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for Impaired excitability of fast-spiking neurons in a novel mouse model of KCNC1 epileptic encephalopathy · this layer across all papers · json

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claims/wengert-2026-kcnc1/pv-in-ap-waveform-altered-downstroke-apd50.md
claims/wengert-2026-kcnc1/pv-in-inhibitory-synapse-altered-adult.md
claims/wengert-2026-kcnc1/pv-in-inhibitory-synapse-intact-juvenile.md

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Read from coverage/wengert-2026-kcnc1.json · 41 KB. claims 32panels.pct 21.6statistics.total 49statistics.pct 18.4spans.segmented 512spans.obligations 233spans.textual 279spans.accounted 130spans.pct 55.8

#	uid	section	text	stats	panels
1	results-003	results	A targeting vector containing part of intron 1 followed by the coding sequence of exons 2–4 flanked by loxP sites was then introduced upstream of the modified endogenous sequence ( Figure 1A ).	`[]`	`["fig1a"]`
2	results-004	results	Thus, in the absence of Cre recombinase, there is expression of the introduced 5’ WT exons 2–4; in the presence of Cre recombinase, there is Cre-mediated excision of the floxed WT exons 2–4 coding seq…	`[]`	`["fig1a"]`
3	results-005	results	Sanger sequencing confirmed the knock-in missense mutation in exon 2, and subsequent PCR showed Cre-dependent genome recombination of the variant ( Figure 1B and C ).	`[]`	`["fig1b","fig1a","fig1d","fig1c"]`
4	results-006	results	We utilized a breeding strategy that allowed us to examine the behavior and physiology of mice expressing the Kcnc1 variant globally (via cross to Actb-Cre mice; JAX#: 003376), as is presumed the case…	`[]`	`["fig1d"]`
5	results-007	results	We also used a transgenic mouse line (C57BL/6-Tg(Pvalb-tdTomato)15Gfng/J; JAX#: 027395) which fluorescently labels PV-INs with the red fluorescent protein tdTomato driven by the endogenous parvalbumin…	`[]`	`["fig1d"]`
6	results-011	results	( A ) Design and structure of the conditional Kcnc1 -A421V allele.	`[]`	`["fig1a"]`
7	results-013	results	( B ) Sequencing results indicate successful targeting of c.1262C>T to introduce the heterozygous A421V variant.	`[]`	`["fig1b"]`
8	results-014	results	( C ) PCR confirmation of two HET founders ( Kcnc1 -A421V/+) and two WT littermates. 167 bp, WT allele fragment; 207 bp, floxed allele fragment.	`[]`	`["fig1c"]`
9	results-015	results	( D ) Breeding strategy to generate control and experimental mice in which the Kcnc1 -A421V variant is expressed globally and PV cells are fluorescently labeled for targeted recording.	`[]`	`["fig1d"]`
10	results-017	results	Figure 1—figure supplement 1. Pvalb-tdTomato reporter effectively labels parvalbumin-positive fast-spiking GABAergic inhibitory interneurons (PV-INs) in wild-type (WT) and Kcnc1 -A421V/+ mice.	`[]`	`["fig1s1"]`
11	results-018	results	( A ) Representative immunohistochemistry images for parvalbumin in WT (top row) and Kcnc1 -A421V/+ (bottom row) mice (postnatal day [P]21–33) showing a high degree of overlap between the tdTomato rep…	`[]`	`["fig1s1a"]`
12	results-022	results	( B ) Counts of PV cells per unit area (mm 2 ) are not different between WT and Kcnc1 -A421V/+ mice (N=3 mice/genotype).	`["N=3"]`	`["fig1s1b"]`
13	results-028	results	( D ).	`[]`	`["fig1s2d"]`
14	results-029	results	Onset of developmental and motor benchmarks for WT (N=7) and Kcnc1 -A421V/+ (N=10) mice.	`["N=7","N=10"]`	`[]`
