phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | multisite optogenetic control of neurons in freely moving animals— “Neuronal control with high temporal precision is possible with optogenetics, yet currently available methods do not enable to control independently multiple locations in the brains of freely moving animals.” | |
| claim-type | method— “Here, we describe a diode-probe system that allows real-time and location-specific control of neuronal activity at multiple sites.” | |
| method — evidence | — “Here, we describe how an array of lightweight diodes is coupled to optical fibers.” | |
| object of study — evidence | — “Neuronal control with high temporal precision is possible with optogenetics, yet currently available methods do not enable to control independently multiple locations in the brains of freely moving animals. Here, we describe a diode-probe system that allows real-time and location-specific control of neuronal activity at multiple sites.” | |
| research question — evidence | — “Since such electrodes can only record and disambiguate spikes of nearby (up to 60 μm) neurons ( Buzsáki 2004 ), stimulation of continuously monitored cells requires placing the light source very close to the recording site. However, stimulation through light sources placed on the surface of the brain ( Huber et al. 2008 ) or large fibers… | |
| contribution — evidence | — “Neuronal control with high temporal precision is possible with optogenetics, yet currently available methods do not enable to control independently multiple locations in the brains of freely moving animals. Here, we describe a diode-probe system that allows real-time and location-specific control of neuronal activity at multiple sites.” | |
| transfer | from optical engineering / fiber photonics: for a uniform planar (Lambertian) light source and a straight cleaved optical fiber having a numerical aperture, the maximum coupling efficiency of Hudson 1974— “For a uniform planar (Lambertian) light source of area A s and a straight (cleaved) optical fiber of cross-sectional area A f having a numerical aperture NA in , the maximum coupling efficiency is ( Hudson 1974 )” | transfers[0] |
| transfer | from fiber optics: reflective losses, quantified by the Fresnel equations at each interface, and skew rays - two factors with opposing practical implications, both ignored in the standard coupling formula— “Two factors, which have opposing practical implications, were ignored in the foregoing: 1 ) reflective losses; and 2 ) skew rays. Since there are inevitable differences between the RIs of the source, coupling medium, and fiber core, there is attenuation due to reflection at each interface. This is quantified by the Fresnel equations; for… | transfers[1] |
| transfer | from tissue optics: a 1/d scattering model fitted to power measured through a block of brain, giving a scattering coefficient per wavelength— “The mean (± SE) scattering coefficients depended on wavelength and were ( Fig. 3 A , bottom left ): blue light, 7.18 ± 0.17; orange, 4.37 ± 0.15; and red, 3.44 ± 0.05. For blue light, the current value is smaller than previously reported values (10.3 for the rat brain; Aravanis et al. 2007 ). The mismatch could be explained by the slightly… | transfers[2] |
| transfer | from solid-state lighting: red laser diodes driven by similar currents, yielding light at the fiber tip that subtended a similar illuminated volume of brain tissue— “The volume of the illuminated brain tissue [at an intensity of >1 mW/mm 2 , the documented threshold for stimulating channelrhodopsin2 (ChR2); Aravanis et al. 2007 ; Boyden et al. 2005 ] was ∼0.001 mm 3 , formed by a truncated cone with 180-μm height and 150-μm base diameter ( Figs. 1 B and 3 ). Red laser diodes driven by similar currents… | transfers[3] |
| transfer | from microelectromechanical systems: waveguides embedded in the probe shank, named as the route to scaling the number of sources— “Because the diode-probe arrays require only electrical connections, they can be used wirelessly ( Wentz et al. 2011 ), enabling recording and stimulation experiments with, for instance, freely moving birds and/or long-term naturalistic experiments with larger animals while permitting precise, large-scale, spatiotemporal control of neuronal… | transfers[4] |
| transfer | from control engineering: closed-loop triggering - the recorded signal decides when the stimulus happens— “To demonstrate physiological closed-loop control in a freely moving animal, we used the activity of a well-isolated neuron recorded on one shank of a diode probe implanted in the CA1 pyramidal layer to trigger optical stimulation on multiple other shanks ( Fig. 7 A ). Comparison of the cross-correlation histograms during illumination ( Fig. 7… | transfers[5] |
| mechanism | Putting the fiber tip within tens of μm of the recording sites means very little light is needed, which in turn removes the need for high currents and lets the device avoid heat sinks, optical artifacts and spike superposition while confining the effect to the monitored neurons— “This enables driving small diodes with low currents, avoiding bulky heat sinks and collimating optics, preventing optical artifacts and spike superposition, and limiting the spatial extent of the photostimulus effect to a relatively small number of neurons, which are concurrently monitored by the extracellular electrodes.” | mechanisms[0] |
| mechanism | An index-matched glue at the diode–fiber interface cuts Fresnel reflection losses and widens the fiber's acceptance angle for skew rays, which is why coupled power doubles— “Since the refractive index (RI) of the glue is higher than air (1.56–1.57), the drop of glue reduced Fresnel losses and approximately doubled the acceptance angle of the fiber to skew rays” | mechanisms[1] |
