Constructing Impactful Machine Learning Research for Astronomy: Best Practices for Researchers and Reviewers

Machine learning has rapidly become a tool of choice for the astronomical community. It is being applied across a wide range of wavelengths and problems, from the classification of transients to neural network emulators of cosmological simulations, and is shifting paradigms about how we generate and report scientific results. At the same time, this class of method comes with its own set of best practices, challenges, and drawbacks, which, at present, are often reported on incompletely in the astrophysical literature. With this paper, we aim to provide a primer to the astronomical community, including authors, reviewers, and editors, on how to implement machine learning models and report their results in a way that ensures the accuracy of the results, reproducibility of the findings, and usefulness of the method.Comment: 14 pages, 3 figures; submitted to the Bulletin of the American Astronomical Societ

Duality and distance formulas in spaces defined by means of oscillation

For the classical space of functions with bounded mean oscillation, it is well known that VMO∗∗=BMOVMO∗∗=BMO and there are many characterizations of the distance from a function f in BMOBMO to VMOVMO. When considering the Bloch space, results in the same vein are available with respect to the little Bloch space. In this paper such duality results and distance formulas are obtained by pure functional analysis. Applications include general Möbius invariant spaces such as QK-spaces, weighted spaces, Lipschitz–Hölder spaces and rectangular BMOBMO of several variables

Magnetic Field Amplification in Galaxy Clusters and its Simulation

We review the present theoretical and numerical understanding of magnetic field amplification in cosmic large-scale structure, on length scales of galaxy clusters and beyond. Structure formation drives compression and turbulence, which amplify tiny magnetic seed fields to the microGauss values that are observed in the intracluster medium. This process is intimately connected to the properties of turbulence and the microphysics of the intra-cluster medium. Additional roles are played by merger induced shocks that sweep through the intra-cluster medium and motions induced by sloshing cool cores. The accurate simulation of magnetic field amplification in clusters still poses a serious challenge for simulations of cosmological structure formation. We review the current literature on cosmological simulations that include magnetic fields and outline theoretical as well as numerical challenges.Comment: 60 pages, 19 Figure

AFM study of morphology and mechanical properties of a chimeric 2 spider silk and bone sialoprotein protein for bone regeneration

Atomic force microscopy (AFM) was used to assess a new chimeric protein consisting of a fusion protein of the consensus repeat for Nephila clavipes spider dragline protein and bone sialoprotein (6merþBSP). The elastic modulus of this protein in film form was assessed through force curves, and film surface roughness was also determined. The results showed a significant difference among the elastic modulus of the chimeric silk protein, 6merþBSP, and control films consisting of only the silk component (6mer). The behavior of the 6merþBSP and 6mer proteins in aqueous solution in the presence of calcium (Ca) ions was also assessed to determine interactions between the inorganic and organic components related to bone interactions, anchoring, and biomaterial network formation. The results demonstrated the formation of protein networks in the presence of Ca2þ ions, characteristics that may be important in the context of controlling materials assembly and properties related to bone formation with this new chimeric silk-BSP protein.Silvia Games thanks the Foundation for Science and Technology (FCT) for supporting her Ph.D. grant, SFRH/BD/28603/2006. This work was carried out under the scope of the European NoE EXPERTISSUES (NMP3-CT-2004-500283), the Chimera project (PTDC/EBB-EBI/109093/2008) funded by the FCT agency, the NIH (P41 EB002520) Tissue Engineering Resource Center, and the NIH (EB003210 and DE017207)

Sotatercept, a novel transforming growth factor beta ligand trap, improves anemia in beta-thalassemia: a phase 2, open-label, dose-finding study

\u3b2-thalassemia, a hereditary blood disorder caused by defective synthesis of hemoglobin \u3b2 globin chains, leads to ineffective erythropoiesis and chronic anemia that may require blood transfusions. Sotatercept (ACE-011) acts as a ligand trap to inhibit negative regulators of late-stage erythropoiesis in the transforming growth factor beta superfamily, correcting ineffective erythropoiesis. In this phase II, open-label, dose-finding study, 16 patients with transfusion-dependent \u3b2-thalassemia and 30 patients with non-transfusion-dependent \u3b2 thalassemia were enrolled at 7 centers in 4 countries from November 2012 to November 2014. Patients were treated with sotatercept at 0.1, 0.3, 0.5, 0.75, or 1.0 mg/kg to determine a safe and effective dose. Doses were administered by subcutaneous injection every 3 weeks. Patients were treated for 6422 months. Response was assessed as a 6520% reduction in transfusion burden sustained for 24 weeks in transfusion-dependent \u3b2-thalassemia patients, and an increase in hemoglobin level of 651.0 g/dL sustained for 12 weeks in non-transfusion-dependent \u3b2-thalassemia patients. Sotatercept was well tolerated. After a median treatment duration of 14.4 months (range 0.6-35.9), no severe life-threatening adverse events were observed; 13% of patients reported serious but manageable adverse events. The active dose of sotatercept was 650.3 mg/kg for non-transfusion-dependent \u3b2-thalassemia and 650.5 mg/kg for transfusion-dependent \u3b2-thalassemia patients. Of 30 non-transfusion-dependent \u3b2-thalassemia patients treated with 650.1 mg/kg sotatercept, 18 (60%) achieved a mean hemoglobin increase 651.0 g/dL, and 11 (37%) an increase 651.5 g/dL, sustained for 6512 weeks. Four (100%) transfusion-dependent \u3b2-thalassemia patients treated with 1.0 mg/kg sotatercept achieved a transfusion-burden reduction of 6520%. Sotatercept was effective and well tolerated in patients with \u3b2-thalassemia. Most non-transfusion-dependent \u3b2-thalassemia patients treated with higher doses achieved sustained increases in hemoglobin level. Transfusion-dependent \u3b2-thalassemia patients treated with higher doses of sotatercept achieved notable reductions in transfusion requirement. The registration number at ClinicalTrials.gov was NCT01571635

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

Background Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems. Methodology/Principal Findings The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share <10% bacterial types defined at 3% sequence similarity level. Surface and deep water, coastal and open ocean, and anoxic and oxic ecosystems host distinct communities that reflect productivity, land influences and other environmental constraints such as oxygen availability. The high variability of bacterial community composition specific to vent and coastal ecosystems reflects the heterogeneity and dynamic nature of these habitats. Both pelagic and benthic bacterial community distributions correlate with surface water productivity, reflecting the coupling between both realms by particle export. Also, differences in physical mixing may play a fundamental role in the distribution patterns of marine bacteria, as benthic communities showed a higher dissimilarity with increasing distance than pelagic communities. Conclusions/Significance This first synthesis of global bacterial distribution across different ecosystems of the World's oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed