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A novel system for measuring net photochemical ozone production rates in the atmosphere based on cavity ring-down spectroscopy (OPR-CRDS) was developed. The system consists of two chambers (a reaction chamber and a reference chamber) and a dual-channel Ox-CRDS detector. To minimize the wall loss of Ox in the chambers, the inner surfaces of both chambers are coated with Teflon film. The performance of the OPR-CRDS system was characterized. It was found that even though the photolysis frequency (J value) decreased by 10%, the decrease in the P(O3) caused by the ultraviolet-blocking film coating was less than 3%. The two chambers had a good consistency in the mean residence time and the measurement of NO2 and Ox under the condition of no sunlight. The detection limit of the OPR-CRDS was determined to be 0.20 ppbv/hr. To further verify the accuracy of the system, the direct measurement values of the OPR-CRDS system were compared with the calculation results based on radical (OH, HO2, and RO2) reactions, and a good correlation was obtained between the measured and calculated values. Finally, the developed instrument was applied to obtain the comprehensive field observations at an urban site in the Yangtze River Delta (China) for 40 days, the time series and change characteristics of the P(O3) were obtained directly, and the good environmental adaptability and stability of the OPR-CRDS system were demonstrated. It is expected that the new instrument will be beneficial to investigations of the relationship between P(O3) and its precursors.

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Oral cancer is the most common malignancy in many developing countries, such as India, due to increased consumption of smokeless tobacco. The trace elemental components in commercially packaged forms of tobacco can play a significant role in the pathogenesis of oral cancer. To qualitatively assess the trace elements in various types of commercially packaged forms of tobacco using laser-induced breakdown spectroscopy (LIBS). Two popular varieties of 'Paan masala' that contained a mixture of slaked lime with areca nut, catechu, and other flavouring agents (tobacco was absent) and four types of packaged tobacco were obtained from 'Paan' shops. The contents in the packets were made into pellets using a hydraulic press and subjected to elemental analysis using LIBS. A ten-trial experiment was carried out on all six pellets. The National Institute of Standards and Technology (NIST) database was used to assess the emission lines. The elements obtained from commercially packaged tobacco and Paan masala were similar: calcium (Ca), iron (Fe), aluminium (Al), nickel (Ni), and chromium (Cr). Substances that cause DNA damage and carcinogenesis are inorganic elements such as nickel. Our study revealed that carcinogens such as nickel are present in the commercially packaged forms of tobacco and 'Paan masala' samples.

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Experimental methods capable of selectively probing water at the DNA minor groove, major groove, and phosphate backbone are crucial for understanding how hydration influences DNA structure and function. Chiral-selective sum frequency generation spectroscopy (chiral SFG) is unique among vibrational spectroscopies because it can selectively probe water molecules that form chiral hydration structures around biomolecules. However, interpreting chiral SFG spectra is challenging since both water and the biomolecule can produce chiral SFG signals. Here, we combine experiment and computation to establish a theoretical framework for the rigorous interpretation of chiral SFG spectra of DNA. We demonstrate that chiral SFG detects the N-H stretch of DNA base pairs and the O-H stretch of water, exclusively probing water molecules in the DNA first hydration shell. Our analysis reveals that DNA transfers chirality to water molecules only within the first hydration shell, so they can be probed by chiral SFG spectroscopy. Beyond the first hydration shell, the electric field-induced water structure is symmetric and, therefore, precludes chiral SFG response. Furthermore, we find that chiral SFG can differentiate chiral subpopulations of first hydration shell water molecules at the minor groove, major groove, and phosphate backbone. Our findings challenge the scientific perspective dominant for more than 40 years that the minor groove "spine of hydration" is the only chiral water structure surrounding the DNA double helix. By identifying the molecular origins of the DNA chiral SFG spectrum, we lay a robust experimental and theoretical foundation for applying chiral SFG to explore the chemical and biological physics of DNA hydration.