| mechanism | Red-light-driven halorhodopsin hyperpolarisation of the membrane delays the ChR2-evoked spike, which is why latencies lengthen when activation and silencing are applied together— “albeit with a longer latency supposedly due to the red light-induced hyperpolarization of the membrane” | mechanisms[2] |
| mechanism | The unusually high fraction of responsive units follows from the high AAV transduction rate combined with the very short distance between fiber tip and recording sites— “This relatively high fraction of light-modulated units may be due to the high ChR2 transduction rates typically obtained with AAV vehicles” | mechanisms[3] |
| mechanism | the light is weak and the fiber tip is close, so the illuminated volume is about 0.001 mm 3 - the cells the light reaches are the cells the shank can hear— “The volume of the illuminated brain tissue [at an intensity of >1 mW/mm 2 , the documented threshold for stimulating channelrhodopsin2 (ChR2); Aravanis et al. 2007 ; Boyden et al. 2005 ] was ∼0.001 mm 3 , formed by a truncated cone with 180-μm height and 150-μm base diameter ( Figs. 1 B and 3 ). Red laser diodes driven by similar currents… | mechanisms[4] |
| mechanism | a drop of index-matching glue at the diode-fiber interface, which cuts the reflective losses at each interface from 8% to under 1%— “Using a coupling interface with an index similar to the indices of the source and fiber ( n in ≈ n source ≈ n core ; e.g., NOA-61, Norland Products; RI of 1.56/1.57 for red/blue light) reduces these reflective losses considerably (to <1%) but at a cost of reducing the effective acceptance angle γ of the fiber by a factor of (1/1.57) 2 =… | mechanisms[5] |
| mechanism | and the same glue admits skew rays from all directions, which is where the doubling in coupling efficiency actually comes from— “θ Is typically much larger than γ (for the above fiber, the values are 12.7 and 43.6°), and thus a considerable part of noncollimated light accepted into a multimode fiber is from nonmeridional rays ( Colvin 1974 ). Although not all rays falling within the θ cone will be transmitted (the exact fraction exhibits a complex dependency on γ, n 0… | mechanisms[6] |
| mechanism | with the light path perpendicular to the recording sites and the power several orders of magnitude below laser stimulation, so there are no local field potential artifacts to interpret— “The weak (<40 μW) light stimulus did not result in local field potential (LFP) artifacts ( Figs. 5 B , 6 A , 7 A , and 8 A ) as often seen when light power several orders of magnitude higher is used (1–10 mW; Cardin et al. 2010 ; Han et al. 2009 ; Kravitz et al. 2010 ).” | mechanisms[7] |
| extends | Royer et al. 2010 (small-core fibers coupled to DPSS lasers at low power)— “These issues were previously addressed in part by coupling small-core fibers to DPSS lasers driven at low power ( Royer et al. 2010 ), but since the number of fibers a freely moving animal can be tethered to is limited (1–2 for small rodents), the range of scientific questions that could be addressed was restricted.” | claim_relations[0] |
| contradicts | Aravanis et al. 2007 (published blue-light scattering coefficient for rat brain)— “For blue light, the current value is smaller than previously reported values (10.3 for the rat brain; Aravanis et al. 2007 ).” | claim_relations[1] |
| builds-on | Fujisawa et al. 2008 (probe implantation methods)— “Probes were implanted following previously described methods ( Fujisawa et al. 2008 ).” | claim_relations[2] |
| contradicts | the previously reported blue-light scattering coefficient for rat brain, 10.3, against 7.18 measured here— “The mean (± SE) scattering coefficients depended on wavelength and were ( Fig. 3 A , bottom left ): blue light, 7.18 ± 0.17; orange, 4.37 ± 0.15; and red, 3.44 ± 0.05. For blue light, the current value is smaller than previously reported values (10.3 for the rat brain; Aravanis et al. 2007 ). The mismatch could be explained by the slightly… | claim_relations[3] |
| critiques | stimulation from the brain surface or from large fibers hundreds of μm away, which activates far more neurons than are monitored— “Since such electrodes can only record and disambiguate spikes of nearby (up to 60 μm) neurons ( Buzsáki 2004 ), stimulation of continuously monitored cells requires placing the light source very close to the recording site. However, stimulation through light sources placed on the surface of the brain ( Huber et al. 2008 ) or large fibers… | claim_relations[4] |
| critiques | large-core fibers driven by strong light sources, which add heat, photoelectrical artifacts and synchronous activation— “Second, strong light of any wavelength carries considerable energy that is dissipated in the form of heat as photons are scattered and absorbed in brain tissue. Local heating has a mixed de-/hyperpolarizing effect on neuronal activity ( Shen and Schwartzkroin 1988 ; Thompson et al. 1985 ), which may confound and/or limit the effect of… | claim_relations[5] |
| distinguishes-from | small-core fibers coupled to lasers at low power, which solved the artifact problem but not the tether limit of one to two fibers— “These issues were previously addressed in part by coupling small-core fibers to DPSS lasers driven at low power ( Royer et al. 2010 ), but since the number of… | claim_relations[6] |
| supports | coincidence between the illuminated volume and the volume a silicon probe shank can monitor, as the condition for separating direct from population-mediated effects | claim_relations[7] |
| predicts | that MEMS integration of diode dies with waveguides in the shank will scale up the number of light sources Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[8] |
