Miracle-dz/UniFAR-FTUs huggingface dataset:
Diseño de un banco de pruebas híbrido para la investigación de seguridad y resiliencia en redes industriales

Resumen—Las redes industriales son entornos interconectados dirigidos a controlar equipamiento fı́sico en entornos industriales. Dada la dificultad de realizar investigación de seguridad en entornos industriales reales, principalmente por el potencial peligro derivado de la interacción con equipamiento fı́sico, los bancos de pruebas son ampliamente utilizados. En estre trabajo, presentamos un banco de pruebas hı́brido, que utiliza diferentes técnicas de implementación: implementación en hardware, emulación, simulación y virtualización. Para ello, se vale del software Emulab y el proceso simulado Tennessee-Eastman (TE). Emulab permite la emulación dinámica de la capa de red y virtualiza los nodos que lo componen, mientras que el proceso TE posibilita estudiar los efectos de diferentes situaciones en el plano fı́sico de forma segura. Además, el banco de pruebas cuenta con soporte para redes definidas por software e integra un módulo de análisis de datos a gran escala, lo que permite el diseño de experimentos de ciberseguridad relacionados con estas tecnologı́as. Palabras clave—banco de pruebas, seguridad en entornos industriales, redes definidas por software, redes industriales
Regulation of pancreatic and intestinal endocrine cell differentiation and function : roles of Pak3 and Rfx6

Pancreatic and intestinal endocrine cells, and their secreted hormones, contribute to the regulation of energy homeostasis. Their differentiation relies on similar genetic programs controlled by the proendocrine transcription factor Ngn3. However, our knowledge of the endocrinogenic programs implemented by Ngn3 is still fragmentary. Therefore, the transcriptome of endocrine progenitors has been determined in the lab. Among the genes which showed a strong enrichment in the endocrine lineage, I studied the expression and function of Pak3, a serine/threonine kinase and further pursued the dissection of the function of the transcription factor Rfx6 in the pancreas and the intestine. I showed that Pak3 is expressed throughout pancreas development and maintained in adult islets. Using ex vivo loss of function experiments and in vivo characterisation of the Pak3-deficient mice, I identified Pak3 as an inhibitor of islet progenitors and beta-cell proliferation in the embryonic mouse pancreas. Furthermore, we performed metabolic studies which revealed that Pak3-deficient micehave an impaired glucose homeostasis, especially under challenging high fat diet. In parallel, using a conditional knockout mouse for Rfx6, we showed that Rfx6 is necessary downstream of Ngn3 for endocrine cell differentiation in the pancreas as well as in the intestine. Finally, additional experiments in adult mice suggest that Rfx6 is necessary to maintain pancreatic beta-cells, enteroendocrine cell turnover and intestinal lipid absorption. In conclusion, these studies revealed two novel key players in the regulation of endocrine cell differentiation and energy homeostasis in the pancreas and the intestine.
Molecular phylogeny of the genus Hordeum and origins of Hordeum polyploidy species

The phylogeny of the diploid species in the genus Hordeum has been studied intensively, however, there has been incongruences between nuclear and chloroplast datasets. In addition, the origins of polyploid species in Hordeum remain unclear. The aims of the present study are to: 1) Investigate the phylogeny ofHordeum diploid species. 2) Investigate the origins of Hordeum polyploids, with combined genetic information from both chloroplast and nuclear datasets. Thirty two Hordeum species from eighty accessions were used in this study. In total 214 sequences from three single copy nuclear genes and two chloroplast regions were obtained. Both nuclear and chloroplast phylogenies of Hordeum diploids are supported by previous studies, and our study suggests the major incongruence between them could be explained by incomplete lineage sorting. For polyploids, our study confirms H. brachyantherum subsp. californicum is the parent of H. brachyantherum subsp. brachyantherum and H. depressum. The present study does not favor previous results that H. roshevitzii is the possible parent of H. tetraploidum and H. fuegianum. Instead, this study suggests H. brevisubulatum is the possible genome donor to tetraploids H. brachyantherum subsp. brachyantherum, H. tetraploidum, H. fuegianum and hexaploids H. lechleri and H. procerum. The present study also suggests the other genome donor of H. tetraploidum and H fuegianum might come from H patagonicum species. The diploid H. pusillum is further confirmed as the maternal parent of H. arizonicum in the present study. Previous suggestion on H. tetraploidum as the possible tetraploid genome donor of H. parodii and H. procerum is supported by our study. In addition, the study also suggests H. flexuosum is one possible genome donor of hexaploid H. parodii.
Neurospora: Contributions of a Model Organism

