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User applications driven by the community contribution framework MPContribs in the Materials Project

This paper discusses how the MPContribs framework in the Materials Project (MP) allows user-contributed data to be shown and analyzed alongside the core MP database. The MP is a searchable database of electronic structure properties of over 65,000 bulk solid materials, which is accessible through a web-based science-gateway. We describe the motivation for enabling user contributions to the materials data and present the framework's features and challenges in the context of two real applications. These use cases illustrate how scientific collaborations can build applications with their own 'user-contributed' data using MPContribs. The Nanoporous Materials Explorer application provides a unique search interface to a novel dataset of hundreds of thousands of materials, each with tables of user-contributed values related to material adsorption and density at varying temperature and pressure. The Unified Theoretical and Experimental X-ray Spectroscopy application discusses a full workflow for the association, dissemination, and combined analyses of experimental data from the Advanced Light Source with MP's theoretical core data, using MPContribs tools for data formatting, management, and exploration. The capabilities being developed for these collaborations are serving as the model for how new materials data can be incorporated into the MP website with minimal staff overhead while giving powerful tools for data search and display to the user community.

97 MATHEMATICS AND COMPUTING↗

BrazilClim : The overcoming of limitations of pre‐existing bioclimate data

Abstract Species distribution modelling has become instrumental in assessing the influence of environmental conditions on the occurrence or abundance of taxa. The set of environmental layers used for this purpose is a crucial aspect, for which different climate‐based (bioclimatic) datasets have been recently developed. These bioclimatic variables result from combinations of precipitation and temperatures surfaces. Here, we explored both the performance and possibility of improving some of the currently available bioclimatic databases, through an evaluation of the precipitation and temperatures surfaces used to generate them. For this purpose, we used a combination of statistic and graphic approaches. We focused on Brazil, not only due to its natural megadiversity, but also due to its continental size and orographic heterogeneity: an excellent ground for refining methods replicable elsewhere. We found a better match between the climatic data measured on‐field and Tropical Rainfall Measuring Mission (TRMM 3B43 v7) in the case of precipitation, and the surfaces provided by the National Oceanic and Atmospheric Administration (NOAA) in the case of temperatures, sources uncommonly used for species niche modelling. We gauge‐calibrated the best performing surfaces using machine‐learning algorithms and generated corrected surfaces that allowed us to create BrazilClim: a database of bioclimatic variables, based on improved primary surfaces, which will result in more assertive predicted distributions and more actual pictures of the species' ecological requirements for megadiverse Brazil, an approach replicable elsewhere. All primary and bioclimatic surfaces generated for this study may be freely downloaded.

Ramoni‐Perazzi, Paolo↗

Machine learning for polymeric materials: an introduction

We report that Polymers are incredibly versatile materials and have become ubiquitous. Increasingly, researchers are using data science and polymer informatics to design new materials and understand their structure-property relationships. Polymer informatics is an emerging field. While there are many useful tools and databases available, many are not widely utilized. Herein, we introduce the field of polymer informatics and discuss some of the available databases and tools. We cover how to share polymer data, approaches for preparing a dataset for machine learning and recent applications of machine learning to polymer property prediction and polymer synthesis.

36 MATERIALS SCIENCE↗

Parameterized complex dielectric functions of CuIn 1−x Ga x Se 2 : applications in optical characterization of compositional non‐uniformities and depth profiles in materials and solar cells

Abstract In‐situ spectroscopic ellipsometry (SE) was employed to extract the complex dielectric functions ε = ε 1 + iε 2 over the spectral range of 0.75–6.5 eV for a set of polycrystalline CuIn 1− x Ga x Se 2 (CIGS) thin films with different alloy compositions x = [Ga]/{[In] + [Ga]}. For highest possible accuracy in ε for each CIGS thin film, specialized SE procedures were adopted including (i) deposition to a thickness of ~600 Å on smooth native oxide covered crystal silicon wafers, which minimizes the surface roughness on the film and thus the required corrections in data analysis, and (ii) measurement in‐situ , which minimizes ambient contamination and oxidation of the film surface. Assuming an analytical form for each of the ε spectra for these CIGS films, oscillator parameters were obtained in best fits, and these parameters were fit in turn to polynomials in x . With the resulting database of polynomial coefficients, the ε spectra for any composition of CIGS can be generated from the single parameter, x . In addition to enabling accurate contactless determination of bulk and surface roughness layer thicknesses of CIGS films by high speed multichannel SE, the database enables characterization of the composition and its profile with depth into these films, and even how the depth profile varies spatially within the plane of the films. In this study, depth profile parameters were found to correlate spatially with solar cell performance parameters. As a result, SE provides the capability of contactless compositional analysis of production‐scale CIGS photovoltaic modules at high speed. Copyright © 2016 John Wiley & Sons, Ltd.

