CAVE: Connectome Annotation Versioning Engine.

Advances in Electron Microscopy, image segmentation and computational infrastructure have given rise to large-scale and richly annotated connectomic datasets which are increasingly shared across communities. To enable collaboration, users need to be able to concurrently create new annotations and correct errors in the automated segmentation by proofreading. In large datasets, every proofreading edit relabels cell identities of millions of voxels and thousands of annotations like synapses.

NEURD offers automated proofreading and feature extraction for connectomics.

We are now in the era of millimeter-scale electron microscopy (EM) volumes collected at nanometer resolution. Dense reconstruction of cellular compartments in these EM volumes has been enabled by recent advances in Machine Learning (ML). Automated segmentation methods produce exceptionally accurate reconstructions of cells, but post-hoc proofreading is still required to generate large connectomes free of merge and split errors.

Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex.

Mammalian cortex features a vast diversity of neuronal cell types, each with characteristic anatomical, molecular and functional properties. Synaptic connectivity powerfully shapes how each cell type participates in the cortical circuit, but mapping connectivity rules at the resolution of distinct cell types remains difficult. Here, we used millimeter-scale volumetric electron microscopy to investigate the connectivity of all inhibitory neurons across a densely-segmented neuronal population of 1352 cells spanning all layers of mouse visual cortex, producing a wiring diagram of inhibitory connections with more than 70,000 synapses.

Oligodendrocyte precursor cells ingest axons in the mouse neocortex.

Neurons in the developing brain undergo extensive structural refinement as nascent circuits adopt their mature form. This physical transformation of neurons is facilitated by the engulfment and degradation of axonal branches and synapses by surrounding glial cells, including microglia and astrocytes. However, the small size of phagocytic organelles and the complex, highly ramified morphology of glia have made it difficult to define the contribution of these and other glial cell types to this crucial process.

Binary and analog variation of synapses between cortical pyramidal neurons.

Learning from experience depends at least in part on changes in neuronal connections. We present the largest map of connectivity to date between cortical neurons of a defined type (layer 2/3 [L2/3] pyramidal cells in mouse primary visual cortex), which was enabled by automated analysis of serial section electron microscopy images with improved handling of image defects (250 × 140 × 90 μm volume). We used the map to identify constraints on the learning algorithms employed by the cortex.

A scalable and modular automated pipeline for stitching of large electron microscopy datasets.

Serial-section electron microscopy (ssEM) is the method of choice for studying macroscopic biological samples at extremely high resolution in three dimensions. In the nervous system, nanometer-scale images are necessary to reconstruct dense neural wiring diagrams in the brain, so -called . The data that can comprise of up to 10 individual EM images must be assembled into a volume, requiring seamless 2D registration from physical section followed by 3D alignment of the stitched sections.

Structure and function of axo-axonic inhibition.

Inhibitory neurons in mammalian cortex exhibit diverse physiological, morphological, molecular, and connectivity signatures. While considerable work has measured the average connectivity of several interneuron classes, there remains a fundamental lack of understanding of the connectivity distribution of distinct inhibitory cell types with synaptic resolution, how it relates to properties of target cells, and how it affects function. Here, we used large-scale electron microscopy and functional imaging to address these questions for chandelier cells in layer 2/3 of the mouse visual cortex.

A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy.

Electron microscopy (EM) is widely used for studying cellular structure and network connectivity in the brain. We have built a parallel imaging pipeline using transmission electron microscopes that scales this technology, implements 24/7 continuous autonomous imaging, and enables the acquisition of petascale datasets. The suitability of this architecture for large-scale imaging was demonstrated by acquiring a volume of more than 1 mm of mouse neocortex, spanning four different visual areas at synaptic resolution, in less than 6 months.

2,4,6-Triphenylaniline nanoemulsion formulation, optimization, and its application in type 2 diabetes mellitus.

