Update projects

_pages/blog.md

@@ -1,7 +1,7 @@
 ---
 layout: default
 permalink: /blog/
-title: blog
+title: Blog
 nav: true
 nav_order: 1
 pagination:

_pages/projects.md

@@ -5,7 +5,7 @@ permalink: /projects/
 description: My collection of professional projects including original research, writing and collaborative work.
 nav: true
 nav_order: 3
-display_categories: [work, fun]
+display_categories: [Neuroscience research, Image and data analysis, Data visualization]
 horizontal: false
 ---
 

_projects/1_project.md

@@ -1,10 +1,10 @@
 ---
 layout: page
 title: Point pattern analysis (PPA) for neuroscience
-description: Implementation of Point pattern analysis (PPA) to examine the spatial arrangement/distribution of cells. 
+description: Point pattern analysis (PPA) to examine the spatial arrangement/distribution of cells. 
 img: assets/img/Pointanalysis.png
-importance: 1
-category: image analysis
+importance: 2
+category: Image analysis
 ---
 
 I am exploring ways to incorporate Point patterns analysis (PPA) for the analysis of microscopy images in neuroscience. PPA allows the investigation of the spatial arrangement/distribution of cells, like neurons and neuroglia, in the healthy and disease central nervous system. Indeed, it has application in multiple biomedical fields. I perform point pattern analysis using the [spatstat](https://spatstat.org/download.html) package in R-programming language. 

_projects/2_project.md

@@ -1,10 +1,10 @@
 ---
 layout: page
 title: Topological data analysis for neuroscience
-description: Implementation of Topological Data Analysis (TDA) to examine the spatial arrangement/distribution of cells. 
+description: Topological Data Analysis (TDA) to examine topological features of point clouds. 
 img: assets/img/TDAimg.jpg
-importance: 2
-category: image analysis
+importance: 3
+category: Image analysis
 ---
 
 Topological data analysis (TDA) is an approach that uses algebraic topology to analyze complex data sets, including point clouds. With TDA, the user can evaluate the degree of noise, variability, and complexity, as well as identifying topological features such as holes, loops, and voids in the point clouds at different scales. This approach is based on tools like vietoris-rips complexes and persistent homology that allow to visualize complex topological structures.

_projects/3_project.md

@@ -1,81 +1,12 @@
 ---
 layout: page
-title: project 3
-description: a project that redirects to another website
-img: assets/img/7.jpg
-redirect: https://unsplash.com
-importance: 3
-category: work
+title: Medium blogs
+description: My writing/blogs about science, data analysis and visualization in Medium
+img: assets/img/20240203_BeyondTheMean_AnimalID2.png
+redirect: https://medium.com/@damanrique
+importance: 1
+category: Image and data analysis
 ---
 
-Every project has a beautiful feature showcase page.
-It's easy to include images in a flexible 3-column grid format.
-Make your photos 1/3, 2/3, or full width.
 
-To give your project a background in the portfolio page, just add the img tag to the front matter like so:
 
-    ---
-    layout: page
-    title: project
-    description: a project with a background image
-    img: /assets/img/12.jpg
-    ---
-
-<div class="row">
-    <div class="col-sm mt-3 mt-md-0">
-        {% include figure.liquid loading="eager" path="assets/img/1.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-    <div class="col-sm mt-3 mt-md-0">
-        {% include figure.liquid loading="eager" path="assets/img/3.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-    <div class="col-sm mt-3 mt-md-0">
-        {% include figure.liquid loading="eager" path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-</div>
-<div class="caption">
-    Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles.
-</div>
-<div class="row">
-    <div class="col-sm mt-3 mt-md-0">
-        {% include figure.liquid loading="eager" path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-</div>
-<div class="caption">
-    This image can also have a caption. It's like magic.
-</div>
-
-You can also put regular text between your rows of images.
-Say you wanted to write a little bit about your project before you posted the rest of the images.
-You describe how you toiled, sweated, _bled_ for your project, and then... you reveal its glory in the next row of images.
-
-<div class="row justify-content-sm-center">
-    <div class="col-sm-8 mt-3 mt-md-0">
-        {% include figure.liquid path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-    <div class="col-sm-4 mt-3 mt-md-0">
-        {% include figure.liquid path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-</div>
-<div class="caption">
-    You can also have artistically styled 2/3 + 1/3 images, like these.
-</div>
-
-The code is simple.
-Just wrap your images with `<div class="col-sm">` and place them inside `<div class="row">` (read more about the <a href="https://getbootstrap.com/docs/4.4/layout/grid/">Bootstrap Grid</a> system).
-To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes.
-Here's the code for the last row of images above:
-
-{% raw %}
-
-```html
-<div class="row justify-content-sm-center">
-  <div class="col-sm-8 mt-3 mt-md-0">
-    {% include figure.liquid path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-  </div>
-  <div class="col-sm-4 mt-3 mt-md-0">
-    {% include figure.liquid path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-  </div>
-</div>
-```
-
-{% endraw %}

