Comprehensive understanding of the crystal structure of perovskite-type Ba3Y4O9 with Zr substitution: a theoretical and experimental study.

We previously reported that Zr substitution improves the chemical stability of Ba3Y4O9 and nominally 20 mol% Zr-substituted Ba3Y4O9 is an oxide-ion conductor at intermediate temperatures (500-700 °C). However, the influence of Zr substitution on the structural properties of Ba3Y4O9 was poorly understood. This paper aims to comprehensively understand the crystal structure of Ba3Y4O9 with Zr substitution by powder X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS) measurements, and first-principles calculations. From the results, firstly we found that the hexagonal unit cell of Ba3Y4O9 reported in the database should be revised as doubled along the c-axis in terms of the periodicity of oxide-ion positions. The revised unit cell of Ba3Y4O9 consists of 18 layers of BaO3 and 24 layers of Y which periodically stack along the c-axis. In this work, we focused on the cationic lattice and noticed that the periodical stacking of Ba and Y layers comprises a similar sequence to that in the body-centered cubic (BCC) structure. There are two regions in the Ba3Y4O9 structure: one is a hetero-stacking region of Ba and Y layers (Ba-Y-Ba-Y-Ba) and the other is a homo-stacking region (Ba-Y-Y-Ba). It is noteworthy that the former region is similar to a cubic perovskite. In Zr-substituted Ba3Y4O9, Zr ions preferentially substitute for Y ions in the hetero-stacking region, and therefore the local environment of Zr ions in Ba3Y4O9 is quite similar to that in BaZrO3. Besides, the Zr substitution for Y in Ba3Y4O9 increases the fraction of the cubic-perovskite-like region in the stacking sequences. The structural change in the long-range order strongly affects the other material properties such as chemical stability and the ionic-conduction mechanism. Our adopted description of perovskite-related compounds based on the stacking sequence of the BCC structure should help in understanding the complex structure and developing new perovskite-related materials.

Enhanced responses to inflammatory cytokine interleukin-6 in micropatterned networks of cultured cortical neurons.

Cortical neurons in dissociated cultures are an indispensable model system for pharmacological research that provides insights into chemical responses in well-defined environments. However, cortical neurons plated on homogeneous substrates develop an unstructured network that exhibits excessively synchronized activity, which occasionally masks the consequences induced by external substances. Here, we show that hyperactivity and excessive synchrony in cultured cortical networks can be effectively suppressed by growing neurons in microfluidic devices. These devices feature a hierarchically modular design that resembles the in vivo network. We focused on interleukin-6, a pro-inflammatory cytokine, and assessed its acute and chronic effects. Fluorescence calcium imaging of spontaneous neural activity for up to 20 days of culture showed detectable modulation of collective activity events and neural correlation in micropatterned neurons, which was not apparent in neurons cultured on homogeneous substrates. Our results indicate that engineered neuronal networks provide a unique platform for detecting and understanding the fundamental effects of biochemical compounds on neuronal networks.

Modular architecture facilitates noise-driven control of synchrony in neuronal networks.

High-level information processing in the mammalian cortex requires both segregated processing in specialized circuits and integration across multiple circuits. One possible way to implement these seemingly opposing demands is by flexibly switching between states with different levels of synchrony. However, the mechanisms behind the control of complex synchronization patterns in neuronal networks remain elusive. Here, we use precision neuroengineering to manipulate and stimulate networks of cortical neurons in vitro, in combination with an in silico model of spiking neurons and a mesoscopic model of stochastically coupled modules to show that (i) a modular architecture enhances the sensitivity of the network to noise delivered as external asynchronous stimulation and that (ii) the persistent depletion of synaptic resources in stimulated neurons is the underlying mechanism for this effect. Together, our results demonstrate that the inherent dynamical state in structured networks of excitable units is determined by both its modular architecture and the properties of the external inputs.

Biological neurons act as generalization filters in reservoir computing.