| qualifies | its own central advantage, which is a limitation whenever the question needs an entire structure driven at once Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[9] |
| sense | THE PAPER'S HEADLINE ADVANTAGE, RE-TAGGED AS A LIMITATION BY ITS OWN AUTHORS: for some applications the use of SPATIALLY RESTRICTED PHOTOSTIMULATION for localized neuronal control IS ACTUALLY A LIMITATION - where synchronous control of an entire structure is wanted, the spatial extent should be two to three ORDERS OF MAGNITUDE HIGHER than the 0.001 mm 3 that can be monitored Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[0] |
| sense | and the resolution is not a better setting but a different question - THE SPECIFIC LIGHT SOURCES AND FIBERS SHOULD BE TAILORED TO THE SCIENTIFIC QUESTION AT HAND Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[1] |
| sense | ONE INTERVENTION, TWO COMPONENTS, OPPOSITE SIGNS: the index-matching glue reduces reflective losses considerably, to under 1%, BUT AT A COST OF REDUCING the effective acceptance angle of the fiber BY 41% Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[2] |
| sense | the same glue on the other component: its effect on the SKEW RAYS acceptance angle is DIAMETRICALLY OPPOSITE from its effect on the meridional one, enabling acceptance from all directions and A TWOFOLD INCREASE in coupling efficiency - the net sign is empirical, not derivable Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[3] |
| sense | with the two ignored factors named as ignored: TWO FACTORS, WHICH HAVE OPPOSING PRACTICAL IMPLICATIONS, WERE IGNORED IN THE FOREGOING - reflective losses, and skew rays Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[4] |
| sense | A MEASURED CONSTANT THAT DISAGREES WITH THE PUBLISHED ONE, AND THE DISAGREEMENT DECLARED NOT TO MATTER: blue-light scattering 7.18 against a previously reported 10.3 for rat brain, explained by the slightly different testing conditions - and IN ANY EVENT estimates were SIMILAR REGARDLESS OF THE PRECISE NUMBER USED Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[5] |
| sense | the model's own failure stated with its range: it CONSISTENTLY OVERESTIMATED power beyond 1 mm while fitting well below it, and scattering was 5 to 10% higher in nonfresh tissue Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[6] |
| sense | and the empirical map declared a proxy: THIS IS ONLY A PROXY to the real geometric distribution of light in the brain, since scattering may contribute, ESPECIALLY AT SHORT WAVELENGTHS Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[7] |
| sense | WHY THE LIGHT HAS TO BE WEAK AND CLOSE: electrodes can only disambiguate spikes of neurons up to 60 μm away, so stimulating from the surface or from a fiber a few hundred μm off INEVITABLY ACTIVATES MANY MORE UNMONITORED NEURONS THAN ARE BEING MONITORED, MAKING THE SEPARATION BETWEEN DIRECT AND POPULATION-MEDIATED EFFECTS IMPOSSIBLE Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[8] |
| sense | and strong light of ANY wavelength carries energy dissipated as HEAT, which has a MIXED DE-/HYPERPOLARIZING effect - a confound that does not depend on the opsin at all Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[9] |
| sense | THE SAME LIGHT, THE OPPOSITE SIGN, DECIDED BY THE PROMOTER: identical parameters in CA1 give robust spiking of pyramidal cells in CaMKII::ChR2 mice, and in PV::ChR2 mice spiking of interneurons FOLLOWED BY SILENCING of the nearby pyramidal cells Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[10] |
| sense | A 25% CHANGE IN DOSE FLIPS THE OUTCOME: 70% of the 0.35 mW/mm 2 blue pulses overcame the red-light hyperpolarization but ONLY 10% of the 0.28 mW/mm 2 pulses did - the same two opsins, the same cells, and a sharp threshold between activation and silencing Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[11] |
| sense | a statistical definition rescued by the data's own shape: the definition of light-modulated spiking WAS STATISTICAL, but the modulation indices exhibited a BIMODAL distribution, 0.045 against 0.76 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[12] |
| sense | with the fraction itself hedged - the relatively high fraction MAY BE DUE TO high transduction rates and the proximity of the fiber tip Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[13] |
| sense | THE UNIT IS DEFINED BY THREE NUMBERED GATES BEFORE ANY RESULT IS COMPUTED: peak-to-peak amplitude above 50 microvolts, L ratio below 0.05, and a clear refractory period - and then a fourth for the statistics, at least 100 spikes above 0.01 spikes/s Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[14] |
| sense | an idealisation declared inside a figure legend: the estimate ASSUMES neuronal density of 20,000 cells/mm 3 and IGNORES SHADOWING by the probe shank Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[15] |
| sense | the temporal resolution stated as three numbers that mean different things - center-of-mass 12 ms, latency 5.5 ms, and precision, the across-trial SD, 2 ms Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[16] |
| sense | AND THE INSTRUMENT'S PURPOSE IS A DEBATE: spatiotemporally sequenced activity at different timescales COULD ADDRESS THE DEBATE ON RATE VS. TEMPORAL CODING - the same debate Levi2022 would later call rooted in definitions Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[17] |
| sense | and the synthetic pattern is taken up by the native one: units driven by nonperiodic photostimuli exhibited PHASE PRECESSION, indicating that NATIVE NETWORK DYNAMICS CAN INCORPORATE SYNTHETIC PATTERNS OF ACTIVITY Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[18] |
