Digital Commons Network^™

Development Of Autochthonous Probiotic Candidates For Tilapia Aquaculture, Rungtawan Yomla

School of Biological and Marine Sciences Theses

This programme of work sought to develop autochthonous probiotic solutions for tilapia aquaculture. Initial work began with the isolation of isolate 34 bacterial cultures from the tilapia intestine, which were tested for probiotic potential in vitro. Fifteen isolates displayed positive probiotic properties in in vitro assays. The selection of high potential probiotic candidates was based on multi-parameter properties using the Z−score method, which ranked isolates identified as Bacillus sp. CHP02 (Z score = 1.48), Bacillus sp. RP01 (1.14) and Bacillus sp. RP00 (1.09) as having the greatest potential. These isolates, along with Enterobacter sp. NP02 (0.50), were then assessed for …

Phaeovirus Infections In Kelp, Dean Andrew Mckeown

School of Biological and Marine Sciences Theses

The latent dsDNA viruses of the genus Phaeovirus (family Phycodnaviridae, clade Nucleo-cytoplasmic Large DNA Viruses; NCLDVs) employ genome integration in their brown algae hosts (class Phaeophyceae). The only phaeoviruses described in detail infected the order Ectocarpales, though Phaeovirus major capsid protein (MCP) occurs in 4 kelp (order Laminariales) species. Phaeoviruses are a major knowledge gap because brown algae are ecologically and economically important and have independently evolved complex multicellularity. This study aimed to investigate kelp Phaeovirus morphology, evolution, host range, distribution, host impacts, and genomics. Microscopy of Laminaria digitata gametophytes revealed particles and cell morphology typical of Phaeovirus infections. This …

Marine Invasive Species: Fluorescence Applications For Ballast Water Regulatory Compliance And Use Of Freshwater As A Biosecurity Tool For Biofouling, Maria Cecilia Trindade De Castro

School of Biological and Marine Sciences Theses

The present thesis addresses the role of shipping as an unintentional and very efficient pathway for spreading aquatic non-native species around the globe, through two major vectors: ballast water and biofouling. The challenge with ballast water is that a myriad of organisms are transported across natural barriers before dispersal, transcending biogeographic regions and this wholesale movement of marine life contributes to the spread of diseases and to the homogenization of coastal habitats. The United Nations nominated the issue as one of the four greatest threats to the oceans, causing extremely severe environmental, economic and public health impacts. This research is …

Microplastic Abundance, Distribution And Composition In The Atlantic And Arctic Oceans, La Daana Kanhai

School of Biological and Marine Sciences Theses

Microplastics are ubiquitous, persistent particles that are capable of posing a threat to organisms that inhabit or depend upon marine ecosystems. Understanding the origin, transport pathways and fate of these particles in the ocean is fundamentally important when evaluating the risks associated with such particles to marine organisms. In the Atlantic Ocean, the Canary and Benguela Upwelling Ecosystems are regions of high primary productivity which sustain large commercial fisheries. The influence of oceanic phenomena such as upwellings on microplastic abundance, distribution and composition remains unknown. Any microplastics that are present within such upwelling ecosystems can potentially interact with the associated …

The Sources And Fate Of Plastic Entering The Marine Environment, Imogen Napper

School of Biological and Marine Sciences Theses

Plastics can come in many forms and bring a wide range of societal benefits in healthcare, agriculture, transport, construction and packaging. However, plastic is a large proportion of marine litter and an internationally recognised pollutant. Marine litter results from the indiscriminate disposal of waste items that are either directly or indirectly transferred into aquatic environments. This debris can cause harmful effects for wildlife, commercial fisheries, maritime industries, tourism and human well-being (Chapter 1). Over the past decade, increased scientific interest has produced an expanding knowledge base for plastic contamination in the environment. However, fundamental questions and issues remain unresolved. This …

Bioturbation In Estuarine Sediments: Modelling Macrofauna-Mediated Oxygen Dynamics, Xiaoyu Fang

School of Biological and Marine Sciences Theses

The aim of this thesis was to provide a comprehensive examination of the roles of macrofauna in estuarine biogeochemistry by adopting a multidisciplinary field and laboratory-based approach and integrating species distribution modelling with biomass-dependent ecosystem function relationships. Eventually, an ecosystem management tool to provide insights into the ecological consequences of anthropogenic disturbance in estuaries was developed using the Western Scheldt as a model system. To establish a baseline understanding of the spatio-temporal patterns of macrobenthos (activities) and ecosystem functioning in the Scheldt estuary, a seasonal survey was carried out during four consecutive seasons in 2015 and 2016, sampling three habitats …

Variation In Sexual Dimorphism In A Wind-Pollinated Plant: The Influence Of Geographical Context And Life-Cycle Dynamics, Gemma Puixeu, Melinda Pickup, David L. Field, Spencer C. H. Barrett

Research outputs 2014 to 2021

Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life‐cycle dynamics.

Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY₁Y₂) of the species.

The direction and degree of sexual …

Seagrass Soil Archives Reveal Centennial-Scale Metal Smelter Contamination While Acting As Natural Filters, Anna Lafratta, O Serrano, Pere Masque, Miguel Mateo, Milena Fernandes, Sam Gaylard, Paul Lavery

Research outputs 2014 to 2021

The upper Spencer Gulf in South Australia hosts the world's largest single stream Pb-Zn smelter, which has caused environmental and health issues related to elevated metal concentrations in the surrounding environment. The area also has extensive seagrass meadows, occupying >4000 km². We reconstructed the fluxes of heavy metals over the last ~3000 years through a multi-parameter study of the soil archives formed by the seagrass Posidonia australis. Pb, Zn and Cd concentrations increased up to 9-fold following the onset of smelter operations in the 1880s, and the stable Pb isotopic signatures confirmed the smelter has been the main …

Time-To-Event Analysis For Sports Injury Research Part 1: Time-Varying Exposures, Rasmus Oestergaard Nielsen, Michael Lejbach Bertelsen, Daniel Ramskov, Merete Møller, Adam Hulme, Daniel Theisen, Caroline F. Finch, Lauren Victoria Fortington, Mohammad Ali Mansournia, Erik Thorlund Parner

Research outputs 2014 to 2021

BACKGROUND: ‘How much change in training load is too much before injury is sustained, among different athletes?’ is a key question in sports medicine and sports science. To address this question the investigator/practitioner must analyse exposure variables that change over time, such as change in training load. Very few studies have included time-varying exposures (eg, training load) and time-varying effect-measure modifiers (eg, previous injury, biomechanics, sleep/stress) when studying sports injury aetiology.

AIM: To discuss advanced statistical methods suitable for the complex analysis of time-varying exposures such as changes in training load and injury-related outcomes.

CONTENT: Time-varying exposures and time-varying effect-measure …

Time-To-Event Analysis For Sports Injury Research Part 2: Time-Varying Outcomes, Rasmus Oestergaard Nielsen, Michael Lejbach Bertelsen, Daniel Ramskov, Merete Møller, Adam Hulme, Daniel Theisen, Caroline F. Finch, Lauren Victoria Fortington, Mohammad Ali Mansournia, Erik Thorlund Parner

Research outputs 2014 to 2021

BACKGROUND: Time-to-event modelling is underutilised in sports injury research. Still, sports injury researchers have been encouraged to consider time-to-event analyses as a powerful alternative to other statistical methods. Therefore, it is important to shed light on statistical approaches suitable for analysing training load related key-questions within the sports injury domain.

CONTENT: In the present article, we illuminate: (i) the possibilities of including time-varying outcomes in time-to-event analyses, (ii) how to deal with a situation where different types of sports injuries are included in the analyses (ie, competing risks), and (iii) how to deal with the situation where multiple subsequent injuries …

Cultural Practices And The Transmission Of Ebola In Sierra Leone: Lessons Learned From A Medical Anthropology Perspective, Abubakarr Jalloh

Dissertations and Theses @ UNI

The link between culture and infectious diseases has long been established. This is primarily due to the notion that culture shapes and influences people’s beliefs, actions, and ways of life. Such beliefs and their accompanying actions ultimately contribute to people’s risk of contracting an infectious disease. As such, there is a need for a cultural perspective in understanding infectious diseases because human behavior plays a significant role in the emergent, transmission, and spread of such diseases. This study explores the cultural practices that may have contributed to the transmission of Ebola Virus Disease (EVD) in Sierra Leone during the 2013-2016 …

Empowering Children's Social Ecology: Reenvisioning Postconflict Reconstruction And Education In Rural Liberia, Kristen N. Mcnutt

Dissertations and Theses @ UNI

Despite the Accra Comprehensive Peace Agreement calling the end to Liberia’s back-to-back civil wars in 2003, Liberia’s peace remains fragile with a high number of out of school children, especially in rural communities. As an indicator of state fragility, rural education needs to be a priority in post-conflict reconstruction. This thesis emerged to support the nongovernmental organization, Supporting Programs in Community Empowerment (SPICE), an emerging Liberian-based nongovernmental organization.