Reservoir computing is a machine learning paradigm that transforms the transient dynamics of high-dimensional nonlinear systems for processing time-series data. Although the paradigm was initially proposed to model information processing in the mammalian cortex, it remains unclear how the nonrandom network architecture, such as the modular architecture, in the cortex integrates with the biophysics of living neurons to characterize the function of biological neuronal networks (BNNs). Here, we used optogenetics and calcium imaging to record the multicellular responses of cultured BNNs and employed the reservoir computing framework to decode their computational capabilities. Micropatterned substrates were used to embed the modular architecture in the BNNs. We first show that the dynamics of modular BNNs in response to static inputs can be classified with a linear decoder and that the modularity of the BNNs positively correlates with the classification accuracy. We then used a timer task to verify that BNNs possess a short-term memory of several 100 ms and finally show that this property can be exploited for spoken digit classification. Interestingly, BNN-based reservoirs allow categorical learning, wherein a network trained on one dataset can be used to classify separate datasets of the same category. Such classification was not possible when the inputs were directly decoded by a linear decoder, suggesting that BNNs act as a generalization filter to improve reservoir computing performance. Our findings pave the way toward a mechanistic understanding of information representation within BNNs and build future expectations toward the realization of physical reservoir computing systems based on BNNs.

The significance of thermomechanical processing on the cellular response of biomedical Co-Cr-Mo alloys.

Strengthening of biomedical Co-Cr-Mo alloys has been explored via thermomechanical processing for enhancing the durability of their biomedical applications. However, the effects of cold and hot deformation on the cellular activity continue to be unclear. In this study, we prepared Co-Cr-Mo alloy rods via cold swaging and hot-caliber rolling and studied the relationship between the microstructure and cellular response of pre-osteoblasts. The cold-swaged rod experienced strain-induced martensitic transformation, which increased the volume fraction of the hexagonal close-packed (hcp) ε-martensite to ∼60 vol.% with an increase in area reduction (r) to 30%. The 111γ fiber texture of the face-centered cubic (fcc) γ-matrix followed the Shoji-Nishiyama orientation relationship with ε-martensite. Cell culture results revealed beneficial effects of cold swaging on the cell response, in terms of adhesion, proliferation and morphology of cells, although increasing r did not significantly affect cellular metabolism levels. The addition of small content of Zr (0.04 wt.%) led to enhanced focal adhesion of cells, which became more significant at higher r. The microstructural evolution during hot-caliber rolling, namely, grain refinement without any phase transformation and strong texture development, did not appreciably affect the cellular activity. These findings are envisaged to facilitate alloy design and microstructural optimization for favorable tuning the osseointegration of biomedical Co-Cr-Mo alloys.

The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies' association with histone locus bodies.

Non-polyadenylated mRNAs of replication-dependent histones (RDHs) are synthesized by RNA polymerase II (Pol II) at histone locus bodies (HLBs). HLBs frequently associate with Cajal bodies (CBs), in which 3'-end processing factors for RDH genes are enriched; however, this association's role in transcription termination of RDH genes remains unclear. Here, we show that Pol II pauses immediately upstream of transcript end sites of RDH genes and Mediator plays a role in this Pol II pausing through CBs' association with HLBs. Disruption of the Mediator docking site for Little elongation complex (LEC)-Cap binding complex (CBC)-Negative elongation factor (NELF), components of CBs, interferes with CBs' association with HLBs and 3' Pol II pausing, resulting in increased aberrant unprocessed RDH gene transcripts. Our findings suggest Mediator's involvement in CBs' association with HLBs to facilitate 3' Pol II pausing and subsequent 3'-end processing of RDH genes by supplying 3'-end processing factors.

A High-throughput Automated ELISA Assay for Detection of IgG Antibodies to the SARS-CoV-2 Spike Protein.

The SARS-CoV-2 pandemic and vaccination campaign has illustrated the need for high throughput serological assays to quantitatively measure antibody levels. Here, we present a protocol for a high-throughput colorimetric ELISA assay to detect IgG antibodies against the SARS-CoV-2 spike protein. The assay robustly distinguishes positive from negative samples, while controlling for potential non-specific binding from serum samples. To further eliminate background contributions, we demonstrate a computational pipeline for fitting ELISA titration curves, that produces an extremely sensitive antibody signal metric for quantitative comparisons across samples and time.

Microfluidic cell engineering on high-density microelectrode arrays for assessing structure-function relationships in living neuronal networks.

