Development of a compact, IoT-enabled electronic nose for breath analysis

In this paper, we report on an in-house developed electronic nose (E-nose) for use with breath analysis. The unit consists of an array of 10 micro-electro-mechanical systems (MEMS) metal oxide (MOX) gas sensors produced by seven manufacturers. Breath sampling of end-tidal breath is achieved using a heated sample tube, capable of monitoring sampling-related parameters, such as carbon dioxide (CO2), humidity, and temperature. A simple mobile app was developed to receive real-time data from the device, using Wi-Fi communication. The system has been tested using chemical standards and exhaled breath samples from healthy volunteers, before and after taking a peppermint capsule. Results from chemical testing indicate that we can separate chemical standards (acetone, isopropanol and 1-propanol) and different concentrations of isobutylene. The analysis of exhaled breath samples demonstrate that we can distinguish between pre- and post-consumption of peppermint capsules; area under the curve (AUC): 0.81, sensitivity: 0.83 (0.59–0.96), specificity: 0.72 (0.47–0.90), p-value: <0.001. The functionality of the developed device has been demonstrated with the testing of chemical standards and a simplified breath study using peppermint capsules. It is our intention to deploy this system in a UK hospital in an upcoming breath research study

Biocompatibility of Osteoblast Cells on Titanium Implants

Adhesion and proliferation of UMR 106-01 osteoblast cells were studied on various surface modified titanium materials such as polished, sandblasted, anodized and alkaline treated. Anodization of polished surface in Hydrofluoric acid developed nano-tubes, while NaOH treatment produced spongy microporous morphology. Test samples were coated with non-adhesive protein bovine serum albumin and compared with fibronectin coated specimens. The adhesion study lasted for 4 hrs, where osteoblast cells were cultured in serum free medium. Polished titanium, anodized titanium and NaOH titanium have shown similar percentages of cell adherence. The proliferation study lasted for 48 hrs, where cells were initially allowed to adhere to the surface in serum free medium for 4 hrs, followed by a medium change to 10 fatal bovine serum. The specific growth rate after 48 hrs in culture on the polished surface was found to be comparable to the tissue culture plastic, which exhibited a high growth rate. No significant difference was found in cell numbers between polished, anodized and NaOH-Ti, but each has varying cell orientation on the surface. Fluorescence images stained with alkaline phosphatase revealed that polished surface had cells flattened to the surface with short filapodia. Anodized surface had cells uniformly distributed across the surface where as NaOH-Ti displayed cells in colonies. Cells were found bonding to the surface of NaOH-Ti firmly using their filapodia as an anchoring agent. These results suggest that NaOH-Ti provides support in initial hours of implantation and bolsters cell proliferation. All together this process may help to better integrate titanium implant surface

Biocompatibility of Osteoblast Cells on Titanium Implants

Adhesion and proliferation of UMR 106-01 osteoblast cells were studied on various surface modified titanium materials such as polished, sandblasted, anodized and alkaline treated. Anodization of polished surface in Hydrofluoric acid developed nano-tubes, while NaOH treatment produced spongy microporous morphology. Test samples were coated with non-adhesive protein bovine serum albumin and compared with fibronectin coated specimens. The adhesion study lasted for 4 hrs, where osteoblast cells were cultured in serum free medium. Polished titanium, anodized titanium and NaOH titanium have shown similar percentages of cell adherence. The proliferation study lasted for 48 hrs, where cells were initially allowed to adhere to the surface in serum free medium for 4 hrs, followed by a medium change to 10 fatal bovine serum. The specific growth rate after 48 hrs in culture on the polished surface was found to be comparable to the tissue culture plastic, which exhibited a high growth rate. No significant difference was found in cell numbers between polished, anodized and NaOH-Ti, but each has varying cell orientation on the surface. Fluorescence images stained with alkaline phosphatase revealed that polished surface had cells flattened to the surface with short filapodia. Anodized surface had cells uniformly distributed across the surface where as NaOH-Ti displayed cells in colonies. Cells were found bonding to the surface of NaOH-Ti firmly using their filapodia as an anchoring agent. These results suggest that NaOH-Ti provides support in initial hours of implantation and bolsters cell proliferation. All together this process may help to better integrate titanium implant surface

