A Data Science Approach to Understanding Residential Water Contamination in Flint

When the residents of Flint learned that lead had contaminated their water system, the local government made water-testing kits available to them free of charge. The city government published the results of these tests, creating a valuable dataset that is key to understanding the causes and extent of the lead contamination event in Flint. This is the nation's largest dataset on lead in a municipal water system. In this paper, we predict the lead contamination for each household's water supply, and we study several related aspects of Flint's water troubles, many of which generalize well beyond this one city. For example, we show that elevated lead risks can be (weakly) predicted from observable home attributes. Then we explore the factors associated with elevated lead. These risk assessments were developed in part via a crowd sourced prediction challenge at the University of Michigan. To inform Flint residents of these assessments, they have been incorporated into a web and mobile application funded by \texttt{Google.org}. We also explore questions of self-selection in the residential testing program, examining which factors are linked to when and how frequently residents voluntarily sample their water.Comment: Applied Data Science track paper at KDD 2017. For associated promotional video, see https://www.youtube.com/watch?v=0g66ImaV8A

Sashimi plots: Quantitative visualization of RNA sequencing read alignments

We introduce Sashimi plots, a quantitative multi-sample visualization of mRNA sequencing reads aligned to gene annotations. Sashimi plots are made using alignments (stored in the SAM/BAM format) and gene model annotations (in GFF format), which can be custom-made by the user or obtained from databases such as Ensembl or UCSC. We describe two implementations of Sashimi plots: (1) a stand-alone command line implementation aimed at making customizable publication quality figures, and (2) an implementation built into the Integrated Genome Viewer (IGV) browser, which enables rapid and dynamic creation of Sashimi plots for any genomic region of interest, suitable for exploratory analysis of alternatively spliced regions of the transcriptome. Isoform expression estimates outputted by the MISO program can be optionally plotted along with Sashimi plots. Sashimi plots can be used to quickly screen differentially spliced exons along genomic regions of interest and can be used in publication quality figures. The Sashimi plot software and documentation is available from: http://genes.mit.edu/burgelab/miso/docs/sashimi.htmlComment: 2 figure

A decision procedure for a sublanguage of set theory involving monotone additive and multiplicative functions, II. The multi-level case

MLSS is a decidable sublanguage of set theory involving the predicates membership, set equality, set inclusion, and the operators union, intersection, set difference, and singleton.In this paper we extend MLSS with constructs for expressing monotonicity, additivity, and multiplicativity properties of set-to-set functions. We prove that the resulting language is decidable by reducing the problem of determining the satisfiability of its sentences to the problem of determining the satisfiability of sentences of MLSS.In addition, we show an interesting model theoretic property of MLSS, the singleton model property, upon which our decidability proof is based. Intuitively, the singleton model property states that if a formula is satisfiable, then it is satisfiable in a model whose non-empty Venn regions are singleton sets

A Decision Procedure for a Fragment of Set Theory Involving Monotone, Additive, and Multiplicative Functions

2LS is a decidable many-sorted set-theoretic language involving one sort for elements and one sort for sets of elements. In this report we extend 2LS with constructs for expressing monotonicity, additivity, and multiplicativity properties of set-to-set functions. We call the resulting language 2LSmf. We prove that 2LSmf is decidable by reducing the problem of determining the satisfiability of its sentences to the problem of determining the satisfiability of sentences of 2LS. Furthermore, we prove that the language 2LSmf is stably infinite with respect to the sort of elements. Therefore, using a many-sorted version of the Nelson-Oppen combination method, 2LSmf can be combined with other languages modeling the sort of elements

Development and Application of Synthetic Affinity Ligands for the Purification of Ferritin-Based Influenza Antigens

A recently developed novel recombinant influenza antigen vaccine has shown great success in preclinical studies in ferrets and mice. It provides broader protection, and is efficient to manufacture compared to the conventional trivalent influenza vaccines (TIV). Each strain of the recombinant antigen has a constant self-assembled bacterial ferritin core which, if used as a target for affinity chromatography, could lead to a universal purification method. Ferritin in silico models were used to explore potential target binding sites against ligands synthesized by the four-component Ugi reaction. Two ligands, SJ047 and SJ055, were synthesized in solution, characterized by 1H, 13C, and 2D NMR spectroscopy, and subsequently immobilized on the PEG-functionalized beads. Ligands SJ047 and SJ055 displayed apparent Kd values of 2.04 × 10–7 M and 1.91 × 10–8 M, respectively, against the ferritin. SJ047 and SJ055-functionalized resins were able to purify hemagglutinin (New Caledonia)-ferritin expressed in a crude Human Embryonic Kidney (HEK) cell supernatant in a single step to a purity of 85 ± 0.5% (97 ± 1% yield) and 87.5 ± 0.5% (95.5 ± 1.5% yield), respectively. Additionally, SJ047 and SJ055-functionalized resins purified the recombinant antigens when spiked at known concentrations into HEK supernatants. All three strains, hemagglutinin (New Caledonia)-ferritin, hemagglutinin (California)-ferritin, and hemagglutinin (Singapore)-ferritin were purified, thereby offering an ideal alternate platform for affinity chromatography. Following elution from the affinity adsorbents, absorbance at 350 nm showed that there was no aggregation of the recombinant antigens and dynamic light scattering studies further confirmed the structural integrity of the recombinant antigen. The use of Ugi ligands coupled to a PEG-spacer arm to target the ferritin core of the strain is entirely novel and provides an efficient purification of these recombinant antigens. This approach represents a potentially universal method to purify any ferritin-based vaccine

