GNU Health and Khadas to deliver Artificial Intelligence in Medicine

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It is official: GNU Solidario, the Spanish NGO behind GNU Health (GH) and Khadas Technologies have signed the “GNU Health Alliance of Academic and Research Institutions”, to research and deliver Artificial Intelligence to the world of medicine.

This is very exciting. GNU Health covers genomics, medical genetics, Dx imaging and social medicine, areas where definitely we can use the power of AI for better diagnostics, personalized treatments, decision support, disease prevention and health promotion.

The GNU Health embedded project using Khadas for Artificial Intelligence in Medicine

What is truly revolutionary is that we will be using affordable single board computers, like the Khadas VIM3, where they could work alone or in the context of the GNU Health Federation, doing massive virtual parallel computing.

Citizens, health professionals and institutions don’t have to spend millions to access the latest in technology. In GNU Health, this has always been our philosophy. Health is must be remain a universal human right, and that is what we do in GNU Health. We deliver state-of-the-art technology all over the world with Libre Software. No hidden lines of code, no hidden agenda.

One of Khadas devices, the VIM3 includes a Neural Processing Unit (NPU) that will be the heart of the AI engine.

GNU Health HMIS with genetics package running on a Khadas VIM3 Pro

We can use our GH Federation model which gathers massive information of protein natural variants, and combine it with the latest tools in Artificial Intelligence. We will be giving a giant leap, unveiling the real clinical significance of many mutations that today remain a mystery about how they would affect our health. In GNU Health we are determine to build this critical bridge between the person, the clinician and the researcher.

Another area that we’ll work on is Dx imaging. Training Khadas devices to differentiate many types of lesions will help the pathologist or the surgeon to take real-time decisions in the operating room based on the picture GNU Health camera takes and the diagnostic that the GH embedded return about the specimen.

In the upcoming GNU Health Conference – GHCon2020– , there will be sessions about this project, so we invite anyone to register at the conference, that this year will be online due to the COVID pandemics. Register at GHCon2020

GHCon2020, the annual GNU Health conference

About GNU Solidario: GNU Solidario is a non-for-profit organization that works globally, focused on Social Medicine and health informatics (using Libre Software).

GNU Solidario is the organization behind GNU Health, the award
winning Libre Health and Hospital Information System, deployed in many
health and research institutions around the globe.

About Khadas: Khadas develops superior quality, high performance single board computers for makers, developers, and tinkerers, that come with open source, professional technical support, and a global community for issue discussion & idea sharing.

GNU Health: Helping Laos Heal from UXO physical and emotional trauma.

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Luis Falcon with the Lao CMR staff in charge at the 2 year anniversary of the implementation
GNU Health implementation anniversary at Laos Center of Medical Rehabilitation

Laos is one of the most heavily bombed countries in the world. During the period from 1964-1973, over 2 million tons of bombs were dropped by B-52 aircrafts across the 2/3 of the country during the “Secret War”. This nine-year period bombing caused thousands of deaths and a unprecedented human displacement that exceeded a hundred thousand civilians from the poorest areas of the country.

The tragic legacy of that period remains today. Thirty percent (30%) of those bombs remains active (Unexploded Ordnances – UXOs – ), causing over 300 victims every year until 2008, and now down to 50 / year. Nearly 60% of the UXOs accidents result in death, and 40% of the victims are children[1].

If the explosion does not kill the person, it causes severe traumatic injuries resulting in the amputation of limbs in many of the victims. Physical and emotional trauma that takes many years to heal. In addition, many UXO victims suffer from Post-traumatic stress disorder (PTSD), a serious condition that can be devastating for the victim and their families[2].

But there is hope. The wonderful people from Laos are resilient, and they are willing to cope and move forward. I have been in Laos several times in the last few years, in the context of GNU Health implementations both in Mahosot Hospital and the Center for Medical Rehabilitation – CMR – .

The Center for Medical Rehabilitation (CMR), located in Vientiane, is a specialized institution that helps people with disabilities and victims survivors of UXOs. The CMR, formerly known as the National Rehabilitation Center initially provided prosthetic limbs for victims of war. Today they have extended the services to provide services to children with disabilities across the country. Some of the services include medical and community based rehabilitation, special education for the deaf and the blind and vocational school for people with disabilities.

At the moment I had the meeting with the hospital directors, I knew that we had to focus both in short term surgery as well as in the long term psychological, physiotherapy and occupational therapy that would allow the person to be fully functional in the society. Again, I was facing a project in need of Social Medicine.

We trained a local multidisciplinary team of nurses, doctors, physiotherapists, social workers, computer scientists, psychologists, administrative personnel, pharmacists and accountants.

CMR nurses. The heart of the institution

It was during that period that I created the package functioning and disability.

General patient information and Functioning & Disability tab. Red boxes on these two sections denote UXO related information

Some of the GNU Health functional modules that CMR decided to use included surgery, socio-economics, ICD-10, nursing, physical therapy, stock, accounting, lifestyle, reporting, health services and diagnostic imaging, among others. In addition to those, we included the “functioning and disability” package.

The GNU Health “Functioning and Disability” package integrates the ideas of WHO Health Organization International Classification of Functioning, Disability and Health. This functionality complements the ICD-10 classification of diseases, with the concept of functionality. For example, after a person has been diagnosed with diabetes, we must go beyond the biology and molecular bases of the disease, and evaluate how diabetes impacts of on her daily activities and integration in the society and environment.

GNU Health contextualizes the health condition in the particular individual, key for personalized medicine. In the UXOs example, the related ICD10 codes are visible from the main chart:

  • S88 : Traumatic amputation of lower limb
  • F43.1: Post-traumatic stress disorder

This diagnostic information is relevant and key for epidemiology and statistics, but if we want to practice medicine, we must take into account the social aspect of these conditions, and how they affect the person in her particular environment.

The GNU Health Functioning and disability assessment has two sections. The first section is a summary of impairments related to the Cognitive, Visual, Hearing, Speech, Hand, Mobility and Activities and Participation .

The second section is a detailed assessment of Body functions, Body structures, Activities and Participation and Environmental factors and barriers. Each of these groups has its own set of qualifiers and components that will provide the health professionals where to put the focus to the time and the context of that person, as well as to evaluate the progression of the conditions.

We can now study, with a multi-disciplinary team, how the body structure and body functioning impairments relate to the person capacities and engagements in social activities; daily household tasks; using the current public transportation system or the level of access to Labor and employment services.

