Miracle-dz/UniFAR-FTUs huggingface dataset:
Bayesian and frequentist methods and analyses of genome-wide association studies

Recent technological advances and remarkable successes have led to genome-wide association studies (GWAS) becoming a tool of choice for investigating the genetic basis of common complex human diseases. These studies typically involve samples from thousands of individuals, scanning their DNA at up to a million loci along the genome to discover genetic variants that affect disease risk. Hundreds of such variants are now known for common diseases, nearly all discovered by GWAS over the last three years. As a result, many new studies are planned for the future or are already underway. In this thesis, I present analysis results from actual studies and some developments in theory and methodology. The Wellcome Trust Case Control Consortium (WTCCC) published one of the first large-scale GWAS in 2007. I describe my contribution to this study and present the results from some of my follow-up analyses. I also present results from a GWAS of a bipolar disorder sub-phenotype, and a recent and on-going fine mapping experiment. Building on methods developed as part of the WTCCC, I describe a Bayesian approach to GWAS analysis and compare it to widely used frequentist approaches. I do so both theoretically, by interpreting each approach from the perspective of the other, and empirically, by comparing their performance in the context of replicated GWAS findings. I discuss the implications of these comparisons on the interpretation and analysis of GWAS generally, highlighting the advantages of the Bayesian approach. Finally, I examine the effect of linkage disequilibrium on the detection and estimation of various types of genetic effects, particularly non-additive effects. I derive a theoretical result showing how the power to detect a departure from an additive model at a marker locus decays faster than the power to detect an association.
Cavity-nesting by the Black-billed Magpie (Pica hudsonia)

Abstract We describe the first known instance of Black-billed Magpies (Pica hudsonia) nesting in a fully enclosed, pre-formed cavity. Magpies built an undomed nest of sticks in a nest box designed for Wood Ducks (Aix sponsa) near Olds, Alberta, Canada, in 2008. All nesting material was removed from the box after an apparently successful nesting attempt. Magpies built a new nest in the box and fledged at least four young in 2009. These observations indicate that cavity nesting is a distinct, novel behavioral trait that can arise in this species. We describe several potential costs of cavity nesting in this species, which may explain in part why this trait has not become established in any of the many studied magpie populations around the world.
The Effect of Low Protein and Skip-a-Day Grower Diets on the Subsequent Performance of Turkey Breeder Hens

Abstract Two experiments were conducted utilizing a total of 720 Marston Broad-white females (hatched late December and July). The day old poults were equally divided among 18 floor pens and fed a turkey starter (27.8% protein) from 0–10 weeks of age. One-third of the birds was assigned to each of the following feeding regimes: control grower (21% protein ad libitum), low protein (10.2% protein ad libitum), or skip-a-day (75% of control grower). All birds remained on these treatments through 24 weeks of age when the control group was placed on a commercial-type breeder diet (16.6% protein); six weeks later the remaining treatment groups were changed to this diet. Feed consumption and body weights were consistently greater for the control group. In all cases, regardless of season of the year or whether the birds were cage or floor reared, the age at sexual maturity was significantly delayed for the restricted birds as compared to the controls. Subsequent egg production tended to be greater in the restricted groups even when the initial two 28-day periods (while the two restricted groups were still on treatment) were included. Egg weight was not affected by treatment; however, it should be noted that the control group laid a much larger number of eggs that were considered too small for setting. It was concluded that nutrient restriction during the growing period is a highly effective method of delaying sexual maturity in the turkey breeder hen and, in addition, reduces production costs. It is hypothesized that any reasonable method of nutrient restriction will be effective if the program is designed to bring a hen to sexual maturity at a specific weight and age.
Identification and mapping of random amplified polymorphic DNA markers linked to a rhizomania resistance gene in sugar beet (Beta vulgaris L.) by bulked segregant analysis