| sense | with the constraint that motivated the whole device stated as a number: the number of fibers a freely moving animal can be tethered to is ONE TO TWO for small rodents, and that RESTRICTED THE RANGE OF SCIENTIFIC QUESTIONS THAT COULD BE ADDRESSED Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[19] |
| control | spike waveforms during light compared with waveforms during spontaneous activity — held — rules out the light distorting or superimposing the spikes it evokes - median waveform consistencies 0.977 against 0.983, U test P = 0.19 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[0] |
| control | units recorded on the shanks that were NOT illuminated, 200 μm and further away — held — rules out the effect spreading beyond the illuminated shank - 52% modulated on the lit shank against 6.8% nearby, at chance level by an exact binomial test Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[1] |
| control | the same cross-correlation histograms computed over a duration-matched baseline period before any stimulation — partial — rules out the correlations being native rather than induced - the baseline histograms were nearly flat WITH AN EXCEPTION, a 1-ms lag between the units on shanks 4 and 3 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[2] |
| control | the wideband traces inspected for photoelectrical artifacts at the light powers actually used — held — rules out light artifacts masquerading as physiology - the weak stimulus produced no LFP artifacts, unlike powers three orders of magnitude higher Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[3] |
| control | the scattering fit repeated across tip morphology, source power and brain region — partial — rules out the attenuation constant depending on how it was measured - it did not, EXCEPT that scattering was 5 to 10% higher in nonfresh tissue and the model overestimates beyond 1 mm Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[4] |
| differs in | the previously reported blue-light scattering coefficient for rat brain, 10.3, against 7.18 measured here — light was shined through brain slices in the previous measurements, which causes reflective losses Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[3] |
| differs in | stimulation from the brain surface or from large fibers hundreds of μm away, which activates far more neurons than are monitored — THE AXIS IS THE MISMATCH BETWEEN THE RECORDED AND THE ILLUMINATED VOLUME. 'such electrodes can only record and disambiguate spikes of nearby (UP TO 60 UM) NEURONS, [so] stimulation of continuously monitored cells requires placing the light source very close to the recording site.' The recording radius is given as a number and the stimulated volume is larger - so a causal claim from optogenetics rests on cells that were driven and never observed. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[4] |
| differs in | large-core fibers driven by strong light sources, which add heat, photoelectrical artifacts and synchronous activation — THE AXIS IS HEAT AS A CONFOUND OF THE LIGHT ITSELF. 'strong light of any wavelength carries considerable energy that is dissipated in the form of heat as photons are scattered and absorbed in brain tissue. Local heating has a mixed de-/hyperpolarizing effect on neuronal activity.' The control for an optogenetic manipulation is light, and light is not inert - the confound is a property of the energy delivered, so it is present in every experiment of this kind at sufficient power. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[5] |
| differs in | small-core fibers coupled to lasers at low power, which solved the artifact problem but not the tether limit of one to two fibers — THE AXIS IS THE TETHER LIMIT, GIVEN AS A NUMBER. 'THESE ISSUES WERE PREVIOUSLY ADDRESSED IN PART BY COUPLING SMALL-CORE FIBERS TO DPSS LASERS DRIVEN AT LOW POWER, BUT SINCE THE NUMBER OF FIBERS A freely moving animal can be tethered to is limited (1-2 FOR SMALL RODENTS), the range of scientific questions that could be addressed was restricted.' The earlier solution is credited with fixing the artifact and charged with a different limit - so the two are not better and worse, they fail at different points. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[6] |
| differs in | its own central advantage, which is a limitation whenever the question needs an entire structure driven at once — THE AXIS IS WHETHER THE QUESTION NEEDS A WHOLE STRUCTURE DRIVEN AT ONCE. 'For some applications, the use of spatially restricted photostimulation for localized neuronal control is actually a limitation. For instance, in experiments requiring synchronous control of an entire structure.' The paper's own headline advantage is a defect for a class of question, said by the authors - so 'higher spatial precision' is not an improvement, it is a trade whose sign depends on the experiment. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[9] |
| audit | photostimulation —is-a→ limitation — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the span calls spatially restricted photostimulation a limitation for some uses; is-a is loose. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[3] |
| note | photostimulation —is-a→ limitation — THE HEADLINE ADVANTAGE RE-TAGGED AS A LIMITATION BY ITS OWN AUTHORS - spatially restricted photostimulation IS ACTUALLY A LIMITATION for experiments requiring synchronous control of an entire structure Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[3] |
| audit | fiber —causes→ volume — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but multiple fibers can illuminate a large volume; causes is loose. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[5] |
| note | fiber —causes→ volume — and the choice is not a better setting but a different question - THE SPECIFIC LIGHT SOURCES AND FIBERS SHOULD BE TAILORED TO THE SCIENTIFIC QUESTION AT HAND Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[5] |
