Coverage

blocked upstream · v5 provisional awaiting approval

What does the paper assert that no claim represents?

for iGABASnFR2 is an improved genetically encoded protein sensor of GABA · this layer across all papers · json

Provisional

This layer needs a corpus-scope decision that has not been ruled on yet, so what it produces would change if the decision changed. It waits on claim-format, relation-vocab.

Awaiting approval

Waiting for approval. That is a statement about the record, not about whether anyone has read this: people read the corpus without stamping what they read, and only a stamp leaves a trace. Approval is an operation on a version, not a step of its own — it is recorded against the version it was granted to, so running this layer again does not carry it forward.

What it produced41 spans.orphans

Read from coverage/kolb-2026-igabasnfr2.json · 16 KB. claims 21panels.pct 36.4statistics.total 2statistics.pct 0spans.segmented 384spans.obligations 79spans.textual 305spans.accounted 38spans.pct 48.1

# uidsectiontextstatspanels
1 results-001 results Results Screening for improved variants The original iGABASnFR1 ( Figure 1a , top) was engineered to increase fluorescence in the presence of GABA and express robustly in mammalian neurons, making it … [] ["fig1a"]
2 results-009 results Numbering is relative to each of the constituent protein domains; the relationship to sequential numbering of the entire polypeptide is shown in Figure 1—figure supplement 1 . [] ["fig1s1"]
3 results-023 results Figure 1—figure supplement 1. Annotated amino acid sequence of iGABASnFRs. [] ["fig1s1"]
4 results-037 results Specifically, we identified 39 sites to target: 14 near the GABA binding site, 6 at or around the protein hinge area, 10 on the cpSFGFP, and 9 at the interface between the two ligand-binding and cpGFP… [] ["fig1a"]
5 results-059 results For 10 action potentials (APs), iGABASnFR2 exhibited a peak ΔF/F 4.1-fold greater than iGABASnFR1 (iGABASnFR2 0.77±0.13; iGABASnFR1 0.19±0.02; p <0.001 Tukey’s HSD post hoc test following one-way ANOV… ["p <0.001","p <0.001"] []
6 results-060 results Rise time constants were slightly faster (iGABASnFR2 43±9 ms; iGABASnFR1 61±13 ms; p <0.001), while decay times were slower (iGABASnFR2 73±26 ms; iGABASnFR1 62±29 ms; p <0.001). ["p <0.001","p <0.001"] []
7 results-061 results The negative-going iGABASnFR2n exhibited slightly reduced performance relative to iGABASnFR2 but still achieved a 3.3-fold greater peak ΔF/F (iGABASnFR2n 0.62±0.12; iGABASnFR1 0.19±0.02; p <0.001), an… ["p <0.001","p <0.01"] []
8 results-066 results Traces and error bars denote mean ± s.e.m., n=20 culture wells for each variant. ["n=20"] []
9 results-067 results ( c ) Rise time constants of the three sensor variants obtained from exponential fits for the 1 AP condition (n=24 culture wells for iGABASnFR1 and iGABASnFR2, n=18 for iGABASnFR2n). ["n=24","n=18"] []
10 results-084 results Within that hinge region, the F101L mutation, introduced in the original iGABASnFR1 ( Marvin et al., 2019 ), increased binding affinity 10-fold ( Figure 3b ). [] ["fig3b"]
11 results-086 results The GABA binding site itself is defined by the side chains of W9, T13, F100, Y102, W202, R205, D228, and Y264 ( Figure 3c ). [] ["fig3c"]
12 results-091 results In iGABASnFR2, the L178 gfp S mutation at this interface is likely involved in a hydrogen-bonding network with nearby hydrophilic residues, enhancing the GABA-induced fluorescence change ( Figure 3b )… [] ["fig3b"]
13 results-103 results Somewhat surprisingly, purified iGABASnFR2 showed a smaller dynamic range than iGABASnFR1, although its affinity was higher ( Figure 4a ; max dF/F0 iGABASnFR2: 0.45, iGABASnFR1: 1.82; EC 50 iGABASnFR2… [] ["fig4a"]
14 results-113 results Lines indicate fits to mean of n=5 titration series, error bars are s.e.m. ["n=5"] []
15 results-122 results Lines indicate fits to mean of n=3 replicates from three separate batches of purified protein. ["n=3"] []
16 results-128 results Each titration has a minimum of n=3 replicates. ["n=3"] []
17 results-130 results Different iGABASnFR variants (200 nM) were titrated with increasing concentrations of GABA in the presence of different potential competing compounds at 1 mM. Lines indicate fits to mean of n=3 titrat… ["n=3"] []
