Data Science Seminar: The data science revolution in Physics and Astronomy

Abstract Heading into the 2020s, Physics and Astronomy are undergoing experimental revolutions that will reshape our picture of the fabric of the Universe. The Large Hadron Collider (LHC), the largest particle physics project in the world, produces 30 petabytes of data annually that need to be sifted through, analysed, and modelled. In astrophysics, the Large Synoptic Survey Telescope (LSST) will be taking a high-resolution image of the full sky every 3 days, leading to data rates of 30 terabytes per night over ten years. These experiments endeavour to answer the question why 96% of the content of the universe currently elude our physical understanding. Both the LHC and LSST share the 5-dimensional nature of their data, with position, energy and time being the fundamental axes. This talk will present an overview of the experiments and data that is gathered, and outlines the challenges in extracting information. Common strategies employed are very similar to industrial data! Science problems (e.g., data filtering, machine learning, statistical interpretation) and provide a seed for exchange of knowledge between academia and industry. Speaker Biography Professor Mark Sullivan Mark Sullivan is a Professor of Astrophysics in the Department of Physics and Astronomy. Mark completed his PhD at Cambridge, and following postdoctoral study in Durham, Toronto and Oxford, now leads a research group at Southampton studying dark energy using exploding stars called "type Ia supernovae". Mark has many years' experience of research that involves repeatedly imaging the night sky to track the arrival of transient objects, involving significant challenges in data handling, processing, classification and analysis.

Egyptian Pagans through Christian Eyes

Construction of Christian identity in Egypt proceeded in pace with construction of the Egyptian pagan “Other” between the second and sixth centuries. Apologies, martyrdoms, apocalypses, histories, sermons, hagiographies, and magical texts provide several different vantage points from which to view the Christian construction of the Egyptian pagan “Other”: as the agent of anti-Christian violence, as an intellectual rival, as an object of anti-pagan violence, as an obstacle to salvation, and—perhaps most dangerously—as but another participant in a shared religious experience. The recent work of social scientists on identity, deviance, violence, social/cultural memory, and religiosity provides insight into the strategies by which construction of the “Other” was part of a larger project of fashioning a “proper” Christian religious domain.

A study of asymptomatic bacteriuria in Egyptian school-going children.

Background: Urinary tract infections (UTI) are a common and important clinical problem in childhood. Upper urinary tract infections (i.e., acute pyelonephritis) may lead to renal scarring, hypertension, and end-stage renal disease. Despite the presence of simple and reliable methods of preliminary screening of children's urine, urinary tract infection continues to be under diagnosed. Objectives: The aim of this study was to establish prevalence rates of significant bacteriuria in asymptomatic school children by simple urine tests in comparison to standard urine culture techniques in Giza, Egypt. Patients and methods: A total of 1000 apparently healthy school going children (6-12) years, 552 boys (55.2%) and 448 girls (44.8%), were enrolled in this cross-sectional prevalence survey. Results: Overall prevalence of significant bacteriuria was 6%. Higher prevalence occurred in girls (11.4%) than boys (1.6%). Escherichia coli was isolated in 35(58%) cases (3 boys and 32 girls), Staph. aureus in 13 (22%) cases (3 boys and 10 girls), Enterobacter in 6 girls (10%), Kelbsiella pneumoniae in 3 boys (5%) and Proteus vulgaris in 3 girls (5%) Conclusion: Asymptomatic bacteriurea could be detected by urine screening program at school age. Overall prevalence of significant bacteriuria was 6%, with predominance in girls than boys.

