Corrigendum: Spatiotemporal analysis of 3D human iPSC-derived neural networks using a 3D multi-electrode array

[This corrects the article DOI: 10.3389/fncel.2023.1287089.].

Spatiotemporal analysis of 3D human iPSC-derived neural networks using a 3D multi-electrode array

While there is a growing appreciation of three-dimensional (3D) neural tissues (i.e., hydrogel-based, organoids, and spheroids), shown to improve cellular health and network activity to mirror brain-like activity in vivo, functional assessment using current electrophysiology techniques (e.g., planar multi-electrode arrays or patch clamp) has been technically challenging and limited to surface measurements at the bottom or top of the 3D tissue. As next-generation MEAs, specifically 3D MEAs, are being developed to increase the spatial precision across all three dimensions (X, Y, Z), development of improved computational analytical tools to discern region-specific changes within the Z dimension of the 3D tissue is needed. In the present study, we introduce a novel computational analytical pipeline to analyze 3D neural network activity recorded from a "bottom-up" 3D MEA integrated with a 3D hydrogel-based tissue containing human iPSC-derived neurons and primary astrocytes. Over a period of ~6.5 weeks, we describe the development and maturation of 3D neural activity (i.e., features of spiking and bursting activity) within cross sections of the 3D tissue, based on the vertical position of the electrode on the 3D MEA probe, in addition to network activity (identified using synchrony analysis) within and between cross sections. Then, using the sequential addition of postsynaptic receptor antagonists, bicuculline (BIC), 2-amino-5-phosphonovaleric acid (AP-5), and 6-cyano-5-nitroquinoxaline-2,3-dione (CNQX), we demonstrate that networks within and between cross sections of the 3D hydrogel-based tissue show a preference for GABA and/or glutamate synaptic transmission, suggesting differences in the network composition throughout the neural tissue. The ability to monitor the functional dynamics of the entire 3D reconstructed neural tissue is a critical bottleneck; here we demonstrate a computational pipeline that can be implemented in studies to better interpret network activity within an engineered 3D neural tissue and have a better understanding of the modeled organ tissue.

Identifying Steady State in the Network Dynamics of Spiking Neural Networks

Analysis of the dynamics of complex networks can provide valuable information. For example, the dynamics can be used to characterize and differentiate between different network inputs and configurations. However, without quantitatively delineating the network's dynamic regimes, analysis of the network's dynamics is based on heuristics and qualitative signatures of transient or steady-state regimes. This is not ideal because interesting phenomena can occur during the transient regime, steady-state regime, or at the transition between the two dynamic regimes. Moreover, for simulated and observed systems, precise knowledge of the network's dynamical regime is imperative when considering metrics on minimal mathematical descriptions of the dynamics, otherwise either too much or too little data is analyzed. Here, we develop quantitative methods to ascertain the starting point and period of steady-state network activity. Using the precise knowledge of the network's dynamic regimes, we build minimal representations of the network dynamics that form the basis for future work. We show applications of our techniques on idealized signals and on the dynamics of a biologically inspired spiking neural network.

Computing Temporal Sequences Associated With Dynamic Patterns on the C. elegans Connectome

Understanding how the structural connectivity and spatial geometry of a network constrains the dynamics it is able to support is an active and open area of research. We simulated the plausible dynamics resulting from the known C. elegans connectome using a recent model and theoretical analysis that computes the dynamics of neurobiological networks by focusing on how local interactions among connected neurons give rise to the global dynamics in an emergent way. We studied the dynamics which resulted from stimulating a chemosensory neuron (ASEL) in a known feeding circuit, both in isolation and embedded in the full connectome. We show that contralateral motorneuron activations in ventral (VB) and dorsal (DB) classes of motorneurons emerged from the simulations, which are qualitatively similar to rhythmic motorneuron firing pattern associated with locomotion of the worm. One interpretation of these results is that there is an inherent—and we propose—purposeful structural wiring to the C. elegans connectome that has evolved to serve specific behavioral functions. To study network signaling pathways responsible for the dynamics we developed an analytic framework that constructs Temporal Sequences (TSeq), time-ordered walks of signals on graphs. We found that only 5% of TSeq are preserved between the isolated feeding network relative to its embedded counterpart. The remaining 95% of signaling pathways computed in the isolated network are not present in the embedded network. This suggests a cautionary note for computational studies of isolated neurobiological circuits and networks.

Generalizable Machine Learning in Neuroscience Using Graph Neural Networks

Although a number of studies have explored deep learning in neuroscience, the application of these algorithms to neural systems on a microscopic scale, i.e. parameters relevant to lower scales of organization, remains relatively novel. Motivated by advances in whole-brain imaging, we examined the performance of deep learning models on microscopic neural dynamics and resulting emergent behaviors using calcium imaging data from the nematode C. elegans. As one of the only species for which neuron-level dynamics can be recorded, C. elegans serves as the ideal organism for designing and testing models bridging recent advances in deep learning and established concepts in neuroscience. We show that neural networks perform remarkably well on both neuron-level dynamics prediction and behavioral state classification. In addition, we compared the performance of structure agnostic neural networks and graph neural networks to investigate if graph structure can be exploited as a favourable inductive bias. To perform this experiment, we designed a graph neural network which explicitly infers relations between neurons from neural activity and leverages the inferred graph structure during computations. In our experiments, we found that graph neural networks generally outperformed structure agnostic models and excel in generalization on unseen organisms, implying a potential path to generalizable machine learning in neuroscience.

