Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrating Neuroimaging and Genetics Data in a Bioinformatics-based Approach for the Study of Alzheimer’s Disease

Recent advances in the imaging-genetics field within Alzheimer’s disease (AD) have resulted in large amounts of data; however the challenge is filtering through the data and identifying meaningful genotype-phenotype relationships within AD. The overall goal of this thesis is to integrate existing tools to prioritize influential genetic variants and associated neuroanatomical measures in order to tease apart the etiology of AD and be able to use these markers in a predictive analysis of AD progression. The thesis is divided into four independent projects. The first project aims to reduce the burden of multiple testing correction by using a false discovery rate approach within strata defined by a novel biologically driven gene prioritization methodology. The overall aim of projects two and three is to estimate the heritability of neuroanatomical measures by preselection of regions with high heritability, allowing for reduction of the multiple testing burden. In project two, I investigated the influence of whole hippocampal volume and total brain volume on the heritability estimates of hippocampal subfields. In project three, I investigated heritability estimates of cortical thickness and surface area using both a vertex-wise and region of interest approach determining unreliability of smaller regions. The fourth project was a pilot study to investigate if combining genome wide association study data with neuroanatomical measures would improve the performance of
Investigation on the Pattern of Intestinal Parasites Present in Refuse Dumps and Abattoir Wastes in Ile-Ife, Nigeria

This project work focuses on the investigation of pattern of intestinal parasites present in refuse dumps and abattoir wastes in Ile-Ife. Samples were collected from 5 abattoirs in Ile-Ife and 5 refuse sites. The collection of samples covered a period of 4 months from March to June 2009. The samples were processed using concentration methods (Simple sedimentation and saturated salt floatation techniques). 64 ova and cyst of intestinal parasite were recovered from abattoir waste and 31 from refuse dumps. Trohozoites of protozoa and larvae of some helminths recovered are 95. In refuse dump samples; Entamoeba histolytica 18 (28.1%) Entamoeba coli 12 (18.8%), Balantidium coli 2 (3.1%), Taenia spp. 2 (3.1%), Hymenolepis nana 3 (4.2%), Hookworm 2 (3.1%) are recovered while in abattoir wastes Ascaris lumbricoides 17 (54.8%), Hookworm 9 (29.0%), Balantidium coli 5 (16.1%) and trophozoite of Balantidium coli 15 (15.8%), Trichomonas hominis 56 (58.9%), larvae of Strongyloides stercoralis 13 (13.7%) and Hookworm 11 (11.6%) were recovered from abattoir effluents. The public is encouraged to take good sanitary and hygienic habits; wastes from our houses should be properly disposed either by burning or burying deep in the soil. Protective material like shoe and hand gloves is suggested for workers that will be having contact with night soil and any waste water, effluents and slurries that will be used as manure or to irrigate farm products should be treated before use and any infected individual should be well treated and prevented from infecting others.
Greenhouse gas emission from a eutrophic coastal lagoon in Rio de Janeiro, Brazil

Greenhouse gases increased in concentrations over pre-industrial values by 257% for methane and 145% for carbon dioxide in 2016. Such increased levels are the main climate change drivers and may affect aquatic systems that accumulate and carry carbon to the ocean and the atmosphere. Additionally, these systems are sensitive to environmental changes since their physical, chemical and biological properties respond rapidly to changes. Therefore, this study focus on the greenhouse gases dynamic over an urban eutrophic tropical lagoon. Samplings were performed in the Rodrigo de Freitas Lagoon by covering four periods in 2016 (April, June, October and December). Mean diffusive flux was -1,466.8 mg m -2 d -1 of carbon dioxide and 113.7 mg m -2 d -1 of methane. Regarding the bubbling, fluxes were 58.28 mg m -2 d -1 for methane and negligible for carbon dioxide (mean value of 5.01 mg m -2 d -1 ). Environmental parameters such as depth, water temperature and sediment particle size were strongly related to the fluxes. In conclusion, the region is a sink of carbon dioxide and a source of methane to the atmosphere. Additionally, the rivers discharge impacts the lagoon by generating a methane hotspot emission region.
A CSR-1 guided H3K36me3 Signature Maintains Germline Gene Expression Programs In Caenorhabditis elegans

