gebhart/patrepeval huggingface dataset:
Automated Slicing for a Multiaxis Metal Deposition System (2006)

A multiaxis adaptive slicing algorithm for multiaxis layered manufacturing, which can generate optimal slices to achieve deposition without support structures, is presented in this paper. Different from current adaptive slicing, this technique varies not only layer thickness but also in slicing/building direction. Aware of potential problems of previous research on slicing, the work in this paper focuses on innovative geometry reasoning and analysis tool-centroidal axis. Similar to medial axis, it contains geometry and topological information but is significantly computationally cheaper. Using a centroidal axis as a guide, the multiaxis slicing procedure is able to generate a three-dimensional layer or change slicing direction as needed automatically to build the part with better surface quality. This paper presents various examples to demonstrate the feasibility and advantages of centroidal axis and its usage in the multiaxis slicing process.
Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries (1982)

We present an algorithm--a generalization of the Needleman-Wunsch-Sellers algorithm--which finds within longer sequences all subsequences that resemble one another locally. The probability that so close a resemblance would occur by chance alone is calculated and used to classify these local homologies according to statistical significance. Repeats and inverted repeats may also be found. Results for both random and biological nucleic acid sequences are presented. Fourteen complete genomes are analyzed for dyad symmetries.
Synthesis and characterisation of twelve SnIV diaryls and formation of a SnIII triaryl (2009)

Ten new crystalline compounds of formula (i) [{Sn(Ar(N2))(2)(micro-E)}(2)] [E = O (), S (), Se (), Te ()], (ii) [Sn(Ar(N2))(2)(ER)(2)] [ER = SCH(2)Ph (), SePh (), TePh ()], (iii) [Sn(Ar(N2))(2)(Br)R] [R = CH(SiMe(3))(2) (), Bu(t) ()] and (iv) [Sn(Ar(N2))(2){CH(SiMe(3))(2)}][BPh(4)] [Ar(N2) = C(6)H(3)(NMe(2))(2)-2,6 ()] have been prepared and identified by microanalysis, EI-mass spectrometry and multinuclear NMR spectroscopy, and for , , , and by single crystal X-ray diffraction. Whereas in the solid state, each of the latter five has only one of its two NMe(2) substituents of each [Ar(N2)](-) ligand close to the tin atom (<3.1 A), in solution at ambient temperature the NMe(2) groups are characterised by a single (1)H and (13)C signal. The known compounds [Sn(Ar(N2))(2)(NCE)(2)] [E = O (), S ()] were synthesised by a new route: the redox reaction between [Sn(Ar(N2))(2)] () and 2AgNCE. Irradiation of a toluene solution of at 298 K afforded a persistent radical assigned as [ Sn(Ar(N2))(3)] ().
Highly stable aptamers selected from a 2′-fully modified fGmH RNA library for targeting biomaterials (2020)

When developed as targeting ligands for the in vivo delivery of biomaterials to biological systems, RNA aptamers immediately face numerous obstacles, in particular nuclease degradation and post-selection 2′ modification. This study aims to develop a novel class of highly stable, 2′-fully modified RNA aptamers that are ideal for the targeted delivery of biomaterials. We demonstrated the facile transcription of a fGmH (2′-F-dG, 2′-OMe-dA/dC/dU) RNA library with unexpected hydrophobicity, the direct selection of aptamers from a fGmH RNA library that bind Staphylococcus aureus Protein A (SpA) as a model target, and the superior nuclease and serum stability of these aptamers compared to 2′-partially modified RNA variants. Characterizations of fGmH RNA aptamers binding to purified SpA and to endogenous SpA present on the surface of S. aureus cells demonstrate fGmH RNA aptamer selectivity and stability. Significantly, fGmH RNA aptamers were able to functionalize, stabilize, and further deliver aggregation-prone silver nanoparticles (AgNPs) to S. aureus with SpA-dependent antimicrobial effects. This study describes a novel aptamer class with considerable potential to improve the in vivo applicability of nucleic acid-based affinity molecules to biomaterials.
SIVrcm infection of macaques (1998)

