Report on the 2012 IEEE AP-S/USNC-URSI

Report on the 2012 IEEE AP-S/USNC-URS

Chemical Vapor Deposition of N‑Doped Graphene and Carbon Films: The Role of Precursors and Gas Phase

Thermally induced chemical vapor deposition (CVD) was used to study the formation of nitrogen-doped graphene and carbon films on copper from aliphatic nitrogen-containing precursors consisting of C₁- and C₂-units and (hetero)aromatic nitrogen-containing ring systems. The structure and quality of the resulting films were correlated to the influence of the functional groups of the precursor molecules and gas phase composition. They were analyzed with SEM, TEM, EDX, XPS, and Raman spectroscopy. The presence of (N-doped) graphene was confirmed by the 2D mode of the Raman spectra. The isolated graphene films obtained from nitrogen-containing precursors reveal a high conductivity and transparency compared to standard graphene CVD samples. Precursors with amine functional groups (<i>e.g.</i>, methylamine) can lead to a direct formation of graphene even without additional hydrogen present in the gas phase. This is not observed for, <i>e.g.</i>, methane under comparable CVD conditions. Therefore, the intermediate gas phase species (<i>e.g.</i>, amine radicals) can significantly enhance the graphene film growth kinetics. Kinetic and thermodynamic effects can be invoked to discuss the decay of the precursors

Adjusting Breast Cancer Patient Prognosis with Non-HER2-Gene Patterns on Chromosome 17

<div><p>Background</p><p><i>HER2</i> and <i>TOP2A</i> gene status are assessed for diagnostic and research purposes in breast cancer with fluorescence in situ hybridization (FISH). However, FISH probes do not target only the annotated gene, while chromosome 17 (chr17) is among the most unstable chromosomes in breast cancer. Here we asked whether the status of specifically targeted genes on chr17 might help in refining prognosis of early high-risk breast cancer patients.</p><p>Methods</p><p>Copy numbers (CN) for 14 genes on chr17, 4 of which were within and 10 outside the core <i>HER2</i> amplicon (HER2- and non-HER2-genes, respectively) were assessed with qPCR in 485 paraffin-embedded tumor tissue samples from breast cancer patients treated with adjuvant chemotherapy in the frame of two randomized phase III trials.</p><p>Principal Findings</p><p><i>HER2</i>-genes CN strongly correlated to each other (Spearman’s rho >0.6) and were concordant with FISH <i>HER2</i> status (Kappa 0.6697 for <i>ERBB2</i> CN). <i>TOP2A</i> CN were not concordant with <i>TOP2A</i> FISH status (Kappa 0.1154). CN hierarchical clustering revealed distinct patterns of gains, losses and complex alterations in HER2- and non-HER2-genes associated with IHC4 breast cancer subtypes. Upon multivariate analysis, non-HER2-gene gains independently predicted for shorter disease-free survival (DFS) and overall survival (OS) in patients with triple-negative cancer, as compared to luminal and HER2-positive tumors (interaction p = 0.007 for DFS and p = 0.011 for OS). Similarly, non-HER2-gene gains were associated with worse prognosis in patients who had undergone breast-conserving surgery as compared to modified radical mastectomy (p = 0.004 for both DFS and OS). Non-HER2-gene losses were unfavorable prognosticators in patients with 1–3 metastatic nodes, as compared to those with 4 or more nodes (p = 0.017 for DFS and p = 0.001 for OS).</p><p>Conclusions</p><p><i>TOP2A</i> FISH and qPCR may not identify the same pathology on chr17q. Non-HER2 chr17 CN patterns may further predict outcome in breast cancer patients with known favorable and unfavorable prognosis.</p></div

Demographic and clinicopathological characteristics of patients and tumors from HE10/00 & HE10/97 cohorts.