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This review explores the historical, botanical, sensory, and quality aspects of Coffea canephora, with a focus on Brazil's rise as a producer of specialty canephora coffees in the Amazon region, Espírito Santo, and Bahia. Brazil has gained global recognition through the first geographical indications for canephora: Matas de Rondônia for robusta amazônico coffee and Espírito Santo for conilon coffee. Despite this, comprehensive insights into how variety, terroir, environmental conditions, and cultivation practices influence the chemical and sensory attributes of Brazilian canephora remain underdeveloped compared to well-studied arabica coffee. Producers and researchers are working to elevate canephora coffees to higher market levels, despite technological, production, and perception challenges stemming from its historical reputation for poor quality. Ensuring the sustainability of Amazonian canephora coffee without deforestation is particularly challenging due to the need to verify practices across numerous small-scale farms. There is also a critical need for standardized production and tasting protocols for Brazilian canephora, leveraging local expertise and professional cuppers to ensure consistent quality and reliable sustainability claims. Significant opportunities exist in valuing the production chain of geographically unique canephora coffees, which could increase specialty exports, enhance economic prospects for local farmers, and support Amazon preservation. Recognizing and marketing these coffees as premium products with unique flavor profiles can boost their global appeal. Another challenge lies in establishing new specialty standards for soluble coffee from specialty canephora to meet consumer demands for convenience without compromising taste or ethical standards. In such a scenario, several analytical methods have been suggested to identify high-quality variants, combating their stigmatization. The potential of spectroscopy techniques and chemometrics-based data science is highlighted in confirming coffee quality, authenticity, traceability, and geographical origin, enhancing model interpretation and predictive accuracy through synergistic and complementary information. Non-targeted spectroscopic analyses, providing comprehensive spectral fingerprints, are contrasted with targeted analyses. Overall, this review offers valuable insights for the coffee scientific community, exporters, importers, roasters, and consumers in recognizing the potential of Brazilian canephora coffees.

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Contamination of the environment with toxic metals such as cadmium or lead is a worldwide issue. The accumulator of metals Cannabis sativa L. has potential to be utilized in phytoremediation, which is an environmentally friendly way of soil decontamination. Novel non-thermal plasma-based technologies may be a helpful tool in this process. Plasma activated water (PAW), prepared by contact of gaseous plasma with water, contains reactive oxygen and nitrogen species, which enhance the growth of plants. In this study, C. sativa was grown in a short-term toxicity test in a medium which consisted of plasma activated water prepared by dielectric barrier discharge with liquid electrode and different concentrations of cadmium or lead. Application of PAW on heavy metal contaminated C. sativa resulted in increased growth under Pb contamination as was determined by ecotoxicology tests. Furthermore, the PAW influence on the bioaccumulation of these metals as well as the influence on the nutrient composition of plants was studied primarily by applying Laser-induced breakdown spectroscopy (LIBS). The LIBS elemental maps show that C. sativa accumulates heavy metals mainly in the roots. The results present a new proof-of-concept in which PAW could be used to improve the growth of plants in heavy metal contaminated environment, while LIBS can be implemented to study the phytoremediation efficiency.

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Toehold-mediated strand displacement (TMSD) is extensively utilized in dynamic DNA nanotechnology and for a wide range of DNA or RNA-based reaction circuits. Investigation of TMSD kinetics typically relies on bulk fluorescence measurements providing effective, bulk-averaged reaction rates. Information on individual molecules or even base pairs is scarce. In this work, we explore the dynamics of strand displacement processes at the single-molecule level using single-molecule force spectroscopy with a microfluidics-enhanced optical trap supported by state-of-the-art coarse-grained simulations. By applying force, we can trigger and observe TMSD in real-time with microsecond and nanometer resolution. We find TMSD proceeds very rapidly under load with single step times of 1 µs. Tuning invasion efficiency by introducing mismatches allows studying thousands of forward/backward invasion events on a single molecule and analyze the kinetics of the invasion process. Extrapolation to zero force reveals single step times for DNA invading DNA four times faster than for RNA invading RNA. We also study the kinetics of DNA invading RNA, a process that in the absence of force would rarely occur. Our results reveal the importance of sequence effects for the TMSD process and have relevance for a wide range of applications in nucleic acid nanotechnology and synthetic biology.

