Single-cell mapping of regulatory DNA:Protein interactions.

Gene expression is coordinated by a multitude of transcription factors (TFs), whose binding to the genome is directed through multiple interconnected epigenetic signals, including chromatin accessibility and histone modifications. These complex networks have been shown to be disrupted during aging, disease, and cancer. However, profiling these networks across diverse cell types and states has been limited due to the technical constraints of existing methods for mapping DNA:Protein interactions in single cells.

Molecular traces of Drosophila hemocytes reveal transcriptomic conservation with vertebrate myeloid cells.

Drosophila hemocytes serve as the primary defense system against harmful threats, allowing the animals to thrive. Hemocytes are often compared to vertebrate innate immune system cells due to the observed functional similarities between the two. However, the similarities have primarily been established based on a limited number of genes and their functional homologies.

Clustering malignant cell states using universally variable genes.

Single-cell RNA sequencing (scRNA-seq) has revealed important insights into the heterogeneity of malignant cells. However, sample-specific genomic alterations often confound such analysis, resulting in patient-specific clusters that are difficult to interpret. Here, we present a novel approach to address the issue.

Customizing Radiative Decay Dynamics of Two-Dimensional Excitons via Position- and Polarization-Dependent Vacuum-Field Interference.

Embodying bosonic and interactive characteristics in two-dimensional space, excitons in transition metal dichalcogenides (TMDCs) have garnered considerable attention. The utilization of the strong-correlation effects, long-range transport, and valley-dependent properties requires customizing exciton decay dynamics. Vacuum-field manipulation allows radiative decay engineering without disturbing intrinsic material properties.

Gate-tunable quantum pathways of high harmonic generation in graphene.

Under strong laser fields, electrons in solids radiate high-harmonic fields by travelling through quantum pathways in Bloch bands in the sub-laser-cycle timescales. Understanding these pathways in the momentum space through the high-harmonic radiation can enable an all-optical ultrafast probe to observe coherent lightwave-driven processes and measure electronic structures as recently demonstrated for semiconductors. However, such demonstration has been largely limited for semimetals because the absence of the bandgap hinders an experimental characterization of the exact pathways.

Photoluminescence Path Bifurcations by Spin Flip in Two-Dimensional CrPS.

Ultrathin layered crystals of coordinated chromium(III) are promising not only as two-dimensional (2D) magnets but also as 2D near-infrared (NIR) emitters due to long-range spin correlation and efficient transition between high- and low-spin excited states of Cr ions. In this study, we report on the dual-band NIR photoluminescence (PL) of CrPS and show that its excitonic emission bifurcates into fluorescence and phosphorescence depending on thickness, temperature, and defect density. In addition to the spectral branching, the biexponential decay of PL transients, also affected by the three factors, could be well described within a three-level kinetic model for Cr(III).

Importance of Chemical Distortion on the Hysteretic Oxygen Capacity in Li-Excess Layered Oxides.

Nonhysteretic redox capacity is a critical factor in achieving high energy density without energy loss during cycling for rechargeable battery electrodes, which has been considered a major challenge in oxygen redox (OR) for Li-excess layered oxide cathodes for lithium-ion batteries (LIBs). Until recently, transition metal migration into the Li metal layer and the formation of O-O dimers have been considered major factors affecting hysteretic oxygen capacity. However, Li-excess layered oxides, particularly Ru oxides, exhibit peculiar voltage hysteresis that cannot be sufficiently described by only these factors.

Tumor immune microenvironment lncRNAs.

Long non-coding ribonucleic acids (RNAs) (lncRNAs) are key players in tumorigenesis and immune responses. The nature of their cell type-specific gene expression and other functional evidence support the idea that lncRNAs have distinct cellular functions in the tumor immune microenvironment (TIME). To date, the majority of lncRNA studies have heavily relied on bulk RNA-sequencing data in which various cell types contribute to an averaged signal, limiting the discovery of cell type-specific lncRNA functions.

Deep-ultraviolet electroluminescence and photocurrent generation in graphene/hBN/graphene heterostructures.

Hexagonal boron nitride (hBN) is a van der Waals semiconductor with a wide bandgap of ~ 5.96 eV. Despite the indirect bandgap characteristics of hBN, charge carriers excited by high energy electrons or photons efficiently emit luminescence at deep-ultraviolet (DUV) frequencies via strong electron-phonon interaction, suggesting potential DUV light emitting device applications.

γ-GeSe: A New Hexagonal Polymorph from Group IV-VI Monochalcogenides.

