Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but does not capture their spatial distribution nor reveal local networks of intercellular communication acting in ...situ. A suite of recently developed techniques that localize RNA within tissue, including multiplexed in situ hybridization and in situ sequencing (here defined as high-plex RNA imaging) and spatial barcoding, can help address this issue. However, no method currently provides as complete a scope of the transcriptome as does scRNA-seq, underscoring the need for approaches to integrate single-cell and spatial data. Here, we review efforts to integrate scRNA-seq with spatial transcriptomics, including emerging integrative computational methods, and propose ways to effectively combine current methodologies.
Nanometer‐sized rutile shows much higher electroactivity towards Li insertion than micrometer‐sized rutile. Up to 0.8 mol of Li per mole of TiO2 can be inserted into nanometer‐sized rutile at room ...temperature (see figure), which is able to reversibly accommodate Li up to Li0.5TiO2 with excellent capacity retention and high rate capability on cycling, rendering it a promising anode material for high‐power lithium‐ion batteries.
An optimized nanostructure design of electrode material for high power, high energy lithium batteries is realized. Highly Li‐permeable materials are obtained by introducing hierarchical mixed ...conducting networks on both nanoscale and microscale levels (see figure). A mesoporous TiO2:RuO2 composite is selected as an example of this new design.
The charge-neutral exciton has been predicted to carry genuine photocurrent due to the geometric Berry phase of the electronic bands, if the inversion symmetry in a crystal is broken. We detect such ...exciton shift current in a prototypical polar semiconductor CdS by using terahertz emission spectroscopy. A distinct peak emerges in the photocurrent spectra at the energy of the exciton resonance, which is demonstrated to result from the distinct displacements of electrons and holes in real space within the excitons to produce a finite transient charge current at subpicosecond time scale. Our findings elucidate the Berry phase physics of the charge-neutral photoexcitations and also shed light on the novel energy harvesting mechanism by exciton generation.
Summary
Background
Serum vitamin D levels are associated with bone complications in patients with primary biliary cirrhosis (PBC). Increasing evidence suggests a nonskeletal role of vitamin D in ...various autoimmune and liver diseases.
Aim
To investigate the clinical relevance of vitamin D levels in PBC, especially their association with the therapeutic effects of ursodeoxycholic acid (UDCA).
Methods
Consecutive PBC patients were retrospectively reviewed. 25‐hydroxyvitamin D 25(OH)D levels were determined in frozen serum samples collected before initiation of UDCA treatment. Response to UDCA was evaluated by Paris‐I and Barcelona criteria. Logistic regressions were performed to identify the treatment response‐associated parameters.
Results
Among 98 patients, the mean serum 25(OH)D concentration was 17.9 ± 7.6 ng/mL. 25(OH)D levels decreased with increasing histological stage (P = 0.029) and were negatively correlated with bilirubin and alkaline phosphatase levels. After 1 year of UDCA therapy, 31 patients failed to achieve complete response according to Paris‐I criteria. The baseline 25(OH)D level was significantly lower in nonresponders (14.8 ± 6.4 vs. 19.3 ± 7.6 ng/mL, P = 0.005). Vitamin D deficiency at baseline was associated with an increased risk of incomplete response independent of advanced stages (OR = 3.93, 95% CI = 1.02–15.19, P = 0.047). Similar results were obtained when biochemical response was evaluated by Barcelona criteria. Furthermore, 25(OH)D levels were lower in patients who subsequently suffered death or liver transplantation (12.1 ± 4.6 vs. 18.4 ± 7.6 ng/mL, P = 0.023).
Conclusions
25(OH)D level is associated with biochemical and histological features in PBC. Pre‐treatment vitamin D status is independently related to subsequent response to UDCA. Our results suggest that vitamin D status may have important clinical significance in PBC.
The biexciton cascade process in self-assembled quantum dots (QDs) provides an ideal system for realizing deterministic entangled photon-pair sources, which are essential to quantum information ...science. The entangled photon pairs have recently been generated in experiments after eliminating the fine-structure splitting (FSS) of excitons using a number of different methods. Thus far, however, QD-based sources of entangled photons have not been scalable because the wavelengths of QDs differ from dot to dot. Here, we propose a wavelength-tunable entangled photon emitter mounted on a three-dimensional stressor, in which the FSS and exciton energy can be tuned independently, thereby enabling photon entanglement between dissimilar QDs. We confirm these results via atomistic pseudopotential calculations. This provides a first step towards future realization of scalable entangled photon generators for quantum information applications.
To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and multiplexed ion beam imaging ...from a series of human cSCCs and matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating normal epidermal states, and a tumor-specific keratinocyte (TSK) population unique to cancer, which localized to a fibrovascular niche. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing TSK cells as a hub for intercellular communication. Multiple features of potential immunosuppression were observed, including T regulatory cell (Treg) co-localization with CD8 T cells in compartmentalized tumor stroma. Finally, single-cell characterization of human tumor xenografts and in vivo CRISPR screens identified essential roles for specific tumor subpopulation-enriched gene networks in tumorigenesis. These data define cSCC tumor and stromal cell subpopulations, the spatial niches where they interact, and the communicating gene networks that they engage in cancer.
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•Profiling of 10 human skin SCCs and matched normals via scRNA-seq, ST, and MIBI•Tumor-specific keratinocytes (TSKs) reside within a fibrovascular niche at leading edges•Distinct ligand-receptor and spatial niche associations for tumor and stromal cells.•Subpopulation essential tumorigenic gene networks defined by in vivo CRISPR screening
Integration of high-dimensional multi-omics approaches to characterize human cutaneous squamous cell carcinoma identifies a tumor-specific keratinocyte population as well as the immune infiltrates and heterogeneity at tumor leading edges.
Viral proteins localize within subcellular compartments to subvert host machinery and promote pathogenesis. To study SARS-CoV-2 biology, we generated an atlas of 2422 human proteins vicinal to 17 ...SARS-CoV-2 viral proteins using proximity proteomics. This identified viral proteins at specific intracellular locations, such as association of accessary proteins with intracellular membranes, and projected SARS-CoV-2 impacts on innate immune signaling, ER-Golgi transport, and protein translation. It identified viral protein adjacency to specific host proteins whose regulatory variants are linked to COVID-19 severity, including the TRIM4 interferon signaling regulator which was found proximal to the SARS-CoV-2 M protein. Viral NSP1 protein adjacency to the EIF3 complex was associated with inhibited host protein translation whereas ORF6 localization with MAVS was associated with inhibited RIG-I 2CARD-mediated IFNB1 promoter activation. Quantitative proteomics identified candidate host targets for the NSP5 protease, with specific functional cleavage sequences in host proteins CWC22 and FANCD2. This data resource identifies host factors proximal to viral proteins in living human cells and nominates pathogenic mechanisms employed by SARS-CoV-2.
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