Search Results (1,970)

The development of new technologies enabling rapid, frequent, and reagent-free monitoring of kidney function is recognized as being of paramount importance. In this work, mid-(MIR) and near-infrared (NIR) spectroscopy were compared for the prediction of key renal biomarkers—creatinine, urea and albumin—using 54 serum solutions mimicking the biochemical profiles of five stages of chronic kidney disease (CKD). MIR spectra were acquired in a high-throughput microplate platform after a simple dehydration step, while the NIR spectra were obtained directly from liquid serum using a fiber optic probe. After evaluating several spectral pre-processing methods and targeted spectral regions, excellent regression models (R² > 0.9 for the best models) were obtained for the three biomarkers. MIR provided highly accurate urea predictions, whereas optimized NIR sub-regions enabled excellent estimation of creatinine and albumin. Both MIR and NIR, associated with supervised classification methods, enabled us to successfully distinguish healthy from diseased profiles and to identify the diseases state with AUC > 0.93. These findings highlight the complementary value of MIR and NIR spectroscopy for kidney disease assessment and their potential integration into point-of-care diagnostic systems. Full article

Benefiting from tunable emission from ultraviolet to near-infrared windows, long luminescence lifetimes, and exceptional photostability, rare earth (RE)-doped nanomaterials overcome the limitations of conventional dyes and quantum dots, enabling deep-tissue, high-resolution, and low-background imaging. As multifunctional fluorescent probes, RE-doped nanomaterials are driving the development of next-generation biomedical imaging. This review summarizes recent advances in the structural design of RE-doped nanomaterials, surface engineering for biocompatibility, and targeting strategies for improved performance, and highlights their integration into advanced imaging modalities, including NIR-I/II fluorescence, FLIM, PAI, super-resolution STED, multimodal FL/MRI/CT, X-ray-excited luminescence, and persistent luminescence. Meanwhile, mechanistic insights, material innovations, and comparative advantages are discussed. Furthermore, challenges related to quantum yield, scalable synthesis, imaging resolution, and clinical translation are considered, while future directions—centered on multifunctional probe design, NIR-II imaging, and AI-assisted data analysis—are proposed, offering a versatile platform for precise multimodal imaging with significant potential to advance early diagnosis, personalized therapy, and clinical applications. Full article

Early detection of dental caries remains a significant clinical challenge, as conventional diagnostic methods lack sensitivity for incipient lesions. Raman spectroscopy offers high chemical specificity for enamel characterization; however, clinical translation is hindered by the complexity of conventional polarized confocal systems. In this work, we present a Raman-based fiber-optic sensing approach for the detection and classification of dental enamel conditions, including sound, affected, and carious tissues. A custom fiber-optic probe was developed for remote measurements and evaluated against a reference polarized confocal Raman system. In addition to spectral discrimination, key factors affecting sensing performance were investigated, including spatial variability across enamel surfaces and angular sensitivity due to probe misalignment. Raman-derived features (carbonate-to-phosphate ratio, phosphate peak intensity, position, and bandwidth) were analyzed using a multinomial logistic regression classifier. The fiber-optic sensor achieved an overall classification accuracy of 73% (F1-scores: 0.55 sound, 0.63 affected, 0.9 carious), confirmed by leave-one-tooth-out cross-validation. Probe misalignment studies revealed robustness up to 10° angular deviation. These results demonstrate that a simplified non-polarized fiber-optic Raman system provides competitive diagnostic performance and clinically relevant robustness, supporting its development as a point-of-care sensing platform for early dental caries detection. Full article

