Miracle-dz/UniFAR-FTUs huggingface dataset:
Význam Kombuchy a její biologicky aktivní látky

This Master's thesis is focuses on mycological characteristics of kombucha and the effects of biologically active substances of kombucha on the human organism. The aim of this thesis is to determine the amount of total polyphenols, antioxidant activity and antiproliferative effect of activity in kombucha. The resulting values were compared and evaluated. The total polyphenol content was determined spectrophotometric and antioxidant activity with help of using the DPPH. Determination of the antiproliferative effect was by spectrometric method of MTT.
Genetic characteristics reflecting the population size and disturbance regime of Siebold’s beech (Fagus crenata Blume) populations at the northernmost distribution

Abstract To understand the population dynamics of tree populations at the range limit of a species’ range, it is important to determine which population size and disturbance regime are critical to genetic diversity. Siebold's beech (Fagus crenata Blume) is a major canopy tree species of cool-temperate forests in Japan, with the northernmost distribution reaching the Kuromatsunai Depression in southwestern Hokkaido, Japan. We examined the genetic variation and dynamics of three beech forests, with different disturbance history and population attributions in the northernmost population. The Tsubamenosawa (TSU) and Sannosuke (SAN), both natural forest, have historically experienced little artificial disturbance, whereas the Soibetsu (SOI), a secondary forest, was intensively logged, and thus strongly disturbed in the past. In total, 35 alleles were detected among 12 loci, encoding 9 enzyme systems. At TSU, He and RS were 0.141 and 2.280, respectively. At SAN, He and RS were 0.142 and 2.604, respectively. At SOI were 0.182 and 2.628, respectively. Parameters of genetic diversity changed with population size, small isolated population indicated low values. Gene flow distance for low density mature trees in the natural forests was greater than that for high-density secondary forest. However, effective population sizes (Ne) were 34.7, 64.3 and 60.3 in TSU, SAN and SOI, respectively, reflecting differences in the density of mature individuals. The results suggested that the population with the low density of mature trees kept genetic diversity through long distance gene flow. The mature tree density affected the effective population size in the northernmost beech populations.
MANAGEMENT OF LEGUME AS LAND COVER CROP AND EMPTY BUNCH FOR THE NITROGEN EFFICIENCY IN INCEPTISOLS AT OIL-PALM PLANTATION

The research aimed to know the kind of legume cover crop which more suitable to be cultivated especially in area of Natar, South Lampung and to know the efficiency of N supply. It used a single Completely Randomized Block Design (CRBD) consisted of 4 treatments (several kinds of debris), covering: kacang benguk ( Mucuna cochinchinensis ), kacang ruji ( Pueraria javanica) , and oil-palm empty bunch compared to one which no debris added (control). Data analyzed by regression, F test (α 5%; or Kruskal-Wallis), DMR test (α 5%; or Mood Median) and correlation test. Result showed that Pueraria javanica ( kacang ruji ) was more suitable to be cultivated. Regression showed that management of empty bunch tend to enhance the ratio of NH 4 + /N-mineral as indicator of N supply efficiency, while the management of Pueraria javanica tend to decrease the ratio of NH 4 + /N-mineral. The degradation of soil NO 3 - concentration in the treatment of empty bunch was followed by the degradation of soil nitrification potential and the enhancement of heterotrofic bacteria. The enhancement of soil nitrification potential in the Pueraria javanica and Mucuna cochinchinensis management was followed by the degradation of soil pH.
Insect herbivory on snow gum (Eucalyptus pauciflora, Myrtaceae) saplings near the alpine treeline: the influence of local- and landscape-scale processes

