Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the Non-vertical Component of BacterialEvolution Using Network Structures

The central tree metaphor has been challenged over the last couple of decades with the observation of incongruent trees derived largely from protein-coding genes in prokaryotic genomes. There are an increasing number of evolutionary processes and entities that confuse and confound the traditional understanding of evolution. As a result, these processes and entities are very often omitted from phylogenetic studies altogether. In this thesis I attempt to uncover the importance of non-tree like evolution. I discuss the types of genes that do not adhere to vertical patterns of inheritance such as fusion genes and mobile genetic elements. Furthermore I explore the alternative of using network structures in describing the evolutionary history of bacteria. This thesis recounts two key uses of networks for revealing the less commonly noted aspects of bacterial evolution. Firstly I present each stage in the development of a new method for identifying fusions of unrelated genes from conception of the idea, through the implementation to its application to data. Secondly I use networks of gene sharing to elucidate patterns of divergence among a group of closely related bacteria that would have once formed a single species cloud. These studies reveal an abundance of the types of genes that contradict traditional tree-thinking and support the notion that a strictly vertical view of evolution is inadequate when describing bacterial relationships.
Itinerary Recommendation for Cruises: User Study

Vacations and leisure activities constitute an important part of human life. Nowadays, a lot of attention is paid to cruising, that is reported to be a favourite vacation choice for families with kids and for Millenials. Like other distributed events (events that gather multiple activities distributed in space and time under one umbrella) such as big festivals, conventions, conferences etc., cruises offer a vast variety of simultaneous on-board activities for all ages and tastes. This results in a cruiser's information overload, in particular given a very limited availability of activities. Recommender systems appear as a desirable solution in such an environment. Due to the number of time constraints, it is more convenient to get a personalised itinerary of activities rather than a list of top-n. In this paper, we present a user study conducted in order to create a preliminary dataset that simulates users' attendance of a cruise and sheds the light on the activity selection behaviour. We discuss challenges faced by the itinerary recommendation and illustrate them with user study examples.
Determinants of CO2 Emissions in Developing Countries using Bayesian Econometric Approach

The attention to sustainable development and the necessity of environmental protection, and also the adverse effects of environmental pollution on development and quality of life all over the world, have made the environmental protection a major concern of economic officials. For this reason, over the recent decades an extensive literature has been devoted to improve environmental quality and its determinants. Therefore, economic analysts have focused on these issues more than before. In this regard, to know the effects of air pollution determinants can contribute economic officials to reduce pollution. This study attempted to investigate the effects of some variables on CO2 (as one of the most important air pollution indicators) in developing countries during 1992-2014 using Bayesian econometrics approach and applying Bayesian Model Averaging (BMA). Finally, according to the theoretical and empirical evidence, it is found that Environmental Kuznets’ hypothesized inverted U-shaped relationship between economic growth and environmental quality is supported by data. The findings of the study also showed that energy consumption, electricity consumption, and the variables related to industrialization have positive and almost important relationship with CO2 emissions. Against, literacy rate and income inequality have negative effects on CO2 emissions.
Grad-CAM: Why did you say that? Visual Explanations from Deep Networks via Gradient-based Localization

