Computing suffix links for suffix trees and arrays

We present a new and simple algorithm to reconstruct suffix links in suffix trees and suffix arrays. The algorithm is based on observations regarding suffix tree construction algorithms. With our algorithm we bring suffix arrays even closer to the ease of use and implementation of suffix trees.     

Overcomplete Independent Component Analysis via Linearly Constrained Minimum Variance Spatial Filtering

Independent Component Analysis (ICA) designed for complete bases is used in a variety of applications with great success, despite the often questionable assumption of having N sensors and M sources with N≥M. In this article, we assume a source model with more sources than sensors (M>N), only L<N of which are assumed to have a non-Gaussian distribution. We argue that this is a realistic source model for a variety of applications, and prove that for ICA algorithms designed for complete bases (i.e., algorithms assuming N=M) based on mutual information the mixture coefficients of the L non-Gaussian sources can be reconstructed in spite of the overcomplete mixture model. Further, it is shown that the reconstructed temporal activity of non-Gaussian sources is arbitrarily mixed with Gaussian sources. To obtain estimates of the temporal activity of the non-Gaussian sources, we use the correctly reconstructed mixture coefficients in conjunction with linearly constrained minimum variance spatial filtering. This results in estimates of the non-Gaussian sources minimizing the variance of the interference of other sources. The approach is applied to the denoising of Event Related Fields recorded by MEG, and it is shown that it performs superiorly to ordinary ICA.     

Trans-Proteomic Pipeline,a standardized data processing pipeline for large-scale reproducible proteomics informatics

Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include MS to define protein sequence, protein:protein interactions, and protein PTMs. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative MS proteomics. It supports all major operating systems and instrument vendors via open data formats. Here, we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of MS/MS datasets, as well as some major upcoming features.     

3D Knitting for Pneumatic Soft Robotics

Soft robots adapt passively to complex environments due to their inherent compliance, allowing them to interact safely with fragile or irregular objects and traverse uneven terrain. The vast tunability and ubiquity of textiles has enabled new soft robotic capabilities, especially in the field of wearable robots, but existing textile processing techniques (e.g., cut-and-sew, thermal bonding) are limited in terms of rapid, additive, accessible, and waste-free manufacturing. While 3D knitting has the potential to address these limitations, an incomplete understanding of the impact of structure and material on knit-scale mechanical properties and macro-scale device performance has precluded the widespread adoption of knitted robots. In this work, the roles of knit structure and yarn material properties on textile mechanics spanning three regimes–unfolding, geometric rearrangement, and yarn stretching–are elucidated and shown to be tailorable across unique knit architectures and yarn materials. Based on this understanding, 3D knit soft actuators for extension, contraction, and bending are constructed. Combining these actuation primitives enables the monolithic fabrication of entire soft grippers and robots in a single-step additive manufacturing procedure suitable for a variety of applications. This approach represents a first step in seamlessly “printing” conformal, low-cost, customizable textile-based soft robots on-demand.     

Automated processing for map generalization using web services

In map generalization various operators are applied to the features of a map in order to maintain and improve the legibility of the map after the scale has been changed. These operators must be applied in the proper sequence and the quality of the results must be continuously evaluated. Cartographic constraints can be used to define the conditions that have to be met in order to make a map legible and compliant to the user needs. The combinatorial optimization approaches shown in this paper use cartographic constraints to control and restrict the selection and application of a variety of different independent generalization operators into an optimal sequence. Different optimization techniques including hill climbing, simulated annealing and genetic deep search are presented and evaluated experimentally by the example of the generalization of buildings in blocks. All algorithms used in this paper have been implemented in a web services framework. This allows the use of distributed and parallel processing in order to speed up the search for optimized generalization operator sequences.

Airway Delivery of Hydrogel-Encapsulated Niclosamide for the Treatment of Inflammatory Airway Disease

Repurposing of the anthelminthic drug niclosamide was proposed as an effective treatment for inflammatory airway diseases such as asthma, cystic fibrosis, and chronic obstructive pulmonary disease. Niclosamide may also be effective for the treatment of viral respiratory infections, such as SARS-CoV-2, respiratory syncytial virus, and influenza. While systemic application of niclosamide may lead to unwanted side effects, local administration via aerosol may circumvent these problems, particularly when the drug is encapsulated into small polyethylene glycol (PEG) hydrospheres. In the present study, we examined whether PEG-encapsulated niclosamide inhibits the production of mucus and affects the pro-inflammatory mediator CLCA1 in mouse airways in vivo, while effects on mucociliary clearance were assessed in excised mouse tracheas. The potential of encapsulated niclosamide to inhibit TMEM16A whole-cell Cl⁻ currents and intracellular Ca²⁺ signalling was assessed in airway epithelial cells in vitro. We achieved encapsulation of niclosamide in PEG-microspheres and PEG-nanospheres (Niclo-spheres). When applied to asthmatic mice via intratracheal instillation, Niclo-spheres strongly attenuated overproduction of mucus, inhibited secretion of the major proinflammatory mediator CLCA1, and improved mucociliary clearance in tracheas ex vivo. These effects were comparable for niclosamide encapsulated in PEG-nanospheres and PEG-microspheres. Niclo-spheres inhibited the Ca²⁺ activated Cl⁻ channel TMEM16A and attenuated mucus production in CFBE and Calu-3 human airway epithelial cells. Both inhibitory effects were explained by a pronounced inhibition of intracellular Ca²⁺ signals. The data indicate that poorly dissolvable compounds such as niclosamide can be encapsulated in PEG-microspheres/nanospheres and deposited locally on the airway epithelium as encapsulated drugs, which may be advantageous over systemic application.     

Propagation and structure of streamers in liquid dielectrics

Our purpose is to present a critical review of the current understanding of streamer propagation in dielectric liquids in order to help define the direction of future research. We show that the molecular structure has a significant effect on streamer propagation. The main parameter affecting propagation is the electronic affinity of the liquid molecules     

Construction features and environmental factors influencingcorrosion on a self-contained fluid-filled submarine cable circuit inLong Island Sound

A 345 kV self-contained fluid-filled cable circuit was installed in an environment where corrosion of the armor may occur. To better understand the conditions that may result in corrosion, stray currents in the cable end zones and in the middle (submarine) of the circuit were measured, and cable samples were analyzed to determine the electrochemical activity of the cable's outer layers. The results of the project revealed that electrolytic corrosion would affect the semiconductive polyethylene if sufficient stray current density (greater than 0.15 A/m²) was induced by stray currents which were present in Long Island Sound where the cables are installed. Measurements revealed stray current densities in excess of this level towards one end of the cable route. Various other considerations for corrosion are also discussed