scholarly journals DNA aptamers against bacterial cells can be efficiently selected by a SELEX process using state-of-the art qPCR and ultra-deep sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Claudia Kolm ◽  
Isabella Cervenka ◽  
Ulrich J. Aschl ◽  
Niklas Baumann ◽  
Stefan Jakwerth ◽  
...  
Keyword(s):  
State Of The Art ◽  
Selection Process ◽  
High Specificity ◽  
Cost Effective ◽  
Cell Labelling ◽  
Dna Aptamers ◽  
Bacterial Cells ◽  
Combined Approach ◽  
Affinity Reagents ◽  
Assessment Techniques

AbstractDNA aptamers generated by cell-SELEX against bacterial cells have gained increased interest as novel and cost-effective affinity reagents for cell labelling, imaging and biosensing. Here we describe the selection and identification of DNA aptamers for bacterial cells using a combined approach based on cell-SELEX, state-of-the-art applications of quantitative real-time PCR (qPCR), next-generation sequencing (NGS) and bioinformatic data analysis. This approach is demonstrated on Enterococcus faecalis (E. faecalis), which served as target in eleven rounds of cell-SELEX with multiple subtractive counter-selections against non-target species. During the selection, we applied qPCR-based analyses to evaluate the ssDNA pool size and remelting curve analysis of qPCR amplicons to monitor changes in pool diversity and sequence enrichment. Based on NGS-derived data, we identified 16 aptamer candidates. Among these, aptamer EF508 exhibited high binding affinity to E. faecalis cells (KD-value: 37 nM) and successfully discriminated E. faecalis from 20 different Enterococcus and non-Enterococcus spp. Our results demonstrate that this combined approach enabled the rapid and efficient identification of an aptamer with both high affinity and high specificity. Furthermore, the applied monitoring and assessment techniques provide insight into the selection process and can be highly useful to study and improve experimental cell-SELEX designs to increase selection efficiency.

scholarly journals A Combined Approach to Predicting Rest in Dogs Using Accelerometers

Sensors ◽  
2018 ◽  
Vol 18 (8) ◽  
pp. 2649 ◽  
Author(s):  
Cassim Ladha ◽  
Christy Hoffman
Keyword(s):  
Resting State ◽  
State Of The Art ◽  
Hybrid Approach ◽  
Well Being ◽  
Housing Conditions ◽  
Combined Approach ◽  
Current State ◽  
Healthy Dogs ◽  
State Of Rest ◽  
Health And Well Being

The ability to objectively measure episodes of rest has clear application for assessing health and well-being. Accelerometers afford a sensitive platform for doing so and have demonstrated their use in many human-based trials and interventions. Current state of the art methods for predicting sleep from accelerometer signals are either based on posture or low movement. While both have proven to be sensitive in humans, the methods do not directly transfer well to dogs, possibly because dogs are commonly alert but physically inactive when recumbent. In this paper, we combine a previously validated low-movement algorithm developed for humans and a posture-based algorithm developed for dogs. The hybrid approach was tested on 12 healthy dogs of varying breeds and sizes in their homes. The approach predicted state of rest with a mean accuracy of 0.86 (SD = 0.08). Furthermore, when a dog was in a resting state, the method was able to distinguish between head up and head down posture with a mean accuracy of 0.90 (SD = 0.08). This approach can be applied in a variety of contexts to assess how factors, such as changes in housing conditions or medication, may influence a dog’s resting patterns.

IN MINIMAL ACCESS SURGERY

1996 ◽  
Vol 17 (12) ◽  
pp. 441-447
Author(s):  
Thom E Lobe
Keyword(s):  
Medical Care ◽  
Pediatric Patient ◽  
Endoscopic Surgery ◽  
State Of The Art ◽  
Outpatient Surgery ◽  
Cost Effective ◽  
Surgical Instruments ◽  
Short Stay ◽  
Minimal Access ◽  
Access Surgery

The pediatrician must be cognizant of the extensive applications of endoscopic surgery in the pediatric patient. The ability to provide either outpatient surgery or short-stay surgery appears to be cost-effective and appropriate state-of-the-art medical care. As the array of surgical instruments continues to evolve, new and innovative endoscopic procedures will become increasingly available.

