diff --git a/archetypes/people.md b/archetypes/people.md
index 11012bd18cc235cfa60dce2c15046a78fa67d2dc..021fbefa82805fa1ade3b0a81526416b14775a84 100644
--- a/archetypes/people.md
+++ b/archetypes/people.md
@@ -8,5 +8,7 @@ pic: "NoPic.jpg"
tit: ""
orcid: ""
weight: ""
+current: true
---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
diff --git a/config.toml b/config.toml
index abcc00b14d6e7505441716b16c9c6e963fb2e1ab..4e80efa6e5013fa9a1982aafea5e13212039135e 100644
--- a/config.toml
+++ b/config.toml
@@ -1,6 +1,7 @@
-baseurl = "https://www.StrandLab.net/"
+baseurl = "http://www.strandlab.net.s3-website.us-east-2.amazonaws.com/"
title = "Strand Lab"
author = "Gervaise H. Henry"
+theme = "blackburn"
# Shown in the side menu
copyright = "© 2019. All rights reserved."
canonifyurls = true
@@ -28,45 +29,41 @@ paginate = 10
custom_css = [""]
custom_js = [""]
- [params.piwikAnalytics]
- siteid = 2
- piwikroot = ""
-
[menu]
# Shown in the side menu.
[[menu.main]]
name = "Research"
- pre = "<i class='fa fa-home fa-fw'></i>"
+ pre = "<i class='fas fa-home fa-fw'></i>"
weight = 1
identifier = "research"
url = "/research"
[[menu.main]]
name = "People"
- pre = "<i class='fa fa-user fa-fw'></i>"
+ pre = "<i class='fas fa-user fa-fw'></i>"
weight = 2
identifier = "people"
url = "/people/"
[[menu.main]]
name = "Publications"
- pre = "<i class='fa fa-book fa-fw'></i>"
+ pre = "<i class='fas fa-book fa-fw'></i>"
weight = 3
identifier = "publications"
url = "/publications/"
[[menu.main]]
name = "Biorepository"
- pre = "<i class='fa fa-stethoscope fa-fw'></i>"
+ pre = "<i class='fas fa-stethoscope fa-fw'></i>"
weight = 4
identifier = "repository"
url = "/repository/"
[[menu.main]]
name = "Single-Cell Data"
- pre = "<i class='fa fa-bar-chart fa-fw'></i>"
+ pre = "<i class='fas fa-chart-bar fa-fw'></i>"
weight = 5
identifier = "data"
url = "/data"
[[menu.main]]
name = "Contact"
- pre = "<i class='fa fa-phone fa-fw'></i>"
+ pre = "<i class='fas fa-phone fa-fw'></i>"
weight = 6
url = "/contact"
@@ -78,4 +75,11 @@ paginate = 10
twitter = "strand_lab"
# Techie
- biohpcgitlab = "StrandLab/"
\ No newline at end of file
+ biohpcgitlab = "StrandLab/"
+
+[deployment]
+ order = [".jpg$", ".gif$"]
+
+ [[deployment.targets]]
+ name = "aws"
+ URL = "s3://www.strandlab.net?region=us-east-2"
\ No newline at end of file
diff --git a/content/contact.md b/content/contact.md
index f7f37af989b06439d44b558c68df7ecdcdbb125a..7bcad1787bf42995f66bf332493e10eef607567c 100644
--- a/content/contact.md
+++ b/content/contact.md
@@ -1,76 +1,7 @@
---
title: "KEEP IN TOUCH WITH US"
date: 2019-05-19T13:49:34-05:00
-draft: true
+draft: false
+type: "custom"
+layout: "contact"
---
-<style>
- .map {
- position: relative;
- padding-bottom: 50%;
- height: 0;
- overflow: hidden;
- }
- .map iframe {
- position: absolute;
- top: 0;
- left: 0;
- width: 100% !important;
- height: 100% !important;
- }
- @media (min-width: 1000px) {
- .column {
- float: left;
- }
- .left {
- width: 10%;
- }
- .right {
- width: 90%;
- }
- .row:after {
- content: "";
- display: table;
- clear: both;
- }
- }
-</style>
-
-<p style='text-align: center;'>
-Questions about our research or need a tip on one of our protocols? Interested in collaborations? Email us, mention any person, project, or activity of interest,and we will get back to you soon!
-</p>
-
-<div class="map">
-<iframe src="https://www.google.com/maps/embed?pb=!1m14!1m12!1m3!1d5666.067598000117!2d-96.84034317995817!3d32.81593873821668!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!5e0!3m2!1sen!2sus!4v1558292028882!5m2!1sen!2sus" frameborder="0" style="border:0" allowfullscreen></iframe>
-</div>
-
-<div class="row">
-<div class="column left">
-<i class="fa fa-map-marker fa-2x"></i><br>
-</div>
-<div class="column right">
-UT Southwestern Medical Center,<br>
-Department of Urology,<br>
-5323 Harry Hines Blvd,<br>
-Mail Code: 9110,<br>
-Dallas, TX 75390-9110<br>
-</div>
-</div>
-___
-<div class="row">
-<div class="column left">
-<i class="fa fa-envelope-open fa-2x"></i><br>
-</div>
-<div class="column right">
-[douglas.strand@utsouthwestern.edu](mailto:douglas.strand@utsouthwestern.edu)
-</div>
-</div>
-___
-<div class="row">
-<div class="column left">
-<i class="fa fa-phone fa-2x"></i><br>
-</div>
-<div class="column right">
-214-648-6096
-</div>
-</div>
-___
\ No newline at end of file
diff --git a/content/data.md b/content/data.md
index 4ac380f0449f898e4c35375b07c753bbf24471b9..ea3ee3b314027c44a77783e49341ae8cd4abd752 100644
--- a/content/data.md
+++ b/content/data.md
@@ -1,122 +1,7 @@
---
title: "Single-Cell RNA-seq Data"
date: 2019-06-10T21:49:01-05:00
-draft: true
+draft: false
type: "custom"
layout: "data"
---
-
-<style>
- .content{
- margin: 0;
- max-width: none;
- }
- .select {
- float: top;
- z-index: 1;
- top: 0px;
- background: #191818;
- overflow-x: hidden;
- padding: 8px 10px;
- }
- .columnS {
- float: left;
- text-align: center;
- width: 33.33%;
- }
- .columnF {
- float: left;
- text-align: center;
- width: 33.33%;
- }
- .row:after {
- content: "";
- display: table;
- clear: both;
- }
- img{
- max-width: 100%;
- height: auto;
- }
- @media (max-width: 1000px) {
- .columnS {
- text-align: right;
- width: 100%;
- }
- .columnF {
- width: 100%;
- }
- br {
- display: none;
- }
- }
-</style>
-<body>
- <div class = "select">
- <div class = "columnS ui-widget">
- <label for = "gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
- <br>
- <input id = "gene">
- </div>
- <div class = "columnS">
- <label for="lineage" style="font-size:18px;"><b>Select a cell lineage to display:</b></label>
- <br>
- <select name="lineage" id="lineage">
- <option selected="selected" value="all">All Cells</option>
- <option value="epi">Epithelial Cells Only</option>
- <option value="st">Stromal Cells Only</option>
- </select>
- </div>
- <div class = "columnS">
- <label for="populations" style="font-size:18px;"><b>Select a group of cell populations:</b></label>
- <br>
- <select name="populations" id="populations">
- <option>Lineage</option>
- <option>Patient</option>
- <option selected="selected" value="Populations"> Cell Populations</option>
- <option value="Zone">Prostatic Zone</option>
- </select>
- </div>
- <br>
- <button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
- <hr>
- <div>
- <span style="font-size:16px; font-weight:bold; " >Experimental details:</span>
- <br>
- <span style="font-size:16px;">Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from the prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were clustered and identified by correlation of their transcriptomes to known cell types. Gene expression can be compared by population identity, cell lineage, patient, or dissected prostatic zone.</span>
- </div>
- </div>
- <div align = "center">
- <h1 id="label.gene">NO GENE SELECTED</h1>
- <h2 id="label.lineage"></h2>
- <div class = "columnF">
- <h3 id="label.ClusterVis"></h3>
- <div class = "img">
- <img id="img.ClusterVis" src=""/>
- </div>
- <br>
- </div>
- <div class = "columnF">
- <h3 id="label.Feature"></h3>
- <div class = "img">
- <img id="img.Feature" src=""/>
- </div>
- <br>
- </div>
- <div class = "columnF">
- <h3 id="label.ViolinBox"></h3>
- <div class = "img">
- <img id="img.ViolinBox" src=""/>
- </div>
- <br>
- </div>
- </div>
- <hr>
- <div align = "left">
- <div><span style="font-size:18px; font-weight:bold; " >Publication found at:</span></div>
- <div><span style="font-size:16px;" > <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875">Cell Reports</a></span></div>
- <div><span style="font-size:18px; font-weight:bold;" >Raw data found at:</span></div>
- <div><span style="font-size:16px;" > <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403">GEO: GSE117403</a></span></div>
- <div><span style="font-size:16px;" ><a href="https://doi.org/10.25548/W-R8CM">GUDMAP: W-R8CM</a></span></div>
- </div>
-</body>
diff --git a/content/people/henry_g.md b/content/people/henry_g.md
index a7ecf00c4a3355140f3cb8afb340560cffb3d6cf..a233cee7f9e1be9eaaa6d163ca59219a59bd6430 100644
--- a/content/people/henry_g.md
+++ b/content/people/henry_g.md
@@ -1,13 +1,15 @@
---
title: "Henry_g"
date: 2019-05-18T21:34:35-05:00
-draft: true
+draft: false
name: "Gervaise H. Henry"
degree: "M.S."
