Experimental Conditions Research Articles

Exploration of reference genes for the development of a diagnostic kit on vascular aging in human saliva.

Identifying reliable biomarkers in saliva can be a promising approach to developing a rapid diagnostic kit for detecting vascular aging. This study investigated the most suitable reference gene for polymerase chain reaction (PCR) in saliva that is not affected by vascular aging variables. Whole saliva samples were collected to assess the expression of reference genes: actin beta (ACTB), 18S ribosomal RNA (18S rRNA), beta-2-microglobulin, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The most abundantly expressed gene was 18S rRNA, and the least expressed gene was GAPDH. Four genes were ranked according to their relative stability, as determined by mathematical algorithms, indicating that ACTB and 18S rRNA were stably expressed as reference genes. 18S rRNA was identified as the most promising reference gene for detecting systemic diseases using saliva from patients with vascular aging in these limited experimental conditions.

Exact ASP Counting with Compact Encodings

Answer Set Programming (ASP) has emerged as a promising paradigm in knowledge representation and automated reason- ing owing to its ability to model hard combinatorial problems from diverse domains in a natural way. Building on advances in propositional SAT solving, the past two decades have wit- nessed the emergence of well-engineered systems for solv- ing the answer set satisfiability problem, i.e., finding mod- els or answer sets for a given answer set program. In re- cent years, there has been growing interest in problems be- yond satisfiability, such as model counting, in the context of ASP. Akin to the early days of propositional model count- ing, state-of-the-art exact answer set counters do not scale well beyond small instances. Exact ASP counters struggle with handling larger input formulas. The primary contribu- tion of this paper is a new ASP counting framework, called sharpASP, which counts answer sets avoiding larger input formulas. This relies on an alternative way of defining answer sets that allows lifting of key techniques developed in the con- text of propositional model counting. Our extensive empirical analysis over 1470 benchmarks demonstrates significant per- formance gain over current state-of-the-art exact answer set counters. Specifically, by using sharpASP, we were able to solve 1062 benchmarks with PAR2 score of 3082 whereas using prior state-of-the-art, we could only solve 895 bench- marks with PAR2 score of 4205, all other experimental con- ditions being the same.

A numerical compass for experiment design in chemical kinetics and molecular property estimation

Kinetic process models are widely applied in science and engineering, including atmospheric, physiological and technical chemistry, reactor design, or process optimization. These models rely on numerous kinetic parameters such as reaction rate, diffusion or partitioning coefficients. Determining these properties by experiments can be challenging, especially for multiphase systems, and researchers often face the task of intuitively selecting experimental conditions to obtain insightful results. We developed a numerical compass (NC) method that integrates computational models, global optimization, ensemble methods, and machine learning to identify experimental conditions with the greatest potential to constrain model parameters. The approach is based on the quantification of model output variance in an ensemble of solutions that agree with experimental data. The utility of the NC method is demonstrated for the parameters of a multi-layer model describing the heterogeneous ozonolysis of oleic acid aerosols. We show how neural network surrogate models of the multiphase chemical reaction system can be used to accelerate the application of the NC for a comprehensive mapping and analysis of experimental conditions. The NC can also be applied for uncertainty quantification of quantitative structure–activity relationship (QSAR) models. We show that the uncertainty calculated for molecules that are used to extend training data correlates with the reduction of QSAR model error. The code is openly available as the Julia package KineticCompass.Graphical

Quantifying noise effects in optical measures of excited state transport.

Time-resolved microscopy is a widely used approach for imaging and quantifying charge and energy transport in functional materials. While it is generally recognized that resolving small diffusion lengths is limited by measurement noise, the impacts of noise have not been systematically assessed or quantified. This article reports modeling efforts to elucidate the impact of noise on optical probes of transport. Excited state population distributions, modeled as Gaussians with additive white noise typical of experimental conditions, are subject to decay and diffusive evolution. Using a conventional composite least-squares fitting algorithm, the resulting diffusion constant estimates are compared with the model input parameter. The results show that heteroscedasticity (i.e., time-varying noise levels), insufficient spatial and/or temporal resolution, and small diffusion lengths relative to the magnitude of noise lead to a surprising degree of imprecision under moderate experimental parameters. Moreover, the compounding influence of low initial contrast and small diffusion length leads to systematic overestimation of diffusion coefficients. Each of these issues is quantitatively analyzed herein, and experimental approaches to mitigate them are proposed. General guidelines for experimentalists to rapidly assess measurement precision are provided, as is an open-source tool for customizable evaluation of noise effects on time-resolved microscopy transport measurements.

