An Intelligent Pill

carlazzopardi
Doctors regularly need to use endoscopes to take a peek inside patients and see what is wrong. Their current tools are pretty uncomfortable. Biomedical engineer Ing. Carl Azzopardi writes about a new technology that would involve just swallowing a capsule.

Michael* lay anxiously in his bed, looking up at his hospital room ceiling. ‘Any minute now’, he thought, as he nervously awaited his parents and doctor to return. Michael had been suffering from abdominal pain and cramps for quite some time. The doctors could not figure it out through simple examinations. He could not take it any more. His parents had taken him to a gut specialist, a gastroenterologist, who after asking a few questions, had simply suggested an ‘endoscopy’ to examine what is wrong. Being new to this, Michael had immediately gone home to look it up. The search results did not thrill him.

The word ‘endoscope’ derives from the Greek words ‘endo’, inside, and ‘scope’, to view. Simply put, looking inside  our body using instruments called endoscopes. In 1804, Phillip Bozzini created the first such device. The Lichtleiter, or light conductor, used hollow tubes to reflect light from a candle (or sunlight) onto bodily openings — rudimentary.

Modern endoscopes are light years ahead. Constructed out of sleek, black polyurethane elastometers, they are made up of a flexible ‘tube’ with a camera at the tip. The tubes are flexible to let them wind through our internal piping, optical fibers shine light inside our bodies, and since the instrument is hollow it allows forceps or other instruments to work during the procedure. Two of the more common types of flexible endoscopes used nowadays are called gastroscopes and colonoscopes. These are used to examine your stomach and colon. As expected, they are inserted through your mouth or rectum.

Michael was not comforted by such advancements. He was not enticed by the idea of having a flexible tube passed through his mouth or colon. The door suddenly opened. Michael jerked his head towards the entrance to see his smiling parents enter. Accompanying them was his doctor holding a small capsule. As he handed it over to Michael, he explained what he was about to give him.

Enter capsule endoscopy. Invented in 2000 by an Israeli company, the procedure is simple. The patient just needs to swallow a small capsule. That is it. The patient can go home, the capsule does all the work automatically.

The capsule is equipped with a miniature camera, a battery, and some LEDs. It starts to travel through the patient’s gut. While on its journey it snaps around four to thirty-five images every second. Then it transmits these wirelessly to a receiver strapped around the patient’s waist. Eventually the patient passes out the capsule and on his or her next visit to the hospital, the doctor can download all the images saved on the receiver.

The capsule sounds like simplicity itself. No black tubes going down patients’ internal organs, no anxiety. Unfortunately, the capsule is not perfect.

“The patient just needs to swallow a small capsule. That is it. The patient can go home, the capsule does all the work automatically”

Autumn 2013 Magazine Master.inddFirst of all, capsule endoscopy cannot replace flexible endoscopes. The doctors can only use the capsules to diagnose a patient. They can see the pictures and figure out what is wrong, but the capsule has no forceps that allow samples to be taken for analysis in a lab. Flexible endoscopes can also have cauterising probes passed through their hollow channels, which can use heat to burn off dangerous growths. The capsule has no such means. The above features make gastroscopies and colonoscopies the ‘gold standard’ for examining the gut. One glaring limitation remains: flexible endoscopes cannot reach the small intestine, which lies squarely in the middle between the stomach and colon. Capsule endoscopy can examine this part of the digestive tract.

A second issue with capsules is that they cannot be driven around. Capsules have no motors. They tend to go along for the ride with your own bodily movements. The capsule could be pointing in the wrong direction and miss a cancerous growth. So, the next generation of capsules are equipped with two cameras. This minimises the problem but does not solve it completely.

The physical size of the pill makes these limitations hard to overcome. Engineers are finding it tricky to include mechanisms for sampling, treatment, or motion control. On the other hand, solutions to a third problem do exist. This difficulty relates to too much information. The capsule captures around 432,000 images over the 8 hours it snaps away. The doctor then needs to go through nearly all of these images to spot the problematic few. A daunting task that uses up a lot of time, increasing costs, and makes it easier to miss signs of disease.

