A dataset of optical spectra and clinical features acquired on human healthy skin and on skin carcinomas

Optical spectroscopy is studied to contribute to skin cancer diagnosis. Indeed, optical spectra are modified along cancer progression and provide complementary information (e.g., on metabolism and tissue structure) to clinical examination for surgical guidance [1,2]. The current original dataset is made of autofluorescence and diffuse reflectance spectra acquired in vivo on 131 patients' skin with the SpectroLive device [3,4]. Spatially-resolved spectroscopy measurements were performed using a multi-fiber optic probe featuring 4 distances (0.4-1 mm) between excitation and collection optical fibers: spatial resolution allows spectra acquired at different distances to carry information from different depths in skin tissues. Five types of autofluorescence spectra were acquired using five different wavelength excitations (on the 365-415 nm spectral range) in order to collect information on several skin endogenous fluorophores (e.g., flavins, collagen). A sixth light source (white broadband) was used to acquire diffuse reflectance spectra carrying information about skin scattering properties and skin endogenous absorbers such as melanin and hemoglobin. Patients were proposed to be included into the clinical trial if they were suspected of suffering from actinic keratoses (precancerous skin lesions) or from basal or squamous cell carcinomas: in all cases, complete diagnostics is provided in the dataset. To increase the interest of the dataset and evaluate the dependence of optical spectra (intensity, shape) not only on pathological states but also on healthy skin features (civil age, skin age, gender, phototype, anatomical site), spectra were acquired for all 131 patients on two so-called "reference" skin sites known to rarely suffer from skin cancer: palm of the hand (featuring a thick skin type) and inner wrist (featuring thin skin). Spectra are available in .tab files: first column displays the spectral range on which intensity spectra were recorded (317-788 nm) and each following column provides an intensity spectrum acquired by each spectrometer for a given combination of light source excitation and distance. Each of the 131 folders corresponding to each of the 131 patients contains a .json file providing patients clinical features: gender, civil age, skin age, phototype score and class. All .tab files names include anatomical site and anatomopathological diagnostics of the skin site on which spectra were acquired: codes were defined to match a letter or an acronym to each diagnostic and anatomical site. To ensure quality control, a spectrum was acquired on the same calibration standard before starting spectra acquisition on each patient. It is therefore possible to follow the impact of the acquisition optical chain ageing during the 4.5 years that the patients were included. This dataset can be used by epidemiologists for the characterization of populations affected by skin cancers (gender ratio, mean age, anatomical sites typically affected, etc.); it may also be used by researchers in artificial intelligence to develop innovative methods to process such data and contribute to non-invasive diagnostics of skin cancers whose incidence is steadily increasing.

Non-invasive assessment of periodontal inflammation by continuum-removal hemodynamic spectral indices

BACKGROUND

Hyperspectral techniques have aroused great interest in non-invasively measuring periodontal tissue hemodynamics. However, current studies mainly focused on three typical inflammation stages (healthy, gingivitis and periodontitis) and practical approaches for using optical spectroscopy for early and precisely detection of periodontal inflammation at finer disease stages have not been well studied.

METHODS

This study provided novel spectroscopic insights into periodontitis at different stages of disease, and developed six simple but physically meaning hemodynamic spectral indices (HSIs) including four spectral absorption depths of oxyhemoglobin ( D HbO 2 ), deoxyhemoglobin ( D Hb ), total hemoglobin ( t Hb ) and tissue water ( D water ), and two normalized difference indices of oxyhemoglobin( N D HbO 2 I ) and deoxyhemoglobin ( N D Hb I ) from continuum-removal spectra (400-1700 nm) of periodontal tissue collected from 47 systemically healthy subjects over different severities from healthy, gingivitis, slight, moderate to severe periodontitis for early and precision diagnostics of periodontitis. Typical statistical analyses were conducted to explore the effectiveness of the proposed HSIs.

RESULTS

D Hb and t Hb exerted significant increasing trends as inflammation progressed, whereas D HbO 2 exhibited significant difference (P < 0.05) from the healthy sites only at moderate and severe periodontitis and D water presented unstable sensitives to disease severity. By contrast, N D HbO 2 I and N D Hb I showed more steadily downward trends as severity increased, and demonstrated the highest correlations with clinical gold standard parameters. Particularly, the proposed normalized HSIs ( N D HbO 2 I and N D Hb I ) yielded high correlations of - 0.49 and - 0.44 with probing depth, respectively, far outperforming results achieved by previous studies. The performances of the HSIs were also confirmed using the periodontal therapy group.

CONCLUSIONS

These results indicated great potentials of combination optical spectroscopy and smart devices to non-invasively probe periodontitis at earlier stages using the simple and practical HSIs. Trial registration This study was retrospectively registered in the Chinese Clinical Trial Registry on October 24, 2021, and the clinical registration number is ChiCTR2100052306.

Fluorescence spectral analysis and logistic regression modeling for diagnosing basal cell carcinoma on head and neck

The optical fluorescence method is distinguished by key features such as non-invasiveness, high sensitivity, and resolution, which are superior to traditional diagnostic approaches. Unlike histopathological examinations and biochemical analyses, optical diagnostic methods obviate the need for tissue sampling, enabling the analysis of virtually unlimited material. The research aims to examine the effectiveness of emission spectra analysis in the diagnosis of basal cell carcinoma (BCC) of the scalp and neck. The analysis was based on data provided by Specialized Hospital No. 2 in Bytom comprising a study sample of 10 patients. For each patient, fluorescence emission spectra were recorded from each of 512 points along a 5 mm line. The results obtained from the histopathological examination, the analysis and morphological evaluation of the tissue, and the diagnosis through microscopic observation were used to define a dichotomous variable (presence or absence of a cancerous lesion), adopted in the study as the modeled variable. The next step of the presented study involved constructing a logistic regression model for identifying cancerous lesions depending on the biochemical indicator's relative fluorescence value (RFV) and emission wavelength (ELW) within the 620 nm to 730 nm range. This wavelength range is often used in fluorescence diagnostics to detect various pathologies, including cancerous lesions. The resulting binary logistic regression model, logit(p)=-33.17+0.04ELW+0.01RFV, indicates a statistically significant relationship between wavelength and relative fluorescence values with the probability of detecting cancer. The estimated model exhibits a good fit and high predictive accuracy. The overall model accuracy is 84.8 %, with the correct classification rates at approximately 96 % for healthy individuals and 74 % for individuals with cancer. These findings underscore the potential of photodynamic diagnostics in cancer detection and monitoring.

Effects of sample pre-treatments on the analysis of liquid organic manures by visible and near-infrared spectrometry

Proper application of a fertilizer requires precise knowledge of its nutrient composition. In the case of liquid organic manures (LOM), this information is often lacking due to heterogeneous nature of these fertilizers. Published "book values" of nutrient contents present the average from a wide range of possible nutrient characteristics, but usually differ considerably from the concentration in a particular manure. Thus, chemical analyses are recommended before applying the specific LOM. Unfortunately, this is usually too costly and time-intensive in practical farming. On-farm analysis by optical spectrometry in the visible and near-infrared (Vis-NIR) range is considered as an efficient alternative. However, calibration of Vis-NIR spectrometry for LOM is challenging as shown in many studies. One reason is LOMs' tendency to rapidly segregate into a fuzzy continuum with liquid and solid properties. By separating LOM into well-defined liquid and solid phases and measuring them separately, calibration of Vis-NIR spectrometry might be improved. In this study, the effects of four sample pre-treatment techniques on the prediction accuracy of macronutrients (N, P, K, Mg, Ca, S), micronutrients (B, Mn, Fe, Cu, Zn), dry matter and pH of LOM using visible and near infrared spectrometry were comprehensively investigated. The concentrations were referred either to wet basis or to dry matter basis. For the study, a total of 163 samples, separated in two similar LOM sets (pig, cattle, digestates), were either dried, filtered, or centrifuged and always compared to non-treated samples. The experiments demonstrate that in comparison to raw samples (Ø r2 = 0.85) neither filtering (Ø r2 = 0.76 for filtrates and Ø r2 = 0.71 for filter residues), centrifugation (Ø r2 = 0.59 for supernatants and Ø r2 = 0.79 for pellets), nor drying (Ø r2 = 0.74) revealed to be a helpful preparation step significantly improving prediction results, independent from referring to wet or dry basis concentrations.

