Miracle-dz/UniFAR-FTUs huggingface dataset:
The evolution of the vertebrate beta globin gene family

This thesis covers different aspects of the evolution of the vertebrate beta globin gene family. A wealth of data on globins has been accumulated over decades of work in diverse areas, this information, together with the use of new methods, allowed a comprehensive analysis of beta globins. First, a review on the current knowledge of gene family evolution is made and the general objectives of the thesis are stated. This introductory chapter is followed by the careful analysis of the beta globin phylogeny comparing different reconstruction methods and discussing the differences between species and gene tree topologies. The molecular evolution of this gene family is investigated using codon models of sequence evolution. Particular emphasis is put on the role of gene conversion and positive selection acting at sites in the genes and along branches in the phylogeny. Also, several models of evolution by gene duplication are tested and results are analysed in the light of the different hypotheses on gene family evolution. The third chapter is devoted to the evolution of the globin protein structure from the analysis of sequence data. The ancestral state reconstruction of structurally relevant amino acids in different globins is conducted and the substitution pathway leading to the observed data is examined. The impact of amino acid changes in the hemoglobin protein is evaluated in terms of structural and functional constraints and the role of positive selection on the protein products of these genes is explored. Also, a possible case of coevolution between residues in the alpha and beta subunits of hemoglobin is proposed. Finally, using new and more sophisticated methods, I estimate dates for gene duplication and gene divergence events in the beta globin family. Two different methods of date estimation based on molecular data are compared and evolutionary rate variation in this gene family is tested.
Antistaling Additives, Flour Type and Sourdough Process Effects on Functionality of Wheat Doughs

Antistaling additives—distilled monoglycerides (MGL), diacetyl tartaric ester of monodiglycerides (DATEM), sodium stearoyl lactylate (SSL), carboxymethylcellulose (CMC), hydroxypropylmethylcellulose (HPMC) and fungal α-amylase—were studied for effects on rheological and fer- mentative properties of white/whole wheat bread doughs, made following straight/sour dough processes. A fractionated factorial design (L32) was used to evaluate single additive effects and interactions. Single addition of DATEM, followed by SSL, α-amylase and hydrocolloids improved oven rise and final volume. In presence of DATEM, synergistic (MGL) and antagonistic (SSL) effects of additional emulsifiers were found on gassing power. SSL was the only effective conditioner for enhancement of mixing properties. Dough plasticity was negatively affected by MGL addition and by CMC/HPMC in white/whole flours respectively. Some combinations resulted in detrimental dough handling properties.
Financial Integrational Effects on Macroeconomic Instability in India

The nexus between international financial integration and economic growth continues to be one of the most debated issues among macroeconomists, and these debates often raise several issues from the theoretical and policy perspectives. Financial integration can catalyse financial development, improve governance and impose discipline on macro-policies. However, in the absence of a basic pre-existing level of supporting conditions, financial integration can aggravate instability (Khadraoui, 2010). In addition, economic theory suggests that increased financial openness intensifies macroeconomic instability. This article investigates the financial integrational effects on macroeconomic instability in terms of output, consumption and investment volatility by employing the vector error correction model (VECM) with empirically reasonably parameters for an emerging economy, India, for the period 1989–2014. From the results, it is evident that financial openness has had a significant effect on output, consumption and investment volatility. Financial development has had a statistically significant negative effect on output, consumption and investment volatility. Similarly, trade openness and terms of trade significantly influence output, consumption and investment volatility. JEL Classification: F36, F41, F43, E32
A Data Envelopment Analysis Evaluation and Financial Resources Reallocation for Brazilian Olympic Sports