Small RNA pathways related to RNA Interference (RNAi) are prevalent in species ranging from protozoa to mammals, including humans. These pathways contribute to organismal development and cellular function and elicit their gene-regulatory impacts through diverse modes of action. The soil nematode, Caenorhabditis elegans, has emerged as a powerful system to study the endogenous activities of these pathways. In the germline, the worm has evolved an intricate network of small RNA pathways, that jointly contribute to the transmission of epigenetic information through cell divisions and across generations. This activity is necessary for the maintenance of existing germline gene expression programs, and involves the dynamic regulation of mRNA transcripts, small RNA populations, and changes to the chromatin landscape. In this thesis, I demonstrate a role for the Argonaute CSR-1 (Chromosome Segregation and RNAi defecient-1) in this process. Using genetic approaches, I demonstrate that CSR-1 licenses genes for germline expression and overcomes the silencing activity of competing small RNA pathways. I explore the mechanisms by which CSR-1 elicits its licensing activity, and identify a role for the pathway in guiding the acquisition of H3K36me3 on a genome-wide scale. Using a combination of genetic and genome-wide approaches I describe the contribution of two H3K36 methyltransferases to the CSR-1 pathway. Finally, I identify a putative self-
Interaction of Rhizoctonia solani and Leuconostoc spp. causing sugar beet root rot and tissue pH changes in Idaho

Abstract Late season Rhizoctonia root rot in sugar beet is a serious yield limiting disease problem caused by an interaction between Rhizoctonia solani and Leuconostoc spp. in Idaho. To better understand this interaction, the two most common Leuconostoc haplotypes were co-inoculated with 17 R. solani strains representing the range of genetic diversity established previously. The study was conducted twice by inoculating sugar beet roots in the field using a plug assay and measuring root rot and tissue pH. L. mesenteroides strain L12311 (17 mm of rot) had significantly (P < 0.0001) more rot than L. pseudomesenteroides strain L12487 (13 mm) when combined with the fungal strains. The R. solani anastomosis group (AG) 2–2 IIIB strains (16 mm of rot) led to significantly (P < 0.0001–0.0073) more rot than strains associated with other AGs: 2–2 IV (11 mm), 4 HG-I (5 mm) and 4 HG-II (3 mm). When R. solani AG-2-2 IIIB strains from three phylogenetic groups were compared, rot ranged from 15 to 17 mm and did not differ (P = 0.1275–0.5565). The pH for root tissue with at least 30 mm of rot was lower (4.0–4.2 ± 0.2–0.4) than tissue with < 2 mm of rot and water checks (6.2–6.4 ± 0.1–0.2). Both isolations and tissue pH suggest late season sugar beet root rot is primarily associated with Leuconostoc and secondary organisms. However, damage was minor without both R. solani AG-2-2 and Leuconostoc strains present when internal rot initiates.
Effect of Inclusion Level and Time on Apparent Digestibility of Solvent-Extracted Soybean Meal for Common Carp ( Cyprinus carpio, Cyprinidae)

Apparent digestibility of solvent-extracted soybean meal (SBM) was determined at four levels of inclusion (10, 20, 30 and 40%) and over two periods of time (days 9-17 and days.19- 24) for common carp (Cyprinus carpio, Cyprinidae). Solvent-extracted SBM was incorporated into a casein-based reference diet, and chromium oxide (1%) was used as an external marker. Apparent digestibility of SBM was found to decrease significantly with inclusion (86.3-73.1%) but not time. The digestibility of dietary protein also decreased significantly with inclusion, and although there was a trend for SBM protein digestibility to decrease with inclusion, this was not significant. Dietary lipid and SBM crude energy digestibility were found to increase and decrease, respectively, with time. These results indicate that digestibility of solvent-extracted SBM and its constituent nutrients for common carp may be affected by both level of inclusion and time, and that these factors must be considered when determining digestibility of protein sources for use in the formulation of experimental and commercial diets for this species.
Spire stimulates nucleation by Cappuccino and binds both ends of actin filaments

