Bypassing spike sorting: Density-based decoding using spike localization from dense multielectrode probes.

Neural decoding and its applications to brain computer interfaces (BCI) are essential for understanding the association between neural activity and behavior. A prerequisite for many decoding approaches is spike sorting, the assignment of action potentials (spikes) to individual neurons. Current spike sorting algorithms, however, can be inaccurate and do not properly model uncertainty of spike assignments, therefore discarding information that could potentially improve decoding performance. Recent advances in high-density probes (e.g., Neuropixels) and computational methods now allow for extracting a rich set of spike features from unsorted data; these features can in turn be used to directly decode behavioral correlates. To this end, we propose a spike sorting-free decoding method that directly models the distribution of extracted spike features using a mixture of Gaussians (MoG) encoding the uncertainty of spike assignments, without aiming to solve the spike clustering problem explicitly. We allow the mixing proportion of the MoG to change over time in response to the behavior and develop variational inference methods to fit the resulting model and to perform decoding. We benchmark our method with an extensive suite of recordings from different animals and probe geometries, demonstrating that our proposed decoder can consistently outperform current methods based on thresholding (i.e. multi-unit activity) and spike sorting. Open source code is available at https://github.com/yzhang511/density_decoding.

Loss of NFE2L3 protects against inflammation-induced colorectal cancer through modulation of the tumor microenvironment.

We investigated the role of the NFE2L3 transcription factor in inflammation-induced colorectal cancer. Our studies revealed that Nfe2l3-/- mice exhibit significantly less inflammation in the colon, reduced tumor size and numbers, and skewed localization of tumors with a more pronounced decrease of tumors in the distal colon. CIBERSORT analysis of RNA-seq data from normal and tumor tissue predicted a reduction in mast cells in Nfe2l3-/- animals, which was confirmed by toluidine blue staining. Concomitantly, the transcript levels of Il33 and Rab27a, both important regulators of mast cells, were reduced and increased, respectively, in the colorectal tumors of Nfe2l3-/- mice. Furthermore, we validated NFE2L3 binding to the regulatory sequences of the IL33 and RAB27A loci in human colorectal carcinoma cells. Using digital spatial profiling, we found that Nfe2l3-/- mice presented elevated FOXP3 and immune checkpoint markers CTLA4, TIM3, and LAG3, suggesting an increase in Treg counts. Staining for CD3 and FOXP3 confirmed a significant increase in immunosuppressive Tregs in the colon of Nfe2l3-/- animals. Also, Human Microbiome Project (HMP2) data showed that NFE2L3 transcript levels are higher in the rectum of ulcerative colitis patients. The observed changes in the tumor microenvironment provide new insights into the molecular differences regarding colon cancer sidedness. This may be exploited for the treatment of early-onset colorectal cancer as this emerging subtype primarily displays distal/left-sided tumors.

Persistence of antibody response to SARS-CoV-2 in a cohort of haemodialysis patients with COVID-19.

BACKGROUND: Haemodialysis patients are extremely vulnerable to COVID-19. Their immune response after infection is unclear. We have found high seroconversion rates in this population with 95% developing antibodies. It is unclear if and how long these antibodies persist. Here we investigate this with serial antibody testing. METHODS: We identified haemodialysis patients who had confirmed SARS-CoV-2 between March-May 2020 and measured monthly antibodies (IgG/IgM) in those who survived. We used a semi-quantitative cut-off index (COI) to create a qualitative result and plotted optical density (OD) over time. We used linear regression to examine the slope, as well as noting peak OD and time to peak OD. We correlated these against baseline demographics, markers of illness severity, and comorbidities. RESULTS: 122 patients were analysed. All remained antibody positive during follow-up; for a minimum of 148 days. 71% had a positive gradient indicating increasing antibody positivity over time. We found that age (p = 0.01), duration of PCR positivity (p = 0.06) and presence of symptoms (p = 0.05) were associated with a longer time to peak OD. Immunosuppression did not alter peak OD but did lead to a non-significant increase in time to peak OD and more patients had a subsequent fall in Ab levels (p = 0.02). Diabetic patients were more likely to have a positive slope (OR 2.26). CONCLUSIONS: These results indicate that haemodialysis patients have a robust and sustained antibody response after confirmed COVID-19 infection with no suggestion that immunosuppression weakens this response. Although unclear what protection these antibodies confer, this encouraging that haemodialysis patients should respond to vaccination.