Robust optical delay lines via topological protection

Phenomena associated with topological properties of physical systems are naturally robust against perturbations. This robustness is exemplified by quantized conductance and edge state transport in the quantum Hall and quantum spin Hall effects. Here we show how exploiting topological properties of optical systems can be used to implement robust photonic devices. We demonstrate how quantum spin Hall Hamiltonians can be created with linear optical elements using a network of coupled resonator optical waveguides (CROW) in two dimensions. We find that key features of quantum Hall systems, including the characteristic Hofstadter butterfly and robust edge state transport, can be obtained in such systems. As a specific application, we show that the topological protection can be used to dramatically improve the performance of optical delay lines and to overcome limitations related to disorder in photonic technologies.Comment: 9 pages, 5 figures + 12 pages of supplementary informatio

On the determination of a cloud condensation nuclei from satellite : Challenges and possibilities

We use aerosol size distributions measured in the size range from 0.01 to 10+ μm during Transport and Chemical Evolution over the Pacific (TRACE-P) and Aerosol Characterization Experiment-Asia (ACE-Asia), results of chemical analysis, measured/modeled humidity growth, and stratification by air mass types to explore correlations between aerosol optical parameters and aerosol number concentration. Size distributions allow us to integrate aerosol number over any size range expected to be effective cloud condensation nuclei (CCN) and to provide definition of a proxy for CCN (CCNproxy). Because of the internally mixed nature of most accumulation mode aerosol and the relationship between their measured volatility and solubility, this CCNproxy can be linked to the optical properties of these size distributions at ambient conditions. This allows examination of the relationship between CCNproxy and the aerosol spectral radiances detected by satellites. Relative increases in coarse aerosol (e.g., dust) generally add only a few particles to effective CCN but significantly increase the scattering detected by satellite and drive the Angstrom exponent (α) toward zero. This has prompted the use of a so-called aerosol index (AI) on the basis of the product of the aerosol optical depth and the nondimensional α, both of which can be inferred from satellite observations. This approach biases the AI to be closer to scattering values generated by particles in the accumulation mode that dominate particle number and is therefore dominated by sizes commonly effective as CCN. Our measurements demonstrate that AI does not generally relate well to a measured proxy for CCN unless the data are suitably stratified. Multiple layers, complex humidity profiles, dust with very low α mixed with pollution, and size distribution differences in pollution and biomass emissions appear to contribute most to method limitations. However, we demonstrate that these characteristic differences result in predictable influences on AI. These results suggest that inference of CCN from satellites will be challenging, but new satellite and model capabilities could possibly be integrated to improve this retrieval

Multi-centre parallel arm randomised controlled trial to assess the effectiveness and cost-effectiveness of a group-based cognitive behavioural approach to managing fatigue in people with multiple sclerosis

Abstract (provisional) Background Fatigue is one of the most commonly reported and debilitating symptoms of multiple sclerosis (MS); approximately two-thirds of people with MS consider it to be one of their three most troubling symptoms. It may limit or prevent participation in everyday activities, work, leisure, and social pursuits, reduce psychological well-being and is one of the key precipitants of early retirement. Energy effectiveness approaches have been shown to be effective in reducing MS-fatigue, increasing self-efficacy and improving quality of life. Cognitive behavioural approaches have been found to be effective for managing fatigue in other conditions, such as chronic fatigue syndrome, and more recently, in MS. The aim of this pragmatic trial is to evaluate the clinical and cost-effectiveness of a recently developed group-based fatigue management intervention (that blends cognitive behavioural and energy effectiveness approaches) compared with current local practice. Methods This is a multi-centre parallel arm block-randomised controlled trial (RCT) of a six session group-based fatigue management intervention, delivered by health professionals, compared with current local practice. 180 consenting adults with a confirmed diagnosis of MS and significant fatigue levels, recruited via secondary/primary care or newsletters/websites, will be randomised to receive the fatigue management intervention or current local practice. An economic evaluation will be undertaken alongside the trial. Primary outcomes are fatigue severity, self-efficacy and disease-specific quality of life. Secondary outcomes include fatigue impact, general quality of life, mood, activity patterns, and cost-effectiveness. Outcomes in those receiving the fatigue management intervention will be measured 1 week prior to, and 1, 4, and 12 months after the intervention (and at equivalent times in those receiving current local practice). A qualitative component will examine what aspects of the fatigue management intervention participants found helpful/unhelpful and barriers to change. Discussion This trial is the fourth stage of a research programme that has followed the Medical Research Council guidance for developing and evaluating complex interventions. What makes the intervention unique is that it blends cognitive behavioural and energy effectiveness approaches. A potential strength of the intervention is that it could be integrated into existing service delivery models as it has been designed to be delivered by staff already working with people with MS. Service users will be involved throughout this research. Trial registration: Current Controlled Trials ISRCTN7651747

Multi-Parton Amplitudes in Gauge Theories

In this report we review recent developments in perturbation theory methods for gauge theories. We present techniques and results that are useful in the calculation of cross sections for processes with many final state partons which have applications in the study of multi-jet phenomena in high-energy Colliders.Comment: 84 pages, 12 figures: Latex, preprint version of 1991 Physics Reports article. Scanned Figure