BioPatML : pattern sharing for the genomic sciences

Computational biology increasingly demands the sharing of sophisticated data and annotations between research groups. Web 2.0 style sharing and publication requires that biological systems be described in well-defined, yet flexible and extensible formats which enhance exchange and re-use. In contrast to many of the standards for exchange in the genomic sciences, descriptions of biological sequences show a great diversity in format and function, impeding the definition and exchange of sequence patterns. In this presentation, we introduce BioPatML, an XML-based pattern description language that supports a wide range of patterns and allows the construction of complex, hierarchically structured patterns and pattern libraries. BioPatML unifies the diversity of current pattern description languages and fills a gap in the set of XML-based description languages for biological systems. We discuss the structure and elements of the language, and demonstrate its advantages on a series of applications, showing lightweight integration between the BioPatML parser and search engine, and the SilverGene genome browser. We conclude by describing our site to enable large scale pattern sharing, and our efforts to seed this repository.

QoS-Based Web Service Scheduling Accommodating Inter-Service Dependencies Using Minimal-Conflict Hill-Climbing Repair Genetic Algorithm

In the filed of semantic grid, QoS-based Web service scheduling for workflow optimization is an important problem.However, in semantic and service rich environment like semantic grid, the emergence of context constraints on Web services is very common making the scheduling consider not only quality properties of Web services, but also inter service dependencies which are formed due to the context constraints imposed on Web services. In this paper, we present a repair genetic algorithm, namely minimal-conflict hill-climbing repair genetic algorithm, to address scheduling optimization problems in workflow applications in the presence of domain constraints and inter service dependencies. Experimental results demonstrate the scalability and effectiveness of the genetic algorithm.

Towards an acoustic environmental observatory

The need for large scale environmental monitoring to manage environmental change is well established. Ecologists have long used acoustics as a means of monitoring the environment in their field work, and so the value of an acoustic environmental observatory is evident. However, the volume of data generated by such an observatory would quickly overwhelm even the most fervent scientist using traditional methods. In this paper we present our steps towards realising a complete acoustic environmental observatory - i.e. a cohesive set of hardware sensors, management utilities, and analytical tools required for large scale environmental monitoring. Concrete examples of these elements, which are in active use by ecological scientists, are also presented

QoS-based web service composition accommodating inter-service dependencies using minimal-conflict , hill-climbing repair genetic algorithm

In the field of semantic grid, QoS-based Web service composition is an important problem. In semantic and service rich environment like semantic grid, the emergence of context constraints on Web services is very common making the composition consider not only QoS properties of Web services, but also inter service dependencies and conflicts which are formed due to the context constraints imposed on Web services. In this paper, we present a repair genetic algorithm, namely minimal-conflict hill-climbing repair genetic algorithm, to address the Web service composition optimization problem in the presence of domain constraints and inter service dependencies and conflicts. Experimental results demonstrate the scalability and effectiveness of the genetic algorithm.

Examining the role of human resource management in continuous improvement

The objective of this paper is to take a first step in developing a theoretical framework describing the role of HRM in successful CI, based on the current literature from both fields. To this end, elements from the CI Maturity Model and a framework depicting the role of HRM in innovation serve as a foundation for examining how specific bundles of HRM practices utilised during different phases of the CI implementation process may contribute to sustained organisational and enhanced operational performance. The primary contribution of this paper is theoretical; however, the framework has practical value in that it suggests important relationships between HRM practices and behaviours necessary for successful CI. A preliminary test of the framework in an empirical setting is summarised at the conclusion of this paper, where a number of possible research avenues are also suggested.