The methodologies for this action research project was a needs assessment, which resulted in the development of the Needs Assessment Report: Paving the Way for the Future of Liberian Children. Through …

Morphological And Morphometric Analysis Of Nekemias Arborea And Ampelopsis Aconitifolia (Vitaceae), Sally Rose Gray

Dissertations and Theses @ UNI

Leaf morphology in angiosperms is not constrained by the leaf’s important function of providing energy through photosynthetic reactions. In just one family, Vitaceae, it is easy to observe among it’s over 900 species, various leaf shapes and sizes even among closely related species as well as within individual species. Observation of these leaf forms within species can be used to determine, for example where a vine transitions from the juvenile state to the adult state as well as their relationship to the spatial and temporal patterning of inflorescence initiation. Analysis of two species within the Ampelopsis clade, one that retained …

Risk Factors Associated With Myopia In Schoolchildren In Ireland, Síofra Harrington, Jim Stack, Veronica O'Dwyer

Articles

Aim To examine the demographic and social factors associated with myopia in schoolchildren in Ireland.

Methods Thirty-seven schools participated, representing a mix of urban and rural schools and schools in socioeconomically disadvantaged and non-disadvantaged areas in Ireland. Examination included cyclopleged autorefraction (1% cyclopentolate hydrochloride). Height and weight of participants were measured. Parents filled in a participant’s lifestyle questionnaire, including questions on daily screen time use and daylight exposure. Myopia was defined as spherical equivalent ≤−0.50 D.

Results Data from 1626 participants (881 boys, 745 girls) in two age groups, 6–7 years (728) and 12–13 years (898), were examined. Myopia prevalence …

Design, Synthesis, Biological Evaluation And Molecular Docking Of Novel Molecules To Parp-1 Enzyme, Fati̇h Tok, Bedi̇a Kaymakçioğlu, Recep İlhan, Si̇nem Yilmaz, Petek Ballar Kirmizibayrak, Tuğba Taşkin Tok

Turkish Journal of Chemistry

Poly (ADP-ribose) polymerase (PARP) enzyme catalyzes the transfer of ADP-ribose into target proteins. Therefore, PARP is responsible for DNA repair, cell proliferation, and cell death. In this study, potential PARP enzyme inhibitors were designed and synthesized. The synthesized compounds were elucidated by Fourier-transform infrared spectroscopy, $^{1}$H NMR, $^{13}$C NMR, heteronuclear single-quantum correlation, and mass spectrometry, and their purity was checked via thin-layer chromatography, high-performance liquid chromatography, and elemental analysis. A total of 63 newly synthesized compounds were screened in terms of PARP inhibition by cellular PARylation assay in the HeLa cell line. It was found that 19 compounds significantly inhibited …

Natural Diterpenoid Alysine A Isolated From Teucrium Alyssifolium Exerts Antidiabetic Effect Via Enhanced Glucose Uptake And Suppressed Glucose Absorption, Alaatti̇n Şen, Buket Ayar, Anil Yilmaz, Özden Özgün Acar, Gurbet Çeli̇k Turgut, Gülaçti Topçu

Turkish Journal of Chemistry

Teucrium species have been used in folk medicine as antidiabetic, antiinflammatory, antiulcer, and antibacterial agents. We have explored in vitro antidiabetic impacts of 2 natural diterpenoids, alysine A and alysine B, isolated from Teucrium alyssifolium. The lactate dehydrogenase (LDH) cytotoxicity assay, glucose uptake test, glucose utilization (glycogen content) test, glucose transport test, glucose absorption ($\alpha $-glucosidase activity) test, insulin secretion test, RNA isolation and cDNA synthesis assay, qPCR quantification assays, and statistical analyses were carried out in the present study. Alysine A exerted the following effects at non-cytotoxic doses: . Enhanced the glucose uptake, as much as the insulin in …

Anticancer And Antiangiogenesis Activities Of Novel Synthesized 2-Substituted Benzimidazoles Molecules, Adem Güner, Eli̇fsu Polatli, Tamer Akkan, Hakan Bektaş, Canan Albay