This paper proposes the use of a Data Envelopment Analysis model to evaluate the Brazilian Olympic sports efficiency and also to reallocate the financial resources received by them. The sports selected were those that received financial resources from the Agnelo/Piva Law in 2011. As proposed in previous works, we use as inputs the funds received and medals offered, as a proxy for difficulty measure in winning a medal; and the results obtained (gold, silver and bronze medal) as outputs. We proposed to use the results from the Pan-American Games, specifically from the 2011 Pan-American Games, since we believe that the Olympic Games results were scarce to assess the sports efficiency as there are many null results for lots of sports. Therefore, the medals related to the 2011 Pan American Games are used in this paper. A DEA non-radial model with weights restrictions is formulated to perform the Olympic sports efficiency evaluation. With these results a financial resources reallocation is proposed using a ZSG-DEA non-radial approach. Results show that using data with minimal null medals leads to a good financial resources reallocation, based on the sports efficiency, without the need of including anymore variables or imposing additional weight restrictions. Key-Words: Data Envelopment Analysis, Olympic sports, sports efficiency, financial resources reallocation
The phylogeny of aglaspidid arthropods and the internal relationships within Artiopoda

The phylogenetic position of aglaspidids, a problematic group of Lower Palaeozoic arthropods of undetermined affinities, is re‐examined in the context of the major Cambrian and Ordovician lamellipedian arthropod groups. A cladistic analysis of ten genera of aglaspidids sensu stricto, six aglaspidid‐like arthropods and 42 Palaeozoic arthropod taxa indicates that Xenopoda, Cheloniellida, Aglaspidida sensu lato and Trilobitomorpha form a clade (Artiopoda Hou and Bergström, 1997 ) nested within the mandibulate stem‐lineage, thus discarding previous interpretations of these taxa as part 'of the chelicerate stem‐group (Arachnomorpha Heider, 1913 ). The results confirm an aglaspidid identity for several recently described arthropods, including Quasimodaspis brentsae, Tremaglaspis unite, Chlupacaris dubia, Australaglaspis stonyensis and an unnamed Ordovician Chinese arthropod. The problematic Bohemian arthropod Kodymirus vagans was recovered as sister taxon to Beckwithia typa, and both form a small clade that falls outside Aglaspidida sensu stricto, thus discarding eurypterid affinities for the former. The analysis does not support the phylogenetic position of Kwanyinaspis maotianshanensis at the base of Conciliterga as proposed in recent studies, but rather occupies a basal position within Aglaspidida sensu lato. The results indicate a close association of aglaspidid arthropods with xenopods (i.e. Emeraldella and Sidneyia) and cheloniellids (e.g. Cheloniellon, Duslia); the new clade “Vicissicaudata” is proposed to encompass these arthropods, which are characterized by a differentiated posterior region. The phylogenetic position of aglaspidid arthropods makes them good outgroup candidates for analysing the internal relationships within the groups that form Trilobitomorpha. This work provides a much clearer picture of the phylogenetic relationships among Lower Palaeozoic lamellipedians.
Benthic macroinvertebrates in Swedish streams: community structure, taxon richness, and environmental relations

Spatial scale, e.g. from the stream channel, riparian zone, and catchment to the regional and global scale is currently an important topic in running water management and bioassessment. An increased knowledge of how the biota is affected by human alterations and management measures taken at different spatial scales is critical for improving the ecological quality of running waters. However, more knowledge is needed to better understand the relationship between environmental factors at different spatial scales, assemblage structure and taxon richness of running water organisms. In this study, benthic macroinvertebrate data from 628 randomly selected streams were analysed for geographical and environmental relationships. The dataset also included 100 environmental variables, from local measures such as in-stream substratum and vegetation type, catchment vegetation and land-use, and regional variables such as latitude and longitude. Cluster analysis of the macroinvertebrate data showed a continuous gradient in taxonomic composition among the cluster groups from north to south. Both locally measured variables (e.g. water chemistry, substratum composition) and regional factors (e.g. latitude, longitude, and an ecoregional delineation) were important for explaining the variation in assemblage structure and taxon richness for stream benthic macroinvertebrates. This result is of importance when planning conservation and management measurements, implementing large-scale biomonitoring programs, and predicting how human alterations (e.g. global warming) will affect running water ecosystems.
The effects of dispersal mode on the spatial distribution patterns of intertidal molluscs

