Miracle-dz/UniFAR-FTUs huggingface dataset:
Introducing GloRiSe – a global database on river sediment composition

Abstract. Rivers transport dissolved and solid loads from terrestrial realms to the oceans and between inland reservoirs, representing major mass fluxes on Earth's surface. The composition of river water and sediment provides clues to a plethora of Earth and environmental processes, including weathering, erosion, nutrient and carbon cycling, environmental pollution, reservoir exchange, and tectonic cycles. While there are documented, publicly available databases for riverine dissolved and suspended nutrients, there is no openly accessible, georeferenced database for riverine suspended sediment composition. Here, we present a globally representative set of 2828 suspended and bed sediment compositional measurements from 1683 locations around the globe. This database, named Global River Sediments (GloRiSe) version 1.1, includes major, minor and trace elements, along with mineralogical data, and provides time series for some sites. Each observation is complemented by metadata describing geographic location, sampling date and time, sample treatment, and measurement details, which allows for grouping and selection of observations, as well as for interoperability with external data sources, and improves interpretability. Information on references, unit conversion and references makes the database comprehensible. Notably, the close to globe-spanning extent of this compilation allows the derivation of data-driven, spatially resolved global-scale conclusions about the role of rivers and processes related to them within the Earth system. GloRiSe version 1.1 can be downloaded from Zenodo (https://doi.org/10.5281/zenodo.4485795, Müller et al., 2021) and GitHub (https://github.com/GerritMuller/GloRiSe, last access: 26 May 2021), where updates with adapted version numbers will become available, along with a technical documentation and an example calculation in the form of MATLAB scripts, which calculate the sediment-flux-weighted major element composition of the annual riverine suspended sediment export to the ocean and related uncertainties.
Multi-Scale Theoretical Investigations of Protein Interactions and Evolution

Evolution of biological systems requires players of multiple layers, from atoms and molecules to organisms and populations. Expression of a gene is operated by molecular machineries for transcription, translation, regulation, and maintenance, which work in concert to produce certain macroscopic and observable phenotypes. And when these phenotypes are exposed to selective pressures, more fit phenotypes (with their genes, molecular machineries, and interaction networks) survive in the population. While the relationship of a gene to its cellular consequences is not fully elucidated, it is known that molecular interactions are one of the key factors that determine the relationship. In this dissertation, we introduce several theoretical tools to study protein interactions and evolution, and show their applications at various scales. The first tool is a coarse-grained scoring function that predicts binding free energy of a protein complex. The scoring function is a simple linear combination of exposed interface areas of different amino acids. In spite of the simplicity, it shows a reasonable predictive power, and predicts correct biochemistry qualitatively. The second is an analytical theory of a spin model on a simple graph, developed by using conventional statistical mechanics. We separated structural and energetic contributions to the free energy of the system, and also obtained a closed form of linear graph contributions. The closed form is applied to predict sequence space free energy of lattice proteins. Lastly, we introduce statistical methods to analyze cellular proteomes and transcriptomes. They can extract global responses of proteomes and transcriptomes to a perturbation, and also responses of specific gene groups. We applied the methods to E. coli and yeast systems to address questions on the genotype-phenotype relationship and evolution.
Understanding the microstructural evolution of hypersaline cemented paste backfill with low-field NMR relaxation

Cemented paste backfill (CPB) comprising mineral tailings, binders and mixing waters is an important potential support material in the mining industry. As the mechanical properties of CPB are significantly influenced by its microstructural characteristics the development of measurement tools to better understand its pore structure evolution is important for its increased utilisation. This study reports the application of low-field nuclear magnetic resonance (NMR) relaxation time measurements to characterise the microstructural evolution of CPB materials over 56 days of hydration, contrasting common tap water and hypersaline water (~22 wt% salt) as mixing waters. Distinct NMR relaxation time populations were evidenced within each CBP sample, revealing the presence of both capillary (T1,2 ≈ 10 ms) and gel pore water (T1,2 ≈ 300 – 500 µs), with time-dependent relaxation measurements facilitating characterisation of capillary pore structure evolution over the hydration period assessed. Hypersaline samples demonstrated a time-lag in this measured capillary pore evolution, relative to those hydrated with tap water, while pore structure evolution rates were observed to increase with increased CPB binder content. Further, both T1 and T2 NMR relaxation times were found to correlate with the uniaxial compressive strength of the CPB materials investigated, facilitating the formulation of a predictive correlation function between NMR relaxation characteristics and mechanical properties.
Deposition and characterisation of RF magnetron sputtered phosphate based glasses

