Constructing lncRNA-miRNA-mRNA networks specific to individual cancer patients and finding prognostic biomarkers.

BACKGROUND: The competitive endogenous RNA (ceRNA) hypothesis suggests that microRNAs (miRNAs) mediate a regulatory relation between long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) which share similar miRNA response elements (MREs) to bind to the same miRNA. Since the ceRNA hypothesis was proposed, several studies have been conducted to construct a network of lncRNAs, miRNAs and mRNAs in cancer. However, most cancer-related ceRNA networks are intended for representing a general relation of RNAs in cancer rather than for a patient-specific relation. Due to the heterogeneous nature of cancer, lncRNA-miRNA-mRNA interactions can vary in different patients. RESULTS: We have developed a new method for constructing a ceRNA network of lncRNAs, miRNAs and mRNAs, which is specific to an individual cancer patient and for finding prognostic biomarkers consisting of lncRNA-miRNA-mRNA triplets. We tested our method on extensive data sets of three types of cancer (breast cancer, liver cancer, and lung cancer) and obtained potential prognostic lncRNA-miRNA-mRNA triplets for each type of cancer. CONCLUSIONS: Analysis of expression patterns of the RNAs involved in the triplets and survival rates of cancer patients revealed several interesting findings. First, even for the same cancer type, prognostic lncRNA-miRNA-mRNA triplets can be different depending on whether lncRNA and mRNA show opposite or similar expression patterns. Second, prognostic lncRNA-miRNA-mRNA triplets are often more predictive of survival rates than RNA pairs or individual RNAs. Our approach will be useful for constructing patient-specific lncRNA-miRNA-mRNA networks and for finding prognostic biomarkers from the networks.

Molecular incompatibility between pig CD200 and human CD200 receptor in in vitro xenogeneic immune responses.

Overexpression of human CD200 (hCD200) in porcine endothelial cells (PECs) has been reported to suppress xenogeneic immune responses of human macrophages against porcine endothelial cells. The current study aimed to address whether the above-mentioned beneficial effect of hCD200 is mediated by overcoming the molecular incompatibility between porcine CD200 (pCD200) and hCD200 receptor or simply by increasing the expression levels of CD200 without any molecular incompatibility across the two species. We overexpressed hCD200 or pCD200 using lentiviral vectors with V5 marker in porcine endothelial cells and compared their suppressive activity against U937-derived human macrophage-like cells (hMCs) and primary macrophages. In xenogeneic coculture of porcine endothelial cells and human macrophage-like cells or macrophages, hCD200-porcine endothelial cells suppressed phagocytosis and cytotoxicity of human macrophages to a greater extent than pCD200-porcine endothelial cells. Secretion of tumor necrosis factor-α, interleukin-1ß, and monocyte chemoattractant protein-1 from human macrophages and expression of M1 phenotypes (inducible nitric oxide synthase, dectin-1, and CD86) were also suppressed by hCD200 to a greater extent than pCD200. Furthermore, in signal transduction downstream of CD200 receptor, hCD200 induced Dok2 phosphorylation and suppressed IκB phosphorylation to a greater extent than pCD200. The above data supported the possibility of a significant molecular incompatibility between pCD200 and human CD200 receptor, suggesting that the beneficial effects of hCD200 overexpression in porcine endothelial cells could be mediated by overcoming the molecular incompatibility across the species barrier rather than by simple overexpression effects of CD200.

A phytosphingosine derivative mYG-II-6 inhibits histamine-mediated TRPV1 activation and MRGPRX2-dependent mast cell degranulation.