A smart solution lies in looking at image content. Not all images are useful. A large majority are snapshots of the stomach uselessly churning away, or else of the colon, far down from the site of interest. Doctors usually use capsule endoscopy to check out the small intestine. Medical imaging techniques come in handy at this point to distinguish between the different organs. Over the last year, the Centre for Biomedical Cybernetics (University of Malta) has carried out collaborative research with Cardiff University and Saint James Hospital to develop software which gives doctors just what they need.

Following some discussions between these clinicians and engineers they quickly realised that images of the stomach and large intestine were mostly useless for capsule endoscopes.

Identifying the boundaries of the small intestines and extracting just these images would simplify and speed up screening. The doctor would just look at these images, discarding the rest.

Engineers Carl Azzopardi, Kenneth Camilleri, and Yulia Hicks developed a computer algorithm that could first and foremost tell the difference between digestive organs. An algorithm is a bit of code that performs a specific task, like calculating employees’ paychecks. In this case, the custom program developed uses image-processing techniques to examine certain features of each image, such as colour and texture, and then uses these to determine which organ the capsule is in.

Take colours for instance. The stomach has a largely pinkish hue, the small intestine leans towards yellowish tones, while the colon (unsurprisingly perhaps) changes into a murky green. Such differences can be used to classify the different organs. Additionally, to quickly sort through thousands of images, the images need to be compacted. A specific histogram is used to amplify differences in colour and compress the information. These procedures make it easier and quicker for algorithm image processing.

Texture is another unique organ quality. The small intestine is covered with small finger-like projections called villi. The projections increase the surface area of the organ, improving nutrient absorption into the blood stream. These villi give a particular ‘velvet-like’ texture to the images, and this texture can be singled out using a technique called Local Binary Patterns. This works by comparing each pixel’s intensity to its neighbours’, to determine whether these are larger or smaller in value than its own. For each pixel, a final number is then worked out which gauges whether an edge is present or not (see image).

Classification is the last and most important step in the whole process. At this point the software needs to decide if an image is part of the stomach, small intestine, or large intestine. To help automatically identify images, the program is trained to link the factors described above with the different organ types by being shown a small subset of images. This data is known as the training set. Once trained, the software can then automatically classify new images from different patients on its own. The software developed by the biomedical engineers was tested first by classification based just on colours or texture, then testing both features together. Factoring both in gave the best results.

“The software is still at the research stage. That research needs to be turned into a software package for a hospital’s day-to-day examinations” 

Dr Yulia Hicks
Dr Yulia Hicks
Prof. Ing. Kenneth Camilleri
Prof. Ing. Kenneth Camilleri

After the images have been labeled, the algorithm can draw the boundaries between digestive organs. With the boundaries in place, the specialist can focus on the small intestine. At the press of a button countless hours and cash are saved.

 

The software is still at the research stage. That research needs to eventually be turned into a software package for a hospital’s day-to-day examinations. In the future, the algorithm could possibly be inserted directly onto the capsule. An intelligent capsule would be born creating a recording process capable of adapting to the needs of the doctor. It would show them just what they want to see.

Ideally the doctor would have it even easier with the software highlighting diseased areas automatically. The researchers at the University of Malta want to start automatically detecting abnormal conditions and pathologies within the digestive tract. For the specialist, it cannot get better than this.

The result? A shorter and more efficient screening process that could turn capsule endoscopy into an easily accessible and routine examination. Shorter specialist screening times would bring down costs in the private sector and lessen the burden on public health systems. Michael would not need to worry any longer; he’d just pop a pill.

* Michael is a fictitious character

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The author thanks Prof. Thomas Attard and Joe Garzia. The research work is funded by the Strategic Educational Pathways Scholarship (Malta). The scholarship is part-financed by the European Union — European Social Fund (ESF) under Operational Programme II — Cohesion Policy  2007–2013, ‘Empowering People for More Jobs and a Better Quality of Life’

Insects in Malta

Insects are vital. Insects also cover the planet, with local research showing that there might be over 6,000 species — a wonderful world awaits. Find out about the incredible world of insects in Malta!