Contemporary iterations of avian phylogenies based on multiple genome sequence assemblies assign three major clades: Palaeognathae (mostly ratite birds), Galloanseres (land and waterfowl) and the largest group—Neoaves. The latter two are sister clades representing subdivisions of Neognathae, while Neoaves further subdivide into Columbaves (pigeons/doves/cuckoos/bustards, etc.), Mirandornithes (flamingos/grebes), Telluraves (“higher land birds”, including finches) and the newly recognized Elementaves (e.g., penguins/pelicans/hummingbirds/swifts/cranes/shorebirds). Molecular studies provide clade information, likely divergence timings and a framework from which gross genomic (chromosomal) changes may be mapped. In this review, we consider the patterns of chromosome change that have occurred throughout all avian clades thus far examined, citing studies from standard karyotyping through molecular cytogenetics to whole genome assemblies. Standard karyotyping led to the realization that most chromosomes (particularly the microchromosomes and dot chromosomes) could not be distinguished by classical means. Indeed, cross-species comparisons were difficult, even among the macrochromosomes, because of indistinct banding patterns. Based on fluorescence (or fluorescent) in situ hybridization (FISH), comparative genomics was thence progressed considerably by cross-species chromosome painting (Zoo-FISH) for the macrochromosomes and interspecific mapping of bacterial artificial chromosome (BAC) probes for the microchromosomes. A key finding was that the most studied species, the chicken, fortuitously, has a genomic organization somewhat akin to that of the ancestral karyotype and tends to be the standard from which all others are measured. A notable exception is the fusion of basal chromosome 4 with a smaller chromosome that convergently appears in some other Galliformes, at least one goose and one dove species. While some groups such as Falconiformes (falcons, etc.) and Psittaciformes (parrots, etc.) underwent extensive interchromosomal change, most, broadly speaking, retain a basic karyotype that differs little from bird to bird. Many, e.g., Passeriformes (finches, songbirds, etc.) and Columbiformes (pigeons, doves), do this despite multiple intrachromosomal rearrangements. The complete karyotype and fully established chromosome-level genome assembly of the chicken allow full integration of DNA sequence assembly with karyotype. They further permit cytogenetic studies to be performed using genome assemblies alone alongside cutting-edge long-read sequencing and optical mapping without the need for chromosome preparation. The classic ZW sex-determination system of birds is easily visible in most Neognathae species, but intrachromosomal change in the sex chromosomes is faster than in the autosomes; indeed, there are numerous examples of autosomal fusions and new sex chromosomes formed. Sex chromosomes aside, the classic avian karyotype represents a very successful mode of genome organization established before the emergence of the dinosaurs and perpetuated to this day in their only living descendants. Full article

Hydrogel-based optical sensors have emerged as a versatile class of analytical materials that combine soft-matter processability, tunable network chemistry, and compatibility with luminescent, colorimetric, photonic, and hybrid transduction strategies. Progress in the field is driven not by a single sensing mechanism, but by the convergence of key advances in material functionalization, embedded selectivity, operation across diverse sample matrices, mechanical and analytical robustness, and usability beyond the laboratory. Current systems include framework-integrated, nanoparticle-doped, probe-functionalized, photonic-crystal, enzyme-immobilized, and device-coupled hydrogels, reflecting growing architectural diversity and application-oriented engineering. Selectivity has likewise advanced from basic interferent screening to recognition-specific, imprinted, and pattern-discriminative formats suited to complex environmental, food, biological, and wearable settings. Evidence of stability, reusability, and deformation tolerance further suggests that many platforms are moving beyond proof-of-concept demonstrations toward credible real-world operation. At the same time, translational priorities such as portability, smartphone readout, implantable and epidermal formats, and multifunctionality spanning antimicrobial action, adsorption, anti-counterfeiting, and device integration are becoming increasingly prominent. Together, these trends show that hydrogel-based optical sensing is maturing into a materially rich, application-responsive domain. The key challenge ahead is to unify materials design, selectivity control, durability, and deployability in standardized, reproducible, and clinically or environmentally credible sensing platforms. Full article

Genetically encoded voltage indicators (GEVIs) have long promised optical access to membrane potential, yet their adoption has lagged significantly behind genetically encoded calcium indicators. A central but underappreciated reason is that the metrics used to evaluate and compare GEVIs—fractional fluorescence change (ΔF/F), kinetics, and signal-to-noise ratio—rest on an assumption that is frequently violated: that GEVI fluorescence reflects a single underlying process. In this perspective, we argue that GEVI signals are composite optical measurements, arising from the superposition of voltage-dependent fluorescence, intracellular and nonresponsive signal, background, and contributions from neighboring cells. Under these conditions, ΔF/F is not a measure of sensor sensitivity but a contrast metric whose value depends on baseline fluorescence composition, optical sampling, and imaging configuration. This reinterpretation has two key consequences. First, it explains a substantial source of variability in GEVI performance that is currently attributed to noise or experimental inconsistency. Second, and more importantly, it reveals that the complexity of GEVI signals is not a limitation to be minimized but a resource to be exploited. By resolving composite signal components, GEVIs can report multiplexed physiological variables, expose hidden conformational states of voltage-sensing domains, probe membrane organization, and reveal intracellular and intercellular electrical coupling. We propose that realizing the full potential of GEVIs requires treating ΔF/F not as a gold standard for sensor performance, but as one interpretable component of a richer optical measurement whose structure encodes multiple layers of cellular physiology. Full article

