Miracle-dz/UniFAR-FTUs huggingface dataset:
Histone ADP-ribosylation by Poly(ADP-ribose) Polymerase 1 (PARP1) Facilitates Inflammatory Gene Transcription by Directly Altering Nucleosome Structure

The packaging of DNA into nucleosomes imposes obstacles to gene transcription as they limit the accessibility of DNA to the transcription machinery. As such, the modulation of nucleosome structure by histone-modifying and chromatin-remodeling complexes is crucial to facilitate transcription. PARP1 is a chromatin-associated enzyme that is thought to modulate chromatin structure through its nicotinamide adenine dinucleotide (NAD)-dependent enzymatic activity. Recently, PARP1 enzymatic activity has been implicated in the regulation of Nuclear Factor kappa B (NF-κB)-dependent gene transcription and the modulation of the inflammatory response in animal models. Despite accumulating evidence supporting a role for PARP1 enzymatic activity in facilitating gene transcription, the underlying molecular mechanisms are not well understood. The studies described in this dissertation provide mechanistic insight into the role of PARP1 enzymatic activity in the regulation of NF-κB-dependent inflammatory gene transcription. Activation of Toll-like Receptor (TLR) 4-dependent intracellular signaling by stimulation of macrophages with lipopolysaccharide (LPS) induced PARP1 enzymatic activity and histone ADP-ribosylation at accessible chromatin regions. The Extracellular Regulated Kinase (ERK) pathway regulated LPS stimulation-induced PARP1 enzymatic activity and histone ADPribosylation in the absence of DNA damage. In vitro nucleosome remodeling assays revealed that histone ADP-ribosylation, but not poly(ADP-ribosyl)ated PARP1 (pADPr-PARP1), directly destabilized histone DNA-interactions in the nucleosome and increased the accessibility of nucleosomal DNA to
Importance of local scattering in high frequency motion lessons from interpacific project sites, application to the kik-net database and derivation of new hard-rock GMPE

The effective shear wave attenuation, often denoted $Q_{Seff}$, is an important parameter for ground motion simulations. However, this parameter is difficult to measure and is often inferred from rules of thumb (e.g., Q$_{Seff}$=V$_S$/X$_Q$, where X$_Q$ is a scalar value, frequently chosen as equal to 10). The recent work by Laurendeau et al. (2017), aiming to derive consistent hard-rock GMPEs from KiK-net surface and down-hole recordings, shows the shortcomings of such a Q$_{Seff}$-V$_S$ scaling at high frequency using the standard scaling Q$_{Seff}$=V$_S$/10 leads to an overestimation of the local amplification, computed from 1D simulations, at high frequency. We show that this issue is likely related to a too simple description of the velocity profile using a limited number of homogeneous layers. Using invasive measurements from the InterPacific project (Garofalo et al., 2017), we show that 1D simulations based on high resolution velocity profiles (as provided by the PSSL method) lead to a significantly higher effective attenuation at high frequency in comparison with the use of lower resolution velocity profiles (as provided by the down-hole method). This observation is clearly due to the back scattering induced by non-smoothed profiles.We then work on the stiff-soil-to-rock KiK-net sites used by Laurendeau et al. (2017) and we introduce a random perturbation to the former simplified profiles provided for each KiK-net site. These perturbations are consistent from a geostatistical point of view with values found in the literature (even though they were not measured on the KiK-net sites) and on the few InterPacific sites. The 1D simulations with these modified profiles, coupled with the standard Q$_{Seff}$-V$_S$ scaling, were found to well reproduce the high frequency attenuation.A new hard-rock GMPE was then derived from the KiK-net surface recordings corrected for the theoretical site response defined from this optimized simulation, and was compared to the previous results of Laurendeau et al. (2017).
Development and application of multiplexed fluorescence imaging to chemotaxis signalling pathways

ii Author declaration . iii Copyright Declaration. iii Acknowledgements . iv Table of contents . vi List of figures . xii List of tables . xv List of abbreviations . xvi Chapter 0 Thesis Overview . 1 Chapter
Dynamic capabilities of early-stage firms: Exploring the business of renting fashion