Determining nutrients, dry matter, and pH of liquid organic manures using visual and near-infrared spectrometry

In agriculture, overfertilization with liquid organic manures (LOM) is causing environmental issues including eutrophication of non-agricultural ecosystems and nitrate pollution of groundwater. To avoid such problems, a precise and demand-oriented fertilization with LOM is needed. This can only be achieved if the nutrient composition of the LOM is known. However, traditional chemical analysis is cost- and time-intensive and furthermore dependent on a representative sample. Optical spectrometry in the visible and near-infrared range could provide an efficient alternative, if a chemometric calibration assures sufficient accuracy. To improve chemometric calibration, this study investigated several spectral preprocessing and regression algorithms, and compared predictions based either on dry or wet weight concentration. In addition, the capability of low-cost spectrometers was evaluated by simulating low-resolution spectra with smaller wavelength ranges. The reflectance spectra of 391 pig manure, 155 cattle manure, and 89 biogas digestate samples were used to predict plant macronutrients (N, P, K, Mg, Ca, S), micronutrients (Mn, Fe, Cu, Zn, B), dry matter (DM) and pH. The experiments demonstrate the general aptness of optical spectrometry to accurately predict DM, pH and all nutrients except boron in pig, cattle, and digestate LOM, even with simulated low-cost spectrometers. Best results show r2 between 0.80 and 0.97, ratios of performance to interquartile distance (RPIQ) between 2.1 and 7.8, and mean absolute errors normalized by the median (nMAE) between 5 and 36 %. The regression methods PLSR, LASSO, and least angle regression predominantly performed best. The innovative preprocessing methods named simple ratios (SR) and normalized differences (ND) proved to be very useful algorithms, especially for N and P predictions, outperforming the accuracy of classical techniques in several cases. Concentrations on dry weight basis improved predictions of K, Mn, and pH.

Osmotic stress studies of G-protein-coupled receptor rhodopsin activation

We summarize and critically review osmotic stress studies of the G-protein-coupled receptor rhodopsin. Although small amounts of structural water are present in these receptors, the effect of bulk water on their function remains uncertain. Studies of the influences of osmotic stress on the GPCR archetype rhodopsin have given insights into the functional role of water in receptor activation. Experimental work has discovered that osmolytes shift the metarhodopsin equilibrium after photoactivation, either to the active or inactive conformations according to their molar mass. At least 80 water molecules are found to enter rhodopsin in the transition to the photoreceptor active state. We infer that this movement of water is both necessary and sufficient for receptor activation. If the water influx is prevented, e.g., by large polymer osmolytes or by dehydration, then the receptor functional transition is back shifted. These findings imply a new paradigm in which rhodopsin becomes solvent swollen in the activation mechanism. Water thus acts as an allosteric modulator of function for rhodopsin-like receptors in lipid membranes.

Fast histological assessment of adipose tissue inflammation by label-free mid-infrared optoacoustic microscopy

Conventional histology, as well as immunohistochemistry or immunofluorescence, enables the study of morphological and phenotypical changes during tissue inflammation with single-cell accuracy. However, although highly specific, such techniques require multiple time-consuming steps to apply exogenous labels, which might result in morphological deviations from native tissue structures. Unlike these techniques, mid-infrared (mid-IR) microspectroscopy is a label-free optical imaging method that retrieves endogenous biomolecular contrast without altering the native composition of the samples. Nevertheless, due to the strong optical absorption of water in biological tissues, conventional mid-IR microspectroscopy has been limited to dried thin (5-10 µm) tissue preparations and, thus, it also requires time-consuming steps-comparable to conventional imaging techniques. Here, as a step towards label-free analytical histology of unprocessed tissues, we applied mid-IR optoacoustic microscopy (MiROM) to retrieve intrinsic molecular contrast by vibrational excitation and, simultaneously, to overcome water-tissue opacity of conventional mid-IR imaging in thick (mm range) tissues. In this proof-of-concept study, we demonstrated application of MiROM for the fast, label-free, non-destructive assessment of the hallmarks of inflammation in excised white adipose tissue; i.e., formation of crown-like structures and changes in adipocyte morphology.

Providing potential solutions by using FT-IR spectroscopy for biofluid analysis: Clinical impact of optical screening and diagnostic tests

BACKGROUND

Currently, the potential of FT-IR spectroscopy for rapid diagnosis of many pathologies has been demonstrated by numerous research studies including those targeting COVID-19 detection. However, the number of clinicians aware of this potential and who are willing to use spectroscopy in their clinics and hospitals is still negligible. In addition, lack of awareness creates a huge gap between clinicians and researchers involved in clinical translation of current FT-IR technology hence hindering initiatives to bring basic and applied research together for the direct benefit of patients.

METHODS

Knowledge and medical training on FT-IR on the side of clinicians should be one of the first steps to be able to integrate it into the list of complementary exams which may be requested by health professionals. Countless FT-IR applications could have a life-changing impact on patients' lives, especially screening and diagnostic tests involving biofluids such as blood, saliva and urine which are routinely non-invasively or minimally-invasively.

RESULTS

Blood may be the most difficult to obtain by the invasive method of collection, but much can be evaluated in its components, and areas such as hematology, infectiology, oncology and endocrinology can be directly benefited. Urine with a relatively simple collection method can provide pertinent information from the entire urinary system, including the actual condition of the kidneys. Saliva collection can be simpler for the patient and can provide information on diseases affecting the mouth and digestive system and can be used to diagnose diseases such as oral cancer in its early-stages. An unavoidable second step is the active involvement of industries to design robust and portable instruments for specific purposes, as the medical community requires user-friendly instruments of advanced computational algorithms. A third step resides in the legal situation involving the global use of the technique as a new diagnostic modality.

CONCLUSIONS

It is important to note that decentralized funds for variety of technologies hinders the training of clinical and medical professionals for the use of newly arising technologies and affect the engagement of these professionals with technology developers. As a result of decentralized funding, research efforts are spread out over a range of technologies which take a long time to get validated and translated to the clinic. Partnership over similar groups of technologies and efforts to test the same technologies while overcoming barriers posed to technology validation in different areas around the globe may benefit the clinical/medical, research and industry community globally.

Characterization of a multi-stage focusing nozzle for collection of spot samples for aerosol chemical analysis

Concentrated collection of aerosol particles on a substrate is essential for their chemical analysis using various microscopy and laser spectroscopic techniques. An impaction-based aerosol concentration system was developed for focused collection of particles using a multi-stage nozzle that consists of a succession of multiple smooth converging stages. Converging sections of the nozzle were designed to focus and concentrate a particle diameter range of 900-2500 nm into a relatively narrower particle beam to obtain particulate deposits with spot diameters of 0.5-1.56 mm. A slightly diverging section before the last contractions was included to allow for better focusing of particles at the lower end of the collectable diameter range. The characterization of this multi-stage nozzle and the impaction-based aerosol concentration system was accomplished both numerically and experimentally. The numerical and experimental trends in collection efficiency and spot diameters agreed well qualitatively; however, the quantitative agreement between numerical and experimental results for wall losses was poor, particularly for larger particle diameters. The resulting concentrated particulate deposit, a spot sample, was analysed using Raman spectroscopy to probe the effect of spot size on analytical sensitivity of measurement. The method's sensitivity was compared against other conventional techniques, such as filtration and aerosol focused impaction, implementing condensational growth. Impaction encompassing the multi-stage focusing nozzle is the only method that can ensure high sensitivity at Reynolds numbers greater than 2000, that can be supported by small pumps which renders such method suitable for portable instrumentation.

Characterization of a Low-Temperature Plasma (LTP) Ambient Ionization Source Using Temporally Resolved Monochromatic Imaging Spectrometry

The low-temperature plasma (LTP) probe is a common plasma-based source used for ambient desorption-ionization mass spectrometry (MS). While the LTP probe has been characterized in detail with MS, relatively few studies have used optical spectroscopy. In this paper, two-dimensional (2D) imaging at selected wavelengths is used to visualize important species in the LTP plasma jet. First, 2D steady-state images of the LTP plume for N2+ (391.2 nm), He I (706.5 nm), and N2 (337.1 nm) emissions were recorded under selected plasma conditions. Second, time-resolved 2D emission maps of radiative species in the LTP plasma jet were recorded through the use of a 200 ns detection gate and varying gate delays with respect to the LTP trigger pulse. Emission from He I, N2+, and N2 in the plasma jet region was found to show a transient behavior (often referred to as plasma bullets) lasting only a few microseconds. The N2+ and He I maps were highly correlated in spatial and temporal structure. Further, emission from N2 showed two maxima in time, one before and one after the maximum emission for N2+ and He I, due to an initial electronic excitation wave and ion-electron recombination, respectively. Third, the interaction of the LTP probe with a sample substrate and an electrically grounded metallic needle was studied. Emission from a fluorophore on the sample substrate showed an initial photon-induced excitation from plasma-generated photons followed by electronic excitation by other plasma species. The presence of a grounded needle near the plasma jet significantly extended the plasma jet lifetime and also generated a long-lived corona discharge on the needle. The effect of LTP operating parameters on emission spectra was correlated with mass-spectral results including reagent-ion signals. Lastly, five movies provide a side-by-side comparison of the temporal behavior of emitting species and insights into the interactions of the emission clouds with a sample surface as well as an external needle. Temporally and spatially resolved imaging provided insights into important processes in the LTP plasma jet, which will help improve analyte ion sampling in LTP-MS.

