Research Data Management Service Sustainability Tina Griffin, MLIS. Asst. Professor. University of Illinois Chicago. Chicago, IL 60612 Margaret Janz. Interpreter II. Great Parks of Hamilton County. Cincinnati, OH 54231 Introduction Libraries at high-level research and other academic institutions have been involved in research data management service (RDMS) for more than ten years. As the demand for these services has increased, libraries have adapted their service models. There have been several studies that have reviewed the “state of RDM services,” but these have only provided a snapshot of activities at a given time. Research Data Management activities require support through infrastructure, personnel, time, and money. Previous studies address these topics individually, but there is little connection between RDMS data collected over time and are few longitudinal studies. These studies also do not address the necessary decisions and changes that must have been made to make RDMS sustainable over time. This study will attempt to fill that gap by updating the RDMS status to describe the current baseline, broadening the facets addressed so that details about sustainability can be highlighted, and presenting the data by cohort to help other institutions identify parallels to their RDMS. Methodology • A 62-question survey was distributed in the fall of 2020 for 6 weeks through data listservs and message boards (DataCure Google Group, Research Data Access and Preservation discussion forum, International Association for Social Science Information Service and Technology listserv, Digital Library Federation listserv, Research Data Alliance forums). Two reminders were sent, one at 3 weeks and one the day before close. • Questions asked about changes in service model, staffing and funding, accountability, and planning for research data management services since service inception. • The survey was reviewed by eight data librarians currently in the field, and edited for bias, errors, and clarity. A copy of he survey instrument can be downloaded here: https://go.library.uic.edu/RDMSUSurveyInstrument. • IRB at both authors’ institutions reviewed the protocol and it was determined to be exempt. • The survey data was collected via Qualtrics Survey Software (Qualtrics, LLC. Provo, UT, USA. https://www.qualtrics.com/). • Received 118 responses. 70 responses were analyzed, including 32 which were partially complete. • Responses were excluded if: • did not contain any data (21) • only answered the question regarding service duration (9) • services were offered less than one year (16) • did not consent (2) • Personally identifying and some institutional demographic information was deleted before analysis, as per the informed consent agreement. Selected Results – Respondent Characteristics 13 14 31 12 1-3Y 3-5Y 5-10Y 10+Y Number of Respondents by Years offering RDMS 12 10 5 34 >7M 8-25M 25-50M unsure Respondents Library budget (Millions) Selected Results – Service profile Almost all respondents indicated that they have increased both technical and advisory services over time. Among all groups, the number of services offered ranged from two to fifteen. The average number of services offered from 1-3Y was 6.5, from 3- 5Y was about 10, cohort 5-10Y or 10+Y offered just under 8 each. Cohorts differ as to which services they offer. Number of Respondents offering RDS by Service level and cohort. Technical Only Advisory Only Both 1 1 3 2 2 1 2 1 3 2 4 6 5 4 4 1 1 1 2 2 2 1 1 2 1 3 4 5 Deidentification Analysis Offer resources Visualization Metadata Purchase Documentation Curation Preservation Citation Storage Finding Data Sharing Education/trai… Planning 1-3Y 2 1 1 1 4 2 6 8 6 4 8 2 9 8 3 2 1 1 1 1 3 3 3 2 2 3 5 2 6 2 3 9 Deidentification Analysis Offer resources Visualization Metadata Purchase Documentation Curation Preservation Citation Storage Finding Data Sharing Education/traini… Planning 3-5Y 1 4 4 6 7 7 4 10 11 6 14 13 13 11 11 2 1 1 5 2 4 2 4 9 1


sentinel-3A SLSTR – Early results The main objective of the Sentinel-3 SLSTR instrument is to maintain continuity with the ENVISAT (A)ATSR series of instruments within the European Copernicus programme. SLSTR will retrieve global coverage sea surface skin temperature (SSTskin) with zero bias and an uncertainty of ± 0.3 K (1σ) for a 5 x 5 degree latitude longitude area, having a temporal stability of 0.1 K/decade in support of Copernicus climate monitoring and operational Numerical Ocean/Weather Prediction (NOP/NWP) applications. In addition, SLSTR using a suite of visible and infrared radiance measurements, monitoring, ice surface temperature, cloud imagery, atmospheric aerosol, land, forestry and hydrology products in support of Copernicus serviceswill provide land surface temperature, active ﬁre. This poster presentation presents initial results from the Sentinel-3A SLSTR as of May 25th 2016. C. Donlon, D. Smith (RAL), B. Berruti, J. Nieke and J. Frerick. Contact: Craig.Donlon@esa.int and for dave.smith@stfc.ac.uk further information. èAbout sentinel-3 Sea and Land Surface Temperature Radiometer è A BIGGER PICTURE FOR COPERNICUS SLSTR Band L Centre [µm] ΔL [µm] SNR [-] / NeΔT [mK] Spatial Sampling Distance (SSD) [km] Function S1 0.555 0.02 20 0.5 Cloud screening, vegetation monitoring, aerosol S2 0.659 0.02 20 0.5 NDVI, vegetation monitoring, aerosol S3 0.865 0.02 20 0.5 NDVI, Cloud flagging, Pixel co- registration S4 1.375 0.015 20 0.5 Cirrus detection over land S5 1.61 0.06 20 0.5 Cloud clearing, Ice and snow, vegetation monitoring, S6 2.25 0.05 20 0.5 Vegetation State and Cloud Clearing S7 3.74 0.38 80 mK 1.0 SST, LST, Active Fire S8 10.95 0.9 50 mK 1.0 SST, LST, Active Fire S9 12 1.0 50 mK 1.0 SST, LST F1 3.74 0.38 < 1 K 1.0 Active Fire F2 10.95 0.9 < 0.5 K 1.0 Active Fire èSpectral channels èSLSTR Optical design ç The complete suite of AATSR and ATSR-2 spectral channels (0.55, 0.66, 0.85, 1.6, 3.7, 10.8 and 12 µm) is included in the SLSTR design in order to maintain continuity. Additional channels at 1.378 µm and 2.25 µm are included to enhance thin cirrus cloud detection. SLSTR has an additional capability to derive active ﬁre measurements using an extended dynamic range of the 3.7 µm channel and dedicated optimized detectors at 10.8 µm that are capable of detecting ﬁres at ~450 K without saturation. è SLSTR uses two independent scan chains each including a separate scan mirror (scanning at a constant velocity of 180 rpm), an off-axis paraboloid mirror, and a fold mirror to focus measured radiance into the instrument Detector Assembly (DA). An innovative recombination “ﬂip” mirror alternately relays each of the scanned optical beams into a common ﬁeld plane at the entrance of the DA where there is a cold bafﬂe. ç While more complex than the single scan system employed by the (A)ATSR instrument series, the SLSTR 3-mirror scan conﬁguration increases the instrument oblique view swath to ~750 km (centred at the SLSTR nadir point) and the nadir swath to~1400 km (offset in a westerly direction). The nadir swath is asymmetrical with respect to the nadir point to provide identical and contemporaneous coverage with OLCI ocean/land colour measurements. Visible and short-wave infrared detectors have a spatial resolution of 0.5 km on ground. Thermal infrared detectors have a spatial resolution of 1 km on ground. 05/04/2016 10:02 am. The first image from the Sentinel-3A SLSTR thermal-infrared channels at 1km spatial resolution reveals thermal signatures over a part of western Namibia and the South Atlantic Ocean. Cold water is seen along the Namibian coast upwelling from deeper waters. The Benguela current flows north along the west coast of South Africa driven by southeasterly winds, creating coastal upwelling. Many eddies and meanders are generated in this complex system and these small-scale features are captured beautifully. Over land, the distinct folds of desert dunes can be seen. In fact, further north, Gobabeb is the locati


25-27 June 2008 Madrid, Spain Knowledge production in evaluating rehabilitation of buildings – Areas of interest and biases Anandasivakumar Ekambaram 1, Andreas Økland 2 1SINTEF, 7031 Trondheim, Norway, siva@sintef.no 2SINTEF, 7031 Trondheim; Norway, Andreas.Okland@sintef.no Background – A structured literature review on evaluating rehabilitation of buildings Journals that are considered: • Building and environment • Cleaner Production • Construction Innovation • Construction Management and Economics • Energy and Buildings • Facility • International Journal of Project Management • Sustainability Selected period of publication: 2016-2018 Number of relevant articles (selected after the final round of study): 58 Preliminary results – Areas of interest Areas of interest that were found after the first round of categorization of the results: • Support for decision making: o Evaluation of potential improvement scenarios / options o Improving decision making • Simulation • User behavior • Life cycle approach: o Life Cycle assessment o Life Cycle Cost • Payback time • Policy These are key areas of interest. This categorization is based on the number of articles that focus on the areas of interest. At the early stage of the study, as each of the articles was read, all areas of interest (that is, what areas that each article focuses on) were noted. Biases • Number of citations of the articles can play a role in determining the areas of interest • Average number of citations per area of interest could lead to a dilemma / bias: • Articles published in 2016 could probably have more citations than the articles published in 2018 • Areas of interest could overlap each other • Choosing what area(s) of interest that an article focuses on could be subjective REZBUILD This study is connected to research project: The REZBUILD project (REfurbishment decision making platform through advanced technologies for near Zero energy BUILDing renovation) grows with the main aim of defining a collaborative refurbishment ecosystem focused on the existing residential building stock. • Awarded by the European Commission with a H2020 Programme Grant of € 6,996,128.25 • Total budget: € 9,038,208.75 • Duration: 4 years (Started in October 2017) REZBUILD will base its refurbishment ecosystem on the integration of cost-effective technologies, business models and life-cycles interaction. https://rezbuildproject.eu/ 20th European Conference on Knowledge Management | Portugal, 2019 An area of interest that was described in one article, and that article has larger number of citations An area of interest that was described in many articles, but those articles have lesser number of citations Versus


