Integration site features for the Acute UD, Acute UD + 5 and Chronic UD cohorts.

Integration site features for the Acute UD, Acute UD + 5 and Chronic UD cohorts.

<p>Individuals are categorized into groups accordingly to the stage when ART was initiated. Donut charts display the number of integration sites (IS) color-coded by their respective characteristic at UD and UD + 5. Distinct clonal populations of infected cells are represented by different patt...

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Manylion Llyfryddiaeth
Prif Awdur:	Tine Struyve (22683295) (author)
Awduron Eraill:	Marion Pardons (6407921) (author), Jozefien De Clercq (17737815) (author), Liesbet Termote (22683298) (author), Laurens Lambrechts (10532207) (author), Ytse Noppe (22683301) (author), Mathias Lichterfeld (57148) (author), Sofie Rutsaert (10667718) (author), Linos Vandekerckhove (105574) (author)
Cyhoeddwyd:	2025
Pynciau:	Biochemistry Medicine Neuroscience Biotechnology Evolutionary Biology Ecology Cancer Infectious Diseases Plant Biology Virology Computational Biology phorbol myristate acetate integration selection mechanisms xlink "> persistence small reservoir sizes treatment initiation timing clonal expansion contributes art ), irrespective individuals treated shortly reservoir persistence early reservoir persistence clonal expansion started treatment pma ), art initiation viral reservoir treated individuals inducible reservoir individuals treated 1 reservoir suggesting post proviruses integrated progressively enriched one year major barrier longitudinal analysis heterochromatin regions five years chronic cohorts cell compartment antiretroviral therapy already detected
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Eitemau Tebyg

Frequencies and phenotypes of p24 + cells following PMA/Tat_LNP stimulation. (A-D) CD4 T cells from Acute UD, Acute UD + 5, Chronic UD and Chronic UD + x individuals were stimulated for 24h with PMA/Tat_LNP (A) Frequencies of p24 + cells in CD4 T cells. Median values are plotted. Open circles represent limit of detection (LOD). (B) Percentages of HIV-infected cells expressing the p24 protein following stimulation. Median values are plotted. Participants with an LOD frequency of p24 + cells in CD4 T cells or unreportable/unavailable total HIV DNA quantification were not included in this analysis. (C) Frequencies of cells with a given phenotype (TN, TCM/TTM, TEM, TTd) in p24+ and p24- fractions. Participants with a minimal number of 4 p24 + cells are represented. Grey bars depict median values. (D) Proportions of all p24 + cells with a given phenotype (TN, TCM/TTM, TEM, TTd). p24 + cells (
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B-
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Integration site analysis, near full-length proviral sequencing and phenotype analysis of p24 + cells. Maximum-likelihood phylogenetic trees for four Acute UD individuals. The trees include sequences with HXB2 coordinates 5089-9602. Naïve (TN), central/transitional memory (TCM/TTM), effector memory (TEM) and terminally differentiated (TTd) T cells are represented by triangles, rectangles, circles and diamonds, respectively. Proviral classification is color-coded. The integration sites are depicted and are color-coded according to their orientation to the host gene. (Peri-) centromeric DNA and KRAB-ZNF genes on chr19 are highlighted with a green and yellow frame, respectively. HXB2 subtype B is HIV-1 reference genome. NFL: near full-length.
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

FACS analysis of p24 + cells across acute and chronic cohorts.
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Clonal expansion dynamics on ART in individuals treated during acute and chronic infection.
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Gating strategy and phenotypic distribution of p24 + cells for the acute and chronic cohorts.
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Integration site analysis and near full-length (NFL) sequencing of p24 + cells. (A) Donut charts displaying the number of HIV integration sites (IS) obtained by ISLA from p24 + cells for four participants in the corresponding Fiebig group. White parts indicate IS detected once and colored parts indicate IS detected more than once. The total number of IS generated by ISLA for each participant is shown in the middle of each donut. (B) Proportion of intact and defective proviral sequences from p24 + cells (n = 47 sequences).
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Schematic overview of participant sampling timeline.
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Source data manuscript.
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Comparison of integration sites from total CD4 T cells and p24 + cells.
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Frequencies of p24 + cells across Fiebig stages.
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Frequencies of p24 + cells in CD4 T cells after PMA/ionomycin, Tat-LNP/PNB and Tat-LNP/PMA stimulation.
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

HIV reservoir quantification and phylogenetic diversity.
gan: Tine Struyve (22683295)
Cyhoeddwyd: (2025)

Numerical model predictions of CO₂ injection well integrity
gan: Lee Hosking (8459091)
Cyhoeddwyd: (2025)

