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Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we apply unsupervised machine learning to a diverse compendium of over 250 high-quality Escherichia coli RNA-seq datasets to identify 92 statistically independent signals that modulate the expression of specific gene sets. We show that 61 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals is validated by exposure of E. coli to new environmental conditions. The resulting decomposition of the transcriptome provides: a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations; a guide to gene and regulator function discovery; and a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation describes the composition of a model prokaryotic transcriptome.

Device-to-Device (D2D) communication is a key enabler to facilitate the realization of the internet of things (IoT). In this paper, we study the deployment of D2D communications as an underlay to long term evolution-advanced (LTE-A) networks based on novel architectures such as cloud radio access network (C-RAN). The challenge is that both energy efficiency (EE) and quality of service (QoS) are severely degraded by the strong intracell and intercell interference due to dense deployment and spectrum reuse. To tackle this problem, we propose an energyefficient resource allocation algorithm through joint channel selection and power allocation design. The proposed algorithm has a hybrid structure that exploits the hybrid architecture of C-RAN: distributed remote radio heads (RRHs) and centralized baseband unit (BBU) pool. The distributed resource allocation problem is modeled as a noncooperative game, and each player optimizes its EE individually with the aid of distributed RRHs. We transform the non-convex optimization problem into a convex one by applying constraint relaxation and nonlinear fractional programming. We propose a centralized interference mitigation algorithm to improve the QoS performance. The centralized algorithm consists of an interference cancellation technique and a transmission power constraint optimization technique, both of which are carried out in the centralized BBU pool. The achievable performance of the proposed algorithm is analyzed through simulations, and the implementation issues and complexity analysis Manuscript

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Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available datasets describing its AMR characteristics demand disparate data-type analyses. Here, we develop a reference strain-agnostic computational platform that uses machine learning approaches, complemented by both genetic interaction analysis and 3D structural mutation-mapping, to identify signatures of AMR evolution to 13 antibiotics. This platform is applied to 1595 sequenced strains to yield four key results. First, a pan-genome analysis shows that M. tuberculosis is highly conserved with sequenced variation concentrated in PE/PPE/PGRS genes. Second, the platform corroborates 33 genes known to confer resistance and identifies 24 new genetic signatures of AMR. Third, 97 epistatic interactions across 10 resistance classes are revealed. Fourth, detailed structural analysis of these genes yields mechanistic bases for their selection. The platform can be used to study other human pathogens.

In this paper, we propose an efficient Two-Phase geographic Greedy Forwarding (TPGF) routing algorithm for WMSNs. TPGF takes into account both the requirements of real time multimedia transmission and the realistic characteristics of WMSNs. It finds one shortest (near-shortest) path per execution and can be executed repeatedly to find more on-demand shortest (near-shortest) node-disjoint routing paths. TPGF supports three features: (1) hole-bypassing, (2) the shortest path transmission, and (3) multipath transmission, at the same time. TPGF is a pure geographic greedy forwarding routing algorithm, which does not include the face routing, e.g., right/left hand rules, and does not use planarization algorithms, e.g., GG or RNG. This point allows more links to be available for TPGF to explore more routing paths, and enables TPGF to be different from many existing geographic routing algorithms. Both theoretical analysis and simulation comparison in this paper indicate that TPGF is highly suitable for multimedia transmission in WMSNs.

Variety and veracity are two distinct characteristics of large-scale and heterogeneous data. It has been a great challenge to efficiently represent and process big data with a unified scheme. In this paper, a unified tensor model is proposed to represent the unstructured, semistructured, and structured data. With tensor extension operator, various types of data are represented as subtensors and then are merged to a unified tensor. In order to extract the core tensor which is small but contains valuable information, an incremental high order singular value decomposition (IHOSVD) method is presented. By recursively applying the incremental matrix decomposition algorithm, IHOSVD is able to update the orthogonal bases and compute the new core tensor. Analyzes in terms of time complexity, memory usage, and approximation accuracy of the proposed method are provided in this paper. A case study illustrates that approximate data reconstructed from the core set containing 18% elements can guarantee 93% accuracy in general. Theoretical analyzes and experimental results demonstrate that the proposed unified tensor model and IHOSVD method are efficient for big data representation and dimensionality reduction.

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