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The Indian Child Welfare Act In The Multiverse (Review Of Adoptive Couple V. Baby Girl By Matthew L.M. Fletcher And Kathryn E. Fort, In Critical Race Judgements: Rewritten U.S. Court Opinions On Race And The Law)), M. Alexander Pearl

Other Faculty Publications

No abstract provided.

Exploring The Metabolic Capabilities And Biotransformation Potential Of Environmental Lactococcus Strains, Desirée Román Naranjo

Theses

The aim of this thesis is to characterize environmental Lactococcus strains to identify different and diverse metabolic capabilities that could be applied to microbial biotransformation, defined as the conversion of a cheap/waste substrate into a value-added product. Due to the increased amounts of food processing waste generated worldwide and the impact of climate change, new sustainable approaches are necessary to contribute to waste valorization and the circular bioeconomy. We ask to what extent and in what ways environment isolated Lactococcus strains could contribute to food biotransformation by metabolizing a different range of substrates. We do so to further understand and …

Nutrient Intakes, Compliance With Recommendations And Key Sources In Women Of Child-Bearing Age (18-50 Y) In Ireland, Abigail O' Mahony

Theses

Women’s pre-conceptional health (including nutritional status) is important for both the health of the individual themselves and also for the lifelong health of any occurring offspring. However, it has been estimated that up to 50% of pregnancies are unplanned, thus optimal nutritional status is important for all women of child-bearing age (WCBA) not just those with pregnancy intentions. Despite the accumulation of evidence of the importance of nutritional status at this life-stage, nutrient recommendations for WCBA for the most part don’t differ from recommendations for other population groups. The notable exception to this is that all WCBA are recommended to …

Genetic Selection For Improved Production Efficiency In The Mature Dairy Herd, Maeve Williams

Theses

Improving dairy cow production efficiency is highly desirable because of its well-documented impact on profitability and sustainability. Long-term gains in dairy cow production efficiency have already been delivered through genetic selection. Nonetheless, achieving further improvements in production efficiency could cement the economic and environmental efficiency of the dairy industry, globally. To date, several components contributing to production efficiency have been overlooked, with many studies focusing on dairy cow production efficiency over short periods rather than lifetime efficiency. Therefore, the objectives of this thesis were to quantify the genetic variance components of complementary dairy cow efficiency metrics; including dry matter intake, …

Identification And Creation Of Novel Bacteriocins With Potential Food And Clinical Applications, David Lynch

Theses

Bacteriocins represent a heterogeneous group of small, ribosomal-synthesized, potent antibacterial peptides produced by bacteria, capable of inhibiting bacteria both closely related or indeed those from other genera than the producer. In addition to their role as food preservatives, bacteriocins have potent activity against medically significant pathogens and are considered attractive alternatives to antibiotics, due to their inherent heat stability, potency at nanomolar scale, resistance to proteases and low levels of acquired resistance in commercial applications. The aim of this thesis was to identify, purify and bioengineer novel bacteriocins from Staphylococcus and Lactic Acid Bacteria (LAB), with a view to expanding …

Investigating Optimal Lipid:Protein Profiles For Infant Milk Formula, Valentina Ivanova

Theses

From the early twentieth century onward, much research has focused on improving infant milk formula (IMF). During the development of IMF, breast milk is commonly considered as the reference and IMF manufacturers are thriving to mimic the composition and/or to match the functionality of breast milk as closely as possible. A variety of bioactive ingredients, found in human breast milk, have been isolated and investigated for their potential functionality and utilised in the production of IMF. This study evaluated the current knowledge on compositional differences between human breast milk and IMF, and recent advances and developments in IMF production. Following …

Nanoparticles In Soil Remediation: Challenges And Opportunities, Wei Wei New, Joseph Ekhebume Ogbezode, Paran Gani

All Rsif Scholars' Publications

Nanoremediation emerges as a promising technology for mitigating soil contamination, encompassing various nanotechnology applications, including chemical degradation, Fenton-type oxidation, photocatalytic degradation, immobilization, and integration with bioremediation techniques like phytoremediation. In addressing soil pollution, the most extensively researched nanomaterials (NMs) are based on carbon, metal and metal oxide, nZVI, and other nanocomposites. Nevertheless, limitations accompany the use of NMs in soil remediation. To assess whether nanotechnology applications outweigh environmental threats, it is crucial to investigate potential effects of NMs on terrestrial vegetation, soil organisms, and human well-being. The impacts of NMs on ecology and the soil environment must be taken into …

