scholarly journals Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS)

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 578 ◽  
Author(s):  
Deshpande ◽  
Reed ◽  
Sullivan ◽  
Kerkhof ◽  
Beigel ◽  
...  
Keyword(s):  
Open Source ◽  
Cost Effective ◽  
Ease Of Use ◽  
Remote Locations ◽  
Resource Limited ◽  
Field Samples ◽  
Sample Characterization ◽  
Internet Availability ◽  
Detection Software ◽  
Downstream Analysis

Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstream analysis problematic, resulting in a lack of sample identification in the field. Due to this dependency, field samples are generally transported back to the lab for analysis where internet availability for downstream analysis is available. These logistics problems and the time lost in sample characterization and identification, pose a significant problem for field scientists. To address this limitation, we have developed a stand-alone data analysis packet using open source tools developed by the Nanopore community that does not depend on internet availability. Like Oxford Nanopore Technologies’ (ONT) cloud-based What’s In My Pot (WIMP) software, we developed the offline MinION Detection Software (MINDS) based on the Centrifuge classification engine for rapid species identification. Several online bioinformatics applications have been developed surrounding ONT’s framework for analysis of long reads. We have developed and evaluated an offline real time classification application pipeline using open source tools developed by the Nanopore community that does not depend on internet availability. Our application has been tested on ATCC’s 20 strain even mix whole cell (ATCC MSA-2002) sample. Using the Rapid Sequencing Kit (SQK-RAD004), we were able to identify all 20 organisms at species level. The analysis was performed in 15 min using a Dell Precision 7720 laptop. Our offline downstream bioinformatics application provides a cost-effective option as well as quick turn-around time when analyzing samples in the field, thus enabling researchers to fully utilize ONT’s MinION portability, ease-of-use, and identification capability in remote locations.

scholarly journals Increasing Access to Medical Training With Three-Dimensional Printing: Creation of an Endotracheal Intubation Model (Preprint)

2018 ◽  
Author(s):  
Lily Park ◽  
Steven Price-Williams ◽  
Alireza Jalali ◽  
Kashif Pirzada
Keyword(s):  
Open Source ◽  
Endotracheal Intubation ◽  
Medical Training ◽  
Three Dimensional ◽  
Simulation Models ◽  
Cost Effective ◽  
Ease Of Use ◽  
Life Saving ◽  
3D Printers ◽  
Simulation Center

BACKGROUND Endotracheal intubation (ETI) is a crucial life-saving procedure, where more than 2 failed attempts can lead to further complications or even death. Like all technical skills, ETI requires sufficient practice to perform adequately. Currently, the models used to practice ETI are expensive and, therefore, difficult to access, particularly in the developing world and in settings that lack a dedicated simulation center. OBJECTIVE This study aimed to improve access to ETI training by creating a comparable yet cost-effective simulation model producible by 3-dimensional (3D) printers. METHODS Open-source mesh files of relevant anatomy from BodyParts3D were modified through the 3D modeling programs Meshlab (ISTI-CNR) and Blender (Blender Foundation). Several prototypes with varying filaments were tried to optimize the ETI simulation. RESULTS We have created the novel 3D-printed pediatric ETI model for learners at all levels to practice this airway management skill at negligible costs compared with current simulation models. It is an open-source design available for all medical trainees. CONCLUSIONS Revolutions in cost and ease of use have allowed home and even desktop 3D printers to become widespread. Therefore, open-source access to the ETI model will improve accessibility to medical training in the hopes of optimizing patient care.

scholarly journals 3D Printed Imaging Platform for Portable Cell Counting

The Analyst ◽  
2021 ◽  
Author(s):  
Diwakar M. Awate ◽  
Cicero C. Pola ◽  
Erica Shumaker ◽  
Carmen L Gomes ◽  
Jaime Javier Juarez
Keyword(s):  
3D Printing ◽  
Point Of Care ◽  
Cost Effective ◽  
Cell Counting ◽  
Biomedical Sciences ◽  
Widespread Application ◽  
Resource Limited ◽  
Cost Effective Approach ◽  
3D Printed

Despite having widespread application in the biomedical sciences, flow cytometers have several limitations that prevent their application to point-of-care (POC) diagnostics in resource-limited environments. 3D printing provides a cost-effective approach...

Quantum Dots as Components of Electrochemical Sensing Platforms for the Detection of Environmental and Food Pollutants: a Review

2017 ◽  
Vol 100 (4) ◽  
pp. 950-961 ◽  
Author(s):  
María Pedrero ◽  
Susana Campuzano ◽  
José M Pingarrón
Keyword(s):  
Quantum Dots ◽  
Signal Amplification ◽  
Cost Effective ◽  
Ease Of Use ◽  
Electrochemical Sensing ◽  
Multiplexed Detection ◽  
Sensing Platforms ◽  
Target Analytes

Abstract The determination of organic and inorganic environmental and food pollutants is a key matter of concern in analytical chemistry due to their effects as a serious threat to human health. Focusing on this issue, several methodologies involving the use of nanostructured electrochemical platforms have been recently reported in the literature. Among these methods, those employing the use of quantum dots (QDs) stand out because of features such as signal amplification, good reproducibility and selectivity, and the possibility for multiplexed detection, and because they preserve the outstanding characteristics of electrochemical methodologies with respect to simplicity, ease-of-use, and cost-effective instrumentation. This review describes recent electrochemical strategies, in which design QDs play a key role, for the determination of pollutants in food and environmental samples. The particular role of QDs in the reported methodologies, their preparation, and the electrochemical platform design, as well as the advantages that QDs provide in the analysis of target analytes, are critically discussed.

scholarly journals Outcome of Acute Peritoneal Dialysis in Northern Tanzania

2012 ◽  
Vol 32 (3) ◽  
pp. 261-266 ◽  
Author(s):  
Kajiru Gad Kilonzo ◽  
Sudakshina Ghosh ◽  
Siya Anaeli Temu ◽  
Venance Maro ◽  
John Callegari ◽  
...  
Keyword(s):  
Peritoneal Dialysis ◽  
Patient Outcomes ◽  
Kidney Injury ◽  
Cost Effective ◽  
High Morbidity ◽  
Poor Countries ◽  
Resource Limited ◽  
Northern Tanzania ◽  
Nephrology Care ◽  
Technical Simplicity

Data on the burden of acute kidney injury (AKI) in resource-poor countries such as Tanzania are minimal because of a lack of nephrology services and an inability to recognize and diagnose AKI with any certainty. In the few published studies, high morbidity and mortality are reported. Improved nephrology care and dialysis may lower the mortality from AKI in these settings. Hemodialysis is expensive and technically challenging in resource-limited settings. The technical simplicity of peritoneal dialysis and the potential to reduce costs if consumables can be made locally, present an opportunity to establish cost-effective programs for managing AKI. Here, we document patient outcomes in a pilot peritoneal dialysis program established in 2009 at a referral hospital in Northern Tanzania.

Silver mirror reaction metallized chromatography paper for supercapacitor application

2021 ◽  
Author(s):  
I-Hsuan Chen ◽  
Jung-Hsien Chang ◽  
Ren-Jie Xie ◽  
Chia-Hui Tseng ◽  
Sheng-Rong Hsieh ◽  
...  
Keyword(s):  
Flexible Electronics ◽  
Photoelectron Spectroscopy ◽  
Cost Effective ◽  
Water Contact ◽  
X Ray ◽  
Supercapacitor Application ◽  
Resource Limited ◽  
Vis Spectroscopy ◽  
Silver Mirror ◽  
Silver Mirror Reaction

Abstract In this study, the easy-to-operate silver mirror reaction (SMR) was used for metallizing chromatography paper. The SMR-metallized paper was characterized by water contact angle measurements, a surface profiler, X-ray photoelectron spectroscopy, UV-vis spectroscopy, X-ray diffraction, and electrical resistance measurement. The characterization results show that Ag was successfully synthesized on cellulose fibers and was electrically conductive after cyclic bending. Moreover, this SMR-metallized paper was used as electrodes for fabricating a supercapacitor. This SMR-metallized paper could be used for realizing cost-effective flexible electronics applied in on-site biochemical sensing in resource-limited settings.

scholarly journals High resolution copy number inference in cancer using short-molecule nanopore sequencing

2020 ◽  
Author(s):  
Timour Baslan ◽  
Sam Kovaka ◽  
Fritz J. Sedlazeck ◽  
Yanming Zhang ◽  
Robert Wappel ◽  
...  
Keyword(s):  
Copy Number ◽  
Cost Effective ◽  
Chromosome Analysis ◽  
Ease Of Use ◽  
Precision Oncology ◽  
Nanopore Sequencing ◽  
Dna Molecules ◽  
Sequencing Data ◽  
Short Read ◽  
Short Read Sequencing

ABSTRACTGenome copy number is an important source of genetic variation in health and disease. In cancer, clinically actionable Copy Number Alterations (CNAs) can be inferred from short-read sequencing data, enabling genomics-based precision oncology. Emerging Nanopore sequencing technologies offer the potential for broader clinical utility, for example in smaller hospitals, due to lower instrument cost, higher portability, and ease of use. Nonetheless, Nanopore sequencing devices are limited in terms of the number of retrievable sequencing reads/molecules compared to short-read sequencing platforms. This represents a challenge for applications that require high read counts such as CNA inference. To address this limitation, we targeted the sequencing of short-length DNA molecules loaded at optimized concentration in an effort to increase sequence read/molecule yield from a single nanopore run. We show that sequencing short DNA molecules reproducibly returns high read counts and allows high quality CNA inference. We demonstrate the clinical relevance of this approach by accurately inferring CNAs in acute myeloid leukemia samples. The data shows that, compared to traditional approaches such as chromosome analysis/cytogenetics, short molecule nanopore sequencing returns more sensitive, accurate copy number information in a cost effective and expeditious manner, including for multiplex samples. Our results provide a framework for the sequencing of relatively short DNA molecules on nanopore devices with applications in research and medicine, that include but are not limited to, CNAs.

scholarly journals ABP para la enseñanza y desarrollo de proyectos tecnológicos interdisciplinares en Arduino [BPL for education and development of interdisciplinary technology projects based in Arduino]

2015 ◽  
Author(s):  
Yair Enrique Rivera Julio ◽  
Luis Gabriel Turizo Martínez
Keyword(s):  
Open Source ◽  
Collaborative Work ◽  
Project Based Learning ◽  
Ease Of Use ◽  
Resource Center ◽  
Building Technology ◽  
Technology Products ◽  
The Social ◽  
Teaching Learning ◽  
Education And Development

El presente trabajo muestra los resultados preliminares del proceso de enseñanza-aprendizaje para la generación de proyectos tecnológicos a través de la metodología de Aprendizaje Basado en Problemas (ABP), cuya importancia radica en la formación integral de los estudiantes en las áreas de programación y robótica constituida por una serie de pasos necesarios para una interacción secuencial y significativa que se originan en una simulación de software con arquitecturas open source como centro de aprendizaje didáctico, junto a una lluvia de ideas condicionadas en el aula de clase, diseñada para facilitar el uso de la electrónica en proyectos que permite diseñar prototipos de hardware basados en Arduino antes de ser armados físicamente. Al utilizar la metodología de aprendizajes ABP en la construcción de productos tecnológicos, se toman problemas planteados dentro del contexto social aplicando la enseñanza a través de temas avanzados como la robótica y la programación en sistemas, además de conjugar muchos aspectos dentro del sistema pedagógico en los proyectos tecnológicos a implementar donde se amerita el trabajo colaborativo, que es asumido dentro de sus integrantes como una conjugación de aspectos como la responsabilidad y las decisiones grupales.Palabras Clave: ABP (Aprendizaje Basado en Problemas), Arduino, prototipo, programación robótica.This work shows preliminary results of the PBL methodology in the teaching-learning process for generating Technological Projects, the importance lies in the comprehensive training of students in the areas of robotics and programming consists of a number of steps required for sequential and meaningful interaction originating from a software simulation with open source architectures as a learning resource center, next to brainstorm conditional on the classroom, designed for ease of use electronics technology projects allows us to design hardware prototypes based on Arduino before being physically armed. By using this method of learning in building technology products, problems are taken within the social context applying teaching through advanced topics such as robotics and programming systems, and combine many aspect in the pedagogical system projects implement technology where collaborative work, which is assumed within its members as a combination of aspects such as responsibility and group decisions is warranted.Keywords: PBL (Project Based Learning), Arduino, Prototype, Robotics programming.

scholarly journals HiSpike Method for High-Throughput Cost Effective Sequencing of the SARS-CoV-2 Spike Gene

2022 ◽  
Vol 8 ◽  
Author(s):  
Ephraim Fass ◽  
Gal Zizelski Valenci ◽  
Mor Rubinstein ◽  
Paul J. Freidlin ◽  
Shira Rosencwaig ◽  
...  
Keyword(s):  
Real Time ◽  
High Throughput ◽  
Cost Effective ◽  
Developed Countries ◽  
Spike Protein ◽  
Medical Community ◽  
Effective Vaccine ◽  
Gene Variants ◽  
Spike Gene ◽  
Field Samples

The changing nature of the SARS-CoV-2 pandemic poses unprecedented challenges to the world's health systems. Emerging spike gene variants jeopardize global efforts to produce immunity and reduce morbidity and mortality. These challenges require effective real-time genomic surveillance solutions that the medical community can quickly adopt. The SARS-CoV-2 spike protein mediates host receptor recognition and entry into the cell and is susceptible to generation of variants with increased transmissibility and pathogenicity. The spike protein is the primary target of neutralizing antibodies in COVID-19 patients and the most common antigen for induction of effective vaccine immunity. Tight monitoring of spike protein gene variants is key to mitigating COVID-19 spread and generation of vaccine escape mutants. Currently, SARS-CoV-2 sequencing methods are labor intensive and expensive. When sequence demands are high sequencing resources are quickly exhausted. Consequently, most SARS-CoV-2 strains are sequenced in only a few developed countries and rarely in developing regions. This poses the risk that undetected, dangerous variants will emerge. In this work, we present HiSpike, a method for high-throughput cost effective targeted next generation sequencing of the spike gene. This simple three-step method can be completed in < 30 h, can sequence 10-fold more samples compared to conventional methods and at a fraction of their cost. HiSpike has been validated in Israel, and has identified multiple spike variants from real-time field samples including Alpha, Beta, Delta and the emerging Omicron variants. HiSpike provides affordable sequencing options to help laboratories conserve resources for widespread high-throughput, near real-time monitoring of spike gene variants.

scholarly journals Comparative evaluation of cost effective extraction free molecular technique for detection of SARS-CoV-2 with reference to standard VTM based RT-qPCR method

2021 ◽  
Author(s):  
Megh Singh Dhakad ◽  
Sanjib Gogoi ◽  
Ansu Kumari ◽  
Aashish Kumar Singh ◽  
Manoj B. Jais ◽  
...  
Keyword(s):  
Detection Method ◽  
Cost Effective ◽  
Molecular Technique ◽  
Rt Pcr ◽  
Index Method ◽  
Resource Limited ◽  
Qpcr Method ◽  
Kappa Value ◽  
The Cost ◽  
Higher Sensitivity

Background and Objectives: The entire globe is undergoing an unprecedented challenge of COVID-19. Considering the need of rapid and accurate diagnostic tests for SARS-CoV-2, this study was planned to evaluate the cost effective extraction free RT-PCR technique in comparison to the standard VTM based RT-qPCR method. Materials and Methods: Paired swabs from nasopharynx and oropharynx were collected for SARS-CoV-2 testing, from 211 adult patients (≥18 years) in VTM and plain sterile tubes (dry swabs). These samples were processed and RT-qPCR was carried out as per standard protocols. Results: 54.5% of the patients were females and 45.5% were males with sex ratio 1:1.19 (M: F). 38.86% were symptomatic, of which fever (86.59%), cough (79.23%) and breathlessness (46.34%) were the most common symptoms. The positivity by VTM based method and index method was 31.27% and 13.27% respectively. Of the 27 inconclusive results from index method, 37.04% were positive, 48.15% were negative by VTM based method. However, in 40 inconclusive results by VTM based method, 90% were negative and rest remained inconclusive by index method. The sensitivity and specificity of the index method were 39.39% and 85.71% respectively. The overall agreement between VTM based method and index method was 49.59% with estimated Kappa value of 0.19. Conclusion: VTM based method showed higher sensitivity compared to the index method. The higher positivity by VTM based method, suggests that VTM based method could plausibly be a better detection method of SARS-CoV-2. Still, the index method might add value in a resource limited setups for detection of SARS-CoV-2.  

Building back smarter—part three: placing modular facilities in a resource-limited healthcare system

2021 ◽  
Vol 27 (12) ◽  
pp. 1-10
Author(s):  
Isobel Clough
Keyword(s):  
Healthcare System ◽  
Effective Means ◽  
Cost Effective ◽  
Public Institution ◽  
Healthcare Staff ◽  
Current State ◽  
Resource Limited ◽  
Potential Benefits ◽  
The Uk ◽  
Physical Spaces

Land should be one of the greatest assets of the UK healthcare system, as a result of its large estates portfolio. Howere, the current state of many of the NHS's buildings means that physical spaces are often more of a burden, with maintenance backlogs costing billions. However, as a resource-limited public institution, it is crucial that all investments into NHS infrastructure are as effective and future-proof as possible. The previous two articles in this series have focused on the potential benefits of modular facilities to healthcare staff, services and patients, drawing on case studies of NHS trusts that have implemented modular facilities on their sites. This article, the third and final instalment of this series, discusses the health economic impact of current NHS infrastructure, and explores the ways in which modular facilities could provide a flexible and cost-effective means of expanding capacity and improving services in a resource-limited environment.

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