NeuroBus - Architecture for an Ultra-Flexible Neural Interface.

This article presents the system architecture for an implant concept called NeuroBus. Tiny distributed direct digitizing neural recorder ASICs on an ultra-flexible polyimide substrate are connected in a bus-like structure, allowing short connections between electrode and recording front-end with low wiring effort and high customizability. The small size (344 µm × 294 µm) of the ASICs and the ultraflexible substrate allow a low bending stiffness, enabling the implant to adapt to the curvature of the brain and achieving high structural biocompatibility. We introduce the architecture, the integrated building blocks, and the post-CMOS processes required to realize a NeuroBus, and we characterize the prototyped direct digitizing neural recorder front-end as well as polyimide-based ECoG brain interface. A rodent animal model is further used to validate the joint capability of the recording front-end and thin-film electrode array.

Change of dominant material properties in laser perforation process with high-energy lasers up to 120 kilowatt.

In laser materials processing, energy losses due to reflection, heat conduction and thermal radiation play an important role. In this publication, we show that with increasing laser intensity, the energy lost within the sample becomes less important for metal perforation processes. We compare the laser-matter interaction of aluminum and steel plates. Material parameters such as density, melting point and especially thermal conductivity differ strongly, leading to much longer perforation times for aluminum in comparison to steel at laser powers of 20 kW. However, this behavior changes at laser powers of more than 80 kW where the perforation times of aluminum become shorter than the corresponding times for steel. By comparing experimental data and simulations, we conclude that thermal conduction is the dominant factor of energy loss at low powers, but is reduced at high laser powers.

Cytosolic RGG RNA-binding proteins are temperature sensitive flowering time regulators in Arabidopsis.

mRNA translation is tightly regulated by various classes of RNA-binding proteins (RBPs) during development and in response to changing environmental conditions. In this study, we characterize the arginine-glycine-glycine (RGG) motif containing RBP family of Arabidopsis thaliana representing homologues of the multifunctional translation regulators and ribosomal preservation factors Stm1 from yeast (ScStm1) and human SERBP1 (HsSERBP1). The Arabidopsis genome encodes three RGG proteins named AtRGGA, AtRGGB and AtRGGC. While AtRGGA is ubiquitously expressed, AtRGGB and AtRGGC are enriched in dividing cells. All AtRGGs localize almost exclusively to the cytoplasm and bind with high affinity to ssRNA, while being capable to interact with most nucleic acids, except dsRNA. A protein-interactome study shows that AtRGGs interact with ribosomal proteins and proteins involved in RNA processing and transport. In contrast to ScStm1, AtRGGs are enriched in ribosome-free fractions in polysome profiles, suggesting additional plant-specific functions. Mutant studies show that AtRGG proteins differentially regulate flowering time, with a distinct and complex temperature dependency for each AtRGG protein. In conclusion, we suggest that AtRGGs function in fine-tuning translation efficiency to control flowering time and potentially other developmental processes in response to environmental changes.

2D and 3D Triangulation Are Suitable In Situ Measurement Tools for High-Power Large Spot Laser Penetration Processes to Visualize Depressions and Protrusions before Perforating.

During laser penetration, the irradiated samples form a melt pool before perforation. Knowledge of the dynamics of this melt pool is of interest for the correct physical description of the process and leads to improved simulations. However, a direct investigation, especially at the location of high-power laser interaction with large spot diameters in the centimeter range is missing until now. Here, the applicability of 2D triangulation for surface topology observations is demonstrated. With the designed bidirectional 2D triangulation setup, the material cross-section is measured by profile detection at the front and back side. This allows a comprehensive description of the penetration process to be established, which is important for a detailed explanation of the process. Specific steps such as surface melting, indentations, protrusions during melt pool development and their dynamics, and the perforation are visualized, which were unknown until now. Furthermore, a scanning 3D triangulation setup is developed to obtain more information about the entire melt pool at the front side, and not just a single intersection line. The measurements exhibit a mirror-symmetric melt pool and the possibility to extrapolate from the central profile to the outer regions in most cases.

A Direct Digitizing Chopped Neural Recorder Using a Body-Induced Offset Based DC Servo Loop.

