Miracle-dz/UniFAR-FTUs huggingface dataset:
Complement factor H regulation in the central nervous system

Approved: ____________________________________ Thesis Supervisor ____________________________________ Title and Department ____________________________________ Date COMPLEMENT FACTOR H REGULATION IN THE CENTRAL NERVOUS SYSTEM by Laura Anne Fraczek A thesis submitted in partial fulfillment of the requirements for the Doctor of Philosophy degree in Immunology in the Graduate College of The University of Iowa
Biological knowledge discovery through mining multiple sources of high-throughput data

As we are moving into the post-genomic era, various high-throughput experimental techniques have been developed to characterize biological systems at the genome scale. The high-throughput data are becoming fundamentally important resources to shed new insights on system-level understanding of the ‘ organization’ and ‘dynamics’ of molecules (i.e. genes, proteins), relationships between them, interaction cascades, pathways, modules and various networks (i.e. regulation, co-expression and metabolism). This dissertation focuses on developing computational tools to facilitate the process of translating the ever-growing volumes of high-throughput data into significant biological knowledge on protein functions, pathways and modules. Although high-throughput data provide a global picture of biological systems about the underlying mechanisms, the details are often noisy, hence the integration of heterogeneous data that characterize cellular systems from different aspects (i.e. gene expression and protein-protein interactions) can lead to the comprehensive and coherent discoveries of biological insights. We developed a Bayesian probability framework to predict function for unannotated proteins in yeast through integrating protein binary interaction data, protein complex data and microarray data. We also extended the computational framework to infer biological pathway in an automated and systematical fashion. Besides bottom-up approaches moving from protein functions to pathways, we also applied top-down approaches to model the cellular network, that is, we started from the architecture of cellular network to identify the functional modules. We applied the k-core algorithm to decompose protein interaction and microarray gene co-expression networks, which provides strong support for modularity principles of networks' structure and function. Dynamic functional modules and protein complexes have been identified by clustering the network constructed from multiple sources of high-throughput data, shedding insights into understanding the organization and dynamics of a living cell. We also proposed a consensus approach to model biological pathway by combining different computational tools and integrating multiple sources of high-throughput data. In the future, with the explosion in the quantity and diversity of high-throughput data, it is vital to develop methodologies and innovative tools in bioinformatics to model biological systems and explore biological knowledge in an iterative fashion.
Seeking health content online: a survey of Internet users’ habits and needs

This paper describes a small-scale survey conducted among non-native speakers of English living in Ireland. We collected data from 86 respondents by means of an online questionnaire. Our goal was to investigate their health information seeking behaviour; potential comprehension issues with health content; and their adoption of machine translation (MT) systems. We found that: the Internet is widely used for health-related searches; Wikipedia is the most consulted website; and information on illnesses and public health threats is frequently sought. We observed that the language in which online searches are conducted is influenced by respondents’ self-reported level of English proficiency, with most limited English proficiency (LEP) Internet users looking for health information in their native languages to facilitate comprehension. We also observed that specialised medical vocabulary might hinder comprehension. Finally, most participants reported adopting MT to translate online health content from English into their native languages, and LEP respondents reported using MT more frequently than proficient respondents. This survey highlights the need to increase the accessibility of online health content for nonnative speakers of English (especially LEP users) with a view to reducing their vulnerability. We argue that text simplification might lead to the production of more comprehensible and more machine translatable health-related texts.
Effect of feeding raw or water soaked rapeseed cake on carcass characteristics and meat quality in kids.

