Optimization-Based Pairwise Interaction Point Process (O-PIPP): A Precise and Universal Retinal Mosaic Modeling Approach.

Purpose: A retinal mosaic, the spatial organization of a population of homotypic neurons, is thought to sample a specific visual feature into the feedforward visual pathway. The purpose of this study was to propose a universal modeling approach for precisely generating retinal mosaics and overcoming the limitations of previous models, especially in modeling abnormal mosaic patterns under disease conditions. Methods: Here, we developed the optimization-based pairwise interaction point process (O-PIPP). It incorporates optimization techniques into previous simulation approaches, enabling directional control of the simulation process according to the user-designed optimization target. For the convenience of the community, we implemented the O-PIPP approach into a Python package and a website application. Results: We showed that the O-PIPP can generate more precise neural spatial patterns of healthy and diseased mosaics compared to previous phenomenological approaches. Notably, through modeling the retinal neural circuitry with O-PIPP-simulated retinitis pigmentosa cone mosaics, we elucidated how the cone mosaic rearrangement impacted the information processing of ganglion cells. Conclusions: The O-PIPP provides a precise and universal tool to simulate realistic mosaics, which could help to investigate the function of retinal mosaics in vision.

A theoretical model reveals specialized synaptic depressions and temporal frequency tuning in retinal parallel channels.

In the Outer Plexiform Layer of a retina, a cone pedicle provides synaptic inputs for multiple cone bipolar cell (CBC) subtypes so that each subtype formats a parallelized processing channel to filter visual features from the environment. Due to the diversity of short-term depressions among cone-CBC contacts, these channels have different temporal frequency tunings. Here, we propose a theoretical model based on the hierarchy Linear-Nonlinear-Synapse framework to link the synaptic depression and the neural activities of the cone-CBC circuit. The model successfully captures various frequency tunings of subtype-specialized channels and infers synaptic depression recovery time constants inside circuits. Furthermore, the model can predict frequency-tuning behaviors based on synaptic activities. With the prediction of region-specialized UV cone parallel channels, we suggest the acute zone in the zebrafish retina supports detecting light-off events at high temporal frequencies.

U-RISC: An Annotated Ultra-High-Resolution Electron Microscopy Dataset Challenging the Existing Deep Learning Algorithms.

Connectomics is a developing field aiming at reconstructing the connection of the neural system at the nanometer scale. Computer vision technology, especially deep learning methods used in image processing, has promoted connectomic data analysis to a new era. However, the performance of the state-of-the-art (SOTA) methods still falls behind the demand of scientific research. Inspired by the success of ImageNet, we present an annotated ultra-high resolution image segmentation dataset for cell membrane (U-RISC), which is the largest cell membrane-annotated electron microscopy (EM) dataset with a resolution of 2.18 nm/pixel. Multiple iterative annotations ensured the quality of the dataset. Through an open competition, we reveal that the performance of current deep learning methods still has a considerable gap from the human level, different from ISBI 2012, on which the performance of deep learning is closer to the human level. To explore the causes of this discrepancy, we analyze the neural networks with a visualization method, which is an attribution analysis. We find that the U-RISC requires a larger area around a pixel to predict whether the pixel belongs to the cell membrane or not. Finally, we integrate the currently available methods to provide a new benchmark (0.67, 10% higher than the leader of the competition, 0.61) for cell membrane segmentation on the U-RISC and propose some suggestions in developing deep learning algorithms. The U-RISC dataset and the deep learning codes used in this study are publicly available.

Genotype-Associated Arginase 1 Expression in Rat Peritoneal Macrophages Induced by Toxoplasma gondii.

Toxoplasma gondii induces polarization of mouse macrophages, including both classically activated macrophages (M1) and alternatively activated macrophages (M2) in a genotype-related manner. Here we present a novel result that the Wh6 strain with type Chinese 1, which is predominantly prevalent in China, induces Arg1 expression in a STAT6-dependent manner in primary rat peritoneal macrophages as compared to the PRU stain with type II, which elicited a high expression of Arg1 in a C/EBPß-dependent manner. In addition, dexamethasone inhibited Arg1 expression in rat macrophages in both treatments. Our data suggest that Arg1 expression, which is abundant in polarized M2 cells, is associated with strain/genotype differences from different pathways.

Toxoplasma gondii isolate with genotype Chinese 1 triggers trophoblast apoptosis through oxidative stress and mitochondrial dysfunction in mice.

