Workflow for the unsupervised clustering of sleep stages identifies light and deep sleep in electrophysiological recordings in mice.

BACKGROUND: Sleep physiology plays a critical role in brain development and aging. Accurate sleep staging, which categorizes different sleep states, is fundamental for sleep physiology studies. Traditional methods for sleep staging rely on manual, rule-based scoring techniques, which limit their accuracy and adaptability. NEW METHOD: We describe, test and challenge a workflow for unsupervised clustering of sleep states (WUCSS) in rodents, which uses accelerometer and electrophysiological data to classify different sleep states. WUCSS utilizes unsupervised clustering to identify sleep states using six features, extracted from 4-second epochs. RESULTS: We gathered high-quality EEG recordings combined with accelerometer data in diverse transgenic mouse lines (male ApoE3 versus ApoE4 knockin; male CNTNAP2 KO versus wildtype littermates). WUCSS showed high recall, precision, and F1-score against manual scoring on awake, NREM, and REM sleep states. Within NREM, WUCSS consistently identified two additional clusters that qualify as deep and light sleep states. COMPARISON WITH EXISTING METHODS: The ability of WUCSSs to discriminate between deep and light sleep enhanced the precision and comprehensiveness of the current mouse sleep physiology studies. This differentiation led to the discovery of an additional sleep phenotype, notably in CNTNAP2 KO mice, showcasing the method's superiority over traditional scoring methods. CONCLUSIONS: WUCSS, with its unsupervised approach and classification of deep and light sleep states, provides an unbiased opportunity for researchers to enhance their understanding of sleep physiology. Its high accuracy, adaptability, and ability to save time and resources make it a valuable tool for improving sleep staging in both clinical and preclinical research.

Rare SH2B3 coding variants in lupus patients impair B cell tolerance and predispose to autoimmunity.

Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with a clear genetic component. While most SLE patients carry rare gene variants in lupus risk genes, little is known about their contribution to disease pathogenesis. Amongst them, SH2B3-a negative regulator of cytokine and growth factor receptor signaling-harbors rare coding variants in over 5% of SLE patients. Here, we show that unlike the variant found exclusively in healthy controls, SH2B3 rare variants found in lupus patients are predominantly hypomorphic alleles, failing to suppress IFNGR signaling via JAK2-STAT1. The generation of two mouse lines carrying patients' variants revealed that SH2B3 is important in limiting the number of immature and transitional B cells. Furthermore, hypomorphic SH2B3 was shown to impair the negative selection of immature/transitional self-reactive B cells and accelerate autoimmunity in sensitized mice, at least in part due to increased IL-4R signaling and BAFF-R expression. This work identifies a previously unappreciated role for SH2B3 in human B cell tolerance and lupus risk.

The possible influence of third-order shim coils on gradient-magnet interactions: an inter-field and inter-site study.

OBJECTIVE: To assess the possible influence of third-order shim coils on the behavior of the gradient field and in gradient-magnet interactions at 7 T and above. MATERIALS AND METHODS: Gradient impulse response function measurements were performed at 5 sites spanning field strengths from 7 to 11.7 T, all of them sharing the same exact whole-body gradient coil design. Mechanical fixation and boundary conditions of the gradient coil were altered in several ways at one site to study the impact of mechanical coupling with the magnet on the field perturbations. Vibrations, power deposition in the He bath, and field dynamics were characterized at 11.7 T with the third-order shim coils connected and disconnected inside the Faraday cage. RESULTS: For the same whole-body gradient coil design, all measurements differed greatly based on the third-order shim coil configuration (connected or not). Vibrations and gradient transfer function peaks could be affected by a factor of 2 or more, depending on the resonances. Disconnecting the third-order shim coils at 11.7 T also suppressed almost completely power deposition peaks at some frequencies. DISCUSSION: Third-order shim coil configurations can have major impact in gradient-magnet interactions with consequences on potential hardware damage, magnet heating, and image quality going beyond EPI acquisitions.

Glutamatergic and GABAergic Receptor Modulation Present Unique Electrophysiological Fingerprints in a Concentration-Dependent and Region-Specific Manner.