Aryal, Puruswottam↗

ENVI-PV: An Interactive Web Client for Multi-Criteria Life Cycle Assessment of Photovoltaic Systems Worldwide

Solar photovoltaics (PV) is the second largest source of new capacity among renewable energies. The worldwide capacity encompassed 135 GW in 2013 and is estimated to increase to 1721 GW in 2030 and 4674 GW in 2050, according to a prospective high-renewable scenario. To achieve this production level while minimizing environmental impacts, decision makers must have access to environmental performance data that reflect their high spatial variability accurately. We propose ENVI-PV (http://viewer.webservice-energy.org/project_iea), a new interactive tool that provides maps and screening level data, based on weighted average supply chains, for the environmental performance of common PV technologies. Environmental impacts of PV systems are evaluated according to a life cycle assessment approach. ENVI-PV was developed using a state-of-the-art interoperable and open standard Web Service framework from the Open Geospatial Consortium (OGC). It combines the latest life cycle inventories, published in 2015 by the International Energy Agency (IEA) under the Photovoltaic Power Systems Program (PVPS) Task 12, and some inventories previously published from Ecoinvent v2.2 database with solar irradiation estimates computed from the worldwide NASA SSE database. ENVI-PV is the first tool to propose a worldwide coverage of environmental performance of PV systems using a multi-criteria assessment. The user can compare the PV environmental performance to the environmental footprint of country electricity mixes. ENVI-PV is designed as an environmental interactive tool to generate PV technological options and evaluate their performance in different spatial and techno-economic contexts. Its potential applications are illustrated in this paper with several examples.

14 SOLAR ENERGY↗

Trajectory analysis via a geometric feature space approach

This study aimed to organize a body of trajectories in order to identify, search for and classify both common and uncommon behaviors among objects such as aircraft and ships. Existing comparison functions such as the Fréchet distance are computationally expensive and yield counterintuitive results in some cases. We propose an approach using feature vectors whose components represent succinctly the salient information in trajectories. These features incorporate basic information such as the total distance traveled and the distance between start/stop points as well as geometric features related to the properties of the convex hull, trajectory curvature and general distance geometry. Additionally, these features can generally be mapped easily to behaviors of interest to humans who are searching large databases. Most of these geometric features are invariant under rigid transformation. Furthermore, we demonstrate the use of different subsets of these features to identify trajectories similar to an exemplar, cluster a database of several hundred thousand trajectories and identify outliers.

97 MATHEMATICS AND COMPUTING↗

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aggregation and analysis of indication-symptom relationships for drugs approved in the USA

Abstract Purpose Drug indications and disease symptoms often confound adverse event reports in real-world datasets, including electronic health records and reports in the FDA Adverse Event Reporting System (FAERS). A thorough, standardized set of indications and symptoms is needed to identify these confounders in such datasets for drug research and safety assessment. The aim of this study is to create a comprehensive list of drug-indication associations and disease-symptom associations using multiple resources, including existing databases and natural language processing. Methods Drug indications for drugs approved in the USA were extracted from two databases, RxNorm and Side Effect Resource (SIDER). Symptoms for these indications were extracted from MedlinePlus and using natural language processing from PubMed abstracts. Results A total of 1361 unique drugs, 1656 unique indications, and 2201 unique symptoms were extracted from a wide variety of MedDRA System Organ Classes. Text-mining precision was maximized at 0.65 by examining Term Frequency Inverse Document Frequency (TF-IDF) scores of the disease-symptom associations. Conclusion The drug-indication associations and disease-symptom associations collected in this study may be useful in identifying confounders in other datasets, such as safety reports. With further refinement and additional drugs, indications, and symptoms, this dataset may become a quality resource for disease symptoms.