This is my concept of medicine, the assessment of the bio, psycho, social determinants of health and disease. Medicine is, first and foremost, a social science, and GNU Health is first and foremost, a social project.

Example of GNU Health person functioning and disability assessment

Celebrating the success of cooperation: During a two-year period of using GNU Health, they have provided over 67,000 medical services, automated their finances, prescriptions, stock management, medical appointments and evaluations, diagnostic imaging, and the demographics tracking for the thousands of patients they assist.

CMR Cope team helping people in Lao rural areas

Local capacity building: CMR trained its own local group of professionals who customize and maintain GNU Health, in their own Lao language. This creates a local and ethical business model, very important for the long-term sustainability of the project.

A well-deserved award. The work that CMR has been doing in Laos for the rehabilitation of their people has been magnificent. Their multidisciplinary approach to trauma, from the acute care and surgery, to the physical therapy and the work in the field is an example for many of us. CMR has helped thousands of people every year healing from the UXO physical and emotional scars, moving forward and being able to get re-inserted in society, and we are so proud to have been part of it.

A delegation of the Laos Ministry of Health presented at GNU Health Con 2016 the implementation in the Lao Center for Medical Rehabilitation – CMR – and in Mahosot hospital. We are so proud that they are part of the GNU Health community.

CMR received the GNU Health Social Medicine Award in 2016 for best Institution.

  1. – Somnuk Vorasarn, Chansaly Phommavong, Khonephet Sely. GNU Health in Mahosot Hospital – GNU Health Con 2016
  2. A cross-sectional community study of post-traumatic stress disorder and social support in Lao People’s Democratic Republic

Reflections towards a Humane and effective Medical Research

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Science can not advance at the cost of the pain and agony of sentient beings. If saving a human life means killing a nonhuman being, then we need to move away from that model and towards a humane and effective medical research.

I am honored to be among the 77 scientists who joined forces with Animal Free Research UK[1], Safer Medicines Trust[2] and the Alliance for Human Relevant Science[3] to call for a change in regulation to enable medical research without the use of animals for all diseases. The open letter [4], a call to international regulatory bodies, was released on this Tuesday (July 14th, 2020) and it was published in The Guardian the same day.

An animal is someone, not something. Human and nonhuman animals are sentient beings. They are capable feel joy and to suffer physical and emotional pain. Can we then call a nonhuman animal a “person” ? I’d say so. A person is someone, not something. A person has the right to live in freedom and dignity. Not doing so will generate discrimination based on species, that is, speciesism. Discrimination wrongfully empowers morally ( and in many occasions, legally) the oppressor. Discrimination based on sex, IQ, race or species varies on the victim. The mechanism of slavery lies on tearing apart the dignity and freedom of someone, turning them into property, a something. Examples of modern slavery are sex trafficking, child labor and factory farming.

Philosopher Mary Midgley wrote a very nice essay on this subject Persons and Non-persons[5]. It is important to reflect about the rationale of the judge.

Wrong educational model: It is appalling how junior medicine school students are “trained” to accept animal suffering as part of being a doctor or a scientist. Undergraduate students “learn” about acute mesenteric ischemia (AMI) with live animals, cutting them open, ligating the artery and then observing the evolution (slow and painful death). The physical and emotional pain that these sentient beings undergo can not be described. Being exposed to such horrendous actions won’t make the students better doctors. On the contrary. There is plenty of literature about AMI on humans that will result on a more relevant learning experience for the future health professional.

The macabre LD50: The term “Lethal Dose 50” is is used extensively in the the pharmaceutical and cosmetic industries. In toxicology, it represents the dose of a substance needed to kill 50% of the exposed population. Dogs, mice, rats, and many other animals are given the drug by different routes (orally, intravenously, intraperitoneal…). The survivors are too sick and end up being “euthanized”.

The cruel failure of science: Sadly, all that that suffering has been in vain. According to the Animals in Science Policy Institute, emerging evidence shows that 95% of drugs testing in animals fail at human clinical trial, and close to 100% Alzheimer’s drugs tested in animals fail when tested in humans[6]

A daily holocaust: During WWII, Hitler’s doctors performed the most heinous experiments on humans, in the name of science. One of the doctors stood out from the rest. His name was Josef Mengele. He used children (had predilection for twins) . Mengele was called the angel of death. In addition to be in charged of sending the prisoners to the gas chamber, he conducted hundreds of experiments in children, killing them afterwards. One night, he killed 14 children by injecting chloroform into their hearts[7]. I am bringing this topic because I want people to remember and never forger the atrocities done by the Nazis. In addition, it’s important to note that his sadistic methods don’t differ much from nonhuman animal experimentation carried out every single day around the world. I am convinced that animals conceive human beings as their Angels of death.

It is ironic that many would have trouble falling asleep thinking about the atrocities committed by Mengele, yet normalize the killing of millions of sentient beings that anticipate torture and suffering equally as those innocent gypsy children in Auschwitz concentration camp. All animals, human and non-human, shiver, cry, vomit and lose control of sphincters in response to emotional and physical stress. The question remains, why our governments perpetuate this holocaust.

Different species, different physiology: Different species have different physiology. That is part of the reason some clinical trials that may show promising results in non-human animals are a failure when tested in humans.

In the context of the COVID-19 pandemic, it’s been shown that the expression of ACE2 receptors is different among rats and humans. In the open letter “A shift in focus is needed to tackle COVID-19” written this May by Animal Defenders International[8] and co-signed by scientists and academics to the World Health Organization and other regulatory entities, they wrote:

[…] mice are one of the most commonly used species in drug and vaccine research. In addition to major differences between human and mouse respiratory systems, species differences specific to research for SARS-COV-2 include that mice do not naturally have the same receptors the virus uses to infect human cells. Researchers are now attempting to “humanize” mice to ensure they contract the virus. Such fundamental differences risk impeding the production of vaccines and other treatments to help prevent and reduce the symptoms of COVID-19 in people.

Humane and effective alternatives: We now know that animal experimentation is both cruel and ineffective as a research strategy. Traditional biomedical has failed to provide solutions for human related conditions and is now anachronistic. As a physician and computer scientist, I see the enormous benefit of applying computer models, artificial intelligence or computer vision as part of the new generation, state-of-the-art technology applied to biomedical research. Thanks to the GNU Health Federation[10], we are capable of building large, distributed networks that interconnect patients, physicians and researches around the globe to provide solutions in key areas of social medicine, cancer, bioinformatics and precision medicine.