This article presents a direct digitizing neural recorder that uses a body-induced offset based DC servo loop to cancel electrode offset (EDO) on-chip. The bulk of the input pair is used to create an offset, counteracting the EDO. The architecture does not require AC coupling capacitors which enables the use of chopping without impedance boosting while maintaining a large input impedance of 238 M Ω over the whole 10 kHz bandwidth. Implemented in a 180 nm HV-CMOS process, the prototype occupies a silicon area of only 0.02 mm2 while consuming 12.8 µW and achieving 1.82 µV[Formula: see text] of input-referred noise in the local field potential (LFP) band and a NEF of 5.75.

Continuous wave high-power laser propagation in water is affected by strong thermal lensing and thermal blooming already at short distances.

When laser beams propagate through media with non-vanishing absorption, the media is heated resulting in a change of the refractive index, which can lead to thermal lensing and thermal blooming. However, experimental details about both phenomena for propagations in water are lacking, especially for high-power lasers in the kilowatt range. We show that significant thermal lensing occurs only for high input powers before the onset of convective flow, while for low input powers, no strong thermal lens arises. After the onset of water flow, thermal blooming occurs at low input powers comparable to that known for propagations over kilometres in the air. However, for high input powers a thermal blooming on a qualitatively higher level is shown. By wavefront sensing, the change of refractive index distribution in water is investigated. This clearly shows the fast development of a strong thermal lens for high input powers and the onset of convection. Furthermore, a qualitatively good agreement of the accompanying simulations is observed. It is found that the absorption coefficient is linear with a value of [Formula: see text] at least up to 7.5 kW, i.e. 8 [Formula: see text]. However, the directed transmission into an aperture is only constant before any thermal lensing of blooming occurs.

A Chopped Neural Front-End Featuring Input Impedance Boosting With Suppressed Offset-Induced Charge Transfer.

Modern neuromodulation systems typically provide a large number of recording and stimulation channels, which reduces the available power and area budget per channel. To maintain the necessary input-referred noise performance despite growingly rigorous area constraints, chopped neural front-ends are often the modality of choice, as chopper-stabilization allows to simultaneously improve (1/f) noise and area consumption. The resulting issue of a drastically reduced input impedance has been addressed in prior art by impedance boosters based on voltage buffers at the input. These buffers precharge the large input capacitors, reduce the charge drawn from the electrodes and effectively boost the input impedance. Offset on these buffers directly translates into charge-transfer to the electrodes, which can accelerate electrode aging. To tackle this issue, a voltage buffer with ultra-low time-averaged offset is proposed, which cancels offset by periodic reconfiguration, thereby minimizing unintended charge transfer. This article explains the background and circuit design in detail and presents measurement results of a prototype implemented in a 180 nm HV CMOS process. The measurements confirm that signal-independent, buffer offset induced charge transfer occurs and can be mitigated by the presented buffer reconfiguration without adversely affecting the operation of the input impedance booster. The presented neural recorder front-end achieves state of the art performance with an area consumption of 0.036 mm2, an input referred noise of [Formula: see text] (1 to 200 Hz) and [Formula: see text] (0.2 to 10 kHz), power consumption of 13.7 µW from 1.8 V supply, as well as CMRR and PSRR ≥ 83 dB at 50 Hz.

In situ speciation and spatial mapping of Zn products during pulsed laser ablation in liquids (PLAL) by combined synchrotron methods.

Pulsed laser ablation in liquids is a hierarchical multi-step process to produce pure inorganic nanoparticle colloids. Controlling this process is hampered by the partial understanding of individual steps and structure formation. In situ X-ray methods are employed to resolve macroscopic dynamics of nanosecond PLAL as well to analyse the distribution and speciation of ablated species with a microsecond time resolution. High time resolution can be achieved by synchrotron-based methods that are capable of 'single-shot' acquisition. X-ray multicontrast imaging by a Shack-Hartmann setup (XHI) and small angle X-ray scattering (SAXS) resolve evolving nanoparticles inside the transient cavitation bubble, while X-ray absorption spectroscopy in dispersive mode opens access to the total material yield and the chemical state of the ejecta. It is confirmed that during ablation nanoparticles are produced directly as well as reactive material is detected, which is identified in the early stage as Zn atoms. Nanoparticles within the cavitation bubble show a metal signature, which prevails for milliseconds, before gradual oxidation sets in. Ablation is described by a phase explosion of the target coexisting with full evaporation. Oxidation occurs only as a later step to already formed nanoparticles.