15	results-031	results	Counts of PV-INs per unit of neocortical area were not different between WT and Kcnc1 -A421V/+ mice (P24–33), indicating that expression of A421V did not alter the density of neocortical PV-INs ( Figu…	`[]`	`["fig1s1"]`
16	results-032	results	We separately used immunohistochemistry to validate our genetic strategy for labeling PV-INs ( Figure 1—figure supplement 1 ): The average sensitivity rates were greater than 0.8 in both groups as pre…	`[]`	`["fig1s1"]`
17	results-037	results	To this end, we assessed spatial memory in juvenile Kcnc1 -A421V/+ mice in the Barnes maze task ( Figure 2A ).	`[]`	`["fig2a"]`
18	results-042	results	( A ) Example pathways for wild-type (WT) (black) and Kcnc1 -A421V/+ (green) during the 4-day acquisition phase of the Barnes maze test.	`[]`	`["fig2a"]`
19	results-048	results	( E ) Total number of arm entries.	`[]`	`["fig2e"]`
20	results-049	results	( G ) Total distance traveled.	`[]`	`["fig2g"]`
21	results-054	results	Importantly, the total number of arm entries ( Figure 2E ) and the distance traveled ( Figure 2F ) did not differ between genotypes, suggesting that the observed deficit was not due to differences in …	`[]`	`["fig2e","fig2f"]`
22	results-057	results	In our recordings of HEK cells expressing WT and A421V Kv3.1 subunits, A421V was a profound loss of function, although a small magnitude K + current was detectable (which cannot be easily distinguishe…	`[]`	`["fig3s1"]`
23	results-058	results	A 50:50 mixture of WT and A421V subunits, more approximating the clinical condition, produced K + currents that were ~42% of the magnitude and slightly shifted in the hyperpolarized direction relative…	`[]`	`["fig3s1"]`
24	results-059	results	Considering that Kv3.1 channels form heterotetramers with other Kv3 channel isoforms (likely Kv3.2) in cerebral cortex PV-INs, we also sought to clarify the impact of the A421V Kcnc1 variant on native…	`[]`	`["fig3a","fig3b","fig3c"]`
25	results-062	results	We did not observe differences in the voltage dependence ( Figure 3F ) or kinetics of activation ( Figure 3G ) when comparing voltage-gated K + channel currents from WT and Kcnc1 -A421V/+ mice.	`[]`	`["fig3f","fig3g"]`
26	results-065	results	( A ) Representative image of a cell being recorded in the outside-out nucleated macropatch configuration.	`[]`	`["fig3a"]`
27	results-066	results	( B–C ) Example family of traces of voltage-gated K + channel currents from a PV-IN from wild-type (WT) (B, black ) and Kcnc1 -A421V/+ (C, green ) mice (postnatal day [P]16–21).	`[]`	`["fig3b","fig3c"]`
28	results-067	results	( D ) Average voltage-gated K + channel current density for WT (n=13 macropatches, N=3 mice) and Kcnc1 -A421V/+ (n=17, N=3 mice).	`["n=13","N=3","n=17","N=3"]`	`["fig3d"]`
29	results-068	results	( E ) Maximum K + channel current density per PV-IN macropatch in WT and Kcnc1 -A421V/+ mice.	`[]`	`["fig3e"]`
30	results-069	results	( F ) Averaged normalized plots of K + conductance relative to voltage command indicating voltage dependence of activation curves for WT and Kcnc1 -A421V/+ mice.	`[]`	`["fig3f"]`
31	results-070	results	( G ) Average activation time constant for the voltage-gated K + channel currents relative to voltage command potential in both WT and Kcnc1 -A421V/+ mice.	`[]`	`["fig3g"]`
32	results-076	results	( A–C ) Example Kv3.1 currents in HEK cells expressing wild-type (WT) (A; black), a 50:50 mixture of WT and A421V (B; blue), and A421V ( C ; green) Kv3.1 subunits.	`[]`	`["fig3a","fig3b","fig3c"]`
33	results-078	results	( D ) Average current density for WT (black), WT+A421V (blue), and A421V (green).	`[]`	`["fig3d"]`
