Controlling the False Discovery Rate in Astrophysical Data Analysis

The False Discovery Rate (FDR) is a new statistical procedure to control the number of mistakes made when performing multiple hypothesis tests, i.e. when comparing many data against a given model hypothesis. The key advantage of FDR is that it allows one to a priori control the average fraction of false rejections made (when comparing to the null hypothesis) over the total number of rejections performed. We compare FDR to the standard procedure of rejecting all tests that do not match the null hypothesis above some arbitrarily chosen confidence limit, e.g. 2 sigma, or at the 95% confidence level. When using FDR, we find a similar rate of correct detections, but with significantly fewer false detections. Moreover, the FDR procedure is quick and easy to compute and can be trivially adapted to work with correlated data. The purpose of this paper is to introduce the FDR procedure to the astrophysics community. We illustrate the power of FDR through several astronomical examples, including the detection of features against a smooth one-dimensional function, e.g. seeing the ``baryon wiggles'' in a power spectrum of matter fluctuations, and source pixel detection in imaging data. In this era of large datasets and high precision measurements, FDR provides the means to adaptively control a scientifically meaningful quantity -- the number of false discoveries made when conducting multiple hypothesis tests.Comment: 15 pages, 9 figures. Submitted to A

Enhanced imaging of microcalcifications in digital breast tomosynthesis through improved image-reconstruction algorithms

PURPOSE: We develop a practical, iterative algorithm for image-reconstruction in under-sampled tomographic systems, such as digital breast tomosynthesis (DBT). METHOD: The algorithm controls image regularity by minimizing the image total $p$-variation (TpV), a function that reduces to the total variation when $p=1.0$ or the image roughness when $p=2.0$. Constraints on the image, such as image positivity and estimated projection-data tolerance, are enforced by projection onto convex sets (POCS). The fact that the tomographic system is under-sampled translates to the mathematical property that many widely varied resultant volumes may correspond to a given data tolerance. Thus the application of image regularity serves two purposes: (1) reduction of the number of resultant volumes out of those allowed by fixing the data tolerance, finding the minimum image TpV for fixed data tolerance, and (2) traditional regularization, sacrificing data fidelity for higher image regularity. The present algorithm allows for this dual role of image regularity in under-sampled tomography. RESULTS: The proposed image-reconstruction algorithm is applied to three clinical DBT data sets. The DBT cases include one with microcalcifications and two with masses. CONCLUSION: Results indicate that there may be a substantial advantage in using the present image-reconstruction algorithm for microcalcification imaging.Comment: Submitted to Medical Physic

The space group classification of topological band insulators

Topological band insulators (TBIs) are bulk insulating materials which feature topologically protected metallic states on their boundary. The existing classification departs from time-reversal symmetry, but the role of the crystal lattice symmetries in the physics of these topological states remained elusive. Here we provide the classification of TBIs protected not only by time-reversal, but also by crystalline symmetries. We find three broad classes of topological states: (a) Gamma-states robust against general time-reversal invariant perturbations; (b) Translationally-active states protected from elastic scattering, but susceptible to topological crystalline disorder; (c) Valley topological insulators sensitive to the effects of non-topological and crystalline disorder. These three classes give rise to 18 different two-dimensional, and, at least 70 three-dimensional TBIs, opening up a route for the systematic search for new types of TBIs.Comment: Accepted in Nature Physic

Revised circulation scheme North of the Denmark Strait

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Elsevier Ltd. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part I: Oceanographic Research Papers 79 (2013): 20-39, doi:10.1016/j.dsr.2013.05.007.The circulation and water mass transports north of the Denmark Strait are investigated using recently collected and historical in-situ data along with an idealized numerical model and atmospheric reanalysis fields. Emphasis is placed on the pathways of dense water feeding theDenmark StraitOverflowWater plume as well as the upper-layer circulation of freshwater. It is found that the East Greenland Current (EGC) bifurcates at the northern end of the Blosseville Basin, some 450 km upstream of the Denmark Strait, advecting overflow water and surface freshwater away from the boundary. This “separated EGC” flows southward adjacent to the previously identified North Icelandic Jet, indicating that approximately 70% of the Denmark Strait Overflow Water approaches the sill along the Iceland continental slope. Roughly a quarter of the freshwater transport of the EGC is diverted offshore via the bifurcation. Two hypotheses are examined to explain the existence of the separated EGC. The atmospheric fields demonstrate that flow distortion due to the orography of Greenland imparts significant vorticity into the ocean in this region. The negative wind stress curl, together with the closed bathymetric contours of the Blosseville Basin, is conducive for spinning up an anti-cyclonic gyre whose offshore branch could represent the separated EGC. An idealized numerical simulation suggests instead that the current is primarily eddy-forced. In particular, baroclinic instability of the model EGC spawns large anticyclones that migrate offshore and coalesce upon reaching the Iceland continental slope, resulting in the separated EGC. Regardless of the formation mechanism, the recently obtained shipboard data and historical hydrography both indicate that the separated EGC is a permanent feature of the circulation north of the Denmark Strait.Support for this work was provided by the Norwegian Research Council (KV), the European Union 7th Framework Programme (FP7 2007-2013) under grant agreement n.308299 NACLIM Project (KV), US National Science Foundation grants OCE-0959381 (RP, MS, DT) and OCE-0850416 (MS), and the Natural Sciences and Engineering Research Council of Canada (KM)