A Narrative Review Of The Synthesis, Characterization, And Applications Of Iron Oxide Nanoparticles, Joseph Ekhebume Ogbezode, Ucheckukwu Stella Ezealigo, Abdulhakeem Bello, Vitalis Chioh Anye, Azikiwe Peter Onwualu

All Rsif Scholars' Publications

The significance of green synthesized nanomaterials with a uniform shape, reduced sizes, superior mechanical capabilities, phase microstructure, magnetic behavior, and superior performance cannot be overemphasized. Iron oxide nanoparticles (IONPs) are found within the size range of 1–100 nm in nanomaterials and have a diverse range of applications in fields such as biomedicine, wastewater purification, and environmental remediation. Nevertheless, the understanding of their fundamental material composition, chemical reactions, toxicological properties, and research methodologies is constrained and extensively elucidated during their practical implementation. The importance of producing IONPs using advanced nanofabrication techniques that exhibit strong potential for disease therapy, microbial pathogen control, …

Assessing Structure, Species Diversity, And Carbon Stocks Across Altitudinal Gradients In Hugumbrda Grat-Kahsu Forest, Tigray, Ethiopia: Implications For Ecosystem Service Management, Haftu Abrha Mengesha, Soro Dodiomon, Victor Ongoma, Emiru Birhane, Shenafi Manaye Manaye

All Rsif Scholars' Publications

The study area, affected by war and siege, necessitates a study of its current ecological sta-
tus. The objective of this study was to assess the present forest structure, species diversity,
and Total Biomass Carbon Stock (TBCS) in relation to environmental variables. The findings
shown 42 woody plant species, with 23 in the highland and 41 in the midland. No signifi-
cant difference in species abundance is observed between the highland and midland areas.
However, there are significant differences in the average diameter and height of trees
between the altitudinal classes. Additionally, diversity indices shown significant difference,
with the midland …

Modeling Impacts Of Climate Change On The Geographic Distribution And Abundances Of Tamarindus Indica In Tigray Region, Ethiopia, Yirga Gufi, Ashenafi Manaye, Berihu Tesfamariam, Haftu Abrha Mengesha, Musse Tesfaye, Sibhatleab Hintsa

All Rsif Scholars' Publications

Tamarindus indica is a multipurpose dry land species in sub-Saharan that is traditionally used to build resilience into the farming system. The species is highly threatened and listed on the IUCN Red List. However, information on how climatic condition locally influences its ecological distribution is limited. This study investigates the current and future suitable habitat for the species in the Tigray region, in northern Ethiopia. A total of 220 species presence points and the number of T. indica within a 50 m × 50 m plot were collected. In addition, 19 bioclimatic variables, 3 topographic variables and soil data …

Effect Of Some Biopesticides Based On Essential Oil And Plant Extracts On Postharvest Mango Stem-End Rot Disease Caused By Lasiodiplodia Theobromae, Yefoungnigui Souleymane Yeo, Dio Dramane Dembele, Brahima Camara, Soualo Ouattara, Jean-Yves Rey, Diana Fernandez, Daouda Koné

All Rsif Scholars' Publications

Lasiodiplodia species causing mango Stem-end rot disease (SER) are mainly controlled using synthetic products, which can harm humans and environmental health. Therefore, developing an eco-friendly control method, such as using plant extract products, is imperative. In this study, we evaluated the inhibitory effect of 3 biopesticides based on essential oils (ASTOUN 50 EC, FERCA 50 EC, and NECO 50 EC) at 300, 500, 700, 1000 ppm and Moringa oleifera leaves extracts (Methanolic and aqueous) at 5, 10, 15 and 20 g/250 ml on mycelial growth of Lasiodiplodia theobromae in vitro. Subsequently, 135 fruits (cv. Kent) per treatment …