Growing male kids (18) of 11.10± 0.77 kg BW, 6 months age were randomly assigned to 3 dietary treatments of 6 each. Groundnut cake of the concentrate mixture of control group (GNC) was replaced by rapeseed-mustard cake (RMC) in group 2 and 3, but the concentrate in group 3 was soaked with water (1:3) overnight and fed as mixed ration (sani) with wheat straw. In other groups, respective concentrate mixtures were offered in the morning and wheat straw was offered ad lib. During an experimental period of 180 days, fortnightly body weight changes of kids were recorded. The glucosinolates (GLS) content of RMC was 149.50 μmol/g DM which was reduced by 31.96% after overnight water soaking. DM intake in group 3 was reduced as compared to other groups. All the kids were slaughtered at the end of the experimental feeding. Preslaughter weight (PSW), carcass yield, carcass length and loin eye area of kids were similar between control and group 2, while all of these were significantly (P<0.05) lower in group 3 than that in control group. While yield of wholesale cuts and, edible and non-edible visceral organs were comparable among groups, weight (g/kg of PSW) of liver and pluck was significantly higher in groups 2 and 3 than in control group. Chemical composition, physico-chemical properties and thiocyanate concentration of Longissimus dorsi (LD) muscle did not differ significantly among groups. Organoleptic scores of pressure cooked LD muscle sample with salt (1.5% w/w) were comparable among the groups; however, tenderness score was slightly poor in groups 2 and 3. It may be concluded that despite reduction in GLS content of RMC based supplement by overnight water soaking, its feeding as mixed ration (sani) to growing kids had no positive effect in terms of meat quality attributes.
Structural elucidation of a common architecture of the nuclear pore complex and COPIl vesicle coats

Nuclear pore complexes (NPCs) are massive protein assemblies that perforate the nuclear envelope and form the exclusive passageway for nucleocytoplasmic transport. NPCs play critical roles in molecular transport and a myriad of other cellular processes. Elucidation of the structure of the NPC is thus expected to provide important insight into cell biology. In this thesis, I investigate the structure of a key subcomplex of the NPC and discuss the evolutionary relationship between the NPC and COPIl vesicle coats it illustrates. The NPC is a modular assembly, with a stable structural scaffold supporting dynamically attached components. The structural scaffold is constructed from multiple copies of the Y-shaped complex and the Nic96 complex. We solved the crystal structure of the heterodimeric Nup85-Sehl module that forms a short arm in the Y complex. Nup85 is found to contain a conserved fold, the ancestral coatomer element 1 (ACE1), also present in three other components of the NPC and in the COPI vesicle coat, providing structural evidence of coevolution from a common ancestor. Sec3l ACE1 units interact to form edge elements in the COPI lattice. Using structural knowledge of this edge element, we identified corresponding interactions between ACE1 proteins Nup84 and Nup145C in the NPC. We solved the crystal structure of the heterotrimeric Nup84-Nupl 45C-Secl 3 module that forms the top of the long arm in the Y complex. The heterotypic ACE1 interaction of Nup145C and Nup84 is analogous to the homotypic Sec31 edge element interaction in the COPIl coat. From these and other structures, we assemble a near complete structural model of the Y complex. Further, based on the demonstrated relationship with the COPIl coatomer lattice, we propose a lattice model for the entire NPC scaffold. The common architectural principles of the edge elements in the NPC and COPI lead us to predict that Y complexes will be arranged as struts in the NPC lattice. In this manner, Nup84-Nup145C edge elements are arranged parallel to the transport axis to stabilize the positively curved nuclear envelope. From a lattice model of the NPC follow hypotheses for how other components are integrated into and function within the NPC. Thesis Supervisor: Thomas U. Schwartz Title: Pfizer-Laubach Career Development Associate Professor of Biology
Reducing Biotic and Abiotic Land‐Use Legacies to Restore Invaded, Abandoned Citrus Groves

