gebhart/patrepeval huggingface dataset:
The feasibility of coherent energy transfer in microtubules (2014)

It was once purported that biological systems were far too 'warm and wet' to support quantum phenomena mainly owing to thermal effects disrupting quantum coherence. However, recent experimental results and theoretical analyses have shown that thermal energy may assist, rather than disrupt, quantum coherent transport, especially in the 'dry' hydrophobic interiors of biomolecules. Specifically, evidence has been accumulating for the necessary involvement of quantum coherent energy transfer between uniquely arranged chromophores in light harvesting photosynthetic complexes. The 'tubulin' subunit proteins, which comprise microtubules, also possess a distinct architecture of chromophores, namely aromatic amino acids, including tryptophan. The geometry and dipolar properties of these aromatics are similar to those found in photosynthetic units indicating that tubulin may support coherent energy transfer. Tubulin aggregated into microtubule geometric lattices may support such energy transfer, which could be important for biological signalling and communication essential to living processes. Here, we perform a computational investigation of energy transfer between chromophoric amino acids in tubulin via dipole excitations coupled to the surrounding thermal environment. We present the spatial structure and energetic properties of the tryptophan residues in the microtubule constituent protein tubulin. Plausibility arguments for the conditions favouring a quantum mechanism of signal propagation along a microtubule are provided. Overall, we find that coherent energy transfer in tubulin and microtubules is biologically feasible.
Parametric mode operation of a hyperbolic Penning trap for Fourier transform mass spectrometry (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTParametric mode operation of a hyperbolic Penning trap for Fourier transform mass spectrometryD. L. Rempel, E. B. Ledford, S. K. Huang, and M. L. GrossCite this: Anal. Chem. 1987, 59, 20, 2527–2532Publication Date (Print):October 15, 1987Publication History Published online1 May 2002Published inissue 15 October 1987https://pubs.acs.org/doi/10.1021/ac00147a018https://doi.org/10.1021/ac00147a018research-articleACS PublicationsRequest reuse permissionsArticle Views138Altmetric-Citations67LEARN 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
한국의 몽골 유학생들에게 나타난 제2 언어정체성과 언어학습 노력에 관한 연구 (2018)

본 논문은 후기구조주의적 관점에서 한국에서 학습하는 네 명의 몽골학생들의 정체성이 한국이라는 학습환경의 이데올로기와 가치체계 안에서 어떻게 영향을 받는지를 살펴보았다. 본 연구를 위하여 Doglas Fir Group(2016)의 준거틀(framework)을 사용하여 데이터를 분석하였다. 거시적 단계(macro-level)에서 한국 학생들에게서 발견한 것은 첫째, ‘외국학생들이 영어를 잘할 것이라는 기대’, 둘째, ‘사회경제적으로 덜 발전된 나라 출신의 아시아 소수민족 학생들이 학문적으로도 수준이 낮을 것’이라고 보는 이데올로기를 발견할 수 있었다. 이것은 한국이라는 학습환경에서 몽골 학생들이 쉽게 소외될 수 있는 불공평한 힘의 구조(power structures)를 보여준다. 중간 단계(meso-level)에서는 한국학습환경의 배타성이 네 명의 학생들의 경험을 통해 나타났다. 하지만 여러 어려움에도 불구하고, 이 학생들이 본인들이 과거 몽골에서의 학습자로써 구축한 긍정적인 학문적 자아상을 바탕으로 학습활동에 능동적으로 임하는 모습이 구체적으로 관찰되었고, 그 결과 새로운 정체성을 협상하는 모습을 발견할 수 있었다(negotiate). 본 연구는 사회적으로 구축된 정체성(socially constructed identities)과 이데올로기가 역동적인 학습주체(learner agency)를 통하여 도전 받는다는 것을 보여준다. 흥미로운 것은, 아시아 학생들에게 목표언어인 한국어 이외에도 영어 능숙도가 한국학습환경에 수월하게 수용될 수 있는 힘을 준다는 것도 밝혀주었다는 점이다.
Computational analysis of slot coating on a tensioned web (1998)

