fix: Show abbr on tap for mobile

This is in prep for a similar feature in BibTex citations

.envrc

@@ -0,0 +1,4 @@
+use flake
+layout node
+mkdir -p "${HOME}/Library/Application Support/SourceGit"
+echo "${PATH}" > "${HOME}/Library/Application Support/SourceGit/PATH"

.github/workflows/build-site.yml

@@ -1,44 +0,0 @@
-name: Build and Deploy Site
-on:
-  push:
-    branches:
-      - master
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-        with:
-          submodules: true
-      - name: Setup Node
-        uses: actions/setup-node@v2
-        with:
-          node-version: lts/*
-      - name: Setup Hugo
-        uses: peaceiris/actions-hugo@v2
-        with:
-          hugo-version: "latest"
-          extended: true
-      - name: Configure npm
-        run: |
-          npm config set "@fortawesome:registry" https://npm.fontawesome.com/
-          npm config set "//npm.fontawesome.com/:_authToken" ${{ secrets.FONTAWESOME_TOKEN }}
-      - name: Install postcss
-        run: |
-          npm -g install postcss-cli
-      - name: Install npm packages
-        run: |
-          npm install
-      - name: Run Hugo
-        run: |
-          hugo --environment production --minify
-      - name: Deploy to gh-pages
-        if: ${{ !env.ACT }}
-        uses: rdarida/simple-github-pages-deploy-action@v1
-        with:
-          git-user: "MillironX"
-          git-email: "25492070+MillironX@users.noreply.github.com"
-          git-base-folder: "public"
-          commit-message: "Build and deploy"
-          branch: "gh-pages"

.gitignore

@@ -151,3 +151,41 @@ dist
 .yarn/build-state.yml
 .yarn/install-state.gz
 .pnp.*
+
+### FontAwesome gitignore ###
+
+fontawesome-pro-6.3.0-web
+
+### direnv gitignore ###
+.direnv
+
+### Nix Flake gitignore ###
+result
+
+### MacOS gitignore ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "themes/ananke"]
-	path = themes/ananke
-	url = https://github.com/theNewDynamic/gohugo-theme-ananke.git

.gitpod.yml

@@ -1,13 +0,0 @@
-# List the start up tasks. Learn more https://www.gitpod.io/docs/config-start-tasks/
-tasks:
-  - name: Install Hugo dependencies
-    before: |
-      mkdir -p $HOME/.local/bin
-      curl -L https://github.com/gohugoio/hugo/releases/download/v0.104.3/hugo_extended_0.104.3_linux-amd64.tar.gz | tar xvz -C $HOME/.local/bin
-      export PATH=$HOME/.local/bin:$PATH
-    init: echo "Your version of Hugo is `hugo version`"
-    command: hugo server -D -F --baseUrl $(gp url 1313) --liveReloadPort=443 --appendPort=false --bind=0.0.0.0
-# List the ports to expose. Learn more https://www.gitpod.io/docs/config-ports/
-ports:
-  - port: 1313
-    onOpen: open-preview

.prettierignore

@@ -1,2 +1 @@
-node_modules
+layouts/_default/index.manifest.json
-themes

.prettierrc

@@ -4,3 +4,6 @@ overrides:
   - files: "*.html"
     options:
       parser: "go-template"
+  - files: "*.gotmpl"
+    options:
+      parser: "go-template"

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+  "editor.formatOnSave": true
+}

.woodpecker.yml

@@ -0,0 +1,18 @@
+when:
+  branch: master
+  event:
+    - push
+    - cron
+  cron: "weekly-build"
+
+steps:
+  - name: Build site
+    image: hugomods/hugo:std-base-non-root-0.141.0
+    commands:
+      - hugo --minify
+  - name: Deploy to pages
+    image: codeberg.org/xfix/plugin-codeberg-pages-deploy:1
+    settings:
+      folder: public
+      ssh_key:
+        from_secret: ssh_key

.zed/settings.json

@@ -0,0 +1,13 @@
+{
+  "languages": {
+    "HTML": {
+      "formatter": {
+        "external": {
+          "command": "prettier",
+          "arguments": ["--stdin-filepath", "{buffer_path}"]
+        }
+      }
+    }
+  },
+  "file_types": { "HTML": ["gotmpl"] }
+}

README.md

@@ -1,3 +1,42 @@
-# millironx.github.io
+# pages
 
-My personal website. Now hosted over at https://millironx.com
+[![status-badge](https://woodpecker.millironx.com/api/badges/30/status.svg?branch=master)](https://woodpecker.millironx.com/repos/30/branches/master)
+
+My personal website. Hosted over at <https://millironx.com>
+
+## Notes to self
+
+### Nix dev shell
+
+All developer dependencies are now bundled as a Nix Flake. The only trouble with
+this is that npm packages don't play well with Nix (and especially Flakes), so
+npm packages are specified twice: once in `package{-lock}.json` and then again
+in `node*.nix`.
+
+Compounding this, there are formatters and commit hooks that require npm to be
+functional. So, to develop right now requires allowing direnv to setup the Nix
+development shell, then immediately installing npm packages via `npm ci`. VSCode
+(with extensions) and Zed are smart enough to figure out how to use direnv, and
+direnv will pass the PATH to SourceGit for Mac, but other programs aren't that
+smart, so you'll need to launch those programs from inside a direnv shell to
+make sure they have Prettier, Husky, and all that jazz to execute the hooks.
+
+Last compounding factors: if `node_modules` is present in the root directory,
+then node2nix won't create a correct derivation, so `node_modules` will need to
+be temporarily deleted after modifying any npm packages, then as soon as
+node2nix is happy, then immediately run `npm ci` to get the commit hooks working
+again. Oh, and also, I renamed the `default.nix` file generated by node2nix to
+node.nix to avoid giving direnv any wrong impressions about what derivation to
+run.
+
+Yes, hopefully I can get completely away from npm here soon, but this is a minor
+inconvenience considering how (not) often I install new packages into this site,
+and really discourages me from contributing to the website obesity crisis.
+
+### Nix building
+
+Nix building will not work because Hugo reaches out to the internet via content
+adapters, and that (by intention) is not perfectly reproducable. As such,
+_development_ tools are installed in a Nix shell, but building has been removed
+from the Flake. Thankfully, hugomods provides "canonical" Docker images for hugo
+now.

archetypes/academia.md

@@ -4,7 +4,7 @@ date: {{ .Date }}
 cardImage: library
 draft: true
 featured: false
-keywords:
+tags:
   - smart
   - profound
 type: "Journal Article"

assets/graphics/brandedbull.svg

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+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:cc="http://creativecommons.org/ns#"
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assets/scripts/fa-icons.js

@@ -1,74 +0,0 @@
-import { library, icon, config, dom } from "@fortawesome/fontawesome-svg-core";
-import {
-  faBook,
-  faBrowser,
-  faComment,
-  faEllipsis,
-  faFileAlt,
-  faFileSignature,
-  faGraduationCap,
-  faHome,
-  faNotebook,
-  faPodium,
-  faPresentation,
-  faUniversity,
-  faUserAstronaut,
-  faVideo,
-  faW,
-} from "@fortawesome/pro-duotone-svg-icons";
-import {
-  faDiscord,
-  faGithub,
-  faGitlab,
-  faGolang,
-  faHtml5,
-  faOrcid,
-  faStackOverflow,
-  faSteam,
-  faVimeo,
-} from "@fortawesome/free-brands-svg-icons";
-
-config.familyDefault = "duotone";
-config.styleDefault = "duotone";
-
-const faBullSperm = {
-  prefix: "fax",
-  iconName: "bull-sperm",
-  icon: [
-    512,
-    512,
-    [],
-    null,
-    "M96 32c-6.691.363-12.375 4.062-15.375 7.062l-64 64c-12.8 12.8-5.333 26.667 0 32l96 64c10.3 10.301 22.938 4.887 37.563-7.812 8.635 9.735 16.63 18.38 23.125 24.875 8.33 8.33 23.436 16.284 41.75 24.313 18.313 8.028 39.82 16.065 60.812 24.062 20.992 7.997 41.474 15.986 57.625 23.938 16.15 7.95 27.882 16.013 31.5 23.25 6.52 13.038 26.468 44.939 48.875 79.75 22.32 34.674 46.99 72.043 63 96.062.02.029.042.096.064.125.045.064.144.185.189.25l2.812-1.5c-10.685-26.697-28.285-68.26-46.44-106.437-18.155-38.179-36.666-72.792-49.937-86.063-16.566-16.566-56.5-32.375-96.5-48.375s-80.066-32.19-95.5-47.625c-6.45-6.45-14.409-15.11-23.063-24.875 12.926-14.779 18.51-27.552 8.125-37.938-16-26.666-51.2-83.2-64-96-5.6-5.6-11.42-7.345-16.625-7.062zm372.688 436.75c.201.487.488 1.079.687 1.563-.291-.44-.644-.995-.937-1.438.023-.012.06.001.064 0 .002 0 .185-.06.188-.064.002-.001-.011-.038 0-.064z",
-  ],
-};
-
-library.add(
-  faBook,
-  faBrowser,
-  faBullSperm,
-  faComment,
-  faDiscord,
-  faEllipsis,
-  faFileAlt,
-  faFileSignature,
-  faGithub,
-  faGitlab,
-  faGolang,
-  faGraduationCap,
-  faHome,
-  faHtml5,
-  faNotebook,
-  faOrcid,
-  faPodium,
-  faPresentation,
-  faStackOverflow,
-  faSteam,
-  faUniversity,
-  faUserAstronaut,
-  faVideo,
-  faVimeo,
-  faW
-);
-
-dom.i2svg();