_projects/4_project.md

@@ -1,80 +1,43 @@
 ---
 layout: page
-title: project 4
-description: another without an image
-img:
+title: Glial reactivity
+description: Research on glial reactivity following brain injury
+img: assets/img/Glial scarring.jpg
 importance: 3
-category: fun
+category: Neuroscience research
 ---
 
-Every project has a beautiful feature showcase page.
-It's easy to include images in a flexible 3-column grid format.
-Make your photos 1/3, 2/3, or full width.
+As a neuroscientist, I am focused on understanding glial reactivity after brain injury. I am particularly interested in astrocytes and their derived extracellular matrix molecules. Recently, I have ventured into the study of PDGFR-B cells and their contribution to fibrotic scar.  
 
-To give your project a background in the portfolio page, just add the img tag to the front matter like so:
-
-    ---
-    layout: page
-    title: project
-    description: a project with a background image
-    img: /assets/img/12.jpg
-    ---
 
 <div class="row">
     <div class="col-sm mt-3 mt-md-0">
-        {% include figure.liquid loading="eager" path="assets/img/1.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-    <div class="col-sm mt-3 mt-md-0">
-        {% include figure.liquid loading="eager" path="assets/img/3.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-    <div class="col-sm mt-3 mt-md-0">
-        {% include figure.liquid loading="eager" path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
+        {% include figure.liquid loading="eager" path="assets/img/Glial scarring.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
     </div>
 </div>
 <div class="caption">
-    Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles.
-</div>
-<div class="row">
-    <div class="col-sm mt-3 mt-md-0">
-        {% include figure.liquid loading="eager" path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-</div>
-<div class="caption">
-    This image can also have a caption. It's like magic.
+    Multicellular reactivity and glial scar formation (Manrique-Castano and Elali (2021).
 </div>
 
-You can also put regular text between your rows of images.
-Say you wanted to write a little bit about your project before you posted the rest of the images.
-You describe how you toiled, sweated, _bled_ for your project, and then... you reveal its glory in the next row of images.
+## Resources
 
-<div class="row justify-content-sm-center">
-    <div class="col-sm-8 mt-3 mt-md-0">
-        {% include figure.liquid path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-    <div class="col-sm-4 mt-3 mt-md-0">
-        {% include figure.liquid path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-    </div>
-</div>
-<div class="caption">
-    You can also have artistically styled 2/3 + 1/3 images, like these.
-</div>
+The following are research/resources I have been involved:
 
-The code is simple.
-Just wrap your images with `<div class="col-sm">` and place them inside `<div class="row">` (read more about the <a href="https://getbootstrap.com/docs/4.4/layout/grid/">Bootstrap Grid</a> system).
-To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes.
-Here's the code for the last row of images above:
+### Research articles and book chapters
 
-{% raw %}
+  - **In progress**: I am writing  popular science book on astrocytes. I hope to finish it soon.
+
+  - My [research article](https://www.biorxiv.org/content/10.1101/2023.10.04.560910v1) applying Point pattern analysis (PPA) and Topological data analysis (TDA) for the examination of glial scar formation.
+
+  - My [research article](https://www.sciencedirect.com/science/article/pii/S0945053X22000555) showing that tenascinc-C (TnC) restrict astrologists following brain injury.
+
+  - In this [book chapter](https://exonpublications.com/index.php/exon/article/view/cerebral-ischemia-neurovascular-reactivity) I summarize the different phases of glial reactivity and how it contributies to glial/fibrotic scar formation.
+
+  - My [research article](https://www.sciencedirect.com/science/article/pii/S0945053X22000555) showing that tenascinc-C (TnC) modulates the infiltration of immune T-cells.
+
+  - My [review](https://journals.sagepub.com/doi/10.1177/1756286418818092) showing how the extracelular matrix contributes to brain remodeling following injury.
+
+### Datasets
 
-```html
-<div class="row justify-content-sm-center">
-  <div class="col-sm-8 mt-3 mt-md-0">
-    {% include figure.liquid path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-  </div>
-  <div class="col-sm-4 mt-3 mt-md-0">
-    {% include figure.liquid path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
-  </div>
-</div>
-```
+  - This [Zenodo repository](https://zenodo.org/records/8399976) contains microscopy images of Gfap (astrocytes) Iba1 (microglia) and NeuN (Neurons) following cerebral ischemia.The repository also contains the point patterns analyzed in [this](https://www.biorxiv.org/content/10.1101/2023.10.04.560910v1) research artcle. 
 
-{% endraw %}