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1. Walleye spawning, ice phenology, and covariate data for Upper Midwestern Lakes: 1939-2019

   https://doi.org/10.6073/pasta/f7a55f08dfe2a9514067e5c633313ef4  

   Feiner, Zachary S ; Barta, Martha ; Sass, Greg ; Reed, Jeffrey ; Cichosz, Thomas ; Shultz, Aaron ; Luehring, Mark ( January 2023 , Environmental Data Initiative)

   The phenology of critical biological events in aquatic ecosystems are rapidly shifting due to climate change. Growing variability in phenological cues can increase the likelihood of trophic mismatches, causing recruitment failures in commercially, culturally, and recreationally important fisheries. We tested for changes in spawning phenology of regionally important walleye (Sander vitreus) populations in 194 Midwest US lakes in Minnesota, Michigan, and Wisconsin spanning 1939-2019 to investigate factors influencing walleye phenological responses to climate change and associated climate variability, including ice-off timing, lake physical characteristics, and population stocking history. Data from Wisconsin and Michigan lakes (185 and 5 out of 194 total lakes, respectively) were collected by the Wisconsin Department of Natural Resources (WDNR) and the Great Lakes Indian Fish and Wildlife Commission (GLIFWC) through standardized spring walleye mark-recapture surveys and spring tribal harvest season records. Standardized spring mark-recapture population estimates are performed shortly after ice-off, where following a marking event, a subsequent recapture sampling event is conducted using nighttime electrofishing (typically AC – WDNR, pulsed-DC – GLIFWC) of the entire shoreline including islands for small lakes and index stations for large lakes (Hansen et al. 2015) that is timed to coincide with peak walleye spawning activity (G. Hatzenbeler, WDNR, personal communication; M. Luehring, GLIFWC, personal communication; Beard et al. 1997). Data for four additional Minnesota lakes were collected by the Minnesota Department of Natural Resources (MNDNR) beginning in 1939 during annual collections of walleye eggs and broodstock (Schneider et al. 2010), where date of peak egg take was used to index peak spawning activity. For lakes where spawning location did not match the lake for which the ice-off data was collected, the spawning location either flowed into (Pike River) or was within 50 km of a lake where ice-off data were available (Pine River) and these ice-off data were used. Following the affirmation of off-reservation Ojibwe tribal fishing rights in the Ceded Territories of Wisconsin and the Upper Peninsula of Michigan in 1987, tribal spearfishers have targeted walleye during spring spawning (Mrnak et al. 2018). Nightly harvests are recorded as part of a compulsory creel survey (US Department of the Interior 1991). Using these records, we calculated the date of peak spawning activity in a given lake-year as the day of maximum tribal harvest. Although we were unable to account for varying effort in these data, a preliminary analysis comparing spawning dates estimated using tribal harvest to those determined from standardized agency surveys in the same lake and year showed that they were highly correlated (Pearson’s correlation: r = 0.91, P < 0.001). For lakes that had walleye spawning data from both agency surveys and tribal harvest, we used the data source with the greatest number of observation years. Ice-off phenology data was collected from two sources – either observed from the Global Lake and River Ice Phenology database (Benson et al. 2000)t, or modeled from a USGS region-wide machine-learning model which used North American Land Data Assimilation System (NLDAS) meteorological inputs combined with lake characteristics (lake position, clarity, size, depth, hypsography, etc.) to predict daily water column temperatures from 1979 - 2022, from which ice-off dates could be derived (https://www.sciencebase.gov/catalog/item/6206d3c2d34ec05caca53071; see Corson-Dosch et al. 2023 for details). Modeled data for our study lakes (see (Read et al. 2021) for modeling details), which performed well in reflecting ice phenology when compared to observed data (i.e., highly significant correlation between observed and modeled ice-off dates when both were available; r = 0.71, p < 0.001). Lake surface area (ha), latitude, and maximum depth (m) were acquired from agency databases and lake reports. Lake class was based on a WDNR lakes classification system (Rypel et al. 2019) that categorized lakes based on temperature, water clarity, depth, and fish community. Walleye stocking history was defined using the walleye stocking classification system developed by the Wisconsin Technical Working Group (see also Sass et al. 2021), which categorized lakes based on relative contributions of naturally-produced and stocked fish to adult recruitment by relying heavily on historic records of age-0 and age-1 catch rates and stocking histories. Wisconsin lakes were divided into three groups: natural recruitment (NR), a combination of stocking and natural recruitment (C-ST), and stocked only (ST). Walleye natural recruitment was indexed as age-0 walleye CPE (number of age-0 walleye captured per km of shoreline electrofished) from WDNR and GLIFWC fall electrofishing surveys (see Hansen et al. 2015 for details). We excluded lake-years where stocking of age-0 fish occurred before age-0 surveys to only include measurements of naturally-reproduced fish. 

