Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics and model analysis of hydropower systems

Globalization and growth in energy consumption in combination with climate challenges, make the use of sustainable energy production a necessity. Important sustainable energy sources (solar, wind) are intermittent in character, and hydropower from high head water reservoirs is a possible energy source for balancing out the variation in intermittent sources. The combination of several energy types as well as counteracting the intermittent energy production make energy management and control much more challenging; optimal energy production will require advanced control based on detailed system models. Another side of globalization is the possibility for everyone to contribute to solutions. This requires lowcost software tools. The combination of open-source software tools with the publication of models and methods provides transparency in research, and increases the possibility of developing optimal and reliable models and methods. In this thesis, a key contribution is the development of a library of mechanistic models for the waterway of hydropower production, using the modelling language Modelica with open-source tool OpenModelica. Another key contribution is the development of analysis methods using open-source languages Python and/or Julia. Mathematical models for various units of a hydropower system are presented and assembled in a hydropower Modelica library — OpenHPL. Detailed studies for modelling different hydropower units are demonstrated in this work, i.e., the study of different complexities of waterway models, and the study of a mechanistic Francis turbine model and its design algorithm. The library can be used in an open-source software OpenModelica, which makes it freely and widely available. In addition, the library also supports modelling and simulation in the commercial environment Dymola. The OpenHPL makes it possible to model different hydropower systems and connect them with models from other libraries, e.g., with models of the power system or other power generating sources. This synergy of our library with other Modelica libraries makes it possible to model the hydropower system starting from precipitations/reservoir to final consumer of electricity. The application and validation of the developed library are presented for case study measurements from the real Trollheim hydropower plant. Various model analysis tools are implemented and tested for the OpenHPL hydropower models. These analysis tools are encoded in open-source scripting languages Python
The Search for Molecular Prognostic Markers of Diabetic Nephropathy in Patients with Type 2 Diabetes Mellitus

The purpose of this study was to search for molecular prognostic markers of diabetic nephropathy (DN) in patients with type 2 diabetes mellitus (T2DM). The study included 205 patients with T2DM and DN (stages 1 to 4). All patients were stratified by the MDRD equation. The control group included 30 healthy individuals. All T2DM patients were divided into 4 groups depending on the DN stages. Group 1 included 42 patients with DN-Stage 1 (prenephropathy), Group 2 included 48 patients with DN-Stage 2 (incipient nephropathy); Group 3 included 65 patients with DN-Stage 3 (overt nephropathy), and Group 4 included 50 patients with DN-Stage 4 (kidney failure). Molecular phenotyping of urine was processed with methods of proteomics: the prefractionation, the separation of proteins with standard sets (MB-HIC C8 Kit, MB-IMAC Cu, MB-Wax Kit, «Bruker», USA), matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS/MS, Ultraflex II, «Bruker», USA). The data of the molecular interactions and functional features of proteins were received with STRING 10.0 database. Potentially new molecular markers of DN development
Historical and current stand structure in Douglas-fir and ponderosa pine forests.

A comparison of historic and current stand structure and species composition was made in Douglas-fir (Pseudotsuga menziesii) and ponderosa pine (Pinus ponderosa) forest series on the eastern slopes of the Cascade Mountains. We used tree ring analysis of 1,192 tree cores from the Okanogan National Forest to reconstruct historical tree diameter and inferred structural attributes during the past 100 years. Sampled stands currently have more trees per acre and more basal area than were found historically. Overall stand density has increased 307% for Douglas-fir, 81% for ponderosa pine and 138% for Engelmann spruce (Picea engelmannii). Western larch (Larix occidentalis) was the only tree species that decreased in density (-48%). Average basal area has also increased 81% above historical levels. Changes in stand density have not been uniform over the past 100 years. The maximum number of trees per acre for most of these stands occurred 40 to 50 years ago, which indicates a shift toward a stem exclusion stage of stand development in recent decades.
Quaternary Activity of the Beihewan Fault in the Southeastern Beishan Wrench Belt, Western China: Implications for Crustal Stability and Intraplate Earthquake Hazards North of Tibet