34	results-080	results	( E ) Average normalized conductance relative to membrane potential for WT (black), WT+A421V (blue), and A421V (green).	`[]`	`["fig3e"]`
35	results-093	results	( A ) Representative images taken at ×10 ( left ) and ×40 ( right ) magnification of a layer IV neocortical PV-IN recorded in the whole-cell configuration to characterize intrinsic excitability.	`[]`	`["fig4a"]`
36	results-094	results	( B–C ) Representative example traces for juvenile (postnatal day [P]16–21) wild-type (WT) ( B , black ) and Kcnc1 -A421V/+ ( C , green ) PV-INs generating action potentials (APs) at current injection…	`[]`	`["fig4b","fig4c"]`
37	results-096	results	( D ) Average relationship between PV-IN AP frequency in response to a range of current injections for juvenile WT (n=20 cells, N = 9 mice) and Kcnc1 -A421V/+ (n=36 cells, N = 12 mice).	`["n=20","N = 9","n=36","N = 12"]`	`["fig4d"]`
38	results-098	results	(F) Representative images for a layer IV neocortical PV-IN from an adult mouse.	`[]`	`["fig4f"]`
39	results-099	results	( G–H ) Representative example traces displaying intrinsic excitability in adult (P32–42) WT and Kcnc1 -A421V/+ PV-INs.	`[]`	`["fig4g","fig4h"]`
40	results-105	results	Figure 4—figure supplement 1. Intrinsic physiology of neocortical layer II-IV parvalbumin-positive fast-spiking GABAergic inhibitory interneurons (PV-INs) remains impaired when resting membrane potent…	`[]`	`["fig4s1"]`
41	results-106	results	( A–B ) Representative example traces showing spiking in layer V neocortical PV-INs from wild-type (WT) (A, black) and Kcnc1 -A421V/+ ( B , green) mice in response to depolarizing current injections.	`[]`	`["fig4s1a","fig4s1b"]`
42	results-107	results	( C ) Average PV-IN spiking frequency relative to current injection.	`[]`	`["fig4s1c"]`
43	results-111	results	( A ) Representative images taken at ×10 ( left ) and ×40 ( right ) magnification of a PV-positive cell in the reticular thalamus recorded in the whole-cell configuration to characterize intrinsic exc…	`[]`	`["fig4s2a"]`
44	results-112	results	( B ) Representative example traces of action potentials (APs) generated in response to current injections of varying magnitudes.	`[]`	`["fig4s2b"]`
45	results-114	results	( D ) Frequency-current relationship shows impaired intrinsic excitability in the RT PV cells relative to depolarizing current injections (0–400 pA).	`[]`	`["fig4s2d"]`
46	results-118	results	( C ) Average frequency-current relationship for WT (n=20 cells, N = 9 mice) and Kcnc1 -A421V/+ (n=32 cells, N = 12 mice) PV-INs with uncorrected resting membrane potential.	`["n=20","N = 9","n=32","N = 12"]`	`["fig4s3c"]`
47	results-134	results	We also recorded these cells in current clamp to characterize intrinsic excitability ( Figure 5H–K ).	`[]`	`["fig5h"]`
48	results-140	results	( A ) Representative image of a neocortical excitatory cell being recorded in the outside-out nucleated macropatch configuration.	`[]`	`["fig5a"]`
49	results-146	results	( H ) Representative images taken at ×10 ( left ) and ×40 ( right ) magnification of a layer IV neocortical excitatory cell recorded in the whole-cell configuration to characterize intrinsic excitabil…	`[]`	`["fig5h"]`
50	results-148	results	( K ) Average relationship between excitatory cell AP frequency in response to a range of current injections for WT (N=23 cells, N=3 mice) and Kcnc1 -A421V/+ (n=22, N=3 mice).	`["N=23","N=3","n=22","N=3"]`	`[]`