The public codes ASOHF and VORTEX for the post-processing of cosmological simulations David Vallés-Pérez 1,† Susana Planelles 1,2 Vicent Quilis 1,2 1Departament d'Astronomia i Astrofísica, Universitat de València 2Observatori Astronòmic, Universitat de València †david.valles-perez@uv.es ASOHF (Vallés-Pérez, Planelles & Quilis, 2022) ASOHF is an adaptive spherical overdensity DM halo finder and galaxy finder. Among its main features, we can count: Haloes are detected from density peaks in configuration space. Dynamical information is subsequently used through several complementary unbinding processes. Physically motivated, self-consistent definition of substructures (see below). Possibility to look for galaxies within DM haloes (see below). Complete merger trees, robust to the loss of haloes in a number of snapshots. Outputs include lists of haloes with several (∼50) properties and, optionally, complete member particle lists. Python packages provided. Optimal scaling properties, ∆twall ∼Npart/ncores in shared-memory platforms (OMP) and low memory footprint. Does not require external, special libraries to be installed. Parallelisation (beyond OMP) Large (≳50 Mpc) simulations with many (≳109) particles can benefit from the domain decompo- sition strategy, which is performed externally to the code. Different subdomains can be run con- currently or sequentially, and the different domain outputs are seamlessly merged afterwards. Substructure Substructures are delimited by their Jacobi radius, RJ, encompassing the region more bound to the satellite than to the host halo. This is usually a more restrictive definition than others based on the density profile alone. Galaxy finder Galaxies are looked for within DM (sub)haloes us- ing a variation of the SO method, and are finally characterised as fully independent objects (with different centre, bulk velocity, etc.). Galaxy ex- tents are delimited by density and density gradi- ent, in addition to phase space arguments. Learn more The paper The code The docs A&A 664 A42 github.com/dvallesp/ASOHF ASOHF.github.io 100 101 102 103 104 105 N( > M) 25 particles 100 particles ASOHF AHF ROCKSTAR SUBFIND Tinker+08 All haloes Subhaloes 101 102 103 104 105 106 Npart 109 1010 1011 1012 1013 1014 M (M ) 0.25 0.50 0.75 1.00 1.25 1.50 1.75 2.00 N( > M) / N( > M) vortex (Vallés-Pérez, Planelles & Quilis, 2021a,b; Vallés-Pérez et al. 2024) vortex is a post-processing code for performing several computationally-intensive analyses on the velocity fields of hydrodynamical simulations. While it was originally designed for block-based AMR simulations, it is now a general tool. Helmholtz-Hodge decomposition v(x) = vsol(x) | {z } Solenoidal part ∇·vsol=0 + vcomp(x) | {z } Compressive part ∇×vcomp=0 + vharm(x) | {z } Harmonic part (mostly irrelevant) The decomposition is straightforward for uniform grids, but much more complex for multi-resolution data, especially if O(N2) is to be avoided. We solve for a vector and a scalar potentials, such that: vcomp = −∇φ vsol = ∇× A ∇2φ = −∇· v ∇2A = −∇× v Elliptic PDEs can be addressed by a combination of FFT techniques (base grid) and iterative solvers (e.g., SOR), so that overall the cost is ≲O(N4/3). Multi-scale Reynolds decomposition v(x) = ⟨v⟩L(x)(x) | {z } Bulk velocity field + δv(x) | {z } Turbulent velocity field The bulk velocity is obtained by performing a top- hat filtering with position-dependent width, ⟨v⟩L(x)(x) = RRR |x′−x|<L(x) w(x′, |x −x′|)v(x′)d3x′ RRR |x′−x|<L(x) w(x′, |x −x′|)d3x′ where L(x) is determined by the smallest of: The scale required for δv(x) to converge, which is an indication of the outer scale of turbulence. The distance to the nearest influential (M ≳2 −3) shock. Learn more The papers The code CPC 263:107892 MNRAS 504(1):510 github.com/dvallesp/vortex Compressive and solenoidal part of the turbulent velocity field (same simulation as the other panels) vortex-p: Helmholtz-Hodge & Reynolds decomposition for particle-based and meshless data B


I-а Міжнародна конференція «Відкрита наука та інновації в Україні 2022», Київ, 27-28 жовтня 2022 р. UNIVERSAL MURANOV ENGINE WITH EXTERNAL HEAT EXCHANGE FOR ENVIRONMENTALLY FRIENDLY GENERATION OF CHEAP ENERGY Muranov Sergey, Muranov Ivan e-mail: smuranov111@gmail.com; tel. +38 050 819 82 10 One of the most important economic problems are : reducing the cost of energy, reducing the consumption of hydrocarbon raw materials, as well as switching to more efficient, reliable and environmentally friendly methods of energy generation Investors are offered an innovative project engine Universal Muranov Engine (UME) that radically reduces the cost of electricity generation (by 2-3 times) while improving environmental friendliness This engine is a deep modernization of the Stirling engine (SE) Matrix SWOT a Stsrling Engine (operating engines in USA, China, Sweden…) + Strength SE: unique properties for efficient power generation high efficiency, the ability to run on any type of fuel and from any external heat sources, noiselessness; - Weakness SE: high manufacturing cost; bulkiness of construction, heavy weight. + Opportunities SE: a wide range of applications, in particular in distributive power generation systems in cogeneration plants. - Threats SE: limitation of the scope of application due to high cost, large dimensions and weight. reduced SE reliability due to the complexity of the mechanical drive design. Universal Muranov Engine (UME) The upgraded Stirling Engine designated as the Universal Muranov Engine with external heat exchange, developed by S. Muranov and I. Muranov, can be the basis of a new highly efficient, reliable and environmentally cleaner energy. The deep modernization of the SE included: development of a crankless mechanism built exclusively on rolling bearings; a unique system for heat recovery from the walls of the working cylinder, a system of reliable seals of pistons operating without lubrication, a new efficient system of heat exchangers with a small dead space. During the modernization, significant shortcomings of the SE were overcome, the cost of manufacturing the engine was radically reduced, efficiency and reliability of operation were increased, the weight and dimensions of the engine were significantly reduced, expanded application areas. The upgraded new UME is able to compete with internal combustion engines. and also with gas and steam turbines in terms of application efficiency. At the same time, UME-based mini-CHP plants generate energy and heat 2-3 times cheaper than traditional power plants. This engine can also be used on any vehicles - cars, ships, yachts, submarines, etc. UME can work autonomously for a long time without any maintenance. The modularity of the design allows you to create engines with a power of 1-50 MW. This project is also of exceptional importance for the EU and Germany, due to the fact that it radically reduces the cost of electricity, reduces the need for hydrocarbons, contributes to the preservation of the environment, and also increases the competitiveness of industry, energy independence and economic efficiency. The project was developed and tested for operability in the 3D design system of SolidWorks. All the main nodes have a novelty at the world level and will be patented. Individual nodes were tested on full- size real samples. An investor is required to finance the prototype.


RepManNet Contact: repmannet_barrierefreiheit@univie.ac.at Authors: Susanne Blumesberger, Sonja Edler, Victoria Eisenheld, Maria Guseva, Doris Haslinger Lizenz: CC BY-NC-ND 4.0 How do I make my repository accessible? Access for All Accessible repositories are an important part of the open science ecosystem! WCAG Accessibility properties for metadata Guidelines on preparing accessible content for repositories • develop easy search, simple navigation and upload – whenever possible in multiple ways • implement metadata indicating accessibility properties • make sure that all necessary information is compact, clear and transparent • encourage to report accessibility issues and offer ongoing support user interface • be sure that your objects are accessible as possible – see guidelines on preparing accessible content for repositories • include comprehensive metadata – don’t forget metadata indicating accessibility properties content fullKeyboardControl fullMouseControl fullSwitchControl chartOnVisual fullTouchControl fullVideoControl fullVoiceControl auditory chemOnVisual colorDependent diagramOnVisual mathOnVisual musicOnVisual textOnVisual visual flashing noFlashingHazard motionSimulation noMotionSimulationHazard sound noSoundHazard annotations textual ARIA bookmarks index pageBreakMarkers pageNavigation readingOrder structuralNavigation tableOfContents taggedPDF alternativeText audioDescription closedCaptions describedMath longDescription openCaptions rubyAnnotations signLanguage transcript displayTransformability synchronizedAudioText timingControl unlocked ChemML latex MathML ttsMarkup highContrastAudio highContrastDisplay fullKeyboardControl fullMouseControl fullSwitchControl fullTouchControl fullVideoControl fullVoiceControl auditory chartOnVisual chemOnVisual colorDependent diagramOnVisual mathOnVisual musicOnVisual textOnVisual textual visual flashing noFlashingHazard motionSimulation noMotionSimulationHazard sound noSoundHazard annotations ARIA bookmarks index pageBreakMarkers pageNavigation readingOrder structuralNavigation tableOfContents taggedPDF alternativeText audioDescription closedCaptions describedMath longDescription openCaptions rubyAnnotations signLanguage transcript All people should be able to be a part of the scientific community without barriers! Constructing an accessible repository is • a collaborative effort of software developers, repository managers and data producers • an ongoing process – consider accessibility before you start a project and integrate it in the workflows on a permanent basis • demanding not only expert knowledge (consider WCAG!), but also participation of people with disabilities


Open Access portal for students and young researchers Mission: Providing Resources, Support and Advice for students and young researchers in their journey from writing to publishing their scientiﬁc papers Sample: 1000 students and young researchers from over 80 different countries PhD candidates 54% / Bachelor & Master students 28% / Post-Doc 15% / Other 3% Respond: Open Access portal for students and young researchers Webinars OA events Videos News Comments Connection to DOAJ search OA journal reviews OA Quiz OA trainings Connection on social media Infographics Certiﬁcation OA networks Online OA resources OAA portal content Open Access ??? OAA Contributors: Anna / @Anna_Pechenina USA Daniel / @d_mutonga Kenya Dusan / @dusandevic The Netherlands Iara / @iaravps Brazil Ivo / @ivocamposneto Portugal Lauren / @parnopaeus USA Meredith / @MeredithNiles1 USA Natalia / @natalianorori Nicaragua Prateek / @MahalwarPrateek Germany Slobodan / @RadicevSlobodan Italy Tom / @tompollard UK OA surveys Results after ﬁrst year: - 1 tutorial - 2 surveys - 2 presentation at conferences - 2 webinars - 10% grow of visitors per month - 12 contributors - 350 unique visitors per day - 1100 newsletter subscribers - 48.000 unique visitors Osman / @aldirdiri Sudan


