gebhart/patrepeval huggingface dataset:
A secure domain name system based on intrusion tolerance (2008)

DNS was not designed to be secure. The biggest security hole in DNS is the lack of support for data integrity authentication, source authentication, and authorization. In this paper, a secure DNS scheme based on intrusion tolerance is proposed. This secure DNS is intrusion-tolerant by using Byzantine intrusion tolerant technique and voting mechanism. The scheme provides high integrity, robustness, and availability of service in the presence of arbitrary failures, including failures due to malicious attacks. The proposed scheme consists of 3f+1 tightly coupled replicas per name server and guarantees safety and liveness properties of the system assuming no more than f replicas are faulty. By adding authentication of client and using symmetric key cryptography, the system guarantees a secure communication mechanism by providing a way to detect whether DNS data has been corrupted during communication over the Internet. Experimental results show that the scheme can provide a much higher degree of security and reliability, as well or even better than an implementation of the DNS security extension.
Controlling a Java enabled Pepsi(R) vending machine over the World Wide Web (2003)

This paper describes an experimental Java client-server system and a special purpose hardware interface to control a Pepsi(R) vending machine over the World Wide Web. This system allows users with pre-paid accounts to vend a soda from the Pepsi(R) machine (without any coins or bills) using a web browser such as Netscape or Internet Explorer. Anyone with a web browser may find out if any of his or her favorite sodas are left in the machine. The server software can also notify the vending corporation, via Internet e-mail, when each brand of soda needs to be restocked. The software includes a Java applet (the client) and a multi-threaded Java server. The computer system, an Intel based Linux machine, runs its own web server and is physically located inside the Pepsi(R) machine.
Towards Designer Cellulosomes in Clostridia: Mannanase Enrichment of the Cellulosomes Produced by <i>Clostridium cellulolyticum</i> (2004)

The man5K gene of Clostridium cellulolyticum was cloned and overexpressed in Escherichia coli. This gene encodes a 424-amino-acid preprotein composed of an N-terminal leader peptide, followed by a dockerin module and a C-terminal catalytic module belonging to family 5 of the glycosyl hydrolases. Mature Man5K displays 62% identity with ManA from Clostridium cellulovorans. Two forms of the protein were purified from E. coli; one form corresponds to the full-length enzyme (45 kDa), and a truncated form (39 kDa) lacks the N-terminal dockerin module. Both forms exhibit the same typical family 5 mannanase substrate preference; they are very active with the galactomannan locust bean gum, and the more galacto-substituted guar gum molecules are degraded less. The truncated form, however, displays fourfold-higher activity with galactomannans than the full-length enzyme. Man5K was successfully overproduced in C. cellulolyticum by using expression vectors. The trans-produced protein was found to be incorporated into the cellulosomes and became one of the major enzymatic components. Modified cellulosomes displayed 20-fold-higher specific activities than control fractions on galactomannan substrates, whereas the specific activity on crystalline cellulose was reduced by 20%. This work clearly showed that the composition of the cellulosomes is obviously regulated by the relative amounts of the enzymes produced and that this composition can be engineered in clostridia by structural gene cloning.
Queueing analysis for ATM switching of mixed continuous-bit-rate and bursty traffic (2002)

Mixed continuous-bit-rate (CBR) and bursty traffic contending for transmission on any output line of a broadband switch based on the asynchronous transfer mode (ATM) is modeled as a superposition of traffic from a number of independent random and binary sources. With the use of a recursive algorithm, a complete queuing analysis is presented. The queue length distribution, the delay distribution, and the cell loss probability for a finite buffer system are exactly calculated. Cases considered and analyzed include: delay priority for CBR traffic, absolute cell loss priority for DS1/DS3 emulation or guaranteed bandwidth CBR traffic with a stringent cell loss requirement, and threshold cell dropping for voice CBR traffic with a high degree of cell loss tolerance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Subtalar joint motion and the relationship to lower extremity overuse injuries (1996)