Turkish Journal of Chemistry

In this study, novel 2-substituted benzimidazoles molecules having triazole, thiadiazole, and oxadiazole rings were synthesized and were evaluated by anticancer, antioxidant/oxidant status, genotoxicity, and antiangiogenesis assays. Anticancer activity of the compounds was determined by MTT (0.5, 5, and 50 $\mu $g/mL) and lactate dehydrogenase (LDH) release assays against human prostate and breast cancer cells. Oxidative status of cells was elicited by total oxidative stress and total antioxidant capacity methods. Chick chorioallantoic membrane assay was used to evaluate the antiangiogenic activity. Genotoxicity was evaluated by the sister chromatid exchange (SCE) and micronucleus (MN) tests in lymphocyte cultured human blood. Our results …

Modeling And Optimizing Microwave-Assisted Extraction Of Antioxidant Compounds From Marigold Calendula Officinalis L. Using Response Surface Methodology, Burcu Bekdeşer

Turkish Journal of Chemistry

Calendula officinalis L. is a commercially important plant that finds application in the treatment of various diseases in traditional medicine. The total antioxidant capacity, radical scavenging activity, and total phenolic content of marigold extracts were investigated by Folin, CUPRAC, and DPPH assays, respectively. The optimum operating conditions of microwave-assisted extraction (MAE) including temperature, extraction time, solvent-to-solid ratio, and solvent concentration were ascertained by employing response surface methodology (RSM). The solvent (ethanol) concentration was the most significant operating factor among all responses of MAE. At the optimum extraction conditions, the maximum yield of total phenolic content, total antioxidant capacity, and radical …

Cover And Contents

Turkish Journal of Chemistry

No abstract provided.

Glucose Oxidase Immobilized Biofuel Cell Flow Channel Geometry Analysis By Cfd Simulations, Sali̇h Obut, Tahsi̇n Bahar

Turkish Journal of Chemistry

Glucose oxidase was covalently immobilized to a porous electrode, which was developed by using ferrocene functionalized polyethyleneimine, multiwall carbon nanotubes, and carbon cloth for biofuel cell applications in our recent studies. The kinetics parameters (i.e. k$_{M}$, V$_{max})$ and other parameters required for the modeling study were determined experimentally. Fuel cell flow channel geometry was analyzed by a computational fluid dynamics modeling approach. Substrate flow rate and mass transfer for each proposed channel type were considered in the simulations. The results showed that serpentine type flow channels are advantageous over pin type or parallel flow channels to acquire sufficient performance from …

Cover And Contents

Turkish Journal of Chemistry

No abstract provided.

The Role Of Diazacrown Ether In The Enhancement Of The Biological Activity Of Silver Nanoparticles, Sarvinaz Hajiyeva, Ulviyya Hasanova, Zarema Gakhramanova, Aygun Israyilova, Khudaverdi Ganbarov, Eldar Gasimov, Fuad Rzayev, Goncha Eyvazova, Alakbar Huseynzada, Gunel Aliyeva, Ilaha Hasanova, Abel Maharramov

Turkish Journal of Chemistry

The nanostructuring of hydroxyl-substituted diazacrown-ether (DC) by silver nanoparticles was obtained by green synthesis method in order to increase the antibacterial activity of silver nanoparticles. The synthesized DC, nanoparticles, and nanosupramolecular complex (Ag@DC) were studied by TEM, powder-XRD, and NMR, IR, and UV spectroscopy methods. The Ag@DC nanostructures were uniform and their sizes ranged from 8 to 18 nm. IR and UV spectra revealed the noncovalent formation of the nanosupramolecular complex. The antibacterial activities of the prepared active agents were investigated on gram-positive and gram-negative bacteria by twofold microdilution method. Ultrastructural study by TEM was performed on \textit{E. coli} BDU12 …

Cover And Contents

Turkish Journal of Chemistry

No abstract provided.

Technical Analysis, Paula Bourke

Datasets

Transcription analysis was performed for Listeria monocytogenes EGD-e wild type strain. Relative expression of stress associated genes (prfA, sigB, rsbR, gadD, lmo0799) following exposure to ACP treatment was quantified using real-time reverse transcription-PCR (RT-PCR).