TOI 560 : Two Transiting Planets Orbiting a K Dwarf Validated with iSHELL, PFS and HIRES RVs Mohammed El Mufti1, Peter Plavchan1, Angelle Tanner2, Eric Gaidos3, Bryson Cale4, Michael Reefe1, Justin Wittrock1, Kevin Issac Collins1, Patrick Newman1, David James Vermilion1,5, Claire Geneser2, Rena Lee3, Ahmad Sohani2, Farzaneh Zohrabi6 George Mason University1, Mississippi State University2, University of Hawai‘i at Mänoa3, NASA JPL4, NASA Godard Center5, Louisiana State University6 Abstract We validate the presence of a two-planet system orbiting the 0.15–1.4 Gyr K4 dwarf TOI 560 (HD 73583). The system con- sists of an inner moderately eccentric transiting mini-Neptune (TOI 560 b, P = 6.397438 ± 0.000037 days, e = 0.294+0.13 −0.062) initially discovered in the Sector 8 mission observations, and a transiting mini-Neptune (TOI 560 c, P = 18.8779 ± 0.0016 days) discovered in the Sector 34 observations, in a rare 1:3 orbital resonance. We utilize photometric data from Spitzer, and ground-based follow-up observations to confirm the ephemerides and period of the transiting planets and vet false positive scenarios. We obtain follow-up spectroscopy and corresponding precise radial velocities (RVs) with the iSHELL spectrograph at the NASA Infrared Telescope Facility and the HIRES Spectrograph at Keck Observatory to validate the plan- etary nature of these signals, which we combine with published PFS RVs from Magellan Observatory. We place upper limits on the masses of both planets of <2.1 and <4.1 MNep for b and c, respectively. We apply a Gaussian Processes (GP) model to the light curves to place priors on a chromatic radial velocity GP model to constrain the stellar activity of the TOI 560 host star. TOI 560 is a nearby moderately young multi-planet sys- tem with two planets suitable for atmospheric characterization with James Webb Space Telescope (JWST) and other upcom- ing missions. pychell Data Pipeline When star light passes through our gas cell and iSHELL cross-dispersed echelle spectrograph, we obtain high-resolution (R=80k) multi-order spectra. For each of the 29 orders, we do optimal spectral extraction (weighted summation) in the verti- cal direction so that in each column eventually we get a single value, which gives us a 1D spectrum for each order. We then forward model the spectrum to measure the radial velocity for each order, and then co-add the RVs from each order. We an- alyze our extracted spectral data using the following standard forward model where each term is a function of wave- length: Intensity = Blaze Function ×(Star × Gas Cell × Tellurics) ⊗Line Spread Function The blaze function ultimately sets the continuum of our spec- trum. The line spread function effectively blurs the spectrum down to resolution of the iSHELL spectrograph. The star has a Doppler shift, and the gas cell also has a Doppler shift which enables us to calibrate for instrumental drift in the wavelength solution and to constrain the line spread function. The tel- lurics, parameterized by a scaling factor optical depth related to airmass, are the remaining lines that causes by the green- house gases in the Earth’s atmosphere. Our RV pipeline is adapted from the CSHELL RV code de- scribed in [1]. We have rewritten the CSHELL code in a Python script pychell to adapt to iSHELL’s larger spectral grasp with multiple orders [2]. TOI 560 host star Parameter Value Reference Spectral type K4 Scolz et al. 2005 Teff[K] 4579+62 −61 this work R∗(R) 0.679+0.018 −0.017 this work Rotation period 12.2 ± 0.1 this work Age 150Myr - 0.5Gyr this work M∗(M⊕) 0.701+0.026 −0.025 this work Luminosity(L∗) 0.1802 ± 0.0058 Stassun et al. 2019 R.A. 08:38:45.260 Stassun et al. 2019 Dec. -13:15:24.09 Stassun et al. 2019 Data analysis • Standard G.P. Kernel: KQP(ti, tj) = ησ2 Decay z }| { exp  −∆t2 2ητ 2   Periodic z }| { exp  −1 2ηl2 sin2        π∆t ηp          , • Modified Chromatic G.P. Kernel: KJ2(ti, tj, λi, λj) = η2 σ,0  


www.helmholtz-hzi.de Introduction The species of the Chaetosphaeriaceae (Chaetosphaeriales, Sordariomycetes, Ascomycota) are microscopic asexually reproducing fungi, some of which belong to the life cycle of sexual morphs with macroscopic fruit bodies (~300 μm diam) perceptible as “black dots” on the surface of decaying plants. They are invisible to most of the people and difficult to find even by a trained eye. In addition, they are usually hard to cultivate and slow growing, what make them difficult to study. Traditionally, they are reported from the decaying plant matter in the forest habitat and some exhibit endophytic lifestyle . Surprisingly, analysis of metabarcoding data showed that they are also common soil fungi, dwelling in a bulk soil in grasslands and croplands. There are about 44 genera classified into this family with monographs available for several genera, but with very little knowledge about their biology. Studies showed that Chaetosphaeriaceae members are important degraders of lignocellulose in wood, litter and soil and have rich structural diversity of natural compounds (e.g. terpenoids, cyclic peptides, naphthoquinones, lactones, lipopeptides, xanthones). Three unpublished and unannotated draft genomes of Chaetosphaeriaceae are available (1000 fungal genome project). Nevertheless, the information about the genetic background of the basic pathways is missing in this fungal lineage. The same is true for the whole Chaetosphaeriales. Our study is filling this gap using analysis of genomes from 16 species. Genome assembly statics of 16 species from the family Chaetosphaeriaceae Comparison of CAZymes classes within the Chaetosphaeriaceae Homology analysis of predicted pyrichalasin H biosynthesis gene cluster in M. ciliata, M. caesia, and P.grisea Conclusion: In this study, we introduced the genomes of sixteen Chaetosphaeriaceae species. The quality of those genomes were assessed, and their carbohydrate-active enzymes (CAZymes) were annotated. There are more than 800 genes that encode CAZymes from each species. The genome mining of the analyzed members of the Chaetosphaeriaceae species revealed a high diversity of biosynthetic pathways that far outmatches the number of compounds known from the individual species. The genome sequences generated in this work will enablea broad range of investigations including studies on fungal evolution, population dynamics, biodegradation and also biosynthesis of secondary metabolites. Acknowledgement: The department Microbial Drugs is gratefully acknowledged for financial support of TC. The work was also supported by ESF project "International mobility of researchers of the Institute of Microbiology of the CAS, v.v.i. No 2" registration number CZ.02.2.69/0.0/0.0/18_053/0017705. First insight into Chaetosphaeriaceae biology using genomic Tian Cheng1,2, František Sklenář2, Martina Réblová2, Tobias Busche3, Marc Stadler1, Jörn Kalinowski3, and Miroslav Kolařík2 1Helmholtz Centre for Infection Research, Inhoffenstr 7, 38124 Braunschweig, Germany. 2Institute of Microbiology, the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha, Czech Republic. 3Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstr 25, D-33615 Bielefeld, Germany. References (1) Réblová M, Barr ME, Samuels GJ. (1999) Chaetosphaeriaceae, a new family for Chaetosphaeria and its relatives. Sydowia 51(1): 49–70. (2) Wijayawardene NN, Hyde KD, Al-Ani LKT, et al. (2020) Outline of Fungi and fungus-like taxa. Mycosphere 11(1): 1060–1456. (3) Wang C, Hantke V, Cox R, et al. (2019) Targeted Gene Inactivations Expose Silent Cytochalasans in Magnaporthe grisea NI980. Org. Lett. 21(11): 4163-4167. (4) Kjærbølling I, Vesth T, Frisvad J, et al. (2018) Linking secondary metabolites to gene clusters through genome sequencing of six diverse. Proc. Natl. Acad. Sci. U.S.A. 115(4): E753-E761. Tian.Cheng@Helmholtz-hzi.de Number of identified enzymes are displayed. (GT: glycosyl transferase, GH: glycoside hydrolas


Burgerdata inzetten voor een veiligere en gezondere schoolomgeving Recrutering & community building Data analyse & empowerment Inwoners toelichting geven bij het voornemen, dialoog aangaan, bezorgdheden capteren en uitnodigen om de effecten te meten aan de hand van sensoren. Iedereen heeft toegang tot de verkeersmetingen, ingewonnen via Telraam-toestellen en kan de situatie voor en tijdens de invoering van de proefopstelling bekijken door middel van het COMPAIR Policy Monitoring Dashboard (PMD). De schoolstraat wordt in het algemeen positief ervaren. Om beperkte overlast in buurtstraten te milderen en verkeersveiligheid verder te verbeteren stellen leerlingen, ouders, leerkrachten en buurtbewoners maatregelen voor (o.a. invoering zone 30 in heel het centrum, knip in parralle straat en sluiting zij- ingang school). Politie advies in voorbereiding Leerlingen, buurtbewoners en gemeente hebben een positieve ervaring opgedaan inzake burgerparticipatie. Lessons learned worden uitgedragen in het SOLVA-werkingsgebied. Meer info … Evaluatie, bijsturing & legacy Gemeente Herzele & Intercommunale SOLVA betrekken burgers, scholen en leerlingen bij de invoering van een schoolstraat. Samen wordt het verkeer & de luchtkwaliteit gemeten en geanalyseerd. Samen wordt de proefopstelling geëvalueerd en bijgestuurd. • Toename fietsverkeer in schoolstraat (3x) • Afname autoverkeer in schoolstraat (60%) • Toename autoverkeer in buurt (14%), met grote verschillen tussen straten +/- 700 students +/- 300 students school street +/- 300 students


Functionalisation of nanochannels for the development of a sustainable and efficient low-grade waste heat harvester Kamil Rahme*, Anjali Ashokan, Ievgen Nedrygailov, Scott Monaghan, Rupa Ranjani, Paul Hurley, Subhajit Biswas and Justin D. Holmes School of Chemistry & Tyndall National Institute, University College Cork, Cork, Ireland AMBER Centre, Environmental Research Institute, University College Cork, Ireland *krahme@ucc.ie This research is supported by the European Union's Horizon 2020 research and innovation programme under grant agreement number 964251, and by Irish Government funding via the DAFM NXTGENWOOD research program (grant agreement: 2019PROG704). Abstract Organic ligands have been used to modify the surface charge in nanochannels formed in cellulose and anodised aluminium oxide (AAO) membranes, using a combination of oxidative, covalent and non-covalent chemistry approaches. Initial electrical and thermoelectric measurements performed on the membranes show that surface functionalisation enhances ionic thermoelectric effects in these nanochannels. 3. Covalent attachment of Polyelectrolyte onto AAO nanochannels Conclusions 2.2. Electrostatic LBL deposition of polyelectrolytes onto silanised AAO Motivation1 Methodologies and results 2.1. Aminosilanes containing two and three amino groups TEMPO/NaBr/NaClO oxidation in water at pH 10–11 oxidise the C6 primary hydroxyl groups in cellulose to carboxyl, generating negatively charged nanochannels under certain conditions.2,4 1. oxidation of cellulose produced from natural wood using TEMPO 1. https://translate-energy.eu/about/ 2. Tian Li et al., Nature Materials 2019, 18, 608. 3. Chih-Feng Huang et al. Polymer Degradation and Stability 2019, 161, 206. 4. Ioana A. Duceac et al. Materials 2022, 15, 5076. 5. Laura Pol et al., Nanomaterials 2019, 9(3), 478. References Acknowledgement FTIR and SEM/EDX, TGA analysis also confirm the presence of PEI 2 KD (~ 3 % weight loss). Nanochannels within AAO and cellulose membranes were functionalised. Surface functionalisation enhances ionic thermoelectric effects in the nanochannels. Further studies to explain this ionic thermoelectric effect enhancement, surface charge/pores densities and zeta potential data are in progress. 1200 1000 800 600 400 200 0 0 10000 20000 30000 40000 50000 Survey Scan CPS Binding Energy (eV) AAO-SiNH2-PAA-PEI AAO-Si-NH2 N 1sC 1s Si 2p 4000 3500 3000 2500 2000 1500 1000 1403 cm -1 C=O in COO - 2858 cm -1 Transmittance (%) Wavenumber (cm-1) AAO AAO-OH AAO-Si-NH-NH-NH2 AAO-Si-NH-NH-NH2-PAA-PEI-PAA 2930 cm -1 C-H stretching is sp 3 1710 cm -1 C=O in COOH 4000 3500 3000 2500 2000 1500 1000 500 80 85 90 95 100 1720 cm-1 C=O in COOH Transmittance (%) Wavenumber (cm-1) TEMPO treated Cellulose Cellulose T = 14K 4 M NaCl 2. Silanisation of AAO membranes with aminosilane ligands5 AAO-NH2 48.8 AAO 19.7 AAO-OH ~ 10 AAO AAO-OH AAO-NH-NH-NH2 3-[2-(2-aminoethylamino)ethylamino]propyl-trimethoxysilane (TAEPT) 3-(2-aminoethylamino)propyl]trimethoxysilane AAO-NH-NH-NH2 4000 3500 3000 2500 2000 1500 1000 500 60 70 80 90 100 110 1160 cm -1 C-N stretching Transmittance (%) Wavenumbers (cm-1) AAO untreated AAO-OH AAO-NH-NH-NH2 1650 cm-1 N-H bending 3300 cm -1 OH Stretching 2930 cm -1 C-H stretching in sp 3 FTIR analysis after TEMPO oxidation shows a new peak at 1720 cm-1 for C=O in carboxylic acid. 3500 3000 2500 2000 1500 1000 0 50 100 Transmittance (%) Wavenumber (cm -1) AAO-OH AAO-Si-EPOXY AAO-Si-EPOXY-PEI 2KD C-H stretching in Sp 3 96 97 98 99 100 101 100 200 300 400 500 600 700 800 AAO membrane untreated AAO-Si-EPOXY-PEI 2KD Weight loss (%) Temperature (oC) AAO-Si-EPOXY-PEI 2KD (2,2,6,6-tetramethylpiperidin-1-yl)oxidanyl