Biocompatibility of Osteoblast Cells on Titanium Implants

Adhesion and proliferation of UMR 106-01 osteoblast cells were studied on various surface modified titanium materials such as polished, sandblasted, anodized and alkaline treated. Anodization of polished surface in Hydrofluoric acid developed nano-tubes, while NaOH treatment produced spongy microporous morphology. Test samples were coated with non-adhesive protein bovine serum albumin and compared with fibronectin coated specimens. The adhesion study lasted for 4 hrs, where osteoblast cells were cultured in serum free medium. Polished titanium, anodized titanium and NaOH titanium have shown similar percentages of cell adherence. The proliferation study lasted for 48 hrs, where cells were initially allowed to adhere to the surface in serum free medium for 4 hrs, followed by a medium change to 10 fatal bovine serum. The specific growth rate after 48 hrs in culture on the polished surface was found to be comparable to the tissue culture plastic, which exhibited a high growth rate. No significant difference was found in cell numbers between polished, anodized and NaOH-Ti, but each has varying cell orientation on the surface. Fluorescence images stained with alkaline phosphatase revealed that polished surface had cells flattened to the surface with short filapodia. Anodized surface had cells uniformly distributed across the surface where as NaOH-Ti displayed cells in colonies. Cells were found bonding to the surface of NaOH-Ti firmly using their filapodia as an anchoring agent. These results suggest that NaOH-Ti provides support in initial hours of implantation and bolsters cell proliferation. All together this process may help to better integrate titanium implant surface

Effects of large solar zenith angles and cloud cover on underwater irradiance

Le processus de la photosynthèse nécessite l'énergie de la lumière solaire et, dans l’océan, se déroule essentiellement dans la couche euphotique. Outre les autres variables (à savoir la chlorophylle a et les paramètres photosynthétiques), une connaissance appropriée du champ lumineux en termes de rayonnement incident disponible sur la photosynthèse (PAR) à un emplacement, une profondeur et une heure et une date donnés, est requise par les modèles d'écosystème marin. Le travail inclus dans cette thèse examine comment des angles de zénith solaires plus grands et différentes conditions nuageuses caractéristiques des régions de haute latitude, en particulier dans l'Arctique, peuvent affecter la précision des estimations de l'éclairement de surface et dans la colonne d’eau. L’accent est également mis sur les variations du champs lumineux à haute fréquence liées à la nébulosité sur les estimations de la productivité primaire. Les PAR de surface estimés à partir de différents modèles ont été comparés à des mesures en série chronologique in situ à haute fréquence de données de PAR d'une bouée située en mer Méditerranée. Nous avons examiné comment les incertitudes dues aux angles de zénith solaires plus grands, en conditions nuageuses variables, pouvaient affecter la précision des estimations de l'éclairement de surface. La méthode de classement objectif a été utilisée pour identifier les meilleures méthodes. Le produit PAR de la NASA-Ocean Biology Processing Group (OBPG) a montré les meilleures performances globales, tandis que les PAR basées sur la méthode de la table de conversion (LUT) ont présenté les meilleures performances en termes de différence carrée moyenne, de biais sous ciel clair et également par temps couvert. D'autres méthodes basées sur des formulations empiriques ont montré la troisième meilleure performance par temps clair, tandis que par temps nuageux, elles présentaient de plus grandes incertitudes. Trois méthodes testées par faible ensoleillement ont montré des incertitudes allant jusqu'à 50% dans toutes les conditions du ciel. Les performances du modèle dépendent des propriétés et des produits de nuage...The process of photosynthesis requires the energy from sunlight and takes place essentially in the euphotic layer of the oceans. In addition to other variables (i.e., chlorophyll a and photosynthetic parameters) a suitable knowledge of light field in terms of photosynthetically available radiation (PAR) at any given location, depth and time is an important input parameter required by marine ecosystem models. The work included in this thesis examines how larger solar zenith angles, different cloud conditions that are characteristic features of high latitude regions, especially in Arctic, might affect the accuracy of surface irradiance estimates. Further, main focus was on the effects of high frequency variations in the light field on primary production. Surface PAR estimated from different models were compared with high frequency in situ time series measurements of PAR a buoy located in Mediterranean Sea. It was examined how uncertainties due to larger solar zenith angles under varying cloud conditions might affect the accuracy of surface irradiance. Objective ranking method was used to identify the best methods. Methods tested under low sun elevations exhibited uncertainties as large as 50% under all sky conditions. Model performances were dependent on cloud properties and products. Accuracy of a semianalytical model for coefficient of vertical diffuse attenuation of surface irradiance (kd!) based on optical properties inherent to the water itself (absorption and scattering), and solar zenith angle was examined under larger solar zenith angels and cloud conditions. Extensive radiative transfer simulations were performed to quantify the uncertainties due to large solar zenith angles and clouds on the estimates of diffuse attenuation coefficient. The uncertainties under both these conditions are due to the variability in the proportions of direct and diffuse parts of the total irradiance reaching the surface and in the water column. Also, an improved model parameterization proposed to estimate !"# under large solar zenith angels and cloud conditions was evaluated with Arctic in situ data exhibited good performances..

