Neuronal dynamics and connectivity analysis of neuronal cultures on multi electrode arrays

Despite a number of attempts over the past two decades, research into reliable, controlled induction of long term evoked responses, mimicking low level learning and memory in dissociated cell cultures remains challenging. In addition, a full understanding of the stimulus-response relationships that underlie synaptic plasticity has not yet been achieved, and many of the underlying principles remain largely unknown. Plasticity studies have been predominantly limited to low density Multi/Micro Electrode Arrays (MEAs). With the advent of complementary metal-oxide-semiconductor (CMOS) based High-Density (HD) MEAs, unprecedented spatial and temporal resolution is now possible. In this thesis, an attempt to bridge the gap between studies of neural plasticity and the use of CMOS based HD-MEAs with thousands of electrodes, is reported. Additionally, since such HD-MEAs generate a large volume of data and require advanced analytics to efficiently process and analyse recordings, computational tools and novel algorithms to infer connectivity during plasticity have been developed. The study showed that the responsiveness, stability and initial firing rate of neuronal cultures are the deciding factors to reliably induce evoked responses. With multi-site stimulation, sustained long term potentiation was achieved, which was validated both by evoked response plots and overall firing rates measured at five different time points - before and after repeated stimulation, and at a three day time points. In contrast, while depression responses were observed, it was found that the effects were not sustained over many days. The findings of the study suggest that appropriate selection of neuronal cultures is crucial for inducing desired evoked responses and criteria for this have been developed. Furthermore, it is concluded that the initial responses to test stimuli can be used to determine whether potentiated or depressed responses are to be expected. To analyse the recordings, pipeline of computational tools was developed. Firstly, neuronal synchrony metrics were adapted for the first time for large HD-MEA recordings and shown to correspond effectively to the firing dynamics. To analyse functional connectivity, an information theoretic approach, Transfer Entropy(TE), was utilised. The method showed accurate estimation of functional connectivity with mid 80th percentile accuracy on simulated data. A superimposition method was proposed to enhance confidence in the connectivity estimation. To statistically evaluate connectivity estimation, a new surrogate method, based on ISI distribution approach, was proposed and validated with a simulated Izhikevich network. The method achieved improved accuracy, compared to the existing ISI shuffling method. This newly developed method was later utilised to infer connectivity and refine connections during the learning process of real neuronal cultures over many days of stimulation. The connectivity inference corresponded accurately to both the spontaneous and stimulated networks during evoked responses and the proposed method permitted observation of the evolution of connections for the potentiated network

Geographic Isolation and Poverty among Indigenous Peoples in Nepal

This study analyzed nationally representative sample of women (N =10793) to quantify the magnitude and predictors of poverty among indigenous peoples of Nepal. The study estimated the risk of poverty among the major ethnic groups in Nepal. Cross-sectional data from the Nepal Demographic and Health Survey 2006 (NDHS 2006) was used. Step-wise multivariate logistic regressions were conducted. The results show that significant variations exist in the risk of poverty between indigenous and non-indigenous peoples. Tamang were at the highest risk of poverty among the indigenous peoples. Controlling for geography further exacerbated the disparity between indigenous and non-non indigenous peoples. Attentions to the intrinsic development practices are needed to determine if these variations are reflective of the institutions that systematically isolate geographic territories of the indigenous peoples

PCR Based Genotyping of Lulu Cattle of Nepal for A1, A2 Type Beta-caseins

Lulu is an indigenous breed of cattle (Bos taurus) found in high altitude regions of western Nepal. Population of Lulu cattle has been declining due to introgression with other exotic breeds to increase milk productivity. Here we aimed at finding potential approach for conserving Lulu cattle and its assets by studying the milk contents and investigating which variant of beta-casein protein is present in this breed. Beta caseins are an abundant protein in cow milk with A1 and A2 being the most common genetic variants of this protein. Consumption of A1 type of milk has numerous health-related complications whereas A2 type of milk has numerous human health promoting factors. We used restriction fragment length polymorphism (RFLP) for determining the A1 and A2 variant of beta casein in Lulu cattle. For performing DNA extraction, we collected (n = 18) blood samples of Lulu from Mustang and (n=17) Nepal Agriculture research council farm. The amplified fragments in 3% agarose at 251bp and 213bp respectively confirmed the presence of both A1 and A2 gene in Lulu; however, A2 was of greater abundance. Our study indicated that Lulu has A2 variant of beta-casein predominantly. The gene frequency of A1A1 is 0, A1A2 is 0.06 and A2A2 is 0.94. We further found that the allele frequency of A1 and A2 is 0.03 and 0.97 respectively. We designed special primer for sequencing CSN2 genes since A2 type beta casein gene was predominantly seen on Lulu. The sequencing result further supports our RFLP result as most of our samples have “C” nucleotide SNP in amplified CSN2 gene sequence. The Chi-square value of the current study is 0.04 which supports Hardy-Weinberg equilibrium inferring that Lulu cattle are still in the pure state, where there is no genetic introgression with the exotic breed for the sake of improvement of productivity