Future Work • Improvements to this study • Larger sample sizes • Vary populations, especially to avoid selection biases • What is the mechanism for the improvement in self-efficacy? Is it sustained long-term? • Hypothesis: Focusing on future impacts enables students to envision themselves as active participants in a changing world. • Can we use our students’ desires to increase motivation and self-efficacy? • E.g. describe how the concepts they’re learning have impacted the world today and/or how these concepts can be leveraged to change the future Experimental Design 1. Pre-class questionnaire. The survey contained SMQII likert-type questions to assess motivation and open-ended questions to investigate student preferences about learning about scientific research. 2. Brief lecture. Students were introduced to historic examples of the impacts of research on society through machine learning as it relates to Netflix recommendations. The areas of scientific impact were then presented. This process served to: i. introduce the concept that scientific research has real-world consequences ii. demonstrate a framework for evaluating the broader impacts of research. 3. Think-pair-share. A problem situated discussion in either the influence of past research on the world today (intervention A) or how current research might impact the future (intervention B). 4. Post-class questionnaire. This survey utilized re-worded, but equivalent, SMQII questions to assess motivation to learn science, and open-ended questions to gauge changes in perceptions of science classes and scientific research. The pre- and post- class questionnaires contained unique codes that link answers to a particular student without revealing identifying information. Results Conclusions • Students indicate that they prefer to learn about current scientific research. • Open-ended responses can be categorized into specific desires. • Students who experienced intervention B, where discussion was grounded in the future impacts of current scientific research, reported an overall increase in self-efficacy, as measured using questions from the SMQII. • Wilcoxon signed-rank test between pre- and post-intervention scores for individuals is significant (p-value = 0.0003049) • This suggests that even quick, one-time interventions can produce measurable changes in self-efficacy The effects of temporal focus on students’ motivation to learn science James C. Schwabacher1 1Northwestern University, Evanston, IL 60208 Motivation in Social Cognitive Theory The motivation to learn science is “an internal state that arouses, directs, and sustains science-learning behavior,” and is typically measured through the Science Motivation Questionnaire II (SMQII).1 Prior studies demonstrate that measures of student motivation to learn science are a fair measure of success in science, technology, engineering, and mathematics (STEM) courses.2,3 Positively influencing student motivation to learn science, thus, is a route to improving student learning outcomes in STEM courses. Psychologists have found that the temporal focus of a situation can drastically affect motivation (i.e. proximal vs distal goals),4 yet no investigations of temporal focus within science classrooms have been reported. References (1) Glynn, S. M.; Brickman, P.; Armstrong, N.; Taasoobshirazi, G. Science Motivation Questionnaire II: Validation with Science Majors and Nonscience Majors. J. Res. Sci. Teach. 2011, 48, 1159–1176. (2) Reardon, R. F.; Traverse, M. A.; Feakes, D. A.; Gibbs, K. A.; Rohde, R. E. Discovering the Determinants of Chemistry Course Perceptions in Undergraduate Students. J. Chem. Educ. 2010, 87, 643–646. (3) Smist, J. M. General Chemistry and Self-Efficacy. Natl. Meet. Am. Chem. Soc. 1993, 1–27. (4) Karniol, R.; Ross, M. THE MOTIVATIONAL IMPACT OF TEMPORAL FOCUS: Thinking About the Future and the Past. Annu. Rev. Psychol. 1996, 47, 593–620. Acknowledgements A special thanks to Dr. Lauren Woods for her patience and cont


Utilizing Patch Metrics to Improve Classification of Remote Sensing Imagery Michael L. Treglia* and Megan E. Young Department of Biological Science, University of Tulsa, Tulsa, OK 74104-9700 Departments of Wildlife and Fisheries, Texas A&M University, College Station, TX 77843-2258 *e-mail: mike-treglia@utulsa.edu Problem: Classified remote sensing imagery is used to inform management of various natural resources, though achieving accurate results is a persistent challenge. In particular, some land cover types that are functionally very distinct can be spectrally similar, thus misclassification errors can yield poor decision-making. Relatively new, object-oriented classification methods that consider the shape of clusters of similar pixels can yield improved results, albeit often at considerable software expense and steep learning curves. Our Approach: We employ a two-stage classification procedure, that takes advantage of free and open source tools to improve upon per-pixel classification techniques. First we perform supervised classification to obtain a layer with patches of our focal land cover classes. We then calculate descriptive metrics for each patch, characterizing size and shape, and for each land cover class we extract the per-pixel probability of class assignment. Lastly, we perform a second supervised classification based on raster layers representing the aforementioned class probabilities and patch metrics. Case Study: A Complex Landscape of West Texas Study Area • We focused on a portion of the Mescalaro/Monahans Sand Dunes ecosystem in western Texas, USA, home to unique biodiversity and threatened by oil and gas development . • The landscape is complex and difficult to classify, particularly with regard to oil/gas roads and well-pads (made of caliche) and natural sand formations. • We strived to classify on Landsat 5 TM data, available for large portions of the globe for up to 27 years, at 30 m resolution. Results Deriving patch statistics from a per-pixel classification for use in a second classification run provided some benefit in our system (Fig. 3). Though there are still classification errors after stage 2, caliche roads and well-pads are better distinguished from sand formations. The stage 2 classification increased overall accuracy on our training dataset, from 94% to 98%. Though these results are positive, neither classification performed well on a smaller evaluation dataset (~50% overall accuracy), with the greatest confusion between living and dead vegetation. Discussion and Next Steps: Our two-stage approach for classifying remote sensing imagery effectively uses information about clusters of similar pixels to improve results. It is conceptually simple, and was done exclusively using freely available tools. The example presented here is a first attempt at this method, involving a complex landscape with fine-scale features, perhaps difficult to detect using Landsat imagery. Thus, we suspect this technique will yield greater benefit in landscapes with larger features, or using higher-resolution imagery. Fig. 1. NAIP 1 m aerial imagery (left) and false color composite from Landsat TM data (right) displaying NDVI, Green and Blue for our study area. Stage 2 Classification • Calculated metrics for each distinct land cover patch classified in stage 1, using Fragstats, and created raster layers for each metric. • Created raster layers of class probabilities from the stage 1 classification for each land cover class. • Performed supervised classification using Random Forests, on raster layers representing class probabilities and patch metrics. Methods Stage 1 Classification • Calculated NDVI and Tasseled Cap metrics for a single Landsat scene (Path 30/Row 38) from 2010 and stacked them with the original Landsat bands using QGIS and R. • Performed supervised classification using Random Forests (in R), based on 260 training areas derived from 1 m aerial imagery and our knowledge of the system. Patch ID AREA PER


KNOWLEDGE ABOUT CERVICAL CANCER AND AWARENESS OF PAP SMEAR SCREENING AMONG FEMALE NURSES IN HOSPITAL PAKAR SULTANAH FATIMAH Authors: Ruzila R, Azlina D, Siti Salmiah S, Noraini A, Rohayu M, Nazrah A. Institution :Nursing Unit, Hospital Pakar Sultanah Muar Johor P-151 NMRR ID:20-3008-56270 Introduction To have a successful cancer control program, nursing staff must be aware of facts about cervical cancer and screening tests themselves. This study was aims to assess the level knowledge about cervical cancer and awareness of Pap smear screening among female nurses in HPSF Methodology A descriptive cross-sectional study, a self- administered semi structured questionnaire, and selected by stratified random sampling method, involved the 239 registered nurses who worked in HPSF. IBM SPSS was used for data analyzed. Results Demographic background among nurse Table 1: Demographic characteristic (n=239) To determine the level of knowledge about cervical cancer and awareness of Pap smear screening. Figure 1: Level of knowledge about cervical cancer (n=239) Figure 2: Level of awareness of pap smear screening(n=239) To identify the association between experience working, knowledge about cervical cancer and awareness of Pap smear screening. Table 2: Association between years of experience working and level awareness (good level and poor level) among participants using simple logistic regression Variables Frequency (%) Mean Age 37.13* Experience working 12.79* Deparment Medical 62( 24.2%) Surgical and Orthopaedic 49(19.1%) Obsetric and Gynae 50( 19.5%) Paediatric 40(15.6%) Multidispline 27(10.5%) Anaesthesia 28(10.9%) Race Malay 252(98.4%) Chinese 1(4%) India 2(8%) Others 1(4%) Maritul status Married 250(97.65%) Widow 6(2.35%) Education Diploma 239(93%) Degree 18(7%) Attended CNE Yes 132(51.6%) No 124(48.4%) Parity 0 17(6.64%) 1 32(12.5%) 2 80(31.25%) 3 82(32.03%) 4 38(14.84%) 5 6(2.34%) 6 1(0.40%) Variable Crude OR (95%CI) P value Experience working 0.926 (0.871,0.985) 0.014 Discussion Cancer cervix is preventable, and one of important aspects is prevention in detection of the premalignant lesion by screening[1]. This study show that majority of the participants have a good knowledge about cervical cancer and most of the participants have a moderate awareness of the Pap smear screening. Moreover, if nurses themselves undergo screening tests regularly, they can be role models for other females in carrying out cervical cancer screening tests[2,3]. The association between years of services and level awareness were significantly (P=0.014). This also implise that more important in teaching curriculum and training programs should be incorporated about cancer cervix and screening[2]. Conclusion Knowledge about cancer cervix, screening and practice of Pap smear is good among female nurses in HPSF. Nurses, if properly aware of cervical cancer and screening methods, can educate the women in the community and increase health-seeking behaviour among eligible women. References [1] Ministry of Health Malaysia, Academy of Medicine of Malaysia. Clinical Practice Guidelines. Management of Cervical Cancer. Kuala Lumpur: Ministry of Health Malaysia;2003. [2] World Health Organization. Comprehensive cervical cancer control. A guide to essential practice. 2nd ed. Geneva: World Health Organization; 2014. [3] Institute for Public Health. The Third National Health and Morbidity Survey (NHMS III) 2006. Women's Health. Kuala Lumpur: Ministry of Health Malaysia; 2008.