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2. Predictors of Jurors’ Understanding of Evidence Strength

   McCowan, K. ( March 2020 , Annual Conference of the American Psychology-Law Society.)

   Abstract Expert testimony varies in scientific quality and jurors have a difficult time evaluating evidence quality (McAuliff et al., 2009). In the current study, we apply Fuzzy Trace Theory principles, examining whether visual and gist aids help jurors calibrate to the strength of scientific evidence. Additionally we were interested in the role of jurors’ individual differences in scientific reasoning skills in their understanding of case evidence. Contrary to our preregistered hypotheses, there was no effect of evidence condition or gist aid on evidence understanding. However, individual differences between jurors’ numeracy skills predicted evidence understanding. Summary Poor-quality expert evidence is sometimes admitted into court (Smithburn, 2004). Jurors’ calibration to evidence strength varies widely and is not robustly understood. For instance, previous research has established jurors lack understanding of the role of control groups, confounds, and sample sizes in scientific research (McAuliff, Kovera, & Nunez, 2009; Mill, Gray, & Mandel, 1994). Still others have found that jurors can distinguish weak from strong evidence when the evidence is presented alone, yet not when simultaneously presented with case details (Smith, Bull, & Holliday, 2011). This research highlights the need to present evidence to jurors in a way they can understand. Fuzzy Trace Theory purports that people encode information in exact, verbatim representations and through “gist” representations, which represent summary of meaning (Reyna & Brainerd, 1995). It is possible that the presenting complex scientific evidence to people with verbatim content or appealing to the gist, or bottom-line meaning of the information may influence juror understanding of that evidence. Application of Fuzzy Trace Theory in the medical field has shown that gist representations are beneficial for helping laypeople better understand risk and benefits of medical treatment (Brust-Renck, Reyna, Wilhelms, & Lazar, 2016). Yet, little research has applied Fuzzy Trace Theory to information comprehension and application within the context of a jury (c.f. Reyna et. al., 2015). Additionally, it is likely that jurors’ individual characteristics, such as scientific reasoning abilities and cognitive tendencies, influence their ability to understand and apply complex scientific information (Coutinho, 2006). Methods The purpose of this study was to examine how jurors calibrate to the strength of scientific information, and whether individual difference variables and gist aids inspired by Fuzzy Trace Theory help jurors better understand complicated science of differing quality. We used a 2 (quality of scientific evidence: high vs. low) x 2 (decision aid to improve calibration - gist information vs. no gist information), between-subjects design. All hypotheses were preregistered on the Open Science Framework. Jury-eligible community participants (430 jurors across 90 juries; Mage = 37.58, SD = 16.17, 58% female, 56.93% White). Each jury was randomly assigned to one of the four possible conditions. Participants were asked to individually fill out measures related to their scientific reasoning skills prior to watching a mock jury trial. The trial was about an armed bank robbery and consisted of various pieces of testimony and evidence (e.g. an eyewitness testimony, police lineup identification, and a sweatshirt found with the stolen bank money). The key piece of evidence was mitochondrial DNA (mtDNA) evidence collected from hair on a sweatshirt (materials from Hans et al., 2011). Two experts presented opposing opinions