Neuronal networks in dissociated culture combined with cell engineering technology offer a pivotal platform to constructively explore the relationship between structure and function in living neuronal networks. Here, we fabricated defined neuronal networks possessing a modular architecture on high-density microelectrode arrays (HD-MEAs), a state-of-the-art electrophysiological tool for recording neural activity with high spatial and temporal resolutions. We first established a surface coating protocol using a cell-permissive hydrogel to stably attach a polydimethylsiloxane microfluidic film on the HD-MEA. We then recorded the spontaneous neural activity of the engineered neuronal network, which revealed an important portrait of the engineered neuronal network-modular architecture enhances functional complexity by reducing the excessive neural correlation between spatially segregated modules. The results of this study highlight the impact of HD-MEA recordings combined with cell engineering technologies as a novel tool in neuroscience to constructively assess the structure-function relationships in neuronal networks.

Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling.

The SNF2 family ATPase Amplified in Liver Cancer 1 (ALC1) is the only chromatin remodeling enzyme with a poly(ADP-ribose) (PAR) binding macrodomain. ALC1 functions together with poly(ADP-ribose) polymerase PARP1 to remodel nucleosomes. Activation of ALC1 cryptic ATPase activity and the subsequent nucleosome remodeling requires binding of its macrodomain to PAR chains synthesized by PARP1 and NAD+ A key question is whether PARP1 has a role(s) in ALC1-dependent nucleosome remodeling beyond simply synthesizing the PAR chains needed to activate the ALC1 ATPase. Here, we identify PARP1 separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1. Investigation of these mutants has revealed multiple functions for PARP1 in ALC1-dependent nucleosome remodeling and provides insights into its multifaceted role in chromatin remodeling.

Elongin functions as a loading factor for Mediator at ATF6α-regulated ER stress response genes.

The bZIP transcription factor ATF6α is a master regulator of endoplasmic reticulum (ER) stress response genes. In this report, we identify the multifunctional RNA polymerase II transcription factor Elongin as a cofactor for ATF6α-dependent transcription activation. Biochemical studies reveal that Elongin functions at least in part by facilitating ATF6α-dependent loading of Mediator at the promoters and enhancers of ER stress response genes. Depletion of Elongin from cells leads to impaired transcription of ER stress response genes and to defects in the recruitment of Mediator and its CDK8 kinase subunit. Taken together, these findings bring to light a role for Elongin as a loading factor for Mediator during the ER stress response.

Computational Efficiency of a Modular Reservoir Network for Image Recognition.

Liquid state machine (LSM) is a type of recurrent spiking network with a strong relationship to neurophysiology and has achieved great success in time series processing. However, the computational cost of simulations and complex dynamics with time dependency limit the size and functionality of LSMs. This paper presents a large-scale bioinspired LSM with modular topology. We integrate the findings on the visual cortex that specifically designed input synapses can fit the activation of the real cortex and perform the Hough transform, a feature extraction algorithm used in digital image processing, without additional cost. We experimentally verify that such a combination can significantly improve the network functionality. The network performance is evaluated using the MNIST dataset where the image data are encoded into spiking series by Poisson coding. We show that the proposed structure can not only significantly reduce the computational complexity but also achieve higher performance compared to the structure of previous reported networks of a similar size. We also show that the proposed structure has better robustness against system damage than the small-world and random structures. We believe that the proposed computationally efficient method can greatly contribute to future applications of reservoir computing.

NRBP1-Containing CRL2/CRL4A Regulates Amyloid ß Production by Targeting BRI2 and BRI3 for Degradation.

Alzheimer's disease (AD) is a progressive neurodegenerative disease caused by accumulations of Aß peptides. Production and fibrillation of Aß are downregulated by BRI2 and BRI3, which are physiological inhibitors of amyloid precursor protein (APP) processing and Aß oligomerization. Here, we identify nuclear receptor binding protein 1 (NRBP1) as a substrate receptor of a Cullin-RING ubiquitin ligase (CRL) that targets BRI2 and BRI3 for degradation. Moreover, we demonstrate that (1) dimerized NRBP1 assembles into a functional Cul2- and Cul4A-containing heterodimeric CRL through its BC-box and an overlapping cryptic H-box, (2) both Cul2 and Cul4A contribute to NRBP1 CRL function, and (3) formation of the NRBP1 heterodimeric CRL is strongly enhanced by chaperone-like function of TSC22D3 and TSC22D4. NRBP1 knockdown in neuronal cells results in an increase in the abundance of BRI2 and BRI3 and significantly reduces Aß production. Thus, disrupting interactions between NRBP1 and its substrates BRI2 and BRI3 may provide a useful therapeutic strategy for AD.

The role of Mediator and Little Elongation Complex in transcription termination.

