gebhart/patrepeval huggingface dataset:
Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation (2016)

For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.
Palmprint Based Multidimensional Fuzzy Vault Scheme (2014)

Fuzzy vault scheme (FVS) is one of the most popular biometric cryptosystems for biometric template protection. However, error correcting code (ECC) proposed in FVS is not appropriate to deal with real-valued biometric intraclass variances. In this paper, we propose a multidimensional fuzzy vault scheme (MDFVS) in which a general subspace error-tolerant mechanism is designed and embedded into FVS to handle intraclass variances. Palmprint is one of the most important biometrics; to protect palmprint templates; a palmprint based MDFVS implementation is also presented. Experimental results show that the proposed scheme not only can deal with intraclass variances effectively but also could maintain the accuracy and meanwhile enhance security.
Radiation Properties of One-Dimensional Quasirandom Antenna Arrays Based on Rudin-Shapiro Sequences (2005)

The development of exotic new materials, such as metamaterials, has created strong interest within the electromagnetics (EM) community for possible new phenomenologies and device applications, with particular attention to periodicity-induced phenomena, such as photonic bandgaps (PBG). Within this context, motivated by the fairly recent discovery in X-ray crystallography of "quasicrystals," whose diffraction patterns display unusual characteristics that are associated with "aperiodic order," we have undertaken a systematic study of how these exotic effects manifest themselves in the radiation properties of aperiodically-configured antenna arrays. The background for these studies, with promising example configurations, has been reported in a previous publication [V. Pierro et al., IEEE Trans. Antennas Propagat., vol. 53, No. 2, pp. 635-644, Feb. 2005]. In the present paper, we pay attention to various configurations generated by Rudin-Shapiro (RS) sequences, which constitute one of the simplest conceivable examples of deterministic aperiodic geometries featuring quasirandom (dis)order. After presentation and review of relevant background material, the radiation properties of one-dimensional RS-based antenna arrays are analyzed, followed by illustrative numerical parametric studies to validate the theoretical models. Design parameters and potential practical applications are also given attention.
Algorithms for Large, Sparse Network Alignment Problems (2009)

We propose a new distributed algorithm for sparse variants of the network alignment problem, which occurs in a variety of data mining areas including systems biology, database matching, and computer vision. Our algorithm uses a belief propagation heuristic and provides near optimal solutions for this NP-hard combinatorial optimization problem. We show that our algorithm is faster and outperforms or ties existing algorithms on synthetic problems, a problem in bioinformatics, and a problem in ontology matching. We also provide a unified framework for studying and comparing all network alignment solvers.
Conjugative transposition of Tn916 requires the excisive and integrative activities of the transposon-encoded integrase (1991)

Transposon Tn916 is a 16.4-kb broad-host-range conjugative transposon originally detected in the chromosome of Enterococcus faecalis DS16. Transposition of Tn916 and related transposons involves excision of a free, nonreplicative, covalently closed circular intermediate that is substrate for integration. Excisive recombination requires two transposon-encoded proteins, Xis-Tn and Int-Tn, whereas the latter protein alone is sufficient for integration. Here we report that conjugative transposition of Tn916 requires the presence of a functional integrase in both donor and recipient strains. We have constructed a mutant, designated Tn916-int1, by replacing the gene directing synthesis of Int-Tn by an allele inactivated in vitro. In mating experiments, transfer of Tn916-int1 from Bacillus subtilis to E. faecalis was detected only when the transposon-encoded integrase was supplied by trans-complementation in both the donor and the recipient. These results suggest that conjugative transposition of Tn916 requires circularization of the element in the donor followed by transfer and integration of the nonreplicative intermediate in the recipient.
Green diesel from Fischer-Tropsch Synthesis: challenges and hurdles. (2007)

Abstract: Kyoto’s protocol respects the view that, within the context of worldwide preservation and improvement, the quality of life is impossible to maintain without bringing forward new and replacement technologies. Energy supply is perhaps the most significant contributing vector and it is, in consequence, intrinsically linked to nearly all environmental actions. Liquid fuels, such as diesel oil, for transportation and heating needs, are in the centre of these preoccupations. The Fischer-Tropsch Synthesis is an “old ” technology but it can be adapted for use with syngas, biosyngas or biogas, for the production of diesel oil. Such diesel fuel oil, when coming from renewable sources, such as “biomass”, is called “green diesel”. This present work outlines the actual status of the FTS technology and details the scientific challenges, and the technical hurdles, associated with the use of renewable feedstocks and the newly developed “nanometric catalysts”. A recently commenced Canadian R&amp;D project in this technical area is also briefly presented.
<title>Statistical metrology for interlevel dielectric thickness variation</title> (1994)