An actin mesh fills both mouse and fly oocytes. The meshes are built by a conserved mechanism and used to establish polarity. Two actin nucleators, Spire and Cappuccino, collaborate to build actin filaments that connect vesicles and the cortex. Direct interaction between Spire and Cappuccino is required for in vitro synergistic actin assembly; however, we understand little about why the interaction is necessary. To mimic the geometry of Spire and Cappuccino in vivo, we immobilized Spire on beads. We found that increased nucleation is a major part of synergy and that Spire alone binds both barbed- and pointed-ends of actin filaments. We identified Spire’s barbed-end binding domain. Partial rescue of fertility by a loss-of-function mutant indicates that barbed-end binding is not necessary for Spire’s in vivo function, but that it may play a role under normal circumstances. We propose that Spire stimulates nucleation by Cappuccino in a manner similar to the collaboration between APC and mDia1. Summary Actin nucleators Cappuccino and Spire collaborate to build an actin mesh in oocytes. Data demonstrate that the collaboration leads to synergistic actin nucleation, as opposed to elongation. Further, Spire binds both ends of polar, actin filaments, resolving a long-outstanding question.
Using Parsimony-Guided Tree Proposals to Accelerate Convergence in Bayesian Phylogenetic Inference

Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topologies. MCMC algorithms using such moves tend to get trapped in tree space, making them slow in finding the globally most probable trees (known as ‘convergence’) and in estimating the correct proportions of the different types of them (known as ‘mixing’). Here, we introduce a new class of moves, which propose trees based on their parsimony scores. The proposal distribution derived from the parsimony scores is a quickly computable albeit rough approximation of the conditional posterior distribution over candidate trees. We demonstrate with simulations that parsimony-guided moves correctly sample the uniform distribution of topologies from the prior. We then evaluate their performance against standard moves using six challenging empirical datasets, for which we were able to obtain accurate reference estimates of the posterior using long MCMC runs, a mix of topology proposals, and Metropolis coupling. On these datasets, ranging in size from 357 to 934 taxa and from 1,740 to 5,681 sites, we find that single chains using parsimony-guided moves usually converge an order of magnitude faster than chains using standard moves. They also exhibit better mixing, that is, they cover the most probable trees more quickly. Our results show that tree moves based on quick and dirty estimates of the posterior probability can significantly outperform standard moves. Future research will have to show to what extent the performance of such moves can be improved further by finding better ways of approximating the posterior probability, taking the trade-off between accuracy and speed into account.
Grafting Can Modulate Watermelon Growth and Productivity under Egyptian Conditions

This study was accomplished in a private farm at Al Salhia area, Sharqia Governorate, Egypt during the two successive spring-summer seasons of 2013 and 2014 to assess the effect of grafting methods and rootstocks on plant growth performance, fruit yield and fruit quality of watermelon (Citrullus lanatus [Thunb.] cv. Peacock wm60. Peacock wm60 plants were grafted onto five rootstocks (6001 F1, Super Shintoza F1, Ferro F1, bottle gourd cv. Local, and Peacock wm60 as self-grafted) either by splice and tongue approach. Non-grafted plants of Peacock wm60 were used as control. Grafting methods pronounced non-significant impact on watermelon vegetative and root growth and fruit yield and quality after transplanting in the field (scope of our study). Based on the data, watermelon propagation via grafting on the rootstocks of 6001, Super Shintosa and Ferro positively impacted on plant growth attributes and fruit yield and quality (fruit weight, rind sickness and TSS content) compared to grafting on local rootstock, self-grafted or direct seed plants. Rootstock of 6001 appeared superior to others on enhancing the measured parameters of plant growth, yield and fruit quality as well as root growth (roots dry weight). Local rootstock of bottle gourd impacted poorly on plant growth, yield and fruit quality compared to other rootstocks but superior to self-grafted or direct seed plants. The data concluded that, choice grafting method either splice or tongue approach for production watermelon seedlings depends on their results in the nursery before planting the grafted seedlings in the field because of differences between the methods on the plant behavior after transplanting were absent.
Mapping the missing branch on the neogastropod tree of life: molecular phylogeny of marginelliform gastropods