Mediator is a coregulatory complex that regulates transcription of Pol II-dependent genes. Previously, we showed that human Mediator subunit MED26 plays a role in the recruitment of Super Elongation Complex (SEC) or Little Elongation Complex (LEC) to regulate the expression of certain genes. MED26 plays a role in recruiting SEC to protein-coding genes including c-myc and LEC to small nuclear RNA (snRNA) genes. However, how MED26 engages SEC or LEC to regulate distinct genes is unclear. Here, we provide evidence that MED26 recruits LEC to modulate transcription termination of non-polyadenylated transcripts including snRNAs and mRNAs encoding replication-dependent histone (RDH) at Cajal bodies. Our findings indicate that LEC recruited by MED26 promotes efficient transcription termination by Pol II through interaction with CBC-ARS2 and NELF/DSIF, and promotes 3' end processing by enhancing recruitment of Integrator or Heat Labile Factor to snRNA or RDH genes, respectively.

Mean-field analysis of directed modular networks.

We considered a modular network with a binomial degree distribution and related the analytical relationships of the network properties (modularity, average clustering coefficient, and small-worldness) with structural parameters that define the network, i.e., number of nodes, number of modules, average node degree, and ratio of intra-modular to total connections. Even though modular networks are universally found in real-world systems and are consequently of broad interest in complex network science, the relationship between network properties and structural parameters has not yet been formulated. Here, we show that a series of equations for predicting the network properties can be related using a mean-field connectivity matrix that is defined on the basis of the structural parameters in the network generation algorithm. The theoretical results are then compared with values calculated numerically using the original connectivity matrix and are found to agree well, except when the connections between modules are sparse. Representation of the structure of the network using simple parameters is expected to be conducive for elucidating the structure-dynamics relationship.

Tuning strain-induced γ-to-ε martensitic transformation of biomedical Co-Cr-Mo alloys by introducing parent phase lattice defects.

In this study, we examined the effect of pre-existing dislocation structures in a face-centered cubic γ-phase on strain-induced martensitic transformation (SIMT) to produce a hexagonal close-packed ε-phase in a hot-rolled biomedical Co-Cr-Mo alloy. The as-rolled microstructure was characterized by numerous dislocations as well as stacking faults and deformation twins. SIMT occurred just after macroscopic yielding in tensile deformation. Using synchrotron X-ray diffraction line-profile analysis, we successfully captured the nucleation of ε-martensite during tensile deformation in terms of structural evolution in the surrounding γ-matrix: many dislocations that were introduced into the γ-matrix during the hot-rolling process were consumed to produce ε-martensite, together with strong interactions between dislocations in the γ-matrix. As a result, the SIMT behavior during tensile deformation was accelerated through the consumption of these lattice defects, and the nucleation sites for the SIMT ε-phase transformed into intergranular regions upon hot rolling. Consequently, the hot-rolled Co-Cr-Mo alloy simultaneously exhibited an enhanced strain hardening and a high yield strength. The results of this study suggest the possibility of a novel approach for controlling the γ → ε SIMT behavior, and ultimately, the performance of the alloy in service by manipulating the initial dislocation structures.

Impact of modular organization on dynamical richness in cortical networks.

As in many naturally formed networks, the brain exhibits an inherent modular architecture that is the basis of its rich operability, robustness, and integration-segregation capacity. However, the mechanisms that allow spatially segregated neuronal assemblies to swiftly change from localized to global activity remain unclear. Here, we integrate microfabrication technology with in vitro cortical networks to investigate the dynamical repertoire and functional traits of four interconnected neuronal modules. We show that the coupling among modules is central. The highest dynamical richness of the network emerges at a critical connectivity at the verge of physical disconnection. Stronger coupling leads to a persistently coherent activity among the modules, while weaker coupling precipitates the activity to be localized solely within the modules. An in silico modeling of the experiments reveals that the advent of coherence is mediated by a trade-off between connectivity and subquorum firing, a mechanism flexible enough to allow for the coexistence of both segregated and integrated activities. Our results unveil a new functional advantage of modular organization in complex networks of nonlinear units.

CTD-dependent and -independent mechanisms govern co-transcriptional capping of Pol II transcripts.

