An inducible genetic tool to track and manipulate specific microglial states reveals their plasticity and roles in remyelination.

Recent single-cell RNA sequencing studies have revealed distinct microglial states in development and disease. These include proliferative-region-associated microglia (PAMs) in developing white matter and disease-associated microglia (DAMs) prevalent in various neurodegenerative conditions. PAMs and DAMs share a similar core gene signature. However, the extent of the dynamism and plasticity of these microglial states, as well as their functional significance, remains elusive, partly due to the lack of specific tools. Here, we generated an inducible Cre driver line, Clec7a-CreERT2, that targets PAMs and DAMs in the brain parenchyma. Utilizing this tool, we profiled labeled cells during development and in several disease models, uncovering convergence and context-dependent differences in PAM and DAM gene expression. Through long-term tracking, we demonstrated microglial state plasticity. Lastly, we specifically depleted DAMs in demyelination, revealing their roles in disease recovery. Together, we provide a versatile genetic tool to characterize microglial states in CNS development and disease.

DDN3.0: determining significant rewiring of biological network structure with differential dependency networks.

MOTIVATION: Complex diseases are often caused and characterized by misregulation of multiple biological pathways. Differential network analysis aims to detect significant rewiring of biological network structures under different conditions and has become an important tool for understanding the molecular etiology of disease progression and therapeutic response. With few exceptions, most existing differential network analysis tools perform differential tests on separately learned network structures that are computationally expensive and prone to collapse when grouped samples are limited or less consistent. RESULTS: We previously developed an accurate differential network analysis method-differential dependency networks (DDN), that enables joint learning of common and rewired network structures under different conditions. We now introduce the DDN3.0 tool that improves this framework with three new and highly efficient algorithms, namely, unbiased model estimation with a weighted error measure applicable to imbalance sample groups, multiple acceleration strategies to improve learning efficiency, and data-driven determination of proper hyperparameters. The comparative experimental results obtained from both realistic simulations and case studies show that DDN3.0 can help biologists more accurately identify, in a study-specific and often unknown conserved regulatory circuitry, a network of significantly rewired molecular players potentially responsible for phenotypic transitions. AVAILABILITY AND IMPLEMENTATION: The Python package of DDN3.0 is freely available at https://github.com/cbil-vt/DDN3. A user's guide and a vignette are provided at https://ddn-30.readthedocs.io/.

CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution.

MOTIVATION: Complex tissues are dynamic ecosystems consisting of molecularly distinct yet interacting cell types. Computational deconvolution aims to dissect bulk tissue data into cell type compositions and cell-specific expressions. With few exceptions, most existing deconvolution tools exploit supervised approaches requiring various types of references that may be unreliable or even unavailable for specific tissue microenvironments. RESULTS: We previously developed a fully unsupervised deconvolution method-Convex Analysis of Mixtures (CAM), that enables estimation of cell type composition and expression from bulk tissues. We now introduce CAM3.0 tool that improves this framework with three new and highly efficient algorithms, namely, radius-fixed clustering to identify reliable markers, linear programming to detect an initial scatter simplex, and a smart floating search for the optimum latent variable model. The comparative experimental results obtained from both realistic simulations and case studies show that the CAM3.0 tool can help biologists more accurately identify known or novel cell markers, determine cell proportions, and estimate cell-specific expressions, complementing the existing tools particularly when study- or datatype-specific references are unreliable or unavailable. AVAILABILITY AND IMPLEMENTATION: The open-source R Scripts of CAM3.0 is freely available at https://github.com/ChiungTingWu/CAM3/(https://github.com/Bioconductor/Contributions/issues/3205). A user's guide and a vignette are provided.

Electrical-Controllable Antiferromagnet-Based Tunnel Junction.

