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Visualizing spatial assay data in anatomical images is vital for understanding biological processes in cell, tissue, and organ organizations. Technologies requiring this functionality include traditional one-at-a-time assays, and bulk and single-cell omics experiments, including RNA-seq and proteomics. The spatialHeatmap software provides a series of powerful new methods for these needs, and allows users to work with adequately formatted anatomical images from public collections or custom images. It colors the spatial features (e.g. tissues) annotated in the images according to the measured or predicted abundance levels of biomolecules (e.g. mRNAs) using a color key. This core functionality of the package is called a spatial heatmap plot. Single-cell data can be co-visualized in composite plots that combine spatial heatmaps with embedding plots of high-dimensional data. The resulting spatial context information is essential for gaining insights into the tissue-level organization of single-cell data, or vice versa. Additional core functionalities include the automated identification of biomolecules with spatially selective abundance patterns and clusters of biomolecules sharing similar abundance profiles. To appeal to both non-expert and computational users, spatialHeatmap provides a graphical and a command-line interface, respectively. It is distributed as a free, open-source Bioconductor package (https://bioconductor.org/packages/spatialHeatmap) that users can install on personal computers, shared servers, or cloud systems.

 

Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genusAsparagus(Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking.

We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genusAsparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature.

We estimate that dioecy evolved once or twice approximately 2.78−3.78 million years ago inAsparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers.

Our findings support previous work implicating a young age and the possibility of two origins of dioecy inAsparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy inAsparagusapproximately 2.78−3.78 million years ago.

 

The superior size and power scaling potential of ferroelectric-gated Mott transistors makes them promising building blocks for developing energy-efficient memory and logic applications in the post-Moore’s Law era. The close to metallic carrier density in the Mott channel, however, imposes the bottleneck for achieving substantial field effect modulation via a solid-state gate. Previous studies have focused on optimizing the thickness, charge mobility, and carrier density of single-layer correlated channels, which have only led to moderate resistance switching at room temperature. Here, we report a record high nonvolatile resistance switching ratio of 38,440% at 300 K in a prototype Mott transistor consisting of a ferroelectric PbZr_0.2Ti_0.8O₃gate and anRNiO₃(R: rare earth)/La_0.67Sr_0.33MnO₃composite channel. The ultrathin La_0.67Sr_0.33MnO₃buffer layer not only tailors the carrier density profile inRNiO₃through interfacial charge transfer, as corroborated by first-principles calculations, but also provides an extended screening layer that reduces the depolarization effect in the ferroelectric gate. Our study points to an effective material strategy for the functional design of complex oxide heterointerfaces that harnesses the competing roles of charge in field effect screening and ferroelectric depolarization effects.

 

Abstract Due to commonalities in pathophysiology, age-related macular degeneration (AMD) represents a uniquely accessible model to investigate therapies for neurodegenerative diseases, leading us to examine whether pathways of disease progression are shared across neurodegenerative conditions. Here we use single-nucleus RNA sequencing to profile lesions from 11 postmortem human retinas with age-related macular degeneration and 6 control retinas with no history of retinal disease. We create a machine-learning pipeline based on recent advances in data geometry and topology and identify activated glial populations enriched in the early phase of disease. Examining single-cell data from Alzheimer’s disease and progressive multiple sclerosis with our pipeline, we find a similar glial activation profile enriched in the early phase of these neurodegenerative diseases. In late-stage age-related macular degeneration, we identify a microglia-to-astrocyte signaling axis mediated by interleukin-1 β which drives angiogenesis characteristic of disease pathogenesis. We validated this mechanism using in vitro and in vivo assays in mouse, identifying a possible new therapeutic target for AMD and possibly other neurodegenerative conditions. Thus, due to shared glial states, the retina provides a potential system for investigating therapeutic approaches in neurodegenerative diseases. 

The development of single-cell RNA-sequencing (scRNA-seq) technologies has offered insights into complex biological systems at the single-cell resolution. In particular, these techniques facilitate the identifications of genes showing cell-type-specific differential expressions (DE). In this paper, we introduce MARBLES, a novel statistical model for cross-condition DE gene detection from scRNA-seq data. MARBLES employs a Markov Random Field model to borrow information across similar cell types and utilizes cell-type-specific pseudobulk count to account for sample-level variability. Our simulation results showed that MARBLES is more powerful than existing methods to detect DE genes with an appropriate control of false positive rate. Applications of MARBLES to real data identified novel disease-related DE genes and biological pathways from both a single-cell lipopolysaccharide mouse dataset with 24 381 cells and 11 076 genes and a Parkinson’s disease human data set with 76 212 cells and 15 891 genes. Overall, MARBLES is a powerful tool to identify cell-type-specific DE genes across conditions from scRNA-seq data.