Co-transcriptional capping of RNA polymerase II (Pol II) transcripts by capping enzyme proceeds orders of magnitude more efficiently than capping of free RNA. Previous studies brought to light a role for the phosphorylated Pol II carboxyl-terminal domain (CTD) in activation of co-transcriptional capping; however, CTD phosphorylation alone could not account for the observed magnitude of activation. Here, we exploit a defined Pol II transcription system that supports both CTD phosphorylation and robust activation of capping to dissect the mechanism of co-transcriptional capping. Taken together, our findings identify a CTD-independent, but Pol II-mediated, mechanism that functions in parallel with CTD-dependent processes to ensure optimal capping, and they support a "tethering" model for the mechanism of activation.

Stacking-fault strengthening of biomedical Co-Cr-Mo alloy via multipass thermomechanical processing.

The strengthening of metallic biomaterials, such as Co-Cr-Mo and titanium alloys, is of crucial importance to the improvement of the durability of orthopedic implants. In the present study, we successfully developed a face-centered cubic (fcc) Co-Cr-Mo alloy with an extremely high yield strength (1400 MPa) and good ductility (12%) by multipass hot-rolling, which is suitable for industrial production, and examined the relevant strengthening mechanisms. Using an X-ray diffraction line-profile analysis, we revealed that a substantial increase in the number of stacking faults (SFs) in the fcc γ-matrix occurred at a greater height reduction (r), while physical modeling demonstrated that the contribution of the accumulated SFs (i.e., the reduction in SF spacing) with an increase in r successfully explains the entire strengthening behavior of the hot-rolled alloy. The present study sheds light on the importance of the SF strengthening mechanism, and will help to guide the design and manufacturing strategy for the high-strength Co-Cr-Mo alloys used in highly durable medical devices.

Carrier properties of B atomic-layer-doped Si films grown by ECR Ar plasma-enhanced CVD without substrate heating.

The atomic-layer (AL) doping technique in epitaxy has attracted attention as a low-resistive ultrathin semiconductor film as well as a two-dimensional (2-D) carrier transport system. In this paper, we report carrier properties for B AL-doped Si films with suppressed thermal diffusion. B AL-doped Si films were formed on Si(100) by B AL formation followed by Si cap layer deposition in low-energy Ar plasma-enhanced chemical-vapor deposition without substrate heating. After fabrication of Hall-effect devices with the B AL-doped Si films on unstrained and 0.8%-tensile-strained Si(100)-on-insulator substrates (maximum process temperature 350°C), carrier properties were electrically measured at room temperature. Typically for the initial B amount of 2 × 1014 cm-2 and 7 × 1014 cm-2, B concentration depth profiles showed a clear decay slope as steep as 1.3 nm/decade. Dominant carrier was a hole and the maximum sheet carrier densities as high as 4 × 1013 cm-2 and 2 × 1013 cm-2 (electrical activity ratio of about 7% and 3.5%) were measured respectively for the unstrained and 0.8%-tensile-strained Si with Hall mobility around 10-13 cm2 V-1 s-1. Moreover, mobility degradation was not observed even when sheet carrier density was increased by heat treatment at 500-700 °C. There is a possibility that the local carrier (ionized B atom) concentration around the B AL in Si reaches around 1021 cm-3 and 2-D impurity-band formation with strong Coulomb interaction is expected. The behavior of carrier properties for heat treatment at 500-700 °C implies that thermal diffusion causes broadening of the B AL in Si and decrease of local B concentration.

Brigatinib combined with anti-EGFR antibody overcomes osimertinib resistance in EGFR-mutated non-small-cell lung cancer.

Osimertinib has been demonstrated to overcome the epidermal growth factor receptor (EGFR)-T790M, the most relevant acquired resistance to first-generation EGFR-tyrosine kinase inhibitors (EGFR-TKIs). However, the C797S mutation, which impairs the covalent binding between the cysteine residue at position 797 of EGFR and osimertinib, induces resistance to osimertinib. Currently, there are no effective therapeutic strategies to overcome the C797S/T790M/activating-mutation (triple-mutation)-mediated EGFR-TKI resistance. In the present study, we identify brigatinib to be effective against triple-mutation-harbouring cells in vitro and in vivo. Our original computational simulation demonstrates that brigatinib fits into the ATP-binding pocket of triple-mutant EGFR. The structure-activity relationship analysis reveals the key component in brigatinib to inhibit the triple-mutant EGFR. The efficacy of brigatinib is enhanced markedly by combination with anti-EGFR antibody because of the decrease of surface and total EGFR expression. Thus, the combination therapy of brigatinib with anti-EGFR antibody is a powerful candidate to overcome triple-mutant EGFR.