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. Thus, a systematic analysis using transcriptomic data could offer novel insights into Drosophila hemocyte function and provide new perspectives on the evolution of the immune system. Here, we performed cross-species comparative analyses using single-cell RNA sequencing data from Drosophila and vertebrate immune cells. We found several conserved markers for the cluster of differentiation (CD) genes in Drosophila hemocytes and validated the role of CG8501 (CD59) in phagocytosis by plasmatocytes, which function much like macrophages in vertebrates. By comparing whole transcriptome profiles in both supervised and unsupervised analyses, we showed that Drosophila hemocytes are largely homologous to vertebrate myeloid cells, especially plasmatocytes to monocytes/macrophages and prohemocyte 1 (PH1) to hematopoietic stem cells. Furthermore, a small subset of prohemocytes with hematopoietic potential displayed homology with hematopoietic progenitor populations in vertebrates. Overall, our results provide a deeper understanding of molecular conservation in the Drosophila immune system.

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. By normalizing gene expression variances to identify universally variable genes (UVGs), we were able to reduce the formation of sample-specific clusters and identify underlying molecular hallmarks in malignant cells. In contrast to highly variable genes vulnerable to a specific sample bias, UVGs led to better detection of clusters corresponding to distinct malignant cell states. Our results demonstrate the utility of this approach for analyzing scRNA-seq data and suggest avenues for further exploration of malignant cell heterogeneity.

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. Single-cell RNA-sequencing (scRNA-seq) is a potential solution for tackling this limitation despite the lack of annotations for low abundance yet cell type-specific lncRNAs. Hence, updated annotations and further understanding of the cellular expression of lncRNAs will be necessary for characterizing cell type-specific functions of lncRNA genes in the TIME. In this review, we discuss lncRNAs that are specifically expressed in tumor and immune cells, summarize the regulatory functions of the lncRNAs at the cell type level and highlight how a scRNA-seq approach can help to study the cell type-specific functions of TIME lncRNAs.

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. However, conventional flat mirrors cannot customize the radiative decay landscape in TMDC's plane or support vacuum-field interference with desired spectrum and polarization properties. Here, we present a meta-mirror platform resolving the issues with more optical degrees of freedom. For neutral excitons of the monolayer MoSe2, the optical layout formed by meta-mirrors manipulated the radiative decay rate in space by 2 orders of magnitude and revealed the statistical correlation between emission intensity and spectral line width. Moreover, the anisotropic meta-mirror demonstrated polarization-dependent radiative decay control. Our platform would be promising to tailor two-dimensional distributions of lifetime, density, diffusion, and polarization of TMDC excitons in advanced opto-excitonic 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. The electrical and optical measurements indicate that synthesized γ-GeSe exhibits high electrical conductivity of 3 × 105 S/m, which is comparable to those of other two-dimensional layered semimetallic crystals. Moreover, γ-GeSe can be directly grown on h-BN substrates, demonstrating a bottom-up approach for constructing vertical van der Waals heterostructures incorporating γ-GeSe. The newly identified crystal symmetry of γ-GeSe warrants further studies on various physical properties of γ-GeSe.

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. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap 2.0, The Cancer Genome Atlas, and GTEx projects, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalog that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of noncoding genomes.

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. METHODS AND RESULTS: Single-cell RNA sequencing analysis of CD45+ leukocytes from murine atherosclerotic aorta revealed that there are macrophage subpopulations with distinct differentially expressed genes involved in various functional pathways. To specifically characterize the intimal foamy macrophages of plaque, we developed a lipid staining-based flow cytometric method for analyzing the lipid-laden foam cells of atherosclerotic aortas. We used the fluorescent lipid probe BODIPY493/503 and assessed side-scattered light as an indication of cellular granularity. BODIPYhiSSChi foamy macrophages were found residing in intima and expressing CD11c. Foamy macrophage accumulation determined by flow cytometry was positively correlated with the severity of atherosclerosis. Bulk RNA sequencing analysis showed that compared with nonfoamy macrophages, foamy macrophages expressed few inflammatory genes but many lipid-processing genes. Intimal nonfoamy macrophages formed the major population expressing IL (interleukin)-1ß and many other inflammatory transcripts in atherosclerotic aorta. CONCLUSIONS: RNA sequencing analysis of intimal macrophages from atherosclerotic aorta revealed that lipid-loaded plaque macrophages are not likely the plaque macrophages that drive lesional inflammation.