Organizations such us Animal Free Research UK are leading medical research in the areas of diabetes, cancer and neurodegenerative conditions by using cell cultures or amazing technologies like “organ-on-a-chip“[11].

There are plenty of reasons to be optimistic, from the technological to the human aspects. These actions reflect how scientific communities, NGOs and citizens are coming together towards a humane, effective and human relevant medical research.

References

  1. Animal Free Research UK https://www.animalfreeresearchuk.org
  2. Safer Medicines Trust . https://safermedicines.org/
  3. Alliance for Human Relevant Science . https://www.humanrelevantscience.org/
  4. Animal Free Research UK. “A call to accelerate human focussed medical research” . https://www.animalfreeresearchuk.org/openletter/
  5. Mary Midgley – “Persons and non-persons” http://www.animal-rights-library.com/texts-m/midgley01.htm
  6. Animals in Science Policy Institute. “Animals in testing” . – https://www.animalsinscience.org/why_we_do_it/animals-in-testing/
  7. Lifton – “What made this man? Mengele” – http://academics.wellesley.edu/Polisci/wj/100/mengle.htm
  8. Animal Defenders International – https://www.ad-international.org
  9. AD International – “A shift in focus is needed to tackle COVID-19” .- https://www.ad-international.org/admin/downloads/adi_aa465255de851a533279bf8e1b053287.pdf
  10. GNU Health – https://www.gnuhealth.org
  11. Animal Free Research UK .- “Organ-on-a-chip” – http://www.animalfreeresearchuk.org/organ-on-a-chip/

GNU Health in Tanzania. An implementation case.

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The following note comes from Mike and Ulf, two Swedish colleagues that implemented GNU Health in Tanzania. The specific institution is Nkinga Hospital. Mike and Ulf have been part of the GH commuity for years. I met personally Mike at the GNUHealthCon 2019 in Brussels. Their work is phenomenal.

The title of his document was “How to Implement GNU Health in Tanzania in 10 days”. We’re very thankful to them for sharing this very inspiring story, and hope is a lesson to all of us!

Background

It all started with that we had studied free software and networks at universities in our spare time for a few years. When we had finished the studies we decided to do something with the knowledge we got. We got in contact with Nkinga hospital in Tanzania and we decided to help them to build the IT-infrastructure.
In September 2011, we went to Tanzania to build a computer network to be able and communicate internal and share documents in the hospital. We set up Wi-Fi points, installed servers and educated technicians.
In August 2014, we traveled to Nkinga to extend the network and set up a PACS server and computers for reviewing x-ray pictures.

Goal
Our goal with this project was to implement GNU Health at the hospital in short time.
The system consists of one server, one spare server, a backup server and about 30 workstations spread out at the hospital. The project also included training of the hospital’s users and to educate technicians to manage the system and network with our remote support.

Challenges
undefinedWe planned to introduce the system in 10 days and expected to start using some basic modules. When the basic modules worked, the plan was to continue implementing more modules . In order to manage to deploy the system at Nkinga in the short time, a medicine manager and an economist from the hospital visited us in Östersund for two weeks to prepare the implementation.


Implementation
When the two personnel went back to the hospital they arranged training sessions for different personnel groups and was a cornerstone for the implementation of the project.
During the first day of using GNU Health, it was discovered where it did not work as it should. For example, it became a bottleneck in the front desk where patients ensign themselves. In the first three days, in parallel with GNU Health, the hospital used paper. In the evening, the data on paper were
fed into the system.
Over the next few days, we moved around the hospital and instructed staff how to use the system. Not everyone was used to computer so it took some time. Everyone in the hospital has been very helpful and we worked up to 16 hours every day.

Afterword
In the first few days after we got home, the hospital contacted us daily about issues that arose and together we solved them. For every week that passed, the problems decreased. After 4 weeks of running GNU Health everything run smoothly. We have weekly telephone meeting to discuss
various issues. At the hospital they have worked very intensively with the training of staff and to optimize the flow. The understanding of the benefits of the hospital system is increasing all the time. The preparation of implementing GNU Health took us approximate one year.

Summary
Examples of work done during ten days:

  • Expanded computer network
  • Installed 25 new computers
  • Assembled and installed 3 servers
  • Training of users
  • Training of Technicians
  • Installed a number of routers and switches
  • During 10 days we (seven people) worked at total 820 hours .

For the implementation of GNU Health, we have purchased hardware for about 8000 EUR sponsored by an aid organization. We shipped 25 used computers and network equipment that we received from different companies.
After 2 months of using GNU Health, 2083 patients was enrolled in the system, 1873 appointments performed, 80 users worked in the system, 1600 invoices print, etc.

GNU Health has been running since November 2017 with only minor disturbance.

Pictures from Mike & Ulf blog (https://nkingahospital2017.wordpress.com/)

Tackling the Beast: Using GNU Health to help the fight against the COVID-19 pandemic

gnuhealth-covid-banner

Introduction

The world is facing one of the the biggest health, economic and social crisis. A minuscule, 50-nanometer in diameter structure is putting the most powerful world economies on their knees, and hundred of thousands are tragically succumbing to COVID-19.

This article is an invitation to governments to embrace GNU Health and Libre Software for the sake of their public healthcare system in the context of the COVID-19 pandemic.

For those of you who already use GNU Health, take this article as some sort of guideline to optimize your implementation and day-by-day usage. Even though it focuses on COVID-19 disease, most topics will apply to any GNU Health implementation.

People before patients: Demographics and health infrastructure

Information is power. Good quality and timely data is crucial to tackle the COVID-19 pandemic. GNU Health has been designed on Social medicine. That is, instead of dealing directly with patients, GNU Health works first on the main pillars of a society. As a result, the government will have better tools for health promotion and disease prevention. The government will be better prepared to fight this pandemic and future outbreaks.

Domiciliary Units : DU are houses, apartments and buildings where people live. GNU Health DU model stores the infrastructure, sanitary conditions as well as the people who is living at anytime at that dwelling, in realtime. This feature is key to track possible contacts of an infected individual. Moreover, the infrastructure, surface and number of rooms provides great information in terms of possible overcrowding conditions that would facilitate the spreading of the disease. Each domiciliary unit can be georeferenced, thanks to GNU Health link OpenStreetMap.