Brain function depends on complex circuit interactions between excitatory and inhibitory neurons embedded in local and long-range networks. Systemic GABAA-receptor (GABAAR) or NMDA-receptor (NMDAR) modulation alters the excitatory-inhibitory balance (EIB), measurable with electroencephalography (EEG). However, EEG signatures are complex in localization and spectral composition. We developed and applied analytical tools to investigate the effects of two EIB modulators, MK801 (NMDAR antagonist) and diazepam (GABAAR modulator), on periodic and aperiodic EEG features in freely-moving male Sprague Dawley rats. We investigated how, across three brain regions, EEG features are correlated with EIB modulation. We found that the periodic component was composed of seven frequency bands that presented region-dependent and compound-dependent changes. The aperiodic component was also different between compounds and brain regions. Importantly, the parametrization into periodic and aperiodic components unveiled correlations between quantitative EEG and plasma concentrations of pharmacological compounds. MK-801 exposures were positively correlated with the slope of the aperiodic component. Concerning the periodic component, MK-801 exposures correlated negatively with the peak frequency of low-γ oscillations but positively with those of high-γ and high-frequency oscillations (HFOs). As for the power, θ and low-γ oscillations correlated negatively with MK-801, whereas mid-γ correlated positively. Diazepam correlated negatively with the knee of the aperiodic component, positively to ß and negatively to low-γ oscillatory power, and positively to the modal frequency of θ, low-γ, mid-γ, and high-γ. In conclusion, correlations between exposures and pharmacodynamic effects can be better-understood thanks to the parametrization of EEG into periodic and aperiodic components. Such parametrization could be key in functional biomarker discovery.

Two dimensional gradient-index beam shapers fabricated using ultrafast laser inscription.

In this paper gradient-index beam shapers are fabricated using the ultrafast laser inscription method. This method enables the fabrication of two-dimensional refractive index profiles inside silica glass, resulting in highly robust and compact beam shapers. The magnitude of this refractive index change can be tailored by adjusting the laser pulse energy, enabling arbitrary two-dimensional refractive index profiles to be manufactured. The process is then demonstrated by fabricating planar waveguides with quadratic index profiles that predictably resize Gaussian beams. Then a more complex two-dimensional refractive index profile is fabricated to transform an input Gaussian beam into a super-Gaussian (flat-top) beam.

Quantitative morphology of femtosecond laser-written point-by-point optical fiber Bragg gratings.

We investigate the morphology of femtosecond laser, single pulse-inscribed, point-by-point (PbP) fiber Bragg gratings. Direct measurement of a PbP grating's refractive index profile was carried out with micro-reflectivity analysis. PbP gratings were imaged at sub-micrometer scale with scanning electron microscopy, Raman and photoluminescence studies were performed to probe the structural and electronic changes. Comparison of results from different characterisation techniques suggests that the creation of an increased refractive index region around the micro-void is due to contributions from both densification and the formation of highly polarizable non-bridging oxygen bonds.

Correction: A Cationic-Independent Mannose 6-Phosphate Receptor Inhibitor (PXS64) Ameliorates Kidney Fibrosis by Inhibiting Activation of Transforming Growth Factor-ß1.

[This corrects the article DOI: 10.1371/journal.pone.0116888.].

Substrate-mediated regulation of the arginine transporter of Toxoplasma gondii.

Intracellular parasites, such as the apicomplexan Toxoplasma gondii, are adept at scavenging nutrients from their host. However, there is little understanding of how parasites sense and respond to the changing nutrient environments they encounter during an infection. TgApiAT1, a member of the apicomplexan ApiAT family of amino acid transporters, is the major uptake route for the essential amino acid L-arginine (Arg) in T. gondii. Here, we show that the abundance of TgApiAT1, and hence the rate of uptake of Arg, is regulated by the availability of Arg in the parasite's external environment, increasing in response to decreased [Arg]. Using a luciferase-based 'biosensor' strain of T. gondii, we demonstrate that the expression of TgApiAT1 varies between different organs within the host, indicating that parasites are able to modulate TgApiAT1-dependent uptake of Arg as they encounter different nutrient environments in vivo. Finally, we show that Arg-dependent regulation of TgApiAT1 expression is post-transcriptional, mediated by an upstream open reading frame (uORF) in the TgApiAT1 transcript, and we provide evidence that the peptide encoded by this uORF is critical for mediating regulation. Together, our data reveal the mechanism by which an apicomplexan parasite responds to changes in the availability of a key nutrient.

Building hybridized 28-baseline pupil-remapping photonic interferometers for future high-resolution imaging.

