Divergently Transcribed ncRNAs in Escherichia coli: Refinement of the Transcription Starts Assumes Functional Diversification

Non-coding regulatory RNAs (ncRNAs) comprise specialized group of essential genetically encoded biological molecules involved in the wide variety of cellular metabolic processes. The progressive increase in the number of newly identified ncRNAs and the defining of their genome location indicate their predominant nesting in intergenic regions and expression under the control of their own regulatory elements. At the same time, the regulation of ncRNA’s transcription cannot be considered in isolation from the processes occurring in the immediate genetic environment. A number of experimental data indicate the notable impact of positional regulation of gene expression mediated by dynamic temporal DNA rearrangements accompanying transcription events in the vicinity of neighboring genes. This issue can be perceived as particularly significant for divergently transcribed ncRNAs being actually subjected to double regulatory pressure. Based on available results of RNAseq experiments for Escherichia coli, we screened out divergent ncRNAs and the adjacent genes for the exact positions of transcription start sites (TSSs) and relative efficiency of RNA production. This analysis revealed extension or shortening of some previously annotated ncRNAs resulting in modified secondary structure, confirmed stable expression of four ncRNAs annotated earlier as putative, and approved the possibility of expression of divergently transcribed ncRNAs containing repetitive extragenic palindromic (REP) elements. The biogenesis of secreted ncRNAs from divergently transcribed ffs, chiX, ralA, and ryhB is discussed taking into account positions of TSSs. Refinement of TSSs for the neighboring genes renders some ncRNAs as true antisense overlapping with 5′UTR of divergently transcribed mRNAs.

Canal blocking optimization in restoration of drained peatlands

Drained peatlands are one of the main sources of carbon dioxide (CO2) emissions globally. Emission reduction and, more generally, ecosystem restoration can be enhanced by raising the water table using canal or drain blocks. When restoring large areas, the number of blocks becomes limited by the available resources, which raises the following question: in which exact positions should a given number of blocks be placed in order to maximize the water table rise throughout the area? There is neither a simple nor an analytic answer. The water table response is a complex phenomenon that depends on several factors, such as the topology of the canal network, site topography, peat hydraulic properties, vegetation characteristics and meteorological conditions. We developed a new method to position the canal blocks based on the combination of a hydrological model and heuristic optimization algorithms. We simulated 3 d dry downs from a water saturated initial state for different block positions using the Boussinesq equation, and the block configurations maximizing water table rise were searched for by means of genetic algorithm and simulated annealing. We applied this approach to a large drained peatland area (931 km2) in Sumatra, Indonesia. Our solution consistently outperformed traditional block locating methods, indicating that drained peatland restoration can be made more effective at the same cost by selecting the positions of the blocks using the presented scheme.

Locating Targets in RFID System in a Sensing Covered Anchor-Free Network

In an RFID system, the RFID readers consume huge energy and are considerably expensive in practical applications. To minimize the total number of readers with guaranteed surveillance such that the position of each tag can be uniquely determined is a challenge. This paper considers a simple but practically useful model of anchor-free network of RFID readers where each tag falls within the sensing zone of at least two readers. To maintain the quality of service in the real applications, a practical condition, the communication range is at least twice its sensing range, is considered. Under this condition, a characterization of a network is proved. An efficient algorithm for recognizing such a network is then developed without any initial position information of the readers. Using these readers as the references, an algorithm is designed for finding the exact positions of the tags in distributed manner. Unlike the existing techniques, it requires no external references for tag tracking. The proposed technique finds at most two possible positions (in some cases, unique position), out of which one is correct, for each tag.

Guided capture of 3-D Ultrasound data and semiautomatic navigation using a mechatronic support arm system

A common treatment for malignant hepatic tumors is radiofrequency thermal ablation (RFA); however this procedure is often exhausting and error-prone, when performed only with hand held devices. In this work, we present a new concept for a computer- and mechatronic-arm-assisted treatment of hepatic tumor with RFA. Challenging factors of state-of-the-art RFA procedures are tackled by utilizing a prototype, which combines state-of-the-art ultrasound image guidance with a mechatronic support arm system. Physicians can image and examine the human abdomen using an ultrasound capturing device which is guided by the mechatronic support arm. The mechatronic arm allows to track the ultrasound transducer via joint position encoders, so that the recorded images’ exact positions are acquired and the patient is automatically registered during imaging. Consequently, physicians can use the acquired ultrasound images to navigate in the imaged abdomen area. The established prototype enables preplanning and semi-automatic alignment of trajectories with sufficient accuracy. In addition, the arm system supports the usually lengthy, exhausting and error-prone holding of the needle during the ablation process. Based on the results of accuracy examination and expert assessments by surgeons, the established concept could be proven to be advantageous for the considered use case.

