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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Rapid anatomical brain imaging using spiral acquisition and an expanded signal model.

We report the deployment of spiral acquisition for high-resolution structural imaging at 7T. Long spiral readouts are rendered manageable by an expanded signal model including static off-resonance and B0 dynamics along with k-space trajectories and coil sensitivity maps. Image reconstruction is accomplished by inversion of the signal model using an extension of the iterative non-Cartesian SENSE algorithm. Spiral readouts up to 25 ms are shown to permit whole-brain 2D imaging at 0.5 mm in-plane resolution in less than a minute. A range of options is explored, including proton-density and T2* contrast, acceleration by parallel imaging, different readout orientations, and the extraction of phase images. Results are shown to exhibit competitive image quality along with high geometric consistency.

Characterization of antagonistic yeasts for biocontrol applications on apples or in soil by quantitative analyses of synthetic yeast communities.

Antagonistic yeasts suppress plant pathogenic fungi by various mechanisms, but their biocontrol efficacy also depends on the ability to compete and persist in the environment. The goal of the work presented here was to quantify the composition of synthetic yeast communities in order to determine the competitiveness of different species and identify promising candidates for plant protection. For this purpose, colony counting of distinct species and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS; MALDI biotyping) were used to distinguish different yeast species and to quantify the composition of a synthetic community of six yeasts (Aureobasidium pullulans, Candida subhashii, Cyberlindnera sargentensis, Hanseniaspora sp., Metschnikowia pulcherrima and Pichia kluyveri) over time, on apples and in soil, and in different growth media. These studies revealed important characteristics that predispose the different species for particular applications. For example, the competitiveness and antagonistic activity of C. subhashii was strongly increased in the presence of N-acetylglucosamin as the sole carbon source, M. pulcherrima and A. pullulans were the strongest competitors on apple, and C. sargentensis competed the best in soil microcosms. Based on these laboratory studies, M. pulcherrima and A. pullulans are promising candidates for biocontrol applications against fungal phyllosphere diseases, while C. sargentensis may hold potential for use against soilborne fungal pathogens. These results document the potential of MALDI-TOF MS for the quantitative analysis of synthetic yeast communities and highlight the value of studying microorganisms with relevant functions in moderately complex, synthetic communities and natural substrates rather than as individual isolates.

Prospective motion correction with NMR markers using only native sequence elements.

PURPOSE: To develop a method of tracking active NMR markers that requires no alterations of common imaging sequences and can be used for prospective motion correction (PMC) in brain MRI. METHODS: Localization of NMR markers is achieved by acquiring short signal snippets in rapid succession and evaluating them jointly. To spatially encode the markers, snippets are timed such that signal phase is accrued during sequence intervals with suitably diverse gradient actuation. For motion tracking and PMC in brain imaging, the markers are mounted on a lightweight headset. PMC is then demonstrated with high-resolution T2 *- and T1 -weighted imaging sequences in the presence of instructed as well as residual unintentional head motion. RESULTS: With both unaltered sequences, motion tracking was achieved with precisions on the order of 10 µm and 0.01° and temporal resolution of 48 and 39 ms, respectively. On this basis, PMC improved image quality significantly throughout. CONCLUSION: The proposed approach permits high-precision motion tracking and PMC with standard imaging sequences. It does so without altering sequence design and thus overcomes a key hindrance to routine motion tracking with NMR markers. Magn Reson Med 79:2046-2057, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Ultrafast Ligand Self-Exchanging Gadolinium Complexes in Ionic Liquids for NMR Field Probes.

Concurrent magnetic field monitoring in MRI with an array of NMR field probes allows for reducing image imperfections. High 19F concentrations together with short relaxation times are basic probe properties. We present the NMR properties of [Gd(NTf2)4]- dissolved in an ionic liquid consisting of an imidazolium cation and the [NTf2]- anion. These solutions achieve fluorine concentrations as high as 26 M and rapid relaxation times in the sub-ms time range. The second order self-exchange rate of coordinated [NTf2]- with [NTf2]- as determined with [Y(NTf2)4]- is 4.5 × 105·M-1·s-1. X-ray structure analyses confirm the coordination number of eight around Gd3+ and Y3+. These ionic-liquid solutions are thus excellent candidates for dynamically probing the NMR fields in MRI.

Physiology recording with magnetic field probes for fMRI denoising.

Physiological noise originating in cardiovascular and respiratory processes is a substantial confound in BOLD fMRI. When unaccounted for it reduces the temporal SNR and causes error in inferred brain activity and connectivity. Physiology correction typically relies on auxiliary measurements with peripheral devices such as ECG, pulse oximeters, and breathing belts. These require direct skin contact or at least a tight fit, impairing subject comfort and adding to the setup time. In this work, we explore a touch-free alternative for physiology recording, using magnetic detection with NMR field probes. Placed close to the chest such probes offer high sensitivity to cardiovascular and respiratory dynamics without mechanical contact. This is demonstrated by physiology regression in a typical fMRI scenario at 7T, including validation against standard devices. The study confirms essentially equivalent performance of noise models based on conventional recordings and on field probes. It is shown that the field probes may be positioned in the subject's back such that they could be readily integrated in the patient table.

Analysis and correction of field fluctuations in fMRI data using field monitoring.

This work investigates the role of magnetic field fluctuations as a confound in fMRI. In standard fMRI experiments with single-shot EPI acquisition at 3 Tesla the uniform and gradient components of the magnetic field were recorded with NMR field sensors. By principal component analysis it is found that differences of field evolution between the EPI readouts are explainable by few components relating to slow and within-shot field dynamics of hardware and physiological origin. The impact of fluctuating field components is studied by selective data correction and assessment of its influence on image fluctuation and SFNR. Physiological field fluctuations, attributed to breathing, were found to be small relative to those of hardware origin. The dominant confounds were hardware-related and attributable to magnet drift and thermal changes. In raw image time series, field fluctuation caused significant SFNR loss, reflected by a 67% gain upon correction. Large part of this correction can be accomplished by traditional image realignment, which addresses slow and spatially uniform field changes. With realignment, explicit field correction increased the SFNR on the order of 6%. In conclusion, field fluctuations are a relevant confound in fMRI and can be addressed effectively by retrospective data correction. Based on the physics involved it is anticipated that the advantage of full field correction increases with field strength, with non-Cartesian readouts, and upon phase-sensitive BOLD analysis.