High Voltage: The Molecular Properties of Redox-Active Dissolved Organic Matter in Northern High-Latitude Lakes

Redox-active functional groups in dissolved organic matter (DOM) are crucial for microbial electron transfer and methane emissions. However, the extent of aquatic DOM redox properties across northern high-latitude lakes and their relationships with DOM composition have not been thoroughly described. We quantified electron donating capacity (EDC) and electron accepting capacity (EAC) in lake DOM from Canada to Alaska and assessed their relationships with parameters from absorbance, fluorescence, and ultrahigh resolution mass spectrometry (FT-ICR MS) analyses. EDC and EAC are strongly tied to aromaticity and negatively related to aliphaticity and protein-like content. Redox-active formulae spanned a range of aromaticity, including highly unsaturated phenolic formulae, and correlated negatively with many aliphatic N and S-containing formulae. This distribution illustrates the compositional diversity of redox-sensitive functional groups and their sensitivity to ecosystem properties such as local hydrology and residence time. Finally, we developed a reducing index (RI) to predict EDC in aquatic DOM from FT-ICR MS spectra and assessed its robustness using riverine DOM. As the hydrology of the northern high-latitudes continues to change, we expect differences in the quantity and partitioning of EDC and EAC within these lakes, which have implications for local water quality and methane emissions.

Diagnostic accuracy of intraoperative margin assessment techniques in surgery for head and neck squamous cell carcinoma: A meta-analysis

BACKGROUND

Positive margins following head and neck squamous cell carcinoma (HNSCC) surgery lead to significant morbidity and mortality. Existing Intraoperative Margin Assessment (IMA) techniques are not widely used due to limitations in sampling technique, time constraints and resource requirements. We performed a meta-analysis of the diagnostic performance of existing IMA techniques in HNSCC, providing a benchmark against which emerging techniques may be judged.

METHODS

The study was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guidelines. Studies were included if they reported diagnostic metrics of techniques used during HNSCC surgery, compared with permanent histopathology. Screening, manuscript review and data extraction was performed by multiple independent observers. Pooled sensitivity and specificity were estimated using the bivariate random effects model.

RESULTS

From an initial 2344 references, 35 studies were included for meta-analysis. Sensitivity (Sens), specificity (Spec), diagnostic odds ratio (DOR) and area under the receiver operating characteristic curve (AUROC) were calculated for each group (n, Sens, Spec, DOR, AUROC): frozen section = 13, 0.798, 0.991, 309.8, 0.976; tumour-targeted fluorescence (TTF) = 5, 0.957, 0.827, 66.4, 0.944; optical techniques = 10, 0.919, 0.855, 58.9, 0.925; touch imprint cytology = 3, 0.925, 0.988, 51.1, 0.919; topical staining = 4, 0.918, 0.759, 16.4, 0.833.

CONCLUSIONS

Frozen section and TTF had the best diagnostic performance. Frozen section is limited by sampling error. TTF shows promise but involves administration of a systemic agent. Neither is currently in widespread clinical use. Emerging techniques must demonstrate competitive diagnostic accuracy whilst allowing rapid, reliable, cost-effective results.

Leveraging visible and near-infrared spectroelectrochemistry to calibrate a robust model for Vanadium(IV/V) in varying nitric acid and temperature levels

Spectroelectrochemistry and optimal design of experiments can be used to rapidly build accurate models for species quantification and enable a greater level of process awareness. Optical spectroscopy can provide vital elemental and molecular information, but several hurdles must be overcome before it can become a widely adopted analytical method for remote analysis in the nuclear field. Analytes with varying oxidation state, acid concentration, and fluctuating temperature must be efficiently accounted for to minimize time and resources in restrictive hot cell environments. The classic one-factor-at-a-time approach is not suitable for frequent calibration/maintenance operations in this setting. Therefore, a novel alternative was developed to characterize a system containing vanadium(IV/V) (0.01-0.1 M), nitric acid (0.1-4 M), and varying temperatures (20-45 °C). Spectroelectrochemistry methods were used to acquire a sample set selected by optimal design of experiments. This new approach allows for the accurate analysis of vanadium and HNO₃ concentration by leveraging UV-Vis-NIR absorption spectroscopy with robust and accurate chemometric models. The top model's root mean squared error of prediction percent values were 3.47%, 4.06%, 3.40%, and 10.9% for V(IV), V(V), HNO₃, and temperature, respectively. These models, efficiently developed using the designed approach, exhibited strong predictive accuracy for vanadium and acid with varying oxidation states and temperature using only spectrophotometry, which advances current technology for real-world hot cell applications. Additionally, Nernstian analysis of the V(IV/V) standard potential was performed using traditional absorbance methods and multivariate curve resolution (MCR). The successful tests demonstrated that MCR Nernst tests may be valuable in highly convoluted spectral systems to better understand the redox processes' behavior.

Frequency chirped Fourier-Transform spectroscopy

Fast (sub-second) spectroscopy with high spectral resolution is of vital importance for revealing quantum chemistry kinetics of complex chemical and biological reactions. Fourier transform (FT) spectrometers can achieve high spectral resolution and operate at hundreds of ms time scales in rapid-scan mode. However, the linear translation of a scanning mirror imposes stringent time-resolution limitations to these systems, which makes simultaneous high spectral and temporal resolution very difficult. Here, we demonstrate an FT spectrometer whose operational principle is based on continuous rotational motion of the scanning mirror, effectively decoupling the spectral resolution from the temporal one. Furthermore, we show that such rotational FT spectrometer can perform Mid-IR dual-comb spectroscopy with a single comb source, since the Doppler-shifted version of the comb serves as the second comb. In our realization, we combine the advantages of dual-comb and FT spectroscopy using a single quantum cascade laser frequency comb emitting at 8.2 μm as a light source. Our technique does not require any diffractive or dispersive optical elements and hence preserve the Jacquinot's-, Fellgett's-, and Connes'-advantages of FT spectrometers. By integrating mulitple broadband sources, such system could pave the way for applications where high speed, large optical bandwidth, and high spectral resolution are desired.

New, fast, and precise method of COVID-19 detection in nasopharyngeal and tracheal aspirate samples combining optical spectroscopy and machine learning

Fast, precise, and low-cost diagnostic testing to identify persons infected with SARS-CoV-2 virus is pivotal to control the global pandemic of COVID-19 that began in late 2019. The gold standard method of diagnostic recommended is the RT-qPCR test. However, this method is not universally available, and is time-consuming and requires specialized personnel, as well as sophisticated laboratories. Currently, machine learning is a useful predictive tool for biomedical applications, being able to classify data from diverse nature. Relying on the artificial intelligence learning process, spectroscopic data from nasopharyngeal swab and tracheal aspirate samples can be used to leverage characteristic patterns and nuances in healthy and infected body fluids, which allows to identify infection regardless of symptoms or any other clinical or laboratorial tests. Hence, when new measurements are performed on samples of unknown status and the corresponding data is submitted to such an algorithm, it will be possible to predict whether the source individual is infected or not. This work presents a new methodology for rapid and precise label-free diagnosing of SARS-CoV-2 infection in clinical samples, which combines spectroscopic data acquisition and analysis via artificial intelligence algorithms. Our results show an accuracy of 85% for detection of SARS-CoV-2 in nasopharyngeal swab samples collected from asymptomatic patients or with mild symptoms, as well as an accuracy of 97% in tracheal aspirate samples collected from critically ill COVID-19 patients under mechanical ventilation. Moreover, the acquisition and processing of the information is fast, simple, and cheaper than traditional approaches, suggesting this methodology as a promising tool for biomedical diagnosis vis-à-vis the emerging and re-emerging viral SARS-CoV-2 variant threats in the future.

