Merge pull request #877 from greenelab/RLordan-patch-1

[ci skip]

This build is based on
15a557f.

This commit was created by the following CI build and job:
https://github.com/greenelab/covid19-review/commit/15a557f66f0d8d3bd487590326e849e80913db1c/checks
https://github.com/greenelab/covid19-review/runs/594565402

citations.tsv

@@ -667,9 +667,9 @@ doi:10.1186/s12937-018-0356-8	doi:10.1186/s12937-018-0356-8	doi:10.1186/s12937-0
 doi:10.1016/j.immuni.2014.02.009	doi:10.1016/j.immuni.2014.02.009	doi:10.1016/j.immuni.2014.02.009	BIVORG2X
 doi:10.1038/nri.2015.4	doi:10.1038/nri.2015.4	doi:10.1038/nri.2015.4	uPOTvvjR
 doi:10.1002/biof.1691	doi:10.1002/biof.1691	doi:10.1002/biof.1691	sxgmhJ68
-doi:10.1016/j.cell.2013.02.027	doi:10.1016/j.cell.2013.02.027	doi:10.1016/j.cell.2013.02.027	fIo3ESPM
 doi:10.1038/nature13479	doi:10.1038/nature13479	doi:10.1038/nature13479	OSEnHt6H
 doi:10.4049/jimmunol.1302795	doi:10.4049/jimmunol.1302795	doi:10.4049/jimmunol.1302795	MK0GQ55y
+doi:10.1016/j.cell.2013.02.027	doi:10.1016/j.cell.2013.02.027	doi:10.1016/j.cell.2013.02.027	fIo3ESPM
 doi:10.1007/s10555-020-09889-4	doi:10.1007/s10555-020-09889-4	doi:10.1007/s10555-020-09889-4	14LjKv9ZH
 doi:10.1016/j.mehy.2020.110340	doi:10.1016/j.mehy.2020.110340	doi:10.1016/j.mehy.2020.110340	PRLlghQS
 doi:10.3389/fimmu.2020.01997	doi:10.3389/fimmu.2020.01997	doi:10.3389/fimmu.2020.01997	oLunKkIG