pic: "henry_g.jpg"
-tit: "Research Technician"
+tit: "Computatonal Biologist"
orcid: "0000-0001-7772-9578"
weight: "10"
+current: true
---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
-Gervaise obtained his master's degree at American University in 2015. He joined Dr. Strand’s lab in 2015.
\ No newline at end of file
+Gervaise obtained his master's degree at American University in 2015. He joined Dr. Strand's lab in 2015. His previous experience involved the utilization of a diverse set of molecular techniques to investigate cancer biology. He also has a strong background in early-stage drug discovery, including the use of lab robotics. After a very successful fellowship with UT Southwestern Bioinformatics Department's Bioinformatics Core Facility (BICF), he transitioned to a more computational role in the lab. He is responsible for the analysis of sequencing, in particular single-cell RNA-sequencing analysis. He also builds pipelines for automated analysis, and tools for easy data exploration.
\ No newline at end of file
diff --git a/content/people/images/henry_g.jpg b/content/people/images/henry_g.jpg
index f6132ba2e0e039735408e93a37b1a48269158721..c3ff2f963e5990dcb485c718ec15049dd5da297b 100644
Binary files a/content/people/images/henry_g.jpg and b/content/people/images/henry_g.jpg differ
diff --git a/content/people/images/joseph_d.jpeg b/content/people/images/joseph_d.jpeg
deleted file mode 100644
index d4685c30e8ae47df617aa65fafcbf3f553ce0bc5..0000000000000000000000000000000000000000
Binary files a/content/people/images/joseph_d.jpeg and /dev/null differ
diff --git a/content/people/images/joseph_d.jpg b/content/people/images/joseph_d.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..4c6e7df6388a767a57762fa945dc63ae4f8b4808
Binary files /dev/null and b/content/people/images/joseph_d.jpg differ
diff --git a/content/people/images/malewska_a.jpg b/content/people/images/malewska_a.jpg
index 2f2bc451bcc9692e058dbc762a0952b989876c24..138c37965bd9cd61bdcf54ce8172bbc601a776a6 100644
Binary files a/content/people/images/malewska_a.jpg and b/content/people/images/malewska_a.jpg differ
diff --git a/content/people/images/strand_d.jpg b/content/people/images/strand_d.jpg
index cef395b3c14102531bd79759d6b2afe58bbbc6fa..e821c7cab8975d548923a28f5605099fd393acd7 100644
Binary files a/content/people/images/strand_d.jpg and b/content/people/images/strand_d.jpg differ
diff --git a/content/people/joseph_d.md b/content/people/joseph_d.md
index 468a786130b54f4df5970ade3c920b0fde57c1b4..3d3c2d536a71e944221a39b47a9ab6d242424712 100644
--- a/content/people/joseph_d.md
+++ b/content/people/joseph_d.md
@@ -1,13 +1,15 @@
---
title: "Joseph_d"
date: 2019-05-18T21:33:56-05:00
-draft: true
-name: "Diya B. Joseph"
+draft: false
+name: "Diya Binoy Joseph"
degree: "Ph.D."
-pic: "joseph_d.jpeg"
+pic: "joseph_d.jpg"
tit: "Postdoctoral Researcher"
orcid: "0000-0002-0587-9558"
weight: "4"
+current: true
---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
-Diya obtained her PhD at the University of Wisconsin: Madison in the Vezina Lab. She joined the Dr. Strand's Lab in 2019.
\ No newline at end of file
+Diya joined the Strand lab in January 2019 as a postdoctoral researcher. Prior to this, she received her Bachelor's degree in Biotechnology from the National Institute of Technology, Calicut in India in 2013 and a Ph.D in Cellular and Molecular Biology in December 2018 from the University of Wisconsin-Madison. During her doctoral studies in Dr. Chad Vezina's lab, Diya studied the development of the lower urinary tract with special emphasis on the role of DNA methylating enzymes during prostate development. During her doctoral studies, Diya was part of a collaborative project with Dr. Strand to produce the first cellular anatomy of the normal human prostate at single cell resolution. This collaboration led to her current position as a postdoctoral researcher in the Strand lab where she studies Benign Prostatic Hyperplasia (BPH) and the role of novel club and hillock urethral cell types in BPH growth.
\ No newline at end of file
diff --git a/content/people/malewska_a.md b/content/people/malewska_a.md
index 24e9faee251b92a3badc457b6bb9dedef9abda37..131f89472b5ab47b91f4c6d81a81737e3b1ddd9a 100644
--- a/content/people/malewska_a.md
+++ b/content/people/malewska_a.md
@@ -1,13 +1,15 @@
---
title: "Malewska_a"
date: 2019-05-18T21:34:09-05:00
-draft: true
+draft: false
name: "Alicia Malewska"
degree: "M.S."
pic: "malewska_a.jpg"
tit: "Research Technician"
orcid: ""
weight: "5"
+current: true
---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
Alicia obtained her master's degree at UT Dallas in 2005 and has worked at UT Southwestern ever since. She joined Dr. Strand’s lab in 2014.
\ No newline at end of file
diff --git a/content/people/mcalanis_c.md b/content/people/mcalanis_c.md
index f41699fb9306552d64118d37eb7065067f23c79b..d5dd11c9a13527a1ec456f2bdf48cf2c3ddb707a 100644
--- a/content/people/mcalanis_c.md
+++ b/content/people/mcalanis_c.md
@@ -1,13 +1,15 @@
---
title: "Mcalanis_c"
date: 2019-06-06T14:38:43-05:00
-draft: true
+draft: false
name: "Caitlin L. Mcalanis"
degree: ""
pic: "mcalanis_c.jpg"
tit: "STARS Student (2019)"
orcid: ""
weight: "15"
+current: false
---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
-Senior at North Forney High School. Caitlin is joining us in the Strand lab for the summer of 2019.
\ No newline at end of file
+While a senior at North Forney High School, Caitlin joined us in the Strand lab for the summer of 2019.
\ No newline at end of file
diff --git a/content/people/strand_d.md b/content/people/strand_d.md
index ee587515b8ef82f1a2e707a47638e13112b452d4..791d971d906c546999d0b10ea5f3518049f3ccf8 100644
--- a/content/people/strand_d.md
+++ b/content/people/strand_d.md
@@ -1,13 +1,15 @@
---
title: "Strand_d"
date: 2019-05-18T21:33:29-05:00
-draft: true
+draft: false
name: "Douglas W. Strand"
degree: "Ph.D."
pic: "strand_d.jpg"
tit: "Assistant Professor of Urology"
orcid: "0000-0002-0746-927X"
weight: "1"
+current: true
---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
-Doug obtained his Ph.D. with David Rowley at Baylor College of Medicine in the department of Molecular and Cellular Biology. He did a postdoctoral fellowship at Vanderbilt University under Simon Hayward. He joined the faculty of UTSW in 2014.