A multi-omics analysis reveals the unfolded protein response regulon and stress-induced resistance to folate-based antimetabolites.

Stress response pathways are critical for cellular homeostasis, promoting survival through adaptive changes in gene expression and metabolism. They play key roles in numerous diseases and are implicated in cancer progression and chemoresistance. However, the underlying mechanisms are only poorly understood. We have employed a multi-omics approach to monitor changes to gene expression after induction of a stress response pathway, the unfolded protein response (UPR), probing in parallel the transcriptome, the proteome, and changes to translation. Stringent filtering reveals the induction of 267 genes, many of which have not previously been implicated in stress response pathways. We experimentally demonstrate that UPR-mediated translational control induces the expression of enzymes involved in a pathway that diverts intermediate metabolites from glycolysis to fuel mitochondrial one-carbon metabolism. Concomitantly, the cells become resistant to the folate-based antimetabolites Methotrexate and Pemetrexed, establishing a direct link between UPR-driven changes to gene expression and resistance to pharmacological treatment.

Shack-Hartmann wavefront sensors based on 2D refractive lens arrays and super-resolution multi-contrast X-ray imaging.

Different approaches of 2D lens arrays as Shack-Hartmann sensors for hard X-rays are compared. For the first time, a combination of Shack-Hartmann sensors for hard X-rays (SHSX) with a super-resolution imaging approach to perform multi-contrast imaging is demonstrated. A diamond lens is employed as a well known test object. The interleaving approach has great potential to overcome the 2D lens array limitation given by the two-photon polymerization lithography. Finally, the radiation damage induced by continuous exposure of an SHSX prototype with a white beam was studied showing a good performance of several hours. The shape modification and influence in the final image quality are presented.

The zinc finger domains in U2AF26 and U2AF35 have diverse functionalities including a role in controlling translation.

Recent work has associated point mutations in both zinc fingers (ZnF) of the spliceosome component U2AF35 with malignant transformation. However, surprisingly little is known about the functionality of the U2AF35 ZnF domains in general. Here we have analysed key functionalities of the ZnF domains of mammalian U2AF35 and its paralog U2AF26. Both ZnFs are required for splicing regulation, whereas only ZnF2 controls protein stability and contributes to the interaction with U2AF65. These features are confirmed in a naturally occurring splice variant of U2AF26 lacking ZnF2, that is strongly induced upon activation of primary mouse T cells and localized in the cytoplasm. Using Ribo-Seq in a model T cell line we provide evidence for a role of U2AF26 in activating cytoplasmic steps in gene expression, notably translation. Consistently, an MS2 tethering assay shows that cytoplasmic U2AF26/35 increase translation when localized to the 5'UTR of a model mRNA. This regulation is partially dependent on ZnF1 thus providing a connection between a core splicing factor, the ZnF domains and the regulation of translation. Altogether, our work reveals unexpected functions of U2AF26/35 and their ZnF domains, thereby contributing to a better understanding of their role and regulation in mammalian cells.

In situ structural kinetics of picosecond laser-induced heating and fragmentation of colloidal gold spheres.

Fragmentation of colloidal 54 nm gold nanoparticles by picosecond laser pulses is recorded by time-resolved X-ray scattering, giving access to structural dynamics down to a 80 ps resolution. Lattice temperature and energy dissipation have been quantified to verify that the maximum applied fluence of 1800 J m-2 heats up the particles close to boiling. Already within 30 ns, particles with significantly lower particle sizes of 2 to 3 nm are detected, which hints towards an ultrafast process either by a thermal phase explosion or Coulomb instability. An arrested growth is observed on a microsecond time scale resulting in a final particle size of 3-4 nm with high yield. In this context, the fragmentation in a NaCl/NaOH solution seems to limit growth by electrostatic stabilization of fragments, whereas it does not modify the initial product sizes. The laser-induced fragmentation process is identified as a single-step, instantaneous reaction.

A sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cells.