Bulked segregant analysis was employed to identify random amplified polymorphic DNA (RAPD) markers linked to a gene that confers rhizomania resistance to a sugar beet line created from a Holly Sugar Company breeding population (USA). Polymorphism revealed with 160 arbitrary 10-mer oligonucleotide primers was screened in two bulks produced by separately pooling the individual DNAs from the six most resistant and the six most susceptible plants of an F2 population segregating for rhizomania resistance. A study of the F2 individuals showed that 19 primers generated 44 polymorphic markers which were then grouped into nine linkage groups. By analysis of variance, 12 were shown to have a significant effect upon the level of resistance and were mapped on a segment 22.3 cM long. A quantitative trait locus (QTL) of resistance was identified and located in a 4.6cM interval between two markers. It accounted for 67.4% of the observed variation and almost all the genetic variation. These results suggest that the identified QTL corresponds to a unique major gene conditioning the Holly resistance studied, which we have named Rz-l.
Comparative methane emissions from cattle, red deer and sheep

Methane (CH4) production (g CH4/d) and yields (g CH4/kg dry matter intake (DMI)) from groups of 11 non-lactating dairy cattle, sheep and red deer were compared in January and June of 2007. During each period, methane emissions measured using the SF6 tracer technique, were measured over four days following 10 days of acclimatisation. All animals were individually housed in metabolism cages and fed ensiled lucerne chaff at a rate of 1.2 times estimated energy requirements according to Australian feeding standards. Total daily methane production from cattle (140.4 g CH4/day) was greater than deer (31.5 g CH4/day) which was greater than sheep (18.3 g CH4/day) (P <0.001) and methane yield from cattle (20.6 g CH4/kg DMI) was greater than sheep (18.4 g CH4/kg DMI) which was greater than deer (16.5 g CH4/kg DMI) (P <0.001). A significant interaction of species by season was driven by the higher methane production and yield of cattle in winter compared with summer (P <0.001). The findings of this experiment show that methane emissions can differ between ruminant species at the same time on the same diet. Reasons for these differences are yet to be elucidated.
Activity, adsorption and mobility of three acetanilide and two new amide herbicides

Activity, adsorption, and mobility of emulsifiable concentrate (EC) and microencapsulated (ME) formulations of alachlor and acetochlor as well as of metolachlor, S-metolachlor, dimethenamid and flufenacet were studied. Petri-dish bioassay, based on root response of oats (Avena sativa L.), was used for their activity in sand and in a silty clay loam soil, and for determination of herbicide concentrations in soil solution (not adsorbed) and in column leachates of the adsorption and mobility studies respectively. Flufenacet and both acetochlor formulations showed the highest activity in both soils and ME-alachlor and metolachlor the lowest; the activity of dimethenamid, EC-alachlor and S-metolachlor was intermediate. Activity of both formulations of alachlor and acetochlor decreased with increasing organic matter content, but alachlor activity was reduced more than that of acetochlor. Lower amounts of dimethenamid and S-metolachlor were adsorbed by soil compared with the other herbicides and, consequently, greater amounts of these two herbicides were leached through that soil. None of the herbicides tested was detected below 30 cm. Less alachlor and acetochlor were biologically available in soil solution after their application as ME-formulations and, therefore, lower amounts of both ME-alachlor and ME-acetochlor were leached through the soil compared with those applied as EC-formulations.
Intelligence's likelihood and evolutionary time frame

Abstract This paper outlines hypotheses relevant to the evolution of intelligent life and encephalization in the Phanerozoic. If general principles are inferable from patterns of Earth life, implications could be drawn for astrobiology. Many of the outlined hypotheses, relevant data, and associated evolutionary and ecological theory are not frequently cited in astrobiological journals. Thus opportunity exists to evaluate reviewed hypotheses with an astrobiological perspective. A quantitative method is presented for testing one of the reviewed hypotheses (hypothesis i; the diffusion hypothesis). Questions are presented throughout, which illustrate that the question of intelligent life's likelihood can be expressed as multiple, broadly ranging, more tractable questions.
Mycorrhizal fungi reduce the negative effects of nitrogen enrichment on plant community structure in dune grassland