\ No newline at end of file
+Doug obtained his Ph.D. with David Rowley at Baylor College of Medicine in the department of Molecular and Cellular Biology. He did a postdoctoral fellowship at Vanderbilt University under Simon Hayward. He joined the faculty of UTSW in 2014 and works closely with the clinicians in the Urology department to characterize the cellular pathogenesis of diseases of the human lower urinary tract.
\ No newline at end of file
diff --git a/content/publications/2010_curmolmed.md b/content/publications/2010_curmolmed.md
index 6d14108f82fd69de07c385823ac0e71555d37bb6..55ae395bdeba08fe49b7c067bfcb77eb878cb09c 100644
--- a/content/publications/2010_curmolmed.md
+++ b/content/publications/2010_curmolmed.md
@@ -1,7 +1,7 @@
---
title: "2010_curmolmed"
date: 2019-05-19T13:28:53-05:00
-draft: true
+draft: false
pname: "Perspectives on tissue interactions in development and disease."
pauthor: "Strand DW. et al"
pjournal: "Curr. Mol. Med."
diff --git a/content/publications/2011_differentiation.md b/content/publications/2011_differentiation.md
index 264befc3f464cc08a78a25a78ec037aa19a6d1c9..bdf42709b6f6207ba9ea338d5922877e79ff3feb 100644
--- a/content/publications/2011_differentiation.md
+++ b/content/publications/2011_differentiation.md
@@ -1,7 +1,7 @@
---
title: "2011_differentiation"
date: 2019-05-19T13:24:23-05:00
-draft: true
+draft: false
pname: "PPARγ: a molecular link between systemic metabolic disease and benign prostate hyperplasia."
pauthor: "Jiang M. et al"
pjournal: "Differentiation"
diff --git a/content/publications/2013_amjpathol.md b/content/publications/2013_amjpathol.md
index 143116d29bca43a0be8df2d3bc45f7838f3f9648..13cdfec317936d4407d1de63ec80267197975612 100644
--- a/content/publications/2013_amjpathol.md
+++ b/content/publications/2013_amjpathol.md
@@ -1,7 +1,7 @@
---
title: "2013_amjpathol"
date: 2019-05-19T13:20:11-05:00
-draft: true
+draft: false
pname: "Deficiency in metabolic regulators PPARγ and PTEN cooperates to drive keratinizing squamous metaplasia in novel models of human tissue regeneration"
pauthor: "Strand DW. et al"
pjournal: "Am. J. Pathol."
diff --git a/content/publications/2013_celldeathdis.md b/content/publications/2013_celldeathdis.md
index 93e452f903b131f0a623254ba54ccfc3e21d069b..d2b73a5206791281a7e1a9bc9caac3f4337dcfc9 100644
--- a/content/publications/2013_celldeathdis.md
+++ b/content/publications/2013_celldeathdis.md
@@ -1,7 +1,7 @@
---
title: "2013_celldeathdis"
date: 2019-05-19T13:22:51-05:00
-draft: true
+draft: false
pname: "PPARγ isoforms differentially regulate metabolic networks to mediate mouse prostatic epithelial differentiation."
pauthor: "Strand DW. et al"
pjournal: "Cell Death Dis."
diff --git a/content/publications/2014_prostate.md b/content/publications/2014_prostate.md
index 7985686f93d075c9ed4cfdf7bea5f04be34c9451..29bf60b8a75cec96549968127ef131faaf592b7a 100644
--- a/content/publications/2014_prostate.md
+++ b/content/publications/2014_prostate.md
@@ -1,7 +1,7 @@
---
title: "2014_prostate"
date: 2019-05-19T13:19:06-05:00
-draft: true
+draft: false
pname: "Surgical intervention for symptomatic benign prostatic hyperplasia is correlated with expression of the AP-1 transcription factor network."
pauthor: "Lin-Tsai O. et al"
pjournal: "Prostate"
diff --git a/content/publications/2016_differentiation.md b/content/publications/2016_differentiation.md
index 79c8458f36ce36c0d037c2f39ee230b8f28e7f90..cf434478ded2ca7994fb7f03a56601002129ae04 100644
--- a/content/publications/2016_differentiation.md
+++ b/content/publications/2016_differentiation.md
@@ -1,7 +1,7 @@
---
title: "2016_differentiation"
date: 2019-05-19T13:17:41-05:00
-draft: true
+draft: false
pname: "Isolation and analysis of discreet human prostate cellular populations."
pauthor: "Strand DW. et al"
pjournal: "Differentiation"
diff --git a/content/publications/2017_cytometry.md b/content/publications/2017_cytometry.md
index 14d49d72a07a4a712817669901a8e6c3dfec30c8..445e0c2aff9bce829c6e8e681e59b0d6a6d5d66e 100644
--- a/content/publications/2017_cytometry.md
+++ b/content/publications/2017_cytometry.md
@@ -1,7 +1,7 @@
---
title: "2017_cytometry"
date: 2019-05-19T12:58:27-05:00
-draft: true
+draft: false
pname: "OMIP-040: Optimized gating of human prostate cellular subpopulations."
pauthor: "Henry GH. et al"
pjournal: "Cytometry"
diff --git a/content/publications/2017_differentiation.md b/content/publications/2017_differentiation.md
index b211c7bab873e2831d30022ab6b42e16076888df..cd616c6d8882933fe3ca5cec6f6ee63f666a627e 100644
--- a/content/publications/2017_differentiation.md
+++ b/content/publications/2017_differentiation.md
@@ -1,7 +1,7 @@
---
title: "2017_differentiation"
date: 2019-05-19T13:11:23-05:00
-draft: true
+draft: false
pname: "Targeting phenotypic heterogeneity in benign prostatic hyperplasia."
pauthor: "Strand DW. et al"
pjournal: "Differentiation"
diff --git a/content/publications/2017_prostate.md b/content/publications/2017_prostate.md
index dd3d841c758d4a8445273393b83095f941ac32a6..3a822bf4ca1406beb8913e745afb03e9d5db9f96 100644
--- a/content/publications/2017_prostate.md
+++ b/content/publications/2017_prostate.md
@@ -1,7 +1,7 @@
---
title: "2017_prostate"
date: 2019-05-19T13:15:41-05:00
-draft: true
+draft: false
pname: "Molecular pathogenesis of human prostate basal cell hyperplasia."
pauthor: "Henry GH. et al"
pjournal: "Prostate"
diff --git a/content/publications/2018_cellreports.md b/content/publications/2018_cellreports.md
index 0b060ec598e0717bb9715f6e48f3753146516a1f..dd038488f7ae28a3fef9dceed08e74c21ad4f60e 100644
--- a/content/publications/2018_cellreports.md
+++ b/content/publications/2018_cellreports.md
@@ -1,7 +1,7 @@
---
title: "2018_cellreports"
date: 2019-05-19T12:58:22-05:00
-draft: true
+draft: false
pname: "A cellular anatomy of the normal adult human prostate and prostatic urethra."