<p>*according to REMARK (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103707#pone-0103707-g001" target="_blank">Figure 1</a>);</p><p>∧NOS2, ERBB2, THRA, RARA, TOP2A; MRM = modified radical mastectomy; BCS = breast conserving surgery;</p><p>**E = epirubicin; T = paclitaxel (Taxol); C = cyclophosphamide; M = methotrexate; F = fluorouracil.</p

Significant interactions between non-HER2 gene CN clusters and clinicopathologic parameters affecting patient survival.

<p>In <b>A,</b> among patients with non-TNBC tumors those with non-HER2 gene CN gains fare best; among patients with TNBC, those with non-HER2 gains fare worse. In <b>B,</b> patients with favorable nodal status (1–3 metastatic lymph nodes) and tumors with non-HER2-gene CN losses have similarly bad outcome as those with unfavorable nodal status. In <b>C,</b> non-HER2-gene CN gains strikingly confer the opposite outcome to patients who have undergone modified radical mastectomy (MRM) as compared to breast-conserving surgery (BCS).</p

Multivariate analysis models involving the main significant non-HER2-gene CN pattern effects on patient OS.

<p>Findings as for DFS in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103707#pone-0103707-g006" target="_blank">Figure 6</a>.</p

Multiple Correspondence Analyses graphs for comparing gene copies as assessed with qPCR and FISH.

<p><b>A:</b> Correspondence of <i>HER2</i> FISH (copies) to CN variables (n = 398). <b>B:</b> Correspondence of TOP2A FISH (copies) with CN variables co-expression (n = 393). Green: normal or loss; red: gain or amplification.</p

Hierarchical clustering of log transformed qPCR copy number (CN) values for chr17 genes in association with relevant breast cancer subtypes.

<p><b>A:</b> clustering of all 14 genes was informative in 376 cases and revealed 4 main CN patterns, out of which high CN for the HER2-related genes form the HER2 cluster and are predominantly found in HER2-positive (Luminal-HER2 and HER2-enriched) tumors; gains for the HER2 gene itself (ERBB2) mostly occur in parallel with STARD3. Luminal A and B, as well as TNBC are evenly represented in the non-HER2 clusters. <b>B:</b> If analyzing CN for the 4 HER2-related genes only, 36 of 93 tumors (38.7%) have non-continuous gains for these genes (complex pattern, red cluster) while the rest exhibit continuous gains in at least two genes, predominantly STARD3 and ERBB2 (gains, green cluster). <b>C:</b> Clustering of the non-HER2-related gene CN, i.e., 10 of 14 genes excluding STARD3, ERBB2, PSMD3 and THRA, yields 3 main clusters with equal representation of all subtypes (distribution of HER2-positive tumors and TNBC is shown). Cluster legend: natural log 0.69 corresponds to 2 copies; log 1.38 to 4 copies.</p

Concordance between FISH and qPCR CN classification of chromosome 17 gene status.

<p>Non-amplified: HER2/CEP17 ratio <2.2, TOP2A/CEP17 ratio <2;</p><p>*McNemar higher P-values indicate higher agreement.</p

Surface Modification of ZnO(0001)–Zn with Phosphonate-Based Self-Assembled Monolayers: Binding Modes, Orientation, and Work Function

We used partially fluorinated alkyl and aromatic phosphonates as model systems with similar molecular dipole moments to form self-assembled monolayers (SAMs) on the Zn-terminated ZnO(0001) surface. The introduced surface dipole moment allows tailoring the ZnO work function to tune the energy levels at the inorganic–organic interface to organic semiconductors, which should improve the efficiency of charge injection/extraction or exciton dissociation in hybrid electronic devices. By employing a wide range of surface characterization techniques supported by theoretical calculations, we present a detailed picture of the phosphonates’ binding to ZnO, the molecular orientation in the SAM, their packing density, as well as the concomitant work function changes. We show that for the aromatic SAM the interaction between neighboring molecules is strong enough to drive the formation of a more densely packed monolayer with a higher fraction of bidentate binding to ZnO, whereas for the alkyl SAM a lower packing density was found with a higher fraction of tridentate binding