Comparative effectiveness of carbon nanoparticles and biochar in alleviating copper stress in corn (Zea mays L.)

The application of carbon nanoparticles (CNPs) and biochar in agriculture for improving plant health and soil quality and alleviating metal stress offers alternative approaches to meet the ever-increasing demand for food. However, poor understanding of their roles in improving crop production under Cu stress represents a significant obstacle to their wide application in agriculture. To clarify how CNPs and biochar affect corn (Zea mays L.) seed germination, seedling growth, plant health, and nutrient uptake under different Cu stress levels, soil-less Petri-dish and greenhouse soil-based bioassays were conducted. The results revealed that CNPs and biochar stimulated corn seed germination and seedling growth. Besides, they were effective in immobilizing Cu2+ sorption in sandy soil and alleviating Cu stress for plant growth, as shown by the increased plant height and dry biomass. The plant nutrient uptake efficiency (NUE) was significantly increased by CNPs, with a maximum increase of 63.1% for N and 63.3% for K at the highest Cu2+ stress level (400 mg Cu2+ L−1). In contrast, non-significant effects on NUE were observed with biochar treatments regardless of Cu stress levels. Interestingly, CNPs significantly increased plant uptake of Cu in the Petri dish test, while biochar inhibited plant uptake of Cu under both experimental conditions. Principle component analysis (PCA) and Pearson correlation analysis indicated that CNPs mitigated Cu stress mainly by elevating antioxidant enzyme activities, enhancing plant photochemical efficiency, and increasing plant uptake of N and K, while biochar was more likely to reduce bioavailability and uptake of Cu in the plant. These findings have great implications for the application of CNPs and biochar as plant growth stimulators and de-toxicity agents in agriculture.

Experimental conditions for efficient retention of vascular endothelial cells on channel wall using lipid bubbles and acoustic interference

In order to fabricate multi-layered artificial blood vessels, bubble-surrounded cells were retained on the wall in a flow channel using the phase sweeping of interferential acoustic field. First, spatial distribution of acoustic intensity was defined to evaluate retention performance. Comparing between various acoustic fields, we found appropriate acoustic intensity for retention of the cells. Next, phase sweeping of the acoustic field was conducted to increase the retained area of the cells by varying sweep velocity, sweep direction, and the amplitudes of sound pressure. As the result, an interferential acoustic field with a balanced sound pressures of 200 kPa-pp at a sweep velocity of 100 mm s−1, which was 10 times higher than the flow, and the sweep direction against the flow, obtained a retained area 1.6 times larger than that without sweeping. We will apply the conditions based on the results for the future 3D fabrication of artificial blood vessels.

Uranium accumulation in environmentally relevant microplastics and agricultural soil at acidic and circumneutral pH

The co-occurrence of microplastics (MPs) with potentially toxic metals in the environment stresses the need to address their physicochemical interactions and the potential ecological and human health implications. Here, we investigated the reaction of aqueous U with agricultural soil and high-density polyethylene (HDPE) through the integration of batch experiments, microscopy, and spectroscopy. The aqueous initial concentration of U (100 μM) decreased between 98.6 and 99.2 % at pH 5 and between 86.2 and 98.9 % at pH 7.5 following the first half hour of reaction with 10 g of soil. In similar experimental conditions but with added HDPE, aqueous U decreased between 98.6 and 99.7 % at pH 5 and between 76.1 and 95.2 % at pH 7.5, suggesting that HDPE modified the accumulation of U in soil as a function of pH. Uranium-bearing precipitates on the cracked surface of HDPE were identified by SEM/EDS after two weeks of agitation in water at both pH 5 and 7.5. Accumulation of U on the near-surface region of reacted HDPE was confirmed by XPS. Our findings suggest that the precipitation of U was facilitated by the weathering of the surface of HDPE. These results provide insights about surface-mediated reactions of aqueous metals with MPs, contributing relevant information about the mobility of metals and MPs at co-contaminated agricultural sites.

