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Lint: immune-reconstitution-inflammatory-syndrome

Acronyms
warning

"low CD4+ count (less than 50 cells/μL) and high plasma HIV RNA prior to initiation of therapy"

Line 7:67 · 'RNA' has no definition. Spell it out if it's unfamiliar to the audience.

"rapid increase in CD4+ count or decrease in HIV RNA following initiation of ART"

Line 8:56 · 'RNA' has no definition. Spell it out if it's unfamiliar to the audience.

"IRIS has been described with several opportunistic pathogens, including tuberculosis 8, PML (JC virus) and cryptococcosis, as well as Kaposi sarcoma. CMV, VZV, and HIV itself rarely cause IRIS."

Line 19:113 · 'PML' has no definition. Spell it out if it's unfamiliar to the audience.

"IRIS has been described with several opportunistic pathogens, including tuberculosis 8, PML (JC virus) and cryptococcosis, as well as Kaposi sarcoma. CMV, VZV, and HIV itself rarely cause IRIS."

Line 19:122 · 'JC' has no definition. Spell it out if it's unfamiliar to the audience.
Inline EG
suggestion

"Immune reconstitution inflammatory syndrome (IRIS) is paradoxical deterioration of a pre-existing illness following abrupt improvement in an individual's immune function. It is classically seen in HIV/AIDS patients following initiation of antiretroviral therapy (ART). Increasingly, however, it is also seen in the setting of other diseases treated with immunomodulation (e.g. natalizumab-associated progressive multifocal leukoencephalopathy immune reconstitution inflammatory syndrome (PML-IRIS) in multiple sclerosis)."

Line 1:399 · Consider replacing a bracketed e.g. with an inline e.g. after a comma.
Semicolons
suggestion

""paradoxical" IRIS has been postulated to arise from the restoration of the previously suppressed inflammatory immune response, in the absence of active infection 1; this is thought to occur due to reactivation of memory cells that had been previously activated by antigen exposure"

Line 16:200 · Use semicolons judiciously.