Many cellular events are driven by changes in protein expression, measurable by mass spectrometry or antibody-based assays. However, using conventional technology, the analysis of transcription factor or membrane receptor expression is often limited by an insufficient sensitivity and specificity. To overcome this limitation, we have developed a high-resolution targeted proteomics strategy, which allows quantification down to the lower attomol range in a straightforward way without any prior enrichment or fractionation approaches. The method applies isotope-labeled peptide standards for quantification of the protein of interest. As proof of principle, we applied the improved workflow to proteins of the unfolded protein response (UPR), a signaling pathway of great clinical importance, and could for the first time detect and quantify all major UPR receptors, transducers and effectors that are not readily detectable via antibody-based-, SRM- or conventional PRM assays. As transcription and translation is central to the regulation of UPR, quantification and determination of protein copy numbers in the cell is important for our understanding of the signaling process as well as how pharmacologic modulation of these pathways impacts on the signaling. These questions can be answered using our newly established workflow as exemplified in an experiment using UPR perturbation in a glioblastoma cell lines.

Inverted Hartmann mask for single-shot phase-contrast x-ray imaging of dynamic processes.

In this Letter, we present the application of the inverted Hartmann mask for time-resolved single-shot phase-contrast x-ray imaging. The inverted Hartmann mask is a periodic array of free-standing gold pillars. The array is manufactured by UV lithography and electroplating. Time-resolved measurements are performed for imaging of pulsed laser ablation in liquids using white-beam synchrotron radiation. The inverted Hartmann mask in combination with a single-shot imaging technique provides sufficient differential phase contrast even at very short exposure times. It can be effectively used for phase-contrast x-ray imaging of fast dynamic processes with temporal resolution on the millisecond scale.

Early appearance of crystalline nanoparticles in pulsed laser ablation in liquids dynamics.

The size and crystallinity of gold and silver nanoparticles during the process of pulsed laser ablation in water (PLAL) is investigated with microsecond and sub-microsecond time resolution. While basic observations have already been established, such as detection of particles inside the cavitation bubble, trapping of ablated matter by the bubble or the action of size quenching on a sub-millisecond time scale, the structure formation mechanism is still a matter of debate. Quantifying the nanoparticle release and crystallinity close to the irradiated metal target by wide and small angle X-ray scattering reveals the presence of nanoparticles ahead of the developing vapour bubble and inside the bubble. While the (temporal) distribution is in agreement with a homogeneously particle-filled bubble, solid particles are detected at the advancing bubble front. Wide-angle X-ray scattering confirms the crystalline nature of these large particles. This reveals that for picosecond ablation the expulsion of condensed phases of material during the ablation process adds significantly to the bimodal size distribution, relating to recent models of film lift-off and liquid metal Rayleigh instabilities.

Incubation Effect of Pre-Irradiation on Bubble Formation and Ablation in Laser Ablation in Liquids.

Pulsed laser ablation in liquids (PLAL) is a multi-scale process, which is widely studied either in batch ablation with prolonged target irradiation as well as mechanistic investigations, in a defined (single-shot) process. However, fundamental studies on defined pulse series are rare. We have investigated the effect of a developing rough morphology of the target surface on the PLAL process with nanosecond pulses and, partially, picosecond pulses. At low fluence the cavitation bubble growth as well as the ablation yield depend on the irradiation history of the target. The bubble size increases with repeated irradiation on one spot for the first 2-30 pulses as well as with the applied dose. This is discussed within the framework of incubation effects. Incubation is found to be important, resulting in a bubble volume increase by a factor of six or more between pristine and corrugated targets. The target surface, changing from smooth to corrugated, induces a more efficient localization of laser energy at the solid-liquid interface. This is accompanied by a suppressed reflectivity and more efficient coupling of energy into the laser-induced plasma. Thus, the cavitation bubble size increases as well as ablation being enhanced. At high fluence, such incubation is masked by the rapid development of surface damage within the first shots, which eventually would lead to a reduction of bubble sizes.

Time and Mechanism of Nanoparticle Functionalization by Macromolecular Ligands during Pulsed Laser Ablation in Liquids.