Nitrogen (N) inputs to ecosystems have increased worldwide, often leading to large changes in plant community structure and reducing plant diversity. Yet, the interaction of increased N availability with other factors that determine plant community composition, are still poorly understood. Here, we test whether the impact of N addition on plant communities depends on the presence of arbuscular mycorrhizal fungi (AMF). AMF are widespread plant symbionts that facilitate growth of many plant species. We hypothesize that AM fungi reduce the negative impact of N addition on plant communities by supporting growth of species that are sensitive to N enrichment.We established experimental grassland microcosms consisting of 18 plant species. These microcosms were subjected to high and low N supply and were inoculated with AMF or remained nonmycorrhizal. Both N addition and AMF had a big impact on plant community composition, but with opposite effects. N addition induced a 2.8‐fold increase in grass biomass and reduced legume biomass. Grasses dominated the microcosms at high N supply, especially when AMF were absent. In contrast, AMF enhanced biomass of all legumes species (on average 6.8‐fold) and reduced the relative abundance of grasses. The proportion of legume biomass out of total shoot biomass at high N supply was 19% with AMF and only 3% without AMF. Our results show that responses of plant communities to N enrichment depend on AMF and that AMF can reduce the negative impact of increased N availability on plant community structure by reducing grass dominance.
A Positive Root-sourced Signal as an Indicator of Soil Drying in Apple, Malus x domestica Borkh.

Plants raised from shoot-tip cultures of apple (Malus x domestica Borkh.) were grown in divided pots so that approximately half the root system could be exposed to soil drying whilst the remainder was well watered. Water was withheld from half the root system in this way for 24 d. During this time, the daily increment in leaf area declined to 65% of that of control plants, which had all their roots in well watered soil. Both leaf expansion and, more particularly, leaf initiation were inhibited. Water loss per plant also fell to 70% of the rate exhibited by control plants. No significant differences were detected between the leaf water status of the partially dried plants and that of the well watered ones. After this drying period, the half-dried plants were treated during the night of the 24th day as follows; one group had its roots in dry soil rewatered, another had them excised, and a third continued half dry. Both the rewatered group and the group with roots excised showed significant recoveries in leaf growth rates compared with the group kept half dry. The inhibition of leaf growth by drying soil is discussed with regard to root-to-shoot signalling. The alleviation of this inhibition by the excision of roots in dry soil, is taken as evidence of a positive inhibitor, produced by drying roots, influencing shoot growth.
The Effect of Chromium on the Photosynthesis and Growth of Diatoms and Green Algae

The effect of hexavalent chromium ions on the photosynthesis and growth of the diatom Nitzschia palea and the green alga Chlorella pyrenoidosa has been studied and compared with the effect of Cu and Hg. The effect of chromium is very similar to that of Cu and Hg, but it is more than one hundred times less toxic for the algae than copper. The toxicity of chromium is not counteracted by adding Fe to the culture solution. The problems regarding cleaning glass-ware in dichromate-sulphuric acid are discussed and it is strongly recommended to use other cleaning agents.
Trajectory of fat-free mass and fat mass indices in small-for-date infants in India

