gebhart/patrepeval huggingface dataset:
Hydrolytic Cleavage of 6-Oxopurines after Intramolecular Acylation at N-3 (1985)

Reaction of 9H-hypoxanthin-9-yl ~ropionic acid ( z ) as well as of its 6-mercapto analogue (g) with N-[3-(dimethylamino) propyll-N'-ethylcarbodiimide hydrochloride results in an intramolecular acylation at N-3 followed by a spontaneous hydroxylation at C-2 and opening of the ~yrimidine ring.The products of these reaction sequences are the imida-
CANbus and microcontroller use in the BaBar detector at SLAC (2000)

The BaBar collaboration has chosen the Controller Area Network (CAN) bus for its controls and monitoring field bus. In addition, the Motorola MC68HC705X32 microcontroller, which has a CAN interface, was chosen for the standard intelligent device for monitoring boards. This paper describes the CAN system used by BaBar and the embedded software that supports it. The General Monitoring Board (GMB) is presented as a specific example. The GMB is a CAN module that digitizes 32 differential analog signals and has eight bits of bi-directional I/O.
Tracking as Repeated Figure/Ground Segmentation (2007)

Tracking over a long period of time is challenging as the appearance, shape and scale of the object in question may vary. We propose a paradigm of tracking by repeatedly segmenting figure from background. Accurate spatial support obtained in segmentation provides rich information about the track and enables reliable tracking of non-rigid objects without drifting. Figure/ground segmentation operates sequentially in each frame by utilizing both static image cues and temporal coherence cues, which include an appearance model of brightness (or color) and a spatial model propagating figure/ground masks through low-level region correspondence. A superpixel-based conditional random field linearly combines cues and loopy belief propagation is used to estimate marginal posteriors of figure vs background. We demonstrate our approach on long sequences of sports video, including figure skating and football.
The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences (2008)

Efficient searching for specific subsequences in a set of longer sequences is an important component of many bioinformatics algorithms. Generalised suffix trees and suffix arrays allow searches for a pattern of length n in time proportional to n independent of the length of the sequences, and are thus attractive for a variety of applications. Here, we present an algorithm termed the generalised k-Truncated Suffix Tree (kTST), that represents an adaption of Ukkonen's linear-time suffix tree construction algorithm. The kTST algorithm creates a k-deep tree in linear time that allows rapid searches for short patterns of length of up to k characters. The kTST can offer advantages in computational time and memory usage for searches for short sequences in DNA or protein sequences compared to other suffix-based algorithms.
Polarization-selective computer-generated holograms: design, fabrication, and applications (1995)

We constructed polarization-selective computer-generated holograms that apply an independent phase profile during readout by horizontal and vertical light polarizations. These elements are composed of two surface-relief-etched birefringent substrates joined face to face. We describe the design methodology for arbitrary birefringent substrate and gap materials. We show how these holograms are fabricated with standard microelectronics technology and discuss the effects of etching and alignment errors on performance. We demonstrated a diffraction efficiency of 60% with a polarization contrast ratio of >100:1 using a multilevel phase hologram made from two birefringent lithium niobate substrates. We also showed that a single-layer SiO(2) thin-film antireflection coating on all surfaces can reduce reflections from the high-index substrates without significant effect on hologram performance. We also consider some possible applications of this technology and demonstrate experimentally a dual focal-length lens and a self-interconnecting binary 2 × 2 polarization switch.
Novel alicyclic polymers having 7,7-dimethyloxepan-2-one acid labile groups for ArF lithography (2002)

The present paper describes a novel class of norbornene- based copolymers containing 7,7-dimethyloxepan-2-one acid labile groups. Poly(3-(bicyclo[2.2.1]hept-5-en-2- ylhydroxymethyl)-7,7-dimethyloxepan-2-one-co-5-((2- decahydronaphth-yl)oxycarbonyl)-norbornene-co-5-norbornene- 2-carboxxylic acid-co-maleic anhydride) was synthesized and evaluated as a potential chemically amplified resist for ArF lithography. The 7,7-dimethyloxepan-2-one group of the matrix polymer was readily cleaved and the carboxylic acid functionality was formed by acid-catalyzed ring-opening reaction in the exposed region after post-exposure bake. 0.12micrometers line and space patterns were obtained at a dose of 10 mJ cm<SUP>-2</SUP> with a conventional developer, 2.38 wt% tetramethylammonium hydroxide aqueous solution, using an ArF excimer laser stepper.
Automated transit vehicle size considerations (1986)

