Site-Specific Iron Substitution in STA-28, a Large Pore Aluminophosphate Zeotype Prepared by Using 1, 10-Phenanthrolines as Framework-Bound Templates

An AlPO4 zeotype has been prepared using the aromatic diamine 1, 10-phenanthroline and some of its methylated analogues as templates. In each case the two template N atoms bind to a specific framework Al site to expand its coordination to the unusual octahedral AlO4N2 environment. Furthermore, using this framework-bound template, Fe atoms can be included selectively at this site in the framework by direct synthesis, as confirmed by annular dark field scanning transmission electron microscopy and Rietveld refinement. Calcination removes the organic molecules to give large pore framework solids, with BET surface areas up to 540 m2 g-1 and two perpendicular sets of channels that intersect to give pore space connected by 12-ring openings along all crystallographic directions

Structural and dielectric properties of Sr2_{2}TiO4_{4} from first principles

We have investigated the structural and dielectric properties of Sr$_{2}$TiO$_{4}$,the first member of the Sr$_{n+1}$Ti$_{n}$O$_{3n+1}$ Ruddlesden-Popper series, within density functional theory. Motivated by recent work in which thin films of Sr$_{2}$TiO$_{4}$ were grown by molecular beam epitaxy (MBE) on SrTiO$_{3}$ substrates, the in-plane lattice parameter was fixed to the theoretically optimized lattice constant of cubic SrTiO$_{3}$ (n=$\infty$), while the out-of-plane lattice parameter and the internal structural parameters were relaxed. The fully relaxed structure was also investigated. Density functional perturbation theory was used to calculate the zone-center phonon frequencies, Born effective charges, and the electronic dielectric permittivity tensor. A detailed study of the contribution of individual infrared-active modes to the static dielectric permittivity tensor was performed. The calculated Raman and infrared phonon frequencies were found to be in agreement with experiment where available. Comparisons of the calculated static dielectric permittivity with experiments on both ceramic powders and epitaxial thin films are discussed.Comment: 11 pages, 1 figure, 8 tables, submitted to Phys. Rev.

Jellyfication of marine ecosystems as a likely consequence of overfishing small pelagic fishes: Lessons from the Benguela

Changes in two contrasting ecosystems of the Benguela upwelling region, one dominated at mid-trophic level by jellyfishes (Namibia, northern Benguela ecosystem, where small pelagic fish abundance has been severely depleted) and one still dominated by small pelagic fishes (South Africa, southern Benguela) were compared in an effort to determine ecosystem trajectories under different exploitation regimes. The role of small pelagic fishes (clupeoids) was highlighted in the context of their importance in maintaining interactions in marine ecosystems. In particular, we examined trophic cascades and possible irreversible changes that promote the proliferation of jellyfishes in marine systems. We found that the presence of large populations of small pelagic fishes has a fundamental role in preserving beneficial trophic interactions in these marine ecosystems. The implications of trophic cascades, such as those observed in the northern Benguela, for ecosystem-based management were apparent. In addition, this comparison provides contrasting case studies to inform the development of management scenarios that avoid ecosystem shifts that affect predators and reduce the value of fisheries production.Web of Scienc

MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data

Exchanging and understanding scientific data and their context represents a significant barrier to advancing research, especially with respect to information siloing. Maintaining information provenance and providing data curation and quality control help overcome common concerns and barriers to the effective sharing of scientific data. To address these problems in and the unique challenges of multicellular systems, we assembled a panel composed of investigators from several disciplines to create the MultiCellular Data Standard (MultiCellDS) with a use-case driven development process. The standard includes (1) digital cell lines, which are analogous to traditional biological cell lines, to record metadata, cellular microenvironment, and cellular phenotype variables of a biological cell line, (2) digital snapshots to consistently record simulation, experimental, and clinical data for multicellular systems, and (3) collections that can logically group digital cell lines and snapshots. We have created a MultiCellular DataBase (MultiCellDB) to store digital snapshots and the 200+ digital cell lines we have generated. MultiCellDS, by having a fixed standard, enables discoverability, extensibility, maintainability, searchability, and sustainability of data, creating biological applicability and clinical utility that permits us to identify upcoming challenges to uplift biology and strategies and therapies for improving human health

MultiCellDS: a standard and a community for sharing multicellular data

Cell biology is increasingly focused on cellular heterogeneity and multicellular systems. To make the fullest use of experimental, clinical, and computational efforts, we need standardized data formats, community-curated "public data libraries", and tools to combine and analyze shared data. To address these needs, our multidisciplinary community created MultiCellDS (MultiCellular Data Standard): an extensible standard, a library of digital cell lines and tissue snapshots, and support software. With the help of experimentalists, clinicians, modelers, and data and library scientists, we can grow this seed into a community-owned ecosystem of shared data and tools, to the benefit of basic science, engineering, and human health

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Statistical Language Modelling

Grammar-based natural language processing has reached a level where it can `understand' language to a limited degree in restricted domains. For example, it is possible to parse textual material very accurately and assign semantic relations to parts of sentences. An alternative approach originates from the work of Shannon over half a century ago [41], [42]. This approach assigns probabilities to linguistic events, where mathematical models are used to represent statistical knowledge. Once models are built, we decide which event is more likely than the others according to their probabilities. Although statistical methods currently use a very impoverished representation of speech and language (typically finite state), it is possible to train the underlying models from large amounts of data. Importantly, such statistical approaches often produce useful results. Statistical approaches seem especially well-suited to spoken language which is often spontaneous or conversational and not readily amenable to standard grammar-based approaches