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Choices, Choices, Choices…

Taking the right decision can be a very challenging and daunting process. Designing a mobile phone, a makeup case, or even a pipe needs engineering teams to continuously make important choices quickly. Lawrence Farrugia (supervised by Prof. Jonathan C. Borg) developed a framework that helps engineers evaluate concepts and take these decisions practically. In a typical design process, the design team generates a number of different concepts that fulfil what is needed from the product. These design concepts are then evaluated against conflicting evaluation criteria. Criteria are chosen from the life cycle of the product and can include cost, quality, ease of use, and recyclability (pictured). Evaluation determines the concept chosen for further development.
Sketch

Although there are design tools that are intended to support engineering design teams in decision making, the reality check is that these tools are rarely used. Such tools are typically too impractical to employ in the real world. Due to the ever increasing complexity of products and the importance of early decision making, this research recognised the need to provide engineering design teams with a practical yet reliable support system.
Farrugia’s research was carried out at the Concurrent Engineering Research Unit (CERU) within the Faculty of Engineering. The framework he developed aids design teams to analyse and rank multiple design concepts against several conflicting evaluation criteria. The proposed framework was then implemented into a prototype computer aided design (CAD) tool named ACADEMI (pictured).

Figure 2

The tool developed by Farrugia allows for design concepts to be mathematically appraised and ranked automatically. The user inputs the various evaluation criteria and the best design is shown in a very short time. This ranking helps the design team rapidly figure out which design concepts should be developed. After the framework and tool were developed the research work was evaluated in the field by engineers from industry and academia. Most industry personnel said that they would be willing to adopt the computer tool in their daily professional work. ï

More information about the research work may be accessed through: www.academi.co.nr

This research was performed as part of an M.Sc. (Research) in Mechanical Engineering at the Faculty of Engineering. This research was partially funded by the Strategic Educational Pathways Scholarship (Malta). This Scholarship is part-financed by the European Union — European Social Fund (ESF) under Operational Programme II — Cohesion Policy 2007–2013, ‘Empowering People for More Jobs and a Better Quality Of Life’.

Keeping heart attacks on hold

Heart attacks and strokes kill millions every year. Most are caused by blockages to blood vessels. Vessels can be pried open by heart stents, tubular devices that are inserted and inflated to prevent vessels from collapsing or blocking. Stents incur many problems ranging from flaring at the edges to fracturing to unexpected shrinking. All lead to complications, further surgery, and even death.

Luke Mizzi (supervised by Prof. Joseph N. Grima, Dr Daphne Attard, and Dr Ruben Gatt) has studied existing stent designs to identify their weaknesses and is currently studying novel designs that overcome these problems. He used computer simulations to replicate the stresses current stents experience in the human body. These stents performed well in response to inflation and bending. However, shortening still occurs and they do not expand uniformly leading to flaring at the edges.

Mizzi found which current designs fared well but no design had all the features needed by heart stents. Crowns with a zigzagging structure allow for high expandability while S-shaped connections between crowns allow for high flexibility.

Mizzi who forms part of the Metamaterials Unit is designing new stent geometries that build on these features incorporating them all and improving stent performance. The next step for these researchers are designs that support part of the throat or oesophagus to continue saving lives.

 

This research was performed as part of Doctoral Studies at the Faculty of Science at the University of Malta. It is funded by the Malta Council for Science and Technology through its R&I programme. This project is in collaboration between the University of Malta, HM RD Ltd, part of the HalMann Vella Group of Companies, and Tek-Moulds Precision Engineering Limited.

Healthier Fitter Happier through Economics

Dr Edward Duca

People do not always act rationally. They overeat, overspend, and find it difficult to plan for the future. THINK met Prof. Liam Delaney to talk about how a new branch of economics might solve the pension crises, the obesity epidemic, the financial situation, help science, and make us feel better. Words by Edward Duca

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The future is bright, The future is research

Mario Cachia

Today’s world is unforgiving; we cannot slack. Be it students in academic pursuits, or executives in professional ones, the need to create new things and innovate is essential to keep up with ever-changing times. The RIDT believes that University and its students are the cradle of all needed change. Our aim is to continue promoting and stimulating research within our Campus community. We believe that our students carry this important message best.

