28,516 results on '"Pearson, P."'
Search Results
2. Meaning-Making Mindsets
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Johnston, Peter H., primary and Pearson, P. David, additional
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- 2024
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3. An Evolutionary, Democratic Learning Community
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Johnston, Peter H., primary and Pearson, P. David, additional
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- 2024
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4. Emotional and Social Life
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Johnston, Peter H., primary and Pearson, P. David, additional
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- 2024
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5. Knowing
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Johnston, Peter H., primary and Pearson, P. David, additional
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- 2024
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6. Identity
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Johnston, Peter H., primary and Pearson, P. David, additional
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- 2024
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7. Noticing and Naming
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Johnston, Peter H., primary and Pearson, P. David, additional
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- 2024
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8. SN2023fyq: A Type Ibn Supernova With Long-standing Precursor Activity Due to Binary Interaction
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Dong, Yize, Tsuna, Daichi, Valenti, Stefano, Sand, David J., Andrews, Jennifer E., Bostroem, K. Azalee, Hosseinzadeh, Griffin, Hoang, Emily, Jha, Saurabh W., Janzen, Daryl, Jencson, Jacob E., Lundquist, Michael, Mehta, Darshana, Ravi, Aravind P., Retamal, Nicolas E. Meza, Pearson, Jeniveve, Shrestha, Manisha, Bonanos, Alceste, Howell, D. Andrew, Smith, Nathan, Farah, Joseph, Hiramatsu, Daichi, Itagaki, Koichi, McCully, Curtis, Newsome, Megan, Gonzalez, Estefania Padilla, Paraskeva, Emmanouela N., Pellegrino, Craig, Terreran, Giacomo, Haislip, Joshua, Kouprianov, Vladimir, and Reichart, Daniel E.
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Astrophysics - High Energy Astrophysical Phenomena ,Astrophysics - Solar and Stellar Astrophysics - Abstract
We present photometric and spectroscopic observations of SN 2023fyq, a type Ibn supernova in the nearby galaxy NGC 4388 (D$\simeq$18~Mpc). In addition, we trace long-standing precursor emission at the position of SN 2023fyq using data from DLT40, ATLAS, ZTF, ASAS-SN, Swift, and amateur astronomer Koichi Itagaki. Precursor activity is observed up to nearly three years before the supernova explosion, with a relatively rapid rise in the final 100 days. The double-peaked post-explosion light curve reaches a luminosity of $\sim10^{43}~\rm erg\,s^{-1}$. The strong intermediate-width He lines observed in the nebular spectrum of SN 2023fyq imply the interaction is still active at late phases. We found that the precursor activity in SN 2023fyq is best explained by the mass transfer in a binary system involving a low-mass He star and a compact companion. An equatorial disk is likely formed in this process ($\sim$0.6$\rm M_{\odot}$), and the interaction of SN ejecta with this disk powers the main peak of the supernova. The early SN light curve reveals the presence of dense extended material ($\sim$0.3$\rm M_{\odot}$) at $\sim$3000$\rm R_{\odot}$ ejected weeks before the SN explosion, likely due to final-stage core silicon burning or runaway mass transfer resulting from binary orbital shrinking, leading to rapid rising precursor emission within $\sim$30 days prior to explosion. The final explosion could be triggered either by the core-collapse of the He star or by the merger of the He star with a compact object. SN 2023fyq, along with SN 2018gjx and SN 2015G, forms a unique class of Type Ibn SNe which originate in binary systems and are likely to exhibit detectable long-lasting pre-explosion outbursts with magnitudes ranging from $-$10 to $-$13., Comment: submitted to ApJ
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- 2024
9. Citizen Science in European Research Infrastructures
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Serjeant, Stephen, Pearson, James, Dickinson, Hugh, and Jarvis, Johanna
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Astrophysics - Instrumentation and Methods for Astrophysics ,Physics - Physics Education - Abstract
Major European Union-funded research infrastructure and open science projects have traditionally included dissemination work, for mostly one-way communication of the research activities. Here we present and review our radical re-envisioning of this work, by directly engaging citizen science volunteers into the research. We summarise the citizen science in the Horizon-funded projects ASTERICS (Astronomy ESFRI and Research Infrastructure Clusters) and ESCAPE (European Science Cluster of Astronomy and Particle Physics ESFRI Research Infrastructures), engaging hundreds of thousands of volunteers in providing millions of data mining classifications. Not only does this have enormously more scientific and societal impact than conventional dissemination, but it facilitates the direct research involvement of what is often arguably the most neglected stakeholder group in Horizon projects, the science-inclined public. We conclude with recommendations and opportunities for deploying crowdsourced data mining in the physical sciences, noting that the primary goal is always the fundamental research question; if public engagement is the primary goal to optimise, then other, more targeted approaches may be more effective., Comment: Accepted by European Physical Journal Plus. Invited review. 26 pages, 1 figure