assets/scripts/phone-masking.js

@@ -1 +1,15 @@
-$("#phone").mask("(000) 000-0000");
+// Built by perplexity.ai
+function maskPhoneNumber(input) {
+  input.addEventListener("input", function (e) {
+    var x = e.target.value
+      .replace(/\D/g, "")
+      .match(/(\d{0,3})(\d{0,3})(\d{0,4})/);
+    e.target.value = !x[2]
+      ? x[1]
+      : "(" + x[1] + ") " + x[2] + (x[3] ? "-" + x[3] : "");
+  });
+}
+
+// Usage
+var phoneInput = document.getElementById("phone");
+maskPhoneNumber(phoneInput);

assets/scripts/scroll-effect.js

@@ -1,5 +0,0 @@
-$(window).scroll(function (e) {
-  oVal = $(window).scrollTop() / 170;
-  $(".blur").css("opacity", oVal);
-});
-$("#motto").fitText();

assets/scripts/tooltip-enable.js

@@ -1,6 +0,0 @@
-var tooltipTriggerList = [].slice.call(
-  document.querySelectorAll('[data-bs-toggle="tooltip"]')
-);
-var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {
-  return new bootstrap.Tooltip(tooltipTriggerEl);
-});

assets/styles/millironx.css

@@ -0,0 +1,747 @@
+:root {
+  /*
+    Color schemes
+  */
+  color-scheme: light dark;
+
+  --ear-tag-red-1: oklch(97.5% 0.016 35.7);
+  --ear-tag-red-2: oklch(95.9% 0.027 37.7);
+  --ear-tag-red-3: oklch(91.8% 0.055 33.4);
+  --ear-tag-red-4: oklch(84% 0.092 29.8);
+  --ear-tag-red-5: oklch(80% 0.123 29.8);
+  --ear-tag-red-6: oklch(71% 0.146 29.8);
+  --ear-tag-red-7: oklch(66% 0.154 29.8);
+  --ear-tag-red-8: oklch(58% 0.162 29.8);
+  --ear-tag-red-9: oklch(53% 0.154 29.8);
+  --ear-tag-red-10: oklch(49% 0.146 29.8);
+  --ear-tag-red-11: oklch(42% 0.131 29.8);
+  --ear-tag-red-12: oklch(35% 0.115 29.8);
+  --ear-tag-red-13: oklch(27% 0.092 29.8);
+  --ear-tag-red-14: oklch(20% 0.07 29.8);
+  --ear-tag-red-15: oklch(16% 0.054 29.8);
+  --ear-tag-red-16: oklch(10% 0.039 29.8);
+  --ear-tag-red: var(--ear-tag-red-12);
+
+  --swiss-brown-1: oklch(98% 0.011 67.7);
+  --swiss-brown-2: oklch(97% 0.023 67.7);
+  --swiss-brown-3: oklch(93% 0.039 67.7);
+  --swiss-brown-4: oklch(84% 0.046 67.7);
+  --swiss-brown-5: oklch(80% 0.061 67.7);
+  --swiss-brown-6: oklch(71% 0.072 67.7);
+  --swiss-brown-7: oklch(66% 0.076 67.7);
+  --swiss-brown-8: oklch(58% 0.08 67.7);
+  --swiss-brown-9: oklch(53% 0.076 67.7);
+  --swiss-brown-10: oklch(49% 0.072 67.7);
+  --swiss-brown-11: oklch(42% 0.065 67.7);
+  --swiss-brown-12: oklch(35% 0.057 67.7);
+  --swiss-brown-13: oklch(27% 0.046 67.7);
+  --swiss-brown-14: oklch(20% 0.035 67.7);
+  --swiss-brown-15: oklch(16% 0.027 67.7);
+  --swiss-brown-16: oklch(10% 0.019 67.7);
+  --swiss-brown: var(--swiss-brown-12);
+
+  --prickly-pear-yellow-1: oklch(98% 0.017 94.5);
+  --prickly-pear-yellow-2: oklch(97% 0.035 94.5);
+  --prickly-pear-yellow-3: oklch(93% 0.059 94.5);
+  --prickly-pear-yellow-4: oklch(84% 0.07 94.5);
+  --prickly-pear-yellow-5: oklch(80% 0.093 94.5);
+  --prickly-pear-yellow-6: oklch(71% 0.11 94.5);
+  --prickly-pear-yellow-7: oklch(66% 0.116 94.5);
+  --prickly-pear-yellow-8: oklch(58% 0.122 94.5);
+  --prickly-pear-yellow-9: oklch(53% 0.116 94.5);
+  --prickly-pear-yellow-10: oklch(49% 0.11 94.5);
+  --prickly-pear-yellow-11: oklch(42% 0.099 94.5);
+  --prickly-pear-yellow-12: oklch(35% 0.083 93.6);
+  --prickly-pear-yellow-13: oklch(27.1% 0.064 92.8);
+  --prickly-pear-yellow-14: oklch(20% 0.047 92.4);
+  --prickly-pear-yellow-15: oklch(16% 0.038 93.3);
+  --prickly-pear-yellow-16: oklch(10% 0.024 89.7);
+  --prickly-pear-yellow: var(--prickly-pear-yellow-7);
+
+  --hayyard-green-1: oklch(98% 0.014 135);
+  --hayyard-green-2: oklch(97% 0.03 135);
+  --hayyard-green-3: oklch(93% 0.049 135);
+  --hayyard-green-4: oklch(84% 0.058 135);
+  --hayyard-green-5: oklch(80% 0.078 135);
+  --hayyard-green-6: oklch(71% 0.092 135);
+  --hayyard-green-7: oklch(66% 0.097 135);
+  --hayyard-green-8: oklch(58% 0.103 135);
+  --hayyard-green-9: oklch(53% 0.097 135);
+  --hayyard-green-10: oklch(49% 0.092 135);
+  --hayyard-green-11: oklch(42% 0.083 135);
+  --hayyard-green-12: oklch(35% 0.073 135);
+  --hayyard-green-13: oklch(27% 0.058 135);
+  --hayyard-green-14: oklch(20% 0.044 135);
+  --hayyard-green-15: oklch(16% 0.034 135);
+  --hayyard-green-16: oklch(10% 0.025 135);
+  --hayyard-green: var(--hayyard-green-11);
+
+  --flaming-gorge-blue-1: oklch(98% 0.012 241);
+  --flaming-gorge-blue-2: oklch(96.8% 0.021 230);
+  --flaming-gorge-blue-3: oklch(92.9% 0.041 242);
+  --flaming-gorge-blue-4: oklch(84% 0.051 245);
+  --flaming-gorge-blue-5: oklch(80% 0.069 245);
+  --flaming-gorge-blue-6: oklch(71% 0.081 245);
+  --flaming-gorge-blue-7: oklch(66% 0.086 245);
+  --flaming-gorge-blue-8: oklch(58% 0.09 245);
+  --flaming-gorge-blue-9: oklch(53% 0.086 245);
+  --flaming-gorge-blue-10: oklch(49% 0.081 245);
+  --flaming-gorge-blue-11: oklch(42% 0.073 245);
+  --flaming-gorge-blue-12: oklch(35% 0.064 245);
+  --flaming-gorge-blue-13: oklch(27% 0.051 245);
+  --flaming-gorge-blue-14: oklch(20% 0.039 245);
+  --flaming-gorge-blue-15: oklch(16% 0.03 245);
+  --flaming-gorge-blue-16: oklch(10% 0.022 245);
+  --flaming-gorge-blue: var(--flaming-gorge-blue-12);
+
+  --coeurdalene-purple-1: oklch(97.8% 0.016 311);
+  --coeurdalene-purple-2: oklch(96.5% 0.026 314);
+  --coeurdalene-purple-3: oklch(92.5% 0.052 308);
+  --coeurdalene-purple-4: oklch(84% 0.097 302);
+  --coeurdalene-purple-5: oklch(80% 0.129 302);
+  --coeurdalene-purple-6: oklch(71% 0.153 302);
+  --coeurdalene-purple-7: oklch(66% 0.162 302);
+  --coeurdalene-purple-8: oklch(58% 0.17 302);
+  --coeurdalene-purple-9: oklch(53% 0.162 302);
+  --coeurdalene-purple-10: oklch(49% 0.153 302);
+  --coeurdalene-purple-11: oklch(42% 0.138 302);
+  --coeurdalene-purple-12: oklch(35% 0.121 302);
+  --coeurdalene-purple-13: oklch(27% 0.097 302);
+  --coeurdalene-purple-14: oklch(20% 0.073 302);
+  --coeurdalene-purple-15: oklch(16% 0.056 302);
+  --coeurdalene-purple-16: oklch(10% 0.041 302);
+  --coeurdalene-purple: var(--coeurdalene-purple-13);
+
+  --eclipse-1: oklch(98% 0 0);
+  --eclipse-2: oklch(97% 0 0);
+  --eclipse-3: oklch(93% 0 0);
+  --eclipse-4: oklch(84% 0 0);
+  --eclipse-5: oklch(80% 0 0);
+  --eclipse-6: oklch(71% 0 0);
+  --eclipse-7: oklch(66% 0 0);
+  --eclipse-8: oklch(58% 0 0);
+  --eclipse-9: oklch(53% 0 0);