A U-Net Deep Learning Framework For High Performance Vessel Segmentation In Patients With Cerebrovascular Disease, Michelle Livne, Jana Rieger, Orhun Utku Aydin, Abdel Aziz Taha, Ela Marie Akay, Tabea Kossen, Jan Sobesky, John D. Kelleher, Kristian Hildebrand, Dietmar Frey, Vince I. Madai

Articles

Brain vessel status is a promising biomarker for better prevention and treatment in cerebrovascular disease. However, classic rule-based vessel segmentation algorithms need to be hand-crafted and are insufficiently validated. A specialized deep learning method—the U-net—is a promising alternative. Using labeled data from 66 patients with cerebrovascular disease, the U-net framework was optimized and evaluated with three metrics: Dice coefficient, 95% Hausdorff distance (95HD) and average Hausdorff distance (AVD). The model performance was compared with the traditional segmentation method of graph-cuts. Training and reconstruction was performed using 2D patches. A full and a reduced architecture with less parameters were trained. We …

Multi-Spectral Visual Crop Assessment Under Limited Data Constraints, Patricia O'Byrne, Patrick Jackman, Damon Berry, Hector-Hugo Franco-Penya, Michael French, Robert J. Ross

Conference papers

In an era of climate change and global population growth, deep learning based multi-spectral imaging has the potential to significantly assist in production management across a wide range of agricultural and food production domains. A key challenge however in applying state-of-the-art methods is that they, unlike classical hand crafted methods, are usually thought of as being only useful when significant amounts of data are available. In this paper we investigate this hypothesis by examining the performance of state-of-the-art deep learning methods when applied to a restricted data set that is not easily bootstrapped through pre-trained image processing networks. We demonstrate …

Cytotoxic And Genotoxic Action Of Tagetes Patula Flower Methanol Extract And Patuletin Using The Allium Test, Mudassar Azhar, Ahsana Dar Farooq, Sayedul Haque, Samina Bano, Lubna Zaheer, Shaheen Faizi

Turkish Journal of Biology

Tagetes patula is used to treat cancer patients in alternative healthcare systems. However, its cytotoxic and genotoxic effects have not been reported. Therefore, the methanol extract of T. patula flower, the ethyl acetate fraction, and the pure compound patuletin were evaluated using the Allium test. The methanol extract and fraction contained ~3% and ~36% patuletin, respectively, with ~98% purity. The methanol extract caused inhibition of Allium root growth displaying an IC50 value of ~500 μg/mL, while the fraction and patuletin were more potent by ~2 and ~5 times, respectively. The Allium root tips demonstrated a decline in prophase, metaphase, anaphase, …

The Nlrp3 Inflammasome: A New Player In Neurological Diseases, Eli̇f Eren, Nesri̇n Özören

Turkish Journal of Biology

Inflammasomes are supramolecular protein complexes implicated in the detection of pathogens or danger-associated molecules and are responsible for mounting the first line of innate immune response to counteract these signals and restore tissue homeostasis. Among different inflammasomes identified so far, NLRP3 is of main interest since mutations in Nlrp3 gene are associated with autoinflammatory diseases such as Muckle-Wells syndrome, neonatal onset multisystem inflammatory disease, and familial cold urticaria/autoinflammatory syndrome. On the other hand, whereas other inflammasomes are mainly detectors of specific molecular motifs, NLRP3 is acting as a general sensor of cellular perturbations including potassium efflux, lysosomal damage, and ROS …

On The Inability Of Markov Models To Capture Criticality In Human Mobility, Vaibhav Klukarni, Abhijit Mahalunkar, Benoit Garbinato, John Kelleher

Conference papers

We examine the non-Markovian nature of human mobility by exposing the inability of Markov models to capture criticality in human mobility. In particular, the assumed Markovian nature of mobility was used to establish an upper bound on the predictability of human mobility, based on the temporal entropy. Since its inception, this bound has been widely used for validating the performance of mobility prediction models. We show that the variants of recurrent neural network architectures can achieve significantly higher prediction accuracy surpassing this upper bound. The central objective of our work is to show that human-mobility dynamics exhibit criticality characteristics which …

Agent-Based Iot Coordination For Smart Cities Considering Security And Privacy, Iván García-Magariño, Geraldine Gray, Rajarajan Muttukrishnan, Waqar Asif

Conference papers

The interest in Internet of Things (IoT) is increasing steeply, and the use of their smart objects and their composite services may become widespread in the next few years increasing the number of smart cities. This technology can benefit from scalable solutions that integrate composite services of multiple-purpose smart objects for the upcoming large-scale use of integrated services in IoT. This work proposes an agent-based approach for supporting large-scale use of IoT for providing complex integrated services. Its novelty relies in the use of distributed blackboards for implicit communications, decentralizing the storage and management of the blackboard information in the …