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- 2024
10. The population of small near-Earth objects: composition, source regions and rotational properties
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Sanchez, Juan A., Reddy, Vishnu, Thirouin, Audrey, Bottke, William F., Kareta, Theodore, De Florio, Mario, Sharkey, Benjamin N. L., Battle, Adam, Cantillo, David C., and Pearson, Neil
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Astrophysics - Earth and Planetary Astrophysics - Abstract
The study of small ($<$300 m) near-Earth objects (NEOs) is important because they are more closely related than larger objects to the precursors of meteorites that fall on Earth. Collisions of these bodies with Earth are also more frequent. Although such collisions cannot produce massive extinction events, they can still produce significant local damage. Here we present the results of a photometric and spectroscopic survey of small NEOs, which include near-infrared (NIR) spectra of 84 objects with a mean diameter of 126 m and photometric data of 59 objects with a mean diameter of 87 m. We found that S-complex asteroids are the most abundant among the NEOs, comprising $\sim$66\% of the sample. Most asteroids in the S-complex were found to have compositions consistent with LL-chondrites. Our study revealed the existence of NEOs with spectral characteristics similar to those in the S-complex, but that could be hidden within the C- or X-complex due to their weak absorption bands. We suggest that the presence of metal or shock-darkening could be responsible for the attenuation of the absorption bands. These objects have been grouped into a new subclass within the S-complex called Sx-types. The dynamical modeling showed that 83\% of the NEOs escaped from the $\nu_{6}$ resonance, 16\% from the 3:1 and just 1\% from the 5:2 resonance. Lightcurves and rotational periods were derived from the photometric data. No clear trend between the axis ratio and the absolute magnitude or rotational period of the NEOs was found., Comment: 61 pages, 43 figures, 5 tables. Accepted for publication in the Planetary Science Journal
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- 2024
11. Determining the time before or after a galaxy merger event
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Pearson, W. J., Rodriguez-Gomez, V., Kruk, S., and Margalef-Bentabol, B.
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Astrophysics - Astrophysics of Galaxies - Abstract
Aims. This work aims to reproduce the time before or after a merger event of merging galaxies from the IllustrisTNG cosmological simulation using machine learning. Methods. Images of merging galaxies were created in the u, g, r, and i bands from IllustrisTNG. The merger times were determined using the time difference between the last simulation snapshot where the merging galaxies were tracked as two galaxies and the first snapshot where the merging galaxies were tracked as a single galaxy. This time was then further refined using simple gravity simulations. These data were then used to train a residual network (ResNet50), a Swin Transformer (Swin), a convolutional neural network (CNN), and an autoencoder (using a single latent neuron) to reproduce the merger time. The full latent space of the autoencoder was also studied to see if it reproduces the merger time better than the other methods. This was done by reducing the latent space dimensions using Isomap, linear discriminant analysis (LDA), neighbourhood components analysis, sparse random projection, truncated singular value decomposition and uniform manifold approximation and projection. Results. The CNN is the best of all the neural networks. The performance of the autoencoder was close to the CNN, with Swin close behind the autoencoder. ResNet50 performed the worst. The LDA dimensionality reduction performed the best of the six methods used. The exploration of the full latent space produced worse results than the single latent neuron of the autoencoder. For the test data set, we found a median error of 190 Myr, comparable to the time separation between snapshots in IllustrisTNG. Galaxies more than $\approx$ 625 Myr before a merger have poorly recovered merger times, as well as galaxies more than $\approx$ 125 Myr after a merger event., Comment: 16 pages, 20 figures, 1 appendix, Accepted for publication in Astronomy & Astrophysics
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- 2024
12. The first degree-scale starlight-polarization-based tomography map of the magnetized interstellar medium
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Pelgrims, V., Mandarakas, N., Skalidis, R., Tassis, K., Panopoulou, G. V., Pavlidou, V., Blinov, D., Kiehlmann, S., Clark, S. E., Hensley, B. S., Romanopoulos, S., Basyrov, A., Eriksen, H. K., Falalaki, M., Ghosh, T., Gjerløw, E., Kypriotakis, J. A., Maharana, S., Papadaki, A., Pearson, T. J., Potter, S. B., Ramaprakash, A. N., Readhead, A. C. S., and Wehus, I. K.