51	results-151	results	( A ) Representative images taken at ×10 ( left ) and ×40 ( right ) magnification of a recorded layer IV excitatory cell.	`[]`	`["fig5s1a"]`
52	results-152	results	( B–C ) Representative example traces of evoked action potentials (APs) in response to depolarizing current injections in cortical layer IV excitatory neurons from wild-type (WT) ( B ) and Kcnc1 -A421…	`[]`	`["fig5s1b","fig5s1c"]`
53	results-153	results	( D ) Average frequency-current relationship for WT (black; n=12, N=4) and Kcnc1 -A421V/+ (n=12, N=4) mice.	`["n=12","N=4","n=12","N=4"]`	`["fig5s1d"]`
54	results-158	results	We collected simultaneous whole-cell patch-clamp electrophysiology recordings from one neocortical layer II-IV PV-IN and one nearby (<100 μm inter-soma distance) excitatory neuron, of which 21 of 64 (…	`[]`	`["fig6a","fig6b","fig6c","fig6d","fig6e"]`
55	results-166	results	( A ) Representative images showing simultaneous whole-cell patch-clamp recordings of cortical PV-IN and nearby excitatory cell ( left , ×10 magnification; right, ×40 magnification).	`[]`	`["fig6a"]`
56	results-167	results	( B ) Example traces of a PV-IN and excitatory cell pair in which generation of action potentials (APs) in the PV-IN (bottom trace) is sufficient to induce clear unitary inhibitory postsynaptic potent…	`[]`	`["fig6b"]`
57	results-169	results	( C–D ) Example traces of unitary inhibitory postsynaptic currents (uIPSCs) in both wild-type (WT) ( C ) and Kcnc1 -A421V/+ pairs of synaptically connected neurons. 10 APs were generated in the PV-IN …	`[]`	`["fig6c","fig6d"]`
58	results-178	results	Figure 6—figure supplement 1. Excitatory neuron to parvalbumin-positive fast-spiking GABAergic inhibitory interneuron (PV-IN) unitary excitatory synaptic neurotransmission is unaltered in juvenile (po…	`[]`	`["fig6s1"]`
59	results-179	results	( A ) Example traces of simultaneous recordings of a synaptically connected PV-IN and excitatory cell neuron pair in which generation of action potentials (APs) in the excitatory cell leads to unitary…	`[]`	`["fig6s1a"]`
60	results-181	results	( B–C ) Representative example traces of unitary excitatory postsynaptic currents (uEPSCs) generated in wild-type (WT) ( B ) and Kcnc1 -A421V/+ pairs of excitatory cells (top trace) and nearby PV-INs …	`[]`	`["fig6s1b","fig6s1c"]`
61	results-184	results	( E ) Average failure rate for WT and Kcnc1 -A421V/+ neuron pairs relative to presynaptic stimulation frequency.	`[]`	`["fig6s1e"]`
62	results-185	results	( F ) Average uEPSC magnitude in response to a train of five APs generated at 20 Hz in WT and Kcnc1 -A421V/+ neuron pairs.	`[]`	`["fig6s1f"]`
63	results-186	results	( G ) Paired-pulse ratio of the second uEPSC to the first uEPSC in WT and Kcnc1 -A421V/+ mice.	`[]`	`["fig6s1g"]`
64	results-187	results	(H) Average synaptic latency between peak of AP to peak of uEPSC in both WT and Kcnc1 -A421V/+ mice.	`[]`	`["fig6s1h"]`
65	results-188	results	In 9 of 61 neuron (14.8%) pairs for WT mice and 6 of 43 pairs (14.0%) for Kcnc1 -A421V/+ mice at P16–21, we observed unitary excitatory synaptic currents (uEPSCs) from the excitatory neuron onto the P…	`[]`	`["fig6s1"]`
66	results-189	results	The frequency-dependent rate of failure showed no significant effect for genotype ( Figure 6—figure supplement 1E ).	`[]`	`["fig6s1"]`
67	results-190	results	Lastly, the magnitude ( Figure 6—figure supplement 1F ), paired-pulse ratio ( Figure 6—figure supplement 1G ), and the latency ( Figure 6—figure supplement 1H ) of the uEPSCs were not significantly di…	`[]`	`["fig6s1"]`
