Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-equilibrium upscaling of compositional transport

Reservoir simulation is a broadly used tool in the oil and gas production industry. It can be used for production history matching, performance forecasting and field development. A common Enhanced Oil Recovery (EOR) method is the injection of miscible gases. With the injection of gas into an oil reservoir, the system has to be considered as multiphase and multicomponent. Compositional simulation gives an accurate representation of the physics of multiphase and multicomponent systems. Solving the system at a high resolution with the compositional description is computationally very intensive. Simulating at a lower resolution with a coarse grid reduces the computational loads, but it becomes less accurate. Upscaling procedures are used to convert the high resolution, fine scale simulation parameters to lower resolution, coarse scale simulation parameters. In this research, an upscaling procedure is examined that uses a thermodynamic non-equilibrium correction to keep a high accuracy for the coarse scale compositional simulation. This non-equilibrium phenomena is represented by a source term in the thermodynamic equilibrium equation. This source term is obtained from a fine scale simulation and upscaling the phase compositions. The source terms are tabulated against the composition and are used in the coarse scale simulation. An isothermal system with number components and number of phases is considered in this research. The capillary and diffusive effects are neglected as well as the chemical reactions and adsorption. For the fine scale, a 2D grid of 102x20 is used and the coarse scale grid is 1D with 102x1 cells. The fine scale simulation is run using Automatic Differentiation General Purpose Research Simulator (AD-GPRS) and the coarse scale simulation is run with an IMPEC simulator written in Matlab. To quantify the accuracy of the coarse scale simulation a misfit value is calculated between the coarse scale saturation distribution and the upscaled fine scale saturation distribution. Comparing the coarse saturation distribution with the upscaled saturation distribution shows that this method allows high accuracy results to be maintained with non-equilibrium upscaling of the compositional flow. A correlation is made between the source term and composition and used in a coarse simulation instead of the tables created from the fine scale simulation. This reduces the accuracy compared to the fine scale, but it still gives a satisfactory improvement of coarse scale results. To improve the accuracy of the simulation using the correlation, an optimization procedure is performed. The optimization improved the accuracy to the level of the accuracy of the simulation using the full source term tables. With a correlation between the source term and composition, the global fine scale compositional solution is no longer necessary for the coarse simulation.
Systems approach to analyzing the TGFbeta/SMAD3 gene regulatory pathway in A549 cells

Public Health Significance: Idiopathic pulmonary fibrosis (IPF) is a devastating lung disease affecting over 100,000 people every year in the U.S. There is no prevention, cure, or effective treatment for the disease, and the life expectancy after diagnosis is about 3 years. The disease is characterized by progressive and irreversible deposition of fibrotic proteins in the lung. The etiology of the disease is poorly understood, but there is abundant evidence the pro-fibrotic cytokine transforming growth factor beta (TGFb) plays a major role in the disease process. TGFb acts principally through the DNA-binding transcription factor SMAD3. The research presented here may lead directly to new pharmacological interventions for IPF, thereby substantially decreasing morbidity and mortality rates for the disease.To gain new insights into how the TGFb/SMAD3 transcriptional regulatory pathway might promote pulmonary fibrosis, I combined high-throughput molecular biology measurements with systems biology computational tools to study transcriptional regulation of the TGFb/SMAD3 pathway in A549 alveolar epithelial cells. The first tier of measurement consisted of chromatin immunoprecipitation combined with whole-genome promoter microarrays (ChIP-on-chip). This technique globally identifies the promoter regions of genes bound by the SMAD3 transcription factor. A second tier of systems-wide information consisted of whole-genome gene expression microarrays, which measures levels of mRNA activated by the TGFb/SMAD3 pathway. These two tiers of transcription information were integrated and analyzed using systems biology computational tools. The analysis yielded three novel findings. The first is that the TGFb/SMAD3 pathway transcriptionally regulates transgelin, a protein that signifies the TGFb-induced transition of epithelial cells into collagen-secreting myofibroblasts. The second is that the TGFb/SMAD3 pathway also regulates the transcription factor FOXA2, which plays a major role in lung development and surfactant production. The third is possible TGFbeta/SMAD3 transcriptional regulation of PINX1, which is a potent suppressor of telomere reverse transcriptase (hTERT). All three of these proteins are mechanistically linked to genes or processes that are already suspected of being involved in the pathophysiology of IPF. Thus, a systems-level approach to studying transcriptional regulatory networks is a valuable tool for discovering new biological pathways or new connections between known biological pathways.
Phytophthora ramorum in England and Wales: which environmental variables predict county disease incidence?

