New tool for the assessment and prioritization of persistence of chemicals under REACH

New computer modelling tool to identify persistent chemicals

Chemicals that persist in the environment can harm humans and wildlife.

This study describes a computer modelling-based approach to predict which chemical compounds are likely to be persistent.

The models were correctly able to predict persistence for 11 of 12 chemicals tested and could provide a cost-effective alternative to laboratory testing.

Abstract

A new integrated in silico strategy for the assessment and prioritization of persistence of chemicals under REACH, science direct, pii/S0160412015301240, 2013.

The fact that chemicals can be recalcitrant and persist in the environment arouses concern since their effects may seriously harm human and environmental health.

We compiled three datasets containing half-life (HL) data on sediment, soil and water compartments in order to build in silico models and, finally, an integrated strategy for predicting persistence to be used within the EU legislation Registration, Evaluation, Authorisation and restriction of CHemicals (REACH). After splitting the datasets into training (80%) and test sets (20%), we developed models for each compartment using the k-nearest neighbor algorithm (k-NN). Accuracy was higher than 0.79 and 0.76 respectively in the training and test sets for all three compartments. To support the k-NN predictions, we identified some structural alerts, using SARpy software, with a high-true positive percentage in the test set and some chemical classes related to persistence using the software IstChemFeat.

All these results were combined to build an integrated model and to reach to an overall conclusion (based on assessment and reliability) on the persistence of the substance. The results on the external validation set were very encouraging and support the idea that this tool can be used successfully for regulatory purposes and to prioritize substances.

Finding good online resources for mental health support

Search engines ‘could help young people find best mental health resources’

Search engines and content providers could have a role to play in helping young people find the most reliable mental health resources online.

With well over 10,000 apps in the mental health area, quantity is not the problem. It’s much more about understanding people’s lives and how they communicate and, of course, it’s about quality.

AyeMind aims to create a digital platform to support young people in mental wellbeing and create digital resources for it; and DocReady is designed to help with a person’s first GP conversation on mental health.

What rules determines a treatment that a medical quiz would recommend?

With great power comes great responsibility

“It seems that no matter what I do, the quiz recommends the client’s drug as the best possible treatment. The only exception is if I say I’m allergic. Or if I say I am already taking it.” Bill Sourour.

Developers are often one of the last lines of defense against potentially dangerous and unethical practices.

We’re approaching a time where software will drive the vehicle that transports your family to soccer practice. There are already AI programs that help doctors diagnose disease. It’s not hard to imagine them recommending prescription drugs soon, too.

“Nothing that we were doing was illegal. In the end, I understood that the real purpose of the site was to push a particular drug.” Bill Sourour.

The more software continues to take over every aspect of our lives, the more important it will be for us to take a stand and ensure that our ethics are ever-present in our code.” 

Read The code I’m still ashamed of, on medium, Nov 13 2016. Code image by Thibault J.

Social media and technology bringing medical information and drugs at our fingertips

Social forums and networking for patients support

International groups of patients are linking up 24/7 through social media to disseminate knowledge, provide peer support, and offer clinical advice. And all of this is delivered quickly, at the touch of a button.

Is social media saving lives? Or is it spreading poor information and damaging private confidentiality? The rapid rise of patient support groups on social media is putting some fundamental ethical questions into the spotlight.

Information and drugs at our fingertips, The BMJ 354:i4527, 18 August 2016.

Tablet image esthervargasc.

Stephen Armstrong explores the role of social media in patient support and considers the benefits, ethical dilemmas, and confidentiality issues that arise.

Maureen Baker, chair of the Royal College of General Practitioners, acknowledges the huge benefit of such groups but cautions that

“these forums should not be seen as a replacement for proper medical care.”

VEGA computer modelling tool to identify persistent chemicals

Chemicals that persist in the environment can harm humans and wildlife

Persistent chemicals (which remain unchanged in the environment for a long time) can accumulate in ecosystems and inside wildlife where they can have damaging effects. People and habitats can remain at risk from these chemicals, even when they are no longer produced, and the substances can also be transported far from their original source.