pauthor: "Henry GH. et al"
pjournal: "Cell Reports"
diff --git a/content/repository.md b/content/repository.md
index c44089bf786cecdf99a5f050dcdde6467e65b96a..a1686f54b4878845215ea0d29d1fc65ff90d1d17 100644
--- a/content/repository.md
+++ b/content/repository.md
@@ -1,8 +1,8 @@
----
-title: "BioRepository"
-date: 2019-07-07T22:25:54-05:00
-draft: true
-type: "custom"
-layout: "repository"
----
-
+---
+title: "BioRepository"
+date: 2019-07-07T22:25:54-05:00
+draft: false
+type: "custom"
+layout: "repository"
+---
+
diff --git a/content/research.images/prostate.jpg b/content/research.images/prostate.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..fbb7eca0d59f9b9587de8fb69de433da99f0e619
Binary files /dev/null and b/content/research.images/prostate.jpg differ
diff --git a/content/research.md b/content/research.md
index 2e6532c7a2dc18fd20f4348f0e158816e229025d..fcae2224512928c2450c6bc7c8937b2e45a932f4 100644
--- a/content/research.md
+++ b/content/research.md
@@ -1,86 +1,7 @@
---
title: "Research"
date: 2019-05-19T01:57:56-05:00
-draft: true
+draft: false
+type: "custom"
+layout: "research"
---
-<style>
- div.section:after {
- content: "";
- display: table;
- clear: both;
- }
- div.fig {
- max-width: 500px;
- padding: 1px;
- border: 1px solid black;
- margin: 1px 10px 1px 1px;
- }
- div.fig img {
- width: 500px;
- max-width: 100%;
- height: auto;
- padding: 1px;
- }
- div.lab {
- text-align: justify;
- padding-left: 10px;
- padding-right: 10px;
- }
- @media (min-width: 1000px) {
- div.fig {
- float: left;
- }
- br {
- display: none;
- }
- }
-</style>
-
-<div class="section">
-<H1 align="center">BENIGN PROSTATIC HYPERPLASIA</H1>
-<div class="fig">
-<img src="/research.images/disease.jpg" alt="disease"/>
-<p class="br"></p>
-</div>
-<p style="text-align:justify; font-size:18px;">
-The goal of the Strand laboratory is to understand the cellular and molecular biology of benign prostatic hyperplasia (BPH). The prostate is a walnut-sized organ wrapped around the bladder neck. A majority of men over 70 years old have BPH, which can cause lower urinary tract symptoms and voiding dysfunction. First line treatment for men with moderately symptomatic BPH is typically an alpha blocker to relax smooth muscle tone. Once the prostate enlarges over 40cc, 5 alpha reductase inhibitors are administered, which reduce prostate volume by ~20% through apoptosis of luminal epithelia. These drugs are mostly tolerable and reduce symptomatic progression by 33% individually. Although the introduction of these drugs decreased surgical intervention, hundreds of thousands of surgeries are performed each year in the US to reduce prostate volume in elderly men. A better understanding of the biology of BPH is needed to develop drugs that actually target the causes of prostatic enlargement and reduce surgical intervention.
-</p>
-</div>
-
-<div class="section">
-<H1 align="center">PATHOLOGICAL HETEROGENEITY AND PERSONALIZED MEDICINE FOR BPH</H1>
-
-<div class="fig">
-<img src="/research.images/pheno.jpg" alt="phenotypes" class="img"/>
-<div class="lab">
-<p>BPH is morphologically diverse. Patients can present with purely glandular hyperplasia, purely stromal hyperplasia, or a mixture of both phenotypes as shown in these images of fresh tissue and a corresponding whole mount H&E.</p>
-</div>
-<p class="br"></p>
-</div>
-
-<p style="text-align:justify; font-size:16px;">
-BPH is morphologically diverse. Patients can present with purely glandular hyperplasia, purely stromal hyperplasia, or a mixture of both phenotypes as shown in these images of fresh tissue and a corresponding whole mount H&E.
-</p>
-<p style="text-align:justify; font-size:18px;">
-One of the factors that likely causes a variable response to medical therapy is phenotypic heterogeneity. Alpha blockers target normal smooth muscle and 5ARIs target normal luminal epithelia. These drugs were not developed to target pathways altered in diseased cells because cell type-specific alterations in BPH have not yet been characterized. Furthermore, each patient can display a highly variable proportion of these cell types in BPH and they are most certainly no longer normal. No clinical trial has ever taken into account the role of cellular composition in treatment response. Our goal is to characterize the cellular composition of BPH, establish clinically useful imaging modalities or biomarkers to diagnose the BPH phenotype, and develop targeted therapies based on cellular and molecular data.
-</p>
-</div>
-
-<div class="section">
-<H1 align="center">CELLULAR ANATOMY OF THE HUMAN PROSTATE</H1>
-
-<div class="fig">
-<img src="/research.images/disection.jpg" alt="disection" class="img"/>
-<div class="lab">
-<p>The human prostate sits at the base of the bladder, which releases urine through the prostatic urethra. Ureters connect to the kidneys, vas deferens connect to the testicles. Sperm from the testicles, and secretory fluids from the seminal vesicles and prostate are forced through into the prostatic urethra during ejaculation. The human prostate is divided into 4 major ‘zones’: the transition zone (TZ), which is an area than encircles the prostatic urethra from the base at the bladder neck to the apex at the start of the penis; the central zone (CZ) encircles the ejaculatory ducts from the seminal vesicles; the peripheral zone (PZ) encompasses the posterior prostate surrounding the TZ and CZ; and the anterior fibromuscular stroma (AFS).</p>
-</div>
-<p class="br"></p>
-</div>
-
-<p style="text-align:justify; font-size:18px;">
-The human prostate sits at the base of the bladder, which releases urine through the prostatic urethra. Ureters connect to the kidneys, vas deferens connect to the testicles. Sperm from the testicles, and secretory fluids from the seminal vesicles and prostate are forced through into the prostatic urethra during ejaculation. The human prostate is divided into 4 major ‘zones’: the transition zone (TZ), which is an area than encircles the prostatic urethra from the base at the bladder neck to the apex at the start of the penis; the central zone (CZ) encircles the ejaculatory ducts from the seminal vesicles; the peripheral zone (PZ) encompasses the posterior prostate surrounding the TZ and CZ; and the anterior fibromuscular stroma (AFS).
-</p>
-<p style="text-align:justify; font-size:18px;">
-The first step towards personalized therapy for BPH phenotypes is to understand the cellular anatomy of the normal prostate. The prostate is mainly composed of epithelial and stromal cell types. Historically, the definition of prostate epithelial cell type has been based on 1) the relative position of cells within glandular acini, 2) cellular shape, and 3) the differential expression of genes and cell surface antigens. Using these criteria, prostate glands are reportedly composed of basal and luminal epithelia with rare neuroendocrine cells. Basal epithelia express cytokeratins 5/14 as well as the transcription factor p63. Luminal epithelia express cytokeratins 8/18 as well as androgen receptor. A putative intermediate cell ‘state’ between luminal and basal lineages has been defined on the basis of shared expression of luminal and basal cytokeratins. Neuroendocrine epithelia are defined by expression of markers such as chromogranin A. The stroma is even more poorly defined as generic smooth muscle and fibroblast cell types. Our laboratory is using single cell sequencing and flow cytometry to define the cellular composition of the normal prostate procured from young organ donors through a partnership with the Southwest Transplant Alliance. These data will establish a baseline against which various diseased phenotypes can be compared. We currently have a biorepository of normal and diseased human prostate containing paraffin blocks, OCT blocks, flash frozen tissue, and cryopreserved single cells available upon request (see Resources page). You can also search our single cell sequencing dataset with our ProstateMapper tool to see where your gene of interest is expressed in the normal prostate.
-</p>
-</div>
\ No newline at end of file
diff --git a/layouts/custom/contact.html b/layouts/custom/contact.html
new file mode 100644
index 0000000000000000000000000000000000000000..f04f7d132a1b364a50b7faad91063f4523bf8dfc
--- /dev/null
+++ b/layouts/custom/contact.html
@@ -0,0 +1,42 @@
+{{ partial "header.html" . }}
+
+<div class="header">
+ <h1>{{ .Title }}</h1>
+ <h2>{{ .Description }}</h2>
+</div>
+
+<div class="content">
+ <p style="text-align: center">
+ Questions about our research or need a tip on one of our protocols?
+ Interested in collaborations? Email us, mention any person, project, or
+ activity of interest,and we will get back to you soon!