Controlling collapse in Bose-Einstein condensates by temporal modulation of the scattering length

We consider, by means of the variational approximation (VA) and direct numerical simulations of the Gross-Pitaevskii (GP) equation, the dynamics of 2D and 3D condensates with a scattering length containing constant and harmonically varying parts, which can be achieved with an ac magnetic field tuned to the Feshbach resonance. For a rapid time modulation, we develop an approach based on the direct averaging of the GP equation,without using the VA. In the 2D case, both VA and direct simulations, as well as the averaging method, reveal the existence of stable self-confined condensates without an external trap, in agreement with qualitatively similar results recently reported for spatial solitons in nonlinear optics. In the 3D case, the VA again predicts the existence of a stable self-confined condensate without a trap. In this case, direct simulations demonstrate that the stability is limited in time, eventually switching into collapse, even though the constant part of the scattering length is positive (but not too large). Thus a spatially uniform ac magnetic field, resonantly tuned to control the scattering length, may play the role of an effective trap confining the condensate, and sometimes causing its collapse.Comment: 7 figure

T-cell subpopulations αβ and γδ in cord blood of very preterm infants : The influence of intrauterine infection

Open Access: This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are creditedPreterm infants are very susceptible to infections. Immune response mechanisms in this group of patients and factors that influence cord blood mononuclear cell populations remain poorly understood and are considered insufficient. However, competent immune functions of the cord blood mononuclear cells are also described. The aim of this work was to evaluate the T-cell population (CD3+) with its subpopulations bearing T-cell receptor (TCR) αβ or TCR γδ in the cord blood of preterm infants born before 32 weeks of gestation by mothers with or without an intrauterine infection. Being a pilot study, it also aimed at feasibility check and assessment of an expected effect size. The cord blood samples of 46 infants age were subjected to direct immunofluorescent staining with monoclonal antibodies and then analyzed by flow cytometry. The percentage of CD3+ cells in neonates born by mothers with diagnosis of intrauterine infection was significantly lower than in neonates born by mothers without infection (p = 0.005; Mann-Whitney U test). The number of cells did not differ between groups. Infection present in the mother did not have an influence on the TCR αβ or TCR γδ subpopulations. Our study contributes to a better understanding of preterm infants' immune mechanisms, and sets the stage for further investigations.Peer reviewedFinal Published versio

Data quality monitoring and performance metrics of a prospective, population-based observational study of maternal and newborn health in low resource settings

