High-throughput volumetric adaptive optical imaging using compressed time-reversal matrix

Deep-tissue optical imaging suffers from the reduction of resolving power due to tissue-induced optical aberrations and multiple scattering noise. Reflection matrix approaches recording the maps of backscattered waves for all the possible orthogonal input channels have provided formidable solutions for removing severe aberrations and recovering the ideal diffraction-limited spatial resolution without relying on fluorescence labeling and guide stars. However, measuring the full input–output response of the tissue specimen is time-consuming, making the real-time image acquisition difficult. Here, we present the use of a time-reversal matrix, instead of the reflection matrix, for fast high-resolution volumetric imaging of a mouse brain. The time-reversal matrix reduces two-way problem to one-way problem, which effectively relieves the requirement for the coverage of input channels. Using a newly developed aberration correction algorithm designed for the time-reversal matrix, we demonstrated the correction of complex aberrations using as small as 2% of the complete basis while maintaining the image reconstruction fidelity comparable to the fully sampled reflection matrix. Due to nearly 100-fold reduction in the matrix recording time, we could achieve real-time aberration-correction imaging for a field of view of 40 × 40 µm2 (176 × 176 pixels) at a frame rate of 80 Hz. Furthermore, we demonstrated high-throughput volumetric adaptive optical imaging of a mouse brain by recording a volume of 128 × 128 × 125 µm3 (568 × 568 × 125 voxels) in 3.58 s, correcting tissue aberrations at each and every 1 µm depth section, and visualizing myelinated axons with a lateral resolution of 0.45 µm and an axial resolution of 2 µm.

Densified Pupil Spectrograph as High-precision Radial Velocimetry: From Direct Measurement of the Universe’s Expansion History to Characterization of Nearby Habitable Planet Candidates

The direct measurement of the universe’s expansion history and the search for terrestrial planets in habitable zones around solar-type stars require extremely high-precision radial-velocity measures over a decade. This study proposes an approach for enabling high-precision radial-velocity measurements from space. The concept presents a combination of a high-dispersion densified pupil spectrograph and a novel line-of-sight monitor for telescopes. The precision of the radial-velocity measurements is determined by combining the spectrophotometric accuracy and the quality of the absorption lines in the recorded spectrum. Therefore, a highly dispersive densified pupil spectrograph proposed to perform stable spectroscopy can be utilized for high-precision radial-velocity measures. A concept involving the telescope’s line-of-sight monitor is developed to minimize the change of the telescope’s line of sight over a decade. This monitor allows the precise measurement of long-term telescope drift without any significant impact on the Airy disk when the densified pupil spectra are recorded. We analytically derive the uncertainty of the radial-velocity measurements, which is caused by the residual offset of the lines of sight at two epochs. We find that the error could be reduced down to approximately 1 cm s−1, and the precision will be limited by another factor (e.g., wavelength calibration uncertainty). A combination of the high-precision spectrophotometry and the high spectral resolving power could open a new path toward the characterization of nearby non-transiting habitable planet candidates orbiting late-type stars. We present two simple and compact highly dispersed densified pupil spectrograph designs for cosmology and exoplanet sciences.

dnabarcoder: an open-source software package for analyzing and predicting DNA sequence similarity cut-offs for fungal sequence identification

The accuracy and precision of fungal molecular identification and classification are challenging, particularly in environmental metabarcoding approaches as these often trade accuracy for efficiency given the large data volumes at hand. In most ecological studies, only a single similarity cut-off value is used for sequence identification. This is not sufficient since the most commonly used DNA markers are known to vary widely in terms of inter- and intra-specific variability. We address this problem by presenting a new tool, dnabarcoder, to analyze and predict different local similarity cut-offs for sequence identification for different clades of fungi. For each similarity cut-off in a clade, a confidence measure is computed to evaluate the resolving power of the genetic marker in that clade. Experimental results showed that when analyzing a recently released filamentous fungal ITS DNA barcode dataset of CBS strains from the Westerdijk Fungal Biodiversity Institute, the predicted local similarity cut-offs varied immensely between the clades of the dataset. In addition, most of them had a higher confidence measure than the global similarity cut-off predicted for the whole dataset. When classifying a large public fungal ITS dataset – the UNITE database - against the barcode dataset, the local similarity cut-offs assigned fewer sequences than the traditional cut-offs used in metabarcoding studies. However, the obtained accuracy and precision were significantly improved.

