Published on 16 Jun 2018.
Tagged:
publication
sepsis
In an earlier post I discussed the damage sepsis can do. It has been a focus of many of the projects I have been involved with for the past few years even though the group I am with is tasked with studying kidney disease. We are interested in sepsis because it is a major cause of acute kidney injury.
We do not yet know all the details of this link. Knowing exactly when kidney function falls after sepsis and what triggers the fall could be very important. It would help in developing clinical procedures and therapies to manage patients with sepsis at risk of acute kidney injury.
I recently published a study exploring one potential cause of falling kidney function during sepsis. The kidney filters the blood and removes excess fluid, solutes, and toxins from the body. The blood passes through the glomerulus where fluid can leak out. The volume at this stage is very large and includes many good things the body wants to keep. This fluid then passes through other specialized structures including the tubules where most of the fluid and useful solutes are re-absorbed. To prevent the body from losing too much fluid if the tubules are not working there is a feedback loop that stops the glomeruli producing filtrate.
Using a genetic model I tested whether this feedback loop is activated during sepsis. The results have just been published in the American Journal of Physiology. Renal Physiology.
Published on 16 Apr 2018.
Tagged:
security
python
Whilst working on my previous post on two factor authentication I was reminded of the broad spectrum of approaches taken to security by many sites. I have one bank that does two factor authentication, another using the standard username/password combination for one factor authentication, and then another that asks for a username, a piece of personal information and then a partial password. In this case, three characters from a password.
Of these three approaches it is the last that seems the weakest. The piece of personal information includes things like the town you grew up in, the name of your first school, etc. These are not generally secret and could be discovered for most people by a bit of research. The partial password scheme seems only slightly stronger than a three character password.
I believe the partial password is intended to prevent a keylogger on your computer from compromising your entire password. This scheme is often paired with selecting characters from a dropdown menu, potentially providing additional protection. The idea is that by requesting different characters on each visit you would need to log in multiple times on a compromised computer before an attacker discovered your entire password.
I don't think such a system would be used in a new application today but I did wonder how such a scheme might be implemented.
Continue reading ...
Published on 08 Apr 2018.
Tagged:
security
python
Postgresql
flask
fido u2f
This is the first semester since the Fall of 2015 that I have not taught a course with the Foundation for Advanced Education in the Sciences. It was a pleasure teaching and I was lucky enough to spend most of my time on a course I had designed. For the Spring 2016 semester I designed the syllabus and began teaching a course on machine learning and object oriented python. I chose to include a web application as I felt it exposed the students to some unfamiliar ideas.
Most of the students were fellow scientists. Many only had previous experience writing scripts for use in their own research. Not trusting user input was often a novel concept. During the course I only had a couple of hours to introduce web applications. This meant I skipped over many important topics. I intend this post to be the first in a collection moving beyond the basics for anyone still new to these concepts. I will start with a basic background but the actual implementation will hopefully be new for most. If implementing web application authentication is familiar to you then skip ahead to the implementation.
Let me know if there are topics you think I should cover moving forward.
In this post I will cover authentication, specifically adding a second authentication factor for additional security.
Continue reading ...
Published on 27 Jan 2018.
Tagged:
python
microscopy
deep learning
I'm just back from the UK where I spent a couple weeks catching up with family and friends. My visit happened to conincide with one of the monthly PyData London events so I attended and gave a lightning talk on image segmentation in medical applications.
They have built a really vibrant community and it was great meeting over 200 data enthusiasts.
The slide deck is available here. Unfortunately there was no video. The content is a more technical version of the presentation I gave at the NIH Pi Day 2017 event where there was video.
Published on 13 Aug 2017.
Tagged:
publication
exosomes
I've studied exosomes since the Summer of 2007 when I did my MSc dissertation project and then PhD in the laboratory of James Dear. When it came time to move on I was fortunate in finding my current position where I could explore new areas without moving away entirely from the exosome field where I had so much experience.
An opportunity to revisit the exosomal field came at the beginning of 2016 when we were invited to write three separate book chapters and review articles on exosomes. The third manuscript, a chapter in the book "Drug Safety Evaluation", has just been published online.
Inevitably the manuscripts have some overlap but they each focus on different aspects of exosomes and their study. The highlight was having a figure from our article in the journal of cellular physiology on the front cover of the issue.
The three manuscripts are:
Urine Exosome Isolation and Characterization is focused on the methods we use to collect, process, and characterize exosomes.
Urine Exosomes: An Emerging Trove of Biomarkers is a review of the potential and challenges in bringing exosome based biomarkers into clinical use.
Quantification of Exosomes is a review of the options available for determining the concentration of exosomes.