Land‐use legacies associated with agriculture, such as increased soil fertility and elevated soil pH, promote invasions by non‐native plant species on former agricultural lands. Restoring natural soil conditions (i.e. low fertility and low pH) may be an effective, long‐term method to control and reduce the abundance of non‐native and ruderal species that invade abandoned agricultural lands. In this study, we examined how soil manipulation treatments of lowering soil fertility with carbon additions and lowering soil pH by applying sulfur affect non‐native and ruderal native plant species abundance in two former citrus groves in central Florida. Non‐native plant biomass was removed by one of two methods (tilling or topsoil removal), and was combined with a soil amendment of sulfur, carbon, sulfur + carbon, or none. The biomass removal treatments significantly decreased non‐native abundance, with topsoil removal as the most effective. Carbon additions did not affect soil fertility or vegetation. Sulfur and sulfur + carbon additions significantly decreased soil pH in both groves for at least 1 year post‐treatment; however, we did not see a significant vegetation response. Overall, our results suggest that removing vegetation by tilling and topsoil removal is an effective method for reducing non‐target species cover. Although we did not see a response of vegetation to our treatments, we were able to restore the initial soil characteristics, which can be a first step toward complete restoration.
Effect of genetic and non-genetic factors on age at first fertile service in Malvi heifers

The data for the present investigation pertained to 409 observations of age at first fertile service (AFFS) on Malvi cattle maintained at Govt. Cattle Breeding Farm, Agar, District Shajapur (M.P.), covering a period of 48 years from 1962 to 2009 (both years inclusive). The least squares analysis of variance revealed the mean AFFS in these cows to be 1451.81±41.23 days and the trait was significantly affected by sire (P< 0.01), period (P< 0.01) and inbreeding (P< 0.05). Heritability estimates for AFFS was obtained as 0.56±0.26 and phenotypic correlation between AFFS and first dry period were positive and significant (P<0.05) while it was non significant with first service period, first calving interval, first lactation yield and first lactation length. It was concluded that inbreeding had deteriorating effect on the age at first fertile service and hence to improve the age at first fertile service in this herd, avoidance of inbreeding along with ameliorative managerial practices should be adopted.
Foraging and Pollination Behaviour of Apis mellifera adansonii Latreille (Hymenoptera, Apidae) on Gossypium hirsutum (Malvaceae) Flowers at Dang (Ngaoundéré, Cameroon)

To evaluate Apis mellifera adansonii Latreille impact on fruit and seed yields of Gossypium hirsutum L. , its foraging and pollinating activities were studied in Ngaoundere for two seasons. Observations were made on 340 flowers each year and divided in three treatments. The treatments included unlimited flowers access by all visitors; bagged flowers to deny all visits and limited visits by Apis mellifera adansonii only. The worker bees seasonal rhythm of activity, its foraging behaviour, its pollination efficiency, the fruiting rate, the number of seeds per fruit and the percentage of normal seeds were evaluated. Results show that this bee foraged G. hirsutum flowers throughout the whole blooming period. This bee species intensely harvested pollen and nectar. The mean foraging speed was 9.41 flowers per min in 2009 and 8.41 flowers per min in 2010. The fruiting rate, the number of seeds per fruit and the percentage of normal seeds of unprotected flowers were significantly higher than those of flowers protected from insects. Through its pollination efficiency, Apis mellifera adansonii provoked a significant increment of the fruiting rate by 60.84% in 2009 and 36.48% in 2010, as well as the number of seeds per fruit by 94.16% in 2009 and 31.41% in 2010, and the percentage of normal seeds by 94.23% in 2009 and 33.49% in 2010. The installation of A. m. adansonii colonies close to G. hirsutum fields could be recommended to increase fruit, seed and honey yields, and pollen production as a hive product in the region.
Limits To Genetic Divergence For Occurrence of Heterosis -Experimental Evidence From Crop Plants