A Distributed Diffusion-Driven Algorithm for Load Balancing in an Electrical Power Grid

In this thesis we propose a distributed algorithm, based on diffusion, to balance loads on an electrical power grid, while maintaining stable operation (system’s ability to maintain bus voltages within preset bounds). This algorithm, called the Diffusion-driven Distributed Load Balancing (DDLB) algorithm, is implemented on the OMNET++ Discrete Event Simulator and the response of the physical grid is simulated on a load flow program, which together simulate a deployment of the DDLB algorithm on the grid. The electrical grid is represented as a graph whose nodes are buses and whose edges are power lines connecting buses. Each node (except the slack bus) has a load (positive if power consumed, negative if power generated) associated with it. The slack bus is a special bus that covers any power surplus or deficit due to a load assignment. A given load assignment, when applied to the grid affects bus voltages and system stability. The problem we address is as follows. Given a preferred load for each node and a load cost (a measure of deviation from this preferred load), the ideal solution is a load assignment with lowest cost that results in a stable system. We measure the performance of our algorithm (DDLB) against the one-shot algorithm, a naive distributed solution in which each node uses its preferred load directly for a load assignment, without any regard for system stability. Through extensive simulations with 1.6 million test cases, we show that the DDLB algorithm vastly outperforms one-shot. Specifically, the one-shot algorithm causes instability in over 57% of the cases tested albeit with zero load cost. For the same cases when applied to the DDLB algorithm only 0.65% were unstable; the average load cost was less than 2%. Our simulations included a study of several scenarios that a grid could be subjected to, including balanced load, overloaded, underloaded grids, local generator failures, and a sparser communication network for the DDLB algorithm; in this context one could view the one-shot algorithm as a distributed algorithm with no communication network. In all these scenarios studied the DDLB algorithm outperforms the one-shot algorithm

DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts

DNA methylation has been associated with transcriptional repression and detection of differential methylation is important in understanding the underlying causes of differential gene expression. Bisulfite-converted genomic DNA sequencing is the current gold standard in the field for building genome-wide maps at a base pair resolution of DNA methylation. Here we systematically investigate the underlying features of detecting differential DNA methylation in CpG and non-CpG contexts, considering both the case of mammalian systems and plants. In particular, we introduce DMRcaller, a highly efficient R/Bioconductor package, which implements several methods to detect Differentially Methylated Regions (DMRs) between two samples. Most importantly, we show that different algorithms are required to compute DMRs and the most appropriate algorithm in each case depends on the sequence context and levels of methylation. Furthermore, we show that DMRcaller outperforms other available packages and we propose a new method to select the parameters for this tool and for other available tools. DMRcaller is a comprehensive tool for differential methylation analysis which displays high sensitivity and specificity for the detection of DMRs and performs entire genome wide analysis within a few hours