Summary Phytophthora ramorum is the oomycete pathogen responsible for Sudden Oak Death on the West Coast of the USA and Sudden Larch Death in the British Isles. It also causes twig dieback and leaf blight on a series of ornamental hosts (e.g. Rhododendron, Viburnum, Pieris and Camellia) commonly grown in plant nurseries, traded by garden centres and cultivated in public and private gardens. The role of the plant trade in the dispersal of P. ramorum has been well documented, but there is a need for regional analyses of which environmental variables can predict disease expression in the trade and in the wild, so as to be able to better predict the further development of this worldwide plant health issue. In this study, we analyse data on the incidence of P. ramorum (2002–2009, thus before the reports in Japanese larch plantations) in counties in England and Wales as a function of environmental variables such as temperature and rainfall, controlling for confounding factors such as county area, human population and spatial autocorrelation. While P. ramorum county incidence in nurseries and retail centres was positively related to county area and human population density, county incidence in gardens and the wild did not show such correlations, declined significantly towards the East and was positively correlated with disease incidence in the trade. The latter finding, although not conclusively proving causation, suggests a role of the trade in the dispersal of this pathogen across English and Welsh landscapes. Combined together, P. ramorum county incidence in the trade and in the semi-natural environment increased with increasing precipitation and with declining latitude. This study shows the importance of environmental variables in shaping regional plant epidemics, but also yields results that are suggestive of a role of people in spreading plant diseases across entire countries.
Modelling the energy budget and prey choice of eider ducks

We developed an energy and heat budget model for eider ducks. All relevant processes have been quantified. Food processing, diving costs, prey heating, the costs of crushing mussel shells, heat losses during diving as well as during resting, and heat production as a result of muscle activity are distinguished. In the report, blue mussels are regarded as food source, and we computed the profitability of small to large sized mussels for a duck. Finally, the possibility for a duck to survive winter conditions when feeding on a mussel population with a known size frequency distribution is calculated during a simulation run. Conditions for four sites in The Netherlands, France, Denmark and Sweden are regarded and there implications for the foraging behaviour of an eider duck are computed. The implications of the presence of barnacle epibionts are briefly discussed.
Resource characteristics and stock assessment of whitebaits

The fishery of whitebait for 1979-88 was studied. The southern maritime states accounted for 97% of the country's whitebait landings. The quartelWise whitebait landings, gearwise catch and catch per unit effort for 1985-88 were studied and discussed. Encrasicholina devisi and Stolephoru. , waitei were the dominant species in the whitebait fishery. The fishery and biological characteristics of these two species at Visakhapatnam, Madras, Vizhinjam, Cochin and Mangalore are presented. Whitebait are short-lived fish, the longevity of E. devisi being 1.9 years and that of S. waite; about 2.3 years. Both the species get recruited into the fishing ground at about 30-35 mrn total length when 2-3 months old. The fish from 40-55 mm length onwards (3-5 months old) are caught in greater abundance. The major bulk of the annuallalldings is constituted by 6-15 months old fish. The growth parameters, mortality rates and exploitation ratios of the two species were estimated for both the coasts. Critical evaluation of the maximum sustainable yield (MSY) estimates in relation to biomass at MSY level indicilted the possible increase in production of E. devi.fi by about 20% over the current yield with higher effort input along the west coast. For E. devi. ,i in the east coast and S. waitei in both the coasts, the expected increase was only marginal.
Evaluation of detergents for the soluble expression of α‐helical and β‐barrel‐type integral membrane proteins by a preparative scale individual cell‐free expression system