| audit | reflective losses —causes→ coupling — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but reflective losses and skew rays have opposing implications for coupling; causes is loose and unsigned. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[6] |
| note | reflective losses —causes→ coupling — TWO FACTORS, WHICH HAVE OPPOSING PRACTICAL IMPLICATIONS, WERE IGNORED IN THE FOREGOING - reflective losses, quantified by the Fresnel equations at 8%, and skew rays Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[6] |
| audit | skew rays —causes→ coupling — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but reflective losses and skew rays have opposing implications for coupling; causes is loose and unsigned. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[7] |
| audit | index —causes→ reflective losses — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but a matched coupling index reduces reflective losses; the edge carries no direction. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[8] |
| audit | index —causes→ acceptance angle — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the span relates the coupling index to the acceptance angle; causes is loose. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[9] |
| note | index —causes→ acceptance angle — ONE INTERVENTION, OPPOSITE SIGNS - the glue reduces reflective losses to under 1% BUT AT A COST OF REDUCING the effective acceptance angle BY 41% Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[9] |
| audit | skew rays —contrasted-with→ meridional — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but skew rays versus meridional rays; contrasted-with is implied. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[11] |
| audit | light —causes→ artifact — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the span discusses artifacts from light near electrodes; causes is loose. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[15] |
| note | light —causes→ artifact — the high intensity used for deep neurons may generate superposition of multiple spike waveforms and CONSIDERABLE LIGHT ARTIFACTS Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[15] |
| note | light —causes→ heat — strong light OF ANY WAVELENGTH carries considerable energy dissipated as heat - a confound that does not depend on the opsin Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[18] |
| audit | heat —causes→ neuron — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but local heating can affect neurons; causes is loose. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[19] |
| note | heat —causes→ neuron — local heating has a MIXED DE-/HYPERPOLARIZING effect, which may confound and/or limit the effect of the optogenetic manipulation itself Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[19] |
| audit | photostimulation —causes→ rate — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but light modulation indices compare firing during photostimulation with baseline; causes 'rate' is terse. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[29] |
| note | photostimulation —causes→ rate — a statistical definition rescued by the data's own shape - the definition WAS STATISTICAL, but the indices were BIMODAL, 0.045 against 0.76 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[29] |
| audit | interneuron —causes→ pyramidal — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but PV-driven interneurons silenced nearby pyramidal cells; causes 'pyramidal' drops the silencing. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[33] |
| note | interneuron —causes→ pyramidal — THE SAME LIGHT, THE OPPOSITE SIGN, DECIDED BY THE PROMOTER - identical parameters give pyramidal spiking in CaMKII::ChR2 and, in PV::ChR2, interneuron spiking FOLLOWED BY SILENCING of nearby pyramidal cells Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[33] |
| audit | rate —contrasted-with→ temporal coding — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span names the 'debate on rate vs. temporal coding'; contrasted-with is attributed. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[40] |
| note | rate —contrasted-with→ temporal coding — THE INSTRUMENT'S PURPOSE IS A DEBATE - the same debate Levi2022 would later call ROOTED IN DEFINITIONS Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[40] |
| audit | diode —part-of→ silicon probe — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but MEMS 'can be used to' integrate diode dies with a silicon probe's shanks; part-of is prospective. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[41] |
| note | diode —part-of→ silicon probe — and the stated next step is to stop gluing - MEMS integration of diode dies with waveguides embedded IN the shanks Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[41] |
| outcome (stated by the tagger, no quotation) | control — held | controls[0] |
| outcome (stated by the tagger, no quotation) | control — held | controls[1] |
| outcome (stated by the tagger, no quotation) | control — partial | controls[2] |
| outcome (stated by the tagger, no quotation) | control — held | controls[3] |
| outcome (stated by the tagger, no quotation) | control — partial | controls[4] |
| for which use | limitation — the confinement that is the method's selling point: FOR SOME APPLICATIONS, THE USE OF SPATIALLY RESTRICTED PHOTOSTIMULATION FOR LOCALIZED NEURONAL CONTROL IS ACTUALLY A LIMITATION - an advantage for one use and a defect for another Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[0] |
| for which use | limitation — every light-intensity figure beyond 1 mm from the tip: THE MODEL CONSISTENTLY OVERESTIMATED POWER AT DISTANCES >1 MM, while POWER AT SHORTER DISTANCES WAS WELL-APPROXIMATED Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[1] |
