Large Experimental Setups Research Articles

Plant Sample Collection and Shipment for Multi-omic Analyses and Phytosanitary Evaluation.

Plant sample preparation for analyses is a fundamental step in high-throughput omics strategies. Especially for plant metabolomics, quenching of hydrolytic enzymes able to affect metabolite concentrations is crucial for the accuracy of results. Given that DNA is usually less labile than metabolites, most sampling and shipment procedures able to preserve the metabolome are also suitable for preventing the degradation of plant DNA or of DNA of pathogens in the plant tissue. In this article, we describe all the steps of sample collection, shipment (including the phytosanitary issues of moving plant samples), and processing for combined genomics and metabolomics from a single sample, as well as the protocols used in our laboratories for downstream approaches for crop plants, allowing collection of multi-omic datasets in large experimental setups. The protocols have been adjusted to apply to both freeze-dried and fresh-frozen material to allow the processing of crop plant samples that will require long-distance transport. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of freeze-dried leaf disks for multiplexed PCR or DArT-Seq genotyping Basic Protocol 2: Medium-throughput preparation of pathogen-free nucleic acids for most genotyping-resequencing applications or pathogen detection Alternate Protocol: Low-throughput extraction of high-quality DNA for resequencing using commercial kits Support Protocol: DNA quality control Basic Protocol 3: Preparation of freeze-dried plant material for metabolomics Basic Protocol 4: Preparation of fresh-frozen plant material for metabolomics Basic Protocol 5: Preparation and shipment of metabolite extracts for metabolomic analyses Basic Protocol 6: Sample shipping and long-term storage.

Eksperimentalna ocjena učinkovitosti prijenosa opterećenja na betonskim kolnicima bez moždanika

Generally, joint performance in concrete pavements is evaluated in laboratory by applying dynamic loads that require large scale experimental setups. In order to propose a simplified laboratory test, a comprehensive literary review of the fundamentals of load transfer at joints is made, and the load transfer efficiency obtained via a reduced scale test is compared under static and dynamic conditions. The results confirm feasibility of static analysis via a reduced scale test for evaluating load transfer efficiency of non-dowelled concrete pavements.

Eddy current characterization on material surface during high power application – A benchmark experiment

Eddy current is creating a lot of problems in high voltage and high current experiments. High eddy current can cause significant heating and deteriorating electromagnetic forces on mechanical structures. The strange behavior of eddy current will sometime leads to collapse of mechanical structures in large experimental set ups. Measurement of eddy current is very important in cases where its magnitude exceeds a certain value. Here we suggest a benchmark experiment for measuring eddy current developed on a metallic surface during a high current discharge. In this experiment, a torus shaped steel (SS 304) tube is considered which resembles super conducting reaction chamber used in fusion experiments. These experiments are under high power applications and hence the mechanical structure will be subjected to eddy current impacts which needs to be studied well in early to understand the possible after effects. Results from a benchmark experiment with similar prototype will help in such situations to derive the system parameters under actual experiment situations. Here, coil is inserted through the torus and a high current discharge is given through that coil using a capacitor and thyristor control circuit. Due to this high current discharge, eddy current will be developed on the torus surface. Practical measurement of current discharged can be calculated using a calibrated Rogowski coil. Another calibrated Rogowski coil is wound across the torus structure to pick the eddy current. Rogowski coil will give the di/dt value. Integrating the output will give the value of current. Subtracting the two Rogowski coil output will give the eddy current value. Further, the experimental set up is modeled and simulated in ANSYS MAXWELL and eddy current obtained from simulation is compared with those we obtained practical values. The proposed experimental setup is a Non Destructive Test (NDT) and therefore this can be easily executed in any test atmosphere. The validated method finds its application in particle accelerators and fusion research.

Huizhou accelerator complex facility and its future development

This paper provides an overview of the frontier research fields and significant questions in nuclear physics regarding particle accelerators, and the status and future development trends for big-science facilities of particle accelerators are reviewed. Two Chinese government-approved “12th Five-Year” major science infrastructure facilities, the “High Intensity heavy-ion Accelerator Facility (HIAF)” and “China Initiative Accelerator Driven System (CiADS)”, are being constructed in Huizhou, Guangdong Province. Based on these two big-science projects (HIAF and CiADS), we proposed to establish a large-scale charged particle accelerator complex facility named the “Bright Electron and Ion research Facility (BEIF).” This facility will be dedicated to the research and development of nuclear physics and its interdisciplinary frontier fields. The research frontier fields of nuclear physics at the BEIF will include nuclear structure and astrophysics, nucleon structure, quark matter phase structure, and interdisciplinary fields between several significant frontiers of fundamental and nuclear physics, such as highly charged atomic physics and heavy ion-driven high energy density physics. BEIF will be a large-scale scientific complex facility comprising several superconducting ion LINAC accelerators, synchrotrons, storage rings, reactors, and various large experimental detectors and setups. BEIF will be built in three construction phases and will become one of the premier global large-scale particle accelerator complex facilities dedicated to the research of nuclear physics and technology.