For this reason, the RIDT has embarked on campaigns and initiatives to gather more interest and feedback from University students and alumni. The RIDT participated in the annual KSU Freshers’ Week. Here we met and greeted thousands of students just starting out their degrees. At the same time, we launched our Facebook page to regularly update and engage with students. We succeeded in attracting nearly 1,000 followers in less than two months from launch. We felt that this was not enough, and in order to further engage our online audience, we enticed them to become closer to University research. With this in mind, we launched a fresh online competition, the UoM Research Challenge, where participants had to answer questions about research happening at University. The competition was sponsored by GO, who donated an iPad Mini for the fastest person to complete the challenge. We have plenty of fresh, innovative concepts lined up for the New Year.

Throughout December, the RIDT is collaborating with KSU and l-Istrina to promote research within the University and the local community. We want to reach out to raise awareness that research is a tool that can make everyone’s lives better. Many people throughout the world suffer from various socio-economic problems, ranging from deadly diseases and famine to poverty and unemployment. Through research, we can truly make a difference to all of these people, and we want to start here, from home.  By fostering a sense of awareness and belonging within our students and alumni, we can look forward to a bright future. In this future, we would be proud of a University making a difference in Malta and the rest of the world.

RIDT is the University’s Research Trust aimed towards fostering awareness and fundraising for high-calibre local research. For more information, visit
www.ridt.eu or find RIDT on Facebook www.facebook.com/RIDTMalta

Christopher Curmi, winner of the UoM Research Challenge, awarded an iPad Mini by the RIDT CEO Wilfred Kenely. Photo by Edward Duca

Author: Mario Cachia, RIDT Campaign Officer

 

Can jetties replace rocky shores?

Leanne Bonnici
Leanne Bonnici

The marine environment needs to be conserved because all enjoy it in summer for leisure and fishermen depend on it for their livelihood. Our rocky shores also hold a unique ecology and it must be studied as a whole to understand how a seemingly insignificant crab or limpet can affect other species we might consider more important.

Our natural environment can be likened to a puzzle having thousands of pieces. If one piece is removed or changed, it will result in a different or incomplete picture. Jetties are artificial structures, in an otherwise natural matrix of rocky shore habitat, which add a new piece to the puzzle. They are built at right angles to the shore and are much smoother than natural rock. These differences are expected to change the environment and species living there. Leanne Bonnici (supervised by Dr Joseph A. Borg and Prof. Patrick J. Schembri) studied these jetties to understand how they would affect the big picture.

Bonnici studied three sites on the northeastern coast of the Maltese Islands (Little Armier, White Tower Bay and Għajn Żejtuna). The organisms on jetties in these areas were sampled from the mediolittoral zone — that part of the shore that is regularly submerged and exposed to the air. Sampling showed that the most abundant algae were low-growing green algae (Cladophoropsis sp.), and a red alga (Jania rubens). The algae serve as a source of food and shelter to other species.

IMG_6874

The most common animals were crustaceans, molluscs, and polychaetes. Polychaetes are worms that possess lots of hair-like structures (chaetae). The most common polychaetes were small voracious predators a few millimetres in length. The diverse crustaceans included small cone shaped barnacles (Chthamalus spp.), which spend most of their life attached to rocks. Other abundant crustaceans included minute shrimp-like swimming animals known as amphipods (Hyale sp. and Ampithoe sp.) that are typically found amidst algae. The molluscs recorded included different species of limpets Patella spp., as well as the chiton Acanthochitona sp.; all of these are usually found attached to the substratum, although they do move to graze on algae.

Bonnici found that jetties share some species with rocky shores; however, jetties always had a lower diversity and fewer numbers of individuals living on them. Therefore one can conclude that jetties cannot replace natural rocky shores.

Keeping to the puzzle analogy, if we know how modifying a ‘piece’ of the environment changes the other pieces, it will help maintain the whole picture. This study will help better manage how jetties affect organisms and make the most out of these artificial structures.