Under the EU chemicals legislation REACH, all chemicals manufactured or imported above 10 tonnes per year must be assessed for persistent, bioaccumulative and toxic (PBT) properties. Substances are generally assessed based on how easily they biodegrade; chemicals that readily degrade in an experimental test system are considered not persistent. Increasingly sophisticated modelling systems are being developed which can predict the activity of a chemical based on its structure, such as quantitative structure-activity relationship (QSAR) models. These may be particularly efficient when experimental data are not available.

A new integrated in silico strategy for the assessment and prioritization of persistence of chemicals under REACH, science direct, pii/S0160412015301240, 2013.

In this study, collaborators from Germany and Italy describe a novel, integrated approach to assess the persistence of chemicals. The software system, combines multiple computational models to predict persistence in several environmental compartments (e.g. water, soil).

To create the VEGA system, the researchers first used thresholds for ‘persistent’ and ‘very persistent’ substances as defined by REACH, and applied them to the experimental data on the half-life (the time needed to remove half of the starting amount of a substance from the environment) of 12 chemicals in sediment, water and soil. If the half-life of a substance was below the criteria for ‘persistent’ then it was considered ‘not persistent’. A range of sources, including the US Geological Survey, Netherlands National Institute for Public Health and the Environment, the European Chemicals Agency and studies published in journals were used to compile the database of substances with experimental values of persistency.

New computer modelling tool to identify persistent chemicals, Science for Environment Policy, Issue 470, 16 September 2016.

VEGA system is tiered, and involves multiple stages of checks before a prediction is made. First of all, the system checks whether an experimental value (a level of persistence established in previous research) is available for the chemical, as this is generally more reliable than a predicted value. If no experimental value is available, the system checks if the compound is perfluorinated (as these compounds are known to be persistent in the environment). If it is, the chemical is automatically classified as ‘persistent’. If not, the biodegradability of the compound is evaluated using a model. If readily biodegradable, the chemical is classified as ‘not persistent’.

If none of these checks can be carried out, three software models are run on the compound, which predict its persistence in sediment, water and soil: IstKNN, machine learning software, which estimates the activity of chemicals based on similar compounds; SARpy, which automatically identifies structural features of chemicals (‘structural alerts’) that are linked to persistence; and IstCHEMfeat, which separates chemicals into classes based on particular features and chemical groups.

The final assessment is made based on a combination of the predictions and their reliability, and is always conservative (e.g. if a chemical is assessed as ‘very persistent’ in water with medium reliability, but ‘not persistent’ in soil with high reliability, the final outcome will be ‘very persistent’).

After ‘training’ the software using chemicals with known properties, the researchers tested its ability to recognise harmful substances from a set of compounds in the Candidate List of substances of very high concern maintained by the European Chemicals Agency. Of 12 compounds, the persistence of 11 were correctly predicted (the remaining compound could not be assessed as it was too dissimilar to the chemicals used during the training phase). These results suggest this tool could be used to prioritise chemicals for regulatory purposes, such as REACH. It may be a more affordable and speedier alternative to experiments for classifying compounds as ‘persistent’.

 

Motivating ASD children to go outdoor via the Pokemon GO app

Could Pokemon Go help children with autism develop their social and physical skill?

An academic specialising in autism research says the hit game Pokemon Go will boost the social skills of children on the autism spectrum.

With Pokemon Go, if you want to find anything, you have to walk outside and explore. This could be a huge bridge for people who aren’t necessarily confident in social spaces…

Craig Smith, Autism Spectrum Australia, has developed Explore Everything with Pokemon GO, an iTunes U course as a resource for families to use with their children, or for young people to enjoy on an individual basis. It follows Gardner’s theory of Multiple Intelligences to align learning experiences across a varied range of modes, from verbal and interpersonal activities through to musical and moral reasoning. Most all the learning experiences in the course use Tag Journal as the primary tool for maintaining a journal of activities and reflections.