+  --eclipse-10: oklch(49% 0 0);
+  --eclipse-11: oklch(42% 0 0);
+  --eclipse-12: oklch(35% 0 0);
+  --eclipse-13: oklch(27% 0 0);
+  --eclipse-14: oklch(20% 0 0);
+  --eclipse-15: oklch(16% 0 0);
+  --eclipse-16: oklch(10% 0 0);
+  --eclipse: var(--eclipse-12);
+
+  --cowhide-1: oklch(98% 0.009 77.5);
+  --cowhide-2: oklch(97% 0.018 77.5);
+  --cowhide-3: oklch(93% 0.029 77.5);
+  --cowhide-4: oklch(84% 0.034 77.5);
+  --cowhide-5: oklch(80% 0.046 77.5);
+  --cowhide-6: oklch(71% 0.054 77.5);
+  --cowhide-7: oklch(66% 0.057 77.5);
+  --cowhide-8: oklch(58% 0.06 77.5);
+  --cowhide-9: oklch(53% 0.057 77.5);
+  --cowhide-10: oklch(49% 0.054 77.5);
+  --cowhide-11: oklch(42% 0.049 77.5);
+  --cowhide-12: oklch(35% 0.043 77.5);
+  --cowhide-13: oklch(27% 0.034 77.5);
+  --cowhide-14: oklch(20% 0.026 77.5);
+  --cowhide-15: oklch(16% 0.02 77.5);
+  --cowhide-16: oklch(10% 0.015 77.5);
+  --cowhide: var(--cowhide-3);
+
+  --body-background: light-dark(var(--cowhide-3), var(--eclipse-11));
+  --link-color: light-dark(
+    var(--flaming-gorge-blue),
+    var(--coeurdalene-purple-4)
+  );
+  --nav-button-text: light-dark(var(--eclipse-2), var(--cowhide-12));
+  --nav-button-background: light-dark(var(--eclipse-11), var(--cowhide-2));
+  --nav-button-background-hover: light-dark(
+    var(--eclipse-13),
+    var(--cowhide-4)
+  );
+  --nav-button-background-active: light-dark(
+    var(--eclipse-14),
+    var(--cowhide-5)
+  );
+  --container-border: light-dark(var(--swiss-brown-6), var(--eclipse-16));
+  --container-background: light-dark(var(--swiss-brown-4), var(--eclipse-12));
+  --container-border-alt: light-dark(var(--eclipse-16), var(--swiss-brown-6));
+  --container-background-alt: light-dark(
+    var(--eclipse-12),
+    var(--swiss-brown-4)
+  );
+  --motto-background: rgba(0, 0, 0, 0.66);
+  --page-button-text: var(--prickly-pear-yellow-1);
+  --page-button-background: var(--prickly-pear-yellow-8);
+  --page-button-background-hover: var(--prickly-pear-yellow-10);
+  --page-button-background-active: var(--prickly-pear-yellow-12);
+  --page-button-background-disabled: var(--prickly-pear-yellow-6);
+  --page-button-text-disabled: var(--eclipse-7);
+
+  /*
+    Fonts
+  */
+  --font-family-antique: Superclarendon, "Bookman Old Style", "URW Bookman",
+    "URW Bookman L", "Georgia Pro", Georgia, serif;
+  --font-family-slab-serif: Rockwell, "Rockwell Nova", "Roboto Slab",
+    "DejaVu Serif", "Sitka Small", serif;
+  --font-family-system-ui: system-ui, sans-serif;
+  --font-family-monospace: "Nimbus Mono PS", "Courier New", monospace;
+}
+
+/*
+  Default element styles (for small screens)
+*/
+
+html {
+  background-color: var(--body-background);
+  font-family: var(--font-family-slab-serif);
+}
+
+body {
+  display: flex;
+  flex-direction: column;
+  min-height: 98vh;
+  margin: 0 8px;
+}
+
+a {
+  color: var(--link-color);
+}
+
+header {
+  display: flex;
+  justify-content: space-evenly;
+  align-items: center;
+}
+
+nav {
+  display: flex;
+  flex-direction: row;
+  overflow: scroll;
+  padding-bottom: 1rem;
+  position: sticky;
+  top: 0;
+}
+
+nav a {
+  color: var(--nav-button-text);
+  background-color: var(--nav-button-background);
+  border-radius: 0.05rem;
+  border-style: outset;
+  border-width: 0.2rem;
+  border-color: var(--nav-button-background);
+  min-width: 7.5rem;
+  max-width: 7.5rem;
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+  margin: 0.2rem;
+  text-decoration: none;
+  padding: 0 0.2rem;
+  font-family: var(--font-family-system-ui);
+}
+
+nav a.active {
+  background-color: var(--nav-button-background-active);
+}
+
+nav a:active {
+  border-style: inset;
+}
+
+nav a:hover {
+  background-color: var(--nav-button-background-hover);
+}
+
+main {
+  display: flex;
+  flex-direction: column;
+}
+
+figure {
+  border-color: var(--container-border);
+  border-width: 1.5pt;
+  border-style: inset;
+  border-radius: 2.5pt;
+  background-color: var(--container-background);
+  padding: 1.25pt;
+}
+
+figure:has(blockquote) {
+  background: linear-gradient(
+    to right,
+    var(--container-border),
+    var(--container-background)
+  );
+  border: none;
+  border-radius: 0;
+  border-left: 6px solid black;
+  padding: 0.25em 1em;
+}
+
+figure:has(blockquote) > blockquote {
+  margin: 0;
+}
+
+figure:has(blockquote) > figcaption::before {
+  content: "\2014 \00A0";
+}
+
+figure:has(blockquote) > figcaption {
+  margin-top: -1em;
+  margin-bottom: 1em;
+  font-size: 80%;
+}
+
+footer {
+  background-color: var(--container-background);
+  margin: 0 0 -1em -1em;
+  width: calc(100% - 1em);
+  padding: 0.25em 1.25em;
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+  flex-shrink: 0;
+}
+
+form {
+  margin: 1rem;
+}
+
+fieldset {
+  padding: 1rem;
+}
+
+input,
+select,
+textarea {
+  width: 100%;
+  margin-bottom: 0.5rem;
+}
+
+input:invalid,
+select:invalid,
+textarea:invalid {
+  border-bottom-width: 2px;
+  border-bottom-color: var(--ear-tag-red);
+}
+
+code {
+  font-family: var(--font-family-monospace);
+}
+
+/*
+  abbr element "tooltip" for mobile
+  heavily modified from https://bitsofco.de/making-abbr-work-for-touchscreen-keyboard-mouse/
+*/
+abbr[title]:focus::after {
+  content: attr(title);
+  background-color: #1e1e1e;
+  color: #fff;
+  border-radius: 0.125em;
+  box-shadow: 1px 1px 5px 0 rgba(0, 0, 0, 0.4);
+  font-size: smaller;
+  padding: 0.5em;
+  display: block;
+}
+
+/*
+  Container-type helper classes
+*/
+.row {
+  display: flex;
+  flex-direction: column;
+  width: 100%;
+}
+
+.motto-wrapper {
+  display: block;
+  flex: 1 0 30vh;
+  margin-bottom: 1em;
+}
+
+.motto {
+  position: relative;
+  display: grid;
+  place-items: center;
+  text-align: center;
+  color: #fff;
+  font-weight: 600;
+  text-shadow: 0 0 10px rgba(0, 0, 0, 0.33);
+  width: 100%;
+  height: 100%;
+  padding: 0 0 0.5em 0;
+  border-radius: 0.25rem;
+  z-index: 10;
+}
+
+.motto::before {
+  content: " ";
+  position: absolute;
+  top: 0;
+  left: 0;
+  width: 100%;
+  height: 100%;
+  box-sizing: border-box;
+  background-size: cover;
+  background-position: 50% 50%;
+}
+
+.motto-inside {
+  position: relative;
+  max-width: 95%;
+  display: grid;
+  place-items: center;