Abstract When a web (thin substrate with considerable flexibility) travels through a coating applicator in free span between the two supporting rollers, the gap between web and coating applicator is determined primarily by the hydrodynamic stresses in the coating flow and externally applied tension on the web. The elastohydrodynamic interaction between the tensioned‐web deformation and the viscous liquid flow in the coating bead has not been extensively studied, in spite of its practical importance. A tensioned‐web wrapped around a slot coater was analyzed here by finite‐element computations. The externally applied tension on the web typically is much greater than the force due to hydrodynamic stresses. Hence, tension in the web is assumed to be constant in the process direction tangential to the web surface. By neglecting the bending and twisting moments as in the approximation of membrane theory, the shape of the flexible web is determined by a normal stress balance equation, quite similar to that of the free surface of coating flow with a constant surface tension. In this work, elastohydrodynamic effects in tensioned‐web slot coating are examined with respect to variations of the liquid feeding rate and externally applied web tension, web wrap angle, and other variables.
Measurements of attractive forces between proteins and end-grafted poly(ethylene glycol) chains (1997)

The surface force apparatus was used to measure directly the molecular forces between streptavidin and lipid bilayers displaying grafted Mr 2,000 poly(ethylene glycol) (PEG). These measurements provide direct evidence for the formation of relatively strong attractive forces between PEG and protein. At low compressive loads, the forces were repulsive, but they became attractive when the proteins were pressed into the polymer layer at higher loads. The adhesion was sufficiently robust that separation of the streptavidin and PEG uprooted anchored polymer from the supporting membrane. These interactions altered the properties of the grafted chains. After the onset of the attraction, the polymer continued to bind protein for several hours. The changes were not due to protein denaturation. These data demonstrate directly that the biological activity of PEG is not due solely to properties of simple polymers such as the excluded volume. It is also coupled to the competitive interactions between solvent and other materials such as proteins for the chain segments and to the ability of this material to adopt higher order intrachain structures.
Automatic sensor clustering : connectivity for the internet of things (2011)

Current predictions from industry envision that within a decade, the Internet will bepopulated by tens of billion of devices. Already today, smart Internet devices havesensors that provide an enormous potential for creating new applications. The chal-lenge at hand is how this information can be shared on the future Internet in order tounlock the full capability of applications to interact with the real world. Therefore,there is an urgent need for scalable and agile support for connecting people, placesand artifacts in applications via a vast number of devices and sensors on the futureInternet. Clearly, this poses a challenge of sharing and thus storage of so-called con-text information. Beyond scalable context storage lays another challenge to identifyand locate devices that are important to the user. In a support for billion of contin-uously changing sensors and actuators, a search engine would not work. Thereforean intelligent way to group devices is required. This thesis deals with mainly three issues: Firstly, propose a method for devicesto be reachable and thus addressable independent of their location in the infrastruc-ture. Secondly, how can the proposed method be used to insure automatic connectiv-ity anywhere between clients and services offered by the device, in particular associ-ated sensors and actuators. Thirdly, how can the grouping and support be combinedand used to dynamically associate sensors from across the Internet with applications,assuming that the aforementioned grouping exists. The proposed solution to the firstissue is to store identifier-locator pairs in an overlay. For the second issue we pro-pose a sensor socket introduced which exploits the identifier/locator pairs to enabledevice mobility. The third issue is addressed by providing a group-cast operation inthe sensor socket. This arrangement allows communication with peers determinedby a grouping algorithm which operates on context information on the context over-lay. Thus we have enabled the creation of automated dynamic clustering of sensorsand actuators in the Internet of Things.The sensor socket is designed as a stand-alone module to support any contextoverlay that provides the same basic functionality. The sensor socket embodiesa support to automatically interconnect and communicate with devices. Using abridging software, remote devices can be dynamically found and inserted into legacylocal area network where current devices can benefit from the connectivity. For fu-ture work the bridge can be extended to actively locate and identify nearby sensorsthat are unable to participate in the overlay network otherwise.
The usefulness of natural philosophy: the Royal Society and the culture of practical utility in the later eighteenth century (1999)