about the scientific evidence related to the mtDNA match estimate for the defendant’s identification. The quality and content of this mtDNA evidence differed based on the two conditions. The high quality evidence condition used a larger database than the low quality evidence to compare to the mtDNA sample and could exclude a larger percentage of people. In the decision aid condition, experts in the gist information group presented gist aid inspired visuals and examples to help explain the proportion of people that could not be excluded as a match. Those in the no gist information group were not given any aid to help them understand the mtDNA evidence presented. After viewing the trial, participants filled out a questionnaire on how well they understood the mtDNA evidence and their overall judgments of the case (e.g. verdict, witness credibility, scientific evidence strength). They filled this questionnaire out again after a 45-minute deliberation. Measures We measured Attitudes Toward Science (ATS) with indices of scientific promise and scientific reservations (Hans et al., 2011; originally developed by National Science Board, 2004; 2006). We used Drummond and Fischhoff’s (2015) Scientific Reasoning Scale (SRS) to measure scientific reasoning skills. Weller et al.’s (2012) Numeracy Scale (WNS) measured proficiency in reasoning with quantitative information. The NFC-Short Form (Cacioppo et al., 1984) measured need for cognition. We developed a 20-item multiple-choice comprehension test for the mtDNA scientific information in the cases (modeled on Hans et al., 2011, and McAuliff et al., 2009). Participants were shown 20 statements related to DNA evidence and asked whether these statements were True or False. The test was then scored out of 20 points. Results For this project, we measured calibration to the scientific evidence in a few different ways. We are building a full model with these various operationalizations to be presented at APLS, but focus only on one of the calibration DVs (i.e., objective understanding of the mtDNA evidence) in the current proposal. We conducted a general linear model with total score on the mtDNA understanding measure as the DV and quality of scientific evidence condition, decision aid condition, and the four individual difference measures (i.e., NFC, ATS, WNS, and SRS) as predictors. Contrary to our main hypotheses, neither evidence quality nor decision aid condition affected juror understanding. However, the individual difference variables did: we found significant main effects for Scientific Reasoning Skills, F(1, 427) = 16.03, p <.001, np2 = .04, Weller Numeracy Scale, F(1, 427) = 15.19, p <.001, np2 = .03, and Need for Cognition, F(1, 427) = 16.80, p <.001, np2 = .04, such that those who scored higher on these measures displayed better understanding of the scientific evidence. In addition there was a significant interaction of evidence quality condition and scores on the Weller’s Numeracy Scale, F(1, 427) = 4.10, p = .04, np2 = .01. Further results will be discussed. Discussion These data suggest jurors are not sensitive to differences in the quality of scientific mtDNA evidence, and also that our attempt at helping sensitize them with Fuzzy Trace Theory-inspired aids did not improve calibration. Individual scientific reasoning abilities and general cognition styles were better predictors of understanding this scientific information. These results suggest a need for further exploration of approaches to help jurors differentiate between high and low quality evidence. Note: The 3rd author was supported by an AP-LS AP Award for her role in this research. Learning Objective: Participants will be able to describe how individual differences in scientific reasoning skills help jurors understand complex scientific evidence. 