1. As many species of marine benthic invertebrates have a limited capacity for movement as adults, dispersal mode is often considered as a determinant of geographical ranges, genetic structure and evolutionary history. Species that reproduce without a larval stage can only disperse by floating or rafting. It is proposed that the colonization processes associated with such direct developing species result in spatial distributions that show relatively greater fine scale patchiness than the distributions of species with a larval dispersal stage. This hypothesis was tested by collecting molluscs at different spatial scales in the Isle of Man. 2. Spatial distribution patterns supported the predictions based on dispersal mode. Estimated variance components for species with larval dispersal suggested that the majority of the spatial variation was associated with variation between shores. In comparison, there was relatively more variability within shores for abundance counts of species with direct development. 3. Multivariate analyses reflected the univariate results. An assemblage of direct developers provided a better discrimination between sites (100 m separation) but the group of species with larval dispersal gave a clearer separation of shores (separated by several km). 4. The fine scale spatial structure of direct developing species was reflected in higher average species diversity within quadrats. Species richness also reflected dispersal mode, with a higher fraction of the regional species pool present for direct developers in comparison to species with larval dispersal. This may reflect the improved local persistence of taxa that avoid the larval dispersal stage.
Firm Heterogeneity and Choice of Ownership Structure

We contribute to the nascent literature on the heterogeneity of multinational enterprises (MNEs) and the relevance of firm characteristics for analysing the determinants of outward foreign direct investment (FDI). The focus is on the role of firm-level heterogeneity when MNEs decide on the share of ownership in foreign affiliates. We combine two firm-specific datasets on German MNEs with varying equity stakes in Indian affiliates. The impact of firm characteristics on ownership shares is assessed in the context of OLS and fractional logit models, controlling for industry and location characteristics. We show that the effect of several characteristics differs between the establishment of new affiliates by German MNEs and their engagement in already existing Indian firms. Most notably, the productivity of the German parents matters only for ownership shares in new affiliates.
Scotland's Rural College Viability of the Happy Factor TM targeted selective treatment approach on several sheep farms in Scotland McBean,

22 The aim of this study was to examine the use of Happy Factor weight based 23 targeted selective treatment (TST) on several commercial farms in Scotland in 24 combination with findings from a long term trial on a research farm to assess the 25 potential for TST use in varying farming operations as an alternative to the current 26 regimen of whole flock treatment. Lambs on each farm were regularly weighed and 27 climatic conditions and pasture availability measured for inclusion into the Happy 28 Factor model to calculate weight targets. Half of the lambs were allocated to TST 29 treatment and any failing to reach the weight target was treated with the anthelmintic 30 of choice on that farm, while the remaining half of each flock was treated with 31 anthelmintic as per normal practice on that farm (routine treatment, RT). The 32 research farm (farm 1) hosted a long term trial using four anthelmintic treatment 33 regimes over 6 years, and data from two regimes are presented here, alongside 34 findings from three further farms: two commercial enterprises (farms 2 and 3) and a 35 research farm operating as a commercial analogue with two breeds (farms 4a and 36 4b). The effect of TST strategy on lamb productivity and the number of anthelmintic 37 treatments was investigated. There was no evidence (p>0.300) that mean 38 bodyweight or growth rate was different between TST and RT groups on any of the 39 farms and 95% confidence intervals of TST and RT groups generally suggested that 40 TST had negligible unfavourable effects on the average growth of lambs for most of 41 the farms. Growth rates ranged from 97.39 to 189.16 g/day reflecting the varied 42 nature of the farms. All commercial farms used significantly less (1.34 RT versus 43 1.14 TST treatments per animal, p<0.05) anthelmintic in lambs following TST, with a 44 reduction from 1, 1, 1.03 and 1.14 to 0.77, 0.57, 0.82 and 0.81 in the number of 45 treatments per animal for farms 2,3 4a and 4b respectively. This study suggests that 46 2 TST is a viable means of controlling parasitic disease without incurring production 47 losses. 48
ANFIS Inverse Kinematics and Precise Trajectory Tracking of a Dual Arm Robot