| for which use | limitation — the measured light cone: THIS IS ONLY A PROXY TO THE REAL GEOMETRIC DISTRIBUTION OF LIGHT IN THE BRAIN SINCE SCATTERING MAY CONTRIBUTE ... ESPECIALLY AT SHORT WAVELENGTHS Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[2] |
| for which use | limitation — experiments requiring synchronous control of an entire structure, where the spatial extent should be two to three orders of magnitude higher than the 0.001 mm 3 a shank can monitor Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[3] |
| for which use | limitation — the same scope as limitations[1], plus the tissue caveat: SCATTERING WAS SLIGHTLY HIGHER (5-10%) IN NONFRESH TISSUE Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[4] |
| duplicate of | limitation — limitations[2] Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[5] |
| for which use | limitation — the same scope as limitations[2] - the fluorescein image stands in for the real distribution Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[5] |
| for which use | limitation — the fraction of units reported as light-modulated: it MAY BE DUE TO THE HIGH ChR2 TRANSDUCTION RATES ... AND THE PROXIMITY OF THE FIBER TIP TO THE RECORDING SITES Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[6] |
| for which use | limitation — the count of illuminated cells: THE ESTIMATION ... ASSUMES NEURONAL DENSITY OF 20,000 CELLS/MM3 AND IGNORES SHADOWING BY THE PROBE SHANK Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[7] |
| for which use | limitation — what could be asked before this method, not only what could be measured: SINCE THE NUMBER OF FIBERS A FREELY MOVING ANIMAL CAN BE TETHERED TO IS LIMITED (1-2 FOR SMALL RODENTS), THE RANGE OF SCIENTIFIC QUESTIONS THAT COULD BE ADDRESSED WAS RESTRICTED Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[8] |
| replication | untested | |
| limitation | The spatial confinement of the photostimulus is itself a drawback for experiments that need a whole structure controlled synchronously. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[0] |
| limitation | The 1/d scattering model used to estimate light intensity overestimates power beyond 1 mm from the fiber tip. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[1] |
| limitation | The fluorescein-bath measurement of the light cone is only an approximation of the real geometric light distribution in brain tissue. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[2] |
| limitation | THE PAPER'S HEADLINE ADVANTAGE, RE-TAGGED AS A LIMITATION: spatially restricted photostimulation IS ACTUALLY A LIMITATION for experiments requiring synchronous control of an entire structure Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[3] |
| limitation | the scattering model consistently overestimated power beyond 1 mm, and scattering ran 5 to 10% higher in tissue that was not fresh Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[4] |
| limitation | the fluorescein image is declared A PROXY ONLY for the real geometric distribution of light in the brain, since scattering contributes to it at short wavelengths Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[5] |
| limitation | the high fraction of light-modulated units MAY BE DUE TO transduction rates and the proximity of the fiber tip rather than to anything general Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[6] |
| limitation | and the count of illuminated cells rests on an assumed neuronal density and IGNORES SHADOWING by the probe shank Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[7] |
| limitation | with the number of fibers a freely moving animal can be tethered to limited to one or two, which RESTRICTED the range of scientific questions that could be addressed Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[8] |
finding · quantity · variable · definition · key-term — grounded in the full text| finding | Weak blue light delivered through the fiber-coupled LEDs drove 42% of recorded hippocampal units (57 of 135) to change their firing rate in freely moving rats. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[0] |
| finding | spike waveforms during light and during spontaneous activity were SIMILAR - median waveform consistencies 0.977 for light-modulated and 0.983 for nonresponsive units, U test P = 0.19 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[1] |
| finding | units recorded on the illuminated shank were often modulated, 20/39 units or 52%, whereas the fraction of modulated units on other shanks was AT CHANCE LEVEL Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[2] |
| finding | Light-evoked spiking was temporally precise, with a median across-trial jitter of 2 ms. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[3] |
| finding | Blue light with identical parameters in CA1 of PV::ChR2 mice drove interneurons to spike and then silenced nearby pyramidal cells. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[4] |
| finding | reliable activation of units on shank 1 during blue light pulses and robust silencing of THE SAME UNITS during the red light pulses Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[5] |
| finding | An index-matching coupling medium at the diode-fiber interface doubled the light output, to 30-50 microwatts for blue LEDs. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[6] |
| finding | these units exhibited phase precession Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[7] |
| finding | the mean scattering coefficients depended on wavelength Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[8] |
| finding | the fraction of significantly light-modulated units exhibited a marked increase between 3.5 and 5.5 mW/mm 2, from 15 to 73% Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[9] |