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. Therefore, this study aims to unlock the critical impeding factors in restraining the non-polarizing oxygen capacity of Li-excess layered oxides (herein, Li2RuO3) that exhibit reversible OR reactions. First, Li2RuO3 undergoes an increase in the chemical potential fluctuation as both the thermodynamic material instability and vacancy content increase. Second, the chemical compression of O-O bonds occurs at the early stage of the OR reaction (0.5 ≤ x ≤ 0.75) for Li1-xRu0.5O1.5, leading to flexible voltage hysteresis. Finally, in the range of 0.75 ≤ x ≤ 1.0, for Li1-xRu0.5O1.5, the formation of an O(2p)-O(2p)* antibonding state derived from the structural distortion of the RuO6 octahedron leads to the irreversibility of the OR reaction and enhanced voltage hysteresis. Consequently, our study unlocks the new decisive factor, namely, the structural distortion inducing the O(2p)-O(2p)* antibonding state, of the hysteretic oxygen capacity and provides insights into enabling the full potential of the OR reaction for Li-excess layered oxides for advanced LIBs.

Photoluminescence Path Bifurcations by Spin Flip in Two-Dimensional CrPS4.

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 Cr3+ ions. In this study, we report on the dual-band NIR photoluminescence (PL) of CrPS4 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). In essence, the PL bifurcations are governed by activated reverse intersystem crossing from the low- to high-spin states, and the transition barrier becomes lower for thinner 2D samples because of surface-localized defects. Our findings can be generalized to 2D solids of coordinated metals and will be valuable in realizing groundbreaking magneto-optic functions and devices.

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. In this study, by combining electrostatic control of chemical potentials with HHG measurement, we resolve quantum pathways of massless Dirac fermions in graphene under strong laser fields. Electrical modulation of HHG reveals quantum interference between the multi-photon interband excitation channels. As the light-matter interaction deviates beyond the perturbative regime, elliptically polarized laser fields efficiently drive massless Dirac fermions via an intricate coupling between the interband and intraband transitions, which is corroborated by our theoretical calculations. Our findings pave the way for strong-laser-field tomography of Dirac electrons in various quantum semimetals and their ultrafast electronics with a gate control.

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. Cell type-specific immune signatures dynamically shifted from premalignant stages to the late HCC stage. Total hepatectomy patients displayed elevated immune infiltration and prolonged disease-free survival compared to the partial hepatectomy patients. However, patients who exhibited an infiltration of regulatory T cells (Tregs) during the pretransplantation period displayed a high risk of tumor relapse with suppressed immune responses, and pretreatment was a potential driver of Treg infiltration in the total hepatectomy group. Treg infiltration appeared to be independent of molecular classifications based on transcriptomic data. Our study provides not only comprehensive immune signatures in adjacent nontumor lesions and early malignant HCC stages but also clinical guidance for HCC patients who will undergo liver transplantation.

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. However, electroluminescence from hBN has not been demonstrated at DUV frequencies so far. In this study, we report DUV electroluminescence and photocurrent generation in graphene/hBN/graphene heterostructures at room temperature. Tunneling carrier injection from graphene electrodes into the band edges of hBN enables prominent electroluminescence at DUV frequencies. On the other hand, under DUV laser illumination and external bias voltage, graphene electrodes efficiently collect photo-excited carriers in hBN, which generates high photocurrent. Laser excitation micro-spectroscopy shows that the radiative recombination and photocarrier excitation processes in the heterostructures mainly originate from the pristine structure and the stacking faults in hBN. Our work provides a pathway toward efficient DUV light emitting and detection devices based on hBN.

A single-cell survey of Drosophila blood.