Abstract Synthesis of cost‐effective transit alternatives using automated vehicles requires consideration of a wide range of factors that are moot in determination of the optimum size of manually driven vehicles where the need to amortize driver wages dominates the economics. Discussions of many of these factors have appeared in previous papers. This article brings them together into consideration of one specific system characteristic: the optimum automated‐transit‐vehicle size.
Polypeptides. XVII. A Study of the Kinetics of the Primary Amine-initiated Polymerization of N-Carboxy-anhydrides with Special Reference to Configurational and Stereochemical Effects (1957)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolypeptides. XVII. A Study of the Kinetics of the Primary Amine-initiated Polymerization of N-Carboxy-anhydrides with Special Reference to Configurational and Stereochemical EffectsR. D. Lundberg and Paul DotyCite this: J. Am. Chem. Soc. 1957, 79, 15, 3961–3972Publication Date (Print):August 1, 1957Publication History Published online1 May 2002Published inissue 1 August 1957https://pubs.acs.org/doi/10.1021/ja01572a004https://doi.org/10.1021/ja01572a004research-articleACS PublicationsRequest reuse permissionsArticle Views413Altmetric-Citations188LEARN 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
Ductility of confined concrete masonry shear walls (1982)

Calculations for the ductility capacity of unconfined concrete masonry shear walls developed in a previous paper are extended to cover the case of confined masonry shear walls. Design charts are presented which show that the available ductility will always be greater than three times the value for a corresponding unconfined wall. Recommendations to govern the required extent of confinement are made.
Cascade control of Escherichia coli glutamine synthetase. Purification and properties of PII protein and nucleotide sequence of its structural gene. (1987)

A procedure was developed to purify large quantities of PII protein from an Escherichia coli strain which contains a multicopy plasmid harboring the structural gene of PII (the glnB gene). Ultraviolet spectra of uridylylated and unuridylylated PII were obtained using the purified PII and empirical formulas to calculate the concentration of protein and the average number of uridylylated subunits per molecule were derived. A continuous fluorometric assay for the measurement of uridylylated PII (PIID) and adenylyltransferase (ATase) was also established. Rate measurements at various concentrations of PIID and at a fixed concentration of ATase showed that a tetrameric PIID molecule interacts with only one ATase molecule at a time. The complete nucleotide sequence of the glnB gene was determined and parts of the deduced amino acid sequence were confirmed by the results of amino acid sequence analysis of peptides. The PII subunit consists of 103 amino acids (Mr = 11,580). Two tyrosines reside at positions 46 and 51, where Tyr51 is the site of uridylylation. Nucleotide sequence analysis of the upstream region showed no obvious sites for the binding of RNA polymerase, indicating that the glnB gene is a part of an as yet unidentified operon.
A new cobalt salicide technology for 0.15 μm CMOS using high-temperature sputtering and in-situ vacuum annealing (2002)

A new cobalt (Co) salicide technology using high-temperature sputtering and in-situ vacuum annealing process has been developed. This technology is a simple process without additional ion implantation and metal deposition to promote silicidation and to suppress oxidation of Co film. No line width dependence of sheet resistances was achieved down to for 0.15 /spl mu/m gate electrode and 0.33 /spl mu/m for diffusion layer. Sheet resistance of 11 /spl Omega//sq. for both gate electrode and diffusion layer was obtained with 5 nm thick Co film (CoSi/sub 2/ 17.5 nm). By using this technology, 0.15 /spl mu/m CMOS devices which have shallow junctions were successfully fabricated.
Optical differentiator based on rapid collapse of Wannier–Stark localization due to space charge field screening (1994)

