Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

It has been difficult, historically, to manage and maintain early-stage experimental data collected by structural biologists in synchrotron facilities. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to manage collected data at synchrotrons and to facilitate the efficient and secure transfer of data to the owner’s home institution

Evolution of Massive Stars at Low Metallicity

This paper reports the contributions made on the occasion of the Special Session entitled "Evolution of Massive Stars at Low Metallicity” which was held on Sunday, December 9, 2007 in Kauai (USA

Human Melanoma-Associated Mast Cells Display a Distinct Transcriptional Signature Characterized by an Upregulation of the Complement Component 3 That Correlates With Poor Prognosis

Cutaneous melanoma is one of the most aggressive human malignancies and shows increasing incidence. Mast cells (MCs), long-lived tissue-resident cells that are particularly abundant in human skin where they regulate both innate and adaptive immunity, are associated with melanoma stroma (MAMCs). Thus, MAMCs could impact melanoma development, progression, and metastasis by secreting proteases, pro-angiogenic factors, and both pro-inflammatory and immuno-inhibitory mediators. To interrogate the as-yet poorly characterized role of human MAMCs, we have purified MCs from melanoma skin biopsies and performed RNA-seq analysis. Here, we demonstrate that MAMCs display a unique transcriptome signature defined by the downregulation of the FcεRI signaling pathway, a distinct expression pattern of proteases and pro-angiogenic factors, and a profound upregulation of complement component C3. Furthermore, in melanoma tissue, we observe a significantly increased number of C3$^{+}$ MCs in stage IV melanoma. Moreover, in patients, C3 expression significantly correlates with the MC-specific marker TPSAB1, and the high expression of both markers is linked with poorer melanoma survival. In vitro, we show that melanoma cell supernatants and tumor microenvironment (TME) mediators such as TGF-β, IL-33, and IL-1β induce some of the changes found in MAMCs and significantly modulate C3 expression and activity in MCs. Taken together, these data suggest that melanoma-secreted cytokines such as TGF-β and IL-1β contribute to the melanoma microenvironment by upregulating C3 expression in MAMCs, thus inducing an MC phenotype switch that negatively impacts melanoma prognosis

Families of superintegrable Hamiltonians constructed from exceptional polynomials

We introduce a family of exactly-solvable two-dimensional Hamiltonians whose wave functions are given in terms of Laguerre and exceptional Jacobi polynomials. The Hamiltonians contain purely quantum terms which vanish in the classical limit leaving only a previously known family of superintegrable systems. Additional, higher-order integrals of motion are constructed from ladder operators for the considered orthogonal polynomials proving the quantum system to be superintegrable

A Spectroscopic Study of Type Ibc Supernova Host Galaxies From Untargeted Surveys

We present the first spectroscopic study of the host environments of Type Ibc supernovae (SN Ibc) discovered exclusively by untargeted SN searches. Past studies of SN Ibc host environments have been biased towards high-mass, high-metallicity galaxies by focusing on SNe discovered in galaxytargeted SN searches. Our new observations more than double the total number of spectroscopic stellar population age and metallicity measurements published for untargeted SN Ibc host environments. For the 12 SNe Ib and 21 SNe Ic in our metallicity sample, we find median metallicities of 0.62 Z⊙ and 0.83 Z⊙, respectively, but determine that the discrepancy in the full distribution of metallicities is not statistically significant. This median difference would correspond to only a small difference in the mass loss via metal-line driven winds (. 30%), suggesting this does not play the dominant role in distinguishing SN Ib and Ic progenitors. However, the median metallicity of the 7 broad-lined SN Ic (SN Ic-BL) in our sample is significantly lower, 0.45 Z⊙. The age of the young stellar population of SN Ic-BL host environments also seems to be lower than for SN Ib and Ic, but our age sample is small. Combining all SN Ibc host environment spectroscopy from the literature to date does not reveal a significant difference in SN Ib and Ic metallicities, but reinforces the significance of the lower metallicities for SN Ic-BL. This combined sample demonstrates that galaxy-targeted SN searches introduce a significant bias for studies seeking to infer the metallicity distribution of SN progenitors, and we identify and discuss other systematic effects that play smaller roles. We discuss the path forward for making progress on SN Ibc progenitor studies in the LSST era. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.Astronom

Spontaneous Inter-layer Coherence in Double-Layer Quantum-Hall Systems I: Charged Vortices and Kosterlitz-Thouless Phase Transitions