Bioresources In Organic Farming: Implications For Sustainable Agricultural Systems, Akinlolu Olalekan Akanmu, Olumayowa Mary Olow, Austin Tenthani Phiri, Drocelle Nirere, Adeyinka John Odebode, Noëlla Josiane Karemera Umuhoza, Michael Dare Asemoloye, Olubukola Oluranti Babalola

All Rsif Scholars' Publications

Over the years, the practice of agriculture has transformed from the era of traditional to that of intensive agriculture in the bid to boost the production index that will satisfy the food needs of the globally growing population. However, the continuous and exaggerated use of chemical fertilizers and pesticides has resulted in major adverse impacts on food and environmental safety, whereas most traditional techniques for reclamation of natural soil nutrients, including shifting cultivation and polyculture, are no longer attractive measures of land rejuvenation. There is, therefore, the need for urgent evaluation and adoption of innovative methods of replenishing the agricultural …

Geospatial Characterization Of Climate-Smart Agroforestry In Two Contrasting Physiographic Zones Of Rwanda, Donatien Ntawuruhunga, Edwin Estomii Ngowi, Halima Omari Mangi, Raymond John Salanga, Mashisia Shikuku

All Rsif Scholars' Publications

Efficient use of rich natural resources notably land, is one of the most important indicators of economic progress. The unmatched population growth with production has triggered increased demand for food. Nations have prioritized sustainable agriculture as a coping strategy. Climate-smart agroforestry (CSAF) can be one of the options to increase productivity, income, and food security, and stabilize the environment. CSAF denotes a practiced farming system of combining trees with crops or animals (AF) evolved in practices to enhance productivity and feed the food-insecure people while coping with the adverse effects of climate change. This study investigates the land suitability for …

Climate-Smart Agroforestry Systems And Practices: A Systematic Review Of What Works, What Doesn’T Work, And Why, Donatien Ntawuruhunga, Edwin Estomii Ngowi, Halima Omari Mangi, Raymond John Salanga, Kelvin Mashisia Shikuku

All Rsif Scholars' Publications

he prevailing global environmental distress, particularly in rural areas, calls for the adoption of integrated sustainable rural development strategies like climate-smart agroforestry (CSA) practices. CSAF is a new name for an old farming practice among the world’s traditional farmers, a holistic approach to land use in which trees, crops, and sometimes animals are combined within a managed farmland, a sustainable farming system and practice, and a pathway toward the mitigation and adaptation of the biggest challenge of our times: climate change. CSAF systems and practices provide a range of goods and services vital for human well-being, particularly for people …

Bushmeat Consumption In Africa: A Microbiological Safety Challenge?, Gwladys Gloria Amen Ahouanse, Abdulsudi Issa-Zacharia, Nuria Majaliwa

All Rsif Scholars' Publications

Objective: This review analyzed the microbiological safety of bushmeat consumed in Africa over the past decades. Methodology:Previous Studies mainly focused on large animals like antelopes and smaller ones like grasscutter. Most microbes studied were similar to those in domestic animal meat, except for rare pathogens such as Salmonella spp, E.coli. Sampling, experiments, and microbe prevalence varied among studies.Results:All studies confirmed the presence of zoonotic pathogens dangerous to human beings. Therefore, more investigations are needed, especially for the chronic and severe cases of pathogens, since only few studies have addressed the bushmeat's microbiological safety in Africa. Conclusion:Efforts should be made to …

Bauhinia Rufescens, Ocimum Basilicum And Salvadora Persica: A Review Of Their Chemical Compounds And Properties For Antimicrobial, Antioxidant And Cytotoxicity, Hissein Hassan Abdel-Razakh, Gaymary George Bakari, Cheol-Ho Pan, Abubakar Shaaban Hoza

All Rsif Scholars' Publications

Bauhinia rufescens, Ocimum basilicum and Salvadora persica are well known plants used in African traditional medicine, especially in Chadian traditional medicine. They are mostly used in the treatment of infectious diseases, inflammatory diseases, fever, and so on. Studies using various in vitro and in vivo bioassay techniques support the scientific rationale for most of these usages. In this review, ethnobotanical uses, chemistry of natural products, and pharmacological and clinical data for these plants are presented

