scholarly journals An Alternative Method to Niskin Sampling for More Accurate Metatranscriptomic Analysis of the Marine Environment

Author(s):  
Jonathan Teague ◽  
Thomas B. Scott ◽  
Sanjay Sharma ◽  
George Graham ◽  
Michael J. Allen

The development of low-cost, open-source Remotely Operated Vehicle (ROV) systems has provided almost unrestricted access for researchers looking to monitor the marine environment in ever greater resolution. Sampling microbial communities from the marine environment, however, still usually relies on Niskin-bottle sampling (ROV or CTD based), a method which introduces an inaccuracy and variability that is incompatible with metatranscriptomic analysis. Here, we describe a versatile, easily-replicated platform which achieves in situ mRNA preservation, via the addition of RNAlater to filtered microbial cells, to enhance ROV or CTD functionality.

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Adriel Latorre-Pérez ◽  
Javier Pascual ◽  
Manuel Porcar ◽  
Cristina Vilanova

Abstract High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.


2021 ◽  
Author(s):  
Mahmoud Wagih ◽  
Thomas Moody

With the massive growth in wireless systems and the internet of things vision, low-cost and rapid antenna measurements in echoic lab environments have attracted significant research, commercial, and educational interest in the last decade. In this paper, we present a low-cost antenna positioning system based on open-source positioning hardware, for in-situ 3-dimensional radiation pattern measurements. The positioner is an off-the-shelf Arduino robotic arm and can perform azimuth and elevation measurements over a hemisphere using different rotation mechanisms. The positioning system is used in conjunction with a commercial Vector Network Analyzer (VNA) and wire λ/2 antennas for the second VNA port. The measured radiation patterns of a flexible microstrip patch antenna using the proposed setup are compared to 3D full-wave simulations as well as anechoic chamber measurements. The measurement setup, excluding the VNA, costs less than $300, and does not require calibrated reference antennas, rotary connectors, or specific PC peripherals. The open-source design library is publicly available at git.soton.ac.uk/mahm1m19/antennameasurement_system/.


SoftwareX ◽  
2021 ◽  
Vol 13 ◽  
pp. 100645
Author(s):  
Partha Pratim Das ◽  
Muthu Ram Prabhu Elenchezhian ◽  
Vamsee Vadlamudi ◽  
Kenneth Reifsnider ◽  
Rassel Raihan

2021 ◽  
Author(s):  
Mahmoud Wagih ◽  
Thomas Moody

With the massive growth in wireless systems and the internet of things vision, low-cost and rapid antenna measurements in echoic lab environments have attracted significant research, commercial, and educational interest in the last decade. In this paper, we present a low-cost antenna positioning system based on open-source positioning hardware, for in-situ 3-dimensional radiation pattern measurements. The positioner is an off-the-shelf Arduino robotic arm and can perform azimuth and elevation measurements over a hemisphere using different rotation mechanisms. The positioning system is used in conjunction with a commercial Vector Network Analyzer (VNA) and wire λ/2 antennas for the second VNA port. The measured radiation patterns of a flexible microstrip patch antenna using the proposed setup are compared to 3D full-wave simulations as well as anechoic chamber measurements. The measurement setup, excluding the VNA, costs less than $300, and does not require calibrated reference antennas, rotary connectors, or specific PC peripherals. The open-source design library is publicly available at git.soton.ac.uk/mahm1m19/antennameasurement_system/.


2020 ◽  
Vol 52 ◽  
pp. 55-61
Author(s):  
Ettore Potente ◽  
Cosimo Cagnazzo ◽  
Alessandro Deodati ◽  
Giuseppe Mastronuzzi

Author(s):  
Jian-Shing Luo ◽  
Hsiu Ting Lee

Abstract Several methods are used to invert samples 180 deg in a dual beam focused ion beam (FIB) system for backside milling by a specific in-situ lift out system or stages. However, most of those methods occupied too much time on FIB systems or requires a specific in-situ lift out system. This paper provides a novel transmission electron microscopy (TEM) sample preparation method to eliminate the curtain effect completely by a combination of backside milling and sample dicing with low cost and less FIB time. The procedures of the TEM pre-thinned sample preparation method using a combination of sample dicing and backside milling are described step by step. From the analysis results, the method has applied successfully to eliminate the curtain effect of dual beam FIB TEM samples for both random and site specific addresses.


Author(s):  
C. Ramachandra ◽  
B.M. Sweety ◽  
U.G. Chandan ◽  
D. Jaypal ◽  
Sarat Kumar Dash ◽  
...  

Abstract Removal of polyimide layer after decapsulation of IC package is essential for many of the failure analysis techniques. An alternative method for polyimide removal is described in this paper. The method suggests appropriate modification of dual acid decapsulation system for this purpose. Device integrity is verified after removal of polyimide layer. This method becomes promising for devices which are sensitive / vulnerable for exposure to plasma.