| finding | THE PAPER'S HEADLINE ADVANTAGE, RE-TAGGED AS A LIMITATION: spatially restricted photostimulation IS ACTUALLY A LIMITATION where synchronous control of an entire structure is wanted Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[10] |
| finding | and the resolution is a question, not a setting - THE SPECIFIC LIGHT SOURCES AND FIBERS SHOULD BE TAILORED TO THE SCIENTIFIC QUESTION AT HAND Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[11] |
| finding | ONE INTERVENTION, OPPOSITE SIGNS: the index-matching glue cuts reflective losses to under 1% BUT AT A COST OF REDUCING the acceptance angle BY 41% Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[12] |
| finding | while its effect on the skew rays acceptance angle is DIAMETRICALLY OPPOSITE, giving A TWOFOLD INCREASE in coupling efficiency Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[13] |
| finding | A MEASURED CONSTANT DISAGREEING WITH THE PUBLISHED ONE: blue-light scattering 7.18 against a reported 10.3, and IN ANY EVENT the estimates were SIMILAR REGARDLESS OF THE PRECISE NUMBER USED Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[14] |
| finding | the fitted model CONSISTENTLY OVERESTIMATED power beyond 1 mm and ran 5 to 10% off in nonfresh tissue Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[15] |
| finding | WHY THE LIGHT MUST BE WEAK AND CLOSE: stimulating further away INEVITABLY ACTIVATES MANY MORE UNMONITORED NEURONS THAN ARE BEING MONITORED, MAKING THE SEPARATION BETWEEN DIRECT AND POPULATION-MEDIATED EFFECTS IMPOSSIBLE Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[16] |
| finding | and strong light of ANY wavelength adds HEAT with a MIXED DE-/HYPERPOLARIZING effect, a confound independent of the opsin Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[17] |
| finding | THE SAME LIGHT, THE OPPOSITE SIGN, DECIDED BY THE PROMOTER: pyramidal cells spike in CaMKII::ChR2 mice and are SILENCED in PV::ChR2 mice under identical parameters Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[18] |
| finding | A 25% CHANGE IN DOSE FLIPS THE OUTCOME: 70% of 0.35 mW/mm 2 pulses efficient against 10% of 0.28 mW/mm 2 pulses Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[19] |
| finding | the statistical definition of light modulation is rescued by a BIMODAL distribution of the indices, 0.045 against 0.76 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[20] |
| finding | with the response fraction hedged - it MAY BE DUE TO transduction rates and the proximity of the fiber tip Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[21] |
| finding | THE UNIT IS DEFINED BY NUMBERED GATES BEFORE ANY RESULT: amplitude, L ratio, refractory period, then a firing floor that cut 535 hippocampal units to 135 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[22] |
| finding | an idealisation declared inside a figure legend - ASSUMES neuronal density of 20,000 cells/mm 3 and IGNORES SHADOWING by the probe shank Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[23] |
| finding | the empirical light map is declared A PROXY ONLY, since scattering contributes ESPECIALLY AT SHORT WAVELENGTHS Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[24] |
| finding | NATIVE NETWORK DYNAMICS CAN INCORPORATE SYNTHETIC PATTERNS OF ACTIVITY - units driven by nonperiodic photostimuli exhibited PHASE PRECESSION Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[25] |
| finding | and the whole device exists to remove one number - a freely moving animal can be tethered to ONE OR TWO fibers, which RESTRICTED the questions that could be addressed Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[26] |
| quantity | 42%; 57/135 — Fraction and count of hippocampal units whose firing rate was modulated by weak blue light Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[0] |
| quantity | median, 2 ms — Across-trial standard deviation of spike centers-of-mass, i.e. the temporal precision of light-evoked spiking Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[1] |
| quantity | median, 5.5 ms — Median latency from light onset to the first significantly elevated PSTH bin Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[2] |
| quantity | ∼0.001 mm 3 — Volume of brain tissue illuminated above the ChR2 activation threshold by a single fiber Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[3] |
| quantity | 20–100 — Estimated number of neurons inside the illuminated volume, given assumed cortical cell density Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[4] |
| quantity | 0.1–0.15% — Diode-to-fiber coupling efficiency for blue LEDs before index matching, versus about 2.5% for laser diodes Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[5] |
| quantity | 100–130 mg — Weight of a single diode-fiber assembly, which is what keeps the headgear light enough for free movement Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[6] |
| quantity | 0.5–1.5 g — Weight of a complete implantation-ready multidiode device Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[7] |
| quantity | 535 hippocampal and 98 neocortical units — Total number of single units isolated that met the amplitude and isolation criteria Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[8] |
| quantity | 1.82 — Median ratio of spiking probability during blue light to duration-matched spontaneous periods Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[9] |
| quantity | 70% ... 10% — Fraction of blue pulses able to break through halorhodopsin silencing at 0.35 versus 0.28 mW/mm2, showing a sharp intensity threshold Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[10] |
| quantity | 0.001 mm 3 — the illuminated volume, and the paper's unit of claim - the tissue a shank of a silicon probe can also monitor Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[11] |