BACKGROUND: To describe quantitative data quality monitoring and performance metrics adopted by the Global Network´s (GN) Maternal Newborn Health Registry (MNHR), a maternal and perinatal population-based registry (MPPBR) based in low and middle income countries (LMICs). METHODS: Ongoing prospective, population-based data on all pregnancy outcomes within defined geographical locations participating in the GN have been collected since 2008. Data quality metrics were defined and are implemented at the cluster, site and the central level to ensure data quality. Quantitative performance metrics are described for data collected between 2010 and 2013. RESULTS: Delivery outcome rates over 95% illustrate that all sites are successful in following patients from pregnancy through delivery. Examples of specific performance metric reports illustrate how both the metrics and reporting process are used to identify cluster-level and site-level quality issues and illustrate how those metrics track over time. Other summary reports (e.g. the increasing proportion of measured birth weight compared to estimated and missing birth weight) illustrate how a site has improved quality over time. CONCLUSION: High quality MPPBRs such as the MNHR provide key information on pregnancy outcomes to local and international health officials where civil registration systems are lacking. The MNHR has measures in place to monitor data collection procedures and improve the quality of data collected. Sites have increasingly achieved acceptable values of performance metrics over time, indicating improvements in data quality, but the quality control program must continue to evolve to optimize the use of the MNHR to assess the impact of community interventions in research protocols in pregnancy and perinatal health.Fil: Goudar, Shivaprasad S.. KLE University. Jawaharlal Nehru Medical College; IndiaFil: Stolka, Kristen B.. Research Triangle Institute International; Estados UnidosFil: Koso Thomas, Marion. Eunice Kennedy Shriver National Institute of Child Health and Human Development; Estados UnidosFil: Honnungar, Narayan V.. KLE University. Jawaharlal Nehru Medical College; IndiaFil: Mastiholi, Shivanand C.. KLE University. Jawaharlal Nehru Medical College; IndiaFil: Ramadurg, Umesh Y.. S. Nijalingappa Medical College; IndiaFil: Dhaded, Sangappa M.. KLE University. Jawaharlal Nehru Medical College; IndiaFil: Pasha, Omrana. Aga Khan University; PakistánFil: Patel, Archana. Indira Gandhi Government Medical College and Lata Medical Research Foundation; IndiaFil: Esamai, Fabian. University School of Medicine; KeniaFil: Chomba, Elwyn. University of Zambia; ZambiaFil: Garces, Ana. Universidad de San Carlos; GuatemalaFil: Althabe, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto de Efectividad Clínica y Sanitaria; ArgentinaFil: Carlo, Waldemar A.. University of Alabama at Birmingahm; Estados UnidosFil: Goldenberg, Robert L.. Columbia University; Estados UnidosFil: Hibberd, Patricia L.. Massachusetts General Hospital for Children; Estados UnidosFil: Liechty, Edward A.. Indiana University; Estados UnidosFil: Krebs, Nancy F.. University of Colorado School of Medicine; Estados UnidosFil: Hambidge, Michael K.. University of Colorado School of Medicine; Estados UnidosFil: Moore, Janet L.. Research Triangle Institute International; Estados UnidosFil: Wallace, Dennis D.. Research Triangle Institute International; Estados UnidosFil: Derman, Richard J. Christiana Care Health Services; Estados UnidosFil: Bhalachandra, Kodkany S.. KLE University. Jawaharlal Nehru Medical College; IndiaFil: Bose, Carl L.. University of North Carolina; Estados Unido

A theoretical investigation of the low lying electronic structure of poly(p-phenylene vinylene)

The two-state molecular orbital model of the one-dimensional phenyl-based semiconductors is applied to poly(p-phenylene vinylene). The energies of the low-lying excited states are calculated using the density matrix renormalization group method. Calculations of both the exciton size and the charge gap show that there are both Bu and Ag excitonic levels below the band threshold. The energy of the 1Bu exciton extrapolates to 2.60 eV in the limit of infinite polymers, while the energy of the 2Ag exciton extrapolates to 2.94 eV. The calculated binding energy of the 1Bu exciton is 0.9 eV for a 13 phenylene unit chain and 0.6 eV for an infinite polymer. This is expected to decrease due to solvation effects. The lowest triplet state is calculated to be at ca. 1.6 eV, with the triplet-triplet gap being ca. 1.6 eV. A comparison between theory, and two-photon absorption and electroabsorption is made, leading to a consistent picture of the essential states responsible for most of the third-order nonlinear optical properties. An interpretation of the experimental nonlinear optical spectroscopies suggests an energy difference of ca. 0.4 eV between the vertical energy and ca. 0.8 eV between the relaxed energy, of the 1Bu exciton and the band gap, respectively.Comment: LaTeX, 19 pages, 7 eps figures included using epsf. To appear in Physical Review B, 199

Data Mining and Machine Learning in Astronomy

We review the current state of data mining and machine learning in astronomy. 'Data Mining' can have a somewhat mixed connotation from the point of view of a researcher in this field. If used correctly, it can be a powerful approach, holding the potential to fully exploit the exponentially increasing amount of available data, promising great scientific advance. However, if misused, it can be little more than the black-box application of complex computing algorithms that may give little physical insight, and provide questionable results. Here, we give an overview of the entire data mining process, from data collection through to the interpretation of results. We cover common machine learning algorithms, such as artificial neural networks and support vector machines, applications from a broad range of astronomy, emphasizing those where data mining techniques directly resulted in improved science, and important current and future directions, including probability density functions, parallel algorithms, petascale computing, and the time domain. We conclude that, so long as one carefully selects an appropriate algorithm, and is guided by the astronomical problem at hand, data mining can be very much the powerful tool, and not the questionable black box.Comment: Published in IJMPD. 61 pages, uses ws-ijmpd.cls. Several extra figures, some minor additions to the tex