Canal blocking optimization in restoration of drained peatlands

Drained peatlands are one of the main sources of carbon dioxide (CO2) emissions globally. Emission reduction and, more generally, ecosystem restoration can be achieved by raising the water table using canal or drain blocks. When restoring large areas, the number of blocks becomes limited by the available resources, which raises the following question: in which exact positions should a given number of blocks be placed in order to maximize the water table raise throughout the area? There is neither a simple nor an analytic answer. The water table response is a complex phenomenon that depends on several factors, such as the topology of the canal network, site topography, peat hydraulic properties, vegetation characteristics and meteorological conditions. We developed a new method to position the canal blocks based on the combination of a hydrological model and heuristic optimization algorithms. We applied this approach to a large drained peatland area (931 km2) in Sumatra, Indonesia. Our solution consistently improved the performance of traditional block locating methods, indicating that drained peatland restoration can be made more effective at the same cost by selecting the positions of the blocks using the presented scheme.

Canal block location optimization for drained peatland restoration

<p><span>Building canal or drain blocks is a powerful tool to raise the water table of a drained peatland and to enhance ecosystem restoration. When restoring large areas, the number of blocks becomes limited by the available resources, which raises the following question: in which exact positions should a given number of blocks be placed in order to maximize the water table raise? There is neither a simple nor an analytic answer. The water table response is a complex phenomenon that depends on several factors, such as the topology of the canal network, site topography, peat hydraulic properties, vegetation and meteorological conditions. We developed a new method to position the canal blocks which is based on the combination of a hydrological model and heuristic optimization algorithms. We applied this approach to a large drained peatland area (1100 km</span><sup><span>2</span></sup><span>) in Indonesia. Our solution consistently improved the performance of traditional block locating methods, indicating that drained peatland restoration can be made more effective at the same cost by selecting the positions of the blocks using a numerical approach.</span></p>

Taylor series method in TDOA approach for indoor positioning system

Localisation technologies have always remained in the limelight of positioning-science as researchers have ever shown keen interest to know the exact positions of things. Ultrasonic sensors are mainly used for localisation of mobile robots since they provide high accuracy. This paper presents Taylor Series Method in Time Difference of Arrival approach using ultrasonic sensors.Signals are send from the sensors periodically.The time difference of arrival of signals from the ultrasonic sensors is used by the receiver unit to estimate the location of the mobile unit. The equations formed by using Time Difference of Approach are solved using Taylor Series Method. Taylor Series Method provides a more accurate result since they give less error compared to other methods and they ignore the measurement errors.

Quantified electrostatic preorganization in enzymes using the geometry of the electron charge density

The exact positions of critical points in the charge density in enzyme active sites reflects electrostatic preorganization.

An Alignment Strategy for Evolution of Multi-Agent Systems

Developed in this paper is the notion that the collective behavior of swarms can be achieved without explicit peer-to-peer communication among agents. It is based on a recently proposed continuum framework for studying swarms where homogeneous maps are the key. The paper focuses on 2D evolution of a multi-agent system (MAS) that consists of N agents with Nl leaders at the two ends of m lines called leading segments, that are on the boundary of a moving convex domain Ωt. Rest of the (N-Nl) agents, the followers, are distributed along the m leading segments while lying inside the convex domain Ωt. Every follower i is initially located at the intersection of two line segments whose end points define four agents that are adjacent to i. Under this setup if the domain Ωt is transformed under a homogenous mapping and if every follower agent moves in such a way to reach the point of intersection of the two line segments connecting the adjacent agents, then the final formation of the MAS will satisfy the same homogenous map. This alignment strategy has the distinct advantage that the followers do not need the exact positions of the adjacent local agents to stay aligned.