Fv)-PE40KDEL4A, respectively, by converting cysteins at amino acids 265, 287, 372, and 379 of PE to alanines. This change resulted in a 20-100-fold loss of activity toward human target cells, but no significant change in binding affinity to p55. To determine the importance of the second toxin disulfide bond, we removed amino acids 365-380 from anti-Tac(Fv)-PE40, anti-Tac(Fv)-PE40KDEL, and anti-Tac(Fv)-PE40KDEL4A, resulting in anti-Tac(Fv)-PE38, anti-Tac(Fv)-PE38KDEL, and anti-Tac(Fv)-PE38KDEL2A, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Characterization of the Met326Ile variant of phosphatidylinositol 3-kinase p85α (2002)

Phosphatidylinositol 3-kinase is a key step in the metabolic actions of insulin. Two amino acid substitutions have been identified in the gene for the regulatory subunit of human p85alpha, Met-326Ile, and Asn-330Asp, and the former has been associated with alterations in glucose/insulin homeostasis. When the four human p85alpha proteins were expressed in yeast, a 27% decrease occurred in the level of protein expression of p85alpha(Ile/Asp) (P = 0.03) and a 43% decrease in p85alpha(Ile/Asn) (P = 0.08) as compared with p85alpha(Met/Asp). Both p85alpha(Ile/Asp) and p85alpha(Ile/Asn) also exhibited increased binding to phospho-insulin receptor substrate-1 by 41% and 83%, respectively (P < 0.001), as compared with p85alpha(Met/Asp). The expression of p85alpha(Ile) was also slightly decreased and the binding to insulin receptor substrate-1 slightly increased in brown preadipocytes derived from p85alpha knockout mice. Both p85alpha(Met) and p85alpha(Ile) had similar effects on AKT activity and were able to reconstitute differentiation of the preadipocytes, although the triglyceride concentration in fully differentiated adipocytes and insulin-stimulated 2-deoxyglucose uptake were slightly lower than in adipocytes expressing p85alpha(Met). Thus, the Met-326Ile variant of p85alpha is functional for intracellular signaling and adipocyte differentiation but has small alterations in protein expression and activity that could play a role in modifying insulin action.
Identification of the metastasis-associated, galactoside-binding lectin as a chimeric gene product with homology to an IgE-binding protein. (1989)

We report the complete primary and secondary structures of a metastasis-associated Mr 34,000 galactoside-binding lectin. The polypeptide sequence (264 amino acids) was derived from the nucleotide sequence of three overlapping complementary DNA clones isolated from lambda gt11 and lambda gt10 phage libraries of UV-induced murine fibrosarcomas. Striking features of the polypeptide sequence are two distinct regions of beta-sheet and globular structures at the amino and carboxy terminals, respectively. Homology search suggests that the polypeptide is a chimeric gene product formed by fusion of the 5'-end of an Mr approximately 14,000 galactoside-binding lectin with an internal domain of the collagen alpha gene. Enzymatic treatment with collagenase confirmed the presence of a collagen-like structure in the polypeptide. Unexpectedly, the entire sequence is greater than 85% homologous to a rat low affinity IgE-binding protein.
Engineering a Direct and Inducible Protein−RNA Interaction To Regulate RNA Biology (2010)

The importance and pervasiveness of naturally occurring regulation of RNA function in biology is increasingly being recognized. A common mechanism uses inducible protein-RNA interactions to shape diverse aspects of cellular RNA fate. Recapitulating this regulatory mode in cells using a novel set of protein-RNA interactions is appealing given the potential to subsequently modulate RNA biology in a manner decoupled from endogenous cellular physiology. Achieving this outcome, however, has previously proven challenging. Here, we describe a ligand-responsive protein-RNA interaction module, which can be used to target a specific RNA for subsequent regulation. Using the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method, RNA aptamers binding to the bacterial Tet Repressor protein (TetR) with low- to subnanomolar affinities were obtained. This interaction is reversibly controlled by tetracycline in a manner analogous to the interaction of TetR with its cognate DNA operator. Aptamer minimization and mutational analyses support a functional role for two conserved sequence motifs in TetR binding. As an initial illustration of using this system to achieve protein-based regulation of RNA function in living cells, insertion of a TetR aptamer into the 5'-UTR of a reporter mRNA confers post-transcriptionally regulated, ligand-inducible protein synthesis in E. coli. Altogether, these results define and validate an inducible protein-RNA interaction module that incorporates desirable aspects of a ubiquitous mechanism for regulating RNA function in Nature and can be used as a foundational interaction for functionally and reversibly controlling the multiple fates of RNA in cells.
Developing a characterization of business intelligence workloads for sizing new database systems (2004)