This review examines recent advances in multifunctional probes that integrate optical and electrochemical channels for in vitro/in vivo studies. Integration of electrodes with optical fibers provides a powerful platform for localized light delivery and simultaneous electrochemical detection of cellular metabolites both within and at the surface of single living cells. These hybrid devices bridge optical stimulation methods, including optogenetics, and electrochemical monitoring of the cellular response within the same experimental preparation. The review systematically categorizes distinct probe architectures: optical nanoendoscopes for intracellular measurements, probes with a shared opto-electrochemical channel, devices where optical and electrochemical channels are physically separated, and probes engineered for neural interfaces and scanning probe microscopy. For each category, fabrication approaches, surface modification strategies, and representative biological applications are discussed. Particular attention is given to the fundamental tension between optical transparency and electrical conductivity in shared-channel designs, to the mechanical requirements imposed by neural tissue on implantable probes, and to the spatial resolution limits of current scanning probe platforms. The review concludes with a critical assessment of current limitations and future directions, including higher spatial resolution, simultaneous multiplexed analyte detection and broader translation of these technologies toward in vivo experimental models. Full article

Magnetic sensors offer a physically grounded and non-invasive approach to probing biological processes that remain inaccessible to optical, electrochemical, and radio-frequency techniques in complex agricultural environments. In recent years, advances in both classical and quantum magnetic sensors have enabled the detection of bioelectromagnetic signals across plants, soils, animals, and aquatic systems, spanning spatial scales from ionic currents to organ-level electrophysiology and population-level dynamics, positioning magnetometry as an emerging modality within the broader biosensor landscape. This review surveys the evolution of magnetic sensing technologies for agricultural and animal systems, from robust classical sensors used in navigation and soil mapping to quantum-enabled platforms, including Optically Pumped Magnetometers (OPMs) and Nitrogen-Vacancy (NV) centers, capable of resolving pT to fT biomagnetic signals. We synthesize the characteristic amplitudes, frequency ranges, and physiological origins of agriculturally relevant magnetic signals, and critically assess how techniques originally developed for medical magnetoencephalography, magnetocardiography, and low-field magnetic resonance imaging (LF-MRI) are being translated into field-deployable agricultural applications. Beyond sensing hardware, we highlight the essential role of artificial intelligence in extracting weak biological signals from dominant environmental noise, enabling synthetic gradiometry, low-field image reconstruction, and scalable interpretation in unshielded settings. Finally, we discuss how the integration of magnetic biosensing with digital twins supports predictive, multiscale monitoring of plant, animal, and ecosystem health. Together, these developments position magnetometry as an enabling technology for next-generation biosensors in precision and sustainable agriculture. Full article

The photoreceptor bacteriorhodopsin (HsBR) from Halobacterium salinarum is a model system for studying ultrafast photoinduced reactions in proteins. Recent time-resolved serial femtosecond crystallography (TR-SFX) experiments require high pump energies, raising concerns about nonlinear excitation and multi-photon effects. Here, we systematically investigate the influence of excitation energy, pulse duration and the sign of the chirp on the initial HsBR photo-reaction using femtosecond Vis-pump IR-probe spectroscopy in the retinal C=C stretching region. An acousto-optic programmable dispersive filter enabled independent control of pulse energy and chirp. Within the tested range, the retinal dynamics were independent of pulse duration and chirp, indicating that fluence alone does not fully describe excitation conditions. Increasing excitation energy leads to nonlinear saturation of the retinal signals and the appearance of an additional band near 1550 ${\mathrm{cm}}^{-1}$. However, this band rises linearly with the excitation energy. Hence, the additional band is not directly caused by non-resonant multi-photon absorption. Spectral decomposition reveals two components: a low-energy contribution consistent with the known retinal isomerization dynamics and a high-energy contribution attributed to a small population of photo-damaged HsBR likely formed via a resonant two-photon process. These findings clarify the role of excitation conditions in ultrafast HsBR spectroscopy and suggest that spectral changes at high pump energies mainly arise from damaged species upon resonant two-photon excitation. Full article