Heat Stress Effects On Milk Yield Traits And Metabolites And Mitigation Strategies For Dairy Cattle Breeds Reared In Tropical And Sub-Tropical Countries, Vincent Habimana, Athumani Nguluma, Zabron Cuthibert Nziku, Gota Morota, Raphael Mrode, Sebastian Chenyambuga

All Rsif Scholars' Publications

Heat stress is an important problem for dairy industry in many parts of the world owing to its adverse effects on productivity and profitability. Heat stress in dairy cattle is caused by an increase in core body temperature, which affects the fat production in the mammary gland. It reduces milk yield, dry matter intake, and alters the milk composition, such as fat, protein, lactose, and solids-not-fats percentages among others. Understanding the biological mechanisms of climatic adaptation, identifying and exploring signatures of selection, genomic diversity and identification of candidate genes for heat tolerance within indicine and taurine dairy breeds is an …

Characterization And Pathogenicity Of Fusarium Species Causing Sugar Beet Root Rot In Morocco, Abdelaaziz Farhaoui, Nabila El Alami, Grace Gachara, Said Ezrari, Mohammed Khadiri, Abdessalem Tahiri, Zineb Belabess

All Rsif Scholars' Publications

The sugar beet crop ranks second globally among the plant species grown mainly
for sugar production. In Morocco, the area under sugar beet farming occupies ap-
proximately 57,000 ha yielding more than 3 million tons of roots. However, sugar beet
root-tip rot (RTR) caused by Fusarium spp. dramatically reduces the anticipated yields,
the purity of the resulting juice, and the sugar concentration. The current study aimed
at identifying and characterizing the Fusarium species responsible for the root rot in
sugar beet grown in the Khenifra-Beni Mellal region of Morocco. In this survey, 69
isolates of Fusarium were sampled from sugar …

Microparticles As Viral Rna Carriers From Stool For Stable And Sensitive Surveillance, Emmanuel Kifaro, Mi Jung Kim, Seungwon Jung, Yoon-Ha Jang, Sungyeon Moon, Dong-Hun Lee, Chang-Seon Song, Gerald Misinzo, Sang Kyung Kim

All Rsif Scholars' Publications

Since its discovery, polymerase chain reaction (PCR) has emerged as an important technol- ogy for the diagnosis and identification of infectious diseases. It is a highly sensitive and reliable nucleic acids (NA) detection tool for various sample types. However, stool, which carries the most abundant micro-organisms and physiological byproducts, remains to be the trickiest clinical specimen for molecular detection of pathogens. Herein, we demonstrate the novel application of hydrogel mi- croparticles as carriers of viral RNA from stool samples without prior RNA purification for real-time polymerase chain reaction (qPCR). In each microparticle of primer-incorporated network (PIN) as a self-sufficient reaction …

Associative Learning Contributes To The Persistence Of Fatigue-Like Behavior In Male Mice In A Model Of Cancer Survivorship, Elisabeth G Vichaya, Josephine K Darpolor, Phillip S Gross, Jessica M Molkentine, Daniel W Vermeer, Paola D Vermeer, John H Lee, Cullen M Taniguchi, Robert Dantzer

Faculty, Staff and Student Publications

Persistent fatigue is a debilitating side effect that impacts a significant proportion of cancer survivors for which there is not yet an FDA-approved treatment. While certainly a multi-factorial problem, persistent fatigue could be due, in part, to associations learned during treatment. Therefore, we sought to investigate the role of associative learning in the persistence of fatigue using a preclinical model of cancer survivorship. For this purpose, we used a murine model of human papilloma virus-related head and neck cancer paired with a curative regimen of cisplatin-based chemoradiation in male C57BL/6J mice. Fatigue-like behavior was assessed by measuring variations in voluntary …

Small Molecule Inhibitor Of Tau Self-Association In A Mouse Model Of Tauopathy: A Preventive Study In P301l Tau Jnpl3 Mice, Eliot J Davidowitz, Patricia Lopez, Heidy Jimenez, Leslie Adrien, Peter Davies, James G Moe