Identification of amino acid residues in a proton release pathway near the bacteriochlorophyll dimer in reaction centers from Rhodobacter sphaeroides

Insight into control of proton transfer, a crucial attribute of cellular functions, can be gained from investigations of bacterial reaction centers. While the uptake of protons associated with the reduction of the quinone is well characterized, the release of protons associated with the oxidized bacteriochlorophyll dimer has been poorly understood. Optical spectroscopy and proton release/uptake measurements were used to examine the proton release characteristics of twelve mutant reaction centers, each containing a change in an amino acid residue near the bacteriochlorophyll dimer. The mutant reaction centers had optical spectra similar to wild-type and were capable of transferring electrons to the quinones after light excitation of the bacteriochlorophyll dimer. They exhibited a large range in the extent of proton release and in the slow recovery of the optical signal for the oxidized dimer upon continuous illumination. Key roles were indicated for six amino acid residues, Thr L130, Asp L155, Ser L244, Arg M164, Ser M190, and His M193. Analysis of the results points to a hydrogen-bond network that contains these residues, with several additional residues and bound water molecules, forming a proton transfer pathway. In addition to proton transfer, the properties of the pathway are proposed to be responsible for the very slow charge recombination kinetics observed after continuous illumination. The characteristics of this pathway are compared to proton transfer pathways near the secondary quinone as well as those found in photosystem II and cytochrome c oxidase.

Integrated photodetectors for compact Fourier-transform waveguide spectrometers

Extreme miniaturization of infrared spectrometers is critical for their integration into next-generation consumer electronics, wearables and ultrasmall satellites. In the infrared, there is a necessary compromise between high spectral bandwidth and high spectral resolution when miniaturizing dispersive elements, narrow band-pass filters and reconstructive spectrometers. Fourier-transform spectrometers are known for their large bandwidth and high spectral resolution in the infrared; however, they have not been fully miniaturized. Waveguide-based Fourier-transform spectrometers offer a low device footprint, but rely on an external imaging sensor such as bulky and expensive InGaAs cameras. Here we demonstrate a proof-of-concept miniaturized Fourier-transform waveguide spectrometer that incorporates a subwavelength and complementary-metal-oxide-semiconductor-compatible colloidal quantum dot photodetector as a light sensor. The resulting spectrometer exhibits a large spectral bandwidth and moderate spectral resolution of 50 cm^-1 at a total active spectrometer volume below 100 μm × 100 μm × 100 μm. This ultracompact spectrometer design allows the integration of optical/analytical measurement instruments into consumer electronics and space devices.

Molecular docking and optical sensor studies based on 2,4-diamino pyrimidine-5-carbonitriles for detection of Hg2

An organic chemical sensor based on pyrimidine was successfully produced through the green reaction between aromatic aldehyde, malononitrile, and guanidine carbonate using SBA-Pr-SO₃H. This fluorescence intensity of chemosensor (2,4-diamino-6-(phenyl)pyrimidine-5-carbonitrile) decreases by the addition of Hg²⁺ and its detection limit is about 14.89 × 10^-5 M, in fact, through the green synthesis, the ligand was yielded to detect Hg²⁺ and the importance of ligand was considered in docking studies. The molecular docking of 2,4-diamino-6-(phenyl)pyrimidine-5-carbonitrile compound has been done with the protein selective estrogen receptor 5ACC complexed with (Azd9496), Human Anaplastic Lymphoma Kinase Pdb; 2xp2 complex with crizotinib (PF-02341066) and human wee1 kinase Pdb; 5vc3 complexed with bosutinib. The ligands 2,4-diamino-6-(phenyl)pyrimidine-5-carbonitrile generate very good docking results with the protein Pdb; 2xp2, which is responsible for effective tumor growth inhibition.

Biological Characteristics and Optical Reflectance Spectroscopy of Human Placenta Derived Mesenchymal Stem Cells for Application in Regenerative Medicine

Introduction: The efficiency of stem cell isolation, culture, and biological characterization techniques for treatment is facing serious challenges. The purpose of this study was to provide a protocol for isolation and culture of three types of mesenchymal stem cells (MSCs) derived from the human placenta, amniotic membrane, and umbilical cord with high efficiency used for cell therapy. Methods: During this experimental laboratory study, 10 complete placenta samples were prepared from cesarean section mothers. The protocol for isolation and culture of mesenchymal cells from the placenta tissue, umbilical cord, and amniotic membrane was enzymatically optimized. The morphological features of mesenchymal cells were investigated using an inverted microscope and their biological features were measured using flow cytometry. The differentiation potential of the cells was evaluated by measuring their differentiation capacity into osteocytes and adipocytes. The absorption and reflectance features of the cells were recorded by optical spectroscopy. Finally, the data were statistically analyzed. Results: The expression of CD44, CD73, CD90 and CD29 markers in human placenta tissue-derived cells was significant. CD14, CD34 and CD45 markers were not expressed or were slightly expressed. These cells were highly viable and successfully differentiated into osteocytes and adipocytes. MSCs absorbed more light than visible light by showing light absorption peaks at wavelengths of about 435 and 550 nm. Conclusion: The protocol used in this study for isolation and culture of human placenta tissue-derived MSCs had significant efficiency for the production of MSCs for use in cell therapy and tissue engineering.

Estimation of the biogeochemical reactivities of dissolved organic matter from modified biochars using color

Modified biochar is widely used as a soil amendment in agricultural systems to improve crop yields and remove environmental pollutants. The water-soluble fraction of biochar, called biochar-derived dissolved organic matter (DOM_BC), is the most active biochar component. However, the correlation between the optical properties of DOM_BC and its biogeochemical activity remain unclear. In this study, one biochar and six modified derivatives were used to extract DOM_BC and characterize its optical properties. The biogeochemical reactivities of DOM_BC were determined using biodegradation, photodegradation, and electron-donating capacity assays. The results show that modification changes the biochar characteristics, leading to a variety of DOM_BC properties. The DOM_BC from modified biochars degrades more rapidly than the original biochar. On the other hand, modification reduces the redox functional groups in DOM_BC, resulting in a lower electron-donating capacity of DOM samples. However, the modifications did not seem to affect photodegradation. Not all spectral parameters provide information about the correlations between the DOM_BC properties and biogeochemical reactivity. However, two fundamental properties, that is, the specific UV absorbance at 254 nm (SUVA₂₅₄, showing aromaticity) and spectral slopes over the ranges of 275-295 nm of the UV absorbance (S_275-295, showing molecular weight), are the dominant factors affecting the biodegradation and electron-donating capacities of DOM_BC. In this study, a rapid and straightforward method is presented, which can be used to characterize DOM_BC and predict the reactivity of biochar that is used as an environmental amendment to minimize toxic organic compounds.

Hypothesis of macroscopic quantum state in biological systems and discussion on the possibility of its experimental verification

Earlier it was noted that the functioning of biological systems is accompanied by a very low level of energy dissipation, and it was assumed that a physical mechanism similar to that which works in superconductivity can operate here. The paper proposes a hypothesis that the phenomenon of life is not based on superconductivity, but on some so far unexplored macroscopic quantum state of organic structures making up the cell. It is assumed that this state is also characterized by the presence of an energy gap in the electronic spectrum, which makes the state stable and provides a low level of energy dissipation. The possibility of using optical spectroscopy methods for identifying the energy gap in biological objects is analyzed. It is assumed that the virus is alive inside the host cell, but not alive outside the host cell. It is proposed to use Raman spectroscopy of the process of bacterial infection with phages to search for the energy gap. This should confirm or refute the main hypothesis, as well as provide an opportunity to answer the question: "Are viruses alive?"

Optical tissue measurements of invasive carcinoma and ductal carcinoma in situ for surgical guidance

Background

Although the incidence of positive resection margins in breast-conserving surgery has decreased, both incomplete resection and unnecessary large resections still occur. This is especially the case in the surgical treatment of ductal carcinoma in situ (DCIS). Diffuse reflectance spectroscopy (DRS), an optical technology based on light tissue interactions, can potentially characterize tissue during surgery thereby guiding the surgeon intraoperatively. DRS has shown to be able to discriminate pure healthy breast tissue from pure invasive carcinoma (IC) but limited research has been done on (1) the actual optical characteristics of DCIS and (2) the ability of DRS to characterize measurements that are a mixture of tissue types.

Methods

In this study, DRS spectra were acquired from 107 breast specimens from 107 patients with proven IC and/or DCIS (1488 measurement locations). With a generalized estimating equation model, the differences between the DRS spectra of locations with DCIS and IC and only healthy tissue were compared to see if there were significant differences between these spectra. Subsequently, different classification models were developed to be able to predict if the DRS spectrum of a measurement location represented a measurement location with “healthy” or “malignant” tissue. In the development and testing of the models, different definitions for “healthy” and “malignant” were used. This allowed varying the level of homogeneity in the train and test data.

