Resonant Raman scattering of core-shell GaN/AlN nanowires

We have analyzed the electron-phonon coupling in GaN/AlN core-shell nanowires by means of Raman scattering excited at various wavelengths in the ultraviolet spectral range (335, 325 and 300 nm) and as a function of the AlN shell thickness. The detailed analysis of the multi-phonon spectra evidences important differences with excitation energy. Under 325 and 300 nm excitation the Raman process is mediated by the allowedA₁(LO) phonon mode, where the atoms vibrate along the NW axis. Considering its selection rules, this mode is easily accessible in backscattering along the wurtzitecaxis. Interestingly, for 335 nm excitation the scattering process is instead mediated by theE₁(LO) phonon mode, where atoms vibrate in thec-plane and that is forbidden in this configuration. This change is ascribed to the band anticrossing caused by the uniaxial strain imposed by the AlN shell and the proximity, at this particular excitation energy, of real electronic transitions separated by the energy of the longitudinal optical phonon modes. The energy and character of the electronic bands can be tuned by varying the AlN shell thickness, a degree of freedom unique to core-shell nanowires. The interpretation of the experimental results is supported by calculations of the electronic transitions of GaN under uniaxial strain performed within the framework of ak · pmodel.

Impact of kinetics on the growth of GaN on graphene by plasma-assisted molecular beam epitaxy

The growth of GaN on graphene by molecular beam epitaxy was investigated. The most stable epitaxial relationship, i.e. [00.1]-oriented grains, is obtained at high temperature and N-rich conditions, which match those for nanowire growth. Alternatively, at moderate temperature and Ga-rich conditions, several metastable orientations are observed at the nucleation stage, which evolve preferentially towards [00.1]-oriented grains. The dependence of the nucleation regime on growth conditions was assigned to Ga adatom kinetics. This statement is consistent with the calculated graphene/GaN in-plane lattice coincidence and supported by a combination of transmission electron microscopy, x-ray diffraction, photoluminescence, and Raman spectroscopy experiments.

Abstract 2607: The cBioPortal for Cancer Genomics: an open source platform for accessing and interpreting complex cancer genomics data in the era of precision medicine

The cBioPortal for Cancer Genomics is an open-access portal (http://cbioportal.org) that enables interactive, exploratory analysis of large-scale cancer genomics data. It integrates genomic and clinical data, and provides a suite of visualization and analysis options, including cohort and patient-level visualization, mutation visualization, survival analysis, enrichment analysis, and network analysis. The user interface is user-friendly, responsive, and makes genomic data easily accessible to translational scientists, biologists, and clinicians.

The cBioPortal is a fully open source platform. All code is available on GitHub (https://github.com/cBioPortal/) under GNU Affero GPL license. The code base is maintained by multiple groups, including Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children’s Hospital of Philadelphia, Princess Margaret Cancer Centre, and The Hyve, an open source bioinformatics company based in the Netherlands. More than 30 academic centers as well as multiple pharmaceutical and biotech companies maintain private instances of the cBioPortal. This includes the recently launched cBioPortal instance at the NCI Genomic Data Commons (https://cbioportal.gdc.nci.nih.gov/), and two large cBioPortal instances hosting genomic and clinical data at MSK and DFCI, supporting the MSK-IMPACT and DFCI Profile projects, two of the largest clinical sequencing efforts in the world.

Our multi-institutional software team has accelerated the progress of evolving the core architectural technologies and developing new features to keep pace with the rapidly advancing fields of cancer genomics and precision cancer medicine. For example, we have integrated multi-platform genomics data with extensive clinical data including patient demographics, treatment history, and survival data. We have also developed a patient-centric view that visualizes both clinical and genomic data with annotation from OncoKB knowledge base. In the next few years, the development team will focus on the following areas:

(1) Implementing major architectural changes to ensure future scalability and performance.

(2) New features to support precision medicine, including (i) improved integration of knowledge base annotation, (ii) enhanced visualization of patient timeline, drug response, and tumor evolution, (iii) new patient similarity metrics, (iv) improved support for immunogenomics and immunotherapy, and (v) new visualization and analysis features for understanding response to therapy.

(3) New analysis and target discovery features for large cohorts, including (i) supporting user-defined virtual cohort by selecting samples from multiple studies, and (ii) comparison of genomic or clinical characteristics of two or more selected cohorts.

(4) Expanding community outreach, user support and training, and documentation.