Laser ablation of gold in liquids with nanosecond laser pulses in aqueous solutions of inorganic electrolytes and macromolecular ligands for gold nanoparticle size quenching is probed inside the laser-induced cavitation bubble by in situ X-ray multicontrast imaging with a Hartmann mask (XHI). It is found that (i) the in situ size quenching power of sodium chloride (NaCl) in comparison to the ablation in pure water can be observed by the scattering contrast from XHI already inside the cavitation bubble, while (ii) for polyvinylpyrrolidone (PVP) as a macromolecular model ligand an in situ size quenching cannot be observed. Complementary ex situ characterization confirms the overall size quenching ability of both additive types NaCl and PVP. The macromolecular ligand as well as its monomer N-vinylpyrrolidone (NVP) are mainly effective for growth quenching of larger nanoparticles on later time scales, leading to the conclusion of an alternative interaction mechanism with ablated nanoparticles compared to the electrolyte NaCl, probably outside of the cavitation bubble, in the surrounding liquid phase. While monomer and polymer have similar effects on the particle properties, with the polymer being slightly more efficient, only the polymer is effective against hydrodynamic aggregation.

Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors.

Influenza polymerase uses short capped primers snatched from nascent Pol II transcripts to initiate transcription of viral mRNAs. Here we describe crystal structures of influenza A and B polymerase bound to a capped primer in a configuration consistent with transcription initiation ('priming state') and show by functional assays that conserved residues from both the PB2 midlink and cap-binding domains are important for positioning the capped RNA. In particular, mutation of PB2 Arg264, which interacts with the triphosphate linkage in the cap, significantly and specifically decreases cap-dependent transcription. We also compare the configuration of the midlink and cap-binding domains in the priming state with their very different relative arrangement (called the 'apo' state) in structures where the potent cap-binding inhibitor VX-787, or a close analogue, is bound. In the 'apo' state the inhibitor makes additional interactions to the midlink domain that increases its affinity beyond that to the cap-binding domain alone. The comparison suggests that the mechanism of resistance of certain mutations that allow virus to escape from VX-787, notably PB2 N510T, can only be rationalized if VX-787 has a dual mode of action, direct inhibition of capped RNA binding as well as stabilization of the transcriptionally inactive 'apo' state.

Thermal dynamics of pulsed-laser excited gold nanorods in suspension.

Photothermal reactions of metallic nanostructures, such as gold nanorods show appealing structural relaxations, such as bubble formation or particle modification. We have employed a pump-probe method to record the structural relaxations of a suspension of gold nanorods upon femtosecond laser excitation by pulsed X-ray scattering both with wide-angle and small-angle sensitivity. Single-pulse reactions include transient bubble formation at 20 J m-2 and irreversible nanorod reshaping at 30 J m-2. Thus the window for reversible excitation is very narrow. Additionally we could map the time-domain and fluence behaviour in a wide range to characterize the relaxations comprehensively. The polarized laser pulse first selectively excites nanorods aligned with the laser electric field, but at higher fluence non-aligned rods are also transformed. At low fluence this transformation happens in the solid state, while at higher fluence the rods melt.

An in vitro fluorescence based study of initiation of RNA synthesis by influenza B polymerase.

Influenza polymerase replicates, via a complementary RNA intermediate (cRNA), and transcribes the eight viral RNA (vRNA) genome segments. To initiate RNA synthesis it is bound to the conserved 5΄ and 3΄ extremities of the vRNA or cRNA (the 'promoter'). 5΄-3΄ base-pairing in the distal promoter region is essential to position the template RNA at the polymerase active site, as shown by a new crystal structure with the 3΄ end threading through the template entry tunnel. We develop fluorescence polarization assays to quantify initiation of cap-primed (transcription) or unprimed (replication) RNA synthesis by recombinant influenza B polymerase bound to the vRNA or cRNA promoter. The rate-limiting step is formation of a primed initiation complex with minimally ApG required to stabilize the 3΄ end of the template within the active-site. Polymerase bound to the vRNA promoter initiates RNA synthesis terminally, while the cRNA promoter directs internal initiation at a significantly lower rate. Progression to elongation requires breaking the promoter 5΄-3΄ base-pairing region and favourable compensation by the emerging template-product base-pairs. The RNA synthesis assay is adaptable to high-throughput screening for polymerase inhibitors. In a pilot study, we find that initiation at the cRNA promoter is unusually susceptible to inhibition by 2΄F-2΄dNTPs.