The distribution and abundance of plant species in high mountain ecosystems are thought to depend largely on abiotic factors that play out at both landscape scales (e.g. steep environmental gradients affected by increasing elevation) and local scales (e.g. changes in topography, aspect and canopy cover). However, relatively little attention has been paid to biotic interactions, and how these might also change with landscape-wide and local factors. Ecological interactions between plants and insect herbivores are likely to alter species performance and affect local abundance, but their role in the Australian Alps remains largely unexplored. Here, we examine the prediction that the amount of herbivory on saplings of the dominant high elevation tree, snow gum Eucalyptus pauciflora Sieb. ex Spreng. (Myrtaceae), are lower at higher elevation because of increasing environmental stress. Using a reciprocal transplant experiment, we tested the prediction that origin of seed (low, mid, high elevation) has less effect on insect herbivory than environmentally-driven changes in plant morphology (height, leaf thickness, specific leaf area). Across all mountains studied, herbivory was best explained by a combination of plant height, canopy openness, leaf thickness and elevation, but not seed origin. This study highlights the individuality of each mountain environment, at landscape and local scales, as well as the complexity of relationships between environmental change, plants and insects. Given the factors that best explain herbivory across mountains, herbivory may decrease with decreasing productivity associated with increasing elevation, a trend in broad agreement with hypotheses associating leaf area loss to the availability of resources and plant vigour.
Systematic transcriptomics reveals a biphasic mode of sarcomere morphogenesis in flight muscles regulated by Spalt

Muscles organise pseudo-crystalline arrays of actin, myosin and titin filaments to build force-producing sarcomeres. To study how sarcomeres are built, we performed transcriptome sequencing of developing Drosophila flight muscles and identified 40 distinct expression profile clusters. Strikingly, two clusters are strongly enriched for sarcomeric components. Temporal gene expression together with detailed morphological analysis enabled us to define two distinct phases of sarcomere development, which both require the transcriptional regulator Spalt major. During the sarcomere formation phase, 1.8 μm long immature sarcomeres assemble myofibrils that spontaneously contract. During the sarcomere maturation phase, these sarcomeres grow to their final 3.2 μm length and 1.5 μm diameter and acquire stretch-sensitivity. Interestingly, the final number of myofibrils per flight muscle fiber is determined at the onset of the first phase. Together, this defines a biphasic mode of sarcomere and myofibril morphogenesis – a new concept that may also apply to vertebrate muscle or heart development.
Self-Supervised Robot In-hand Object Learning

In order to complete tasks in a new environment, robots must be able to recognize unseen, unique objects. Fully supervised methods have made great strides on the object segmentation task, but require many examples of each object class and don't scale to unseen environments. In this work, we present a method that acquires pixelwise object labels for manipulable in-hand objects with no human supervision. Our two-step approach does a foreground-background segmentation informed by robot kinematics then uses a self-recognition network to segment the robot from the object in the foreground. We are able to achieve 49.4\% mIoU performance on a difficult and varied assortment of items.
A comparison of SNP based genome clustering tools

Bacterial infections are returning as a global hazard, with international travel enabling infections to spread much wider and faster than before. In addition, the bacteria causing these infections are to an increasing extent resistant to antibiotics. There is an estimate of 12 600 deaths every day for children in Asia, Africa and Latin America combined. With the advent of low-cost DNA sequencing machines, we are now able to efficiently study large-scale genomes from epidemiological outbreaks in a cost-effective way. Many methods for clustering genomes on the basis of SNPs exist. This thesis provides an in-depth comparison of two different SNP clustering methods, ksnp and parsnp. Ksnp compares kmers to finds SNPs whilst parsnp uses MUMs. The objective of this thesis is to investigate how the two methods compare on both real and simulated Escherichia coli and Campylobacter jejuni data sets. In addition, to explore the differences between these two methods, a genome simulator is designed and implemented. This enables the possibility to predict which tools are more suitable for data sets with various sizes and mutation rates of SNPs. Furthermore, it makes it possible to determine the method that is more suitable if their results diverge on real-world data. This thesis implements two comparative SNP clustering suites, one for the Galaxy framework and one standalone for Unix systems. Both tools are modified in order to fit a streamlined process. The SNPs provides an insight into how the methods compare before creating phylogenies, therefore the SNP-comparator was created. This provides useful statistics on the SNPs from both tools. However, even if the SNPs are inconsistent from the methods they can still produce the same phylogeny. To determine the difference in phylogenetic trees for both methods, the TreeCmp package is used. This paper found that it matters which SNP clustering method is used. The methods diverge on both the Campylobacter jejuni and the Escherichia coli data sets. Ksnp and parsnp are more similar with respect to the topological metrics for Campylobacter than for E.coli. In the genome simulations, parsnp is better overall in terms of accuracy. By removing the more distant genomes, parsnp will subsequently have less material to analyze and less complicated path to re-creating the true phylogeny unlike ksnp. Both the real and simulated data sets reveal that the SNP clustering methods result in different SNPs and tree structures on the same data. This is a result of parsnps similarity filter and the SNP clustering distance features. Based on the
Isolement reproductif et architecture génomique de la différenciation chez deux espèces du complexe Jaera albifrons (isopodes marins) - Etude de populations mixtes présentant des niveaux d'isolement interspécifique contrastés