 

gnuhealth_domiciliary_unit_osm

Domiciliary Unit in GNU Health: conditions, members and its geolocation linked to OSM

 

Operational Areas: GNU Health can divide a country in administrative areas and sectors (provinces, cities, neighborhoods,..) composed by domiciliary units and health institutions. GNU health can do real-time epidemiological reporting based on these sectors. Understanding this concept is key for COVID-19 contention or mitigation programs, since it would be able to identify early outbreaks in new areas, or focus on sections of relevant incidence. Operational areas and sectors allow us to find correlations from many indicators (ethnicity, sex, age, income, education level, population density) in the COVID-19 incidence, prevalence, susceptibility of infection or disease progression.

Health institutions: GNU Health can keep track and manage health institutions across the country. Human resources, financial and stock management, pharmacies and laboratories. In the context of the COVID-19 pandemic, you can do reporting on occupation levels of those institutions, number of beds, operating rooms, devices such as ventilators, number of health professionals and their specialties, the incidence, prevalence and mortality per institution, average time of hospitalization, and many other studies. Of course, you need to have the institutions set up.

gnuehalth_institution

GNU Health institution model

Health professionals : In crises such the COVID-19, GNU Health allows the Ministry of health to know each health professional, their specialties, the health institution where they work and where are they located (operational sectors). Time is precious and keeping updated information of the professionals will allow rapid assignment.

Person Demographics: Age, address and domiciliary units, work and insurance. Make sure this information is stored. Age is a factor on this epidemics, as COVID-19 is particularly pernicious with the elderly population. The profession of the person is also important. For instance, health professionals are highest infected group. Demographics will also help to identify people without health coverage, unemployed, homeless and other underprivileged groups that are particularly vulnerable.

 

Person contacts: For each person, GNU Health keeps record of their contacts and their relations (work, classmates, friends, classmates). In the scenario of a positive case for COVID-19, this information would allow to call the patient close contacts. It is key to have this information updated. Remember to fill in all possible contact mechanisms for each person (email, mobile phone, Telegram, …). Tracking and getting in touch with the person close contacts is vital.

Person Universal ID: This is one key feature of GNU Health, specially in the context of the GNU Health Federation. The person Unique ID (Federation Account) would be valid not only for the region or country, but across the world. The clinical information could be available and updated in any health institution across the country or region, immediately available for the rest.

Screening

The World Health Organization (WHO) keeps saying “test,test,test” the population. The earlier we test the population, the better we can control the spread of the disease in the community. Special population groups, such as health professionals, the elderly or those with existing health conditions should have priority.

There are rapid, point-of-care tests available in many countries that can deliver the results in less than 30 minutes. Some of them around 10 minutes. In GNU Health, you can use the SARS-CoV-2 antibodies lab test type.

GNU Health workstations can be deployed at the mobile test stations, and send the information in real-time to the Ministry of Health, with the result, signed and validated.

If the person has tested positive for IgM antibodies, it means she is in the early stage of the infection. IgG antibodies build up later in the infection and are part of the “immunological memory”. If IgM is positive, you must update the health conditions, include the following ICD10 code and activate the COVID-19 protocol for patient isolation and contact tracking.

The ICD10 code for COVID-19 is U07.1

U07.1 : 2019-nCoV acute respiratory disease COVID-19 : In GNU Health, the U07.1 condition (COVID-19) belongs to the infectious, respiratory and notifiable disease groups.

Indicate the lab test type and order in the related condition.

gnuhealth_patient_screen

GNU Health patient screen sample, including critical information related to COVID-19 disease

Clinical Management

If the patient is tested positive but is asymptomatic or mild clinical, the patient might be sent home for home care. Please verify at that moment if the Domiciliary Unit meets the requirements (ventilation, number of rooms, number of people in the house, … ).

If the person has tested positive and/or presents signs to warrant her hospitalization, admit her to the health facility and assign her a bed in the appropriate ward. A new inpatient record will be created, with the corresponding in charge physician, treatment and nutrition plan. When admitting a patient suffering from COVID-19 is important to enter its code (U07.1 : 2019-nCoV acute respiratory disease COVID-19) as the reason of admission and discharge. This will be very valuable for statistics.

Medical History: The patient medical history is ready in GNU Health, from all the patient evaluations in the different health institutions. In the context of the COVID-19, this information is key, especially for people with chronic health conditions, such as cardiovascular disease or diabetes. The current and past medication is also stored in GNU Health, as well as surgeries.

Roundings: For each rounding, enter the vital signs, the medication provided,  assess the environment and the “Six P’s” and record all the procedures done in the rounding itself.  In addition, if the patient is on Intensive Care Unit (“ICU” tab), record relevant information on nervous, respiratory, cardiovascular, urinary and digestive systems, as well as any signs of infection.

The vital signs can be taken in different contexts. They can be assessed in an outpatient evaluation, inpatient nurse rounding or ICU setting.

Intensive Care Unit: If the disease progression is life threatening, the patient will be admitted to the Intensive Care Unit. GNU Health has an Intensive Care Unit module. After recording the main information of the rounding, move to the “ICU” tab for a detailed assessment of the patient in this unit. Scores such as Glasgow Coma Scale and Apache II are available.   For each ICU rounding the health professional should record both the basic information as well as a detailed RoS. GNU Health allows to enter ECG information and the copy of the ECG strip per rounding, if needed.

A percentage of hospitalized patients by COVID-19 will need mechanical ventilation. GNU Health records the type and duration of the intubation, per patient on each institution. This information is very valuable for both clinical management as well as for statistics. Most countries are facing today is the shortage of mechanical ventilators. GNU Health permits to know the incidence of hospitalizations due to COVID-19, as well as the discharge rate.

Medical Imaging and Laboratory tests

Radiological findings of many COVID-19 patients are compatible with atypical pneumonia. Streaky opacities, specially at the bases are common findings. Many people with mild disease won’t show any radiological signs.

GNU Health provides different types of Dx tests. Images and observations are recorded in the system and linked to the patient history. In addition to the standard GNU health radiology package, the Intensive Care module also permits to add Xray images on each rounding to evaluate and compare the disease progression.