Encryption schemes and key exchange protocols in the certificateless setting

The contributions of this thesis fall into three areas of certificateless cryptography. The first area is encryption, where we propose new constructions for both identity-based and certificateless cryptography. We construct an n-out-of- n group encryption scheme for identity-based cryptography that does not require any special means to generate the keys of the trusted authorities that are participating. We also introduce a new security definition for chosen ciphertext secure multi-key encryption. We prove that our construction is secure as long as at least one authority is uncompromised, and show that the existing constructions for chosen ciphertext security from identity-based encryption also hold in the group encryption case. We then consider certificateless encryption as the special case of 2-out-of-2 group encryption and give constructions for highly efficient certificateless schemes in the standard model. Among these is the first construction of a lattice-based certificateless encryption scheme. Our next contribution is a highly efficient certificateless key encapsulation mechanism (KEM), that we prove secure in the standard model. We introduce a new way of proving the security of certificateless schemes based that are based on identity-based schemes. We leave the identity-based part of the proof intact, and just extend it to cover the part that is introduced by the certificateless scheme. We show that our construction is more efficient than any instanciation of generic constructions for certificateless key encapsulation in the standard model. The third area where the thesis contributes to the advancement of certificateless cryptography is key agreement. Swanson showed that many certificateless key agreement schemes are insecure if considered in a reasonable security model. We propose the first provably secure certificateless key agreement schemes in the strongest model for certificateless key agreement. We extend Swanson's definition for certificateless key agreement and give more power to the adversary. Our new schemes are secure as long as each party has at least one uncompromised secret. Our first construction is in the random oracle model and gives the adversary slightly more capabilities than our second construction in the standard model. Interestingly, our standard model construction is as efficient as the random oracle model construction.

Publicly verifiable ciphertexts

In many applications, where encrypted traffic flows from an open (public) domain to a protected (private) domain, there exists a gateway that bridges the two domains and faithfully forwards the incoming traffic to the receiver. We observe that indistringuishability against (adaptive) chosen-ciphertext attacks (IND-CCA), which is a mandatory goal in face of active attacks in a public domain, can be essentially relaxed to indistinguishability against chosen-plaintext attacks (IND-CPA) for ciphertexts once they pass the gateway that acts as an IND-CCA/CPA filter by first checking the validity of an incoming IND-CCA ciphertext, then transforming it (if valid) into an IND-CPA ciphertext, and forwarding the latter to the receipient in the private domain. "Non-trivial filtering" can result in reduced decryption costs on the receivers' side. We identify a class of encryption schemes with publicaly verifiable ciphertexts that admit generic constructions of (non-trivial) IND-CCA/CPA filters. These schemes are characterized by existence of public algorithms that can distinguish between valid and invalid ciphertexts. To this end, we formally define (non-trivial) public verifiability of ciphertexts for general encryption schemes, key encapsulation mechanisms, and hybrid encryption schemes, encompassing public-key, identity-based, and tag-based encryption flavours. We further analyze the security impact of public verifiability and discuss generic transformations and concrete constructions that enjoy this property.

Computationally sound automated proofs of cryptographic schemes

Proving security of cryptographic schemes, which normally are short algorithms, has been known to be time-consuming and easy to get wrong. Using computers to analyse their security can help to solve the problem. This thesis focuses on methods of using computers to verify security of such schemes in cryptographic models. The contributions of this thesis to automated security proofs of cryptographic schemes can be divided into two groups: indirect and direct techniques. Regarding indirect ones, we propose a technique to verify the security of public-key-based key exchange protocols. Security of such protocols has been able to be proved automatically using an existing tool, but in a noncryptographic model. We show that under some conditions, security in that non-cryptographic model implies security in a common cryptographic one, the Bellare-Rogaway model [11]. The implication enables one to use that existing tool, which was designed to work with a different type of model, in order to achieve security proofs of public-key-based key exchange protocols in a cryptographic model. For direct techniques, we have two contributions. The first is a tool to verify Diffie-Hellmanbased key exchange protocols. In that work, we design a simple programming language for specifying Diffie-Hellman-based key exchange algorithms. The language has a semantics based on a cryptographic model, the Bellare-Rogaway model [11]. From the semantics, we build a Hoare-style logic which allows us to reason about the security of a key exchange algorithm, specified as a pair of initiator and responder programs. The other contribution to the direct technique line is on automated proofs for computational indistinguishability. Unlike the two other contributions, this one does not treat a fixed class of protocols. We construct a generic formalism which allows one to model the security problem of a variety of classes of cryptographic schemes as the indistinguishability between two pieces of information. We also design and implement an algorithm for solving indistinguishability problems. Compared to the two other works, this one covers significantly more types of schemes, but consequently, it can verify only weaker forms of security.

