Initial commit

content/repository.md

+---
+title: "BioRepository"
+date: 2019-07-07T22:25:54-05:00
+draft: true
+type: "custom"
+layout: "repository"
+---
+

content/research.md

+---
+title: "Research"
+date: 2019-05-19T01:57:56-05:00
+draft: true
+---
+<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

layouts/custom/data.html

+{{ partial "header.html" . }}
+
+<div class="header">
+    <h1>{{ .Title }}</h1>
+    <h2>{{ .Description }}</h2>
+</div>
+<div class="content">
+    {{ .Content }}
+</div>
+
+{{ partial "footer.html" . }}
+
+<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>
+        .ui-autocomplete {
+            max-height: 200px;
+            overflow-y: auto;
+            overflow-x: hidden;
+        }
+    </style>
+    <script>
+        $(function(){
+            $("#lineage" ).selectmenu({width: 230});
+        });
+        $(function(){
+            $("#populations" ).selectmenu({width: 230});
+        });
+        $(function(){
+            var genes = {{ index .Site.Data.scRNAseq_huPr_D.genes }};
+            var selectedGene = $("#gene").autocomplete({
+                source: genes.genes,
+                maxResults: 10,
+                maxShowItems: 10,
+                minLength: 1,
+            });
+        });
+        $("#analysis").click(function (event) {
+            event.preventDefault();
+            var genes = {{ index .Site.Data.scRNAseq_huPr_D.genes }};
+            _gene = $('#gene').val().toUpperCase();
+            if($.inArray(_gene,genes.genes) < 0){
+                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.ClusterVis").innerHTML = "Cluster Visualization"
+            var img = document.getElementById("img.ClusterVis");
+            img.src="/images/scRNAseq_huPr_D/png/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"
+            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"
+            return(_gene)
+        });
+    </script>
+</head>
\ No newline at end of file

layouts/custom/people.html

+{{ partial "header.html" . }}
+
+<style>
+    @media (min-width: 1000px) {
+        .column {
+            float: left;
+        }
+        .left {
+            width: 25%;
+        }
+        .right {
+            width: 75%;
+        }
+        .row:after {
+            content: "";
+            display: table;
+            clear: both;
+        }
+    }
+    img.pic {
+        width: 175px;
+        padding: 7px;
+        border: 1px solid #ddd;
+        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="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}}"><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>
+</div>
+
+{{ partial "footer.html" . }}
\ No newline at end of file

layouts/custom/publications.html

+{{ partial "header.html" . }}
+
+<style>
+    @media (min-width: 1000px) {
+        .column {
+            float: left;
+        }
+        .left {
+            width: 25%;
+        }
+        .right {
+            width: 75%;
+        }
+        .row:after {
+            content: "";
+            display: table;
+            clear: both;
+        }
+    }
+</style>
+
+<div class="header">
+    <h1>{{ .Title }}</h1>
+    <h2>{{ .Description }}</h2>
+</div>
+<div class="content">
+    <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%;">
+                </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}}">
+            {{else}}
+                <h4><i><a href="{{.Params.plink}}">
+            {{end}}
+            {{.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>
+                {{end}}
+            {{end}}
+            <hr><br>
+        {{end}}
+    </div>
+</div>
+
+{{ partial "footer.html" . }}
\ No newline at end of file

layouts/custom/repository.html

+{{ partial "header.html" . }}
+
+<div class="header">
+    <h1>{{ .Title }}</h1>
+    <h2>{{ .Description }}</h2>
+</div>
+<div class="content">
+    {{ .Content }}
+</div>
+
+{{ partial "footer.html" . }}
+
+<head>
+
+</head>
\ No newline at end of file

layouts/index.html

+{{ partial "header.html" . }}
+
+<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>
+  <h4>{{ .Site.Params.description }}</h3>
+</div>
+
+<div class="content">
+  {{ range ( .Paginate (where .Data.Pages "Type" "post")).Pages }}
+    {{ .Render "summary"}}
+  {{ end }}
+
+  {{ partial "pagination.html" . }}
+
+</div>
+
+{{ partial "footer.html" . }}

layouts/partials/copyright.html

+<div>
+  <div class="small-print">
+    <small>{{ .Site.Copyright | safeHTML }}</small>
+  </div>
+  <div class="small-print">
+  </div>
+</div>

layouts/partials/social.html

+<div class="pure-menu social">
+  <ul class="pure-menu-list">
+
+     <!-- 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>
+    </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>
+    </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>
+    </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>
+    </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>
+    </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>
+    </li>
+    {{ end }}
+
+    <!-- SNS photo/video sharing -->
+
+    {{ 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>
+    </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>
+    </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>
+    </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>
+    </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>
+    </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>
+    </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>
+    </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>
+    </li>
+    {{ end }}
+
+    <!-- SNS career oriented -->
+
+    {{ 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>
+    </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>
+    </li>
+    {{ end }}
+
+    <!-- SNS news -->
+
+    {{ 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>
+    </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>
+    </li>
+    {{ end }}
+
+    <!-- Techie -->
+
+    {{ 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>
+    </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>
+    </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>
+    </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>
+    </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>
+    </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>
+    </li>
+    {{ end }}
+
+    <!-- Gaming -->
+
+    {{ 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>
+    </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>
+    </li>
+    {{ end }}
+
+    <!-- Music -->
+
+    {{ 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>
+    </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>
+    </li>
+    {{ end }}
+
+    <!-- Other -->
+
+    {{ 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>
+    </li>
+    {{ end }}
+
+  </ul>
+</div>

blackburn @ 643be7f9

+Subproject commit 643be7f9157c9cb3c2c2f020ffab8725018c1b66