Faculty, Staff and Student Publications

Advances in tau biology and the difficulties of amyloid-directed immunotherapeutics have heightened interest in tau as a target for small molecule drug discovery for neurodegenerative diseases. Here, we evaluated OLX-07010, a small molecule inhibitor of tau self-association, for the prevention of tau aggregation. The primary endpoint of the study was statistically significant reduction of insoluble tau aggregates in treated JNPL3 mice compared with Vehicle-control mice. Secondary endpoints were dose-dependent reduction of insoluble tau aggregates, reduction of phosphorylated tau, and reduction of soluble tau. This study was performed in JNPL3 mice, which are representative of inherited forms of 4-repeat tauopathies with …

Artificial Intelligence-Driven Meta-Analysis Of Brain Gene Expression Identifies Novel Gene Candidates And A Role For Mitochondria In Alzheimer’S Disease, Caitlin A Finney, Fabien Delerue, Wendy A Gold, David A Brown, Artur Shvetcov

Faculty, Staff and Student Publications

Alzheimer's disease (AD) is the most common form of dementia. There is no treatment and AD models have focused on a small subset of genes identified in familial AD. Microarray studies have identified thousands of dysregulated genes in the brains of patients with AD yet identifying the best gene candidates to both model and treat AD remains a challenge. We performed a meta-analysis of microarray data from the frontal cortex (n = 697) and cerebellum (n = 230) of AD patients and healthy controls. A two-stage artificial intelligence approach, with both unsupervised and supervised machine learning, combined with a functional …

A Unified Mediation Analysis Framework For Integrative Cancer Proteogenomics With Clinical Outcomes, Licai Huang, James P Long, Ehsan Irajizad, James D Doecke, Kim-Anh Do, Min Jin Ha

Faculty, Staff and Student Publications

MOTIVATION: Multilevel molecular profiling of tumors and the integrative analysis with clinical outcomes have enabled a deeper characterization of cancer treatment. Mediation analysis has emerged as a promising statistical tool to identify and quantify the intermediate mechanisms by which a gene affects an outcome. However, existing methods lack a unified approach to handle various types of outcome variables, making them unsuitable for high-throughput molecular profiling data with highly interconnected variables.

RESULTS: We develop a general mediation analysis framework for proteogenomic data that include multiple exposures, multivariate mediators on various scales of effects as appropriate for continuous, binary and survival outcomes. …

Sparse Tree-Based Clustering Of Microbiome Data To Characterize Microbiome Heterogeneity In Pancreatic Cancer, Yushu Shi, Liangliang Zhang, Kim-Anh Do, Robert Jenq, Christine B Peterson

Faculty, Staff and Student Publications

There is a keen interest in characterizing variation in the microbiome across cancer patients, given increasing evidence of its important role in determining treatment outcomes. Here our goal is to discover subgroups of patients with similar microbiome profiles. We propose a novel unsupervised clustering approach in the Bayesian framework that innovates over existing model-based clustering approaches, such as the Dirichlet multinomial mixture model, in three key respects: we incorporate feature selection, learn the appropriate number of clusters from the data, and integrate information on the tree structure relating the observed features. We compare the performance of our proposed method to …

Erratum: Cxcl12-Mediated Monocyte Transmigration Into Brain Perivascular Space Leads To Neuroinflammation And Memory Deficit In Neuropathic Pain, Chun-Lin Mai, Zhi Tan, Ya-Nan Xu, Jing-Jun Zhang, Zhen-Hua Huang, Dong Wang, Hui Zhang, Wen-Shan Gui, Jun Zhang, Zhen-Jia Lin, Ying-Tong Meng, Xiao Wei, Ying-Tao Jie, Peter M Grace, Long-Jun Wu, Li-Jun Zhou, Xian-Guo Liu

Faculty, Staff and Student Publications

In the original Figure 7E of our article, the authors mistakenly reused the GFAP immunostaining representative image of the Vehi+Sham group for the anti-CXCL12+Sham group. This is because an error occurred in converting the original purple fluorescence of GFAP for each group to red fluorescence during preparation of representative pictures of Figure 7E. Unfortunately, this error was not found in multiple revisions. The correct version of Figure 7E is shown below. The correction made in this Erratum does not affect the results and conclusions in this study. The authors apologize for any inconvenience the errors may have caused.