Citation Format: Jianjiong Gao, Ersin Ciftci, Pichai Raman, Pieter Lukasse, Istemi Bahceci, Adam Abeshouse, Hsiao-Wei Chen, Ino de Bruijn, Benjamin Gross, Zachary Heins, Ritika Kundra, Aaron Lisman, Angelica Ochoa, Robert Sheridan, Onur Sumer, Yichao Sun, Jiaojiao Wang, Manda Wilson, Hongxin Zhang, James Xu, Andy Dufilie, Priti Kumari, James Lindsay, Anthony Cros, Karthik Kalletla, Fedde Schaeffer, Sander Tan, Sjoerd van Hagen, Jorge Reis-Filho, Kees van Bochove, Ugur Dogrusoz, Trevor Pugh, Adam Resnick, Chris Sander, Ethan Cerami, Nikolaus Schultz. The cBioPortal for Cancer Genomics: an open source platform for accessing and interpreting complex cancer genomics data in the era of precision medicine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2607. doi:10.1158/1538-7445.AM2017-2607

Abstract LB-008: The Pediatric Brain Tumor Atlas: building an integrated, multi-platform data-rich ecosystem for collaborative discovery in the cloud

Pediatric brain tumors are the leading cause of disease-related death in children. However, despite large scale data-driven efforts for pediatric cancers by the NIH (e.g. TARGET, Therapeutically Applicable Research To Generate Effective Treatments), public access to large-scale pediatric brain tumor genomic data remains limited. As a result, precision medicine initiatives and clinical trials in pediatric brain tumors are hampered by the absence of publicly available genomic resources that can dynamically inform novel discovery and clinical implementation of genomic and molecular approaches for diagnostic and therapeutic purposes in affected children. The Pediatric Brain Tumor Atlas is a concerted multi-institution effort by the Children’s Brain Tumor Consortium (CBTTC) and the Pacific Pediatric Neuro-Oncology Consortium to characterize and deeply profile a newly defined cohort of >1600 brain tumor samples across diverse histopathologies via a combination of whole exome sequencing, whole genome sequencing, RNA sequencing and limited proteomic analysis. Importantly, the Atlas initiative provides for near real-time integration, dissemination, and sharing of the associated raw and analyzed data through an ecosystem of data discovery platforms. As data of this size and complexity require a bolus of scalable computational power and storage, a new cloud-based collaborative scientific environment termed CAVATICA (cavatica.org) has been launched to support integrative analysis and open access to data alongside shared computation and algorithms that empower users to further integrate and analyse their own uploaded data. Importantly, CAVATICA provides further portal access to dbGaP approved users to TCGA and other NCI datasets hosted by the NCI’s Cancer Genomics’ Cloud. Additionally, it provides for scalable integration of these and additional disease-specific datasets on the platform via transdisciplinary analyses. Currently, one of the biggest barriers and challenges to collaborative research in large datasets is the transfer and processing of ‘big data’. By committing to the rapid release of these large pediatric brain tumor data and their deposition in CAVATICA’s cloud-based environment supporting shared pipelines, computation, and visualizations, PNOC and the CBTTC’s collaborating membership are seeking to provide a centralized, collaborative rapid discovery environment for researchers to engage new discovery and data reuse. In addition to unprocessed genomic, whole genome and RNA sequencing data in CAVATICA, processed annotations and and additional biospecimen querying is enabled for the Pediatric Brain Tumor Atlas via PedcBioPortal (PedcBioPortal.org), a data visualization and analysis application further integrating across additional public and deposited datasets. The combination of large-scale genomic data and integrative cloud-based analytic platforms with what is one of the largest genomic date cohorts to date for pediatric brain tumors serves to define a new paradigm for pediatric cancer research and collaborative discovery.