references.json

@@ -103,6 +103,194 @@
     "abstract": "  COVID-19 has revealed limitations of existing mechanisms for rationing medical resources under emergency scenarios. Many argue that these mechanisms abandon various ethical values such as equity by discriminating against disadvantaged communities. Illustrating that these limitations are aggravated by a restrictive choice of mechanism, we formulate pandemic rationing of medical resources as a new application of market design and propose a reserve system as a resolution. We develop a general theory of reserve design, introduce new concepts such as cutoff equilibria and smart reserves, extend analysis of previously-known ones such as sequential reserve matching, relate these concepts to current debates, and present preliminary policy impact. ",
     "note": "license: http://arxiv.org/licenses/nonexclusive-distrib/1.0/\nThis CSL JSON Item was automatically generated by Manubot v0.4.1 using citation-by-identifier.\nstandard_id: arxiv:2008.00374\nLoaded from an external bibliography file by Manubot.\nsource_bibliography: manual-references-2021-02-08.json\noriginal_id: FaGAJ7AI"
   },
+  {
+    "id": "r366f5T3",
+    "URL": "https://arxiv.org/abs/2102.01521",
+    "number": "2102.01521",
+    "title": "Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through analysis of Viral Genomics and Structure",
+    "issued": {
+      "date-parts": [
+        [
+          2021,
+          2,
+          15
+        ]
+      ]
+    },
+    "author": [
+      {
+        "given": "Halie M.",
+        "family": "Rando"
+      },
+      {
+        "given": "Adam L.",
+        "family": "MacLean"
+      },
+      {
+        "given": "Alexandra J.",
+        "family": "Lee"
+      },
+      {
+        "given": "Sandipan",
+        "family": "Ray"
+      },
+      {
+        "given": "Vikas",
+        "family": "Bansal"
+      },
+      {
+        "given": "Ashwin N.",
+        "family": "Skelly"
+      },
+      {
+        "given": "Elizabeth",
+        "family": "Sell"
+      },
+      {
+        "given": "John J.",
+        "family": "Dziak"
+      },
+      {
+        "given": "Lamonica",
+        "family": "Shinholster"
+      },
+      {
+        "given": "Lucy D'Agostino",
+        "family": "McGowan"
+      },
+      {
+        "given": "Marouen Ben",
+        "family": "Guebila"
+      },
+      {
+        "given": "Nils",
+        "family": "Wellhausen"
+      },
+      {
+        "given": "Sergey",
+        "family": "Knyazev"
+      },
+      {
+        "given": "Simina M.",
+        "family": "Boca"
+      },
+      {
+        "given": "Stephen",
+        "family": "Capone"
+      },
+      {
+        "given": "Yanjun",
+        "family": "Qi"
+      },
+      {
+        "given": "YoSon",
+        "family": "Park"
+      },
+      {
+        "given": "Yuchen",
+        "family": "Sun"
+      },
+      {
+        "given": "David",
+        "family": "Mai"
+      },
+      {
+        "given": "Christian",
+        "family": "Brueffer"
+      },
+      {
+        "given": "James Brian",
+        "family": "Byrd"
+      },
+      {
+        "given": "Jinhui",
+        "family": "Wang"
+      },
+      {
+        "given": "Ronan",
+        "family": "Lordan"
+      },
+      {
+        "given": "Ryan",
+        "family": "Velazquez"
+      },
+      {
+        "given": "Gregory L",
+        "family": "Szeto"
+      },
+      {
+        "given": "John P.",
+        "family": "Barton"
+      },
+      {
+        "given": "Rishi Raj",
+        "family": "Goel"
+      },
+      {
+        "given": "Serghei",
+        "family": "Mangul"
+      },
+      {
+        "given": "Tiago",
+        "family": "Lubiana"
+      },
+      {
+        "given": "COVID-19 Review",
+        "family": "Consortium"
+      },
+      {
+        "given": "Anthony",
+        "family": "Gitter"
+      },
+      {
+        "given": "Casey S.",
+        "family": "Greene"
+      }
+    ],
+    "container-title": "arXiv",
+    "publisher": "arXiv",
+    "type": "report",
+    "abstract": "  The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world infecting tens of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease. ",
+    "note": "license: http://creativecommons.org/licenses/by/4.0/\nThis CSL Item was generated by Manubot v0.5.0 from its persistent identifier (standard_id).\nstandard_id: arxiv:2102.01521"
+  },
+  {
+    "id": "1B22G6dja",
+    "URL": "https://arxiv.org/abs/2102.02250",
+    "number": "2102.02250",
+    "title": "Dietary Supplements and Nutraceuticals Under Investigation for COVID-19 Prevention and Treatment",
+    "issued": {
+      "date-parts": [
+        [
+          2021,
+          2,
+          5
+        ]
+      ]
+    },
+    "author": [
+      {
+        "given": "Ronan",
+        "family": "Lordan"
+      },
+      {
+        "given": "Halie M.",
+        "family": "Rando"
+      },
+      {
+        "given": "COVID-19 Review",
+        "family": "Consortium"
+      },
+      {
+        "given": "Casey S.",
+        "family": "Greene"
+      }
+    ],
+    "container-title": "arXiv",
+    "publisher": "arXiv",
+    "type": "report",
+    "abstract": "  Coronavirus disease 2019 (COVID-19) has caused global disruption and a significant loss of life. Existing treatments that can be repurposed as prophylactic and therapeutic agents could reduce the pandemic's devastation. Emerging evidence of potential applications in other therapeutic contexts has led to the investigation of dietary supplements and nutraceuticals for COVID-19. Such products include vitamin C, vitamin D, omega 3 polyunsaturated fatty acids, probiotics, and zinc, all of which are currently under clinical investigation. In this review, we critically appraise the evidence surrounding dietary supplements and nutraceuticals for the prophylaxis and treatment of COVID-19. Overall, further study is required before evidence-based recommendations can be formulated, but nutritional status plays a significant role in patient outcomes, and these products could help alleviate deficiencies. For example, evidence indicates that vitamin D deficiency may be associated with greater incidence of infection and severity of COVID-19, suggesting that vitamin D supplementation may hold prophylactic or therapeutic value. A growing number of scientific organizations are now considering recommending vitamin D supplementation to those at high risk of COVID-19. Because research in vitamin D and other nutraceuticals and supplements is preliminary, here we evaluate the extent to which these nutraceutical and dietary supplements hold potential in the COVID-19 crisis. ",
+    "note": "license: http://creativecommons.org/licenses/by/4.0/\nThis CSL Item was generated by Manubot v0.5.0 from its persistent identifier (standard_id).\nstandard_id: arxiv:2102.02250"
+  },
   {
     "id": "65ggO2DM",
     "type": "webpage",

spelling-error-locations.txt

@@ -19,5 +19,3 @@ content/20.pharmaceuticals.md:775:immunocompetent
 content/20.pharmaceuticals.md:776:ADG
 content/20.pharmaceuticals.md:781:REGN
 content/22.vaccines.md:22:niaid
-content/22.vaccines.md:247:propiolactone
-content/22.vaccines.md:254:poliovirus

spelling-errors.txt

@@ -10,6 +10,5 @@ immunocompetent
 JS
 Junshi
 NIAID
-poliovirus
-propiolactone
+Nrf
 REGN