BACKGROUND: Phytosphingosine and its derivative are known for their skin-protective properties. While mYG-II-6, a phytosphingosine derivative, has shown anti-inflammatory and antipsoriatic effects, its potential antipruritic qualities have yet to be explored. This study aimed to investigate mYG-II-6's antipruritic properties. METHODS: The calcium imaging technique was employed to investigate the activity of ion channels and receptors. Mast cell degranulation was confirmed through the ß-hexosaminidase assay. Additionally, in silico molecular docking and an in vivo mouse scratching behavior test were utilized. RESULTS: Using HEK293T cells transfected with H1R and TRPV1, we examined the impact of mYG-II-6 on histamine-induced intracellular calcium rise, a key signal in itch-mediating sensory neurons. Pretreatment with mYG-II-6 significantly reduced histamine-induced calcium levels and inhibited TRPV1 activity, suggesting its role in blocking the calcium influx channel. Additionally, mYG-II-6 suppressed histamine-induced calcium increase in primary cultures of mouse dorsal root ganglia, indicating its potential antipruritic effect mediated by histamine. Interestingly, mYG-II-6 exhibited inhibitory effects on human MRGPRX2, a G protein-coupled receptor involved in IgE-independent mast cell degranulation. However, it did not inhibit mouse MrgprB2, the ortholog of human MRGPRX2. Molecular docking analysis revealed that mYG-II-6 selectively interacts with the binding pocket of MRGPRX2. Importantly, mYG-II-6 suppressed histamine-induced scratching behaviors in mice. CONCLUSIONS: Our findings show that mYG-II-6 can alleviate histamine-induced itch sensation through dual mechanisms. This underscores its potential as a versatile treatment for various pruritic conditions.

Interleukin-2/anti-interleukin-2 immune complex attenuates cold ischemia-reperfusion injury after kidney transplantation by increasing renal regulatory T cells.

BACKGROUND: Cold ischemia-reperfusion injury (IRI) is an unavoidable complication of kidney transplantation. We investigated the role of regulatory T cells (Treg) in cold IRI and whether the interleukin (IL)-2/anti-IL-2 antibody complex (IL-2C) can ameliorate cold IRI. METHODS: We developed a cold IRI mouse model using kidney transplantation and analyzed the IL-2C impact on cold IRI in acute, subacute and chronic phases. RESULTS: Treg transfer attenuated cold IRI, while Treg depletion aggravated cold IRI. Next, IL-2C administration prior to IRI mitigated acute renal function decline, renal tissue damage and apoptosis and inhibited infiltration of effector cells into kidneys and pro-inflammatory cytokine expression on day 1 after IRI. On day 7 after IRI, IL-2C promoted renal regeneration and reduced subacute renal damage. Furthermore, on day 28 following IRI, IL-2C inhibited chronic fibrosis. IL-2C decreased reactive oxygen species-mediated injury and improved antioxidant function. When IL-2C was administered following IRI, it also increased renal regeneration with Treg infiltration and suppressed renal fibrosis. In contrast, Treg depletion in the presence of IL-2C eliminated the positive effects of IL-2C on IRI. CONCLUSION: Tregs protect kidneys from cold IRI and IL-2C inhibited cold IRI by increasing the renal Tregs, suggesting a potential of IL-2C in treating cold IRI. KEY POINTS: Interleukin (IL)-2/anti-IL-2 antibody complex attenuated acute renal injury, facilitated subacute renal regeneration and suppressed chronic renal fibrosis after cold ischemia-reperfusion injury (IRI) by increasing the renal Tregs. IL-2/anti-IL-2 antibody complex decreased reactive oxygen species-mediated injury and improved antioxidant function. This study suggests the therapeutic potential of the IL-2/anti-IL-2 antibody complex in kidney transplantation-associated cold IR.

Mechanistic Insight into how ß-Ketoacyl ACP Synthase I (KasA) Recognizes the Fatty Acid Chain Length of its Substrate.

ß-ketoacyl ACP synthase I (KasA) has been considered as a promising drug target against Tuberculosis because it is known to play a pivotal role in the survival of Mycobacterium Tuberculosis, a causative agent of Tuberculosis. KasA catalyzes the reaction elongating only the acyl chain that is 16 carbon atoms in length or longer, but the molecular details of how KasA selectively recognizes only the substrate longer than a certain length still remain unknown. In the present study, this challenging subject is addressed, and to this end, molecular dynamics (MD) simulations and free energy calculations for actual substrate binding process are carried out. The results illustrate that the substrate specificity of KasA is highly linked to its cooperativity and this cooperativity is realized through the activation of catalytic residues. Through these results, the mechanistic details of how KasA can be selectively activated only by the substrate with a proper length are suggested.

Lithospermum erythrorhizon Siebold & Zucc. extract reduces the severity of endotoxin-induced uveitis.

