2D-Material-Assisted GaN Growth on GaN Template by MOCVD and Its Exfoliation Strategy.

The production of freestanding membranes using two-dimensional (2D) materials often involves techniques such as van der Waals (vdW) epitaxy, quasi-vdW epitaxy, and remote epitaxy. However, a challenge arises when attempting to manufacture freestanding GaN by using these 2D-material-assisted growth techniques. The issue lies in securing stability, as high-temperature growth conditions under metal-organic chemical vapor deposition (MOCVD) can cause damage to the 2D materials due to GaN decomposition of the substrate. Even when GaN is successfully grown using this method, damage to the 2D material leads to direct bonding with the substrate, making the exfoliation of the grown GaN nearly impossible. This study introduces an approach for GaN growth and exfoliation on 2D material/GaN templates. First, graphene and hexagonal boron nitride (h-BN) were transferred onto the GaN template, creating stable conditions under high temperatures and various gases in MOCVD. GaN was grown in a two-step process at 750 and 900 °C, ensuring exfoliation in cases where the 2D materials remained intact. Essentially, while it is challenging to grow GaN on 2D material/GaN using only MOCVD, this study demonstrates that with effective protection of the 2D material, the grown GaN can endure high temperatures and still be exfoliated. Furthermore, these results support that vdW epitaxy and remote epitaxy principle are not only possible with specific equipment but also applicable generally.

Stability of Graphene and Influence of AlN Surface Pits on GaN Remote Heteroepitaxy for Exfoliation.

Remote epitaxy is a promising technology that has recently attracted considerable attention, which enables the growth of thin films that copy the crystallographic characteristics of the substrate through two-dimensional material interlayers. The grown films can be exfoliated to form freestanding membranes, although it is often challenging to apply this technique if the substrate materials are prone to damage under harsh epitaxy conditions. For example, remote epitaxy of GaN thin films on graphene/GaN templates has not been achieved by a standard metal-organic chemical vapor deposition (MOCVD) method due to such damages. Here, we report GaN remote heteroepitaxy on graphene/AlN templates by MOCVD and investigate the influence of surface pits in AlN on the growth and exfoliation of GaN thin films. We first show the thermal stability of graphene before GaN growth, based on which two-step growth of GaN on graphene/AlN is developed. The GaN samples are successfully exfoliated after the first step of the growth at 750 °C, whereas the exfoliation failed after the second step at 1050 °C. In-depth analysis confirms that the pits in AlN templates lead to the degradation of graphene near the area and thus the alteration of growth modes and the failure of exfoliation. These results exemplify the importance of chemical and topographic properties of growth templates for successful remote epitaxy. It is one of the key factors for III-nitride-based remote epitaxy, and these results are expected to be of great help in realizing complete remote epitaxy using only MOCVD.

Impact of Na Doping on the Carrier Transport Path in Polycrystalline Flexible Cu2ZnSn(S,Se)4 Solar Cells.

It is well-known that the alkali doping of polycrystalline Cu2ZnSn(S,Se)4 (CZTSSe) and Cu(In,Ga)(Se,S)2 has a beneficial influence on the device performance and there are various hypotheses about the principles of performance improvement. This work clearly explains the effect of Na doping on the fill factor (FF) rather than on all of the solar cell parameters (open-circuit voltage, FF, and sometimes short circuit current) for overall performance improvement. When doping is optimized, the fabricated device shows sufficient built-in potential and selects a better carrier transport path by the high potential difference between the intragrains and the grain boundaries. On the other hand, when doping is excessive, the device shows low contact potential difference and FF and selects a worse carrier transport path even though the built-in potential becomes stronger. The fabricated CZTSSe solar cell on a flexible metal foil optimized with a 25 nm thick NaF doping layer achieves an FF of 62.63%, thereby clearly showing the enhancing effect of Na doping.

Flexible High-Efficiency CZTSSe Solar Cells on Diverse Flexible Substrates via an Adhesive-Bonding Transfer Method.