Citation Format: Adam C. Resnick, Phillip B. Storm, Angela J. Waanders, Jena V. Lilly, Rishi R. Lulla, Sabine Mueller, Michael Prados, Leonard S. Sender, Allison Heath, Alex S. Felmeister, Anthony Cros, Yuankun Zhu, Pichai Raman. The Pediatric Brain Tumor Atlas: building an integrated, multi-platform data-rich ecosystem for collaborative discovery in the cloud [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-008. doi:10.1158/1538-7445.AM2017-LB-008

Optical contrast of 2D InSe on SiO2/Si and transparent substrates using bandpass filters

The particular optical and electronic properties recently reported for 2D InSe depict this 2D material as being very versatile for future electronic and optoelectronic devices with tunable and optimized functionalities. For its fundamental study and the development of practical applications, rapid and accurate identification methods of atomically thin InSe are essential. Here, we demonstrate an enhancement of the optical contrast between InSe nanosheets and the underlying SiO₂/Si substrate by illuminating with a 40 nm wide bandpass filter centered at 500 nm. Moreover, we study the optical contrast of 2D InSe on transparent substrates. Our results suggest that a good optical contrast is achieved for transparent substrates with low real refractive indices such as LiF or a viscoelastic polydimethylsiloxane stamp. In this case, an optimum optical contrast would be achieved by using a bandpass filter centered at 450 nm. These results can be very useful for speeding up the continuously growing research on 2D InSe and its applications.

Assessment of Polarity in GaN Self-Assembled Nanowires by Electrical Force Microscopy

In this work, we demonstrate the capabilities of atomic force microscopies (AFMs) for the nondestructive determination of the polarity of GaN nanowires (NWs). Three complementary AFMs are analyzed here: Kelvin probe force microscopy (KPFM), light-assisted KPFM, and piezo-force microscopy (PFM). These techniques allow us to assess the polarity of individual NWs over an area of tens of μm(2) and provide statistics on the polarity of the ensemble with an accuracy hardly reachable by other methods. The precise quantitative analysis of the tip-sample interaction by multidimensional spectroscopic measurements, combined with advanced data analysis, has allowed the separate characterization of electrostatic and van der Waals forces as a function of tip-sample distance. Besides their polarity, the net surface charge density of individual NWs was estimated.

Growth, structural and optical properties of AlGaN nanowires in the whole composition range

We report on the growth of AlxGa1-xN nanowires by plasma-assisted molecular beam epitaxy for x in the 0.3-0.8 range. Based on a combination of macro- and micro-photoluminescence, Raman spectroscopy, x-ray diffraction and scanning electron microscopy experiments, it is shown that the structural and optical properties of AlGaN NWs are governed by the presence of compositional fluctuations associated with strongly localized electronic states. A growth model is proposed, which suggests that, depending on growth temperature and metal adatom density, macroscopic composition fluctuations are mostly of kinetic origin and are directly related to the nucleation of the AlGaN nanowire section on top of the GaN nanowire base which is used as a substrate.

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal.

BioMart: a data federation framework for large collaborative projects

BioMart is a freely available, open source, federated database system that provides a unified access to disparate, geographically distributed data sources. It is designed to be data agnostic and platform independent, such that existing databases can easily be incorporated into the BioMart framework. BioMart allows databases hosted on different servers to be presented seamlessly to users, facilitating collaborative projects between different research groups. BioMart contains several levels of query optimization to efficiently manage large data sets and offers a diverse selection of graphical user interfaces and application programming interfaces to ensure that queries can be performed in whatever manner is most convenient for the user. The software has now been adopted by a large number of different biological databases spanning a wide range of data types and providing a rich source of annotation available to bioinformaticians and biologists alike.

BioMart Central Portal: an open database network for the biological community

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.

The structural properties of GaN/AlN core-shell nanocolumn heterostructures

The growth and structural properties of GaN/AlN core-shell nanowire heterostructures have been studied using a combination of resonant x-ray diffraction, Raman spectroscopy and high resolution transmission electron microscopy experiments. For a GaN core of 20 nm diameter on average surrounded by a homogeneous AlN shell, the built-in strain in GaN is found to agree with theoretical calculations performed using a valence force field model. It is then concluded that for an AlN thickness up to at least 12 nm both core and shell are in elastic equilibrium. However, in the case of an inhomogeneous growth of the AlN shell caused by the presence of steps on the sides of the GaN core, plastic relaxation is found to occur. Consistent with the presence of dislocations at the GaN/AlN interface, it is proposed that this plastic relaxation, especially efficient for AlN shell thickness above 3 nm, is promoted by the shear strain induced by the AlN inhomogeneity.

The structural properties of GaN insertions in GaN/AlN nanocolumn heterostructures

The strain state of 1 and 2.5 nm thick GaN insertions in GaN/AlN nanocolumn heterostructures has been studied by means of a combination of high resolution transmission electron microscopy, Raman spectroscopy and theoretical modeling. It is found that 2.5 nm thick GaN insertions are partially relaxed, which has been attributed to the presence of dislocations in the external AlN capping layer, in close relationship with the morphology of GaN insertions and with the AlN capping mechanism. The observed plastic relaxation in AlN is consistent with the small critical thickness expected for GaN/AlN radial heterostructures.