We present evidence for the Late Quaternary activity of the Beihewan Fault (BHWF), along the southeastern margin of the Beishan block, western China. Field observations and analysis of UAV‐derived DEMs and Google Earth images reveal an ~10‐km‐long active fault trace in a region previously considered tectonically inactive. Offset landforms and trench exposures reveal that the fault is dominantly strike‐slip, with local thrust or normal displacements. Average rates of left‐lateral motion and thrusting since the Holocene are estimated to be ~2.69 and ~0.35 mm/a, respectively. The most recent surface‐rupturing event generated ~2.5 m of strike‐slip offset since 6.2–8.6 ka; with estimated M = 6.3–6.9. Modeling and two‐dimensional inversion of new magnetotelluric data indicate that the BHWF is a subvertical low‐resistivity zone that penetrates into the lower crust. Existing geological and geophysical evidence do not support subsurface linkage between the BHWF and Altyn Tagh–Jinta‐Nanshan Fault system further south in the Hexi Corridor. Close examination of high‐resolution satellite imagery west and east of the BHWF reveals other Quaternary surface fault scarps, pressure ridges, offset drainages, and truncated lithological strike belts. Collectively, these features constitute a previously unrecognized 150‐km‐long sinistral deforming belt along the southeastern Beishan and northern Hexi Corridor boundary that we call the Southeast Beishan Wrench Belt. Recognition of Quaternary activity along the BHWF within the larger Southeast Beishan Wrench Belt challenges long‐held assumptions that the Beishan region is a relatively stable and tectonically inactive block within the Late Cenozoic Indo‐Eurasian deformation field north of Tibet.
Managing the Agri-Food System of Watersheds to Combat Coastal Eutrophication: A Land-to-Sea Modelling Approach to the French Coastal English Channel

The continental coastal waters of the Eastern Channel, from Normandy to Hauts-de-France, are subject to the major influence of unbalanced nutrient inputs from inflowing rivers. Several episodes of harmful algal blooms (HABs) compromising fishing and shellfish farming activities have been observed at the coast. For a better understanding of how the land-to-sea aquatic continuum functions, the GRAFS-RIVERSTRAHLER river biogeochemical model was implemented to cover the watersheds of 11 rivers flowing into this area (including the Seine) and chained with the ecological marine ECO-MARS3D model, applied to the French Northern coastal zone. Human activities strongly impact on the functioning of coastal ecosystems. Specifically, for these fertile soils of Northern France, intensive agricultural nitrogen (N) deliveries in excess over silica (Si) and phosphorus (P), essentially of diffuse origin, are potentially responsible for coastal eutrophication. Phosphorous is today equally supplied by diffuse and point sources, after a drastic reduction of inputs from wastewater treatment plants since the 2000s, and is better balanced regarding Si, as shown by the indicators of coastal eutrophication potential (P-ICEP versus N-ICEP). However, despite this drastic P reduction, HABs still appear repeatedly. Exploration of several scenarios of agro-food chain reorganization shows that (i) further progress in urban wastewater treatment to fully comply with current European regulations will not result in a significant reduction of nutrient fluxes to the sea, hence including HABs, and (ii) radical structural changes in agriculture, based on generalization of long and diversified organic crop rotations, reconnection of crop and livestock farming and changes in the human diet have the capacity to significantly reduce nutrient flows, coastal eutrophication and HABs.
Idiosyncrasies in cities: evaluating patterns and drivers of ant biodiversity along urbanization gradients