+ </p>
+ <hr>
+ <div style="text-align: center">
+ <iframe
+ src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d3353.0540362781526!2d-96.84412528424524!3d32.81733318923467!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x864e9c04b088e599%3A0x2e63ea34f8b2150b!2sUT%20Southwestern%20Medical%20Center!5e0!3m2!1sen!2sus!4v1576207208811!5m2!1sen!2sus"
+ width="600" height="450" frameborder="0" style="border:0"
+ allowfullscreen=""></iframe>
+ </div>
+ <hr>
+ <div style="text-align: center">
+ <i class="fa fa-map-marker"></i>
+ UT Southwestern Medical Center,<br>
+ Department of Urology,<br>
+ 5323 Harry Hines Blvd,<br>
+ Mail Code: 9110,<br>
+ Dallas, TX 75390-9110<br>
+ </div>
+ <hr>
+ <div style="text-align: center">
+ <i class="fa fa-envelope-open"></i>
+ <a href="mailto: douglas.strand@utsouthwestern.edu">douglas.strand@utsouthwestern.edu</a>
+ </div>
+ <hr>
+ <div style="text-align: center">
+ <i class="fa fa-phone"></i>
+ 214-648-6096
+ </div>
+ <hr>
+
+ {{ partial "footer.html" . }}
\ No newline at end of file
diff --git a/layouts/custom/data.html b/layouts/custom/data.html
index ba1628e2b3c9dc75d0b334d0bd5c784b78815bf7..3c4f2961065d5dc750f5967ddc697d8fa35b90d2 100644
--- a/layouts/custom/data.html
+++ b/layouts/custom/data.html
@@ -1,27 +1,158 @@
{{ partial "header.html" . }}
<div class="header">
- <h1>{{ .Title }}</h1>
- <h2>{{ .Description }}</h2>
+ <h1>{{ .Title }}</h1>
+ <h2>{{ .Description }}</h2>
</div>
<div class="content">
- {{ .Content }}
+ {{ .Content }}
</div>
-{{ partial "footer.html" . }}
+<style>
+ .content{
+ margin: 0;
+ max-width: none;
+ }
+ .select {
+ float: top;
+ z-index: 1;
+ top: 0px;
+ background: #191818;
+ overflow-x: hidden;
+ padding: 8px 10px;
+ }
+ .columnS {
+ float: left;
+ text-align: center;
+ width: 33.33%;
+ }
+ .columnF {
+ float: left;
+ text-align: center;
+ width: 33.33%;
+ }
+ .row:after {
+ content: "";
+ display: table;
+ clear: both;
+ }
+ img{
+ max-width: 100%;
+ height: auto;
+ }
+ @media (max-width: 1000px) {
+ .columnS {
+ text-align: right;
+ width: 100%;
+ }
+ .columnF {
+ width: 100%;
+ }
+ br {
+ display: none;
+ }
+ }
+</style>
+<body>
+ <div class="select">
+ <div class="columnS ui-widget">
+ <label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
+ <br>
+ <input id="gene" size="19">
+ </div>
+ <div class="columnS">
+ <label for="lineage" style="font-size:18px;"><b>Select a cell lineage to
+ display:</b></label>
+ <br>
+ <select name="lineage" id="lineage">
+ <option selected="selected" value="all">All Cells</option>
+ <option value="epi">Epithelial Cells Only</option>
+ <option value="st">Stromal Cells Only</option>
+ </select>
+ </div>
+ <div class="columnS">
+ <label for="populations" style="font-size:18px;"><b>Select a group of cell
+ populations:</b></label>
+ <br>
+ <select name="populations" id="populations">
+ <option>Lineage</option>
+ <option>Patient</option>
+ <option selected="selected" value="Populations"> Cell Populations</option>
+ <option value="Zone">Prostatic Zone</option>
+ </select>
+ </div>
+ <br>
+ <button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
+ <hr>
+ <div>
+ <span style="font-size:16px; font-weight:bold;">Experimental details:</span>
+ <br>
+ <span style="font-size:16px;">Single Cell RNA-Sequencing was conducted on
+ 32,194 cells from peripheral zone and transition zone from the prostate
+ of three 18-38 year old organ donors using the 10x Genomics platform.
+ The cells were clustered and identified by correlation of their
+ transcriptomes to known cell types. Gene expression can be compared by
+ population identity, cell lineage, patient, or dissected prostatic zone.</span>
+ </div>
+ </div>
+ <div align="center">
+ <h1 id="label.gene">NO GENE SELECTED</h1>
+ <h2 id="label.lineage"></h2>
+ <h3 id="label.populations"></h3>
+ <div class="columnF">
+ <h4 id="label.ClusterVis"></h3>
+ <div class="img">
+ <img id="img.ClusterVis" src="" />
+ </div>
+ <br>
+ </div>
+ <div class="columnF">
+ <h4 id="label.Feature"></h3>
+ <div class="img">
+ <img id="img.Feature" src="" />
+ </div>
+ <br>
+ </div>
+ <div class="columnF">
+ <h4 id="label.ViolinBox"></h3>
+ <div class="img">
+ <img id="img.ViolinBox" src="" />
+ </div>
+ <br>
+ </div>
+ </div>
+ <hr>
+ <div align="left">
+ <div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
+ <div><span style="font-size:16px;"> <a
+ href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
+ target="_blank">Cell Reports</a></span></div>
+ <div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
+ <div><span style="font-size:16px;"> <a
+ href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
+ target="_blank">GEO:
+ GSE117403</a></span></div>
+ <div><span style="font-size:16px;"><a
+ href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP: W-R8CM</a></span></div>
+ </div>
+</body>
+
<head>
- <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
- <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
- <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
- <style>
+ <link rel="stylesheet"
+ href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
+ <script
+ src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+ <script
+ src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
+ <style>
.ui-autocomplete {
max-height: 200px;
overflow-y: auto;
overflow-x: hidden;
}
</style>
- <script>
+ <script>
$(function(){
$("#lineage" ).selectmenu({width: 230});
});
@@ -40,24 +171,27 @@
$("#analysis").click(function (event) {
event.preventDefault();
var genes = {{ index .Site.Data.scRNAseq_huPr_D.genes }};
- _gene = $('#gene').val().toUpperCase();
+ _gene = $("#gene").val().toUpperCase();
if($.inArray(_gene,genes.genes) < 0){
- alert("Gene "+ _gene +" does not exist in the data.")
+ alert("Gene "+ _gene +" not exist in the data.")
return
}
<!-- alert(_gene) -->
document.getElementById("label.gene").innerHTML = _gene
document.getElementById("label.lineage").innerHTML = $("#lineage").val().toUpperCase() + " Cells"
+ document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
var img = document.getElementById("img.ClusterVis");
- img.src="/images/scRNAseq_huPr_D/png/ID/" + $("#lineage").val() + "/" + $("#populations").val() + "/ClusterVis.png"
+ img.src="https://s3.us-east-2.amazonaws.com/data-10.1016-j.celrep.2018.11.086/ID/" + $("#lineage").val() + "/" + $("#populations").val() + "/ClusterVis.png"
document.getElementById("label.Feature").innerHTML = "Feature Plot"
var img = document.getElementById("img.Feature");
- img.src="/images/scRNAseq_huPr_D/png/Feature/" + $("#lineage").val() + "/genes/" + _gene + ".png"
+ img.src="https://s3.us-east-2.amazonaws.com/data-10.1016-j.celrep.2018.11.086/Feature/" + $("#lineage").val() + "/genes/" + _gene + ".png"
document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
var img = document.getElementById("img.ViolinBox");
- img.src="/images/scRNAseq_huPr_D/png/ViolinBox/" + $("#lineage").val() + "/" + $("#populations").val() + "/" + _gene + ".png"
+ img.src="https://s3.us-east-2.amazonaws.com/data-10.1016-j.celrep.2018.11.086/ViolinBox/" + $("#lineage").val() + "/" + $("#populations").val() + "/" + _gene + ".png"
return(_gene)
});
</script>
-</head>
\ No newline at end of file
+</head>
+
+{{ partial "footer.html" . }}
diff --git a/layouts/custom/people.html b/layouts/custom/people.html
index 729d68827e5c79550912cf9561a539cac6a53636..382df21f7ad2fc6f61ba2a6b84c62c1836f35b30 100644
--- a/layouts/custom/people.html