The effects of cold air (-110°C) and water (8°C) cryotherapy on knee skin temperature

Exposure to cold air, whole body cryotherapy (WBC), is a novel treatment employed by athletes. In WBC individuals dressed in minimal clothing are exposed to a temperature below -100°C for 2-4 min. The use of WBC has been advocated as a treatment for various knee injuries. PURPOSE: To compare the effects of two modalities of cryotherapy, -110°C WBC and 8°C cold water immersion (CWI) on knee skin temperature (Tsk). METHODS: With ethical approval and written informed consent 10 healthy active male participants (26.5±4.9 yr, 183.5±6.0 cm, 90.7±19.9 kg, 26.8±5.0 kg/m2, 23.0±9.3% body fat (measured by DXA), 7.6 ± 2.0 mm patellar skin fold; mean±SD) were exposed to 4 min of CWI and WBC. The treatment order was randomised in a controlled crossover design, with a minimum of 7 days between treatments. During WBC participants stood in a chamber (-60±3°C) for 20 s before entering the main chamber (-110°C±3°C) where they remained for 3 min and 40 s. For CWI participants were seated in a tank filled with cold water (8±0.3°C) and immersed to the level of the sternum for 4 min. Right knee Tsk was assessed via non-contact, infrared thermal imaging. A quadrilateral region of interest was created using inert markers placed 5 cm above and below the most superior and inferior aspect of the patella. Tsk within this quadrilateral was recorded pre, immediately post and every 10 min thereafter for 60 min. Tsk changes were examined using a two-way (treatment x time) repeated measures analyses of variance. In addition, a paired sample t-test was used to compare baseline Tsk before both treatments. RESULTS: Knee Tsk was similar before treatment (WBC: 29.9±0.7°C, CWI: 29.6±0.9°C, p>0.05). There was a significant main effect for treatment (p<0.05) and time (p<0.001). Compared to baseline, Tsk was significantly reduced (p<0.05) immediately post and at 10, 20, 30, 40, 50 and 60 min after both cooling modalities. Knee Tsk was lower (p<0.05) immediately after WBC (19.0±0.9°C) compared to CWI (20.5±0.6°C). However, from 10 to 60 min post, knee Tsk was lower (p<0.05) following the CWI treatment. CONCLUSION: WBC elicited a greater decrease in knee Tsk compared to CWI immediately after treatment. However, both modalities display different recovery patterns and Tsk after CWI was significantly lower than WBC at 10, 20, 30, 40, 50 and 60 min after treatment.

Publicly verifiable ciphertexts

In many applications, where encrypted traffic flows from an open (public) domain to a protected (private) domain, there exists a gateway that bridges the two domains and faithfully forwards the incoming traffic to the receiver. We observe that indistinguishability against (adaptive) chosen-ciphertext attacks (IND-CCA), which is a mandatory goal in face of active attacks in a public domain, can be essentially relaxed to indistinguishability against chosen-plaintext attacks (IND-CPA) for ciphertexts once they pass the gateway that acts as an IND-CCA/CPA filter by first checking the validity of an incoming IND-CCA ciphertext, then transforming it (if valid) into an IND-CPA ciphertext, and forwarding the latter to the recipient in the private domain. “Non-trivial filtering'' can result in reduced decryption costs on the receivers' side. We identify a class of encryption schemes with publicly verifiable ciphertexts that admit generic constructions of (non-trivial) IND-CCA/CPA filters. These schemes are characterized by existence of public algorithms that can distinguish between valid and invalid ciphertexts. To this end, we formally define (non-trivial) public verifiability of ciphertexts for general encryption schemes, key encapsulation mechanisms, and hybrid encryption schemes, encompassing public-key, identity-based, and tag-based encryption flavours. We further analyze the security impact of public verifiability and discuss generic transformations and concrete constructions that enjoy this property.