p o li c y i n n o v a ti o n s tr a t e g ic d e si g n h a p p i n e s s & w e ll b e i n g textile artisans’ communities material tool by hands machinery digital tools quality skilled control personal identity material culture local ﬁbres: vegetal animal discarded research framework methodology a r t i s a n c o m m u n i t y large diﬀusion wide applications sustainability challenges t e x t i l e s utilitarian culturally meaningful aesthetic discover deﬁne develop deliver contextual interviews co-creation experts’ focus group shadowing service blueprint service ecosystem map o n t o l o g y diﬀerent stakeholders acknowledge multiple realities constructivism interpretivism participatory action research e p i s t e m o l o g y r e s e a r c h p a r a d i g m interaction with participants inﬂuences the research qualitative and ﬂexible process of in situ data collection Francesco Mazzarella PhD Student (1st Year) AHRC Design Star CDT F.Mazzarella@lboro.ac.uk Supervisors: Dr Escobar-Tello - Dr Mitchell an enabling ecosystem towards sustainability and social innovation service design for the future of textile artisans’ communities Textile artisanship is the human-centred economic activity of giving form and meaning to local natural ﬁbres, by hands or by directly controlling mechanised and digital tools, and managing the process of apparel making. research questions What are the barriers and enablers for textile artisans’ communities to become sustainable? How can service design be used to encourage such communities toward a sustainable future? How can an enabling ecosystem be codesigned to scale up innovation at a glocal level? area of study The global economic and environmental crisis is leading to the transition from a linear economy based on consumption and waste, towards new ethics of sustainability and cutting-edge business opportunities. Textile artisanship is an interesting opportunity for opening up ﬂexible and redistributed micro-enterprises, while bridging local realities with global markets. It is a key contributor to sustainable development as it catalyses cultural heritage, provides social employment, boosts creative economies and enhances environmental stewardship. This PhD aims to explore how service design can strategically contribute to encourage textile artisans’ communities towards a sustainable future. This means empowering artisans’ creative assets and social bonds, codesigning collaborative services and scaling up initiatives within an enabling ecosystem at a glocal level. small scale localised diversiﬁed ﬂexible service design sustainable development social innovation e n a b li n g e c o s y s t e m r e si li e n c y g l o c al m a r k e ts c r a ft c lu st e r s m a t e ri al c u lt u r e c r e a ti v e e c o n o m y ci r c u la r e c o n o m y h y b ri d t o u c h p o i n ts c o ll a b o r a ti v e s e r vi c e s d i g it al i n n o v a ti o n a i m f o c u s a p p r o a c h a i m making


CompressedSensinginWirelessCommunication Thomas Arildsen∗, Tobias Lindstrøm Jensen, Karsten Fyhn, Peng Li, Pawel Pankiewicz, Jacek Pierzchlewski, Hao Shen, Ruben Grigoryan, Søren Holdt Jensen, Torben Larsen Dept. of Electronic Systems, Aalborg University, Denmark ∗tha@es.aau.dk Abstract Compressed sensing has gained a lot of attention in recent years. While the famous Shannon-Nyquist boundary for sampling of analog signals provides a suﬃcient condition for the sampling frequency, it can be reduced substantially in situations where a signal is sparse in a given domain. This can lead to compressive sensing which can be formulated as an optimization problem where an under-determined system of linear equations is solved under the con- dition of a sparse solution. In our research group at Aalborg University we are using compressed sensing theory to address some important practical challenges in radio frequency communication and more generally in analog-to- digital conversion. Radio frequency receivers for modern telecommu- nication standards in power-constrained devices are increasingly challenged by the necessary sam- pling frequencies and hardware power consump- tion. Compressed sensing techniques may help ad- dress some of these challenges, for example by re- ducing the necessary sampling rate. This is a move towards the original, but hardware-wise unrealistic, ideas of software deﬁned radios. In order to utilise compressed sensing, we must be able to represent the relevant signals sparsely – or, alternatively, ﬁnd new signal structures that allow compressed sensing. In practice, various hardware imperfections as well as noise and interference limit the applicability of compressed sensing. These issues must be ad- dressed to make compressed sensing practicable. Multi-Coset Sampling Scheme ▶The multi-coset sampling scheme is one of sev- eral possible sub-Nyquist sampling schemes. ▶The multi-coset sampling scheme can be used to sample and reconstruct frequency sparse sig- nals. Reconstruction is possible with various al- gorithms that may have diﬀerent performance. ▶We are focusing on the impact of hardware im- perfections on the reconstruction quality. Var- ious real-life restrictions such as practical sam- pling patterns are also important. ▶This research will bring multi-coset sampling schemes closer to real-life applications. ADC 1 x(t) x((m·L+c1)·T) = y1[m] ADC 2 ADC P x((m·L+c2)·T) = y2[m] x((m·L+cP)·T) = yP[m] Sparse Sampling Receivers ▶Applying multi-coset sampling on a conven- tional time-interleaved ADC may increase the input bandwidth. ▶Time-interleaved ADC traditionally uses uni- form sampling. We investigate introduction of randomized sampling. ▶We consider a sample-time error in each sub- ADC. Sample-time error is a random time delay for each sub-ADC, and it is a constant error for each sampling instance. ▶We identify these sample-time errors and ex- ploit them to introduce randomized sampling similar to multi-coset sampling. L 1c 2c 3c c1 0 0 o T 0 max s max s max s T ( 1) L T  max s max s - - - max s CS Direct Conversion Receiver ▶Increasing computational power of modern data receivers enables moving more and more pro- cessing from the analog to the digital domain. ▶In this project, compressed sensing is used to relax the analog ﬁltering requirements prior to the ADCs in a direct conversion receiver. ▶The ﬁltered down-converted radio signals are randomly sampled with an average sampling frequency below its Nyquist rate. ▶This approach exploits frequency domain spar- sity of the down-converted radio signals. ▶The approach allows identifying and remov- ing interfering signals from the sampled signal, thereby enabling reduced low-pass ﬁlter order. f f 0 Frequencies allowed by the radio band-pass filter B B f r f r f r f r Blockers Desired signal Noise s b2 s b1 s f r f r f 2f 0 Low frequency components f r f r Downconverted blockers All the high frequency components can be removed by the 1st order low- pass filters N


The Governance of Digital Immortality & the Digital Afterlife Researcher: Khadiza Laskor khadiza.laskor@bristol.ac.uk https://www.bristol.ac.uk/cdt/cyber-security/ Supervisors: Professor Richard Owen Professor Andrew Charlesworth Digital Immortality & Digital Afterlife… …are terms that grew in prominence since the turn of the century. This prompted the emergence of ‘grief tech’ which includes the possibility to preserve and curate a virtual online persona from digital remains, enabling individuals to ‘live’ after their physical death. Governance & Regulation However, history is at risk of repeating itself: the ‘pacing problem’ (Collingridge, 1980) has often been observed when governing technology. This is the main theme being explored using ‘grief tech’ as a use case. Research Progress A systematic literature review on the framing of ‘Digital Immortality’ and ‘Digital Afterlife’, and the state of art of its governance, has revealed strong technological influences, with little emphasis on governance or regulation. This Year’s Focus Analysis of over 50 expert stakeholder interviews, with results from focus group discussions with the public (to be scheduled later) are expected to highlight how this innovation ought to be controlled, if at all. Further… …the combined results will be used to assess whether existing governance artefacts are able to protect an identifiable virtual online persona created by the individual before they died, or posthumously by a loved one. This multi-disciplinary PhD thesis utilises a flexible design process, based upon ‘Responsible Innovation’ (Owen et al, 2013). The approaches being adopted are empirico-inductive: thus, allowing for a comprehensive analysis in how such a nascent industry, loosely labelled as ‘grief tech’, could be governed. While the foci is on data left behind by the deceased, due to sensitivities associated with grief and bereavement, creative means are also being pursued.


Astyanax mexicanus: surface fish and Pachón Methods: • Cardiac cryoinjury • Histochemistry analysis • RNAsequencing • Real-time quantitative polymerase chain reaction (qPCR) • RNAscope • QTL analysis RESULTS (CONTINUED) MATERIALS AND METHODS SUMMARY FINANCIAL SUPPORT RESULTS BACKBROUND Distinct dynamics of the extracellular matrix during heart regeneration in different Astyanax mexicanus populations Zhilian Hu1, Madeleine E. Lemieux2, Mathilda T. M. Mommersteeg1 1. Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK 2. Bioinfo, Plantagenet, Ontario, Canada The cardiac regenerative capacity of Astyanax mexicanus populations is completely distinct in response to the injury. Surface fish can regenerate the ablated heart tissue, similar to zebrafish, while Pachón cannot and instead forms a permanent scar with excess extracellular matrix (ECM), similar to human. ECM is a dynamic three-dimension network of extracellular macromolecules including collagen and non-collagenous components. Its content, relative proportion, and spatial arrangement play a pivotal role during tissue regeneration. Any changes in ECM deposition can have a big impact on the ability to regenerate. Astyanax mexicanus allows us to identify the differences in ECM deposition and removal between a degradable scar in a regenerative setting and a permanent scar in a non-regenerative setting. Our research indicates ECM components and their regulating Matrix metalloproteinases (MMPs) are dynamically and differentially expressed during heart regeneration between surface fish and Pachón. Next, we will link the key scarring differences directly to both the genome and the ability for heart regeneration using new and prior Quantitative Trait Loci analyses. This will allow to find the most fundamental molecular mechanisms directing the wound healing process towards regeneration versus scarring. Result 1: Differential regenerative capacity of the heart after cryoinjury between surface fish and Pachón Figure 1. A-A’, Adult Astyanax mexicanus surface fish (A) and cave-dwelling Pachón (B). B-C’, AFOG staining of the cardiac ventricle after cryoinjury (Fibrin in red, intact muscle in orange and collagen in blue). The hearts are similar in fibrin formation at 3 days post cryoinjury (dpci) (B-B’), followed by intermingling of fibrin with collagen fibrils at 14 dpci (C-C’). Resolution of fibrotic scar in surface fish (D), but permanent scar in Pachón (D’) at 100 dpci. E, Quantification of the scar area at 100 dpci shows a large scar is still present in Pachón, while the surface fish restored the injured ventricular apex. Scar bar: 100 µm. Result 2:Excess deposition of collagens and disorganisation of collagen fibrils in the wound area of Pachón heart Figure 2. A-B, Picro Sirius red (PSR) staining of the ventricle at 14 dpci for both fish (collagen in bright red under light microscopy). ven, ventricle. A’-B’, Imaging of collagen fibrils under a polarised microscope shows remarkable high deposition of collagens and disorganization of collagen fibrils in Pachón (Green-thin fibrils in green and thick fibrils in yellow-orange- red). Result 3: Deregulation of collagen and non-collagenous extracellular matrix encoding genes after cryoinjury Figure 3. A-A’, Diagram of the workflow of RNAseq. B, Example of candidate genes validated by qPCR at six time points (6 hpci, 24 hpci, 3 dpci, 7 dpci, 14 dpci and 30 dpci). Expression levels of non-collagen fibronectin (fn1a) and FACIT collagen 12 (col12) are dynamically and differentially expressed between both fish during the regenerative process. C-D”, RNAscope revealed that col12 is primarily expressed in the outside wall of wound. E-F”, Multiplexin collagen 18 (col18) is undetectable in the wound region of surface fish (D-D”) but is expressed in the Pachón scar (E-E”). These results indicate the composition of the scar is different between both fish. FACIT, Fibril Associated Collagens with Interrupted Triple Helices; Mu