- The dual arm manipulation of a totally six degrees of freedom revolute robot will be considered in this study. For the inverse kinematics purposes of the robot, the Cartesian trajectory assumed for the end effectors of both arms will be transformed to joint space by Adaptive Neuro Fuzzy Inference System (ANFIS) modeling of the system. The Fuzzy control system designed to drive the joint servomotors will utilize this information as a reference input for the joint angular positions and realize the overall assumed Cartesian space trajectory. The whole system will be modeled by using Simulink with some embedded MATLAB functions and the SimMechanics model of the real mechanical construction. The simulations belonging to the assumed trajectories will be realized and the error will be evaluated for the applied Fuzzy control.
ADOPTION OF INTEGRATED FOOD-ENERGY SYSTEMS: IMPROVED COOKSTOVES AND PIGEONPEA IN SOUTHERN MALAWI

SUMMARY We analyse the adoption of an Integrated Food-Energy System (IFES) in southern Malawi. The IFES combined the improved cookstove (chitetezo mbaula in Chichewa), designed to reduce demand for fuelwood, with the pigeonpea variety Mthawajuni, which increased both food supply and supply of fuelwood from pigeonpea stems. Adoption of the improved cookstove was found to be higher among households that were better off and where women had greater control over decision-making. However, adoption of the IFES was not associated with reduced demand for fuelwood from forests and hills or reduced frequency of collection. IFES adopters might have high fuelwood consumption because they were better off, but fuelwood consumption in better-off households did not differ significantly between IFES adopters and non-adopters. Pigeonpea increased food supply for adopter households, including children aged less than five years. Consequently, the IFES has had mixed results, improving food supply but not reducing demand for fuelwood. Households ranked early maturity, fuelwood and yield as the three most important reasons for preferring Mthawajuni over other varieties of pigeonpea. The plant breeding programme for pigeonpea in Malawi should evaluate improved varieties not only for earliness and grain yield but also for the production of fuelwood. Improved varieties with desirable market traits have had limited success in the absence of reliable markets and price incentives.
Human behavior and sustainability

7 Sustainability demands changes in human behavior. To this end, priority areas include reforming formal insti- tutions, strengthening the institutions of civil society, improving citizen engagement, curbing consumption and population growth, addressing social justice issues, and reflecting on value and belief systems. We review existing knowledge across these areas and conclude that the global sustainability deficit is not primarily the result of a lack of academic knowledge. Rather, unsustainable behaviors result from a vicious cycle, where tra- ditional market and state institutions reinforce disincentives for more sustainable behaviors while, at the same time, the institutions of civil society lack momentum to effectively promote fundamental reforms of those insti- tutions. Achieving more sustainable behaviors requires this cycle to be broken. We call on readers to contribute to social change through involvement in initiatives like the Ecological Society of America's Earth Stewardship Initiative or the nascent Millennium Alliance for Humanity & the Biosphere.
Latitudinal, longitudinal and weather-related variation in breeding parameters of Great Reed Warblers in Europe: a meta-analysis

Capsule Clutch initiation date decreased with longitude, clutch size increased with latitude and decreased with maximum temperature, whereas the number of fledglings increased both with latitude and longitude, and decreased with maximum temperature in 19 European studies of the Great Reed Warbler. Our study confirmed previous findings about the increasing trend in clutch size with latitude, but also found earlier clutch initiation dates and higher number of fledglings longitudinally from west to east, with precipitation closely associated with clutch initiation date and maximum temperature closely associated with the number of fledglings.
Introduction to Special Issue

