User:Jcreagmile/sandbox

Topics
- epilepsy - carbon nanotubes

- deep brain stimulation
 * currently epilepsy is not listed in the applications listed for use of DBS, which is the topic of my (Jack's) fellowship research. That being said, I don't know how applicable this would be for other people, as it is fairly specific and still in the early stages.

- immunodeficiency / immunosuppression - virology
 * Both pages have been listed as "start-class" on the quality scale - whoever has these topics should give it a read and see what we could contribute to improve the quality of the pages
 * Both pages are listed as needing additional citations for verification

- Floater

- Optical coherence tomography
 * There is a section labeled "Layperson's explanation," which attempts to explain OCT in a simpler manner. The problem is this section of the article has no citations, additional ones could be added for verification. However, the sections outside this one have many sources so there is a possibility that citations would be repeated.
 * The "theory" section has a lot of complicated physics that lack a clear explanation. Maybe some explanation of the formulas would be beneficial.

- Neurodevelopmental disorder
 * This page is listed as having too few medical sources or too reliant on primary sources

- behavioral testing

- sensory assessments

- Hyperarousal
 * This page has been listed as "start-class" on the quality scale - whoever has this topic should give it a read and see what we could contribute to improve the quality of the page

- Health Literacy

- CT by language
 * Can be used as a marker of quality of care (health care quality)
 * perhaps we can add surrogate markers of quality

= Selected Topic - JC Virus = From the intro of the Wiki page:

The JC virus or John Cunningham virus (JCV, not to be confused with Jamestown Canyon virus that bears the same initials) is a type of human polyomavirus (formerly known as papovavirus) and is genetically similar to BK virus and SV40. It was identified by electron microscopy in 1965 by ZuRhein and Chou, and by Silverman and Rubinstein, and later isolated in culture and named using the two initials of a patient, John Cunningham, with progressive multifocal leukoencephalopathy (PML). The virus causes PML and other diseases only in cases of immunodeficiency, as in AIDS or during treatment with drugs intended to induce a state of immunosuppression (e.g. organ transplant patients).

Casey

 * Different strains of JC virus associated with novel syndromes (pyramidal neurons of cortex --> encephalopathy, granule cell layer of cerebellum, meninges and choroid plexus --> meningitis)
 * Talk about differences in pathogenic strains from the one that remains quiescent
 * Latent strains can lay dormant in several organs other than kidneys and GI tract (which are the only ones listed on wiki)
 * No mention of subcellular localization

Other strains and Novel Pathological Syndromes
Although JC virus infection is classically associated with white matter demyelination and PML pathogenesis, recent literature has identified viral variants as etiological agents of other novel syndromes. For example, JCV has been found to infect the granule cell layer of the cerebellum, while sparing purkinje fibers, ultimately causing severe cerebellar atrophy. This syndrome, called JCV granule cell layer neuronopathy (JCV GCN), is characterized by a productive and lytic infection by a JC variant with a mutation in the VP1 coding region. JCV also appears to mediate encephalopathy, an infection of cortical pyramidal neurons (CPN) and astrocytes. Analysis of the JCV CPN variant revealed differences from JCV GCN: no mutations were found in the VP1 coding region, however, a 143 base-pair deletion was identified in the agnogene, coding for a 10 amino acid truncated peptide, which is believed to mediate CPN tropism. Additionally, analysis of the sub-cellular localization of JC CPN virions in nuclei, cytoplasm, and axons suggests that the virus may travel through axons to increase infectivity. The JCV virus may also be an etiological agent of meningitis (JCVM), as JCV was the only pathogen identified in the CSF of patients with meningitis. Analysis of the JCVM variant revealed archetype-like regulatory regions with no mutations in coding sequences. The precise molecular mechanisms mediating JCV meningeal tropism needs to be further explored.

Jack

 * No significance given for what the differences are between for the types/strains of JCV
 * We should see if there has been any more evidence for its link to colorectal cancer since 2000

Paul

 * The significance of the promoter in viral fitness is mentioned but not expanded upon. This seems to be important in terms of how likely the virus is to proliferate in immunodeficiency and cause PML.
 * No mention of treatments (this may however be more pertinent for PML, given this is the clinical manifestation of the JCV).
 * A histology slide picture of healthy vs. PML brain tissue would be helpful to illustrate the damage caused.