Resistance of Hindu Traditionalist Against Sampradaya Hare Krishna Bali

This research was conducted to understand the tension between two internal Hindu religious groups in Bali since 1984. The tension shows resistance of Balinese traditional Hindus to the Sampradaya or the spiritualist group of the Hare Krishna consciousness movement. The feud started from a hate speech on social media from both sides that leads to physical persecution. The research was conducted using a case study method, with interviews and observations at the scene and religious practices. This study found out that the conflict was rooted in different religious understandings between the Hare Krishna Gaudy Vaisnava theology and Balinese Hindu Traditional, as well as differences in acceptance of Balinese religious traditions. The contestation of the two parties escalated the feud on social media, then heated up to the closing of Hare Krishna's religious activities. The accumulation of tension was also triggered by religious activities and the appearance of Hare Krishna followers was considered to be in contrast to the Balinese traditional community, and the rite system was considered not to reflect Balinese customs. The research concludes that the institutional interaction between the two parties is deadlocked, although so far there is still a safety valve, namely Nyama Baraya, but the potential for conflict still arises. Similarity of ethnic background; dialogue intentions do not find common ground, the reintegration process is threatened with failure. A solution through dialogue is still the best step compared to resolving power or law enforcement, therefore efforts to bring the two parties together in dialogue must continue.

Engineering of Vaginal Lactobacilli to Express Fluorescent Proteins Enables the Analysis of Their Mixture in Nanofibers

Lactobacilli are a promising natural tool against vaginal dysbiosis and infections. However, new local delivery systems and additional knowledge about their distribution and mechanism of action would contribute to the development of effective medicine. This will be facilitated by the introduction of the techniques for effective, inexpensive, and real-time tracking of these probiotics following their release. Here, we engineered three model vaginal lactobacilli (Lactobacillus crispatus ATCC 33820, Lactobacillus gasseri ATCC 33323, and Lactobacillus jensenii ATCC 25258) and a control Lactobacillus plantarum ATCC 8014 to express fluorescent proteins with different spectral properties, including infrared fluorescent protein (IRFP), green fluorescent protein (GFP), red fluorescent protein (mCherry), and blue fluorescent protein (mTagBFP2). The expression of these fluorescent proteins differed between the Lactobacillus species and enabled quantification and discrimination between lactobacilli, with the longer wavelength fluorescent proteins showing superior resolving power. Each Lactobacillus strain was labeled with an individual fluorescent protein and incorporated into poly (ethylene oxide) nanofibers using electrospinning, as confirmed by fluorescence and scanning electron microscopy. The lactobacilli retained their fluorescence in nanofibers, as well as after nanofiber dissolution. To summarize, vaginal lactobacilli were incorporated into electrospun nanofibers to provide a potential solid vaginal delivery system, and the fluorescent proteins were introduced to distinguish between them and allow their tracking in the future probiotic-delivery studies.

Mobile and high-spectral-resolution Fabry–Pérot interferometer spectrographs for atmospheric remote sensing

Grating spectrographs (GS) are presently widely in use for atmospheric trace gas remote sensing in the ultraviolet (UV) and visible spectral range (e.g. differential optical absorption spectroscopy, DOAS). For typical DOAS applications, GSs have a spectral resolution of about 0.5 nm, corresponding to a resolving power R (ratio of operating wavelength to spectral resolution) of approximately 1000. This is sufficient to quantify the vibro-electronic spectral structure of the absorption of many trace gases with good accuracy and further allows for mobile (i.e. compact and stable) instrumentation. However, a much higher resolving power (R≈105, i.e. a spectral resolution of about the width of an individual rotational absorption line) would facilitate the measurement of further trace gases (e.g. OH radicals), significantly reduce cross interferences due to other absorption and scattering processes, and provide enhanced sensitivity. Despite these major advantages, only very few atmospheric studies with high-resolution GSs are reported, mostly because increasing the resolving power of a GS leads to largely reduced light throughput and mobility. However, for many environmental studies, light throughput and mobility of measurement equipment are central limiting factors, for instance when absorption spectroscopy is applied to quantify reactive trace gases in remote areas (e.g. volcanoes) or from airborne or space-borne platforms. For more than a century, Fabry–Pérot interferometers (FPIs) have been successfully used for high-resolution spectroscopy in many scientific fields where they are known for their superior light throughput. However, except for a few studies, FPIs have hardly received any attention in atmospheric trace gas remote sensing, despite their advantages. We propose different high-resolution FPI spectrograph implementations and compare their light throughput and mobility to GSs with the same resolving power. We find that nowadays mobile high-resolution FPI spectrographs can have a more than 2 orders of magnitude higher light throughput than their immobile high-resolution GS counterparts. Compared with moderate-resolution GSs (as routinely used for DOAS), an FPI spectrograph reaches a 250 times higher spectral resolution while the signal-to-noise ratio (SNR) is reduced by only a factor of 10. Using a first compact prototype of a high-resolution FPI spectrograph (R≈148 000, <8 L, <5 kg), we demonstrate that these expectations are realistic. Using mobile and high-resolution FPI spectrographs could have a large impact on atmospheric near-UV to near-infrared (NIR) remote sensing. Applications include the enhancement of the sensitivity and selectivity of absorption measurements of many atmospheric trace gases and their isotopologues, the direct quantification of OH radicals in the troposphere, high-resolution O2 measurements for radiative transfer and aerosol studies, and solar-induced chlorophyll fluorescence quantification using Fraunhofer lines.