Recent research in the past decade has highlighted the significance of principals in improving schools and schooling outcomes (Branch, Hanushek, & Rivken, 2012; Coelli & Green, 2012; Fuller & Hollingworth, 2013; Grissom, Kalogrides, & Loeb, 2014; Jacobson, 2011; Louis et al., 2010; Portin, Feldman, & Knapp, 2006; Rice, 2010) as well as the importance of leadership preparation programs (LPPs) in ensuring graduates are well prepared to be effective school leaders (Fuller, Young, & Baker, 2011; Hitt, Tucker, & Young, 2012; Orr & Orphanos, 2011). Concomitant with this increase in research has been the widespread adoption of both personnel and program accountability mechanisms as levers for the improvement of the U.S. education system (Fuller & Hollingworth, 2014b; Fuller, Hollingworth, & Liu, 2015). Little research, however, has examined the validity and reliability of these accountability mechanisms or the effects these systems might have on individuals and programs. This special issue includes two articles that begin to address this paucity of research by examining trends across the United States and how these efforts are enacted in specific contexts across the nation. The two articles in this volume examine the state policies and political context concerning principal evaluation and principal preparation programs. Both articles rely on a mixed-methods approach that relies heavily on document review and descriptive statistics.
Inclusion in and out of the classroom: A longitudinal study of students with visual impairments in inclusive education

This longitudinal study examined psychological well-being and social relations in school for six students with blindness or severe visual impairment (VI) in Swedish inclusive education. The students were followed through compulsory school, with data collection in Grades 1, 2, 3, and 9. A total of 151 interviews were conducted with the students, teachers, and parents during these years. At the end of ninth grade, the Strengths and Difficulties Questionnaire (SDQ) was also administered to all informants. The results revealed several challenges regarding social inclusion, with a majority of families being critical of the social situation in the schools. During lower school years, many examples of educational interventions aiming to facilitate social inclusion were described. However, as the children grew older, the parents’ and teachers’ possibilities to influence the group dynamics and create organized social arenas diminished drastically. Regarding the students’ general psychological well-being, the SDQ ratings showed minor or no differences compared to sighted norms. However, the interviews revealed that a majority of the students were stressed about school work and keeping up with their sighted peers and described feelings of loneliness. Some displayed emotional symptoms of which parents and teachers were not always aware. Three students had additional disabilities besides their VI. These students reported more overt psycho-social problems than the students with only VI. The students developed different strategies to handle the social challenges, for example, focusing on school work and getting good grades, or withdrawing and seeking friends with VI outside school. The conclusion is that students with visual impairments are a heterogeneous group comprising individuals with different needs, and that many of these students face social challenges in school. Interventions on different levels are necessary in order to improve the possibilities for these students’ social inclusion.
The American Midland Naturalist

—The Crooked Creek Barrens Preserve in the northeastern Knobs region of Kentucky contains an aggregation of species-rich grass and forb-dominated glade openings surrounded by secondary forest. Encroachment of woody species and invasion by non-native species threaten the rare forbs and sedges of the glades. The locations of these plant assemblages are commonly known to correspond to the unique properties of their underlying soils, yet few studies consider how soil factors may influence habitat conservation or restoration. This study describes vegetation and soil properties across the glade-edge-forest transition of three individual glade openings. Juniperus virginiana was the most abundant woody species within the glade openings. Juniperus virginana, Quercus stellata, Fraxinus americana and Cercis canadensis co-dominated the edge-forest boundary. Glade surface soils had dramatically higher pH (2 units) and lower extractable soil P (50% less) than forest soils. Also, total soil N content and net mineralization rates were significantly lower in glades than in forest or edge soils. The highly erodable nature of alkaline shale sediments appears to have contributed to the current location and extent of the glade openings. These findings suggest that management efforts to enhance rare plant habitat by expanding the glade openings should be accompanied by monitoring of soil changes following clearing. Further study should assess whether glade species of conservation concern are restricted to the nutrientpoor alkaline soils within extant glade openings or if they readily colonize the more nutrientrich habitat of the cleared edge.