We propose a technique for making Convolutional Neural Network (CNN)-based models more transparent by visualizing the regions of input that are "important" for predictions from these models - or visual explanations. Our approach, called Gradient-weighted Class Activation Mapping (Grad-CAM), uses the class-specific gradient information flowing into the final convolutional layer of a CNN to produce a coarse localization map of the important regions in the image. Grad-CAM is a strict generalization of the Class Activation Mapping. Unlike CAM, Grad-CAM requires no re-training and is broadly applicable to any CNN-based architectures. We also show how Grad-CAM may be combined with existing pixel-space visualizations to create a high-resolution class-discriminative visualization (Guided Grad-CAM). We generate Grad-CAM and Guided Grad-CAM visual explanations to better understand image classification, image captioning, and visual question answering (VQA) models. In the context of image classification models, our visualizations (a) lend insight into their failure modes showing that seemingly unreasonable predictions have reasonable explanations, and (b) outperform pixel-space gradient visualizations (Guided Backpropagation and Deconvolution) on the ILSVRC-15 weakly supervised localization task. For image captioning and VQA, our visualizations expose the somewhat surprising insight that common CNN + LSTM models can often be good at localizing discriminative input image regions despite not being trained on grounded image-text pairs. Finally, we design and conduct human studies to measure if Guided Grad-CAM explanations help users establish trust in the predictions made by deep networks. Interestingly, we show that Guided Grad-CAM helps untrained users successfully discern a "stronger" deep network from a "weaker" one even when both networks make identical predictions.
Neurosteriod enhancement of glutamatergic transmission via transient receptor potential melastatin 3 chanels in the developing cerebellum

Neurosteroids are compounds synthesized de novo within the central nervous system and affect brain function via genomic and non-genomic mechanisms. Sulfated neurosteroids modulate synaptic neurotransmission via interactions with various membrane receptors located at preand/ or postsynaptic sites, including metabotropic and ionotropic neurotransmitter receptors and ion permeable channels. The interactions of sulfated neurosteroids with these types of targets can induce rapid changes in neurotransmitter release and/or in postsynaptic responses. Since the 1940's, pregnenolone sulfate (PregS), the sulfated version of the steroid precursor, pregnenolone, has been suggested to have anti-stress, anti-aging, antidepressive, neuroprotective and memory enhancing effects in the mature brain. However, little is known on the physiological role of PregS in the development of the brain. Previous studies from our laboratory have postulated PregS as a novel enhancer of excitatory neurotransmission in the hippocampus, a brain area important for learning and memory. In the work presented here, we evaluated the effects of PregS in the developing rat cerebellum. The cerebellum
Adulthood Relocation: Implications for Personality, Future Orientation, and Social Partner Choices

The purpose of this study was to learn the reasons why individuals relocate and whether relocaters differ from nonrelocaters on demographic, social, and personality factors. One hundred participants from three age groups, 34 to 46 (young/middle-aged), 54 to 66 (young-old), and 69 to 93 (older) years, were designated as relocaters or residents as a function of months of residence. Relocaters did not differ from residents in age, income, health, or marital status. Reasons provided for relocating revealed the following differences: young/middle-aged moved for employ ment reasons, young-old moved for reasons of retirement, and older adults relocated to be closer to family members. No differences in network size occurred and older relocaters selected more cards in a social partner selection task. Most interesting was the finding that relocaters scored higher on Openness to Experience and future orientation. These data suggest personality may be an important trait that explains why some individuals are more likely to relocate.
Spatio-temporal patterns of mink and muskrat in Canada during a quarter century

Summary 1 Fur-return data on muskrat (Ondatra zibethicus) and mink (Mustela vison) from 80 posts of the Hudson’s Bay Company were analysed. From each post we obtained the number of furs bought from trappers during 25 years (1925–49). 2 The ecological information content of the data was assessed using questionnaires sent to each post. We conclude that fur-return data reflect relative abundance of muskrat and mink, and not primarily information about the trappers. 3 The most-common temporal pattern of the two species are cycles with a period of 8–9 years, with muskrat cycling 1–2 years ahead of the mink. This pattern, as would be expected in a typical predator–prey relationship, is found throughout the boreal forest region, with the exception of several posts in eastern Canada. In the eastern region, the two species were found to fluctuate in synchrony. 4 The data show broad-scale synchrony. Peaks (and troughs) are roughly aligned in phase over the entire Canadian boreal forest. 5 In some areas the phase of the cycle is either ahead or behind the average cycle. Peaks (and troughs) of mink and muskrat cycles generally appear first in the Athabasca Basin region (for mink in the Hudson’s Bay region of Manitoba and Ontario) and from this epicentre spread throughout Canada within 2–3 years. 6 Synchrony (i.e. mean correlation) declines with distance; for distances less than 450 km, similarity among populations is higher than the average.
Determination of the optimum pollen germination medium for different fruit forms of oil palm ( Elaeis guineensis )