 

This research is part of an M.Sc. in Biology at the Faculty of Science. It was partly funded by the Strategic Educational Pathways Scholarship (Malta), which is part-financed by the European Union – European Social Fund (ESF) under Operational Programme II – Cohesion Policy 2007-2013, “Empowering People for More Jobs and a Better Quality Of Life”.

It’s all in the family

AlexandraFiott

Whatever you inherit comes from your biological family. Unfortunately, this includes disease. Talking about inherited conditions can make people anxious, making them unwilling to discuss the issue with their relatives. After speaking to a number of people my impression is that it seems taboo to discuss these things. People seem to feel that they will be stigmatised or treated differently because of a genetic condition.

A fear of social stigma hinders beneficial research. Research needs the collaboration of patients, since by investigating their condition researchers can in the long run develop a treatment or therapy. Not only that, but avoiding certain discussions means that relatives who might be at risk of developing the same problem would not be aware of it. If a condition is detected too late there might be very little that can be done.

It is very useful to discuss these matters with your family and speak to your doctor together. By building a medical family tree you can easily see who might inherit what. This way, your relatives will learn more about their health and then seek treatment. For example, a cousin might learn that she has an increased risk of breast cancer and would therefore attend screening sessions to catch the cancer before it spreads. Not knowing that something is there does not make it go away but discussing medical matters with your family could save a relative’s life.

“It is very useful to discuss these matters with your family and speak to your doctor together”

Scientific studies need family medical information. Scientific studies using family trees have already shown how useful this information is in identifying families with a high risk for inheritable cancers, like colon and breast cancer. Other research showed that families can benefit from preventative treatments against cardiovascular diseases like diabetes.

Local research has recently used this technique to find new genes, knowledge that can be developed for new treatments. The researchers were studying the genetic background of the protein which carries oxygen in our blood, haemoglobin. This protein switches from foetal haemoglobin to adult haemoglobin 3–6 months after birth. People with thalassemia have a problem with the adult version. Therefore, by studying local families that naturally cope well with the disease, they discovered the KLF1 gene that compensates for the malfunctioning adult protein by raising foetal haemoglobin levels. This was only possible with the help of family trees.

Speaking to a doctor to prepare a medical family tree (pictured) is done in the strictest confidentiality. You may also create your family medical history on https://familyhistory.hhs.gov/fhh-web/home.action to discuss with your family and doctor. I believe that it is in our best interest, apart from being potentially beneficial to the rest of humankind, to help in the creation of our own family medical trees.

If you have any queries when your physician or consultant asks you to prepare a family tree feel free to discuss them rather than avoiding family trees.

Should Malta Be The Next China?

JonathanCBorgAfter repeatedly visiting Asia, I totally disagree with comments occasionally made that China’s industrial success is wholly attributed to its ability to replicate low quality versions of branded products at rock-bottom prices. In China there are many good examples of good quality products and brands being produced such as Audi, Airbus, and Armani. Based on these facts, what Maltese industry and policy makers should focus on is making our industry more competitive by improving the current situation and analyzing products being developed elsewhere.

The Maltese industry is not really dying. Our industry has indeed changed, for example from textiles to pharmaceuticals. Overall, the number of employees has declined. However, this is either due to industry becoming more efficient hence able to produce more with less, or due to the way statistical data is being collected.

Malta’s industrial sector can become more competitive. However, what does it mean to ‘be competitive’? Goods should be produced with shorter delivery periods, better costs and quality compared to competitors. Since we lack raw materials cost is very challenging to compete on. On the other hand, improving quality provides much more opportunity. Quality can be improved by increasing the external quality of the products manufactured, the product’s functionality, the interactions that take place with clients during product development, the quality of support and after sales services, management of operations, and how operators work. Core to adopting this quality-based approach is the need to focus on shifting from just manufacturing products to designing and manufacturing products in Malta.

“Goods should be produced with shorter delivery periods, better costs, and quality compared to competitors”

To design their own products, Maltese manufacturing firms need to set up an internal Research & Development unit. At the same time, industry needs support through government policies and incentives. In their publication ‘Vision 2015’ American consultants clearly specify product design as an enabler to higher value added manufacturing. The Malta Chamber of Commerce, Enterprise & Industry has also recommended starting a Malta Business Research & Innovation Body. These recommendations need urgent implementation to shift Malta’s manufacturing industry towards becoming ‘design driven’.