Data Sheet 2_Beyond prescriptions: chronic medication adherence predicts mortality risk in a large-scale cohort study.pdf
gan: Jessica Hamuy Blanco (17279713)
Cyhoeddwyd: (2025)

Data Sheet 1_Beyond prescriptions: chronic medication adherence predicts mortality risk in a large-scale cohort study.pdf
gan: Jessica Hamuy Blanco (17279713)
Cyhoeddwyd: (2025)

Concordance between histopathology and nude mice inoculation results.
gan: Andrea Maia Fernandes de Araújo Fonseca (10333122)
Cyhoeddwyd: (2025)

Clinical and laboratory characteristics at diagnosis and after completion of 24-dose MDT (post-MDT index re-evaluation).
gan: Andrea Maia Fernandes de Araújo Fonseca (10333122)
Cyhoeddwyd: (2025)

Reactional profiles at the post-MDT index visit (mutually exclusive).
gan: Andrea Maia Fernandes de Araújo Fonseca (10333122)
Cyhoeddwyd: (2025)

Socio-demographic and clinical characteristics.
gan: Andrea Maia Fernandes de Araújo Fonseca (10333122)
Cyhoeddwyd: (2025)

Tests performed at the post-MDT index re-evaluation: operational definitions and analytic denominators.
gan: Andrea Maia Fernandes de Araújo Fonseca (10333122)
Cyhoeddwyd: (2025)

Proportions of patients at diagnosis and after completing 24 doses of MDT are shown.
gan: Andrea Maia Fernandes de Araújo Fonseca (10333122)
Cyhoeddwyd: (2025)

Case 1 (A and B): After the treatment (24 doses of MDT), neural branches with an intense peri and endoneural lymphohistiocytic inflammatory process were observed (A) (→).
gan: Andrea Maia Fernandes de Araújo Fonseca (10333122)
Cyhoeddwyd: (2025)

Overlap of clinical domains among patients with paired Simplified Neurological Assessment (SNA) at the post-MDT index visit (n = 99).
gan: Andrea Maia Fernandes de Araújo Fonseca (10333122)
Cyhoeddwyd: (2025)

Striking image - new.
gan: Andrea Maia Fernandes de Araújo Fonseca (10333122)
Cyhoeddwyd: (2025)

HIV in the Eastern Cape: what the numbers tell us
gan: Human Sciences Research Council (18851275)
Cyhoeddwyd: (2025)

Drug retention rate of Janus kinase inhibitors in patients with rheumatoid arthritis: the KEIO-RA cohort study
gan: Satoshi Takanashi (15221350)
Cyhoeddwyd: (2025)

Multilevel logistic regression models with each negative emotions as a predictor.
gan: Chan-Young Ahn (22683343)
Cyhoeddwyd: (2025)

Confusion Matrix for Binary Classification.
gan: Chan-Young Ahn (22683343)
Cyhoeddwyd: (2025)

Associations between pre-assessment self-report measures and EMA (14-day) ratings.
gan: Chan-Young Ahn (22683343)
Cyhoeddwyd: (2025)

Descriptive statistics of demographic and clinical characteristics.
gan: Chan-Young Ahn (22683343)
Cyhoeddwyd: (2025)

Feature importance scores of the predictors.
gan: Chan-Young Ahn (22683343)
Cyhoeddwyd: (2025)

Supplementary material JImaging-3990735
gan: Adrien Deliege (22675676)
Cyhoeddwyd: (2025)

Melt Memory Effect on Biaxially Oriented Random Copolyamides: Direct Evidence for Stretch-Induced Crystal Retention above the Equilibrium Melting Point
gan: Yunqi Xu (349428)
Cyhoeddwyd: (2025)

Summary of the multi-level models to predict cognition on seven difference neuropsychological outcome measures over five years.
gan: Lisa Ohlhauser (22676519)
Cyhoeddwyd: (2025)

Participant demographics and descriptive statistics.
gan: Lisa Ohlhauser (22676519)
Cyhoeddwyd: (2025)

Multi-level model specification equations to predict neuropsychological outcome measures.
gan: Lisa Ohlhauser (22676519)
Cyhoeddwyd: (2025)

Description of neuropsychological measures and cognitive domains assessed.
gan: Lisa Ohlhauser (22676519)
Cyhoeddwyd: (2025)

Cognitive Assessment Scores over time.
gan: Lisa Ohlhauser (22676519)
Cyhoeddwyd: (2025)

Schematic of the 2-level linear mixed model.
gan: Lisa Ohlhauser (22676519)
Cyhoeddwyd: (2025)

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