Miracle-dz/UniFAR-FTUs huggingface dataset:
Shotgun lipidomics and mass spectrometry imaging unveil diversity and dynamics in lipid composition in Gammarus fossarum

Sentinel species are playing an indispensable role in monitoring environmental pollution in aquatic ecosystems. Many pollutants found in water prove to be endocrine disrupting chemicals that could cause disruptions in lipid homeostasis in aquatic species. A comprehensive profiling of the lipidome of these species is thus an essential step towards understanding the mechanism of toxicity induced by pollutants. We here extensively examined both the composition and spatial distribution of lipids in freshwater crustacean Gammarus fossarum. The baseline lipidome of gammarids of different gender and reproductive stage was established by high throughput shotgun lipidomics. Spatial lipid mapping by high resolution mass spectrometry imaging led to the discovery of sulfate-based lipids in hepatopancreas and their accumulation in mature oocytes. We uncovered in G. fossarum a diverse and dynamic lipid composition that deepens our understanding of the biochemical changes during development and which could serve as a reference for future ecotoxicological studies.
Shear coaxial injector instability mechanisms

There is no definitive knowledge of which of several concurrent processes ultimately results in unstable combustion within liquid rocket chambers employing shear coaxial injectors. Possible explanations are a detrimental change in the atomization characteristics due to a decrease in the gas-to-liquid velocity ratio, a change in the gas side injector pressure drop allowing acoustic coupling to the propellant feed system or the disappearance of a stabilizing recirculation region at the base of the LOX post. The aim of this research effort is to investigate these proposed mechanisms under conditions comparable to actual engine operation. Spray characterization was accomplished with flash photography and planar laser imaging to examine the overall spray morphology and liquid jet breakup processes and with a PDPA to quantify the spatial distribution of droplet size and mean axial velocity. A simplified stability model based on the Rayleigh criterion was constructed for the flow dynamics occurring within the chamber and injector to evaluate the potential coupling between the chamber and injector acoustic modes and was supported by high frequency measurements of chamber and injector pressure oscillations. To examine recirculation within the LOX post recess, velocity measurements were performed in the recess region by means of LDV. Present experiments were performed under noncombusting conditions using LOX/GH2 stimulants at pressures up to 4 MPa.
Critical impeller speed for solid suspension in mechanically agitated contactors

Critical impeller speed for the suspension of solid particles, Ncs, has been measured in 0.3, 0.4, 0.57, 1.0, and 1.5 m ID mechanically agitated contactors. Tap water and quartz particles (100, 340, 700, 850, 2,000 μm) were used as liquid and solid phase, respectively. The impeller speed was varied from 3.5 to 13.3 r/s and solid loading from 0 to 50 wt. %. Three types of impellers were employed: disk turbine, pitched turbine downflow, and pitched turbine upflow. The impeller diameter to vessel diameter ratio was varied in the range 0.175 to 0.58 and the impeller blade width to impeller diameter ratio was varied in the range 0.25 to 0.4. The impeller clearance from the tank bottom was varied from 0.5 to 0.167 of tank diameter. The effect of impeller blade thickness was also studied. The pitched-blade impellers were found to be more efficient than a conventional disk turbine, and the pitched turbine downflow type was found to be more efficient than a pitched turbine upflow impeller. An attempt has been made to explain the mechanism of suspension on a rational basis and a correlation has been proposed for the estimation of Ncs that is expected to be useful in design.
The effect of seven substituted urea herbicides on the soil microflora