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3. Search for point sources of ultra-high-energy photons with the Telescope Array surface detector

   https://doi.org/10.1093/mnras/stz3618  

   Abbasi, R.U. ( February 2020 , Monthly notices of the Royal Astronomical Society)

   Ultra-high-energy (UHE) photons are an important tool for studying the high-energy Universe. A plausible source of photons with exa-eV (EeV) energy is provided by UHE cosmic rays (UHECRs) undergoing the Greisen–Zatsepin–Kuzmin process (Greisen 1966; Zatsepin & Kuzmin 1966) or pair production process (Blumenthal 1970) on a cosmic background radiation. In this context, the EeV photons can be a probe of both UHECR mass composition and the distribution of their sources (Gelmini, Kalashev & Semikoz 2008; Hooper, Taylor & Sarkar 2011). At the same time, the possible flux of photons produced by UHE protons in the vicinity of their sources by pion photoproduction or inelastic nuclear collisions would be noticeable only for relatively near sources, as the attenuation length of UHE photons is smaller than that of UHE protons; see, for example, Bhattacharjee & Sigl (2000) for a review. There also exists a class of so-called top-down models of UHECR generation that efficiently produce the UHE photons, for instance by the decay of heavy dark-matter particles (Berezinsky, Kachelriess & Vilenkin 1997; Kuzmin & Rubakov 1998) or by the radiation from cosmic strings (Berezinsky, Blasi & Vilenkin 1998). The search for the UHE photons was shown to be the most sensitive method of indirect detection of heavy dark matter (Kalashev & Kuznetsov 2016, 2017; Kuznetsov 2017; Kachelriess, Kalashev & Kuznetsov 2018; Alcantara, Anchordoqui & Soriano 2019). Another fundamental physics scenario that could be tested with UHE photons (Fairbairn, Rashba & Troitsky 2011) is the photon mixing with axion-like particles (Raffelt & Stodolsky 1988), which could be responsible for the correlation of UHECR events with BL Lac type objects observed by the High Resolution Fly’s Eye (HiRes) experiment (Gorbunov et al. 2004; Abbasi et al. 2006). In most of these scenarios, a clustering of photon arrival directions, rather than diffuse distribution, is expected, so point-source searches can be a suitable test for photon - axion-like particle mixing models. Finally, UHE photons could also be used as a probe for the models of Lorentz-invariance violation (Coleman & Glashow 1999; Galaverni & Sigl 2008; Maccione, Liberati & Sigl 2010; Rubtsov, Satunin & Sibiryakov 2012, 2014). The Telescope Array (TA; Tokuno et al. 2012; Abu-Zayyad et al. 2013c) is the largest cosmic ray experiment in the Northern Hemisphere. It is located at 39.3° N, 112.9° W in Utah, USA. The observatory includes a surface detector array (SD) and 38 fluorescence telescopes grouped into three stations. The SD consists of 507 stations that contain plastic scintillators, each with an area of 3 m2 (SD stations). The stations are placed in the square grid with 1.2 km spacing and cover an area of ∼700 km2. The TA SD is capable of detecting extensive air showers (EASs) in the atmosphere caused by cosmic particles of EeV and higher energies. The TA SD has been operating since 2008 May. A hadron-induced EAS significantly differs from an EAS induced by a photon because the depth of the shower maximum Xmax for a photon shower is larger, and a photon shower contains fewer muons and has a more curved front (see Risse & Homola 2007 for a review). The TA SD stations are sensitive to both muon and electromagnetic components of the shower and therefore can be triggered by both hadron-induced and photon-induced EAS events. In the present study, we use 9 yr of TA SD data for a blind search for point sources of UHE photons. We utilize the statistics of the SD data, which benefit from a high duty cycle. The full Monte Carlo (MC) simulation of proton-induced and photon-induced EAS events allows us to perform the photon search up to the highest accessible energies, E ≳ 1020 eV. As the main tool for the present photon search, we use a multivariate analysis based on a number of SD parameters that make it possible to distinguish between photon and hadron primaries. While searches for diffuse UHE photons were performed by several EAS experiments, including Haverah Park (Ave et al. 2000), AGASA (Shinozaki et al. 2002; Risse et al. 2005), Yakutsk (Rubtsov et al. 2006; Glushkov et al. 2007, 2010), Pierre Auger (Abraham et al. 2007, 2008a; Bleve 2016; Aab et al. 2017c) and TA (Abu-Zayyad et al. 2013b; Abbasi et al. 2019a), the search for point sources of UHE photons has been done only by the Pierre Auger Observatory (Aab et al. 2014, 2017a). The latter searches were based on hybrid data and were limited to the 1017.3 < E < 1018.5 eV energy range. In the present paper, we use the TA SD data alone. We perform the searches in five energy ranges: E > 1018, E > 1018.5, E > 1019, E > 1019.5 and E > 1020 eV. We find no significant evidence of photon point sources in all energy ranges and we set the point-source flux upper limits from each direction in the TA field of view (FOV). The search for unspecified neutral particles was also previously performed by the TA (Abbasi et al. 2015). The limit on the point-source flux of neutral particles obtained in that work is close to the present photon point-source flux limits. 

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4. Biodistribution, cardiac and neurobehavioral assessments, and neurotransmitter quantification in juvenile rats following oral administration of aluminum oxide nanoparticles

   https://doi.org/10.1002/jat.4122  

   Mortensen, Ninell P. ; Moreno Caffaro, Maria ; Patel, Purvi R. ; Snyder, Rodney W. ; Watson, Scott L. ; Aravamudhan, Shyam ; Montgomery, Stephanie A. ; Lefever, Timothy ; Sumner, Susan J. ; Fennell, Timothy R. ( December 2020 , Journal of Applied Toxicology)