Urbanization is expected to reduce biodiversity. However, an increasing number of studies report urban biodiversity comparable to that of surrounding nonurban areas, leaving open the question: what maintains biodiversity in cities? We characterized patterns of ant biodiversity across urbanization gradients of three major cities in the Midwestern United States and evaluated the support for two mechanisms underlying the maintenance of biodiversity in cities, specifically via introduced non-native species and differential phenology of communities along each urbanization gradient. We observed idiosyncrasies in ant species diversity such that each city displayed either increased, decreased or no change in biodiversity across the urbanization gradient. We found partial support (one of the three cities) for the hypothesis that non-native species can contribute positively to overall species diversity in cities, though even with introduced species removed from consideration, native ant biodiversity was maintained along the urbanization gradient. We found no support for systematic differential phenology across urbanization gradients, although species diversity did vary over time across all sites. Our results further challenge the assumption of biodiversity loss in cities, as two of our three cities exhibited maintained species diversity along the urbanization gradient. Most importantly, our study demonstrates that urban biodiversity can be maintained entirely by native communities.
Biophysical characterisation of measles virus receptors

Measles virus (MV) is an important human pathogen that still claims almost one million lives annually, primarily in the developing world. To date two human proteins have been identified that can serve as the receptor for measles virus, namely membrane cofactor protein (MCP) and signalling lymphocyte activation molecule (SLAM). It is thought that a more through understanding of the sructure and behaviour of the interacting regions of these receptors, will facilitate a more detailed understanding of the pathogenesis of MV. This thesis describes efforts to clone, express and characterise the relevant fragments of these receptors. The natural function of MCP is to prevent activation of complement on self cells. MCP contains four extracellular complement control protein (CCP) modules. The region of MCP that interact with MV has previously been identified to be the first two N-terminal CCP modules. MCP carries a functionally critical N-glycan on its second module (MCP2) and the crystal structure of MCP12 (expressed in mammalian cells) implies a structural role for this carbohydrate moiety. MCP 12 and MCP2 were successfully cloned and expressed as secreted proteins in Pichia pastoris at levels sufficient for biophysical characterisation. Proton and ' 5N Nuclear magnetic resonance spectroscopy (NMR) studies, differential scanning calorimetry and mass spectrometry were employed to investigate the recombinant proteins. Both the natural sequences of MCP 12 and MCP2 fragments expressed in P. pastoris were hyperglycosylated, and therefore these recombinant fragments were investigated in both glycosylated and deglycolylated forms in order to study the effect of the glycans on module 2 of MCP, and with a view to detailed structural and dynamic studies using NMR. The data obtained with the P. pastoris-expressed fragments are not inconsistant with the hypothesis that the N-glycan on module 2 of the wild-type MCP is required for this module to be properly folded. After extensive investigations, it was concluded that the inability of P. pastoris to attach the natural glycan is a barrier to more detailed structural studies. In an effort to produce MCP2 with a better defined glycosylation profile, efforts were made to express, this fragment in insect cells which are known to produce a 'more natural' glycosylation profile on proteins. Moreover, the MCP2 fragment was also expressed in E. coli, in order to produce a form of MCP2 that had never been glycosylated. Following the discovery that SLAM may be the more physiologically relevant receptor for MV, it had been established that the first V-type immunoglobulin-type domain (SLAM 1) is necessary and sufficient for interaction with the virus. SLAM 1 was successfully cloned from a human cDNA library using touchdown PCR, and efforts were made towards its expression in P. pastoris. Expression levels of 20 mg/i of induction medium were achieved, however the recombinant SLAM 1 was also hyperglycosyiated by P. pastoris which has hampered its purification.
Subduction history reveals Cretaceous slab superflux as a possible cause for the mid-Cretaceous plume pulse and superswell events

