Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualization for Simulation-Based Decision Support in Manufacturing

Nowadays, the increasing demand for ever more customizable products has emphasized the need for more flexible and fast-changing manufacturing systems. In this environment, simulation has become a strategic tool for the design, development, and implementation of such systems. Simulation represents a relatively low-cost and risk-free alternative for testing the impact and effectiveness of changes in different aspects of manufacturing systems. Systems that deal with this kind of data for its use in decision making processes are known as Simulation-Based Decision Support Systems (SB-DSS). Although most SB-DSS provide a powerful variety of tools for the automatic and semi-automatic analysis of simulations, visual and interactive alternatives for the manual exploration of the results are still open to further development. The work in this dissertation is focused on enhancing decision makers’ analysis capabilities by making simulation data more accessible through the incorporation of visualization and analysis techniques. To demonstrate how this goal can be achieved, two systems were developed. The first system, viPhos – standing for visualization of Phos: Greek for light –, is a system that supports lighting design in factory layout planning. viPhos combines simulation, analysis, and visualization tools and techniques to facilitate the global and local (overall factory or single workstations, respectively) interactive exploration and comparison of lighting design alternatives. The second system, STRAD - standing for Spatio-Temporal Radar -, is a web-based systems that considers the spatio/attribute-temporal analysis of event data. Since decision making processes in manufacturing also involve the monitoring of the systems over time, STRAD enables the multilevel exploration of event data (e.g., simulated or historical registers of the status of machines or results of quality control processes). A set of four case studies and one proof of concept prepared for both systems demonstrate the suitability of the visualization and analysis strategies adopted for supporting decision making processes in diverse application domains. The results of these case studies indicate that both, the systems as well as the techniques included in the systems can be generalized and extended to support the analysis of different tasks and scenarios.
GeoDiver: Differential Gene Expression Analysis & Gene-Set Analysis For GEO Datasets

Summary GeoDiver is an online web application for performing Differential Gene Expression Analysis (DGEA) and Generally Applicable Gene-set Enrichment Analysis (GAGE) on gene expression datasets from the publicly available Gene Expression Omnibus (GEO). The output produced includes numerous high quality interactive graphics, allowing users to easily explore and examine complex datasets instantly. Furthermore, the results produced can be reviewed at a later date and shared with collaborators. Availability GeoDiver is freely available online at http://www.geodiver. co.uk. The source code is available on Github: https://github.com/GeoDiver/GeoDiver and a docker image is available for easy installation.
Variations in the vertical profile of ozone at four high-latitude Arctic sites from 2005 to 2017

Abstract. Understanding variations in atmospheric ozone in the Arctic is difficult because there are only a few long-term records of vertical ozone profiles in this region. We present 12 years of ozone profiles from February 2005 to February 2017 at four sites: Summit Station, Greenland; Ny-Ålesund, Svalbard, Norway; and Alert and Eureka, Nunavut, Canada. These profiles are created by combining ozonesonde measurements with ozone profile retrievals using data from the Microwave Limb Sounder (MLS). This combination creates a high-quality dataset with low uncertainty values by relying on in situ measurements of the maximum altitude of the ozonesondes (∼30 km) and satellite retrievals in the upper atmosphere (up to 60 km). For each station, the total column ozone (TCO) and the partial column ozone (PCO) in four atmospheric layers (troposphere to upper stratosphere) are analyzed. Overall, the seasonal cycles are similar at these sites. However, the TCO over Ny-Ålesund starts to decline 2 months later than at the other sites. In summer, the PCO in the upper stratosphere over Summit Station is slightly higher than at the other sites and exhibits a higher standard deviation. The decrease in PCO in the middle and upper stratosphere during fall is also lower over Summit Station. The maximum value of the lower- and middle-stratospheric PCO is reached earlier in the year over Eureka. Trend analysis over the 12-year period shows significant trends in most of the layers over Summit and Ny-Ålesund during summer and fall. To understand deseasonalized ozone variations, we identify the most important dynamical drivers of Arctic ozone at each level. These drivers are chosen based on mutual selected proxies at the four sites using stepwise multiple regression (SMR) analysis of various dynamical parameters with deseasonalized data. The final regression model is able to explain more than 80 % of the TCO and more than 70 % of the PCO in almost all of the layers. The regression model provides the greatest explanatory value in the middle stratosphere. The important proxies of the deseasonalized ozone time series at the four sites are tropopause pressure (TP) and equivalent latitude (EQL) at 370 K in the troposphere, the quasi-biennial oscillation (QBO) in the troposphere and lower stratosphere, the equivalent latitude at 550 K in the middle and upper stratosphere, and the eddy heat flux (EHF) and volume of polar stratospheric clouds throughout the stratosphere.
Chemical constituents of Securidaca longipedunculata root bark and evaluation of their antibacterial activities

The Bioassay-guided sequential extraction and column chromatographic separation of theroot bark of Securidaca longipedunculata led to the isolation of three phenolic compounds; two benzoic acid derivatives (1 and 2) and a xanthone (3). The structures ofthese compounds were established based on the spectroscopic analyses including NMR( 1 H and 13 C NMR, 1 H- 1 H COSY, HMQC, and HMBC), MS, IR, UV-Vis and comparison with reported literature. In an in vitro antibacterial assay of the crude extracts and the pure compounds against four bacterial strains (S. aureus ATCC 25923, B. subtilis ATCC 6633,E. coli ATCC 35218, P. aeruginosa ATCC 27853), almost all crude extracts showed significant anti bacterial activity with acetone extract exhibited highest activity against B.subtilis and P. aeruginosa. Whereas, only compound 3 showed activity against the tested bacterial strains with the highest activity observed against B. subtilis with inhibition zone diameter 15 mm, which is comparable to that of the reference drug (gentamycin).
Investigation of multicomponent adsorption isotherms in chromatography using high-throughput formats

Adsorption isotherms in chromatography are critical in determining the separation of solutes during column separations. Multicomponent protein adsorption isotherms, which are relevant during the downstream processing of biopharmaceutical products, have received limited study historically. The studies and methodologies which have been assessed have mainly focused on small, simple, chromophore containing proteins which have limited applicability to industrially relevant bio-therapeutics. The reasons why this area of study has received limited attention include the experimental effort associated with generating such large data sets as well as the difficulty in obtaining data of good enough quality. The work explored here presents and optimises the deployment of highthroughput chromatography formats as well as automated liquid handling systems in order to elucidate adsorption isotherms of proteins. Additionally, alternative rapid analytical methods involving the collection of protein UV spectra in conjunction with multivariate data analysis have been applied to quantify protein mixtures. These rapid high-throughput methods decrease the experimental effort associated with multicomponent isotherm studies. 3 binary isotherms and 1 ternary isotherm have been studied for larger, non-chromophore containing model proteins. The propagation of error in single component and multicomponent isotherms has been investigated to understand what drives the propensity for error as well as methods to mitigate problematic regions of investigation. The fitting of the multicomponent ion exchange isotherms across multiple salt levels to isotherm formalisms proved elusive which precluded their application for in silico modelling of column separation. Short of that a heuristic optimisation of a binary mixture was achieved quantifying eluted fractions using the UV spectra multivariate method.
Review: Sensors for the improvement of irrigation efficiency in nurseries

Traditional timer-based systems for irrigation management, which are more commonly used in commercial nurseries in South Africa, are not ideal as they may not irrigate seedlings efficiently. A sensor-based irrigation system is presented as an alternative, as this can provide several benefits to nurseries and nursery-grown seedlings. Small-sized soil water sensors that could fit in small-volume nursery containers (25 to 100 mL), and could be integrated into an automated irrigation system, are reviewed. Several experiments have been conducted internationally to measure soil water status of small-volume containers in soilless substrates, and a large body of knowledge is now available. In this review, we describe the principles of several currently commercially available sensors that can be adapted to this purpose, giving advantages and disadvantages of each type. We conclude that a sensor-based irrigation system has great potential to address the challenges associated with irrigation scheduling, while improving water usage in most nurseries.
Beam splitting of flexural waves with a coding meta-slab