Dans l’etude de la speciation, l'existence de zones dans lesquelles deux especes en sympatrie montrent differents niveaux de differenciation genetique constitue une bonne opportunite pour comprendre la nature et l'evolution des barrieres a la reproduction entre especes. Jaera (albifrons) albifrons et Jaera (albifrons) praehirsuta sont deux especes d’isopodes marins qui coexistent en sympatrie le long des cotes nord-europeennes. Des barrieres ecologiques, comportementales, et genetiques cloisonnent efficacement ces deux especes, a l'exception d'une region unique (Normandie, France) dans laquelle des morphotypes intermediaires avaient ete decrits dans les annees 60.Au cours de cette these, l'utilisation de microsatellites et de SNPs obtenus par sequencage RAD ont permis de demontrer que le niveau d'isolement interspecifique varie fortement entre sites, de l'hybridation introgressive a l'isolement quasi-complet. Une analyse comparative de ces sites combinant echantillonnage en populations naturelles, croisements experimentaux et analyses genomiques a ensuite permis de : i) mettre en avant le role preponderant de l'isolement sexuel (qui reste fort dans les populations introgressees) accompagne d'une barriere post-zygotique relativement faible, ii) decouvrir la presence de bacteries Wolbachia au sein des deux especes, iii) demontrer que la coexistence des deux especes resulte d'une speciation allopatrique suivie de contacts secondaires avec reprise de flux de genes d'intensite variable, et iv) montrer que ces flux de genes varient egalement fortement au sein du genome, les chromosomes sexuels et des chromosomes rearranges semblant limiter fortement l'introgression.
Evolutionary history as a driver of ecological networks: a case study of plant–hummingbird interactions

Multiple factors drive species interactions in ecological networks, such as morphological barriers, spatio–temporal distribution, abundances and evolutionary histories of species. Novel methods are making it possible to evaluate the relative importance of each of these drivers. However, the lack of appropriate methods has prevented evaluating the extent to which interaction networks are shaped by species’ evolutionary histories. This study includes the evolutionary histories of species among the potential drivers of interactions, allowing the comparative analysis of its importance in structuring ecological networks. We hypothesized different possible phylogenetic scenarios to predict frequencies of interactions between species by combining concepts from the fields of ecological networks and ecophylogenetics. The usage of these scenarios is illustrated in a plant–hummingbird interaction network database from the Atlantic Forest, southeastern Brazil. We first evaluated which phylogenetic hypotheses better predict the observed network; subsequently, we evaluated the relative importance of species evolutionary histories, abundances, and matching on species morphologies and phenologies as drivers of their frequencies of interactions. The results suggest that the evolutionary histories of hummingbirds are more important than the species abundances in structuring the studied plant–hummingbird network but less important than the morphological and phenological matching among species. The approach developed here offers the potential to advance our understanding of the multiple factors structuring ecological networks.
Characterization and Similarity Analysis of 15 Tomato Genotypes in Lowlands Based on Morphological Characters