68	results-192	results	As in the younger mice, we recorded pairs of cortical PV-IN and excitatory neurons that were synaptically connected – 14 of 36 pairs (38.9%) in WT mice (N = 8 mice) and 13 of 36 pairs (36.1%) in Kcnc1…	`["N = 8","N=8"]`	`["fig7a","fig7b","fig7c","fig7d"]`
69	results-193	results	We did not detect differences in failure rates between WT and Kcnc1 -A421V/+ mice over a range of stimulation frequencies ( Figure 7E ).	`[]`	`["fig7e"]`
70	results-199	results	( A ) Example presynaptic cortical PV-IN and postsynaptic excitatory neuron.	`[]`	`["fig7a"]`
71	results-201	results	( B–C ) Example traces of unitary inhibitory postsynaptic currents (uIPSCs) in both adult wild-type (WT) ( B ) and Kcnc1 -A421V/+ ( C ) pairs of synaptically connected neurons. 10 APs were generated i…	`[]`	`["fig7b","fig7c"]`
72	results-202	results	( D ) Connection probability between WT (14 of 36, N=8 mice) and Kcnc1 -A421V/+ (13 of 36, N=8 mice) pairs PV-INs and nearby excitatory cells.	`["N=8","N=8"]`	`["fig7d"]`
73	results-203	results	( E ) Average frequency-dependent rate of failure for the first five APs in adult WT and Kcnc1 -A421V/+ neuron pairs.	`[]`	`["fig7e"]`
74	results-208	results	Two-photon in vivo calcium imaging reveals paroxysmal hypersynchronous discharges and altered neuronal excitability in Kcnc1 -A421V/+ mice We then utilized two-photon (2P) calcium imaging to investiga…	`[]`	`["fig8a"]`
75	results-213	results	( A ) Experimental setup for in vivo 2P calcium imaging with representative calcium transients from cells expressing AAV-hSyn-GCaMP8m and mean dF/F 0 of the whole field of view (FOV) aligned to locomo…	`[]`	`["fig8a"]`
76	results-218	results	( E ) Experimental design for in vivo 2P calcium imaging of somata positive (PV+) and negative (PV–) for parvalbumin.	`[]`	`["fig8e"]`
77	results-219	results	( F ) Example calcium transients of PV+ (bottom) and PV– (top) somata aligned to locomotion speed in a WT (left) and Kcnc1 -A421V mouse (right).	`[]`	`["fig8f"]`
78	results-224	results	Figure 8—figure supplement 1. Analysis of in vivo two-photon calcium imaging data.	`[]`	`["fig8s1"]`
79	results-225	results	( A ) PV– (wild-type [WT], n=847 cells, N=4 mice; Kcnc1 -A421V, n=901 cells, N=3 mice) and ( B ) PV+ cells (WT, n=65 cells; Kcnc1 -A421V, n=60 cells).	`["n=847","N=4","n=901","N=3","n=65","n=60"]`	`["fig8s1a","fig8s1b"]`
80	results-227	results	( E–F ) Mean transient height in ( E ) PV– and ( F ) PV+ cells.	`[]`	`["fig8s1e","fig8s1f"]`
81	results-231	results	( G–H ) Boxplot of percent of active ( G ) PV– and ( H ) PV+ cells for each mouse.	`[]`	`["fig8s1g","fig8s1h"]`
82	results-236	results	Of note, this held true even if only cells that displayed at least one transient throughout the recording were included in the analysis ( Figure 8—figure supplement 1A and B ).	`[]`	`["fig8s1"]`
83	results-240	results	These decreases in the frequency of PV– cell transients and the height of PV+ cell transients were not seen during epochs where the mouse was running ( Figure 8—figure supplement 1C–F ).	`[]`	`["fig8s1"]`
84	results-241	results	We also observed no differences in the overall percentage of cells that were active in Kcnc1 -A421V/+ relative to WT mice ( Figure 8—figure supplement 1G and H ).	`[]`	`["fig8s1"]`
85	results-255	results	Recordings in wild-type (WT) (N = 4) control mice did not show epileptic seizures or runs of spikes.	`["N = 4"]`	`[]`
86	captions-008	captions	[panels detected: a, b, c, d, e] === Figure 1s1 === Figure 1—figure supplement 1. Pvalb-tdTomato reporter effectively labels parvalbumin-positive fast-spiking GABAergic inhibitory interneurons (PV-INs…	`[]`	`["fig1s1"]`