Estimated path information gain-based robot exploration under perceptual uncertainty

Robotica ◽  
2022 ◽  
pp. 1-17
Author(s):  
Jie Liu ◽  
Chaoqun Wang ◽  
Wenzheng Chi ◽  
Guodong Chen ◽  
Lining Sun
Keyword(s):  
Decision Making ◽  
Topological Structure ◽  
Information Gain ◽  
State Of The Art ◽  
Selection Process ◽  
Random Trees ◽  
Experimental Results ◽  
Restricted Area ◽  
Structure Information ◽  
Path Information

Abstract At present, the frontier-based exploration has been one of the mainstream methods in autonomous robot exploration. Among the frontier-based algorithms, the method of searching frontiers based on rapidly exploring random trees consumes less computing resources with higher efficiency and performs well in full-perceptual scenarios. However, in the partially perceptual cases, namely when the environmental structure is beyond the perception range of robot sensors, the robot often lingers in a restricted area, and the exploration efficiency is reduced. In this article, we propose a decision-making method for robot exploration by integrating the estimated path information gain and the frontier information. The proposed method includes the topological structure information of the environment on the path to the candidate frontier in the frontier selection process, guiding the robot to select a frontier with rich environmental information to reduce perceptual uncertainty. Experiments are carried out in different environments with the state-of-the-art RRT-exploration method as a reference. Experimental results show that with the proposed strategy, the efficiency of robot exploration has been improved obviously.

scholarly journals CRISPR-mediated isogenic cell-SELEX approach for generating highly specific aptamers against native membrane proteins

2020 ◽  
Author(s):  
Jonah C. Rosch ◽  
Emma H. Neal ◽  
Daniel A. Balikov ◽  
Mohsin Rahim ◽  
Ethan S. Lippmann
Keyword(s):  
Membrane Proteins ◽  
Glucose Transporter ◽  
High Specificity ◽  
Epithelial Cell Line ◽  
Target Cells ◽  
Wild Type ◽  
Simultaneous Exposure ◽  
Affinity Reagents ◽  
A Cell

AbstractIntroductionThe generation of affinity reagents that bind native membrane proteins with high specificity remains challenging. Most in vitro selection paradigms utilize different cell types for positive and negative rounds of selection (where the positive selection is against a cell that expresses the desired membrane protein and the negative selection is against a cell that lacks the protein). However, this strategy can yield affinity reagents that bind unintended membrane proteins on the target cells. To address this issue, we developed a systematic evolution of ligands by exponential enrichment (SELEX) scheme that utilizes isogenic pairs of cells generated via CRISPR techniques.MethodsUsing a Caco-2 epithelial cell line with constitutive Cas9 expression, we knocked out the SLC2A1 gene (encoding the GLUT1 glucose transporter) via lipofection with synthetic gRNAs. Cell-SELEX rounds were carried out against wild-type and GLUT1-null cells using a single-strand DNA (ssDNA) library. Next-generation sequencing (NGS) was used to quantify enrichment of prospective binders to the wild-type cells.Results10 rounds of cell-SELEX were conducted via simultaneous exposure of ssDNA pools to wild-type and GLUT1-null Caco-2 cells under continuous perfusion. The top binders identified from NGS were validated by flow cytometry and immunostaining for their specificity to the GLUT1 receptor.ConclusionsOur data indicate that highly specific aptamers can be isolated with a SELEX strategy that utilizes isogenic cell lines. This approach should be broadly useful for generating affinity reagents that selectively bind to membrane proteins in their native conformations on the cell surface.

scholarly journals Using plants to remediate or manage metal-polluted soils: an overview on the current state of phytotechnologies

2021 ◽  
Vol 43 ◽  
pp. e58283
Author(s):  
Clístenes Williams Araújo do Nascimento ◽  
Caroline Miranda Biondi ◽  
Fernando Bruno Vieira da Silva ◽  
Luiz Henrique Vieira Lima
Keyword(s):  
Large Scale ◽  
State Of The Art ◽  
Cost Effective ◽  
Time Frame ◽  
Contaminated Site ◽  
Polluted Soils ◽  
Mining Sites ◽  
Current State ◽  
Remedial Actions ◽  
The Tropics

Soil contamination by metals threatens both the environment and human health and hence requires remedial actions. The conventional approach of removing polluted soils and replacing them with clean soils (excavation) is very costly for low-value sites and not feasible on a large scale. In this scenario, phytoremediation emerged as a promising cost-effective and environmentally-friendly technology to render metals less bioavailable (phytostabilization) or clean up metal-polluted soils (phytoextraction). Phytostabilization has demonstrable successes in mining sites and brownfields. On the other hand, phytoextraction still has few examples of successful applications. Either by using hyperaccumulating plants or high biomass plants induced to accumulate metals through chelator addition to the soil, major phytoextraction bottlenecks remain, mainly the extended time frame to remediation and lack of revenue from the land during the process. Due to these drawbacks, phytomanagement has been proposed to provide economic, environmental, and social benefits until the contaminated site returns to productive usage. Here, we review the evolution, promises, and limitations of these phytotechnologies. Despite the lack of commercial phytoextraction operations, there have been significant advances in understanding phytotechnologies' main constraints. Further investigation on new plant species, especially in the tropics, and soil amendments can potentially provide the basis to transform phytoextraction into an operational metal clean-up technology in the future. However, at the current state of the art, phytotechnology is moving the focus from remediation technologies to pollution attenuation and palliative cares.