Marginelliform gastropods are a heterogeneous and diverse group of molluscs encompassing over 1,600 living species, among which are the smallest known neogastropods. The relationships of marginelliform gastropods within the order Neogastropoda are controversial, and the monophyly of the two marginelliform families the Marginellidae J. Fleming, 1828 and the Cystiscidae Stimpson, 1865, remains unconfirmed. DNA sequence data have never been used to assess the relationships of the marginelliform gastropods, making this group the only major branch missing in our current understanding of the neogastropod tree of life. Here we report results of the first multilocus phylogenetic analysis of marginelliform gastropods, which is based on a dataset comprising 63 species (20 genera) of Marginellidae and Cystiscidae, and a wide range of neogastropod lineages. The Marginellidae and Cystiscidae form a moderately supported clade that is sister to the family Volutidae. Marginellona gigas appears to be sister to all other marginelliforms. The subfamily Marginellinae was recovered as a well-supported clade, and good resolution of this part of the tree makes it possible to propose amendments to the family-level classification of the group. The relationship between Granulina and other marginelliforms could not be resolved and requires further study. Due to poor resolution of basal relationships within the Marginellidae–Cystiscidae clade, the monophyly of the Cystiscidae was neither confirmed nor convincingly rejected. The shell morphology of most marginellid and cystiscid genera is taxonomically not very informative but, nevertheless, of the traditionally recognized genera only Gibberula and Dentimargo were shown to be polyphyletic. Although a comprehensive systematic revision of the group requires more extensive taxonomic sampling (e.g. with better representation of the type species of nominal genus-group names), our results support the superfamily Volutoidea, comprising four families (Volutidae, Cystiscidae, Marginellidae and Marginellonidae), with the placement of the Granulinidae uncertain for the time being.
ISOLATION AND IDENTIFICATION OF Salmonella enterica TYPHIMURIUM FROM RABBITS

The current study aimed to isolate and identify Salmonella Typhimurium from rabbits and evaluate their antimicrobial resistance. Seventy five New-Zealand breed rabbits of both sex (40 apparently healthy and 35 clinically diseased) were collected from Sharkia Province, Egypt. The collected samples from diseases cases (No=135) included raw meat, intestinal content (diarrheic), and liver (35 each). Vaginal swabs (No = 10) from aborted cases and abscess samples (No =20) were also collected. Isolation and identification of Salmonella enterica was carried out by standard methods. The isolates were characterized by using serological test, phagetyping, genus specific PCR and antimicrobial sensitivity tests. The overall prevalence of S. Typhimurium in the examined rabbit samples was 7.40% (10/135). S. Typhimurium was more frequently detected in vaginal swab (aborted cases) and diarrheic faeces with a frequency of 40% (4/10) and 14.29(5/35), respectively. Nevertheless, it was lower in the examined liver samples with a percentage of 5(1/35). S. Typhimurium was absent in apparently healthy rabbit samples. It was found that all S. Typhimurium isolates phage-typed as DT104. All PCR products of isolates include positive control, screened by PCR, resulted in 186 bp amplified fragment. No amplified DNA fragments were obtained from non-Salmonella species. Conclusively, it was concluded that rabbit is a potential reservoir for salmonellosis. The conservative Salmonella serotypes in the present study, was S. Typhimurium DT104. Multiresistance phenonmena was emergent in the circulating Salmonella strains in rabbit sources.
Rice Hybrids and High Yielding Varieties for Augmenting Public Distribution System Demand in Andaman and Nicobar Islands, India