87	captions-013	captions	( B ) Counts of PV cells per unit area (mm 2 ) are not different between WT and Kcnc1 -A421V/+ mice (N=3 mice/genotype).	`["N=3"]`	`[]`
88	captions-020	captions	Onset of developmental and motor benchmarks for WT (N=7) and Kcnc1 -A421V/+ (N=10) mice.	`["N=7","N=10"]`	`[]`
89	captions-025	captions	( B ) Average escape latency during the acquisition phase for WT (black; N=15) and Kcnc1 -A421V/+ (green; N=13) mice.	`["N=15","N=13"]`	`[]`
90	captions-027	captions	(D–F) Group data for WT (black; N=16) and Kcnc1 -A421V/+ mice (green; N=15) during the Y-maze test for spatial working memory.	`["N=16","N=15"]`	`[]`
91	captions-035	captions	( D ) Average voltage-gated K + channel current density for WT (n=13 macropatches, N=3 mice) and Kcnc1 -A421V/+ (n=17, N=3 mice).	`["n=13","N=3","n=17","N=3"]`	`[]`
92	captions-054	captions	( D ) Average relationship between PV-IN AP frequency in response to a range of current injections for juvenile WT (n=20 cells, N = 9 mice) and Kcnc1 -A421V/+ (n=36 cells, N = 12 mice).	`["n=20","N = 9","n=36","N = 12"]`	`[]`
93	captions-063	captions	[panels detected: a, b, c, d, e, f, g, h, i, j] === Figure 4s1 === Figure 4—figure supplement 1. Intrinsic physiology of neocortical layer II-IV parvalbumin-positive fast-spiking GABAergic inhibitory …	`[]`	`["fig4s1"]`
94	captions-076	captions	( C ) Average frequency-current relationship for WT (n=20 cells, N = 9 mice) and Kcnc1 -A421V/+ (n=32 cells, N = 12 mice) PV-INs with uncorrected resting membrane potential.	`["n=20","N = 9","n=32","N = 12"]`	`[]`
95	captions-081	captions	( D ) Average voltage-gated K + channel current density for WT (n=8 macropatches, N=3 mice) and Kcnc1 -A421V/+ (n=10, N=3 mice) relative to membrane potential.	`["n=8","N=3","n=10","N=3"]`	`[]`
96	captions-087	captions	( K ) Average relationship between excitatory cell AP frequency in response to a range of current injections for WT (N=23 cells, N=3 mice) and Kcnc1 -A421V/+ (n=22, N=3 mice).	`["N=23","N=3","n=22","N=3"]`	`[]`
97	captions-092	captions	( D ) Average frequency-current relationship for WT (black; n=12, N=4) and Kcnc1 -A421V/+ (n=12, N=4) mice.	`["n=12","N=4","n=12","N=4"]`	`[]`
98	captions-107	captions	[panels detected: a, b, c, d, e, f, g, h, i, j, k, l] === Figure 6s1 === Figure 6—figure supplement 1. Excitatory neuron to parvalbumin-positive fast-spiking GABAergic inhibitory interneuron (PV-IN) u…	`[]`	`["fig6s1"]`
99	captions-121	captions	( D ) Connection probability between WT (14 of 36, N=8 mice) and Kcnc1 -A421V/+ (13 of 36, N=8 mice) pairs PV-INs and nearby excitatory cells.	`["N=8","N=8"]`	`[]`
100	captions-139	captions	[panels detected: a, b, c, d, e, f, g, h, i, j] === Figure 8s1 === Figure 8—figure supplement 1. Analysis of in vivo two-photon calcium imaging data.	`[]`	`["fig8s1"]`
101	captions-140	captions	( A ) PV– (wild-type [WT], n=847 cells, N=4 mice; Kcnc1 -A421V, n=901 cells, N=3 mice) and ( B ) PV+ cells (WT, n=65 cells; Kcnc1 -A421V, n=60 cells).	`["n=847","N=4","n=901","N=3","n=65","n=60"]`	`[]`
102	captions-151	captions	( C ) Raster plot indicating nonfatal seizures (blue bars), seizure-induced sudden death (red bars), interictal runs of spikes (green bars) without clear behavior manifestation, and periods of repetit…	`["N=12"]`	`[]`
103	captions-152	captions	Recordings in wild-type (WT) (N = 4) control mice did not show epileptic seizures or runs of spikes.	`["N = 4"]`	`[]`

