Comparison of Empirical Data from Two Honeynets and a Distributed Honeypot Network

In this paper we present empirical results and speculative analysis based on observations collected over a two month period from studies with two high interaction honeynets, deployed in a corporate and an SME (small to medium enterprise) environment, and a distributed honeypots deployment. All three networks contain a mixture of Windows and Linux hosts. We detail the architecture of the deployment and results of comparing the observations from the three environments. We analyze in detail the times between attacks on different hosts, operating systems, networks or geographical location. Even though results from honeynet deployments are reported often in the literature, this paper provides novel results analyzing traffic from three different types of networks and some initial exploratory models. This research aims to contribute to endeavours in the wider security research community to build methods, grounded on strong empirical work, for assessment of the robustness of computer-based systems in hostile environments

Stretching force dependent transitions in single stranded DNA

Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living cell. Single stranded DNA (ssDNA), which, till recently was presumed to be an simple flexible polymer continues to spring surprises. Synthetic ssDNA, like polydA (polydeoxyadenosines) has revealed an intriguing force-extension (FX) behavior exhibiting two plateaus, absent in polydT (polydeoxythymidines) for example. Loop closing time in polydA had also been found to scale exponentially with inverse temperature, unexpected from generic models of homopolymers. Here we present a new model for polydA which incorporates both a helix-coil transition and a over-stretching transition, accounting for the two plateaus. Using transfer matrix calculation and Monte-Carlo simulation we show that the model reproduces different sets of experimental observations, quantitatively. It also predicts interesting reentrant behavior in the temperature-extension characteristics of polydA, which is yet to be verified experimentally.Comment: 5 pages, 3 figure

Competition for hydrogen bond formation in the helix-coil transition and protein folding

The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure; and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.Comment: 21 pages, 3 figures, submitted to Phys Rev

Wigner crystal model of counterion induced bundle formation of rod-like polyelectrolytes

A simple electrostatic theory of condensation of rod-like polyelectrolytes under influence of polyvalent ions is proposed. It is based on the idea that Manning condensation of ions results in formation of the Wigner crystal on a background of a bundle of rods. It is shown that, depending on a single dimensionless parameter, this can be the densely packed three-dimensional Wigner crystal or the two-dimensional crystal on the rod surfaces. For DNA the location of charge on the spiral results in a model of the one-dimensional Wigner crystal. It is also argued that the Wigner crystal idea can be applied to self-assembly of other polyelectrolytes, for example, colloids and DNA-lipid complexes.Comment: 4 pages; typos corrected, references adde

Local Cooperativity Mechanism in the DNA Melting Transition

We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which mimic the geometrical constraints in the real molecule. This microscopic mechanism intrinsically accounts for the cooperativity related to the free energy penalty of bubble nucleation. The model describes both the unpairing and unstacking parts of the spectroscopically determined experimental melting curves. Furthermore, the model explains the observed temperature dependence of the effective thermodynamic parameters used in models of the nearest neighbor (NN) type. We compute the partition function for the model through the transfer matrix formalism, which we also generalize to include non local chain entropy terms. This part introduces a new parametrization of the Yeramian-like transfer matrix approach to the Poland-Scheraga description of DNA melting. The model is exactly solvable in the homogeneous thermodynamic limit, and we calculate all observables without use of the grand partition function. As is well known, models of this class have a first order or continuous phase transition at the temperature of complete strand separation depending on the value of the exponent of the bubble entropy.Comment: Extended version of Phys. Rev. E pape

The Effects of Stacking on the Configurations and Elasticity of Single Stranded Nucleic Acids

Stacking interactions in single stranded nucleic acids give rise to configurations of an annealed rod-coil multiblock copolymer. Theoretical analysis identifies the resulting signatures for long homopolynucleotides: A non monotonous dependence of size on temperature, corresponding effects on cyclization and a plateau in the extension force law. Explicit numerical results for poly(dA) and poly(rU) are presented.Comment: 4 pages and 2 figures. Accepted in Phys. Rev. E Rapid Com

Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case

The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the ideal case where opening events are known to a very good time resolution (very large bandwidth), and study how the sequence can be reconstructed from the unzipping data. Our approach relies on the use of statistical Bayesian inference and of Viterbi decoding algorithm. Performances are studied numerically on Monte Carlo generated data, and analytically. We show how multiple unzippings of the same molecule may be exploited to improve the quality of the prediction, and calculate analytically the number of required unzippings as a function of the bandwidth, the sequence content, the elasticity parameters of the unzipped strands

Microglial activity in people at ultra high risk of psychosis and in schizophrenia; an [11C]PBR28 PET brain imaging study

Objective: The purpose of this study was to determine whether microglial activity, measured using translocator-protein positron emission tomography (PET) imaging, is increased in unmedicated persons presenting with subclinical symptoms indicating that they are at ultra high risk of psychosis and to determine whether microglial activity is elevated in schizophrenia after controlling for a translocator-specific genetic polymorphism. Method: The authors used the second-generation radioligand [11C]PBR28 and PET to image microglial activity in the brains of participants at ultra high risk for psychosis. Participants were recruited from early intervention centers. The authors also imaged a cohort of patients with schizophrenia and matched healthy subjects for comparison. In total, 56 individuals completed the study. At screening, participants were genotyped to account for the rs6971 polymorphism in the gene encoding the 18Kd translocator protein. The main outcome measure was total gray matter [11C]PBR28 binding ratio, representing microglial activity. Results: [11C]PBR28 binding ratio in gray matter was elevated in ultra-high-risk participants compared with matched comparison subjects (Cohen’s d >1.2) and was positively correlated with symptom severity (r=0.730). Patients with schizophrenia also demonstrated elevated microglial activity relative to matched comparison subjects (Cohen’s d >1.7). Conclusions: Microglial activity is elevated in patients with schizophrenia and in persons with subclinical symptoms who are at ultra high risk of psychosis and is related to at-risk symptom severity. These findings suggest that neuroinflammation is linked to the risk of psychosis and related disorders, as well as the expression of subclinical symptoms

Charge Fluctuation Forces Between Stiff Polyelectrolytes in Salt Solution: Pairwise Summability Re-examined

We formulate low-frequency charge-fluctuation forces between charged cylinders - parallel or skewed - in salt solution: forces from dipolar van der Waals fluctuations and those from the correlated monopolar fluctuations of mobile ions. At high salt concentrations forces are exponentially screened. In low-salt solutions dipolar energies go as $R^{-5}$ or $R^{-4}$; monopolar energies vary as $R^{-1}$ or $\ln{R}$, where $R$ is the minimal separation between cylinders. However, pairwise summability of rod-rod forces is easily violated in low-salt conditions. Perhaps the most important result is not the derivation of pair potentials but rather the demonstration that some of these expressions may not be used for the very problems that originally motivated their derivation.Comment: 8 pages and 1 fig in ps forma

Trauma-informed care for adult survivors of developmental trauma with psychotic and dissociative symptoms: a systematic review of intervention studies

Developmental trauma is associated with an increased risk of psychosis and predicts poor prognosis. Despite this association, little is known about which treatments work best for survivors of developmental trauma with psychosis. We sought to do the first review, to our knowledge, to investigate treatments for people with psychotic and dissociative symptoms who have a history of developmental trauma. We searched MEDLINE, PsychINFO, and Google Scholar for studies reporting psychological and pharmacological treatments of psychotic or dissociative symptoms in adult survivors of developmental trauma. We identified 24 studies, most of which investigated various modalities of psychotherapy with two case reports of pharmacological treatments. There is preliminary evidence in favour of third wave cognitive therapies. However, because of low methodological quality and reporting in most of the studies found, it remains unknown which treatments are most effective in this clinical group. Nonetheless, our findings of potential treatment targets, including emotion regulation, acceptance, interpersonal skills, trauma re-processing, and the integration of dissociated ego states, could guide future work in this area. Methodologically rigorous studies are needed to enable clinicians and patients to collaboratively form evidence-based treatment plans. Our Review is registered with PROSPERO, number CRD42018104533