Miracle-dz/UniFAR-FTUs huggingface dataset:
An integrated airborne laser scanning approach to forest management and cultural heritage issues: a case study at Porolissum, Romania

This paper explores the opportunities that arise where forest ecosystem management and cultural heritage monuments protection converge. The case study area for our analysis was the landscape surrounding the Moigrad-Porolissum Archaeological site. We emphasize that an Airborne Laser Scanning (ALS or LiDAR-Light Detection and Ranging) approach to both forest management and cultural heritage conservation is an outstanding tool, assisting policy-makers and conservationists in decision making for integrated planning and management of the environment. LiDAR-derived surface models enabled a synoptic, never-seen-before view of the ancient Roman frontiers defensive systems while also revealing the present forest road network. The thorough and accurate road inventory data are very useful for updating and modifying forest base maps and registries and also for identifying the priority sectors for archaeological discharge. The ability to identify and determine optimal routes for forest management and to locate previously unmapped ancient archaeological remains aids in reducing costs and creating operational efficiencies as well as in complying with the legislation and avoiding infringements. The potential of LiDAR to demonstrate the long-term and comprehensive human impact on wooded areas is discussed. We identified a significant historical landscape change, consisting of a deforestation period, spanning over more than 160 years, during the Roman Period in Dacia (106-271 AD). The transdisciplinary analysis of the LiDAR data provides the base for combining knowledge from archaeology, forestry and environmental history in order to achieve a thorough analysis of the landscape changes and history. In the “nature versus culture” dichotomy, the landscape, outfield areas and forests are primarily perceived as nature, while in reality they are often heavily marked by human impact. LiDAR offers an efficient method for broadening our knowledge regarding the character and extent of human interaction with landscapes – forested or otherwise.
Chemogenetical investigations of flower colours in Cyclamen

Flower pigments in cyclamen species, cultivars and crosses between cultivars were investigated to provide a basis for the description of cultivars and for breeding work. By paper chromatography, 14 anthocyanins and 8 flavonol glycosides were isolated. Two leuco-anthocyanins were found. The results of the analysis of flower-colouring flavonoids in wild species and cultivars were listed in tables. Analysis of the chemistry and genetics of crosses between cultivars confirmed the presence of genes W, F, S and M . Additional data were found on their effect in biosynthesis of flavonoids. Three new genes were detected: X, determining the glycosidic pattern of a flavonol glycoside, Y , determining the glycosidic pattern of an anthocyanin, and Z , determining the distribution of flower pigment. A hypothesis on the effect of the genes in the biosynthesis of the flowercolouring flavonoids was proposed.
Size selection from fishways and potential evolutionary responses in a threatened Atlantic salmon population

The evolutionary effects of harvest on wild fish populations have been documented around the world; however, sublethal selective pressures can also cause evolutionary changes in phenotypes. For migratory fishes, passage facilities may represent instances of nonlethal selective pressure. Our analysis of 6 years of passage data suggests that certain fish passage facilities on the Penobscot River have been exerting selective pressure against large‐bodied, anadromous Atlantic salmon (Salmo salar). At the second and third dams in the river, a 91‐cm salmon was 21%–27% and 12%–16% less likely to pass than a 45‐cm salmon, respectively. Fish size positively influences egg survival and number and is a heritable trait. Therefore, in a wild‐reproducing population, exclusion of large fish from spawning areas may have population‐level impacts. In the Penobscot River, most returning adults derive from a hatchery program that collects its broodstock after passing the first dam in the river. Analysis of fork lengths of salmon returning to the Penobscot River from 1978 to 2012 provided mixed support for evolution of size at maturity in different age classes in a pattern that may be expected from interactions with conservation hatchery operations. Additionally, slow‐maturing and iteroparous individuals that represent the largest salmon size classes were essentially lost from the population during that time, and Penobscot River fish have shorter fork lengths at maturity than Atlantic salmon in undammed systems.
The Effects of Magnetic Field on Germination of Seeds and Growth of Seedlings of Stone Pine

