gebhart/patrepeval huggingface dataset:
Learning Probabilistic Models of Relational Structure (2001)

Most real-world data is stored in relational form. In contrast, most statistical learning methods work with &quot;flat&quot; data representations, forcing us to convert our data into a form that loses much of the relational struc- ture. The recently introduced framework of probabilistic relational models (PRMs) allows us to represent probabilistic models over multiple entities that utilize the relations between them. In this paper, we propose the use of probabilistic models not only for the attributes in a relational model, but for the rela- tional structure itself. We propose two mechanisms for modeling structural uncertainty: reference uncertainty and existence uncertainty. We describe the appropriate conditions for using each model and present learning algorithms for each. We present experimental results showing that the learned models can be used to pre- dict relational structure and, moreover, the observed relational structure can be used to provide better pre- dictions for the attributes in the model.
Adaptive Control Tutorial (2006)

Preface Acknowledgements List of acronyms 1. Introduction 2. Parametric models 3. Parameter identification: continuous time 4. Parameter identification: discrete time 5. Continuous-time model reference adaptive control 6. Continuous-time adaptive pole placement control 7. Adaptive control for discrete-time systems 8. Adaptive control of nonlinear systems Appendix Bibliography Index.
Complex Optimization in Answer Set Programming (2011)

Preference handling and optimization are indispensable means for addressing non-trivial applications in Answer Set Programming (ASP). However, their implementation becomes difficult whenever they bring about a significant increase in computational complexity. As a consequence, existing ASP systems do not offer complex optimization capacities, supporting, for instance, inclusion-based minimization or Pareto efficiency. Rather, such complex criteria are typically addressed by resorting to dedicated modeling techniques, like saturation. Unlike the ease of common ASP modeling, however, these techniques are rather involved and hardly usable by ASP laymen. We address this problem by developing a general implementation technique by means of meta-programming, thus reusing existing ASP systems to capture various forms of qualitative preferences among answer sets. In this way, complex preferences and optimization capacities become readily available for ASP applications.
Next-Generation Copper, Nickel and Lead-Free Metallization Products for Next-Generation Devices and Applications (2015)

Flip-chip interconnect and 3-D packaging applications must utilize reliable, high-performance metallization products in order to produce highly-efficient, low-cost microelectronic devices. As the market moves to shrinking device architectural features and increasingly difficult pattern layouts, more demand is placed on the plating performance of the copper, nickel and lead-free solder products used to create these interconnects. Additionally, the move from traditional C4 bumping processes with lead-free solder to capping processes utilizing copper pillars with lead-free solder requires metal interfaces that are highly compatible in order to avoid defects that could occur. In this paper, next-generation products developed for copper pillar, nickel barrier, and lead-free solder plating will be introduced that are capable of delivering high-performance and highly reliable metallic interconnects. The additive packages that were selected and optimized allowing for increased rate of electrodeposition, uniform height control with controllable pillar shape and smooth surface morphology will be discussed. Furthermore, compatibility will be shown for a lead-free solder cap electrodeposited onto copper pillar structures, both with and without nickel barrier layers, on large pore features (≥50 μm diameter) and micro pore features (≤20 μm diameter) for both bumping and capping applications.
A maximum-entropy chinese parser augmented by transformation-based learning (2004)

Parsing, the task of identifying syntactic components, e.g., noun and verb phrases, in a sentence, is one of the fundamental tasks in natural language processing. Many natural language applications such as spoken-language understanding, machine translation, and information extraction, would benefit from, or even require, high accuracy parsing as a preprocessing step. Even though most state-of-the-art statistical parsers were initially constructed for parsing in English, most of them are not language-specific, in that they do not rely on properties of the language that are specific to English. Therefore, construction of a parser in a given language becomes a matter of retraining the statistical parameters with a Treebank in the corresponding language. The development of the Chinese treebank [Xia et al. 2000] spurred the construction of parsers for Chinese. However, Chinese as a language poses some unique problems for the development of a statistical parser, the most apparent being word segmentation. Since words in written Chinese are not delimited in the same way as in Western languages, the first problem that needs to be solved before an existing statistical method can be applied to Chinese is to identify the word boundaries. This is a step that is neglected by most pre-existing Chinese parsers, which assume that the input data has already been pre-segmented. This article describes a character-based statistical parser, which gives the best performance to-date on the Chinese treebank data. We augment an existing maximum entropy parser with transformation-based learning, creating a parser that can operate at the character level. We present experiments that show that our parser achieves results that are close to those achievable under perfect word segmentation conditions.
Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology (2014)