Cell‐free expression has become a highly promising tool for the fast and efficient production of integral membrane proteins. The proteins can be produced as precipitates that solubilize in mild detergents usually without any prior denaturation sttif. Alternatively, membrane proteins can be synthesized in a soluble form by adding detergents to the cell‐free system. However, the effects of a representative variety of detergents on the production, solubility and activity of a wider range of membrane proteins upon cell‐free expression are currently unknown. We therefore analyzed the cell‐free expression of three structurally very different membrane proteins, namely the bacterial α‐helical multidrug transporter, EmrE, the β‐barrel nucleoside transporter, Tsx, and the porcine vasopressin receptor of the eukaryotic superfamily of G‐protein coupled receptors. All three membrane proteins could be produced in amounts of several mg per one ml of reaction mixture. In general, the detergent 1‐myristoyl‐2‐hydroxy‐sn‐glycero‐3‐[phospho‐rac‐(1‐glycerol)] was found to be most effective for the resolubilization of membrane protein precipitates, while long chain polyoxyethylene‐alkyl‐ethers proved to be most suitable for the soluble expression of all three types of membrane proteins. The yield of soluble expressed membrane protein remained relatively stable above a certain threshold concentration of the detergents. We report, for the first time, the high‐level cell‐free expression of a β‐barrel type membrane protein in a functional form. Structural and functional variations of the analyzed membrane proteins are evident that correspond with the mode of expression and that depend on the supplied detergent.
Activité constitutive et adressage axonal du récepteur cannabinoïque neuronal CB1

L'activite constitutive est une propriete pharmacologique que possedent de nombreuxrecepteurs couples aux proteines G. Cependant, son role biologique reste largement inconnu.Nous avons etudie les relations entre la pharmacologie et le trafic intracellulaire du recepteurcannabinoique CB1, un recepteur abondamment exprime dans le cerveau qui possede uneactivite constitutive averee. Exprime dans les cellules HEK-293, l'activite constitutive durecepteur CB1 provoque un cycle continu d'endocytose et de recyclage du recepteur entre lamembrane plasmique et les endosomes intracellulaires : a l'equilibre, le recepteur CB1 estmajoritairement present dans les endosomes. Le cycle fait intervenir une endocytose par puitsrecouverts de clathrine et un trafic intracellulaire dependant de Rab5 et de Rab4, mais pas deRab11. Dans les neurones d'hippocampe en culture, ce cycle d'endocytose/recyclage durecepteur CB1 est limite au compartiment somatodendritique, et le recepteur est stable a lasurface de l'axone. Ce cycle depend de l'activite constitutive du recepteur CB1 etl'endocytose selective du recepteur dirige l'etablissement de l'expression axonale durecepteur CB1 a la surface du neurone.
Microscopic swimming in biological fluids

Fluid interactions are ubiquitous in the natural world; all organisms must find strategies to generate, utilise or resist flow in order to be successful. A process fundamental to all life on earth is reproduction, which in many cases entails the swimming of sperm cells. Cell swimming arises from coupled interactions between physical and biological processes. We will focus on the effects of changing fluid rheology onmicroscopic swimmers, with a particular application to the study of internal mammalian fertilisation. To reach the egg, mammalian sperm must navigate the convoluted geometry of the female reproductive tract, actively bending their flagella in order to propel themselves through cervical mucus: a suspension of polymer chains that twist, tangle and align with flow, giving it complex properties. Whilst recent work has examined the effects of fluid viscoelasticity on sperm-like swimmers, relatively less attention has been given to the shear-thinning property. We develop a new finite element technique to simulate free swimmers with prescribed beat kinematics in shear-thinning fluids with nonlinear governing equations. This technique is then applied to three qualitatively different viscous swimmers in order to examine the different phenomena that arise from swimmer interactions with of shear-thinning fluid.
Die Scyphomedusen-Sammlung des naturhistorischen Reichsmuseums in Leiden : I. Die Carybdeiden (Cubomedusen)