Stone pine (Pinus Pinea L.) is a multi-purpose species for Mediterranean forestry owing to both economic and socio-economic importance. Thus, in this study the effects of magnetic field on the germination of seeds and growth of seedlings of stone pine were investigated. For this purpose, its seeds were treated by a magnetic field of 9.42 mT for a different period of time – 0 min (control), 15 min, 30 min and 40 min in a cylindrical shaped sample, made of a nonmagnetic thin transparent plastic sheet. Germination experiments were conducted in the greenhouse of Bartin University. Considered the germination results as a whole, while seeds exposed to a magnetic field for 30 and 45 minutes resulted in higher germination energy (43%) and percentage (55%), respectively. Both the lowest germination energy (6%) and germination percentage (32%) were found out to be in the seeds without applying magnetic field. Magnetic field increased shoot height, root collar diameter and also tap root length of stone pine seedlings. In terms of shoot height, 85% of 1+0 seedlings was proper for afforestation activities based the classification of TSI. Moreover, magnetic field treatments may be considered as an alternative method to enhance germination Stone pine seeds and to obtain better growth characteristics of their seedlings.
The role of folic acid in maintaining colorectal cancer cell DNA methylation patterns, and cancer stem cell phenotype in vitro

The role of folic acid in maintaining colorectal cancer cell DNA methylation patterns and cancer stem cell phenotype in vitro Nathan Farias Advisor: University of Guelph, 2013 Dr. B. L. Coomber Folic acid is a B vitamin involved in DNA CpG methylation. Mandated dietary fortification has led to a subsequent increase in blood folate concentration which has been correlated to a simultaneous spike in colorectal cancer incidence in Canada and the US. Several human colorectal cancer cell lines were cultivated under low (0 mg/L), standard (4 mg/L), and high (16 mg/L) folate conditions for seven days, then assessed for DNA methyltransferase1 protein expression, changes in DNA methylation, and ability to generate colonospheres in culture. Low folic acid levels generally led to reduced DNMT1 protein expression, CpG hypomethylation, and reduced colonosphere yield. High folic acid levels led to increased DNMT1 protein expression, CpG hypermethylation, and maintained colonosphere yield. This data demonstrates that varying levels of folic acid in vitro can influence the methylation status and cancer stem cell self-renewal ability of human colorectal cancer cells.
Starch‐based carbohydrates display the bifidogenic and butyrogenic properties in pH‐controlled faecal fermentation

Summary Starch-based carbohydrates, native rice starch (NRS), isomaltooligosaccharide produced from native rice starch (rIMO), commercial isomaltooligosaccharide (cIMO), resistant starch type 2 (RS2) and type 3 (RS3) were investigated the bifidogenic and butyrogenic properties. The result confirmed that the bifidogenic effect of rIMO (9.8 ± 0.18) was comparable to cIMO (10.3 ± 0.2). In addition, rIMO showed the highest support on growth of bifidobacteria during early fermentation (10 h), and it was not significantly different (P > 0.05) from cIMO after up to 70 h. Prebiotic index (PI) at 24 h fermentation of rIMO and cIMO was shown positive value and higher than RS3 and RS2. Meanwhile, NRS showed negative value means it has no prebiotic property. Interestingly, RS3 showed approximately twofold in butyrate production (132.3 mm) compared to rIMO and cIMO. In conclusion, IMO showed high bifidogenic effect; meanwhile, RS3 showed high butyrogenic property.
Calcium channel levels at single synapses predict release probability and are upregulated in homeostatic potentiation

Abstract Communication in neural circuits depends on neurotransmitter release at specialized domains of presynaptic terminals called active zones. Evidence in multiple systems indicates that neurotransmitter release properties vary significantly, even between neighboring active zones of the same neuron. To investigate the role of voltage-gated calcium channels in determining diverse release properties, we combined endogenous tagging of the Ca V 2 channel Cacophony with functional imaging at Drosophila neuromuscular junctions. We find that calcium channels are differentially localized to active zones and robustly predict release probability at single synapses. Synaptic calcium channel levels, in turn, are highly correlated with ELKS/Bruchpilot levels at the active zone cytomatrix. During acute homeostatic potentiation, active zone cytomatrix remodeling is accompanied by a rapid increase in calcium channel levels. We propose that dynamic reorganization of the active zone cytomatrix during short-term plasticity generates new sites for the incorporation of calcium channels to modulate release properties and circuit function.
The spatial structure of phylogenetic and functional diversity in the United States and Canada: An example using the sedge family (Cyperaceae)

