Merge branch 'develop' into 'master'

Develop

See merge request !9

content/publications/2013_celldeathdis.md

 ---
 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."

content/publications/2014_prostate.md

 ---
 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"

content/publications/2016_differentiation.md

 ---
 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"

content/publications/2017_cytometry.md

 ---
 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"

content/publications/2017_differentiation.md

 ---
 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"

content/publications/2017_prostate.md

 ---
 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"

content/publications/2018_cellreports.md

 ---
 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"

content/repository.md

----
-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"
+---
+

content/research.md

 ---
 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

content/sc.data/_index.md

+---
+title: "Single-Cell RNA-sequencing Data"
+date: 2019-05-19T12:09:34-05:00
+draft: false
+type: "custom"
+layout: "sc.data"
+---
+

content/sc.data/hu.bph.pr.md

+---
+title: "Human BPH"
+description: "Single-Cell RNA-sequencing Data"
+name: "Human BPH (PENDING)"
+date: 2019-12-24T22:35:01-06:00
+draft: false
+weight: "4"
+type: "custom"
+layout: ""
+---
+
+**PENDING**
\ No newline at end of file

content/sc.data/hu.cancer.pr.md

+---
+title: "Human Prostate Cancer"
+description: "Single-Cell RNA-sequencing Data"
+name: "Human Prostate Cancer (PENDING)"
+date: 2019-12-24T22:35:22-06:00
+draft: false
+weight: "5"
+type: "custom"
+layout: ""
+---
+
+**PENDING**
\ No newline at end of file

content/sc.data/hu.donor.bl.md

+---
+title: "Human Donor Bladder"
+description: "Single-Cell RNA-sequencing Data"
+name: "Human Donor Bladder (PENDING)"
+date: 2019-12-24T22:35:48-06:00
+draft: false
+weight: "3"
+type: "custom"
+layout: ""
+---
+
+**PENDING**
\ No newline at end of file

content/sc.data/hu.donor.pr.deep.md

+---
+title: "Human Donor Prostate"
+description: "Single-Cell RNA-sequencing Data"
+name: "Human Donor (additional sequencing depth of data published in Henry GH. et al, Cell Reports,2018 and projected in UMAP space)"
+date: 2019-12-24T21:46:39-06:00
+draft: false
+weight: "1"
+type: "custom"
+layout: "hu.donor.deep"
+---
+

content/sc.data/hu.donor.pr.shallow.md

+---
+title: "Human Donor Prostate (shallow)"
+description: "Single-Cell RNA-sequencing Data"
+name: "Human Donor (original sequencing depth published in Henry GH. et al, Cell Reports,2018)"
+date: 2019-12-24T21:46:39-06:00
+draft: true
+weight: "2"
+type: "custom"
+layout: "hu.donor.shallow"
+---
+

content/sc.data/mu.bl.md

+---
+title: "Mouse Bladder"
+description: "Single-Cell RNA-sequencing Data"
+name: "Mouse Bladder (PENDING)"
+date: 2019-12-24T22:36:05-06:00
+draft: false
+weight: "7"
+type: "custom"
+layout: ""
+---
+
+**PENDING**
\ No newline at end of file

content/sc.data/mu.pr.md

+---
+title: "Mouse Prostate"
+description: "Single-Cell RNA-sequencing Data"
+name: "Mouse Prostate (PENDING)"
+date: 2019-12-24T22:36:01-06:00
+draft: false
+weight: "6"
+type: "custom"
+layout: ""
+---
+
+**PENDING**
\ No newline at end of file