NIMBLE: A language for algorithms for graphical models embedded in R Problem-specific hierarchical statistical models (graphical models) are used by domain experts in many scientific fields: • State-space or hidden Markov models for time-series data • Random field models for spatial data • Generalized linear mixed models for complex designed studies • Capture-recapture models • Non-parametric regression and distribution models • Combinations of these and many more ideas There are many unmet statistical challenges for hierarchical models: • Efficient Markov chain Monte Carlo (MCMC) for parameter estimation • Maximum likelihood (or empirical Bayes) estimation when the likelihood requires integration. • Approximation of normalizing constants (likelihood or marginal likelihood) for model comparisons. • Tools for model selection, an unresolved area of Bayesian methodology. • Tools for model averaging. • Tools for assessing/validating model fit or assumptions. Perry de Valpine1, Christopher J. Paciorek1, Daniel Turek2, Nick Michaud1, & Duncan Temple Lang3 1University of California, Berkeley. 2Williams College. 3University of California, Davis. Previous software typically follows one of two basic designs: 1. Define a single model or family of models and provide specific methods for them. • Typical of R packages. • E.g. Generalized linear mixed models (GLMMS; lme4, MCMCglmm). • E.g. Generalized additive mixed models (mgcv). • E.g. Spatial models (spBayes, INLA). • E.g. Dirichlet process type models (dpPackage) • User cannot extend the model. 2. Provide a domain-specific language for writing general models and one or a few black-box algorithms. • E.g. MCMC is provided by BUGS (WinBUGS, OpenBUGS, JAGS), Stan, PyMC and others. • E.g. particle filtering is provided by BiiPS, LibBI, pomp, and others. • User cannot write new algorithms for the models. New computational statistics methods for general models Software for statistically savvy domain scientists Statisticians and computer scientists publish many new methods that are not accessible via software to domain scientists. • Model-specific methods can be distributed as R packages. • Model-generic methods are hard to code because the model must be abstracted. There has been no general system for model-generic programming. Model flexibility Algorithm flexibility BUGS/JAGS PyMC ADMB Stan Typical R packages NIMBLE = BUGS language + Algorithm programming 1. Domain-specific language (DSL) for statistical models • We adopt and extend the widely-used BUGS language 2. Domain-specific language embedded within R for model-generic algorithms 3. Code-generator (compiler) that generates C++ from the model and algorithms DSLs. • C++ objects are managed from R by dynamically-generated interface classes 4. Algorithm library (MCMC, SMC, etc.) metropolis_hastings_sampler <- nimbleFunction( contains = sampler_BASE, setup = function(model, mvSaved, targetNode, scale) { calcNodes <- model$getDependencies(targetNode) }, run = function() { model_lp_current <- model$getLogProb(calcNodes) proposal <- rnorm(1, model[[targetNode]], scale) model[[targetNode]] <<- proposal model_lp_prop <- model$calculate(calcNodes) log_MH_ratio <- model_lp_prop - model_lp_initial if(decide(log_MH_ratio)) jump <- TRUE else jump <- FALSE if(jump) copy(from = model, to = mvSaved, row = 1, nodes = calcNodes, logProb = TRUE) else copy(from = mvSaved, to = model, row = 1, nodes = calcNodes, logProb = TRUE) }) The gap between methods and software Limitations of previous software designs NIMBLE enables algorithm programming for general graphical models Four components of NIMBLE Numerical Inference for statistical Models using Bayesian and Likelihood Estimation Existing and future (in colors) NIMBLE processing flows Why R? Benefits of embedding NIMBLE in R: • R is widely used in applied statistics. • The BUGS language uses extremely R-like syntax that can be natively parsed in R. • R handles code as an object. • NIMBLE constructs and evaluat


Manual Quality Control with Freesurfer 7.1: Key Problem Areas and Importance of Corrections V. Vahermaa¹ ², B. Aydogan³ , T. Raij³ ⁴, R-L. Armio⁵, H. Laurikainen⁵, J. Saramäki ¹, J. Suvisaari² ¹ Department of Computer Science, School of Science, Aalto University, Finland ² Department of National Health and Welfare (THL), Helsinki, Finland ³ Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, Finland ⁴ University of Helsinki and Helsinki University Hospital, Psychiatry, Helsinki, Finland ⁵ Department of Psychiatry, University of Turku, Finland Contact Information: Vesa Vahermaa vesa.vahermaa@aalto.fi Results Methods Introduction Conclusions Dataset FreeSurfer (FS) is a free software suite that provides a comprehensive processing stream for structural magnetic resonance imaging (MRI) images. ⁶ This stream includes brain extraction and grey-white matter segmentation, which outlines the brain. 51 FEP patients and 78 images were included in the dataset. All subjects were scanned with the same Siemens brand 3T scanner. The impact of pial surface errors related to overextension of gray matter boundary on automatically calculated brain volumes is very small. Unless the study requires highly precise volume measurements or focuses on the areas that were shown to have a significant number of errors, manual quality control may not be necessary. References Figure 1. Three regions of the brain with error clusters: lateral orbitofrontal cortex (A), paracentral lobule (B), and cerebellar tentorium (C). Table 1. Error frequency among inspected MRI images. A total of 233 errors related to overextension of gray matter boundary were recorded from the images. Here, we determine the number, location, and volume distorting effect of such errors in the brains of 51 first-episode psychosis (FEP) patients and 78 MRI images. 28 of the subjects had both baseline and 1-year follow-up images. The subjects had FEP in 2010–2016, and were recruited by the Finnish Institute for health and welfare (THL). The changes in local brain volumes as listed in aparc.stats between non-controlled and controlled images were on average very small (-0.09% +- 0.33). The average change in cortical thickness was -0.07% +- 0.14. 127 errors were in the left hemisphere, and 106 in the right hemisphere. The images went through manual quality control by a single researcher (V.V.), with error locations recorded. All MRI images underwent the full FS processing stream (recon-all) including automatic volume calculation. Mistakes in this automated process lead to the miscalculation of brain volume in the areas with incorrectly determined edges. 6 http://surfer.nmr.mgh.harvard.edu/ 7 Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig. User- guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. Neuroimage 2006 Jul 1;31(3):1116-28. The pial surfaces of each brain were systematically scanned for gray matter boundary errors present in at least 3 consecutive slices, and any non-brain tissue was removed. The error coordinates were recorded, and location labels determined from the aparc+aseg —file of each subject. The errors were not uniformly distributed in the brain: the most affected areas were the middle cerebral artery (59 errors) and the immediate vicinity of the cerebellar tentorium (50 errors). Watch a video about Figure 1: The effect is calculated by having a researcher manually examine the MRI images and manually correct the errors, and comparing the pre- and post intervention datasets and their volume measurements. Each set of error coordinates was converted to MNI 305 space as a single voxel. A heatmap was generated by applying gaussian kernel smoothing to the voxels in MNI305 space, and overlaying the heatmap in ITK-Snap. ⁷ A B C Subjects with visible motion artefacts were excluded from the dataset. The errors were also


Results Analysis of variance tests compared mean abundance data across multiple semesters. Results show that only three of the key species (Nassau grouper, Red lionfish, and Queen triggerfish) had a significant change. Abundance of Nassau grouper initially decreased from Fall 2004 to Spring 2005 and since has been increasing through Fall 2010. Significant increases were seen when comparing Fall 2010 to Fall 2005, Spring 2006, and Fall 2006 (P=0.06, P<0.01, and P=0.004; Figure 1). Results for Red lionfish showed a significant difference in all semesters when compared to Fall 2008 (P=0.001, P=0.001, P=0.041, and P=0.043; Figure 2). The mean abundance of Queen triggerfish is significantly different when comparing all semesters to spring 2007, when there was a significant rise in mean abundance ( P<0.05; Figure 3). Visual Surveys of Patch Reef Species Abundance in South Eleuthera, The Bahamas Phoebe Fitz, Marianne Foss-Skiftesvik, Meaghan Kachadoorian, Chris Lorient, Chris Pibl, Jackson Rafter Advisors: Matt Dawson and Skylar Miller Methods This study was performed off Powell Point in Cape Eleuthera, Bahamas during a seven-week period in Fall 2010. Twenty patch reefs, all within a proposed marine protected area, were surveyed twice during the seven-week observation period in order to maintain accurate results (Figure 5). Extensive fish identification training was conducted before research commenced to ensure proper field identification. Visual surveys were conducted in buddy pairs while snorkeling to record population abundance of the six key species (Figure 4). Mean abundance values of each species across all survey sites over the seven-week period were calculated. This data was then analyzed and compared to data from the past seven years. Discussion One reason for the increase in abundance of Nassau grouper may be the effectiveness of current fishing regulations. Fishing regulations are determined annually by the Bahamian government. For the year 2011, fishing is closed December 1 to February 28. Another regulation limits the size of the Nassau grouper caught to a minimum of three pounds (Department of Marine Resources 2010). The initial increase in Red lionfish population seen from 2007 to 2008 may be due to their invasive nature and therefore lack of natural predators. Because the Red lionfish originated in the Indo-pacific, locals had no previous knowledge of this species. However, now that handling techniques are more familiar, some local Bahamians are beginning to recognize Red lionfish as a good food source. Because Red lionfish spawn every four days and therefore have a very high reproduction rate, even the smallest catch by locals impacts their population. Despite this, the most probable reason for the decrease in Red lionfish population is that maximum carrying capacity was reached. As the Red lionfish population increased in South Eleuthera, competition for food and space may have caused the significant decrease. The population abundance of the Queen triggerfish has proved to be fairly constant over this ongoing study, with the exception of the atypical data collected in 2007. However, their population should continue to be monitored to ensure its stability, especially since the Queen triggerfish is economically important to the Bahamas. Their vibrant colors attract many tourists to snorkel on the patch reefs and they have been used in the past as a fishing alternative to Nassau grouper when their numbers were dwindling. The data supported the hypothesis for some of the key species, while was inconclusive for others. The increase in Nassau grouper populations is an example of how fishing regulations may have positive effects on species population abundance. However, this data is not conclusive enough to provide recommendations for future marine protected areas and/or fishing regulations in South Eleuthera, The Bahamas. Literature Cited Albins, M.A., Hixon, M.A. 2008. Invasive Indo-Pacific lionfish reduce recruitment of