In recent years the share economy has gained widespread success across different industries. Since small firms and new ventures obtain fewer resources, an increased focus on service allows them to differentiate and compete with cost pressure in traditionally manufacturing based industries. There still is a lack of understanding how these firms manage to successfully shift towards service-oriented business models. This paper adopts a dynamic capabilities approach to examine the particular microfoundations that underlie sensing, seizing and reconfiguring dynamic capabilities of early-stage service firms within a traditional retail market. The context of this study is the fashion industry. It is an ideal setting since it is characterized by severe competition, short life cycles, strong cost pressure and high volatility. There are few but increasing examples of entrepreneurial initiatives that try to compete by providing offers to resell, rent or swap clothes. Qualitative data of five early-stage fashion ventures is analyzed. Findings reveal that the ability to develop and maintain long-term relationships is essential. It has also been found crucial to acquire knowledge from external network partners, delegate tasks and share information. Furthermore, skills for interacting with customers and adopting consumer feedback are critical. This study provides empirical evidence of dynamic capabilities of early-stage firms and contributes to knowledge on the factors that facilitate servitization in traditionally manufacturing based industries. For practitioners, the presented microfoundations provide a framework of critical tasks that allow them to develop and maintain a service-oriented business model.
The Utility of Cladistic Analysis of Nonmetric Skeletal Traits for Biodistance Analysis

A significant focus of bioarchaeology is biodistance analysis, which seeks to determine the biological affinities of human groups and to support arguments about prehistoric and historic cultural topics, such as migration, marriage, and residential patterns. Although genetic comparisons are becoming more common, metric and nonmetric skeletal traits remain the primary source of information on human populations.Biodistance analysis is grounded theoretically and methodologically in phenetics, which is an approach developed by systematists to group organisms on the basis of overall similarity. However, while phenetics was adopted by physical anthropologists and bioarchaeologists as the foundation of biodistance analysis, systematists have long since moved away from phenetic approaches for determining relatedness to hypothetico-deductively based cladistic analyses. It is time for physical anthropologists and bioarchaeologists engaged in biodistance analysis do so as well.It is perhaps an irony that biodistance analysis, which seeks to delineate the biological relationships of group, begins by defining the groups (samples) on the basis of archaeological, cultural, or linguistic information prior to any morphological/biological comparison. However, the delineation and comparison of groups should be based from the beginning on the biology (morphology) of individuals and then of groups and, more specifically, on unique biological features, not cultural or linguistic criteria. A cladistic analysis can provide a biologically based delineation of groups.In this study I investigate whether unique, nonmetric characters can be delineated for small groups such as those traditionally the focus of biodistance analysis and, thus, whether cladistic analysis is an appropriate substitute for the phenetic approach in biodistance analysis. Four samples of skeletal material were examined. One, the Spitalfields collection, consists of burials of individuals whose familial relationships are well documented. The other samples are undocumented and compared to the Spitalfields sample in an attempt to delineate unique characters that might define groups.The result was that no unique characters could be delineated, which means that cladistic analysis, while perhaps applicable to study of higher-level groups within the species, fails at the population level. Consequently, while unsatisfactory, biodistance analysis must continue to rely on abiological criteria for defining populations.
Evolutionary convergence of body shape and trophic morphology in cichlids from Lake Tanganyika

A recent phylogenetic analysis of mitochondrial DNA sequences from eretmodine cichlids from Lake Tanganyika indicated independent origins of strikingly similar trophic specializations, such as dentition characters. Because genetic lineages with similar trophic morphologies were not monophyletic, but instead were grouped with lineages with different trophic phenotypes, raises the question of whether trophic morphology covaries with additional morphological characters. Here, we quantified morphological variation in body shape and trophically associated traits among eretmodine cichlids using linear measurements, meristic counts and landmark‐based geometric morphometrics. A canonical variates analysis (CVA) delineated groups consistent with dentition characters. Multivariate regression and partial least squares analyses indicated that body shape was significantly associated with trophic morphology. When the phylogenetic relationships among taxa were taken into account using comparative methods, the covariation of body shape and trophic morphology persisted, indicating that phylogenetic relationships were not wholly responsible for the observed pattern. We hypothesize that trophic ecology may be a key factor promoting morphological differentiation, and postulate that similar body shape and feeding structures have evolved multiple times in independent lineages, enabling taxa to invade similar adaptive zones.
Protein Kinase C-θ Participates in the Activation of Cyclic AMP-Responsive Element-Binding Protein and Its Subsequent Binding to the −180 Site of the IL-2 Promoter in Normal Human T Lymphocytes1