An optical differentiator operation is demonstrated using a GaAs/AlAs short-period superlattice near an optical absorption band edge. This operation is clearly explained by a rapid collapse of Wannier–Stark localization due to electric field screening by photogenerated space charges, because the screening causes a positive feedback loop between restoration of blueshifted wavelength of absorption band edge to the red side and an increase in optical absorption which causes an additional field screening.
Vitamin B<sub>6</sub> biosynthesis: formation of pyridoxine 5′‐phosphate from 4‐(phosphohydroxy)‐<scp>l</scp>‐threonine and 1‐deoxy‐<scp>d</scp>‐xylulose‐5‐phosphate by PdxA and PdxJ protein (1999)

In Escherichia coli the coenzyme pyridoxal 5'-phosphate (PLP) is synthesised de novo by a pathway that is thought to involve the condensation of 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose, catalysed by the enzymes PdxA and PdxJ, to form either pyridoxine (vitamin B6) or pyridoxine 5'-phosphate (PNP). Here we show that incubation of PdxJ with PdxA, 4-(phosphohydroxy)-L-threonine, NAD and 1-deoxy-D-xylulose-5-phosphate, but not 1-deoxy-D-xylulose, results in the formation of PNP. The PNP formed was characterised by (i) cochromatography with an authentic standard, (ii) conversion to pyridoxine by alkaline phosphatase treatment, and (iii) UV and fluorescence spectroscopy. Furthermore, when [2-(14)C]1-deoxy-D-xylulose-5-phosphate was used as a substrate, the radioactivity was incorporated into PNP. These results clarify the previously unknown role of PdxJ in the de novo PLP biosynthetic pathway. The sugar used as substrate by PdxJ is 1-deoxy-D-xylulose-5-phosphate rather than the previously assumed 1-deoxy-D-xylulose. The first vitamin B6 vitamer synthesised is PNP, and not pyridoxine.
Polytype Controlled SiC Epitaxy on On-axis 6H-SiC(0001) by Adding HCl during Growth (1999)

The homoepitaxial growth of is demonstrated on on‐axis substrates at by adding during the growth by chemical vapor deposition. In prior studies. a pregrowth stepped surface obtained either by several‐degree off‐cut substrates or a pregrowth etch was required to suppress inclusions and to achieve homoepitaxial growth of . In contrast, the addition of during the growth decorates the grown surface via etching to provide an in situ stepped surface where step‐flow growth of occurs. Atomic force microscopy of the deposited films shows the addition of produces a much more regular step and terrace structure that is characteristic of near equilibrium, step‐flow growth. In addition, can reduce the surface supersaturation and growth rate. remove the undesired nucleation sites for , and etch inclusions over , all of which benefit the homoepitaxial growth of on on‐axis substrates. ©2000 The Electrochemical Society
Statistical Foundations of Thermodynamics II. Equivalence Problem. Stability Conditions (1969)

On the basis of the results obtained in a previous paper it is shown that in the thermodynamic limit the analogues of the Massieu-Plandc functions are linked with each other by means of the Legendre transformation. The existence of the limiting function φ k (∞) implies the existence of the limiting function φ l (∞) (l<k) under the same assumptions. Passage to the limit and derivation with respect to all independent variables commute. A statistical derivation of the thermodynamic stability condition in its most general form is given which leads naturally to a statistical interpretation of the concept of thermodynamic stability.
Role of Primers in Glucan Synthesis by Glucosyltransferases from Streptococcus mutans strain OMZ176 (1983)

