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Towards Stratified Healthcare and Precision Medicine for Developing Economies during the Covid-19 pandemic through Network Modelling and Natural Language Processing

Nowadays, the ever-increasing volume of information recorded every second has brought significant opportunities and challenges to both life and science. For instance, during the current Covid-19 situation, several medical records are being registered in large databases, and this data brings up two essential, yet straightforward, questions: How to identify and warn possible patients at risk from current patients data? And is there a way to identify successful procedures to threat Covid-19? In this work, we discuss how Network Modelling and Natural Language Processing, which are valuable tools from Data Science, can deliver an answer to these questions in a Stratified Healthcare and Precision Medicine context. Furthermore, we also provide an ethical discussion of to what extent these methods may impact the public.

Let us present one example which is currently happening in clinics and hospitals worldwide: In a third-world country, there are numerous medical facilities currently overwhelmed with Covid-19 patients. As the World Health Organization has not identified a standard procedure to tackle the virus, many doctors and nurses are dazzled trying to treat patients effectively and develop a prognosis. This process is affected by several factors: limited medical resources, lack of a standard procedure nationwide, patients from different medical backgrounds, and a pressing need for quick medical response. However, every step of treatment gets its digital footprint in a local database. This example is an open door for Stratified Healthcare and Precision Medicine. The first is the ability to identify essential differences across populations and to act accordingly in healthcare provision; whereas, the second focuses on establishing a prognosis for each patient based on genetic, environmental, and lifestyle factors. To see how to implement these, we now introduce Network Modelling and Natural Language Processing.

Network Modelling (NM) is the study of the interaction between objects or entities. It uses graphs to represent relationships. Here we present two uses of NM for our example above. Firstly, Systems Biology approach to the study of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has effectively revealed the life span of the virus in different surfaces, and determined the structure of its proteins, explaining its transmission rate and effect on human cells. With this information, hospitals can take measures which could prevent community spread of the virus. Also, labs can research on proteins reaction to assist the production of new therapies and drugs, complemented by hospital records on patient-specific datasets during trials, ultimately reaching Precision Medicine. Secondly, by using a communication network, it is possible to identify and prevent future cases of people with risk of dying of Covid-19. Through the Resource Description Framework (RDF), we can trace a path between a current Covid-19 patient and their household. Hence, if a patient is certainly in touch with someone of a population of high risk, additional measures can be taken to prevent contagion or to do a preventive intervention, thus accomplishing stratified healthcare.

Natural Language Processing (NLP) is an area of Data Science focused on processing, analyzing, and interpreting human languages. Focusing on Precision Medicine, NLP is useful when analyzing pathology reports to relate records to an individual's health. However, it is essential to identify a standard set of procedures that have, historically from a data point of view, been successful in treating the virus; hence, allowing for a more informed decision to be made when considering treatment options. There are several ways to do this, like using rule-based techniques or machine learning. For instance, university hospitals, in partnership with IBM, can use Watson to determine the best method to perform this analysis quickly. Laterwards, this knowledge could be applied nationwide with the use of open-source packages like NLTK. However, if there is no access to this kind of tools, engineers, mathematicians, and statisticians can collaborate with health professionals to provide an NLTK-based nationwide tool. Whatever the method, we would focus on accurately classifying a patient and find the steps that the medical team took to treat it. This way, we can use this technique of Precision Medicine to develop Stratified Healthcare.

At this point, we have seen how combining NM and NLP are useful tools to develop Precision Medicine and Stratified Healthcare for our example above. Moreover, they have been essential in answering the questions proposed at the beginning of this piece of work. Notwithstanding, we have not considered the difficulties related to both approaches, which are of technical and ethical nature.