Results

It was found that the optical characteristics of IC and DCIS were similar. Regarding the classification of tissue with a mixture of tissue types, it was found that using mixed measurement locations in the development of the classification models did not tremendously improve the accuracy of the classification of other measurement locations with a mixture of tissue types. The evaluated classification models were able to classify measurement locations with > 5% malignant cells with a Matthews correlation coefficient of 0.41 or 0.40. Some models showed better sensitivity whereas others had better specificity.

Conclusion

The results suggest that DRS has the potential to detect malignant tissue, including DCIS, in healthy breast tissue and could thus be helpful for surgical guidance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13058-021-01436-5.

Tautomeric influence on the photoinduced birefringence of 4-substituted phthalimide 2-hydroxy Schiff bases in PMMA matrix

The photoinduced birefringence of two 4-substituted phthalimide 2-hydroxy Schiff bases, containing salicylic (4) and 2-hydroxy-1-naphthyl (5) moieties has been investigated in PMMA matrix. Their optical behaviour as nanocomposite films was revealed by combined use of DFT quantum chemical calculations (in ground and excited state) and experimental optical spectroscopy (UV-Vis and fluorescence). The results have shown that solid-state reversible switching takes place by enol/keto tautomerization and Z/E isomerization. Birefringence study was performed in the PMMA nanocomposite films using pump lasers at λ_rec = 355 nm and λ_rec = 442 nm. Fast response time and high stability of anisotropy up to 58% for (4) and 95% for (5) after turning off the excitation laser, was observed, which makes these materials appropriate candidates for cutting-edge optical information technology materials. The possibility for multiple cycles of recording, reading and optical erasure of the photoinduced birefringence at λ_rec = 442 nm in 5 has been demonstrated. The obtained results have shown that the maximum value of the measured birefringence is close to the anisotropic characteristics of the most frequently used azo materials.

Brain neurochemical monitoring

Brain neurochemical monitoring aims to provide continuous and accurate measurements of brain biomarkers. It has enabled significant advances in neuroscience for application in clinical diagnostics, treatment, and prevention of brain diseases. Microfabricated electrochemical and optical spectroscopy sensing technologies have been developed for precise monitoring of brain neurochemicals. Here, a comprehensive review on the progress of sensing technologies developed for brain neurochemical monitoring is presented. The review provides a summary of the widely measured clinically relevant neurochemicals and commonly adopted recognition technologies. Recent advances in sampling, electrochemistry, and optical spectroscopy for brain neurochemical monitoring are highlighted and their application are discussed. Existing gaps in current technologies and future directions to design industry standard brain neurochemical sensing devices for clinical applications are addressed.

Optical properties and electronic structure of Eu(III) complexes with HMPA and TPPO

Two adducts of Eu(III) tris-hexofluoroacetylacetonate with HMPA (OP(N(CH₃)₂)₃, hexamethylphosphotriamide) and TPPO (OP(C₆H₅)₃, triphenylphosphine oxide) were studied by optical spectroscopy and quantum chemistry (DFT/TD-DFT). The structure of the higher occupied molecular orbitals (MO) of the two adducts determines differences in the position of the excitation band maximum of hfac ligands. According to the calculation data, all excited states are caused by the transition to 3 vacant π₄* MOs of hfac ligands. Optical spectra of absorption, excitation and luminescence are obtained and interpreted. The peculiarity of the HOMO-LUMO structure, the low value of the energy gap, and the broadened absorption region of hfac ligands compensate the low absorbance ability of the groups N(CH₃)₂ in a region of 220-360 nm for the adduct Eu(hfac)₃(HMPA)₂, reducing the luminescence intensity by only 5-10% relative to the adduct of the Eu(III) complex with TPPO ligands.

Characterization data of an (AlFeNiTiVZr)1-xCrx multi-principal element alloy continuous composition spread library

The data provided in this article is related to the research article entitled "Phase stabilization and oxidation of a continuous composition spread multi-principal element (AlFeNiTiVZr)1-xCrx alloy" [1]. This data article describes the high-throughput synthesis and characterization processes of an (AlFeNiTiVZr)1-xCrx alloy system. Continuous composition spread (CCS) thin-film libraries were synthesized by co-depositing an AlFeNiTiVZr metal alloy target and Cr target via magnetron sputtering. Post-processing was performed on the sample libraries with a vacuum anneal at 873 K and an air anneal at 873 K. Compositional data was determined via WDS in order to verify parameters provided by an in-house sputter model. Crystallographic data was captured via synchrotron diffraction and diffractograms were compared as a function of the change in Cr concentration. These measurements were taken in order to observe phase behavior after oxidation throughout the composition library. Furthermore, vibrational spectrographic data is provided of the oxidized library to show surface speciation along the composition gradient of the alloy system. The structural and oxidative behavior of the (AlFeNiTiVZr)1-xCrx alloy can be analysed using the data provided in this article. Additionally, this characterization dataset can be utilized in machine learning algorithms for determining important features and parameters for future hypothesis generation of functional multi-principal element alloys (MPEAs).

Optical technologies for the detection of viruses like COVID-19: Progress and prospects

The outbreak of life-threatening pandemic like COVID-19 necessitated the development of novel, rapid and cost-effective techniques that facilitate detection of viruses like SARS-CoV-2. The presently popular approach of a collection of samples using the nasopharyngeal swab method and subsequent detection of RNA using the real-time polymerase chain reaction suffers from false-positive results and a longer diagnostic time scale. Alternatively, various optical techniques namely optical sensing, spectroscopy, and imaging shows a great promise in virus detection. Herein, a comprehensive review of the various photonics technologies employed for virus detection, particularly the SARS-CoV family, is discussed. The state-of-art research activities in utilizing the photonics tools such as near-infrared spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, fluorescence-based techniques, super-resolution microscopy, surface plasmon resonance-based detection, for virus detection accounted extensively with an emphasis on coronavirus detection. Further, an account of emerging photonics technologies of SARS-CoV-2 detection and future possibilities is also explained. The progress in the field of optical techniques for virus detection unambiguously show a great promise in the development of rapid photonics-based devices for COVID-19 detection.

Incoherent excess noise spectrally encodes broadband light sources

Across optics and photonics, excess intensity noise is often considered a liability. Here, we show that excess noise in broadband supercontinuum and superluminescent diode light sources encodes each spectral channel with unique intensity fluctuations, which actually serve a useful purpose. Specifically, we report that excess noise correlations can both characterize the spectral resolution of spectrometers and enable cross-calibration of their wavelengths across a broad bandwidth. Relative to previous methods that use broadband interferometry and narrow linewidth lasers to characterize and calibrate spectrometers, our approach is simple, comprehensive, and rapid enough to be deployed during spectrometer alignment. First, we employ this approach to aid alignment and reduce the depth-dependent degradation of the sensitivity and axial resolution in a spectrometer-based optical coherence tomography (OCT) system, revealing a new outer retinal band. Second, we achieve a pixel-to-pixel correspondence between two otherwise disparate spectrometers, enabling a robust comparison of their respective measurements. Thus, excess intensity noise has useful applications in optics and photonics.

Acenaphtoquinoxaline as a selective fluorescent sensor for Hg (II) detection: experimental and theoretical studies

A new fluorescent chemosensor based on quinoxaline was successfully synthesized through a facile and green catalytic reaction of ortho-phenylenediamine (O-PDA) and acenaphthylene-1,2-dione in the presence of SBA-Pr-SO3H. Prepared a "switch-off" quinoxaline-based receptor to recognized Hg2+ ion in high selectively and, without any interference from other metal ions, was developed. The photophysical behavior of this fluorophore was studied in acetonitrile by using fluorescence spectra. The fluorescence properties of several cations to acenaphtoquinoxaline were investigated in acetonitrile, and the competition test displayed that the probe fluorescence changes were specific for Hg2+ ion. The obtained results have shown high selectivity and sensitivity only for Hg2+. Also, the detection limit was as low as 42 ppb, and a top linear trend was observed between the concentration of Hg2+ ions and fluorescence intensity. The binding stoichiometry between chemosensor L and Hg2+ was found to be 1:1. Moreover, a computational study was performed to obtain an electronic description of the fluorescence emission and quenching mechanisms. The optimized structures and binding mechanisms were supported with a high correlation and agreement by spectroscopy and DFT calculations.