The effects of isomaltosaccharides of various molecular weights (isomaltose to dextran T2000) on glucan synthesis by a water-soluble glucan-synthesizing glucosyltransferase enzyme (GTase-S) and a water-insoluble glucan-synthesizing enzyme (GTase-I), both from Streptococcus mutans OMZ176, were examined. The activity of GTase-S was not affected by the addition of the isomaltosaccharides, but GTase-I was stimulated increasingly by isomaltosaccharides with degrees of polymerization more than 10. The GTase-I activity first increased and thereafter decreased slightly with increasing amounts of a soluble dextran. Maximal stimulation occurred at concentrations in the range 0.1 to 0.2 mg ml-1, when dextran T10 was used as a primer. The rate of glucan synthesis was highly enhanced by the combined action of GTase-S and GTase-I. The profile of the net activity of GTase-I in the presence of various amounts of GTase-S was similar to that of GTase-I in the presence of increasing amounts of an exogenous dextran. These results collectively suggest that soluble glucan produced by GTase-S from sucrose acts as an intrinsic primer for the glucan synthesis by GTase-I, indicating the contribution of autopriming in glucan synthesis by crude GTase of S. mutans.
Extraction of Equine Infectious Anemia Immunodiffusion Antigen with the Aid of the Chaotropic Agent, Thiocyanate (1973)

Immunodiffusion antigen from spleens of horses infected with equine infectious anemia virus was prepared by methods employing freeze-thaw cycles and thiocyanate treatment. Thiocyanate (0.5 M) permitted the recovery of the greatest amount of antigen. Furthermore, it was most effective for recovery of immunodiffusion antigen from spleens which yielded unsatisfactory concentrations of antigen by the conventional freeze-thaw or water-extraction methods. The reactivity of the antigen did not appear to be affected by this chemical treatment.
A Study of Process-Induced Oxygen Updiffusion in Pseudomorphic Boron-Doped Sub-50 nm SiGeC Layers Grown by LPCVD (2005)

This work is believed to be the first report of localized elevated oxygen concentration (or pileup), which occurs with thermal anneals of strained, boron-doped SiGeC layers. The thermally activated oxygen updiffusion is directly correlated to concentrations of germanium, carbon, and boron. A strong dependency on the prebake temperature was also found. Secondary ion mass spectrometry measurements were made to verify O, C, B, and Ge concentrations in SiGeC layers following low temperature growth by low pressure chemical vapor deposition and also following thermal anneal.
SseL, a <i>Salmonella</i> deubiquitinase required for macrophage killing and virulence (2007)

Expression of the Salmonella enterica serovar Typhimurium pathogenicity island 2 (SPI-2) type III secretion system is controlled by the two-component regulatory system SsrA-SsrB. We used a transcriptomic approach to help define the SsrA-SsrB regulon. We identified a gene encoding an uncharacterized effector (SseL) whose translocation into host cells depends on the SPI-2 secretion system. SseL has similarities to cysteine proteases with deubiquitinating activity. A GST-SseL fusion protein specifically hydrolyzed mono- and polyubiquitin substrates in vitro with a preference for K63-linked ubiquitin chains. Ubiquitin-modified proteins accumulated in macrophages infected with Salmonella sseL mutant strains but to a lesser extent when infected with bacteria expressing active protein, demonstrating that SseL functions as a deubiquitinase in vivo. Salmonella sseL mutant strains did not show a replication defect or induce altered levels of cytokine production upon infection of macrophages but were defective for a delayed cytotoxic effect and were attenuated for virulence in mice.
The effect of dietary fruits and vegetables on urinary galactitol excretion in galactose‐1‐phosphate uridyltransferase deficiency (1992)

Even on a lactose-restricted diet, urinary galactitol excretion and erythrocyte galactose-1-phosphate levels are persistently elevated in patients with galactose-1-phosphate uridyltransferase deficiency. In order to determine the contribution of galactose in dietary fruits and vegetables to this phenomenon, (1) the content of galactose in a lactose-free diet was directly measured when a galactosaemic patient's diet was specifically enriched in those fruits and vegetables which contain relatively large amounts of free galactose and (2) galactitol excretion was determined during ingestion of this diet for 3 weeks and while on a synthetic diet for 1 week that provided < 8 mg galactose/day. For comparison the effect of a 3-week supplementation of 200 mg galactose/day was determined. The measured intake in total foodstuffs matched the theoretical content of galactose in the patient's diet based on amounts in fruits and vegetables alone, thus supporting the concept that fruits and vegetables are primarily responsible for galactose intake in a lactose-free diet. All of the dietary manipulations, however, had relatively little effect on metabolite levels, suggesting that endogenous galactose production is primarily responsible for the elevated levels of galactose metabolites routinely detected in patients on lactose-restricted diets.
FIExPat: flexible extraction of sequential patterns (2002)

