Security and the Transnational Information Polity

Global information and communications technologies create criminal opportunities in which criminal violation and physical proximity are decoupled. As in all our endeavors, the good become the prey of the bad. Murderous and venal exploitation of ICT has followed from the inception of the Internet, threatening all the good it brings and the trust we need so badly as a people. As the work continues to expand the implementation of Smart Cities and the Internet of Things, there will be more opportunities for exploitation of these technologies. We examine the social and liberty risks our data and technology-driven responses may entail

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

<p>Abstract</p> <p>Background</p> <p>High throughput sequencing (HTS) platforms produce gigabases of short read (<100 bp) data per run. While these short reads are adequate for resequencing applications, <it>de novo </it>assembly of moderate size genomes from such reads remains a significant challenge. These limitations could be partially overcome by utilizing mate pair technology, which provides pairs of short reads separated by a known distance along the genome.</p> <p>Results</p> <p>We have developed SOPRA, a tool designed to exploit the mate pair/paired-end information for assembly of short reads. The main focus of the algorithm is selecting a sufficiently large subset of simultaneously satisfiable mate pair constraints to achieve a balance between the size and the quality of the output scaffolds. Scaffold assembly is presented as an optimization problem for variables associated with vertices and with edges of the contig connectivity graph. Vertices of this graph are individual contigs with edges drawn between contigs connected by mate pairs. Similar graph problems have been invoked in the context of shotgun sequencing and scaffold building for previous generation of sequencing projects. However, given the error-prone nature of HTS data and the fundamental limitations from the shortness of the reads, the ad hoc greedy algorithms used in the earlier studies are likely to lead to poor quality results in the current context. SOPRA circumvents this problem by treating all the constraints on equal footing for solving the optimization problem, the solution itself indicating the problematic constraints (chimeric/repetitive contigs, etc.) to be removed. The process of solving and removing of constraints is iterated till one reaches a core set of consistent constraints. For SOLiD sequencer data, SOPRA uses a dynamic programming approach to robustly translate the color-space assembly to base-space. For assessing the quality of an assembly, we report the no-match/mismatch error rate as well as the rates of various rearrangement errors.</p> <p>Conclusions</p> <p>Applying SOPRA to real data from bacterial genomes, we were able to assemble contigs into scaffolds of significant length (N50 up to 200 Kb) with very few errors introduced in the process. In general, the methodology presented here will allow better scaffold assemblies of any type of mate pair sequencing data.</p

Establishing norms with metanorms in distributed computational systems

Norms provide a valuable mechanism for establishing coherent cooperative behaviour in decentralised systems in which there is no central authority. One of the most influential formulations of norm emergence was proposed by Axelrod (Am Political Sci Rev 80(4):1095–1111, 1986). This paper provides an empirical analysis of aspects of Axelrod’s approach, by exploring some of the key assumptions made in previous evaluations of the model. We explore the dynamics of norm emergence and the occurrence of norm collapse when applying the model over extended durations . It is this phenomenon of norm collapse that can motivate the emergence of a central authority to enforce laws and so preserve the norms, rather than relying on individuals to punish defection. Our findings identify characteristics that significantly influence norm establishment using Axelrod’s formulation, but are likely to be of importance for norm establishment more generally. Moreover, Axelrod’s model suffers from significant limitations in assuming that private strategies of individuals are available to others, and that agents are omniscient in being aware of all norm violations and punishments. Because this is an unreasonable expectation , the approach does not lend itself to modelling real-world systems such as online networks or electronic markets. In response, the paper proposes alternatives to Axelrod’s model, by replacing the evolutionary approach, enabling agents to learn, and by restricting the metapunishment of agents to cases where the original defection is observed, in order to be able to apply the model to real-world domains . This work can also help explain the formation of a “social contract” to legitimate enforcement by a central authority

Design of compensated ferrimagnetic Heusler alloys for giant tunable exchange bias

The discovery of materials with improved functionality can be accelerated by rational material design. Heusler compounds with tunable magnetic sublattices allow to implement this concept to achieve novel magnetic properties. Here, we have designed a family of Heusler alloys with a compensated ferrimagnetic state. In the vicinity of the compensation composition in Mn-Pt-Ga, a giant exchange bias (EB) of more than 3 T and a similarly large coercivity are established. The large exchange anisotropy originates from the exchange interaction between the compensated host and ferrimagnetic clusters that arise from intrinsic anti-site disorder. We demonstrate the applicability of our design concept on a second material, Mn-Fe-Ga, with a magnetic transition above room temperature, exemplifying the universality of the concept and the feasibility of room-temperature applications. Our study points to a new direction for novel magneto-electronic devices. At the same time it suggests a new route for realizing rare-earth free exchange-biased hard magnets, where the second quadrant magnetization can be stabilized by the exchange bias.Comment: Four figure

Linking variation in planktonic primary production to coral reef fish growth and condition

Within low-nutrient tropical oceans, islands and atolls with higher primary production support higher fish biomass and reef organism abundance. External energy subsidies can be delivered onto reefs via a range of physical mechanisms. However, the influence of spatial variation in primary production on reef fish growth and condition is largely unknown. It is not yet clear how energy subsidies interact with reef depth and slope. Here we test the hypothesis that with increased proximity to deep-water oceanic nutrient sources, or at sites with shallower reef slopes, parameters of fish growth and condition will be higher. Contrary to expectations, we found no association between fish growth rate and sites with higher mean chlorophyll-a values. There were no differences in fish δ 15N or δ 13C values between depths. The relationship between fish condition and primary production was influenced by depth, driven by increased fish condition at shallow depths within a primary production 'hotspot' site. Carbon δ 13C was depleted with increasing primary production, and interacted with reef slope. Our results indicate that variable primary production did not influence growth rates in planktivorous Chromis fieldi within 10-17.5 m depth, but show site-specific variation in reef physical characteristics influencing fish carbon isotopic composition

Altered Env conformational dynamics as a mechanism of resistance to peptide‑triazole HIV‑1 inactivators.

