@article{1171,
author = {Tkacik, Gasper},
journal = {Physics of Life Reviews},
pages = {166 -- 167},
publisher = {Elsevier},
title = {{Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.}},
doi = {10.1016/j.plrev.2016.06.005},
volume = {17},
year = {2016},
}
@article{1172,
abstract = {A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.},
author = {Sachdeva, Himani and Barma, Mustansir and Rao, Madan},
journal = {Scientific Reports},
publisher = {Nature Publishing Group},
title = {{Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae}},
doi = {10.1038/srep38840},
volume = {6},
year = {2016},
}
@article{1177,
abstract = {Boldyreva, Palacio and Warinschi introduced a multiple forking game as an extension of general forking. The notion of (multiple) forking is a useful abstraction from the actual simulation of cryptographic scheme to the adversary in a security reduction, and is achieved through the intermediary of a so-called wrapper algorithm. Multiple forking has turned out to be a useful tool in the security argument of several cryptographic protocols. However, a reduction employing multiple forking incurs a significant degradation of (Formula presented.) , where (Formula presented.) denotes the upper bound on the underlying random oracle calls and (Formula presented.) , the number of forkings. In this work we take a closer look at the reasons for the degradation with a tighter security bound in mind. We nail down the exact set of conditions for success in the multiple forking game. A careful analysis of the cryptographic schemes and corresponding security reduction employing multiple forking leads to the formulation of ‘dependence’ and ‘independence’ conditions pertaining to the output of the wrapper in different rounds. Based on the (in)dependence conditions we propose a general framework of multiple forking and a General Multiple Forking Lemma. Leveraging (in)dependence to the full allows us to improve the degradation factor in the multiple forking game by a factor of (Formula presented.). By implication, the cost of a single forking involving two random oracles (augmented forking) matches that involving a single random oracle (elementary forking). Finally, we study the effect of these observations on the concrete security of existing schemes employing multiple forking. We conclude that by careful design of the protocol (and the wrapper in the security reduction) it is possible to harness our observations to the full extent.},
author = {Kamath Hosdurg, Chethan and Chatterjee, Sanjit},
journal = {Algorithmica},
number = {4},
pages = {1321 -- 1362},
publisher = {Springer},
title = {{A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound}},
doi = {10.1007/s00453-015-9997-6},
volume = {74},
year = {2016},
}
@inproceedings{1179,
abstract = {Computational notions of entropy have recently found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The two main types of results which make computational notions so useful are (1) Chain rules, which quantify by how much the computational entropy of a variable decreases if conditioned on some other variable (2) Transformations, which quantify to which extend one type of entropy implies another.
Such chain rules and transformations typically lose a significant amount in quality of the entropy, and are the reason why applying these results one gets rather weak quantitative security bounds. In this paper we for the first time prove lower bounds in this context, showing that existing results for transformations are, unfortunately, basically optimal for non-adaptive black-box reductions (and it’s hard to imagine how non black-box reductions or adaptivity could be useful here.)
A variable X has k bits of HILL entropy of quality (ϵ,s)
if there exists a variable Y with k bits min-entropy which cannot be distinguished from X with advantage ϵ
by distinguishing circuits of size s. A weaker notion is Metric entropy, where we switch quantifiers, and only require that for every distinguisher of size s, such a Y exists.
We first describe our result concerning transformations. By definition, HILL implies Metric without any loss in quality. Metric entropy often comes up in applications, but must be transformed to HILL for meaningful security guarantees. The best known result states that if a variable X has k bits of Metric entropy of quality (ϵ,s)
, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2). We show that this loss of a factor Ω(ϵ−2)
in circuit size is necessary. In fact, we show the stronger result that this loss is already necessary when transforming so called deterministic real valued Metric entropy to randomised boolean Metric (both these variants of Metric entropy are implied by HILL without loss in quality).
The chain rule for HILL entropy states that if X has k bits of HILL entropy of quality (ϵ,s)
, then for any variable Z of length m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still leaves a gap of ϵ between the known bound and our lower bound.},
author = {Pietrzak, Krzysztof Z and Maciej, Skorski},
location = {Beijing, China},
pages = {183 -- 203},
publisher = {Springer},
title = {{Pseudoentropy: Lower-bounds for chain rules and transformations}},
doi = {10.1007/978-3-662-53641-4_8},
volume = {9985},
year = {2016},
}
@article{1181,
abstract = {This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies.},
author = {Dwyer, Noelle and Chen, Bin and Chou, Shen and Hippenmeyer, Simon and Nguyen, Laurent and Ghashghaei, Troy},
journal = {Journal of Neuroscience},
number = {45},
pages = {11394 -- 11401},
publisher = {Society for Neuroscience},
title = {{Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity}},
doi = {10.1523/JNEUROSCI.2359-16.2016},
volume = {36},
year = {2016},
}