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At least 127 records · Page 7

Comparing published scientific journal articles to their pre-print versions

Academic publishers claim that they add value to scholarly communications by coordinating reviews and contributing and enhancing text during publication. These contributions come at a considerable cost: US academic libraries paid $1.7 billion for serial subscriptions in 2008 alone. Library budgets, in contrast, are flat and not able to keep pace with serial price inflation. Here, we have investigated the publishers’ value proposition by conducting a comparative study of pre-print papers from two distinct science, technology, and medicine corpora and their final published counterparts. This comparison had two working assumptions: (1) If the publishers’ argument is valid, the text of a pre-print paper should vary measurably from its corresponding final published version, and (2) by applying standard similarity measures, we should be able to detect and quantify such differences. Our analysis revealed that the text contents of the scientific papers generally changed very little from their pre-print to final published versions. These findings contribute empirical indicators to discussions of the added value of commercial publishers and therefore should influence libraries’ economic decisions regarding access to scholarly publications.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Capturing phenotypes for precision medicine

Deep phenotyping followed by integrated computational analysis of genotype and phenotype is becoming ever more important for many areas of genomic diagnostics and translational research. The overwhelming majority of clinical descriptions in the medical literature are available only as natural language text, meaning that searching, analysis, and integration of medically relevant information in databases such as PubMed is challenging. The new journal Cold Spring Harbor Molecular Case Studies will require authors to select Human Phenotype Ontology terms for research papers that will be displayed alongside the manuscript, thereby providing a foundation for ontology-based indexing and searching of articles that contain descriptions of phenotypic abnormalities —an important step toward improving the ability of researchers and clinicians to get biomedical information that is critical for clinical care or translational research.

59 BASIC BIOLOGICAL SCIENCES↗

Supporting Development of Satellite's Guidance Navigation and Control Software: A Product Line Approach

The NASA Goddard Space Flight Center Flight Software Branch (FSB) is developing a Guidance, Navigation, and Control (GNC) Flight Software (FSW) product line. The demand for increasingly more complex flight software in less time while maintaining the same level of quality has motivated us to look for better FSW development strategies. The GNC FSW product line has been planned to address the core GNC FSW functionality very similar on many recent low/near Earth missions in the last ten years. Unfortunately these missions have not accomplished significant drops in development cost since a systematic approach towards reuse has not been adopted. In addition, new demands are continually being placed upon the FSW which means the FSB must become more adept at providing GNC FSW functionality's core so it can accommodate additional requirements. These domain features together with engineering concepts are influencing the specification, description and evaluation of FSW product line. Domain engineering is the foundation for emerging product line software development approaches. A product line is 'A family of products designed to take advantage of their common aspects and predicted variabilities'. In our product line approach, domain engineering includes the engineering activities needed to produce reusable artifacts for a domain. Application engineering refers to developing an application in the domain starting from reusable artifacts. The focus of this paper is regarding the software process, lessons learned and on how the GNC FSW product line manages variability. Existing domain engineering approaches do not enforce any specific notation for domain analysis or commonality and variability analysis. Usually, natural language text is the preferred tool. The advantage is the flexibility and adapt ability of natural language. However, one has to be ready to accept also its well-known drawbacks, such as ambiguity, inconsistency, and contradictions. While most domain analysis approaches are functionally oriented, the idea of applying the object-oriented approach in domain analysis is not new. Some authors propose to use UML as the notation underlying domain analysis. Our work is based on the same idea of merging UML and domain analysis. Further, we propose a few extensions to UML in order to express variability, and we define precisely their semantics so that a tool can support them. The extensions are designed to be implemented on the API of a popular industrial CASE tool, with obvious advantages in cost and availability of tool support. The paper outlines the product line processes and identifies where variability must be addressed. Then it describes the product line products with respect to how they accommodate variability. The Celestial Body subdomain is used as a working example. Our results to date are summarized and plans for the future are described.