A Rapid and Easy Procedure of Enzyme Biosensor based on Nitrogen-Doped Graphene for Detection of Methyl Parathion in CHM

Methyl parathion (MP), an organophosphorus pesticide that is frequently used to control pests during the planting process of Chinese herbal medicine (CHM), has been used without sufficient control, leading to excessive residues on the surface of CHM, which has a serious impact on the quality and safety of CHM and their preparations. Consequently, it is crucial to carefully control MP during the cultivation, processing, and manufacture of CHM. Based on this, nitrogen-doped graphene (N-Gr) with a high conductivity and chitosan (CS) with good stability were used to modify the glassy carbon electrode (GCE). Subsequently, the prussian blue (PB) with catalytic activity and gold nanoparticles (AuNPs) with excellent biocompatibility were deposited by the electrodeposition method to form the AuNPs/PB/CS@N-Gr/GCE. Then, the acetylcholinesterase (AChE) was effectively immobilized on the electrode surface by covalent bonding between AuNPs and AChE through gold-sulfhydryl bonds. Finally, a rapid and easy procedure of enzyme biosensor (AChE/AuNPs/PB/CS@N-Gr/GCE) for sensitive detection of MP pesticide residues was fabricated. Herein, PB catalyzes the redox reaction of thiocholine, which is produced when acetylthiocholine iodide (ATCHI) undergoes efficient hydrolysis catalyzed by AChE. This process effectively promoted electron transfer, amplifying the sensor’s response signal. After the experimental conditions are optimized, the limit of detection (LOD) for MP is found to be 9.47 × 10−5 μg ml−1. Exhibits a good linear relationship within the concentration range of 1 × 10−3 μg ml−1 ∼ 1 × 101 μg ml−1. Significantly, the fabricated enzyme biosensor excels in swiftly and sensitively detecting trace amounts of MP in real examples. Furthermore, it exhibits robust stability and reproducibility. The excellent performance of this enzyme biosensor not only offers a rapid and easy way to identify and find minute amounts of trace MP pesticide residues in CHM, but also serves as a technical guide for the creation of new, portable, and on-site pesticide residue detection technology for law enforcement.

Genome-scale metabolic modeling of Thraustochytrium sp. RT2316-16: Effects of nutrients on metabolism.

Marine thraustochytrids produce metabolically important lipids such as the long-chain omega-3 polyunsaturated fatty acids, carotenoids, and sterols. The growth and lipid production in thraustochytrids depends on the composition of the culture medium that often contains yeast extract as a source of amino acids. This work discusses the effects of individual amino acids provided in the culture medium as the only source of nitrogen, on the production of biomass and lipids by the thraustochytrid Thraustochytrium sp. RT2316-16. A reconstructed metabolic network based on the annotated genome of RT2316-16 in combination with flux balance analysis was used to explain the observed growth and consumption of the nutrients. The culture kinetic parameters estimated from the experimental data were used to constrain the flux via the nutrient consumption rates and the specific growth rate of the triacylglycerol-free biomass in the genome-scale metabolic model (GEM) to predict the specific rate of ATP production for cell maintenance. A relationship was identified between the specific rate of ATP production for maintenance and the specific rate of glucose consumption. The GEM and the derived relationship for the production of ATP for maintenance were used in linear optimization problems, to successfully predict the specific growth rate of RT2316-16 in different experimental conditions.

A Curb-Detection Network with a Tri-Plane BEV Encoder Module for Autonomous Delivery Vehicles

Curb detection tasks play a crucial role in the perception of the autonomous driving environment for logistics vehicles. With the popularity of multi-modal sensors under the BEV (Bird’s Eye View) paradigm, curb detection tasks are increasingly being integrated into multi-task perception networks, achieving robust detection results. This paper modifies and integrates the tri-plane spatial feature representation method of the EG3D network from the field of 3D reconstruction into a BEV-based multi-modal sensor detection network, including LiDAR, pinhole cameras, and fisheye cameras. The system collects a total of 24,350 frames of data under real road conditions for experimentation, proving the effectiveness of the proposed method.