For large images and studies, such MRI or CT scans, we highly recommend the GNU Health Orthanc package. Orthanc is a fantastic Libre DICOM server and GNU Health can interoperate with it, thanks to the magic of the Free Software philosophy.

gnuhealth-dx-imaging-atypical_pneumonia_covid19

GNU Health radiology. Findings compatible with atypical pneumonia in a COVID-19 patient

In addition to the standard lab test types (CBC, renal and liver function …..), there are markers that can predict COVID-19 progression and severity. For instance, high ferritin levels, low platelet number and a high ESR are common in patients who develop severe disease and the cytokine storm syndrome.

CBC-lab-test

GNU Health LIMS showing a Complete Blood Count sample

All the lab test results can be exported to different formats. In the context of the GNU Health Federation a new POL (Page of Life) is created and the information can be exchanged directly in JSON format. The following pictures show the same lab test report in PDF and JSON format from the GNU Health Federation message server (“Thalamus”)

 

In addition to the tests done in hospitalized patients, remember that GNU Health LIMS package can be used in diagnostic and population screening, as in the case of PCR and rapid tests.

Death Certificates

The death certificate is a key document, since it has legal, administrative, demographic and epidemiological significance.

The following is an example of how we could use the GNU Health Vital Record System to generate a death certificate associated to the COVID-19 disease.

gnuhealth_covid_death_certificate

Person Death certificate related to COVID-19 disease

Digitally signing the digital certificate with the health professional and/or civil officer will make it a legal document. GNU Health uses GNUPG (GNU Privacy Guard) to digitally sign and encrypt documents.

death-certificate_digital_signature

Digital signature section of the death certificate

Research

Although the respiratory system is the most affected in patients with COVID-19, other organs can be impacted. The ACE2 receptor (cell’s entry point for SARS-CoV-2) is expressed in other tissues in addition than lungs, such colon and heart. Not surprisingly, gastrointestinal symptoms and cardiac involvement, as acute myocarditis, have been reported. Recording all findings will help to improve the management of the disease of the patient, but also to share information with colleagues from the scientific community.

Sharing the patient treatments and individual outcomes will help speed up clinical trials and response to possible therapeutic agents (eg, remdesivir, lopinavir/ritonavir, hydroxychloroquine, tocilizumab…)

gnuhealth_federation_components

The GNU Health Federation connects thousands of nodes from health and research institutions

To be able to achieve such breakthroughs in science and in our society, we need our politicians and governments to embrace open science, open data and Libre software.

A call for Open Science, Open Data and Libre Software

The current COVID-19 pandemic is a terrible tragedy for human kind, but opens an opportunity to cooperation, to join forces and to our innate resilience.There are many gray areas and many uncertainties in the origin of the virus, disease progression and therapeutic approaches. On the other hand, the GNU Health Federation allows the scientific community to come together and tackle this beast. We can securely  share huge, anonymized amount of information from all over the world to find not only the molecular basis of the COVID-19 disease, but environmental and social factors that impact on the susceptibility and disease progression.

I am returning from Japan, where I was invited to give a lecture at Kyoto university Medical Innovation Center (MIC). It was an honor to share ideas with students and professionals from a leading institution on molecular biology and biomedicine. Although I talked about GNU Health in cancer research, my presentation focused on the importance of Libre Health informatics, open science, open data in Public Health. It was surprisingly exciting the great level of engagement of the audience in these topics.

A robust, sustainable public health infrastructure must be based in cooperation. Cooperation involves open knowledge and open science. I am convinced that true evolution comes from cooperation, and not from competition. In this sense, we as members of the scientific community should share our work, whether is a computer program source code, the discovery of a protein natural variant or the development of a new therapeutic molecule.

GNU Health uses the GPL license (General Public License), which permits downloading the program, study the source code, adapt it to your center needs and share it with the community.

Keep in mind that libre software not only provides collective freedom, but is the only way to achieve privacy in healthcare. Proprietary, non-libre programs are blackboxes that jeopardize both personal privacy and public health information. In addition to that, using proprietary software in Public Health is an obscene contradiction.

To accomplish collective freedom, every single component must be Free/Libre. That is, the operating systems (both for servers and clients) as well as the applications around. We will need to share information among colleagues around the world, so the format that we use in the corresponding files should also be open.

In the meantime, stay safe. Stay home !

 

La venganza del Pangolín

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El todopoderoso, arrogante ser humano ahora está asustado y  frágil.

La nueva epidemia del coronavirus covid-19, causado por el virus SARS-COV-2, es la última de una serie de zoonosis que amenaza en convertirse en una pandemia. Algunas enfermedades zoonóticas recientes causadas por coronavirus han sido el SARS (Síndrome Respiratorio Agudo Grave) o el MERS (Síndrome Respiratorio de Oriente Medio). Todas ellas tienen como origen común animales que han sido explotados por humanos.

Pangolin

Credit : Associated Press – AP

Parece que el brote inicial del COVID-19 tuvo su origen en el un mercado de la ciudad de Wuhan, donde animales vivos son mantenidos en condiciones deplorables. Gatos, perros, murciélagos, serpientes, ciervos, pollos, etc.. son enjaulados y observan aterrorizados como queman vivos y matan a otros animales inocentes, sabiendo que ellos tendrán la misma suerte.

Wuhan wet market -Source : Weibo

El pangolín está en peligro de extinción, víctima de la “medicina tradicional” en China y en muchos otros países de Asia. Cazadores furtivos han hecho que el pangolín sea el mayor víctima de esta atrocidad. Por supuesto, no es la única víctima de la codicia e ignorancia humana. Los tiburones también están enfrentando la extinción por sus aletas, así como los rinocerontes y elefantes que son mutilados o asesinados por sus cuernos. Un mercado tan cruel y inhumano como bárbaro en el nombre de  una falsa medicina, sin ningún tipo de evidencia científica.

Ganadería industrial, resistencia antibiótica, calentamiento global y priones

Asia no está sola cuando hablamos de crueldad animal. Europa y los Estados Unidos tienen las mayores granjas industriales, donde literalmente millones de seres sintientes son secuestrados, esclavizados y asesinados cada día.

En la industria láctea, las vacas son violadas, sus terneros son enviados al matadero pocas horas después de nacer, y se les colocan pinchos en el hocico que generan dolorosas lesiones a la madre, con el fin de evitar la lactancia.