McComas, David↗

Novel Analysis and Visualization of Chemical Events for Public Health Surveillance

Pacific Northwest National Laboratory hosted an intern-based web application development contest in the summer of 2016 centered around developing novel chemical surveillance applications to aid in health situational awareness. Making up the three teams were three graduate students (n=9) from various US schools majoring in non-public health domains, such as computer science and user design. The interns successfully developed three applications that demonstrated a value-add to chemical surveillance—ChemAnalyzer (text analytics), RetroSpect (retrospective analysis of chemical events),and ToxicBusters (geo-based trend analytics). These applications will be the basis for the first chemical surveillance application to be incorporated into the DTRA Biosurveillance Ecosystem (BSVE).Pacific Northwest National Laboratory (PNNL), on behalf the Defense Threat Reduction Agency (DTRA; project number CB10190), hosts an annual intern- based web app development contest. Previous competitions have focused on mobile biosurveillance. The 2016 competition pivoted away from biosurveillance to focus on addressing challenges within the field of chemical surveillance and increasing public health chemical situational awareness. The result of the app will be integrated within the DTRA BSVE. PNNL hosted nine graduate interns for a 10-week period in the summer of 2016 as participants in a summer web application development contest. Students were drawn from such fields as software engineering and user experience and design and placed into three teams of three students. The challenge presented to the interns was to design and develop a fully-functional web application that would address a critical need within the chemical surveillance community. The interns developed their own ideas (vetted by PNNL and DTRA), discovered and integrated their own data sources, and produced their own visualizations and analytics, independent of any assistance outside of that provided in an advisory capacity. The competition end with a judging event with a panel of subject matter experts and cash awards were distributed to the teams. Each team produced a unique application. Although there was mild overlap between some of the ideas, the applications were developed independently and each reflected the unique contributions of the teams. ChemAnalyzer is a text-analytics platform designed to facilitate more data-driven decision, given a corpus of text data about a chemical event. Their platform provided the ability to automatically identify and highlight key words in documents related to chemical events. The keywords are drawn from an ontology installed with the system, as well as any user-identified keywords. The ChemAnalyzer team finished in third place. The RetroSpect team developed a visual analytic tool for performing retrospective analysis and monitoring of chemical events. Their app provided the ability to search and analyze past events, as well as visualization of state and county information for the recorded chemical events. The RetroSpect team finished in second place. The Toxic busters team - the winners of the competition - created a geo-based situational awareness tool for tracking chemical events. Their app featured an updateable map overlay, search functionality for finding specific or related events, incident and city/state/national-level statistics and trends, as well as news and social media integration based on keywords related to chemical surveillance. Each of the apps developed by the teams provides value to an analyst tasked with monitoring chemical events. The apps integrated unique data sources to provides a full picture of a chemical event, and its effects upon the surrounding population. This integrated analytics provides a valuable benefit over existing workflows, where analysts must monitor news, social, and other information sources manually for real-time information. The apps developed by these interns are designed to enable identification and analysis of the incident as quickly as possible, allowing for more timely assessments of the incident and its impacts. The web app development contest provided a unique opportunity for students to learn about the emerging needs in chemical surveillance as it relates to health situational awareness. Students were drawn from a variety of fields and were tasked with developing novel web apps addressing some of the most pressing challenges in the field of chemical surveillance. The ideas generated by the students will help form the basis for future chemical surveillance application development to be integrated with the DTRABSVE.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Measurement of the Higgs boson production rate in association with top quarks in final states with electrons, muons, and hadronically decaying tau leptons at $\sqrt{s} =$ 13 TeV