Neuroprotective Role of SRT1720 Against Hydrogen Peroxide Induced Oxidative Stress in NT2 Cells

Neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD) are characterized by a significant increase in neuronal loss. Oxidative stress (OS) plays a significant role on neuronal damage. Reactive oxygen species (ROS) generated from agents such as hydrogen peroxide (H2O2) leads to cell damage and reduction of cell viability. Sirtuin 1 (SIRT1) is a therapeutic target for neurodegenerative disorders because it regulates several cellular functions and biological processes that promote cellular longevity. This study was undertaken to examine the role of SRT1720 in protecting cells from H2O2 induced stress in Ntera-2 cl.D1(NT2), which has been proven to be a useful in vitro system for the investigation of functions related to human neuronal and glial systems. The results provide evidence that H2O2 significantly induced oxidative stress in a concentration dependent manner. Moreover, pre-treatment with low concentrations of SRT1720 for 48 hours protected against the effects of H2O2. Also, a combination of H2O2 and SRT1720 improved cell viability. Interestingly, apoptotic or necrotic cell death was not detected after H2O2 treatment in the cell culture model system employed

Extensions of I-Reversible Rings

A ring $R$ is said to be i-reversible if for every $a,b$ $\in$ $R$, $ab$ is a non-zero idempotent implies $ba$ is an idempotent. It is known that the rings $M_n(R)$ and $T_n(R)$ (the ring of all upper triangular matrices over $R$) are not i-reversible for $n \geq 3$. In this article, we provide a non-trivial i-reversible subring of $M_n(R)$ when $n \geq 3$ and $R$ has only trivial idempotents. We further provide a maximal i-reversible subring of $T_n(R)$ for each $n\geq 3$, if $R$ is a field. We then give conditions for i-reversibility of Trivial, Dorroh and Nagata extensions. Finally, we give some independent sufficient conditions for i-reversibility of polynomial rings, and more generally, of skew polynomial rings

On the survivability and detectability of terrestrial meteorites on the moon

Materials blasted into space from the surface of early Earth may preserve a unique record of our planet's early surface environment. Armstrong et al. (2002) pointed out that such materials, in the form of terrestrial meteorites, may exist on the Moon and be of considerable astrobiological interest if biomarkers from early Earth are preserved within them. Here, we report results obtained via the AUTODYN hydrocode to calculate the peak pressures within terrestrial meteorites on the lunar surface to assess their likelihood of surviving the impact. Our results confirm the order-of-magnitude estimates of Armstrong et al. (2002) that substantial survivability is to be expected, especially in the case of relatively low velocity (ca. 2.5 km/s) or oblique (≤45°) impacts, or both. We outline possible mechanisms for locating such materials on the Moon and conclude that searching for them would be a scientifically valuable activity for future lunar exploration

FACTORS AFFECTING METFORMIN AND CLOMIPHENE’S REPRODUCTIVE EFFICACY IN PCOS WOMEN

Polycystic Ovarian Syndrome (PCOS) is a heterogeneous multifactorial disorder in which the ovarian dysfunction is the main cause of an ovulatory infertility. Metformin and Clomiphene Citrate (CC) are two effective drugs to induce ovulation in these patients. The study aimed to ascertain the effect of obesity, serum insulin and free testosterone levels on fertility success with metformin and CC as first line approaches in PCOS. This clinical study was a retrospective multicenter cohort study conducted in nine gynecology and endocrinology clinics. It included (61) PCOS women, aged (18-32) years, having desire to conceive, and free from the study medications for more than six months. Patients were divided to metformin receiving and CC receiving groups. Main outcomes of measure were; pregnancy rate, and improvement in PCOS as detected by ultrasound on their second visit. Results showed that CC was more effective in non-obese users (P0.05). Overall improvement was affected by Serum Free Testosterone (SFT) in both study groups (P\u3e0.05). Metformin was effective regardless of patient’s SFT levels, while CC was effective in patients with high SFT levels. There was a significant association between obesity and pregnancy rate in metformin users (P0.05). However, CC was less effective than metformin in overall improvement (OR=0.53, P\u3e0.05,) suggesting metformin as the possible drug of choice regardless to obesity, serum insulin and SFT levels

