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It is well known that quality of hearing decreases with increasing age due to changes in the peripheral or central auditory pathway. Along with the decrease in the number of neurons the neurotransmitter profile is also affected in the various parts of the auditory system. Particularly, changes in the inhibitory neurons in the inferior colliculus (IC) are known to affect quality of hearing with aging. To date, there is no information about the status of the inhibitory neurotransmitter GABA in the human IC during aging. We have collected and processed inferior colliculi of persons aged 11-97 years at the time of death for morphometry and immunohistochemical expression of glutamic acid decarboxylase (GAD67) and parvalbumin. We used unbiased stereology to estimate the number of cresyl-violet and immunostained neurons. Quantitative real-time PCR was used to measure the relative expression of the GAD67 mRNA. We found that the number of total, GABAergic and PV-positive neurons significantly decreased with increasing age (p 0.05). The proportion of GAD67-ir neurons to total number of neurons was also negatively associated with increasing age (p = 0.004), but there was no change observed in the proportion of PV-ir neurons relative to GABAergic neurons (p = 0.25). Further, the fold change in the levels of GAD67 mRNA was negatively correlated to age (p = 0.024). We conclude that the poorer quality of hearing with increasing age may be due to decreased expression of inhibitory neurotransmitters and the decline in the number of inhibitory neurons in the IC.

Estimation of total number of neurons in the spiral ganglion (SG) at various ages and their functional status is important as these neurons are constantly exposed to noise and other environmental factors that may lead to neuronal loss with aging due to excitotoxic damage. Parvalbumin (PV) is a calcium-binding protein (CBP), found in highly metabolically active neurons. It helps in buffering cytosolic calcium, which is essential for neurotransmitter release. The neurons in the adult human SG express PV more strongly than other CBPs like calbindin and calretinin. These CBPs can be used as signatures to recognise neurons. In the present study, we quantified the number of neurons expressing PV by unbiased stereology and compared it to the number of neurons stained by cresyl violet (CV), which is a Nissl stain, in the adult human SG. Five adult human cadaveric temporal bones were obtained from the forensic science mortuary, after due clearance from the institute ethics committee. Independent CV stained and PV immunostained sections were used to estimate the total number of neurons (optical fractionator), with StereoInvestigator (SI) software. The estimated total number of SG neurons was 27,485±3251 and 26,705±1823 in the PV and CV stained sections, respectively. There was no significant difference between the estimates (p=0.552). Therefore, CV staining is simpler and more cost effective when estimating neuronal number. Although PV stains spiral ganglion neurons (SGNs) with a greater intensity and provides a functional status, its tedious protocol limits its use for quantification.

Animal-studies associate age-related hearing loss (presbycusis) with decreasing number of spiral ganglion neurons (SGNs) in Rosenthal’s canal (RC) of cochlea. The excitatory neurotransmitter for SGNs is glutamate (through its receptor NMDAR 2B), which can be neurotoxic through Ca2+ overload. Neurotoxicity is balanced by calcium-binding proteins (CBPs) like Parvalbumin (PV), which is the predominant CBP of the SGNs. To estimate the volume of the RC and total number of SGNs that are immunoreactive to PV and NMDAR 2B, we used unbiased stereology in 35 human cochleae derived from cadavers of persons from 2nd to 8th decade of life (subsequently statistically divided into two groups) and compared them to the total number of cresyl violet (CV) stained SGNs. We also estimated the volume of individual neurons and their nuclei. Regression analysis was made on estimated parameters against age. Hierarchical-cluster analysis was done on the neuronal against neuronal nuclear volumes.The average volume of the RC did not change with increasing age (p = 0.4115). The total number of SGNs (CV-stained and those separately expressing PV and NMDAR 2B) significantly decreased with age (p

The Next Generation Sequencing (NGS) technologies have provided affordable ways to generate errorful raw genetical data. To extract Variant Information from billions of NGS reads is still a daunting task which involves various hand-crafted and parameterized statistical tools. Here we propose a Deep Neural Networks (DNN) based alignment and SNV tool known as DAVI. DAVI consists of models for both global and local alignment and for Variant Calling. We have evaluated the performance of DAVI against existing state of the art tool-set and found that its accuracy and performance is comparable to existing tools used for benchmarking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies. Moreover, this approach is a migration from expert driven statistical models to generic, automated, self-learning models.

