gebhart/patrepeval huggingface dataset:
Storage and query processing optimizations for hierarchically-organized data (2006)

Hierarchical data can be found anywhere multiple pieces of information are connected by a relationship. The first chapter of my thesis deals with processing relational queries in the context of a native XML storage system. We take advantage of hierarchical XML to equate the nested structure of the XML documents with the key relationship between two data items. A join query can then be rewritten as a storage scan, allowing acceleration of the query. The second chapter provides a comparison of row and oriented storage optimizations given an assumption of read-mostly data access. We focus on two, and column abstraction, to elucidate the difference between row and storage layouts. Column abstraction allows optimization of hierarchically organized data by storing repeating values only once. We extend the read-optimized relational store in the third chapter to evaluate two predicate evaluation strategies---a scan-based solution over both standard super tuples and the PAX layout, and an index-based strategy with and without a slot array in super tuples.
UAV Communications in Integrated Terrestrial and Non-terrestrial Networks (2022)

With growing interest in integrating terrestrial networks (TNs) and non-terrestrial networks (NTNs) to connect the unconnected, a key question is whether this new paradigm could also be opportunistically exploited to augment service in urban areas. We assess this possibility in the context of an integrated TN-NTN, comprising a ground cellular deployment paired with a Low Earth Orbit (LEO) satellite constellation, providing sub-6 GHz connectivity to an urban area populated by ground users (GUEs) and uncrewed aerial vehicles (UAVs). Our study reveals that offloading UAV traffic to the NTN segment drastically reduces the downlink outage of UAVs from 70% to nearly zero, also boosting their uplink signal quality as long as the LEO satellite constellation is sufficiently dense to guarantee a minimum elevation angle. Offloading UAVs to the NTN also benefits coexisting GUEs, preventing uplink outages of around 12% that GUEs would otherwise incur. Despite the limited bandwidth available below 6 GHz, NTN-offloaded UAVs meet command and control rate requirements even across an area the size of Barcelona with as many as one active UAV per cell. Smaller UAV populations yield proportionally higher rates, potentially enabling aerial broadband applications.
Exocyclic Carbons Adjacent to theN6of Adenine are Targets for Oxidation by the Escherichia coli Adaptive Response Protein AlkB (2012)

The DNA and RNA repair protein AlkB removes alkyl groups from nucleic acids by a unique iron- and α-ketoglutarate-dependent oxidation strategy. When alkylated adenines are used as AlkB targets, earlier work suggests that the initial target of oxidation can be the alkyl carbon adjacent to N1. Such may be the case with ethano-adenine (EA), a DNA adduct formed by an important anticancer drug, BCNU, whereby an initial oxidation would occur at the carbon adjacent to N1. In a previous study, several intermediates were observed suggesting a pathway involving adduct restructuring to a form that would not hinder replication, which would match biological data showing that AlkB almost completely reverses EA toxicity in vivo. The present study uses more sensitive spectroscopic methodology to reveal the complete conversion of EA to adenine; the nature of observed additional putative intermediates indicates that AlkB conducts a second oxidation event in order to release the two-carbon unit completely. The second oxidation event occurs at the exocyclic carbon adjacent to the N(6) atom of adenine. The observation of oxidation of a carbon at N(6) in EA prompted us to evaluate N(6)-methyladenine (m6A), an important epigenetic signal for DNA replication and many other cellular processes, as an AlkB substrate in DNA. Here we show that m6A is indeed a substrate for AlkB and that it is converted to adenine via its 6-hydroxymethyl derivative. The observation that AlkB can demethylate m6A in vitro suggests a role for AlkB in regulation of important cellular functions in vivo.
Cinachyramine, the Novel Alkaloid Possessing a Hydrazone and Two Aminals from Cinachyrella sp. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Fluoride penetration into the hybrid layer from a dentin adhesive. (1998)