An electrical-controllable antiferromagnet tunnel junction is a key goal in spintronics, holding immense promise for ultradense and ultrastable antiferromagnetic memory with high processing speed for modern information technology. Here, we have advanced toward this goal by achieving an electrical-controllable antiferromagnet-based tunnel junction of Pt/Co/Pt/Co/IrMn/MgO/Pt. The exchange coupling between antiferromagnetic IrMn and Co/Pt perpendicular magnetic multilayers results in the formation of an interfacial exchange bias and exchange spring in IrMn. Encoding information states "0" and "1" is realized through the exchange spring in IrMn, which can be electrically written by spin-orbit torque switching with high cyclability and electrically read by antiferromagnetic tunneling anisotropic magnetoresistance. Combining spin-orbit torque switching of both exchange spring and exchange bias, a 16 Boolean logic operation is successfully demonstrated. With both memory and logic functionalities integrated into our electrically controllable antiferromagnetic-based tunnel junction, we chart the course toward high-performance antiferromagnetic logic-in-memory.

Restricted Boltzmann Machines Implemented by Spin-Orbit Torque Magnetic Tunnel Junctions.

Artificial intelligence has surged forward with the advent of generative models, which rely heavily on stochastic computing architectures enhanced by true random number generators with adjustable sampling probabilities. In this study, we develop spin-orbit torque magnetic tunnel junctions (SOT-MTJs), investigating their sigmoid-style switching probability as a function of the driving voltage. This feature proves to be ideally suited for stochastic computing algorithms such as the restricted Boltzmann machines (RBM) prevalent in pretraining processes. We exploit SOT-MTJs as both stochastic samplers and network nodes for RBMs, enabling the implementation of RBM-based neural networks to achieve recognition tasks for both handwritten and spoken digits. Moreover, we further harness the weights derived from the preceding image and speech training processes to facilitate cross-modal learning from speech to image generation. Our results clearly demonstrate that these SOT-MTJs are promising candidates for the development of hardware accelerators tailored for Boltzmann neural networks and other stochastic computing architectures.

Creation of Room-Temperature Sub-100 nm Antiferromagnetic Skyrmions in an Antiferromagnet IrMn through Interfacial Exchange Coupling.

Antiferromagnetic (AFM) skyrmions are magnetic vortices composed of antiparallell-aligned neighboring spins. In stark contrast to conventional skyrmions based on ferromagnetic order, AFM skyrmions have vanished stray fields, higher response frequencies, and rectified translational motion driven by an external force. Therefore, AFM skyrmions promise highly efficient spintronics devices with high bit mobility and density. Nevertheless, the experimental realization of intrinsic AFM skyrmions remains elusive. Here, we show that AFM skyrmions can be nucleated via interfacial exchange coupling at the surface of a room-temperature AFM material, IrMn, exploiting the particular response from uncompensated moments to the thermal annealing and imprinting effects. Further systematic magnetic characterizations validate the existence of such an AFM order at the IrMn/CoFeB interfaces. Such AFM skyrmions have a typical size of 100 nm, which presents pronounced robustness against field and temperature. Our work opens new pathways for magnetic topological devices based on AFM skyrmions.

Exceptional Hole-Selective Properties of Ta2O5 Films via Sn4+ Doping for High Performance Silicon Heterojunction Solar Cells.

Carrier-selective passivating contacts using transition metal oxides (TMOs) have attracted great attention for crystalline silicon (c-Si) heterojunction solar cells recently. Among them, tantalum oxide (Ta2O5) exhibits outstanding advantages, such as a wide bandgap, good surface passivation, and a small conduction band offset with c-Si, which is typically used as an electron-selective contact layer. Interestingly, it is first demonstrated that solution-processed Ta2O5 films exhibit a high hole selectivity, which blocks electrons and promotes hole transport simultaneously. Through the ozone pre-treatment of Ta2O5/p-Si interface and optimization of the film thickness (≈9 nm), the interfacial recombination is suppressed and the contact resistivity is reduced from 178.0 to 29.3 mΩ cm2. Moreover, the Sn4+ doping increases both the work function and oxygen vacancies of the film, contributing to the improved hole-selective contact performance. As a result, the photoelectric conversion efficiencies of Ta2O5/p-Si heterojunction solar cells are significantly improved from 14.84% to 18.47%, with a high thermal stability up to 300 °C. The work has provided a feasible strategy to explore new features of TMOs for carrier-selective contact applications, that is, bipolar carrier transport properties.