Azobenzene has been widely used as a photoregulator due to its reversible photoisomerization, large structural change between E and Z isomers, high photoisomerization yield, and high chemical stability. On the other hand, some azobenzene derivatives can be used as universal quenchers for many fluorophores. Nucleic acid is a good candidate to be modified because it is not only the template of gene expression but also widely used for building well-organized nanostructures and nanodevices. Because the size and polarity distribution of the azobenzene molecule is similar to a nucleobase pair, the introduction of azobenzene into nucleic acids has been shown to be an ingenious molecular design for constructing light-switching biosystems or light-driven nanomachines. Here we review recent advances in azobenzene-modified nucleic acids and their applications for artificial regulation of gene expression and enzymatic reactions, construction of photoresponsive nanostructures and nanodevices, molecular beacons, as well as obtaining structural information using the introduced azobenzene as an internal probe. In particular, nucleic acids bearing multiple azobenzenes can be used as a novel artificial nanomaterial with merits of high sequence specificity, regular duplex structure, and high photoregulation efficiency. The combination of functional groups with biomolecules may further advance the development of chemical biotechnology and biomolecular engineering.
Approach to maximize increased details and minimize color distortion for IKONOS and QuickBird image fusion (2004)

Both IKONOS and QuickBird offer 11-bit panchromatic and multispectral data in which more details can be extracted from scenes that are very dark under shadows or very washed out due to excessive sun reflectance. In this work, a discrete cosine transform (DCT)-based single-scale Retinex (SSR) technique is presented to extract the highest possible spatial details from the panchromatic image, and a minimum/maximum percent cutoff approach is used to preserve the most spectral information in the multispectral imagery. By fusing those two images, the typical bright target recovery (BTR) response can be avoided. Furthermore, to address the color distortion problem by the fusion process, a fast intensity hue saturation (IHS) image fusion technique with direct saturation stretching in RGB space is also proposed. To verify the efficacy of the proposed techniques, experiments are conducted using real IKONOS and QuickBird imagery covering different areas. Experimental results have shown that the perfect performance, maximizing increased details and minimizing color distortion, is achieved.
RNA templating the epigenome (2011)

Cellular pathways must be synergized, controlled and organized to manage homeostasis. To achieve high selectivity within the crowded cellular milieu the cell utilizes scaffolding complexes whose role is to bring molecules in proximity thereby controlling and enhancing intermolecular interactions and signaling events. To date, scaffolds have been shown to be composed of proteinaceous units; however, recent evidence has supported the idea that non-coding RNAs may also play a similar role. In this point of view article we discuss recent data on ncRNA scaffolds, with particular focus on ncRNA HOTAIR. Using our current knowledge of signaling networks we discuss the role that RNA may play in writing and regulating histone modifications and the information needed for correct gene expression. Further, we speculate on additional, yet undiscovered roles that ncRNAs may be playing as molecular scaffolds.
Concurrency control for B-trees with differential indices (2002)

We present an indexing system where a database index is divided into two parts: the main index located on disk and the differential index in the main memory. Both indices are implemented as B-trees. All updates performed by active transactions are written in the differential index. Periodically, writes of committed transactions are transferred from differential index to the main index as a batch-update operation. Thus, updates falling into the same leaf of the tree can be performed simultaneously. In addition, the system offers a simple recovery scheme. After a system crash, no undo operations are needed and redo operations need only write to the main memory.
Immune privilege induced by cotransplantation of islet and allogeneic testicular cells. (2001)