+  text-align: center;
+}
+
+.motto .motto-inside h1 {
+  background-color: var(--motto-background);
+  padding: 0.5rem;
+}
+
+.card {
+  background-color: var(--container-background);
+  border-color: var(--container-border);
+  border-width: 1.5pt;
+  border-radius: 0.1rem;
+  border-style: outset;
+  margin: 1rem 0;
+  padding: 0.5rem;
+  padding-top: 0;
+  display: flex;
+  flex-direction: column;
+}
+
+.card-content {
+  display: flex;
+  flex-direction: column;
+  flex-grow: 1;
+}
+
+.card-header {
+  display: flex;
+  flex-direction: row;
+  justify-content: space-between;
+  flex-grow: 1;
+}
+
+.card-link {
+  white-space: nowrap;
+  display: inline-flex;
+  gap: 0.375rem;
+  align-items: center;
+  text-underline-offset: 0.25em;
+  backface-visibility: hidden;
+  margin: 0.1em 0.25em;
+  padding: 0.33em;
+  padding-right: 0.45em;
+}
+
+.card-body {
+  margin-top: 0.33em;
+}
+
+.category-button {
+  display: grid;
+  align-items: center;
+  justify-items: center;
+  color: white;
+  background-color: var(--ear-tag-red);
+  border-radius: 0.5em;
+  padding: 1em;
+  margin: 1em;
+  height: 2em;
+  aspect-ratio: 1 / 1;
+}
+
+.card-title > a {
+  color: inherit;
+}
+
+.img-thumbnail {
+  width: 100%;
+  height: auto;
+  margin-top: 0.5rem;
+}
+
+.thumb-icon-wrapper {
+  margin-top: 1rem;
+  display: flex;
+  justify-content: center;
+  align-content: center;
+}
+
+.thumb-icon-badge {
+  font-size: xx-large;
+  justify-self: center;
+  align-self: center;
+  padding: 1.5rem 3rem;
+  border-radius: 3rem;
+  background-color: var(--ear-tag-red);
+  color: white;
+}
+
+.fa-container svg {
+  overflow: visible;
+  box-sizing: content-box;
+  display: inline-block;
+  height: 1em;
+  width: 1.25em;
+  vertical-align: -0.125em;
+}
+
+.fa-container svg path {
+  fill: currentColor;
+}
+
+.account-bucket {
+  display: grid;
+  grid-template-columns: 3em 1em 1fr;
+  background-color: var(--container-background-alt);
+  padding: 1em 0;
+  border-radius: 0.5em;
+  border-color: var(--container-border-alt);
+  border-style: solid;
+  color: light-dark(white, black);
+  margin: 1em 0;
+  align-items: center;
+}
+
+.account-bucket h3 {
+  align-self: center;
+  writing-mode: sideways-lr;
+}
+
+.account-bucket details {
+  grid-column: 3;
+}
+
+.account-bucket .crypto-list {
+  grid-column: 3;
+  max-width: 100%;
+}
+
+.account-list {
+  display: flex;
+  justify-content: space-between;
+  flex-wrap: wrap;
+  width: calc(100% - 1.5em);
+}
+
+.account-bucket .account-list {
+  grid-column: 3;
+}
+
+.account-list a {
+  font-size: xx-large;
+  text-decoration: none;
+  color: inherit;
+  padding: 0.5em;
+}
+
+.account-list a:hover {
+  background-color: var(--container-background);
+  border-color: var(--container-border);
+  border-width: 2.5px;
+  border-radius: 0.5em;
+  border-style: solid;
+  padding: calc(0.5em - 2.5px);
+}
+
+figcaption .mono {
+  color: light-dark(black, white);
+  overflow-wrap: anywhere;
+}
+
+.crypto-list details {
+  max-width: 100%;
+}
+
+/*
+  Helper classes
+*/
+.font-small-caps {
+  font-variant-caps: small-caps;
+}
+
+.img-fluid {
+  max-width: 100%;
+  height: auto;
+  display: grid;
+  align-items: center;
+  justify-items: center;
+}
+
+.float-left {
+  float: none;
+  max-width: 100%;
+}
+
+.float-right {
+  float: none;
+  max-width: 100%;
+}
+
+.pagination {
+  display: flex;
+  justify-content: center;
+  gap: 0.5em;
+  padding-left: 0;
+}
+
+.pagination li {
+  list-style-type: none;
+  color: var(--nav-button-text);
+}
+
+.pagination li a {
+  color: var(--page-button-text);
+  background-color: var(--page-button-background);
+  border-radius: 0.05rem;
+  border-style: outset;
+  border-width: 0.2rem;
+  border-color: var(--page-button-background);
+  width: 2rem;
+  max-width: 1.8vw;
+  aspect-ratio: 1 / 1;
+  display: flex;
+  justify-content: center;
+  align-items: center;
+  margin: 0.2rem;
+  text-decoration: none;
+  padding: 0 0.2rem;
+  font-family: var(--font-family-system-ui);
+}
+
+.pagination li a:hover {
+  background-color: var(--page-button-background-hover);
+}
+
+.pagination li.active a {
+  background-color: var(--page-button-background-active);
+}
+
+.pagination li.disabled a {
+  cursor: not-allowed;
+  background-color: var(--page-button-background-disabled);
+  color: var(--page-button-text-disabled);
+  border-style: solid;
+}
+
+.mono {
+  font-family: var(--font-family-monospace);
+  font-weight: 600;
+}
+
+.bolder {
+  font-weight: bolder;
+  background-color: rgba(0, 0, 0, 0.33);
+  border-radius: 0.25em;
+}
+
+/* Specific elements */
+#content {
+  flex: 1 0 max-content;
+}
+
+/*
+  Desktop screen size adjustments
+*/
+@media (min-width: 768px) {
+  /*
+    Default element styles
+  */
+  nav {
+    flex-direction: column;
+    padding-right: 1rem;
+    padding-bottom: 0;
+
+    /*
+      Workaround for Chrome always showing scrollbar even when scrolling not needed
+    */
+    -ms-overflow-style: none;
+    scrollbar-width: none;
+  }
+
+  /*
+    Continued Chrome workaround
+  */
+  nav::-webkit-scrollbar {
+    display: none;
+  }
+
+  main {
+    width: calc(100% - 10rem);
+  }
+
+  /*
+    Container-type helper classes
+  */
+  .row {
+    flex-direction: row;
+  }
+
+  .person-profile {
+    position: sticky;
+    top: 0;
+    width: 300px;
+    min-width: 20vw;
+    max-width: 30vw;
+    margin-bottom: 5vh;
+  }
+
+  /*
+    Helper classes
+  */
+  .float-left {
+    float: left;
+    max-width: 50%;
+  }
+
+  .float-right {
+    float: right;
+    max-width: 50%;
+  }
+
+  .card {
+    flex-direction: row;
+  }
+
+  .img-thumbnail {
+    margin-right: 1rem;
+  }
+
+  .card-thumbnail {
+    width: 20vw;
+    flex-shrink: 0;
+  }
+
+  .card-thumbnail:not(
+      :has(~ .card-content > .card-header > .card-title > .dt-published)
+    ) {
+    width: 10vw;
+  }
+
+  .card-content {
+    margin-left: 1rem;
+  }
+
+  /*
+    Clearfix implementation
+  */
+  h1::before,
+  h2::before,
+  h3::before,
+  h4::before,
+  h5::before,
+  h6::before,
+  blockquote::before {
+    content: " "; /* Older browser do not support empty content */
+    visibility: hidden;
+    display: block;
+    height: 0;
+    clear: both;
+  }
+} /* end @media */