Punyala, Ananth↗

Anastomosing hemangioma of the liver: a case series

Purpose: To report imaging and pathologic features of five pathologically proven anastomosing hemangiomas of the liver (AHL). Methods: A retrospective review for AHL was conducted using our institutional database from 6/2004 to 3/2018. Histology proven AHL with radiologic imaging available for review were included. A total of five patients who met our criteria were identified from our institutional database. Computed tomography, ultrasound, and magnetic resonance imaging findings, including location, size, attenuation/signal intensity, enhancement characteristics, and additional imaging data were reviewed. The clinical and pathological data were also reviewed. Results: The imaging characteristics of AHL are variable, but features such as peripheral or diffuse hyperintensity on diffusion weighted imaging, arterial hyperenhancement without globular interrupted enhancement, and persistent enhancement without complete filling in the delayed phases were more characteristic of AHL. Imaging also demonstrated a lack of aggressive features. Conclusions: AHL present a diagnostic dilemma as they can mimic more malignant lesions, such as angiosarcoma, both on imaging and at pathology. While the imaging characteristics of AHL are variable, there are some features which can help distinguish AHL from other liver lesions. When the diagnosis of anastomosing hemangioma is known, the management of choice is primarily surveillance, as intervention can cause unnecessary morbidity, and no degeneration to malignancy has been identified to date.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Systematic Review of Infrapopliteal Drug-Eluting Stents: A Meta-Analysis of Randomized Controlled Trials

IntroductionDrug-eluting stents (DES) have been proposed for the treatment of infrapopliteal arterial disease. We performed a systematic review to provide a qualitative analysis and quantitative data synthesis of randomized controlled trials (RCTs) assessing infrapopliteal DES.Materials and MethodsPubMed (Medline), EMBASE (Excerpta Medical Database), AMED (Allied and Complementary medicine Database), Scopus, CENTRAL (Cochrane Central Register of Controlled Trials), online content, and abstract meetings were searched in September 2012 for eligible RCTs according to the preferred reporting items for systematic reviews and meta-analyses selection process. Risk of bias was assessed using the Cochrane Collaboration's tool. Primary endpoint was primary patency defined as absence of {>=}50 % vessel restenosis at 1 year. Secondary outcome measures included patient survival, limb amputations, change of Rutherford-Becker class, target lesion revascularization (TLR) events, complete wound healing, and event-free survival at 1 year. Risk ratio (RRs) were calculated using the Mantel-Haenszel fixed effects model, and number-needed-to-treat values are reported.ResultsThree RCTs involving 501 patients with focal infrapopliteal lesions were analyzed (YUKON-BTX, DESTINY, and ACHILLES trials). All three RCTs included relatively short and focal infrapopliteal lesions. At 1 year, there was clear superiority of infrapopliteal DES compared with control treatments in terms of significantly higher primary patency (80.0 vs. 58.5 %; pooled RR = 1.37, 95 % confidence interval [CI] = 1.18-1.58, p < 0.0001; number-needed-to-treat (NNT) value = 4.8), improvement of Rutherford-Becker class (79.0 vs. 69.6 %; pooled RR = 1.13, 95 % CI = 1.002-1.275, p = 0.045; NNT = 11.1), decreased TLR events (9.9 vs. 22.0 %; pooled RR = 0.45, 95 % CI = 0.28-0.73, p = 0.001; NNT = 8.3), improved wound healing (76.8 vs. 59.7 %; pooled RR = 1.29, 95 % CI = 1.02-1.62, p = 0.04; NNT = 5.9), and better overall event-free survival (72.2 vs. 57.3 %; pooled RR = 1.26, 95 % CI = 1.10-1.44, p = 0.0006; NNT = 6.7). Conclusion. DES for focal infrapopliteal lesions significantly inhibit vascular restenosis and thereby improve primary patency, decrease repeat procedures, improve wound healing, and prolong overall event-free survival.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Outcome Following a Negative CT Angiogram for Gastrointestinal Hemorrhage

ObjectiveThis study was designed to evaluate the role of a negative computed tomography angiogram (CTA) in patients who present with gastrointestinal (GI) hemorrhage.MethodsA review of all patients who had CTAs for GI hemorrhage over an 8-year period from January 2005 to December 2012 was performed. Data for patient demographics, location of hemorrhage, hemodynamic stability, and details of angiograms and/or the embolization procedure were obtained from the CRIS/PACS database, interventional radiology database, secure electronic medical records, and patient’s clinical notes.ResultsA total of 180 patients had 202 CTAs during the 8-year period: 87 CTAs were performed for upper GI hemorrhage (18 positive for active bleeding, 69 negative) and 115 for lower GI hemorrhage (37 positive for active bleeding, 78 negative); 58.7 % (37/63) of patients with upper GI bleed and 77.4 % (48/62) of patients with lower GI bleed who had an initial negative CTA did not rebleed without the need for radiological or surgical intervention. This difference was statistically significant (p = 0.04). The relative risk of rebleeding, following a negative CTA, in lower GI bleeding versus upper GI bleeding patients is 0.55 (95 % confidence interval 0.32–0.95).ConclusionsPatients with upper GI bleed who had negative CTAs usually require further intervention to stop the bleeding. In contrast, most patients presenting with lower GI hemorrhage who had a negative first CTA were less likely to rebleed.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Endovascular Therapy Research in Lower Limb Peripheral Arterial Disease Published Over a 5-Year Period: Who is Publishing and Where?