The purpose of this study was to determine if there was a difference between the subtalar joint ratio (transverse plane component to frontal plane component) in subjects with overuse symptoms in the foot compared with subjects with overuse symptoms in the leg and knee. Superior and posterior photographs were taken with the subtalar joint in pronation and supination while the subjects were in a seated position. The ratio of the transverse plane to frontal plane components of subtalar joint motion was calculated. A significant (p < 0.05) difference in the subtalar joint ratio existed between subjects with foot overuse symptoms and subjects with leg and knee overuse symptoms.
Tumour necrosis factor induction by malaria exoantigens depends upon phospholipid. (1992)

In patients with malaria, the clinical manifestations of the disease are associated with the presence of high concentrations of tumour necrosis factor (TNF) in the serum. Blood-stage parasites of human and rodent malarial parasites release serologically related exoantigens which induce the production of TNF in vitro and in vivo and which can kill mice made hypersensitive to TNF by pretreatment with D-galactosamine. They also elicit the production of T-independent antibody, which blocks these effects. The capacity of the exoantigens to stimulate macrophages to secrete TNF does not require the presence of protein or carbohydrate, but is associated with a lipid whose activity can be abolished by treatment with phospholipase C. Treatments of the exoantigens which destroyed their activity in vitro also abrogated their immunogenicity and their toxicity for mice. No TNF-inducing activity could be detected in preparations of parasitized erythrocytes that was not associated with phospholipid, and the TNF-inducing properties of the malarial phospholipids are quite distinct from those of bacterial lipopolysaccharide. We conclude that release of potentially toxic phospholipids by parasites may be responsible for some of the pathology of malaria.
Geometric integrators (2005)

In Chapter 2, we introduced the concept of a numerical integrator as a mapping which approximates the flow-map of a given system of differential equations. We have also seen a few instances of how such integrators behave, demonstrating concepts such as convergence and order of accuracy. We observed that the typical picture is a locally accurate approximation that gradually drifts further from the true trajectory (see Fig. 2.3, Fig. 2.5 and the left panel of Fig. 2.7); the rate of drift can be reduced by reducing the stepsize (and thereby also increasing the amount of computational work), but the qualitative picture does not change in any significant way.
A New Enantioselective Synthesis of the Anticonvulsant Drug Pregabalin (Lyrica) Based on a Hydrolytic Kinetic Resolution Method (2013)

A practical and efficient enantioselective synthesis of the anticonvulsant drug pregabalin is described for the first time using Jacobsen's hydrolytic kinetic resolution of a terminal epoxide as a key step and a source of chirality.
The Elasticity and Related Properties of Rubbers (1974)

Abstract In Section I the relation of rubbers to other classes of polymers and the molecular basis of rubber elasticity are briefly examined. In Section II the methods used in the quantitative development of the statistical-thermodynamic theory of a molecular network are outlined, and the main conclusions, in the form of stress—strain relations, etc. , are presented and compared with experimental data. Section III examines the photoelastic properties of rubbers from both theoretical and experimental standpoints and discusses in detail the evidence derived from photoelastic studies on the statistical segment length in the molecular chain and its relation to intramolecular energy barriers. Section IV is concerned with the thermodynamic analysis of stress—temperature data for rubber and other polymers, with particular reference to the internal energy and entropy changes during extension under constant pressure or constant volume conditions. Methods of deriving these quantities are compared and the results related to the modified molecular network theory due to Flory. Section V deals with the phenomena of swelling in liquids and considers both the effect of swelling on the mechanical properties and the effect of different types of stress or strain on the swelling equilibrium. Sections I–V are concerned mainly with the statistical theory and its applications. The final section examines in considerable detail the formulation of more general theories of large elastic deformations on a purely empirical or phenomenological basis, so as to overcome some of the limitations of the statistical theory. The logical basis of these formulations is presented and the conclusions are discussed in relation to the available experimental evidence. Some common pitfalls to be avoided are emphasized.
Design and Synthesis of a Potent and Selective Peptidomimetic Inhibitor of Caspase-3 (2004)