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Precise prediction of soil salinity using visible, and near-infrared (vis-NIR) spectroscopy is crucial for ensuring food security and effective environmental management. This paper focuses on the precise prediction of soil salinity utilizing visible and near-infrared (vis-NIR) spectroscopy, a critical factor for food security and effective environmental management. The objective is to utilize vis-NIR spectra alongside a multiple regression model (MLR) and a random forest (RF) modeling approach to predict soil salinity across various land use types, such as farmlands, bare lands, and rangelands accurately. To this end, we selected 150 sampling points representatives of these diverse land uses. At each point, we collected soil samples to measure the soil salinity (ECe) and employed a portable spectrometer to capture the spectral reflectance across the full wavelength range of 400 to 2400 nm. The methodology involved using both individual spectral reflectance values and combinations of reflectance values from different wavelengths as input variables for developing the MLR and RF models. The results indicated that the RF model (RMSE = 4.85 dS m-1, R2 = 0.87, and RPD = 3.15), utilizing combined factors as input variables, outperformed others. Furthermore, our analysis across different land uses revealed that models incorporating combined input variables yielded significantly better results, particularly for farmlands and rangelands. This study underscores the potential of combining vis-NIR spectroscopy with advanced modeling techniques to enhance the accuracy of soil salinity predictions, thereby supporting more informed agricultural and environmental management decisions.

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Diffuse correlation spectroscopy (DCS) is a non-invasive technology for the evaluation of blood perfusion in deep tissue. However, it requires high computational resources for data analysis, which poses challenges in its implementation for real-time applications. To address the unmet need, we developed a novel device-on-chip solution that fully integrates all the necessary computational components needed for DCS. It takes the output of a photon detector and determines the blood flow index (BFI). It is implemented on a field-programmable gate array (FPGA) chip including a multi-tau correlator for the calculation of the temporal light intensity autocorrelation function and a DCS analyzer to perform the curve fitting operation that derives the BFI at a rate of 6000 BFIs/s. The FPGA DCS system was evaluated against a lab-standard DCS system for both phantom and cuff ischemia studies. The results indicate that the autocorrelation of the light correlation and BFI from both the FPGA DCS and the reference DCS matched well. Furthermore, the FPGA DCS system was able to achieve a measurement rate of 50 Hz and resolve pulsatile blood flow. This can significantly lower the cost and footprint of the computational components of DCS and pave the way for portable, real-time DCS systems.

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Correlative imaging of cutaneous tumors provides additional information to the standard histopathologic examination. However, the joint progress in the establishment of analytical techniques, such as Laser-Induced Breakdown Spectroscopy (LIBS) and Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in clinical practice is still limited. Their combination provides complementary information as it is also shown in our study in terms of major biotic (Ca, Mg, and P) and trace (Cu and Zn) elements. To elucidate changes in the elemental composition in tumors, we have compiled a set of malignant tumors (Squamous Cell Carcinoma, Basal Cell Carcinoma, Malignant Melanoma, and Epithelioid Angiosarcoma), one benign tumor (Pigmented Nevus) and one healthy-skin sample. The data processing was based on a methodological pipeline involving binary image registration and affine transformation. Thus, our paper brings a feasibility study of a practical methodological concept that enables us to compare LIBS and LA-ICP-MS results despite the mutual spatial distortion of original elemental images. Moreover, we also show that LIBS could be a sufficient pre-screening method even for a larger number of samples according to the speed and reproducibility of the analyses. Whereas LA-ICP-MS could serve as a ground truth and reference technique for preselected samples.

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4-Fluoro-N-(thiazol-2-yl)benzenesulfonamide (3) is a novel fluorinated compound, containing various biological activities. Therefore, absorption spectroscopy, fluorescence quenching, molecular docking, and molecular simulation were employed to investigate the interaction between 3 and human serum albumin (HSA). Firstly, compound 3 meets all criteria for drug-likeness prediction. UV absorption spectra revealed the interaction of 3 with HSA altered the microenvironment of protein, as well as circular dichroism spectroscopic analysis indicated slightly conformational changes and a reduction in α-helical content. The binding parameters of the HSA-3 complex suggested that fluorescence quenching is driven by combined static and dynamic processes. Additionally, the stability of the complex is attributed to conventional hydrogen and hydrophobic bonding interactions. Furthermore, esterase-like activity indicated that the binding of 3 might disrupt HSA's bond networks, leading to structural alterations. Consequently, the strong binding constant (Ka ≈ 1.204 × 106 M-1) aligns with the predicted unbound fraction (0.28) in serum, indicating that thiazole 3 has good bioavailability in plasma and can be effectively transported to target sites, thereby exerting its pharmaceutical effects. However, careful dosage management is essential to prevent potential adverse effects. Overall, these findings highlight the potential of 3 as a therapeutic agent, emphasizing the need for further research to optimize its uses.