The rate for Higgs (${\mathrm{H}} $) bosons production in association with either one (${\mathrm{t}} {\mathrm{H}} $) or two (${\mathrm{t}} {{\overline{{{\mathrm{t}}}}}} {\mathrm{H}} $) top quarks is measured in final states containing multiple electrons, muons, or tau leptons decaying to hadrons and a neutrino, using proton–proton collisions recorded at a center-of-mass energy of $13\,\text {Te}\text {V} $ by the CMS experiment. The analyzed data correspond to an integrated luminosity of 137$\,\text {fb}^{-1}$. The analysis is aimed at events that contain ${\mathrm{H}} \rightarrow {\mathrm{W}} {\mathrm{W}} $, ${\mathrm{H}} \rightarrow {\tau } {\tau } $, or ${\mathrm{H}} \rightarrow {\mathrm{Z}} {\mathrm{Z}} $ decays and each of the top quark(s) decays either to lepton+jets or all-jet channels. Sensitivity to signal is maximized by including ten signatures in the analysis, depending on the lepton multiplicity. The separation among ${\mathrm{t}} {\mathrm{H}} $, ${\mathrm{t}} {{\overline{{{\mathrm{t}}}}}} {\mathrm{H}} $, and the backgrounds is enhanced through machine-learning techniques and matrix-element methods. The measured production rates for the ${\mathrm{t}} {{\overline{{{\mathrm{t}}}}}} {\mathrm{H}} $ and ${\mathrm{t}} {\mathrm{H}} $ signals correspond to $0.92 \pm 0.19\,\text {(stat)} ^{+0.17}_{-0.13}\,\text {(syst)} $ and $5.7 \pm 2.7\,\text {(stat)} \pm 3.0\,\text {(syst)} $ of their respective standard model (SM) expectations. The corresponding observed (expected) significance amounts to 4.7 (5.2) standard deviations for ${\mathrm{t}} {{\overline{{{\mathrm{t}}}}}} {\mathrm{H}} $, and to 1.4 (0.3) for ${\mathrm{t}} {\mathrm{H}} $ production. Assuming that the Higgs boson coupling to the tau lepton is equal in strength to its expectation in the SM, the coupling $y_{{\mathrm{t}}}$ of the Higgs boson to the top quark divided by its SM expectation, $\kappa _{{\mathrm{t}}}=y_{{\mathrm{t}}}/y_{{\mathrm{t}}}^{\mathrm {SM}}$, is constrained to be within $-0.9< \kappa _{{\mathrm{t}}}< -0.7$ or $0.7< \kappa _{{\mathrm{t}}}< 1.1$, at 95% confidence level. This result is the most sensitive measurement of the ${\mathrm{t}} {{\overline{{{\mathrm{t}}}}}} {\mathrm{H}} $ production rate to date.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Measurement of differential cross sections for inclusive isolated-photon and photon+jet production in proton-proton collisions at $\sqrt{s} = 13\,\text {TeV} $

Measurements of inclusive isolated-photon and photon+jet production in proton–proton collisions at $\sqrt{s} = 13\,\text {TeV} $ are presented. The analysis uses data collected by the CMS experiment in 2015, corresponding to an integrated luminosity of 2.26 $\,\text {fb}^{-1}$ . The cross section for inclusive isolated photon production is measured as a function of the photon transverse energy in a fiducial region. The cross section for photon+jet production is measured as a function of the photon transverse energy in the same fiducial region with identical photon requirements and with the highest transverse momentum jet. In conclusion, all measurements are in agreement with predictions from next-to-leading-order perturbative QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Applications of Automation Methods for Nonlinear Fracture Test Analysis

Using automated and standardized computer tools to calculate the pertinent test result values has several advantages such as: 1. allowing high-fidelity solutions to complex nonlinear phenomena that would be impractical to express in written equation form, 2. eliminating errors associated with the interpretation and programing of analysis procedures from the text of test standards, 3. lessening the need for expertise in the areas of solid mechanics, fracture mechanics, numerical methods, and/or finite element modeling, to achieve sound results, 4. and providing one computer tool and/or one set of solutions for all users for a more "standardized" answer. In summary, this approach allows a non-expert with rudimentary training to get the best practical solution based on the latest understanding with minimum difficulty.Other existing ASTM standards that cover complicated phenomena use standard computer programs: 1. ASTM C1340/C1340M-10- Standard Practice for Estimation of Heat Gain or Loss Through Ceilings Under Attics Containing Radiant Barriers by Use of a Computer Program 2. ASTM F 2815 - Standard Practice for Chemical Permeation through Protective Clothing Materials: Testing Data Analysis by Use of a Computer Program 3. ASTM E2807 - Standard Specification for 3D Imaging Data Exchange, Version 1.0 The verification, validation, and round-robin processes required of a computer tool closely parallel the methods that are used to ensure the solution validity for equations included in test standard. The use of automated analysis tools allows the creation and practical implementation of advanced fracture mechanics test standards that capture the physics of a nonlinear fracture mechanics problem without adding undue burden or expense to the user. The presented approach forms a bridge between the equation-based fracture testing standards of today and the next generation of standards solving complex problems through analysis automation.