IL-2 gene expression is regulated by the cooperative binding of discrete transcription factors to the IL-2 promoter/enhancer and is predominantly controlled at the transcriptional level. In this study, we show that in normal T cells, the −180 site (−164/−189) of the IL-2 promoter/enhancer is a p-cAMP-responsive element-binding protein (p-CREB) binding site. Following activation of the T cells through various membrane-initiated and membrane-independent pathways, protein kinase C (PKC)-θ phosphorylates CREB, which subsequently binds to the −180 site and associates with the transcriptional coactivator p300. Rottlerin, a specific PKC-θ inhibitor, diminished p-CREB protein levels when normal T cells were treated with it. Rottlerin also prevented the formation of p-CREB/p300 complexes and the DNA-CREB protein binding. Cotransfection of fresh normal T cells with luciferase reporter construct driven by two tandem −180 sites and a PKC-θ construct caused a significant increase in the transcription of the reporter gene, indicating that this site is functional and regulated by PKC-θ. Cotransfection of T cells with a luciferase construct driven by the −575/+57 region of the IL-2 promoter/enhancer and a PKC-θ construct caused a similar increase in the reporter gene transcription, which was significantly limited when two bases within the −180 site were mutated. These findings show that CREB plays a major role in the transcriptional regulation of IL-2 and that a major pathway for the activation of CREB and its subsequent binding to the IL-2 promoter/enhancer in normal T cells is mediated by PKC-θ.
Analysis of morphometry and dimorphism in Enhydrus sulcatus (Wiedeman, 1821) (Coleoptera: Gyrinidae)

Enhydrus sulcatus (Wiedeman, 1821) (Coleoptera: Gyrinidae) were found swimming in circles on the surface of streams shaded by forests in preserved sites. The sexual dimorphism was evaluated in that species through the quantification of differences occurring among the length of the first pair of legs, width of the mesonotum, total lengthand body mass of 112 individuals, 71 being females and 41 males. There was significant difference among the width of the mesonotum (KW-H(1.112) = 32.80; p < 0.05), total length (KW-H (1.112) = 38.00; p < 0.05), length of the first leg (KW-H(1.112) = 47.58; p <0.05) and body weight (KW-H (1.82) = 23.86; p < 0.05) of male and female E. sulcatus . The length of the first leg relates positively and significantly with the width of the mesonotum (r2 = 0.40; p < 0.05), with the total weight (r2 = 0.36; p < 0.05) and with the total body length of individuals E. sulcatus (r2 = 0.33; p < 0.05). The total length of individuals of E. sulcatus relates positively and significantly with width of the mesonotum (r2 = 0.65; p <0.05). In this study a clear sexual dimorphism was shown in Enhydrus sulcatus and was present in various other body structures besides the tarsal dilations. Key words: sexual dimorphism, Gyrinidae, Enhydrus sulcatus , measured morphometrics.
Rating the rat: Global patterns and research priorities in impacts and management of rodent pests