BACKGROUND: Uveitis is an inflammatory eye condition that threatens vision, and effective anti-inflammatory treatments with minimal side effects are necessary to treat uveitis. PURPOSE: This study aimed to investigate the effects of Lithospermum erythrorhizon Siebold & Zucc. against endotoxin-induced uveitis in rat and mouse models. METHODS: Endotoxin-induced uveitis models of rats and mice were used to evaluate the effects of l. erythrorhizon treatment. Clinical inflammation scores and retinal thickness were assessed in the extract of l. erythrorhizon-treated rats. Histopathological examination revealed inflammatory cell infiltration into the ciliary body. Protein concentration, cellular infiltration, and prostaglandin-E2 levels were measured in the aqueous humor of the extract of l. erythrorhizon-treated rats. Protective effects of l. erythrorhizon on the anterior segment of the eye were examined in mice with endotoxin-induced uveitis. Additionally, we investigated the effect of l. erythrorhizon on the expression of pro-inflammatory cytokines [tumor necrosis factor alpha, interleukin-6, and interleukin-8] in lipopolysaccharide-stimulated THP1 human macrophages and examined the involvement of nuclear factor kappaB/activator protein 1 and interferon regulatory factor signaling pathways. Furthermore, three components of l. erythrorhizon were identified and assessed for their inhibitory effects on LPS-induced inflammation in RAW264.7 macrophage cells. RESULTS: Treatment of the extract of l. erythrorhizon significantly reduced clinical inflammation scores and retinal thickening in rats with endotoxin-induced uveitis. Histopathological examination revealed decreased inflammatory cell infiltration into the ciliary body. The extract of l. erythrorhizon effectively reduced the protein concentration, cellular infiltration, and PG-E2 levels in the aqueous humor of rats with endotoxin-induced uveitis. In mice with endotoxin-induced uveitis, the extract of l. erythrorhizon demonstrated a protective effect on the anterior segment of the eye by reducing inflammation and retinal thickening. The extract of l. erythrorhizon suppressed the expression of pro-inflammatory cytokines (tumor necrosis factor alpha, interleukin-6, and interleukin-8) in lipopolysaccharide-induced inflammation in THP1 human macrophages, by modulating nuclear factor kappaB/activator protein 1 and interferon regulatory factor signaling pathways. Moreover, shikonin, acetylshikonin, and ß, ß-dimethylacryloylshikonin showed dose-dependent inhibition of nitric oxide, tumor necrosis factor alpha and interleukin-6 production in RAW264.7 macrophage cells. CONCLUSION: The extract of l. erythrorhizon is a potential therapeutic agent for uveitis management. Administration of the extract of l. erythrorhizon led to reduced inflammation, retinal thickening, and inflammatory cell infiltration in rat and mouse models of uveitis. The compounds (shikonin, acetylshikonin, and ß, ß-dimethylacryloylshikonin) identified in this study played crucial roles in mediating the anti-inflammatory effects of l. erythrorhizon. These findings indicate that the extract of l. erythrorhizon and its constituent compounds are promising candidates for further research and development of novel treatment modalities for uveitis.

FSLLRY-NH2, a protease-activated receptor 2 (PAR2) antagonist, activates mas-related G protein-coupled receptor C11 (MrgprC11) to induce scratching behaviors in mice.