Systematically quantifying diversity across landscapes is necessary to understand how clade history and ecological heterogeneity contribute to the origin, distribution, and maintenance of biodiversity. Here, we chart the spatial structure of diversity among all species in the sedge family (Cyperaceae) throughout the USA and Canada. We first identify areas of remarkable species richness, phylogenetic diversity, and functional trait diversity, and highlight regions of conservation priority. We then test predictions about the spatial structure of this diversity based on the historical biogeography of the family. Incorporating a phylogeny, over 400 000 herbarium records, and a database of functional traits mined from online floras, we find that species richness and functional trait diversity peak in the Northeastern USA, while phylogenetic diversity peaks along the Gulf of Mexico. Floristic turnover among assemblages increases significantly with distance, but phylogenetic turnover is twice as rapid along latitudinal gradients as along longitudinal gradients. These patterns reflect the expected distribution of Cyperaceae, which originated in the tropics but radiated in temperate regions. We identify assemblages with an abundance of rare, range‐restricted lineages, and assemblages composed of species generally lacking from diverse regions. We argue that both of these metrics are useful for developing targeted conservation strategies. We use the data generated here to establish future research priorities, including the testing of a series of hypotheses regarding the distribution of chromosome numbers, photosynthetic pathways, and resource partitioning in sedges.
Ecophysiological Characteristics and CSR Strategies of Four Dune Species

Plants that live in coastal dune ecosystems may develop several strategies to deal with environmental stress. The aim of this study was to compare contents of nonenzymatic antioxidants including chlorophyll, carotenoid, anthocyanin and total phenolic compounds, and CSR (competitive, stress-tolerant, ruderal) strategy types of four dune species: Pancratium maritimum, Eryngium maritimum, Polygonum maritimum and Achillea maritima subsp. maritima. CSR strategies were determined using canopy height, leaf dry matter content, flowering period, flowering initiation, leaf dry weight, lateral spread, and specific leaf area (SLA). The lowest values for all measured parameters were found in Pancratium maritimum, while the highest contents of chlorophyll a, carotenoid, anthocyanin and total phenolic compounds were in Polygonum maritimum. The studied species had different ecological strategies to cope with stressful environmental conditions.
Sexing of common gull, Larus canus, using linear measurements

Abstract. The common gull is a widespread species, occurring in almost the whole of Europe that shows no sexual dimorphism in plumage and some dimorphism in size. To propose a method for sexing birds from this species by linear measurements, a discriminant function analysis was applied to a set of morphometric traits in birds captured in northern Poland during the non-breeding season. In total, 138 males and 76 females were measured and sexed molecularly. The averages of measurements of males were larger than the average measurements of females. All individuals with a total head length shorter than 90.6 mm were females. However, the occurrence of larger individuals of the subspecies heinei among common gulls of the nominate subspecies canus wintering in Europe makes separating males according to a single border value of this measurement less efficient. The proposed discriminant function containing the total head length allowed for correct sexing of 95.7 % of males and 90.9 % of females. This discriminant equation may be used for sexing common gulls when DNA sampling is not possible, and could be applied to data collected in the past, providing the opportunity to re-examine the results of previous analyses. However the higher misclassification rate than in other gull species should be taken into account.
Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP)

