Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency

<p>Abstract</p> <p>Background</p> <p>Investigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroughs in the field. However, at present, taxonomic binning tools for metagenomes discard 30-40% of Sanger sequencing data due to the stringency of BLAST cut-offs. In an attempt to provide a comprehensive overview of metagenomic data, we re-analyzed the discarded metagenomes by using less stringent cut-offs. Additionally, we introduced a new criterion, namely, the evolutionary conservation of adjacency between neighboring genes. To evaluate the feasibility of our approach, we re-analyzed discarded contigs and singletons from several environments with different levels of complexity. We also compared the consistency between our taxonomic binning and those reported in the original studies.</p> <p>Results</p> <p>Among the discarded data, we found that 23.7 ± 3.9% of singletons and 14.1 ± 1.0% of contigs were assigned to taxa. The recovery rates for singletons were higher than those for contigs. The <it>Pearson </it>correlation coefficient revealed a high degree of similarity (0.94 ± 0.03 at the phylum rank and 0.80 ± 0.11 at the family rank) between the proposed taxonomic binning approach and those reported in original studies. In addition, an evaluation using simulated data demonstrated the reliability of the proposed approach.</p> <p>Conclusions</p> <p>Our findings suggest that taking account of conserved neighboring gene adjacency improves taxonomic assignment when analyzing metagenomes using Sanger sequencing. In other words, utilizing the conserved gene order as a criterion will reduce the amount of data discarded when analyzing metagenomes.</p

Sedimentological characteristics and seafloor failure offshore SW Taiwan

In this study, analysis results reveal two main deposition zones are located at the flank of upper Gaoping Submarine Canyon and Lower Fangliao Basin offshore SW Taiwan. The non-event related sediments deposited in past 150 years (i.e., 632 Mt km-2) was delivered and transported from Gaoping River by suspension process with tides and coastal currents and gradually spread out offshore. Meanwhile, the total mass of accumulation sediments is 1922 Mt km-2, accounting for 40% Gaoping Riverâs sediment load and suggesting that the deposition process is mainly controlled by natural hazards. Sedimentation rates in much of the study area, except in the main deposition zones, are less than 0.5 cm yr-1 (5 m kyr-1). Compared with the studies at the instability seafloor caused by high sedimentation rates (~30 m kyr-1), the offshore southwestern Taiwan is relatively stable. In this study, we also discovered a series of sediment waves located on the upper continental slope between Gaoping and Fangliao Submarine Canyons, which is related to the creeping process on seafloor. In summary, our results reveal the fluid activities, existence of weak layers and earthquake triggering are potential factors which might induced seafloor failures offshore southwestern Taiwan

An Integrated Edge and Fog System for Future Communication Networks

Put together, the edge and fog form a large diverse pool of computing and networking resources from different owners that can be leveraged towards low latency applications as well as for alleviating high traffic volume in future networks including 5G and beyond. This paper sets out a framework for the integration of edge and fog computing and networking leveraging on ongoing specifications by ETSI MEC ISG and the OpenFog Consortium. It also presents the technological gaps that need to be addressed before such an integrated solution can be developed. These noticeably include challenges relating to the volatility of resources, heterogeneity of underlying technologies, virtualization of devices, and security issues. The framework presented is a Launchpad for a complete solution under development by the 5G-CORAL consortium.This work has been partially funded by the H2020 collaborative Europe/Taiwan research project 5G-CORAL (grant num. 761586

On‐Demand Reconfiguration of Nanomaterials: When Electronics Meets Ionics

Rapid advances in the semiconductor industry, driven largely by device scaling, are now approaching fundamental physical limits and face severe power, performance, and cost constraints. Multifunctional materials and devices may lead to a paradigm shift toward new, intelligent, and efficient computing systems, and are being extensively studied. Herein examines how, by controlling the internal ion distribution in a solid‐state film, a material’s chemical composition and physical properties can be reversibly reconfigured using an applied electric field, at room temperature and after device fabrication. Reconfigurability is observed in a wide range of materials, including commonly used dielectric films, and has led to the development of new device concepts such as resistive random‐access memory. Physical reconfigurability further allows memory and logic operations to be merged in the same device for efficient in‐memory computing and neuromorphic computing systems. By directly changing the chemical composition of the material, coupled electrical, optical, and magnetic effects can also be obtained. A survey of recent fundamental material and device studies that reveal the dynamic ionic processes is included, along with discussions on systematic modeling efforts, device and material challenges, and future research directions.By controlling the internal ion distribution in a solid‐state film, the material’s chemical composition and physical (i.e., electrical, optical, and magnetic) properties can be reversibly reconfigured, in situ, using an applied electric field. The reconfigurability is achieved in a wide range of materials, and can lead to the development of new memory, logic, and multifunctional devices and systems.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141225/1/adma201702770.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141225/2/adma201702770_am.pd

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field