+++ b/layouts/custom/people.html
@@ -1,5 +1,10 @@
{{ partial "header.html" . }}
+<div class="header">
+ <h1>{{ .Title }}</h1>
+ <h2>{{ .Description }}</h2>
+</div>
+
<style>
@media (min-width: 1000px) {
.column {
@@ -24,14 +29,34 @@
box-shadow: 4px 4px 5px #888;
}
</style>
-
-<div class="header">
- <h1>{{ .Title }}</h1>
- <h2>{{ .Description }}</h2>
-</div>
<div class="content">
- <div>
- {{ range .Pages.ByWeight }}
+ <div class="current">
+ {{ range where .Pages.ByWeight "Params.current" true }}
+ <div class="row">
+ <h3><strong>{{.Params.name}} {{.Params.degree}}</strong></h3>
+ <h4>{{.Params.tit}}</h4>
+ {{ if not (eq .Params.orcid "") }}
+ <p>
+ <a href="https://orcid.org/{{.Params.orcid}}" target="_blank"><img
+ src="https://orcid.org/sites/default/files/images/orcid_16x16.png">orcid.org/{{.Params.orcid}}</a>
+ </p>
+ {{ end }}
+ <div class="column left">
+ {{ if not (eq .Params.pic "") }}
+ <img src="images/{{.Params.pic}}" alt="" class="pic">
+ {{ end }}
+ </div>
+ <div class="column right" style="text-align: justify">
+ <p>{{.Content}}</p>
+ </div>
+ </div>
+ <hr><br>
+ {{end}}
+ </div>
+ <hr>
+ <h1>Former Members</h1>
+ <div class="former">
+ {{ range where .Pages.ByWeight "Params.current" false }}
<div class="row">
<h3><strong>{{.Params.name}} {{.Params.degree}}</strong></h3>
<h4>{{.Params.tit}}</h4>
@@ -46,8 +71,8 @@
<img src="images/{{.Params.pic}}" alt="" class="pic">
{{ end }}
</div>
- <div class="column right" style='text-align: justify;'>
- <p >{{.Content}}</p>
+ <div class="column right" style="text-align: justify">
+ <p>{{.Content}}</p>
</div>
</div>
<hr><br>
diff --git a/layouts/custom/publications.html b/layouts/custom/publications.html
index 88e1bcf3e3887c0f01f003cc6077b599d348cf6e..3fd85c124180a20eb4b40222ffe7c89fe5e593be 100644
--- a/layouts/custom/publications.html
+++ b/layouts/custom/publications.html
@@ -18,36 +18,39 @@
}
}
</style>
-
<div class="header">
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
</div>
<div class="content">
+ <br>
<div>
{{ range first 10 (.Pages.ByParam "odate" ).Reverse }}
<div class="row">
<div class="column left">
- <img src="images/{{.Params.ppic}}" alt="" width="100px;" style="border:5px double black; border-radius:20%;">
+ <img src="images/{{.Params.ppic}}" alt="" width="100px;"
+ style="border:5px double black; border-radius:20%;">
</div>
<div class="column right">
<h3>{{.Params.pname}}</h3>
</div>
</div>
{{ if not (eq .Params.ppubmed "") }}
- <h4><i><a href="https://www.ncbi.nlm.nih.gov/pubmed?term={{.Params.ppubmed}}">
+ <h4><i><a
+ href="https://www.ncbi.nlm.nih.gov/pubmed?term={{.Params.ppubmed}}"
+ target="_blank">
{{else}}
<h4><i><a href="{{.Params.plink}}">
{{end}}
- {{.Params.pauthor}}, {{.Params.pjournal}}, {{.Params.pdate}}</a></i></h4>
- {{ range first 1 .Params.prepo }}
+ {{.Params.pauthor}}, {{.Params.pjournal}},{{.Params.pdate}}</a></i></h4>
+ {{ range first 1 .Params.prepo }}
{{ if not (eq .title "") }}
<u>Data Repository:</u><br>
{{end}}
{{end}}
{{ range .Params.prepo }}
{{ if not (eq .title "") }}
- <a href="{{.loc}}">{{.title}}</a><br>
+ <a href="{{.loc}}" target="_blank">{{.title}}</a><br>
{{end}}
{{end}}
<hr><br>
diff --git a/layouts/custom/repository.html b/layouts/custom/repository.html
index 35d278c34e7f3a888a692bf513187741b39c7cd0..58b8c413354d2b19dbf6535ec9cf471ccca87dfa 100644
--- a/layouts/custom/repository.html
+++ b/layouts/custom/repository.html
@@ -134,5 +134,4 @@
-{{ partial "footer.html" . }}
-
+{{ partial "footer.html" . }}
\ No newline at end of file
diff --git a/layouts/custom/research.html b/layouts/custom/research.html
new file mode 100644
index 0000000000000000000000000000000000000000..e1c9ca34f87c47aea7697aa57ba12600fdf8d698
--- /dev/null
+++ b/layouts/custom/research.html
@@ -0,0 +1,168 @@
+{{ partial "header.html" . }}
+
+<div class="header">
+ <h1>{{ .Title }}</h1>
+ <h2>{{ .Description }}</h2>
+</div>
+
+<style>
+ div.section:after {
+ content: "";
+ display: table;
+ clear: both;
+ }
+ div.fig {
+ padding: 1px;
+ border: 1px solid black;
+ margin: auto;
+ background-color: LightGrey;
+ }
+ div.fig img {
+ width: 500px;
+ max-width: 100%;
+ height: auto;
+ padding: 1px;
+ }
+ div.lab {
+ text-align: justify;
+ padding-left: 10px;
+ padding-right: 10px;
+ }
+ @media (min-width: 1000px) {
+ div.fig {
+ float: left;
+ margin: 1px 10px 1px 1px;
+ }
+ br {
+ display: none;
+ }
+ }
+</style>
+<div class="content">
+ <div class="section">
+ <H1 align="center">Overview</H1>
+ <p style="text-align:justify; font-size:18px">
+ The main goals of the Strand lab are to create accurate cellular
+ atlases of the human and mouse lower
+ urinary tract, characterize the molecular and cellular alterations
+ in human lower urinary tract disease, and
+ build appropriate models of the human disease in novel mouse models.
+ </p>
+ </div>
+ <div class="section">
+ <H1 align="center">Benign Prostatic Hyperplasia</H1>
+ <div class="fig" style="max-width:250px">
+ <img src="/research.images/prostate.jpg" alt="prostate" class="img"
+ />
+ <div class="lab">
+ <p>Cross-section of a prostate gland, showing the transition
+ zone (TZ) and the peripheral zone (PZ)</p>
+ </div>
+ <p class="br"></p>
+ </div>
+ <p style="text-align:justify; font-size:18px">
+ A goal of the Strand laboratory is to understand the cellular and
+ molecular biology of lower urinary tract
+ symptoms (LUTS) due to benign prostatic hyperplasia (BPH) or bladder
+ dysfunction. BPH/LUTS is present in the
+ vast majority of men over 70 years old resulting in medical
+ treatment or surgical intervention.
+ </p>
+ <p style="text-align:justify; font-size:18px">
+ We focus on translational questions related to progression of
+ BPH/LUTS in order to develop new targets for
+ therapeutic intervention. In particular, we are interested in
+ characterizing the cellular composition of
+ particular phenotypes that are resistant to current therapies. We
+ use a combination of single cell RNA
+ sequencing, flow cytometry and immunohistochemistry on normal and
+ diseased human specimens to build a
+ cellular atlas of prostate and bladder disease.
+ </p>
+ </div>
+
+ <div class="section">
+ <H1 align="center">Pathological Heterogeneity in BPH</H1>
+ <div class="fig" style="max-width:500px">
+ <img src="/research.images/pheno.jpg" alt="phenotypes" class="img"
+ />
+ <div class="lab">
+ <p>Phenotypic diversity in BPH. Left: glandular enlargement.
+ Middle: Stromal enlargement. Right: Mixed
+ type.</p>
+ </div>
+ </div>
+ <p style="text-align:justify; font-size:18px">
+ We believe that the basis for heterogeneous clinical responses in
+ BPH is pathologic diversity. There are a
+ number of phenotypes evident across and even within patients. In one
+ area, a patient can display a stromal
+ tumor while the other area display an epithelial nodule.
+ </p>
+ <p style="text-align:justify; font-size:18px">
+ Our goal is to provide a rational basis for therapeutically treating
+ these individual phenotypes by
+ dissecting them macroscopically and then comparing their
+ cell-specific molecular profiles to reduce the
+ noise of cellular heterogeneity and inflammation. Our first goal is
+ to identify a cell or cells of origin
+ for the varying phenotypes by phenotyping the tissues with single
+ cell RNA sequencing. This includes a
+ comprehensive evaluation of the immune and inflammatory infiltrate
+ as well as fluctuations in epithelial and
+ stromal subpopulations.