scholarly journals Belt and Road Initiative: Interim Results and Challenges During Pandemic

2021 ◽  
Vol 65 (3) ◽  
pp. 42-51
Author(s):  
N. Pyzhikov ◽  
E. Gushchin
Keyword(s):  
Selection Process ◽  
Foreign Debt ◽  
Cost Effective ◽  
Point Of View ◽  
Current Status ◽  
Belt And Road Initiative ◽  
Middle Income ◽  
Chinese Investment ◽  
The World ◽  
Belt And Road

The article analyses the current status of the Belt and Road Initiative (BRI), its key achievements and challenges, including those related to the COVID 19 pandemic. In the 2010s China has become one of world’s largest investors and BRI is one of the most important tools of Chinese investment policy. Due to its flexible structure, BRI has been able to adjust and develop in the context of the U.S. – China trade war and the growing anti-Chinese sentiment in the world that included the concerns over so called China’s debt diplomacy. But this lack of rigidity is also a challenge to those who study BRI because there is no official list of projects (estimations vary between 118 and 374) and countries participating in BRI (up to 138). China’s key BRI partner is Pakistan. The total value of projects implemented by China in Pakistan as part of the China-Pakistan Economic Corridor was initially estimated at $46 billion but now exceeds $70 billion (new projects were signed even during the pandemic). BRI is increasing the number of its participants. In March 2019 Italy became the first G7 country to sign a BRI MoU with China. While implementing BRI China has faced such challenges as rising concerns of “China’s debt trap”, as well as ecological and political issues. In 2020 BRI is facing a new challenge with the COVID-19 pandemic. Some BRI projects were postponed because of the pandemic, but in some cases they were unaffected. There are 64 out of 138 countries participating in BRI that come from low and lower-middle income groups according to the World Bank classification. Their average ratio of foreign debt to GDP was 54% in 2018–2019. It is most likely that these countries will be hit hard by the coronacrisis. Thus the pandemic will encourage China to tighten the selection process for BRI projects with a focus on the most strategically important and cost effective ones. From the point of view of China’s BRI partners, the effect can be two-fold: the most unstable economies will increase their dependence on China, while with the economically strong countries China will be more willing to make concessions and offer more favorable conditions for cooperation.

scholarly journals A ruthenium-based catalyst on carbon electrodes for electrochemical water splitting

2021 ◽  
Author(s):  
Lin Li ◽  
Biswanath Das ◽  
Ahibur Rahaman ◽  
Andrey Shatskiy ◽  
Fei Ye ◽  
...  
Keyword(s):  
Water Splitting ◽  
Water Oxidation ◽  
State Of The Art ◽  
Cost Effective ◽  
Molecular Catalyst ◽  
Electrolysis Cells ◽  
Multi Walled Carbon Nanotubes ◽  
Energy Economy ◽  
Electrochemical Water Splitting ◽  
Walled Carbon Nanotubes

Electrochemical water splitting constitutes one of the most promising strategies for converting water into hydrogen-based fuels, and this technology is predicted to play a key role in our transition towards a carbon-neutral energy economy. To enable the design of cost-effective electrolysis cells based on this technology, new and more efficient anodes with augmented water splitting activity and stability will be required. Herein, we report an active molecular Ru-based catalyst for electrochemically-driven water oxidation and two simple methods for preparing anodes by attaching this catalyst onto multi-walled carbon nanotubes. The anodes modified with the molecular catalyst were characterized by a broad toolbox of microscopy and spectroscope techniques, and interestingly no RuO2 formation was detected during electrocatalysis over 4 h. These results demonstrate that the herein presented strategy can be used to prepare anodes that rival the performance of state-of-the-art metal oxide anodes.

scholarly journals INTERACTIVE CADASTRAL BOUNDARY DELINEATION FROM UAV DATA

2018 ◽  
Vol IV-2 ◽  
pp. 81-88 ◽  
Author(s):  
S. Crommelinck ◽  
B. Höfle ◽  
M. N. Koeva ◽  
M. Y. Yang ◽  
G. Vosselman
Keyword(s):  
Unmanned Aerial Vehicles ◽  
Land Tenure ◽  
State Of The Art ◽  
Cost Effective ◽  
Contour Detection ◽  
Local Boundary ◽  
Manual Delineation ◽  
Cost Paths ◽  
Cadastral Surveying ◽  
Least Cost Paths