Chloroxuron, diuron, fluometuron, metobromuron and monuron added to soil at 500 parts/million a.i. on a dry weight basis caused an initial stimulation of CO2 production, followed by indications of inhibition. Nitrification was clearly inhibited, particularly by monuron and metobromuron. Metoxuron at 5 and 50 parts/million a.i. had no effect on CO2 output and nitrification, but at 500 parts/million a.i. both were greatly reduced. Numbers of fungal propagules were temporarily lower at 50 parts/million a.i., and severely curtailed at 500 parts/million a.i. but total counts of bacterial propagules were greatly increased. Linuron had an inhibitory effect on CO2 evolution at 500 parts/million a.i. but this varied in extent and duration; some reduction was also found at 50 parts/ million a.i. At 500 parts/million a.i. there was no effect on mineralisation of N but in soil supplemented with ammonium sulphate nitrification was reduced. Changes in microbial equilibrium occurred, but were less marked than with metoxuron. Cellulose decomposition was also reduced. Small amounts of 3,4dichloroaniline were found in linuron-treated soils, but microbial activities were not affected when 5 parts/million 3,4-dichloroaniline was added to the soil. However, at 140 parts/million microbial activities were affected adversely, but in a different pattern to that for linuron; nitrification was severely reduced, but numbers of fungal propagules were hardly affected, suggesting that the effects observed in linuron-treated soil were not due to this metabolite.
A CMOS Process-Compatible Wet-Etching Recipe for the High-k Gate Dielectrics Pr2O3 and Pr2 − x Ti x O3

The fabrication of complementary metal oxide semiconductor (CMOS) structures with praseodymium oxide (Pr 2 O 3 ) or titanium-doped praseodymium oxide (Pr 2 - x Ti x O 3 ) (0 ≤ x ≤ 1) layers as integrated high-k gate dielectrics requires the development of a process-compatible etching recipe. Different wet-etching processes in acid-based chemistry were evaluated and solutions of diluted sulfuric acid were identified as suitable etchants for Pr 2 O 3 and Pr 2 - x Ti x O 3 layers on Si substrates. Metal-oxide-semiconductor stacks with poly-Si as the potential gate electrode were patterned with the help of tetramethyl ammonium hydroxide as the selective etchant attacking the poly-Si gate electrode material but not the underlying Pr-based high-k gate dielectric layers.
Assignment of Helical Sense for Poly(phenylacetylene) Bearing Achiral Galvinoxyl Chromophore Synthesized by Helix-Sense-Selective Polymerization

{4-[(3,5-Di-tert-butyl-4-hydroxyphenyl)(3,5-di-tert-butyl-4-oxocyclohexa-2,5-dienylidene)methyl]phenyl}acetylene (abbreviated as (4-ethynylphenyl)hydrogalvinoxyl) was polymerized using [Rh(norbornadiene)Cl]2 catalyst in the presence of (R)-1-phenylethylamine or (S)-1-phenylethylamine to give red polymers. The circular dichroism (CD) spectra of polymers indicated that an excess of one-handed helical polyacetylene backbone was induced by helix-sense-selective polymerization under the asymmetric condition despite the achiral monomer. Results show that the CD signal intensity depends on temperature and decreases reversibly with increasing temperature, although the energy difference between the right-handed and left-handed conformations of each other is almost zero. The sign of the CD signal in the absorption region (420 nm) of the hydrogalvinoxyl chromophore, which was calculated from the polymer geometry, suggests that the excess of right-handed helix was induced by polymerization in the presence of (R)-1-ph.
Phase behavior and interfacial tension as a function of pressure and temperature in a ternary alkane system

Interfacial tension and PT phase diagrams have been measured in a ternary system composed of methane, propane, and decane. Measurements at constant temperature with varying pressure have been performed at two different compositions. The Soave-Redlich-Kwong (SRK) equation of state is fitted to the phase diagram. The interfacial tension seems to follow critical scaling laws even far from the critical point. The temperature range scanned is 20-100{degree}C, and the pressure range is from approximately 100 to 260 bar. The interfacial tension varies from 10{sup {minus}3} to 1 mN/m.
Freeze-Frame Imaging of Dendritic Calcium Signals With TubuTag

The extensive dendritic arbor of neurons is thought to be actively involved in the processing of information. Dendrites contain a rich diversity of ligand- and voltage-activated ion channels as well as metabotropic receptors. In addition, they are capable of releasing calcium from intracellular stores. Under specific conditions, large neurons produce calcium spikes that are locally restricted to a dendritic section. To investigate calcium signaling in dendrites, we introduce TubuTag, a genetically encoded calcium sensor anchored to the cytoskeleton. TubuTag integrates cytoplasmic calcium signals by irreversible photoconversion from green to red fluorescence when illuminated with violet light. To image the mm-long dendritic tree of pyramidal neurons at subcellular resolution, we used a custom two-photon microscope with a large field of view. As the read-out of fluorescence can be performed several hours after photoconversion, TubuTag will help investigating dendritic signal integration and calcium homeostasis in large populations of neurons.
Numerical Study of Coolant Mixing Caused by the Flow Deflectors in a Nuclear Fuel Bundle