Not surprisingly, to apply any of the tools previously described for the example discussed, we need a stable internet connection, a server to store data, and computation capability. In third-world economies, this is sometimes too much to ask. Furthermore, if we could overcome these issues, then the lacking of a systematic medical terminology, like SNOMED-CT, would limit processing. Without medical supervision, the output of the analysis would be limited, yet guaranteeing medical assistance for research during the pandemic is not practical, even less if professionals do not know how to use a computer. Without a doubt, if the country overcomes these challenges, then a great opportunity would be ahead. We could not only tackle the pandemic efficiently, we could, more importantly, develop a Data Science-based Health System, and we would have the tools for future disease control.

From the ethical point of view, what pops up pretty quickly are privacy concerns. Consent is essential to apply NM in identifying risky cases, as patients may not want to disclose their personal information nor identify the participants of their households. Information breaches, hacking, discrimination by neighbours, and personal motives are among the fears of compliance. Likewise, the proposed use of NLP includes these drawbacks alongside a possible misuse of information from organizations and researchers. Even though these tools may bring a benefit, they can also affect the wellbeing of the public. Thus, the state and research facilities should guarantee an ethical treatment of data, similar to the General Data Protection Regulation, always assuring consent accurately and adequately. This way, an equilibrium can be reached to both, benefit the nation and ensure people's rights.

Some references:

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. https://www.ncbi.nlm.nih.gov/pubmed/32075877

Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1. https://www.ncbi.nlm.nih.gov/pubmed/32182409

These open-access articles are available at:

https://science.sciencemag.org/content/367/6483/1260.long

https://www.nejm.org/doi/pdf/10.1056/NEJMc2004973

[andy-we-ardilla]

[andy-we-ardilla]

oye chiquillx,

te molestaría 

pasarme a buscar

y llevarme lejos

de la monotonía

o simplemente 

a mirar la luna?

[andy-we-ardilla]

¿Y este barro bilear?

[andy-we-ardilla]

“La vida sin un poco de riesgo es monotonía”

—

Taro-Y-Capa

[andy-we-ardilla]

Mi familia es atípica en algunos aspectos. Uno de ellos es la entrega y desinterés: No solemos hacer las cosas para sacar beneficio de otros. Solo… damos. Y ya. A veces para bien, otras para mal.

El día de hoy, hablaba con mi madre al respecto de unos primos míos. Y me dijo:

«Por último, si quiere algo, hasta por interés, se hace algo.» (MRTO, 2018)

Me dio mucha intriga. En mi familia ese «Por último» es ya de últimas. Lo peor, algo malo, ajeno, molestoso.

[andy-we-ardilla]

Sci-hub isn’t taking money from authors.

[andy-we-ardilla]

Una pequeña obsesión

Cuando era pequeño no le encontraba el gusto a la lectura. Me parecía burdo pasar horas sin producir sonido alguno frente a papel con palabras. Un marco de absurdo con gotero de tinta temporal.

Cuando era pequeño, veía televisión durante cuatro o más horas al día. A veces con atención, otras veces como acompañante o distractor. Otras veces como ruido de fondo mientras jugaba a construir con plastilina. Sin libros, sin instrucciones, sin otros mundos.

Cuando era pequeño, mi madre buscaba formas de sugerirnos la lectura, formas de entender más allá. Mi hermana colgaba de un auricular, yo de creaciones y mundos imaginarios en mi casita de plástico.

Cuando llegaron mis once, tras dos películas y varias épocas de aburrimiento frente a un adiós forzado y la imposibilidad de escapar más, mi madre me regaló un libro. Uno que tomaría y ejercería su lugar en mi librero que no tenía libros. Uno. Desde mi cama lo puedo observar, siempre fiel. Siempre mío. Uno. Y podría tal vez donar todos los otros… pero ese libro se quedaría conmigo. Sé su textura, conozco su olor. Sus colores y hasta de qué tinta cogea.

Cuando llegaron más libros el librero se dio a lucir. 1, 2, 5 de repente, 1, 1, 3, 1… y mi madre los ordenaría. Al inicio indistintamente, aunque agrupándolos en base a su cercanía. Teniendo en cuenta su tamaño. A veces su color.