EINLEITUNG. Die in der vorliegenden Mitteilung besprochenen Cubomedusen bilden einen kleinen gut abgegrenzten Teil der grossen Scyphomedusen-Sammlung des Rijksmuseums van Natuurlijke Historie in Leiden, uber welche zu einem spateren Zeitpunkte ausfuhrlich berichtet werden wird. Von diesen aberranten und seltenen Formen liegt eine relativ ganz ansehnliche Anzahl (25 Exemplare) vor, die verschiedenen Genera und vielleicht auch verschiedenen Species angehoren. Bei der Seltenheit dieser Medusen ist dies reichhaltig zu nennen. Zum grossen Teil stammen sie aus dem malayischen Archipel, doch liegen auch Formen aus dem Mittelmeer und West-Indien vor. Die meisten Stucke wurden von dem Schiffsarzt P. Buitendijk, der jahrelang im Archipel gereist ist, gesammelt, 1 Exemplar stammt von E. Jacobson, 3 Exemplare von van Kampen, 3 Exemplare von M. F. Horst. Leider sind die Objekte, namentlich die grosseren, nicht immer im besten Erhaltungszustande, so dass die Determinierung nicht selten Schwierigkeiten begegnete und der anatomischen Untersuchung enge Grenzen gezogen wurden. Das Material ist schon aus dem Grunde von Interesse, weil mit Sicherheit nur sehr wenige Cubomedusen aus dem hinterindischen Archipel bekannt sind. Haeckel (10) fuhrt in seiner grossen Medusen-Monographie allerdings einige Species aus diesem Gebiete an, doch sind seine Angaben meist so unsicher und ungenau, dass A. G. Mayer in seinem standard-work „Medusae of the World", 1910, fast alle diese Species annulliert hat. Richard Semon (23) und die franzosischen Forscher Bedot und Pictet
ISOLATION OF PLANT GROWTHPROMOTING STRAINS OF BRADYRHIZOBIUM (ARACHIS) SP. WITH BIOCONTROL POTENTIAL AGAINST MACROPHOMINA PHASEOLINA CAUSING CHARCOAL ROT OF PEANUT

Among ten strains of Bradyrhizobium (Arachis) sp. in peanut, only three produced siderophore and IAA, and exhibited phosphate solubilization in vitro. Bradyrhizobium strains AHR-2 a m P + , AHR-5 a m P + and AHR-6 a m p + showed antagonistic activity against Macrophomina phaseolina. Peanut seeds coated with Bradyrhizobium strains were significant by enhanced seed germination, seedling biomass, nodule number, nodule fresh weight, average nodule weight compared to uninoculated and uninfected controls. These findings confirm the antagonistic as well as plant growth-promotory properties of Bradyrhizobium strains.
Introduction of threatened species in a fragmented and deteriorated landscape

In The Netherlands, heathlands and species-rich grassland are strongly reduced in both area and habitat quality mainly due to fragmentation, eutrophication and acidification. As a result, many plant and animal species have become (locally) extinct, or are threatened by extinction as they are forced into small and isolated habitat patches. In this thesis several genetic reasons for the loss and threatening of these plant species are described. The possibility to use reintroduction as a management measure in order to preserve these small and isolated populations from extinction is investigated. Moreover, several reintroduction strategies by using plant material from local and non-local populations of different size are discussed. In The Netherlands, heathlands and species-rich grassland are strongly reduced in both area and habitat quality mainly due to fragmentation, eutrophication and acidification. As a result, many plant and animal species have become (locally) extinct, or are threatened by extinction as they are forced into small and isolated habitat patches. In this thesis several genetic reasons for the loss and threatening of these plant species are described. The possibility to use reintroduction as a management measure in order to preserve these small and isolated populations from extinction is investigated. Moreover, several reintroduction strategies by using plant material from local and non-local populations of different size are discussed. In The Netherlands, heathlands and species-rich grassland are strongly reduced in both area and habitat quality mainly due to fragmentation, eutrophication and acidification. As a result, many plant and animal species have become (locally) extinct, or are threatened by extinction as they are forced into small and isolated habitat patches. In this thesis several genetic reasons for the loss and threatening of these plant species are described. The possibility to use reintroduction as a management measure in order to preserve these small and isolated populations from extinction is investigated. Moreover, several reintroduction strategies by using plant material from local and non-local populations of different size are discussed.
DIALLEL ANALYSIS AND MAPPING OF ALUMINUM TOLERANCE IN CORN INBRED LINES

