gebhart/patrepeval huggingface dataset:
The Tetramethylammonium Chloride (™AC) Method for Screening cDNA Libraries with Highly Degenerate Oligonucleotide Probes Obtained by Reverse Translation of Amino Acid Sequences (2003)

If an unknown protem is purified and available in relatively small amounts, it is possible to determine the sequences of short internal peptides (). In order to determine the whole sequence of the protein by cDNA cloning, one of the peptides of perhaps five to seven amino acids may be reverse translated into nucleotide sequence resulting in a 15–21 base long deoxyribonucleotide. Because of codon degeneracy, the number of possible oligonucleotides may be more than several hundred, which must be present in order to ensure that the correct sequence is represented. Only one of these oligonucleotides corresponds to the correct sequence. Traditionally long stretches of DNA are hybridized in buffered saline solution where physicochemical parameters affecting the annealing are well known (, ). However, for shorter DNA sequences, the melting temperature of each oligonucleotide depends on the G + C content, since G:C base pairs possessing three hydrogen bonds interact more strongly than A:T base pairs with two hydrogen bonds. The different oligonucleotides in a mixture will thus possess different melting temperatures. This means that in buffered saline solution, one usually chooses a melting temperature that is so low that the oligonucleotide with the lowest G + C content can hybridize. However, in doing so, it is possible that oligonucleotides with a higher G + C content may form stable hybrids with mismatches resulting in the cloning of artifact cDNAs. Even though this procedure has been used successfully (-), it is more convenient to use a different buffer type that contains tetramethylammonium chloride (TMAC), since it has been reported that this salt selectively binds to and stabilizes A:T base pairs so that their melting temperature becomes similar to that of G:C base pairs (-).
Efficient Run-time Monitoring Using Shadow Processing. (1995)

General purpose multiprocessors are becoming increasingly common. We propose using pairs of processors, one running an ordinary application program and the other monitoring the application&apos;s execution. We call the processor doing the monitoring a &quot;shadow processor, &quot; as it &quot;shadows&quot; the main processor&apos;s execution. We have developed a prototype shadow processing system which supports full-size programs written in C. Our system instruments an executable user program in C to obtain a &quot;main process&quot; and a &quot;shadow process.&quot; The main process performs computations from the original program, occasionally communicating a few key values to the shadow process. The shadow process follows the main process, checking pointer and array accesses and detecting memory leaks. The overhead to the main process is very low --- almost always less than 10%. Further, since the shadow process avoids repeating some of the computations from the input program, it runs much faster than a single process pe...
Assessment of the response to imatinib in chronic myeloid leukemia patients – comparison between the FISH, multiplex and RT‐PCR methods (2004)

Molecular remission according to FISH and multiplex RT-PCR can be achieved by imatinib within 1 yr of therapy. There is a good correlation between the FISH, multiplex and RQ-PCR results in terms of the kinetics of disappearance of the BCR-ABL transcript and the predictability of each method for the other. Although RQ-PCR is the most sensitive method for molecular follow-up, FISH and multiplex RT-PCR can be used as complementary tools, at least during the early period of treatment.
Preparation of electrodeposited cobalt nanowires (2006)

Nanostructured magnetic materials have great interest because of their applications in high-density magnetic information storage and for magnetic sensors. The electrodeposition of materials into porous alumina arrays is a suitable technique to produce nanomaterials, since highly ordered uniform nanomaterials can be obtained simply and cheaply. In this work, template-assisted Co nanowire arrays were prepared by electrodeposition into nanometer-sized pores of an alumite film using a two-electrode electrochemical cell. The Co nanowires were electrodeposited from a solution of 400 g/L of CoSO4.7H2O and 40 g/L of H3BO3. The morphology of the samples was investigated by means of TEM and AFM. The structural characteristic of the samples was examined using XRD, EDX and FTIR, which confirm the cobalt nanowire formation.
FIR multichannel identification using weighted cumulant matrix (2000)

Blind identification of FIR multichannel using higher-order statistics (HOS) is investigated. A new linear approach is proposed which generalizes the weighted slices method for single FIR channel estimation. By finding the proper linear combinations, channel response is obtained from the weighted cumulant matrix with Toeplitz structure. This general algorithm works for both single user and multiuser scenario. It relaxes the identification condition of the original method and demonstrates performance improvement.
Learning Bayesian Networks: Search Methods and Experimental Results (1995)

We discuss Bayesian approaches for learning Bayesian networks from data. First, we review a metric for computing the relative posterior probability of a network structure given data developed by Heckerman et al. (1994a,b,c). We see that the metric has a property useful for inferring causation from data. Next, we describe search methods for identifying network structures with high posterior probabilities. We describe polynomial algorithms for finding the highestscoring network structures in the special case where every node has at most k = 1 parent. We show that the general case (k > 1) is NP-hard, and review heuristic search algorithms for this general case. Finally, we describe a methodology for evaluating learning algorithms, and use this methodology to evaluate various scoring metrics and search procedures.
Simultaneous control of time-dependent population transfer dynamics and wave-packet quantum interferences in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Li</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>by shaped ultrafast pulses (2002)