A Strategy for Enhancing Perpendicular Magnetic Anisotropy in Yttrium Iron Garnet Films.

In future information storage and processing, magnonics is one of the most promising candidates to replace traditional microelectronics. Yttrium iron garnet (YIG) films with perpendicular magnetic anisotropy (PMA) have aroused widespread interest in magnonics. Obtaining strong PMA in a thick YIG film with a small lattice mismatch (η) has been fascinating but challenging. Here, a novel strategy is proposed to reduce the required minimum strain value for producing PMA and increase the maximum thickness for maintaining PMA in YIG films by slight oxygen deficiency. Strong PMA is achieved in the YIG film with an η of only 0.4% and a film thickness up to 60 nm, representing the strongest PMA for such a small η reported so far. Combining transmission electron microscopy analyses, magnetic measurements, and a theoretical model, it is demonstrated that the enhancement of PMA physically originates from the reduction of saturation magnetization and the increase of magnetostriction coefficient induced by oxygen deficiency. The Gilbert damping values of the 60-nm-thick YIG films with PMA are on the order of 10-4. This strategy improves the flexibility for the practical applications of YIG-based magnonic devices and provides promising insights for the theoretical understanding and the experimental enhancement of PMA in garnet films.

Wearable fiber-free optical sensor for continuous monitoring of neonatal cerebral blood flow and oxygenation.

BACKGROUND: Unstable cerebral hemodynamics places preterm infants at high risk of brain injury. We adapted an innovative, fiber-free, wearable diffuse speckle contrast flow-oximetry (DSCFO) device for continuous monitoring of both cerebral blood flow (CBF) and oxygenation in neonatal piglets and preterm infants. METHODS: DSCFO uses two small laser diodes as focused-point and a tiny CMOS camera as a high-density two-dimensional detector to detect spontaneous spatial fluctuation of diffuse laser speckles for CBF measurement, and light intensity attenuations for cerebral oxygenation measurement. The DSCFO was first validated against the established diffuse correlation spectroscopy (DCS) in neonatal piglets and then utilized for continuous CBF and oxygenation monitoring in preterm infants during intermittent hypoxemia (IH) events. RESULTS: Significant correlations between the DSCFO and DCS measurements of CBF variations in neonatal piglets were observed. IH events induced fluctuations in CBF, cerebral oxygenation, and peripheral cardiorespiratory vitals in preterm infants. However, no consistent correlation patterns were observed among peripheral and cerebral monitoring parameters. CONCLUSIONS: This pilot study demonstrated the feasibility of DSCFO technology to serve as a low-cost wearable sensor for continuous monitoring of multiple cerebral hemodynamic parameters. The results suggested the importance of multi-parameter measurements for understanding deep insights of peripheral and cerebral regulations. IMPACT: The innovative DSCFO technology may serve as a low-cost wearable sensor for continuous bedside monitoring of multiple cerebral hemodynamic parameters in neonatal intensive care units. Concurrent DSCFO and DCS measurements of CBF variations in neonatal piglet models generated consistent results. No consistent correlation patterns were observed among peripheral and cerebral monitoring parameters in preterm neonates, suggesting the importance of multi-parameter measurements for understanding deep insights of peripheral and cerebral regulations during IH events. Integrating and correlating multiple cerebral functional parameters with clinical outcomes may identify biomarkers for prediction and management of IH associated brain injury.

The impact of intermittent hypoxemia on type 1 retinopathy of prematurity in preterm infants.