Near-infrared Instrumentation For Rapid-response Astronomy

Ɣ-ray bursts (GRBs) are the Universe's most luminous transient events. Since the discovery of GRBs was announced in 1973, efforts have been ongoing to obtain data over a broader range of the electromagnetic spectrum at the earliest possible times following the initial detection. The discovery of the theorized ``afterglow'' emission in radio through X-ray bands in the late 1990s confirmed the cosmological nature of these events. At present, GRB afterglows are among the best probes of the early Universe (z ≳ 9). In addition to informing theories about GRBs themselves, observations of afterglows probe the circum-burst medium (CBM), properties of the host galaxies and the progress of cosmic reionization. To explore the early-time variability of afterglows, I have developed a generalized analysis framework which models near-infrared (NIR), optical, ultra-violet (UV) and X-ray light curves without assuming an underlying model. These fits are then used to construct the spectral energy distribution (SED) of afterglows at arbitrary times within the observed window. Physical models are then used to explore the evolution of the SED parameter space with time. I demonstrate that this framework produces evidence of the photodestruction of dust in the CBM of GRB 120119A, similar to the findings from a previous study of this afterglow. The framework is additionally applied to the afterglows of GRB 140419A and GRB 080607. In these cases the evolution of the SEDs appears consistent with the standard fireball model. Having introduced the scientific motivations for early-time observations, I introduce the Rapid Infrared Imager-Spectrometer (RIMAS). Once commissioned on the 4.3 meter Discovery Channel Telescope (DCT), RIMAS will be used to study the afterglows of GRBs through photometric and spectroscopic observations beginning within minutes of the initial burst. The instrument will operate in the NIR, from 0.97 μm to 2.37 μm, permitting the detection of very high redshift (z ≳ 7) afterglows which are attenuated at shorter wavelengths by Lyman-ɑ absorption in the intergalactic medium (IGM). A majority of my graduate work has been spent designing and aligning RIMAS's cryogenic (~80 K) optical systems. Design efforts have included an original camera used to image the field surrounding spectroscopic slits, tolerancing and optimizing all of the instrument's optics, thermal modeling of optomechanical systems, and modeling the diffraction efficiencies for some of the dispersive elements. To align the cryogenic optics, I developed a procedure that was successfully used for a majority of the instrument's sub-assemblies. My work on this cryogenic instrument has necessitated experimental and computational projects to design and validate designs of several subsystems. Two of these projects describe simple and effective measurements of optomechanical components in vacuum and at cryogenic temperatures using an 8-bit CCD camera. Models of heat transfer via electrical harnesses used to provide current to motors located within the cryostat are also presented.

An Assessment of Professional Development for Astronomy and Physics Faculty: Expanding Our Vision of How to Support Faculty's Learning About Teaching

In this thesis, we will explore approaches to faculty instructional change in astronomy and physics. We primarily focus on professional development (PD) workshops, which are a central mechanism used within our community to help faculty improve their teaching. Although workshops serve a critical role for promoting more equitable instruction, we rarely assess them through careful consideration of how they engage faculty. To encourage a shift towards more reflective, research-informed PD, we developed the Real-Time Professional Development Observation Tool (R-PDOT), to document the form and focus of faculty's engagement during workshops. We then analyze video-recordings of faculty's interactions during the Physics and Astronomy New Faculty Workshop, focusing on instances where faculty might engage in pedagogical sense-making. Finally, we consider insights gained from our own local, team-based effort to improve a course sequence for astronomy majors. We conclude with recommendations for PD leaders and researchers.

Atmospheric calibration for sub-millimeter radio astronomy

This thesis is focused on improving the calibration accuracy of sub-millimeter astronomical observations. The wavelength range covered by observational radio astronomy has been extended to sub-millimeter and far infrared with the advancement of receiver technology in recent years. Sub-millimeter observations carried out with airborne and ground-based telescopes typically suffer from 10% to 90% attenuation of the astronomical source signals by the terrestrial atmosphere. The amount of attenuation can be derived from the measured brightness of the atmospheric emission. In order to do this, the knowledge of the atmospheric temperature and chemical composition, as well as the frequency-dependent optical depth at each place along the line of sight is required. The altitude-dependent air temperature and composition are estimated using a parametrized static atmospheric model, which is described in Chapter 2, because direct measurements are technically and financially infeasible. The frequency dependent optical depth of the atmosphere is computed with a radiative transfer model based on the theories of quantum mechanics and, in addition, some empirical formulae. The choice, application, and improvement of third party radiative transfer models are discussed in Chapter 3. The application of the calibration procedure, which is described in Chapter 4, to the astronomical data observed with the SubMillimeter Array Receiver for Two Frequencies (SMART), and the German REceiver for Astronomy at Terahertz Frequencies (GREAT), is presented in Chapters 5 and 6. The brightnesses of atmospheric emission were fitted consistently to the simultaneous multi-band observation data from GREAT at 1.2 ∼ 1.4 and 1.8 ∼ 1.9 THz with a single set of parameters of the static atmospheric model. On the other hand, the cause of the inconsistency between the model parameters fitted from the 490 and 810 GHz data of SMART is found to be the lack of calibration of the effective cold load temperature. Besides the correctness of atmospheric modeling, the stability of the receiver is also important to achieving optimal calibration accuracy. The stabilities of SMART and GREAT are analyzed with a special calibration procedure, namely the “load calibration". The effects of the drift and fluctuation of the receiver gain and noise temperature on calibration accuracy are discussed in Chapters 5 and 6. Alternative observing strategies are proposed to combat receiver instability. The methods and conclusions presented in this thesis are applicable to the atmospheric calibration of sub-millimeter astronomical observations up to at least 4.7 THz (the H channel frequency of GREAT) for observations carried out from ∼ 4 to 14 km altitude. The procedures for receiver gain calibration and stability test are applicable to other instruments using the same calibration approach as that for SMART and GREAT. The structure of the high performance, modular, and extensible calibration program used and further developed for this thesis work is presented in the Appendix C.