Isotropic Scalar Quantum Sensing of Magnetic Fields for Industrial Application

AbstractMagnetic field sensors based on quantum mechanic effects are often susceptible to misalignments of the magnetic field or need advanced procedures to compensate for these. Also, the record breaking sensitivities reported for superconducting quantum interference devices and alkali vapor magnetometers come along with large and complex experimental setups. The nitrogen vacancy center in diamond can be used to design a simple, small, and robust sensor without employing microwave radiation. By using compressed nanodiamond particles, it is possible to eliminate the need of an alignment of the magnetic field and still obtain the absolute magnetic flux density in a single measurement. In order to demonstrate the capabilities of this approach, a centimeter‐sized modified automotive demo board is employed as a complete sensor with a sensitivity of 78 T/.

A control hardware based on a field programmable gate array for experiments in atomic physics.

Experiments in Atomic, Molecular, and Optical (AMO) physics require precise and accurate control of digital, analog, and radio frequency (RF) signals. We present control hardware based on a field programmable gate array core that drives various modules via a simple interface bus. The system supports an operating frequency of 10 MHz and a memory depth of 8 M (223) instructions, both easily scalable. Successive experimental sequences can be stacked with no dead time and synchronized with external events at any instructions. Two or more units can be cascaded and synchronized to a common clock, a feature useful to operate large experimental setups in a modular way.

Observation of internal multiplication of nonequilibrium charge in irradiated silicon detectors at a temperature of 1.9K

The development of modern high-energy physics is a powerful incentive for the progress of its experimental base. The use of semiconductor devices is standard for large accelerators and experimental setups at LHC, CERN, and perspective as sensors for monitoring beam loss and radiation fields in superconducting magnets and accelerating resonators operating at superfluid helium temperature (1.9 K). In these problems, the optimal type of radiation sensor is a compact silicon detector, the use of which in harsh radiation environment in combination with helium temperatures is a non-trivial task. The most important characteristics of such devices are the distribution of the electric field in the volume and the parameters of charge carrier transport, which determines the detector signal. The study considers specific kinetics of charge collection in silicon detectors at a temperature of 1.9 K in situ irradiated by relativistic hadrons.

Freeware tool for analysing numbers and sizes of cell colonies

The clonogenic cell survival assay is a basic method to study the cytotoxic effect of radiation and chemical toxins. In large experimental setups, counting of colonies by eye is tiresome and prone to bias. Moreover, it is often interesting to quantify the size of individual colonies. Such analyses are largely facilitated by computerised image analysis systems. Although a number of such systems exist, they all focus on enumerating colonies and not on analysing the colony size. We have developed a new software package for both counting colonies and plotting their size distributions. The software called count and Plot HIstograms of Colony Size (countPHICS) consists of two parts: (1) a macro written for ImageJ which analyses computerised images of cell culture dishes or 6-well plates, counts colonies, estimates their size and saves the results in a text file; (2) a program written with QT Creator which reads the text file, plots histograms of colony size distribution and fits the best function. The full program is freely available at: http://www.fuw.edu.pl/~bbrzozow/FizMed/countPHICS.html. In conclusion, our new publically available software will facilitate colony counting and provide additional information on the colony growth rate, which is relevant especially for radiosensitisation studies.

CMOS based capacitance to digital converter circuit for MEMS sensor

Most of the MEMS cantilever based system required costly instruments for characterization, processing and also has large experimental setups which led to non-portable device. So there is a need of low cost, highly sensitive, high speed and portable digital system. The proposed Capacitance to Digital Converter (CDC) interfacing circuit converts capacitance to digital domain which can be easily processed. Recent demand microcantilever deflection is part per trillion ranges which change the capacitance in 1-10 femto farad (fF) range. The entire CDC circuit is designed using CMOS 250nm technology. Design of CDC circuit consists of a D-latch and two oscillators, namely Sensor controlled oscillator (SCO) and digitally controlled oscillator (DCO). The D-latch is designed using transmission gate based MUX for power optimization. A CDC design of 7-stage, 9-stage and 11-stage tested for 1-18 fF and simulated using mentor graphics Eldo tool with parasitic. Since the proposed design does not use resistance component, the total power dissipation is reduced to 2.3621 mW for CDC designed using 9-stage SCO and DCO.

A miniature bioassay for testing the acute phytotoxicity of photosystem II herbicides on seagrass.