Morphological studies in developing brain determine critical periods of proliferation, neurogenesis, gliogenesis, and apoptosis. During these periods both intrinsic and extrinsic pathological factors can hamper development. These time points are not available for the human cochlear nucleus (CN). We have used design-based stereology and determined that 18–22 weeks of gestation (WG) are critical in the development of the human CN. Twenty-three fetuses and seven postnatal brainstems were processed for cresyl violet (CV) staining and immunoexpression of NeuN (neurons), GFAP (astrocytes), Ki-67 (proliferation) and TUNEL (apoptosis) and 3-D reconstruction. The volume of CN, total number of neurons selected profiles and the volume of neurons and their nuclei were estimated. Data were grouped (G) into: G1:18-20 WG, G2: 21–24 WG, G3: 25–28 WG and G4 >29 WG. The dimensions of morphologically identified neurons were also measured. The CN primordium was first identifiable at 10WG. Definitive DCN (Dorsal cochlear nucleus) and VCN (ventral cochlear nucleus) were identifiable at 16 WG. There was a sudden growth spurt in total volume of CN, number of neurons and astrocytes from 18 WG. We also observed an increase in proliferation and apoptosis after 22 WG. The number of neurons identifiable by CV was significantly lower than that by NeuN-immunostaining till 25 WG (p = 0.020), after which, both methods were equivalent. Eight morphological types of neurons were identifiable by 26 WG and could be resolved into four clusters by volume and diameter. The CN changed orientation from small, flat and horizontal at 10–16 WG to larger and oblique from 18WG onwards. Prevention of exposure to noxious factors at 18–22 WG may be important in preventing congenital deafness.

Introduction Age associated progressive fibrosis may be a major causative factor that leads to pathogenesis of many diseases. Activated pancreatic stellate cells (α-SMA positive) play a major role in fibrogenesis that affects the cytoarchitecture and functioning of pancreas. This study dealt with age-related fibrotic changes in the ductular system of the tail and body of pancreas and the morphology of pancreatic stellate cells. Methods Pancreata ( n = 36) from cadavers aged 30–80 years were obtained after due clearances and processed for Masson's trichome staining. Fibrosis was quantified using Adobe Photoshop (CS2) and Image-J software. Hierarchical cluster analysis was done on the luminal area and total ductal area that were measured by the nucleator probe of StereoInvestigator software (MBF, Vermont, USA). Pancreatic stellate cells (α-SMA positive cells) were identified by immunohistochemistry and quantified stereologically around periacinar, periductular, perivascular, and peri-Islet areas. Results An increased fibrosis was noted in body and tail regions of the pancreas with increasing age. Three duct populations were identified in clustering. Their area and corresponding lumen showed a significant increase with progressive decades ( p p = 0.002, 0.004 and 0.002, respectively). Discussion Pancreatic stellate cells may be important contributors to increased fibrosis in pancreas. The classification of pancreatic ducts into three clusters may serve to be a useful tool.

Next-generation sequencing (NGS) technologies have provided affordable but errorful ways to generate raw genetic data. To extract variant information from billions of NGS reads is still a daunting task which involves various hand-crafted and parameterized statistical tools. Here we propose a deep neural networks (DNN) based alignment and single nucleotide variant (SNV) identifier tool known as DAVI: deep alignment and variant identification. DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies as well as across different species. The use of DAVI will therefore help non-human sequencing projects to benefit from the wealth of human ground truth data. Moreover, this approach is a migration from expert-driven statistical models to generic, automated, self-learning models.

The Next Generation Sequencing Technique (NGS) has provided affordable and fast method for generating genetic data. Generation of whole Genome Sequence and extract relevant information from this data is still a computationally expensive process. In this paper we demonstrate a novel approach for local alignment of DNA reads with respect to reference genome. For this process we have used Skip-gram model for creating encoding(Nucl2Vec) and k-nearest neighbor for the alignment. With our new approach we have reduced computation cost for local alignment, while achieving accuracy comparable to existing defacto standard BWA-MEM tool.Index TermsGenome, Alignment, Local Alignment, k-nearest Neighbor, Distributed vector representation, Skip-gram

Pancreas gets affected by fibrosis associated with aging. This study analyzed the age-related fibrotic changes in the ductular system of the pancreas. After obtaining necessary ethical clearances, twelve human fetal and thirty post-natal and adult pancreas were collected and processed to obtain resin-embedded sections for transmission electron microscopy and paraffin-embedded sections for H&E staining and light microscopy. The sections were analyzed qualitatively and quantitatively. The human pancreas had mature zymogen granules in the exocrine part and secretory granules in the endocrine part by 20th week of gestation. The amount of connective tissue and acini increased with age. After the 3rd decade, there was increased fibrosis. This began around small and medium sized ducts. Changes in the epithelium of ducts were seen in later decades. There was a direct correlation between area of the ducts and increasing age. There was increased fibrosis in and around the islets of Langerhans. The number of fibroblasts and stellate cells increased with age. The increased fibrosis with increasing age that first appears around the small and medium sized ducts may be due to increased number of pancreatic stellate cells.