Key Experimental Parameters Research Articles

Review of Smog Chamber Experiments for Secondary Organic Aerosol Formation

In this study, we reviewed smog chamber systems and methodologies used in secondary organic aerosol (SOA) formation studies. Many important chambers across the world have been reviewed, including 18 American, 24 European, and 8 Asian chambers. The characteristics of the chambers (location, reactor size, wall materials, and light sources), measurement systems (popular equipment and working principles), and methodologies (SOA yield calculation and wall-loss correction) are summarized. This review discussed key experimental parameters such as surface-to-volume ratio (S/V), temperature, relative humidity, light intensity, and wall effect that influence the results of the experiment, and how the methodologies have evolved for more accurate simulation of atmospheric processes. In addition, this review identifies the sources of uncertainties in finding SOA yields that are originated from experimental systems and methodologies used in previous studies. The intensity of the installed artificial lights (photolysis rate of NO2 varied from 0.1/min to 0.40/min), SOA density assumption (varied from 1 g/cm3 to 1.45 g/cm3), wall-loss management, and background contaminants were identified as important sources of uncertainty. The methodologies developed in previous studies to minimize those uncertainties are also discussed.

Assessment of the Purity of IMM-H014 and Its Related Substances for the Treatment of Metabolic-Associated Fatty Liver Disease Using Quantitative Nuclear Magnetic Resonance Spectroscopy.

An accurate, rapid, and selective quantitative nuclear magnetic resonance method was developed and validated to assess the purity of IMM-H014, a novel drug for the treatment of metabolic-associated fatty liver disease (MAFLD), and four related substances (impurities I, II, III, and IV). In this study, we obtained spectra of IMM--H014 and related substances in deuterated chloroform using dimethyl terephthalate (DMT) as the internal standard reference. Quantification was performed using the 1H resonance signals at δ 8.13 ppm for DMT and δ 6.5-7.5 ppm for IMM-H014 and its related substances. Several key experimental parameters were investigated and optimized, such as pulse angle and relaxation delay. Methodology validation was conducted based on the International Council for Harmonization guidelines and verified with satisfactory specificity, precision, linearity, accuracy, robustness, and stability. In addition, the calibration results of the samples were consistent with those obtained from the mass balance method. Thus, this research provides a reliable and practical protocol for purity analysis of IMM-H014 and its critical impurities and contributes to subsequent clinical quality control research.

A comprehensive assessment of exome capture methods for RNA sequencing of formalin-fixed and paraffin-embedded samples

RNA-Seq analysis of Formalin-Fixed and Paraffin-Embedded (FFPE) samples has emerged as a highly effective approach and is increasingly being used in clinical research and drug development. However, the processing and storage of FFPE samples are known to cause extensive degradation of RNAs, which limits the discovery of gene expression or gene fusion-based biomarkers using RNA sequencing, particularly methods reliant on Poly(A) enrichment. Recently, researchers have developed an exome targeted RNA-Seq methodology that utilizes biotinylated oligonucleotide probes to enrich RNA transcripts of interest, which could overcome these limitations. Nevertheless, the standardization of this experimental framework, including probe designs, sample multiplexing, sequencing read length, and bioinformatic pipelines, remains an essential requirement. In this study, we conducted a comprehensive comparison of three main commercially available exome capture kits and evaluated key experimental parameters, to provide the overview of the advantages and limitations associated with the selection of library preparation protocols and sequencing platforms. The results provide valuable insights into the best practices for obtaining high-quality data from FFPE samples.

Optimizing the use of a gas diffusion electrode setup for CO2 electrolysis imitating a zero-gap MEA design

The lack of a robust and standardized experimental test bed to investigate the performance of catalyst materials for the electrochemical CO2 reduction reaction (ECO2RR) is one of the major challenges in this field of research. To best reproduce and mimic commercially relevant conditions for catalyst screening and testing, gas diffusion electrode (GDE) setups attract rising attention as an alternative to conventional aqueous-based setups such as the H-cell configuration. Zero-gap electrolyzer designs show promising features for upscaling to the commercial scale. In this study, we scrutinize further our recently introduced “zero-gap GDE” setup or more correct half-cell MEA design for the CO2RR. Using an Au electrocatalyst as a model system we simulate the anode conditions in a zero-gap electrolyzer and identify/report the key experimental parameters to control the catalyst layer preparation to optimize the activity and selectivity of the catalyst. Among others, it is demonstrated that supported Au nanoparticles (NPs) result in significantly higher current densities when compared to unsupported counterparts, however, the supporting also renders the NPs prone to agglomeration during electrolysis.