In this paper we report the synthesis and characterization of a novel potent and selective inhibitor of caspase-3, a member of the caspase family of cysteine proteases which plays an important role in many human disorders. This molecule represents 3(S)-acetylamino-N-[1-[(((3S)-2-hydroxy-5-oxo-tetrahydrofuran-3-yl)carbamoyl)methyl]-2-oxo-5-phenyl-2,3-dihydro-1H-benzo[e][1,4]diazepin-3-yl]succinamic acid, a monocyclic conformationally constrained form of the tetrapeptide Ac-DEVD-H, in which a 1,4-benzodiazepine nucleus is introduced internally to the peptidic sequence.
Single Fluorescent Probe Responds to H <sub>2</sub> O <sub>2</sub> , NO, and H <sub>2</sub> O <sub>2</sub> /NO with Three Different Sets of Fluorescence Signals (2011)

Hydrogen peroxide (H(2)O(2)) acts as a signaling molecule in a wide variety of signaling transduction processes and an oxidative stress marker in aging and disease. However, excessive H(2)O(2) production is implicated with various diseases. Nitric oxide (NO) serves as a secondary messenger inducing vascular smooth muscle relaxation. However, mis-regulation of NO production is associated with various disorders. To disentangle the complicated inter-relationship between H(2)O(2) and NO in the signal transduction and oxidative pathways, fluorescent reporters that are able to display distinct signals to H(2)O(2), NO, and H(2)O(2)/NO are highly valuable. Herein, we present the rational design, synthesis, spectral properties, and living cell imaging studies of FP-H(2)O(2)-NO, the first single-fluorescent molecule, that can respond to H(2)O(2), NO, and H(2)O(2)/NO with three different sets of fluorescence signals. FP-H(2)O(2)-NO senses H(2)O(2), NO, and H(2)O(2)/NO with a fluorescence signal pattern of blue-black-black, black-black-red, and black-red-red, respectively. Significantly, we have further demonstrated that FP-H(2)O(2)-NO, a single fluorescent probe, is capable of simultaneously monitoring endogenously produced NO and H(2)O(2) in living macrophage cells in multicolor imaging. We envision that FP-H(2)O(2)-NO will be a unique molecular tool to investigate the interplaying roles of H(2)O(2) and NO in the complex interaction networks of the signal transduction and oxidative pathways. In addition, this work establishes a robust strategy for monitoring the multiple ROS and RNS species (H(2)O(2), NO, and H(2)O(2)/NO) using a single fluorescent probe, and the modularity of the strategy may allow it to be extended for other types of biomolecules.
ChemInform Abstract: HALOHYDRINS OF ISOQUINOLINE REISSERT COMPOUNDS: BASE‐INDUCED REARRANGEMENT REACTIONS PROVIDING ISOCHROMENES AND NEW ISOQUINOLINES (1979)

Abstract Umsetzung der Reissertprodukt (VI) zu dem Isocumarin (VII) hydrolysiert wird.
β‐Cyclodextrin adducts of Gd(III) chelates: useful models for investigating the structural and dynamic determinants of the relaxivity of gadolinium‐based systems (2003)

Abstract Gadolinium‐chelates bearing hydrophobic substituents on their surfaces form inclusion complexes with β‐cyclodextrin. When the chelate contains more than one substituent, the observed relaxation enhancement has to be analysed on the basis of the contributions arising from the actual speciation of the resulting inclusion complexes. This analysis allows the assessment of the binding constants for the individual inclusion complexes, as well as their specific relaxation enhancements. The relaxivities obtained of the supramolecular adducts display a good linearity with their molecular weights to outline that, in these systems, the main determinant of the relaxation enhancement is represented by the overall molecular reorientational time. Copyright © 2003 John Wiley & Sons, Ltd.
Studies on the Partial Carboxymethylation of Cotton (1952)