Drosophila 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. Further, we discovered rare subsets within crystal cells and lamellocytes that express fibroblast growth factor (FGF) ligand branchless and receptor breathless, respectively. We demonstrate that these FGF components are required for mediating effective immune responses against parasitoid wasp eggs, highlighting a novel role for FGF signaling in inter-hemocyte crosstalk. Our scRNA-seq analysis reveals the diversity of hemocytes and provides a rich resource of gene expression profiles for a systems-level understanding of their functions.

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. Additionally, we identify the developmental trajectory of hemocytes during normal development as well as the emergence of the lamellocyte lineage following active cellular immunity caused by wasp infestation. Finally, we establish similarities and differences between embryonically derived- and larval lymph gland hemocytes. Altogether, our study provides detailed insights into the hemocyte development and cellular immune responses at single-cell resolution.

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. The objective of this study was to estimate the heritability of LV mass in Japanese families living in Hawaii. DESIGN AND METHODS: We analyzed data by components of variance in a sample of 169 hypertensive families (n = 476 subjects) and, separately, in a population-based sample of 256 families (n = 501 subjects) participating in the Honolulu Heart Program. RESULTS: In multivariate models, established predictors of LV mass explained about half the total variance of LV mass. Using SOLAR, our estimates of the narrow sense heritability of LV mass ranged from 42.5% (SE 9.8, P < 0.0001) in our sample of hypertensive families to 60.6% (SE 11.7, P < 0.0001) in our population-based sample of families. Parametric bootstrap analyses confirmed that the inference for each sample was appropriate. CONCLUSIONS: Assuming the absence of shared familial environmental effects, close to half of the unexplained variance of LV mass in Japanese subjects living in Hawaii is genetic in nature. This estimate was observed in two independent samples. Therefore, the pursuit of novel genetic determinants of LV mass through either whole genome or candidate gene association studies of this population may be worthwhile. Such studies are certainly feasible.

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. Defining data come from measurements that play major roles in medical practice. A precise statement of what the data are is in Section 1. Their family structures are described in detail. They concern levels of lipids and the results of an oral glucose tolerance test (OGTT). We apply GMVQ to residuals obtained from regressions of outcomes of an OGTT and lipids on functions of age and BMI that are inferred from the data. A bootstrap procedure developed for our family data supplemented by insights from other approaches leads us to believe that two clusters are appropriate for defining IR precisely. One cluster consists of women who are IR, and the other of women who seem not to be. Genes and other features are used to predict cluster membership. We argue that prediction with "main effects" is not satisfactory, but prediction that includes interactions may be.

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. This purified HcE recombinant protein was evaluated for their immunogenicity and protective efficacy in guinea pig. The survival rates of guinea pig immunized with HcE protein was significantly increased over that of JE vaccine. This result indicates helpful information for developing a subunit vaccine against JEV.

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 1.5 ug/kg remifentanil (R 1.5), or 2.0 ug/kg remifentanil (R 2). Before induction, IV midazolam 0.05 mg/kg was given for sedation. After glycoppylorate 5 ug/kg, thiopental 4.0 mg/kg was injected within 10 seconds and followed by remifentanil. Following check the unconsciousness, patients were received rocuronium 0.6 mg/kg and tracheal intubation were performed 90s later, and anesthesia was maintained with 2% sevoflurane in air/oxygen. Systolic arterial pressure (SAP), mean arterial pressure (MAP) and heart rate (HR) were measured at before induction of anesthesia (B), before, just after and at 1, and 3 minutes after tracheal intubation. RESULTS: SAP and HR were increased than B values in the three groups just after intubation (P < 0.05). The percentage increases of SAP and HR were 30% and 30% of B values, respectively, in R 1; 19% and 24% in R 1.5; 10% and 22% in R 2. There were significant differences between R 2 group and other two groups in SAP and HR (P < 0.05). CONCLUSIONS: In pediatric anesthesia, a bolus injection of 2 ug/kg remifentanil (R 2) was a dosage to attenuate the cardiovascular responses after intubation in pediatric patients.