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coverage/wengert-2026-kcnc1.json

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

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

ran via scripts/pipeline.py

cd extract && python3 -m elife_extract.cli coverage --paper wengert-2026-kcnc1 --json ../coverage/wengert-2026-kcnc1.json
v4 · 2026-09-12 · scripts/pipeline.py run

re-run after prepare v2

cd extract && python3 -m elife_extract.cli coverage --paper wengert-2026-kcnc1 --json ../coverage/wengert-2026-kcnc1.json
v3 · 2026-09-11 · scripts/pipeline.py run

re-run to record input-set membership

cd extract && python3 -m elife_extract.cli coverage --paper wengert-2026-kcnc1 --json ../coverage/wengert-2026-kcnc1.json
v2 · 2026-09-11 · scripts/pipeline.py run

re-run to record input-set membership

cd extract && python3 -m elife_extract.cli coverage --paper wengert-2026-kcnc1 --json ../coverage/wengert-2026-kcnc1.json
v1 · 2026-09-11 · scripts/pipeline.py run

coverage for the nine papers that had none

cd extract && python3 -m elife_extract.cli coverage --paper wengert-2026-kcnc1 --json ../coverage/wengert-2026-kcnc1.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

Paper	State	Version	Last run	Output	Cell
A three-dimensional immunofluorescence atlas of the …ran via scripts/pipeline.py	blocked upstream	v3	2026-09-13	artiushin-2026-spider-atlas.json	json
Distinct representational properties of cues and con…ran via scripts/pipeline.py	stale	v4	2026-09-13	bouyeure-2026-fear-rsa.json	json
Computational modelling identifies key determinants …ran via scripts/pipeline.py	stale	v3	2026-09-13	ejdrup-2026-dopamine.json	json
Contributions of insula and superior temporal sulcus…rebuild after edge completion pass	stale	v7	2026-09-13	gadeke-2026-guilt-insula.json	json
Spatially targeted inhibitory rhythms differentially…ran via scripts/pipeline.py	stale	v3	2026-09-13	headley-2026-inhibitory-rhythms.json	json
Feedback of peripheral saccade targets to early fove…ran via scripts/pipeline.py	blocked upstream	v3	2026-09-13	kammer-2026-foveal-feedback.json	json
iGABASnFR2 is an improved genetically encoded protei…ran via scripts/pipeline.py	blocked upstream	v5	2026-09-13	kolb-2026-igabasnfr2.json	json
A deep learning pipeline for mapping in situ network…ran via scripts/pipeline.py	blocked upstream	v5	2026-09-13	rozak-2026-neurovascular-dl.json	json
Self-association enhances early attentional selectio…ran via scripts/pipeline.py	stale	v3	2026-09-13	scheller-2026-self-prioritization.json	json
Impaired excitability of fast-spiking neurons in a n…ran via scripts/pipeline.py	stale	v5	2026-09-13	wengert-2026-kcnc1.json	json

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.