Jeff

 * incidence of JV virus in US
 * Could mention current research and what is being done to combat JC virus
 * What is being targeted in terms of treatment?
 * Update drugs that might be associated with reactivation of JC
 * Expand upon type differences and any significance

Casey

 * Novel strains of the JC virus

Jack

 * Colorectal cancer and latent strains that are dormant in organs, GI, and other tissue (See Casey's point 2).
 * Associated cancers

Paul

 * Research moving forward - talks about Paul's first point
 * picture

Jeff

 * Clinical treatment/therapy
 * Incidence in US

Topic Outline
The JC virus or John Cunningham virus (JCV, not to be confused with Jamestown Canyon virus that bears the same initials) is a type of human polyomavirus (formerly known as papovavirus) and is genetically similar to BK virus and SV40. It was identified by electron microscopy in 1965 by ZuRhein and Chou, and by Silverman and Rubinstein, and later isolated in culture and named using the two initials of a patient, John Cunningham, with progressive multifocal leukoencephalopathy (PML). The virus causes PML and other diseases only in cases of immunodeficiency, as in AIDS or during treatment with drugs intended to induce a state of immunosuppression (e.g. organ transplant patients).

Paul
Certain transcription factors present in the early promoter sequences of the JC virus can induce trophism and viral proliferation that leads to PML. The Spi-B factor was shown to be crucial in initiating viral replication in certain strains of transgenic mice. The protein encoded by these early sequences, T-antigen, also plays a key role in viral proliferation, directing the initiation of DNA replication for the virus as well as performing a transcriptional switch to allow for the formation of the various capsid and regulatory proteins needed for viral fitness. Further research is needed to determine the exact etiological role of T-antigen, but there seems to be a connection to the early initiation of the active virus from its archetypal dormant state.
 * Histology picture citing damage caused by JCV (from Casey's PI!)
 * http://www.bidmc.org/~/media/Images/CentersandDepartments/Neurology/Research/Koralnik%20Lab/jcv%20pml%20staining.jpg
 * Good articles referencing promoter sequence influence on JCV expression
 * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376594/
 * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3052566/

Jeff

 * Clinical treatment/therapy
 * https://www.uptodate.com/contents/progressive-multifocal-leukoencephalopathy-treatment-and-prognosis?source=see_link
 * No treatment for "JC virus" but you can treat PML
 * Put a link to PML treatment page. Perhaps a quick synopsis of the treatment
 * "Initiating or optimizing effective antiretroviral therapy (ART) for patients with HIV infection ●Withdrawing immunosuppressive drugs (when possible) for patients without HIV infection  ●Discontinuing natalizumab and starting plasma exchange for patients with natalizumab-associated PML"
 * Incidence in US
 * https://academic.oup.com/jid/article-abstract/167/1/13/845066


 * https://www.ncbi.nlm.nih.gov/pubmed/28228564
 * PML incidence (cases/number of treated patients) in studies can be surprisingly high, as in the STRATA trial, with 12.8/1,000 treated patients.9 Vennegoor et al.10 calculated an incidence of 20.7/1,000 treated patients in their study. These incidences almost double when only JC virus (JCV)–seropositive (JCV+) patients are used as denominator, reflecting the seroprevalence of about 50% in the whole population. In the following, we give some general considerations concerning incidence calculations
 * 55%–70% of patients are JCV+, but fewer than 1% will ultimately develop PML
 * treatment with natalizumab has been associated with JCV seroconversion rates of about 8%–10% per year
 * suggests that either long-term treatment is a risk factor (qualitative evaluation: either a patient has the risk factor or not, similar to prior IS) or the longer a patient is treated with natalizumab, the higher the PML risk (quantitative evaluation: PML risk rises with each infusion).
 * 14% of PML cases developed in the first 24 months of natalizumab treatment.
 * There is no doubt that long-term treatment is a risk factor, but how valuable this risk factor is for stratification highly depends on the overall avArerage treatment duration
 * D62L?
 * The greater the anti-JCV antibody index is, the higher the risk to PML
 * http://www.mdedge.com/neurologyreviews/article/76141/multiple-sclerosis/anti-jcv-antibody-index-may-further-define-pml
 * https://www.ncbi.nlm.nih.gov/pubmed/20401541
 * The human polyoma virus JC is the causative agent of PML