More Information

  • EXPLORE EVERYTHING WITH POKEMON GO!, autismpedagogy, July 10, 2016.
  • Pokemon Go app set to help children on autism spectrum, abc.net.au, 15 Jul 2016.

Bioengineering Infographic

The future of disease prevention and treatment ?

Editing Out Diseases with the Help of Bioengineering…

This infographic by The University of California, Riverside highlights not only how engineering is crossing into the health and medical industry, but how engineering is “the future of disease prevention and treatment“.

Most fertility awareness apps do not employ evidence-based methodology

Smartphone apps not so smart at helping users avoid or achieve pregnancy

You might not want to depend on your smartphone app alone to help you avoid or achieve pregnancy, say the authors of a new study. A review of nearly 100 fertility awareness apps finds that most don’t employ evidence-based methodology.

The findings, published in the Journal of the American Board of Family Medicine, also found that many apps include a disclaimer discouraging use for avoiding pregnancy.

New Fertility App Study – Coming Soon!, factsaboutfertility.

The study was led by Marguerite Duane, MD, MHA, FAAFP, adjunct associate professor at Georgetown University School of Medicine and executive director of Fertility Appreciation Collaborative to Teach the Science (FACTS). Additional researchers include Alison Contreras, PhD, FCP, of FACTS, Elizabeth T. Jensen, MPH, PhD, of Wake Forest School of Medicine, and Amina White, MD, MA, of University of North Carolina at Chapel Hill.

says Duane, a family physician.

But as the authors write,

“The effectiveness of fertility awareness based methods (FABMs) depends on women observing and recording fertility biomarkers and following evidence-based guidelines. Apps offer a convenient way to track fertility biomarkers, but only some employ evidence-based FABMs.”

Success using FABMs depends on many factors, including the ability to accurately make and classify daily observations. But the authors say relying solely on an FABM app may not be sufficient to avoid pregnancy.

“Smartphone apps are increasing in popularity because more and more women are interested in using natural or fertility awareness based methods of family planning because they want to feel empowered with greater knowledge of their bodies,”

For the review, more than 95 apps were identified on iTunes, Google, or Google play. Of those, 55 were excluded from evaluation because they either had a disclaimer prohibiting use for avoiding pregnancy or did not claim to employ an evidence-based FABM.

Smartphone contraceptive apps rarely work and can cause unplanned pregnancy, scientists warn, independent, 30 June 2016.

The researchers evaluated the remaining 40 apps for accuracy using a rating system based on criteria used by Family Practice Management. Each app was rated on a five-point scale for 10 clearly defined criteria, which were weighted based on their level of importance for avoiding pregnancy.

“Of those reviewed, 30 apps predict days of fertility for the user and 10 do not. Only six apps had either a perfect score on accuracy or no false negatives (days of fertility classified as infertile),”

the researchers wrote.

Apps that do not predict fertile days scored high on accuracy only if they required women receive training in an FABM prior to using the app.

“When learning how to track your fertility signs, we recommend that women first receive instruction from a trained educator and then look for an app that scored 4 or more on mean accuracy and authority in our review,”

says Dr. Duane.

Information about evidence based FABMs and a list of all the apps reviewed can be found at the FACTS website.

Most health apps provide little or no protection for the sensitive data they collect

Is the data gathered by mobile health apps and wearables being sold for commercial profit?

Abstract

Is there something dangerous at the heart of your mobile phone? Health and wellness apps and wearables are a burgeoning phenomenon. According to the IMS Institute for Healthcare Informatics there are roughly 170 000 health apps on the Apple and Android app stores, and a recent US survey found that 58% of smartphone users have downloaded at least one of them.

At the same time, there’s an explosion in so called health wearables such as the fitness tracker Fitbit. They measure more and more things, from posture and sleep patterns, to steps taken, blood pressure, vision, body temperature, and heart activity. Forecasts from digital health consultants Tractica suggest we’ll be buying 98 million wearable health devices every year by 2021. Fitbit alone sold 21 million units in 2015.