Abstract A numerical study was conducted to investigate the nuclear fuel assembly coolant flow mixing that is promoted by the flow deflectors on the grid spacer. Four typical flow deflectors (split vane, side-supported vane, swirl vane, and twisted vane) were chosen for this study. A single subchannel of one grid span is modeled using the flow symmetry. The predicted axial and lateral mean flow velocities, and the turbulent kinetic energy in the subchannel for the split-vane design, are in good agreement with the experimental results. The split vane and the twisted vane generate a large cross flow between the subchannels and a skewed elliptic swirling flow in the subchannel near the grid spacer. The cross flow rapidly decreases and the swirling flow becomes dominant downstream of the spacer. The side-supported vane induces a horizontally elongated elliptic swirl in the subchannel and a secondary flow in the near downstream of the spacer. The swirl vane produces a circular swirling flow in the subchannel and a negligible cross flow. For the twisted-vane and side-supported vane designs, the change in direction of the cross flow was predicted. The average turbulent kinetic energy in the subchannel sharply increases near the spacer and rapidly decreases to a fully developed level. In summary, the numerical results showed a somewhat large difference from the experimental results near the spacer but represented the overall characteristics of coolant mixing well in a nuclear fuel bundle with the flow deflectors on the grid spacer.
Modalflow: Cross-Origin Flow Data Visualization for Urban Mobility

Pervasive data have become a key source of information for mobility and transportation analyses. However, as a secondary source, it has a different methodological origin than travel survey data, usually relying on unsupervised algorithms, and so it requires to be assessed as a dataset. This assessment is challenging, because, in general, there is not a benchmark dataset or a ground truth scenario available, as travel surveys only represent a partial view of the phenomenon and suffer from their own biases. For this critical task, which involves urban planners and data scientists, we study the design space of the visualization of cross-origin, multivariate flow datasets. For this purpose, we introduce the Modalflow system, which incorporates and adapts different visualization techniques in a notebook-like setting, presenting novel visual encodings and interactions for flows with modal partition into scatterplots, flow maps, origin-destination matrices, and ternary plots. Using this system, we extract general insights on visual analysis of pervasive and survey data for urban mobility and assess a mobile phone network dataset for one metropolitan area.
Automatic generation of ground truth data for the evaluation of clonal grouping methods in B-cell populations

Motivation The adaptive B-cell response is driven by the expansion, somatic hypermutation, and selection of B-cell clones. Their number, size and sequence diversity are essential characteristics of B-cell populations. Identifying clones in B-cell populations is central to several repertoire studies such as statistical analysis, repertoire comparisons, and clonal tracking. Several clonal grouping methods have been developed to group sequences from B-cell immune repertoires. Such methods have been principally evaluated on simulated benchmarks since experimental data containing clonally related sequences can be difficult to obtain. However, experimental data might contains multiple sources of sequence variability hampering their artificial reproduction. Therefore, the generation of high precision ground truth data that preserves real repertoire distributions is necessary to accurately evaluate clonal grouping methods. Results We proposed a novel methodology to generate ground truth data sets from real repertoires. Our procedure requires V(D)J annotations to obtain the initial clones, and iteratively apply an optimisation step that moves sequences among clones to increase their cohesion and separation. We first showed that our method was able to identify clonally-related sequences in simulated repertoires with higher mutation rates, accurately. Next, we demonstrated how real benchmarks (generated by our method) constitute a challenge for clonal grouping methods, when comparing the performance of a widely used clonal grouping algorithm on several generated benchmarks. Our method can be used to generate a high number of benchmarks and contribute to construct more accurate clonal grouping tools. Availability and implementation The source code and generated data sets are freely available at github.com/NikaAb/BCR_GTG
Heavy Metals Concentration at Electronic- Waste Dismantling Sites and Dumpsites in Lagos, Nigeria