1 SUMMARY The study was conducted to determine the optimum medium for in vitro pollen germination in African oil palm, Elaeis guineensis Jacq. based on germination percentages and length of pollen tube. The viability of pollens from three fruit forms of 20-year old dura, pisifera, and tenera palms was investigated at 60,120 and 180 min after incubation at 35°C using three kinds of medium: 11% of sucrose solid media, 11% of glucose solid media and 2.5 % of sucrose liquid media with 0.1% of boric acid. The longest mean pollen tube length was observed in dura pollen on all three media at 60, 120, and 180 min after incubation. The pollens germinated on sucrose solid medium had longer tube length than those germinated on glucose and sucrose liquid media. Adoption of sucrose solid medium as germination medium for the estimation of germinability and tube length of pollen in oil palm is suggested.
THE POTENTIAL VALUE OF PHYTOCHEMICAL AND MICROMORPHOLOGICAL CHARACTERS IN TAXONOMIC TREATMENT OF GENUS VITEX L. (LAMIACEAE)

Vitex L. (Lamiaceae) in Iran was reviewed using morphological and phytochemical characters. Verbena officinalis (Verbenaceae) was also studied for comparison. The pollen grains, were examined using SEM and LM Furthermore, the petiolar anatomy, trichome structure and morphology of different plant parts were studied. The essential oils of aerial plant parts were extracted and identified. Pollen grains among the studied species of Vitex are tricolpate, isopolar, circular in the polar view, while in Verbena officinalis they are tricolporate and triangular. The exine ornamentation provides characteristic features useful for delimitation of the species in our group. The SEM micrographs of fruits, leaves and stems show uniand tetra-cellular glandular and simple multi-cellular trichomes. The petiolar anatomy of the first to the third lower nodes showed different patterns in the shapes and arrangement of the vascular bundles. Form phytochemical point of view α-pinene, sabinene and limonene are the characteristic compounds in Vitex spp. and are present in examined species in high concentrations. In most species monoterpenoids are the major constituents of the oil. There are differences in monoand sesquiterpenoid compounds of the oils among species. Examining the morphological and micromorphological characters of leaf, stem, corolla and calyx in combination with the phytochemical characters revealed the occurrence of four species in the flora of Iran including V. agnus-castus, V. negundo, V. trifolia and V. pseudo-negundo. Among these species high morphological, anatomical and phytochemical variations were observed in V. pseudo-negundo. Moreover, the affinity of Vitex within Lamiaceae genera is supported.
Modular design approach for Watt-level millimeter-wave power amplifiers

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Mathematical modelling of the floral transition — with a Bayesian flourish —

Flowering plants are abundant on Earth. In the model dicot plant species, Arabidopsis thaliana, multiple endogenous and exogenous signals converge to initiate a change from vegetative to reproductive growth in optimal environmental conditions. Much genetic and experimental research has gone into elucidating the biological mechanisms controlling the floral transition. However there has been little mathematical modelling of this process. The aim of this thesis was to gain an understanding of the essential features and dynamic properties underlying this developmental phase change from a systems and computational biology perspective. Combining mathematical modelling with experimental results a core regulatory network was defined with multiple feedback loops. Simplified models inevitably miss finer details of the biological system yet they provide a route to understanding the overall system behaviour.This reductionist path allowed a tractable genetic regulatory network to be investigated without large numbers of parameters. Not overfitting to data and parameter inference are two current challenges in systems biology. Treating all unknowns as a probability within the setting of Bayes’ theorem as a statistical framework allows for a solution to both of these issues. This thesis investigates the use of a contemporary Bayesian inference algorithm, nested sampling, for inference problems typically found in systems biology where the data are few and noisy. Nested sampling simultaneously calculates the key term for model comparison and also produces parameter inferences allowing uncertainty in models and predictions to be robustly quantified. Network models are developed that can accurately reproduce experimental leaf number data, show important properties of the floral transition such as the ability to filter environmental noise and provide a clue on spatial patterning of an Arabidopsis shoot apex. Incorporating network knowledge into a plant breeding program is an exciting goal for future developments addressing global food security.
Mango Resources Left on Okinawa Island and Their Diversity