18 results-136 results Data points represent the mean of n=3 technical replicates; error bars indicate s.e.m. ["n=3"] []
19 results-144 results Additional biophysical properties are reported in Table 1 . [] ["table1"]
20 results-147 results Table 1. Photophysical properties of iGABASnFR variants as purified proteins. λ abs (nm) λ Ex (nm) λ Em (nm) ΔF/F ε (M/cm 2 ) Φ τ (ns) GABA PBS GABA PBS GABA PBS iGABASnFR1 490 489 508 1.9 14,070±600 … [] ["table1"]
21 results-152 results Specifically, the hypothesis is that GABA release is stronger when a visual stimulus moves so that excitation sweeps down the dendritic branch from root to tip (centrifugal motion) rather than when it… [] ["fig5a"]
22 results-153 results The resulting direction-selective inhibition is relayed to direction-selective retinal ganglion cells (DSGCs) through asymmetric synaptic connections ( Briggman et al., 2011 ; Yonehara et al., 2011 ; … [] ["fig5b"]
23 results-160 results ( f–h ) Results of imaging using iGABASnFR2. ( i ) Histograms of response amplitude index (left) and response reliability (right) from SACs expressing iGABASnFR. n=147 ROIs collected across five retin… ["n=147"] []
24 results-161 results ( j ) As in i but with SACs expressing iGABASnFR2. n=346 ROIs collected from three retinae. ["n=346"] []
25 results-164 results Line and shading indicate mean ± s.d (n=147 for iGABASnFR, n=346 for iGABASnFR2). ["n=147","n=346"] []
26 results-165 results ( l ) Comparison of signal-to-noise ratio (SNR) of the motion response detected with the two sensor versions. p =0. Two-tailed Mann-Whitney-Wilcoxon test. ["p =0"] []
27 results-166 results ( m ) Comparison of direction selectivity (CV, circular variance) for the two sensor versions. p =7.812×10 –6 . ["p =7.812"] []
28 captions-004 captions Numbering is relative to each of the constituent protein domains; the relationship to sequential numbering of the entire polypeptide is shown in Figure 1—figure supplement 1 . [] ["fig1s1"]
29 captions-018 captions [panels detected: a, b, c, d] === Figure 1s1 === Figure 1—figure supplement 1. Annotated amino acid sequence of iGABASnFRs. [] ["fig1s1"]
30 captions-029 captions Traces and error bars denote mean ± s.e.m., n=20 culture wells for each variant. ["n=20"] []
31 captions-030 captions ( c ) Rise time constants of the three sensor variants obtained from exponential fits for the 1 AP condition (n=24 culture wells for iGABASnFR1 and iGABASnFR2, n=18 for iGABASnFR2n). ["n=24","n=18"] []
32 captions-044 captions Lines indicate fits to mean of n=5 titration series, error bars are s.e.m. ["n=5"] []
33 captions-053 captions Lines indicate fits to mean of n=3 replicates from three separate batches of purified protein. ["n=3"] []
34 captions-060 captions Different iGABASnFR variants (200 nM) were titrated with increasing concentrations of GABA in the presence of different potential competing compounds at 1 mM. Lines indicate fits to mean of n=3 titrat… ["n=3"] []
35 captions-065 captions Data points represent the mean of n=3 technical replicates; error bars indicate s.e.m. ["n=3"] []
36 captions-072 captions ( f–h ) Results of imaging using iGABASnFR2. ( i ) Histograms of response amplitude index (left) and response reliability (right) from SACs expressing iGABASnFR. n=147 ROIs collected across five retin… ["n=147"] []
37 captions-073 captions ( j ) As in i but with SACs expressing iGABASnFR2. n=346 ROIs collected from three retinae. ["n=346"] []
38 captions-076 captions Line and shading indicate mean ± s.d (n=147 for iGABASnFR, n=346 for iGABASnFR2). ["n=147","n=346"] []
39 captions-077 captions ( l ) Comparison of signal-to-noise ratio (SNR) of the motion response detected with the two sensor versions. p =0. Two-tailed Mann-Whitney-Wilcoxon test. ["p =0"] []
40 captions-078 captions ( m ) Comparison of direction selectivity (CV, circular variance) for the two sensor versions. p =7.812×10 –6 . ["p =7.812"] []
41 tables-001 tables Table 1. Photophysical properties of iGABASnFR variants as purified proteins. λ abs (nm) λ Ex (nm) λ Em (nm) ΔF/F ε (M/cm 2 ) Φ τ (ns) GABA PBS GABA PBS GABA PBS iGABASnFR1 490 489 508 1.9 14,070±600 … [] ["table1"]

Artifacts

Versions

From the run ledger. There is no changelog beside it to keep in step.