Ultrafast pulse shapes are used to control simultaneously the optimal population transfer coefficients and rotational wave-packet quantum interferences in the $E{}^{1}{\ensuremath{\Sigma}}_{g}^{+}$ state of ${\mathrm{Li}}_{2}$ $({\ensuremath{\nu}}_{E}=9,$ ${J}_{E}=27$ and 29). By dividing the spectral bandwidth of the ultrafast pulses into multiple ``control domains'' centered on each resonant wavelength, the population transfer coefficients can be manipulated independently of the wave-packet interferences to maximize the ${\mathrm{Li}}_{2}$ photoionization yield at arbitrary short pump-probe time delays. To investigate the population transfer coefficients with and without wave-packet interferences, respectively, the pump polarization is set to be either parallel to or at the magic angle (\ensuremath{\sim}55\ifmmode^\circ\else\textdegree\fi{}) relative to the probe polarization. A comparison is made between phases that are symmetric and antisymmetric about the resonances. The effects of resonant and nonresonant frequencies are separately established and quantified. It is estimated that up to 90% of the possible nonresonant Rabi oscillations can be brought into phase simultaneously for each rovibrational state in the wave packet, while at the same time a constant phase offset added to one of the control domains establishes the phase of the wave-packet interference.
IL-17-producing CD8+ T lymphocytes from psoriasis skin plaques are cytotoxic effector cells that secrete Th17-related cytokines (2009)

IL-17-producing CD4+ T lymphocytes (Th17) are currently considered relevant participants in the pathogenesis of psoriasis skin lesions. However, little is known about the potential role of IL-17-producing CD8+ T cells, which are also present at the psoriatic plaque. We have addressed the functional characterization of this CD8+ subtype of T lymphocytes from psoriasis patients. Our results show that CD8+IL-17+ cells from psoriasis-inflamed skin tissue produce TNF-alpha and IFN-gamma (Th1-related cytokines) as well as IL-17, IL-21, and IL-22 (Th17-related cytokines) efficiently. A significant up-regulation of the RORC transcription factor is also observed. These cells are refractory to Tregs but show a proliferative response to anti-CD3/CD28 stimulation that is enhanced by IL-12 and IL-15. Blocking of TNF-alpha activity inhibits TCR-mediated activation and IL-17 production. CD8+IL-17+ T cells are cytotoxic cells that display TCR/CD3-mediated cytotoxic abilities to kill target cells. Thus, CD8+IL-17+ T cells share some key features with Th17 cells and exhibit remarkable differential abilities attributable to the CD8+ lineage of T lymphocytes, adding new insights into the functional resources of IL-17-producing cells from human epidermis that could be of potential interest to our understanding of the pathogenesis of psoriasis.
Formation of single crystalline ZnO nanotubes without catalysts and templates (2007)

Oxide and nitride nanotubes have gained attention for their large surface areas, wide energy band gaps, and hydrophilic natures for various innovative applications. These nanotubes were either grown by templates or multistep processes with uncontrollable crystallinity. Here the authors show that single crystal ZnO nanotubes can be directly grown on planar substrates without using catalysts and templates. These results are guided by the theory of nucleation and the vapor-solid crystal growth mechanism, which is applicable for transforming other nanowires or nanorods into nanotubular structures.
Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences (2013)

Next-Generation Sequencing (NGS) technologies have dramatically revolutionised research in many fields of genetics. The ability to sequence many individuals from one or multiple populations at a genomic scale has greatly enhanced population genetics studies and made it a data-driven discipline. Recently, researchers have proposed statistical modelling to address genotyping uncertainty associated with NGS data. However, an ongoing debate is whether it is more beneficial to increase the number of sequenced individuals or the per-sample sequencing depth for estimating genetic variation. Through extensive simulations, I assessed the accuracy of estimating nucleotide diversity, detecting polymorphic sites, and predicting population structure under different experimental scenarios. Results show that the greatest accuracy for estimating population genetics parameters is achieved by employing a large sample size, despite single individuals being sequenced at low depth. Under some circumstances, the minimum sequencing depth for obtaining accurate estimates of allele frequencies and to identify polymorphic sites is [Formula: see text], where both alleles are more likely to have been sequenced. On the other hand, inferences of population structure are more accurate at very large sample sizes, even with extremely low sequencing depth. This all points to the conclusion that under various experimental scenarios, in cost-limited population genetics studies, large sample sizes at low sequencing depth are desirable to achieve high accuracy. These findings will help researchers design their experimental set-ups and guide further investigation on the effect of protocol design for genetic research.
Physicochemical properties of copper oxide loaded alumina in methane combustion (1990)