Abstract Subduction is a fundamental mechanism of material exchange between the planetary interior and the surface. Despite its significance, our current understanding of fluctuating subducting plate area and slab volume flux has been limited to a range of proxy estimates. Here we present a new detailed quantification of subduction zone parameters from the Late Triassic to present day (230–0 Ma). We use a community plate motion model with evolving plate topologies to extract trench-normal convergence rates through time to compute subducting plate areas, and we use seafloor paleo-age grids to estimate the thickness of subducting lithosphere to derive the slab flux through time. Our results imply that slab flux doubled to values greater than 500 km3/yr from 180 Ma in the Jurassic to 130 Ma in the mid-Cretaceous, subsequently halving again towards the Cretaceous-Paleogene boundary, largely driven by subduction zones rimming the Pacific ocean basin. The 130 Ma spike can be attributed to a two-fold increase in mid-ocean ridge lengths following the break-up of Pangea, and a coincident increase in convergence rates, with average speeds exceeding 10 cm/yr. With one third of the total 230 - 0 Ma subducted volume entering the mantle during this short ∼50 Myr period, we suggest this slab superflux drove a surge in slab penetration into the lower mantle and an associated increase in the vigour of mantle return flow. This mid-Cretaceous event may have triggered, or at least contributed to, the formation of the Darwin Rise mantle superswell, dynamic uplift of the South African Plateau and the plume pulse that produced the Ontong-Java-Hikurangi-Manihiki and Kerguelen plateaus, among others. The models presented here contribute to an improved understanding of the time-evolving flux of material consumed by subduction, and suggest that slab superflux may be a general feature of continental dispersal following supercontinent breakup. These insights may be useful for better understanding how supercontinent cycles are related to transient episodes of Large Igneous Province and superswell formation, and the associated deep cycling of minerals and volatiles, as well as leading to a better understanding of tectonic drivers of long-term climate and icehouse-to-greenhouse transitions.
Rising mean and extreme near‐surface air temperature across Nepal

Owing to unique topographic and ecological diversity, central Himalayan state of Nepal is exposed to adverse impacts of climate change and associated disasters. However, countrywide historical assessment of mean and extreme temperature changes, a prerequisite for devising adequate adaptation strategies, is still lacking. Here, we present a comprehensive picture of mean and extreme temperature trends across Nepal over the 1980–2016 period, based on high‐quality daily temperature observations from 46 stations. Our results suggest that besides winter cooling in southern lowlands, the country features a widespread warming, which is higher for maximum temperature (~0.04°C⋅year−1) than for minimum temperature (~0.02°C⋅year−1), over the mountainous region than in valleys and lowlands and during the pre‐monsoon season than for the rest of the year. Consistently, we found a higher increasing trend for warm days (13 days⋅decade−1) than for warm nights (4 days⋅decade−1), whereas the rates of decrease for cold days and cold nights are the same (6 days⋅decade−1). Further investigations reveal that pronounced warming in maximum temperature over mountain regions can be attributed to less cloud cover and snowfall in recent decades during non‐monsoon seasons as a result of positive geopotential height anomalies and strengthening of anticyclonic circulations in the mid‐to‐upper troposphere. Similarly, increased stability of lower atmosphere during winter and post‐monsoon seasons caused prolonged and frequent periods of fog over lowlands, resulting in significant winter cooling there.
Dental pulp stem cells in serum-free medium for regenerative medicine

ABSTRACT Mesenchymal stem cells in dentistry have multiple potential applications including alveolar ridge preservation and repair, cleft palate reconstruction, sinus grafting and ultimately pulp and dentine regeneration. The autologous application of tissue resident stem cells for regeneration is a relatively new field of research focus. Clinical application of these stem cells with multi-lineage capability requires that they be harvested and amplified in a serum- and xeno-free environment that minimises the possibility of cellular mutations and of introducing disease. The use of tissue-specific stem cells from different sites also has implications in relation to the site of harvesting and the differentiation status of the stem cells obtained. This review will examine the serum- and xeno-free culture of human dental pulp stem cells (DPSC). It will overview both the development and current practise in relation to DPSC culture and identification, to enable the future application of these cells in regenerative medicine. The phenotypic characteristics, stem-cell markers, harvesting considerations and differentiation capacity will be summarised. We will also investigate the ability of DPSCs to undergo multi-lineage differentiation in vitro and the possible clinical implications of DPSCs being derived from the neural crest.
Range expansions in the evolutionary history of western palaeartic aquatic coleoptera