Phosphate based glasses are emerging in the field of biomaterials for their potential to resorb in biological environments, fulfilling applications from the fibre reinforcement of resorbable polymeric matrices to carriers for therapeutic drug delivery. Here we show the optimisation and characterisation of thin film glasses deposited by RF magnetron sputtering onto medical implant materials such as Ti6Al4V to function as ion leaching coatings to promote osseointegration or inhibit bacterial attachment. Vaporisation of the target preform occurred by momentum exchange interactions leading to non stoichiometric transfer to the condensed coating, sputtering in the order Na > Mg > Ca > Fe > P. Structural analyses revealed short range variation between compositionally equivalent glasses such that coatings with 32.5, 34 and 37 mol% P2O5 showed bulk polymerisation increasing in Q2 species by (23% to 45%) versus (9% to 32%) in quenched glasses. P O P bridging oxygens on the surface of coatings formed (PO3) metaphosphates (Q2), compared to (PO4)3 orthophosphates (Q0) and (P2O7)4 pyrophosphates (Q1) in quenched glasses. Quinternary coatings of up to 2.67 μm, containing Fe3+ and Ti4+ intermediate and cross linking elements were degraded in distilled water and phosphate buffered saline. Fe2O3 was increased from 4 to 8 mol% to stabilise dissolution, however an observed increase was attributed to variable condensation energies leading to inequivalent enthalpy and internal stress states. A comparison of a compositionally equivalent condensed and quenched glass suggested that the surface ratios of P O P to (P=O and PO ) were 34.2% to 65.8% versus 20.5% to 79.5% respectively leading to more soluble coating surfaces, exhibiting an exponential degradation dependence in the first 2 h in distilled water, followed by a linear profile. Post deposition heat treatments at 500, 550 and 610 °C were employed to stabilise dissolution and to tailor mechanical properties. All phosphate glass coatings showed interfacial tensile adhesion in excess of 73.6 MPa; surpassing ISO and FDA requirements for HA coatings. The initial exponential degradation from 0 2 h was stabilised via heat treatment. From 2 24 h coatings exhibited linear ion release rates ordering P > Na > Mg > Ca > Fe whilst dissolution rates reduced by factors of 2.44 to 4.55, attributed the formation of crystals and the depletion of hydrophilic P O P bonds within the surface layer. Vapour deposition has shown its ability to condense tailorable compositions of glasses, maintaining their amorphous tetrahedral structures whilst demonstrating exceptional adhesion to Ti6Al4V substrates. Coatings have demonstrated linear ion release capabilities and the ability to accommodate a vast array of potentially therapeutic ions to promote osteogenic or antimicrobial capabilities.
A ReaxFF-Based Molecular Dynamics Simulation of the Pyrolysis Mechanism for Polycarbonate

Polycarbonate (PC) is considered a promising substitute for insulating materials due to its excellent insulation and mechanical properties. The main cause for PC insulation aging is the breakage of chemical bonds at high temperatures. The reactive force field (ReaxFF) method is first employed in a molecular dynamics (MD) simulation of polycarbonate pyrolysis to elucidate the mechanism for thermal aging at the atomic level. The results show that the main reaction pathway for breakage of the polycarbonate main chain is C–O bond breakage of the terminal group or between PC monomers. CO2, CO, CH4, and H2 are the major products generated following polycarbonate pyrolysis. The formation mechanisms of these dominant products are detailed for the first time based on the simulation trajectories. The activation energy and pre-exponential factor extracted from the ReaxFF simulations show good agreement with experimental results. The fracturing of the main chain and the production of small molecule gases both decreas.
Application of Hypoxic Exposure Combined with Osteogenic Induction for the Enhancement of Multiple Osteoinductive Capabilities in Rat Mesenchymal Cells