Computer system sizing involves estimating the amount of hardware resources needed to support a new workload not yet deployed in a production environment. In order to determine the type and quantity of resources required, a methodology is required for describing the new workload. In this paper, we discuss the sizing process for database management systems and describe an analysis for characterizing business intelligence (BI) workloads, using the TPC-H benchmark as our workload basis. The characterization yields four general classes of queries, each with different characteristics. Our approach for sizing a BI application's database tier quantifies a new BI workload in terms of the response time goals and mix of the different query classes obtained from the characterization analysis.
iCirrus Wop: Workload Analysis for Virtual Machine Placements (2012)

True essence of the technology of virtualization is the ability to allow one or more workloads to share the underlying physical resources, thereby bringing about significant cost saving. However, in order to maximize the cost savings from this disruptive technology, it is essential to adopt optimal resource management techniques. These techniques broadly encompass approaches to virtual machine (VM) sizing and placement in a manner that maximizes the physical infrastructure utilization, alongside ensuring that the desired service-level objectives of the candidate workloads are met. In this paper, we propose a novel workload analysis approach for VM placement, which relies on examining the time varying processing demands and variability of the workloads to determine the most optimal placement. Such a solution will result in maximizing infrastructure utilization and ensure that the SLAs of the candidate workloads are met after placement. The technique has been effectively applied to real-life workloads that pertain to SaaS based business platforms offered to clients spread across different geographical locations. A paper based assessment reported over 25% improvement in the overall infrastructure utilization by using the proposed algorithm as compared to other well-known approaches.
PNP- A NEWCLASSOFCODEDAPERTURE ARRAYS (1986)

Wereportona newclassofcodedaperture arrays whichhasallthedesirable imaging characteristics of theUniformly Redundant Array(URA), yetis constructible indimensions whichareforbidden to thatdesign.Inaddition, thenewarrays(called PNP arrays,forPseudo-Noise Product) areofselfsupporting geometry, simplifying fabrication and makingthemidealcandidates forsituations where active collimators areemployed, asforexample in high-energy y-rayimaging. A unique andimportant feature ofallPNParraysistheability toproduce reconstructed images whosenoiseisuniformregardless oftheoriginal sourcestructure. A comparison ofthe predicted performance ofthePNP,URA,GEOMETRIC, and PINHOLE designs ispresented. Introducti on
Effects of Microbial Agent-Chemical Pesticide Mixtures on Heliothis virescens (F.) (Lepidoptera: Noctuidae)1 (1983)

Journal Article Effects of Microbial Agent-Chemical Pesticide Mixtures on Heliothis virescens (F.) (Lepidoptera: Noctuidae) Get access A. I. Mohamed, A. I. Mohamed Department of Entomology, University of Arkansas, Fayetteville, Arkansas 72701 Search for other works by this author on: Oxford Academic PubMed Google Scholar S. Y. Young, S. Y. Young Department of Entomology, University of Arkansas, Fayetteville, Arkansas 72701 Search for other works by this author on: Oxford Academic PubMed Google Scholar W. C. Yearian W. C. Yearian Department of Entomology, University of Arkansas, Fayetteville, Arkansas 72701 Search for other works by this author on: Oxford Academic PubMed Google Scholar Environmental Entomology, Volume 12, Issue 2, 1 April 1983, Pages 478–481, https://doi.org/10.1093/ee/12.2.478 Published: 01 April 1983 Article history Received: 27 July 1982 Published: 01 April 1983
Optical Two-Way Time-Frequency Transfer across a Three-Node Free-Space Network (2020)

We demonstrate optical two-way time-frequency transfer (O-TWTFT) across a three-node free-space network. The network spans 28 km of outdoor air and relays time and frequency from a master node, through an intermediate fielded node, to an end node. Despite strong atmospheric turbulence along the close-to-ground free-space links and large ambient temperature swings at the fielded node, the network transfers time with relative timing offsets below 5 fs. Additionally, the network transfers frequency with instability below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-18</sup> at averaging times greater than 200 s-i.e. below the level needed to compare state-of-the-art optical atomic clocks.
Performance enhancement of first order three-level envelope delta sigma modulator based transmitter (2014)

