Strategy for Optimizing LC-MS Data Processing in Metabolomics: A Design of Experiments Approach

A strategy for optimizing LC-MS metabolomics data processing is proposed. We applied this strategy on the XCMS open source package written in R on both human and plant biology data. The strategy is a sequential design of experiments (DoE) based on a dilution series from a pooled sample and a measure of correlation between diluted concentrations and integrated peak areas. The reliability index metric, used to define peak quality, simultaneously favors reliable peaks and disfavors unreliable peaks using a weighted ratio between peaks with high and low response linearity. DoE optimization resulted in the case studies in more than 57% improvement in the reliability index compared to the use of the default settings. The proposed strategy can be applied to any other data processing software involving parameters to be tuned, e.g., MZmine 2. It can also be fully automated and used as a module in a complete metabolomics data processing pipeline.     

Double slit interferometry to measure the EUV refractive indices of solids using high harmonics

Accurate values of the extreme ultraviolet (EUV) optical properties of materials are required to make EUV optics such as filters and multilayer mirrors. The optical properties of aluminum studied in this report are required, in particular, as aluminum is used as an EUV filter material. The complex refractive index of solid aluminum and the imaginary part of the refractive index of solid iron between 17 eV and 39 eV have been measured using EUV harmonics produced from an 800 nm laser focused to 10(14) Wcm(2) in an argon gas jet impinging on a double slit interferometer.     

Seismic response of floating wind turbines due to seaquakes

Vertical seismic waves, which are primarily due to pressure waves in the ground, can propagate with the same intensity in the seawater and impact floating bodies such as floating wind turbines (FWTs). Part of this wave can further propagate in the tower and generate large vertical accelerations in the nacelle. This paper presents a methodology for computation of the pressure waves generated by vertical earthquake shaking, referred to as seaquake, its impact on submerged bodies, and the induced dynamic response in the structure. A FWT concept with catenary mooring is used for the assessment of the effects of earthquake shaking. The pressure during a seaquake is determined using a 2D acoustic finite element (FE) model in Abaqus. The acoustic model is benchmarked against a 1D analytical solution. The response due to the environmental loads, namely, wind, current, and waves, is also studied and used as a reference for assessment of the relative significance of the seaquake. Considerable vertical accelerations can occur in the nacelle due to amplification of the platform accelerations through the tower. It is shown that this acceleration could exceed a commonly used operational limit range of 0.2 g to 0.3 g even for moderate accelerations at the seabed. This indicates that earthquake loading should be considered in the design of FWTs in seismic regions. The mooring tensile forces, due to motion of the platform during a seaquake, do not exceed the design tension computed for the extreme environmental conditions. However, the leeward mooring lines could experience zero tension, which could cause snap tension.     

From Meso to Macro: Controlling Hierarchical Porosity in Supraparticle Powders

A drying droplet containing colloidal particles can consolidate into a spherical assembly called a supraparticle. Such supraparticles are inherently porous due to the spaces between the constituent primary particles. Here, the emergent, hierarchical porosity in spray-dried supraparticles is tailored via three distinct strategies acting at different length scales. First, mesopores (<10 nm) are introduced via the primary particles. Second, the interstitial pores are tuned from the meso- (35 nm) to the macro scale (250 nm) by controlling the primary particle size. Third, defined macropores (>100 nm) are introduced via templating polymer particles, which can be selectively removed by calcination. Combining all three strategies creates hierarchical supraparticles with fully tailored pore size distributions. Moreover, another level of the hierarchy is added by fabricating supra-supraparticles, using the supraparticles themselves as building blocks, which provide additional pores with micrometer dimensions. The interconnectivity of the pore networks within all supraparticle types is investigated via detailed textural and tomographic analysis. This work provides a versatile toolbox for designing porous materials with precisely tunable, hierarchical porosity from the meso- (3 nm) to the macroscale (≈10 µm) that can be utilized for applications in catalysis, chromatography, or adsorption.     

Seasonal offshore/inshore migration of round gobies

Since the invasion of round gobies (Neogobius melanostomus) to Lake Michigan, they have become integrated into both nearshore and offshore food webs. Round gobies can be found in relatively shallow water (<20 m) during summer, but nearly disappear from these depths in early fall. They have been collected, occasionally, offshore in depths greater than 70 m during warm seasons. These observations and other anecdotal evidence suggest that round gobies migrate offshore during fall and return to nearshore water in spring. To study this, a remotely operated vehicle was used to conduct video transects at various depths.Sampling showed that round gobies migrated away from the shallowest (10 m) site in early October, with larger gobies moving offshore first, and were almost exclusively found deeper than 20 m by November. Round gobies remained offshore (>30 m) until mid-May, when they began the return to nearshore habitat. The cues to start offshore and return migrations were not the focus of this project, but fall offshore migrations coincided with decreasing temperatures nearshore in fall, and in spring, the offshore movement of the thermal bar.     

Giant barocaloric effects in natural graphite/polydimethylsiloxane rubber composites

Journal of Materials Science - Solid-state cooling based on caloric effects is considered a viable alternative to replace the conventional vapor-compression refrigeration systems. Regarding...     

Dynamic Process Operation Under Demand Response – A Review of Methods and Tools

Participating in electricity markets through demand response causes new requirements for optimizing process control of chemical plants. The last ten years have brought great advances in the formulation and solution of economic nonlinear model predictive control and state estimation to support operation of processes under dynamic constraints. However, gaps remain regarding the availabilities of suitable plant models capable of describing processes active in demand response as well as of robust schemes for state estimation and economic nonlinear model predictive control in commercial tools.     

Crystallinity,reversibility, and injectability of physically crosslinked poly(vinyl alcohol) and poly(ethylene glycol) hydrogels

Crystallite regions within a hydrogel network contribute to its mechanical strength, which is crucial for use in load-bearing applications. However, high amounts of crystallinity can negatively impact the ability for hydrogels to be injected, an attractive property that could replace the need for highly invasive surgical procedures. The reversibility of crystallinity and its lasting impact on the injectability of poly(vinyl alcohol) and poly(ethylene glycol) hydrogels was evaluated in this paper. The relative percent crystallinity in hydrogels was evaluated after storage and autoclaving in syringes in weekly intervals using X-ray diffraction. Results indicate that crystallinity increased over time and significantly decreased after autoclaving for all samples, where postautoclaved samples contained comparable crystallinity percentages to freshly made gels (p > 0.05). Injectability was evaluated using calculated viscosity. Aged samples were able to be injected after autoclaving, yet there was no determination established between viscosity and storage times based on the data. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020 , 137, 48706.     

DockVis: Visual Analysis of Molecular Docking Trajectories

Computation of trajectories for ligand binding and unbinding via protein tunnels and channels is important for predicting possible protein–ligand interactions. These highly complex processes can be simulated by several software tools, which provide biochemists with valuable information for drug design or protein engineering applications. This paper focuses on aiding this exploration process by introducing the DockVis visual analysis tool. DockVis operates with the multivariate output data from one of the latest available tools for the prediction of ligand transport, CaverDock. DockVis provides the users with several linked views, combining the 2D abstracted depictions of ligands and their surroundings and properties with the 3D view. In this way, we enable the users to perceive the spatial configurations of ligand passing through the protein tunnel. The users are initially visually directed to the most relevant parts of ligand trajectories, which can be then explored in higher detail by the follow-up analyses. DockVis was designed in tight collaboration with protein engineers developing the CaverDock tool. However, the concept of DockVis can be extended to any other tool predicting ligand pathways by the molecular docking. DockVis will be made available to the wide user community as part of the Caver Analyst 3.0 software package ( www.caver.cz ).