Fluoride leached from the adhesive at a decreasing rate with time. The final rate over 112 days was 0.02 ppm/day (0.2 microgram/cm2/day). Leakage at the enamel and dentin margins was similar for both adhesives (Mann-Whitney U-test; P < or = 0.05). SEM evaluation showed the presence of a discontinuous hybrid layer of 2-3 microns. Fluoride was present within, but limited to, the hybrid layer for the FB adhesive. The penetration of fluoride could only be confirmed in areas where leakage had occurred.
Variable Acoustics by Wave Field Synthesis (2000)

Variable acoustics systems can be applied to adapt the acoustical properties of an enclosure, assuring an optimal perception of each possible performance. This thesis describes the design of a variable acoustics system, based on electro-acoustic techniques. Its contents can be related to three elements that play a role in room acoustics: analysis, synthesis and perception. A new concept of wave field analysis is described, applying linear microphone arrays. The application of microphone arrays reveals the spatial coherence of wave fields and spatial processing techniques are made accessible. The spatial processing technique applied in this thesis is the Radon transform, performing a plane wave decomposition. Array measurements show a considerable amount of nonspecular reflections within the first 100 ms of the impulse response, and some clear anisotropy until 200-300 ms after the direct sound. These results do not endorse a sharp distinction between early reflections and reverberation. Wave field synthesis denotes a technique of generating wave fronts by means of loudspeaker arrays. The application of loudspeaker arrays is inevitable in order to accurately generate sound fields with predefined temporal, spectral and spatial properties. Hence, wave field synthesis offers a volume solution, instead of the point solution offered by conventional multi-channel systems. The design of a variable acoustics system should be based on perceptually relevant parameters. Parameters relevant for perception have been described with respect to the reverberant sound field. The spatial properties are parametrized seperately from the temporal and spectral properties. Perceptual experiments reveal that the described parameters are perceptually highly relevant. A laboratory prototype system, based on a rectangular loudspeaker array configuration, has been designed and built. The reverberant sound field is generated by means of 11 plane waves, while different FIR filters are attributed to each plane wave to control the temporal and spectral properties. The early reflections are presently generated by synthesizing a limited number of mirror image sources, ignoring the presence of non-specular reflections.
The effect of water on the enantioselective hydrogenation of ethyl pyruvate and butane-2,3-dione using cinchona-modified Pt/Al2O3 (2002)

A detailed study of Pt/alumina modified with cinchona alkaloids for the catalytic enantioselective hydrogenation of ethyl pyruvate to ethyl lactate and of butane-2,3-dione to 3-hydroxybutan-2-one is reported. Catalytic and 1H NMR spectroscopic studies have been carried out on both systems to investigate the influence of water on modifier conformation and enantioselectivity. Interestingly, the presence of small amounts of water has been shown to result in an increase the proportion of the open 3 conformer of cinchonidine when it is present in dilute solutions. Increased enantioselectivity, coupled with an increase in the proportion of the open 3 conformation of cinchonidine, is observed after pretreatment of the pyruvate ester with the modifier prior to admission to the reaction vessel. In contrast, no analogous effects are observed with butane-2,3-dione. It is proposed that the enhancements in enantioselectivity are a consequence of hydrolysis of ethyl pyruvate by a process that is catalysed by the basic cinchona modifier. The pyruvic acid formed during the hydrolysis interacts with the modifier and this leads to a further enhancement in the concentration of open 3 conformer present. The results contribute to an understanding of the widely variable enantioselectivities reported in the literature for this reaction.
Sulforaphane potentiates the sensitivity of apoptosis through suppression of tnf-α-induced nf-κb activation (2007)

B5 Sulforaphane (SFN) induces apoptosis in tumor cells and inhibits inflammatory response through a poorly understood mechanism. Because the nuclear transcription factor nuclear factor κB (NF-κB) has been shown to suppress apoptosis and promote proliferation and is linked with inflammation and differentiation, we postulated that SFN modulates NF-κB activity and NF-κB-regulated geneexpression. Using human leukemia cell lines, we show that SFN potently inhibits inducible NF-κB activated by tumor necrosis factor-α (TNF-α). NF-κB suppression occurredthrough inhibition of IκBα phosphorylation, IκBα degradation, p65 phosphorylation and p65 nuclear translocation. This inhibition correlated with suppression of NF-κB-dependent genes involved in antiapoptosis (IAP1, XIAP, Bcl-2, and Bcl-xL), proliferation (cyclin D1 and c-Myc). Overall, our results suggestthat SFN inhibits NF-κB through inhibition of IκBα, leading to the suppression of expression of NF-κB-regulated gene products and enhancement of apoptosis induced by TNF-α.
Functional recovery of denervated muscle by neurotization using nerve guidance channels (2013)