At strong magnetic fields double-layer two-dimensional-electron-gas systems can form an unusual broken symmetry state with spontaneous inter-layer phase coherence. In this paper we explore the rich variety of quantum and finite-temperature phase transitions associated with this broken symmetry. We describe the system using a pseudospin language in which the layer degree-of-freedom is mapped to a fictional spin 1/2 degree-of-freedom. With this mapping the spontaneous symmetry breaking is equivalent to that of a spin 1/2 easy-plane ferromagnet. In this language spin-textures can carry a charge. In particular, vortices carry e/2 electrical charge and vortex-antivortex pairs can be neutral or carry charge e. We derive an effective low-energy action and use it to discuss the charged and collective neutral excitations of the system. We have obtained the parameters of the Landau-Ginzburg functional from first-principles estimates and from finite-size exact diagonalization studies. We use these results to estimate the dependence of the critical temperature for the Kosterlitz-Thouless phase transition on layer separation.Comment: 56 pages, 19 figures available upon request at [email protected]. RevTex 3.0. IUCM94-00

Protocol for population testing of an Internet-based Personalised Decision Support system for colorectal cancer screening

Extent: 8p.Background: Australia has a comparatively high incidence of colorectal (bowel) cancer; however, population screening uptake using faecal occult blood test (FOBT) remains low. This study will determine the impact on screening participation of a novel, Internet-based Personalised Decision Support (PDS) package. The PDS is designed to measure attitudes and cognitive concerns and provide people with individually tailored information, in real time, that will assist them with making a decision to screen. The hypothesis is that exposure to (tailored) PDS will result in greater participation in screening than participation following exposure to non-tailored PDS or resulting from the current non-tailored, paper-based approach. Methods/design: A randomised parallel trial comprising three arms will be conducted. Men and women aged 50-74 years (N = 3240) will be recruited. They must have access to the Internet; have not had an FOBT within the previous 12 months, or sigmoidoscopy or colonoscopy within the previous 5 years; have had no clinical diagnosis of bowel cancer. Groups 1 and 2 (PDS arms) will access a website and complete a baseline survey measuring decision-to-screen stage, attitudes and cognitive concerns and will receive immediate feedback; Group 1 will receive information 'tailored' to their responses in the baseline survey and group 2 will received 'non-tailored' bowel cancer information. Respondents in both groups will subsequently receive an FOBT kit. Group 3 (usual practice arm) will complete a paper-based version of the baseline survey and respondents will subsequently receive 'non-tailored' paper-based bowel cancer information with accompanying FOBT kit. Following despatch of FOBTs, all respondents will be requested to complete an endpoint survey. Main outcome measures are (1) completion of FOBT and (2) change in decision-to-screen stage. Secondary outcomes include satisfaction with decision and change in attitudinal scores from baseline to endpoint. Analyses will be performed using Chi-square tests, analysis of variance and log binomial generalized linear models as appropriate. Discussion: It is necessary to restrict participants to Internet users to provide an appropriately controlled evaluation of PDS. Once efficacy of the approach has been established, it will be important to evaluate effectiveness in the wider at-risk population, and to identify barriers to its implementation in those settings.Carlene J Wilson, Ingrid HK Flight, Ian T Zajac, Deborah Turnbull, Graeme P Young, Stephen R Cole, Tess Gregor

Anti-phospholipid human monoclonal antibodies inhibit CCR5-tropic HIV-1 and induce β-chemokines

Traditional antibody-mediated neutralization of HIV-1 infection is thought to result from the binding of antibodies to virions, thus preventing virus entry. However, antibodies that broadly neutralize HIV-1 are rare and are not induced by current vaccines. We report that four human anti-phospholipid monoclonal antibodies (mAbs) (PGN632, P1, IS4, and CL1) inhibit HIV-1 CCR5-tropic (R5) primary isolate infection of peripheral blood mononuclear cells (PBMCs) with 80% inhibitory concentrations of <0.02 to ∼10 µg/ml. Anti-phospholipid mAbs inhibited PBMC HIV-1 infection in vitro by mechanisms involving binding to monocytes and triggering the release of MIP-1α and MIP-1β. The release of these β-chemokines explains both the specificity for R5 HIV-1 and the activity of these mAbs in PBMC cultures containing both primary lymphocytes and monocytes

Ontology-based end-user visual query formulation: Why, what, who, how, and which?

Value creation in an organisation is a time-sensitive and data-intensive process, yet it is often delayed and bounded by the reliance on IT experts extracting data for domain experts. Hence, there is a need for providing people who are not professional developers with the flexibility to pose relatively complex and ad hoc queries in an easy and intuitive way. In this respect, visual methods for query formulation undertake the challenge of making querying independent of users’ technical skills and the knowledge of the underlying textual query language and the structure of data. An ontology is more promising than the logical schema of the underlying data for guiding users in formulating queries, since it provides a richer vocabulary closer to the users’ understanding. However, on the one hand, today the most of world’s enterprise data reside in relational databases rather than triple stores, and on the other, visual query formulation has become more compelling due to ever-increasing data size and complexity—known as Big Data. This article presents and argues for ontology-based visual query formulation for end-users; discusses its feasibility in terms of ontology-based data access, which virtualises legacy relational databases as RDF, and the dimensions of Big Data; presents key conceptual aspects and dimensions, challenges, and requirements; and reviews, categorises, and discusses notable approaches and systems