Okinawa Island had old mango trees of unknown cultivars before the introduction of ‘Irwin’ which is the most important cultivar for commercial production. The continuous wet climate in Okinawa during the flowering season requires roof protection for stable fruit production, however, local Okinawa mango trees set fruit without protection. To identify these old mango trees, the morphological and physiological characteristics were recorded and their backgrounds of the introductions were interviewed to the local people. Their distributions were intensive around Nago and southern area from Urazoe, with thin distribution from Yomitan to Urazoe. Trees of about 100 years old were found such as in gardens and private homes. Some set fruit out of roof protection, and some set fruit off-season. ISSR analysis found that Okinawa mango trees exceeded the international standard cultivars in both the number of bands and polymorphism ratio, indicating wider diversity than the world major commercial cultivars. Interviews to the local people on the background of introduction and the result of ISSR suggest the relevance between most local Okinawa mango trees and Taiwanese resources.
Genetic disposition and response of blood lipids to diet : studies on gene-diet interaction in humans

Even though a cholesterol-lowering diet is effective for most people, it is not for all. Identification of genetic determinants of the serum lipid response to diet may be of help in the identification of subjects who will not benefit from a cholesterol-lowering diet. It may also clarify the role of certain proteins in cholesterol metabolism. The objective of our research was to determine whether genetic polymorphisms affect the response of serum lipids to diet in humans. We first assessed sex differences in the response of serum lipids to changes in the diet. Men had larger responses of total and low-density lipoprotein cholesterol to saturated fat and cafestol than women. There were no sex differences in the responses to trans fat and dietary cholesterol. We also used these data to study the effect of 11 genetic polymorphisms on responses of serum lipids to the various dietary treatments. Apoprotein E, A4 347 and 360, and cholesteryl-ester transfer protein TaqIb polymorphisms affected the lipid response to diet slightly. We further studied the effect of the apoprotein A4 360-1/2 polymorphism on response of serum lipids to dietary cholesterol in a controlled trial specially designed for this purpose. The apoprotein A4 360-1/2 polymorphism did not affect the response of serum lipids to a change in the intake of cholesterol in a group of healthy Dutch subjects who consumed a background diet high in saturated fat. Although it is not directly related to genetic polymorphisms and lipid response, we finally reviewed the effect of dietary cholesterol on the ratio of total to high-density lipoprotein cholesterol, which is a more specific predictor of coronary heart disease than either lipid value alone. Dietary cholesterol raised the ratio of total to high-density lipoprotein cholesterol. In conclusion, the effect of genetic polymorphisms on serum lipid response to diet is small. It is therefore not possible to identify individuals who will not benefit from a cholesterol-lowering diet on the basis of a specific genetic polymorphism.
The role of grassland sward islets in the distribution of arthropods in cattle pastures

1. It is well documented that cattle reduce their grazing activity in the vicinity of cattle dung, which gives rise to distinct patches, or islets as they have been termed, of longer sward. The influence of such islets on pasture utilisation and agronomic performance has been widely studied, but very little information is available concerning their influence on grassland biodiversity.
Diopsis (Diopsidae, Diptera) with unusual wing spots: two new species from Malawi with a longer eye span in females than in males

