Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• HIV-1 sequence evolution in vivo after superinfection with three viral strains.

  PMID 17716368 · PMC2020475 · Retrovirology · 2007 · 8 claims · 8 setups

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  gag and env-V3 nucleotide evolution follows a similar pattern in all three strains: low substitution rate in the first 2-3 years of infection, then an increase driven mainly by synonymous substitutions

  blood seminal pbmcs biological strain-specific bulk in-house

• Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

  PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

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  PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

  hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag

• Development of a microtiter plate-based glycosaminoglycan array for the investigation of glycosaminoglycan-protein interactions.

  PMID 19729381 · PMC3428902 · Glycobiology · 2009 · 8 claims · 5 setups

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  Plasma-polymerized allyl amine:octadiene surfaces support non-covalent immobilization of diverse GAGs (heparin, chondroitin-4-sulfate, dermatan sulfate, hyaluronan) in a functionally active, protein-binding state

  microtiter allyl solid-phase x-ray radiolabel

• Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

  PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

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  Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

  hiv-1 same sequenced gag single-genome mhc hypermutation

• Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

  PMID 19812689 · PMC2753653 · PloS one · 2009 · 7 claims · 5 setups

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  Natural CTL immunodominance toward variable proteome regions increases epitope mismatch with challenge strains and recapitulates the escape-driven CTL failure seen in natural infection, contributing to HIV vaccine failure

  hiv-1 polyclonally shannon cross-clade ctl

• HIV-1 evolution following transmission to an HLA-B*5801-positive patient.

  PMID 19909081 · PMC2779566 · The Journal of infectious diseases · 2009 · 8 claims · 8 setups

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  Multiple escape mutations developed rapidly in HLA-B*5801-restricted epitopes in Gag, Nef, and Pol following transmission

  plasma transmitter subject genomic full-length population ifn-γ

• Loss of mutual protection between human osteoclasts and chondrocytes in damaged joints initiates osteoclast-mediated cartilage degradation by MMPs.

  PMID 34811438 · PMC8608887 · Scientific reports · 2021 · 6 claims · 8 setups

  Has reproduction · 50

  Human osteoclasts can differentiate on acellular cartilage, express osteoclast markers, and degrade cartilage matrix in a contact-dependent manner without forming F-actin rings or resorption pits.

  knee cd14+ osteoclasts conditioned histology osteoclast gag

• Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil.

  PMID 10081673 · PMC2627691 · Emerging infectious diseases · 1999 · 8 claims · 8 setups

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  Among 79 HIV-1 infected patients, 3 (3.8%) had dual infections, 6 (7.6%) had recombinant infections, and 70 (88.6%) had single-subtype infections

  pbmc uncultured pcr-amplified aligned rflp heteroduplex nested

• Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response.

  PMID 15545352 · PMC2211924 · The Journal of experimental medicine · 2004 · 7 claims · 4 setups

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  CD8+ CTL responses contribute to containment of viral replication in acute/early HIV-1 infection, and HIV-1 rapidly selects escape variants within epitope-containing regions beginning within weeks of infection.

  pbmcs autologous vaccinia plasma ifn-γ 51cr recombinant

• The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

  PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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  Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

  hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral

• Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers.

  PMID 36373634 · PMC9723646 · Nucleic acids research · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells (OSCs)

  drosophila ovarian osc melanogaster chip-seq sirna western

• HIV-1 Nef binds the DOCK2-ELMO1 complex to activate rac and inhibit lymphocyte chemotaxis.

  PMID 14737186 · PMC314466 · PLoS biology · 2004 · 8 claims · 8 setups

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  HIV-1 Nef binds the DOCK2-ELMO1 complex (which also contains Rac) in T cells

  jurkat hek resting ns1 two-step ni-nta anti-flag

• Widely variable endogenous retroviral methylation levels in human placenta.

  PMID 17617638 · PMC1950553 · Nucleic acids research · 2007 · 6 claims · 6 setups

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  Three HERV-E LTRs that function as alternative gene promoters (LTR-PTN, LTR-EBR, LTR-MID1) are unmethylated in placenta but heavily methylated in blood cells, where they are not active promoters

  term placenta genome bisulfite rt-pcr genome-wide

• Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

  PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

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  Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

  archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr

• BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools.

  PMID 15757512 · PMC555852 · Retrovirology · 2005 · 8 claims · 3 setups

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  BioAfrica's HIV-1 Proteomics Resource integrates protein structure, gene expression, post-translational modification, functional activity and protein-macromolecule interaction data with bioinformatics tools in a single website.

  hiv-1 motif sequence literature-derived

• Depletion of HIV reservoir by activation of ISR signaling in resting CD4(+)T cells.

  PMID 36590168 · PMC9800255 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 89

  Activation of ISR/ATF4 signaling (via HA15) reverses HIV latency in Jurkat models of HIV latency (J-Lat A1, 2D10)

  jurkat cd4+ hiv-negative resting flow trypan western

• Automated recognition of retroviral sequences in genomic data--RetroTector.

  PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences

  reference genome chimpanzee red motif whole-genome simulated