assets/styles/mix-twbs.scss

@@ -1,8 +1,17 @@
+$web-font-path: "/fonts/nunito-sans/index.css";
+
+@import "bootstrap/functions";
+@import "bootswatch/lux/variables";
+@import "bootstrap/bootstrap";
+@import "bootswatch/lux/bootswatch";
+
+$peek-height: 25rem;
+
 .blurred-container {
   position: relative;
   width: 100%;
   min-height: 35vh;
-  height: 350px;
+  height: $peek-height;
   top: 0;
   left: 0;
 }
@@ -25,25 +34,30 @@
 
 .motto h1 {
   background: #0000007d;
+  -webkit-text-stroke: 0.3px $gray-100;
+  line-height: 1;
 }
 
 .blurred-container .img-src {
   position: fixed;
   width: 100%;
   min-height: 35vh;
-  height: 350px;
+  height: $peek-height;
   background-repeat: no-repeat;
   background-size: cover;
   background-position: center center;
 }
 
-.blur {
-  opacity: 0;
-}
-
 .list-main {
   position: relative;
   background-color: #fff;
+  padding-bottom: calc(1rem + 95px);
+  padding-top: 1rem;
+}
+
+.footer-contents {
+  position: relative;
+  background-color: $gray-200;
 }
 
 /* Gives me greater control over fonts */
@@ -121,3 +135,45 @@ h1 {
 .fa-stack-top {
   vertical-align: top;
 }
+
+.table-condensed th {
+  padding: 0.5rem;
+}
+
+.table-condensed td {
+  padding: 0.5rem;
+}
+
+@media (min-width: map-get($grid-breakpoints, md)) {
+  .fixed-bottom {
+    left: 25%;
+  }
+
+  .md-max-width-33 {
+    max-width: 33%;
+  }
+}
+
+.card-link {
+  white-space: nowrap;
+}
+
+.category-button {
+  position: absolute;
+  top: 1em;
+  right: 1em;
+  display: grid;
+}
+
+.card-title {
+  margin-right: 2.25em;
+}
+
+.thumb-icon-wrapper {
+  display: flex;
+  justify-content: center;
+}
+
+.thumb-icon-badge {
+  font-size: xx-large;
+}

assets/styles/scrolling-header.css

@@ -0,0 +1,65 @@
+@media (prefers-reduced-motion: no-preference) {
+  @supports (animation-timeline: scroll()) and (animation-range: 0 50vh) {
+    @keyframes sticky-header {
+      from {
+        flex-basis: 30vh;
+      }
+
+      to {
+        flex-basis: 0;
+      }
+    }
+
+    .motto-wrapper {
+      position: sticky;
+      top: 0;
+      z-index: 100;
+
+      animation: sticky-header linear forwards;
+      animation-timeline: scroll();
+      animation-range: 0 30vh;
+    }
+
+    @keyframes blurry-header {
+      from {
+        filter: blur(0);
+      }
+
+      to {
+        filter: blur(3.5px);
+      }
+    }
+
+    .motto::before {
+      animation: blurry-header linear forwards;
+      animation-timeline: scroll();
+      animation-range: 0 30vh;
+    }
+
+    @keyframes transparent-text-bg {
+      from {
+        background-color: var(--motto-background);
+        text-shadow: 0 0 10px rgba(0, 0, 0, 0.33);
+      }
+      to {
+        background-color: rgba(0, 0, 0, 0);
+        text-shadow: 0 0 10px rgba(0, 0, 0, 1);
+      }
+    }
+    .motto-inside h1 {
+      animation: transparent-text-bg linear forwards;
+      animation-timeline: scroll();
+      animation-range: 0 30vh;
+    }
+
+    .motto-inside h1 small {
+      display: block;
+      font-size: calc(1vh + 1vw);
+      line-height: calc(1vh + 1vw);
+    }
+
+    main section {
+      margin: 0 0.25em;
+    }
+  } /* end @supports */
+} /* end @media */

config.toml

@@ -1,7 +1,9 @@
 baseURL = "https://millironx.com"
 languageCode = "en-us"
-title = "MillironX"
+title = "Milliron X"
-paginate = 5
+
+[pagination]
+pagerSize = 5
 
 [build]
 writeStats = true
@@ -9,53 +11,47 @@ writeStats = true
 [Params]
 cardImage = "saddles"
 motto = ""
+images = ["saddles.jpg"]
+categories = []
 
-[module]
+[taxonomies]
+people = "people"
+tag = "tags"
+category = "categories"
 
-[[module.mounts]]
+[mediaTypes]
-source = "assets/graphics"
-target = "assets/graphics"
 
-[[module.mounts]]
+[mediaTypes."application/atom+xml"]
-source = "assets/images"
+suffixes = ["xml"]
-target = "assets/images"
 
-[[module.mounts]]
+[outputs]
-source = "assets/scripts"
+home = ["atom", "html", "manifest"]
-target = "assets/scripts"
+page = ["html"]
+section = ["html", "atom"]
+term = ["html", "atom"]
 
-[[module.mounts]]
+[outputFormats]
-source = "assets/styles"
-target = "assets/styles"
 
-[[modules.mounts]]
+[outputFormats.atom]
-source = "assets/scripts/custom"
+mediaType = "application/atom+xml"
-target = "assets/scripts/custom"
+baseName = "feed"
 
-[[module.mounts]]
+[outputFormats.manifest]
-source = "./node_modules/@fortawesome/fontawesome-pro/js"
+name = "manifest"
-target = "assets/scripts/fontawesome"
+baseName = "manifest"
+mediaType = "application/json"
+notAlternative = "true"
 
-[[module.mounts]]
+[markup]
-source = "./node_modules/@popperjs/core/dist/umd"
-target = "assets/scripts/popper"
 
-[[module.mounts]]
+[markup.goldmark]
-source = "./node_modules/bootstrap/scss"
-target = "assets/styles/bootstrap"
 
-[[module.mounts]]
+[markup.goldmark.parser]
-source = "./node_modules/bootstrap/dist/js"
-target = "assets/scripts/bootstrap"
 
-[[module.mounts]]
+[markup.goldmark.parser.attribute]
-source = "./node_modules/fittext.js"
+block = true
-target = "assets/scripts/fittext"
 
-[[module.mounts]]
+[markup.goldmark.renderHooks]
-source = "./node_modules/jquery/dist"
-target = "assets/scripts/jquery"
 