A principal component approach to space-based gravitational wave astronomy

The current approach to data analysis for the Laser Interferometry Space Antenna (LISA) depends on the time delay interferometry observables (TDI) which have to be generated before any weak signal detection can be performed. These are linear combinations of the raw data with appropriate time shifts that lead to the cancellation of the laser frequency noises. This is possible because of the multiple occurrences of the same noises in the different raw data. Originally, these observables were manually generated starting with LISA as a simple stationary array and then adjusted to incorporate the antenna's motions. However, none of the observables survived the flexing of the arms in that they did not lead to cancellation with the same structure. The principal component approach is another way of handling these noises that was presented by Romano and Woan which simplified the data analysis by removing the need to create them before the analysis. This method also depends on the multiple occurrences of the same noises but, instead of using them for cancellation, it takes advantage of the correlations that they produce between the different readings. These correlations can be expressed in a noise (data) covariance matrix which occurs in the Bayesian likelihood function when the noises are assumed be Gaussian. Romano and Woan showed that performing an eigendecomposition of this matrix produced two distinct sets of eigenvalues that can be distinguished by the absence of laser frequency noise from one set. The transformation of the raw data using the corresponding eigenvectors also produced data that was free from the laser frequency noises. This result led to the idea that the principal components may actually be time delay interferometry observables since they produced the same outcome, that is, data that are free from laser frequency noise. The aims here were (i) to investigate the connection between the principal components and these observables, (ii) to prove that the data analysis using them is equivalent to that using the traditional observables and (ii) to determine how this method adapts to real LISA especially the flexing of the antenna. For testing the connection between the principal components and the TDI observables a 10x 10 covariance matrix containing integer values was used in order to obtain an algebraic solution for the eigendecomposition. The matrix was generated using fixed unequal arm lengths and stationary noises with equal variances for each noise type. Results confirm that all four Sagnac observables can be generated from the eigenvectors of the principal components. The observables obtained from this method however, are tied to the length of the data and are not general expressions like the traditional observables, for example, the Sagnac observables for two different time stamps were generated from different sets of eigenvectors. It was also possible to generate the frequency domain optimal AET observables from the principal components obtained from the power spectral density matrix. These results indicate that this method is another way of producing the observables therefore analysis using principal components should give the same results as that using the traditional observables. This was proven by fact that the same relative likelihoods (within 0.3%) were obtained from the Bayesian estimates of the signal amplitude of a simple sinusoidal gravitational wave using the principal components and the optimal AET observables. This method fails if the eigenvalues that are free from laser frequency noises are not generated. These are obtained from the covariance matrix and the properties of LISA that are required for its computation are the phase-locking, arm lengths and noise variances. Preliminary results of the effects of these properties on the principal components indicate that only the absence of phase-locking prevented their production. The flexing of the antenna results in time varying arm lengths which will appear in the covariance matrix and, from our toy model investigations, this did not prevent the occurrence of the principal components. The difficulty with flexing, and also non-stationary noises, is that the Toeplitz structure of the matrix will be destroyed which will affect any computation methods that take advantage of this structure. In terms of separating the two sets of data for the analysis, this was not necessary because the laser frequency noises are very large compared to the photodetector noises which resulted in a significant reduction in the data containing them after the matrix inversion. In the frequency domain the power spectral density matrices were block diagonals which simplified the computation of the eigenvalues by allowing them to be done separately for each block. The results in general showed a lack of principal components in the absence of phase-locking except for the zero bin. The major difference with the power spectral density matrix is that the time varying arm lengths and non-stationarity do not show up because of the summation in the Fourier transform.