| quantity | 7.18 ± 0.17 — the scattering coefficient measured for blue light, against a previously reported 10.3 for rat brain Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[12] |
| quantity | 41% — the acceptance angle the index-matching glue COSTS, at the same time as it removes the reflective losses Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[13] |
| quantity | 2 ms — the temporal precision of light-evoked spiking, the across-trial SD of the centers-of-mass Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[14] |
| quantity | 70% — the fraction of 0.35 mW/mm 2 blue pulses that overcame the red-light hyperpolarization, against 10% at 0.28 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[15] |
| quantity | 20,000 cells/mm 3 — the neuronal density ASSUMED by the illuminated-cell estimate, in a legend that also says it ignores shadowing Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[16] |
| variable | light intensity (independent) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[0] |
| variable | Firing rate during light (dependent) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[1] |
| variable | spiking probability (dependent) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[2] |
| variable | baseline period (control) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[5] |
| variable | intensity Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[6] |
| variable | precision Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[7] |
| variable | rate Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[8] |
| variable | coupling Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[9] |
| definition | diode-probe system Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[0] |
| definition | light-modulated unit Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[1] |
| definition | light modulation index Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[2] |
| definition | waveform consistency Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[3] |
| definition | center-of-mass Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[4] |
| definition | spiking probability Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[5] |
| definition | closed-loop control Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[6] |
| definition | threshold Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[7] |
| definition | coupling Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[8] |
| definition | unit Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[9] |
| definition | precision Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[10] |
| key-terms | light, diode, laser diode, fiber, coupling, skew rays, meridional, acceptance angle, index, reflective losses, scattering, wavelength, model, intensity, threshold, volume, shank, silicon probe, photostimulation, spike, waveform, neuron, unit, precision, latency, interneuron, pyramidal, ChR2, transduction, cell type, artifact, heat, closed-loop, circuit, network, phase precession, plasticity, rate, temporal coding, limitation, tether, freely moving |
| Mann-Whitney U test P | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[0] |
| Wilcoxon signed-rank test P | as written: Wilcoxon paired signed-rank test Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[1] |
| chi-squared test χ 2 | as written: χ 2 -test Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[2] |
| Kruskal-Wallis test P | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[3] |
| exact binomial test P | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[4] |
| permutation test P | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[5] |
| correlation | as written: Pearson correlation Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[6] |
| principal component analysis | as written: principal component analysis (PCA) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[7] |
| multiple-comparison correction | as written: Bonferroni correction Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[8] |
| regression r 2 | as written: robust linear regression Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[9] |
| standard deviation SD | as written: mean ± SD Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[10] |
| standard error SE | as written: mean ± SE Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[11] |
| goodness of fit r 2 | as written: r 2 > 0.98 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[12] |
| U test | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[13] |
| exact binomial test | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[14] |
| permutation test | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[15] |
| r 2 | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[16] |
| L ratio | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[17] |
| claim type | method — a second reading reaching the same value; recorded: method Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | alternatives.claim_type |
| method | couple a miniature diode to a small-core fiber etched to a point, glue it 50 μm above the top recording site, and drive each diode from its own precision current channel — a second reading DIFFERING from the recorded value; recorded: system-or-tool-building Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | alternatives.method |
| phenomenon | light-evoked spiking in intact tissue, and how far in space and time the evoked spikes stay where they were aimed — a second reading DIFFERING from the recorded value; recorded: multisite optogenetic control of neurons in freely moving animals Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | alternatives.phenomenon |
When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.
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