Y es que ahora…

Cuando toco los que llamo mis libros,

Cuando los limpio,

Cuando les sonrío con nostalgia y placer,

Cuando los veo de reojo y compruebo que no se han movido,

(aunque no puedan)

Pero por si acaso…

Cuando mis libros son libros, yo los ordeno aún con ese cuidado. Esa necesidad de tenerlos en un orden, considerando su color, su cercanía, su impacto. El amor que les tengo… el color que me han dejado.

[andy-we-ardilla]

🍁

[andy-we-ardilla]

Speech

Hola,

Empezar con una antítesis me es esencial para que mis palabras sean naturales, cercanas, cálidas. Es así que este saludo informal contrasta con esta ocasión especial. Hoy es un día de gozo para muchos de nosotros, para otros es un día de expectativas y para algunos, incluidos nuestros familiares, es un día de alivio. Hoy somos colegas.

El tiempo pasa como retumban las cuerdas. Un día entramos a la Escuela Politécnica Nacional, con perspectivas sobre la vida, la ciencia y el mundo. Nuestras metas y visiones sucedieron a una vida colegial igual de fugaz. Recuerdo que al empezar a estudiar Matemática, tomé una apuesta a lo desconocido, que aparentaba encontrarme con lo no-obvio y desenmascaré que buscamos lo que creemos. Soy quien entró a estudiar lo que no son números por su pasión por la imagen. En dicho marco viví, trabajé, serví, investigué, viajé y establecí lazos con personas espléndidas. Además, también tuve malos momentos, desveladas por un código y pruebas aleatorias de doble filo. ¿Cambiaría algo? Algunas cosas. Aunque volvería a vivir muchas. Porque tanto los buenos como los malos momentos me han traído aquí, y a ustedes también. En este punto es grato mirar atrás y sentir los pasos, la trama que nos ha llevado a este desenlace y, en este punto, los felicito. Graduarse es un proceso, superar el papeleo es otro, sobresalir ante la presión, la tesis y el estrés frente a la perseverancia en los años de estudio, eso es nuestro logro.

En este punto y para terminar, recolijo mi barroco y expreso una idea hambrienta que tuve desde que supe que estaría al frente de ustedes: Hoy, estimadas y estimados colegas, les hago un llamado a la equidad. A que todas y todos trabajemos en conjunto sin complejos, sin prejuicios. Que al integrarnos hoy al ámbito profesional del país, creemos puentes entres nosotros y no muros de concreto. Porque ahora adquirimos un compromiso con nuestro país, de ser más que aquello que no nos gusta; de estar encima del dinero y un género, de aportar con nuestra sociedad cambiante. Como profesionales seremos el país… y ello no es cuestión de unos académicos o unas pocas potencias, es de todas las científicas, ingenieras, científicos e ingenieros que ahora en esta sala, comparten un nuevo aire, y están, estoy seguro, dispuestos a mejorar nuestra patria. 

Graduadas y graduados, sus acciones definirán el progreso de nuestra sociedad. Aventúrense a seguir persiguiendo sus metas, vivir sus colores, borrar sus barreras y no sombrear sus sueños.

Muchas gracias

[andy-we-ardilla]

[andy-we-ardilla]

UniCorgi

instagram @stefanieshank

[andy-we-ardilla]

I’m comfortable with the unknown—that’s the point of science. There are places out there, billions of places out there, that we know nothing about. And the fact that we know nothing about them excites me, and I want to go out and find out about them. And that’s what science is. So I think if you’re not comfortable with the unknown, then it’s difficult to be a scientist… I don’t need an answer. I don’t need answers to everything. I want to have answers to find.

Brian Cox

[andy-we-ardilla]

Kindness is so underrated! I feel like we emphasize the importance of being smart, working hard, or being strong… but in my experience, kindness can have the most impact. I won’t forget the times that people were exceptionally kind to me. 💕

Instagram | Patreon | Webtoon

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[andy-we-ardilla]

Geometry