Background: We previously developed drug-like peptide triazoles (PTs) that target HIV-1 Envelope (Env) gp120, potently inhibit viral entry, and irreversibly inactivate virions. Here, we investigated potential mechanisms of viral escape from this promising class of HIV-1 entry inhibitors. Results: HIV-1 resistance to cyclic (AAR029b) and linear (KR13) PTs was obtained by dose escalation in viral passaging experiments. High-level resistance for both inhibitors developed slowly (relative to escape from gp41-targeted C-peptide inhibitor C37) by acquiring mutations in gp120 both within (Val255) and distant to (Ser143) the putative PT binding site. The similarity in the resistance profiles for AAR029b and KR13 suggests that the shared IXW pharmacophore provided the primary pressure for HIV-1 escape. In single-round infectivity studies employing recombinant virus, V255I/S143N double escape mutants reduced PT antiviral potency by 150- to 3900-fold. Curiously, the combined mutations had a much smaller impact on PT binding affinity for monomeric gp120 (four to ninefold). This binding disruption was entirely due to the V255I mutation, which generated few steric clashes with PT in molecular docking. However, this minor effect on PT affinity belied large, offsetting changes to association enthalpy and entropy. The escape mutations had negligible effect on CD4 binding and utilization during entry, but significantly altered both binding thermodynamics and inhibitory potency of the conformationally-specific, anti-CD4i antibody 17b. Moreover, the escape mutations substantially decreased gp120 shedding induced by either soluble CD4 or AAR029b. Conclusions: Together, the data suggest that the escape mutations significantly modified the energetic landscape of Env’s prefusogenic state, altering conformational dynamics to hinder PT-induced irreversible inactivation of Env. This work therein reveals a unique mode of virus escape for HIV-1, namely, resistance by altering the intrinsic conformational dynamics of the Env trimerpost-print4093 K

Linking variation in planktonic primary production to coral reef fish growth and condition

Within low-nutrient tropical oceans, islands and atolls with higher primary production support higher fish biomass and reef organism abundance. External energy subsidies can be delivered onto reefs via a range of physical mechanisms. However, the influence of spatial variation in primary production on reef fish growth and condition is largely unknown. It is not yet dear how energy subsidies interact with reef depth and slope. Here we test the hypothesis that with increased proximity to deep-water oceanic nutrient sources, or at sites with shallower reef slopes, parameters of fish growth and condition will be higher. Contrary to expectations, we found no association between fish growth rate and sites with higher mean chlorophyll-a values. There were no differences in fish delta N-15 or delta C-13 values between depths. The relationship between fish condition and primary production was influenced by depth, driven by increased fish condition at shallow depths within a primary production 'hotspot' site. Carbon delta C-13 was depleted with increasing primary production, and interacted with reef slope. Our results indicate that variable primary production did not influence growth rates in planktivorous Chromis fieldi within 10-17.5 m depth, but show site-specific variation in reef physical characteristics influencing fish carbon isotopic composition

Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association

<p>Abstract</p> <p>Background</p> <p>The genome of <it>Mycobacterium avium </it>subspecies <it>paratuberculosis </it>(<it>MAP</it>) is remarkably homogeneous among the genomes of bovine, human and wildlife isolates. However, previous work in our laboratories with the bovine K-10 strain has revealed substantial differences compared to sheep isolates. To systematically characterize all genomic differences that may be associated with the specific hosts, we sequenced the genomes of three U.S. sheep isolates and also obtained an optical map.</p> <p>Results</p> <p>Our analysis of one of the isolates, <it>MAP </it>S397, revealed a genome 4.8 Mb in size with 4,700 open reading frames (ORFs). Comparative analysis of the <it>MAP </it>S397 isolate showed it acquired approximately 10 large sequence regions that are shared with the human <it>M. avium </it>subsp. <it>hominissuis </it>strain 104 and lost 2 large regions that are present in the bovine strain. In addition, optical mapping defined the presence of 7 large inversions between the bovine and ovine genomes (~ 2.36 Mb). Whole-genome sequencing of 2 additional sheep strains of <it>MAP </it>(JTC1074 and JTC7565) further confirmed genomic homogeneity of the sheep isolates despite the presence of polymorphisms on the nucleotide level.</p> <p>Conclusions</p> <p>Comparative sequence analysis employed here provided a better understanding of the host association, evolution of members of the <it>M. avium </it>complex and could help in deciphering the phenotypic differences observed among sheep and cattle strains of <it>MAP</it>. A similar approach based on whole-genome sequencing combined with optical mapping could be employed to examine closely related pathogens. We propose an evolutionary scenario for <it>M. avium </it>complex strains based on these genome sequences.</p