2019 ◽  
Author(s):  
Nikki Theofanopoulou ◽  
Katherine Isbister ◽  
Julian Edbrooke-Childs ◽  
Petr Slovák

BACKGROUND A common challenge within psychiatry and prevention science more broadly is the lack of effective, engaging, and scale-able mechanisms to deliver psycho-social interventions for children, especially beyond in-person therapeutic or school-based contexts. Although digital technology has the potential to address these issues, existing research on technology-enabled interventions for families remains limited. OBJECTIVE The aim of this pilot study was to examine the feasibility of in-situ deployments of a low-cost, bespoke prototype, which has been designed to support children’s in-the-moment emotion regulation efforts. This prototype instantiates a novel intervention model that aims to address the existing limitations by delivering the intervention through an interactive object (a ‘smart toy’) sent home with the child, without any prior training necessary for either the child or their carer. This pilot study examined (i) engagement and acceptability of the device in the homes during 1 week deployments; and (ii) qualitative indicators of emotion regulation effects, as reported by parents and children. METHODS In this qualitative study, ten families (altogether 11 children aged 6-10 years) were recruited from three under-privileged communities in the UK. The RA visited participants in their homes to give children the ‘smart toy’ and conduct a semi-structured interview with at least one parent from each family. Children were given the prototype, a discovery book, and a simple digital camera to keep at home for 7-8 days, after which we interviewed each child and their parent about their experience. Thematic analysis guided the identification and organisation of common themes and patterns across the dataset. In addition, the prototypes automatically logged every interaction with the toy throughout the week-long deployments. RESULTS Across all 10 families, parents and children reported that the ‘smart toy’ was incorporated into children’s emotion regulation practices and engaged with naturally in moments children wanted to relax or calm down. Data suggests that children interacted with the toy throughout the duration of the deployment, found the experience enjoyable, and all requested to keep the toy longer. Child emotional connection to the toy—caring for its ‘well-being’—appears to have driven this strong engagement. Parents reported satisfaction with and acceptability of the toy. CONCLUSIONS This is the first known study investigation of the use of object-enabled intervention delivery to support emotion regulation in-situ. The strong engagement and qualitative indications of effects are promising – children were able to use the prototype without any training and incorporated it into their emotion regulation practices during daily challenges. Future work is needed to extend this indicative data with efficacy studies examining the psychological efficacy of the proposed intervention. More broadly, our findings suggest the potential of a technology-enabled shift in how prevention interventions are designed and delivered: empowering children and parents through ‘child-led, situated interventions’, where participants learn through actionable support directly within family life, as opposed to didactic in-person workshops and a subsequent skills application.


2020 ◽  
Author(s):  
Andrew Fang ◽  
Jonathan Kia-Sheng Phua ◽  
Terrence Chiew ◽  
Daniel De-Liang Loh ◽  
Lincoln Ming Han Liow ◽  
...  

BACKGROUND During the Coronavirus Disease 2019 (COVID-19) outbreak, community care facilities (CCF) were set up as temporary out-of-hospital isolation facilities to contain the surge of cases in Singapore. Confined living spaces within CCFs posed an increased risk of communicable disease spread among residents. OBJECTIVE This inspired our healthcare team managing a CCF operation to design a low-cost communicable disease outbreak surveillance system (CDOSS). METHODS Our CDOSS was designed with the following considerations: (1) comprehensiveness, (2) efficiency through passive reconnoitering from electronic medical record (EMR) data, (3) ability to provide spatiotemporal insights, (4) low-cost and (5) ease of use. We used Python to develop a lightweight application – Python-based Communicable Disease Outbreak Surveillance System (PyDOSS) – that was able perform syndromic surveillance and fever monitoring. With minimal user actions, its data pipeline would generate daily control charts and geospatial heat maps of cases from raw EMR data and logged vital signs. PyDOSS was successfully implemented as part of our CCF workflow. We also simulated a gastroenteritis (GE) outbreak to test the effectiveness of the system. RESULTS PyDOSS was used throughout the entire duration of operation; the output was reviewed daily by senior management. No disease outbreaks were identified during our medical operation. In the simulated GE outbreak, PyDOSS was able to effectively detect an outbreak within 24 hours and provided information about cluster progression which could aid in contact tracing. The code for a stock version of PyDOSS has been made publicly available. CONCLUSIONS PyDOSS is an effective surveillance system which was successfully implemented in a real-life medical operation. With the system developed using open-source technology and the code made freely available, it significantly reduces the cost of developing and operating CDOSS and may be useful for similar temporary medical operations, or in resource-limited settings.


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