Additional studies have been made on partial carboxymethylation—the reaction between mono chloroacetic acid and cotton in the presence of sodium hydroxide—and on the products ob tained. A thorough investigation of the time and temperature of reaction and concentration of reagents showed that relatively small amounts of monochloroacetic acid, properly applied, alter the properties of cotton considerably. Pilot-scale carboxymethylation of cloth was conducted which showed that it is possible to use standard textile machinery in the process. The cloth resulting from this treatment had a crisp liand with a slightly starched feel. More detailed investigations than reported previously were made, and it was found that the tensile strength and elongation of treated cotton are increased, dyeing properties are changed, and soiling-resistance and soil removal are increased. It was also learned that the treated materials are unaffected after one year's storage.
New Techniques for Graph Edit Distance Computation (2019)

Due to their capacity to encode rich structural information, labeled graphs are often used for modeling various kinds of objects such as images, molecules, and chemical compounds. If pattern recognition problems such as clustering and classification are to be solved on these domains, a (dis-)similarity measure for labeled graphs has to be defined. A widely used measure is the graph edit distance (GED), which, intuitively, is defined as the minimum amount of distortion that has to be applied to a source graph in order to transform it into a target graph. The main advantage of GED is its flexibility and sensitivity to small differences between the input graphs. Its main drawback is that it is hard to compute. In this thesis, new results and techniques for several aspects of computing GED are presented. Firstly, theoretical aspects are discussed: competing definitions of GED are harmonized, the problem of computing GED is characterized in terms of complexity, and several reductions from GED to the quadratic assignment problem (QAP) are presented. Secondly, solvers for the linear sum assignment problem with error-correction (LSAPE) are discussed. LSAPE is a generalization of the well-known linear sum assignment problem (LSAP), and has to be solved as a subproblem by many GED algorithms. In particular, a new solver is presented that efficiently reduces LSAPE to LSAP. Thirdly, exact algorithms for computing GED are presented in a systematic way, and improvements of existing algorithms as well as a new mixed integer programming (MIP) based approach are introduced. Fourthly, a detailed overview of heuristic algorithms that approximate GED via upper and lower bounds is provided, and eight new heuristics are described. Finally, a new easily extensible C++ library for exactly or approximately computing GED is presented.
The watchful forensic analyst: Multi-clue information fusion with background knowledge (2013)

Image Forensics (IF) is a challenging research topic, that suffers from strong limitations when facing with real world applications. A possible way to cope with these limitations is to resort to data fusion, whereby the outputs of different forensic tools are used to reach a final decision about the analyzed image. Nevertheless, existing schemes do not take full advantage of all the information available to the analyst, like the knowledge of the dependence of the performance of forensic tools on side conditions. Specifically, in this paper we show how the performance of forensic tools varies according to a number of parameters, most of which are directly observable by the analyst. After showing some practical examples, we propose a method to cast this background information into two multi-clue information fusion frameworks, yielding a significant improvement of the overall performance at virtually no cost.
Primary and secondary structure of dinoflagellate U5 small nuclear RNA (1984)

U5 RNA is one of the six capped small nuclear RNAs present in most eukaryotic cells. Like U1, U2, U4 and U6 RNAs, U5 RNA is associated with hnRNP particles and is thus probably involved in some, as yet undefined, aspects of pre-messenger RNA processing. In this study, the complete nucleotide sequence of U5 RNA of a dinoflagellate, Crypthecodinium cohnii was determined. The analysis of this dinoflagellate U5 RNA sequence showed that a) the sequence homology between human, rat and chicken U5 RNA sequences and dinoflagellate U5 RNA sequence is 64%; b) the extent and the position of post-transcriptional modifications are similar to those found in U5 RNA of higher eukaryotes; c) although the dinoflagellate U5 RNA is shorter in length (108 nucleotides long vs 117 long in human, rat and chicken cells), the RNA fits well into the same secondary structure proposed for U5 RNA of higher eukaryotes (Krol et al. (1981) Nucl. Acids Res. 9, 769); and d) the AUn nucleotide sequence protected by the Sm-antigen and the tight secondary structure found near the 3'-end of other U-RNAs was also found in dinoflagellate U5 RNA. The high order of homology observed between dinoflagellate U5 RNA and U5 RNA of higher eukaryotes indicates that dinoflagellates are more closely related to metazoans than to early eukaryotes.
Assembly Line Polyketide Synthases: Mechanistic Insights and Unsolved Problems (2014)