IntroductionPeripheral arterial disease (PAD) is being increasingly managed by endovascular therapies. In this study, we identified the clinical services publishing research as well as the journals of publication over a 5-year period.MethodsTwenty keywords and phrases related to endovascular intervention were identified, and a literature search was performed through the PubMed database from January 2009 to January 2014. Inclusion criteria were English language, study population more than five patients, and matching the keyword search. Eligible studies were collated into a database and classified by journal of publication, PubMed number, article title, publishing clinical service, type of publication, country of origin, and authors.Results825 studies from 114 different journals were identified. 297 papers were excluded. Of the 528 included papers, 204 (39%) were published by Vascular Surgery (VS), 157 (30%) by Interventional Radiology (IR), 101 (19%) by Cardiology, 43 (8%) by Angiology, 6 (1%) by Vascular Medicine, and 17 (3%) from miscellaneous services. 283 (54%) studies originated from Europe, 157 (30%) from North America, 76 (14%) from Asia, 6 from Australia, 3 each from South America and Africa. IR published the most papers on PAD endovascular intervention in Europe with VS second while this trend was reversed in the USA. The 528 papers were published in 98 different journals with retrospective case series (72%), the majority.ConclusionIR continues to play a significant research role in endovascular intervention in PAD, particularly in Europe, and specifically in below the knee intervention, pedal intervention, and drug-eluting technologies.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Pseudomonas atagosis sp. nov., and Pseudomonas akappagea sp. nov., New Soil Bacteria Isolated from Samples on the Volcanic Island Izu Oshima, Tokyo

During the exploration of microbial natural resources, two strains of Pseudomonas, PS14 T and PS24 T , were isolated from samples taken from Izu Oshima, a volcanic island located 120 km southwest of central Tokyo. Phylogenetic analysis based on 16S rRNA gene sequences showed that PS14 T was most similar to Pseudomonas baetica a390T (99.6%) and Pseudomonas helmanticensis OHA11 T (99.5%), and that PS24T was most similar to Pseudomonas qingdaonensis JJ3 T (98.8%) and Pseudomonas lutea OK2 T (98.7%). The major fatty acids of these two strains were C 16:0 and C 17:0 cyclo, summed feature 3 (C 16:1 ω6c and/or C 16:1 ω7c), and summed feature 8 (C18:1 ω7c and/or 18:1 ω6c). The phylogenetic analyses, DNA-DNA hybridization results and phenotypic traits indicated that PS14 T and PS24 T constitute two novel species, Pseudomonas atagosis sp. nov. (type strain PS14 T = CECT 9940 T , = LMG 31496 T ) and Pseudomonas akappagea sp. nov. (type strain PS24T = CECT 9941T, = LMG 31497T), respectively. The sequence data of the draft genomes of PS14 T and PS24 T were deposited in the GenBank database under accession numbers VXCA00000000 and VXCP00000000, respectively, and the sequence data of their 16S rRNA genes were deposited in the GenBank database under accession numbers MN396717 and MN382268, respectively.

59 BASIC BIOLOGICAL SCIENCES↗

The solubility of titanite in silicate melt determined from growth and dissolution experiments

The solubility of titanite (CaTiSiO 5 ) in Si-rich melts was measured experimentally through growth experiments at 800–1000 °C, 0.5–1.0 GPa, log fO 2 ~ CCO–0.8, t = 72–168 h, and H 2 O = 0 to 4 wt.%, and in dissolution experiments at 925–1300 °C, 0.8 GPa, t = 18–118 h, and H 2 O = 1–10 wt.% in a piston-cylinder apparatus. Run product glasses in growth experiments were homogeneous, and iron loss suppressed ilmenite crystallization. Saturation concentrations in dissolution experiments were estimated by fitting measured diffusion profiles. Titanite solubility increases with increasing temperature and melt composition parameter \(M = {\text{ molar }}\left( {{\text{Na }} + {\text{ K }} + {\text{ 2Ca}}} \right)/\left( {{\text{Al }} \times {\text{ Si}}} \right)\) . Multiple linear regression of glass composition data from growth and dissolution experiments ( n = 29) plus 39 experiments from the LEPR database (Hirschmann et al. 2008 ) yielded the titanite solubility equation (adj. r 2 = 0.95): \(\left( {TiO_{2} } \right)^{melt} \left( {wt.\% } \right) = 0.978 \times M + 0.0048 \times T\left( K \right){-}5.90\) . This model correctly predicted undersaturation in 95% of 2344 experiments from the LEPR database that did not have titanite or rutile. Application to natural rocks yields saturation temperatures that are similar to independent temperature estimates. Finally, this equation should be useful for constraining the temperatures of titanite-saturated melts, for determining whether titanite saturation in magmatic source regions is likely, and for determining when titanite can crystallize and begin to exert an influence on melt geochemistry.