The UoM’s Faculty of Engineering has been actively contributing towards a design driven approach. Our undergraduate engineers are purposely trained in this design-centric approach. Additionally, some final year student projects focusing on design are sponsored by industry: an excellent win-win mechanism. A number of both mechanical and electrical engineers have also benefited through an evening M.Sc. in Integrated Product Development. The Faculty also collaborates with industry through MCST funded Research & Innovation projects. More financial support to University would help every academic active in research to regularly receive decent research funds.

Considering the above, Malta does not and should not aim to be the next China. On the other hand, Malta should nurture its unique strengths such as a highly educated, flexible English-speaking workforce. We should aim to address weaknesses related to Malta’s manufacturing sector. This requires short-term and long-term commitments from our policy makers. Business leaders can also proactively embrace change by aiming to offer quality and innovative solutions, rather than aiming for higher production rates of existing products. The Maltese industry should support continuous training and collaborate on research activities with University. The UoM can help them become more innovative. Like Airbus, Armani, and Audi, Maltese business leaders should exploit, rather than fear, Asian industry. Some Malta based entities, such as Toly Products Ltd, are already going down these routes and are reaping the rewards of growth during a recession. Clearly others should aim to do the same to keep Malta competitive.

Incubator Helps Start-ups take off

BenMcClure

 

The old saying goes: it takes a village to raise a child. In other words, to get it right a community effort is needed, shared by family and friends who pass on their experience and knowledge to the youngster.

The same saying applies to building technology companies. Budding technology entrepreneurs in Malta need plenty of nurturing and guidance to get their innovations off the ground and into the marketplace. A supportive and well-connected entrepreneurial community is what is needed to transform Malta’s innovations into start-up ventures that will expand the economy.

The good news for Malta is that the basic components of a technology start-up community already exist. The University of Malta is a hothouse of world-class scientific, engineering, and creative research that holds the potential to spin out exciting commercial ventures. A new generation of bright, technically-skilled graduates is starting to pursue entrepreneurship as a career path. Malta lacks a professional venture capital investment industry, but does have high net worth entrepreneurs and private ‘angel’ investors. Many of these have valuable experience gained abroad and are hungry to find and fund high-potential technology companies. The government is exploring ways of encouraging early-stage investment by way of tax incentives and seed fund development. Ideas, entrepreneurial energy, and money — the key ingredients for raising technology start-ups — are all here on the island.

“Tucked away in their laboratories, garages, and workshops, Malta’s innovators are not networking”

So, what is holding us back? I recently spoke to Steve Blank, a highly successful Silicon Valley entrepreneur and investor. I asked him what he thought was missing. His reply: ‘much of the Valley’s alchemy lies in connectivity’.

Innovators, entrepreneurs, investors – Malta has got them all. Unfortunately, they are not finding each other. Tucked away in their laboratories, garages, and workshops, Malta’s innovators are not networking. They need skilled and experienced business people to push their technologies past the idea stage. Wealthy angel investors are here in Malta, but they frequently operate ‘under the radar’ and can be hard to access. In the absence of connections, both investors and innovators miss out on potentially rewarding opportunities. Promising young ventures, which might takeoff with a little support and funding, consequently get left to struggle on their own.

The University of Malta Business Incubator will start operations this year and create a platform for new start-ups. Opening its doors to researchers, students, and aspiring technology entrepreneurs, the incubator will provide them with space to plan, launch, and grow businesses. There, a network of seasoned entrepreneurs, business mentors, and angel investors will join them. These ‘parents and village elders’ will be mobilised to concentrate efforts to guide start-ups to create a company, raise capital, and reach the marketplace. We aim to make the incubator a lively hub to create businesses.

Building a company, like raising a child, is a lot of hard work. Bringing the community together under one roof, where it can do the job right, will ease the labour of start-up development, and improve the odds of scoring triumphs.

 

Ben McClure is Manager at the University of Malta Business Incubator

benjamin.mcclure@um.edu.mt