A total of 502 Campylobacter jejuni isolates from poultry in 12 different European countries (10 of them the largest poultry production countries in Europe) were whole genome sequenced to examine the genomic diversity of fluoroquinolone resistant (FQ-R) and susceptible (FQ-S) C. jejuni across the poultry producing European countries and to determine whether the emergence of fluoroquinolone resistance among C. jejuni is related to the transmission through countries or to the selection through fluoroquinolone use in the individual countries. A high genomic diversity was observed. The isolates clustered in four main clusters. All trees revealed that the isolates were clustered according to the presence/absence of the gyrA mutations causing fluoroquinolone resistance and ST-types. The cgMLST trees of only FQ-R and FQ-S isolates showed that isolates from the same country of origin were distributed into multiple clusters similarly to the trees combining FQ-R and FQ-S isolates. The different phylogenetic methods, ranging from single nucleotide polymorphisms analysis to gene-bygene approaches such as rMLST, cgMLST, wgMLST and core genome tree, provided concordant results, but it is not known which is the most accurate method for identifying the country of origin of the isolates. Allele frequency analysis of isolates under this study and a selection of previously published C. jejuni genomes in ENA showed association of geographical origin of poultry C. jejuni populations between Romania-Poland, Italy-Germany-England, Portugal-The Netherlands and USALuxemburg. Allele frequency and phylogenetic analysis indicated that the isolates from Finland were genetically different from C. jejuni populations from other European countries included in this study. GenCamp – Genomics of quinolone-resistant and susceptible C. jejuni of poultry origin in EU countries www.efsa. europa.eu/publications 2 EFSA Supporting publication 2018:EN-1398 Trade pattern and antimicrobial use in livestock were not significantly associated with allele frequency or populations of C. jejuni, but data available to investigate these associations were limited. © Technical University of Denmark National Food Institute, 2018
Potential of an infectious laryngotracheitis (ILT) recombinant virus depleted of open reading frame (ORF) C gene as a live attenuated vaccine for in ovo usage

A recombinant Infectious laryngotracheitis virus (ILTV) depleted of the open reading frame C (ORF C) gene was previously developed and showed significant levels of attenuation post intratracheal/ocular and eye-drop delivery and induced satisfactory protection against Infectious laryngotracheitis (ILT). In ovo vaccination is a highly effective method for mass immunization of poultry, providing increased coverage, fast delivery and lower costs as compared to other field vaccination methods. In the USA, in ovo vaccination with Marek`s disease virus (MDV) is a standard procedure, capable of inducing early and effective immune response against Marek’s disease. The objectives of this study were to evaluate the attenuation and protection efficacy of the ∆ORF C recombinant virus when delivered in ovo in the absence or presence of ILTV maternally derived antibodies (MAb). In ovo delivery of ∆ORF C recombinant virus did not affect hatchability or weight-gain, and transmission of the virus to contact chickens was low. However, 5 to 19 % mortality was observed in specific pathogen free (SPF) chickens vaccinated with 3.5 (log10) and 3.8 (log10) TCID50 of ∆ORF C per embryo, respectively. While in commercial layers, in the presence of MAbs, no mortalities were observed. In ovo vaccination with ∆ORF C ILTV induced satisfactory protection after challenge, particularly in the absence of maternal antibodies, as SPF chickens vaccinated with 3.8 (log10) TCID50 dose showed significant reduction in clinical signs of the disease and tracheal virus load after challenge, while reduction of challenge virus load in commercial layers was not as significant. These results indicate that the ∆ORF C recombinant virus is still not properly attenuated for in ovo vaccination and the protection efficacy of ∆ORF C recombinant virus was affected by maternally derived antibodies.
Computational Analysis of Genome-wide Methylation Enrichment Experiments (Computergestützte Analyse genomweiter Methylierungsanreicherungsexperimente)