5-Aminolevulinic Acid-Induced Fluorescence in Focal Cortical Dysplasia: Report of 3 Cases

BACKGROUND

Three patients enrolled in a clinical trial of 5-aminolevulinic-acid (5-ALA)-induced fluorescence-guidance, which has been demonstrated to facilitate intracranial tumor resection, were found on neuropathological examination to have focal cortical dysplasia (FCD).

OBJECTIVE

To evaluate in this case series visible fluorescence and quantitative levels of protoporphyrin IX (PpIX) during surgery and correlate these findings with preoperative magnetic resonance imaging (MRI) and histopathology.

METHODS

Patients were administered 5-ALA (20 mg/kg) approximately 3 h prior to surgery and underwent image-guided, microsurgical resection of their MRI- and electrophysiologically identified lesions. Intraoperative visible fluorescence was evaluated using an operating microscope adapted with a commercially available blue light module. Quantitative PpIX levels were assessed using a handheld fiber-optic probe and a wide-field imaging spectrometer. Sites of fluorescence measurements were co-registered with both preoperative MRI and histopathological analysis.

RESULTS

Three patients with a pathologically confirmed diagnosis of FCD (Types 1b, 2a, and 2b) underwent surgery. All patients demonstrated some degree of visible fluorescence (faint or moderate), and all patients had quantitatively elevated concentrations of PpIX. No evidence of neoplasia was identified on histopathology, and in 1 patient, the highest concentrations of PpIX were found at a tissue site with marked gliosis but no typical histological features of FCD.

CONCLUSION

FCD has been found to be associated with intraoperative 5-ALA-induced visible fluorescence and quantitatively confirmed elevated concentrations of the fluorophore PpIX in 3 patients. This finding suggests that there may be a role for fluorescence-guidance during surgical intervention for epilepsy-associated FCD.

A stability-indicating UPLC method for the determination of curcumin diethyl disuccinate, an ester prodrug of curcumin, in raw materials

A stability-indicating reversed-phase ultra-performance liquid chromatographic (UPLC) method for quantitative analysis of curcumin diethyl disuccinate (CDD) in raw materials was developed for applications in product development and quality control. Chromatographic separation was performed using the Waters ACQUITY UPLC® H-Class system consisting of an ACQUITY UPLC® BEH C18 (1.7 μm, 2.1 × 50 mm) column and a photodiode array detector set at a wavelength of 400 nm. The mobile phase consisting of 2%v/v acetic acid in water and acetonitrile was delivered at a flow rate of 0.3 mL/min under gradient elution program. The method was validated according to the ICH Q2(R1) guideline for the validation of analytical procedures. The method was found to be linear over the concentration range of 8-12 μg/mL with the coefficient of determination >0.995. The accuracy of the method established as %recovery ranged from 98.3 - 100.8%. The precision of the method expressed as %CV was found to be <1%. The coelution of degradation products from six stress test conditions was not observed. The method was robust under the variation of chromatographic parameters. The method was successfully applied in the determination of CDD content in raw materials.

Two diagnostic criteria of optical spectroscopy for bladder tumor detection: Clinical study using 5-ALA induced fluorescence and mathematical modeling

BACKGROUND

The study proposes to improve bladder cancer diagnosis by photodynamic diagnosis (PDD) using red-light excitation (632.8 nm) of 5-ALA induced-protoporphyrin IX. Employing 9 patients' bladders, two types of signals were used to improve diagnostic accuracy for malignancy and we also present numerical modeling of the scattering coefficient to provide biological explanation of the results obtained.

METHODS

Two modalities of bladder cancer spectral diagnosis are presented: conventional PDD and intensity assessment of the diffusely reflected laser light by fiber-optic spectroscopy. Experiments are done in clinical conditions and as a series of numerical simulations.

RESULTS

High-grade cancerous bladder tissues display twice a higher relative fluorescence intensity (mean value 1, n = 9) than healthy (0.39, n = 9), dysplastic (0.44, n = 5) tissues and CIS (0.39, n = 2). The laser back-scattering signal allows to discriminate most effectively high-grade cancerous and dysplastic tissues from normal. Numerical modeling of diffuse reflectance spectra reveals that spectral behavior of the back-scattered light depends on both, nuclear size and nuclear density of tumoral cells.

CONCLUSIONS

Unlike the fluorescence signal, where its value is higher in the case of pathological tissues, the tendency of the laser signal to, both, decrease or increase in comparison with the signal from normal urothelium, should be perceived as a sign towards neoplasm. Numerical simulation reveals that such a double-analysis at a multiwavelength mode potentially may be used to provide diagnostic accuracy.

First observation of tropospheric nitrogen dioxide from the Environmental Trace Gases Monitoring Instrument onboard the GaoFen-5 satellite

The Environmental Trace Gases Monitoring Instrument (EMI) is the first Chinese satellite-borne UV-Vis spectrometer aiming to measure the distribution of atmospheric trace gases on a global scale. The EMI instrument onboard the GaoFen-5 satellite was launched on 9 May 2018. In this paper, we present the tropospheric nitrogen dioxide (NO2) vertical column density (VCD) retrieval algorithm dedicated to EMI measurement. We report the first successful retrieval of tropospheric NO2 VCD from the EMI instrument. Our retrieval improved the original EMI NO2 prototype algorithm by modifying the settings of the spectral fit and air mass factor calculations to account for the on-orbit instrumental performance changes. The retrieved EMI NO2 VCDs generally show good spatiotemporal agreement with the satellite-borne Ozone Monitoring Instrument and TROPOspheric Monitoring Instrument (correlation coefficient R of ~0.9, bias < 50%). A comparison with ground-based MAX-DOAS (Multi-Axis Differential Optical Absorption Spectroscopy) observations also shows good correlation with an R of 0.82. The results indicate that the EMI NO2 retrieval algorithm derives reliable and precise results, and this algorithm can feasibly produce stable operational products that can contribute to global air pollution monitoring.

Absolute and Relative Methods for Fluorescence Quantum Yield Evaluation of Quantum Dots

Optical spectroscopy techniques are crucial for the evaluation and use of quantum dots (QDs) in life and materials science. In that context, the fluorescence quantum yield (Φ_f) is an essential parameter in the assessment of the luminescent features of QDs. The fluorescence quantum yield can be defined as the ratio of the number of emitted photons to the number of absorbed photons by a luminescent material. In this chapter, we describe absolute and relative methods to measure the fluorescence quantum yield of QDs in solution phase. The advantages and limitations of the techniques are reviewed.

Ultra-long-working-distance spectroscopy of single nanostructures with aspherical solid immersion microlenses

In light science and applications, equally important roles are played by efficient light emitters/detectors and by the optical elements responsible for light extraction and delivery. The latter should be simple, cost effective, broadband, versatile and compatible with other components of widely desired micro-optical systems. Ideally, they should also operate without high-numerical-aperture optics. Here, we demonstrate that all these requirements can be met with elliptical microlenses 3D printed on top of light emitters. Importantly, the microlenses we propose readily form the collected light into an ultra-low divergence beam (half-angle divergence below 1°) perfectly suited for ultra-long-working-distance optical measurements (600 mm with a 1-inch collection lens), which are not accessible to date with other spectroscopic techniques. Our microlenses can be fabricated on a wide variety of samples, including semiconductor quantum dots and fragile van der Waals heterostructures made of novel two-dimensional materials, such as monolayer and few-layer transition metal dichalcogenides.

The evolution of total internal reflection Raman spectroscopy for the chemical characterization of thin films and interfaces

Total internal reflection (TIR) optical spectroscopies have been widely used for decades as non-destructive and surface-sensitive measurements of thin films and interfaces. Under TIR conditions, an evanescent wave propagates into the sample layer within a region approximately 50 nm to 2 μm from the interface, which limits the spatial extent of the optical signal. The most common TIR optical spectroscopies are fluorescence (i.e., TIRF) and infrared spectroscopy (i.e., attenuated total reflection infrared). Despite the first report of TIR Raman spectroscopy appearing in 1973, this method has not received the same attention to date. While TIR Raman methods can provide chemical specific information, it has been outshined in many respects by surface-enhanced Raman spectroscopy (SERS). TIR Raman spectroscopy, however, is garnering more interest for analyzing the chemical and physical properties of thin polymer films, self-assembled monolayers (SAMs), multilayered systems, and adsorption at an interface. Herein, we discuss the early experimental and computational work that laid the foundation for recent developments in the use of TIR Raman techniques. Recent applications of TIR Raman spectroscopy as well as modern TIR Raman instruments capable of measuring monolayer-sensitive vibrational modes on smooth metallic surfaces are also discussed. The use of TIR Raman spectroscopy has been on a rise and will continue to push the limits for chemical specific interfacial and thin film measurements. Graphical abstract Total internal reflection (TIR) Raman spectroscopy can extract the chemical and physical information from thin films and adsorbates.