Preface 1. A Brief History 2. The Biology of Neurospora 3. Genome and Mitosis 4. Meiosis, Genetic Analysis, and Recombination Models 5. Mutational, Biochemical, and Molecular Rationales 6. Carbon Metabolism 7. Nitrogen, Sulfur and Phosphate Metabolism 8. Mitochondria 9. DNA, RNA, and Protein Synthesis 10. Stress 11. Metabolic Investigations 12. Growth and Form 13. Cell Recognition, Population Biology and Evolution 14. Genetic, Biochemical, and Molecular Techniques Appendix A. Neurospora Genetic Nomenclature Appendix B. Genetic Maps of N. crassa
Community and trophic responses of benthic Foraminifera to oxygen gradients and organic enrichment

Global warming and eutrophication are driving an expansion of hypoxia in the World Ocean. This will favour organisms, such as Foraminifera (testate protists), that tolerate low-oxygen conditions and may lead to an overall decline in marine biodiversity. With this in mind, community and trophic responses of benthic Foraminifera were investigated at two contrasting sites in the upper boundary (140 m water depth; bottom-water oxygen concentrations = 2.05 mll-1 during the spring intermonsoon and 0.11 mll-1 during the SW monsoon) and the core (300 m water depth; bottom-water oxygen concentration consistently ~ 0.11 mll-1) of an intense, natural, mid-water oxygen minimum zone (OMZ) on the Pakistan Margin, NE Arabian Sea. Live macrofaunal (>300 µm fraction) Foraminifera (including softwalled species) and metazoans were examined at each site during the 2003 spring intermonsoon (April) and SW monsoon (October) seasons (4 replicate multicores/site/season, 25.5cm2 surface area, 0-5 cm depth). Wet-sorting revealed a low diversity assemblage dominated (> 60 %) by calcareous Foraminifera at both sites. A total of 36 species was recognised and diversity was not greatly affected by water depth or season. At both sites, >86 % of Foraminifera were restricted to the upper 0-1 cm layer of sediment and the Average Living Depth (ALD) decreased from the spring intermonsoon to the SW monsoon (140 m, ALD5 = 0.41 to 0.33; 300 m, ALD5 = 0.65 to 0.44). Foraminifera increased in mean abundance from 124 to 153 individuals per 10 cm2 from the spring intermonsoon to the SW monsoon at 140 m and from 86 to 122 individuals per 10 cm2 at 300 m. The calcareous species Uvigerina ex. gr. semiornata dominated communities and increased in mean abundance from 54 to 118 individuals (140 m) and from 41 to 69 individuals (300 m) per 10 cm2 following the SW monsoon. At 140 m, Foraminifera were 3.6 times more abundant than metazoans during the spring intermonsoon, rising to 13.9 times during the SW monsoon. The corresponding proportions at 300 m, where metazoans were rare, were 12.4 and 14.5. Fatty acid biomarkers suggest that foraminiferal diets vary between species. The calcareous species U. ex. gr. semiornata, Bolivina aff. dilatata and Globobulimina cf. G. pyrula selectively ingested phytodetrital material, whereas the agglutinated species, Ammodiscus aff. cretaceus, Bathysiphon sp. nov. 1, and Reophax dentaliniformis favoured bacteria. Moreover, U. ex. gr. semiornata, rapidly ingested (within two days) 13C-labelled diatoms in shipboard laboratory and in situ pulse-chase experiments at the 140-m site following the SW monsoon. This enabled the uptake and processing of organic matter (OM) to be tracked in the foraminiferal cell into individual fatty acids, using Gas Chromatography - Mass Spectrometry (selective ion scan). These results suggest that calcareous Foraminifera, in particular U. ex. gr. semiornata, play a central role in OM cycling on the sea-floor in the upper part of the Pakistan margin OMZ.
GENETIC EVIDENCE OF ROTAVIRUS IN CHICKEN FROM TWO LOCALITIES IN SOUTHWESTERN NIGERIA

