On the computational power of insertion-deletion systems

Gene insertion and deletion are basic phenomena found in DNA processing or RNA editing in molecular biology. The genetic mechanism and development based on these evolutionary transformations have been formulated as a formal system with two operations of insertion and deletion, called insertion-deletion systems (Kari and Thierrin, 1996; Kari et al., 1997).We investigate the generative power of insertion-deletion systems (InsDel systems), and show that the family INS ¹ ₁ DEL ¹ ₁ is equal to the family of recursively enumerable languages. This gives a positive answer to an open problem posed in Kari et al. (1997) where it was conjectured contrary. This revised version was published online in June 2006 with corrections to the Cover Date.     

Failure-analysis-based test chip design for quick yield improvement

A new design approach for a test chip developed to shorten the debugging cycle time in fabrication is described. This approach meets the requirements for failure analysis as well as parametric and statistical analyses. Particular attention is devoted to accurate defect density estimation and to locating individual defects. This is done by designing test structures suitable for both electrical measurements and failure analysis. A specially designed test chip, named YTEG, is used to evaluate 0.5-μm CMOS process technologies, and confirms the effectiveness of the chip.     

A simple approach to observe non-conductive hydrated materials with FE-SEM: Case study on porous hydroxyapatite green bodies

The purpose of this study is to develop a simple method to observe the surface morphology of non-conductive material in its hydrated condition. Here porous hydroxyapatite (HAp) green body prepared by gelcasting process was considered as a case study, and, the resultant body was subsequently treated with hydrophilic ionic liquid (IL). The surface morphology and the pore structure of the IL-treated porous HAp green body were successfully observed even in hydrated condition without any charging using field emission scanning electron microscope (FE-SEM). Results showed that the pore diameter from 300 to 600 μm in as-prepared green body was reduced to 100–300 μm in the sample sintered at 1000 °C. Raman results showed that the IL forms weak hydrogen bond with water molecules within the sample and, that prevents from drying in vacuum condition. In addition, the IL acts as a conducting media for HAp ceramics to be observed under FE-SEM.     

Inhibitory Effects of Cholesterol Derivatives on DNA Polymerase and Topoisomerase Activities, and Human Cancer Cell Growth

This paper describes the inhibitory activities of cholesterol derivatives such as cholesterol, sodium cholesteryl sulfate, cholesteryl-5α, 6α-epoxide, cholesteryl chloride, cholesteryl bromide, and cholesteryl hemisuccinate (compounds 1–6, respectively) against DNA polymerase (pol), DNA topoisomerase (topo), and human cancer cell growth. Among the compounds tested, compounds 2 and 6 revealed themselves to be potent inhibitors of animal pols, and the IC₅₀ values for pols were 0.84–11.6 and 2.9–148 μM, respectively. Compounds 2, 3 and 6 inhibited the activity of human topo II, with IC₅₀ values of 5.0, 12.5 and 120 μM, respectively. Compounds 2, 3 and 6 also suppressed human cancer cell (promyelocytic leukemia cell line, HL-60) growth, and LD₅₀ values were 8.8, 20.2 and 72.3 μM, respectively, suggesting that cell growth inhibition had the same tendency as the inhibition of topos rather than pols. Compounds 2 and 6 arrested the cells in S and G2/M phases, compound 3 arrested the cells in the G2/M phase, and these compounds also increased sub-G1 phase in the cell cycle. These results suggested that the effect of cell cycle arrest might be effective on both pols and topos activities. From these findings, the action mode of cholesterol derivatives as anti-cancer compounds is discussed.     

Identification of SYS1 as a Host Factor Required for Shiga Toxin-Mediated Cytotoxicity in Vero Cells

