scholarly journals Evaluation of various RNA-seq approaches for identification of gene outrons in the flatworm Opisthorchis felineus

2020 ◽  
Vol 24 (8) ◽  
pp. 897-904
Author(s):  
N. I. Ershov ◽  
D. E. Maslov ◽  
N. P. Bondar
Keyword(s):  
High Efficiency ◽  
The Other ◽  
Opisthorchis Felineus ◽  
Transcription Start Sites ◽  
Spliced Leader ◽  
Trans Splicing ◽  
Rrna Depletion ◽  
Causative Agents ◽  
Bona Fide ◽  
Nascent Transcripts

The parasitic flatworm Opisthorchis felineus is one of the causative agents of opisthorchiasis in humans. Recently, we assembled the O. felineus genome, but the correct genome annotation by means of standard methods was hampered by the presence of spliced leader trans-splicing (SLTS). As a result of SLTS, the original 5’-end (outron) of the transcripts is replaced by a short spliced leader sequence donated from a specialized SL RNA. SLTS is involved in the RNA processing of more than half of O. felineus genes, making it hard to determine the structure of outrons and bona fide transcription start sites of the corresponding genes and operons, being based solely on mRNA-seq data. In the current study, we tested various experimental approaches for identifying the sequences of outrons in O. felineus using massive parallel sequencing. Two of them were developed by us for targeted sequencing of already processed branched outrons. One was based on sequence-specific reverse transcription from the SL intron toward the 5’-end of the Y-branched outron. The other used outron hybridization with an immobilized single-stranded DNA probe complementary to the SL intron. Additionally, two approaches to the sequencing of rRNA-depleted total RNA were used, allowing the identification of a wider range of transcripts compared to mRNAseq. One is based on the enzymatic elimination of overrepresented cDNAs, the other utilizes exonucleolytic degradation of uncapped RNA by Terminator enzyme. By using the outron-targeting methods, we were not able to obtain the enrichment of RNA preparations by processed outrons, which is most likely indicative of a rapid turnover of these trans-splicing intermediate products. Of the two rRNA depletion methods, a method based on the enzymatic normalization of cDNA (Zymo-Seq RiboFree) showed high efficiency. Compared to mRNA-seq, it provides an approximately twofold increase in the fraction of reads originating from outrons and introns. The results suggest that unprocessed nascent transcripts are the main source of outron sequences in the RNA pool of O. felineus.

scholarly journals Search for Promising Strains of Probiotic Microbiota Isolated from Different Biotopes of Healthy Cats for Use in the Control of Surgical Infections

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 667
Author(s):  
Pavel Rudenko ◽  
Yuriy Vatnikov ◽  
Nadezhda Sachivkina ◽  
Andrei Rudenko ◽  
Evgeny Kulikov ◽  
...  
Keyword(s):  
Antimicrobial Agents ◽  
High Efficiency ◽  
Biological Marker ◽  
High Sensitivity ◽  
Antagonistic Activity ◽  
Adhesive Properties ◽  
Surgical Infection ◽  
Surgical Infections ◽  
Causative Agents ◽  
Inflammatory Processes

Despite the introduction of modern methods of treatment, the creation of new generations of antibacterial agents, and the constant improvement of aseptic and antiseptic methods, the treatment of purulent–inflammatory processes remains one of the most complex and urgent problems in veterinary practice. The article presents the results of the isolation of indigenous microbiota from various biotopes of healthy cats, as well as the study of their biological marker properties for the selection of the most optimal strains in probiotic medicines for the control of surgical infections. It was demonstrated that isolated cultures of bifidobacteria and lactobacilli, which we isolated, revealed high sensitivity to antibiotics of the β-lactam group (excepting L. acidophilus No. 24, L. plantarum “Victoria” No. 22, L. rhamnosus No. 5, L. rhamnosus No. 20, and L. rhamnosus No. 26, which showed a significant variability in sensitivity to antibacterial drugs of this group, indicating the great potential of these microorganisms) and resistance to aminoglycosides, lincosamides, and fluoroquinolones (with the exception of gatifloxacin, which showed high efficiency in relation to all lactic acid microorganisms). The adhesive properties of the isolated lactobacteria and bifidobacteria were variable, even within the same species. It was found that the B. adolescentis No. 23 strain of the Bifidobacterium genus, as well as the L. plantarum No. 8, L. plantarum “Victoria” No. 22, L. rhamnosus No. 6, L. rhamnosus No. 26, L. acidophilus No. 12, and L. acidophilus No. 24 strains of the Lactobacillus genus had the highest adhesive activity. Thus, when conducting a detailed analysis of the biological marker properties of candidate cultures (determining their sensitivity to antimicrobial agents, studying the adhesive properties, and antagonistic activity in relation to causative agents of surgical infection in cats), it was found that the most promising are L. plantarum “Victoria” No. 22, L. rhamnosus No. 26, and L. acidophilus No. 24.

