Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

<p>Abstract</p> <p>Background</p> <p>Analyses of gene expression data from microarray experiments has become a central tool for identifying co-regulated, functional gene modules. A crucial aspect of such analysis is the integration of data from different experiments and different laboratories. How to weigh the contribution of different experiments is an important point influencing the final outcomes. We have developed a novel method for this integration, and applied it to genome-wide data from multiple Arabidopsis microarray experiments performed under a variety of experimental conditions. The goal of this study is to identify functional globally co-regulated gene modules in the Arabidopsis genome.</p> <p>Results</p> <p>Following the analysis of 21,000 Arabidopsis genes in 43 datasets and about 2 × 10⁸gene pairs, we identified a globally co-expressed gene network. We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations. Two types of modules were identified in the regulatory network that differed in their sensitivity to the node-scoring parameter; we further showed these two pertain to general and specialized modules. Some of these modules were further investigated using the <it>Genevestigator </it>compendium of microarray experiments. Analyses of smaller subsets of data lead to the identification of condition-specific modules.</p> <p>Conclusion</p> <p>Our method for identification of gene clusters allows the integration of diverse microarray experiments from many sources. The analysis reveals that part of the <it>Arabidopsis </it>transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules. Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.</p

Genomic DNA k-mer spectra: models and modalities

Tetrapods, unlike other organisms, have multimodal spectra of k-mers in their genome

Tight lower bounds for certain parameterized NP-hard problems

Based on the framework of parameterized complexity theory, we derive tight lower bounds on the computational complexity for a number of well-known NP-hard problems. We start by proving a general result, namely that the parameterized weighted satisfiability problem on depth-t circuits cannot be solved in time no(k) poly(m), where n is the circuit input length, m is the circuit size, and k is the parameter, unless the (t − 1)-st level W [t − 1] of the W-hierarchy collapses to FPT. By refining this technique, we prove that a group of parameterized NP-hard problems, including weighted sat, dominating set, hitting set, set cover, and feature set, cannot be solved in time no(k) poly(m), where n is the size of the universal set from which the k elements are to be selected and m is the instance size, unless the first level W [1] of the W-hierarchy collapses to FPT. We also prove that another group of parameterized problems which includes weighted q-sat (for any fixed q ≥ 2), clique, and independent set, cannot be solved in time no(k) unless all search problems in the syntactic class SNP, introduced by Papadimitriou and Yannakakis, are solvable in subexponential time. Note that all these parameterized problems have trivial algorithms of running time either n k poly(m) or O(n k).

ClaimChain: Improving the Security and Privacy of In-band Key Distribution for Messaging

The social demand for email end-to-end encryption is barely supported by mainstream service providers. Autocrypt is a new community-driven open specification for e-mail encryption that attempts to respond to this demand. In Autocrypt the encryption keys are attached directly to messages, and thus the encryption can be implemented by email clients without any collaboration of the providers. The decentralized nature of this in-band key distribution, however, makes it prone to man-in-the-middle attacks and can leak the social graph of users. To address this problem we introduce ClaimChain, a cryptographic construction for privacy-preserving authentication of public keys. Users store claims about their identities and keys, as well as their beliefs about others, in ClaimChains. These chains form authenticated decentralized repositories that enable users to prove the authenticity of both their keys and the keys of their contacts. ClaimChains are encrypted, and therefore protect the stored information, such as keys and contact identities, from prying eyes. At the same time, ClaimChain implements mechanisms to provide strong non-equivocation properties, discouraging malicious actors from distributing conflicting or inauthentic claims. We implemented ClaimChain and we show that it offers reasonable performance, low overhead, and authenticity guarantees.Comment: Appears in 2018 Workshop on Privacy in the Electronic Society (WPES'18

Noun incorporation in Ainu

アイヌ語では名詞を抱合した動詞形というのが見られる。先行研究では他動詞の主語抱合、他動詞の目的語抱合、自動詞の主語抱合があり、抱合される名詞の意味役割は他動詞の対象、自動詞の対象、充当接頭辞によって道具や場所も可能であり、名詞+自動詞の場合、その動詞は非対格自動詞であることがすでに指摘されている。本稿ではこれを踏まえ、動詞に名詞が抱合され結果として、名詞句を一つ取る一項動詞が形成される場合、残りの一つを埋める名詞はその意味役割が動作主である場合、対象である場合、(抱合された名詞の)所有主である場合もあり、ときには基本形の項ではない場合もあるが、いずれの場合も格表示は主格となり、主語となることを述べる。そして、一項動詞が使役接尾辞を取らずに名詞を抱合する際には、一項動詞に名詞が直接抱合される場合であっても、動詞に充当接頭辞が接頭した上で名詞が抱合される場合であっても、その動詞は対象を主語とする非対格動詞であることを述べる

Hamiltonicity below Dirac's condition

Dirac's theorem (1952) is a classical result of graph theory, stating that an $n$-vertex graph ($n \geq 3$) is Hamiltonian if every vertex has degree at least $n/2$. Both the value $n/2$ and the requirement for every vertex to have high degree are necessary for the theorem to hold. In this work we give efficient algorithms for determining Hamiltonicity when either of the two conditions are relaxed. More precisely, we show that the Hamiltonian cycle problem can be solved in time $c^k \cdot n^{O(1)}$, for some fixed constant $c$, if at least $n-k$ vertices have degree at least $n/2$, or if all vertices have degree at least $n/2-k$. The running time is, in both cases, asymptotically optimal, under the exponential-time hypothesis (ETH). The results extend the range of tractability of the Hamiltonian cycle problem, showing that it is fixed-parameter tractable when parameterized below a natural bound. In addition, for the first parameterization we show that a kernel with $O(k)$ vertices can be found in polynomial time