Cotransplantation of islets with FasL+ sertoli cells induces local immune privilege and allows long-term graft survival without systemic immunosuppression.
Performance of Three Nucleic Acid Amplification Tests for Detection of <i>Chlamydia trachomatis</i> and <i>Neisseria gonorrhoeae</i> by Use of Self-Collected Vaginal Swabs Obtained via an Internet-Based Screening Program (2009)

Use of self-obtained vaginal specimens processed by nucleic acid amplification tests (NAATs) has significantly increased the utilization of nontraditional locations for Chlamydia trachomatis and Neisseria gonorrhoeae screening programs. One important emerging source of such venues includes home-based self-sampling kits available via the Internet. The objective of our study was to evaluate the performance of three commercially available NAATs (Becton-Dickinson ProbeTec SDA, Gen-Probe Aptima Combo2 TMA, and Roche Amplicor PCR) for detection of C. trachomatis and N. gonorrhoeae in vaginal samples obtained via an Internet-based screening program. From July 2004 to August 2005, 500 self-collected vaginal swabs were tested for C. trachomatis and N. gonorrhoeae by using all three NAATs. Another 500 samples were collected between August 2005 and November 2007 and tested by ProbeTec and Combo2; PCR testing was discontinued due to low specificity for N. gonorrhoeae. All tests were conducted according to the manufacturers' procedures; the "gold standard" for an infected C. trachomatis or N. gonorrhoeae patient was defined as > or = 2 positive NAAT results. Of the first 500 swabs submitted, 46 were C. trachomatis infected (9.2%) and 5 were N. gonorrhoeae infected (1.0%), and 3 of these were coinfected (0.6%). All C. trachomatis and N. gonorrhoeae Combo2-positive/ProbeTec-negative samples were confirmed as true positives by an alternative NAAT. For C. trachomatis, ProbeTec, Combo2, and PCR had sensitivities of 82.6%, 100%, and 100%, with specificities of 100%, 100%, and 99.3%, respectively. For N. gonorrhoeae, ProbeTec, Combo2, and PCR had sensitivities of 80%, 100%, and 100%, with specificities of 100%, 100%, and 98.8%, respectively. Of the total 1,000 swabs submitted, 92 were C. trachomatis infected (9.2%) and 15 were N. gonorrhoeae infected (1.5%), and 7 of these were coinfected (0.7%). There were no ProbeTec-positive/Combo2-negative samples. For C. trachomatis, ProbeTec and Combo2 had sensitivities of 81.5% and 100%, with specificities of 100% and 100%, respectively. For N. gonorrhoeae, ProbeTec and Combo2 had sensitivities of 80% and 100%, with specificities of 100% and 100%, respectively. Overall, ProbeTec had 17 C. trachomatis false-negative results (1.7%) and 3 N. gonorrhoeae false-negative results (0.3%), while Combo2 had none. Our results were consistent with the sensitivities and specificities stated by the manufacturers. NAATs perform well for detection of chlamydia and gonorrhea with self-obtained vaginal swabs shipped in a dry state to a laboratory. For 1,000 self-collected vaginal swabs tested by NAATs, the sensitivities for C. trachomatis and N. gonorrhoeae for Combo2 were 100% and 100%, while they were 81.5% and 80%, respectively, for ProbeTec. For 500 PCR samples, the C. trachomatis sensitivity was 100% and the N. gonorrhoeae sensitivity was 100%, with specificities of 99.3% and 98.8%, respectively.
Comparison of Microwave Assisted Solvothermal and Hydrothermal Syntheses of LiFePO<sub>4</sub>/C Nanocomposite Cathodes for Lithium Ion Batteries (2008)