La industria ganadera y láctea son asesinos en serie. Necesitan optimizar el crecimiento del producto, el animal, así que mientras más rápido crezca, antes son asesinadas. Para acortar el ciclo de los animales, estas industrias usan hormonas de crecimiento y antibióticos. Literalmente se emplean toneladas de antibióticos, no sólo para aumentar el peso, sino para luchar las enfermedades generadas por las condiciones inhumanas y hacinamiento en las que los animales están confinados. Esto hace que el ganado sea el mayor mercardo de antibióticos, así como la mayor fuente de resistencia antibiótica que tiene un impacto directo en la salud humana.

Irónicamente, la dieta basada en productos animales no es sólo innecesaria, sino que también es poco saludable. El consumo de productos lácteos y cárnicos están asociados a enfermedad cardiovascular y distintos tipos de cáncer. Esto es un hecho irrefutable. Por muchos años la industria ganadera y láctea han estado mostrando una falsa realidad acerca de los supuestos beneficios a la salud. El lobby ha sido tal que penetró las facultades de medicina, nutrición y la literatura científica. Ahora sabemos que ha sido todo una mentira.

En un esfuerzo para optimizar el “ciclo de producción”, las vacas, que son herbívoros, han sido alimentadas con productos de origen animal. Esta práctica anti-natural generó la encefalopatía espongiforme bovina, una enfermedad devastadora e invariablemente fatal. Muchas personas, especialmente en Europa ha sucumbido a la variante humana de la enfermedad (Variant Creutzfeldt–Jakob disease (vCJD)) después de comer la carne de animales infectados. Más de 4.5 millones de vacas fueron sacrificadas por miedo  a que fueran portadoras del prión.

Pero eso no es todo. La ganadería extensiva (“Factory farming”) es una fuente principal de calentamiento global. Según The Humane Society, la ganadería industrial es responsable del 34% de las emisiones de metano (CH4), con una capacidad veinte veces mayor de efecto invernadero que el dióxido de carbono (CO2)[1] . La tasa de deforestación del Amazonas ha alcanzado su punto más alto. Los bosques amazónicos se queman para plantar soja, y millones de litros de recursos naturales preciosos como el agua son desperdiciados para alimentar a un ganado que posteriormente será sacrificado. Tan cruel como absurdo.

factory_farming

“La venganza del Pangolín”, título de este artículo, representa la venganza de todas las especies que han sido explotadas por el ser humano. Es la respuesta de la Madre Naturaleza a nuestras estúpidas acciones, basadas en la codicia e ignorancia que están llevando a la especie humana a su auto-destrucción. Pareciera que una maldición ha caído sobre la humanidad como consecuencia de su nefasto comportamiento con otras especies y con la Naturaleza.

La epidemia del Covid-19 es la última respuesta de la Naturaleza al arrogante, ignorante, egoísta ser humano. Es una forma de decirnos que somos víctimas de nuestros propios actos malvados.

Todavía soy optimista, pero tenemos que actuar ya. Deberíamos empezar por ser humildes. Tenemos que arrepentirnos y pedir perdón por todo el daño y hechos execrables a otras especies. Debemos recomenzar, generando una relación empática y compasiva con ellas.

En vez de ponernos mascarillas – que no sirven de nada a personas sanas y se las quitan a las personas que realmente las necesitan – debemos tomar acciones de manera inmediata. Esa acción no pasa únicamente por pedir a la comunidad científica para que genere un antiviral o una vacuna, que llegará tarde a muchos. La medida debe ser sostenible a largo plazo.

Los gobiernos y organizaciones supranacionales como la Organización Mundial de la Salud deben poner un fin a la industria láctea y ganadera. Deben prohibir la caza, en todas sus formas, así como imponer las mayores penas a los cazadores furtivos y mercados animales, así como a los países que los fomenten.

Paralelamente, se debe promover prácticas agrícolas orgánicas sostenibles. Los gobiernos deben poner el foco en mejorar el sistema educativo donde los niños aprendan, principalmente, a ser personas humildes, compasivas y respetuosas.

Nosotros, como individuos, debemos parar de ser parte de esta industria y sociedad perversa. Podemos erradicar estos crueles sistemas económicos basados en el sufrimiento animal si dejamos de ser sus clientes. Una de las acciones más importantes que puedes hacer es cambiar a una dieta de origen vegetal. Con los hechos sobre la mesa, ya no hay excusa para no adoptarla.

“Be kind to all kind”. Hazte vegano. Por los animales, por el planeta, por tu salud.

 

1.- Greenhouse Gas Emissions from Animal Agriculture.  https://www.humanesociety.org/sites/default/files/archive/assets/pdfs/farm/hsus-fact-sheet-greenhouse-gas-emissions-from-animal-agriculture.pdf

2.- Preserving Antibiotics, Rationally . Aidan Hollis, Ziana Ahmed.- The  New England Journal of Medicine, Dec. 2013 .https://www.nejm.org/doi/full/10.1056/NEJMp1311479

 

The revenge of the Pangolin

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The all-mighty, arrogant human race is now feeling fragile and scared.

The novel coronavirus epidemic (covid-19) is the latest of a series of zoonotic virus known to be pathogenic in humans and threatens to become a pandemic. Recent coronavirus known to cause disease in human have been the source of SARS (Severe Acute Respiratory Syndrome) or MERS (Middle East Respiratory Syndrome) . All of them linked to animals that have been exploited by humans.

Pangolin

Pangolin carrying her baby – Picture credit : Associated Press – AP

It seems like the initial  covid-19 outbreak had its source in a market in the city of Wuhan, where live animals are kept in deplorable conditions. Cats, dogs, bats, snakes, deers,  chickens are jailed and have to watch terrified how they scald, burn alive and kill the other innocent animals, knowing they will suffer the same fate.

Wuhan wet market -Source : Weibo

Wuhan wet market -Source : Weibo

The pangolin is facing extinction, victim of the “traditional medicine” in China and many other Asian countries. Poachers around the world have made the pangolin the most poached mammal in the world. Of course, is not the only victim of human greed and ignorance. Sharks are also facing extinction, as well as rhinos and elephants which are brutally killed for their fins or horns. Cruel,  inhumane, barbaric ludicrous market in a name of a fake medicine, without any scientific evidence.

Factory Farming, antibiotic resistance global warming and prions

Asia is not alone in animal cruelty. Europe and the United States have the largest factory farms, where literally millions of sentient beings are sequestered, enslaved and killed every day.

In the dairy industry, cows are raped, their male baby calves are sent to the slaughter house shortly after birth, and many are kept with spikes around their mouth so they can not drink the milk from their mothers.