Exploring the future: introduction of a new paradigm to examine intergroup experiences

Intergroup contact theory, as one of the most established research strands in social psychology, has mostly relied on overall measured averages of intergroup contact over larger time spans. Yet, in everyday life, intergroup contact experiences are far more complex: they are sequential and cumulative and may vary on a range of dimensions, such as, for example, their perceived valence. In this article, I introduce a new experimental paradigm, primarily developed as a research manipulation, to examine intergroup contact, manipulated on the unit of single interactions in a video-game setting, which can also be run from a web server, so that participants can join from their home computers. Depending on experimental condition, in a first study, participants rated the perceived quality of multiple positive or negative intergroup interactions with an alien species and intergroup attitudes in a storytelling questionnaire setting (Pilot Study, N = 242). Study 1 implemented these positive and negative interactions in a video game, which was played in the laboratory (N = 44), and examined their effects on the perceived contact quality and intergroup attitudes. Study 2 (N = 64) utilized a web-based version of the video game to test the effects on intergroup attitudes. In all three studies participants in the positive condition evaluated the interactions, as well as the overall outgroup, more positive than participants in the negative condition. Furthermore, Study 1 and 2 explored participants' perception of the virtual environment and previous experiences with video games. The results suggest that specifically developed video games offer new pathways to study intergroup interactions.

Three-Layer Electrorefining of Molten Zinc Held on Porous Carbon or Silica Sheets in Molten LiCl–KCl–ZnCl2

We investigated a three-layer electrolysis process utilizing porous holding materials with poor wettability to molten metal, which enables to establish a three-layer configuration of metal(l)/electrolyte(l)/metal(l) by holding metals above the electrolyte regardless of their densities. In this study, porous carbon or silica sheets were used as the holding materials for electrorefining experiments of Zn metal in molten LiCl–KCl–ZnCl2 at 723 K. Three types of experiments were carried out focusing on anodic polarization, electrorefining with cathodic carbon, and three-layer electrolysis using liquid Zn as cathode. The concentration of impurity elements in the Zn was reduced by a factor of 8 to 200 in this experimental condition, highlighting the purification effectiveness of the method. From the results obtained, we have identified certain challenges associated with the three-layer electrolysis process. Furthermore, we discuss potential prospects for industrialization.

Effect of annealing temperature and doping concentrations on structure and optical properties of Eu3+-doped TiO2 nanomaterials

In this study, we successfully synthesized europium-doped TiO2 (TiO2:Eu3+) nanomaterials (NMs) with crystalline sizes ranging from 6.5 to 71.7 nm through a sol-gel method. Analysis of X-ray diffraction (XRD) patterns and ultraviolet-visible (UV-Vis) spectra indicates that the substitution of smaller-sized Ti4+ ions (0.745 Å) by larger-sized Eu3+ ions (0.947 Å) was more efficient at higher doping concentrations and annealing temperatures. Photoluminescence (PL) and photoluminescence excitation (PLE) spectra of the synthesized TiO2:7%Eu3+NMs exhibit a strong red emission band peaking at 613 nm and remarkable absorption in the blue light region centered at 463 nm, making them suitable for use in white light-emitting diode (WLED) applications. Our findings reveal that both annealing temperature and doping concentration significantly influence the structure and properties of these materials. Besides, the research team has seen, under the experimental conditions, the TiO2:7%Eu3+ sample annealed at 800°C exhibits the highest PL intensity. These results underscore the potential of the synthesized TiO2:Eu3+ NMs as red-emitting materials for WLED applications.

The interpretation of animate nouns in child and adult Mandarin: from the Universal Grinder to syntactic structure

Abstract Using animate nouns to refer to entities in the world involves a complex interaction of ontology, cognition and language. The present study evaluates two accounts of the use of animate nouns, with Mandarin Chinese as the vehicle for testing between the competing accounts. One account was proposed by Cheng et al. (2008. How universal is the Universal Grinder? In Marjo van Koppen & Bert Botma (eds.), Linguistics in the Netherlands, 50–62. Amsterdam & Philadelphia: John Benjamins). These researchers contend that the count interpretation is basic for Mandarin animate nouns, due to a lexical blocking effect. To access the alternative, mass interpretation requires some kind of pragmatic coercion. A second account was proposed by Pelletier, based on English (1975. Non-Singular reference: Some preliminaries. Philosophia 5(4). 451–465; 2012. Lexical nouns are both +MASS and +COUNT, but they are neither +MASS nor + COUNT. In Diane Massam (ed.), Count and mass across languages, 9–26. Oxford: Oxford University Press). We extend this account to Mandarin animate nouns, proposing that they are encoded in the mental lexicon with both a count sense and a mass sense. To adjudicate between the accounts, we conducted four experiments that were designed to assess the interpretation assigned to animate nouns by Mandarin-speaking children and adults. The experimental conditions manipulated both the syntactic structures of the sentences and the non-linguistic contexts in which those sentences were presented. The experimental findings support our proposal that both mass and count interpretations of animate nouns are available to children and adults when sentences are presented in contexts that are congruent with these interpretations. The findings also suggest that syntactic structure is an even more critical factor in determining the interpretation that is assigned to animate nouns in Mandarin.