Tissue-engineered muscle has been proposed as a means of repairing volumetric muscle defects to restore anatomical and functional recovery. We have previously demonstrated that denervated muscle, which is analogous to engineered muscle construct, can be reinnervated by direct transplantation of host nerve (neurotization) in a rat model. However, the use of this approach is not possible if the length of host nerve is inadequate and cannot be mobilized to the insertion site of the engineered muscle. In this study we investigated whether neurotization coupled with nerve guidance channels would increase the regeneration of neuromuscular junctions (NMJs) in completely denervated muscle and encourage neurofunctional recovery. Seventy-two Lewis rats were evaluated in three groups, a normal control group (n = 8), a denervated group (n = 32) and a neurotization coupled with nerve guidance group (n = 32). Neurofunctional behaviour and histological evaluations were performed at 4, 8, 12 and 20 weeks postoperatively. Extensor postural thrust (EPT) and compound muscle action potential (CMAP) amplitude were significantly improved in the nerve guidance group when compared with the denervated group, even though these values were different from those of the normal control group at 20 weeks postoperation. Regeneration of axons and NMJs was demonstrated histologically in the nerve guidance group. Neurotization coupled with nerve guidance channels leads to regeneration of axons and NMJs in completely denervated muscle. To our knowledge, this is the first report to show that nerve guidance can allow re-innervation in denervated muscle containing long-gap nerve injuries.
Task-based optimization of flip angle for texture analysis in MRI (2016)

Chronic liver disease is a worldwide health problem, and hepatic fibrosis (HF) is one of the hallmarks of the disease. The current reference standard for diagnosing HF is biopsy followed by pathologist examination, however this is limited by sampling error and carries risk of complications. Pathology diagnosis of HF is based on textural change in the liver as a lobular collagen network that develops within portal triads. The scale of collagen lobules is characteristically on order of 1-5 mm, which approximates the resolution limit of <i>in vivo</i> gadolinium-enhanced magnetic resonance imaging in the delayed phase. We have shown that MRI of formalin fixed human <i>ex vivo</i> liver samples mimic the textural contrast of <i>in vivo</i> Gd-MRI and can be used as MRI phantoms. We have developed local texture analysis that is applied to phantom images, and the results are used to train model observers. The performance of the observer is assessed with the area-under-the-receiveroperator- characteristic curve (AUROC) as the figure of merit. To optimize the MRI pulse sequence, phantoms are scanned with multiple times at a range of flip angles. The flip angle that associated with the highest AUROC is chosen as optimal based on the task of detecting HF.
Design and use of macromonomers as steric stabilizers for the synthesis of novel functional particles in dispersed media (2005)

Abstract The synthesis of core–shell latex particles is discussed in this paper. Various macromonomers have been engineered and used as steric reactive stabilizers to render these particles surface active. Latexes of polystyrene, polynorbornene and polyurethane have been obtained in aqueous, organic and supercritical CO 2 dispersant media. The fields of application of these original materials are also discussed. Copyright © 2005 Society of Chemical Industry
Self-vertical phase separation study of nanoparticle/polymer solar cells by introducing fluorinated small molecules (2012)

A new approach to induce self-vertical phase separation of nanoparticle/polymer hybrid solar cells is reported by introducing fluorinated small molecules into the active layer. The formation of a vertically gradient structure improves not only polymer organization but also charge transport efficiency, thus increasing the photovoltaic cell performance by a factor of 5.
Developing an AIDS Vaccine: Need, Uncertainty, Hope (2004)

It is more than 20 years since the identification of HIV, the virus that causes AIDS. In their Perspective, [Emini and Koff][1] discuss how far we have come in understanding the interaction of HIV with the host immune system, and what we must learn to develop an effective vaccine that will halt the spread of AIDS.