Photosystem II (PSII) herbicides have been detected in nearshore tropical waters such as those of the Great Barrier Reef and may add to the pressure posed by runoff containing sediments and nutrients to threatened seagrass habitats. There is a growing number of studies into the potential effects of herbicides on seagrass, generally using large experimental setups with potted plants. Here we describe the successful development of an acute 12-well plate phytotoxicity assay for the PSII herbicide Diuron using isolated Halophila ovalis leaves. Fluorescence images demonstrated Diuron affected the entire leaf surface evenly and responses were not influenced by isolating leaves from the plant. The optimum exposure duration was 24 h, by which time the inhibition of effective quantum yield of PSII (∆F/Fm’) was highest and no deterioration of photosystems was evident in control leaves. The inhibition of ∆F/Fm’ by Diuron in isolated H. ovalis leaves was identical to both potted and hydroponically grown plants (with leaves remaining attached to rhizomes), indicating similar reductions in photosynthetic activity in these acute well-plate assays. The sensitivity of the assay was not influenced by irradiance (range tested 40 to 400 μmol photons m-2 s-1). High irradiance, however, caused photo-oxidative stress in H. ovalis and this generally impacted in an additive or sub-additive way with Diuron to damage PSII. The bioassay using isolated leaves is more rapid, uses far less biological material and does not rely on specialised aquarium facilities in comparison with assays using potted plants. The development and validation of this sensitive bioassay will be useful to reliably screen and monitor the phytotoxicity of existing and emerging PSII herbicides and contribute to risk assessments and water quality guideline development in the future.

Fibre laser hydrophones for cosmic ray particle detection

The detection of ultra high energetic cosmic neutrinos provides a unique means to search for extragalactic sources that accelerate particles to extreme energies. It allows to study the neutrino component of the GZK cut-off in the cosmic ray energy spectrum and the search for neutrinos beyond this limit. Due to low expected flux and small interaction cross-section of neutrinos with matter large experimental set-ups are needed to conduct this type of research. Acoustic detection of cosmic rays may provide a means for the detection of ultra-high energetic neutrinos. Using relative low absorption of sound in water, large experimental set-ups in the deep sea are possible that are able to detect these most rare events, but it requires highly sensitive hydrophones as the thermo-acoustic pulse originating from a particle shower in water has a typical amplitude as low as a mPa. It has been shown in characterisation measurements that the fibre optic hydrophone technology as designed and realised at TNO provides the required sensitivity. Noise measurements and pulse reconstruction have been conducted that show that the hydrophone is suited as a particle detector.

GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data

Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)(1). The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net.

Cryopreservation of hairy root cultures of Maesa lanceolata and Medicago truncatula

To study the production of secondary metabolites of Maesa lanceolata and Medicago truncatula, hairy root cultures of both plant species were established. Because maintenance of large numbers of cultures is laborious and costly, we developed a cryopreservation protocol and stored different isolated lines over time. Using encapsulation-dehydration, high survival rates were observed for both Maesa and Medicago hairy roots. Root tips were isolated and encapsulated in calcium-alginate beads, containing 0.1 M sucrose. The encapsulated hairy roots were precultured for 3 days using basal medium containing high sucrose concentrations. Medicago root tip growth during the preculturing time lead to unwanted outgrowth which could be tempered by addition of plant growth inhibitors. After preculturing, the beads were dehydrated in the air flow of a laminar flow until 35–40% of the initial bead weight was reached. Dehydrated beads were plunged into liquid nitrogen and after different storage times thawed in a water bath at 40°C. The survival rates were 90% for Maesa and 53% for Medicago, which are sufficient to allow implementation in large storage experimental set-ups.

Large strain dynamic compression for soft materials using a direct impact experiment

Measurement of strain rate dependent material data of low density low strength materials like polymeric foams and rubbers still poses challenges of a different kind to the experimental set up. For instance, in conventional Split Hopkinson Pressure Bar tests the impedance mismatch between the bars and the specimen makes strain measurement almost impossible. Application of viscoelastic bars poses new problems with wave dispersion. Also, maximum achievable strains and strain rates depend directly on the bar lengths, resulting in large experimental set ups in order to measure relevant data for automobile crash applications. In this paper a modified SHPB will be presented for testing low impedance materials. High strains can be achieved with nearly constant strain rate. A thin film stress measurement has been applied to the specimen/bar interfaces to investigate the initial sample ring up process. The process of stress homogeneity within the sample was investigated on EPDM and PU rubber.

A 1 GHz flash-ADC module in VMEbus

A data acquisition module based on monolithic high-speed flash-analog-to-digital-converter-chips is described. Four fully independent channels, with 250 MHz sampling rate and a 2 kbyte buffer memory each, can be combined (interleaved) in one channel to achieve an effective 1-GHz sampling rate with a total of 8 kbyte memory depth. The double Eurocard board supports standard 16-b or 32-b VMEbus protocol for high-speed readout. The board is essentially self-contained and can be used cost-effectively in small applications and in large experimental setups. The performance of the data acquisition module has been tested.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Random pulse generator with a uniformly distributed amplitude spectrum

The described pulse generator produces a while pulse amplitude spectrum in addition to an optional calibration peak. Amplitudes and pulse distances are nearly randomly distributed. The amplitude of the output pulses, with a width of 2 μs, ranges from 0.1 to 10 Vp. The rate may be varied from 0.1 to 110 kips. The unit has been developed for applications in nuclear physics. It will mainly be used to test large experimental setups, and for calibration of parameters. In some cases, measurements of nonlinearities will be possible. Distortions of the white spectrum which may occur if the pulses are converted by an ADC with amplitude dependent dead time (Wilkinson type) have been considerably reduced.