This study aimed to obtain information about the characteristics of 15 genotypes and to study a genetic similarity of each genotype that will be used for producing superior tomato varieties in lowlands. The research was conducted from March to August 2012 at the Experimental Field Leuwikopo Bogor Agricultural University, Darmaga Bogor. The experiment used The Randomized Complete Block Design (RCBD) using a single factor of genotype with three replications. Characterization and similarity analysis used the method of principal component analysis and cluster analysis. Based on principal component analysis and cluster analysis of tomato genotypes, it can be classified into three groups: group I (IPBT1, IPBT4, IPBT8, IPBT13, IPBT58, IPBT83 and IPBT84), Group II (IPBT3, IPBT23, IPBT30, IPBT33, IPBT34, IPBT53 and IPBT57) and group III (IPBT80). Characters with an influence on the genetic diversity of each component are the size of the cork layer between the scar stalk and the size of the center of the fruit in transverse slices. The genotypes with a high genetic similarity were IPBT1 and IPBT8, while IPBT30 with IPBT80 had a low genetic similarity
MAT-Fly: An Educational Platform for Simulating Unmanned Aerial Vehicles Aimed to Detect and Track Moving Objects

The main motivation of this work is to propose a simulation approach for a specific task within the Unmanned Aerial Vehicle (UAV) field, i.e., the visual detection and tracking of arbitrary moving objects. In particular, it is described MAT-Fly, a numerical simulation platform for multi-rotor aircraft characterized by the ease of use and control development. The platform is based on Matlab® and the MathWorks™ Virtual Reality (VR) and Computer Vision System (CVS) toolboxes that work together to simulate the behavior of a quad-rotor while tracking a car that moves along a nontrivial path. The VR toolbox has been chosen due to the familiarity that students have with Matlab and because it does not require a notable effort by the user for the learning and development phase thanks to its simple structure. The overall architecture is quite modular so that each block can be easily replaced with others simplifying the code reuse and the platform customization. Some simple testbeds are presented to show the validity of the approach and how the platform works. The simulator is released as open-source, making it possible to go through any part of the system, and available for educational purposes.
Spiking allows neurons to estimate their causal effect

Neural plasticity can be seen as ultimately aiming at the maximization of reward. However, the world is complicated and nonlinear and so are neurons’ firing properties. A neuron learning to make changes that lead to the maximization of reward is an estimation problem: would there be more reward if the neural activity had been different? Statistically, this is a causal inference problem. Here we show how the spiking discontinuity of neurons can be a tool to estimate the causal influence of a neuron’s activity on reward. We show how it can be used to derive a novel learning rule that can operate in the presence of non-linearities and the confounding influence of other neurons. We establish a link between simple learning rules and an existing causal inference method from econometrics, yielding proofs of both the correctness of the approach as well as its asymptotic behavior.
Genomics, transcriptomics and CRISPR/CAS9 geneediting approaches to investigate embryonic sexdetermination in insect pest Ceratitis capitata.

During my PhD, I have carried out studies of genomic and transcriptomic in the non-model system Ceratitis capitata. C. capitata (Diptera, Tephritidae), also called “medfly”, is an insect pest that spread over almost every continent and represents a great danger to the cultivation of fruits for human alimentation. Its vast diffusion, together with its ability to parasitize many fruit hosts and the difficulties humans encountered when trying to control and eradicate it from local areas, made C. capitata one of the most dangerous species to agriculture on a global scale, and therefore, to a significant portion of national and international economies. The reproduction and the sex determination are two crucial aspects to understand the biology of insects and represent optimal targets to limit their growth and diffusion. The project of my PhD consists into two parallel and synergic research lines: 1) transcriptomic (Illumina®) and genomic (PacBio®) approaches to the identification of novel Y-linked genes potentially involved in male sex determination, and X-linked genes in “medfly”; 2) the development and perfecting of a powerful technique of gene editing, the CRISPR/Cas9, to study these novel gene functions.
Chemical Analysis of Bioactive Compound Produced by Lactobacillusreuteri Isolated From Domestic Chickens in Iran