Statistical metrology seeks to assess the sources and magnitude of variation in semiconductor manufacturing. The methodology emphasizes electrical measurements resulting from short process flows, statistical design of experiments and analysis of data, and close coupling to technology computer aided design tools for the interpretation of data. In this paper, we apply statistical metrology to interlevel dielectric thickness variation. Capacitive test structures, in conjunction with resistive line width structures and two-dimensional capacitance simulations, are used to estimate ILD thickness for a variety of layout and process factors in a poly-metal BPSG planarization process. The methodology is successful in highlighting the key factors, including underlying structure line width spacing,and finger length that impact ILD thickness. Future work will examine other planarization processes, including chemical mechanical polishing.
Economic, Ecological, Food Safety, and Social Consequences of the Deployment of Bt Transgenic Plants (2002)

Transgenic plants expressing insecticidal proteins from the bacterium, Bacillus thuringiensis (Bt), are revolutionizing agriculture. Bt, which had limited use as a foliar insecticide, has become a major insecticide because genes that produce Bt toxins have been engineered into major crops grown on 11.4 million ha worldwide in 2000. Based on the data collected to date, generally these crops have shown positive economic benefits to growers and reduced the use of other insecticides. The potential ecological and human health consequences of Bt plants, including effects on nontarget organisms, food safety, and the development of resistant insect populations, are being compared for Bt plants and alternative insect management strategies. Scientists do not have full knowledge of the risks and benefits of any insect management strategies. Bt plants were deployed with the expectation that the risks would be lower than current or alternative technologies and that the benefits would be greater. Based on the data to date, these expectations seem valid.
Limited angle breast ultrasound tomography with <i>a priori</i> information and artifact removal (2017)

In B-mode images from dual-sided ultrasound, it has been shown that by delineating structures suspected of being relatively homogeneous, one can enhance limited angle tomography to produce speed of sound images in the same view as X-ray Digital Breast Tomography (DBT). This could allow better breast cancer detection and discrimination, as well as improved registration of the ultrasound and X-ray images, because of the similarity of SOS and X-ray contrast in the breast. However, this speed of sound reconstruction method relies strongly on B-mode or other reflection mode segmentation. If that information is limited or incorrect, artifacts will appear in the reconstructed images. Therefore, the iterative speed of sound reconstruction algorithm has been modified in a manner of simultaneously utilizing the image segmentations and removing most artifacts. The first step of incorporating a priori information is solved by any nonlinearnonconvex optimization method while artifact removal is accomplished by employing the fast split Bregman method to perform total-variation (TV) regularization for image denoising. The proposed method was demonstrated in simplified simulations of our dual-sided ultrasound scanner. To speed these computations two opposed 40-element ultrasound linear arrays with 0.5 MHz center frequency were simulated for imaging objects in a uniform background. The proposed speed of sound reconstruction method worked well with both bent-ray and full-wave inversion methods. This is also the first demonstration of successful full-wave medical ultrasound tomography in the limited angle geometry. Presented results lend credibility to a possible translation of this method to clinical breast imaging.
TotalRecall: A Bilingual Concordance in National Digital Learning Project - CANDLE (2003)

This paper describes a Web-based English-Chinese concordance system, TotalRecall, being developed in National Digital Learning Project – CANDLE, to promote translation reuse and encourage authentic and idiomatic use in second language learning. We exploited and structured existing high-quality translations from the bilingual Sinorama Magazine to build the concordance of authentic text and translation. Novel approaches were taken to provide high-precision bilingual alignment on the sentence, phrase and word levels. A browser-based user interface also developed for ease of access over the Internet. Users can search for word, phrase or expression in English or Chinese. The Web-based user interface facilitates the recording of the user actions to provide data for further research.
Lasing in Al following photoionization and neutralization in the presence of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">H</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>: The role of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mrow><mml:mi mathvariant="normal">H</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="normal">−</mml:mi></mml:mrow></mml:msup></mml:mrow></mml:math> (1994)

Atomic Al develops a population inversion and stimulated emission in the resonance lines when a solid target in a ${\mathrm{H}}_{2}$ buffer gas is irradiated with ArF 1930-\AA{} laser light. We present experimental evidence that the ${\mathrm{H}}^{\mathrm{\ensuremath{-}}}$ ion is responsible for this effect, through charge-neutralizing collisions with ${\mathrm{Al}}^{+}$.
Unsymmetrical Diaryl Sulfones through Palladium-Catalyzed Coupling of Aryl Boronic Acids and Arylsulfonyl Chlorides (2004)