Two experiments in groundnut (Arachis hypogaea L.) and one in rapeseed (Brassica campestris L.) involving varying number of crosses made to diailel and line × tester designs were studied with the aim of relating genetic divergence among parents with the frequency and magnitude of heterosis in the F1 generation. A method was devised to delineate the divergence among parents into four divergence classes, DC1, DC2, DC3 and DC4. Heterosis was computed as per cent improvement over the value of better parent, for three important components of yield in each crop. Genetic divergence was measured by D2 statistic. If m is the mean and s the standard deviation of divergence values (given by D2) among parents, it was postulated that two parents whose genetic divergence falls between (m−s) and (m+s), i.e., in the classes, DC2 or DC3, when crossed will have higher chances of producing high frequency and magnitude of heterosis when compared to a cross whose parental divergence falls outside the limits, (m−s, m+s).
CHEMICAL CONTROL OF STEM END ROT OF MANGO CAUSED BY LASIODIPLODIA THEOBROMAE

Stem end rot is the most severe and widely prevailed postharvest disease of mango throughout the Pakistan. Lasiodiplodia theobromae was predominantly isolated from the mango fruits having typical symptoms of the stem end rot disease. Pathogenicity assay depict that faster and severe symptoms appear on mango fruit when they inoculated with disks of L. theobromae as compared to injection method. Range of chemical fungicides is use in pre- and post-harvest disease management. In present comparative studies of six fungicides [Carbendazim (Carbendazim), Gemstar (Azoxystrobin), Native (Tebuconazole+Trifloxystobin), Score (Difenoconazole), Tecto (Thiabendazole) and Tilt (Propiconazole)], lower used concentrations of Carbendazim followed by Tecto appeared as highly effective to inhibit the growth of L. theobromae on agar medium while at higher used concentration (30000 ppm) no growth of L. theobromae was observed with any fungicide. Generally, higher concentration of fungicides were more effective than the lower concentrations All fungicides more or less checked the pathogen infection on mango fruits inoculated with L. theobromae , as significantly minimum disease development was observed on treated fruits as compared to the untreated once (control). Nativo, Gemstar and Carbedazim at the lowest used dose (10000 ppm) reduced the lesion area while no lesion develops at 20000 and 30000 ppm in hot dip treatment at 50 oC for 5 min.
Scale-dependent thermal tolerance variation in Australian mountain grasshoppers

Physiological variation among and within species is thought to play a key role in determining distribution patterns across environmental gradients. We tested inter- and intraspecific variation in cold and heat tolerances for three grasshopper species (genus Kosciuscola) with overlapping elevation distributions, across their respective ranges in the Australian mountains. Of the three cold tolerance traits measured, the critical thermal minimum was the only trait to vary among species, with greater cold tolerance associated with a distribution extending to a higher elevation. Cold tolerance limits were regularly exceeded in exposed microhabitats, suggesting a role for cold adaptation in structuring species distribution patterns. In contrast to cold tolerance, heat tolerance variation was primarily partitioned within species. For two species, populations from treeless alpine habitat were more heat tolerant than their lower-elevation counterparts, supporting recent models that suggest greater exposure to temperature extremes at higher elevations. These contrasting patterns of physiological variation among and within species emphasise the importance of considering variation within species when attempting to understand how species distributions are affected by thermal extremes.
Leaving local authority care : the experiences of separated young people seeking asylum in the UK

Children and young people arriving in the UK seeking asylum, who are separated from their parents or lawful guardians (separated children and young people) are placed into the care of the receiving local authority. They will remain in this care until 18 years of age, at which point they make the transition to leaving care. There is much evidence to suggest that this is a difficult move. Anecdotal evidence also suggests that because of the multiple stressors faced by separated children and young people, this can be a particularly distressing time, impacting on their psychological well-being. However, there is little empirical evidence to support this. There is even less research which explores this transition from the experiences of the young people themselves. This study took a contextualist epistemological position to explore the experiences and understanding of the transition to leaving care for six separated young people. Semi-structured interviews were completed and the resulting accounts analysed using Interpretative Phenomenological Analysis. Three super-ordinate themes were identified: ‘An Unwanted Move’, ‘Loss and Hardship’ and ‘Surviving’. Within these themes the young men reported experiences suggesting lack of preparation for the move, multiple losses and the impact of building pressure from the challenges of living independently. This was compounded by limited support and the uncertainty of their future, and had significant repercussions for their psychological well-being. Despite this, the young men demonstrated an ability to survive, drawing on the support of others around them and their own resources. The findings of this study suggest more should be done to provide support for this potentially vulnerable group of young people. The findings are considered in the context of current literature and government policy, and recommendations made for greater inclusion of psychology within the social care setting to promote better understanding of and support for this transition.
Comparative DNA Sequence Analysis of the G4 and ϕ X174 Genomes