This work is concerned with the analysis, based on MATLAB simulation, of 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> and 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> order Multi-level envelope delta sigma modulators (EDSMs) that are used for high efficiency and linearity wireless mobile transmitter architectures with an Orthogonal Frequency Division Modulation (OFDM) signal and long term evolution (LTE) signal. The analysis is based on measuring the linearity and the efficiency of the three-level EDSM. It was shown that, at different input signal power levels of the three-level EDSM, 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> order three-level EDSM is able to achieve a performance that is close to the performance of the 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> order counterpart. While 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> order DSM requires less circuitry, it is recommended to employ 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> order three-level EDSM instead of using 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> order three-level EDSM. 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> order three-level EDSM has a signal to noise distortion ratio (SNDR) and coding efficiency of 58 dB and 77%, respectively. While 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> order three-level EDSM showed SNDR of 61.5 dB and coding efficiency of 76.4%. Also, with a long term evolution (LTE) signal, the 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> order EDSM has better performance, in terms of SNDR and CE, than that of the 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> order EDSM circuit.
Microwave imaging via space-time beamforming for early detection of breast cancer (2003)

A method of microwave imaging via space-time (MIST) beamforming is proposed for detecting early-stage breast cancer. An array of antennas is located near the surface of the breast and an ultrawideband (UWB) signal is transmitted sequentially from each antenna. The received backscattered signals are passed through a space-time beamformer that is designed to image backscattered signal energy as a function of location. The beamformer spatially focuses the backscattered signals to discriminate against clutter and noise while compensating for frequency-dependent propagation effects. As a consequence of the significant dielectric-properties contrast between normal and malignant tissue, localized regions of large backscatter energy levels in the image correspond to malignant tumors. A data-adaptive algorithm for removing artifacts in the received signals due to backscatter from the skin-breast interface is also presented. The effectiveness of these algorithms is demonstrated using a variety of numerical breast phantoms based on anatomically realistic MRI-derived FDTD models of the breast. Very small (2 mm) malignant tumors embedded within the complex fibroglandular structure of the breast are easily detected above the background clutter. The MIST approach is shown to offer significant improvement in performance over previous UWB microwave breast cancer detection techniques based on simpler focusing schemes.
Colonization of Tomato Seedlings by Bioluminescent <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i> Under Different Humidity Regimes (2011)

Tomato bacterial canker, caused by Clavibacter michiganensis subsp. michiganensis, is transmitted by infected or infested seed and mechanically from plant to plant. Wounds occurring during seedling production and crop maintenance facilitate the dissemination of the pathogen. However, the effects of environmental factors on C. michiganensis subsp. michiganensis translocation and growth as an endophyte have not been fully elucidated. A virulent, stable, constitutively bioluminescent C. michiganensis subsp. michiganensis strain BL-Cmm 17 coupled with an in vivo imaging system allowed visualization of the C. michiganensis subsp. michiganensis colonization process in tomato seedlings in real time. The dynamics of bacterial infection in seedlings through wounds were compared under low (45%) and high (83%) relative humidity. Bacteria multiplied rapidly in cotyledon petioles remaining after clip inoculation and moved in the stem toward both root and shoot. Luminescent signals were also observed in tomato seedling roots over time, and root development was reduced in inoculated plants maintained under both humidity regimes. Wilting was more severe in seedlings under high-humidity regimes. A strong positive correlation between light intensity and bacterial population in planta suggests that bioluminescent C. michiganensis subsp. michiganensis strains will be useful in evaluating the efficacy of bactericides and host resistance.
When can tentative decisions be used to cancel (linear or nonlinear) intersymbol interference? (With application to magnetic recording channels) (2002)

Adaptive cancellation of intersymbol interference using tentative decisions has been proposed by several researchers. These authors report satisfactory results in voiceband data transmission and satellite communications. However there are other applications where this technique is completely ineffective. One such case is cancellation of nonlinear distortion in magnetic recording channels. We formulate precise conditions under which tentative decisions can be effectively used to cancel linear or nonlinear intersymbol interference. In the case of magnetic recording channels, we show that these conditions are satisfied by the precursor interference generated by inductive read heads, resulting in an improvement of the noise margin, of 2 dB at the output of a symbol-by-symbol detector or 1 dB at the output of a Viterbi decoder at a bit error rate of 10/sup -9/. This technique has been incorporated in an experimental VLSI partial response maximum likelihood (PRML) receiver and the results confirmed by laboratory measurements. We also show that no improvement is obtained when this technique is used to compensate nonlinear distortion, which is another common impairment of magnetic recording channels, and we establish fundamental limits for the improvement achievable by any nonlinear equalization technique in magnetic recording.
Surface permanent magnet synchronous machine design for saliency-tracking self-sensing position estimation at zero and low speeds (2010)