-[[module.mounts]]
+[markup.goldmark.renderHooks.link]
-source = "./node_modules/jquery-mask-plugin/dist"
+enableDefault = true
-target = "assets/scripts/jquery-mask-plugin"

content/_index.html

@@ -1,164 +0,0 @@
----
-title: Home
-cardImage: charolette
-motto: <small>My name is Thomas Christensen</small><br />I am Milliron X
-description: The homepage of Thomas A. Christensen II
-layout: _default/list
----
-
-<h2>What is a "Milliron X"?</h2>
-
-<h3>
-  It's a
-  <a href="https://en.wikipedia.org/wiki/Livestock_branding">cattle brand</a>,
-  of course! My cattle brand!
-</h3>
-
-<p>
-  The <dfn>milliron</dfn> is the bar with a bend in the middle. It does not
-  represent anything physical or textual <i>per se</i>, and is therefore a
-  rather unique element in cattle brands. Millirons are difficult to modify into
-  another brand, and provide a guarantee of authentic ownership.
-</p>
-
-<p>
-  <dfn>X</dfn> is the letter of mystery and mystique. For nerds, it's the
-  unknown in any algebra problem. Ranchers and cowboys will associate it with
-  big names like the "Bar X" and the "Double X." In either case, it lends itself
-  to a sense of withholding, prestige, and power.
-</p>
-
-<p>
-  Together, these two symbols represent the qualities I strive for in each of my
-  works: authenticity, originality, power, depth, and prestige.
-</p>
-
-<h2>Who am I?</h2>
-
-{{% imgproc me-and-lady Resize "768x" "float-md-end w-md-50 p-3" %}}
-Image courtesy [Guy McCutcheon Photography](https://www.guymccutcheon.com/)
-{{% /imgproc %}}
-
-
-<p>I am</p>
-
-<ul>
-  <li>🧬 A bioinformatician (by profession)</li>
-  <li>📐 An engineer (by education)</li>
-  <li>🐂 A rancher (by lifestyle)</li>
-  <li>🖥️ A techie (self-taught)</li>
-  <li>🎥 And a filmmaker (at heart)</li>
-</ul>
-
-<p>
-  I've got a soft spot for Brown Swiss dairy cows (just in case you couldn't
-  tell by the pictures), and am sometimes called "one of those crazy, Wyoming
-  dairy cow people." I love anything to do with cattle or technology, but
-  especially anything to do with both of them.
-</p>
-
-<p>
-  <em>
-    <abbr
-      title="Born again, fundamentalist, dispensationalist, King James Bible-believing, independent Baptist"
-      >Christian</abbr
-    >, American, Convervative, Pro-gun, Heterosexual - any questions?
-  </em>
-</p>
-
-<h2>Where am I?</h2>
-
-{{% imgproc wy-in-ks Resize "768x" "float-md-start w-md-50 p-3" /%}}
-
-<p>
-  I am a Wyomingite sojurning in Kansas. That ought to lead to some interesting
-  stories.
-</p>
-
-Around the web you can find me at (in order of subjective importance)
-
-<ul class="float-md-end w-md-50">
-  <li>
-    <i class="fab fa-fw fa-github"></i> GitHub:
-    <a href="https://github.com/MillironX">@MillironX</a>
-  </li>
-  <li>
-    <i class="fab fa-fw fa-orcid"></i>
-    ORCiD:
-    <a href="https://orcid.org/0000-0003-1219-9320">0000-0003-1219-9320</a>
-  </li>
-  <li>
-    <i class="fab fa-fw fa-gitlab"></i>
-    GitLab: <a href="https://gitlab.com/MillironX">@MillironX</a>
-  </li>
-  <li>
-    <i class="fab fa-fw fa-vimeo"></i>
-    Vimeo: <a href="https://vimeo.com/tchristensenii">Thomas Christensen II</a>
-  </li>
-  <li>
-    <i class="fab fa-fw fa-stack-overflow"></i>
-    Stack Exchange:
-    <a href="https://stackexchange.com/users/4863541/milliron-x">Milliron X</a>
-  </li>
-  <li>
-    <i class="fad fa-fw fa-user-astronaut"></i>
-    Odysee: <a href="https://odysee.com/@millironx:f">@millironx</a>
-  </li>
-  <li>
-    <span class="fa-layers fa-fw">
-      <i class="fad fa-fw fa-comment"></i>
-      <span class="fa-layers-text" data-fa-transform="shrink-6 up-2">g</span>
-    </span>
-    Gab: <a href="https://gab.com/millironx">@MillironX</a>
-  </li>
-  <li>
-    <i class="fab fa-fw fa-steam"></i>
-    Steam: <a href="https://steamcommunity.com/id/millironx">MillironX</a>
-  </li>
-  <li>
-    <span class="fa-layers fa-fw">
-      <i class="fad fa-fw fa-w" data-fa-transform="shrink-2 down-2"></i>
-      <i class="fad fa-fw fa-ellipsis" data-fa-transform="grow-3 up-8"></i>
-    </span>
-    MeWe:
-    <a href="https://mewe.com/i/thomaschristensenii">Thomas Christensen II</a>
-  </li>
-  <li>
-    <i class="fab fa-fw fa-discord"></i>
-    Discord:
-    <a href="https://discord.com/users/484492414837587978">@MillironX</a>
-  </li>
-</ul>
-
-<div style="clear: both;"></div>
-
-<div class="card border-warning m-3">
-  <div class="card-body">
-    <p class="card-text">
-      This list is intended to verify my identity on other sites. Please do
-      <em>not</em> use it as fodder to try and "follow" me on each of these
-      platforms. I stand with RMS:
-    </p>
-    <figure>
-      <blockquote class="blockquote">
-        <p>
-          Facebook is a bad place for a person to be. When people find us on
-          Facebook, we lead them away from Facebook and then talk with them
-          elsewhere.
-        </p>
-      </blockquote>
-      <figcaption class="blockquote-footer">
-        Richard Stallman in
-        <cite
-          ><a href="https://stallman.org/facebook-presence.html"
-            >If you feel your organization needs a 'presence' in Facebook</a
-          ></cite
-        >
-      </figcaption>
-    </figure>
-    <p class="card-text">
-      I typically don't respond to inqueries made on these platforms. Please use
-      <a href="/contact">my contact form</a>, instead.
-    </p>
-  </div>
-</div>

content/_index.md

@@ -0,0 +1,30 @@
+---
+cardImage: charolette
+cardImageDescription: She almost looks like she's in her native country again.
+motto: <small>My name is Thomas Christensen</small><br />I am Milliron X
+description: The homepage of Thomas A. Christensen II
+menu:
+  main:
+    name: Home
+    params:
+      icon: home
+    weight: -1000
+---
+
+## What is a "Milliron X"?
+
+It's a [cattle brand](https://en.wikipedia.org/wiki/Livestock_branding), of
+course! My cattle brand!
+
+The {{< dfn >}}milliron{{< /dfn >}} is the bar with a bend in the middle. It
+does not represent anything physical or textual _per se_, and is therefore a
+rather unique element in cattle brands. Millirons are difficult to modify into
+another brand, and provide a guarantee of authentic ownership.
+
+{{< dfn >}}X{{< /dfn >}} is the letter of mystery and mystique. For nerds, it's
+the unknown in any algebra problem. Ranchers and cowboys will associate it with
+big names like the "Bar X" and the "Double X." In either case, it lends itself
+to a sense of withholding, prestige, and power.
+
+Together, these two symbols represent the qualities I strive for in each of my
+works: authenticity, originality, power, depth, and prestige.

content/academia/_index.md

@@ -1,7 +1,28 @@
 ---
 title: Academic Publications and Presentations
-motto: Academic Publications and Presentations
+motto: Publications and Presentations
 cardImage: library
+cardImageDescription:
+  Personally, I preferred the Owen Library in Pullman seven miles west
+description: A list of my academic publications
+menu:
+  main:
+    name: Academia
+    params:
+      icon: university
+    weight: 20
+fa-thumbnail: university
 ---
 