Shiga toxin (STx) or Vero toxin is a virulence factor produced by enterohemorrhagic Escherichia coli. The toxin binds to the glycosphingolipid globotriaosylceramide (Gb3) for its entry, and causes cell death by inhibiting ribosome function. Previously, we performed a loss-of-function screen in HeLa cells using a human CRISPR knockout (KO) library and identified various host genes required for STx-induced cell death. To determine whether this library targeted to the human genome is applicable to non-human primate cells and to identify previously unrecognized factors crucial for STx-induced cell death, we herein performed a similar screen in the African green monkey kidney-derived Vero C1008 subline. Many genes relevant to metabolic enzymes and membrane trafficking were enriched, although the number of enriched genes was less than that obtained in the screening for HeLa cells. Of note, several genes that had not been enriched in the previous screening were enriched: one of these genes was SYS1, which encodes a multi-spanning membrane protein in the Golgi apparatus. In SYS1 KO Vero cells, expression of Gb3 and sphingomyelin was decreased, while that of glucosylceramide and lactosylceramide was increased. In addition, loss of SYS1 inhibited the biosynthesis of protein glycans, deformed the Golgi apparatus, and perturbed the localization of trans-Golgi network protein (TGN) 46. These results indicate that the human CRISPR KO library is applicable to Vero cell lines, and SYS1 has a widespread effect on glycan biosynthesis via regulation of intra-Golgi and endosome–TGN retrograde transports.     

Team O2AS at the world robot summit 2018: an approach to robotic kitting and assembly tasks using general purpose grippers and tools

ABSTRACT

In this article, we propose a versatile robotic system for kitting and assembly tasks which uses no jigs or commercial tool changers. Instead of specialized end effectors, it uses its two-finger grippers to grasp and hold tools to perform subtasks such as screwing and suctioning. A third gripper is used as a precision picking and centering tool, and uses in-built passive compliance to compensate for small position errors and uncertainty. A novel grasp point detection for bin picking is described for the kitting task, using a single depth map. Using the proposed system we competed in the Assembly Challenge of the Industrial Robotics Category of the World Robot Challenge at the World Robot Summit 2018, obtaining 4th place and the SICE award for lean design and versatile tool use. We show the effectiveness of our approach through experiments performed during the competition.     

Team O2AS' approach for the task-board task of the World Robot Challenge 2018

ABSTRACT

In this paper, we describe the approach of Team O2AS to complete the task-board task of the World Robot Challenge 2018, held in Tokyo. We use a custom gripper and graspable tools with in-built compliance to work with various kinds of parts, increase robustness against uncertainties, and to avoid complicated control strategies. The robots are able to finish all the sub-tasks without the need to exchange grippers. The main idea is to use mechanical compliance and self-centering mechanisms to deal with uncertainty. This is achieved by aligning the objects using either the gripper and tools, or by the design of the robot motions.     

Two complementary operations inspired by the DNA hairpin formation: Completion and reduction

We consider two complementary operations: Hairpin completion introduced in [D. Cheptea, C. Martin-Vide, V. Mitrana, A new operation on words suggested by DNA biochemistry: Hairpin completion, in: Proc. Transgressive Computing, 2006, pp. 216–228] with motivations coming from DNA biochemistry and hairpin reduction as the inverse operation of the hairpin completion. Both operations are viewed here as formal operations on words and languages. We settle the closure properties of the classes of regular and linear context-free languages under hairpin completion in comparison with hairpin reduction. While the class of linear context-free languages is exactly the weak-code image of the class of the hairpin completion of regular languages, rather surprisingly, the weak-code image of the class of the hairpin completion of linear context-free languages is a class of mildly context-sensitive languages. The closure properties with respect to the hairpin reduction of some time and space complexity classes are also studied. We show that the factors found in the general cases are not necessary for regular and context-free languages. This part of the paper completes the results given in the earlier paper, where a similar investigation was made for hairpin completion. Finally, we briefly discuss the iterated variants of these operations.     

A pregnancy-specific glycoprotein is expressed in the brain and serves as a receptor for mouse hepatitis virus

Mouse hepatitis virus (MHV), a murine coronavirus known to cause encephalitis and demyelination, uses murine homologues of carcinoembryonic antigens as receptors. However, the expression of these receptors is extremely low in the brain. By low-stringency screening of a mouse brain cDNA library, we have identified a member of the pregnancy-specific glycoprotein (PSG) subgroup of the carcinoembryonic antigen gene family. Unlike other PSG that are expressed in the placenta, it is expressed predominantly in the brain. Transfection of the cDNA into COS-7 cells, which lack a functional MHV receptor, conferred susceptibility to infection by some MHV strains, including A59, MHV-2, and MHV-3, but not JHM. Thus, this is a virus strain-specific receptor. The detection of multiple receptors for MHV suggests the flexibility of this virus in receptor utilization. The identification of this virus in receptor utilization. The identification of a PSG predominantly expressed in the brain also expands the potential functions of these molecules.