Copper oxide was deposited on gamma alumina with loadings between 2.1 and 9.2 wt % of CuO. The activity of these solids was measured in the catalytic combustion of methane before and after an aging test performed at 1340 K. The state and the environment of the copper species was followed by UV–VIS reflectance spectroscopy. Carbon monoxide adsorption on fresh and aged samples was performed and studied by infrared spectroscopy. For fresh samples, the number of active centres decreases when the copper loading increases. At low amounts of CuO, copper oxide does not have the spectral features of bulk oxide whereas the 9.2 wt % CuO sample behaves like bulk CuO. At moderate conversion levels the catalytic activity is directly proportional to the absorbance of the vCO band of carbon monoxide bonded to surface CuII ions of the copper oxide phase, showing that the sites responsible for the catalytic activity are revealed by carbon monoxide adsorption. After the ageing test, the catalytic activity strongly decreases because of the formation of copper aluminate, copper being in the oxidation state + 1 or +2 according to the stoichiometry of the reactants mixture. In that case, the remaining activity is also proportional to the absorbance of the vCO band of carbon monoxide bonded to CuII ions of the copper oxide phase.
Relative rates of biosynthesis of collagen type I, type V and type VI in calf cornea (1991)

The biosynthesis of type I, type V and type VI collagens was studied by incubation of calf corneas in vitro with [3H]proline as a marker. Pepsin-solubilized collagen types were isolated by salt fractionation and quantified by SDS/PAGE. Expressed as proportions of the total hydroxyproline solubilized, corneal stroma comprised 75% type I, 8% type V and 17% type VI collagen. The rates of [3H]proline incorporation, linear up to 24 h for each collagen type, were highest for type VI collagen and lowest for type I collagen. From pulse-chase experiments, the calculated apparent half-lives for types I, V and VI collagens were 36 h, 10 h and 6 h respectively.
Chemotherapeutic agents circumvent emergence of dasatinib-resistant BCR-ABL kinase mutations in a precise mouse model of Philadelphia chromosome–positive acute lymphoblastic leukemia (2011)

The introduction of cultured p185(BCR-ABL)-expressing (p185+) Arf (-/-) pre-B cells into healthy syngeneic mice induces aggressive acute lymphoblastic leukemia (ALL) that genetically and phenotypically mimics the human disease. We adapted this high-throughput Philadelphia chromosome-positive (Ph(+)) ALL animal model for in vivo luminescent imaging to investigate disease progression, targeted therapeutic response, and ALL relapse in living mice. Mice bearing high leukemic burdens (simulating human Ph(+) ALL at diagnosis) entered remission on maximally intensive, twice-daily dasatinib therapy, but invariably relapsed with disseminated and/or central nervous system disease. Although relapse was frequently accompanied by the eventual appearance of leukemic clones harboring BCR-ABL kinase domain (KD) mutations that confer drug resistance, their clonal emergence required prolonged dasatinib exposure. KD P-loop mutations predominated in mice receiving less intensive therapy, whereas high-dose treatment selected for T315I "gatekeeper" mutations resistant to all 3 Food and Drug Administration-approved BCR-ABL kinase inhibitors. The addition of dexamethasone and/or L-asparaginase to reduced-intensity dasatinib therapy improved long-term survival of the majority of mice that received all 3 drugs. Although non-tumor-cell-autonomous mechanisms can prevent full eradication of dasatinib-refractory ALL in this clinically relevant model, the emergence of resistance to BCR-ABL kinase inhibitors can be effectively circumvented by the addition of "conventional" chemotherapeutic agents with alternate antileukemic mechanisms of action.
Convergence of Laplacian Eigenmaps (2007)

Geometrically based methods for various tasks of machine learning have attracted considerable attention over the last few years. In this paper we show convergence of eigenvectors of the point cloud Laplacian to the eigenfunctions of the Laplace-Beltrami operator on the underlying manifold, thus establishing the first convergence results for a spectral dimensionality reduction algorithm in the manifold setting.
A model for ionic polymer metal composites as sensors (2006)

This paper introduces a comprehensive model of sensors based on ionic polymer metal composites (IPMCs) working in air. Significant quantities ruling the sensing properties of IPMC-based sensors are taken into account and the dynamics of the sensors are modelled.
Investigation of Performance of SCN-1 Pure Glass as Sealant Used in SOFC (2010)