1) INTRODUCTION 1.1) Motivation 1.2) Research Objective 1.3) Thesis Outline 2) BIOLOGICAL BACKGROUND : EPIGENETICS 2.1) Epigenetics in Development 2.2) Epigenetics in Disease 2.3) Chromatin structure 2.4) Histone Modification 2.5) DNA Methylation 3) FUNDAMENTAL PRINCIPLES 3.1) Approaching the Epigenome: Experimental Principles 3.2) Modeling Read Enrichment: Statistical Principles 3.3) Benchmark Dataset 4) ESTIMATING ABSOLUTE METHYLATION VALUES 4.1) Coupling Factor Scaling 4.2) Relation of Methylation Level and Enrichment 4.3) Modeling the Read Coverage 4.4) Estimating Local C P G Density 4.5) Estimating Abundance of Background Reads 4.6) Assessing Sample Specific Enrichment 4.7) Fitting Enrichment Profiles 4.8) Statistical Model of the Absolute Methylation Level 4.9) Bayesian Estimators for the Absolute Methylation Level 4.10) Assessment of Methylation Level Estimation Methods 4.11) Conclusion 5) DIFFERENTIAL METHYLATION ANALYSIS 5.1) Wilcoxon’s Rank Sum Test 5.2) Generalized Linear Model Likelihood Ratio Test 5.3) Comparison of Statistical Tests 5.4) Conclusion 6) IMPLEMENTATION 6.1) MEDIPS package 6.2) QSEA package 6.3) Conclusion 7) APPLICATIONS 7.1) DNA-Methylome Analysis of Mouse Intestinal Adenoma 7.2) QSEA – Modeling genome-wide DNA methylation enrichment 7.3) Predicting Therapy Resistance in NSCLC by Epigenomic Profiling 7.4) Epigenomic Analysis of Immune Cells from Asthma Patients 8) DISCUSSION BIBLIOGRAPHY APPENDICES MATHEMATICAL PROOFS CURRICULUM VITAE PUBLICATIONS SUMMARY ZUSAMMENFASSUNG
Genetic studies on self-fertility in perennial ryegrass (Lolium perenne L.) with implications for hybrid breeding in allogamous grasses

Perennial grasses have diverse uses and are relevant from the agronomic and economic point of view, with main uses as forage, turf and bioenergy. In the grass family polyploidy is prevalent and both autopolyploids and allopolyploids are present. Also, within grasses there are a range of breeding systems, but hermaphrodite flower is the most frequent floral condition. Cross-pollination in species with hermaphrodite flowers is imposed by a gametophytic genetic self-incompatibility (SI). SI is controlled by two multiallelic and independent loci, S and Z. The incompatibility phenotype of the pollen grain is determined by its haploid genome. A pollen grain is incompatible when the same S and Z alleles carried by pollen are present in the pistil. This SI mechanism keeps its functionality at higher ploidy levels. Understanding the mechanisms involved in the breakdown of SI are crucial for implementing novel breeding practices. The aim of this work is to increase the knowledge of SF in outcrossing grasses for the purpose of inbred line development and making hybrid breeding possible. Mutations at S, Z and at a third locus are known to cause self-fertility (SF). In perennial ryegrass (Lolium perenne), a locus conferring SF is located in linkage group 5. Using segregation and linkage analysis, the SF locus region was reduced to 1.6 cM. This locus explained 94% of the observed variability. By aligning the flanking marker sequences to the Brachypodium distachium reference genome, it was found that it corresponds to an 807 Kbp region in B. distachium. This locus was studied at the tetraploid level and it was found that SF remained functional, the SF locus genotype was the main determinant of pollen compatibility explaining 54% of the variation, and there is incomplete
EEG Decoding Reveals the Temporal Dynamics and Functional Relevance of Goal-Relevant Representations

Models of action control assume that abstract task-set settings regulate lower-level stimulus/response representations. Yet, we know little about the functional and dynamic properties of task-set representations in humans. Using a cued task-switching paradigm, we show that information about task sets and lower-level stimulus/response aspects can be extracted through decoding analyses from the scalp electrophysiological signal (EEG) on the single-trial level and with high temporal resolution. Task-sets are active throughout the entire processing cascade and trial-to-trial variations in task-set strength emerges as a remarkably strong predictor of variability in performance, both within and between individuals. Also, taskset strength is related to stimulus representation strength at an early period and to the strength of response representations at a later period, consistent with the notion that task-sets coordinate successive, lower-level representations in a concurrent manner. These results demonstrate a powerful approach towards uncovering stages of information processing and their relative importance for performance.