Unmanned aerial vehicles (UAV) are evolving as an alternative tool to acquire land tenure data. UAVs can capture geospatial data at high quality and resolution in a cost-effective, transparent and flexible manner, from which visible land parcel boundaries, i.e., cadastral boundaries are delineable. This delineation is to no extent automated, even though physical objects automatically retrievable through image analysis methods mark a large portion of cadastral boundaries. This study proposes (i) a methodology that automatically extracts and processes candidate cadastral boundary features from UAV data, and (ii) a procedure for a subsequent interactive delineation. Part (i) consists of two state-of-the-art computer vision methods, namely gPb contour detection and SLIC superpixels, as well as a classification part assigning costs to each outline according to local boundary knowledge. Part (ii) allows a user-guided delineation by calculating least-cost paths along previously extracted and weighted lines. The approach is tested on visible road outlines in two UAV datasets from Germany. Results show that all roads can be delineated comprehensively. Compared to manual delineation, the number of clicks per 100 m is reduced by up to 86 %, while obtaining a similar localization quality. The approach shows promising results to reduce the effort of manual delineation that is currently employed for indirect (cadastral) surveying.

scholarly journals Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

2016 ◽  
Vol 10 (1) ◽  
pp. 176-182 ◽  
Author(s):  
Reza Ranjbar ◽  
Payam Behzadi ◽  
Caterina Mammina
Keyword(s):  
Dna Microarray ◽  
Francisella Tularensis ◽  
High Specificity ◽  
Cost Effective ◽  
High Rate ◽  
Molecular Diagnostic ◽  
Microarray Technology ◽  
Microarray Probe ◽  
Specificity And Sensitivity ◽  
Oligo Microarray

Background:Francisella tularensis(F. tularensis) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing.Objective:The main goal of this original article was to design suitable long oligo microarray probes for detection and identification ofF. tularensis.Method:For performing this research, the complete genomes ofF. tularensissubsp.tularensisFSC198,F. tularensissubsp.holarcticaLVS,F. tularensissubsp.mediasiatica,F. tularensissubsp.novicida(F. novicidaU112), andF. philomiragiasubsp.philomiragiaATCC 25017 were studiedviaNCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processedviaAlleleID 7.7 software and Oligoanalyzer tool, respectively.Results:In thisin silicoinvestigation, a number of long oligo microarray probes were designed for detecting and identifyingF. tularensis. Among these probes, 15 probes were recognized as the best candidates for microarray chip designing.Conclusion:Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip.

Employing Space-Based Hyperspectral Imagery for Pipeline Leak Prevention, Detection and Compliance

2020 ◽  
Author(s):  
R. Peter Weaver ◽  
Dan Katz ◽  
Tushar Prabahakar ◽  
Katie A. Corcoran
Keyword(s):  
Environmental Protection Agency ◽  
Oil And Gas ◽  
State Of The Art ◽  
Hyperspectral Imagery ◽  
Cost Effective ◽  
Protection Agency ◽  
High Resolution Data ◽  
Hydrocarbon Detection ◽  
Detection Capabilities ◽  
Vapor Emissions

Abstract We are now living in what has been described as the Experience Era, where lines between the digital and physical are increasingly blurred. As such, we are just beginning to see how customized access to space will improve asset stewardship in ways that are still evolving, as customization of on-orbit technology pushes the bounds of how we receive and process information. Specific to oil and gas operators, one technology being launched by microsatellite, hyperspectral imagery (HSI), is poised to enable unparalleled daily global pipeline leak prevention, detection and speciation, intrusion and change detection capabilities. This will replace conventional DOT pipeline patrol for compliance while contributing to our understanding of vapor emissions as regulated by the Environmental Protection Agency. This paper discusses both the evolving space marketplace and the state of the art for HSI, including current examples of hyperspectral findings regarding pipeline and terminal leaks. Successful deployment of HSI will drive a decrease in the number and magnitude of pipeline leaks using persistent, global, high-resolution data collection, rapid and reliable analysis, and immediate reporting of actionable information. For decades, satellite HSI technology has offered a promise of remote hydrocarbon detection and other features of interest. It is only now becoming scalable, accessible to, and cost-effective for the pipeline industry, and thus a reality for cost-effective pipeline stewardship.

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