Plaintext awareness in identity-based key encapsulation

The notion of plaintext awareness ( PA ) has many applications in public key cryptography: it offers unique, stand-alone security guarantees for public key encryption schemes, has been used as a sufficient condition for proving indistinguishability against adaptive chosen-ciphertext attacks ( IND-CCA ), and can be used to construct privacy-preserving protocols such as deniable authentication. Unlike many other security notions, plaintext awareness is very fragile when it comes to differences between the random oracle and standard models; for example, many implications involving PA in the random oracle model are not valid in the standard model and vice versa. Similarly, strategies for proving PA of schemes in one model cannot be adapted to the other model. Existing research addresses PA in detail only in the public key setting. This paper gives the first formal exploration of plaintext awareness in the identity-based setting and, as initial work, proceeds in the random oracle model. The focus is laid mainly on identity-based key encapsulation mechanisms (IB-KEMs), for which the paper presents the first definitions of plaintext awareness, highlights the role of PA in proof strategies of IND-CCA security, and explores relationships between PA and other security properties. On the practical side, our work offers the first, highly efficient, general approach for building IB-KEMs that are simultaneously plaintext-aware and IND-CCA -secure. Our construction is inspired by the Fujisaki-Okamoto (FO) transform, but demands weaker and more natural properties of its building blocks. This result comes from a new look at the notion of γ -uniformity that was inherent in the original FO transform. We show that for IB-KEMs (and PK-KEMs), this assumption can be replaced with a weaker computational notion, which is in fact implied by one-wayness. Finally, we give the first concrete IB-KEM scheme that is PA and IND-CCA -secure by applying our construction to a popular IB-KEM and optimizing it for better performance.

A cognitive processing framework for learning analytics

Incorporating a learner’s level of cognitive processing into Learning Analytics presents opportunities for obtaining rich data on the learning process. We propose a framework called COPA that provides a basis for mapping levels of cognitive operation into a learning analytics system. We utilise Bloom’s taxonomy, a theoretically respected conceptualisation of cognitive processing, and apply it in a flexible structure that can be implemented incrementally and with varying degree of complexity within an educational organisation. We outline how the framework is applied, and its key benefits and limitations. Finally, we apply COPA to a University undergraduate unit, and demonstrate its utility in identifying key missing elements in the structure of the course.

NTRUCCA : how to strengthen NTRUEncrypt to chosen-ciphertext security in the standard model

NTRUEncrypt is a fast and practical lattice-based public-key encryption scheme, which has been standardized by IEEE, but until recently, its security analysis relied only on heuristic arguments. Recently, Stehlé and Steinfeld showed that a slight variant (that we call pNE) could be proven to be secure under chosen-plaintext attack (IND-CPA), assuming the hardness of worst-case problems in ideal lattices. We present a variant of pNE called NTRUCCA, that is IND-CCA2 secure in the standard model assuming the hardness of worst-case problems in ideal lattices, and only incurs a constant factor overhead in ciphertext and key length over the pNE scheme. To our knowledge, our result gives the first IND-CCA2 secure variant of NTRUEncrypt in the standard model, based on standard cryptographic assumptions. As an intermediate step, we present a construction for an All-But-One (ABO) lossy trapdoor function from pNE, which may be of independent interest. Our scheme uses the lossy trapdoor function framework of Peikert and Waters, which we generalize to the case of (k − 1)-of-k-correlated input distributions.

Predictive validity of accelerometer prediction equations for energy expenditure (EE) during overland walking and running in children and adolescents

Purpose The aim of this study was to assess the predictive validity of three accelerometer prediction equations (Freedson et aL, 1997; Trost et aL, 1998; Puyau et al., 2002) for energy expenditure (EE) during overland walking and running in children and adolescents. Methods 45 healthy children and adolescents aged 10-18 completed the following protocol, each task 5-mins in duration, with a 5-min rest period in between; walking normally; walking briskly; running easily and running fast. During each task participants wore MTI (WAM 7164) Actigraphs on the left and right hips. VO2 was monitored breath by breath using the Cosmed K4b2 portable indirect calorimetry system. For each prediction equation, difference scores were calculated as EE measured minus EE predicted. The percentage of 1-min epochs correctly categorized as light (<3 METs), moderate (3-5.9 METs), and vigorous (≥6 METS) was also calculated. Results The Freedson and Trost equations consistently overestimated MET level. The level of overestimation was statistically significant across all tasks for the Freedson equation, and was significant for only the walking tasks for the Trost equation. The Puyau equation consistently underestimated AEE with the exception of the walking normally task. In terms of categorisation, the Freedson equation (72.8% agreement) demonstrated better agreement than the Puyau (60.6%). Conclusions These data suggest that the three accelerometer prediction equations do not accurately predict EE on a minute-by-minute basis in children and adolescents during overland walking and running. However, the cut points generated by these equations maybe useful for classifying activity as either, light, moderate, or vigorous.