Determinants of mortality in patients with cirrhosis and uncontrolled variceal bleeding.

BACKGROUND & AIMS: Failure to control oesophago-gastric variceal bleeding (OGVB) and acute-on-chronic liver failure (ACLF) are both important prognostic factors in cirrhosis. The aims of this study were to determine whether ACLF and its severity define the risk of death in OGVB and whether insertion of rescue transjugular intrahepatic shunt (TIPS) improves survival in patients with failure to control OGVB and ACLF. METHODS: Data on 174 consecutive eligible patients, with failure to control OGVB between 2005 and 2015, were collected from a prospectively maintained intensive care unit registry. Rescue TIPS was defined as technically successful TIPS within 72 hours of presentation with failure to control OGVB. Cox-proportional hazards regression analyses were applied to explore the impact of ACLF and TIPS on survival in patients with failure to control OGVB. RESULTS: Patients with ACLF (n = 119) were significantly older, had organ failures and higher white cell count than patients with acute decompensation (AD, n = 55). Mortality at 42-days and 1-year was significantly higher in patients with ACLF (47.9% and 61.3%) than in those with AD (9.1% and 12.7%, p <0.001), whereas there was no difference in the number of endoscopies and transfusion requirements between these groups. TIPS was inserted in 78 patients (AD 21 [38.2%]; ACLF 57 [47.8%]; p = 0.41). In ACLF, rescue TIPS insertion was an independent favourable prognostic factor for 42-day mortality. In contrast, rescue TIPS did not impact on the outcome of patients with AD. CONCLUSIONS: This study shows that in patients with failure to control OGVB, the presence and severity of ACLF determines the risk of 42-day and 1-year mortality. Rescue TIPS is associated with improved survival in patients with ACLF. LAY SUMMARY: Variceal bleeding that is not controlled by initial endoscopy is associated with high risk of death. The results of this study showed that in the occurrence of failure of the liver and other organs defines the risk of death. In these patients, insertion of a shunt inside the liver to drain the portal vein improves survival.

The integration of visual and target signals in V4 and IT during visual object search.

Searching for a specific visual object requires our brain to compare the items in view with a remembered representation of the sought target to determine whether a target match is present. This comparison is thought to be implemented, in part, via the combination of top-down modulations reflecting target identity with feed-forward visual representations. However, it remains unclear whether top-down signals are integrated at a single locus within the ventral visual pathway (e.g., V4) or at multiple stages [e.g., both V4 and inferotemporal cortex (IT)]. To investigate, we recorded neural responses in V4 and IT as rhesus monkeys performed a task that required them to identify when a target object appeared across variation in position, size, and background context. We found nonvisual, task-specific signals in both V4 and IT. To evaluate whether V4 was the only locus for the integration of top-down signals, we evaluated several feed-forward accounts of processing from V4 to IT, including a model in which IT preferentially sampled from the best V4 units and a model that allowed for nonlinear IT computation. IT task-specific modulation was not accounted for by any of these feed-forward descriptions, suggesting that during object search, top-down signals are integrated directly within IT.NEW & NOTEWORTHY To find specific objects, the brain must integrate top-down, target-specific signals with visual information about objects in view. However, the exact route of this integration in the ventral visual pathway is unclear. In the first study to systematically compare V4 and inferotemporal cortex (IT) during an invariant object search task, we demonstrate that top-down signals found in IT cannot be described as being inherited from V4 but rather must be integrated directly within IT itself.

Rethinking assumptions about how trial and nuisance variability impact neural task performance in a fast-processing regime.