Dispersive liquid-liquid microextraction coupled with gas chromatography-mass spectrometry (GC-MS) for the determination of soy sauce aroma compounds

In the present work, a dispersive liquid-liquid microextraction (DLLME) method combined with gas chromatography-mass spectrometry (GC-MS) was successfully developed for accurate determination of aroma-active components in soy sauce. Several key experimental parameters were optimized, including the type of dispersant, vortex time and the volume ratio of extractant and dispersant. The optimal conditions were 1200 μL acetone as dispersant, 800 μL dichloromethane as extractant and 3 min of vortex mixing. The proposed method was validated, achieving good linearities with R2 ≥ 0.9941, recoveries between 82 and 129% with 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF) and 4-hydroxy-2 (or 5)-ethly-5 (or 2)-methyl-3(2H)-furanone (HEMF) within 84–103%, relative standard deviations ranging from 0.02 to 8.60% with HDMF and HEMF between 0.26 and 1.44%, and limits of detection and limits of quantification in the range of 0.08–35.95 μg/L and 0.25–119.83 μg/L, respectively. The entire sample processing with DLLME was completed in roughly 15 min with a total consumption of 2 mL of organic solvent, and 93 volatiles identified in the obtained extracts, with 87.1% (81 volatiles) showing relative standard deviations lower than 10%. Compared to conventional liquid-liquid extraction (LLE), DLLME exhibited obvious advantages of simplicity, rapidity, stability and low solvent consumption, favouring the extraction of acids and ketones. This is the first application of the DLLME technique for the analysis of aroma compounds in soy sauce and is suitable for rapid determination of key aroma compounds like HDMF and HEMF, especially for routine detection and large batch analysis of soy sauce, which can provide reliable information for soy sauce flavour analysis.

Dial-In Synthesis of 'Polymer Opal' Core-Interlayer-Shell Composite Nanoparticles.

The emulsion polymerization process via which core-interlayer-shell polymer nanoparticles are synthesized is engineered to offer a crucial control of the eventual size and monodispersity of the polystyrene (PS) cores. We examine the role of key experimental parameters, optimizing the temperature, reactant purity, and agitation (stirring) rate. The subsequent addition of a poly(methyl-methacrylate) (PMMA) grafting layer and a poly(ethyl-acrylate) (PEA) shell layer produces composite particles, which are shear-orderable into opaline films, known as 'polymer opals'. We thus demonstrate pathways toward a 'dial-in' process, where the time taken to obtain the target core size is mapped to the expected resultant structural color. At reaction temperatures of 60 and 70 °C, viable conditions are found where all syntheses give an excellent level of monodispersity (polydispersity index < 0.02), suitable for interlayer and shell growth. These reports may be readily applied to a wider industrial scale fabrication pipeline for these polymeric photonic materials.

Utilization of Synthesized Copper Ferrite/Calcium Alginate Nanocomposite for Adsorption and Photocatalytic Degradation of Malachite Green

In this article, the effectiveness of two different application methods (photocatalytic degradation and adsorption) onto the created solid nanomaterials for the removal of malachite green (MG) was investigated. Copper ferrite nanoparticles (CF) and copper ferrite/calcium alginate composite (CG) were synthesized as two studied solid samples. By using XRD, TGA, FTIR, DRS, nitrogen adsorption/desorption isotherm, pHPZC, SEM, and TEM, the physicochemical and morphological properties of the solid samples were tested. Sample dose, pH, initial MG concentration, shaking time, ionic strength, UV light power, and temperature were the key experimental parameters that were established. The obtained results demonstrated that at 40 °C, CG reached a greater adsorption capacity (297.62 mg/g). The spontaneous, endothermic, and advantageous adsorption process of MG was proved by the best fitting of pseudo-second order, Elovich, intra-particle diffusion, Langmuir, Dubinin-Radushkevich, and Temkin models onto all the produced materials. The maximum percentage of MG degradation by CG (89.9%) was accomplished by utilizing 1.0 g/L of catalyst mass, an initial MG concentration of 10 mg/L, and 33 W. Arrhenius and Eyring–Polanyi models well applied the MG photodegradation onto the catalyst surface.