Highly crystalline LiFePO4 nanorods have been synthesized within a short reaction time of 5−15 min at <300 °C by a novel microwave-solvothermal (MW-ST) process and a microwave-hydrothermal (MS-HT) process. In order to improve the electrical conductivity, both an ex situ carbon coating by heating at 700 °C with sucrose the LiFePO4 obtained by the MW-ST method and an in situ carbon coating by carrying out the MW-HT process in presence of glucose (MW-HT carbonization) followed by heating at 700 °C have been pursued. The products have been characterized by X-ray diffraction, scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy, and charge−discharge measurements in lithium cells. The MW-ST method offers smaller size nanorods (25 ± 6 nm width and up to 100 nm length) compared to the MW-HT method (225 ± 6 nm width and up to 300 nm length). Annealing at 700 °C improves the rate capability and cyclability significantly without much particle growth due to an improvement in the structural order of carbon and electronic conductivity. Moreover, the LiFePO4/C nanocomposite obtained by the MW-ST method offers higher initial discharge capacity than that obtained by the MW-HT method due to a smaller particle size, illustrating that both lithium ion diffusion and electronic conductivity play a critical role in controlling the electrochemical properties.
An Efficient SSHI Interface With Increased Input Range for Piezoelectric Energy Harvesting Under Variable Conditions (2016)

Piezoelectric vibration energy harvesters have been widely researched and are increasingly employed for powering wireless sensor nodes. The synchronized switch harvesting on inductor (SSHI) circuit is one of the most efficient interfaces for piezoelectric vibration energy harvesters. However, the traditional incarnation of this circuit suffers from a significant startup issue that limits operation in low and variable amplitude vibration environments. This paper addresses this start-up issue for the SSHI rectifier by proposing a new architecture with SSHI startup circuitry. The startup circuitry monitors if the SSHI circuit is operating correctly and re-starts the SSHI interface if required. The proposed circuit is comprehensively analyzed and experimentally validated through tests conducted by integrating a commercial piezoelectric vibration energy harvester with the new interface circuit designed in a 0.35-μm HV CMOS process. Compared to conventional SSHI rectifiers, the proposed circuit significantly decreases the required minimum input excitation amplitude before energy can be harvested, making it possible to extract energy over an increased excitation range.
Dimerization and trimerization of norbornadiene by soluble rhodium catalysts (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDimerization and trimerization of norbornadiene by soluble rhodium catalystsNancy Acton, Ronald J. Roth, Thomas J. Katz, JoAnn K. Frank, Carol A. Maier, and Iain C. PaulCite this: J. Am. Chem. Soc. 1972, 94, 15, 5446–5456Publication Date (Print):July 1, 1972Publication History Published online1 May 2002Published inissue 1 July 1972https://pubs.acs.org/doi/10.1021/ja00770a048https://doi.org/10.1021/ja00770a048research-articleACS PublicationsRequest reuse permissionsArticle Views340Altmetric-Citations52LEARN 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
Molecular recognition in homogeneous transition metal catalysis: a biomimetic strategy for high selectivity (2007)

Traditional methods for selectivity control in homogeneous transition metal catalysis either employ steric effects in a binding pocket or chelate control. In a supramolecular strategy, encapsulation of the substrate can provide useful shape and size selectivity. A fully developed molecular recognition strategy involving hydrogen bonding or solvophobic forces has given almost completely regioselective functionalization of remote, unactivated C-H bonds.
Divergence of Substrate Specificity and Function in the <i>Escherichia coli</i> Hotdog-fold Thioesterase Paralogs YdiI and YbdB (2014)