A deep learning approach for quantum dots sizing from wide-angle X-ray scattering data

AbstractDisclosing the full potential of functional nanomaterials requires the optimization of synthetic protocols and an effective size screening tool, aiming at triggering their size-dependent properties. Here we demonstrate the successful combination of a wide-angle X-ray total scattering approach with a deep learning classifier for quantum dots sizing in both colloidal and dry states. This work offers a compelling alternative to the lengthy process of deriving sizing curves from transmission electron microscopy coupled with spectroscopic measurements, especially in the ultra-small size regime, where empirical functions exhibit larger discrepancies. The core of our algorithm is an all-convolutional neural network trained on Debye scattering equation simulations, incorporating atomistic models to capture structural and morphological features, and augmented with physics-informed perturbations to account for different predictable experimental conditions. The model performances are evaluated using both wide-angle X-ray total scattering simulations and experimental datasets collected on lead sulfide quantum dots, resulting in size classification accuracies surpassing 97%. With the developed deep learning size classifier, we overcome the need for calibration curves for quantum dots sizing and thanks to the unified modeling approach at the basis of the total scattering method implemented, we include simultaneously structural and microstructural aspects in the classification process. This algorithm can be complemented by incorporating input information from other experimental observations (e.g., small angle X-ray scattering data) and, after proper training with the pertinent simulations, can be extended to other classes of quantum dots, providing the nanoscience community with a powerful and broad tool to accelerate the development of functional (nano)materials.

Adhesion measurement of living cells based on electrical impedance.

Cells adherence provides specific information about physiology and pathology, the adhesion measurement between living cells and nanostructures can be measured by atomic force microscopy, but this detection technique is difficult to operate and costly. The adhesion height and effective contact area between cells and substrates are also the key factors affecting measurement value of the overall impedance. These factors change with structural parameters of the substrates, so the adhesion measurement between living cells and substrate can be indirectly reflected by the impedance value. To establish a mapping relationship between the impedance measurement and the adhesion measurement of living cells. The possibility of dynamic measurement of adhesion is realized by this method, and the experimental process is simplified. Laser interference technology was used to prepare nanoarray structures with different periods on the surface of silicon wafers for cells culture. Under the same experimental conditions, the impedance of living cells on the substrates of different cycle sizes were measured. The adhesion between cells and different substrates were analyzed by measuring impedance after the interaction between cells and substrate. The adhesion of living cells on the substrates of different sizes be analyzed, and the mapping relationship between the impedance and the adhesion measurement was established. The results showed that, the larger the impedance value between cells and substrate, the larger the effective contact area and the smaller the gap between them. The difference of adhesion height and effective adhesion area between living cells and substrates were obtained. This paper, a new method to measure the adhesion properties of living cells is presented, which provides theoretical basis for the related research.

High-resolution ro-vibrational spectrum of H[formula omitted]S in highly excited vibrational states: Re-visiting the first decade

High resolution spectra of the H232S hydrogen sulfide are re-analyzed in the region of its first decade. Thanks to the improvement of the experimental conditions (in particular, an increase in both the instrumental resolution and the effective absorption path length by 1.5 times), on the one hand, and of the use of a more correct Hamiltonian model (which additionally takes into account the interactions of the bands under study with the ν1+4ν2 and 4ν2+ν3 bands), on the other hand, the information obtained as a result of the analysis of experimental data has been significantly expanded and improved compared to the previous status. In particular, (1) the total number of assigned lines has been increased by approximately 15 percent, (2) the maximum values of quantum numbers Jmax and Kamax for the assigned lines have been increased for the studied bands in average by 20–25 percent, (3) the number of obtained ”experimental“ energy levels of the upper vibrational states (especially for the (121) and (022) vibrational states) has been significantly increased, (4) despite the increase in the number of initial vibrational–rotational energies and quantum numbers Jmax and Kamax, the value of the standard deviation drms has improved 2.7 times for the obtained upper vibrational–rotational energies.