We present a high-precision theoretical study of attosecond transient absorption spectroscopy (ATAS) of atomic hydrogen by numerically solving the time-dependent Schrödinger Equation (TDSE). A broadband extreme ultraviolet (XUV) attosecond pulse creates a wave packet of singly-excited bound states, which is subsequently probed by a time-delayed synthesized optical attosecond pulse (SOAP) with varying bandwidths and durations. When the SOAP has a narrow bandwidth (1.3–1.5 eV) and a long duration (~17 fs), the absorption spectrum exhibits conventional features, namely AC Stark shifts, half-cycle modulations (1.48 fs), and light-induced intermediate states, consistent with previous ATAS studies. In contrast, when the SOAP has a broad bandwidth (0.5–5.5 eV) and an attosecond duration (400 as), the dynamics are completely different. The spectrum reveals transverse wavelike modulations along the absorption lines and, remarkably, quantum beats with distinct frequencies, which are different from previous reports in hydrogen ATAS. To interpret these observations, we employ a dipole-control model. The model quantitatively reproduces the dominant modulation frequencies, identifying resonant couplings via two-photon processes (TPPs, 1.89 eV, period 2.18 fs) and three-photon processes (THPPs, 10.2 eV and 12.1 eV), as well as higher-order couplings. The validity of the $\delta$-like pulse approximation is quantitatively assessed. The model remains accurate for pulse durations shorter than 700 as (bandwidth broader than 3.5 eV) but fails for longer pulses (exceeding 4 fs), where energy level splittings emerge. Our results demonstrate that the dipole-control model provides a reliable and intuitive framework for interpreting complex multiphoton interactions in ATAS, and highlight the unique capability of broadband SOAP probes to resolve attosecond-scale quantum beats inaccessible with conventional few-cycle infrared pulses. Full article

Extragalactic background light (EBL), formed by the light radiated and re-radiated by stars, galaxies, and active galactic nuclei throughout the evolution of the Universe, brings the imprint of the history of the rate of the formation of emitting astrophysical objects and the Universe’s expansion. It makes EBL one of the fundamental quantities in cosmology. The optical depth for high-energy emission from the distant active galactic nuclei provides a constraint for the EBL density that is clear from the foreground galactic and other emissions, and, therefore, for the cosmological parameters. In this work, we investigate the high-redshift active galaxy 4C +55.17 (z = 0.902), whose unusually hard and stable high-energy spectrum makes it a valuable probe of EBL-induced absorption effects. Using observations extending from GeV to TeV energies, we reconstruct the optical depth associated with gamma-ray propagation and compare the inferred attenuation with predictions from existing EBL models. The results favor relatively low EBL intensities in the optical and infrared bands, consistent with low-level EBL models and suggesting reduced star formation activity and dust contributions over cosmic evolution. We further explore the cosmological implications of the reconstructed optical depth and derive constraints on the Hubble constant in the range $H_0\approx$ 64–74 km s⁻¹ Mpc⁻¹, with an average value of $H_0=69\pm 4$ km s⁻¹ Mpc⁻¹. These findings demonstrate the potential of hard-spectrum, high-redshift gamma-ray sources such as 4C +55.17 as cosmological probes for studying EBL evolution and addressing current tensions in cosmological parameter measurements. Full article

Simulations of intermediate-mass black holes (IMBHs) in dwarf galaxies within 10 Mpc that host bright nuclear star clusters (NSCs), prime candidates for IMBH formation, using the High Angular Resolution Monolithic Optical and Near-infrared Integral (HARMONI) field spectrograph on the Extremely Large Telescope, probe black hole formation in the early universe. Our approach combines observed surface-brightness profiles from the Hubble Space Telescope (HST), synthetic stellar population spectra, and Jeans Anisotropic Modeling (JAM) for stellar dynamics. Mock HARMONI observations were generated with the HSIM simulator and analyzed in a Bayesian framework to infer IMBH masses down to 0.5% of the NSC mass. In this work, we extend these simulations by constructing improved stellar mass models using SimCADO to simulate imaging with the Multi-AO Imaging Camera for Deep Observations (MICADO). The MICADO data are jointly analyzed with HARMONI kinematics via JAM to reassess IMBH masses and uncertainties. This combined framework enables us to examine how variations in the NSC inner surface-brightness slope influence IMBH mass estimates, providing tighter constraints on low-mass black holes and advancing models for IMBH detection in NSCs. Full article