scholarly journals Fast Accurate and Automatic Brushstroke Extraction

2021 ◽  
Vol 17 (2) ◽  
pp. 1-24
Author(s):  
Yunfei Fu ◽  
Hongchuan Yu ◽  
Chih-Kuo Yeh ◽  
Tong-Yee Lee ◽  
Jian J. Zhang
Keyword(s):  
Neural Network ◽  
Efficient Algorithm ◽  
Deep Neural Network ◽  
High Efficiency ◽  
State Of The Art ◽  
High Reliability ◽  
The Other ◽  
Manual Annotation ◽  
Stroke Extraction ◽  
Art Research

Brushstrokes are viewed as the artist’s “handwriting” in a painting. In many applications such as style learning and transfer, mimicking painting, and painting authentication, it is highly desired to quantitatively and accurately identify brushstroke characteristics from old masters’ pieces using computer programs. However, due to the nature of hundreds or thousands of intermingling brushstrokes in the painting, it still remains challenging. This article proposes an efficient algorithm for brush Stroke extraction based on a Deep neural network, i.e., DStroke. Compared to the state-of-the-art research, the main merit of the proposed DStroke is to automatically and rapidly extract brushstrokes from a painting without manual annotation, while accurately approximating the real brushstrokes with high reliability. Herein, recovering the faithful soft transitions between brushstrokes is often ignored by the other methods. In fact, the details of brushstrokes in a master piece of painting (e.g., shapes, colors, texture, overlaps) are highly desired by artists since they hold promise to enhance and extend the artists’ powers, just like microscopes extend biologists’ powers. To demonstrate the high efficiency of the proposed DStroke, we perform it on a set of real scans of paintings and a set of synthetic paintings, respectively. Experiments show that the proposed DStroke is noticeably faster and more accurate at identifying and extracting brushstrokes, outperforming the other methods.

scholarly journals An in vivo genetic screen for genes involved in spliced leader trans-splicing indicates a crucial role for continuous de novo spliced leader RNP assembly

2017 ◽  
Vol 45 (14) ◽  
pp. 8474-8483 ◽  
Author(s):  
Lucas Philippe ◽  
George C. Pandarakalam ◽  
Rotimi Fasimoye ◽  
Neale Harrison ◽  
Bernadette Connolly ◽  
...  
Keyword(s):  
Crucial Role ◽  
De Novo ◽  
Genetic Screen ◽  
Spliced Leader ◽  
Trans Splicing

scholarly journals A directed approach for the identification of transcripts harbouring the spliced leader sequence and the effect of trans-splicing knockdown in Schistosoma mansoni

2013 ◽  
Vol 108 (6) ◽  
pp. 707-717 ◽  
Author(s):  
Marina de Moraes Mourao ◽  
Maina Bitar ◽  
Francisco Pereira Lobo ◽  
Ana Paula Peconick ◽  
Priscila Grynberg ◽  
...  
Keyword(s):  
Schistosoma Mansoni ◽  
Leader Sequence ◽  
Spliced Leader ◽  
Trans Splicing

Hemodialysis during cardiopulmonary resuscitation in patients with severe metabolic acidosis

2018 ◽  
Vol 41 (8) ◽  
pp. 431-436 ◽  
Author(s):  
Tuncay Sahutoglu ◽  
Elif Sahutoglu
Keyword(s):  
Metabolic Acidosis ◽  
Cardiopulmonary Resuscitation ◽  
High Efficiency ◽  
Spontaneous Circulation ◽  
The Other ◽  
Unresolved Issue ◽  
Severe Metabolic Acidosis ◽  
Hospital Records ◽  
Return Of Spontaneous Circulation ◽  
Potential Use

Background/Aims: Severe metabolic acidosis during cardiopulmonary resuscitation is an important and yet unresolved issue. The potential use of hemodialysis for severe metabolic acidosis during cardiopulmonary resuscitation was investigated. Methods: Acute hemodialyses between January 2012 and April 2017 were reviewed for patients with concomitant hemodialysis and cardiopulmonary resuscitation. In addition, MEDLINE was searched for similar reports. Data were extracted from hospital records. Results: Two patients (36M, 70F) were found to study, without similar reports in MEDLINE. Cardiac arrests (in-hospital) occurred due to severe metabolic acidosis in both patients (due to ethylene glycol and metformin intoxications, respectively). Return of spontaneous circulation could not be obtained within the first 28 and 30 min of cardiopulmonary resuscitation only, whereas both patients had return of spontaneous circulation following at least 45 min of concomitant hemodialysis and cardiopulmonary resuscitation. One patient (70F) was discharged with good neurological outcome, but the other died. Conclusion: The addition of high-efficiency hemodialysis during cardiopulmonary resuscitation may contribute to the return of spontaneous circulation in patients with severe metabolic acidosis due to intoxication.