Late Effects Of Craniospinal Irradiation Using Electron Spinal Fields For Pediatric Patients With Cancer, Brian De, Marcus A Florez, Ethan B Ludmir, Moshe H Maor, Susan L Mcgovern, Mary Frances Mcaleer, David R Grosshans, Eric L Chang, Anita Mahajan, Arnold C Paulino

Faculty, Staff and Student Publications

Purpose: For children, craniospinal irradiation (CSI) with photons is associated with significant toxic effects. The use of electrons for spinal fields is hypothesized to spare anterior structures but the long-term effects remain uncertain. We studied late effects of CSI using electrons for spinal radiation therapy (RT).

Methods and materials: Records of 84 consecutive patients treated with CSI using electrons for the spine at a single institution between 1983 and 2014 were reviewed. Median age at RT was 5 (range, 1-14) years. The most common histologies were medulloblastoma/primitive neuroectodermal tumor (59%) and ependymoma (8%). The median prescribed dose to the entire …

Protective Role Of Colitis In Inflammatory Arthritis Via Propionate-Producing Bacteroides In The Gut, Hoh-Jeong Shon, Yu-Mi Kim, Kyeong Seog Kim, Jin-Ouk Choi, Sang-Hyun Cho, Sujin An, Se-Hyeon Park, Yong-Joon Cho, Joo-Hong Park, Sang-Uk Seo, Joo-Youn Cho, Wan-Uk Kim, Donghyun Kim

Faculty, Staff and Student Publications

OBJECTIVES: To investigate whether and how inflammatory disease in the intestine influences the development of arthritis, considering that organ-to-organ communication is associated with many physiological and pathological events.

METHODS: First, mice were given drinking water containing dextran sodium sulfate (DSS) and then subjected to inflammatory arthritis. We compared the phenotypic symptoms between the cohoused and separately-housed mice. Next, donor mice were divided into DSS-treated and untreated groups and then cohoused with recipient mice. Arthritis was then induced in the recipients. The fecal microbiome was analyzed by 16S rRNA amplicon sequencing. We obtained type strains of the candidate bacteria and generated …

Accurate Prediction Of Functional Effect Of Single Amino Acid Variants With Deep Learning, Houssemeddine Derbel, Zhongming Zhao, Qian Liu

Faculty, Staff and Student Publications

The assessment of functional effect of amino acid variants is a critical biological problem in proteomics for clinical medicine and protein engineering. Although natively occurring variants offer insights into deleterious variants, high-throughput deep mutational experiments enable comprehensive investigation of amino acid variants for a given protein. However, these mutational experiments are too expensive to dissect millions of variants on thousands of proteins. Thus, computational approaches have been proposed, but they heavily rely on hand-crafted evolutionary conservation, limiting their accuracy. Recent advancement in transformers provides a promising solution to precisely estimate the functional effects of protein variants on high-throughput experimental data. …

Optimal Ranking And Directional Signature Classification Using The Integral Strategy Of Multi-Objective Optimization-Based Association Rule Mining Of Multi-Omics Data, Saurav Mallik, Soumita Seth, Amalendu Si, Tapas Bhadra, Zhongming Zhao

Faculty, Staff and Student Publications

No abstract provided.

3pnmf-Mkl: A Non-Negative Matrix Factorization-Based Multiple Kernel Learning Method For Multi-Modal Data Integration And Its Application To Gene Signature Detection\, Saurav Mallik, Anasua Sarkar, Sagnik Nath, Ujjwal Maulik, Supantha Das, Soumen Kumar Pati, Soumadip Ghosh, Zhongming Zhao

Faculty, Staff and Student Publications

In this current era, biomedical big data handling is a challenging task. Interestingly, the integration of multi-modal data, followed by significant feature mining (gene signature detection), becomes a daunting task. Remembering this, here, we proposed a novel framework, namely, three-factor penalized, non-negative matrix factorization-based multiple kernel learning with soft margin hinge loss (3PNMF-MKL) for multi-modal data integration, followed by gene signature detection. In brief, limma, employing the empirical Bayes statistics, was initially applied to each individual molecular profile, and the statistically significant features were extracted, which was followed by the three-factor penalized non-negative matrix factorization method used for data/matrix fusion …