One key advantage of single-mode photonic technologies for interferometric use is their ability to easily scale to an ever-increasing number of inputs without a major increase in the overall device size, compared to traditional bulk optics. This is particularly important for the upcoming extremely large telescope (ELT) generation of telescopes currently under construction. We demonstrate the fabrication and characterization of a hybridized photonic interferometer, with eight simultaneous inputs, forming 28 baselines, which is the largest amount to date, to the best of our knowledge. Using different photonic fabrication technologies, we combine a 3D pupil remapper with a planar eight-port ABCD pairwise beam combiner, along with the injection optics necessary for telescope use, into a single integrated monolithic device. We successfully realized a combined device called Dragonfly, which demonstrates a raw instrumental closure-phase stability down to 0.9° over $8\pi$ phase piston error, relating to a detection contrast of ${\sim}6.5 \times {10^{- 4}}$ on an adaptive-optics-corrected 8 m telescope. This prototype successfully demonstrates advanced hybridization and packaging techniques necessary for on-sky use for high-contrast detection at small inner working angles, ideally complementing what can currently be achieved using coronagraphs.

Achromatic photonic tricouplers for application in nulling interferometry.

Integrated-optic components are being increasingly used in astrophysics, mainly where accuracy and precision are paramount. One such emerging technology is nulling interferometry that targets high contrast and high angular resolution. Two of the most critical limitations encountered by nullers are rapid phase fluctuations in the incoming light causing instability in the interference and chromaticity of the directional couplers that prevent a deep broadband interferometric null. We explore the use of a tricoupler designed by ultrafast laser inscription that solves both issues. Simulations of a tricoupler, incorporated into a nuller, result in an order of a magnitude improvement in null depth.

Scalable photonic-based nulling interferometry with the dispersed multi-baseline GLINT instrument.

Characterisation of exoplanets is key to understanding their formation, composition and potential for life. Nulling interferometry, combined with extreme adaptive optics, is among the most promising techniques to advance this goal. We present an integrated-optic nuller whose design is directly scalable to future science-ready interferometric nullers: the Guided-Light Interferometric Nulling Technology, deployed at the Subaru Telescope. It combines four beams and delivers spatial and spectral information. We demonstrate the capability of the instrument, achieving a null depth better than 10-3 with a precision of 10-4 for all baselines, in laboratory conditions with simulated seeing applied. On sky, the instrument delivered angular diameter measurements of stars that were 2.5 times smaller than the diffraction limit of the telescope. These successes pave the way for future design enhancements: scaling to more baselines, improved photonic component and handling low-order atmospheric aberration within the instrument, all of which will contribute to enhance sensitivity and precision.

Simultaneous feedback control for joint field and motion correction in brain MRI.

T2*-weighted gradient-echo sequences count among the most widely used techniques in neuroimaging and offer rich magnitude and phase contrast. The susceptibility effects underlying this contrast scale with B0, making T2*-weighted imaging particularly interesting at high field. High field also benefits baseline sensitivity and thus facilitates high-resolution studies. However, enhanced susceptibility effects and high target resolution come with inherent challenges. Relying on long echo times, T2*-weighted imaging not only benefits from enhanced local susceptibility effects but also suffers from increased field fluctuations due to moving body parts and breathing. High resolution, in turn, renders neuroimaging particularly vulnerable to motion of the head. This work reports the implementation and characterization of a system that aims to jointly address these issues. It is based on the simultaneous operation of two control loops, one for field stabilization and one for motion correction. The key challenge with this approach is that the two loops both operate on the magnetic field in the imaging volume and are thus prone to mutual interference and potential instability. This issue is addressed at the levels of sensing, timing, and control parameters. Performance assessment shows the resulting system to be stable and exhibit adequate loop decoupling, precision, and bandwidth. Simultaneous field and motion control is then demonstrated in examples of T2*-weighted in vivo imaging at 7T.

On the signal-to-noise ratio benefit of spiral acquisition in diffusion MRI.