According to the generalized Snell’s law, we provide an alternative way of beam splitting of flexural waves based on a proposed coding meta-slab. The coding meta-slab is composed of two logical units “0” and “1” with different thicknesses and with ±π phase shift differences between them. The logical units are designed theoretically. Experiments for beam splitting of flexural waves are performed for the perpendicular and oblique incidence. They verify that the designed coding meta-slab can effectively split incident flexural waves in a broadband frequency range.
Visual object detection from lifelogs using visual non-lifelog data

Limited by the challenge of insufficient training data, research into lifelog analysis, especially visual lifelogging, has not progressed as fast as expected. To advance research on object detection on visual lifelogs, this thesis builds a deep learning model to enhance visual lifelogs by utilizing other sources of visual (non-lifelog) data which is more readily available. By theoretical analysis and empirical validation, the first step of the thesis identifies the close connection and relation between lifelog images and non-lifelog images. Following that, the second phase employs a domain-adversarial convolutional neural network to trans- fer knowledge from the domain of visual non-lifelog data to the domain of visual lifelogs. In the end, the third section of this work considers the task of visual object detection of lifelog, which could be easily extended to other related lifelog tasks. One intended outcome of the study, on a theoretical level of lifelog research, is to iden- tify the relationship between visual non-lifelog data and visual lifelog data from the perspective of computer vision. On a practical point of view, a second intended outcome of the research is to demonstrate how to apply domain adaptation to enhance learning on visual lifelogs by transferring knowledge from visual non-lifelogs. Specifically, the thesis utilizes variants of convolutional neural networks. Furthermore, a third intended outcome contributes to the release of the corresponding visual non-lifelog dataset which corresponds to an existing visual lifelog one. Finally, another output from this research is the suggestion that visual object detection from lifelogs could be seamlessly used in other tasks on visual lifelogging.
Endotoxin Increases Oxidative Stress And Oxygen Tension While Reducing Milk Protein Gene Expression In The Mammary Gland

Mastitis, the inflammation of the mammary gland by bacterial infection, is one of the costliest diseases to the dairy industry primarily due to a loss in milk production. The aim of this study was to investigate the mechanisms underlying reduced milk production during mastitis. We hypothesized that bacterial endotoxin induces cell apoptosis, oxidative stress and increases hypoxia while inhibiting milk gene expression in the mammary gland. To test this hypothesis, mice were bred to pregnancy, and 3 days postpartum the left and right sides of the 4th pair of mammary glands were alternately injected with either the endotoxin liposaccharide (LPS, E. coli 055:B5, 100 ul of 0.2 mg/ml) or sterile PBS through the teat meatus. At 10.5 and 22.5 h post-injection, pimonidazole HCl, a hypoxyprobe, was injected intraperitoneally. At 12 or 24 h after the LPS injection, the fourth glands were individually collected (n=8 pairs) and analyzed for hypoxia, gene expression and oxidative stress. LPS treatment induced mammary gland inflammation as shown by increases in inflammatory cytokine expression (P < 0.001) and neutrophil recruitment at 12 and 24 h. LPS promoted cell apoptosis in a transient manner; an abundance of cleaved caspase 3 was evident only at 12 h after LPS challenge (P = 0.02). Increased H2O2 content was seen at 12 h (P < 0.001) but decreased dramatically after 24 h of LPS treatment (P < 0.001). Total antioxidative capacity tended to decrease at both 12 and 24 h (P = 0.067 and 0.061, respectively). In agreement with these findings, LPS activated Nuclear factor erythroid 2-related factor 2 (Nrf2) antioxidative signaling in the mammary gland, demonstrated by increased expression of its target gene Nqo1 at 12 h (P = 0.05) and xCT at 24 h (P = 0.076). Hypoxyprobe staining, indicative of hypoxia, was greater in the alveoli of PBS-treated glands than LPS-treated glands at both 12 and 24 h. This suggests oxygen tension rises in response to LPS treatment. Conversely, milk expression genes, β-casein gene (CSN2) and α-lactalbumin (LALBA), were inhibited by LPS treatment across time. Expression of α-S1 casein (CSN1S1) mRNA increased with LPS treatment at 24 h, but protein expression was reduced at this same time point (P < 0.05). In summary, intramammary LPS challenge incurs inflammation, augments cell apoptosis, induces oxidative stress and activation of the Nrf2 antioxidation pathway, increases oxygen tension, and inhibits milk protein expression in the mammary gland. This study provides functional insight into mechanisms of reduced milk production during mastitis and provides possible approaches to combat reduction in milk production, such as enhancing the Nrf2-antioxidative signaling pathway and reducing inhibition of milk protein expression.
New strategies for co-immobilization of dehydrogenases, NAD+ cofactor and redox mediators in sol-gel thin films for bioelectrocatalytic applications