Molecular interaction of human serum albumin with gemini surfactant, 1,6 bis (N,N-hexadecyl dimethyl ammonium) bromide: Influence of micelles and pH

The interaction between human seram albumin (HSA) and a cationic gemini (dimeric) surfactant, 1,6 bis (N,N-hexadecyl dimethyl ammonium) bromide (16–6-16) has been investigated. Various analytical techniques, including UV–vis spectroscopy, fluorescence spectroscopy, lifetime fluorescence measurement, circular dichroism (CD), and atomic force microscope (AFM), were employed to investigate these interaction studies. The experiments were conducted in aqueous environments at three distinct pH levels (viz., below (4.0), at (4.7), and above (7.0) the isoelectric point (IP)), as well as both above and below the critical micellar concentration (CMC) of the surfactant (16–6-16). In these experimental conditions, HSA experiences conformational changes, leading to unfolding and denaturation as a result of its interaction with the gemini surfactant molecules (16–6-16). The extent of these conformational changes is found to be associated with both the degree of surfactant partial intercalation and the characteristics (size and charge) of the surfactant aggregates formed. The AFM microscopy studies provide insights into the topographical structural alterations occurring above, at, and below the CMC. Molecular docking analysis further validates the interaction between the protein (HSA) and the gemini surfactant (16–6-16) at a molecular level.

Micro/nanofluidic device for tamsulosin therapeutic drug monitoring in patients with benign prostatic hyperplasia at point of care.

Discovering the balance between toxicity and efficacy for many drugs requires therapeutic drug monitoring (TDM) of their concentrations in the blood. Here, a hot-embossed microfluidic device with a new design integrated to a nanofracture is presented for purification of blood samples from numerous proteins and cells, allowing to the separation of small molecules from blood matrix. The device was used to separate and quantitatively detect tamsulosin drug after derivatization with fluorescamine reagent, allowing converting it from a neutral molecule into a charged fluorescent complex under the experimental conditions, and thus its separation by electrophoresis. The device is portable and easy operated, and the presented method showed good linearity (R2 = 0.9948) over a concentration range of 0.1-1μg/mL. The relative standard deviation (RSD%) was below 10% (n = 3), indicating good precisions, and the limit of detection (LOD) and limit of quantitation (LOQ) values were estimated to be 0.1 and 0.55μg/mL, respectively. Whole blood samples from 10 patients with benign prostatic hyperplasia (BPH) were analyzed, showing good percentage recoveries of tamsulosin in whole blood. This point-of-care (POC), low-cost method could increase the convenience of patients and doctors, make therapies safer, and make TDM available in different regions and places.

Combining a Commercial Mixer with a Wall-Tube Electrode Allows the Arbitrary Control of Concentrations in Protein Film Electrochemistry.

Protein film electrochemistry is a technique in which an enzyme is immobilized on an electrode in a configuration that allows following the changes in turnover frequency as a response to changes in the experimental conditions. Insights into the reactivity of the enzyme can be obtained by quantitatively modeling such responses. As a consequence, the more the technique allows flexibility in changing conditions, the more useful it becomes. The most commonly used setup, based on the rotating disc electrode, allows easy stepwise increases in the concentration of nongaseous substrates, or exposure to constant concentration of dissolved gas, but does not permit to easily decrease the concentration of nongaseous substrates, or to change the concentration of dissolved gas in a stepwise fashion. To overcome the limitation by mass transport of the substrate toward the electrode when working with fast enzymes, we have designed another kind of electrochemical cell based on the wall-tube electrode (WTE). We demonstrate here that by using a system combining two syringe pumps, a commercial mixer, and the WTE, it is possible to change the concentration of species in a stepwise fashion in all directions, opening new possibilities to study redox enzymes. As a proof of concept, this device was applied to the study of the electrochemical response of the cytochrome c nitrite reductase of Desulfovibrio desulfuricans.