58 GEOSCIENCES↗

Computer-Aided Diagnosis of Lung Nodules in Computed Tomography by Using Phylogenetic Diversity, Genetic Algorithm, and SVM

Lung cancer is pointed as the major cause of death among patients with cancer throughout the world. This work is intended to develop a methodology for diagnosis of lung nodules using images from the Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI). The proposed methodology uses image processing and pattern recognition techniques. In order to differentiate between the patterns of malignant and benign nodules, we used phylogenetic diversity by means of particular indexes, that are: intensive quadratic entropy, extensive quadratic entropy, average taxonomic distinctness, total taxonomic distinctness, and pure diversity indexes. After that, we applied the genetic algorithm for selection of the best model. In the tests’ stage, we applied the proposed methodology to 1405 (394 malignant and 1011 benign) nodules. The proposed work presents promising results at the classification into malignant and benign, achieving accuracy of 92.52%, sensitivity of 93.1% and specificity of 92.26%. The results demonstrated a good rate of correct detections using texture features. Since a precocious detection allows a faster therapeutic intervention, thus a more favorable prognostic to the patient, we propose herein a methodology that contributes to the area in this aspect.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Detection of Lung Contour with Closed Principal Curve and Machine Learning

Radiation therapy plays an essential role in the treatment of cancer. In radiation therapy, the ideal radiation doses are delivered to the observed tumor while not affecting neighboring normal tissues. In three-dimensional computed tomography (3D-CT) scans, the contours of tumors and organs-at-risk (OARs) are often manually delineated by radiologists. The task is complicated and time-consuming, and the manually delineated results will be variable from different radiologists. We propose a semi-supervised contour detection algorithm, which firstly uses a few points of region of interest (ROI) as an approximate initialization. Then the data sequences are achieved by the closed polygonal line (CPL) algorithm, where the data sequences consist of the ordered projection indexes and the corresponding initial points. Finally, the smooth lung contour can be obtained, when the data sequences are trained by the backpropagation neural network model (BNNM). We use the private clinical dataset and the public Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) dataset to measure the accuracy of the presented method, respectively. To the private dataset, experimental results on the initial points which are as low as 15% of the manually delineated points show that the Dice coefficient reaches up to 0.95 and the global error is as low as 1.47 × 10{sup −2}. The performance of the proposed algorithm is also better than the cubic spline interpolation (CSI) algorithm. While on the public LIDC-IDRI dataset, our method achieves superior segmentation performance with average Dice of 0.83.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Nuclear-Physical Foundation of Atomic Energy

The current status of the nuclear database used for engineering calculations in the field of nuclear energy is reported. It is shown that the nuclear database and its attendant computational methods, stabilization, and transmission to the next generation of specialists who will have to solve the problems of the future development of nuclear power must be improved and updated.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Capabilities of multivariate Bayesian inference toward seismic hazard assessment

Multivariate Bayesian analysis can bring significant benefits to seismic hazard analysis: Its multivariate feature enables computing scalar and vector hazard without making any approximations; Correlations between intensity measures are implicitly modeled, permitting direct simulation of ground motion selection tools such as the conditional mean spectrum and the generalized conditioning intensity measure; and Its updating feature enables a seamless integration of new ground motion data into the hazard results. Here, we first develop a multivariate Bayesian ground motion model through the NGA-West2 database. The model functional form considers fault-type, magnitude, and distance dependencies, and also the linear and the rock intensity dependent site response. We use a hybrid Markov Chain Monte Carlo sampling to perform Bayesian inference consisting of Gibbs step and a multilevel Metropolis-Hastings step. We then perform several checks on the model and note that its performance is satisfactory. Finally, we illustrate the merits of this multivariate Bayesian analysis, which include: ground motion model updating with ground motion data recorded in the last four years not part of the NGA-West2 database; computation of scalar and vector seismic hazard using the un-updated and updated ground motion models for Los Angeles, CA; and simulation of the conditional mean spectrum under scalar and vector IM conditioning while accounting for different sources of aleatoric and epistemic uncertainties.

58 GEOSCIENCES↗