Optimal Uncertainty Quantification

We propose a rigorous framework for Uncertainty Quantification (UQ) in which the UQ objectives and the assumptions/information set are brought to the forefront. This framework, which we call \emph{Optimal Uncertainty Quantification} (OUQ), is based on the observation that, given a set of assumptions and information about the problem, there exist optimal bounds on uncertainties: these are obtained as values of well-defined optimization problems corresponding to extremizing probabilities of failure, or of deviations, subject to the constraints imposed by the scenarios compatible with the assumptions and information. In particular, this framework does not implicitly impose inappropriate assumptions, nor does it repudiate relevant information. Although OUQ optimization problems are extremely large, we show that under general conditions they have finite-dimensional reductions. As an application, we develop \emph{Optimal Concentration Inequalities} (OCI) of Hoeffding and McDiarmid type. Surprisingly, these results show that uncertainties in input parameters, which propagate to output uncertainties in the classical sensitivity analysis paradigm, may fail to do so if the transfer functions (or probability distributions) are imperfectly known. We show how, for hierarchical structures, this phenomenon may lead to the non-propagation of uncertainties or information across scales. In addition, a general algorithmic framework is developed for OUQ and is tested on the Caltech surrogate model for hypervelocity impact and on the seismic safety assessment of truss structures, suggesting the feasibility of the framework for important complex systems. The introduction of this paper provides both an overview of the paper and a self-contained mini-tutorial about basic concepts and issues of UQ.Comment: 90 pages. Accepted for publication in SIAM Review (Expository Research Papers). See SIAM Review for higher quality figure

Magnetic coiffure: Engineering of human hair surfaces with polyelectrolyte-stabilised magnetite nanoparticles

Here we report a spontaneous electrostatic coating of human hair with aqueous Fe3O4 colloids capable to tailor magnetic properties to hair, orienting and even moving them under the influence of the external magnetic field. Magnetite particles were modified by cationic and anionic polyelectrolytes and then successfully deposited in dense arrays, starting from cuticle gaps and spreading further over a major hair surface. These biocompatible and biodegradable magnetic nanoparticles may serve as carriers for drug loading and delivery for topical pharmaceutical treatments. The deposition process was imaged in real-time using dark-field microscopy. The hair specimens were further studied using a number of characterisation techniques. Under application of an external magnetic field, the nanoparticle magnetic ordering was obtained resulting in the hair alignment and attraction along the field applied. We believe the technology reported here will find a range of applications in topical drug delivery and hair care

Reciprocal regulation of airway rejection by the inducible gas-forming enzymes heme oxygenase and nitric oxide synthase

Obliterative bronchiolitis (OB) develops insidiously in nearly half of all lung transplant recipients. Although typically preceded by a CD8+ T cell–rich lymphocytic bronchitis, it remains unresponsive to conventional immunosuppression. Using an airflow permissive model to study the role of gases flowing over the transplanted airway, it is shown that prolonged inhalation of sublethal doses of carbon monoxide (CO), but not nitric oxide (NO), obliterate the appearance of the obstructive airway lesion. Induction of the enzyme responsible for the synthesis of CO, heme oxygenase (Hmox) 1, increased carboxyhemoglobin levels and suppressed lymphocytic bronchitis and airway luminal occlusion after transplantation. In contrast, zinc protoporphyrin IX, a competitive inhibitor of Hmox, increased airway luminal occlusion. Compared with wild-type allografts, expression of inducible NO synthase (iNOS), which promotes the influx of cytoeffector leukocytes and airway graft rejection, was strikingly reduced by either enhanced expression of Hmox-1 or exogenous CO. Hmox-1/CO decreased nuclear factor (NF)-κB binding activity to the iNOS promoter region and iNOS expression. Inhibition of soluble guanylate cyclase did not interfere with the ability of CO to suppress OB, implicating a cyclic guanosine 3′,5′-monophosphate–independent mechanism through which CO suppresses NF-κB, iNOS transcription, and OB. Prolonged CO inhalation represents a new immunosuppresive strategy to prevent OB