BACKGROUND: Intermittent hypoxemia (IH) may influence retinopathy of prematurity (ROP) development in preterm infants, however, previous studies had mixed results. This study tests the hypothesis that increased IH is associated with Type 1 ROP; a stage beyond which treatment is indicated. METHODS: IH was quantified by continuously monitoring oxygen saturation (SpO2) using high-resolution pulse oximeters during the first 10 weeks of life. Statistical analyses assessed the relationship and predictive ability of weekly and cumulative IH for Type 1 ROP development. RESULTS: Most analyses showed no association between IH and Type 1 ROP adjusting for gestational age (GA) and birth weight (BW). However, cumulative IH of longer duration during weeks 5-10, 6-10, and 7-10 were significantly associated with Type 1 ROP adjusting for GA and BW, e.g., the adjusted odds ratio of Type 1 ROP was 2.01 (p = 0.03) for every 3.8 seconds increase in IH duration from week 6-10. IH did not provide statistically significant added predictive ability above GA and BW. CONCLUSIONS: For most analyses there was no significant association between IH and Type 1 ROP adjusting for GA and BW. However, infants with longer IH duration during the second month of life had higher risk for Type 1 ROP. IMPACT: The relationship and predictive ability of intermittent hypoxemia (IH) on retinopathy of prematurity (ROP) is controversial. This study shows no significant association between IH events and Type 1 ROP after adjusting for gestational age (GA) and birth weight (BW), except for cumulative IH of longer duration in the second month of life. In this cohort, IH does not provide a statistically significant improvement in ROP prediction over GA and BW. This study is the first to assess the cumulative impact of IH measures on Type 1 ROP. Interventions for reducing IH duration during critical postnatal periods may improve ROP outcomes.

All-Electrical 9-Bit Skyrmion-Based Racetrack Memory Designed with Laser Irradiation.

Racetrack memories with magnetic skyrmions have recently been proposed as a promising storage technology. To be appealing, several challenges must still be faced for the deterministic generation of skyrmions, their high-fidelity transfer, and accurate reading. Here, we realize the first proof-of-concept of a 9-bit skyrmion racetrack memory with all-electrical controllable functionalities implemented in the same device. The key ingredient is the generation of a tailored nonuniform distribution of magnetic anisotropy via laser irradiation in order to (i) create a well-defined skyrmion nucleation center, (ii) define the memory cells hosting the information coded as the presence/absence of skyrmions, and (iii) improve the signal-to-noise ratio of anomalous Hall resistance measurements. This work introduces a strategy to unify previous findings and predictions for the development of a generation of racetrack memories with robust control of skyrmion nucleation and position, as well as effective skyrmion electrical detection.

An Ultrathin Flexible Programmable Spin Logic Device Based on Spin-Orbit Torque.

Flexible electronic devices have shown increasingly promising value facilitating our daily lives. However, flexible spintronic devices remain in their infancy. Here, this research demonstrates a type of nonvolatile, low power dissipation, and programmable flexible spin logic device, which is based on the spin-orbit torque in polyimide (PI)/Ta/Pt/Co/Pt heterostructures fabricated via capillary-assisted electrochemical delamination. The magnetization switching ratio is shown to be about 50% for the flexible device and does not change after 100 cycles of bending, indicating the device has stable performance. By designing the path of pulse current, five Boolean logic gates AND, NAND, NOT, NOR, and OR can be realized in an integrated two-element device. Moreover, such peeling-off devices can be successfully transferred to almost any substrate, such as paper and human skin, and maintain high performance. The flexible PI/Ta/Pt/Co/Pt spin logic device serves as logic-in-memory architecture and can be used in wearable electronics.

Evolution of Emergent Monopoles into Magnetic Skyrmion Strings.

Topological defects are fundamental concepts in physics, but little is known about the transition between distinct types across different dimensionalities. In topological magnetism, as in field theory, the transition between 1D strings and 0D monopoles is a key process whose observation has remained elusive. Here, we introduce a novel mechanism that allows for the controlled stabilization of emergent monopoles and show that magnetic skyrmion strings can be folded into monopoles. Conversely, they act as seeds out of which the entire string structure can unfold, containing its complete information. In chiral magnets, this process can be observed by resonant elastic X-ray scattering when the objects are in proximity to a polarized ferromagnet, whereby a pure monopole lattice is emerging on the surface. Our experimental proof of the reversible evolution from monopole to string sheds new light on topological defects and establishes the emergent monopole lattice as a new 3D topological phase.