The analysis of protein recruitment to laser microirradiation-induced DNA damage in live cells: Best practices for data analysis

Laser microirradiation coupled with live-cell fluorescence microscopy is a powerful technique that has been used widely in studying the recruitment and retention of proteins at sites of DNA damage. Results obtained from this technique can be found in published works by both seasoned and infrequent users of microscopy. However, like many other microscopy-based techniques, the presentation of data from laser microirradiation experiments is inconsistent; papers report a wide assortment of analytic techniques, not all of which result in accurate and/or appropriate representation of the data. In addition to the varied methods of analysis, experimental and analytical details are commonly under-reported. Consequently, publications reporting data from laser microirradiation coupled with fluorescence microscopy experiments need to be carefully and critically assessed by readers. Here, we undertake a systematic investigation of commonly reported corrections used in the analysis of laser microirradiation data. We validate the critical need to correct data for photobleaching and we identify key experimental parameters that must be accounted for when presenting data from laser microirradiation experiments. Furthermore, we propose a straightforward, four-step analytical protocol that can readily be applied across platforms and that aims to improve the quality of data reporting in the DNA damage field.

Simulation research on surface growth process of positive and negative frequency detuning chromium atom lithographic gratings

Chromium atom photolithography gratings are a promising technology for the development of nanoscale length standard substances due to their high accuracy, uniformity, and consistency. However, the inherent difference between the interaction of positive and negative frequency detuning standing wave field and the atoms can cause a difference in the adjacent peak-to-valley heights of the grating in positive and negative frequency detuning chromium atom lithography, which greatly reduces its accuracy. In this study, we performed a controlled variable growth simulation using the semi-classical theoretical model and Monte Carlo method with trajectory tracking and ballistic deposition methods to investigate the influence of key experimental parameters on the surface growth process of positive and negative frequency detuning atomic lithography gratings. We established a theoretical model based on simulation results and summarized empirical equations to guide the selection of experimental parameters. Our simulations achieved uniform positive and negative frequency detuning atomic lithography gratings with a period of 1/4 of the wavelength corresponding to the atomic transition frequency, and adjacent peak-to-valley heights differing by no more than 2 nm, providing an important theoretical reference for the controllable fabrication of these gratings.

A benchmark of computational pipelines for single-cell histone modification data

BackgroundSingle-cell histone post translational modification (scHPTM) assays such as scCUT&Tag or scChIP-seq allow single-cell mapping of diverse epigenomic landscapes within complex tissues and are likely to unlock our understanding of various mechanisms involved in development or diseases. Running scHTPM experiments and analyzing the data produced remains challenging since few consensus guidelines currently exist regarding good practices for experimental design and data analysis pipelines.ResultsWe perform a computational benchmark to assess the impact of experimental parameters and data analysis pipelines on the ability of the cell representation to recapitulate known biological similarities. We run more than ten thousand experiments to systematically study the impact of coverage and number of cells, of the count matrix construction method, of feature selection and normalization, and of the dimension reduction algorithm used. This allows us to identify key experimental parameters and computational choices to obtain a good representation of single-cell HPTM data. We show in particular that the count matrix construction step has a strong influence on the quality of the representation and that using fixed-size bin counts outperforms annotation-based binning. Dimension reduction methods based on latent semantic indexing outperform others, and feature selection is detrimental, while keeping only high-quality cells has little influence on the final representation as long as enough cells are analyzed.ConclusionsThis benchmark provides a comprehensive study on how experimental parameters and computational choices affect the representation of single-cell HPTM data. We propose a series of recommendations regarding matrix construction, feature and cell selection, and dimensionality reduction algorithms.