Histopathological changes in the testes of prepubertal male rats after chronic administration of cocaine

PURPOSE

This study was conducted to evaluate histopathologic findings in the testes of prepubertal male rats after long-term cocaine exposure.

METHODS

At 25 days of age, male Sprague-Dawley rats were administered cocaine hydrochloride daily (15 mg/kg body weight corresponding to an average single dose for a heavy cocaine user). The treatment was continued for 100 days when all the rats were sacrificed. Morphological analysis of the testes were assessed by qualitative and quantitative histological means.

RESULTS

In all the groups, a minimum of 5 to 10 representative seminiferous tubules were examined. The mean diameter of the seminiferous tubules was less in the treated group than in their respective controls (p < 0.05). The thickness of the germinal epithelium was much reduced in the cocaine-treated groups when compared with their controls (p < 0.05). The number of degenerating germ cells was greater in the treated group than in the controls. There was evidence of failure to release the mature spermatids in the treated groups. There was no evidence of sloughed Sertoli cells or germ cells in the tubular lumen or the epididymis.

CONCLUSION

There were distinct histopathological changes noted after chronic administration of cocaine. These changes are characteristic of toxic effects on the testes, but the exact mechanism is not clear. Further studies are underway in our laboratory to delineate the exact mechanism of action by cocaine on the testes.

Effect of cocaine on testicular blood flow in rats: evaluation by percutaneous injection of xenon-133

PURPOSE

Cocaine abuse has reached epidemic proportions in the United States. Our recent study has shown that cocaine has adverse action on spermatogenesis and fertility in male rats. The indirect action of cocaine occurs by blocking the reuptake of neurotransmitter, which causes local vasoconstriction. In this study we evaluate blood flow to the testes after subcutaneous injection of cocaine to male rats.

METHODS

Male Sprague-Dawley rats were divided into two main groups. The treatment group received subcutaneous cocaine (30 mg/kg body weight) and the control animals received normal saline. Xenon-133 wash out experiments were carried out on testes at 5, 10, 15, 20, 30, 45, 60, 90 min and 4.5 hours after injection of cocaine or normal saline. Statistical analysis was done by SPSS V. 7.S for windows. P < 0.05 was considered statistically significant.

RESULTS

There was a reduction in testicular blood flow after cocaine administration to male rats. This vasoconstrictor effect was most pronounced at 15 min after injection of cocaine and persisted up to 60 min. At 90 min, the early restitution of blood flow to ischemic tissue occurred. There was a significant increase in testicular blood flow in cocaine-treated groups than in the control group during restitution phases at 90 min. At 4.5 hours, there was no difference in blood flow in both groups.

CONCLUSION

This study demonstrates that cocaine, when given subcutaneously at a 30 mg/kg body weight dose, results in prolonged vasoconstriction of the blood vessels to the testes. Adverse effects of cocaine on the testes may be in part due to ischemic and postischemic reperfusion injury to the organ.

Characterization of cocaine binding sites in the rat testes

PURPOSE

An estimated 29 million individuals use cocaine in the United States. Studies have shown a high affinity for dose dependent binding of cocaine in the testes. Recent work done in our laboratory has shown that chronic administration of cocaine to male rats has an adverse effect on fertility and spermatogenesis by producing extensive morphological changes in the testes, leading to reduction in sperm production. As a first step toward understanding this process, we characterized and identified the pharmacological properties of [3H]cocaine binding sites in the testes.

MATERIALS AND METHODS

Crude membranes from the testes were prepared from 35 days old male Sprague-Dawley rats. [3H]cocaine binding was measured by using the method of Madras et al. (1989) with modifications. The data from saturation binding assays were analyzed by Inplot (GraphPad Software, San Diego, CA) to determine the Kd and Bmax.

RESULTS

Specific binding of [3H]cocaine was linearly dependent on membrane protein concentrations ranging from 0.2 to 8 mg./ml. The pooled data from three independent experiments revealed a mean affinity of 36 +/- 2.0 nM and Bmax of 1.84 +/- 0.13 pmol/mg. The present study demonstrates that testicular tissue has receptor protein that binds [3H]cocaine saturably and specifically. Competition displacement experiments revealed a shallow displacement curve for (-)cocaine and Win 35,428 with r2 = 0.96, indicative of multiple binding components. Computer analysis confirmed that a two component binding model was preferred statistically over a one component model in all three experiments (p < 0.001).

CONCLUSION

The results from these studies suggest that the testicular tissue contains a protein that binds [3H]cocaine in a saturable and specific manner. It has a different sensitivity from the [3H]cocaine binding protein in the brain and placenta. Further clarification of the relationship between cocaine and its recognition site is necessary to understand the mechanism of testicular damage after cocaine exposure.