In this thesis, the research work was focused on designing functional layers based on silica sol-gel thin films to co-immobilize dehydrogenase, cofactor and electron mediator to get the most highly active systems. Immobilization of dehydrogenase in an active form in a sol-gel matrix was obtained by using a positively-charged polyelectrolyte as additive in the starting sol. The optimal sol can be deposited by evaporation or by electrodeposition and was successfully deposited in macroporous electrodes. The immobilization of the cofactor was investigated by simple entrapment, adsorption to carbon nanotube (CNTs), encapsulation of NAD+ chemically attached to dextran(NAD-dextran), and by in-situ coupling with glycidoxypropyltrimethoxysilane (GPS). The last approach allowed stable immobilization of the cofactor. Several mediators (Fc-PEI, Fc-Silane or Osmium polymer) were successfully co-immobilized with dehydrogenase and cofactor in the sol-gel matrix deposited by drop-coating. However, such co-immobilization did not operate in the electrogenerated sol-gel films. The strategies based on CNTs for mediator immobilization were finally developed. They include (1) micro-wave treatment (MWCNTs-µW), (2) electrochemical deposition of poly(methylene green) (MWCNTs-PMG), and (3) wrapping by osmium(III) polymer (MWCNTs-Os). MWCNTs-Os has been the only system that was successfully combined with sol-gel electrodeposition for co-immobilization of dehydrogenase and cofactor.
LDPC Soft Decoding with Improved Performance in 1X-2X MLC and TLC NAND Flash-Based Solid State Drives

The reliability of non-volatile NAND flash memories is reaching critical levels for traditional error detection and correction. Therefore, to ensure data trustworthiness in nowadays NAND flash-based Solid State Drives, it is essential to exploit powerful correction algorithms such as the Low Density Parity Check. However, the burdens of this approach materialize in a disk performance reduction. In this work a standard decoding approach is compared with an optimized solution exploiting hardware resources available in NAND flash chips. The simulation results on 2X, 1X and mid-1X MLC and TLC NAND flash-based Solid State Drives in terms of disk bandwidth, average latency, and Quality of Service favor the adoption of the presented solution in different host scenarios and realistic workloads. The proposed solution is particularly effective when high error correction interventions and read- or write-intensive workloads are considered.
The Storage Efficiency of Immobilized Bradyrhizobium japonicum Strain Using Encapsulation Method

There is a growing need for new formulations of carriers with better protection for bacterial inoculum. One of the newer techniques in inoculum making is encapsulation method. With this method, the whole bacterial cells are immobilized in defined space – matrix, where the cells are protected from environmental activities before use. Encapsulation of the inoculum was performed with ionic gelation method. The alginate-based microparticles (500-600 µm) containing viable B. japonicum strain were solidified in CaCl2. The initial number of viable bacteria in every sample was 9.0 log CFU/ml. Chitosan coated particles had a higher mortality rate than non-coated particles, with 1.3 log CFU/ml in lyophilized and wet microparticles stored at room temperature. High viability of B. japonicum was registered in wet particles stored at constant −20°C for thirty days with a viability rate of 8.84 log CFU/ml.
Co-effects of fuel research octane number and ethanol injection ratio on dual-fuel spark-ignition engine