The importation and refurbishing of second -hand electrical and electronic equipment (EEE) is a major concern all over the world and Nigeria is not in exception owing to the generation of e-wastes. The assessment of the levels of Pb, Cr, Ni, Cd and Zn in th e dust at dismantling sites and soil from dumpsites in Lagos municipal was performed using Atomic Absorption Spectroscopy. Control samples were also taken at 1km away from each site. At the dismantling sites, the concentration of Pb, Cr, Ni, Cd and Zn were found
Algorithm for Mapping Kidney Tissue Water Content during Normothermic Machine Perfusion Using Hyperspectral Imaging

The preservation of kidneys using normothermic machine perfusion (NMP) prior to transplantation has the potential for predictive evaluation of organ quality. Investigations concerning the quantitative assessment of physiological tissue parameters and their dependence on organ function lack in this context. In this study, hyperspectral imaging (HSI) in the wavelength range of 500–995 nm was conducted for the determination of tissue water content (TWC) in kidneys. The quantitative relationship between spectral data and the reference TWC values was established by partial least squares regression (PLSR). Different preprocessing methods were applied to investigate their influence on predicting the TWC of kidneys. In the full wavelength range, the best models for absorbance and reflectance spectra provided Rp2 values of 0.968 and 0.963, as well as root-mean-square error of prediction (RMSEP) values of 2.016 and 2.155, respectively. Considering an optimal wavelength range (800–980 nm), the best model based on reflectance spectra (Rp2 value of 0.941, RMSEP value of 3.202). Finally, the visualization of TWC distribution in all pixels of kidneys’ HSI image was implemented. The results show the feasibility of HSI for a non-invasively and accurate TWC prediction in kidneys, which could be used in the future to assess the quality of kidneys during the preservation period.
Separating Enthalpy and Volume Contributions in Photothermal Experiments: A Perspective

Abstract— Signals in photothermal experiments originate from both enthalpies and volumes of reaction. Two methods have been reported through which enthalpy and volume contributions can be separated: (1) analysis of signals as a function of temperature in aqueous solution or (2) analysis of signals from a series of linear alkanes or solvent mixtures. This manuscript describes potential difficulties in the application of the latter method to charge transfer reactions and proposes two alternative approaches by which the separation might be effected in a single organic solvent: (a) measurement of signals in isotopomeric solvents or (b) measurement of thermally induced changes in refractive index under conditions of constant density. The utility of neither approach has been demonstrated in any solvent other than water.
Preparation and Characterization of Poly(Methyl Methacrylate) Coated TiO2 Nanoparticles

Titanium dioxide (TiO2) nanoparticles were modified with poly(methyl methacrylate) (PMMA) to improve the dispersion stability of the nanoparticles in a dielectric medium and to reduce the density mismatch between TiO2 and a dielectric medium for a microcapsule‐type electrophoretic display application. Nanoparticles were coated with PMMA by in situ dispersion polymerization. The PMMA‐coated TiO2 nanoparticles were characterized by fourier transform‐infrared spectrometrey (FT‐IR), electrophoretic light scattering (ELS), and scanning electron microscopy (SEM). Density of PMMA‐coated TiO2 nanoparticles was found to be dependent on the thickness of the PMMA coating on the nanoparticles. An increase of thermal stability of the PMMA layer and the contents of PMMA on the surface of the nanoparticles were measured via thermogravimetric analysis (TGA).
Fate of carbon and nitrogen in water‐stable aggregates during decomposition of 13C15N‐labelled wheat straw in situ

When incorporated in soil, plant residues and their decomposition products are in close contact with mineral particles with which they can be bound to form aggregates. We measured the incorporation of carbon (C) and nitrogen (N) derived from crop residues in water‐stable aggregate fractions of a silty soil in a field experiment in Northern France using 13C15N‐labelled wheat straw (Triticum aestivum L.). Soil samples were taken seven times for 18 months and separated into slaking‐resistant aggregate size fractions which were analysed for total C and N contents, and 13C and 15N enrichments. During the early stages of decomposition (approximately 200 days), the enrichment of 13C increased rapidly in the macro aggregates (> 250 pm) but decreased thereafter. The macro aggregates represented only < 20% of the soil mass and at any one time, they accounted for <25% of the residual 13C in the soil. The proportion of 13C recovered in the <50‐μm and 50–250‐μm fractions increased during decomposition of the residues; at day 574, the 50–250‐μm fraction accounted for close to 50% of the residual 13C. A greater proportion of 15N than 13C was recovered in the <50‐μm fraction. The results indicate that during decomposition in soil, C and N from crop residues become rapidly associated with stable aggregates. In this silty soil the 50–250‐μm stable aggregates appear to be involved in the storage and stabilization of C from residues.
Leaching-induced migration and compositional form change of Cu, Zn, and Cd from sludge to loess