AIMS: Protease-activated receptor 2 (PAR2), a type of G protein-coupled receptor (GPCR), plays a significant role in pathophysiological conditions such as inflammation. A synthetic peptide SLIGRL-NH2 (SLIGRL) can activate PAR2, while FSLLRY-NH2 (FSLLRY) is an antagonist. A previous study showed that SLIGRL activates both PAR2 and mas-related G protein-coupled receptor C11 (MrgprC11), a different type of GPCR expressed in sensory neurons. However, the impact of FSLLRY on MrgprC11 and its human ortholog MRGPRX1 was not verified. Hence, the present study aims to verify the effect of FSLLRY on MrgprC11 and MRGPRX1. METHODS: The calcium imaging technique was applied to determine the effect of FSLLRY in HEK293T cells expressing MrgprC11/MRGPRX1 or dorsal root ganglia (DRG) neurons. Scratching behavior was also investigated in wild-type and PAR2 knockout mice after injecting FSLLRY. KEY FINDINGS: It was surprisingly discovered that FSLLRY specifically activates MrgprC11 in a dose-dependent manner, but not other MRGPR subtypes. Furthermore, FSLLRY also moderately activated MRGPRX1. FSLLRY stimulates downstream pathways including Gαq/11, phospholipase C, IP3 receptor, and TRPC ion channels to evoke an increase in the intracellular calcium levels. The molecular docking analysis predicted that FSLLRY interacts with the orthosteric binding pocket of MrgprC11 and MRGPRX1. Finally, FSLLRY activated primary cultures of mouse sensory neurons, and induced scratching behaviors in mice. SIGNIFICANCE: The present study has revealed that FSLLRY is capable of triggering itch sensation through activation of MrgprC11. This finding highlights the importance of considering the unexpected activation of MRGPRs in future therapeutic approaches aimed at the inhibition of PAR2.

Gene Signatures and Associated Transcription Factors of Allergic Rhinitis: KLF4 Expression Is Associated with Immune Response.

This study is aimed at investigating the potential molecular features of allergic rhinitis (AR) and identifying gene signatures and related transcription factors using transcriptome analysis and in silico datasets. Transcriptome profiles were obtained using three independent cohorts (GSE101720, GSE19190, and GSE46171) comprising healthy controls (HC) and patients with AR. The pooled dataset (n = 82) was used to identify the critical signatures of AR compared with HC. Subsequently, key transcription factors were identified by a combined analysis using transcriptome and in silico datasets. Gene ontology: bioprocess (GO: BP) analysis using differentially expressed genes (DEGs) revealed that immune response-related genes were significantly enriched in AR compared with HC. Among them, IL1RL1, CD274, and CD44 were significantly higher in AR patients. We also identified key transcription factors between HC and AR using the in silico dataset and found that AR samples frequently express KLF transcription factor 4 (KLF4), which regulates immune response-related genes including IL1RL1, CD274, and CD44 in human nasal epithelial cells. Our integrative analysis of transcriptomic regulation provides new insights into AR, which may help in developing precision management for patients with AR.

Protective effects of isoflavones on alcoholic liver diseases: Computational approaches to investigate the inhibition of ALDH2 with isoflavone analogues.

Excessive and chronic alcohol intake can lead to the progression of alcoholic liver disease (ALD), which is a major cause of morbidity and mortality worldwide. ALD encompasses a pathophysiological spectrum such as simple steatosis, alcoholic steatohepatitis (ASH), fibrosis, alcoholic cirrhosis, and hepatocellular carcinoma (HCC). Aldehyde dehydrogenase (ALDH2) is the most vital enzyme that produces acetate from acetaldehyde and is expressed at high levels in the liver, kidneys, muscles, and heart. The ALDH2*2 allele is found in up to 40% of East Asian populations, and has a significant impact on alcohol metabolism. Interestingly, several studies have shown that individuals with ALDH2 deficiency are more susceptible to liver inflammation after drinking alcohol. Furthermore, there is growing evidence of an association between ALDH2 deficiency and the development of cancers in the liver, stomach, colon, and lung. Isoflavone analogues are low molecular-weight compounds derived from plants, similar in structure and activity to estrogen in mammals, known as phytoestrogens. Recent studies have reported that isoflavone analogues have beneficial effects on the progression of ALD. This mini-review summarizes the current knowledge about the roles of isoflavone analogues in ALD and discusses the therapeutic potential of isoflavone analogues in liver pathophysiology. In particular, we highlight the significance of computational approaches in this field.

Rg3-enriched Korean red ginseng alleviates chloroquine-induced itch and dry skin pruritus in an MrgprA3-dependent manner in mice.