Background . Human growth during the first 2 years of life involves not only quantitative changes in body size, but also qualitative changes in body composition. Measuring fat-free mass (FFM) and fat mass (FM) in infants and children is of both scientific and public-health interest. The incidence of hypertension, type 2 diabetes and coronary heart disease is very high among south Asians compared with white people. In light of these findings, the measurement of body composition such as FFM and FM during the early development phase assumes importance. Objectives. To establish the trajectories of the fat mass index (FMI), fat-free mass index (FFMI) and body mass index (BMI) of normalbirthweight (NBW) and low-birthweight (LBW) infants, and compare the age-related indices among NBW and LBW children. Methods. This was a longitudinal study. A total of 240 NBW and LBW in six cohorts, aged 0, 45, 90, 180, 270 and 360 days at baseline, were enrolled from the neonatal care unit of a large charitable government hospital serving the urban poor population in the city of Kolkata, India. Weight and length (L) were measured, and total body water was determined by bio-electrical impedance analysis for estimation of FFM and FM. The indices FFM/L2 and FM/L2 were calculated, as were the indices FFM/LP and FM/LP, where p was selected in order to eliminate the correlation of these indices with length. Results. The percentage of FFM gradually decreased in both NBW and LBW babies with an increase in age, and the percentage of FM gradually increased. The percentage of FFM in NBW babies was found to be lower than that in the LBW babies, and the percentage of FM in NBW babies was greater than in LBW babies. Conclusion. The percentage of FM was consistently lower in LBW than the NBW infants. The fat percentage in all these infants was consistently lower, from birth to age 360 days, than in the reference data on healthy American infants in the West. BMI and FFMI gradually increased from 45 to 180 days of age, and then decreased up to 360 days. Similarly, FMI increased from 45 to 180 days of age, and from 180 to 270 days its growth remained constant. After that point, FMI gradually increased up to 360 days, but very slowly.
THE BIOLOGY OF PHYTOPHTHORA CINNAMOMI IN AUSTRALASIAN FORESTS

The request for this review is evidence of the worldwide concern for and fascination with the invasion by Phytophthora cinnamomi Rands of Au­ stralasian native forests. The area of Australia is large, but most of the interior is barren desert. Quite extensive forests occur on the eastern coastal zone from Papua New Guinea in the north to Tasmania in the south, and in the south­ west, with a smaller region in the far north of the continent. The forest tree genera are varied, and those of the rain forest may have Indo-Malaysian affinities, but dry, sclerophyll, or open forests are dominated by some of the 600 species of Eucalyptus. The southwest open forests are dominated by Eucalyptus marginata (jarrah), andjarrah dieback, recorded as early as 1920, was the first, and remains the worst, example of the cinnamon fungus epidemic. The role of P. cinnamomi in jarrah dieback was not elucidated until 1 965 (53). The same pathogen was then isolated from the eastern states. These early isolations did not prove that P. cinnamomi was responsible for the epidemic dieback and death of 75% of the flora that occurred in the jarrah forests of Western Australia, the stringy bark forests of the Brisbane Ranges, and the silvertop forests of East Gippsland. Proof was obtained when washed mycelium of P. cinnamomi, added to the topsoil, produced typical symptoms that gradually extended into the forest and from which the pathogen
Elevated δ15N values in aquatic plants from cleared catchments : why?

δ15N values of plants and animals are being increasingly used to identify the flow of nitrogen through aquatic ecosystems. The δ15N values of crops, riparian trees, emergent and submerged aquatic vegetation in streams from both cleared (agricultural) and forested (rainforest) catchments were sampled. Riparian and aquatic plants had similar δ15N values in forested streams,suggesting a similar source of inorganic nitrogen.In cleared catchments, however, aquatic plants had δ15N values 4–8‰ higher than adjacent riparian vegetation and aquatic plants from streams in forested catchments. The elevated δ15N values of aquatic vegetation in streams with cleared catchments suggest that these plants either have access to a different source of N than those in undisturbed catchments or that high rates of microbial decomposition and nutrient cycling in the cleared catchments influence the δ15N value of available N. This also suggests that the aquatic plants in disturbed catchments are incorporating a different source of nitrogen than the adjacent riparian vegetation. This supports the proposal that in-stream processing of N affects the δ15N value of available N in streams with cleared catchments. These results begin to identify potential pathways for nitrogen transport to streams and the effect that internal cycling may have on a stream’s nitrogen load.
Allometric models for non-destructive leaf area estimation in coffee (Coffea arabica and Coffea canephora)