   Little is known about the uptake, biodistribution, and biological responses of nanoparticles (NPs) and their toxicity in developing animals. Here, male and female juvenile Sprague–Dawley rats received four consecutive daily doses of 10 mg/kg Al₂O₃NP (diameter: 24 nm [transmission electron microscope], hydrodynamic diameter: 148 nm) or vehicle control (water) by gavage between postnatal days (PNDs) 17–20. Basic neurobehavioral and cardiac assessments were performed on PND 20. Animals were sacrificed on PND 21, and selected tissues were collected, weighed, and processed for histopathology or neurotransmitter analysis. The biodistribution of Al₂O₃NP in tissue sections of the intestine, liver, spleen, kidney, and lymph nodes were evaluated using enhanced dark‐field microscopy (EDM) and hyperspectral imaging (HSI). Liver‐to‐body weight ratio was significantly increased for male pups administered Al₂O₃NP compared with control. HSI suggested that Al₂O₃NP was more abundant in the duodenum and ileum tissue of the female pups compared with the male pups, whereas the abundance of NP was similar for males and females in the other tissues. The abundance of NP was higher in the liver compared with spleen, lymph nodes, and kidney. Homovanillic acid and norepinephrine concentrations in brain were significantly decreased following Al₂O₃NP administration in female and male pups, whereas 5‐hydroxyindoleacetic acid was significantly increased in male pups. EDM/HSI indicates intestinal uptake of Al₂O₃NP following oral administration. Al₂O₃NP altered neurotransmitter/metabolite concentrations in juvenile rats' brain tissues. Together, these data suggest that orally administered Al₂O₃NP interferes with the brain biochemistry in both female and male pups.

    

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5. Linking Biodiversity Data Using Evolutionary History

   https://doi.org/10.3897/biss.3.36207  

   McTavish, Emily Jane ( June 2019 , Biodiversity Information Science and Standards)

   All life on earth is linked by a shared evolutionary history. Even before Darwin developed the theory of evolution, Linnaeus categorized types of organisms based on their shared traits. We now know these traits derived from these species’ shared ancestry. This evolutionary history provides a natural framework to harness the enormous quantities of biological data being generated today. The Open Tree of Life project is a collaboration developing tools to curate and share evolutionary estimates (phylogenies) covering the entire tree of life (Hinchliff et al. 2015, McTavish et al. 2017). The tree is viewable at https://tree.opentreeoflife.org, and the data is all freely available online. The taxon identifiers used in the Open Tree unified taxonomy (Rees and Cranston 2017) are mapped to identifiers across biological informatics databases, including the Global Biodiversity Information Facility (GBIF), NCBI, and others. Linking these identifiers allows researchers to easily unify data from across these different resources (Fig. 1). Leveraging a unified evolutionary framework across the diversity of life provides new avenues for integrative wide scale research. Downstream tools, such as R packages developed by the R OpenSci foundation (rotl, rgbif) (Michonneau et al. 2016, Chamberlain 2017) and others tools (Revell 2012), make accessing and combining this information straightforward for students as well as researchers (e.g. https://mctavishlab.github.io/BIO144/labs/rotl-rgbif.html). Figure 1. Example linking phylogenetic relationships accessed from the Open Tree of Life with specimen location data from Global Biodiversity Information Facility. For example, a recent publication by Santorelli et al. 2018 linked evolutionary information from Open Tree with species locality data gathered from a local field study as well as GBIF species location records to test a river-barrier hypothesis in the Amazon. By combining these data, the authors were able test a widely held biogeographic hypothesis across 1952 species in 14 taxonomic groups, and found that a river that had been postulated to drive endemism, was in fact not a barrier to gene flow. However, data provenance and taxonomic name reconciliation remain key hurdles to applying data from these large digital biodiversity and evolution community resources to answering biological questions. In the Amazonian river analysis, while they leveraged use of GBIF records as a secondary check on their species records, they relied on their an intensive local field study for their major conclusions, and preferred taxon specific phylogenetic resources over Open Tree where they were available (Santorelli et al. 2018). When Li et al. 2018 assessed large scale phylogenetic approaches, including Open Tree, for measuring community diversity, they found that synthesis phylogenies were less resolved than purpose-built phylogenies, but also found that these synthetic phylogenies were sufficient for community level phylogenetic diversity analyses. Nonetheless, data quality concerns have limited adoption of analyses data from centralized resources (McTavish et al. 2017). Taxonomic name recognition and reconciliation across databases also remains a hurdle for large scale analyses, despite several ongoing efforts to improve taxonomic interoperability and unify taxonomies, such at Catalogue of Life + (Bánki et al. 2018). In order to support innovative science, large scale digital data resources need to facilitate data linkage between resources, and address researchers' data quality and provenance concerns. I will present the model that the Open Tree of Life is using to provide evolutionary data at the scale of the entire tree of life, while maintaining traceable provenance to the publications and taxonomies these evolutionary relationships are inferred from. I will discuss the hurdles to adoption of these large scale resources by researchers, as well as the opportunities for new research avenues provided by the connections between evolutionary inferences and biodiversity digital databases. 

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