Objective: The enhancement of multiple functions, including osteogenesis, angiogenesis, and cell recruitment, is required for efficient bone regeneration therapy. Recently, special attention has been focused on the microenvironment of stem cells to facilitate bone regeneration. Herein, we examined the effects of various combinations of hypoxic conditions and osteogenic induction on rat mesenchymal cells, to develop a specific protocol for enhancing the multiple cellular functions beneficial to bone regeneration. Methods: Rat mesenchymal cells, isolated from bone marrow, adipose tissue, and periodontal ligament, were examined. The cells were cultured under varied conditions of O2 tension (hypoxia) and duration and timing of hypoxic exposure, with or without osteogenic induction. Consequently, four different protocols were examined by measuring the gene expression levels of Runx2, Vegfa, and Cxcl12, indicating a capability for osteogenesis, angiogenesis, and cell recruitment, respectively. Finally, the mineralization ability of the rat mesenchymal cells was assessed by quantitating their calcified nodule formation. Results: The simultaneous application of hypoxic exposure and osteogenic induction promoted Vegfa expression in all types of cells, but suppressed Runx2. In contrast, hypoxic preconditioning, followed by osteogenic induction, did not increase the expression of these genes; in fact, Vegfa expression decreased significantly. Among the various protocols, 0.5% O2 exposure for 12 h after osteogenic induction exhibited the largest fold changes of gene expression level, especially of Vegfa. Hypoxic post-conditioning enhanced the formation of calcified nodules in periodontal ligament-derived cells. Conclusion: Short-term hypoxic exposure after osteogenic induction could be used to improve the efficiency of mesenchymal cells for bone regeneration.
Geological map of the San Donato – Costa Thrust Zone, Belluno Thrust System, eastern Southern Alps (northern Italy)

ABSTRACT We present a 1:7500 scale geological map of part of the footwall of the south verging Belluno Thrust of the seismically active eastern Southern Alps of northern Italy. We report a previously unknown thrust zone, the “San Donato-Costa Thrust Zone”, that cuts across the local Meso-Cenozoic stratigraphic succession. 1:2500 and 1:5000 geological mapping, in combination with the revision and improvement of the local lithostratigraphy and detailed structural analysis, provided new insights into the thrust geometry and the setting of the greater area it deforms. We show that the recorded deformation style (e.g. folding vs. faulting) exhibits notable variations within the affected Meso-Cenozoic stratigraphic succession, with shortening accommodated by fold trains and several subparallel thrust splays with variable amounts of stratigraphic offset cumulated during repeated faulting. Our results contribute to a better definition of folding and faulting within the Mesozoic carbonate multilayer system of the eastern Southern Alps.
Synthesis and Structure-Dependent Optical Properties of ZnO Nanocomb and ZnO Nanoflag

The structure-dependent optical properties of ZnO nanostructures have attracted considerable attention due to their fascinating optoelectronic properties and great structural diversity. Novel ZnO nanocomb and ZnO nanoflag have been successfully synthesized by chemical vapor deposition (CVD) method using Au nanoparticles (NPs) as the catalyst at the deposition temperatures of 900 and 950 °C, respectively. X-ray diffraction and high-resolution transmission electron microscopy results show that the ZnO nanocomb handle and its teeth grow in [0111] and [0001] orientations, respectively, while the ZnO nanoflag sheet and its pole grow along [0001] and [2110] orientations, respectively. Au NPs as well as deposition temperature played an important role in the growth of the nanocomb handle and nanoflag pole. Synchrotron-based scanning transmission X-ray microscopy (STXM) reveals the thickness distribution and the crystallinity of ZnO nanocomb and ZnO nanoflag. For the near-surface emission, photoluminescence and.
MCM7 Ubiquitination Regulates CMG Helicase Disassembly In Human