The meat and dairy are mass murder industries. They need to optimize the growth of the animal, so the faster they grow, the faster they are slaughtered. To shorten the lifecycle of the animals, they use growth hormones and antibiotics. Literally tons of antibiotic are used, not only for gaining weight, but to fight the diseases the animals carry due to the inhumane conditions under they are kept. That makes the livestock the largest antibiotic market as well as the largest source for antibiotic resistance that has a direct impact on human health.

 

Ironically, animal based diet is not only unnecessary in humans, but also unhealthy. Consumption of dairy products and meat leads to cardiovascular disease and different types of cancer. This fact is irrefutable. For many years the meat and dairy industry has been portraying a false reality about the health benefits of animal based diet. The lobby was such that even penetrated medical schools and the scientific literature. Now we know it has been a lie.

In an effort to optimize the “production” cycle, cows – herbivore animals –  had been feed with animal byproducts. This anti-natural practice led to the bovine spongiform disease, a devastating prion disease, invariably fatal. Many people, specially in Europe have succumbed to Variant Creutzfeldt–Jakob disease (vCJD) after eating meat of infected cows, and millions of cows put to death feared they carry the prion.

But that is not all. Factory farming is the leading source of global warming and deforestation. According to the Humane Society, factory farming accounts for 34% of methane (CH4) emissions, which has twenty times the global warming effect than carbon dioxide (CO2)[1] . Deforestation in the Amazon is happening at the highest rate. Amazon forests are being burnt to plant soy, and millions and millions of tons of precious natural resources like water is being wasted to livestock.

factory_farming

“The revenge of the Pangolin” actually represents the revenge of all species who have been exploited by the human being. It is the response of Mother Nature to our senseless acts, based on greed and ignorance that are leading the human race to self destruction. It would almost seem a curse has been put on humanity for the complete disrespect of other sentient beings  and Nature.

The novel Covid-19 coronavirus epidemic is the latest Nature response to the arrogant, ignorant, greedy, now scared to death humanity. It is a way of telling us that we are victims of our own evil actions.

I am still optimistic, but the time for acting is now.We should start by being humble. We have to honestly ask for forgiveness to all other species, and start a new empathetic, compassionate relationship with them.

Instead of walking around wearing (mostly useless) masks, we must take immediate action,  and the action is not just asking the scientific community to look for a vaccine, which would come late for many, and won’t work for the next strain. The action must be sustainable in the long term.

Governments and organizations such United Nations and World Health Organization should immediately put to stop to factory farming, meat and dairy industries. They must ban  poaching or animal markets anywhere in the World, and impose the highest penalties the countries who don’t comply. In parallel, they need to promote sustainable, organic agriculture practices. Governments should also focus on improving the education system where children learn, first and foremost, how to become kinder,  compassionate human beings.

We, as individuals, must stop being part of this wicked industry. These cruel economies based on animal suffering won’t survive if they don’t have clients.  On of the most important actions you can do is to change to a plant-based diet. You have the facts now, there is no excuse.

Be kind to all kind. Be vegan. For the animals, for the planet, for your health.

1.- Greenhouse Gas Emissions from Animal Agriculture.  https://www.humanesociety.org/sites/default/files/archive/assets/pdfs/farm/hsus-fact-sheet-greenhouse-gas-emissions-from-animal-agriculture.pdf

2.- Preserving Antibiotics, Rationally . Aidan Hollis, Ziana Ahmed.- The  New England Journal of Medicine, Dec. 2013 . https://www.nejm.org/doi/full/10.1056/NEJMp1311479

GNU HEALTH HMIS 3.6 series released

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Dear community:

I am very proud to announce the release of the GNU Health 3.6 series !

This version is the result of many developments and integration of ideas from the community.

We are now 11 years old. We should all be very proud because not only we have built the best Libre Health and Hospital Information System, but we have created a strong, committed and friendly international community around it.
What is new in GNU Health 3.6 series

  • Both GNU Health client and server are now in Python3
  • Remove Python2 support
  • GH HMIS server uses Tryton 5.0 LTS kernel (5 year support)
  • Client is based on Tryton GTK client 5.2
  • Automation on the GH Federation queue management
  • Integration to Orthanc DICOM server
  • Pages of Life models fully integrated with patient evaluation & GH Federation
  • GNU Health camera plugin integrated with the latest OpenCV
  • GH Client uses GI. Removed pygtkcompat.
  • GH Federation HIS has been migrated from MongoDB to PostgreSQL
  • New demo database downloader
  • Thalamus uses now uwsgi as the default WSGI
  • SSL is the default method for Thalamus and the GH Federation

Upgrading from GNU Health 3.4

  • Make a FULL BACKUP your kernel, database and attach directories !!!
  • Follow the instructions on the Wikibooks
  • Read specific instructions found under scripts/upgrade/3.6 of the main source installation tarball, an apply the scripts in the specified order.

Development focus

In addition of the GH HMIS server, we will focus the development in the following areas of the GNU Health ecosystem:

  • The GNU Health Federation Portal
  • The mobile client
  • Interoperability

The GH Federation Portal has already started. It is a VueJS application and provides a single point of entry for individuals, health professionals and epidemiologists to the GNU Health Information system.

The GNU Health Federation now receives information coming from many health institutions and people from a region or country. The GH Federation portal will allow to manage resources, as well as the main point for analytics and reporting of massive amount of demographics health data generated nationwide. People, health centers and research institutions (e.g. genomics) already can enjoy the benefits from the GNU Health Federation.

The mobile client (MyGNUHealth) development will remain in QT and will be focus on KDE plasma mobile technology, and run in Libre mobile operating systems and devices (such as Pine64). We need fully libre mobile devices if we want to preserve privacy in healthcare.

As far as Interoperability goes, GNU Health is now very interoperable. It uses open coding standards, as well as open formats (XML, JSON, .. ) to exchange messages. We currently have support for read operations in HL7 FHIR for a number of resources. Needless to say, we are open to other open standard communities that are willing to integrate to GNU Health.

Last but not least….no matter how hard we try to avoid them, there will be bugs, so please test the new system, upgrade process, languages, and give us your feedback via them via health@gnu.org

Happy and Healthy Hacking !


Dr. Luis Falcon, M.D.
President, GNU Solidario
GNU Health: Freedom and Equity in Healthcare
https://www.gnuhealth.org
GNUPG Fingerprint :ACBF C80F C891 631C 68AA 8DC8 C015 E1AE 0098 9199

GNU Health: 10 years of Freedom and Equity in Healthcare

Update: Last year (May 2018), the FSF asked me to write a post about GNU Health. Finally, here it is !