  1. v5 · 2026-09-13 · scripts/pipeline.py run

    ran via scripts/pipeline.py

    cd extract && python3 -m elife_extract.cli coverage --paper kolb-2026-igabasnfr2 --json ../coverage/kolb-2026-igabasnfr2.json

  2. v4 · 2026-09-13 · scripts/pipeline.py run

    ran via scripts/pipeline.py

    cd extract && python3 -m elife_extract.cli coverage --paper kolb-2026-igabasnfr2 --json ../coverage/kolb-2026-igabasnfr2.json

  3. v3 · 2026-09-12 · scripts/pipeline.py run

    re-run after prepare v2

    cd extract && python3 -m elife_extract.cli coverage --paper kolb-2026-igabasnfr2 --json ../coverage/kolb-2026-igabasnfr2.json

  4. v2 · 2026-09-11 · scripts/pipeline.py run

    coverage for the nine papers that had none

    cd extract && python3 -m elife_extract.cli coverage --paper kolb-2026-igabasnfr2 --json ../coverage/kolb-2026-igabasnfr2.json

  5. v1 · 2026-09-11 · scripts/pipeline.py run

    ran via scripts/pipeline.py

    cd extract && python3 -m elife_extract.cli coverage --doi 10.7554/eLife.108319 --paper-slug kolb-2026-igabasnfr2 --claims-dir ../claims/kolb-2026-igabasnfr2 --json ../coverage/kolb-2026-igabasnfr2.json

This layer across the corpus

Across the corpus

4 blocked upstream · 6 stale·a paper links to its own cell, where this layer's output for it is rendered

PaperStateVersionLast runOutputCell
A three-dimensional immunofluorescence atlas of the …ran via scripts/pipeline.pyblocked upstreamv32026-09-13artiushin-2026-spider-atlas.jsonjson
Distinct representational properties of cues and con…ran via scripts/pipeline.pystalev42026-09-13bouyeure-2026-fear-rsa.jsonjson
Computational modelling identifies key determinants …ran via scripts/pipeline.pystalev32026-09-13ejdrup-2026-dopamine.jsonjson
Contributions of insula and superior temporal sulcus…rebuild after edge completion passstalev72026-09-13gadeke-2026-guilt-insula.jsonjson
Spatially targeted inhibitory rhythms differentially…ran via scripts/pipeline.pystalev32026-09-13headley-2026-inhibitory-rhythms.jsonjson
Feedback of peripheral saccade targets to early fove…ran via scripts/pipeline.pyblocked upstreamv32026-09-13kammer-2026-foveal-feedback.jsonjson
iGABASnFR2 is an improved genetically encoded protei…ran via scripts/pipeline.pyblocked upstreamv52026-09-13kolb-2026-igabasnfr2.jsonjson
A deep learning pipeline for mapping in situ network…ran via scripts/pipeline.pyblocked upstreamv52026-09-13rozak-2026-neurovascular-dl.jsonjson
Self-association enhances early attentional selectio…ran via scripts/pipeline.pystalev32026-09-13scheller-2026-self-prioritization.jsonjson
Impaired excitability of fast-spiking neurons in a n…ran via scripts/pipeline.pystalev52026-09-13wengert-2026-kcnc1.jsonjson

Inputs and outputs

Produces
  • coverage/{paper}.json

One per paper — the table above links each one that exists.

Views
  • document — declared, and this artifact is not the shape this view needs
  • table — rendered above, over the 128 spans.orphans in the artifact

Running it

The command comes from the declaration, so this text and what actually runs cannot diverge. pipeline.py run also runs the unmet dependencies first. 

python3 scripts/pipeline.py run <paper> coverage

Underneath, that runs cd extract && python3 -m claim_graphs.cli coverage --paper {paper} --json ../coverage/{paper}.json.