X-ray absorption near-edge structure of GaN with high Mn concentration grown on SiC

By means of x-ray absorption near-edge structure (XANES) several Ga(1-x)Mn(x)N (0.03<x<0.09) layers have been analyzed. The Mn-doped GaN samples consisted of different epilayers grown by molecular beam epitaxy on [0001] SiC substrates. The low mismatch between GaN and SiC allows for a good quality and homogeneity of the material. The measurements were performed in fluorescence mode around both the Ga and Mn K edges. All samples studied present a similar Mn ionization state, very close to 2+, and tetrahedral coordination. In order to interpret the near-edge structure, we have performed ab initio calculations using the full potential linear augmented plane wave method as implemented in the Wien2k code. The calculations show the appearance of a Mn bonding [Formula: see text] band localized in the gap region, and the corresponding anti-bonding state [Formula: see text], which seem to be responsible for the double structure which appears at the pre-edge absorption region. The shoulders and main absorption peak of the XANES spectra are attributed to transitions from the Mn(1s) band to the conduction bands, which are partially dipole allowed because of the Mn(4p) contribution to these bands.

Therapeutic efficacy of intra-cochlear administration of methylprednisolone after acoustic trauma caused by gunshot noise in guinea pigs

The therapeutic efficacy of cochlear infusion of methylprednisolone (MP) after an impulse noise trauma (170dB SPL peak) was evaluated in guinea pigs. The compound action potential threshold shifts were measured over a 14 days recovery period after the gunshot exposure. For each animal, one of the cochlea was perfused directly into the scala tympani with MP during 7 days via a mini-osmotic pump, whereas the other cochlea was not pump-implanted. The functional study of hearing was supplemented by histological analysis. Forty eight hours after the trauma, significant differences between auditory threshold shifts in the implanted and non-implanted ears were observed for frequencies above 8kHz. At day 7, the difference was significant for only one frequency and no difference was observed after 14 days recovery. Cochleograms showed that the hair cell losses were significantly lower in the MP treated ears. This work indicates that direct infusion of MP into perilymphatic space accelerates hearing recovery, reduces hair cell losses after impulse noise trauma but does not limit permanent threshold shifts.

Defect turbulence in a spiral wave pattern in the torsional Couette flow

Our experimental study is devoted to the transition to defect turbulence of a periodic spiral wave pattern occurring in the flow between a rotating and a stationary disk. As the rotation rate Omega of the disk is increased, the radial phase velocity of the waves changes its sign: The waves that propagate first outward on average, then become stationary and finally propagate inward. As they become stationary, the nucleation of topological defects breaks the periodicity of the pattern. For higher Omega, more and more defects are generated in the flow pattern. This article presents the statistical study of this defect mediated turbulence.

Magnetic Field and Plasma Observations at Mars: Initial Results of the Mars Global Surveyor Mission

The magnetometer and electron reflectometer investigation (MAG/ER) on the Mars Global Surveyor spacecraft has obtained magnetic field and plasma observations throughout the near-Mars environment, from beyond the influence of Mars to just above the surface (at an altitude of approximately 100 kilometers). The solar wind interaction with Mars is in many ways similar to that at Venus and at an active comet, that is, primarily an ionospheric-atmospheric interaction. No significant planetary magnetic field of global scale has been detected to date (<2 x 10(21) Gauss-cubic centimeter), but here the discovery of multiple magnetic anomalies of small spatial scale in the crust of Mars is reported.

Magnetic Field and Plasma Observations at Mars: Initial Results of the Mars Global Surveyor Mission

The magnetometer and electron reflectometer investigation (MAG/ER) on the Mars Global Surveyor spacecraft has obtained magnetic field and plasma observations throughout the near-Mars environment, from beyond the influence of Mars to just above the surface (at an altitude of approximately 100 kilometers). The solar wind interaction with Mars is in many ways similar to that at Venus and at an active comet, that is, primarily an ionospheric-atmospheric interaction. No significant planetary magnetic field of global scale has been detected to date (<2 x 10(21) Gauss-cubic centimeter), but here the discovery of multiple magnetic anomalies of small spatial scale in the crust of Mars is reported.