Congenital toxoplasmosis may result in abortion, severe mental retardation and neurologic damage in the offspring. Placental damage is considered as the key event in this disease. Here we show that maternal infection with Toxoplasma gondii Wh3 isolate of genotype Chinese 1, which is predominantly prevalent in China, induced trophoblast apoptosis of pregnant mouse. PCR array analysis of 84 key genes in the biogenesis and functions of mouse mitochondrion revealed that ten genes were up-regulated at least 2-fold in the Wh3 infection group, compared with those in the control. The elevated levels of reactive oxygen species (ROS), malondialdehyde (MDA) and 8-hydroxydeoxyguanosine (8-OHdG), as well as the decreased glutathione (GSH), were observed in the infected mice. The mRNA levels of NADPH oxidase 1 and glutathione peroxidase 6 (GPx6) were significantly increased. The production of excessive ROS was NADPH oxidase-dependent, which contributed to mitochondrial structural damage and mitochondrial dysfunction in placentas, followed by the cleavage of caspase-9 and caspase-3, and finally resulted in apoptosis of trophoblasts. All the above-mentioned phenomena were inhibited by pretreatment with the antioxidant of N-acetylcysteine (NAC). Taken together, we concluded that Wh3 infection during pregnancy may contribute to trophoblast apoptosis by oxidative stress-induced mitochondrial dysfunction and activation of the downstream signaling pathway.

Seroprevalence and genetic characterization of Toxoplasma gondii in cancer patients in Anhui Province, Eastern China.

BACKGROUND: Recent studies have indicated the predominance of Toxoplasma gondii genotype Chinese 1 in animals in China. However, little is known of the genetic features of the parasite in humans. This study aims to determine the prevalence of anti-T. gondii antibodies based on which the genetic character of the parasite was identified in cancer patients in China. METHODS: A total of 1014 serum samples with malignant neoplasms were collected from six tertiary-care hospitals (HAUCM, APH, HAMU, XAH, FHH and HBMC) from January, 2012 to August, 2013. Antibodies against T. gondii were examined by enzyme-linked immunosorbent assay (ELISA). Blood samples were subsequently used for PCR assay to detect T. gondii DNA (gra6). The DNA positive samples were subjected to genotyping using a multiplex multilocus nested PCR-RFLP at 10 loci, including sag1, sag2, sag3, btub, gra6, l358, c22-8, c29-2, pk1 and apico. Samples from the patients were anonymous and only data with regard to age and gender was available at sample collection. RESULTS: Overall, 8.38% (85/1014) of the examined patients showed positive antibodies against T. gondii. Among them, 61 (6.02%) were seropositive only for IgG, 16 (1.58%) were only for IgM, and 8 (0.79%) were found to be positive for both IgG and IgM. The seroprevalence of antibodies to Toxoplasma ranged from 5.8% to 11.0%, without regional difference (χ(2) = 4.764, P = 0.445). No significant differences of the positive rates of T. gondii infection were noted in genders (male, 8.96%; female, 7.45%) (χ(2) = 0.707, P = 0.400) and in ages (χ(2) = 1.172, P = 0.947). Of 1014 DNA samples, 36 (3.55%) were positive for T. gondii by nested PCR at gra6 locus and nine gave rise to complete genotyping results. All samples with achieved PCR-RFLP genotyping showed a common genetic character of type Chinese 1 (ToxoDB#9). CONCLUSION: Seroprevalence of toxoplasmosis in immunosuppressed individuals is rarely reported in China and we presented a positive rate of 8.38% in cancer patients. Toxoplasma genomic DNA genotyping demonstrated a common genetic character of Chinese 1, indicating a possible pathogenic origin of animals in human infection.

Defective fast inactivation recovery of Nav 1.4 in congenital myasthenic syndrome.

OBJECTIVE: To describe the unique phenotype and genetic findings in a 57-year-old female with a rare form of congenital myasthenic syndrome (CMS) associated with longstanding muscle fatigability, and to investigate the underlying pathophysiology. METHODS: We used whole-cell voltage clamping to compare the biophysical parameters of wild-type and Arg1457His-mutant Nav 1.4. RESULTS: Clinical and neurophysiological evaluation revealed features consistent with CMS. Sequencing of candidate genes indicated no abnormalities. However, analysis of SCN4A, the gene encoding the skeletal muscle sodium channel Nav 1.4, revealed a homozygous mutation predicting an arginine-to-histidine substitution at position 1457 (Arg1457His), which maps to the channel's voltage sensor, specifically D4/S4. Whole-cell patch clamp studies revealed that the mutant required longer hyperpolarization to recover from fast inactivation, which produced a profound use-dependent current attenuation not seen in the wild type. The mutant channel also had a marked hyperpolarizing shift in its voltage dependence of inactivation as well as slowed inactivation kinetics. INTERPRETATION: We conclude that Arg1457His compromises muscle fiber excitability. The mutant fast-inactivates with significantly less depolarization, and it recovers only after extended hyperpolarization. The resulting enhancement in its use dependence reduces channel availability, which explains the patient's muscle fatigability. Arg1457His offers molecular insight into a rare form of CMS precipitated by sodium channel inactivation defects. Given this channel's involvement in other muscle disorders such as paramyotonia congenita and hyperkalemic periodic paralysis, our study exemplifies how variations within the same gene can give rise to multiple distinct dysfunctions and phenotypes, revealing residues important in basic channel function.