18th International Open Repositories Conference (OR2023), Stellenbosch University, South Africa, 12‐15 June 2023 Marcin Werla (mwerla@qnl.qa), Dr. Alwaleed Alkhaja (aalkhaja@qnl.qa), Dr. Arif Shaon (ashaon@qnl.qa) Qatar National Library In November 2022, Qatar National Library (QNL) launched a new repository service called Manara – the Arabic word for ‘lighthouse’ – with the ambition of capturing, curating, preserving and providing open access to all research outputs created in Qatar. This service builds on a national-level e-resources consortium that the Library has been coordinating since 2016, ensuring optimum licensing and ﬁnancial terms for subscription-based access to research and educational content for 10 major institutions. Besides institutional-level cooperation, Manara welcomes all kinds of research-related open access contributions from all researchers based in Qatar on an individual voluntary basis. The Library is responsible for the basic content review before publishing. Introduction Manara is a new service and will initially operate as a pilot. The wider goal is to develop Manara as a core Library service that is strategically important for QNL's long-term mission and vision. The exact long-term sustainability model will be developed in cooperation with participating institutions after the initial pilot period, which runs until mid-2024. THE FUTURE Find out more at manara.qnl.qa Manara, as a comprehensive and sustainable research repository, contributes signiﬁcantly to several UNESCO Sustainable Development Goals by enriching scientiﬁc, educational and cultural knowledge environments, supporting research communication and information sharing. The open access model promoted through the repository makes the contribution even stronger, opening Qatari research outputs to the world. UNESCO SDGs An important role of Manara is to help preserve institutional archives in the dynamic landscape of Qatar. To support the Library’s mission, Manara can preserve research and educational content from institutions that no longer exist, like the Qatar branch of University College London, UCL-Q, which was active between 2010 and 2020, and played the role of Center of Excellence for Cultural Heritage and Knowledge Management in the country, conducting around 100 research and education projects. LEGACY ARCHIVING The concept at the heart of a refreshed Qatar Foundation strategy revolves around creating a collaborative and diverse higher education ecosystem in Qatar that promotes interdisciplinary learning, research excellence, and global connectivity. The concept emphasizes the integration of multiple universities, research institutions, and educational facilities within a shared campus or network. It aims to contribute to the development of Qatar as a knowledge-based society and a hub for education and research in the region. This is a comprehensive development plan introduced by the government of Qatar to guide the country's growth and progress across various sectors by the year 2030. The vision emphatically focuses on four key pillars: human development, social development, economic development, and environmental development. The vision profoundly emphasizes the importance of creating a knowledgeable and skilled society, developing a knowledge-based economy, and promoting entrepreneurship and innovation. Qatar National Library actively promotes open access through a broad variety of services, to support global dissemination of, and unrestricted access to, Qatar-based research, including: • signing open access agreements with publishers and providing an article processing charges fund for Qatar-based researchers; • supporting international open access initiatives, like INTACT’s OpenAPC and Open Access 2020; • running events and training sessions; • providing information and advice to researchers about open access publishing and open licensing. Qatar National Vision 2030 Promoting Open Access The Qatar Foundation Multiversity Manara


Crowdsourcing in History. New participatory and inclusive method- ological challenges for research in History in Spain (CrowdHistory) DH2023 COLLABORATION AS OPPORTUNITY ALLIANCE OF DIGITAL HUMANITIES ORGANIZATIONS, UNIVERSITY OF GRAZ AUSTRIA, 10-14 JULY 2023. Credits Scientific Publications The main objective of CrowdHistory project is to identify, analyse, test and standardise methodological practices of citizen participa- tion in Spanish R&D projects from the per- spective of Digital Humanities, both within and outside the academic field. by PhD. Lidia Bocanegra Barbecho - Digital Humanities responsible at Medialab UGR (Universidad de Granada- Spain) and tenure Track position at Contemporary History Department, UGR. lbocanegra@ugr.es | @Lidia_Bocanegra THE PROJECT AIM CROWDHISTORY METHODOLOGY To achieve the proposed objectives, CrowdHistory implements a four-phase methodology as follow: - Phase 1 - Detection of research projects in history that use public participation from citizen science. Design and structuring of a relational web database (DB), implemented through the Drupal Content Management System, version 9, PHP 7 and MariaDB 5.5. The established database (DB) allows classification parame- ters in closed lists and with free text fields, where explanatory information about the strategies of approaching the public has been added. - Phase 2 - Standardisation methodology on public participation in historical re- search. This phase will lead to first analyses and, as a result, to a first catalogu- ing of participatory processes (of citizen involvement) as well as engagement activities (public engagement). - Phase 3 - Testing and improving the methodology of public participation in his- torical research from citizen science through pilot cases. use of hybrid (physical/ digital) citizen laboratories where some of the classified participatory approach- es and techniques will be put into practice. - Phase 4 - Evaluation of the public participation and public engagement methodology and development of good practice guidelines. STATE OF THE ART The current state of research lacks scientific investigations that reflect methodologically and conceptually on public participa- tion in historical research in Spain. When we talk about public participation in research, we refer to Citizen Science (CS): this is scientific research coordinated by scientists in which ordinary people, amateur and non-professional researchers, participate in some aspect of the research (Eitzel 2017). This type of methodological research is practically new in the humanities; however, there are a discrete number of research projects that use CS that are currently underway or have already been car- ried out, which offer a suitable breeding ground with relevant data to carry out analyses in Citizen Science (Bocanegra et al. 2017). This citizen participatory aspect is one of the main characteris- tics of the Digital Humanities (DH) (Bocanegra 2020); in the last decade there has been a change in the way of doing research in the human sciences as society begins to have a participatory role during the research process; beyond being the subject of analysis to even participate in part or all stages of scientific production. This new way of doing science is strongly driven by the growing boom of web 2.0 and, within it, digital social net- works stand out as a place for interaction (Bocanegra 2020); betting on collective intelligence (Surowiecki 2004) and micro- PRELIMINARY RESULTS Currently, we have identified and classified 473 international projects that use CS through the project's web database: https://cohistoria.es/; of which 161 are Spanish initiatives or with Spanish participation. Data collection continues as new initiatives are found. An ad hoc classification has been made on the basis of two models: PPS – Public Participation Strategies and PES – Public Engagement Strategies, through which a series of participatory and public engagement activities have been i


ERSP - baseline, 0-50ms & 4-8Hz ERSP - random, 0-50ms & 4-8Hz -0.9 -0.4 0.1 0.7 1.2 (p-value) perm with fdr 1 0.1 0.01 0.001 ERSP - 1, 0-50ms & 8-12Hz ERSP - 4, 0-50ms & 8-12Hz -0.4 0.1 0.6 1.1 1.6 (p-value) perm with fdr 1 0.1 0.01 0.001 Background Method 32 cap-mounted electrodes Two sessions: count aloud 1-10 randomly count aloud 1-10 Count upon visual presentation question mark Epochs time-locked to question mark onset Preprocessing & power spectrum analysis in EEGLAB Bobby Ruijgrok & Olga Kepinska bobbyruijgrok@gmail.com Alpha and theta enhancement during self-ordered number generation [1] Petrides, M., Alivisatos, B., Meyer, E., & Evans, A. C. (1993). Functional activation of the human frontal cortex during the performance of verbal working memory tasks. Proceedings of the National Academy of Sciences of the United States of America, 90(3), 878–882. [2] Meyer, L. (2017). The neural oscillations of speech processing and language comprehension: state of the art and emerging mechanisms. European Journal of Neuroscience. https://doi.org/10.1111/ejn.13748 . Descriptive statistics 93 Dutch participants (71 female; 85 righthanded) Mage = 23.65, SE = 0.16 Accuracy count aloud: 100% Accuracy randomly count aloud: 59.12% Discussion Method Replicated finding of enhanced bilateral activity within the mid-dorsolateral frontal cortex Additional temporal and parietal activity Frontal distribution: Theta retrieval Alpha storage Verbal working memory (VWM) capacity tested by means of self-ordered number generation. PET-study Petrides et al. (1993) reported bilateral activa- tion mid-dorsolateral frontal cortex[1] Current study: power spectrum analysis on theta band (4-8Hz) and alpha band (8-12Hz). Storage and retrieval interplay of alpha and theta[2] . [Figure taken from Petrides et al. (1993)] Self-ordered minus control task. Merged PETMRI horizontal sections showing activation foci within the mid-dorsolateral frontal cortex. The schematic outlines of the brain indicate the level (interrupted lines) of the sections presented. The subject's left is on the left side in these sections. The coordinates (x, y, z) of the foci shown on the schematic outlines of the brain are 1, 40, 32, 30; 2, 35, 42, 22; and 1, 38, 39, 26. Results Theta Alpha


Innovative Research for a Sustainable Future www.epa.gov/research knudsen.thomas@epa.gov l 919-541-9776 hunter.sid@epa.gov l 919-541-3490 Framework for Predictive Developmental Toxicity of Chemicals Regulated under TSCA Thomas B. Knudsen1 and E. Sidney Hunter2 U.S. Environmental Protection Agency, Office of Research and Development 1NCCT and 2NHEERL Mining ToxCast to define sensitive pathways Summary OBJECTIVE: build a framework for pre-prioritizing chemicals for developmental toxicity (DevTox) for potential application to chemicals regulated under TSCA (amended 2016). INPUTS: ToxCast data including new information on chemical effects in zebrafish embryos and in diverse mammalian embryonic stem cell lines (hESC, mESC). OUTPUT: generalized workflow to sort compounds by their predicted potential for DevTox and in silico modeling of quantitative cellular, tissue and phenotypic responses. Evaluating model performance • Assigning chemicals under amended TSCA to low and high priority comes with uncertainties in complexity of predicting toxicity during pregnancy. • A DevTox predictive framework will implement data from in vitro assays assessing embryonic cell growth and differentiation. • The framework will operationalize a defined interpretation protocol for computational synthesis and integration DevTox decision tree. • Multiscale modeling and simulation will provide tools and approaches to virtually reconstruct and analyze complexity and quantitative prediction. OBSERVATIONS: • ZFISH platforms were more sensitive but less specific than mESC or hESC platforms. • Model performance improves against more stringent in vivo criteria for DevTox. • Overall accuracy approaches 62% (ZFISH), 72% (mESC), and 84% (hESC). • The hESC model also predicts the critical concentration for human dosimetry. DEFINITIONS: (a) LEL, lowest effect level (mg/kg/day) in ToxRefDB prenatal developmental toxicity study: dLEL (fetal endpoint) and mLEL (maternal endpoint) in the same ToxRefDB study for ‘n’ compounds; (b) evidence for DevTox: ‘CLEAR’ (dLEL< 200, dLEL<mLEL); ‘SOME’ (dLEL< 200, dLEL> mLEL); ‘EQUIVOCAL’ (dLEL> 200 but <1000); and ‘NO’ (dLEL>1000) in rat and/or rabbit study; (c) TP (true positive), FP (false positive), FN (false negative), TN (true negative); SENS, sensitivity [TP/(TP+FN)]; SPEC, specificity [TN/(TN+FP)]; ACC, accuracy [(TP+FN)/(TP+FP+FN+TN)]. Anatomical development Overview Computational synthesis and integration This poster does not represent EPA Policy i) assess qualitative performance of the predictive model; ii) set an exposure-based prediction of teratogenicity; iii) characterize sensitive response pathways; and iv) virtually reconstruct quantitative phenotypic response. Chemicals ranked by enumerated response Toxicity Prioritization index (ToxPi): • chart maps 753 ToxCast chemicals tested across 6 in vitro platforms; • slices indicate response (1) or no response (0) for each platform: blue - zebrafish platforms (2) yellow - ToxCast pathways (multiple) red - hESC (pluripotent H9 cells) green - mESC (differentiating J1 cells). Pyridaben (strong evidence) Captan (moderate evidence) Hexaconazole (weak evidence) 2,4-Dichlorophenoxy- acetic acid (false negative) Specific aims examples Human palatal closure (left) simulated in a virtual embryo (right). Running the simulation with ToxCast data for ‘Captan’ predicts a tipping point at 4 µM. Captan (+) EGF (-) TGF-beta Human HTTK model predicts exposure of a pregnant woman to Captan at 2.39 mg/kg/day would achieve a steady state of 4 µM in fetal plasma. example


