Complementary intrastrand base pairing during initiation of Herpes simplex virus type 1 DNA replication

The herpes simplex virus type 1 origin of DNA replication, oriS, contains three copies of the recognition sequence for the viral initiator protein, origin binding protein (OBP), arranged in two palindromes. The central box I forms a short palindrome with box III and a long palindrome with box II. Single-stranded oriS adopts a conformation, oriS*, that is tightly bound by OBP. Here we demonstrate that OBP binds to a box III–box I hairpin with a 3′ single-stranded tail in oriS*. Mutations designed to destabilize the hairpin abolish the binding of OBP to oriS*. The same mutations also inhibit DNA replication. Second site complementary mutations restore binding of OBP to oriS* as well as the ability of mutated oriS to support DNA replication. OriS* is also an efficient activator of the hydrolysis of ATP by OBP. Sequence analyses show that a box III–box I palindrome is an evolutionarily conserved feature of origins of DNA replication from human, equine, bovine, and gallid alpha herpes viruses. We propose that oriS facilitates initiation of DNA synthesis in two steps and that OBP exhibits exquisite specificity for the different conformations oriS adopts at these stages. Our model suggests that distance-dependent cooperative binding of OBP to boxes I and II in duplex DNA is succeeded by specific recognition of a box III–box I hairpin in partially unwound DNA.

Computation of Surface Electrical Potentials of Plant Cell Membranes : Correspondence to Published Zeta Potentials from Diverse Plant Sources

A Gouy-Chapman-Stern model has been developed for the computation of surface electrical potential (ψ0) of plant cell membranes in response to ionic solutes. The present model is a modification of an earlier version developed to compute the sorption of ions by wheat (Triticum aestivum L. cv Scout 66) root plasma membranes. A single set of model parameters generates values for ψ0 that correlate highly with published ζ potentials of protoplasts and plasma membrane vesicles from diverse plant sources. The model assumes ion binding to a negatively charged site (R− = 0.3074 μmol m−2) and to a neutral site (P0 = 2.4 μmol m−2) according to the reactions R− + IΖ ⇌ RIΖ−1 and P0 + IΖ ⇌ PIΖ, where IΖ represents an ion of charge Ζ. Binding constants for the negative site are 21,500 m−1 for H+, 20,000 m−1 for Al3+, 2,200 m−1 for La3+, 30 m−1 for Ca2+ and Mg2+, and 1 m−1 for Na+ and K+. Binding constants for the neutral site are 1/180 the value for binding to the negative site. Ion activities at the membrane surface, computed on the basis of ψ0, appear to determine many aspects of plant-mineral interactions, including mineral nutrition and the induction and alleviation of mineral toxicities, according to previous and ongoing studies. A computer program with instructions for the computation of ψ0, ion binding, ion concentrations, and ion activities at membrane surfaces may be requested from the authors.

The evolution of emergent computation.

A simple evolutionary process can discover sophisticated methods for emergent information processing in decentralized spatially extended systems. The mechanisms underlying the resulting emergent computation are explicated by a technique for analyzing particle-based logic embedded in pattern-forming systems. Understanding how globally coordinated computation can emerge in evolution is relevant both for the scientific understanding of natural information processing and for engineering new forms of parallel computing systems.

Rapid local synchronization of action potentials: toward computation with coupled integrate-and-fire neurons.

The collective behavior of interconnected spiking nerve cells is investigated. It is shown that a variety of model systems exhibit the same short-time behavior and rapidly converge to (approximately) periodic firing patterns with locally synchronized action potentials. The dynamics of one model can be described by a downhill motion on an abstract energy landscape. Since an energy landscape makes it possible to understand and program computation done by an attractor network, the results will extend our understanding of collective computation from models based on a firing-rate description to biologically more realistic systems with integrate-and-fire neurons.

An integral security kernel

As the user base of the Internet has grown tremendously, the need for secure services has increased accordingly. Most secure protocols, in digital business and other fields, use a combination of symmetric and asymmetric cryptography, random generators and hash functions in order to achieve confidentiality, integrity, and authentication. Our proposal is an integral security kernel based on a powerful mathematical scheme from which all of these cryptographic facilities can be derived. The kernel requires very little resources and has the flexibility of being able to trade off speed, memory or security; therefore, it can be efficiently implemented in a wide spectrum of platforms and applications, either software, hardware or low cost devices. Additionally, the primitives are comparable in security and speed to well known standards.

Fast pseudorandom generator based on packed matrices

Pseudorandom generators are a basic foundation of many cryptographic services and information security protocols. We propose a modification of a previously published matricial pseudorandom generator that significantly improves performance and security. The resulting generator is successfully compared to world class standards.