The presence of rotavirus in some poultry flocks in Abeokuta and Oyo was evaluated using the reverse transcription-polymerase chain reaction (RT-PCR) technique. A total of 49 fecal samples in form of cloacal swabs were collected from chickens and turkeys with age groups ranging between 5days and 43weeks. Six samples from diarrheic chicken aged 8 and 9 days old were positive for the virus, while others were negative. To our knowledge, this is the first study to report rotavirus infection in Nigerian poultry. It is recommended that epidemiological surveys be carried out to provide more data on rotavirus infection in poultry flocks in Nigeria.
Fodder yield and quality of ryegrass (Lolium perenne) grown pure and in mixture with different seed rates of oat (Avena sativa) and sarson (Brassica campestris)

The experiment was conducted during rabi 2002-03 to 2005-06 to get higher fodder yield of ryegrass in the first cut and to see the effect of oat and sarson crops sown at different seed rates on the succeeding cuts. The experi- ment consisted of nine treatment combinations viz., ryegrass-monoculture, ryegrass + oats (22.5, 30.0, 37.5 and 45.0 kg/ha), and ryegrass + sarson (0.625, 1.25, 1.875 and 2.5 kg/ha) conducted in a randomized block design with four replications. The addition of oats at the rate of 22.5, 30.0, 37.5 and 45.0 kg/ha and sarson at the rate of 0.625 kg, 1.25 kg, 1.875 kg and 2.50 kg/ha with full seed rate of ryegrass increased green fodder yield by 14.3, 21.1, 25.1 and 27.2% and; 22.6, 33.7, 54.5 and 63.1%, respectively over the ryegrass monoculture. The addition of different seed rates of oats and sarson had no adverse effect on the fodder yield of subsequent cuttings. Sarson contributed 60 to 81% in the first cutting and oats contributed 22 to 60% in first cutting and 7 to 15% in second cut- ting in mixture with ryegrass. The highest net returns (Rs 49,398/ha) and benefit: cost ratio (2.12) were obtained with berseem + 2.5 kg/ha sarson mixture. The uptake of N by ryegrass + oats/sarson mixtures were higher than pure ryegrass. Crude protein and in vitro dry matter digestibility contents were higher in pure crop of ryegrass in first cutting and the trend was reverse in subsequent cuttings.
Handbook for Rhizobia: Methods in Legume-Rhizobium Technology

Rhizobia are bacteria which inhabit the roots of plants in the pea family and "fix" atmospheric nitrogen for plant growth. They are thus of enormous economic importance internationally and the subject of intense research interest. Handbook for Rhizobia is a monumental book of practical methods for working with these bacteria and their plant hosts. Topics include the general microbiological properties of rhizobia and their identification, their potential as symbionts, methods for inoculating rhizobia onto plants, and molecular genetics methods for Rhizobium in the laboratory. The book will be invaluable to Rhizobium scientists, soil microbiologists, field and laboratory researchers at agricultural research centers, agronomists, and crop scientists.
Isolation and characterization endonuclease EclHKI from an cloacae strain of restriction Enterobacter

An Enterobacter cloacae strain, producing restriction enzyme Ec]HKI, was isolated from a decaying potato. The enzyme is an isoschizomer of Eam1105I, which recognizes and cleaves GACNNNINNGTC. Ec]HKI was produced at high activity (4 x 104 U/g wet cells) and was purified from contaminants which interfere with restriction digestion by passing the cell lysate through DEAE-Sephacel and heparin columns. Activity was optimal at 37°C in a medium salt buffer.
Characterization of the endosymbiotic forms of sinorhizobium sp. Strain NGR234

In association with legumes, symbiotic nitrogen fixation by rhizobia is a major contributor to the combined pool of assimilable nitrogen in the biosphere. It takes place in specialized root- or stem-organs called nodules, in which large polyploid nodule cells house thousands of endosymbiotic nitrogen-fixing bacteroids. Our model system, Sinorhizobium sp. strain NGR234, is a promiscuous bacterium capable of forming nodules on more than 150 genera of legumes and fixing nitrogen in many nodules of determinate type (DNs) as well as indeterminate type (IDNs). By combining microscopy and cytology we have examined the fate of bacteroids of NGR234 in distinct host backgrounds. The regulatory networks that govern gene expression in bacteroids were also explored, particularly the BxqH-regulon which is under the control of a LuxR-like regulator. Finally we also examined the role in symbiosis of a second type-three secretion system (T3SS-II) that was identified during the analysis of the NGR234 genome.
Demographic characteristics of molting black brant near Teshekpuk Lake, Alaska