We aimed to evaluate the currently used allometric models, as well as to propose a reliable and accurate model using non-destructive measurements of leaf length (L) and/or width (W), for estimating the area of leaves of eight field-grown coffee cultivars. For model construction, a total of 1563 leaves were randomly selected from different levels of the tree canopies and encompassed the full spectrum of measurable leaf sizes (0.3-263 cm 2 ) for each genotype. Power models better fit coffee leaf area (LA) than linear models. To validate the model, an independent data set of 388 leaves was used. We demonstrated that the currently used allometric models are biased, underestimating the area of a coffee leaf. We developed a single power model (Y =β 0 x β 1) based on two leaf dimensions [LA = 0.6626 (LW) 1.0116 ; standard errors: β 0 = 0.0064, β 1 = 0.0019; R 2 = 0.996] with high precision and accuracy, random dispersion pattern of residuals and also unbiased, irrespective of cultivar and leaf size and shape. Even when the L (but not width) alone was used as the single leaf dimension, the power model developed still predicted with good accuracy the LA but at the expense of some loss of precision, as particularly found for 8% of the leaves sampled with length-to-width ratios below 2.0 or above 3.0.
IL-2 receptor α chain expression during early B lymphocyte differentiation

The IL-2/IL-2 receptor (IL-2R) has been studied intensively because of its potential function in the development and regulation of the immune system. The IL-2R alpha chain has been shown to be expressed on CD4-CD8- thymocytes and activated T and B cells. In this report, we show that IL-2R alpha is also expressed on precursor B cells in the bone marrow. Its expression is initiated by functional rearrangement and expression of Ig mu heavy chain gene and is down-regulated when immature B cells mature and express IgD. Its potential function in early B cell differentiation is discussed in comparison with its role in thymocyte differentiation.
Morphological and Epidermal Studies on Certain Species of Napoleona P. Beauv. (Lecythidaceae) in Nigeria

A comparative study of the morphological and foliar epidermal characteristics of three species of Napoleona Beauv. , N. imperialis P. Beauv. , N. vogelli Hook. and Planch and N. gossweileri Baker f. was carried out by simple light microscopy. While N. imperialis and N. vogelli are shrubs, with the bark, smooth, shallow and fibrous, N. gossweileri is a woody climbing liane, with thick-barked stem. Significant variations in leaf size, flo wer colour, fruit shape and colour when ripe and stomatal type which could be exploited for taxono mic purposes were observed among the species. The study aims at contributing morphological and epidermal in formation on the scanty literature available on the species which have potentials for med icinal, ornamental and food purposes.
EPIZOOTIOLOGY OF FELINE LEUKEMIA VIRUS IN THE FLORIDA PANTHER

of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Master of Science EPIZOOTIOLOGY OF FELINE LEUKEMIA VIRUS IN THE FLORIDA PANTHER By Mark William Cunningham August, 2005 Chair: Donald J. Forrester Major Department: Wildlife Ecology and Conservation Feline leukemia virus (FeLV) has been reported only rarely in non-domestic felids and was not detected in Florida panthers (Puma concolor coryi) during almost 20 yr of routine surveillance. The finding of two FeLV antigen-positive panthers during the 20022003 capture season led to a prospective and retrospective investigation of the epizootiology of this disease in the population. Archived serum was tested for FeLV antibodies to assess history of exposure. To determine prevalence and distribution, panthers were captured throughout their range and tested for FeLV antigen by ELISA. Positive tests were confirmed by immunofluorescent antibody (IFA) test and viral culture. The outcome following exposure in panthers was inferred from ELISA antigen and antibody, IFA, and PCR results. All infected panthers were monitored by radiotelemetry and necropsied following detection of a mortality signal. Between 1990 and 2005, the prevalence of positive antibody tests increased significantly and were concentrated in the northern portion of panther range. The prevalence of antigenemia (positive ELISA antigen) among panthers and Texas pumas ≥1 yr of age, not previously