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Diffuse correlation spectroscopy (DCS) is a powerful tool for assessing microvascular hemodynamic in deep tissues. Recent advances in sensors, lasers, and deep learning have further boosted the development of new DCS methods. However, newcomers might feel overwhelmed, not only by the already-complex DCS theoretical framework but also by the broad range of component options and system architectures. To facilitate new entry to this exciting field, we present a comprehensive review of DCS hardware architectures (continuous-wave, frequency-domain, and time-domain) and summarize corresponding theoretical models. Further, we discuss new applications of highly integrated silicon single-photon avalanche diode (SPAD) sensors in DCS, compare SPADs with existing sensors, and review other components (lasers, sensors, and correlators), as well as data analysis tools, including deep learning. Potential applications in medical diagnosis are discussed and an outlook for the future directions is provided, to offer effective guidance to embark on DCS research.

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The evaluation of the diffusion properties of different molecules in tissues is a subject of great interest in various fields, such as dermatology/cosmetology, clinical medicine, implantology and food preservation. In this review, a discussion of recent studies that used kinetic spectroscopy measurements to evaluate such diffusion properties in various tissues is made. By immersing ex vivo tissues in agents or by topical application of those agents in vivo, their diffusion properties can be evaluated by kinetic collimated transmittance or diffuse reflectance spectroscopy. Using this method, recent studies were able to discriminate the diffusion properties of agents between healthy and diseased tissues, especially in the cases of cancer and diabetes mellitus. In the case of cancer, it was also possible to evaluate an increase of 5% in the mobile water content from the healthy to the cancerous colorectal and kidney tissues. Considering the application of some agents to living organisms or food products to protect them from deterioration during low temperature preservation (cryopreservation), and knowing that such agent inclusion may be reversed, some studies in these fields are also discussed. Considering the broadband application of the optical spectroscopy evaluation of the diffusion properties of agents in tissues and the physiological diagnostic data that such method can acquire, further studies concerning the optimization of fruit sweetness or evaluation of poison diffusion in tissues or antidote application for treatment optimization purposes are indicated as future perspectives.

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Elemental profiling of fungal species as a phenotyping tool is an understudied topic and is typically performed to examine plant tissue or non-biological materials. Traditional analytical techniques such as inductively coupled plasma-optical emission spectroscopy (ICP-OES) and inductively coupled plasma-mass spectrometry (ICP-MS) have been used to identify elemental profiles of fungi; however, these techniques can be cumbersome due to the difficulty of preparing samples. Additionally, the instruments used for these techniques can be expensive to procure and operate. Laser-induced breakdown spectroscopy (LIBS) is an alternative elemental analytical technique-one that is sensitive across the periodic table, easy to use on various sample types, and is cost-effective in both procurement and operation. LIBS has not been used on axenic filamentous fungal isolates grown in substrate media. In this work, as a proof of concept, we used LIBS on two genetically distinct fungal species grown on a nutrient-rich and nutrient-poor substrate media to determine whether robust elemental profiles can be detected and whether differences between the fungal isolates can be identified. Our results demonstrate a distinct correlation between fungal species and their elemental profile, regardless of the substrate media, as the same strains shared a similar uptake of carbon, zinc, phosphorus, manganese, and magnesium, which could play a vital role in their survival and propagation. Independently, each fungal species exhibited a unique elemental profile. This work demonstrates a unique and valuable approach to rapidly phenotype fungi through optical spectroscopy, and this approach can be critical in understanding these fungi's behavior and interactions with the environment. IMPORTANCE: Historically, ionomics, the elemental profiling of an organism or materials, has been used to understand the elemental composition in waste materials to identify and recycle heavy metals or rare earth elements, identify the soil composition in space exploration on the moon or Mars, or understand human disorders or disease. To our knowledge, ionomic profiling of microbes, particularly fungi, has not been investigated to answer applied and fundamental biological questions. The reason is that current ionomic analytical techniques can be laborious in sample preparation, fail to measure all potential elements accurately, are cost-prohibitive, or provide inconsistent results across replications. In our previous efforts, we explored whether laser-induced breakdown spectroscopy (LIBS) could be used in determining the elemental profiles of poplar tissue, which was successful. In this proof-of-concept endeavor, we undertook a transdisciplinary effort between applied and fundamental mycology and elemental analytical techniques to address the biological question of how LIBS can used for fungi grown axenically in a nutrient-rich and nutrient-poor environment.