Cu2ZnSn(S,Se)4 (CZTSSe) thin-film solar cells are showing great promise due to using earth-abundant and nontoxic materials and tuning the band gap through the amount of S and Se. Flexible high-efficiency CZTSSe solar cells are one of the outstanding research challenges because they currently require the use of thick glass substrates due to the high-temperature heat treatment process, and for this reason, few flexible CZTSSe solar cells have been reported. Furthermore, most researchers have used thin glass and metal substrates with little flexibility; the power conversion efficiency (PCE or η) values of the solar cells made with them have been slightly lower. To overcome these hurdles, we transferred high-efficiency CZTSSe solar cells formed on a soda-lime glass substrate to flexible substrates via an adhesive-bonding transfer method. Through this method, we were able to achieve the PCE of 5.8-7.1% on completely flexible substrates such as cloth, paper, and poly(ethylene terephthalate) (PET). In particular, we were able to produce a CZTSSe solar cell on a PET substrate with a PCE of 7.1%, which is the highest among fully flexible CZTSSe solar cells currently known to us. In addition, we deeply analyzed the PCE degradation of the flexible CZTSSe solar cell fabricated by the transfer method through a panoramic focused ion-beam image and nanoindentation. From the results of our work, we provide an insight into the possibility of making flexible high-efficiency CZTSSe solar cells using our transfer method.

ZNF542P is a pseudogene associated with LDL response to simvastatin treatment.

Statins are the most commonly prescribed cardiovascular disease drug, but their inter-individual efficacy varies considerably. Genetic factors uncovered to date have only explained a small proportion of variation in low-density lipoprotein cholesterol (LDLC) lowering. To identify novel markers and determinants of statin response, we used whole transcriptome sequence data collected from simvastatin and control incubated lymphoblastoid cell lines (LCLs) established from participants of the Cholesterol and Pharmacogenetics (CAP) simvastatin clinical trial. We looked for genes whose statin-induced expression changes were most different between LCLs derived from individuals with high versus low plasma LDLC statin response during the CAP trial. We created a classification model of 82 "signature" gene expression changes that distinguished high versus low LDLC statin response. One of the most differentially changing genes was zinc finger protein 542 pseudogene (ZNF542P), the signature gene with changes most correlated with statin-induced change in cellular cholesterol ester, an in vitro marker of statin response. ZNF542P knock-down in a human hepatoma cell line increased intracellular cholesterol ester levels upon simvastatin treatment. Together, these findings imply a role for ZNF542P in LDLC response to simvastatin and, importantly, highlight the potential significance of noncoding RNAs as a contributing factor to variation in drug response.

Tenofovir disoproxil fumarate (TDF) vs. emtricitabine (FTC)/TDF in lamivudine resistant hepatitis B: A 5-year randomised study.

BACKGROUND & AIMS: Long-term treatment with tenofovir disoproxil fumarate (TDF) alone, or in combination with emtricitabine (FTC) is associated with sustained viral suppression in patients with lamivudine resistant (LAM-R) chronic hepatitis B (CHB). METHODS: LAM-R CHB patients were randomised 1:1 to receive TDF 300mg or FTC 200mg and TDF 300mg once daily in a prospective, double blind, study. The proportion of patients with plasma hepatitis B virus (HBV) DNA<69IU/ml (<400copies/ml) at week 96 (primary efficacy endpoint) was reported previously. Here we present week 240 follow-up data. RESULTS: Overall, 280 patients were randomised to receive TDF (n=141) or FTC/TDF (n=139), and 85.4% completed 240weeks of treatment. At week 240, 83.0% of patients in the TDF arm, and 82.7% of patients in the FTC/TDF treatment arm had HBV DNA<69IU/ml (p=0.96). Rates of normal alanine aminotransferase (ALT) and normalised ALT were similar between groups (p=0.41 and p=0.97 respectively). Hepatitis B e antigen loss and seroconversion at week 240 were similar between groups, (p=0.41 and p=0.67 respectively). Overall, six patients achieved hepatitis B surface antigen (HBsAg) loss and one patient (FTC/TDF arm) had HBsAg seroconversion by week 240. No TDF resistance was observed up to week 240. Treatment was generally well tolerated, and renal events were mild and infrequent (∼8.6%). The mean change in bone mineral density at week 240 was -0.98% and -2.54% at the spine and hip, respectively. CONCLUSIONS: TDF monotherapy was effective and well tolerated in LAM-R CHB patients for up to 240weeks. LAY SUMMARY: The goal of oral antiviral treatment for chronic hepatitis B (CHB) is to achieve and maintain undetectable HBV DNA levels. Treatment options with enhanced potency, and low risk of resistance development for patients infected with lamivudine resistant (LAM-R) HBV are required. Tenofovir disoproxil fumarate (TDF) monotherapy was effective and well tolerated without TDF resistance development in CHB patients with LAM-R, for up to 240weeks. Clinical trial number: NCT00737568.