Correlating laser energy with compositional and atomic-level information of oxides in atom probe tomography

Atom probe tomography (APT) is a 3D analysis technique that offers unique chemical accuracy and sensitivity with sub-nanometer spatial resolution. There is an increasing interest in the application of APT to complex oxides materials, giving new insight into the relation between local variations in chemical composition and emergent physical properties. However, in contrast to the field of metallurgy, where APT is routinely applied to study materials at the atomic level, complex oxides and their specific field evaporation mechanisms are much less explored. Here, we perform APT measurements on the hexagonal manganite ErMnO3 and systematically study the effect of different experimental parameters on the measured composition and structure. We demonstrate that both the mass resolving power (MRP) and compositional accuracy can be improved by increasing the charge-state ratio (CSR) working at low laser energy (< 5 pJ) for a given fixed detection rate. Furthermore, we observe a substantial preferential retention of Er atoms, which is suppressed at higher CSRs. We explain our findings based on fundamental field evaporation concepts, expanding the knowledge about the impact of key experimental parameters and the field evaporation process in complex oxides in general.

Application of quality-by-design for adopting an environmentally green fluorogenic determination of benoxinate hydrochloride in eye drops and artificial aqueous humour

Herein, a sensitive and selective spectrofluorimetric method has been developed for the determination of the ocular local anesthetic benoxinate hydrochloride (BEN-HCl) in eye drops and artificial aqueous humour. The proposed method is based on the interaction of fluorescamine with the primary amino group of BEN-HCl at room temperature. Following the excitation of the reaction product at 393 nm, the emitted relative fluorescence intensity (RFI) was measured at 483 nm. The key experimental parameters were carefully examined and optimized by adopting an analytical quality-by-design approach. The method used a two-level full factorial design (24 FFD) to obtain the optimum RFI of the reaction product. The calibration curve was linear at the range of 0.10–1.0 μg/mL of BEN-HCl with sensitivity down to 0.015 μg/mL. The method was applied for analyzing the BEN-HCl eye drops and could also assess its spiked levels in artificial aqueous humour with high % recoveries (98.74–101.37%) and low SD values (≤ 1.11). To investigate the green profile of the proposed method, a greenness assessment was performed with the aid of the Analytical Eco-Scale Assessment (ESA) and GAPI. The developed method obtained a very high ESA rating score in addition to being sensitive, affordable, and environmentally sustainable. The proposed method was validated according to ICH guidelines.

Overview of ICARUS-A Curated, Open Access, Online Repository for Atmospheric Simulation Chamber Data.

Atmospheric simulation chambers continue to be indispensable tools for research in the atmospheric sciences. Insights from chamber studies are integrated into atmospheric chemical transport models, which are used for science-informed policy decisions. However, a centralized data management and access infrastructure for their scientific products had not been available in the United States and many parts of the world. ICARUS (Integrated Chamber Atmospheric data Repository for Unified Science) is an open access, searchable, web-based infrastructure for storing, sharing, discovering, and utilizing atmospheric chamber data [https://icarus.ucdavis.edu]. ICARUS has two parts: a data intake portal and a search and discovery portal. Data in ICARUS are curated, uniform, interactive, indexed on popular search engines, mirrored by other repositories, version-tracked, vocabulary-controlled, and citable. ICARUS hosts both legacy data and new data in compliance with open access data mandates. Targeted data discovery is available based on key experimental parameters, including organic reactants and mixtures that are managed using the PubChem chemical database, oxidant information, nitrogen oxide (NOx) content, alkylperoxy radical (RO2) fate, seed particle information, environmental conditions, and reaction categories. A discipline-specific repository such as ICARUS with high amounts of metadata works to support the evaluation and revision of atmospheric model mechanisms, intercomparison of data and models, and the development of new model frameworks that can have more predictive power in the current and future atmosphere. The open accessibility and interactive nature of ICARUS data may also be useful for teaching, data mining, and training machine learning models.