As its name implies, self-healing glass seal has the potential of restoring its mechanical properties upon being reheated to stack operating temperature, even when it has experienced some cooling induced damage/crack at room temperature. Such a self-healing feature is desirable for achieving high seal reliability during thermal cycling. On the other hand, self-healing glass is also characterized by its low mechanical stiffness and high creep rate at the typical operating temperature of SOFCs. Therefore, from a design’s perspective, it is important to know the long term geometric stability and thermal mechanical behaviors of the self-healing glass under the stack operating conditions. These predictive capabilities will guide the design and optimization of a reliable sealing system that potentially utilizes self-healing glass as well as other ceramic seal components in achieving the ultimate goal of SOFC. In this report, we focused on predicting the effects of various generic seal design parameters on the stresses in the seal. For this purpose, we take the test cell used in the leakage test for compliant glass seals conducted in PNNL as our initial modeling geometry. The effect of the ceramic stopper on the geometry stability of the self-healing glass sealants is studied first. Then we explored the effect of various interfaces such as stopper and glass, stopper and PEN, as well stopper and IC plate, on the geometry stability and reliability of glass during the operating and cooling processes.
Single event mitigation for Xilinx 7-series FPGAs (2018)

This study establishes the optimal Single Event Upset (SEU) mitigation strategy for Xilinx's 7-Series Field Programmable Gate Arrays (FPGAs). This enables 7-Series FPGAs to be utilised in systems with high exposure to ionising radiation over Xilinx's smaller, radiation-hardened 4-Series and 5-Series FPGAs. The optimal strategy maximises system up-time, with minimal complexity and minimal risk of damaging the target FPGA device. Four SEU mitigation techniques are analysed and compared. Three of these are external scrubbing techniques; blind, readback, and blind with Frame Address Register (FAR) verification; with the fourth being Xilinx's internal scrubber, the Soft Error Mitigation (SEM) Intellectual Property (IP) core. The initial comparisons are quantitative, comparing the four methods for traits that lend themselves to meeting the criteria of the optimal scrubber. The techniques are then compared quantitatively to establish theoretical whole-device scan times for each technique given a range of errors to be corrected. These scan times can be utilised to determine which technique performs the fastest given the error rate and technique parameters. The calculations and resultant data can be computed for every device in the 7-series range. The findings suggest that the optimal solution is to opt not for a traditional mitigation strategy, but for a dynamic mitigation strategy. The fastest scrubber is the SEM IP Core, predominantly due to being internal to the FPGA, and as error rates increase, there becomes a crossover point whereby the blind scrubber with FAR verification comes into play to scrub at higher error rates in a deterministic way. Additionally, it finds that the configuration scrubber can operate at higher frequencies in comparison to NASAs recommendation of scrubbing at an order of magnitude higher than the expected SEU rate. These results provide the optimal scrubber for the 7-Series FPGA, and bring into question the recommendation of scrubbing at a higher order of magnitude than the expected error rate. Additionally, Xilinx's guidance for their FPGAs brings in an essential bit ratio which determines what proportion of the FPGAs is actually being utilised by the design, thereby decreasing the proportion of the errors that impact the design as opposed to empty areas of the FPGA, and hence increasing the speed at which scrubbing can take place with reference to NASAs recommendation.
Simultaneous feature-based identification and track fusion (2002)

A tactical pilot typically experiences difficulty in maintaining accurate identification on multiple-interacting targets in the presence of clutter. We propose a multilevel feature-based association (MFBA) algorithm to aid a pilot in a dynamic multi-target environment. We investigate MFBA for an air-to-ground scenario in which a plane, equipped with a high-range resolution radar sensor, processes kinematic and target features at different levels, and fuses these features to simultaneously track and identify targets.
Improved Detection for H.264 Encoded Video Sequences over Mobile Networks (2005)

Real-time video conferencing or streaming over mobile network introduces a challenge to the endto-end design of the whole system. Due to the realtime character of these applications, there are no retransmissions possible at the transport layer and therefore any errors result in packet loss at the receiver. This article investigates error resilience methods, especially improvements of the detection granularity to minimize perceptual visual quality degradation at the receiver. Costs of the additional error resilience is evaluated and a combination of H.264 resilience features, improved error detection and error concealment is finally tested. 1
Enzymes in organic synthesis: synthesis of highly enantiomerically pure 1,2-epoxy aldehydes, epoxy alcohols, thiirane, aziridine, and glyceraldehyde 3-phosphate (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymes in organic synthesis: synthesis of highly enantiomerically pure 1,2-epoxy aldehydes, epoxy alcohols, thiirane, aziridine, and glyceraldehyde 3-phosphateRichard L. Pederson, Kevin K. C. Liu, James F. Rutan, Lihren Chen, and Chi Huey WongCite this: J. Org. Chem. 1990, 55, 16, 4897–4901Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/jo00303a026https://doi.org/10.1021/jo00303a026research-articleACS PublicationsRequest reuse permissionsArticle Views976Altmetric-Citations66LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts