Development of a programmable Loop mediated isothermal amplification (LAMP) reader for biomedical applications – MRes Scholarship

 

Development of a programmable Loop mediated isothermal amplification (LAMP) reader for biomedical applications.

Faculty of Computing, Engineering and Science at the University of South Wales

Project ID: 22525
Annual Stipend: £11.8k p.a
Application Deadline: midnight Thursday 16th June 2022

MbyRes wedi’i gyllido yw hwn, sy’n cynnwys cyflog hael a ffioedd dysgu, gydag amgylchiadau sydd â digon o adnoddau ar gyfer ysgoloriaeth lwyddiannus. This is a funded MbyRes, including a generous stipend and tuition fees, with well-resourced circumstances for a successful scholarship.

Here is an exciting opportunity to carry out research and development in biomedical electronics which could lead to entirely new approaches in molecular diagnostics.

The selected candidate will apply their programming and embedded systems skills and ambition to design and release a real application product that would make molecular diagnostics faster and more affordable  . This project will allow the student to develop transferable knowledge and skills in this most exciting and active field of biotechnology.

This Knowledge Economy Skills Scholarship (KESS) project will be held in the Faculty of Computing, Engineering and Science at the University of South Wales.  KESS is a programme funded by the European Social Fund (ESF) awarded by the Welsh European Funding Office (WEFO) in the Welsh Government.

The project is backed by Llusern Scientific Ltd, a Welsh biotech new start-up, that has developed a molecular testing platform technology that is based on the “Loop mediated isothermal amplification” (LAMP) of nucleic acids, with the aim of making molecular diagnostic rapid and affordable worldwide.

Programme of research:

To carry out the day to day tasks of this project.  An MbyRes student with background in embedded electronic systems design will be recruited after an open competitive process. The direct supervision of the student will be carried out by Dr Ali Roula who has expertise in signal processing and embedded systems design. Dr Nieuwland will assist with requirement specification and supplying LAMP samples for experimentation and validation. The work in the project will be subdivided into 4 phases of 3 months each:

Phase 1: Background research and requirement specification: During this phase, the student will undertake the required literature survey on LAMP detection and its challenges and limitations. The student will also work closely with LLusern Scientific to understand the operation of the existing LAMP system and in particular, develop an intimate understanding of the firmware code.

Phase 2: Firmware redesign for programmableLAMP:  The student will use the existing code version for LodeStar Dx to first design a more sophisticated heating control algorithm to replace the existing simple differential fix temperature control algorithm. This will require investigating various control system approaches including PID control and Fuzzy Logic Control technique. Then the next step would be to investigate and design suitable digital signal processing pre-processing algorithm for photo-detection to ensure optimal signal to noise ratio and maximum dynamic range and signal sensitivity for a range of LAMP reactions.

Phase 3: Data collection and validation:  After the firmware has been modified to show that the proof-of concept updated machine can operate reliably for variable temperature ranges and reaction times, the next step would be to test and fine-tune the performance on a selected number of reagents targets, namely 1- Urinary Track Infections (UTI),  2- Respiratory Syncitial Virus (RSV) and  3- EColi. Once variable reaction profiles could be generated, statistically significant learning data set can then be produced with both positive and negative reactions. With such training data available, the student’s last task will be to develop a detection algorithm using machine learning techniques to minimise false negatives. Various approaches will be investigated including Quadratic Discriminant Function, Support Vector Machines (SVM) and Machine Learning approaches such as Artificial Neural Networks or Deep belief Networks.

Phase 4: Thesis Write-up and output publication:  As a consolidation of the outcomes of the project and if time allows, the student will work to fully characterise the system and gauge the trade-off between sensitivity vs specificity, the algorithm parameters will be varied and fine-tuned, to obtain ROC curves and compare the new system performance to conventional (slow) gold standards PCR.  Findings from the project will be disseminated to suitable journals such as IEEE Transaction in Biomedical Engineering. Sufficient time will be allocated exclusively for the final thesis will be written up viva preparation.

Ysgoloriaeth ymchwil:

Bydd yr ysgoloriaeth ymchwil yn cynnwys ffioedd ar gyfer rhaglen MbyRes llawn-amser am flwyddyn ac yn talu cyflog o oddeutu £11.8k y flwyddyn. Mae hefyd tua £3k o gostau cymorth ar gael i’r prosiect ar gyfer treuliau, teithio, mân offer, hyfforddiant (gan gynnwys Ysgol Raddedig KESS) a mynychu cynadleddau.

Mae’r swydd ar gael o Gorffennaf 2022.

Studentship:

The studentship will cover the fees for a full-time MbyRes programme and pay a stipend of circa £11.8k p.a. There is also around £3k project support costs available for consumables, travel, minor equipment, training (including the KESS Grad School) and conference attendance.

The position is available from July 2022

Cymhwyster Myfyrwyr:

I fod yn gymwys i gael ysgoloriaeth ymchwil KESS, mae’n rhaid:

· cael cyfeiriad cartref yn yr ardal Dwyrain Cymru (manylion isod)* ar adeg cofrestru.