Remediation of Cr(VI)-contaminated soil using self-sustaining smoldering

Self-sustaining smoldering is an emerging technology for nonaqueous-phase liquid remediation; however, it is rarely applied for Cr(VI)-contaminated soil treatment. In this study, self-sustaining smoldering using rice straw (RS) as a surrogate fuel was applied to remediate Cr(VI)-contaminated soil for the first time. Thirteen one-dimensional vertical smoldering experiments were conducted to investigate the effectiveness of the smoldering method and the effects of key experimental parameters on smoldering remediation performance. Smoldering was observed to be self-sustaining within the range of RS particle size from <0.16 to 2.00–4.00 mm, airflow from 0.2 to 1 m3/h, and Cr(VI)-impacted soil/RS ratios from 2:1 to 6:1. The Cr(VI)-contaminated soil was effectively remediated, which was confirmed by lowered Cr(VI) contents in the treated samples (decreased by 52.22–86.57%) and the elevated fraction of Cr oxidizable and residual form (increased by 1.14–3.30 and 2.97–4.00 times, respectively), compared to the control. The reducing gases (CO and CxHy) generated during the smoldering played a crucial role in the remediation process. The contents of available P and K in the remediated soil containing the remaining biochar and ash increased, thus improving soil reusability. Hence, this study shows that smoldering with RS as supplemental fuel is a promising Cr(VI)-contaminated soil management technique without supplying substantial external energy.

A TLC-direct bioassay method for detection of anti-lipid peroxidation constituents from fruits of Perilla frutescens

A practical TLC-direct bioassay method was established for screening and evaluating antioxidant activity. The method was based on series of reactions. Irradiation of linoleic acid with UV 254 nm produced lipid peroxides. Upon heating, the peroxides were converted into malondialdehyde, which combined with thiobarbituric acid to a red pigment with a maximum absorption at 535 nm. Following a TLC separation, substance with anti-lipid peroxidation activity showed white spots/zones against red background on the TLC plate. The proposed method was established by the dot blot test, and validated with respect to selectivity, sensitivity, linearity, precision, and recovery after optimizing key experimental parameters. In an exemplary screening for antioxidant constituents from Perilla fruits, two active zones were discovered and tentatively characterized as salviaflaside and rosmarinic acid by TLC-interface-ESI-MS, respectively. Further verification by HPTLC-bioassay-guided-isolation was carried out and in addition to salviaflaside and rosmarinic acid, also luteolin 5-O-β-d-glucopyranoside and 3′-dehydroxyl-rosmarinic acid-3-O-β-D-glucoside were discovered to show prominent anti-lipid peroxidation activity.

Harmonizing Biopredictive Methodologies Through the Product Quality Research Institute (PQRI) Part I: Biopredictive Dissolution of Ibuprofen and Dipyridamole Tablets

Assessing in vivo performance to inform formulation selection and development decisions is an important aspect of drug development. Biopredictive dissolution methodologies for oral dosage forms have been developed to understand in vivo performance, assist in formulation development/optimization, and forecast the outcome of bioequivalence studies by combining them with simulation tools to predict plasma profiles in humans. However, unlike compendial dissolution methodologies, the various biopredictive methodologies have not yet been harmonized or standardized. This manuscript presents the initial phases of an effort to develop best practices and move toward standardization of the biopredictive methodologies through the Product Quality Research Institute (PQRI, https://pqri.org) entitled “The standardization of in vitro predictive dissolution methodologies and in silico bioequivalence study Working Group.” This Working Group (WG) is comprised of participants from 10 pharmaceutical companies and academic institutes. The project will be accomplished in a total of five phases including assessing the performance of dissolution protocols designed by the individual WG members, and then building “best practice” protocols based on the initial dissolution profiles. After refining the “best practice” protocols to produce equivalent dissolution profiles, those will be combined with physiologically based biopharmaceutics models (PBBM) to predict plasma profiles. In this manuscript, the first two of the five phases are reported, namely generating biopredictive dissolution profiles for ibuprofen and dipyridamole and using those dissolution profiles with PBBM to match the clinical plasma profiles. Key experimental parameters are identified, and this knowledge will be applied to build the “best practice” protocol in the next phase.Graphical

Moiré fringes in conductive atomic force microscopy

Moiré physics plays an important role in characterization of functional materials and engineering of physical properties in general, ranging from strain-driven transport phenomena to superconductivity. Here, we report on the observation of moiré fringes in conductive atomic force microscopy (cAFM) scans gained on the model ferroelectric Er(Mn,Ti)O3. By performing a systematic study of the impact of key experimental parameters on the emergent moiré fringes, such as scan angle and pixel density, we demonstrate that the observed fringes arise due to a superposition of the applied raster scanning and sample-intrinsic properties, classifying the measured modulation in conductance as a scanning moiré effect. Our findings are important for the investigation of local transport phenomena in moiré engineered materials by cAFM, providing a general guideline for distinguishing extrinsic from intrinsic moiré effects. Furthermore, the experiments provide a possible pathway for enhancing the sensitivity, pushing the resolution limit of local transport measurements by probing conductance variations at the spatial resolution limit via more long-ranged moiré patterns.