 [1]: http://www.sciencemag.org/cgi/content/full/304/5679/1913
ChemInform Abstract: β‐Lactamase Inhibitors: Agents to Overcome Bacterial Resistance (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Adapting Risk Management and Computational Intelligence Network Optimization Techniques to Improve Traffic Throughput and Tail Risk Analysis (2014)

Risk management techniques are used to analyze fluctuations in uncontrollable variables and keep those fluctuations from impeding the core function of a system or business. Examples of this are making sure that volatility in copper and aluminum prices do not force an aircraft manufacturer to abruptly shut down manufacturing and making sure a failed bank or state does not cause an entire financial system to fail. Computer network optimization techniques involve many nodes and routes communicating to maximize throughput of data while making sure not to deadlock high priority or time sensitive data. This project will involve exploring possible remappings of these application spaces from risk and computer networks to traffic. Some of these possible mappings include mapping flash crashes and black swans to traffic jams, bank failure to construction or traffic accidents, data packets to vehicles, network routers to traffic lights and other intersection policies. Due to the large data and large solution/ state/ policy spaces computational intelligence techniques are a natural fit for traffic as they are for risk management and computer network optimization.
Microsoft Research at TREC 2009. Web and Relevance Feedback Tracks (2009)

We took part in the Web and Relevance Feedback tracks, using the ClueWeb09 corpus. To process the corpus, we developed a parallel processing pipeline which avoids the generation of an inverted file. We describe the components of the parallel architecture and the pipeline and how we ran the TREC experiments, and we present effectiveness results. 1
Error-based or target-based? A unified framework for learning in recurrent spiking networks (2022)

The field of recurrent neural networks is over-populated by a variety of proposed learning rules and protocols. The scope of this work is to define a generalized framework, to move a step forward towards the unification of this fragmented scenario. In the field of supervised learning, two opposite approaches stand out, error-based and target-based. This duality gave rise to a scientific debate on which learning framework is the most likely to be implemented in biological networks of neurons. Moreover, the existence of spikes raises the question of whether the coding of information is rate-based or spike-based. To face these questions, we proposed a learning model with two main parameters, the rank of the feedback learning matrix and the tolerance to spike timing τ⋆. We demonstrate that a low (high) rank accounts for an error-based (target-based) learning rule, while high (low) tolerance to spike timing promotes rate-based (spike-based) coding. We show that in a store and recall task, high-ranks allow for lower MSE values, while low-ranks enable a faster convergence. Our framework naturally lends itself to Behavioral Cloning and allows for efficiently solving relevant closed-loop tasks, investigating what parameters are optimal to solve a specific task. We found that a high is essential for tasks that require retaining memory for a long time (Button and Food). On the other hand, this is not relevant for a motor task (the 2D Bipedal Walker). In this case, we find that precise spike-based coding enables optimal performances. Finally, we show that our theoretical formulation allows for defining protocols to estimate the rank of the feedback error in biological networks. We release a PyTorch implementation of our model supporting GPU parallelization.
Spontaneous T Cell Proliferation and Release of Soluble Interleukin-2 Receptors in Patients with HTLV-I-Associated Myelopathy (1990)

"Spontaneous T Cell Proliferation and Release of Soluble Interleukin-2 Receptors in Patients with HTLV-I-Associated Myelopathy" published on Apr 1990 by The American Society of Tropical Medicine and Hygiene.
Influence of Preparation Conditions on Microdomain Formation in Poly(urethane urea) Block Copolymers (2001)