· bod gennych hawl i ymgymryd â gwaith cyflogedig yn yr ardal Dwyrain Cymru* ar ôl cwblhau’r ysgoloriaeth.

· bod y Brifysgol yn eich ystyried yn fyfyriwr ‘cartref’ neu ‘UE’ at ddibenion ffioedd dysgu yn unol â chanllawiau’r Brifysgol.

· eich bod yn bodloni meini prawf mynediad Prifysgol De Cymru: gweler isod, cymwysterau a phrofiad a’r broses ymgeisio

*Dwyrain Cymru ardal yn cwmpasu:  Bro Morgannwg / Caerdydd / Casnewydd/ Sir Fynwy/ Powys/ Wrecsam/ Sir Y Fflint

Eligibility of Student:

To be eligible to hold a KESS studentship, you must:

· have a home address in East Wales area (details below)* at the time of registration.

· have the right to take up paid work in the East Wales area* on completion of the scholarship.

· be classified by the University as ‘home’ or ‘EU’ for tuition fees purposes according to the University’s guidelines.

· satisfy University of South Wales’s admissions criteria: see below, qualifications and experience and application process

*East Wales area covers:  Vale of Glamorgan / Cardiff/ Newport/ Monmouthshire/ Powys/ Wrexham/ Flintshire

 

Cymwysterau a phrofiad:

Bydd ymgeiswyr cymwys yn:

1) Meddu ar radd (2i neu uwch) mewn Peirianneg Electroneg neu faes cysylltiedig.

2) Meddu ar ddealltwriaeth resymol o systemau a dyluniad wedi’u Hymgorffori gyda RTOS.

3) Hunanysgogol iawn, gyda’r gallu i ddysgu a datblygu sgiliau a thechnegau newydd.

4) Meddu ar sgiliau rhyngbersonol datblygedig a chydweithredol gadarnhaol. 

5) Meddu ar y gallu i gyflwyno adroddiadau technegol a chyfleu canfyddiadau.

6) Bod yn barod i deithio a gweithio mewn lleoliadau cymorth diwydiannol/clinigol/cymunedol.

Qualifications and experience:

Eligible applicants will:

1) Have a degree (2i or higher) in Electronics Engineering or related field

2) Possess a reasonable understanding of Embedded systems and design with RTOS

3) Be highly self-motivated, with capacity to learn and develop new skills and techniques

4) Have well-developed and positively collaborative interpersonal skills

5) Have an ability to deliver technical reports and communicate findings

6) Be willing to travel and work in industrial / clinical / community support settings

 

Y Broses Ymgeisio:

I lawrlwytho’r pecyn ymgeisio, ewch i:  Pecyn Ymgeisio Cyfranogwr

Am unrhyw ymholiadau ynghylch cymhwysedd, cysylltwch â:  Tîm KESS, Gwasanaethau Ymchwil ac Arloesedd, Prifysgol De Cymru: kess@decymru.ac.uk Ffôn: 01443 482578

Ar gyfer ymholiadau anffurfiol neu ragor o wybodaeth am y rhaglen, cysylltwch â: Dr Ali Roula (Ali.Roula@southwales.ac.uk ).

Mae tudalen staff Dr Roula i’w gweld yma:

https://pure.southwales.ac.uk/en/persons/ali-roula(5003f2a1-4896-4616-aa7b-24cba289fbe0).html

Application Process:

To download an application package, please visit:  Participant Application Package

For any queries on eligibility, please contact:  KESS Team at Research and Innovation Services, University of South Wales: kess@southwales.ac.uk  Tel: 01443 482578

For informal enquiries or further programme information, please contact: Dr Ali Roula (Ali.Roula@southwales.ac.uk).

Dr Roula staff page can be found here:

https://pure.southwales.ac.uk/en/persons/ali-roula(5003f2a1-4896-4616-aa7b-24cba289fbe0).html

Dyddiad cau ar gyfer ceisiadau: hanner nos dydd Iau 16 Mehefin 2022

Cyfweliadau i’w gadarnhau

Closing date for applications: midnight Thursday 16th June 2022

Interviews TBC

Mae Ysgoloriaethau Sgiliau Economi Gwybodaeth (KESS) yn fenter sgiliau lefel uwch ar draws Cymru a arweinir gan Brifysgol Bangor ar ran y sector AU yng Nghymru. Fe’i cyllidir yn rhannol gan raglen Cronfa Gymdeithasol Ewropeaidd (ESF) Llywodraeth Cymru ar gyfer Dwyrain Cymru. Knowledge Economy Skills Scholarships (KESS) is a pan-Wales higher-level skills initiative led by Bangor University on behalf of the HE sector in Wales. It is part funded by the Welsh Government’s European Social Fund (ESF) programme for East Wales.

*USW reserves the right to close the vacancy if sufficient applications are received before the deadline/Mae PDC yn cadw’r hawl i gau’r swydd os derbynnir nifer digonol o geisiadau cyn y dyddiad cau