-Molting Brant (Branta bernicla) in the Teshekpuk Lake Special Area (TLSA) on the Arctic Coastal Plain of Alaska were studied from 1987 to 1992 using capture-mark-recapture techniques to determine origin, age and sex composition, return rates and site fidelity. Brant originated from 10 nesting colonies in Canada and Alaska. The captured birds were 76% adults and 57% males. Ninety-one percent of known-age recaptures were <6-yr-old. Fewer 1-yr-olds and more 2-yr-olds were present than expected. Sixty-one percent of adult females were failed breeders. Brant were not segregated by nesting colony on lakes in the TLSA, but those returning exhibited high site fidelity (T = 0.945) to the lake of initial capture. Recapture rates for Brant banded in the Teshekpuk area were greater ('r = 0.156) than for Brant banded at nesting colonies. Highest recapture rates (T = 0.059) of Brant banded at nesting colonies were from those located closest to the molting area. CARACTERiSTICAS DEMOGRAFICAS DE INDIVIDUOS DE BRANTA BERNICLA DURANTE EL PERIODO DE MUDA CERCA DEL LAGO TESHEKPUK, ALASKA Sinopsis. -De 1987 a 1992 se estudiaron individuos de Branta bernicla en el Lago Teshekpuk de Alaska, durante el periodo de muda de las aves. Se utiliz6 el metodo de marca y recaptura para determinar el origen, edad, composici6n sexual, tasa de retorno y fidelidad a la localidad de estos gansos. Las aves se originaron de 10 colonias de anidamiento en Canada y Alaska. De las aves capturadas el 76% resultaron ser adultos y el 57% machos. El 91% de las aves de edad conocida fue menor a 6 afios. Se encontr6 un ndmero menor de individuos de un afno y un numero mayor de individuos de dos afios, a lo esperado. El 61% de las hembras capturadas fracas6 en reproducirse. Los gansos no estuvieron agregados por colonias reproductivas en los lagos de Teshekpuk. Sin embargo, aquellos que regresaron exhibieron una alta fidelidad (P = 0.945) al lago en donde fueron capturados. La tasa mas alta de recaptura (T = 0.059) de aves anilladas en colonias de anidamiento fue de aquellos individuos localizados cerca de los lugares de muda. Few waterfowl studies have focused on molt migration, although this behavior has been attributed to seven of 13 tribes in the Anatidae (Hohman et al. 1992, Salomonsen 1968). Brant (Branta bernicla) are coastal marine geese that nest in colonies in Alaska, Canada and Siberia (Derksen and Ward 1993). Some Brant, which do not attempt to nest or that fail at nesting, migrate to remote, high arctic areas before molting (King 1970, Uspenski 1965). The largest known concentration of molting Brant is in the Teshekpuk Lake area on Alaska's Arctic Coastal Plain that annually supports '22% of the Pacific Brant (B. b. nigricans) population during the summer molt period (R. J. King, unpubl. data). King and Hodges (1979) reported band recoveries from this population and suggested that all non-breeding Brant from nesting areas north of the Bering Strait in Alaska, Canada and Siberia molted in the Teshekpuk Lake area. An international marking program at nesting colonies in Canada and
Microclimate and vegetation function as indicators of forest thermodynamic efficiency

Summary 1. Resilient and functional landscapes are essential for climate change adaptation. Thermodynamic theory has been applied increasingly to ecological studies to understand ecosystem resilience and integrity. Resilient ecosystems have complex structure and greater levels of biomass and functional diversity, which act to enhance the degradation of solar energy. Forests that exhibit these characteristics express thermodynamic efficiency through a greater capacitance effect that promotes cooler surface temperatures under extreme weather conditions. 2. With forest disturbance, complex structures and functional linkages are simplified, reducing the capacity of the system to degrade energy. Such changes can lead to dysfunctional ecosystem states, impaired provision of ecosystem services and a weakened resilience. 3. This study has applied indicators based on thermodynamic theory to a chronosequence of forest ecosystems in the UK, Germany and Ukraine. Surface temperatures were measured to test thermodynamic theories relating to energy degradation and temperature moderation. Grime’s CSR model was applied to plant data to compare functional complexity in vegetation between stands. 4. Old-growth woodlands are shown to attenuate surface temperature more effectively than native species plantations. Consistently lower temperatures were observed in European old-growth forests with high proportions of biomass when compared to managed stands of similar species composition, suggesting a greater efficiency of energy degradation in complex forest ecosystems, particularly at higher temperatures. 5. Analysis of plant species data using Grime’s CSR model indicated that old-growth forests ordinate towards competitive and stress-tolerant communities in contrast to intensively managed forests, which had a greater proportion of generalist and ruderal species. High CSR functional scores were associated with moderated temperature extremes. 6. Synthesis and applications. Our results suggest an important thermodynamic basis for conservation in the context of climate change. Conservation practice and management policy, which is based on preserving ecosystem complexity and function, can aid in mitigating the effects of extreme temperatures, enhancing vital services such as climate regulation, primary production and water retention. Old-growth forests have a significant climate mitigation role alongside other recognised ecosystem services such as carbon sequestration.
Production of bioactive peptides through sequencial action of Yarrowia lipolytica proteases and chemical glycation