Allen, Phillip A.↗

Does Peer Review of Radiation Plans Affect Clinical Care? A Systematic Review of the Literature

Purpose: Peer review is a recommended component of quality assurance in radiation oncology; however, it is resource-intensive and its effect on patient care is not well understood. We conducted a systematic review of the published data to assess the reported clinical impact of peer review on radiation treatment plans. Methods and Materials: A systematic review of published English studies was performed in accordance with the PRISMA guidelines using the MEDLINE and EMBASE databases and abstracts published from major radiation oncology scientific meeting proceedings. For inclusion, the studies were required to report the effect of peer review on ≥1 element of treatment planning (eg, target volume or organ-at-risk delineation, dose prescription or dosimetry). Results: The initial search strategy identified 882 potentially eligible studies, with 11 meeting the inclusion criteria for full-text review and final analysis. Across a total of 11,491 patient cases, peer review programs led to modifications in a weighted mean of 10.8% of radiation treatment plans. Five studies differentiated between major and minor changes and reported weighted mean rates of change of 1.8% and 7.3%, respectively. The most common changes were related to target volume delineation (45.2% of changed plans), dose prescription or written directives (24.4%), and non-target volume delineation or normal tissue sparing (7.5%). Conclusions: Our findings suggest that peer review leads to changes in clinical care in approximately 1 of every 9 cases overall. This is similar to the reported rates of change in peer review studies from other oncology-related specialties, such as radiology and pathology.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Erratum: Polarization transfer observables in elastic electron-proton scattering at Q 2 =2.5 , 5.2, 6.8, and 8.5GeV 2 [Phys. Rev. C 96 , 055203 (2017)]

Subsequent to the release of our original paper, we discovered in the context of preparing our technical supplement [1] for journal publication that a typographical error had existed in the text file that the analysis program used to construct the beam polarization "database" for both the original analysis, published in Ref. [2], and our final analysis. The electron-beam polarization P e and the analyzing power A y cancel exactly in the ratio R, which is proportional to the ratio P t / P l of the transferred polarization components. On the other hand, the extraction of the relative e dependence of P l / P Born l relies on knowledge of the beam polarization. As such, data taking was interrupted roughly every two days during the GEp - 2γ experiment to perform invasive measurements of the beam polarization using the Hall C Moller polarimeter [3].

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Physical properties of the layered $\mathcal{f}$-electron van der Waals magnet Ce 2 Te 5

Here. we report a detailed study of the magnetic, transport, and thermodynamic properties of Ce 2 Te 5 single crystals, a layered $\mathcal{f}$-electron van der Waals magnet. Four consecutive transitions at ~5.2, 2.1, 0.9, and 0.4 K were observed in the ac-plane electrical resistivity $\rho(T)$, which were further confirmed in specific heat $C_\text{p}(T)$ measurements. Analysis of the magnetic susceptibility $\chi(T)$, the magnetic-field variation of $\rho(T)$, and the increase of the first transition temperature ($T_c$ ~ 5.2 K) with applied magnetic field indicates ferromagnetic order, while the decrease of the other transitions with field suggests different states with dominant antiferromagnetic interactions below $T_2$ ~ 2.1 K, $T_3$ ~ 0.9 K, and $T_4$ = 0.4 K. Critical behavior analysis around Tc that gives critical exponents $\beta$ = 0.31(2), $\gamma$ = 0.99(2), $\delta$ = 4.46(1), and $T_c$ = 5.32(1) K indicates that Ce 2 Te 5 shows a three-dimensional magnetic critical behavior. Moreover, the Hall resistivity ρxy indicates that Ce2Te5 is a multiband system with a relatively high electron mobility ~2900 cm 2 V –1 s –1 near $T_c$, providing further opportunities for future device applications.