Linking the molecular composition of autochthonous dissolved organic matter to source identification for freshwater lake ecosystems by combination of optical spectroscopy and FT-ICR-MS analysis

Autochthonous dissolved organic matter (DOM) is increasingly released in lakes due to eutrophication, and thus affects the composition and environmental behaviors of DOM in eutrophic lakes. However, there are only limited studies on the molecular characteristics of autochthonous DOM and its influencing mechanisms. Herein, end-member DOM samples of macrophytes, algae, sediments and freshwater DOM samples in eutrophic lakes (Ch:Taihu and Dianchi) were collected and characterized by optical spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The results revealed the chemical structures of autochthonous DOM were more aliphatic and less oxidized, which was marked by increases in lipid compounds and decreases in the lignin components as compared to the allochthonous DOM-dominated freshwaters. More specially, algae-derived DOM contains more lipid compounds, while macrophyte-derived DOM was dominated by lignin and tannin compounds according to Van Krevelen plots. Sediment-derived DOM contained more N-containing compounds. The traditional optical indices indicated the relative aromaticity covaried with polyphenolic and polycyclic aromatics, whereas those reflecting autochthonous DOM covaried with more aliphatic compounds. Multivariate analysis of FT-ICR-MS data of end-members and freshwaters revealed the predominant terrestrial input to Lake Taihu and greater contribution of algae released DOM to Dianchi. This study provides critical information about the characteristics of autochthonous DOM at a molecular level and confirmed autochthonous DOM was compositionally distinct from allochthonous DOM. Overall autochthonous DOM should be gained more attention in the eutrophic lakes.

Bound manganese oxides capable of reducing the bacteriochlorophyll dimer of modified reaction centers from Rhodobacter sphaeroides

A biohybrid model system is described that interfaces synthetic Mn-oxides with bacterial reaction centers to gain knowledge concerning redox reactions by metal clusters in proteins, in particular the Mn₄CaO₅ cluster of photosystem II. The ability of Mn-oxides to bind to modified bacterial reaction centers and transfer an electron to the light-induced oxidized bacteriochlorophyll dimer, P⁺, was characterized using optical spectroscopy. The environment of P was altered to obtain a high P/P⁺ midpoint potential. In addition, different metal-binding sites were introduced by substitution of amino acid residues as well as extension of the C-terminus of the M subunit with the C-terminal region of the D1 subunit of photosystem II. The Mn-compounds MnO₂, αMn₂O₃, Mn₃O₄, CaMn₂O₄, and Mn₃(PO₄)₂ were tested and compared to MnCl₂. In general, addition of the Mn-compounds resulted in a decrease in the amount of P⁺ while the reduced quinone was still present, demonstrating that the Mn-compounds can serve as secondary electron donors. The extent of P⁺ reduction for the Mn-oxides was largest for αMn₂O₃ and CaMn₂O₄ and smallest for Mn₃O₄ and MnO₂. The addition of Mn₃(PO₄)₂ resulted in nearly complete P⁺ reduction, similar to MnCl₂. Overall, the activity was correlated with the initial oxidation state of the Mn-compound. Transient optical measurements showed a fast kinetic component, assigned to reduction of P⁺ by the Mn-oxide, in addition to a slow component due to charge recombination. The results support the conjecture that the incorporation of Mn-oxides by ancient anoxygenic phototrophs was a step in the evolution of oxygenic photosynthesis.

A dip-and-read optical aptasensor for detection of tau protein

Neurodegeneration currently remains without a differential diagnosis or cure. Tau protein is one of the biomarkers of neurodegenerative diseases commonly known as tauopathies. Tau protein plays an integral role in stabilizing microtubules and cell structure; however, due to post-translational modifications, tau protein undergoes self-assembly into cytotoxic structures and is co-localized intra- and extracellularly. Hence, tau protein is a viable biomarker associated with protein pathogenesis and neurodegeneration. The novel optical biosensor for tau441 protein is based on the aptamer recognition probe and the biolayer interferometry (BLI) method for detection. The current biotin-aptasensor in combination with the streptavidin surface provides real-time monitoring of tau441 protein in the nanomolar range, with the limit of detection at 6.7 nM in vitro. The tau441 detection is achieved with high selectivity over other neurodegeneration biomarkers which include amyloid-β and α-synuclein. The aptasensor also allows for tau441 protein detection in a complex matrix such as fetal bovine serum, indicating its utility in other biological fluids for diagnostic applications. The optical method is simple, rapid and highly selective for point-of-care application which is critical for achieving the early and differential diagnosis of neurodegenerative diseases and identifying their treatments. Graphical abstract.

Understanding and tuning blue-to-near-infrared photon cutting by the Tm3+/Yb3+ couple

Lanthanide-based photon-cutting phosphors absorb high-energy photons and 'cut' them into multiple smaller excitation quanta. These quanta are subsequently emitted, resulting in photon-conversion efficiencies exceeding unity. The photon-cutting process relies on energy transfer between optically active lanthanide ions doped in the phosphor. However, it is not always easy to determine, let alone predict, which energy-transfer mechanisms are operative in a particular phosphor. This makes the identification and design of new promising photon-cutting phosphors difficult. Here we unravel the possibility of using the Tm³⁺/Yb³⁺ lanthanide couple for photon cutting. We compare the performance of this couple in four different host materials. Cooperative energy transfer from Tm³⁺ to Yb³⁺ would enable blue-to-near-infrared conversion with 200% efficiency. However, we identify phonon-assisted cross-relaxation as the dominant Tm³⁺-to-Yb³⁺ energy-transfer mechanism in YBO₃, YAG, and Y₂O₃. In NaYF₄, in contrast, the low maximum phonon energy renders phonon-assisted cross-relaxation impossible, making the desired cooperative mechanism the dominant energy-transfer pathway. Our work demonstrates that previous claims of high photon-cutting efficiencies obtained with the Tm³⁺/Yb³⁺ couple must be interpreted with care. Nevertheless, the Tm³⁺/Yb³⁺ couple is potentially promising, but the host material-more specifically, its maximum phonon energy-has a critical effect on the energy-transfer mechanisms and thereby on the photon-cutting performance.

Deep spectral learning for label-free optical imaging oximetry with uncertainty quantification

Measurement of blood oxygen saturation (sO2) by optical imaging oximetry provides invaluable insight into local tissue functions and metabolism. Despite different embodiments and modalities, all label-free optical-imaging oximetry techniques utilize the same principle of sO2-dependent spectral contrast from haemoglobin. Traditional approaches for quantifying sO2 often rely on analytical models that are fitted by the spectral measurements. These approaches in practice suffer from uncertainties due to biological variability, tissue geometry, light scattering, systemic spectral bias, and variations in the experimental conditions. Here, we propose a new data-driven approach, termed deep spectral learning (DSL), to achieve oximetry that is highly robust to experimental variations and, more importantly, able to provide uncertainty quantification for each sO2 prediction. To demonstrate the robustness and generalizability of DSL, we analyse data from two visible light optical coherence tomography (vis-OCT) setups across two separate in vivo experiments on rat retinas. Predictions made by DSL are highly adaptive to experimental variabilities as well as the depth-dependent backscattering spectra. Two neural-network-based models are tested and compared with the traditional least-squares fitting (LSF) method. The DSL-predicted sO2 shows significantly lower mean-square errors than those of the LSF. For the first time, we have demonstrated en face maps of retinal oximetry along with a pixel-wise confidence assessment. Our DSL overcomes several limitations of traditional approaches and provides a more flexible, robust, and reliable deep learning approach for in vivo non-invasive label-free optical oximetry.

Mineral composition of organic and conventional white wines from Italy

Despite of the increased interest of consumers for organic agro-food products and of the growing demand for organic wines, scientific literature reports a limited number of studies aimed to evaluate the chemical composition of organic wine with respect to conventional wine in terms of major and trace metals. In the present study the concentrations of 19 elements (Al, As, B, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Na, Ni, Pb, Sr, V, and Zn) were determined in samples of white wines from Italy, conventionally and organically produced. No significant difference in the mineral composition was found between the two groups, except for Ni, which showed a higher concentration in organic wines. By comparing our data with data from literature it can be pointed out that there is no agreement among the results presented in the different studies referring to comparisons between organically and conventionally produced wines, concluding that the mineral composition of wines depends on factors different from organic/conventional production method.

