Tree-systems of morphisms

Starting from the idea of determinism in membrane systems, we introduce a language generating device consisting of morphisms placed in the nodes of a tree. Initial strings are given in the leaves; by iteratively applying the morphisms to them, we produce new strings, which are collected in the root of the tree. Such a device is called a tree-system of morphisms (in short, a T system). We investigate here the power of T systems, both in the extended (a terminal alphabet is considered and only strings over it are accepted) and non-extended case, mainly in comparison with classes of languages in Lindenmayer hierarchy. Received: 8 February 2001 / 18 September 2001     

A New Approximation Algorithm for Finding Heavy Planar Subgraphs

We provide the first nontrivial approximation algorithm for MAXIMUM WEIGHT PLANAR SUBGRAPH, the NP-hard problem of finding a heaviest planar subgraph in an edge-weighted graph G . This problem has applications in circuit layout, facility layout, and graph drawing. No previous algorithm for MAXIMUM WEIGHT PLANAR SUBGRAPH had a performance ratio exceeding 1/3 , which is obtained by any algorithm that produces a maximum weight spanning tree in G . Based on the Berman—Ramaiyer Steiner tree algorithm, the new algorithm has performance ratio at least 1/3+1/72 and at most 5/12 . We also show that if G is complete and its edge weights satisfy the triangle inequality, then the performance ratio is at least 3/8 . Furthermore, we derive the first nontrivial performance ratio (7/12 instead of 1/2 ) for the NP-hard SC MAXIMUM WEIGHT OUTERPLANAR SUBGRAPH problem.     

ONT-Based Alternative Assemblies Impact on the Annotations of Unique versus Repetitive Features in the Genome of a Romanian Strain of Drosophila melanogaster

To date, different strategies of whole-genome sequencing (WGS) have been developed in order to understand the genome structure and functions. However, the analysis of genomic sequences obtained from natural populations is challenging and the biological interpretation of sequencing data remains the main issue. The MinION device developed by Oxford Nanopore Technologies (ONT) is able to generate long reads with minimal costs and time requirements. These valuable assets qualify it as a suitable method for performing WGS, especially in small laboratories. The long reads resulted using this sequencing approach can cover large structural variants and repetitive sequences commonly present in the genomes of eukaryotes. Using MinION, we performed two WGS assessments of a Romanian local strain of Drosophila melanogaster, referred to as Horezu_LaPeri (Horezu). In total, 1,317,857 reads with a size of 8.9 gigabytes (Gb) were generated. Canu and Flye de novo assembly tools were employed to obtain four distinct assemblies with both unfiltered and filtered reads, achieving maximum reference genome coverages of 94.8% (Canu) and 91.4% (Flye). In order to test the quality of these assemblies, we performed a two-step evaluation. Firstly, we considered the BUSCO scores and inquired for a supplemental set of genes using BLAST. Subsequently, we appraised the total content of natural transposons (NTs) relative to the reference genome (ISO1 strain) and mapped the mdg1 retroelement as a resolution assayer. Our results reveal that filtered data provide only slightly enhanced results when considering genes identification, but the use of unfiltered data had a consistent positive impact on the global evaluation of the NTs content. Our comparative studies also revealed differences between Flye and Canu assemblies regarding the annotation of unique versus repetitive genomic features. In our hands, Flye proved to be moderately better for gene identification, while Canu clearly outperformed Flye for NTs analysis. Data concerning the NTs content were compared to those obtained with ONT for the D. melanogaster ISO1 strain, revealing that our strategy conducted to better results. Additionally, the parameters of our ONT reads and assemblies are similar to those reported for ONT experiments performed on various model organisms, revealing that our assembly data are appropriate for a proficient annotation of the Horezu genome.     

Reactive Oxygen Species and Long Non-Coding RNAs,an Unexpected Crossroad in Cancer Cells

Long non-coding RNAs (lncRNA) have recently been identified as key regulators of oxidative stress in several malignancies. The level of reactive oxygen species (ROS) must be constantly regulated to maintain cancer cell proliferation and chemoresistance and to prevent apoptosis. This review will discuss how lncRNAs alter the ROS level in cancer cells. We will first describe the role of lncRNAs in the nuclear factor like 2 (Nrf-2) coordinated antioxidant response of cancer cells. Secondly, we show how lncRNAs can promote the Warburg effect in cancer cells, thus shifting the cancer cell’s “building blocks” towards molecules important in oxidative stress regulation. Lastly, we explain the role that lncRNAs play in ROS-induced cancer cell apoptosis and proliferation.     

Adaptive observer design for discrete time LTV systems

In this paper, the discrete-time exponential forgetting factor observer is specialised for the joint estimation of state and parameters, leading to an adaptive observer in which the decay rates of the estimation errors for the two distinct objects can be quasi-separated. The effectiveness of the observer is demonstrated through numerical simulation.     

A Review of Microfluidic Experimental Designs for Nanoparticle Synthesis

Microfluidics is defined as emerging science and technology based on precisely manipulating fluids through miniaturized devices with micro-scale channels and chambers. Such microfluidic systems can be used for numerous applications, including reactions, separations, or detection of various compounds. Therefore, due to their potential as microreactors, a particular research focus was noted in exploring various microchannel configurations for on-chip chemical syntheses of materials with tailored properties. Given the significant number of studies in the field, this paper aims to review the recently developed microfluidic devices based on their geometry particularities, starting from a brief presentation of nanoparticle synthesis and mixing within microchannels, further moving to a more detailed discussion of different chip configurations with potential use in nanomaterial fabrication.     

Covalently-Bonded “Onion Type” Double Fullerenic Carbon Cages

Abstract

Three “onion type” double carbon cages (consisting of an inner sp³-hybridized C₆₀ buckminsterfullerene skeleton and an outer larger carbon cage with icosahedral symmetry, with covalent bonds between the carbon atoms of the 5-membered rings) are described and their strain energies are discussed: (i) when the outer cage is a C₁₂₀ cage derived from buckminsterfullerene by replacing each bond between two six-membered rings by an acetylenic group, the strain is smallest.; (ii) when the same derivation concerns each bond between 5- and 6-membered rings leading to a C₁₈₀ outer cage, the strain is largest.; (iii) when the outer cage is C₁₈₀ with benzenoid rings, the strain is intermediate.