Tenofovir alafenamide versus tenofovir disoproxil fumarate for the treatment of patients with HBeAg-negative chronic hepatitis B virus infection: a randomised, double-blind, phase 3, non-inferiority trial.

BACKGROUND: The novel prodrug tenofovir alafenamide delivers the nucleotide reverse transcriptase inhibitor tenofovir to target cells more efficiently at a lower dose than tenofovir disoproxil fumarate, thereby reducing systemic exposure. We compared the efficacy and safety of the two drugs in patients with HBeAg-negative chronic hepatitis B virus (HBV) infection in a non-inferiority study. METHODS: In this ongoing randomised, double-blind, phase 3, non-inferiority study in 105 centres in 17 countries, patients with HBeAg-negative chronic HBV were randomly assigned (2:1) by a computer-generated allocation sequence (block size six), stratified by plasma HBV DNA concentration and previous treatment status, to receive once-daily oral doses of tenofovir alafenamide 25 mg or tenofovir disoproxil fumarate 300 mg, each with matching placebo. Participants, investigators, and those assessing outcomes were masked to group assignment. Eligible patients were aged at least 18 years with HBeAg-negative chronic HBV infection (with plasma HBV DNA concentrations of >20 000 IU/mL), serum alanine aminotransferase concentrations of greater than 60 U/L in men or greater than 38 U/L in women and at no more than ten times the upper limit of normal, and estimated creatinine clearance of at least 50 mL/min (by the Cockcroft-Gault method). The primary efficacy endpoint was the proportion of patients who had HBV DNA less than 29 IU/mL at week 48 in those who received at least one dose of study drug; the study was powered to show non-inferiority with a 10% efficacy margin of tenofovir alafenamide compared with tenofovir disoproxil fumarate. Bone and renal safety, and key secondary safety endpoints were assessed sequentially. The study will be conducted for a total of 3 years as a double-blind comparison to assess the longer term response to treatment. This study is registered with ClinicalTrials.gov, number NCT01940341. FINDINGS: Between Sept 12, 2013, and Oct 31, 2014, 426 patients were randomly assigned (285 assigned to tenofovir alafenamide and 141 assigned to tenofovir disoproxil fumarate; one patient assigned to tenofovir disoproxil fumarate did not receive the treatment. 268 (94%) of 285 patients receiving tenofovir alafenamide had HBV DNA less than 29 IU/mL at week 48 versus 130 (93%) of 140 patients receiving tenofovir disoproxil fumarate (difference 1·8% [95% CI -3·6 to 7·2]; p=0·47), which demonstrates non-inferiority. Patients receiving tenofovir alafenamide had significantly smaller mean percentage declines in bone mineral density than those receiving tenofovir disoproxil fumarate (hip -0·29% [95% CI -0·55 to -0·03] vs -2·16% [-2·53 to -1·79], adjusted percentage difference 1·87% [95% CI 1·42 to 2·32; p<0·0001]; spine -0·88% [-1·22 to -0·54] vs -2·51% [-3·09 to -1·94], adjusted percentage difference 1·64% [95% CI 1·01 to 2·27]; p<0·0001). At week 48, mean change in serum creatinine was small in both groups (tenofovir alafenamide 0·01 mg/dL [95% CI 0·00 to 0·02] vs tenofovir disoproxil fumarate 0·02 mg/dL [0·00 to 0·04], adjusted percentage difference -0·01 mg/dL [95% CI -0·03 to 0·01]; p=0·32), but patients receiving tenofovir alafenamide had a smaller reduction in creatinine clearance (median change in estimated glomerular filtration rate -1·8 mL/min [IQR -7·8 to 6·0] vs -4·8 mL/min [-12·0 to 3·0]; p=0·004). Most adverse events were mild to moderate in severity in the two treatment groups. The most common adverse events overall were headache (tenofovir alafenamide 40 [14%] patients vs tenofovir disoproxil fumarate 14 [10%] patients), nasopharyngitis (30 [11%] vs 15 [11%]), and upper respiratory tract infection (35 [12%] vs ten [7%]). 14 (5%) patients receiving tenofovir alafenamide and nine (6%) patients receiving tenofovir disoproxil fumarate had serious adverse events, none of which was deemed by investigators to be related to study treatment; one patient in the tenofovir disoproxil fumarate group died, but this was not deemed to be related to study treatment. INTERPRETATION: In patients with HBeAg-negative chronic HBV, the efficacy of tenofovir alafenamide was non-inferior to that of tenofovir disoproxil fumarate, and had improved bone and renal effects. Longer term follow-up is needed to better understand the clinical impact of these changes. FUNDING: Gilead Sciences.