PURPOSE: Spiral readouts combine several favorable properties that promise superior net sensitivity for diffusion imaging. The purpose of this study is to verify the signal-to-noise ratio (SNR) benefit of spiral acquisition in comparison with current echo-planar imaging (EPI) schemes. METHODS: Diffusion-weighted in vivo brain data from three subjects were acquired with a single-shot spiral sequence and several variants of single-shot EPI, including full-Fourier and partial-Fourier readouts as well as different diffusion-encoding schemes. Image reconstruction was based on an expanded signal model including field dynamics obtained by concurrent field monitoring. The effective resolution of each sequence was matched to that of full-Fourier EPI with 1 mm nominal resolution. SNR maps were generated by determining the noise statistics of the raw data and analyzing the propagation of equivalent synthetic noise through image reconstruction. Using the same approach, maps of noise amplification due to parallel imaging (g-factor) were calculated for different acceleration factors. RESULTS: Relative to full-Fourier EPI at b = 0 s/mm2 , spiral acquisition yielded SNR gains of 42-88% and 40-89% in white and gray matter, respectively, depending on the diffusion-encoding scheme. Relative to partial-Fourier EPI, the gains were 36-44% and 34-42%. Spiral g-factor maps exhibited less spatial variation and lower maxima than their EPI counterparts. CONCLUSION: Spiral readouts achieve significant SNR gains in the order of 40-80% over EPI in diffusion imaging at 3T. Combining systematic effects of shorter echo time, readout efficiency, and favorable g-factor behavior, similar benefits are expected across clinical and neurosciences uses of diffusion imaging.

Record-high positive refractive index change in bismuth germanate crystals through ultrafast laser enhanced polarizability.

Unlike other crystals, the counter intuitive response of bismuth germanate crystals ([Formula: see text], BGO) to form localized high refractive index contrast waveguides upon ultrafast laser irradiation is explained for the first time. While the waveguide formation is a result of a stoichiometric reorganization of germanium and oxygen, the origin of positive index stems from the formation of highly polarisable non-bridging oxygen complexes. Micro-reflectivity measurements revealed a record-high positive refractive index contrast of [Formula: see text]. The currently accepted view that index changes [Formula: see text] could be brought about only by engaging heavy metal elements is strongly challenged by this report. The combination of a nearly perfect step-index profile, record-high refractive index contrast, easily tunable waveguide dimensions, and the intrinsic high optical non-linearity, electro-optic activity and optical transparency up to [Formula: see text] of BGO make these waveguides a highly attractive platform for compact 3D integrated optics.

Boson band mapping: revealing ultrafast laser induced structural modifications in chalcogenide glass.

The formation of femtosecond laser direct-written waveguides in gallium lanthanum sulfide (GLS) chalcogenide glass with a peak index contrast of Δnmax=0.023 and an average positive refractive index change of Δnwaveguide=0.0049 is explained for the first time, to the best of our knowledge. Evidence of structural change and ion migration is presented using Raman spectroscopy and electron probe microanalysis (EPMA), respectively. Raman microscopy reveals a frequency shift and a change in full-width at half maximum variation of the symmetric vibration of the GaS4 tetrahedra. The boson band is successfully used to identify and understand the material densification profile in a high refractive index glass waveguide. EPMA provides evidence of ion migration due to sulfur, where the observation of an anion (S2-) migration causing material modification is reported for the first time. These results will enable optimization of future mid-infrared and nonlinear integrated optical devices in GLS glass based on femtosecond laser written waveguides.

Multiple links between 5-methylcytosine content of mRNA and translation.

BACKGROUND: 5-Methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise. RESULTS: We obtained ~ 1000 candidate m5C sites in the wider transcriptome, most of which were found in mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCaP and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m5C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in both mRNAs and noncoding RNAs. Candidate m5C sites in mRNAs are enriched in 5'UTRs and near start codons and are embedded in a local context reminiscent of the NSUN2-dependent m5C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that modification levels, at bulk and for many individual sites, were inversely correlated with ribosome association. CONCLUSIONS: Our findings emphasise the major role of NSUN2 in placing the m5C mark transcriptome-wide. We further present evidence that substantiates a functional interdependence of cytosine methylation level with mRNA translation. Additionally, we identify several compelling candidate sites for future mechanistic analysis.

Revisiting ultrafast laser inscribed waveguide formation in commercial alkali-free borosilicate glasses.