Determination of 60 Migrant Substances in Plastic Food Contact Materials by Vortex-Assisted Liquid-Liquid Extraction and GC-Q-Orbitrap HRMS

A GC-HRMS analytical method for the determination of 60 migrant substances, including aldehydes, ketones, phthalates and other plasticizers, phenol derivatives, acrylates, and methacrylates, in plastic food contact materials (FCM) has been developed and validated. The proposed method includes migration tests, according to Commission Regulation (EU) 10/2011, using four food simulants (A, B, C, and D1), followed by vortex-assisted liquid–liquid extraction (VA-LLE) and GC-Q-Orbitrap HRMS analysis in selected ion monitoring (SIM) mode, with a resolving power of 30,000 FWHM and a mass accuracy ≤5 ppm. The method was validated, showing satisfactory linearity (R2 ≥ 0.98 from 40 to 400 µg L−1), limits of quantification (40 µg L−1), precision (RSD, 0.6–12.6%), and relative recovery (81–120%). The proposed method was applied to the analysis of field samples, including an epoxy-coated tin food can, a drinking bottle made of Tritan copolyester, a disposable glass made of polycarbonate, and a baby feeding bottle made of polypropylene, showing that they were in compliance with the current European regulation regarding the studied substances.

Optical cavity-referenced terahertz synthesizer with 15-digit short-term stability

Stable terahertz sources are required to advance high precision terahertz applications such as molecular spectroscopy, terahertz radars, and wireless communications. Here, we demonstrate a photonic scheme of terahertz synthesis using an optical comb in stabilization to an ultra-low expansion optical cavity offering a 15-digit accuracy. By heterodyne photomixing of comb lines, terahertz frequencies of 0.10 – 1.10 THz are synthesized with a 2-mHz linewidth and a fractional instability of 3.26×10-15 at 1.3-s integration. Compared to other state-of-the-art counterparts, our terahertz synthesizer offers a fine frequency tuning capability in steps of 100 MHz and an extremely low level of phase noise below -70 dBc/Hz even at 1 Hz offset. Such unprecedented performance is expected to drastically improve the signal-to-noise ratio of terahertz radars, the resolving power of terahertz molecular spectroscopy, and the transmission capacity of wireless communications.

Undergraduate Nursing Students Endorse Education Standards in Blended e-Learning Theory Teaching during COVID-19 Pandemic

Aim: The aim of this study was to survey student learning perspectives as measured by ‘student satisfaction’ following the rapid introduction of remote blended e-learning into the existing undergraduate nursing curriculum at Umm Al-Qura University, Saudi Arabia. Background: National legislation resulting from the spread of Covid-19 required all theoretical and practical nurse training to move immediately to online provision using an unfamiliar e-learning environment and associated tools. Objective: The objective of this study was to use a validated satisfaction questionnaire developed elsewhere, but within a similar educational context involving both theoretical and practical components, for the purpose of checking that educational objectives were being satisfactorily achieved across five relevant domains of educational enquiry, and to use survey findings to improve the online delivery of the nursing program in future academic years. Methods: A validated 35 item questionnaire was circulated online to all male and female nursing students in their 2nd, 3rd and 4th years of study. The questionnaire content was subdivided into the five domains of ‘Interaction’, ‘Instruction’, ‘Instructor’, ‘Course Management’ and ‘Technology’. Descriptive and comparative statistics were used to compare levels of satisfaction between genders and among undergraduate years of study, and against findings from undergraduate information technology undergraduates. Results: 199 female and 84 male students completed the questionnaire (response rate 59.2%). Mean satisfaction scores for male and female nursing undergraduates were significantly greater than 3 (neutral score) in all domains of enquiry, indicating good satisfaction with blended e-learning (p<0.001). However, multivariate regressions of domain satisfaction scores taking gender and year of study as explanatory variables had poor resolving power. Domain scores were also significantly greater than those of a comparator study in three of the five domains (p<0.030) and similar in the domains of course management (p=0.717) and technology (p=0.677). Levels of satisfaction in males and females were similar in 80% of the survey questions, but in females, satisfaction was significantly lower in some questions concerning technology (p<0.003), willingness to interrupt the instructor (p=0.021), comparison of blended learning and face-to-face teaching (p=0.002) and timely feedback on tests and assignments (p=0.031). Fourth-year students showed the highest levels of satisfaction across all five domains. Conclusion: Undergraduate nursing students reported above-average satisfaction levels across all five domains of education provision. Despite an unfamiliar blended e-learning curriculum environment, they demonstrated compatible technological skills, satisfactory interaction with teachers and other students and engagement in the learning process. A number of recommendations identified in the literature as underlying a successful program of blended e-learning are recorded for the benefit of readers.

A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry

Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.