Time-Resolved Study of Site-Specific Corrosion in a Single Crystalline Silver Nanoparticle

We followed over 24 h a corrosion process in monocrystalline triangular-shaped nanoparticles at a single-particle level by atomic force microscopy and optical spectroscopy techniques under ambient laboratory conditions. The triangular-shaped form of the particles was selected, because the crystallographic orientation of the particles is well defined upon their deposition on a substrate. We observed that the particles already start to alter within this time frame. Surprisingly, the corrosion starts predominantly from the tips of the particles and it creates within few hours large protrusions, which strongly suppress the plasmon character of the particles. These observations support the crystallographic model of these particles consisting of a high-defect hexagonal closed packed layer, and they could help material scientists to design more stable silver nanoparticles. Moreover, this described technique can be used to reveal kinetics of the corrosion in the nanoscale of other materials.

Comparison of optical spectroscopy techniques for monitoring the stages of thermoxidation of soybean biodiesel

The thermoxidation of biodiesel was monitored using different spectroscopic techniques: UV-Vis and MIR absorption, Raman spectroscopy, and visible fluorescence. As the oxidation progressed, the UV-Vis absorption spectra showed an increase in the spectral range between 34,000 and 26,000 cm-1, while two main fluorescence bands (under ultraviolet excitation) were observed at around 21,000 and 15,000 cm-1. The UV-Vis absorption and fluorescence intensities presented opposite behavior during the processes, irrespective of the temperature used (90, 140, or 190 °C). These effects could be explained by the consumption of natural antioxidants, followed by the formation of primary oxidation compounds. The Raman and MIR absorption results indicated the existence of a cis-trans isomerization effect, followed by the formation of hydroperoxides during the oxidation, with the behavior being the same as that revealed by the UV-Vis absorption and fluorescence analyses. The comparison, under the same conditions, of different spectroscopy techniques that can be used to monitor the stages of thermoxidation of soybean biofuel provides important information for selection of an appropriate technique for evaluating biodiesel integrity.

Impressive near-infrared brightness and singlet oxygen generation from strategic lanthanide-porphyrin double-decker complexes in aqueous solution

Although lanthanide double-decker complexes with hetero-macrocyclic ligands as functional luminescent and magnetic materials have promising properties, their inferior water solubility has negated their biomedical applications. Herein, four water-soluble homoleptic lanthanide (Ln = Gd, Er, Yb and La) sandwiches with diethylene-glycol-disubstituted porphyrins (DD) are reported, with their structures proven by both quantum chemical calculations and scanning tunneling microscopy. Our findings demonstrate that the near-infrared emission intensity and singlet oxygen (¹O₂) quantum yields of YbDD and GdDD in aqueous media are higher than those of the reported capped lanthanide monoporphyrinato analogues, YbN and GdN; the brightness and luminescence lifetime in water of YbDD are greater than those of YbN. This work provides a new dimension for the future design and development of molecular theranostics-based water-soluble double-decker lanthanide bisporphyrinates.

Optical spectroscopy study of Ca3(Ru0.91Mn0.09)2O7 single crystal in high magnetic fields

The magneto-optical spectrum, with magnetic fields up to 42 T, of double layered ruthenates Ca₃(Ru_0.91Mn_0.09)₂O₇ (CRMO) single crystal is studied. Both the temperature and magnetic field induced insulator-to-metal transitions (IMTs) are observed via magneto-optical properties of the crystal. The critical magnetic field (H // c) of IMT for CRMO is found to be as large as 35 T at 5 K. The fine structure of optical spectra identified the antiferromagnetic/ferro-orbital-ordering configurations of Ru 4d orbitals at low temperatures. Meanwhile, the configuration of orbital polarization of such double-layer CRMO single crystal is discussed. These results suggest that the orbital degree of freedom plays an important role in the field induced IMT of multi-orbital system.

A Wearable Fiberless Optical Sensor for Continuous Monitoring of Cerebral Blood Flow in Mice

Continuous and longitudinal monitoring of cerebral blood flow (CBF) in animal models provides information for studying the mechanisms and interventions of various cerebral diseases. Since anesthesia may affect brain hemodynamics, researchers have been seeking wearable devices for use in conscious animals. We present a wearable diffuse speckle contrast flowmeter (DSCF) probe for monitoring CBF variations in mice. The DSCF probe consists of a small low-power near-infrared laser diode as a point source and an ultra-small low-power CMOS camera as a 2D detector array, which can be affixed on a mouse head. The movement of red blood cells in brain cortex (i.e., CBF) produces spatial fluctuations of laser speckles, which are captured by the camera. The DSCF system was calibrated using tissue phantoms and validated in a human forearm and mouse brains for continuous monitoring of blood flow increases and decreases against the established technologies. Significant correlations were observed among these measurements (R² ≥ 0.80, p < 10^-5). This small fiberless probe has the potential to be worn by a freely moving conscious mouse. Moreover, the flexible source-detector configuration allows for varied probing depths up to ~8 mm, which is sufficient for transcranially detecting CBF in the cortices of rodents and newborn infants.

Multispectral Endoscopy with Light Gating for Early Cancer Detection

This paper reports the application of endoscopic light scattering spectroscopy (LSS) with light gating to detect malignancies in the biliary and pancreatic ducts, and also reviews the application of endoscopic LSS for differentiating cystic neoplasms in the pancreas and detecting invisible dysplasia in Barrett's esophagus. Information about tissue structure within the superficial epithelium where malignancy starts is present within the spectra of reflected light. Fortunately, this component of the reflected light is not yet randomized. However multiple scattering randomizes the signal from the underlying connective tissue which obscures the desired signal. In order to extract diagnostic information from the reflected signal the multiple scattering component related to connective tissue scattering and absorption must be removed. This is accomplished using described here spatial or polarization gating implemented with endoscopically compatible fiber optic probes.

Satellite UV-Vis spectroscopy: implications for air quality trends and their driving forces in China during 2005-2017

Abundances of a range of air pollutants can be inferred from satellite UV-Vis spectroscopy measurements by using the unique absorption signatures of gas species. Here, we implemented several spectral fitting methods to retrieve tropospheric NO₂, SO₂, and HCHO from the ozone monitoring instrument (OMI), with radiative simulations providing necessary information on the interactions of scattered solar light within the atmosphere. We analyzed the spatial distribution and temporal trends of satellite-observed air pollutants over eastern China during 2005-2017, especially in heavily polluted regions. We found significant decreasing trends in NO₂ and SO₂ since 2011 over most regions, despite varying temporal features and turning points. In contrast, an overall increasing trend was identified for tropospheric HCHO over these regions in recent years. Furthermore, generalized additive models were implemented to understand the driving forces of air quality trends in China and assess the effectiveness of emission controls. Our results indicated that although meteorological parameters, such as wind, water vapor, solar radiation and temperature, mainly dominated the day-to-day and seasonal fluctuations in air pollutants, anthropogenic emissions played a unique role in the long-term variation in the ambient concentrations of NO₂, SO₂, and HCHO in the past 13 years. Generally, recent declines in NO₂ and SO₂ could be attributed to emission reductions due to effective air quality policies, and the opposite trends in HCHO may urge the need to control anthropogenic volatile organic compound (VOC) emissions.

A Wearable Fiberless Optical Sensor for Continuous Monitoring of Cerebral Blood Flow in Mice

Continuous and longitudinal monitoring of cerebral blood flow (CBF) in animal models provides information for studying the mechanisms and interventions of various cerebral diseases. Since anesthesia may affect brain hemodynamics, researchers have been seeking wearable devices for use in conscious animals. We present a wearable diffuse speckle contrast flowmeter (DSCF) probe for monitoring CBF variations in mice. The DSCF probe consists of a small low-power near-infrared laser diode as a point source and an ultra-small low-power CMOS camera as a 2D detector array, which can be affixed on a mouse head. The movement of red blood cells in brain cortex (i.e., CBF) produces spatial fluctuations of laser speckles, which are captured by the camera. The DSCF system was calibrated using tissue phantoms and validated in a human forearm and mouse brains for continuous monitoring of blood flow increases and decreases against the established technologies. Significant correlations were observed among these measurements (R² ≥ 0.80, p < 10^-5). This small fiberless probe has the potential to be worn by a freely moving conscious mouse. Moreover, the flexible source-detector configuration allows for varied probing depths up to ~8 mm, which is sufficient for transcranially detecting CBF in the cortices of rodents and newborn infants.