-### Academic Papers
+During my time in academia, I have amassed a few notable accomplishments. Of
+course, as the old saying goes, "if it isn't published, then it never happened,"
+so here is a list of everything that actually happened.
+
+Academia is not the be-all and end-all of life (contrary to what your professor
+might have told you). I've found the side-effects to be similar to this guy's:
+
+<!-- prettier-ignore-start -->
+> I have spent too long in school and not enough time in the middle of nowhere,
+> and it has inhibited my ability to learn the simple things.
+{author="Baxter Black, DVM"}
+<!-- prettier-ignore-end -->

content/academia/bpv-genetics.md

@@ -0,0 +1,42 @@
+---
+title: "Genetic analysis of bovine papillomas"
+date: 2024-09-19
+categories:
+  - poster
+people:
+  - Thomas A. Christensen II
+  - Rachel Palinski
+  - Bob Gentry
+journal:
+  "National Association of Animal Breeders Technical Conference Student Poster
+  session"
+location: "Middleton, Wisconsin"
+---
+
+Bovine papillomavirus (BPV) is a major cause of reproductive failure in cattle.
+In bulls, penile papillomas caused by BPV may cause reluctance to breed, and is
+always a cause to fail an animal on a breeding soundness exam. Historically, it
+has been thought that BPV was transmitted via direct contact and could be
+controlled by managing clinically presenting animals in the herd, but more
+recent evidence suggests alternative modes of transmission. BPV has been found
+repeatably in clinically healthy animals, and in non-cutaneous secretions
+including milk, blood, urine and semen. Currently, no commercially available BPV
+vaccine uses isolated viral particles and naturally occurring virus does not
+produce cross-protective immunity. In order to develop a proper vaccine for
+penile papillomas further studies are required to understand the epidemiology of
+BPV in herds. While vulvar, cutaneous, and mammary papillomas have been
+genotyped in recent years, this information is not available for penile
+papillomas. In this study there were 31 submissions, collected from 7 states,
+NE, KS, NY, TX, AL, MO and SD (14 different cattle operations) Samples were
+collected between August of 2022 and April 2024. Twenty-two submissions were
+penile papillomas and with pooling of samples represented over 50 penile
+papillomas. Samples were metagenomically sequenced at the Kansas State
+Veterinary Diagnostic Lab, and the genotype of each sample was determined using
+the phylogenetic analysis. The clade of each sample was determined by aligning
+consensus sequences of the L1 gene (used for both for phylogeny and as a vaccine
+target) using MAFFT and a maximum-likelihood phylogeny generated in Mega X.
+Analysis found that all penile papilloma submissions were composed of BPV type
+2, with one sample showing co-infection with BPV type 1. Conversely, cutaneous
+and teat papillomas had BPV genotypes that were more variable with genotypes of
+1,2,7,12,14,29 and 40. These results indicate that BPV type 2 and type 1 provide
+a unified target for bovine penile papilloma vaccine development.

content/academia/cheme-car/index.md

@@ -4,16 +4,17 @@ date: 2019-05-14
 cardImage: cannulated-cows
 draft: false
 featured: true
-keywords:
+tags:
   - chemical engineering
   - AIChE
   - radiation
   - rumen
   - microbial electrolysis cells
-medium: thesis
+categories:
-authors:
+  - thesis
+people:
   - Thomas A. Christensen II
-link: "/academia/cheme-car/cud_cheme_car_web.pdf"
+link: https://doi.org/10.15786/13700938.v1
 journal: "University of Wyoming Honors Program"
 location: "Laramie, Wyoming"
 ---

content/academia/got-warts-naab.md

@@ -0,0 +1,14 @@
+---
+title:
+  "Got Warts? Bovine Papillomavirus Pathogenesis, Transmission, and Vaccination"
+date: 2024-09-19
+featured: false
+categories:
+  - presentation
+people:
+  - Bob Gentry
+  - Thomas A. Christensen II
+journal:
+  "National Association of Animal Breeders Technical Conference Sponsor session"
+location: "Middleton, Wisconsin"
+---

content/academia/how-to-build-a-cow-cud-fuel-cell.md

@@ -4,8 +4,9 @@ date: 2018-08-01
 cardImage: library
 draft: false
 featured: false
-medium: presentation
+categories:
-authors:
+  - presentation
+people:
   - Thomas A. Christensen II
 journal: "Idaho INBRE Summer Research Conference"
 location: "Moscow, Idaho"

content/academia/hydronium-pva.md

@@ -1,15 +1,18 @@
 ---
-title: "Investigation of Hydronium Diffusion in Poly(vinyl alcohol) Hydrogels: A Critical First Step to Describe Acid Transport for Encapsulated Bioremediation"
+title:
+  "Investigation of Hydronium Diffusion in Poly(vinyl alcohol) Hydrogels: A
+  Critical First Step to Describe Acid Transport for Encapsulated Bioremediation"
 date: 2022-09-02
 featured: false
-keywords:
+tags:
   - diffusion
   - hydrogels
   - ionic strength
   - polymers
   - transport properties
-medium: paper
+categories:
-authors:
+  - paper
+people:
   - Carson J. Silsby
   - Jonathan R. Counts
   - Thomas A. Christensen II
@@ -20,4 +23,23 @@ link: https://doi.org/10.1021/acsestengg.2c00107
 journal: "ACS ES&T Engineering"
 ---
 
-Bioremediation of chlorinated aliphatic hydrocarbon-contaminated aquifers can be hindered by high contaminant concentrations and acids generated during remediation. Encapsulating microbes in hydrogels may provide a protective, tunable environment from inhibiting compounds; however, current approaches to formulate successful encapsulated systems rely on trial and error rather than engineering approaches because fundamental information on mass-transfer coefficients is lacking. To address this knowledge gap, hydronium ion mass-transfer rates through two commonly used hydrogel materials, poly(vinyl alcohol) and alginic acid, under two solidification methods (chemical and cryogenic) were measured. Variations in hydrogel crosslinking conditions, polymer composition, and solvent ionic strength were investigated to understand how each influenced hydronium ion diffusivity. A three-way ANOVA indicated that the ionic strength, membrane type, and crosslinking method significantly (_p_ < 0.001) contributed to changes in hydronium ion mass transfer. Hydronium ion diffusion increased with ionic strength, counter to what is observed in aqueous-only (no polymer) solutions. Co-occurring mechanisms correlated to increased hydronium ion diffusion with ionic strength included an increased water fraction within hydrogel matrices and hydrogel contraction. Measured diffusion rates determined in this study provide first principal design information to further optimize encapsulating hydrogels for bioremediation.
+Bioremediation of chlorinated aliphatic hydrocarbon-contaminated aquifers can be
+hindered by high contaminant concentrations and acids generated during
+remediation. Encapsulating microbes in hydrogels may provide a protective,
+tunable environment from inhibiting compounds; however, current approaches to
+formulate successful encapsulated systems rely on trial and error rather than
+engineering approaches because fundamental information on mass-transfer
+coefficients is lacking. To address this knowledge gap, hydronium ion
+mass-transfer rates through two commonly used hydrogel materials, poly(vinyl
+alcohol) and alginic acid, under two solidification methods (chemical and
+cryogenic) were measured. Variations in hydrogel crosslinking conditions,
+polymer composition, and solvent ionic strength were investigated to understand
+how each influenced hydronium ion diffusivity. A three-way ANOVA indicated that
+the ionic strength, membrane type, and crosslinking method significantly (_p_ <
+0.001) contributed to changes in hydronium ion mass transfer. Hydronium ion
+diffusion increased with ionic strength, counter to what is observed in
+aqueous-only (no polymer) solutions. Co-occurring mechanisms correlated to
+increased hydronium ion diffusion with ionic strength included an increased
+water fraction within hydrogel matrices and hydrogel contraction. Measured
+diffusion rates determined in this study provide first principal design
+information to further optimize encapsulating hydrogels for bioremediation.

content/academia/metagenomics/index.md

@@ -6,13 +6,14 @@ date: 2019-06-12
 cardImage: cannulated-cows
 draft: false
 featured: true
-keywords:
+tags:
   - gestation
   - metagenomics
   - microbiome
   - rumen
-medium: poster
+categories:
-authors:
+  - poster
+people:
   - Thomas A. Christensen II
   - Kathy J. Austin
   - Kristi M. Cammack

content/academia/pva-aiche/index.md

@@ -6,14 +6,15 @@ date: 2018-10-29
 cardImage: library
 draft: false
 featured: false
-keywords:
+tags:
   - bioremediation
   - polyoxometalate
   - hydrogel polymers
   - proton transport
   - chemical engineering
-medium: poster
+categories:
-authors:
+  - poster
+people:
   - Thomas A. Christensen II
   - Samuel R. Wolfe
   - Jonathan Counts

content/academia/pva-inbre.md

@@ -4,8 +4,9 @@ date: 2018-07-31
 cardImage: library
 draft: false
 featured: false
-medium: poster
+categories:
-authors:
+  - poster
+people:
   - Thomas A. Christensen II
   - Jonathan Counts
   - James G. Moberly