[reaction: see text] A simple and efficient method for the synthesis of unsymmetrical diaryl sulfones using the palladium-catalyzed coupling of aryl boronic acids and arylsulfonyl chlorides has been developed. High product yields, a short reaction time, and mild reaction conditions are important features of this method.
Queue management for QoS provision build on network processor (2004)

Network processor is a kind of programmable processor performing network computing with special design and optimization. It can be viewed as a tight-coupled multi-processor system due to its architecture of multiple in-chip processors, high-speed buses and other function components. The design and development of networking systems using network processors is an emerging field that offers numerous challenges and opportunities. This paper provides the design and implementation of queue management module combining buffer management and packet scheduling for QoS provision, which uses Intel's network processor and follows the relative differentiated service model. As the key issues, system synchronization, task assignment to threads, and design difficulties are discussed in the paper.
Characterization of the nanoscale properties of individual amyloid fibrils (2006)

We report the detailed mechanical characterization of individual amyloid fibrils by atomic force microscopy and spectroscopy. These self-assembling materials, formed here from the protein insulin, were shown to have a strength of 0.6 ± 0.4 GPa, comparable to that of steel (0.6–1.8 GPa), and a mechanical stiffness, as measured by Young's modulus, of 3.3 ± 0.4 GPa, comparable to that of silk (1–10 GPa). The values of these parameters reveal that the fibrils possess properties that make these structures highly attractive for future technological applications. In addition, analysis of the solution-state growth kinetics indicated a breakage rate constant of 1.7 ± 1.3 × 10 −8 s −1 , which reveals that a fibril 10 μm in length breaks spontaneously on average every 47 min, suggesting that internal fracturing is likely to be of fundamental importance in the proliferation of amyloid fibrils and therefore for understanding the progression of their associated pathogenic disorders.
FAST COLOUR RASTER GRAPHICS USING AN ARRAY PROCESSOR (1980)

This paper shows how an array processor technique can be used as the basis of an animated (fast) colour raster display. It is amenable to expansion for more colours, greater speed and resolution, and large scale integration techniques because of the regularity and low interconnectivity of an array. This technique could bring the speed and display file advantages of vector graphics to colour raster graphics at a reasonable price.
Manipulating Biomolecules with Aqueous Liquids Confined within Single-Walled Nanotubes (2009)

Confinement of molecules inside nanoscale pores has become an important method for exploiting new dynamics not happening in bulk systems and for fabricating novel structures. Molecules that are encapsulated in nanopores are difficult to control with respect to their position and activity. On the basis of molecular dynamics simulations, we have achieved controllable manipulation, both in space and time, of biomolecules with aqueous liquids inside a single-walled nanotube by using an external charge or a group of external charges. The remarkable manipulation abilities are attributed to the single-walled structure of the nanotube that the electrostatic interactions of charges inside and outside the single-walled nanotube are strong enough, and the charge-induced dipole-orientation ordering of water confined in the nanochannel so that water has a strong interaction with the external charge. These designs are expected to serve as lab-in-nanotube for the interactions and chemical reactions of molecules especially biomolecules, and have wide applications in nanotechnology and biotechnology.
Operon prediction using both genome-specific and general genomic information (2006)

We have carried out a systematic analysis of the contribution of a set of selected features that include three new features to the accuracy of operon prediction. Our analyses have led to a number of new insights about operon prediction, including that (i) different features have different levels of discerning power when used on adjacent gene pairs with different ranges of intergenic distance, (ii) certain features are universally useful for operon prediction while others are more genome-specific and (iii) the prediction reliability of operons is dependent on intergenic distances. Based on these new insights, our newly developed operon-prediction program achieves more accurate operon prediction than the previous ones, and it uses features that are most readily available from genomic sequences. Our prediction results indicate that our (non-linear) decision tree-based classifier can predict operons in a prokaryotic genome very accurately when a substantial number of operons in the genome are already known. For example, the prediction accuracy of our program can reach 90.2 and 93.7% on Bacillus subtilis and Escherichia coli genomes, respectively. When no such information is available, our (linear) logistic function-based classifier can reach the prediction accuracy at 84.6 and 83.3% for E.coli and B.subtilis, respectively.
Tendon stem/progenitor cell ageing: Modulation and rejuvenation (2019)