Land utilization of sewage sludge has become one of the major issues in environmental mitigation in China. This is particularly important in the Loess Plateau of Northwest China. Sludge enriched with organic matter and nutrients might effectively help to resolve the problems of silty loess soils as evidenced by porosity defect, structural alterations and absence of fertility. After sludge flows into the loess, irrigation water contains heavy metals that leach and migrate into sludge and consequently related human health risks may occur that raise concerns; and this situation needs to be rectified. The characteristics of the vertical migration and composition form change of Cu, Zn, and Cd from composted sludge to loess, and corresponding influencing factors, were investigated by performing a soil column simulation test under the leaching treatment of a one-year irrigation water capacity. Results demonstrated that: (1) composted sludge significantly improved loess fertility, and irrigation leaching transported only a small quantity of organic matter in sludge in the plough layer; (2) although some of the Cu, Zn, and Cd in composted sludge migrated to and concentrated in the middle and upper layers of the soil column during leaching, these metals were mostly retained in the plough layer; and (3) after the leaching treatment of the one-year irrigation water capacity, the compositions of Cu, Zn, and Cd (particularly Cu and Zn) in both plough layer and loess began to stabilize with low concentrations in the exudate. These findings confirmed the applicability of composted sludge in loess regions. This study provided a new insight into the sludge reuse in alkaline soils in arid and semi-arid region.
Adsorption of Cs and U(VI) on soils of the Australian arid zone

Distribution coefficients (Kd values) for Cs and U(VI) on soils from an arid region of Australia were measured under a range of conditions. The Kd values for trace 137Cs in 0.02 M NaCl were typically around 104 mL/g, and were not affected by the pH. However, the Kd decreased with increasing ionic strength, and was strongly dependent on the total Cs concentration. Much lower Kd values (around 102 mL/g) were measured in systems containing total Cs of 1 mmol/L in a background electrolyte of 0.10 M NaCl. The main factor determining the sorption behaviour of U(VI) in systems equilibrated with air was the pH, with the Kd decreasing from above 103 mL/g at pH 7 to around 10 mL/g at pH 9.
Effects of ridging on crop performance and symbiotic N2 fixation of fababean (Vicia faba L.)

Abstract. The success of organic cropping systems depends on symbiotic N2 fixation by leguminous crops, and it is important to explore new management systems to improve the nitrogen input through N2 fixation. During two growing seasons the possible advantage of growing fababean (Vicia faba L.) in ridges was studied in comparison to the traditional method on flat soil. Differences in soil physical parameters resulted in a significantly greater microbial activity and a deeper root system at the flowering stage when grown in the ridge than on the flat. Consequently, the amount of fixed N at flowering was significantly greater in ridges than in flat soil. However, during the period from flowering until harvest, when the major part of the N uptake and N2 fixation took place, the differences between the treatments disappeared. Average values for the growing season of fluorescein diacetate hydrolysis, arylamidase activity and arylsulphatase activity were significantly greater in the ridge than on the flat, and the microbial biomass‐C, derived from substrate induced respiration (SIR), was on average 232 and 223 μg C g−1 soil in the ridge and on the flat, respectively. Measured total‐N uptake, including root N (0–30 cm depth), ranged from 206 to 247 kg N ha−1, of which 182–201 kg N ha−1 was fixed N. From 154 to 173 kg N ha−1 was removed in grain resulting in a soil‐N balance of +28 kg N ha−1 in both years. However, by including estimates of total root N and rhizodeposition‐N the soil‐N balance ranged from +52 to +62 kg N ha−1.
Protein Structure: Nanosecond Crystallographic Snapshots of Protein Structural Changes

In this issue of Science, Srajer et al. (p. 1726) present nanosecond-long snapshots of carbon monoxide dissociating from myoglobin, the first glimpse of a protein at work. In his Perspective, Eaton et al. discuss why this is such a landmark feat and how it was made possible.