Prediction of LDL cholesterol response to statin using transcriptomic and genetic variation.

BACKGROUND: Statins are widely prescribed for lowering LDL-cholesterol (LDLC) levels and risk of cardiovascular disease. There is, however, substantial inter-individual variation in the magnitude of statin-induced LDLC reduction. To date, analysis of individual DNA sequence variants has explained only a small proportion of this variability. The present study was aimed at assessing whether transcriptomic analyses could be used to identify additional genetic contributions to inter-individual differences in statin efficacy. RESULTS: Using expression array data from immortalized lymphoblastoid cell lines derived from 372 participants of the Cholesterol and Pharmacogenetics clinical trial, we identify 100 signature genes differentiating high versus low statin responders. A radial-basis support vector machine prediction model of these signature genes explains 12.3% of the variance in statin-mediated LDLC change. Addition of SNPs either associated with expression levels of the signature genes (eQTLs) or previously reported to be associated with statin response in genome-wide association studies results in a combined model that predicts 15.0% of the variance. Notably, a model of the signature gene associated eQTLs alone explains up to 17.2% of the variance in the tails of a separate subset of the Cholesterol and Pharmacogenetics population. Furthermore, using a support vector machine classification model, we classify the most extreme 15% of high and low responders with high accuracy. CONCLUSIONS: These results demonstrate that transcriptomic information can explain a substantial proportion of the variance in LDLC response to statin treatment, and suggest that this may provide a framework for identifying novel pathways that influence cholesterol metabolism.

Statin-induced changes in gene expression in EBV-transformed and native B-cells.

Human lymphoblastoid cell lines (LCLs), generated through Epstein-Barr Virus (EBV) transformation of B-lymphocytes (B-cells), are a commonly used model system for identifying genetic influences on human diseases and on drug responses. We have previously used LCLs to examine the cellular effects of genetic variants that modulate the efficacy of statins, the most prescribed class of cholesterol-lowering drugs used for the prevention and treatment of cardiovascular disease. However, statin-induced gene expression differences observed in LCLs may be influenced by their transformation, and thus differ from those observed in native B-cells. To assess this possibility, we prepared LCLs and purified B-cells from the same donors, and compared mRNA profiles after 24 h incubation with simvastatin (2 µm) or sham buffer. Genes involved in cholesterol metabolism were similarly regulated between the two cell types under both the statin and sham-treated conditions, and the statin-induced changes were significantly correlated. Genes whose expression differed between the native and transformed cells were primarily implicated in cell cycle, apoptosis and alternative splicing. We found that ChIP-seq signals for MYC and EBNA2 (an EBV transcriptional co-activator) were significantly enriched in the promoters of genes up-regulated in the LCLs compared with the B-cells, and could be involved in the regulation of cell cycle and alternative splicing. Taken together, the results support the use of LCLs for the study of statin effects on cholesterol metabolism, but suggest that drug effects on cell cycle, apoptosis and alternative splicing may be affected by EBV transformation. This dataset is now uploaded to GEO at the accession number GSE51444.

Using biologically interrelated experiments to identify pathway genes in Arabidopsis.

MOTIVATION: Pathway genes are considered as a group of genes that work cooperatively in the same pathway constituting a fundamental functional grouping in a biological process. Identifying pathway genes has been one of the major tasks in understanding biological processes. However, due to the difficulty in characterizing/inferring different types of biological gene relationships, as well as several computational issues arising from dealing with high-dimensional biological data, deducing genes in pathways remain challenging. RESULTS: In this work, we elucidate higher level gene-gene interactions by evaluating the conditional dependencies between genes, i.e. the relationships between genes after removing the influences of a set of previously known pathway genes. These previously known pathway genes serve as seed genes in our model and will guide the detection of other genes involved in the same pathway. The detailed statistical techniques involve the estimation of a precision matrix whose elements are known to be proportional to partial correlations (i.e. conditional dependencies) between genes under appropriate normality assumptions. Likelihood ratio tests on two forms of precision matrices are further performed to see if a candidate pathway gene is conditionally independent of all the previously known pathway genes. When used effectively, this is a promising approach to recover gene relationships that would have otherwise been missed by standard methods. The advantage of the proposed method is demonstrated using both simulation studies and real datasets. We also demonstrated the importance of taking into account experimental dependencies in the simulation and real data studies.