Task performance is determined not only by the amount of task-relevant signal present in our brains but also by the presence of noise, which can arise from multiple sources. Internal noise, or "trial variability," manifests as trial-by-trial variations in neural responses under seemingly identical conditions. External factors can also translate into noise, particularly when a task requires extraction of a particular type of information from our environment amid changes in other task-irrelevant "nuisance" parameters. To better understand how signal, trial variability, and nuisance variability combine to determine neural task performance, we explored their interactions, both in simulation and when applied to recorded neural data. This exploration revealed that trial variability is typically larger than a neuron's task-relevant signal for tasks with fast reaction times, where spike count integration windows are short. In this low signal-to-trial variability regime, nuisance variability has the counterintuitive property of having a negligible impact on single-neuron task performance, even when it dominates the task-relevant signal. The inconsequential impact of nuisance variability on individual neurons also extends to descriptions of population performance, under the assumption that both trial and nuisance variability are uncorrelated between neurons. These results demonstrate that some basic intuitions about neural coding are misguided in the context of a fast-processing, low-spike-count regime. NEW & NOTEWORTHY Many everyday tasks require us to extract specific information from our environment while ignoring other things. When the neurons in our brains that carry task-relevant signals are also modulated by task-irrelevant "nuisance" information, nuisance modulation is expected to act as performance-limiting noise. Using both simulated and recorded neural data, we demonstrate that these intuitions are misguided when the brain operates in a fast-processing, low-spike-count regime, where nuisance variability is largely inconsequential for performance.

Inferotemporal cortex multiplexes behaviorally-relevant target match signals and visual representations in a manner that minimizes their interference.

Finding a sought visual target object requires combining visual information about a scene with a remembered representation of the target to create a "target match" signal that indicates when a target is in view. Target match signals have been reported to exist within high-level visual brain areas including inferotemporal cortex (IT), where they are mixed with representations of image and object identity. However, these signals are not well understood, particularly in the context of the real-world challenge that the objects we search for typically appear at different positions, sizes, and within different background contexts. To investigate these signals, we recorded neural responses in IT as two rhesus monkeys performed a delayed-match-to-sample object search task in which target objects could appear at a variety of identity-preserving transformations. Consistent with the existence of behaviorally-relevant target match signals in IT, we found that IT contained a linearly separable target match representation that reflected behavioral confusions on trials in which the monkeys made errors. Additionally, target match signals were highly distributed across the IT population, and while a small fraction of units reflected target match signals as target match suppression, most units reflected target match signals as target match enhancement. Finally, we found that the potentially detrimental impact of target match signals on visual representations was mitigated by target match modulation that was approximately (albeit imperfectly) multiplicative. Together, these results support the existence of a robust, behaviorally-relevant target match representation in IT that is configured to minimally interfere with IT visual representations.

Evaluation of motion and its effect on brain magnetic resonance image quality in children.

BACKGROUND: Motion artifacts pose significant problems for the acquisition of MR images in pediatric populations. OBJECTIVE: To evaluate temporal motion metrics in MRI scanners and their effect on image quality in pediatric populations in neuroimaging studies. MATERIALS AND METHODS: We report results from a large pediatric brain imaging study that shows the effect of motion on MRI quality. We measured motion metrics in 82 pediatric patients, mean age 13.4 years, in a T1-weighted brain MRI scan. As a result of technical difficulties, 5 scans were not included in the subsequent analyses. A radiologist graded the images using a 4-point scale ranging from clinically non-diagnostic because of motion artifacts to no motion artifacts. We used these grades to correlate motion parameters such as maximum motion, mean displacement from a reference point, and motion-free time with image quality. RESULTS: Our results show that both motion-free time (as a ratio of total scan time) and average displacement from a position at a fixed time (when the center of k-space was acquired) were highly correlated with image quality, whereas maximum displacement was not as good a predictor. Among the 77 patients whose motion was measured successfully, 17 had average displacements of greater than 0.5 mm, and 11 of those (14.3%) resulted in non-diagnostic images. Similarly, 14 patients (18.2%) had less than 90% motion-free time, which also resulted in non-diagnostic images. CONCLUSION: We report results from a large pediatric study to show how children and young adults move in the MRI scanner and the effect that this motion has on image quality. The results will help the motion-correction community in better understanding motion patterns in pediatric populations and how these patterns affect MR image quality.

Watch this! Observed tool use affects perceived distance.

Recent research has shown that being able to interact with an object causes it to be perceived as being closer than objects that cannot be interacted with. In the present study, we examined whether that compression of perceived space would be experienced by people who simply observed such interactions by others with no intention of performing the action themselves. Participants judged the distance to targets after observing an actor reach to an otherwise unreachable target with a tool (Experiment 1) or illuminate a distant target with a laser pointer (Experiment 2). Observing either type of interaction caused a compression of perceived space, revealing that a person's perception of space can be altered through mere observation. These results indicate that shared representations between an actor and observer are engaged at the perceptual level easily and perhaps automatically, even in the absence of cooperation or an observer's own intention to interact.