Indeed, using wearables in routine healthcare is UK government policy. In September 2015, the health secretary, Jeremy Hunt, outlined plans to get a quarter of smartphone users—15% of all NHS patients—routinely accessing NHS advice, services, and medical records through apps by the end of the next financial year. Hunt said:

“I also want patients not just to be able to read their medical record on their smartphone but to add to it, whether by recording their own comments or by plugging in their own wearable devices to it.”

The NHS plans to start issuing free apps and wearables to patients in 2017.

Read What happens to data gathered by health and wellness apps?,
The BMJ 2016;353:i3406, 23 June 2016. Image via @bmj_latest.

Apple is opening up its CareKit framework to developers

Apple’s plan to turn the iPhone into a medical wonder starts now

Apple Advances Health Apps with CareKit, New Software Framework Helps Developers Empower People to Take a More Active Role in their Health, Apple Press Release, 2016.

CUPERTINO, California — March 21, 2016 — Apple today announced CareKit, a new software framework designed to help developers enable people to actively manage their own medical conditions. iPhone apps using CareKit make it easier for individuals to keep track of care plans and monitor symptoms and medication; providing insights that help people better understand their own health. With the ability to share information with doctors, nurses or family members, CareKit apps help people take a more active role in their health.

“We’re thrilled with the profound impact ResearchKit has already had on the pace and scale of conducting medical research, and have realised that many of the same principles could help with individual care, We believe that giving individuals the tools to understand what is happening with their health is incredibly powerful, and apps designed using CareKit make this a reality by empowering people to take a more active role in their care.”

said Jeff Williams, Apple’s chief operating officer.

CareKit will be released as an open source framework next month allowing the developer community to continue building on the first four modules designed by Apple, that include:

  • Care Card helps people track their individual care plans and action items, such as taking medication or completing physical therapy exercises. Activities can automatically be tracked and entered using sensors in Apple Watch or iPhone;
  • Symptom and Measurement Tracker lets users easily record their symptoms and how they’re feeling, like monitoring temperature for possible infections or measuring pain or fatigue. Progress updates could include simple surveys, photos that capture the progression of a wound or activities calculated by using the iPhone’s accelerometer and gyroscope, like quantifying range of motion;
  • Insight Dashboard maps symptoms against the action items in the Care Card to easily show how treatments are working; and
  • Connect makes it easy for people to share information and communicate with doctors, care teams or family members about their health and any change in condition.

“With ResearchKit, we quickly realised the power of mobile apps for running inexpensive, high-quality clinical studies with unprecedented reach. We hope that CareKit will help us close the gap between our research findings and how we care for our Parkinson’s patients day-to-day. It’s opening up a whole new opportunity for the democratisation of research and medicine.”

said Ray Dorsey, MD, David M. Levy Professor of Neurology at the University of Rochester Medical Center.

Developers of health and wellness apps are excited to build these CareKit modules into apps for Parkinson’s patients, post-surgery progress, home health monitoring, diabetes management, mental health and maternal health.

  • Sage Bionetworks and the University of Rochester are using CareKit to turn the mPower ResearchKit study into a valuable tool to help better inform patients about their condition and care providers about treatment.
  • The Texas Medical Center is designing apps to guide and support care pathways for its 8 million patients to improve their health through enhanced connectivity with their care teams.
  • Beth Israel Deaconess Medical Center will provide patients with more insight into their own chronic care management through home health monitoring devices that securely store data in HealthKit.
  • One Drop is empowering people with a better approach to managing their diabetes.
  • Start, by Iodine, helps people on antidepressants understand if their medication is working for them or not, and helps their doctors deliver more informed care.
  • Glow, Inc. will incorporate CareKit modules into its pregnancy app, Glow Nurture, to guide women through a healthier pregnancy.

These are a few of the first apps. For more information, visit www.apple.com/carekit.