The disassembly of the replisome plays an essential role in maintaining genome stability at the termination of DNA replication. However, the mechanism of replisome disassembly remains unknown in human. In this study, we screened E3 ligases and deubiquitinases (DUBs) for the ubiquitination of minichromosome maintenance protein (MCM) 7 and provided evidence of this process driving CMG helicase disassembly in human tumor cells. Our data identified two important features of helicase disassembly in human. First, RNF8 catalyzes the K63-linkedpolyubiquitylation of MCM7 on chromatin, which is transiently modified mainly in the late S phase of the cell cycle. Moreover, the proteasome, p97 segregase, USP29 and ATXN3 are required for the removal of MCM7 ubiquitination to promote the disassembly of CMG on chromatin. Our study will help to uncover the novel role of the regulation of CMG helicase disassembly via MCM7 ubiquitination.
Potential symmetry reduction of a convection-dispersion equation with spatial dependent water velocity

Abstract We consider a class of a convection-dispersion equation describing the transport model of oil spilled in sea water with concentration-dependent dispersion and spatial velocity. A potential variable is introduced to the governing equation such that the governing equation is written in conserved form (or auxiliary system). The conserved form admits a number of classical symmetries which induce potential symmetries for the governing equation. We construct group invariant solutions using admitted potential symmetries for the governing equation. The potential symmetry reduction is coupled with invariant surface condition to construct solutions via classical reduction method. The solutions are new and exact.
A trigonometric hardware acceleration in 32-bit RISC-V microcontroller with custom instruction

This work presents a 32-bit Reduced Instruction Set Computer ﬁfth-generation (RISC-V) microprocessor with a COordinate Rotation DIgital Computer (CORDIC) accelerator. The accelerator is implemented inside the core and being used by the software via custom instruction. The used microprocessor is the VexRiscv with the Instruction Set Architecture (ISA) of RV32IM; that means 32-bit RISC-V including Integer and Multiplication. The experimental results were collected using Field-Programmable Gate Array (FPGA) on the DE2-115 development kit and ApplicationSpeciﬁcIntegratedChip(ASIC)synthesizeron180-nmCMOSprocesslibrary.
Hybrid Photonic Nanostructures by In Vivo Incorporation of an Organic Fluorophore into Diatom Algae

Biotechnological processes harnessing living organisms' metabolism are low‐cost routes to nanostructured materials for applications in photonics, electronics, and nanomedicine. In the pursuit of photonic biohybrids, diatoms microalgae are attractive given the properties of the porous micro‐to‐nanoscale structures of the biosilica shells (frustules) they produce. The investigations have focused on in vivo incorporation of tailored molecular fluorophores into the frustules of Thalassiosira weissflogii diatoms, using a procedure that paves the way for easy biotechnological production of photonic nanostructures. The procedure ensures uniform staining of shells in the treated culture and permits the resulting biohybrid photonic nanostructures to be isolated with no damage to the dye and periodic biosilica network. Significantly, this approach ensures that light emission from the dye embedded in the isolated biohybrid silica is modulated by the silica's nanostructure, whereas no modulation of photoluminescence is observed upon grafting the fluorophore onto frustules by an in vitro approach based on surface chemistry. These results pave the way to the possibility of easy production of photonic nanostructures with tunable properties by simple feeding the diatoms algae with tailored photoactive molecules.
Solid phase extraction method for detection of ciprofloxacin residue in milk

The present study was conducted for detection of Ciprofloxacin residue in milk using Solid Phase Extraction (SPE) method. Raw milk samples of cow were collected from milk vendors in sterile containers and then preserved until analysis. Ultra High Performance Liquid Chromatography (UHPLC) with diode array detection system was employed for detection of ciprofloxacin in the milk samples. A mixture of water and acetonitrile (70:30 v/v) was used as the mobile phase. The flow rate was maintained in an isocratic mode at a speed of 1.0 ml.min-1. The wavelength for the detector was set at 277 nm. The standard calibration curve showed good linearity (r2 > 0.996). Accuracy and recovery was in the range of 94-99% for ciprofloxacin in milk indicating that the method can be used as a validated method. The present method very precisely identifies and quantifies low level of Ciprofloxacin in milk which is useful for monitoring purpose.
Do Foreign Cash Holdings Generate Uncertainty for Analysts?