In situ hybridization (ISH) has undergone a rapid evolution from a low-throughput histological staining technique to a diverse family of modern methods for sensitive, specific and multiplexed molecular detection in intact cells and tissues, and to a cornerstone technology for image-based spatial transcriptomics. This transformation has been driven by advances in probe design, signal amplification, cyclic imaging, combinatorial barcoding, automated fluidics and computational decoding, which together allow RNA molecules to be measured within preserved cellular and tissue architecture. In this review, we examine the molecular and engineering principles that underlie modern ISH methods and their extension into ISH-based spatial profiling, with emphasis on hybridization chain reaction, branched-DNA amplification, SABER-FISH, rolling-circle-amplification-based approaches, seqFISH, MERFISH, RAEFISH and selected commercial implementations. We discuss how sensitivity, specificity, tissue compatibility, optical crowding, imaging burden, cost, reproducibility and computational uncertainty shape the practical use of each method. Sequencing-based spatial capture platforms are not reviewed comprehensively, but are considered where comparative benchmarks help clarify trade-offs in spatial resolution, transcriptome breadth, tissue area or analytical interpretation. We also consider how recent benchmarking and standardization efforts are beginning to define quantitative criteria for comparing platforms, and how advances in segmentation, barcode decoding, spatial integration and cell–cell communication analysis convert raw images into biological insight. Finally, we highlight applications in targeted transcript detection, tissue-based validation, neuroscience, cancer, developmental biology, non-model organisms and spatial functional genomics, where modern ISH methods and ISH-based spatial profiling provide information that bulk and dissociated single-cell approaches cannot capture. Together, these developments trace how ISH has expanded from targeted molecular visualization into a broad methodological framework for in situ detection and spatially resolved transcriptomic analysis. Full article

Clear aligner therapy (CAT) increasingly relies on composite-based attachments to improve force transmission and aligner retention, yet the role of flowable composite properties in clinical performance remains poorly understood. In this study, five commercially available flowable composites used for orthodontic attachments—Aligner FLOW LC, SIMPLY SHADE, SOFT ENA Flow, TETRIC EvoFlow, and VENUS Bulk Flow One—were comparatively investigated through physicochemical, morphological, optical, thermal, and rheological characterization. Scanning electron microscopy coupled with energy-dispersive X-ray analysis, thermogravimetric analysis, UV–Vis–NIR and ATR–FTIR spectroscopy, and rheological measurements before and after curing were employed to probe composition, filler content, viscoelastic behavior, and mechanical response. The results revealed marked differences among the investigated materials, with post-curing storage modulus spanning nearly two orders of magnitude, from 0.06 MPa for SOFT ENA Flow to approximately 5 MPa for SIMPLY SHADE. Similarly, the elastic modulus ranged from about 20 MPa to nearly 1000 MPa for the softest and stiffest resins, respectively. Interestingly, SOFT ENA Flow, the softest material after curing, also exhibited the highest pre-curing viscosity, nearly one order of magnitude greater than the least viscous resin, Aligner FLOW LC. These findings highlight an intrinsic trade-off between pre-cure processability and post-cure mechanical stability, providing a rational framework for material selection in orthodontic attachments and supporting more predictable and durable CAT outcomes. Full article

Surface-enhanced Raman spectroscopy (SERS) has evolved from a fundamental optical phenomenon to a powerful, molecule-specific analytical technique capable of detecting ultra-trace-level species across biomedicine, catalysis, environmental monitoring, and national security applications. In this review, we summarize recent advances in SERS probe design and fabrication along three major directions: (i) engineering plasmonic hotspots with enhanced field confinement to achieve stronger and more uniform signals; (ii) analyte-directed strategies that precisely position and retain target molecules via tailored surface chemistries, nanoscale confinement, and on-surface reactions for single hotspot SERS; and (iii) hybrid architectures integrating plasmonic metals with functional materials, including high entropy materials, semiconductors, and graphene and other 2D materials, to synergistically couple electromagnetic and chemical enhancement mechanisms. Despite significant progress, key challenges remain for practical applications outside laboratories, including substrate reproducibility and stability, diverse analyte compatibility, unknown molecule identification and standardized quantitative performance in complex environments. We highlight emerging solutions, such as large-area nanomanufacturing for controlled nanoscale gaps, high-resolution Raman mapping for spatial–temporal characterization, density-functional-theory-guided molecular interpretation, and machine-learning-enabled spectral analysis. Advances in foundational AI models and data-driven discovery are positioning SERS to become an increasingly versatile platform, from decoding unknown molecular structures to analyzing complicated multi-component systems for environmental, biomedical, and national security applications with high sensitivity and selectivity. Full article