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OBJECTIVES: Inadequate resection margins of less than 5 mm impair local tumor control. This weak point in oncological safety is exacerbated in bone-infiltrating tumors because rapid bone analysis procedures do not exist. This study aims to assess the bony resection margin status of bone-invasive oral cancer using laser-induced breakdown spectroscopy (LIBS). MATERIALS AND METHODS: LIBS experiments were performed on natively lasered, tumor-infiltrated mandibular cross-sections from 10 patients. In total, 5,336 spectra were recorded at defined distances from the tumor border. Resection margins < 1 mm were defined as very close, from 1-5 mm as close, and > 5 mm as clear. The spectra were histologically validated. Based on the LIBS spectra, the discriminatory power of potassium (K) and soluble calcium (Ca) between bone-infiltrating tumor tissue and very close, close, and clear resection margins was determined. RESULTS: LIBS-derived electrolyte emission values of K and soluble Ca as well as histological parameters for bone neogenesis/fibrosis and lymphocyte/macrophage infiltrates differ significantly between bone-infiltrating tumor tissue spectra and healthy bone spectra from very close, close, and clear resection margins (p < 0.0001). Using LIBS, the transition from very close resection margins to bone-infiltrating tumor tissue can be determined with a sensitivity of 95.0%, and the transition from clear to close resection margins can be determined with a sensitivity of 85.3%. CONCLUSIONS: LIBS can reliably determine the boundary of bone-infiltrating tumors and might provide an orientation for determining a clear resection margin. CLINICAL RELEVANCE: LIBS could facilitate intraoperative decision-making and avoid inadequate resection margins in bone-invasive oral cancer.

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Nucleic acid detection technology has become a crucial tool in cutting-edge research within the life sciences and clinical diagnosis domains. Its significance is particularly highlighted during the respiratory virus pandemic, where nucleic acid testing plays a pivotal role in accurately detecting the virus. Isothermal amplification technologies have been developed and offer advantages such as rapidity, mild reaction conditions and excellent stability. Among these methods, recombinase polymerase amplification (RPA) has gained significant attention due to its simple primer design and resistance to multiple reaction inhibitors. However, the detection of RPA amplicons hinders the widespread adoption of this technology, leading to a research focus on cost-effective and convenient detection methods for RPA nucleic acid testing. In this study, we propose a novel computational absorption spectrum approach that utilizes the polar GelRed dye to efficiently detect RPA amplicons. By exploiting the asymmetry of GelRed molecules upon binding with DNA, polar electric dipoles are formed, leading to precipitate formation through centrifugal vibration and electrostatic interaction. The quantification of amplicon content is achieved by measuring the residual GelRed concentration in the supernatant. Our proposed portable and integrated microfluidic device successfully detected five respiratory virus genes simultaneously. The optimized linear detection was achieved and the sensitivity for all the targets reached 100 copies/µL. The total experiment could be finished in 27 min. The clinical experiments demonstrated the practicality and accuracy. This cost-effective and convenient detection scheme presents a promising biosensor for rapid virus detection, contributing to the advancement of RPA technology.

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Conventional bulk protein structure determination methods are not suitable for understanding the distinct and diverse interactions of proteins with interfaces. Notably, interfacial activation is a feature common to many lipases involving movement of a helical "lid" region upon contact with a hydrophobic surface to expose the catalytic site. Here we use the surface specificity of vibrational sum frequency generation spectroscopy (VSFG) spectroscopy to directly probe the conformation of Thermomyces lanuginosus lipase (TLL) at hydrophobic interfaces. The TLL-catalyzed reaction at the air/water interface is monitored by VSFG spectroscopy, showing loss of ester carbonyl modes and appearance of carboxylate stretching modes of the fatty acid products. Furthermore, comparison of experimental and calculated VSFG spectra of the amide I band of TLL allows us to discern the subtle structural changes involved with lid-opening at a hydrophobic surface. Finally, we report a likely orientation of this lid-open state, which interacts with the surface through a loop region away from the lid and active site. This experimental framework for probing protein structure and function at interfaces addresses a significant problem in protein science that is not only impeding the design of better enzymes for biotechnology applications but also drug discovery targeting membrane associated proteins.