This study examines whether foreign cash holdings increase the complexity of analysts’ forecasting tasks, thereby affecting their earnings forecasts’ properties. In forecasting future earnings, analysts face uncertainty in understanding the firm’s economic situation, especially if cash is held by foreign subsidiaries – given that it may be subject to investment inefficiencies. The lack of disclosure about foreign cash makes it difficult for analysts to anticipate and fully incorporate in their estimates the negative performance consequences of foreign cash holdings. Using a sample of U.S. multinational corporations and estimating their foreign cash holdings, we show that a firm with an average level of estimated foreign cash to total assets has a 12.5% higher forecast error and a 13.7% higher forecast dispersion (relative to firms without foreign cash). Moreover, we document that estimated foreign cash is negatively associated with future performance and that, in the presence of large amounts of foreign cash, financial analysts issue more optimistic forecasts. Cross-section analyses show that estimated foreign cash holdings affect analysts’ forecasts to a larger extent in the absence of disclosure, consistent with the idea that the lack of disclosure restricts financial analysts’ ability to fully incorporate in their estimates the effect of foreign cash.
Temperature, lipid charge and septin dependence of lateral lipid diffusion in biomimetic membrane systems

Plasma membrane dynamics have become increasingly of interest due to recent discoveries on anomalous lipid diffusion in live cells. A specific characteristic has been found in the exponential relation between lateral lipid diffusion and temperature. The finding was reported to be surprising as a linear dependence was theoretically predicted. In this study, the gap between simple theoretical models and experimental in vivo results on lipid diffusion is investigated by studying model membrane systems experimentally. Specifically, lateral lipid diffusion is further characterized as function of temperature, lipid charge and asymmetry. To induce anomalous diffusion, a peripheral protein known to act as a diffusion barrier, fly-septin, was associated to the lipid bilayer to explore its effect on lipid slow-down. Lateral lipid diffusion was measured by fluorescence recovery after photobleaching (FRAP) on a bare, or with associated septin, model phospholipid membrane system. The supported lipid bilayer (SLB) model membrane systems were formed by vesicle fusion (VF) or Langmuir-Blodgett/vesicle fusion (LBVF), specifically for asymmetric SLBs. Temperature variations were induced by using an in-house built sample heater. The quality of the lipid bilayers was defined by investigating influencing variables; lipid batches, substrate surface treatment, SLB formation methods and lipid tracers. Results show that membrane viscosity exhibits linear scaling to lipid diffusion. Furthermore, lateral lipid diffusion appears to be charge dependent and influenced by lipid composition of both leaflets. Considering the influence of septin, lateral lipid diffusion is reproducibly increased as compared to a bare membrane, in contrast to the reported septin induced lipid slow-down due to a diffusion barrier mechanism. These findings have brought the gap between theoretical models and membrane dynamics one step closer together.
Examining the Applicability of Wavelet Packet Decomposition on Different Forecasting Models in Annual Rainfall Prediction

Accurate precipitation prediction can help plan for different water resources management demands and provide an extension of lead-time for the tactical and strategic planning of courses of action. This paper examines the applicability of several forecasting models based on wavelet packet decomposition (WPD) in annual rainfall forecasting, and a novel hybrid precipitation prediction framework (WPD-ELM) is proposed coupling extreme learning machine (ELM) and WPD. The works of this paper can be described as follows: (a) WPD is used to decompose the original precipitation data into several sub-layers; (b) ELM model, autoregressive integrated moving average model (ARIMA), and back-propagation neural network (BPNN) are employed to realize the forecasting computation for the decomposed series; (c) the results are integrated to attain the final prediction. Four evaluation indexes (RMSE, MAE, R, and NSEC) are adopted to assess the performance of the models. The results indicate that the WPD-ELM model outperforms other models used in this paper and WPD can significantly enhance the performance of forecasting models. In conclusion, WPD-ELM can be a promising alternative for annual precipitation forecasting and WPD is an effective data pre-processing technique in producing convincing forecasting models.