The combustion and emission characteristics of a dual-fuel spark-ignition engine with direct injection of gasoline surrogates and port injection of ethanol were studied. Toluene reference fuel with different research octane number namely TRF#1, TRF#2, TRF#3, TRF#4 and TRF#5 were employed as gasoline surrogates, in which TRF#1 with high octane number was to simulate commercial gasoline under direct-injection spark-ignition mode as comparison. For dual-fuel spark-ignition mode, the ethanol port-injection ratios were 21%, 25%, 29%, 32% and 35%, respectively. The results demonstrated that with the increase of the ethanol ratio, the knock-limited spark timing was advanced gradually. The emissions of hydrocarbon, ethane, propylene, isopentane, cyclohexane and aromatic hydrocarbons reduced while CO, NOx, ethylene, acetaldehyde and ethanol increased. Compared to TRF#1 in direct-injection spark-ignition mode, the indicated thermal efficiencies of dual-fuel spark-ignition mode were slightly lower under most test conditions. When direct injection of TRF#3, TRF#4, TRF#5 and the ethanol ratio was higher than 29%, some of the indicated thermal efficiencies of the engine were consistent with or higher than that of TRF#1 in direct-injection spark-ignition mode. Based on dual-fuel spark-ignition mode and with the assistance of port injection of ethanol, the indicated thermal efficiency of low research octane number fuels was comparable to that of TRF#1 in direct-injection spark-ignition mode.
Fine Particulate Matter and Ozone Pollution in the 18 Cities of the Sichuan Basin in Southwestern China: Model Performance and Characteristics

The Sichuan Basin (SCB) is located in southwestern China and has a total population of 108.1 million across 18 cities, including the 2 largest in western China (Chengdu and Chongqing). As most air quality monitoring stations are located in urban areas, we simulated the PM2.5 (i.e., particulate matter with an aerodynamic diameter 70% of the days during winter and > 40% of the days during summer, respectively. Based on the aforementioned spatial patterns of the PM2.5 and O3 concentrations, and the wind directions within the basin, strictly controlling emissions originating in the SCB may greatly reduce PM2.5 and O3 concentrations within the basin.
One-pot synthesis of a new generation of hybrid bisphosphonate polyoxometalate gold nanoparticles as antibiofilm agents

A reduced polyoxovanadate functionalized with bisphosphonate molecules was synthesized and used to prepare in one step hybrid organic–inorganic polyoxometalate decorated gold nanoparticles. These new composites were shown to strongly inhibit P. aeruginosa and S. epidermidis biofilm growth, with the three components constituting the nanoparticles (Au0 core, vanadium and alendronate) acting synergistically.
Model discrimination for drying and rehydration kinetics of freeze‐dried tomatoes

The aim of this work is to investigate the effect of a highly interconnected porous microstructure on the quality of rehydrated tomatoes by (a) designing a freeze‐dried cycle that ensure product integrity (i.e., no collapse, no puffing) (b) characterizing both freeze‐drying and rehydration kinetics. Fresh tomatoes were first freeze‐dried and subsequently rehydrated to get generate kinetics data. Afterwards, six thin‐layer drying models and four rehydration models were fitted using regression analysis to the experimental data. The goodness‐of‐fit was evaluated according to root mean squared error, adjusted R², Akaike information criterion, and Bayesian information criterion. The most accurate representations of the system kinetics were observed using the Page model for freeze‐drying and the exponential and Weibull models for rehydration. Rehydration capacities and equilibrium moisture contents of the rehydrated samples were found to increase with temperature, and the corresponding activation energy values were calculated. PRACTICAL APPLICATIONS: Freeze‐dried porous microstructures can enhance water absorption and transport, contributing to restore the fresh product functional properties and leading to higher quality rehydrated products, especially in highly heat‐sensitive food products as vegetables and fruits. The use of mathematical models to (a) design freeze‐drying cycles and (b) characterize and/or predict drying and rehydration kinetics in cellular freeze‐dried microstructures is then key for processing and optimization of convenience and ready‐to‐eat foods, which represents the main application of dried foods/powders and also a growing market. This approach to the manufacture of freeze‐dried products also presents potential to set the basis of an alternative decentralized supply scenario for high‐quality dried products, where freeze‐dried foods will be manufactured and shipped and finally rehydrated closer to the consumption point.