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The adventitious root formaton (ARF) in excised plant parts is essential for the survival of isolated plant fragments. In this study, we explored the complex mechanisms of ARF in Larix kaempferi by conducting a comprehensive proteomic analysis across three distinct stages: the induction of adventitious root primordia (C1, 0-25 d), the formation of adventitious root primordia (C2, 25-35 d), and the elongation of adventitious roots (C3, 35-45 d). We identified 1976 proteins, with 263 and 156 proteins exhibiting increased abundance in the C2/C1 and C3/C2 transitions, respectively. In contrast, a decrease in the abundance of 106 and 132 proteins suggests a significant demand for metabolic processes during the C2/C1 phase. The abundance of IAA-amino acid hydrolase and S-adenosylmethionine synthase were increased in the C2/C1 phase, underscoring the role of auxin in adventitious root induction. The decrease in abundance of photosynthesis-related proteins during the C2/C1 phase highlights the significance of initial light conditions in adventitious root induction. Moreover, variation in cell wall synthesis and metabolic proteins in the C2/C1 and C3/C2 stages suggests that cell wall metabolism is integral to adventitious root regeneration. Gene Ontology enrichment analysis revealed pathways related to protein modification enzymes, including deubiquitinases and kinases, which are crucial for modulating protein modifications to promote ARF. Furthermore, the increased abundance of antioxidant enzymes, such as peroxidases and glutathione peroxidases, indicates a potential approach for enhancing ARF by supplementing the culture medium with antioxidants. Our study provides insights into metabolic changes during ARF in L. kaempferi, offering strategies to enhance adventitious root regeneration. These findings have the potential to refine plant propagation techniques and expedite breeding processes. SIGNFICANCE: The main challenge in the asexual reproduction technology of Larix kaempferi lies in adventitious root formation (ARF). While numerous studies have concentrated on the efficiency of ARF, proteomic data are currently scarce. In this study, we collected samples from three stages of ARF in L. kaempferi and subsequently performed proteomic analysis. The data generated not only reveal changes in protein abundance but also elucidate key metabolic processes involved in ARF. These insights offer a novel perspective on addressing the challenge of adventurous root regeneration.

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Tropospheric ozone (O3) causes widespread damage to vegetation; however, monitoring of O3 induced damage is often reliant on manual leaf inspection. Reflectance spectroscopy of vegetation can identify and detect unique spectral signatures of different abiotic and biotic stressors. In this study, we tested the use of hyperspectral leaf reflectance to detect O3 stress in alder, beech, birch, crab apple, and oak saplings exposed to five long-term O3 regimes (ranging from daily target maxima of 30 ppb O3 to 110 ppb). Hyperspectral reflectance varied significantly between O3 treatments, both in whole spectra analysis and when simplified to representative components. O3 damage had a multivariate impact on leaf reflectance, underpinned by changes in pigment balance, water content and structural composition. Vegetation indices derived from reflectance which characterised the visible green peak were able to differentiate between O3 treatments. Iterative normalised difference spectral indices across the hyperspectral wavelength range were correlated to visual damage scores to identify significant wavelengths for O3 damage detection. We propose a new Ozone Damage Index (OzDI), which characterises the reflectance peak in the shortwave infrared region and outperformed existing vegetation indices in terms of correlation to O3 treatment. These results demonstrate the potential application of hyperspectral reflectance as a high throughput method of O3 damage detection in a range of common broadleaf. species.

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Vibrational spectroscopy combined with machine learning has a great potential for forensic research. Portable Raman spectrometers are already being used by law-enforcement agencies to identify drugs. Several new technologies based on vibrational spectroscopy, that can be used in forensic science to analyze documents, gunshot traces, cloths, soil, hair, nails and lacquer, are being developed nowadays. The article considers the use of vibrational spectroscopy in forensic practice for conducting serological studies with an emphasis on the development of a universal method of identifying the main secretions of the body. The method allows to determine the time elapsed since the trace was made, as well as the phenotypic profile of host, including sex, race and age.

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