Paraffin-embedded tissues from the posterior basal ganglia (primarily, the caudate and putamen) of HIV+   and seronegative individuals were dewaxed and rehydrated in xylene (100%; 3   ×   10 min), ethanol (100%; 2   ×   10 min, 95%; 2   ×   5 min, 70%; 2   ×   5 min, 50%; 2   ×   5 min), and dH2O (2   ×   5 min) prior to immunofluorescence assay. Snap-frozen tissues were embedded in O.C.T compound, sectioned, and postfixed (with ice-cold 4% paraformaldehyde for 20 min) prior to use. All tissues (12–18 μm-thick) were heated (at 50% microwave power for 3 min) in Tris-based antigen unmasking solution (pH 9.0, # H3301, Vector Laboratories, Burlingame, CA), followed by permeabilization in a neutral pH phosphate-buffered saline (PBS) containing 0.25% Triton X 100. Tissue sections were incubated (2 h) in Animal-Free Blocker® and Diluent solution (# SP-5035-100, Vector Laboratories) and then incubated overnight (at 4oC) in primary antibodies for the 32 kDa dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32) (1:200, # sc271111 AF647, Santa Cruz, Dallas, TX), TDP-43 (1:100, # 67345, Proteintech, Rosemont, IL), phospho-TDP-43 Ser409/410 (pTDP-43) (1:100, # 66318, Proteintech), CK2 (1:100, #10992, Proteintech), and CK1δ (1:100, #14388, Proteintech) followed by a 1 h incubation in species-specific secondary antibodies. Autofluorescence in tissue sections was eliminated using ReadyProbes Tissue Autofluorescence Quenching Kit (#R37630, Thermo Fisher, Waltham, MA) per the manufacturer's instructions. Mean fluorescence/pixel intensity values for pTDP-43, TDP-43, CK2, and CK1δ (corresponding to the level of immunostaining) were acquired in optical sections using confocal microscopy and measured in the cytoplasm and nuclear compartments using CellProfilerTM software (V 6.1) (Broad Institute, Cambridge, MA) (see supplementary Figure 1 for details on the CellProfilerTM workflow). At least 300 Hoechst+   cells were analyzed for each subject.