In a prior report, we described the isolation and characterization of SIVrcm, a distinct primate lentivirus found in a household pet Red-Capped Mangabey (RCM) in Gabon. SIVrcm is divergent from HIV-1 and HIV-2/SIV families of primate lentiviruses. In this report, additional in vitro replication studies and the results of SIVrcm infection in macaques are presented. SIVrcm causes little cytopathic effedct in Molt 4 Clone 8 cells and in rhesus and human PBMCs. In vivo, SIVrcm is non-pathogenic after 200 days in rhesus macaques and after one year in cynomolgous macaques, but does cause a chronic infection in both macaques.
Substrate-Promoted Formation of a Catalytically Competent Binuclear Center and Regulation of Reactivity in a Glycerophosphodiesterase from <i>Enterobacter aerogenes</i> (2008)

The glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a promiscuous binuclear metallohydrolase that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. GpdQ has attracted recent attention as a promising enzymatic bioremediator. Here, we have investigated the catalytic mechanism of this versatile enzyme using a range of techniques. An improved crystal structure (1.9 A resolution) illustrates the presence of (i) an extended hydrogen bond network in the active site, and (ii) two possible nucleophiles, i.e., water/hydroxide ligands, coordinated to one or both metal ions. While it is at present not possible to unambiguously distinguish between these two possibilities, a reaction mechanism is proposed whereby the terminally bound H2O/OH(-) acts as the nucleophile, activated via hydrogen bonding by the bridging water molecule. Furthermore, the presence of substrate promotes the formation of a catalytically competent binuclear center by significantly enhancing the binding affinity of one of the metal ions in the active site. Asn80 appears to display coordination flexibility that may modulate enzyme activity. Kinetic data suggest that the rate-limiting step occurs after hydrolysis, i.e., the release of the phosphate moiety and the concomitant dissociation of one of the metal ions and/or associated conformational changes. Thus, it is proposed that GpdQ employs an intricate regulatory mechanism for catalysis, where coordination flexibility in one of the two metal binding sites is essential for optimal activity.
Carrot Seed Germination at High Temperature: Effect of Genotype and Association with Ethylene Production (2008)

Carrot ( Daucus carota L.) seed germination may be erratic or reduced under high temperatures (above 35 °C). Even in tropical genotypes (tolerant to high temperatures during crop development), the negative effects of high temperatures on carrot stand establishment have been observed, especially during summer. The objectives of this study were to characterize commercial carrot cultivars and accession lines for their ability to germinate at high temperature and determine the ethylene production during imbibition at high temperature. Seeds from 34 commercial cultivars and 125 carrot accessions from the North Central Regional Plant Introduction Station were germinated at 25 °C (optimal) and 35 ± 0.5 °C (high) in constant light. Ethylene production during seed imbibition at high temperature was evaluated in some genotypes. Many of the commercial cultivars had reduced germination at 35 °C. ‘XPC-3617’, ‘Alvorada’, ‘Brasilia’, and ‘Esplanada’ had the greatest germination at 35 °C. A greater number of accessions germinated at 35 °C than did the commercial genotypes. The accession PI 319858 germinated 95% at both temperatures and was considered thermotolerant. Six accessions (Ames 7665, Ames 7698, Ames 25031, PI 167082, PI 294637, and PI 319858) germinated above 80% at 35 °C and were also identified as potential sources of thermotolerance. Fifteen other accessions (Ames 7694, Ames 25031, Ames 25036, Ames 25049, Ames 25705, PI 167082, PI 179687, PI 180834, PI 261782, PI 269486, PI 273658, PI 277710, PI 288242, PI 294637, and PI 319858) had thermotolerance ratios of T35/T25 0.85 or greater (where T35 = germination at 35 °C and T25 = germination at 25 °C) and were identified for further testing. The identified thermotolerant genotypes might be useful for carrot seed germination mechanism studies as well as for breeding programs. Ethylene production during seed germination at high temperature was greater in thermotolerant genotypes than in thermosensitive genotypes. High correlations were observed between first germination count at 35 °C and ethylene production, total germination at 35 °C and ethylene production, and thermotolerance ratio and ethylene production.
Comparison of Various Types of Hydrogen Bonds Involving Aromatic Amino Acids (2002)