Toxicity by aluminum is one of the main limitations for production in cropping areas, including corn (Zea mays L.) cultivation. There is genetic variability for the aluminum tolerance traits in corn but selection is troublesome because field assessment is difficult. The ob- jective of the present study was to characterize aluminum tolerance in five corn inbred lines and to identify chromo- somal regions associated to this resistance. A diallel ex- periment was conducted between three aluminum sensi- tive and two aluminum tolerant lines using the root re- growth method. The hybrid populations were superior compared with the parents and, from the partitioning of the heterosis effects; there were significant variety hetero- sis and specific heterosis effects. Lines L06 and L09 showed greater general combining ability and the L10 x L08 cross presented the best specific combination. Molec- ular mapping was performed with SSR in an F3 genera- tion from the cross L10 x L08. Data analysis showed five QTL, which explained 41% and 37% for root re-growth and hematoxylin staining. The results suggested that alu- minum resistance in corn have complex inheritance deter- mined by additive and non additive genetic effects.
Diversity and distribution of epiphytic diatoms

Epiphytic diatoms perform a variety of ecological functions. Diatoms are important primary producers and sources of oxygen which can modify the chemistry of the surrounding aquatic environment. They may live attached to plant surfaces with the help of extracellular polymeric substances and compete with plants for resources (e.g., light, nutrients). Thus, they represent an excellent model system for studies on interactions between epiphytes and their host plants under different environmental conditions. Further, the practical usage of epiphytic diatoms in biomonitoring begs questions concerning substrate specificity, diatom biodiversity, and species delimitations. This review focuses on specific aspects of freshwater epiphytic diatom ecology as adaptations for epiphytic way of life, epiphyte-host relationships, and implications for biomonitoring. epiphytic diatoms / ecology / substrate specificity / biomonitoring / species complexes
Plant regeneration from mature embryo-derived callus of Australian rice (Oryza sativa L.) varieties

In vitro plant regeneration from callus induced from embryos of mature seeds of 4 Australian varieties of rice was studied. Observations of callus induction on MS and N6 media indicated that MS medium supplemented with 0.5–2 mg/L of 2,4-D is suitable for callus formation from the varieties tested. Comparison of shoot initiation on medium containing BAP, BAP + NAA, and TDZ + NAA indicated that these varieties prefer BAP + NAA or TDZ + NAA in the shoot initiation medium. Partial desiccation, resulting in up to 20% loss of fresh weight of callus, significantly increased the regeneration frequency of the 4 rice varieties tested. The varieties showed varied response to number of shoots produced per callus. Regenerated shoots were rooted on plant growth regulator free medium. The plants regenerated were phenotypically normal and fertile. Our study showed that callus derived from mature embryos of these rice varieties are amenable to multiple shoot formation, and could be used for genetic transformation studies.
"Who am I?" : personal accounts of the dementia assessment process and the impact of the dementia label

There are competing models through which a dementia diagnosis can be understood, but what dominates the assessment process for dementia diagnosis is the medical model, which neglects the social, cultural, and political aspects of the diagnosis. In a Western society where value is ascribed to qualities associated with youth, such as good physical health, the rhetoric around older adults and dementia has long been dominated by stories of dependence and burden. Assuming them to be passive and unreliable, little research into the opinions of those diagnosed with dementia has been undertaken, but studies eliciting first-hand accounts suggest that the practice of diagnosis is inconsistent and often fails to meet the needs of the people receiving the diagnosis. Aiming to add depth to this research, four people aged over 65 with a dementia diagnosis were interviewed to evaluate the impact of socio-cultural discourse on their experience of being assessed for and living with a dementia diagnosis. Narrative analysis was then used, attending to the performative, descriptive, and contextual elements of the accounts. The study revealed the narrative abilities of people diagnosed with dementia and showed that hegemonic discourse on dementia alongside personal philosophies affect how the label is received and understood, and whether it is accepted or rejected. Participants also demonstrated value in interdependence, and a variety of post-diagnostic needs, reflecting the heterogeneity of those who receive the diagnosis. The implications of this study are then discussed, considering the impact that utilising the social model of disability could have on the treatment of people diagnosed with dementia.