Observation of the Fluctuation Spin Hall Effect in a Low-Resistivity Antiferromagnet.

The spin Hall effect (SHE) can generate a pure spin current by an electric current, which is promisingly used to electrically control magnetization. To reduce the power consumption of this control, a giant spin Hall angle (SHA) in the SHE is desired in low-resistivity systems for practical applications. Here, critical spin fluctuation near the antiferromagnetic (AFM) phase transition in chromium (Cr) is proven to be an effective mechanism for creating an additional part of the SHE, named the fluctuation spin Hall effect. The SHA is significantly enhanced when the temperature approaches the Néel temperature (TN) of Cr and has a peak value of -0.36 near TN. This value is higher than the room-temperature value by 153% and leads to a low normalized power consumption among known spin-orbit torque materials. This study demonstrates the critical spin fluctuation as a prospective way to increase the SHA and enriches the AFM material candidates for spin-orbitronic devices.

Deterministic Magnetization Switching via Tunable Noncollinear Spin Configurations in Canted Magnets.

Spin obit torque (SOT) driven magnetization switching has been used widely for encoding consumption-efficient memory and logic. However, symmetry breaking under a magnetic field is required to realize the deterministic switching in synthetic antiferromagnets with perpendicular magnetic anisotropy (PMA), which limits their potential applications. Herein, we report all electric-controlled magnetization switching in the antiferromagnetic Co/Ir/Co trilayers with vertical magnetic imbalance. Besides, the switching polarity could be reversed by optimizing the Ir thickness. By using the polarized neutron reflection (PNR) measurements, the canted noncollinear spin configuration was observed in Co/Ir/Co trilayers, which results from the competition of magnetic inhomogeneity. In addition, the asymmetric domain walls demonstrated by micromagnetic simulations result from introducing imbalance magnetism, leading to the deterministic magnetization switching in Co/Ir/Co trilayers. Our findings highlight a promising route to electric-controlled magnetism via tunable spin configuration, improve our understanding of physical mechanisms, and significantly promote industrial applications in spintronic devices.

swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution.

MOTIVATION: Complex biological tissues are often a heterogeneous mixture of several molecularly distinct cell subtypes. Both subtype compositions and subtype-specific (STS) expressions can vary across biological conditions. Computational deconvolution aims to dissect patterns of bulk tissue data into subtype compositions and STS expressions. Existing deconvolution methods can only estimate averaged STS expressions in a population, while many downstream analyses such as inferring co-expression networks in particular subtypes require subtype expression estimates in individual samples. However, individual-level deconvolution is a mathematically underdetermined problem because there are more variables than observations. RESULTS: We report a sample-wise Convex Analysis of Mixtures (swCAM) method that can estimate subtype proportions and STS expressions in individual samples from bulk tissue transcriptomes. We extend our previous CAM framework to include a new term accounting for between-sample variations and formulate swCAM as a nuclear-norm and ℓ2,1-norm regularized matrix factorization problem. We determine hyperparameter values using cross-validation with random entry exclusion and obtain a swCAM solution using an efficient alternating direction method of multipliers. Experimental results on realistic simulation data show that swCAM can accurately estimate STS expressions in individual samples and successfully extract co-expression networks in particular subtypes that are otherwise unobtainable using bulk data. In two real-world applications, swCAM analysis of bulk RNASeq data from brain tissue of cases and controls with bipolar disorder or Alzheimer's disease identified significant changes in cell proportion, expression pattern and co-expression module in patient neurons. Comparative evaluation of swCAM versus peer methods is also provided. AVAILABILITY AND IMPLEMENTATION: The R Scripts of swCAM are freely available at https://github.com/Lululuella/swCAM. A user's guide and a vignette are provided. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Activities of Family 18 Chitinases on Amorphous Regenerated Chitin Thin Films and Dissolved Chitin Oligosaccharides: Comparison with Family 19 Chitinases.