Diopsis malawiensis spec. nov. and D. vanbruggeni spec. nov. are described from Malawi. Subgeneric grouping of Diopsis Linnaeus, 1775, is briefly discussed, but the genus awaits revision. A redescription is given of Diopsis micronotata Brunett i, 1926, from the D.R. of Congo, as this species might be confused with D. vanbruggeni. The two new species and D. micronotata are closely related and are tentatively placed in the absens Brunett i group. Diopsis surcoufi Seguy, 1955, from Mozambique and Tanzania, is redescribed because of its superficial resemblance to D. malawiensis. All four species are characterised by tiny, but distinct, apical or subapical wing spots. In D. malawiensis, D. micronotata and D. vanbruggeni, eye span is, in absolute and relative terms, slightly longer in females than in males. Sexual dimorphism in Diopsidae, as related to eye span, is briefly discussed.
Effect of Biliary Drainage on Individual Reactions in the Conversion of Cholesterol to Taurocholic Acid

The effect of biliary drainage on incorporation of acetate into cholesterol and on four different enzyme systems in the metabolic pathway from cholesterol to taurocholic acid has been studied in homogenates of rat liver. In homogenates of liver taken from bile fistula rats 48 hours after operation the extent of incorporation of acetate into cholesterol was about eighteen times greater and the extent of 7α-hydroxylation of cholesterol about eight times greater than in homogenates of liver from control rats. The other reactions studied, the conversion of cholest-5-ene-3β,7α-diol to 7α-hydroxycholest-4-en-3-one, the 12α-hydroxylation of 7α-hydroxycholest-4-en-3-one, and the 7α-hydroxylation of taurodeoxycholic acid, were influenced much less by biliary drainage. It is suggested that the hydroxylation of cholesterol to cholest-5-ene-3β, 7α-diol might be a rate-determining step in the conversion of cholesterol to bile acids.
Elimination of a Tapinoma melanocephalum (hymenoptera: formicidae) infestation using imidacloprid bait

Tapinoma melanocephalum F. (Ghost Ant) infestations have increased in Western Europe. Generally, Ghost Ant infestations resemble those of Monomorium pharaonis (Pharaoh's Ant) with a focus to older, multi-unit apartment blocks which offer a multitude of nesting opportunities and easy migration of ants within the building. Control of these infestations is often regarded as difficult. Laboratory trials of a novel semi-liquid broad-spectrum ant bait product containing 0.03% imidacloprid against nest cells of Ghost ants demonstrated complete destruction of workers, queens and brood by week 6. The same ant bait product was tested in a field trial in Groningen, Netherlands. An apartment block containing 108 apartments had a seven year history of failing Ghost ant control. Using a conventional bait gun, one bait spot of 200 mg per m 2 treated area was applied. An area of 10 m 2 was treated; the average amount of product dispensed was 2 g per apartment. Several apartments were chosen as indicator sites and were closely followed. The remaining apartments were treated by a local pest control company using the same product with identical use pattern. Decline of ant numbers in the indicator flats was rapid (86 % reduction in 3 days) and total absence of ants was demonstrated from week eight after treatment. Similarly, all flats treated by the pest control company were shown to be free of ants at the last monitoring time point 5 months after initial treatment.
Bacterial wilt of enset (Ensete ventricosum) incited by Xanthomonas musacearum sp. n

Heavy losses in E. ventricosum, an important staple crop in Ethiopia, are caused by a wilt disease in which the inner folds of the drooping heartleaf are covered with greyish-brown patches. Eventually the leaf breaks at the petiole and yellowish bacterial slime oozes from the vascular bundles. All the leaves wilt, bend over, and wither, causing the death of the plant. A previously undescribed bacterium was isolated from affected plants and was pathogenic to enset and banana. The name X. musacearum Yirgou & Bradbury is proposed and details are given of the physiological and biochemical characteristics of.the pathogen. None of 19 other plant spp. inoculated showed symptoms within 5-6 weeks.