This paper addresses sequential data mining, a sub-area of data mining where the data to be analyzed is organized in sequences. In many problem domains a natural ordering exists over data. Examples of sequential databases (SDBs) include: (a) collections of temporal data sequences, such as chronological series of daily stock indices or multimedia data (sound, music, video, etc.); and (b) macromolecule banks, where amino acid or proteic sequences are represented as strings. In a SDB it is often valuable to detect regularities through one or several sequences. In particular, finding exact or approximate repetitions of segments can be utilized directly (e.g. for determining the biochemical activity of a protein region) or indirectly, e.g. for prediction in finance. To this end, we present concepts and an algorithm for automatically extracting sequential patterns from a sequential database. Such a pattern is defined as a group of significantly similar segments from one or several sequences. Appropriate functions for measuring similarity between sequence segments are proposed, generalizing the edit distance framework. There is a trade off between flexibility, particularly in sequence data representation and in associated similarity metrics, and computational efficiency. We designed the FlExPat algorithm to satisfactorily cope with this trade-off. FlExPat's complexity is in practice lesser than quadratic in the total length of the SDB analyzed, while allowing high flexibility. Some experimental results obtained with FlExPat on music data are presented and commented.
Dengue virus photo-inactivated in presence of 1,5-iodonaphthylazide (INA) or AMT, a psoralen compound (4′-aminomethyl-trioxsalen) is highly immunogenic in mice (2013)

Two novel methods of dengue virus inactivation using iodonaphthyl azide (INA) and aminomethyl trioxsalen (AMT) were compared with traditional virus inactivation by formaldehyde. The AMT inactivated dengue-2 virus retained its binding to a panel of 5 monoclonal antibodies specific for dengue-2 envelope protein, whereas inactivation by formaldehyde and INA led to 30-50% decrease in binding. All three inactivated viruses elicited high level virus neutralizing antibodies in vaccinated mice. However, only mice vaccinated with AMT inactivated virus mounted T cell responses similar to live, uninactivated virus.
Application of temporal constrained predicate nets to production systems (2002)

This paper discusses the advantage of using a hybrid model to express the discrete aspects (events) as well as continuous aspects (time) of production systems. We propose an extension of the Petri Net model to take these two information types into account. Finally we use this new model to describe, to simulate and to check the properties of a production system in a simple example. The proposed model is close to the predicate transition one. However it is more general because it is not limited to finite domains. So, it allows continuous temporal properties to be explicitly defined. Moreover, we show how the constraints intervening in the behaviour modelling can be handled to demonstrate safety properties depending on time.
Synthestic approaches to the teleocidin-related tumour promoters: a total synthesis of (±)-indolactam V (1986)

A synthesis of the macrolactam tumour promoter indolactam V is described in 11 steps from 4-aminoindole.
Atomic Resolution (0.98 Å) Structure of Eosinophil-Derived Neurotoxin<sup>,</sup> (2002)

Human eosinophil-derived neurotoxin (EDN) is a small, basic protein that belongs to the ribonuclease A superfamily. EDN displays antiviral activity and causes the neurotoxic Gordon phenomenon when injected into rabbits. Although EDN and ribonuclease A have appreciable structural similarity and a conserved catalytic triad, their peripheral substrate-binding sites are not conserved. The crystal structure of recombinant EDN (rEDN) has been determined at 0.98 A resolution from data collected at a low temperature (100 K). We have refined the crystallographic model of the structure using anisotropic displacement parameters to a conventional R-factor of 0.116. This represents the highest resolution structure of rEDN determined to date and is only the second ribonuclease structure to be determined at a resolution greater than 1.0 A. The structure provides a detailed picture of the conformational freedom at the various subsites of rEDN, and the water structure accounts for more than 50% of the total solvent content of the unit cell. This information will be crucial for the design of tight-binding inhibitors to restrain the ribonucleolytic activity of rEDN.