Mitochondrial demographic history of the Egyptian mongoose (Herpestes ichneumon), an expanding carnivore in the Iberian Peninsula

Describing the genetic patterns and the demographic history of expanding species is essential for providing insights into the processes linked with range dynamics. We analysed the mitochondrial diversity of the Egyptian mongoose (Herpestes ichneumon) across the Iberian Peninsula, where the species is currently expanding northwest. A total of 242 individuals were analysed, together with nine representatives from the North African dispersal source. Haplotype segregation and strong differentiation between Iberian and North African populations confirmed the longterm presence of the species in the Iberian Peninsula. The distribution of mitochondrial diversity fitted the pattern of a historically diversified population in southern Iberia, from which the recent dispersals into northern areas may have occurred. Higher levels of haplotype and nucleotide diversities in the northern areas, together with the heterogeneous distribution of pairwise population differentiations and the weak signal for isolationbydistance suggest the existence of longdispersal migrants across the Iberian Peninsula. Sudden and spatial expansion scenarios of H. ichneumon in the Iberian Peninsula were supported by mismatch analysis and marginally supported by neutrality tests. However, the precise time of occurrence of the detected expansion remains unclear. Future studies should incorporate additional markers in order to further clarify the population dynamics of the Egyptian mongoose in its Iberian range.

Genetic signature of the northward expansion of the Egyptian mongoose Herpestes ichneumon (Herpestidae) in the Iberian Peninsula

In the last three decades, the range of the Egyptian mongoose (Herpestes ichneumon) has increased in the Iberian Peninsula. A panel of microsatellites was used to confront the patterns of genetic diversity of the species with the scenario of its recent northward expansion in its Iberian range. Evidence of substructure and significant genetic differentiation within the studied population were recorded, with a central-northern subpopulation (CNorth) and a southern subpopulation (S). Northward range expansion was supported by the observed allelic frequencies, diversity parameters, and observed heterozygosity of the studied loci, with S showing a higher allelic diversity and a higher number of private alleles than CNorth. Patterns of isolation-by-distance and isolation-by-barrier as a result of the Tagus River were demonstrated, suggesting that the river acted as a semi-permeable barrier, possibly leading to genetic differentiation of the studied population. The observed individuals from CNorth in southern locations and individuals from S in central/northern areas might comprise evidence for long range dispersals across the studied range. A bottleneck event after population expansion was supported by a significant heterozygosity deficiency in CNorth, which is in agreement with a scenario of founder events occurring in recently colonized areas after the crossing of the Tagus River.

High porosity chained aggregates from the topsoil of the Lunar regolith Dust

The unusual behaviour of fine lunar regolith like stickiness and low heat conductivity is dominated by the structural arrangement of its finest fraction in the outer-most topsoil layer. Here, we show the previously unknown phenomenon of building a globular 3-D superstructure within the dust fraction of the regolith. New technology, Transmission X-ray Microscopy (TXM) with tomographic reconstruction, reveals a highly porous network of cellular void system in the lunar finest dust fraction aggregates. Such porous chained aggregates are composed of sub-micron in size particles that build cellular void networks. Voids are a few micrometers in diameter. Discovery of such a superstructure within the finest fraction of the lunar topsoil allow building a model of heat transfer which is discussed.

Astrophysics on the lab bench

In this article some basic laboratory bench experiments are described that are useful for teaching high school students some of the basic principles of stellar astrophysics. For example, in one experiment, students slam a plastic water-filled bottle down onto a bench, ejecting water towards the ceiling illustrating the physics associated with a type II supernova explosion. In another experiment, students roll marbles up and down a double ramp in an attempt to get a marble to enter a tube half way up the slope, which illustrates quantum tunnelling in stellar cores. The experiments are reasonably low cost to either purchase or manufacture.

The Space Day at QUT

The Space Day has been running at QUT for about a decade. The Space Day started out as a single lecture on the stars delivered to a group of high school students from Brisbane State High School (BSHS), just across the river from QUT and therefore convenient for the school to visit. I was contacted by Victor James of St. Laurence’s College (SLC), Brisbane asking if he could bring a group of boys to QUT for a lecture similar to that delivered to BSHS. However, for SLC a hands-on laboratory session was added to the lecture and thus the Space Day was born. For the Space Day we have concentrated on year 7 – 10 students. Subsequently, many other schools from Brisbane and further afield in Queensland have attended a Space Day.

An evaluation framework for sustaining the impact of educational development

Notwithstanding significant efforts by international aid agencies, aid ineffectiveness became apparent in 1990s as the impact of continued development intervention did not endure the expected outcomes. Conventional monitoring and evaluation by those agencies is critiqued for focusing on measuring project outcomes and giving little attention to aspects of sustainability. As a result, devising a rigorous evaluation framework for educational development has been sought in light of recent paradigm shifts in international development. This paper reports on a case study of an Egyptian educational development project highlighting the importance of transforming the evaluation procedures to process evaluation so as to enhance project impact and longevity. This requires building evaluation capacity of the aid recipient country.