+ </p>
+ <p style="text-align:justify; font-size:18px">
+ We are subsequently isolating the cell types of interest and
+ performing molecular profiling. Based on these
+ targets, we will use our mouse and cell culture models to
+ experimentally test our hypotheses.
+ </p>
+ </div>
+
+ <div class="section">
+ <H1 align="center">Clinical Heterogeneity in BPH</H1>
+ <p style="text-align:justify; font-size:18px">
+ It is clear from clinical trials of medications for BPH that
+ personalized therapies will be needed due to
+ the highly variable responses. Typically, patients complaining of
+ lower urinary tract symptoms are placed on
+ an alpha-adrenergic receptor blocker as a first line therapy due to
+ its fast-acting relief of symptoms.
+ These drugs relieve smooth muscle tone and are most effective in
+ patients with early stage disease
+ displaying a high smooth muscle to epithelial tissue composition.
+ However, as the prostate enlarges,
+ epithelial nodules predominate the tissue decreasing the likelihood
+ of alpha-blocker efficacy.
+ </p>
+ <p style="text-align:justify; font-size:18px">
+ The second-line therapy for BPH is a 5 alpha reductase inhibitor
+ (5ARI), which induces epithelial apoptosis
+ by decreasing the levels of intra-prostatic dihyrotestosterone
+ (DHT). This therapy is effective at reducing
+ prostate size by 25 percent in most patients.
+ </p>
+ <p style="text-align:justify; font-size:18px">
+ Importantly, either therapy only reduces symptomatic progression by
+ 34 percent, suggesting
+ androgen-independent mechanisms of prostate growth and symptoms need
+ to be targeted. Responses to current
+ drugs are further reduced in patients with obesity, diabetes, and
+ dyslipidemia.
+ </p>
+ <p style="text-align:justify; font-size:18px">
+ These data suggest that there are further measures that are
+ necessary for every patient, and completely
+ novel measures necessary for individual patients. Our goal is to
+ characterize the cellular composition of
+ particular phenotypes, and more deeply understand the molecular
+ changes driving these phenotypes. We use a
+ combination of single cell RNA sequencing, flow cytometry, and
+ immunohistochemistry on specimens from young
+ organ donors and older men with prostatic enlargement.
+ </p>
+ </div>
+</div>
+
+{{ partial "footer.html" . }}
\ No newline at end of file
diff --git a/layouts/index.html b/layouts/index.html
index 779b51628f3e50442bc5432b9b0f5e178f588e8b..7a8c18c6ad7a3c76c1176fad797f2070643786e5 100644
--- a/layouts/index.html
+++ b/layouts/index.html
@@ -2,8 +2,8 @@
<div class="header">
<h1>{{ .Title }}</h1>
- <h2><a href="{{ .Site.Params.isite }}">{{ .Site.Params.institution }}</a></h2>
- <h3><a href="{{ .Site.Params.dsite }}">{{ .Site.Params.department }}</a></h3>
+ <h2><a href="{{ .Site.Params.isite }}" target="_blank">{{ .Site.Params.institution }}</a></h2>
+ <h3><a href="{{ .Site.Params.dsite }}" target="_blank">{{ .Site.Params.department }}</a></h3>
<h4>{{ .Site.Params.description }}</h3>
</div>
diff --git a/layouts/partials/social.html b/layouts/partials/social.html
index dd580bbc4226ec68cb801ca3d36288fb104d7eb3..e714ab6461a7e5527040136e8c4079bbe4b922b7 100644
--- a/layouts/partials/social.html
+++ b/layouts/partials/social.html
@@ -1,41 +1,48 @@
<div class="pure-menu social">
<ul class="pure-menu-list">
- <!-- SNS microblogging -->
+ {{ if .OutputFormats.Get "RSS" }}
+ <li class="pure-menu-item">
+ <a class="pure-menu-link" href='{{ with .OutputFormats.Get "RSS" }}{{ .RelPermalink }}{{ end }}'><i
+ class="fas fa-rss"></i>RSS</a>
+ </li>
+ {{ end }}
+
+ <!-- SNS microblogging -->
{{ with .Site.Social.twitter }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://twitter.com/{{ . }}" rel="me" target="_blank"><i class="fa fa-twitter-square fa-fw"></i>Twitter</a>
+ <a class="pure-menu-link" href="https://twitter.com/{{ . }}" rel="me" target="_blank"><i class="fab fa-twitter-square fa-fw"></i>Twitter</a>
</li>
{{ end }}
{{ with .Site.Social.gnusocial }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="{{ . }}" rel="me" target="_blank"><i class="fa fa-comment fa-fw"></i>GNU social</a>
+ <a class="pure-menu-link" href="{{ . }}" rel="me" target="_blank"><i class="fas fa-comment"></i>GNU social</a>
</li>
{{ end }}
{{ with .Site.Social.facebook }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://facebook.com/{{ . }}" rel="me" target="_blank"><i class="fa fa-facebook-square fa-fw"></i>Facebook</a>
+ <a class="pure-menu-link" href="https://facebook.com/{{ . }}" rel="me" target="_blank"><i class="fab fa-facebook-square fa-fw"></i>Facebook</a>
</li>
{{ end }}
{{ with .Site.Social.googleplus }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://plus.google.com/+{{ . }}" rel="me" target="_blank"><i class="fa fa-google-plus-square fa-fw"></i>Google+</a>
+ <a class="pure-menu-link" href="https://plus.google.com/+{{ . }}" rel="me" target="_blank"><i class="fab fa-google-plus-square fa-fw"></i>Google+</a>
</li>
{{ end }}
{{ with .Site.Social.weibo }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="http://weibo.com/{{ . }}" rel="me" target="_blank"><i class="fa fa-weibo fa-fw"></i>Weibo</a>
+ <a class="pure-menu-link" href="http://weibo.com/{{ . }}" rel="me" target="_blank"><i class="fab fa-weibo fa-fw"></i>Weibo</a>
</li>
{{ end }}
{{ with .Site.Social.tumblr }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://{{ . }}.tumblr.com/" rel="me" target="_blank"><i class="fa fa-tumblr-square fa-fw"></i>Tumblr</a>
+ <a class="pure-menu-link" href="https://{{ . }}.tumblr.com/" rel="me" target="_blank"><i class="fab fa-tumblr-square fa-fw"></i>Tumblr</a>
</li>
{{ end }}
@@ -43,49 +50,49 @@
{{ with .Site.Social.instagram }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://instagram.com/{{ . }}" rel="me" target="_blank"><i class="fa fa-instagram fa-fw"></i>Instagram</a>
+ <a class="pure-menu-link" href="https://instagram.com/{{ . }}" rel="me" target="_blank"><i class="fab fa-instagram fa-fw"></i>Instagram</a>
</li>
{{ end }}
{{ with .Site.Social.flickr }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://flickr.com/photos/{{ . }}" rel="me" target="_blank"><i class="fa fa-flickr fa-fw"></i>Flickr</a>
+ <a class="pure-menu-link" href="https://flickr.com/photos/{{ . }}" rel="me" target="_blank"><i class="fab fa-flickr fa-fw"></i>Flickr</a>
</li>
{{ end }}
{{ with .Site.Social.photo500px }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://500px.com/{{ . }}" rel="me" target="_blank"><i class="fa fa-500px fa-fw"></i>500px</a>
+ <a class="pure-menu-link" href="https://500px.com/{{ . }}" rel="me" target="_blank"><i class="fab fa-500px fa-fw"></i>500px</a>
</li>
{{ end }}
{{ with .Site.Social.pinterest }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://pinterest.com/{{ . }}" rel="me" target="_blank"><i class="fa fa-pinterest-square fa-fw"></i>Pinterest</a>
+ <a class="pure-menu-link" href="https://pinterest.com/{{ . }}" rel="me" target="_blank"><i class="fab fa-pinterest-square fa-fw"></i>Pinterest</a>
</li>
{{ end }}