Background: Previous studies have found that Korean red ginseng extract (KRG) has antipruritic effects, which can be attributed to the presence of Rg3, one of the most potent ginsenosides. Therefore, Rg3-enriched KRG extract (Rg3EKRG) is anticipated to have enhanced antipruritic effects. The present study was conducted to examine the effects of Rg3EKRG in acute chloroquine (CQ)-induced and chronic dry skin pruritus. Methods: Calcium imaging technique was used in HE293T cells expressing MrgprA3 and TRPA1 ("MrgprA3/TRPA1") and in primary cultures of mouse dorsal root ganglia (DRG) neurons. Mouse scratching behavior tests were performed on dry skin models. To verify the altered expression of itch-related genes, real-time RNA sequencing analysis and PCR were performed on DRG sections obtained from dry skin models. Results: Rg3EKRG suppressed CQ-induced intracellular calcium changes to a greater degree than KRG. Rg3EKRG dose-dependently inhibited CQ-induced responses in MrgprA3/TRPA1 cells. Rg3EKRG likely targeted MrgprA3 rather than TRPA1 to exert its inhibitory effect. Further, Rg3EKRG strongly inhibited the scratching behavior in mice induced by acute CQ injection. Importantly, DRG neurons obtained from dry skin mice models showed increased mRNA levels of MrgprA3, and treatment with Rg3EKRG alleviated chronic dry skin conditions and suppressed spontaneous scratching behaviors. Conclusion: The results of the present study imply that Rg3EKRG has a stronger antipruritic effect than KRG, inhibiting both acute CQ-induced and chronic dry skin pruritus in an MrgprA3-dependent manner. Therefore, Rg3EKRG is a potential antipruritic agent that can suppress acute and chronic itching at the peripheral sensory neuronal level.

Constructing a Cancer Patient-Specific Network Based on Second-Order Partial Correlations of Gene Expression and DNA Methylation.

Typically patient-specific gene networks are constructed with gene expression data only. Such networks cannot distinguish direct gene interactions from indirect interactions via others such as the effect of epigenetic events to gene activity. There is an increasing evidence of inter-individual variations not only in gene expression but also in epigenetic events such as DNA methylation. In this paper we propose a new method for constructing a cancer patient-specific gene correlation network using both gene expression and DNA methylation data. We derive a patient-specific network from differential second-order partial correlations of gene expression and DNA methylation between normal samples and the patient sample. The network represents direct interactions between genes by controlling the effect of DNA methylation. Using this method, we constructed 4,000 patient-specific networks for 10 types of cancer. The networks are highly effective in classifying different types of cancer and in deriving potential prognostic gene pairs. In particular, potential prognostic gene pairs derived from the networks were powerful in predicting the survival time of cancer patients. This approach will help identify patient-specific gene correlations and predict prognosis of cancer patients.

Mechanistic Aspects of the Effect of Flanking Nucleotide Sequence on CPD Formation and CPD Self-Repair in DNA.

A cyclobutane pyrimidine dimer (CPD) is a photolesion which is produced by a cycloaddition reaction between two stacked pyrimidine bases upon UV light absorption. Because of its harmful effect on important cellular processes involving DNA and especially its relevance to skin cancer, the mechanisms of how a CPD is formed or repaired have been studied extensively, and it has been demonstrated that flanking nucleotide sequences play a crucial role in CPD formation or self-repair. Understanding the mechanisms behind this sequence dependence of CPD formation or self-repair is of great importance because it can give us valuable information on which sequence will be vulnerable to this DNA photodamage. This Perspective focuses on the mechanisms of how flanking nucleotide sequences affect CPD formation or self-repair, especially highlighting the role of computational studies in this field.

Constructing Integrative ceRNA Networks and Finding Prognostic Biomarkers in Renal Cell Carcinoma.

Inspired by a newly discovered gene regulation mechanism known as competing endogenous RNA (ceRNA) interactions, several computational methods have been proposed to generate ceRNA networks. However, most of these methods have focused on deriving restricted types of ceRNA interactions such as lncRNA-miRNA-mRNA interactions. Competition for miRNA-binding occurs not only between lncRNAs and mRNAs but also between lncRNAs or between mRNAs. Furthermore, a large number of pseudogenes also act as ceRNAs, thereby regulate other genes. In this study, we developed a general method for constructing integrative networks of all possible interactions of ceRNAs in renal cell carcinoma (RCC). From the ceRNA networks we derived potential prognostic biomarkers, each of which is a triplet of two ceRNAs and miRNA (i.e., ceRNA-miRNA-ceRNA). Interestingly, some prognostic ceRNA triplets do not include mRNA at all, and consist of two non-coding RNAs and miRNA, which have been rarely known so far. Comparison of the prognostic ceRNA triplets to known prognostic genes in RCC showed that the triplets have a better predictive power of survival rates than the known prognostic genes. Our approach will help us construct integrative networks of ceRNAs of all types and find new potential prognostic biomarkers in cancer.