From its very beginning the Royal Society was regarded by many, if not most, of its founders as centrally concerned with practical improvement. How could it be otherwise? The study of nature was not only a pious act in and of itself – a reading of the book of nature – but it was also the way in which God's Providence would provide discoveries for the relief of man's estate. The early ideologues of the Society, such as Robert Boyle and Thomas Sprat, continually returned to the usefulness of natural philosophy in that sense. They were no doubt stimulated in this not only by the narrow purpose of gaining support for their novel institution but also by quite genuine beliefs about the role that natural philosophy could play in creating a stable political and economic order through which prosperity might increase and the years of civil war be left behind. However, by the late seventeenth century the Society, especially after the demise of the history of trades programme, became much more a deliberative forum than a projective organization.
A transform approach for analyzing and constructing quasi-cyclic low-density parity-check codes (2011)

An approach for studying quasi-cyclic codes based on matrix transformations via Fourier transforms and row and column permutations is presented. These transformations put a parity-check matrix in the form of an array of circulant matrices into a diagonal array of matrices of the same size over an extension field. The approach is used to characterize certain structural properties of low-density parity-check (LDPC) codes such as the girths of their Tanner graphs. Many constructions of quasi-cyclic LDPC codes can be unified under the proposed approach.
The Design Concept and the Phonological System of Huangji Jingshi: Shengyin Changhe Tu: On the Influence of Image-Number Yijing Studies on the Creation of the Korean Alphabet (2012)

Among the extant rhyme tables of the Song Dynasty, Shao Yong’s (1011–1077) Huangji Jingshi: Shengyin Changhe Tu is the most unique. It is different from other phonological tables, such as Yunjing and Qiyin Lue , that were designed for the interpretation of fanqie formulae in terms of arrangement and phonological terminology. However, most contemporary scholars have failed to notice the unique design in Shengyin Changhe Tu and merely follow Karlgren’s paradigm, which contends that a phonological table objectively reflects certain dialectal phonological features through the prism of historical phonology. Instead, the present paper approaches the question of how the rhyme table is structured from the perspective of the history of phonological philosophy rather than historical phonology. By so doing, the role of philologists is reconsidered as that of a rhyme designer constructing an ideal sound system, rather than that of a dialectologist investigating a real sound system. The following questions are then discussed: What is the purpose for compiling such a work as Shengyin Changhe Tu and what are its design motivations? Can other scholars’ reconstructions of the sound system and sound values of Shengyin Changhe Tu be considered reasonable? In addition to Shengyin Changhe Tu , did the Image-Number Yijing School have any impact on the design of the later phonological tables? In this way the author wishes to develop a new humanistic approach toward understanding of the rhyme tables in order to correct the blind spots and flaws resulting from an overly extreme tendency toward scientism.
ESSCertIDv2 Update for RFC 3161 (2010)

This document updates RFC 3161.It allows the use of ESSCertIDv2, as defined in RFC 5035, to specify the hash of a signer certificate when the hash is calculated with a function other than the Secure Hash Algorithm (SHA-1).
Nuclear Organization and Dynamics of 7SK RNA in Regulating Gene Expression (2010)