36 MATERIALS SCIENCE↗

SU-E-T-778: Use of the 2D MatriXX Detector for Measuring Scanned Ion Beam Parameters

Purpose: The quality assurance (QA) procedure has to check the most relevant beam parameters to ensure the delivery of the correct dose to patients. Film dosimetry, which is commonly used for scanned ion beam QA, does not provide immediate results. The purpose of this work is to answer whether, for scanned ion beam therapy, film dosimetry can be replaced with the 2D MatriXX detector as a real-time tool. Methods: MatriXX, equipped with 32×32 parallel plate ion-chambers, is a commercial device intended for pre-treatment verification of conventional radiation therapy.The MatriXX, placed at the isocenter, and GAFCHROMIC films, positioned on the MatriXX entrance, were exposed to 131.44 MeV proton and 221.45 MeV/u Carbon-ion beams.The OmniPro-I’mRT software, applied for the data taking of MatriXX, gives the possibility of acquiring consecutive snapshots. Using the NI LabVIEW, the data from snapshots were logged as text files for further analysis. Radiochromic films were scanned with EPSON scanner and analyzed using software programs developed in-house for comparative purposes. Results: The field dose uniformity, flatness, beam position and beam width were investigated. The field flatness for the region covering 6×6 cm{sup 2} square field was found to be better than 2%. The relative standard deviations, expected to be constant over 2×2, 4×4 and 6×6 pixels from MatriXX measurement gives a uniformity of 1.5% in good agreement with the film results.The beam center position is determined with a resolution better than 200 µm for Carbon and less than 100 µm for proton beam.The FWHM determination for a beam wider than 10 mm is satisfactory, whilst for smaller beams the determination is uncertain. Conclusion: Precise beam position and fast 2D dose distribution can be determined in real-time using MatriXX detector. The results show that MatriXX is quick and accurate enough to be used in charged-particle therapy QA.

60 APPLIED LIFE SCIENCES↗

Measurements of $\pi ^\pm $, $K^\pm $, p and $\bar{p}$ spectra in $^{40}\hbox {Ar+}^{45}\hbox {Sc}$ collisions at 13A to 150A $\text{ Ge }\hspace{-1.00006pt}\text{ V }\!/\!c$

The NA61/SHINE experiment at the CERN Super Proton Synchrotron studies the onset of deconfinement in strongly interacting matter through a beam energy scan of particle production in collisions of nuclei of varied sizes. This paper presents results on inclusive double-differential spectra, transverse momentum and rapidity distributions and mean multiplicities of $\pi ^\pm $, $K^\pm $, p and $\bar{p}$ produced in $^{40}\hbox {Ar+}^{45}\hbox {Sc}$ collisions at beam momenta of 13A, 19A, 30A, 40A, 75A and 150A $\text{ Ge }\hspace{-1.00006pt}\text{ V }\!/\!c$. The analysis uses the 10% most central collisions, where the observed forward energy defines centrality. The energy dependence of the $K^\pm $/$\pi ^\pm $ ratios as well as of inverse slope parameters of the $K^\pm $ transverse mass distributions are placed in between those found in inelastic $p+p$ and central Pb + Pb collisions. The results obtained here establish a system-size dependence of hadron production properties that so far cannot be explained either within statistical or dynamical models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Postdoctoral insights on mentoring excellence: a framework for best practices at Sandia National labs