May 2018

social_medicine

Health is a non-negotiable human right. Access to quality healthcare must be public and universal.

I am back from my trip to India, where I spent a week with the team of All India Institute of Medical Sciences – AIIMS –, the largest public hospital in Asia and a leading research institution. They have taken the decision to adopt GNU Health, the Free Hospital and Health Information System.

One key aspect in Free Software is ownership. From the moment they adopted GNU Health, it now also belongs to AIIMS. They have full control over it. They can download and upgrade the system; access the source code; customize it to fit their needs; and contribute back to the community. This is the definition of Free Software.

The definition of Free Software is universal. GNU Health is equally valid for very large institutions, national public health networks and small, rural or primary care centers. The essence is the same.

GNU Health as a social movement: GNU Health is a social project with technology behind. It’s about Social Medicine and delivering universal healthcare. It’s about social activism. One of the main reasons that led me to create GNU Health were the tremendous inequalities in access to healthcare. Over 20000 children die every day from preventable, social diseases. To name a few : malnutrition, contaminated water, child slavery, prostitution, war, malaria, HIV-AIDS, tuberculosis, dengue and other neglected tropical diseases. These are causes and/or results of social diseases, conditions that have a higher impact and higher prevalence on the poor and the underprivileged.

Studying and getting a deeper understanding on the living conditions of people in rural areas and in urban ghettos around the world, reinforced my intention to write a system that included the socio-economic determinants of health and disease. Most of the time, health (and the lack of) is determined by the environment, and biology plays a lesser role. Proper nutrition, housing, sanitation, access to education and to primary healthcare are key for the dignity, development and health of the individual, family and society at large. I like to summarize it as “people before patients”.

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GNU Health implementation at Laos CMR Public Health hospital (CC BY-SA 4.0 GNU Solidario )

Nature and Nurture: Having Social Medicine on its DNA does not stop GNU Health from also working on the molecular basis of health and disease, precision medicine, bioinformatics and genetics. For instance, we incorporate state-of-the-art information from Unitprot containing thousands of gene natural variants involved in human disease. The bio-psycho-social GNU Health approach makes personalized medicine possible, and it builds the bridge between the clinician and the research institution, to better understand and fight multifactorial conditions such as Alzheimer’s disease or cancer. Both nature and nurture are present in GNU Health.

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GNU Health – Freedom and Equity in Healthcare

Trans-disciplinary team: GNU Health works at different levels. Social workers doing prevention in the field; health professionals taking care of the patients; Administrative team dealing with stock, human resources, finances and other internal health institution processes; and the ministry of health improving health campaigns based on the collected data. All these processes and tasks are interconnected, and the result of others.

The fight for Public Health System: I am observing how many countries are dismantling the Public Health system in favor of private corporations. This is not only sad, it is a crime. The only way we can guarantee proper and universal health care is by maintaining the Public Health system. Privatization of the public healthcare is evil, creates a health system for the rich, and excludes the underprivileged that can not afford insurance costs. Let me be very clear: healthcare is just a business for the corporation. Dr. René Favaloro said “Medicine without humanism is unworthy of being practiced”. I am not against the small private doctor office, that is complementary to the public health system. I am condemning the destruction of the current public health system, and putting it on the hands of large corporations that only care about money.

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GNU Solidario first project. Santiago del Estero 2006 . (CC BY-SA 4.0 Luis Falcon)

Public Health is a public good, so, as a result, anything related to public health should also be public. It is a contradiction to have proprietary software running in the public health system. Not only is contradictory and unethical, it poses many dangers to privacy and security of the individual health information. Private software is a black box. We don’t know what happens when a medical evaluation is recorded. Where else does this data go? Who can access it ? We simply don’t know, because we can not see the code behind the action.

Niños de una escuela de Camerún

Children in a Cameroon rural school (2018 CC BY-SA 4.0 Luis Falcon)

Collective Freedom and ethical software: Free software is a philosophy based on community, cooperation and solidarity. We all benefit from the work, effort and talent of others. GNU Health uses many Free Software (operating systems, programming languages, database engines, encryption libraries, etc.). Moreover, GNU Health is today the result of the contribution of many people and institutions. We must be grateful to the community, and make sure that nobody breaks the evolution chain. This is where the concept I call “collective freedom” comes into play. People or companies that take the work of others, and purposely make it non-free are breaking the chain of evolution. They have taken advantage of the good will from the community to lock-in them in. Purposely obfuscating the code, not providing upgrade scripts, hiding documentation are ways violating the “collective freedom” and making a system non-ethical. That is one of the reasons we differentiate between Free Software philosophy, which is ethical by definition, from “Open Source”, that has a more pragmatic approach to programming. Richard Stallman wrote an article “When Free Software depends on nonfree” (https://www.gnu.org/philosophy/when-free-depends-on-nonfree) , related to this concept. For Spanish speakers, you can read my article “El Software Libre no se Mancha” (http://www.rebelion.org/noticia.php?id=233717 ), also related to this concept of Collective Freedom.

Ten years of Freedom and Equity in Healthcare: During this 10-year period, we have seen GNU Health adopted in many different scenarios: Primary care centers and academic institutions in Argentina; in the tropical rainforest of Cameroon; Infectious diseases laboratory in Gabon; the eHealth system in Jamaica Ministry of Public Health; The Center for Physical Rehabilitation in Laos taking care of UXO victims; Red Cross hospitals in Mexico or the largest public hospital in India and Asia. They are all different contexts and peculiarities, yet they all share the same spirit, that is, delivering Freedom and Equity in healthcare to the people.

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GNU Health at the United Nations – International Institute for Global Health

Let’s celebrate this 10 years of GNU Health, a social movement with technology behind. Let’s keep on fighting for health to be a non-negotiable human right.

 

 

Reconocimiento OpenAwards 2019 en Medicina y Ciencia

Hoy me siento honrado con este importante reconocimiento en OpenExpo 2019 , el mismo Día mundial de Refugiado .Se lo dedico a ellos y a los profesionales de la Sanidad Pública, que día tras día defienden la Salud como un derecho humano no negociable. Seguiremos trabajando por GNU Health y por llevar dignidad y salud alrededor del mundo.
Openaward 2019a Luis Falcon en Medicina y Ciencia