The purpose was Chemical analysis of the bioactive compounds produced by Lactobacillus reuteri isolated from domestic chickens. In addition, the antimicrobial property of the bioactive compounds was assessed against pathogenic bacteria. A total twenty two samples were collected from digestive tracts of domestic chickens and subjected to microbiology analysis. The bioactive producing bacterium was identified and the bioactive compound was analyzed by SDS-PAGE and HPLC methods. Finally, antimicrobial property of the bioactive compound against the pathogenic bacteria was assessed. The results obtained indicated that the bioactive compound producing bacterium was Lactobacillus reuteri . The results obtained from SDS-PAGE indicated that the molecular weight of purified bioactive compound produced by the isolatewas3.5< kDa. The bioactive compound showed antimicrobial effect against Escherichia coli, Salmonellatyphimurium, Staphylococcus aureus and Bacillus cereus. Salmonella typhimuriumi and cereus were more and less sensitive to the bioactive compounds. Overall, chemical analysis of the bioactive compounds illustrated that the bioactive compound produced by Lactobacillus reuteri was probably Lactocins.
Carbamate Pesticide Carbaryl Induces Alterations in Antioxidant and Oxidative Stress Related Responses of Indian Buffalo ( Bubalus bubalis ) after Sub-Chronic Exposure

The aim of the present work was to study the alterations of the antioxidant defenses and the overall susceptibility to oxidative stress of the Bubalus bubalis exposed to the carbamate pesticide Carbaryl at the dose rate of 1mg/kg/day for 105 consecutive days produced no observable signs of toxicity in buffalo calves. However, it produced a significant increase in the extent of lipid peroxidation (42.9%) and in the activity of anti-oxidant enzymes namely glutathione peroxidase (39.2%), glutathione reductase (45.3%), glutathione-S-transferase (29%), superoxide dismutase (65%) and catalase (34.5%). On the other hand, carbaryl administration resulted in significant decrease in the blood glutathione level (26%), an important intra-cellular component of defense against oxidative damage, which is indicative of variations in the overall anti-oxidant profile of buffalo calves induced with sub-chronic carbaryl toxicosis. Overall the current results demonstrated the susceptibility of B. Bubalis to oxidative stress induced by the exposure to Carbaryl at an environmentally realistic concentrations, exposing the animal to the risk of oxidative stress damages. The observed responses can be used as sensitive biomarkers for the detection and assessment of effects caused by Carbaryl pesticide exposure.
IDENTIFICATION AND LOCALIZATION OF QUANTITATIVE TRAIT LOCI CONFERRING RESISTANCE TO SHEATH ROT DISEASE AND ITS ATTRIBUTING TRAITS ON LINKAGE MAP AND CHARACTERIZATION OF PATHOGEN [Sarocladium oryzae (SAWADA) GAMS & HAWKSW] CAUSING SHEATH ROT DISEASE IN RICE (Oryza sativa L.)

Sheath rot disease of rice caused by Sarocladium oryzae [(Sawada) W. Gams & D. Hawksw] has emerged as one of the major disease, causing significant qualitative and quantitative yield loss. In the present study screening methods, Genetics, QTLs associated with disease, pathogen variability and the whole genome nucleotide sequence were dissected. Foliar inoculation with conidial suspension of 10 5 conidia/ml and detached tiller assay were found suitable to assess absolute resistance using RILs of BPT5201/HP14. Simple disease severity scoring system and novel disease indices were developed for accurate measurement of disease resistance. Aerobic and wetland systems of rice cultivation had no significant effect on severity and incidence, and maximum incidence in late kharif. Among 31 landraces screened, Dappaneyabilijeddu and male parent HP-14 were highly resistant. Reciprocal F2 populations revealed three complementary genes to control the disease and exhibited the cytoplasmic inheritance. Anthocyanin pigmentation was positively associated with sheath rot and explained significant portion of phenotypic variation, and could serve as phenotypic marker. A strong QTL qShR-12 flanked by SSR marker RM1036 and RM28118 on Chro. # 12 explained 28.26% cumulative phenotypic variation. Geographic isolates of Sarocladium oryzae showed wide variation for colony characters, length of conidiophores and phialades. Virulent strain Saro-13 from Srirangapatna, location was whole genome de nova sequenced using Illumina Nextseq Paired-End sequencing platform and was estimated to be 32.85 Mb, 10526 genes predicted and 10650 SSR markers developed and validated. This is the first report on standardization of screening protocol, genetics, QTL detection using SSR markers and whole genome sequence.