Tendon ageing is a complicated process caused by multifaceted pathways and ageing plays a critical role in the occurrence and severity of tendon injury. The role of tendon stem/progenitor cells (TSPCs) in tendon maintenance and regeneration has received increasing attention in recent years. The decreased capacity of TSPCs in seniors contributes to impaired tendon functions and raises questions as to what extent these cells either affect, or cause ageing, and whether these age-related cellular alterations are caused by intrinsic factors or the cellular environment. In this review, recent discoveries concerning the biological characteristics of TSPCs and age-related changes in TSPCs, including the effects of cellular epigenetic alterations and the mechanisms involved in the ageing process, are analyzed. During the ageing process, TSPCs ageing might occur as a natural part of the tendon ageing, but could also result from decreased levels of growth factor, hormone deficits and changes in other related factors. Here, we discuss methods that might induce the rejuvenation of TSPC functions that are impaired during ageing, including moderate exercise, cell extracellular matrix condition, growth factors and hormones; these methods aim to rejuvenate the features of youthfulness with the ultimate goal of improving human health during ageing.
Nanofabricated periodic arrays of silver elliptical discs as SERS substrates (2008)

Abstract Signal enhancement observed in surface‐enhanced Raman spectroscopy (SERS) is attributable to the presence of noble‐metal nanostructures on substrate surfaces. The rational development of SERS‐active substrates depends critically on the homogeneity and intensity of surface plasmon resonances, properties that are strongly dependent on both the morphology and dielectric properties of the metals and composite materials making up the SERS substrates. Enhancement can be controlled by the shape, size, and spacing of metallic nanoparticles. Previous studies in our group have shown that arrays of elliptical nanodiscs have promising geometries for this purpose. Using electron beam lithography (EBL), we fabricate close‐packed arrays of these discs with lateral dimensions ranging from 300:50 to 300:300 nm (long axis : short axis). The arrays are composed of a negative photoresist that, once the lithography process is complete, are coated with a noble metal through physical vapor deposition (PVD). In this work, optimum thickness and deposition rate of noble metal are determined for these substrates. The lithographically produced nanopatterns are studied by Raman spectroscopy to examine the effect of altering the elliptical aspect ratio on SERS activity, while scanning electron microscopy (SEM) is used to examine pattern surfaces post lithographic development and post noble‐metal deposition. Atomic force microscopy (AFM) is used to inspect the roughness of substrate surfaces. Reproducibility between different arrays of the same pattern ranges from 12 to 28%. Homogeneity of our uniform‐morphology EBL/PVD‐fabricated substrates is examined and compared to our random‐morphology polymer nanocomposite substrates. Using rhodamine 6G as an analyte, an increase in SERS signal is noted as the aspect ratio of ellipses goes from 6:1 to 6:6. Our experimental data, in terms of trends in SERS activity, correlate with trends in field enhancements calculated using a simple electrostatic model and with the magnitude of the broad red‐shifted spectral continuum observed for the substrates. Copyright © 2008 John Wiley & Sons, Ltd.
Video compression via constructs (2002)

Current video compression standards compress video sequences at NTSC quality with factors in the range of 10-100, like in MPEG-1 and MPEC-2. To operate beyond this range, that is, MPEG-4, radically new techniques are needed. We discuss one such technique called generative video (GV). Video compression is realized in GV in two steps. First, the video sequence is reduced to constructs. Constructs are world images, corresponding to augmented images containing the non-redundant information on the sequence, and window, figure, motion, and signal processing operators, representing video sequence properties. Second, the world images are spatially compressed. The video sequence is reconstructed by applying the various operators to the decompressed world images. We apply GV to a 10 sec video sequence of a real 3-D scene and obtain compression ratios of about 2260 and 4520 for two experiments done with different quantization codebooks. The reconstructed video sequence exhibits very good perceptual quality.
Spider: A Large-Scale Human-Labeled Dataset for Complex and Cross-Domain Semantic Parsing and Text-to-SQL Task (2018)

Tao Yu, Rui Zhang, Kai Yang, Michihiro Yasunaga, Dongxu Wang, Zifan Li, James Ma, Irene Li, Qingning Yao, Shanelle Roman, Zilin Zhang, Dragomir Radev. Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing. 2018.
Crawling Facebook for social network analysis purposes (2011)

We describe our work in the collection and analysis of massive data describing the connections between participants to online social networks. Alternative approaches to social network data collection are defined and evaluated in practice, against the popular Facebook Web site. Thanks to our ad-hoc, privacy-compliant crawlers, two large samples, comprising millions of connections, have been collected; the data is anonymous and organized as an undirected graph. We describe a set of tools that we developed to analyze specific properties of such social-network graphs, i.e., among others, degree distribution, centrality measures, scaling laws and distribution of friendship.