Ab initio calculations are used to compare the abilities of the aromatic groups of the Phe, Tyr, Trp, and His amino acids (modeled respectively by benzene, phenol, indole, and imidazole) to form H-bonds of three different types. Strongest of all are the conventional H-bonds (e.g., OH..O and OH..N). His forms the strongest such H-bond, followed by Tyr, and then by Trp. Whereas OH..phi bonds formed by the approach of a proton donor to the pi electron cloud above the aromatic system are somewhat weaker, they nonetheless represent an important class of stabilizing interactions. The strengths of H-bonds in this category follow the trend Trp > His > Tyr approximately Phe. CH.O interactions are weaker still, and only those involving His and Trp are strong enough to make significant contributions to protein structure. A protonated residue such as HisH(+) makes for a very powerful proton donor, such that even its CH..O H-bonds are stronger than the conventional H-bonds formed by neutral groups.
Deep Learning Under Privileged Information Using Heteroscedastic Dropout (2018)

Unlike machines, humans learn through rapid, Abstract model-building. The role of a teacher is not simply to hammer home right or wrong answers, but rather to provide intuitive comments, comparisons, and explanations to a pupil. This is what the Learning Under Privileged Information (LUPI) paradigm endeavors to model by utilizing extra knowledge only available during training. We propose a new LUPI algorithm specifically designed for Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs). We propose to use a heteroscedastic dropout (i.e. dropout with a varying variance) and make the variance of the dropout a function of privileged information. Intuitively, this corresponds to using the privileged information to control the uncertainty of the model output. We perform experiments using CNNs and RNNs for the tasks of image classification and machine translation. Our method significantly increases the sample efficiency during learning, resulting in higher accuracy with a large margin when the number of training examples is limited. We also theoretically justify the gains in sample efficiency by providing a generalization error bound decreasing with O(1/n), where n is the number of training examples, in an oracle case.
Rapid Measurements of Intracellular Calcium Using a Fluorescence Plate Reader (1999)

Intracellular calcium is a universal second messenger that can serve as a broad-based measure of receptor activity. Recent developments in multi-well plate fluorescence readers facilitate measurement of intracellular free-calcium levels and reduce reliance on slower, more cumbersome or expensive data collection methods. In this report, we describe a rapid and sensitive method to assay intracellular calcium ions in human embryonic kidney (HEK293) and Chinese hamster ovary (CHO) cells from multi-well plates using a fluorometer equipped with on-line injectors. We examine the compatibility of visible-light excitable dyes Calcium Green-1 and Oregon Green 488 BAPTA-1. Using this assay, we were able to detect and quantify activity from muscarinic and beta-adrenergic receptors endogenous to HEK293 cells and detect calcium signals generated by activation of Gi-coupled recombinant mu-opioid and dopamine D2L receptors, and the Gs-coupled melanocortin subtype 4 (MC4) receptor. Fluorescence signals, stable in HEK293 cells, required the use of Oregon Green 488 BAPTA-1 and an inhibitor of organic anion transport in CHO cells. Under appropriate conditions, both cell types can be used to collect complete concentration-response data for a variety of receptors (including a recombinant muscarinic M1 receptor expressed in CHO cells) from a single plate of dye-loaded cells.
An economy-based accounting infrastructure for the datagrid (2004)

A distributed grid computing environment, like the European datagrid (EDG), that manages enormous numbers of computing resources (in terms of processing power, disk space, memory usage, etc.) and astronomical amounts of scientific data, requires mechanisms for a balanced access of many thousands of simultaneous users. The datagrid accounting system (DGAS), that we present, is designed to support an economy-based approach to regulating the distribution of the resources among the authorized grid users. We describe two possible models for resource pricing and a utility function for economic brokering.
Preparation of Functionally Graded Aluminum Nitride-Oxide Coatings Using a Precursor Derived from a Chloroaluminate Ionic Liquid (2007)

