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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
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
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
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
Exaggeration of PFS by blinded, independent, central review (BICR)
Background Recent published studies have shown meaningful discrepancies between local investigator and blinded, independent, central review (BICR) assessed median progression-free survival (PFS). When the local review but not BICR shows progression, generally, no further assessments are carried out and patients are censored in the BICR analysis, leading to violation of the statistical assumptions of independence between censoring and outcome used in survival analysis methods. Methods We carried out a simulation study to assess methodological reasons behind these discrepancies and corroborated our findings in a case study of three BRCA-mutated ovarian cancer trials. We briefly outline possible methodological solutions that may lead to improved estimation of the BICR medians. Results The Kaplan-Meier (KM) curve for the BICR PFS can often be exaggerated. The degree of bias is largest when there is reasonably strong correlation between BICR and local PFS, especially when PFS is long compared with assessment frequency. This can result in an exaggeration of the medians and their difference; however, the hazard ratio (HR) is much less susceptible to bias. Our simulation shows that when the true BICR median PFS was 19 months, and patients assessed every 12 weeks, the estimated KM curves were materially biased whenever the correlation between BICR and local PFS was 0.4 or greater. This was corroborated by case studies where, in the active arm, the BICR median PFS was between 6 and 11 months greater than the local median PFS. Further research is required to find improved methods for estimating BICR survival curves. Conclusions In general, when there is a difference between local and BICR medians, the true BICR KM curve is likely to be exaggerated and its true median will probably lie somewhere between the observed local and BICR medians. Presentation of data should always include both BICR and local results whenever a BICR is carried out.</p
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 or ; monopolar
energies vary as or , where 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
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