Antiallergic Effects of N,N-dicoumaroylspermidine Isolated from Lithospermum erythrorhizon on Mast Cells and Ovalbumin-Induced Allergic Rhinitis.

In East Asia, the dried root of Lithospermum erythrorhizon has been utilized as an anti-inflammatory, antipyretic, detoxifying, and anti-inflammatory agent. Recently, we reported that L. erythrorhizon protects against allergic rhinitis; however, the component within L. erythrorhizon that exerts antiallergic activity remains unknown. The purpose of the current study was to isolate and characterize the antiallergic active components in an ethanolic extract of L. erythrorhizon roots. We examined the antiallergic effects of L. erythrorhizon reflux ethanol extracts in an ovalbumin (OVA)-induced allergic rhinitis mouse model, and compared the chemical compounds extracted using the hot reflux and cold extraction methods. Chromatographic separation identified two novel anthraquinones, erythrin A and B, one newly discovered compound from the Lithospermum genus, N1″,N3″-dicoumaroylspermidine, and nineteen other recognized compounds. Their chemical structures were elucidated by single (1D) and 2D analysis of nuclear magnetic resonance (NMR) spectroscopic data, as well as high resolution mass spectrometry. Among the identified compounds, N,N'-dicoumaroylspermidine strongly inhibited the release of ß-hexosaminidase, as well as the production of IL-3, IL-4, and IL-13 by IgE-sensitized and BSA-stimulated RBL-2H3 cells. Using the OVA-induced allergic rhinitis mouse model, we showed that N,N'-dicoumaroylspermidine reduced the production of serum OVA-specific IgE and the number of inflammatory cells in nasal lavage fluid. N,N'-dicoumaroylspermidine isolated from L. erythrorhizon exhibits antiallergic properties, making it potentially effective for allergic rhinitis.

Predicting lymph node metastasis and prognosis of individual cancer patients based on miRNA-mediated RNA interactions.

BACKGROUND: Lymph node metastasis is usually detected based on the images obtained from clinical examinations. Detecting lymph node metastasis from clinical examinations is a direct way of diagnosing metastasis, but the diagnosis is done after lymph node metastasis occurs. RESULTS: We developed a new method for predicting lymph node metastasis based on differential correlations of miRNA-mediated RNA interactions in cancer. The types of RNAs considered in this study include mRNAs, lncRNAs, miRNAs, and pseudogenes. We constructed cancer patient-specific networks of miRNA mediated RNA interactions and identified key miRNA-RNA pairs from the network. A prediction model using differential correlations of the miRNA-RNA pairs of a patient as features showed a much higher performance than other methods which use gene expression data. The key miRNA-RNA pairs were also powerful in predicting prognosis of an individual patient in several types of cancer. CONCLUSIONS: Differential correlations of miRNA-RNA pairs identified from patient-specific networks of miRNA mediated RNA interactions are powerful in predicting lymph node metastasis in cancer patients. The key miRNA-RNA pairs were also powerful in predicting prognosis of an individual patient of solid cancer.

Exploring dopant effects in stannic oxide nanoparticles for CO2 electro-reduction to formate.

The electrosynthesis of formate from CO2 can mitigate environmental issues while providing an economically valuable product. Although stannic oxide is a good catalytic material for formate production, a metallic phase is formed under high reduction overpotentials, reducing its activity. Here, using a fluorine-doped tin oxide catalyst, a high Faradaic efficiency for formate (95% at 100 mA cm-2) and a maximum partial current density of 330 mA cm-2 (at 400 mA cm-2) is achieved for the electroreduction of CO2. Furthermore, the formate selectivity (≈90%) is nearly constant over 7 days of operation at a current density of 100 mA cm-2. In-situ/operando spectroscopies reveal that the fluorine dopant plays a critical role in maintaining the high oxidation state of Sn, leading to enhanced durability at high current densities. First-principle calculation also suggests that the fluorine-doped tin oxide surface could provide a thermodynamically stable environment to form HCOO* intermediate than tin oxide surface. These findings suggest a simple and efficient approach for designing active and durable electrocatalysts for the electrosynthesis of formate from CO2.