Room temperature ionic liquids (RTILs), also called ambient temperature molten salts, have been demonstrated to be potentially useful for a wide variety of chemical and electrochemical functions, ranging from power source electrolytes to alternative solvents for chemical synthesis. We will report on recent work on a materials application of RTILs in which a functionally graded, corrosion-resistant coating for the interior of hot ferrous metal pipes was prepared using precursors derived from an ambient temperature chloroaluminate melt.
The cascaded predictor: economical and adaptive branch target prediction (1998)

Two-level predictors improve branch prediction accuracy by allowing predictor tables to hold multiple predictions per branch. Unfortunately, the accuracy of such predictors is impaired by two detrimental effects. Capacity misses increase since each branch may occupy many entries, depending on the number of different path histories leading up to the branch. The working set of a given program therefore increases with history length. Similarly, cold start misses increase with history length since the predictor must first store a prediction separately for each history pattern before it can predict branches with that history. We describe a new hybrid predictor architecture, cascaded branch prediction, which can alleviate both of these effects while retaining the superior accuracy of two level predictors. Cascaded predictors dynamically classify and predict easily predicted branches using an inexpensive predictor, preventing insertion of these branches into a more powerful second stage predictor. We show that for path-based indirect branch predictors, cascaded prediction obtains prediction rates equivalent to that of two-level predictors at approximately one fourth the cost. For example, a cascaded predictor with 64+1024 entries achieves the same prediction accuracy as a 4096-entry two-level predictor. Although we have evaluated cascaded prediction only on indirect branches, we believe that it could also improve conditional branch prediction and value prediction.
A cryptographically secure EW database with selective random access (2002)

This paper describes the design and implementation of a high security electronic warfare (EW) database based on building up a hierarchical information system employing multilevel security classifications. Users' activities in each classification are authorised via personal identification numbers (PINs). The information is encrypted using the software optimised encryption algorithm (SEAL) which enables random access to and decryption of records in the database as well as guaranteeing the integrity of the retrieved records. Only the required record is decrypted; the database as stored on the permanent media remains fully encrypted at all times providing a very high degree of database confidentiality and integrity. The application has been particularly targeted towards electronic warfare libraries and tests conducted to determine its utility in real-time systems.
RTX Toxins Recognize a β2 Integrin on the Surface of Human Target Cells (1997)

Actinobacillus actinomycetemcomitans leukotoxin and Escherichia coli alpha-hemolysin are RTX toxins that kill human immune cells. We have obtained a monoclonal antibody (295) to a cell surface molecule present on toxin-sensitive HL60 cells that can inhibit cytolysis by both RTX toxins. Utilization of this monoclonal antibody for immunoaffinity purification of detergent-solubilized target cell membranes yielded two polypeptide chains of approximate molecular masses of 100 and 170 kDa. Microsequencing of tryptic peptides from the two proteins showed complete homology with CD11a and CD18, the two subunits of the beta2 integrin, lymphocyte function-associated antigen 1 (LFA-1). Anti-CD11a and CD18 monoclonal antibodies also inhibited RTX toxin-mediated cytolysis. Direct binding experiments demonstrated the ability of an immobilized RTX to bind LFA-1 heterodimers present in a detergent lysate of human HL60 target cells. Transfection of CD11a and CD18 integrin genes into a cell line (K562) that is not sensitive to either RTX toxin resulted in LFA-1 expressing cells, KL/4, that were sensitive to both toxins. These experiments identify LFA-1 as a cell surface receptor that mediates toxicity of members of this family of pore-forming toxins.
Reaction kinetics of a polyurea reaction injection molding system (1988)