Elimination of externally mounted position sensors and their associated cables is a goal for virtually all drive manufacturers. This paper addresses design methods of surface permanent magnet (SPM) synchronous machines for saliency-tracking self-sensing (position sensorless) position estimation. Machine saliency is created by stator magnetic saturation due to the rotor zigzag leakage flux from surface permanent magnets. Using the machine saliency created by zigzag leakage flux can allow a SPM machine to be suitable for saliency-tracking position estimation without the need of any further special rotor design modification. In addition, another major benefit is achieved, i.e. a saliency role reversal whereby L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> >L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</sub> . This has the advantage of reducing machine cross-saturation and increasing the feasible region for accurate position estimation. All the design procedures are verified by the finite element analysis (FEA), and a 50 W SPM machine prototype is used for performance validation.
Scanning System for Laser Velocimeter (1987)

Interference fringes remain parallel and focus-spot diameter same. Scanning system proposed for laser velocimeter (laser Doppler anemometer) to maintain constant beam-crossing angle and beam-waist diameter maintaining beam waist locations at crossing points. As target fluid scanned, interference fringes formed by crossing beams remain parallel and the focus-spot diameter same. System allows accurate velocity profiles obtained in wind tunnels and other fluid flow systems.
Abstract 2155: The origins and functional consequences of ETS gene fusions in prostate cancer (2011)

Abstract The purpose of this study is to unravel the cellular mechanisms underlying the oncogenic ETS gene fusions, which are a hallmark of prostate cancer development. Recurrent gene fusions involving the 5’untranslated region of the androgen-regulated gene TMPRSS2 and the ETS family genes are observed in a majority of prostate cancers. Among the ETS family gene fusions, the TMPRSS2-ERG fusions involving the 5’untranslated region of TMPRSS2 with the ERG gene are the most common and found in approximately 50% of prostate cancers. However, the origins and functional consequences of ETS gene fusions are not clear. Using dual color fluorescence in situ hybridization (FISH), we demonstrate that stimulation with dihydrotestosterone (DHT) induces proximity between TMPRSS2 and ERG genomic loci in LNCaP cells, which are androgen sensitive and lack the TMPRSS2-ERG gene fusions. This effect was dependent on androgen receptor (AR). Importantly, androgen did not induce proximity between the TMPRSS2 and ERG loci in DU145 human prostate cancer cells, which are androgen insensitive. Further, a combination of androgen signaling and genotoxic stress that induces DNA double strand breaks results in the formation of TMPRSS2-ERG gene fusions in LNCaP cells. Interestingly, we observe that the ERG protein formed as a result of gene fusion binds to the promoter of wild type ERG and activates its transcription. The VCaP cell line that endogenously harbors the TMPRSS2-ERG gene fusion has high levels of wild type ERG. Treatment with androgens induces the expression of both the TMPRSS2-ERG and wild type ERG transcripts in VCaP cells. Lenti virus mediated stable over expression of TMPRSS2-ERG in PC3 cells results in an increase in the expression levels of wild type ERG. This auto-activation of wild type ERG is observed in about 50% of clinically localized and 25% of metastatic prostate cancers harboring the TMPRSS2-ERG gene fusions, but not in ETS negative prostate cancers. Taken together, our studies provide a mechanistic framework for the up-regulation of ERG transcription in prostate cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2155. doi:10.1158/1538-7445.AM2011-2155
Transfer of Chemically Modified Graphene with Retention of Functionality for Surface Engineering (2016)

Single-layer graphene chemically reduced by the Birch process delaminates from a Si/SiOx substrate when exposed to an ethanol/water mixture, enabling transfer of chemically functionalized graphene to arbitrary substrates such as metals, dielectrics, and polymers. Unlike in previous reports, the graphene retains hydrogen, methyl, and aryl functional groups during the transfer process. This enables one to functionalize the receiving substrate with the properties of the chemically modified graphene (CMG). For instance, magnetic force microscopy shows that the previously reported magnetic properties of partially hydrogenated graphene remain after transfer. We also transfer hydrogenated graphene from its copper growth substrate to a Si/SiOx wafer and thermally dehydrogenate it to demonstrate a polymer- and etchant-free graphene transfer for potential use in transmission electron microscopy. Finally, we show that the Birch reduction facilitates delamination of CMG by weakening van der Waals forces between graphene and its substrate.