Changes in mass and viscoelasticity of chitin layers in fungal cell walls during chitinase attack are vital for understanding bacterial invasion of and human defense against fungi. In this work, regenerated chitin (RChitin) thin films mimicked the fungal chitin layers and facilitated studies of degradation by family 18 chitinases from Trichoderma viride (T. viride) and family 19 chitinases from Streptomyces griseus (S. griseus) that possessed chitin-binding domains (CBDs) that were absent in the family 18 chitinases. Degradation was monitored via a quartz crystal microbalance with dissipation monitoring (QCM-D) in real time at various pH and temperatures. Compared to substrates of colloidal chitin or dissolved chitin derivatives and analogues, the degradation of RChitin films was deeply affected by chitinase adsorption. While the family 18 chitinases had greater solution activity on chitin oligosaccharides, the family 19 chitinases exhibited greater surface activity on RChitin films, illustrating the importance of CBDs for insoluble substrates.

Axially Bound Magnetic Skyrmions: Glueing Topological Strings Across an Interface.

A major challenge in topological magnetism lies in the three-dimensional (3D) exploration of their magnetic textures. A recent focus has been the question of how 2D skyrmion sheets vertically stack to form distinct types of 3D topological strings. Being able to manipulate the vertical coupling should therefore provide a route to the engineering of topological states. Here, we present a new type of axially bound magnetic skyrmion string state in which the strings in two distinct materials are glued together across their interface. With quasi-tomographic resonant elastic X-ray scattering, the 3D skyrmion profiles before and after their binding across the interface were unambiguously determined and compared. Their attractive binding is accompanied by repulsive twisting; i.e., the coupled skyrmions mutually affect each other via a compensating twisting. This state exists in chiral magnet-magnetic thin film heterostructures, providing a new arena for the engineering of 3D topological phases.

Field-Free Spin-Orbit Torque Switching Enabled by the Interlayer Dzyaloshinskii-Moriya Interaction.

Perpendicularly magnetized structures that are switchable using a spin current under field-free conditions can potentially be applied in spin-orbit torque magnetic random-access memory (SOT-MRAM). Several structures have been developed; however, new structures with a simple stack structure and MRAM compatibility are urgently needed. Herein, a typical structure in a perpendicular spin-transfer torque MRAM, the Pt/Co multilayer and its synthetic antiferromagnetic counterpart with perpendicular magnetic anisotropy, was observed to possess an intrinsic interlayer chiral interaction between neighboring magnetic layers, namely, the interlayer Dzyaloshinskii-Moriya interaction (DMI) effect. Furthermore, using a current parallel to the eigenvector of the interlayer DMI, we switched the perpendicular magnetization of both structures without a magnetic field, owing to the additional symmetry breaking introduced by the interlayer DMI. This SOT switching scheme realized in the Pt/Co multilayer and its synthetic antiferromagnet structure may open a new avenue toward practical perpendicular SOT-MRAM and other SOT devices.

Astroglial dysfunctions drive aberrant synaptogenesis and social behavioral deficits in mice with neonatal exposure to lengthy general anesthesia.

Lengthy use of general anesthetics (GAs) causes neurobehavioral deficits in the developing brain, which has raised significant clinical concerns such that the United States Food and Drug Administration (FDA) is warning on the use of GAs in children younger than 3 years. However, the molecular and cellular mechanisms for GAs-induced neurotoxicity remain largely unknown. Here, we report that sevoflurane (Sevo), a commonly used GA in pediatrics, caused compromised astrocyte morphogenesis spatiotemporally correlated to synaptic overgrowth, with reduced synaptic function in developing cortex in a regional-, exposure-length-, and age-specific manner. Sevo disrupted astrocyte Ca2+ homeostasis both acutely and chronically, which led to the down-regulation of Ezrin, an actin-binding membrane-bound protein, which we found was critically involved in astrocyte morphogenesis in vivo. Importantly, overexpression of astrocyte Ezrin rescued astrocytic and neuronal dysfunctions and fully corrected deficits in social behaviors in developing mice with lengthy Sevo exposure. Our data uncover that, in addition to neurons, astrocytes may represent important targets for GAs to exert toxic effects and that astrocyte morphological integrity is crucial for synaptogenesis and neurological behaviors.