We report the results of the first systematic assessment of global patterns and research priorities emerging in the field of rodent pest management. We carried out an extensive literature review targeted towards identifying the most relevant rodent pests, their impacts and the most common methods used to control them. We identified three disproportionally important pest species that are characterized by severe, generalist and geographically widespread impacts: the black rat Rattus rattus, the Norway rat Rattus norvegicus and the house mouse Mus musculus. Overall, only 7% of known rodent species may be considered pests. Scansorial (i.e. terrestrial and semi-arboreal) and fossorial species are generally important as pests, while aquatic and arboreal species have only specific impacts. Impacts of rodent pests on arable crops were studied most, followed by impacts on ecosystems. Studies on arable crops were typical in countries with low net income and health expenditure, while the opposite was observed for studies on ecosystems. Poisons were the most commonly used control method, followed by traps and habitat management. The need to control rodent species is expanding, especially to protect ecosystems and public health. Unlike in other fields of pest management (e.g. insect control), in rodent control we are approaching new problems with old solutions; control strategies and methods have not kept pace with emerging impacts. The need to control a rodent pest species is higher when it is non-native than within its original geographical range. The impact of a rodent species in its native range is a good predictor of the impact it may have in areas of introduction. Our review will contribute towards guiding researchers and stakeholders to focus research efforts and investments on a subset of species, and on new, less hazardous control techniques.
Estudo e Caracterização das Principais Ferramentas para Reconhecimento de Atividade Humana usando Sensores de Acelerômetro

O Human Activity Recognition (RAH) tem como objetivo classificar as atividades realizadas por um usuario coletando dados de sensores heterogeneos. O RAH permite o monitoramento das acoes dos usuarios, oferecendo servicos na area de assistencia medica, no acompanhamento de idosos, acompanhamento de saude, acompanhamento de condicionamento fisico, automacao residencial e do trabalho, entre outros. O RAH pode ser visto como um Sistema de Informacao composto por tres etapas: coleta e pre-processamento de dados, extracao de caracteristicas e classificacao. Apesar da abundância de trabalhos propostos para este assunto, uma questao importante a ser abordada e como escolher as ferramentas e metodos a serem utilizados em cada etapa do RAH. Essa escolha e um processo dificil, porque envolve a comparacao dos resultados obtidos por outros trabalhos, a maioria dos quais usa conjuntos de dados privados, extrai conjuntos diferentes de recursos e usa algoritmos de classificacao diferentes. Este trabalho tem como objetivo caracterizar e comparar as principais ferramentas, metodos e bases de dados para a tarefa RAH. Alem disso, visa fornecer orientacoes e diretrizes para pesquisas futuras na area. Experimentos foram realizados para identificar os principais atributos a serem utilizados na classificacao. Pode-se observar que os atributos media, desvio padrao e variância produzem os melhores modelos para a tarefa de classificacao.
Structure-function relationship of viral cis-acting RNA elements. The role of the ori I and ori R in enterovirus replication.

The genus Enterovirus belongs to Picornaviridae, a family of small, non-enveloped, lytic RNA viruses. They contain a single-stranded RNA genome of positive polarity of approximately 7,500 nucleotides. A viral protein VPg is specifically linked to the 5'terminus of the viral RNA. IRES-mediated initiation of viral RNA translation yields a single polyprotein, which is processed to yield structural and non-structural proteins. The non-structural proteins are involved in viral RNA replication. Enterovirus RNA replication is initiated with the synthesis of a complementary negative RNA strand from virion RNA. Multiple rounds of positive-strand RNA synthesis using the negative-strand as a matrix generates a large pool of progeny RNA, which is encapsidated to produce infectious virus particles. Finally, virus progeny is released into the extracellular medium by cell- lysis. The enterovirus RNA genome contains RNA structures dubbed cis-acting replication elements, which, in concert with replication proteins, have been speculated to regulate RNA replication. The main objective of the studies described in this thesis was to obtain more insight into the functional and structural aspects of two RNA elements, the OriI and the OriR using coxsackie B3 virus as a model. The results indicated that both the OriI and the OriR form RNP complexes to execute their function. Besides encoding part of the enterovirus 2C protein the OriI also serves as the primary template for uridylylation of the peptide primer VPg, required for the initiation of both negative- and positive- strand RNA synthesis. The OriR was found to be a multifunctional RNA element involved in several important steps of the enterovirus life-cycle; i) initiation of negative-strand RNA synthesis, ii) polyadenylation of progeny RNA and iii) enterovirus pathogenicity. Multi-functionality of both the OriI and OriR indicates that the small RNA viruses use their genomes very efficiently to maximize the output of the genetic information
La fracturation lato sensu de l'os et du bois de cervidé : un bref historique des recherches