Measuring similarities between gene expression profiles through new data transformations.

BACKGROUND: Clustering methods are widely used on gene expression data to categorize genes with similar expression profiles. Finding an appropriate (dis)similarity measure is critical to the analysis. In our study, we developed a new measure for clustering the genes when the key factor is the shape of the profile, and when the expression magnitude should also be accounted for in determining the gene relationship. This is achieved by modeling the shape and magnitude parameters separately in a gene expression profile, and then using the estimated shape and magnitude parameters to define a measure in a new feature space. RESULTS: We explored several different transformation schemes to construct the feature spaces that include a space whose features are determined by the mutual differences of the original expression components, a space derived from a parametric covariance matrix, and the principal component space in traditional PCA analysis. The former two are the newly proposed and the latter is explored for comparison purposes. The new measures we defined in these feature spaces were employed in a K-means clustering procedure to perform analyses. Applying these algorithms to a simulation dataset, a developing mouse retina SAGE dataset, a small yeast sporulation cDNA dataset, and a maize root affymetrix microarray dataset, we found from the results that the algorithm associated with the first feature space, named TransChisq, showed clear advantages over other methods. CONCLUSION: The proposed TransChisq is very promising in capturing meaningful gene expression clusters. This study also demonstrates the importance of data transformations in defining an efficient distance measure. Our method should provide new insights in analyzing gene expression data. The clustering algorithms are available upon request.

Transcription profile analyses identify genes and pathways central to root cap functions in maize.

Affymetrix GeneChips arrayed with about one-half (~23K) of the rice genes were used to profile gene transcription activity in three tissues comprising the maize root tip; the proximal meristem (PM), the quiescent center (QC), and the root cap (RC). Here we analyze the gene transcription profile of the RC, compared to both the PM and the QC, from three biological replicates. In the RC, a total of 669 genes were identified as being differentially upregulated, and 365 differentially downregulated. Real-time quantitative RT-PCR analysis was used to confirm upregulated genes in the RC. In addition, using the technique of laser microdissection (LMD) we localized upregulated gene expression to the lateral RC cells. Taken as a whole, transcription profile analyses revealed the upregulation in the maize RC of clusters of genes linked to major metabolic processes and pathways, including: (1) transport, both the export of carbohydrates and the uptake of nutrients; (2) sensing and responding to (often stressful) biotic and abiotic environmental stimuli; (3) integrating the responses of at least 3 major growth regulators (auxin, ethylene, jasmonic acid); (4) processing the large amount of carbohydrate transported into the RC. Although the profile data are derived using heterologous rice GeneChips, with about half of the total rice gene set, this study, nevertheless, provides a genomic scale characterization of the entire RC, and serves as a new platform from which to advance studies of the network of pathways operating in the maize RC.

Growth of poly(pseudorotaxane) on gold using host-stabilized charge-transfer interaction.

A novel supramolecular polymer (poly(pseudorotaxane)) in which the repeating units are linked by host-stabilized charge-transfer interaction between the guest molecules is grown on gold and characterized.

Designed self-assembly of molecular necklaces using host-stabilized charge-transfer interactions.

A novel approach to the noncovalent synthesis of molecular necklaces successfully led to the first quantitative self-assembly of a molecular necklace [6]MN, in which five small rings are threaded on a large ring, from 10 components. Our strategy involves the host-guest complex formation between the molecular host cucurbit[8]uril (CB[8]) and a guest molecule in which an electron donor and an electron acceptor unit are connected by a rigid linker with a proper angle, to form a cyclic oligomer through the host-stabilized intermolecular charge-transfer (CT) complex formation. In the structure of the molecular necklace [6]MN, five molecules of the guest form a cyclic framework by the intermolecular CT interactions, on which five CB[8] molecules are threaded with an arrangement reminiscent of a five-fold propeller. The molecular necklace measures approximately 3.7 nm in diameter and approximately 1.8 nm in thickness.

Unprecedented host-induced intramolecular charge-transfer complex formation.

For the first time, host-induced intramolecular charge-transfer complex formation in a guest containing both an electron donor and an electron acceptor is demonstrated in the cucurbit[8]uril cavity, leading to unusual back-folding of the guest molecule.