Evaluation of partial volume correction and analysis of longitudinal [18F]GTP1 tau PET imaging in Alzheimer's disease using linear mixed-effects models.

Purpose: We evaluated the impact of partial volume correction (PVC) methods on the quantification of longitudinal [18F]GTP1 tau positron-emission tomography (PET) in Alzheimer's disease and the suitability of describing the tau pathology burden temporal trajectories using linear mixed-effects models (LMEM). Methods: We applied van Cittert iterative deconvolution (VC), 2-compartment, and 3-compartment, and the geometric transfer matrix plus region-based voxelwise methods to data acquired in an Alzheimer's disease natural history study over 18 months at a single imaging site. We determined the optimal PVC method by comparing the standardized uptake value ratio change (%ΔSUVR) between diagnostic and tau burden-level groups and the longitudinal repeatability derived from the LMEM. The performance of LMEM analysis for calculating %ΔSUVR was evaluated in a natural history study and in a multisite clinical trial of semorinemab in prodromal to mild Alzheimer's disease by comparing results to traditional per-visit estimates. Results: The VC, 2-compartment, and 3-compartment PVC methods had similar performance, whereas region-based voxelwise overcorrected regions with a higher tau burden. The lowest within-subject variability and acceptable group separation scores were observed without PVC. The LMEM-derived %ΔSUVR values were similar to the per-visit estimates with lower variability. Conclusion: The results indicate that the tested PVC methods do not offer a clear advantage or improvement over non-PVC images for the quantification of longitudinal [18F]GTP1 PET data. LMEM offers a robust framework for the longitudinal tau PET quantification with low longitudinal test-retest variability. Clinical trial registration: NCT02640092 and NCT03289143.

Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences.

SUMMARY: Antibody repertoires reveal insights into the biology of the adaptive immune system and empower diagnostics and therapeutics. There are currently multiple tools available for the annotation of antibody sequences. All downstream analyses such as choosing lead drug candidates depend on the correct annotation of these sequences; however, a thorough comparison of the performance of these tools has not been investigated. Here, we benchmark the performance of commonly used immunoinformatic tools, i.e. IMGT/HighV-QUEST, IgBLAST and MiXCR, in terms of reproducibility of annotation output, accuracy and speed using simulated and experimental high-throughput sequencing datasets.We analyzed changes in IMGT reference germline database in the last 10 years in order to assess the reproducibility of the annotation output. We found that only 73/183 (40%) V, D and J human genes were shared between the reference germline sets used by the tools. We found that the annotation results differed between tools. In terms of alignment accuracy, MiXCR had the highest average frequency of gene mishits, 0.02 mishit frequency and IgBLAST the lowest, 0.004 mishit frequency. Reproducibility in the output of complementarity determining three regions (CDR3 amino acids) ranged from 4.3% to 77.6% with preprocessed data. In addition, run time of the tools was assessed: MiXCR was the fastest tool for number of sequences processed per unit of time. These results indicate that immunoinformatic analyses greatly depend on the choice of bioinformatics tool. Our results support informed decision-making to immunoinformaticians based on repertoire composition and sequencing platforms. AVAILABILITY AND IMPLEMENTATION: All tools utilized in the paper are free for academic use. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Antimicrobial Release From Prefabricated Spacers Is Variable and the Dose Is Low.

BACKGROUND: High-dose antimicrobial-loaded bone cement (ALBC) is recommended to treat orthopaedic infections. Elution characteristics from prefabricated ALBC spacers and how they compare with hand-mixed ALBC are not well described. QUESTIONS/PURPOSES: (1) How does antimicrobial release from prefabricated spacers compare with release from hand-mixed ALBC over time? (2) Is antimicrobial release uniform across the surface of prefabricated ALBC spacers? (3) Do variations exist between different prefabricated spacer components? (4) Do textured surfaces release more antimicrobial than smooth surfaces? METHODS: Six prefabricated ALBC spacer components, two hip and four knee, and three hand-mixed ALBC formulations were studied in this comparative laboratory study. Gentamicin was eluted from 41 discrete sites over the surfaces of six spacer components and compared with elution from 15 ALBC specimens, five from each of three hand-mixed formulations. Elution was compared between spacer sites, components, and surface texture. Statistical analysis was performed by analysis of variance and Tukey's multiple-comparison test or t-test. RESULTS: Gentamicin release was highest in the first 24 hours for both prefabricated ALBC spacers and hand-mixed ALBC. Elution decreased over 7 days similarly for both. At Day 7, prefabricated ALBC spacers eluted more than hand-mixed 1 g ALBC (1 g ALBC: 1.49 ± 0.34, prefabricated: 3.59 ± 1.48, mean difference = 2.1 [0.2-4.0], p = 0.04) but eluted less than 5 g ALBC (9.21 ± 1.31, mean difference = -5.6 [-3.5 to -7.7], p < 0.001) and less than 10 g ALBC (35.8 ± 1.69, mean difference = -32.2 [-29.8 to -34.6], p < 0.001). Release varied from 2.7 to 9.9 µg/mm(2) over the surface of the spacers and from 3.5 to 5.5 µg/mm(2) between components with no component different than the others (Tukey). Release from textured surfaces was inconsistent. CONCLUSIONS: Antimicrobial release from prefabricated ALBC spacers is consistent with low-dose ALBC. Variation across the surface and between components is small compared with changes in antimicrobial load. CLINICAL RELEVANCE: Antimicrobial release from prefabricated ALBC spacers is consistent with local antimicrobial delivered from other low-dose ALBC formulations.