The family of group IV-VI monochalcogenides has an atomically puckered layered structure, and their atomic bond configuration suggests the possibility for the realization of various polymorphs. Here, we report the synthesis of the first hexagonal polymorph from the family of group IV-VI monochalcogenides, which is conventionally orthorhombic. Recently predicted four-atomic-thick hexagonal GeSe, so-called γ-GeSe, is synthesized and clearly identified by complementary structural characterizations, including elemental analysis, electron diffraction, high-resolution transmission electron microscopy imaging, and polarized Raman spectroscopy.

Preoperative immune landscape predisposes adverse outcomes in hepatocellular carcinoma patients with liver transplantation.

Immune class in hepatocellular carcinoma (HCC) has been shown to possess immunogenic power; however, how preestablished immune landscapes in premalignant and early HCC stages impact the clinical outcomes of HCC patients remains unexplored. We sequenced bulk transcriptomes for 62 malignant tumor samples from a Korean HCC cohort in which 38 patients underwent total hepatectomy, as well as for 15 normal and 47 adjacent nontumor samples. Using in silico deconvolution of expression mixtures, 22 immune cell fractions for each sample were inferred, and validated with immune cell counting by immunohistochemistry.

Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila.

The Drosophila lymph gland, the larval hematopoietic organ comprised of prohemocytes and mature hemocytes, has been a valuable model for understanding mechanisms underlying hematopoiesis and immunity. Three types of mature hemocytes have been characterized in the lymph gland: plasmatocytes, lamellocytes, and crystal cells, which are analogous to vertebrate myeloid cells, yet molecular underpinnings of the lymph gland hemocytes have been less investigated. Here, we use single-cell RNA sequencing to comprehensively analyze heterogeneity of developing hemocytes in the lymph gland, and discover previously undescribed hemocyte types including adipohemocytes, stem-like prohemocytes, and intermediate prohemocytes.

A single-cell survey of blood.

blood cells, called hemocytes, are classified into plasmatocytes, crystal cells, and lamellocytes based on the expression of a few marker genes and cell morphologies, which are inadequate to classify the complete hemocyte repertoire. Here, we used single-cell RNA sequencing (scRNA-seq) to map hemocytes across different inflammatory conditions in larvae. We resolved plasmatocytes into different states based on the expression of genes involved in cell cycle, antimicrobial response, and metabolism together with the identification of intermediate states.

Transcriptome Analysis Reveals Nonfoamy Rather Than Foamy Plaque Macrophages Are Proinflammatory in Atherosclerotic Murine Models.

Rationale: Monocyte infiltration into the subintimal space and its intracellular lipid accumulation are the most prominent features of atherosclerosis. To understand the pathophysiology of atherosclerotic disease, we need to understand the characteristics of lipid-laden foamy macrophages in the subintimal space during atherosclerosis.

Objective: We sought to examine the transcriptomic profiles of foamy and nonfoamy macrophages isolated from atherosclerotic intima.

High-confidence coding and noncoding transcriptome maps.

The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps.

Insulin resistance: regression and clustering.

In this paper we try to define insulin resistance (IR) precisely for a group of Chinese women. Our definition deliberately does not depend upon body mass index (BMI) or age, although in other studies, with particular random effects models quite different from models used here, BMI accounts for a large part of the variability in IR. We accomplish our goal through application of Gauss mixture vector quantization (GMVQ), a technique for clustering that was developed for application to lossy data compression.

Immunogenicity of Japanese encephalitis virus envelope protein by Hyphantria cunea nuclear polyhedrosis virus vector in guinea pig.

Japanese encephalitis virus (JEV) is an important pathogen causing febrile syndrome, encephalitis, and death. Envelop (E) glycoprotein is the major target of inducing neutralizing antibodies and protective immunity in host. In this study, E glycoprotein of JEV was expressed in Spodoptera frugiperd 9 cells as a fusion protein containing a gX signal sequence of pseudorabies virus.

Dose of remifentanil for minimizing the cardiovascular changes to tracheal intubation in pediatric patients.

Background: The purpose of this study was to investigate a dosage of remifentanil for attenuating cardiovascular changes during anesthetic induction in pediatric anesthesia.

Methods: We examined the effect of remifentanil on the cardiovascular responses to intubation in 90 children ASA 1 patients, aged 4-15 years, randomly allocated to receive 1.0 ug/kg remifentanil as a bolus (R 1), or 1.

Heritability of left ventricular mass in Japanese families living in Hawaii: the SAPPHIRe Study.

Objective: Established determinants of left ventricular (LV) mass explain only a modest fraction of its variability. Family studies to date suggest that a proportion of the unexplained variability can be accounted for by additive polygenic effects. An estimate of this proportion has not been reported previously in an East Asian population.