The secondary metabolite 2,4,6-triphenylaniline (TPA) was isolated from an endophytic fungi Alternaria longipes strain VITN14G of mangrove plant Avicennia officinalis, that exhibited satisfactory in vitro antidiabetic activity for type 2 diabetes mellitus (T2DM). The TPA was encapsulated using nanoemulsion (NE) to overcome the problem of stability and permeability to increase its therapeutic applications. Response surface methodology (RSM) was used for the optimization of the variables given, such as hydrodynamic diameter, surface charge, and polydispersity index (PDI).

Secondary metabolite as therapeutic agent from endophytic fungi Alternaria longipes strain VITN14G of mangrove plant Avicennia officinalis.

Endophytic fungi, especially from mangrove plants, are rich source of secondary metabolites, which plays a major role in various pharmacological actions preferably in cancer and bacterial infections. To perceive its role in antidiabetic activity we isolated and tested the metabolites derived from a novel strain Alternaria longipes strain VITN14G obtained from mangrove plant Avicennia officinalis. The crude extract was analyzed for antidiabetic activity and subjected to column chromatography.

Florid Osseous Dysplasia-Report of Two Cases and Review of Literature.

Florid osseous dysplasia is a rare benign fibro-osseous multiquadrant dysplastic lesion confined to the alveolar process of jaws, generally asymptomatic and usually detected incidentally during radiologic examination and requires no treatment unless symptomatic or cosmetically concerning. In this article, we present two rare cases of florid osseous dysplasia in Indian women with their clinical, radiographic and histologic findings and a brief review of literature. The first case was asymptomatic and the lesion was detected during routine radiographic examination and required no treatment whereas, the second case presented with features of osteomyelitis.

Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs.

Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences.

An integrated workflow for DNA methylation analysis.

The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes. DNA methylation has a demonstrated role in the genome stability and protection, regulation of gene expression and many other aspects of genome function and maintenance. BS-seq is a relatively unbiased method for profiling the DNA methylation, with a resolution capable of measuring methylation at individual cytosines.

2-hydroxy 4-methoxy benzoic acid isolated from roots of Hemidesmus indicus ameliorates liver, kidney and pancreas injury due to streptozotocin-induced diabetes in rats.

Protective effect was evaluated in streptozoticin (STZ)-induced diabetes rats. 2-Hydroxy 4-methoxy benzoic acid (HMBA) was isolated from the roots of Hemidesmus indicus and administered (500 microg/kg body weight) orally for 7 weeks to STZ-induced diabetic and non-diabetic rats to study its effect on protein metabolism, serum electrolytes and on liver and kidney lipid peroxides. Oral administration of HMBA restored the altered biochemical parameters such as urea, uric acid, creatinine, plasma proteins and serum electrolytes to near-normal levels.

Computational methods for comparative analysis of plant small RNAs.

Small RNAs play an important role in plant development, stress responses, and epigenetic regulation, primarily through their role in transcriptional and post-transcriptional silencing of specific target genes and loci. Most if not all plants utilize these small RNA signaling networks. We have developed a deep-sequencing based dataset of plant small RNAs, based on the hypothesis that comparisons among the complex pool of small RNAs from diverse plants will identify novel types of conserved, regulated, or species-specific molecules.

Antidiabetic and ameliorative potential of Ficus bengalensis bark extract in streptozotocin induced diabetic rats.

The aim of the present study was to evaluate the antidiabetic and ameliorative potential of aqueous extract of Ficus bengalensis bark in streptozotocin induced diabetic rats. The effect of oral administration of aqueous extract of F. bengalensis bark on blood glucose, serum electrolytes, serum glycolytic enzymes, liver microsomal protein, hepatic cytochrome P-450 dependent monooxygenase enzymes and lipid peroxidation in liver and kidney of streptozotocin -induced diabetic rats was studied.

Hypoglycemic activity of Hemidesmus indicus R. Br. on streptozotocin-induced diabetic rats.

Objective: To evaluate the antidiabetic activity of an aqueous extract of the roots of Hemidesmus indicus on blood glucose, serum electrolytes, serum marker enzymes, liver microsomal P-450 enzymes, and lipid peroxidation in the liver and kidney of streptozotocin-induced diabetic rats.

Materials And Methods: Effect of H. indicus extract on blood glucose was studied with fed, fasted and glucose-loaded diabetic and nondiabetic rat models.