De novo genome sequencing of Skeletonema marinoi and Surirella brebissonii Mats Töpel¹*, Magnus Alm Rosenblad¹, Ulrika Lind¹, Susanna Gross², Sandra Karlsten¹, Jens Persson¹, Mattias Backman¹, Anna Godhe², Anders Blomberg¹ 1. Department of Chemistry and Molecular Biology, University of Gothenburg 2. Department of Biology and Environmental Sciences, University of Gothenburg *mats@topel.se Introduction De novo whole genome sequencing of the two diatom species Suri- rella brebissonii (CCMP2919) and Skeletonema marinoi (GUMACC St54) are currently conducted as part of the Linnaeus Centre for Marine Evolutionary Biology (CeMEB) initiative at the University of Gothenburg. This work is part of the Infrastructure for Marine Genetic model Organisms (IMAGO) project, aimed at developing new marine model systems and provide genomic and genetic tools to study vital phenomena and components of coastal marine ecosystems. Protein translocation in diatoms A chloroplast’s genome only encodes ~100 proteins, but the organ- elle requires many more proteins in order to perform its functions in the cell. Translocons at the Outer and Inner Chloroplast enve- lope membranes (TOC and TIC, respectively) are the two multi- protein complexes in plants, red- and green algae that enable chlo- roplasts to import these essential nuclear-encoded proteins. Diatom plastids, on the other hand, are surrounded by four mem- branes where the outermost is continuous with the endoplasmic reticulum (ER) [8]. The second membrane (known as the periplas- tid membrane [PPM]) is the remnant of the secondary endosymbiont’s plasma membrane (proposed to be of red algal origin) [9]. The two innermost membranes are homologous to the outer and inner envelope membranes in plant plastids and are de- rived from the membranes surrounding the cyanobiont of primary plastids [10]. The identity of the TOC and TIC translocons in diatoms and most other chromalveolate organism groups (e.g brown algae, dinofla- gellates and apicomplexan parasites) is mainly unknown. How- ever, bioinformatics analyses of whole genome sequences from dia- toms has shown that these systems are also present in diatoms. Bullman et al. [11] reported the discovery of an Omp85 protein that is localized in the third outermost plastid membrane (homologous to the outer envelope membrane in plants) of the diatom Phaeodactylum tricornutum. To date, this Omp85 protein is the only reported putative member of the TOC complex in diatoms. Our phylogenetic analyses (including bacterial, plant and diatom sequences) reveals that the diatom sequences are of red algal origin and more specifically belongs to the Toc75 gene family. Unexpectedly long branches in the diatom part of the tree indicates a rapid, albeit even, evolu- tionary rate. This phenomenon has been reported on previously, but the significance of the phenomenon has not yet been thor- oughly investigated. Assembly statistics DNA libraries (insert size 150 and 3000 bp), of which one were gen- erated from an axenic culture, and one RNA library (300 bp) from Surirella brebissonii has been sequenced. One axenic 300 bp library from Skeletonema marinoi has been generated. Both genomes have been assembled using the CLC de novo assembler software package. Sequence reads where preprocessed using cutadapt [1] and the fastx toolkit [2] (for details see http://matstopel.se/notebook). Skeletonema Surirella Total nt sequenced (Gb) 33 46 Total input to assembly (Gb) 26 33 Assembly size (Mb) 49 136 Number of contigs (K) 53 244 Average coverage (x/cont) 443 207 N50 (bp) 1673 694 Average contig lenght (bp) 929 557 Longest contig (Kb) 506* 76 *Putative bacterial symbiont. Preliminary findings Organelles − The plastid of Surirella brebissonii contains a group II intron with an ORF, the first group II intron to be identified in dia- toms. Interestingly, the mitochondrial genome of S. brebissonii has lost the group II intron present in both Thalassiosira pseudonana and Phaeodactylum tricornutu


08-11 November 2021 Online Event Prediction of photoelectric effect log and facies classification in the Panoma gas field Felipe F. Melo CGG GeoSoftware (Formerly at PUC Rio) Contact: felipe146@hotmail.com 1) AIM Predict the photoelectric effect log on two wells and then perform facies classification. 2) Introduction Departing from seven wells in the training set, I impute missing values in the photoelectric effect log (PE) in one well and predict the PE log from two wells. Then, I aggregate these wells to the training data in order to perform facies classification. Distinct feature augmentation techniques are used in both log prediction and facies classification. I used the random forest algorithm for log prediction and the extreme gradient boosting for facies classification. Focusing on the generalization of the models, the hyperparameters were tuned with the nested and the leave two out cross validation, respectively. The well Churchman Bible is picked as test data, this well is chosen because it has all facies and a large number of samples related to facies of interest. 3) Dataset 4) Method 5) Prediction of photoelectric effect log 6) Facies Classification 7) Conclusions • The feature augmentation was successful in both prediction and classification. • The PE prediction score (72%) in the test well shows the good result of this approach. • The results for facies classification are acceptable because of the samples limitations, accuracy of 58%. • The accuracy of 86% on adjacent facies and 90% on BS, 57% on PS and 6% on D (critical facies) shows the effectiveness of the proposed approach. 9) References Dubois, M. K.; Bohling, G. C.; Chakrabarti, S. 2007. Comparison of four approaches to a rock facies classification problem. Computers & Geosciences, 33 (5), 599–617. Hall, B. 2016a Facies classification using machine learning. The Leading Edge, 35, 906–909. Hall, M.; Hall, B. 2017. Distributed collaborative prediction: Results of the machine learning contest. The Leading Edge, 36, 267–269. 8) Acknowledgments I would like to acknowledge Brendon and Matt Hall, the participants of the SEG contest and the Swung community for push the knowledge and free software. This research has been benefited from knowledge and source codes shared by them. 10) Reproduce The codes used on this work are available at: https://github.com/ffigura/SBGf_ ML_gas/ Figure 1 – Distribution of facies for each well, the well names are shown over each plot. The last panel shows the distribution of all facies. Figure 2 – Cross-plots from the well logs colored with facies classification. Figure 3 – Well logs and facies from the well Nolan. Figure 4 – Feature augmentation for well Nolan. Figure 5 – Prediction results. a) Feature importance for the test set. b) True and predicted logs from the well Nolan, this well is part of the training set. c) True and predicted logs from the test set, well Churchman Bible. Figure 7 – Confusion matrix. The facies as BS, PS and D are more critical in this work. The well Churchman Bible is used as test dataset, i.e., the quality of the regressor and of the classifier will be evaluated on this well. All other nine wells are used as training dataset for facies classification. In the first part, the photoelectric effect (PE) log is imputed for the well Recruit F9 (12 missing samples) and computed for the wells Alexander D and Kimzey A using the Random Forest regressor. Before log prediction, I perform feature augmentation. In this case, it adds non-linearities computing quadratic expansion and by considering all second order interaction terms and applies a low pass filter with the 1D discrete wavelet transform in the logs. Therefore, the training set moves from six to twenty features before estimate the PE logs. The logs NM_N and RELPOS are not used in feature augmentation because it would make no geophysical sense. After prediction of the PE logs into the two missing wells, these wells are grouped with the seven wells used as trai


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Simple tool quantifying sediment resuspension effects on marine organic carbon storage A rapid and efficient solution for integrating sediment heterogeneity in resuspension and C storage assessments. Global trawling CO2 footprint estimations3 lack • measurements of resuspension effect on org. C mineralization rates4 • accountancy for spatial variation of sediment types/ habitats5 Seafloor plays pivotal role for Earth’s climate by storing organic carbon long-term.1 Resuspension enhances mineralisation of stored organic carbon to CO2.2 Ines Bartl Tegan Evans Jenny Hillman Simon Thrush Institute of Marine Science, The University of Auckland, Auckland 1142, New Zealand ines.bartl@auckland.ac.nz Acknowledgments: This research was funded by the University of Auckland, the George Mason Centre for the Environment, the Ministry of Business, Innovation and Employment (UOAX2307), and the Oceans of Change Project. We thank Stefano Schenone, Sam Ladewig, Simon Thomas, Alessandra Valim, Li Yeoh, Keshav Chandran, Gemma Cunnington, Eliana Ferreti, Caitlin Grosvenor, Paul Caiger, Andrew Reid, Sophie Thomson, and Alanta Loucks for their assistance during the field campaigns, with special thanks to Brady Doak for both his professional support and his hospitality during the cruise. References: 1 Bianchi, T. S., Cui, X., Blair, et al. (2018). Organic Geochemistry, 115, 138–155. https://doi.org/10.1016/J.ORGGEOCHEM.2017.09.008 2 Ståhlberg, C., Bastviken, D., Svensson, B. H., & Rahm, L. (2006). Estuarine, Coastal and Shelf Science, 70(1–2), 317–325. https://doi.org/10.1016/J.ECSS.2006.06.0224 3 Sala, E., Mayorga, J., Bradley, D., et al. (2021). Nature, 592. https://doi.org/10.1038/s41586-021-03371-z 4 Hiddink, J. G., van de Velde, S. J., McConnaughey, R. A., et al. (2023). Nature 2023 617:7960, 617(7960), E1–E2. https://doi.org/10.1038/s41586-023-06014-7 5 Epstein, G., Middelburg, J. J., Hawkins, J. P., et al. (2022). In Global Change Biology (Vol. 28, Issue 9, pp. 2875–2894). https://doi.org/10.1111/gcb.161056 6 Jørgensen, B. B., Wenzhöfer, F., Egger, M., & Glud, R. N. (2022).. Earth-Science Reviews, 228, 103987. https://doi.org/10.1016/J.EARSCIREV.2022.103987 7 Sawyer, C. N., McCarty, P. L., & Parkin, G. F. (2003). Chemistry for Environmental Engineering and Science. 5th (edn) McGraw-Hill Inc. New York, 1–752. The Resuspension Assay What’s next? Identifying vulnerability of Hauraki Gulf sediments to demersal fishing. Simple  based on BOD method7 Rapid  short incubations of 3-5 hrs Efficient  7-8 sites per day in 50 km radius Affordable  inexpensive equipment https://www.usgs.gov/media/images/conceptual-drawing-ocean-trawling