Noncoding RNAs play important roles in various aspects of gene regulation. We have identified 7SK RNA to be enriched in nuclear speckles or interchromatin granule clusters (IGCs), a subnuclear domain enriched in pre-mRNA processing factors. 7SK RNA, in association with HEXIM 1 and 2, is involved in the inhibition of transcriptional elongation by RNA polymerase II. Inhibition occurs via sequestration of the active P-TEFb kinase complex (CDK 9 and Cyclin T1/T2a/b or K) that is involved in phosphorylating the C-terminal domain of RNA polymerase II. Our results demonstrate that knock-down of 7SK RNA, by specific antisense oligonucleotides, results in the mislocalization of nuclear speckle constituents in a transcription-dependent manner, and the transcriptional up-regulation of a RNA polymerase II transcribed reporter gene locus. Furthermore, 7SK RNA transiently associates with a stably integrated reporter gene locus upon transcriptional down-regulation and its presence correlates with the efficient displacement of P-TEFb constituents from the locus. Our results suggest that 7SK RNA plays a role in modulating the available level of P-TEFb upon transcriptional down-regulation by sequestering its constituents in nuclear speckles.
An In-solution Ultrasonication-assisted Digestion Method for Improved Extracellular Matrix Proteome Coverage (2009)

Epithelial cell behavior is coordinated by the composition of the surrounding extracellular matrix (ECM); thus ECM protein identification is critical for understanding normal biology and disease states. Proteomic analyses of ECM proteins have been hindered by the insoluble and digestion-resistant nature of ECM. Here we explore the utility of combining rapid ultrasonication- and surfactant-assisted digestion for the detailed proteomics analysis of ECM samples. When compared with traditional overnight digestion, this optimized method dramatically improved the sequence coverage for collagen I, revealed the presence of hundreds of previously unidentified proteins in Matrigel, and identified a protein profile for ECM isolated from rat mammary glands that was substantially different from that found in Matrigel. In a three-dimensional culture assay to investigate epithelial cell-ECM interactions, mammary epithelial cells were found to undergo extensive branching morphogenesis when plated with mammary gland-derived matrix in comparison with Matrigel. Cumulatively these data highlight the tissue-specific nature of ECM composition and function and underscore the need for optimized techniques, such as those described here, for the proteomics characterization of ECM samples.
Automatic image quality assessment and measurement of fetal head in two-dimensional ultrasound image (2017)

Owing to the inconsistent image quality existing in routine obstetric ultrasound (US) scans that leads to a large intraobserver and interobserver variability, the aim of this study is to develop a quality-assured, fully automated US fetal head measurement system. A texton-based fetal head segmentation is used as a prerequisite step to obtain the head region. Textons are calculated using a filter bank designed specific for US fetal head structure. Both shape- and anatomic-based features calculated from the segmented head region are then fed into a random forest classifier to determine the quality of the image (e.g., whether the image is acquired from a correct imaging plane), from which fetal head measurements [biparietal diameter (BPD), occipital-frontal diameter (OFD), and head circumference (HC)] are derived. The experimental results show a good performance of our method for US quality assessment and fetal head measurements. The overall precision for automatic image quality assessment is 95.24% with 87.5% sensitivity and 100% specificity, while segmentation performance shows 99.27% ([Formula: see text]) of accuracy, 97.07% ([Formula: see text]) of sensitivity, 2.23 mm ([Formula: see text]) of the maximum symmetric contour distance, and 0.84 mm ([Formula: see text]) of the average symmetric contour distance. The statistical analysis results using paired [Formula: see text]-test and Bland-Altman plots analysis indicate that the 95% limits of agreement for inter observer variability between the automated measurements and the senior expert measurements are 2.7 mm of BPD, 5.8 mm of OFD, and 10.4 mm of HC, whereas the mean differences are [Formula: see text], [Formula: see text], and [Formula: see text], respectively. These narrow 95% limits of agreements indicate a good level of consistency between the automated and the senior expert's measurements.
On stability in the presence of analog erasure channels (2008)

Consider a discrete-time networked control scheme, in which the controller has direct access to noisy measurements of the plant¿s output, but the controller and the actuator are connected via a link that features Bernoulli erasure events. We determine necessary and sufficient conditions for the stabilizability of an unstable linear and time-invariant plant. We show that these conditions are identical for two types of actuators: (1) (Type I) Processing at the actuator has access to the plant¿s model; (2) (Type II) Processing at the actuator uses a universal algorithm that does not depend on the model of the plant. We also identify cases where availability of acknowledgements over the controller-actuator channel is not required for stability. We also consider decentralized networked control structures, where two or more independent controller-link-actuator assemblies have access to different measurements of the plant¿s output.
Mining policies from enterprise network configuration (2009)