A basic question in geographic range issues is to understand why some species are widespread while others closely related are very restricted geographically. In this work I want to contribute to the understanding of the factors that lead some species to expand their original geographic range and suggest some hypothesis to explain the extreme differences in range size among closely related species. For this aim I reconstruct the evolutionary history of various lineages of aquatic beetles distributed in the Western Palearctic area, in the context of the complex geological and climatical history of this area, in order to shed light about the factors that have contributed to the current distribution of species in these groups. All these lineages are typical of running waters (i.e. with poor dispersal abilities), and include both narrowly distributed endemics and widespread species, showing their potential for range expansions. The different biogeographical reconstructions performed suggests the occurrence of several events of range expansions between the eastern and western sides of the Mediterranean Basin under favourable conditions, followed by fragmentation when conditions deteriorate. Range expansions were mainly across the north shore of the Mediterranean as in the south there is virtual absence in the studied groups of species eastern of Tunisia. Despite that it is not possible to establish a common temporal origin for all studied groups, the Miocene, with its various connections and subsequent isolation among the eastern and western sides of the Mediterranean basin, seems to be involved in the origin and east-west disjunction of some groups. However most of the current species were estimated to have originated during the Pleistocene, including those with widespread distributions, being therefore the epoch with a stronger influence in the present-day distribution. The successive rounds of range expansion and fragmentation resulted mainly in the accumulation of narrow range species in the Mediterranean area, especially the Iberian and Anatolian peninsulas. Despite evidence in some cases of speciation with range stasis within the southern Mediterranean area, some species were able to expand their original range reaching widespread distributions in northern areas, likely as a consequence of a privileged geographical position during a narrow window of favourable conditions. However, differences in physiological or ecological tolerances could also have favoured range expansions in some species and limited them in others although further experimental research in the differences in physiological tolerances in these lineages would be necessary to test this hypothesis.
Ulinastatin ameliate lung damage induced by mechanical ventialtion for serious burned rats:an experimental study

Objective To explore the potential protective effects of ulinastatin on ventilation-induced lung injuries of severe burned rats.Methods Ninety Wistar rats were randomly divided into three experimental groups:control group(n=30),ventilation group(n=30)and ventilation-ulinastatin group(n=30). After establishing the severe burn model,the rats of latter two groups were mechanically ventilated for 1 hour with or without the pre-treatment of ulinastatin.The lung injury was evaluated by pathological changes,lung index and the expression level of cytokines including TNF-α,IL-2,and IFN-γ at 2 hours,6 hours and 12 hours post-ventilation.The samples of lung tissue at the last time point(12 hours)were used for both HE staining and electron microscopy analysis.Results The lung tissues of the control and ventilation groups exhibited markedly pulmonary edema and scattered hemorrhagic foci.In contrast,ventilation-ulinastatin group demonstrated milder pulmonary edema.HE staining revealed that the pathological changes of ventilation-ulinastatin group were milder than ventilation group.Under electron microscopy,severe organelle destruction was noted for the lung tissue of control group and ventilation group.In contrast,ventilation-ulinastatin group demonstrated milder pathological changes.Pulmanary index showed that the value of ventilation-ulinastatin group decreased significantly compared with ventilation group.Immunohistochemical staining demonstrated lower expression of TNF-α,IL-2,IFN-γ in ventilation-ulinastatin group compared with ventilation group.Conclusions Ulinastatin attenuated ventilation-induced lung injury in a severe burn model of rat.The protective effects of ulinastatin maybe related to the capacity of ulinastatin to reduce the expression of cytokines including TNF-α,IL-2,and IFN-γ.