Two hallmarks of assembly line polyketide synthases have motivated an interest in these unusual multienzyme systems, their stereospecificity and their capacity for directional biosynthesis. In this review, we summarize the state of knowledge regarding the mechanistic origins of these two remarkable features, using the 6-deoxyerythronolide B synthase as a prototype. Of the 10 stereocenters in 6-deoxyerythronolide B, the stereochemistry of nine carbon atoms is directly set by ketoreductase domains, which catalyze epimerization and/or diastereospecific reduction reactions. The 10th stereocenter is established by the sequential action of three enzymatic domains. Thus, the problem has been reduced to a challenge in mainstream enzymology, where fundamental gaps remain in our understanding of the structural basis for this exquisite stereochemical control by relatively well-defined active sites. In contrast, testable mechanistic hypotheses for the phenomenon of vectorial biosynthesis are only just beginning to emerge. Starting from an elegant theoretical framework for understanding coupled vectorial processes in biology [Jencks, W. P. (1980) Adv. Enzymol. Relat. Areas Mol. Biol. 51, 75-106], we present a simple model that can explain assembly line polyketide biosynthesis as a coupled vectorial process. Our model, which highlights the important role of domain-domain interactions, not only is consistent with recent observations but also is amenable to further experimental verification and refinement. Ultimately, a definitive view of the coordinated motions within and between polyketide synthase modules will require a combination of structural, kinetic, spectroscopic, and computational tools and could be one of the most exciting frontiers in 21st Century enzymology.
Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. (1994)

Unfixed chicken erythrocyte chromatin fibers in very low salt have been imaged with a scanning force microscope operating in the tapping mode in air at ambient humidity. These images reveal a three-dimensional organization of the fibers. The planar "zig-zag" conformation is rare, and extended "beads-on-a-string" fibers are seen only in chromatin depleted of histones H1 and H5. Glutaraldehyde fixation reveals very similar structures. Fibers fixed in 10 mM salt appear somewhat more compacted. These results, when compared with modeling studies, suggest that chromatin fibers may exist as irregular three-dimensional arrays of nucleosomes even at low ionic strength.
How to scale distributed deep learning? (2016)

Training time on large datasets for deep neural networks is the principal workflow bottleneck in a number of important applications of deep learning, such as object classification and detection in automatic driver assistance systems (ADAS). To minimize training time, the training of a deep neural network must be scaled beyond a single machine to as many machines as possible by distributing the optimization method used for training. While a number of approaches have been proposed for distributed stochastic gradient descent (SGD), at the current time synchronous approaches to distributed SGD appear to be showing the greatest performance at large scale. Synchronous scaling of SGD suffers from the need to synchronize all processors on each gradient step and is not resilient in the face of failing or lagging processors. In asynchronous approaches using parameter servers, training is slowed by contention to the parameter server. In this paper we compare the convergence of synchronous and asynchronous SGD for training a modern ResNet network architecture on the ImageNet classification problem. We also propose an asynchronous method, gossiping SGD, that aims to retain the positive features of both systems by replacing the all-reduce collective operation of synchronous training with a gossip aggregation algorithm. We find, perhaps counterintuitively, that asynchronous SGD, including both elastic averaging and gossiping, converges faster at fewer nodes (up to about 32 nodes), whereas synchronous SGD scales better to more nodes (up to about 100 nodes).
A novel method for footstep detection with extremely low false alarm rate (2003)

Development of advanced seismic footstep detection systems for perimeter and zone protection can offer new method for improved homeland security and defense applications. High false alarm rates associated with current seismic security systems has been a formidable obstacle in their widespread adoption. This paper describes a novel method for seismic footstep detection in which false alarms are inhibited and virtually eliminated. In addition, a significant increase in detection range for seismic security systems is also reported. Proprietary software was specifically developed to improve processing of the seismic signals. This software allows one to uniquely analyze over three-dozen signal shape parameters within the detected seismic signal. This novel software enables real time signal analysis, thus effectively offering a more efficient and effective alternative to using trained personnel.