Alkali-free borosilicate glasses are one of the most used dielectric platforms for ultrafast laser inscribed integrated photonics. Femtosecond laser written waveguides in commercial Corning Eagle 2000, Corning Eagle XG and Schott AF32 glasses were analyzed. They were studied in depth to disclose the dynamics of waveguide formation. We believe that the findings presented in this paper will help bridge one of the major and important gaps in understanding the ultrafast light-matter interaction with alkali-free boroaluminosilicate glass. It was found that the waveguides are formed mainly due to structural and elemental reorganization upon laser inscription. Aluminum along with alkaline earth metals were found to be responsible for the densification and silicon being the exchanging element to form a rarefied zone. Strong affinity towards alkaline earth elements to form the densified zone for waveguides written with high feed rate (>200 mm/min) were identified and explained. Finally we propose a plausible solution to form positive refractive index change waveguides in different glasses based on current and previous reports.

Motion detection with NMR markers using real-time field tracking in the laboratory frame.

PURPOSE: To enhance the utility of motion detection with nuclear magnetic resonance (NMR) markers by removing the need for sequence-dependent calibration. METHODS: Two sets of NMR markers are used for simultaneous observation of magnetic field dynamics during imaging procedures. A set of stationary markers at known positions in the laboratory frame serves to determine the field evolution in that frame. Concurrent recording from a set of head-mounted markers then permits calculating their lab-frame positions and derived rigid-body motion parameters. The precision and accuracy of this approach are evaluated relative to current calibration-based solutions. Use for prospective motion correction is then demonstrated in high-resolution imaging of long scan duration. RESULTS: Motion detection with real-time field tracking overcomes the need for explicit calibration without compromising precision, which is assessed at 10 to 30 µm. Relative to full conventional calibration, it is found to offer superior robustness against thermal drift. Relative to more economical modes of calibration, it achieves substantially higher accuracy. Prospective motion correction based on real-time field tracking resulted in consistently high image quality even when head motion exceeded the image resolution by one order of magnitude. CONCLUSION: Real-time field tracking enables motion detection with NMR markers without calibration overhead and thus overcomes a key obstacle toward routine use. In addition, it renders this mode of motion tracking more robust against system imperfections.

Towards a photonic mid-infrared nulling interferometer in chalcogenide glass.

Nulling interferometry enables astronomers to advance beyond the resolving power of ground-based telescopes with the goal of directly detecting exo-planets. By diminishing the overwhelming emission of the host star through destructive interference, radiation from young companions can be observed. The atmospheric transmission window centered around 4 µm wavelength is of particular interest because it has a favorable contrast between star and planet as well as a reduced atmospheric disturbance. For robustness and high stability, it is desirable to employ integrated devices based on optical waveguide technology. Their development is hindered at this wavelength range due to the lack of suitable host materials and compatible fabrication techniques to create low-loss photonic devices. This paper details our work on femtosecond laser direct-written optical waveguides and key components for an on-chip nulling interferometer inside gallium lanthanum sulphur glass. By combining cumulative heating fabrication with the multiscan technique, single-mode optical waveguides with propagation losses as low as 0.22 ± 0.02 dB/cm at 4 µm and polarization-dependent losses of < 0.1 dB/cm were realized. Furthermore, S-bends with negligible bending loss and broadband Y-splitters with 50/50 power division across a 600 nm wavelength window (3.6 - 4.2 µm) and low losses of < 0.5 dB are demonstrated. Directional couplers with an equal splitting ratio complement these main building blocks to create a future compact nulling interferometer with a total projected intrinsic loss of < 1 dB, a value that is sufficient to perform future on-sky experiments in relatively short observation runs on ground-based telescopes.

Beam shaping of a broad-area laser diode using 3D integrated optics.

Typical high power broad-area semiconductor lasers exhibit a highly astigmatic beam profile. However, many applications require a homogenous and circular symmetric beam. Thus coupling into circular multimode optical fibers is often employed. The strip-like astigmatic output of the diode laser underfills the circular multimode fiber, thus a decrease in beam quality occurs after fiber coupling due to mode mixing inside the optical fiber. This Letter presents a 3D integrated optics approach to shape the output of a broad-area laser diode. Ultrafast laser inscription is utilized to create a pair of photonic lanterns connected back to back inside a glass chip that captures and shapes the output of a commercial 976 nm wavelength broad-area laser diode with 95 µm emitter width. Compared to coupling to a 105 µm diameter, 0.15 numerical aperture step-index multimode fiber, the photonic chip-based approach results in a 13× higher beam quality and 7× greater brightness.