data/repository/filters.json

+[
+    {"id": "disease", "parent": "#", "text": "Disease Phenotype",  "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "disease.d", "parent":"disease", "text": "Donor (normal)"},
+    {"id": "disease.b", "parent":"disease", "text": "BPH"},
+    {"id": "disease.c", "parent":"disease", "text": "Prostate Cancer"},
+    {"id": "demographics", "parent": "#", "text": "Demographics",  "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "ethnicity", "parent":"demographics", "text": "Ethnicity", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "ethn.aa", "parent":"ethnicity", "text": "African American"},
+    {"id": "ethn.as", "parent":"ethnicity", "text": "Asian"},
+    {"id": "ethn.ca", "parent":"ethnicity", "text": "Caucasian"},
+    {"id": "ethn.hi", "parent":"ethnicity", "text": "Hispanic"},
+    {"id": "ethn.uk", "parent":"ethnicity", "text": "Unknown Ethnicity"},
+    {"id": "age", "parent":"demographics", "text": "Age", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "age.40", "parent":"age", "text": "<40yo"},
+    {"id": "age.50", "parent":"age", "text": "41-50yo"},
+    {"id": "age.60", "parent":"age", "text": "51-60yo"},
+    {"id": "age.70", "parent":"age", "text": "61-70yo"},
+    {"id": "age.80", "parent":"age", "text": "71-80yo"},
+    {"id": "age.90", "parent":"age", "text": "81-90yo"},
+    {"id": "age.100", "parent":"age", "text": "91+yo"},
+    {"id": "age.uk", "parent":"age", "text": "Unknown Age"},
+    {"id": "clinical", "parent":"#", "text": "Clinical Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bmi", "parent":"clinical", "text": "BMI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bmi.uw", "parent":"bmi", "text": "Underweight"},
+    {"id": "bmi.nw", "parent":"bmi", "text": "Normal"},
+    {"id": "bmi.ow", "parent":"bmi", "text": "Overweight"},
+    {"id": "bmi.ob", "parent":"bmi", "text": "Obese"},
+    {"id": "bmi.vo", "parent":"bmi", "text": "Very Obese"},
+    {"id": "bmi.so", "parent":"bmi", "text": "Severely Obese"},
+    {"id": "bmi.uk", "parent":"bmi", "text": "Unknown BMI"},
+    {"id": "t2d", "parent":"clinical", "text": "Type 2 Diabetes", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "t2d.y", "parent":"t2d", "text": "Yes"},
+    {"id": "t2d.n", "parent":"t2d", "text": "No"},
+    {"id": "t2d.uk", "parent":"t2d", "text": "Unknown"},
+    {"id": "bph", "parent":"clinical", "text": "BPH Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bphsurgery", "parent":"bph", "text": "BPH Surgery", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bphsurg.simp", "parent":"bphsurgery", "text": "Simple Prostatectomy"},
+    {"id": "bphsurg.turp", "parent":"bphsurgery", "text": "TURP"},
+    {"id": "bphsurg.uk", "parent":"bphsurgery", "text": "Unknown Surgery"},
+    {"id": "5ari", "parent":"bph", "text": "5ARI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "5ari.y", "parent":"5ari", "text": "Yes 5ARI"},
+    {"id": "5ari.n", "parent":"5ari", "text": "No 5ARI"},
+    {"id": "5ari.uk", "parent":"5ari", "text": "Unknown 5ARI"},
+    {"id": "5aril", "parent":"bph", "text": "5ARI Length (months)", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "5aril.10", "parent":"5aril", "text": "<10mnths 5ARI"},
+    {"id": "5aril.20", "parent":"5aril", "text": "10-20mnths 5ARI"},
+    {"id": "5aril.30", "parent":"5aril", "text": "20+mnths 5ARI"},
+    {"id": "5aril.uk", "parent":"5aril", "text": "Unknown 5ARI"},
+    {"id": "5aril.na", "parent":"5aril", "text": "NA 5ARI"},
+    {"id": "prostatevol", "parent":"clinical", "text": "Prostate Volume", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "prvol.low", "parent":"prostatevol", "text": "Low Volumne"},
+    {"id": "prvol.med", "parent":"prostatevol", "text": "Medium Volume"},
+    {"id": "prvol.hi", "parent":"prostatevol", "text": "High Volume"},
+    {"id": "prvol.vhi", "parent":"prostatevol", "text": "Very High Volume"},
+    {"id": "prvol.uk", "parent":"prostatevol", "text": "Unknown Volume"},
+    {"id": "repo", "parent":"#", "text": "Repository", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "repo.pr", "parent":"repo", "text": "Prostate", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "repo.pr.cry", "parent":"repo.pr", "text": "Pr Cryopreserved Cells"},
+    {"id": "repo.pr.ff", "parent":"repo.pr", "text": "Pr Flash Frozen Tissue"},
+    {"id": "repo.pr.ffpe", "parent":"repo.pr", "text": "Pr FFPE"},
+    {"id": "repo.pr.oct", "parent":"repo.pr", "text": "Pr OCT"},
+    {"id": "repo.bl", "parent":"repo", "text": "Bladder"},
+    {"id": "repo.sv", "parent":"repo", "text": "Seminal Vesicle"},
+    {"id": "repo.vd", "parent":"repo", "text": "Vas Deferencec"},
+    {"id": "repo.ut", "parent":"repo", "text": "Ureter"}
+]
\ No newline at end of file