G4 was isolated in 1974 (Godson 1974b) and was quickly shown to be different from ϕ X174 in some aspects of its physiology and DNA replication (see below). At this time DNA sequencing methods employing ϕ X DNA as a model system were being developed in this laboratory, which resulted in the determination of the entire 5386-nucleotide sequence of the ϕ X genome (Sanger et al. 1977b; an updated version of this sequence is given in this volume in Appendix I). A natural next step was to apply these methods to a closely related virus such as G4 and to compare the sequences. 1 We will present the results of this comparison after first reviewing the biological differences between G4 and ϕ X. Biological Differences and Similarities between G4 and ϕ X G4 has the same host range as ϕ X; it forms plaques on Escherichia coli C strains but not on K or B strains (Godson 1974b). Its growth is restricted by the E. coli K ( Eco K) and B ( Eco B) restriction systems, and it forms plaques with low efficiency on E. coli K and B spheroplasts and on some K/C hybrid cells (L. Dumas, pers. comm.). Growth of G4 is also restricted in cells containing the plasmid RY13 because G4 has a single Eco RI cleavage site (Godson and Boyer 1974). Multiplication of ϕ X is not restricted in any of these systems. The G4 genome is 5577 nucleotides long, compared with 5386 for ϕ X, and it has a different G + T content. This causes.
Analysis of genetic divergence of dolichos bean (Lablab purpureus) genotypes

The variance analysis showed significant difference for all the characters among the genotypes. High estimates of heritability coupled with the higher genetic advance observed for flowering and yield per plant. Yield per plant, the most important economic trait, exhibited positive association with pod weight (0.31) and number of pods per plant (0.41). The high and positive correlation was observed for pod length with pod weight (0.58) and seeds per pod (0.56). From the dendogram it can be concluded that the genotypes were mainly divided at the first node into 3 clusters with 20, 21 and 1 genotype in different groups. Cluster with 21 genotypes was again divided into 2 Sub-groups with 18 and 3 genotypes. However, cluster of 21 genotypes further divided into 2 groups with 19 and 1 member, respectively.
Community assembly after long-term fragmentation: a case study of tropical rainforest in Xishuangbanna, south-west China

Background: Tropical rainforests represent the most species-rich and at the same time the most fragmented terrestrial biome on Earth. Fragmentation of tropical rainforests is having wide-ranging consequences for the maintenance of local species diversity and community assembly patterns. Aims: To examine floristic changes and changes in community phylogenetic structure in the forest fragment over the past five decades. Methods: A new taxonomic diversity algorithm (within-family diversity) was developed to assess floristic changes in the forest fragment. Community phylogenetic structure was then compared before and after fragmentation. Results: Taxonomic diversity changed greatly among families, with changes occurring randomly across the phylogeny. The forest fragment had higher phylogenetic diversity, higher mean pair-wise phylogenetic distance, but lower mean nearest-neighbour distance. The community phylogenetic structure has changed significantly from clustering to dispersion. Conclusions: High species turnover occurred in the forest fragment. While shade-tolerant species have been lost, and ruderal and alien species have been added, overall phylogenetic diversity has increased with species being more phylogenetically distant. Competitive exclusion, which was related to the relatively drier conditions in the forest after fragmentation, led the plant community phylogenetic structure to be more dispersed.