The Sandia National Laboratories Strategic Plan FY24-FY27, updated for FY25, outlines Sandia’s two Big Labs-wide Goals, Accelerate Innovation and Lead in Modern Engineering. The goal of Accelerate Innovation is that “by FY27, Sandia will be a leader in scientific, engineering and operational innovation and an employer of choice for highly innovative and creative talent.” Sandia’s postdocs are leaders in innovation, well-versed in emerging techniques and cutting-edge methods, and capable of acting as a highly agile technical force across domains at the lab. As a federally funded research and development center (FFRDC), Sandia National Laboratories attracts top doctoral talent by offering a unique opportunity for postdoctoral researchers to develop at the crossroads of government, academia, and industry, working in multi-disciplinary teams and performing cutting-edge, mission-specific research that responds to immediate needs of national interest. However, this creates unique opportunities and demands of both postdoctoral appointees and the Sandia staff who act as their mentors, making mentorship key to attract talent. Since 2007 the Sandia Postdoctoral Development (SPD) Board, originally Postdoc To Professional (PD2P), a networking group at Sandia composed of a voluntary board of current postdocs and two staff liaisons, has advocated for postdoctoral development within Sandia National Labs. In this white paper, SPD board members and the Sandia Postdoctoral Development Office, organized in 2019, have come together to develop a comprehensive overview of the postdoctoral mentoring landscape at Sandia National Labs as we currently know it. By scouring various forms of data from efforts since 2018, we’ve compiled a community-derived perspective on what makes postdoctoral mentorship at Sandia unique. First, we analyze working sessions held between mentors and mentees to develop a comprehensive map of who is involved in postdoctoral mentorship at the lab and how the responsibilities are divided amongst mentors and mentees. We then combine multiple forms of data, including exit surveys, annual surveys, and community workshops, to identify the specific challenges that mentors and mentees encounter at the national lab. Finally, we use text mining and sentiment analysis to analyze mentoring award data to develop an idea of what postdocs are self-identifying as excellent mentorship within the lab. It is our goal that this white paper act as an ongoing resource to the postdoc and postdoc mentoring communities and provide a firm foundation for further conversations on the future of postdoctoral mentorship at Sandia National Labs.

99 GENERAL AND MISCELLANEOUS↗

Machine Reading at Scale: A Search Engine for Scientific and Academic Research

The Internet, much like our universe, is ever-expanding. Information, in the most varied formats, is continuously added to the point of information overload. Consequently, the ability to navigate this ocean of data is crucial in our day-to-day lives, with familiar tools such as search engines carving a path through this unknown. In the research world, articles on a myriad of topics with distinct complexity levels are published daily, requiring specialized tools to facilitate the access and assessment of the information within. Recent endeavors in artificial intelligence, and in natural language processing in particular, can be seen as potential solutions for breaking information overload and provide enhanced search mechanisms by means of advanced algorithms. As the advent of transformer-based language models contributed to a more comprehensive analysis of both text-encoded intents and true document semantic meaning, there is simultaneously a need for additional computational resources. Information retrieval methods can act as low-complexity, yet reliable, filters to feed heavier algorithms, thus reducing computational requirements substantially. In this work, a new search engine is proposed, addressing machine reading at scale in the context of scientific and academic research. It combines state-of-the-art algorithms for information retrieval and reading comprehension tasks to extract meaningful answers from a corpus of scientific documents. The solution is then tested on two current and relevant topics, cybersecurity and energy, proving that the system is able to perform under distinct knowledge domains while achieving competent performance.

Sousa, Norberto (ORCID:0000000329194817)↗

Tools to perform data reduction of time-of-flight data taken on BL4A (MagRef)—a Jupyter notebook approach

A collection of modules or tools to produce reflectivity profiles from data acquired with unpolarized and polarized neutron beams using the BL4A (MagRef) instrument at the Spallation Neutron Source. The Jupyter notebook approach offers transparency to the user on what is done with the data, and once the event mode data are stored as NumPy binary files empowers the user to perform the steps from their own laptop without the need for Mantid. The notebook offers two options for background subtraction, applies corrections for the wavelength dependence of the polarizer and flipper efficiencies, accounts for Zeeman energy splitting of the spin-flip channels, Qz-bins the data along contours of constant Qz, propagates errors and writes results in text format suitable for analysis with tools such as GenX.

Fitzsimmons, Michael [Oak Ridge Associated Univ., ↗

Recent test results on lithium BCX cells

Texts included: short circuit analysis, voltage reversal, high temperature exposure, parallel loading sharing, capacity tests, shock and vibration tests, and assembly tests. Both the AA and D cell configurations were tested. Certification of the cells is discussed and applications are highlighted.

Bragg, B. J.↗

Causality Extraction from Nuclear Licensee Event Reports Using a Hybrid Framework

In this paper, we proposed a hybrid framework for causality detection and extraction in LER documents. The main contributions are summarized below. We 1) built an LER corpus with 20,129 text samples for causality analysis, 2) developed an interactive tool was developed for labeling cause-effect pairs, 3) built a deep learning-based approach for causal relation detection, and 4) built a knowledge-based cause-effect extraction approach.

99 GENERAL AND MISCELLANEOUS↗