Few studies so far have examined the nature of reachability policies in enterprise networks. A better understanding of reachability policies could both inform future approaches to network design as well as current network configuration mechanisms. In this paper, we introduce the notion of a policy unit, which is an abstract representation of how the policies implemented in a network apply to different network hosts. We develop an approach for reverse-engineering a network's policy units from its router configuration. We apply this approach to the configurations of five productions networks, including three university and two private enterprises. Through our empirical study, we validate that policy units capture useful characteristics of a network's policy. We also obtain insights into the nature of the policies implemented in modern enterprises. For example, we find most hosts in these networks are subject to nearly identical reachability policies at Layer 3.
Scalable gradient-based tuning of continuous regularization hyperparameters (2016)

Hyperparameter selection generally relies on running multiple full training trials, with selection based on validation set performance. We propose a gradient-based approach for locally adjusting hyperparameters during training of the model. Hyperparameters are adjusted so as to make the model parameter gradients, and hence updates, more advantageous for the validation cost. We explore the approach for tuning regularization hyperparameters and find that in experiments on MNIST, SVHN and CIFAR-10, the resulting regularization levels are within the optimal regions. The additional computational cost depends on how frequently the hyperparameters are trained, but the tested scheme adds only 30% computational overhead regardless of the model size. Since the method is significantly less computationally demanding compared to similar gradient-based approaches to hyperparameter optimization, and consistently finds good hyperparameter values, it can be a useful tool for training neural network models.
Adaptive trellis-coded multiple-phase-shift keying for Rayleigh fading channels (1994)

An adaptive scheme for trellis-coded modulation of MPSK signals, called adaptive trellis-coded multiple-phaseshift keying (ATCMPSK), is proposed for slowly Rayleigh fading channels. The adaptive scheme employs a slightly modified rate 1/2 convolutional encoder and the corresponding Viterbi decoder to realize a family of codes of different rates which are employed according to channel conditions. During poor channel conditions, trellis-coded QPSK (TCQPSK) together with repetition schemes are employed. As channel conditions improve, higher rate schemes such as trellis-coded 16 PSK are used. An interleaving/ deinterleaving method suitable for the adaptive scheme is proposed. Theoretical bounds for the error performance and an exact expression for the throughput of the proposed adaptive scheme are derived, and are compared against simulation results. Simulations have been performed to measure the performance of the scheme for different parameters and some nonideal conditions. It is shown that ATCMPSK results in considerable improvement in bit-error-rate (BER) performance of MPSK signals. Under ideal conditions, gains in the range of 3-20 dB are achieved over conventional fixed rate pragmatic trellis-coded schemes.
Design alternatives for shared memory multiprocessors (2002)

We consider the design alternatives available for building the next generation DSM machine (e.g., the choice of memory architecture, network technology, and amount and location of per-node remote data cache). To investigate this design space, we have simulated five applications on a wide variety of possible DSM architectures that employ significantly different caching techniques. We also examine the impact of using a special purpose system interconnect designed specifically to support low latency DSM operation versus using a powerful off the shelf system interconnect. We found that two architectures have the best combination of good average performance and reasonable worst case performance: CC-NUMA employing a moderate sized DRAM remote access cache (RAC) and a hybrid CC-NUMA/S-COMA architecture called AS-COMA or adaptive S-COMA. Both pure CC-NUMA and pure S-COMA have serious performance problems for some applications, while CC-NUMA employing an SRAM RAC does not perform as well as the two architectures that employ larger DRAM caches. The paper concludes with several recommendations to designers of next generation DSM machines, complete with a discussion of the issues that led to each recommendation so that designers can decide which ones are relevant to them given changes in technology and corporate priorities.