Evaluation of the Service Performance of Ships

2005 ◽  
Vol 42 (04) ◽  
pp. 177-183
Author(s):  
Poul Andersen ◽  
Anne-Sophie Borrod ◽  
Hervé Blanchot
Keyword(s):  
Input Data ◽  
High Efficiency ◽  
Service Performance ◽  
The Other ◽  
Simple Method ◽  
Propulsive Efficiency ◽  
Order Of Magnitude ◽  
Time Periods

A simple method has been established for the evaluation of the service performance of ships. Input data are easily collected daily on board and transformed to a well-defined condition that makes possible the comparison between ships, for instance, sister ships, and between different time periods of voyages for the same ship. The procedure has been applied to two ships that are identical, with the only exception that one has a conventional propeller, whereas the other one is fitted with a high-efficiency propeller of the KAPPEL type. The results are obtained from a period of 2 years steaming for both vessels. They clearly confirm the increase of propulsive efficiency obtained with the KAPPEL propeller in the order of magnitude of 4%.

scholarly journals 22. The relation between orbits and physical characteristics of meteors

1968 ◽  
Vol 33 ◽  
pp. 217-235 ◽  
Author(s):  
Ľ. Kresák
Keyword(s):  
Major Axis ◽  
Progressive Increase ◽  
Physical Characteristics ◽  
The Other ◽  
Asteroid Belt ◽  
Angle Of Incidence ◽  
Semi Major Axis ◽  
Short Period ◽  
Broad Variety ◽  
Bona Fide

The relation of physical characteristics of meteors to their orbital elements is investigated using Harvard Super-Schmidt data. A set of characteristic indices is defined, allowing for the effects of geocentric velocity, angle of incidence, magnitude and mass, wherever a correction appears appropriate according to the correlations found by Jacchia et al. (1967). The medians for representative meteor samples are plotted in the semi-major axis/eccentricity diagram and the distribution of each parameter is derived. Although the differences are moderate compared to the measuring errors, six regions of different nature can be distinguished.The existence of two families of asteroidal meteors is indicated, one of them brought to crossing with the Earth's orbit by drag effects and the other by collision effects in the main asteroid belt. These meteors are characterized by low and uniform beginning heights, high fragmentation, low ablation, low deceleration, and bright wakes. A direct counterpart to this is represented by meteors moving in short-period orbits of higher eccentricity and shorter perihelion distance, which bear resemblance to the long-period and retrograde cometary meteors. Meteors with perihelion distances of less than 0·15 AU tend to resemble the bona fide asteroidal meteors by a progressive increase of fragmentation and decrease of reduced beginning heights and decelerations as the perihelion approaches the Sun. This is attributed to the selective destruction effects of solar radiation.With the exception of the Draconids, the mean characteristics of meteor showers agree well with those of sporadic meteors moving in similar orbits. It is suggested that the Draconid stream includes a broad variety of meteoric material and that the two peculiar Super-Schmidt meteors on record represent only the less resistive, short-lived component which has already been eliminated from the other showers.

scholarly journals A High-Efficiency Three-Level ANPC Inverter Based on Hybrid SiC and Si Devices

Energies ◽  
2020 ◽  
Vol 13 (5) ◽  
pp. 1159 ◽  
Author(s):  
Zhijian Feng ◽  
Xing Zhang ◽  
Jianing Wang ◽  
Shaolin Yu
Keyword(s):  
Silicon Carbide ◽  
High Efficiency ◽  
The Other ◽  
Switching Frequency ◽  
Parallel Operation ◽  
Switching Loss ◽  
Hybrid Scheme ◽  
Excellent Performance ◽  
Switching Losses ◽  
The Cost

Silicon carbide (SiC) devices have excellent performance, such as higher switching frequency and lower switching loss compared with traditional silicon (Si) devices. The application of SiC devices in inverters can achieve higher efficiency and power density. In recent years, the production process of SiC devices has become more mature, but the cost is still several times that of traditional Si devices. In order to balance cost and efficiency, replacing only some of the Si devices with SiC devices in a topology is a better choice. This paper proposed a high-efficiency hybrid active neutral point clamped (ANPC) three-level inverter which has only two SiC devices and the other devices are Si devices. A specific modulation strategy was applied to concentrate switching losses on the SiC devices and reduce the on-state loss through parallel operation during freewheeling intervals. Theoretical efficiency curves and experimental verification of the proposed hybrid scheme with Si-only and SiC-only schemes were carried out.

scholarly journals Constitutive Expression of Escherichia coli tat Genes Indicates an Important Role for the Twin-Arginine Translocase during Aerobic and Anaerobic Growth

2001 ◽  
Vol 183 (5) ◽  
pp. 1801-1804 ◽  
Author(s):  
Rachael L. Jack ◽  
Frank Sargent ◽  
Ben C. Berks ◽  
Gary Sawers ◽  
Tracy Palmer
Keyword(s):  
Constitutive Expression ◽  
Protein Export ◽  
The Other ◽  
Anaerobic Growth ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Expression Studies ◽  
Twin Arginine Translocase ◽  
Aerobic And Anaerobic Growth ◽  
Aerobic And Anaerobic

ABSTRACT The transcription start sites for the tatABCD andtatE loci, encoding components of the Tat (twin-arginine translocase) protein export pathway, have been identified. Expression studies indicate that the tatABCD and tatEtranscription units are expressed constitutively. Translational fusion experiments suggest that TatA is synthesized at a much higher level than the other Tat proteins.

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