An optimized pseudorandom generator using packed matrices

Most cryptographic services and information security protocols require a dependable source of random data; pseudorandom generators are convenient and efficient for this application working as one of the basic foundation blocks on which to build the required security infrastructure. We propose a modification of a previously published matricial pseudorandom generator that significantly improves performance and security by using word packed matrices and modifying key scheduling and bit extraction schemes. The resulting generator is then successfully compared to world class standards.

Efficient tool path computation using multi-core GPUs

Tool path generation is one of the most complex problems in Computer Aided Manufacturing. Although some efficient strategies have been developed, most of them are only useful for standard machining. However, the algorithms used for tool path computation demand a higher computation performance, which makes the implementation on many existing systems very slow or even impractical. Hardware acceleration is an incremental solution that can be cleanly added to these systems while keeping everything else intact. It is completely transparent to the user. The cost is much lower and the development time is much shorter than replacing the computers by faster ones. This paper presents an optimisation that uses a specific graphic hardware approach using the power of multi-core Graphic Processing Units (GPUs) in order to improve the tool path computation. This improvement is applied on a highly accurate and robust tool path generation algorithm. The paper presents, as a case of study, a fully implemented algorithm used for turning lathe machining of shoe lasts. A comparative study will show the gain achieved in terms of total computing time. The execution time is almost two orders of magnitude faster than modern PCs.

Crypto at the Time of Surveillance: Sharing with the Cloud

These days as we are facing extremely powerful attacks on servers over the Internet (say, by the Advanced Persistent Threat attackers or by Surveillance by powerful adversary), Shamir has claimed that “Cryptography is Ineffective”and some understood it as “Cryptography is Dead!” In this talk I will discuss the implications on cryptographic systems design while facing such strong adversaries. Is crypto dead or we need to design it better, taking into account, mathematical constraints, but also systems vulnerability constraints. Can crypto be effective at all when your computer or your cloud is penetrated? What is lost and what can be saved? These are very basic issues at this point of time, when we are facing potential loss of privacy and security.

Comparison Between Dcrit Considering the Abrupt Variation and Inflexion in the Concrete Mercury Intrusion Porosimetry Curve

Mercury intrusion porosimetry (MIP) has been widely used to evaluate the quality of concrete through the pore size distribution parameters. Two of these parameters are the critical pore diameter (Dcrit) and the percentage of the most interconnected net of pores compared to the total volume of pores. Some researchers consider Dcrit as the diameter obtained from the inflexion point of the cumulative mercury intrusion curve while others consider Dcrit as the diameter obtained from the point of abrupt variation in the same curve. This study aims to analyze two groups of concretes of varying w/c ratios, one cast with pozzolanic cement and another with high initial strength cement, in order to determine which of these diameters feature a better correlation with the quality parameters of the concretes. The concrete quality parameters used for the evaluations were (1) the w/c ratios and (2) chloride diffusion coefficients measured at approximately 90 days. MIP cumulative distributions of the same concretes were also measured at about 90 days, and Dcrit values were determined (1) from the point of abrupt variation and alternatively, (2) from the inflexion point of each of these plots. It was found that Dcrit values measured from the point of abrupt variation were useful indicators of the quality of the concrete, but the Dcrit values based on the inflexion points were not. Hence, it is recommended that Dcrit and the percentage of the most interconnected volume of pores should be obtained considering the point of abrupt variation of the cumulative curve of pore size distribution.

Mr. Monis's computation about printing his Hebrew Grammar, [ca. 1734]

A one-page handwritten computation by Judah Monis for printing the Hebrew Grammar and binding it in sheep and calf skins. The document was written on one folio-sized leaf that is torn in two pieces.

Geometry of Dirac Operators

Thesis (Master, Mathematics & Statistics) -- Queen's University, 2016-07-04 20:27:20.386

A Proper Yield Curve for Greece to Kick-Start Financial Intermediation. ECMI Policy Brief No. 21, 10 December 2013

At present, the market is severely mispricing Greece’s sovereign risk relative to the country’s fundamentals. As a result of the mispricing, financial intermediation in Greece has become dysfunctional and the privatisation of state-owned assets has stalled. This mispricing is partially due to an illiquid and fragmented government yield curve. A well-designed public liability management exercise can lead to a more efficient pricing of Greece’s government bonds and thereby help restore stable and affordable financing for the country’s private sector, which is imperative in order to overcome Greece’s deep recession. This paper proposes three measures to enhance the functioning of the Greek government debt market: i) Greece should issue a new five-year bond, ii) it should consolidate the 20 individual series of government bonds into four liquid securities and iii) it should offer investors a swap of these newly created bonds into dollar-denominated securities. Each of these measures would be beneficial to the Hellenic Republic, since the government would be able to reduce the face value and the net present value of its debt stock. Furthermore, this exercise would facilitate the resumption of market access, which is a necessary condition for continuous multilateral disbursements to Greece.