Rice (Oryza sativa L.) is the most important staple crop of Andaman & Nicobar Islands grown under rain fed lowlands during kharif season on 5340 ha with a production 16845 t (DOES, 2018) and this production is far behind the local requirements. This is evident from the fact that during 2016-17, 12594 t rice was produced in islands, while 22, 821 t of rice (6,737 t wheat) were shipped from mainland and supplied though public distribution system (PDS) indicating a demand of 42152 t of cereals (DOES, 2017). The transhipment of food grains from mainland to Islands and from there to fair price shops located in each village by Food Corporation of India (FCI) is a herculean task and involves huge cost and human effort. All India transit losses of rice in India were estimated as 0.38% in 2017-18 (DFPD, 2019), though separate estimates are unavailable for Islands; the losses will be many times higher (5 times) due to multi-mode of transport Increases in rice grain yield depend on introduction of potential cultivars including hybrids into Andaman and Nicobar islands that with small acreage (5340 ha) won’t merit developing hybrids locally. The objective of this study was to evaluate newly released hybrids and high yielding varieties of rice elsewhere in the country and identify promising ones for augmenting the huge production shortages in the islands. Twenty rice cultivars (17 hybrids and 3 high yielding varieties) were field evaluated using randomised complete block design with two replicates at Port Blair, Andaman & Nicobar Islands during kharif season of 2017. Results revealed that five hybrids (28P09, NK-16520, 27P36, KPH-272 and PAN-2423) and two varieties (NDR-359 and Gontra Bidhan-3) have 14-26% higher grain yields than local check variety ‘CARI Dhan-6’ (3.1 t/ha). Based on 10 and 20% increase in yield as criteria for release of a variety and hybrid in the country, NDR-359 (21%) and Gontra Bidhan-3 (23%) varieties and 28P09 hybrid (26%) merits are introduction. From economics point of view, Gontra Bidhan-3 (250%) followed by NDR359 (217%) and 28P09 hybrid (214%) with 227% higher net income than local check (Rs. 9121) proved their merit. This study provided evidence to suggest that new cultivars introduction could augment the rice production shortages in the islands to some extent. K e y w o r d s
Accumulated degeneration of transcriptional regulation contributes to disease development and detrimental clinical outcomes of Alzheimer’s disease

Alzheimer’s disease (AD) is extremely complex for both causal mechanism and clinical manifestation, requiring efforts to uncover its diversity and the corresponding mechanisms. Here, we applied a modelling analysis to investigate the regulation divergence among a large-scale cohort of AD patients. We found that transcription regulation tended to get degenerated in AD patients, which contributed to disease development and the detrimental clinical outcomes, mainly by disrupting protein degradation, neuroinflammation, mitochondrial and synaptic functions. To measure the accumulated effects, we came up with a new concept, regulation loss burden, which better correlated with AD related clinical manifestations and the ageing process. The epigenetic studies to multiple active regulation marks also supported a tendency of regulation loss in AD patients. Our finding can lead to a unified model as AD causal mechanism, where AD and its diversity are contributed by accumulated degeneration of transcriptional regulation. The significance of this study is that: (1) it is the first system biology investigation to transcription regulation divergence among AD patients; (2) we observed an accumulated degeneration of transcription regulation, which well correlates with detrimental clinical outcomes; (3) transcriptional degeneration also contributes to the ageing process, where its correlation with ages is up to 0.78.
The development of inhibitory cortical interneurons in the early fetal human telencephalon

The extent of similarities and differences between cortical GABAergic interneuron generation in rodent and primate telencephalon remains contentious. We examined expression of three interneuron precursor transcription factors, alongside other markers, using immunohistochemistry on 8–12 post-conceptional weeks (PCW) human telencephalon sections. NKX2.1, OLIG2, and COUP-TFII expression occupied distinct (although overlapping) neurogenic domains which extended into the cortex and revealed three CGE compartments: lateral, medial, and ventral. NKX2.1 expression was very largely confined to the MGE, medial CGE, and ventral septum confirming that, at this developmental stage, interneuron generation from NKX2.1? precursors closely resembles the process observed in rodents. OLIG2 immunoreactivity was observed in GABAergic cells of the proliferative zones of the MGE and septum, but not necessarily co-expressed with NKX2.1, and OLIG2 expression was also extensively seen in the LGE, CGE, and cortex. At 8 PCW, OLIG2? cells were only present in the medial and anterior cortical wall suggesting a migratory pathway for interneuron precursors via the septum into the medial cortex. By 12 PCW, OLIG2? cells were present throughout the cortex and many were actively dividing but without co-expressing cortical progenitor markers. Dividing COUP-TFII? progenitor cells were localized to ventral CGE as previously described but were also numerous in adjacent ventral cortex; in both the cases, COUP-TFII was co-expressed with PAX6 in proliferative zones and TBR1 or calretinin in post-mitotic cortical neurons. Thus COUPTFII? progenitors gave rise to pyramidal cells, but also interneurons which not only migrated posteriorly into the cortex from ventral CGE but also anteriorly via the LGE.