Selected poly(urethane urea) block copolymers were prepared under different conditions and their microphase-separated morphologies analyzed primarily with small-angle X-ray scattering (SAXS). Preparation conditions were varied by adjusting the temperature and vacuum pressure during solution casting. Copolymers with relatively high hard segment contents prepared under “low” vacuum conditions, where solvent is removed comparatively slowly and the copolymers spend a longer period of time in the presence of a plasticizer (i.e., solvent), produced films with higher degrees of phase separation. The longer casting times associated with the low vacuum pressure conditions also resulted in larger mean interdomain spacings. We speculate that this may be due to secondary hard domain coalescence. Attenuated total reflectance FT-IR and wide-angle X-ray diffraction experiments were performed, but these were not sensitive to the microdomain organization of these copolymers.
Cloning, Sequencing, and Heterologous Expression of the elmGHIJ Genes Involved in the Biosynthesis of the Polyketide Antibiotic Elloramycin from Streptomyces olivaceus Tü2353 (2001)

Elloramycin A (1) belongs to a small family of naphthacenequinones characterized by a unique highly hydroxylated cyclohexenone moiety. A cosmid clone 16F4, harboring genes for the production of 1 from Streptomyces olivaceus Tü2353, has been previously isolated. DNA sequence analysis of a 3.2-kb fragment from 16F4 revealed four open reading frames--the elmGHIJ genes. Heterologous expressions of the elmGHI genes in either Escherichia coli or Streptomyces lividans, followed by biochemical characterizations of the ElmGHI proteins, established ElmG as tetracenomycin B2 oxygenase, ElmH as tetracenomycin F1 monooxygenase, and ElmI as tetracenomycin F2 cyclase. These results provide direct biochemical evidence for the hypothesis that the biosynthesis of 1 in S. olivaceus parallels that of tetracenomycin C (2) in Streptomyces glaucescens and support the notion that the biosynthesis of the highly hydroxylated cyclohexenone moiety in other polyketides most likely follows the same paradigm as the tetracenomycin B2 or A2 oxygenase.
The Effect of Pitch Composition on the Adsorption Behavior of Pd-Doped ACF (2007)

Recent studies indicate that metal-containing activated carbon fibers (ACF) are promising adsorbents for hydrogen storage applications. In these studies, Pd compounds were added to a petroleum precursor and formed into ACFs. Results showed that the molecular composition of the pitch had a significant affect on critical characteristics of the ACFs, such as pore size and Pd particle size. In an ongoing Department of Energy project, we are testing pitch precursors with carefully controlled chemical compositions in order to develop an optimum precursor for hydrogen storage applications. A low softening point pitch made by Marathon Oil is being separated into narrow molecular weight fractions using a dense gas extraction (DGE) process. In the current series of tests the heavier portion of the extracted pitch was used to prepare both undoped and Pd-doped carbon fibers. These fibers were activated over a range of temperatures to determine the effect of temperature and pitch composition on ACF properties. Lower activation temperatures resulted in increased microporosity (desirable for hydrogen adsorption) for all Pd-doped pitch precursors. Comparing ACFs produced from various DGE-extracted pitches showed that even small quantities of mesophase-forming components inhibited activation and significantly reduced microporosity. Additional DGE pitch fractions are now being tested tomore » further refine the optimum composition for hydrogen storage applications.« less
High-Z metal-based underlayer patterning for improving EUV stochastics (Conference Presentation) (2020)

Extending extreme ultraviolet (EUV) single exposure patterning to its limits is dependent on eliminating its stochastic defectivity. Along with developments in photoresist platforms, the patterning film stack also needs to be considered. The material immediately underneath the photoresist is expected to have significant impact on both lithographic and pattern transfer performance. By designing the resist substrate interface with high EUV absorbance, there is potential to increase the EUV quantum yield of the exposure process. Increasing the selectivity to organic layer offers the opportunity to modulate stochastic defects through etch strategies. This paper will demonstrate the patterning of various chemically amplified resists on a high-Z metal-based hardmask. The potential for dose reduction, higher etch selectivity, and defectivity improvement from a high-Z hardmask will be discussed. Deposition-trim etch techniques will be used for decreasing the transfer of stochastic defects to the underlying substrate. Sub-32nm pitch trench patterning, defectivity, and electrical yield for this patterning stack will be highlighted.