Multiple stress creep and recovery test for bituminous binders – influence of several key experimental parameters

The Multiple Stress Creep and Recovery test is recognised to better characterise the high-temperature property of bituminous binders than the traditional methods, especially for polymer modified bitumen (PmB). However, some experimental parameters may affect the test results, such as the preloading, measurement location, stress level. In this study, the effects of these parameters were evaluated through an interlaboratory experiment. Four bituminous binders were short-term aged and analysed by five different laboratories. The variability in most results met the requirements of the European standard, while some failed to pass the American precision criteria. The preloading at 0.1 kPa with ten cycles was found to have a recordable impact on PmB samples, but a less significant effect was observed for the unmodified ones. With the measurement locations, the influence is limited compared to other parameters. As for stress sensitivity, higher stresses lead to remarkable differences.

Electrostatically Driven Vertical Combinatorial Patterning of Colloidal Nano-Objects

The hierarchically directed assembly of multiple types of colloidal nano-objects on surfaces is of interest for developing disruptive applications combining their original properties. We propose herein a versatile, electrostatically driven strategy to arrange various kinds of colloids vertically in the shape of 3D micropatterns by nanoxerography. We made the proof of concept of this vertical combinatorial nano-object patterning using two types of photoluminescent CdSe(S)/CdZnS core/shell nanoplatelets emitting in the red and green wavelengths as model colloidal nanoparticles. The key experimental parameters were investigated to tune the thickness of each independent level of nanoplatelets within the vertical stack. We finally applied such a concept to make dual-colored nanoplatelet patterns. Interestingly, we proved numerically that the relatively high index of the nanoplatelet level is responsible for the partially directed emissions observed in photoluminescence experiments.

Revisiting “Non-Thermal” Batch Microwave Oven Inactivation of Microorganisms

Over the last few decades there has been active discussion concerning the mechanisms involved in “non-thermal” microwave-assisted inactivation of microorganisms. This work presents a novel non-invasive acoustic measurement of a domestic microwave oven cavity-magnetron operating at fo = 2.45 ± 0.05 GHz (λo ~ 12.2 cm) that is modulated in the time-domain (0 to 2 minutes). The measurements reveal the cavity-magnetron cathode filament cold-start warm-up period and the pulse width modulation periods (time-on time-off and base-time period, where time-on minus base-time = duty cycle). The waveform information is used to reconstruct historical microwave “non-thermal” homogeneous microorganism inactivation experiments: where tap-water is used to mimic the microorganism suspension; and ice, crushed ice, and ice slurry mixture are used as the cooling media. The experiments are described using text, diagrams, and photographs. Four key experimental parameters are indentified that influence the suspension time-dependent temperature profile. First, where the selected process time > the time-base, the cavity-magnetron continuous wave rated power should be used for each second of microwave illumination. Second, external crushed ice and ice slurry baths induce different cooling profiles due to difference in their heat absorption rates. In addition external baths may shield the suspension resulting in a retarding of the time-dependent heating profile. Third, internal cooling systems dictate that the suspension is directly exposed to microwave illumination due to the absence of surrounding ice volume. Fourth, four separated water dummy-loads isolate and control thermal heat transfer (conduction) to and from the suspension, thereby diverting a portion of the microwave power away from the suspension. Energy phase-space projections were used to compare the “non-thermal” energy densities of 0.03 to 0.1 kJ·m-1 at 800 W with reported thermal microwave-assisted microorganism inactivation energy densities of 0.5 to 5 kJ·m-1 at 1050 ± 50 W. Estimations of the “non-thermal” microwave-assisted root mean square of the electric field strength are found to be in the range of 22 to 41.2 V·m-1 for 800 W.