This PhD thesis is aimed at studying the suitability of proteases realised by Yarrowia lipolytica to hydrolyse proteins of different origins available as industrial food by-products. Several strains of Y. lipolytica have been screened for the production of extracellular proteases by zymography. On the basis of the results some strains released only a protease having a MW of 37 kDa, which corresponds to the already reported acidic protease, while other produced prevalently or only a protease with a MW higher than 200 kDa. The proteases have been screened for their "cold attitude" on gelatin, gluten and skim milk. This property can be relevant from a biotechnological point of view in order to save energy consumption during industrial processes. Most of the strains used were endowed with proteolytic activity at 6 °C on all the three proteins. The proteolytic breakdown profiles of the proteins, detected at 27 °C, were different related to the specific strains of Y. lipolytica. The time course of the hydrolysis, tested on gelatin, affected the final bioactivities of the peptide mixtures produced. In particular, an increase in both the antioxidant and antimicrobial activities was detected when the protease of the strain Y. lipolytica 1IIYL4A was used. The final part of this work was focused on the improvement of the peptides bioactivities through a novel process based on the production of glycopeptides. Firstly, the main reaction parameters were optimized in a model system, secondly a more complex system, based on gluten hydrolysates, was taken into consideration to produce glycopeptides. The presence of the sugar moiety reduced the hydrophobicity of the glycopeptides, thus affecting the final antimicrobial activity which was significantly improved. The use of this procedure could be highly effective to modify peptides and can be employed to create innovative functional peptides using a mild temperature process.
Fusing Infrared and Visible Images for DNN-based Nighttime Human Detection

The accurate human detection based on artificial intelligence plays a crucial role in various applications such as selfdriving and augmented reality. In poor lighting conditions, infrared images are more suitable than visible light images. However, infrared images-based human detection has many shortcomings and improving infrared images-based human detection is still a fundamental task. In this study, three types of pre-processing are applied to infrared images to improve the accuracy of deep learning-based human detection. To further improve the accuracy, we propose an image fusion algorithm using both visible and infrared images. Experimental results show that the proposed method performs better than conventional methods.
Characterization of Mice with Altered Dopamine Transporter and Vesicular Monoamine Transporter 2 Levels

Dopamine is a key neurotransmitter that regulates motor coordination and dysfunction of the dopamine system gives rise to Parkinson’s disease. Nigrostriatal dopamine neurons are vulnerable to various genetic and environmental insults, suggesting that these cells are inherently at-risk. A cell-specific risk factor for these neurons is the neurotransmitter, dopamine itself. If intracellular dopamine is not appropriately sequestered into vesicles, it can accumulate in the cytosol. Cytosolic dopamine is highly reactive and can trigger oxidative stress, leading to cellular toxicity. Cytosolic dopamine levels are modulated by the plasma membrane dopamine transporter (DAT) that takes up dopamine from the extracellular space, and the vesicular monoamine transporter 2 (VMAT2) that stores dopamine into vesicles. In this thesis, we altered DAT and VMAT2 levels to investigate the detrimental consequences of potentially amplifying cytosolic dopamine in transgenic mice. Project 1 focused on selective over-expression of DAT in dopaminergic cells of transgenic mice (DAT-tg). DAT-tg mice displayed phenotypes of dopaminergic damage: increased dopamine-specific oxidative stress, L-DOPA-reversible fine motor deficits and enhanced sensitivity to toxicant insult, suggesting that increasing DATmediated dopamine uptake is detrimental for dopamine cells. As an extension of Project 1,