Abstract Polyureas have the potential for Improving reaction Injection molding (RIM) productivity through shorter demo Id times and elimination of external mold release agents and post‐cure. Kinetics of urea formation are necessary for process modeling of polyurea RIM systems. Adiabatic temperature rise measurements were used to monitor the extent of reaction of an aliphatic diamine and an aromatic diamine reacting competitively with a single diisocyanate. The aliphatic diamine reacted much faster; essentially complete polymerization occurred in the RIM mixhead. A similar three‐component system was studied in dimethylacetamide and diethylene glycol dimethyl ether, and the sequential nature of the two competing reactions was confirmed. The RIM polymerization of the aromatic diamine, 3,5 diethyltoluene (2,4 and 2,6) diamine and;4,4′‐diphenylmethane diisocyanate was studied using an unreactive poly ether as the solvent. The exotherms could be fit with a third order model. Adiabatic temperature rises for all RIM experiments were in good agreement with the values predicted by heats of reaction measured in solution.
Phase retarders highly insensitive to the input angle (1998)

In the few exceptional cases of total internal reflection phase retarders that are weakly sensitive to variations in the input angle of incidence i, the devices are of increasingly larger size; deviate or translate the emergent beam; are difficult to align in optical systems; or, in coated rhombs, have an impermanent stability of the retardance. Based on new compensating effects, novel devices of high retardance stability and advantageous characteristics are presented. One device is stable to within 0.09 degrees of 90 degrees for i ? 3 degrees . It is a two-reflection quarter-wave retarder that does not alter the path of the compact size light beam, is of compact size (one seventh the size occupied by the achromatic device AD-1 for equal aperture lengths), and can be easily aligned in optical systems or used as a rotating element. The path length of the beam inside the device is less than one third the corresponding length inside the achromatic device AD-1.
Critical elements of a disaster recovery and business/servicecontinuity plan (1995)

Outlines ideas for a well‐designed crisis plan applicable to many corporations, institutions or government agencies. In the light of numerous community‐wide disasters, as well as the singular disasters that corporations, institutions, municipalities and government agencies have suffered in the last few years, details disaster recovery needs. Also discusses issues of site assessment – whether or not a building is occupied, repairs, fire and water cleanup.
Depolymerization of Hyaluronic Acid by<scp>D</scp>-Fructose 6-Phosphate (1993)

Depolymerization of hyaluronic acid obtained from Streptococcus zooepidemicus by D-fructose 6-phosphate was investigated for characterization of reducing sugar-mediated degradation of biopolymers under physiological conditions. The extent of depolymerization was monitored by the decrease of viscosity of a reaction mixture containing 1.0% hyaluronic acid, D-fructose 6-phosphate, and 1.0 × 10−2 mM of Cu2+ in phosphate buffer, pH 7.4. It was found that the depolymerization of hyaluronic acid was dependent on the concentration of the reducing sugar and was specifically accelerated by the presence of Cu2+. The reaction was found to be significantly inhibited by catalase, superoxide dismutase (SOD), 1,2-dihy­ droxybenzene 3,5-disulfonic acid (Tiron), and chelating agents such as EDTA and diethylene triamine penta­ acetic acid (DETAPAC), although the inhibition by SOD was low. Almost the same depolymerization rates were observed in hyaluronic acid preparations of different molecular weight (1.1 × 106, 8.8 × 105, and 6.8 × 105). The rates, however, were different for hyaluronic acids obtained from S. zooepidemicus, rooster comb, and umbilical cord. It was concluded that depolymerization of the polysaccharide was caused by active oxygen species generated by the autoxidation of D-fructose 6-phosphate in the presence of Cu2+, in a mechanism similar to that previously reported for the degradation of DNA and inactivation of virus in vitro.
Auxiliary function approach to parameter estimation of constrained sinusoidal model for monaural speech separation (2008)

We introduce in this paper an auxiliary function approach to parameter estimation of the constrained sinusoidal model, which enables us to derive a complex-spectrum-domain EM-like multiple F <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> estimation algorithm. Through simulations, we evaluated the performance of the presented method in the ability to avoid locally optimal solutions. We implemented a monaural speech separation system based on the presented method and confirmed its performance on compound signals of real speech.