{{ with .Site.Social.youtube }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://youtube.com/user/{{ . }}" rel="me" target="_blank"><i class="fa fa-youtube-square fa-fw"></i>YouTube</a>
+ <a class="pure-menu-link" href="https://youtube.com/user/{{ . }}" rel="me" target="_blank"><i class="fab fa-youtube-square fa-fw"></i>YouTube</a>
</li>
{{ end }}
{{ with .Site.Social.vimeo }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://vimeo.com/{{ . }}" rel="me" target="_blank"><i class="fa fa-vimeo-square fa-fw"></i>Vimeo</a>
+ <a class="pure-menu-link" href="https://vimeo.com/{{ . }}" rel="me" target="_blank"><i class="fab fa-vimeo-square fa-fw"></i>Vimeo</a>
</li>
{{ end }}
{{ with .Site.Social.vine }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://vine.co/{{ . }}" rel="me" target="_blank"><i class="fa fa-vine fa-fw"></i>Vine</a>
+ <a class="pure-menu-link" href="https://vine.co/{{ . }}" rel="me" target="_blank"><i class="fab fa-vine fa-fw"></i>Vine</a>
</li>
{{ end }}
{{ with .Site.Social.slideshare }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="http://slideshare.net/{{ . }}" rel="me" target="_blank"><i class="fa fa-slideshare fa-fw"></i>SlideShare</a>
+ <a class="pure-menu-link" href="http://slideshare.net/{{ . }}" rel="me" target="_blank"><i class="fab fa-slideshare fa-fw"></i>SlideShare</a>
</li>
{{ end }}
@@ -93,13 +100,13 @@
{{ with .Site.Social.linkedin }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://linkedin.com/in/{{ . }}" rel="me" target="_blank"><i class="fa fa-linkedin-square fa-fw"></i>LinkedIn</a>
+ <a class="pure-menu-link" href="https://linkedin.com/in/{{ . }}" rel="me" target="_blank"><i class="fab fa-linkedin"></i></i>LinkedIn</a>
</li>
{{ end }}
{{ with .Site.Social.xing }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://xing.com/profile/{{ . }}" rel="me" target="_blank"><i class="fa fa-xing-square fa-fw"></i>Xing</a>
+ <a class="pure-menu-link" href="https://xing.com/profile/{{ . }}" rel="me" target="_blank"><i class="fab fa-xing-square fa-fw"></i>Xing</a>
</li>
{{ end }}
@@ -107,13 +114,13 @@
{{ with .Site.Social.reddit }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://reddit.com/user/{{ . }}" rel="me" target="_blank"><i class="fa fa-reddit-square fa-fw"></i>Reddit</a>
+ <a class="pure-menu-link" href="https://reddit.com/user/{{ . }}" rel="me" target="_blank"><i class="fab fa-reddit-square fa-fw"></i>Reddit</a>
</li>
{{ end }}
{{ with .Site.Social.hackernews }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://news.ycombinator.com/user?id={{ . }}" rel="me" target="_blank"><i class="fa fa-hacker-news fa-fw"></i>Hacker News</a>
+ <a class="pure-menu-link" href="https://news.ycombinator.com/user?id={{ . }}" rel="me" target="_blank"><i class="fab fa-hacker-news fa-fw"></i>Hacker News</a>
</li>
{{ end }}
@@ -121,37 +128,37 @@
{{ with .Site.Social.github }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://github.com/{{ . }}" rel="me" target="_blank"><i class="fa fa-github-square fa-fw"></i>GitHub</a>
+ <a class="pure-menu-link" href="https://github.com/{{ . }}" rel="me" target="_blank"><i class="fab fa-github-square fa-fw"></i>GitHub</a>
</li>
{{ end }}
{{ with .Site.Social.gitlab }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://gitlab.com/{{ . }}" rel="me" target="_blank"><i class="fa fa-gitlab fa-fw"></i>GitLab</a>
+ <a class="pure-menu-link" href="https://gitlab.com/{{ . }}" rel="me" target="_blank"><i class="fab fa-gitlab fa-fw"></i>GitLab</a>
</li>
{{ end }}
{{ with .Site.Social.biohpcgitlab }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://git.biohpc.swmed.edu/{{ . }}" rel="me" target="_blank"><i class="fa fa-gitlab fa-fw"></i>GitLab</a>
+ <a class="pure-menu-link" href="https://git.biohpc.swmed.edu/{{ . }}" rel="me" target="_blank"><i class="fab fa-gitlab fa-fw"></i>GitLab</a>
</li>
{{ end }}
{{ with .Site.Social.bitbucket }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://bitbucket.org/{{ . }}" rel="me" target="_blank"><i class="fa fa-bitbucket-square fa-fw"></i>Bitbucket</a>
+ <a class="pure-menu-link" href="https://bitbucket.org/{{ . }}" rel="me" target="_blank"><i class="fab fa-bitbucket"></i>Bitbucket</a>
</li>
{{ end }}
{{ with .Site.Social.stackoverflow }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://stackoverflow.com/users/{{ . }}" rel="me" target="_blank"><i class="fa fa-stack-overflow fa-fw"></i>Stack Overflow</a>
+ <a class="pure-menu-link" href="https://stackoverflow.com/users/{{ . }}" rel="me" target="_blank"><i class="fab fa-stack-overflow fa-fw"></i>Stack Overflow</a>
</li>
{{ end }}
{{ with .Site.Social.serverfault }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://serverfault.com/users/{{ . }}" rel="me" target="_blank"><i class="fa fa-server fa-fw"></i>Server Fault</a>
+ <a class="pure-menu-link" href="https://serverfault.com/users/{{ . }}" rel="me" target="_blank"><i class="fab fa-server fa-fw"></i>Server Fault</a>
</li>
{{ end }}
@@ -159,13 +166,13 @@
{{ with .Site.Social.steam }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://steamcommunity.com/id/{{ . }}" rel="me" target="_blank"><i class="fa fa-steam-square fa-fw"></i>Steam</a>
+ <a class="pure-menu-link" href="https://steamcommunity.com/id/{{ . }}" rel="me" target="_blank"><i class="fab fa-steam-square fa-fw"></i>Steam</a>
</li>
{{ end }}
{{ with .Site.Social.mobygames }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://www.mobygames.com/developer/sheet/view/developerId,{{ . }}" rel="me" target="_blank"><i class="fa fa-gamepad fa-fw"></i>MobyGames</a>
+ <a class="pure-menu-link" href="https://www.mobygames.com/developer/sheet/view/developerId,{{ . }}" rel="me" target="_blank"><i class="fas fa-gamepad"></i>MobyGames</a>
</li>
{{ end }}
@@ -173,13 +180,13 @@
{{ with .Site.Social.lastfm }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="http://last.fm/user/{{ . }}" rel="me" target="_blank"><i class="fa fa-lastfm-square fa-fw"></i>Last.fm</a>
+ <a class="pure-menu-link" href="http://last.fm/user/{{ . }}" rel="me" target="_blank"><i class="fab fa-lastfm-square fa-fw"></i>Last.fm</a>
</li>
{{ end }}
{{ with .Site.Social.discogs }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://www.discogs.com/user/{{ . }}" rel="me" target="_blank"><i class="fa fa-music fa-fw"></i>Discogs</a>
+ <a class="pure-menu-link" href="https://www.discogs.com/user/{{ . }}" rel="me" target="_blank"><i class="fab fa-music fa-fw"></i>Discogs</a>
</li>
{{ end }}
@@ -187,7 +194,7 @@
{{ with .Site.Social.keybase }}
<li class="pure-menu-item">
- <a class="pure-menu-link" href="https://keybase.io/{{ . }}" rel="me" target="_blank"><i class="fa fa-key fa-fw"></i>Keybase</a>
+ <a class="pure-menu-link" href="https://keybase.io/{{ . }}" rel="me" target="_blank"><i class="fas fa-key"></i>Keybase</a>
</li>
{{ end }}
diff --git a/themes/blackburn b/themes/blackburn
index 643be7f9157c9cb3c2c2f020ffab8725018c1b66..4c748f2e02b2e6964c424ac5e40b807919c3418f 160000
--- a/themes/blackburn
+++ b/themes/blackburn
@@ -1 +1 @@
-Subproject commit 643be7f9157c9cb3c2c2f020ffab8725018c1b66
+Subproject commit 4c748f2e02b2e6964c424ac5e40b807919c3418f