Le present article propose un bilan historiographique des recherches sur la fracturation de deux matieres dures d'origine animale depuis les premieres interrogations concernant sa reconnaissance a partir des restes osseux au xix e siecle, l'identification de son origine anthropique ou taphonomique au debut du XXe siecle, jusqu'aux recherches ciblees sur ses objectifs, technique et/ou alimentaire, au debut du xxi e siecle. Dans ce but, l'axe de recherche « Ressources animales : acquisition, transformation et utilisation » de l'equipe Ethnologie prehistorique (UMR 7041, ArScAn) a developpe, a partir des annees 2010-2011, une nouvelle dynamique de recherche sur la fracturation. Les travaux menes ont beneficie des recherches anterieures, mais en s'inscrivant plus specifiquement dans une optique tres technique. Cet article est ainsi oriente vers l'exploitation technique de l'os et du bois de cervide et la production de supports potentiels pour des outils dits « peu elabores ». Mais s'interesser a cet objectif amene necessairement a poser la question de la fracturation d'origine alimentaire des os puisqu'on considere souvent qu'ils etaient avant tout casses dans le but de recuperer la moelle contenue dans les diaphyses. Ce sont les differentes facettes de la fracturation sensu lato de l'os et du bois animal qui sont traitees ici (la coquille, le bois vegetal et l'ivoire sont presentes plus loin dans ce volume). Ce bilan ne pretend pas a l'exhaustivite car la profusion des documents est telle, depuis le XIXe siecle jusqu'a nos jours, qu'un seul ouvrage n'y aurait pas suffi.
Contribution of Inorganic Phosphorus Fractions to Plant Nutrition in Alkaline-Calcareous Soils

To evaluate the relationships between soil inorganic phosphorus P (Pi) fractions, the soil P test and plant parameters such as plant P uptake, dry matter yield, tissue P concentration and relative yield, glasshouse experiments and chemical analyses were conducted on 13 calcareous soils from six agricultural and seven adjacent bushland (virgin soil) sites. Four rates of P (0, 15, 30, 60 mg/kg soil) were applied as reagent-grade KH2PO4 to the soils in a randomised complete block design with three replications. Perennial ryegrass (Lolium perenne cv. Roper) was grown and forage was harvested five times over a period of 210 days. Successive harvesting resulted in the depletion of plant available P as measured by NaHCO3-extractable P, which coincided with the decrease in the plant dry matter yield and P uptake. After five harvests, the order of reduction in Pi fractions induced by cropping without added P was Ca10-P>Al-P>Ca2-P>Ca8-P>occluded-P>Fe-P for the virgin soils and Ca2-P>Al-P>Ca10-P>Ca8-P>Fe-P>occluded-P for the agricultural soils. The order of abundance of Pi fractions for P treated-soils was non-occluded Al and Fe phosphate (Al-P+Fe-P)>secondary Ca-bound P (Ca2-P+Ca8-P)>acid-extractable P (Ca10P)>occluded-P for both virgin and agricultural soils. Although a marked proportion of added P was transformed into less soluble Al and Fe phosphates, successive harvesting had depleted considerable percentages of these fractions. Highly significant (p<0.001) relationships were found for P uptake vs. Olsen-P, P uptake vs. Pi fractions (Ca2-P, Ca10-P, Al-P, Ca8-P, Fe-P) and Olsen-P vs. Pi fractions. NaHCO3-extractable P seems to be adequate for evaluating plant available P in calcareous soils. However, the closer relationship for the Fe-P fraction vs plant P uptake than for Olsen-P versus plant P uptake indicates that NaHCO3 may not provide the best estimate of plant available P for calcareous soils. Using stepwise regression analysis, it was found that the Ca2-P fraction was most predictive of P uptake (60%), total dry matter (68%), relative yield (74%) and Olsen-P (69%), followed by the Fe-P fraction.