InAsP Quantum Dot-Embedded InP Nanowires toward Silicon Photonic Applications.

Quantum dot (QD) emitters on silicon platforms have been considered as a fascinating approach to building next-generation quantum light sources toward unbreakable secure communications. However, it has been challenging to integrate position-controlled QDs operating at the telecom band, which is a crucial requirement for practical applications. Here, we report monolithically integrated InAsP QDs embedded in InP nanowires on silicon. The positions of QD nanowires are predetermined by the lithography of gold catalysts, and the 3D geometry of nanowire heterostructures is precisely controlled. The InAsP QD forms atomically sharp interfaces with surrounding InP nanowires, which is in situ passivated by InP shells. The linewidths of the excitonic (X) and biexcitonic (XX) emissions from the QD and their power-dependent peak intensities reveal that the proposed QD-in-nanowire structure could be utilized as a non-classical light source that operates at silicon-transparent wavelengths, showing a great potential for diverse quantum optical and silicon photonic applications.

A New Approach to Deriving Prognostic Gene Pairs From Cancer Patient-Specific Gene Correlation Networks.

Many of the known prognostic gene signatures for cancer are individual genes or combination of genes, found by the analysis of microarray data. However, many of the known cancer signatures are less predictive than random gene expression signatures, and such random signatures are significantly associated with proliferation genes. With the availability of RNA-seq gene expression data for thousands of human cancer patients, we have analyzed RNA-seq and clinical data of cancer patients and constructed gene correlation networks specific to individual cancer patients. From the patient-specific gene correlation networks, we derived prognostic gene pairs for three types of cancer. In this paper, we propose a new method for inferring prognostic gene pairs from patient-specific gene correlation networks. The main difference of our method from previous ones includes (1) it is focused on finding prognostic gene pairs rather than prognostic genes, (2) it can identify prognostic gene pairs from RNA-seq data even when no significant prognostic genes exist, and (3) prognostic gene pairs can serve as robust prognostic biomarkers in the sense that most prognostic gene pairs show little association with proliferation genes, the major boosting factor of the predictive power of random gene signatures. Evaluation of our method with extensive data of three types of cancer (liver cancer, pancreatic cancer, and stomach cancer) showed that our approach is general and that gene pairs can serve as more reliable prognostic signatures for cancer than genes. Analysis of patient-specific gene networks suggests that prognosis of individual cancer patients is affected by the existence of prognostic gene pairs in the patient-specific network and by the size of the patient-specific network. Although preliminary, our approach will be useful for finding gene pairs to predict survival time of patients and to tailor treatments to individual characteristics. The program for dynamically constructing patient-specific gene networks and for finding prognostic gene pairs is available at http://bclab.inha.ac.kr/LPS.

Bottom-Up Evolution of Diamond-Graphite Hybrid Two-Dimensional Nanostructure: Underlying Picture and Electrochemical Activity.

The diamond-graphite hybrid thin film with low-dimensional nanostructure (e.g., nitrogen-included ultrananocrystalline diamond (N-UNCD) or the alike), has been employed in many impactful breakthrough applications. However, the detailed picture behind the bottom-up evolution of such intriguing carbon nanostructure is far from clarified yet. Here, the authors clarify it, through the concerted efforts of microscopic, physical, and electrochemical analyses for a series of samples synthesized by hot-filament chemical vapor deposition using methane-hydrogen precursor gas, based on the hydrogen-dependent surface reconstruction of nanodiamond and on the substrate-temperature-dependent variation of the growth species (atomic hydrogen and methyl radical) concentration near substrate. The clarified picture provides insights for a drastic enhancement in the electrochemical activities of the hybrid thin film, concerning the detection of important biomolecule, that is, ascorbic acid, uric acid, and dopamine: their limits of detections are 490, 35, and 25 nm, respectively, which are among the best of the all-carbon thin film electrodes in the literature. This work also enables a simple and effective way of strongly enhancing AA detection.