content/academia/rotavirus-virome.md

@@ -5,13 +5,14 @@ title:
 date: 2022-04-27
 cardImage: cannulated-cows
 featured: true
-keywords:
+tags:
   - porcine rotavirus
   - porcine enteric disease
   - virome
   - rotavirus
-medium: paper
+categories:
-authors:
+  - paper
+people:
   - Tyler Doerksen
   - Thomas A. Christensen II
   - Andrea Lu

content/academia/taxprofiler.md

@@ -0,0 +1,41 @@
+---
+title:
+  "nf-core/taxprofiler: highly parallelised and flexible pipeline for
+  metagenomic taxonomic classification and profiling"
+date: 2023-10-23
+featured: true
+tags:
+  - genomics
+categories:
+  - paper
+people:
+  - Sofia Stamouli
+  - Moritz E. Beber
+  - Tanja Normark
+  - Thomas A. Christensen II
+  - Lili Andersson-Li
+  - Maxime Borry
+  - Mahwash Jamy
+  - nf-core community
+  - James A. Fellows Yates
+link: https://doi.org/10.1101/2023.10.20.563221
+journal: bioRxiv
+---
+
+Metagenomic classification tackles the problem of characterising the taxonomic
+source of all DNA sequencing reads in a sample. A common approach to address the
+differences and biases between the many different taxonomic classification tools
+is to run metagenomic data through multiple classification tools and databases.
+This, however, is a very time-consuming task when performed manually -
+particularly when combined with the appropriate preprocessing of sequencing
+reads before the classification. Here we present nf-core/taxprofiler, a highly
+parallelised read-processing and taxonomic classification pipeline. It is
+designed for the automated and simultaneous classification and/or profiling of
+both short- and long-read metagenomic sequencing libraries against a 11
+taxonomic classifiers and profilers as well as databases within a single
+pipeline run. Implemented in Nextflow and as part of the nf-core initiative, the
+pipeline benefits from high levels of scalability and portability, accommodating
+from small to extremely large projects on a wide range of computing
+infrastructure. It has been developed following best-practise software
+development practises and community support to ensure longevity and adaptability
+of the pipeline, to help keep it up to date with the field of metagenomics.

content/academia/thesis.md

@@ -6,14 +6,15 @@ date: 2020-08-07
 cardImage: library
 draft: false
 featured: true
-keywords:
+tags:
   - bioremediation
   - polyoxometalate
   - hydrogel polymers
   - proton transport
   - chemical engineering
-medium: thesis
+categories:
-authors:
+  - thesis
+people:
   - Thomas A. Christensen II
 link: "https://www.proquest.com/dissertations-theses/polyoxometalate-incorporation-effects-on-proton/docview/2502214356/se-2"
 journal: "University of Idaho"

content/academia/yavsap/index.md

@@ -0,0 +1,54 @@
+---
+title: "YAVSAP: versatile viral quasispecies analysis for veterinary samples"
+date: 2024-03-05
+featured: false
+categories:
+  - presentation
+people:
+  - Thomas A. Christensen II
+  - Steven Stancic
+  - Andrea Lu
+  - Dana Mitzel
+  - William Wilson
+  - Rachel Palinski
+journal: "Phi Zeta Research Day"
+location: "Manhattan, Kansas"
+tags:
+  - virus
+  - quasispecies
+  - next-generation sequencing
+  - pipeline
+awards:
+  - "2nd Place Large Animal Applied Research Presentation"
+link: "/academia/yavsap/yavsap.pdf"
+---
+
+Viral populations within an infected host are composed of viral particles with a
+spectrum of genetic mutations rather than a unified genome. This phenomenon is
+referred to as viral "quasispecies," and has been useful for the understanding
+of viral transmission and early detection of new viral variants. Next generation
+sequencing (NGS) has enabled the study of these quasispecies for many viral
+species, notably Influenza A and B, Human Immunodeficiency Virus (HIV), Foot and
+Mouth Disease Virus (FMDV), and Severe Acute Respiratory Syndrome Coronavirus 2
+(SARS CoV2), and established protocols and computer analysis tools have been
+developed for these species. Some of the most important viruses, such as
+emerging and exotic disease agents, however, do not have replicatable protocols
+or software tools capable of producing valid output from their sequence data.
+Here, we present Yet Another Viral Subspecies Analysis Pipeline (YAVSAP). YAVSAP
+is a fully automated bioinformatic pipeline built from the ground up to identify
+and analyze viral quasispecies of any arbitrary virus in human and veterinary
+samples. YAVSAP provides reference-based genome mapping of both long- and
+short-read sequencing reads to any reference genome that the user chooses,
+identifies subconsensus variants and haplotypes, and assesses the phylogenies of
+all viral sequences found within a sample. YAVSAP is written in Nextflow and
+conforms to the nf-core initiative's standards, which allows it to run on
+low-end computers, high performance computing (HPC) clusters, or anything in
+between with zero configuration. YAVSAP has been tested on viruses of interest
+to veterinary medicine and public health, including Japanese Encephalitis Virus
+(JEV), Influenza D Virus (IDV), Bovine Coronavirus (BCoV), SARS CoV2, and Rift
+Valley Fever Virus (RVFV), and can correctly identify consensus genomes and
+quasispecies within samples containing each of these viruses. This tool provides
+a means for biologists with little bioinformatic experience to analyze deep
+sequence data while correcting for many of the pitfalls associated with previous
+and current analysis platforms. YAVSAP is open source software and is publicly
+available at https://github.com/ksumngs/yavsap.

content/ai/_index.md

@@ -1,12 +0,0 @@
----
-title: Artificial Insemination
-cardImage: Ai-calf
-motto: Artificial Insemination
----
-
-I am licensed in the Great State of Wyoming as a food animal artificial
-insemination technician, which means I can legally AI cows, goats, and sheep.
-Practically speaking, I have only ever AIed cows, but my conception rates are
-very good for both beef and dairy cows. When (if?) I standardize my rates, I
-will include them here. Until then, you will have to [contact me](/contact)
-directly and we can negotiate prices then.

content/blogroll/_index.md

@@ -1,5 +1,15 @@
 ---
-draft: true
+title: "Blogroll"
+menu:
+  main:
+    name: Blogroll
+    params:
+      icon: scroll
+    weight: -800
+cardImage: eclipse
+cardImageDescription: |
+  Randall Monroe was right. Eclipses are way cooler than they sound.
+suppressRss: true
 ---
 
 ## Stuff I like on the internet
@@ -7,39 +17,4 @@ draft: true
 This section of a website used to be called a "blogroll." I don't know what it's
 called now. In order to be on this list, I must have been subscribed or
 otherwise follow it for over a year. It's amazing how little stuff on the
-internet can't make that cut.
+internet can make that cut.
-
-### [Thru the Bible](https://ttb.org/)
-
-I'm convinced that the word of God is timeless, and we need less commentary and
-cherry-picking of favorite verses, and more study of the complete Bible. Dr.
-McGee does just that.
-
-### [Enoch the Cow Vet](https://youtube.com/channel/UC6PPmHUbcdOSzX5tLB3uXdw)
-
-A veternarian/agricultural channel that doesn't make me cringe. "God built these
-things for cows for vets ... [there are] so many aspects of the cow that are
-just designed for vets." Amen, Enoch. Amen.
-
-### [Proglogion](https://blog.drwile.com/)
-
-The blog of my high school science teacher (of sorts). It is refreshing to find
-a creationist who can still think critically. I love his "bad sermon
-illustrations" posts.
-
-### [The Milk Check](https://www.jacoby.com/learning-center/podcasts-overview/)
-
-A pragmatic inside look at dairy marketing. I only understand half of what
-they're talking about, but I learn something new every episode.
-
-### [Brian Harry's Blog](https://devblogs.microsoft.com/bharry/)
-
-Where else are you going to find a blog about cows _and_ version control? The
-blog is basically dead now, but it's still fun to go back and read the farm
-stories.
-
-### [Car Talk](https://cartalk.com/)
-
-The antics of these guys are enough to make anyone have to pull over to the side
-of the road from laughing too much. I dread the day when NPR fully axes the only
-good program to cross their airwaves.

content/blogroll/brian-harry/index.md

@@ -0,0 +1,8 @@
+---
+title: Brian Harry's blog
+link: https://devblogs.microsoft.com/bharry/
+---
+
+Where else are you going to find a blog about cows _and_ version control? The
+blog is basically dead now, but it's still fun to go back and read the farm
+stories.