 

Abstract. Coupled physical–biogeochemical models can fill thespatial and temporal gap in ocean carbon observations. Challenges ofapplying a coupled physical–biogeochemical model in the regional oceaninclude the reasonable prescription of carbon model boundary conditions,lack of in situ observations, and the oversimplification of certainbiogeochemical processes. In this study, we applied a coupledphysical–biogeochemical model (Regional Ocean Modelling System, ROMS) to theGulf of Mexico (GoM) and achieved an unprecedented 20-year high-resolution(5 km, 1/22∘) hindcast covering the period of 2000 to 2019. Thebiogeochemical model incorporated the dynamics of dissolved organic carbon(DOC) pools and the formation and dissolution of carbonate minerals. Thebiogeochemical boundaries were interpolated from NCAR's CESM2-WACCM-FV2solution after evaluating the performance of 17 GCMs in the GoM waters. Modeloutputs included carbon system variables of wide interest, such aspCO2, pH, aragonite saturation state (ΩArag), calcitesaturation state (ΩCalc), CO2 air–sea flux, and carbon burialrate. The model's robustness is evaluated via extensive model–datacomparison against buoys, remote-sensing-based machine learning (ML)products, and ship-based measurements. A reassessment of air–sea CO2flux with previous modeling and observational studies gives us confidencethat our model provides a robust and updated CO2 flux estimation, andNGoM is a stronger carbon sink than previously reported. Model resultsreveal that the GoM water has been experiencing a ∼ 0.0016 yr−1 decrease in surface pH over the past 2 decades, accompanied by a∼ 1.66 µatm yr−1 increase in sea surfacepCO2. The air–sea CO2 exchange estimation confirms in accordance with severalprevious models and ocean surface pCO2 observations that theriver-dominated northern GoM (NGoM) is a substantial carbon sink, and theopen GoM is a carbon source during summer and a carbon sink for the rest ofthe year. Sensitivity experiments are conducted to evaluate the impacts ofriver inputs and the global ocean via model boundaries. The NGoM carbonsystem is directly modified by the enormous carbon inputs (∼ 15.5 Tg C yr−1 DIC and ∼ 2.3 Tg C yr−1 DOC) from theMississippi–Atchafalaya River System (MARS). Additionally,nutrient-stimulated biological activities create a ∼ 105 timeshigher particulate organic matter burial rate in NGoM sediment than in thecase without river-delivered nutrients. The carbon system condition of theopen ocean is driven by inputs from the Caribbean Sea via the Yucatan Channeland is affected more by thermal effects than biological factors. 

The palette of applications for bipolar membranes (BPMs) has expanded recently beyond electrodialysis as they are now being considered for fuel cell and electrolysis applications. Their deployment in emerging electrochemical technologies arises from the need to have a membrane separator that provides disparate pH environments and to prevent species crossover. Most materials research for BPMs has focused on water dissociation catalysts and less emphasis has been given to the design of the polycation–polyanion interface for improving BPM performance. Here, soft lithography fabricated a series of micropatterned BPMs with precise control over the interfacial area in the bipolar junction. Polarization experiments showed that a 2.28× increase in interfacial area led to a 250 mV reduction in the onset potential. Additionally, the same increase in interfacial area yielded marginal improvements in current density due to the junction region being under kinetics-diffusion control. A simple physics model based on the electric field of the junction region rationalized the reduction in the overpotential for water dissociation as a function of interfacial area. Finally, the soft lithography approach was also conducive for fabricating BPMs with different chemistries ranging from perfluorinated polymer backbones to alkaline stable poly(arylene) hydrocarbon polymers. These polymer chemistries are better suited for fuel cell and electrolysis applications. The BPM featuring the alkaline stable poly(terphenyl) anion exchange membrane had an onset potential of 0.84 V, which was near the thermodynamic limit, and was about 150 mV lower than a commercially available variant. 

In this review, an attempt has been made to compare the electronic structures of various 5d iridates (iridium oxides), with an effort to note the common features and differences. Both experimental studies, especially angle-resolved photoemission spectroscopy (ARPES) results, and first-principles band structure calculations have been discussed. This brings to focus the fact that the electronic structures and magnetic properties of the high- Z 5d transition iridates depend on the intricate interplay of strong electron correlation, strong (relativistic) spin–orbit coupling, lattice distortion, and the dimensionality of the system. For example, in the thin film limit, SrIrO 3 exhibits a metal–insulator transition that corresponds to the dimensionality crossover, with the band structure resembling that of bulk Sr 2 IrO 4 .