The management of extensive penile fibrosis: a new technique of 'minimal scar-tissue excision'

OBJECTIVE

To evaluate the results of excising minimal scar tissue in patients undergoing insertion of a penile prosthesis for extensive corporal fibrosis.

PATIENTS AND METHODS

Twelve patients (mean age 58 years, range 44-73) with extensive corporal fibrosis who underwent the insertion of a penile prosthesis were evaluated. Eleven patients had a defect of varying extent after the insertion of the penile prosthesis, and a polytetrafluoroethylene graft was used to cover the area.

RESULTS

All 12 patients tolerated the procedure well and currently have a functioning penile implant.

CONCLUSIONS

Minimal excision of scar tissue provided better results and fewer complications when compared to other studies which used extensive excision.

Effects of long-term cocaine exposure on spermatogenesis and fertility in peripubertal male rats

PURPOSE

This study was conducted to investigate the effects of long-term administration of cocaine on spermatogenesis and fertility in adult male rats.

MATERIALS AND METHODS

Thirty-day-old male Sprague-Dawley rats were given cocaine hydrochloride (15 mg./kg. body weight, corresponding to an average single dose for a heavy cocaine user) either daily or twice weekly (weekend group, cocaine given on Saturday and Sunday) and mated with pregnancy-proven female rats after 100 and 150 days of exposure to the drug. Pregnancy rates and litter birth weights were evaluated. Serum testosterone, follicle stimulating hormone and luteinizing hormone levels were measured in all adult rats. Morphologic analysis of the testis entailed the evaluation of quantitative and qualitative histologic parameters to assess the effect of cocaine on various stages of spermatogenesis.

RESULTS

After 100 days of treatment, the rats receiving daily cocaine had a pregnancy rate of only 33% versus 86% for the controls (p < 0.05). In rats exposed to cocaine for 150 days the pregnancy rate was 50% compared with 100% for controls (p < 0.05). The birth weights of offspring from the group receiving daily cocaine was 10% less than that of controls (p < 0.05). The weight of the testis and epididymis was not affected by cocaine exposure. Morphometric analysis showed significant differences between the cocaine-treated groups (both the daily cocaine and twice weekly cocaine groups) and their respective controls. The mean diameter of seminiferous tubules in the daily and twice weekly cocaine groups was reduced when compared with their respective controls. These differences between treated groups and their controls were statistically significant (p < 0.05). Similarly the thickness of the germinal epithelium was less in the cocaine-treated groups than in the controls (p < 0.05). Degenerating cells were more numerous in both daily and twice weekly cocaine groups than the controls. Furthermore, the number of step VII spermatids was reduced in both daily and twice weekly cocaine groups, a difference that was statistically significant (p < 0.05).

CONCLUSION

Our findings demonstrate that chronic administration of cocaine to peripubertal male rats has a profound effect on their testicular function. Even with twice weekly administration there was a significant adverse effect on spermatogenesis although this was not manifested by diminished fertility in this group. These findings confirm that chronic administration of cocaine to male rats can have a deleterious effect on spermatogenesis and fertility.

Follow-up with Mentor two-piece inflatable penile prosthesis

Between October, 1987 and June, 1993, we implanted 50 Mentor two-piece inflatable penile prostheses with a mean follow-up of 52.18 months (6-72 months). In 7 pts (14%), the implants were removed for various reasons. One pt (2%) had total fluid leak due to breakage of the tube at its junction with the cylinder. One implant (2%) was replaced due to loss of rigidity. Two implants (4%) were removed due to infection and later replaced with semirigid prostheses. Three pts (6%) had pump erosion. There was loss of rigidity in seven implants (14%), which appears to be due to stretching of the tunica albuginea from repeated use. The limited amount of fluid in the resipump precludes compensation for the stretching, leading to loss of rigidity. The overall complication rate of 28% in this long-term series appears to be much higher than that in other reported short-term follow ups. Thirty-six pts (72%) are fully satisfied with the device and 7 pts (14%) are partially satisfied, with an overall satisfaction rate of 86%. In our series, 46/50 (92%) pts have functioning prostheses at the time of review.

The effect of ranitidine on urine mucus concentration in patients with enterocystoplasty

We describe the effect of ranitidine in reducing mucus in urine in 8 patients with enterocystoplasty and present a simple technique for measuring the concentration of mucus in urine. After a 10-day course of ranitidine (300 mg daily in divided doses) the concentration of mucus had fallen significantly from an initial level of 1.38 +/- 0.18 to 0.39 +/- 0.04 mg/ml.

Clam ileocystoplasty

Clam enterocystoplasty has been used successfully in the treatment of refractory urge incontinence. We report 31 patients who underwent ileocystoplasty between 1982 and 1989. The majority of patients were pleased with the outcome of the operation. The main post-operative complication was voiding dysfunction due to relative bladder outflow obstruction. Urinary tract infection and mucus production were significant long-term problems.