The work described in this paper, and its companion paper (Wu, R., Latham, J. A., Chen, D., Farelli, J., Zhao, H., Matthews, K. Allen, K. N., and Dunaway-Mariano, D. (2014) Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry, DOI: 10.1021/bi500334v), focuses on the evolution of a pair of paralogous hotdog-fold superfamily thioesterases of E. coli, YbdB and YdiI, which share a high level of sequence identity but perform different biological functions (viz., proofreader of 2,3-dihydroxybenzoyl-holoEntB in the enterobactin biosynthetic pathway and catalyst of the 1,4-dihydoxynapthoyl-CoA hydrolysis step in the menaquinone biosynthetic pathway, respectively). In vitro substrate activity screening of a library of thioester metabolites showed that YbdB displays high activity with benzoyl-holoEntB and benzoyl-CoA substrates, marginal activity with acyl-CoA thioesters, and no activity with 1,4-dihydoxynapthoyl-CoA. YdiI, on the other hand, showed a high level of activity with its physiological substrate, significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB. These results were interpreted as evidence for substrate promiscuity that facilitates YbdB and YdiI evolvability, and divergence in substrate preference, which correlates with their assumed biological function. YdiI support of the menaquinone biosynthetic pathway was confirmed by demonstrating reduced anaerobic growth of the E. coli ydiI-knockout mutant (vs wild-type E. coli) on glucose in the presence of the electron acceptor fumarate. Bioinformatic analysis revealed that a small biological range exists for YbdB orthologs (i.e., limited to Enterobacteriales) relative to that of YdiI orthologs. The divergence in YbdB and YdiI substrate specificity detailed in this paper set the stage for their structural analyses reported in the companion paper.
Characteristics of hexokinase, pyruvate kinase, and glucose‐6‐phosphate dehydrogenase during adult and neonatal reticulocyte maturation (1985)

Erythrocytes from adults and newborn infants (at term and premature) were separated by Percoll density gradient centrifugation into four fractions of increasing density. Glycolytic enzymes, especially the age-dependent ones, hexokinase (EC 2.7.1.1, HK), pyruvate kinase (EC 2.7.1.40, PK), and glucose-6-phosphate dehydrogenase (EC 1.1.1.49, G6PD) were studied during reticulocyte maturation and further red cell senescence. Analysis of the fraction with lowest density showed an almost linear and steep decline of HK, PK, and G6PD activity with a decreasing number of reticulocytes. In the next three fractions of increasing density, the activity decline was far less. These data are therefore illustrative for a biphasic activity decay pattern of HK, PK, and G6PD during both adult and neonatal red cell aging. The strong decline in HK activity could not be ascribed to the disappearance of a particulate (mitochondrial) bound fraction of the enzyme during reticulocyte maturation. All hexokinase activity in human reticulocytes was found to be cytosolic in contrast with rabbit reticulocytes in which 70% of HK activity was particulate.
Methylation of single sites within the herpes simplex virus tk coding region and the simian virus 40 T-antigen intron causes gene inactivation. (1994)

In order to determine whether partial methylation of the herpes simplex virus (HSV) tk gene prevents tk gene expression, the HSV tk gene was cloned as single-stranded DNA. By in vitro second-strand DNA synthesis, specific HSV tk gene segments were methylated, and the hemimethylated DNA molecules were microinjected into thymidine kinase-negative rat2 cells. Conversion of the hemimethylated DNA into symmetrical methylated DNA and integration into the host genome occurred early after gene transfer, before the cells entered into the S phase. HSV tk gene expression was inhibited either by promoter methylation or by methylation of the coding region. Using the HindIII-SphI HSV tk DNA fragment as a primer for in vitro DNA synthesis, all cytosine residues within the coding region, from +499 to +1309, were selectively methylated. This specific methylation pattern caused inactivation of the HSV tk gene, while methylation of the cytosine residues within the nucleotide sequence from +811 to +1309 had no effect on HSV tk gene activity. We also methylated single HpaII sites within the HSV tk gene using a specific methylated primer for in vitro DNA synthesis. We found that of the 16 HSV tk HpaII sites, methylation of 6 single sites caused HSV tk inactivation. All six of these "methylation-sensitive" sites are within the coding region, including the HpaII-6 site, which is 571 bp downstream from the transcription start site. The sites HpaII-7 to HpaII-16 were all methylation insensitive. We further inserted separately the methylation-sensitive HSV tk HpaII-6 site and the methylation-insensitive HpaII-13 site as DNA segments (32-mer) into the intron region of the simian virus 40 T antigen (TaqI site). Methylation of these HpaII sites caused inhibition of simian virus 40 T-antigen synthesis.