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
We present the first degree-scale tomography map of the dusty magnetized interstellar medium (ISM) from stellar polarimetry and distance measurements. We used the RoboPol polarimeter at Skinakas Observatory to conduct a survey of starlight polarization in a region of the sky of 4 square degrees. We propose a Bayesian method to decompose the stellar-polarization source field along the distance to invert the 3D volume occupied by the observed stars. We used it to obtain the first 3D map of the dusty magnetized ISM. Specifically, we produced a tomography map of the orientation of the plane-of-sky (POS) component of the magnetic field threading the diffuse, dusty regions responsible for the stellar polarization. For the targeted region centered on Galactic coordinates $(l,b) \approx (103.3^\circ, 22.3^\circ)$, we identified several ISM clouds. Most of the lines of sight intersect more than one cloud. A very nearby component was detected in the foreground of a dominant component from which most of the polarization signal comes. Farther clouds, with a distance of up to 2~kpc, were similarly detected. Some of them likely correspond to intermediate-velocity clouds seen in HI spectra in this region of the sky. We found that the orientation of the POS component of the magnetic field changes along distance for most of the lines of sight. Our study demonstrates that starlight polarization data coupled to distance measures have the power to reveal the great complexity of the dusty magnetized ISM in 3D and, in particular, to provide local measurements of the POS component of the magnetic field. This demonstrates that the inversion of large data volumes, as expected from the PASIPHAE survey, will provide the necessary means to move forward in the modeling of the Galactic magnetic field and of the dusty magnetized ISM as a contaminant in observations of the cosmic microwave background polarization., Comment: Preprint of the accepted version at Astronomy & Astrophysics. The 3D map obtained in this paper can be visualized online at https://pasiphae.science/visualization and a video featuring it is accessible at https://www.youtube.com/watch?v=dB_6J1zhmPI
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- 2024
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13. Fifth Generation IMC: Expanding the scope to Profit, People, and the Planet
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Pearson, Stewart and Malthouse, Edward
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Computer Science - Computers and Society - Abstract
This editorial outlines an expanded scope for the next (fifth) generation of integrated marketing communication. It identifies key market forces that gave rise to this evolution and describes a trajectory of where Integrated Marketing Communication (IMC) has been and where it is going. The central shift is moving from primarily focusing on one stakeholder to multiple ones, including people (employees and society), the planet (environment), and profits. It identifies examples from industry that exemplify multi-stakeholder decision-making and uses the examples to suggest research questions that academics and practitioners should address. Examples and research directions are organized around marketing strategy, communication media and messages, and measurement systems.
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- 2024
14. Unified equations of state for cold nonaccreting neutron stars with Brussels-Montreal functionals. V. Improved parametrization of the nucleon density distributions
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Shchechilin, N. N., Chamel, N., Pearson, J. M., Chugunov, A. I., and Potekhin, A. Y.
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Astrophysics - High Energy Astrophysical Phenomena ,Nuclear Theory - Abstract
We previously studied the inner crust and the pasta mantle of a neutron star within the 4th-order extended Thomas-Fermi (ETF) approach with consistent proton shell corrections added perturbatively via the Strutinsky integral (SI) theorem together with the contribution due to pairing. To speed up the computations and avoid numerical problems, we adopted parametrized nucleon density distributions. However, the errors incurred by the choice of the parametrization are expected to become more significant as the mean baryon number density is increased, especially in the pasta mantle where the differences in the energy per nucleon of the different phases are very small, typically a few keV. To improve the description of these exotic structures, we discuss the important features that a nuclear profile should fulfill and introduce two new parametrizations. Performing calculations using the BSk24 functional, we find that these parametrizations lead to lower ETF energy solutions for all pasta phases than the parametrization we adopted before and more accurately reproduce the exact equilibrium nucleon density distributions obtained from unconstrained variational calculations. Within the ETFSI method, all parametrizations predict the same composition in the region with quasi-spherical clusters. However, the two new parametrizations lead to a different mantle structure at mean baryon densities above about 0.07 fm^-3, at which point lasagna is energetically favored. Interestingly, spherical clusters reappear in the pasta region. The inverted pasta phases such as bucatini and Swiss cheese are still found in the densest region above the core in all cases., Comment: 12 pages, 9 figures, published in Phys. Rev. C
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- 2024
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15. Scaling Laws for Galaxy Images
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Walmsley, Mike, Bowles, Micah, Scaife, Anna M. M., Makechemu, Jason Shingirai, Gordon, Alexander J., Ferguson, Annette M. N., Mann, Robert G., Pearson, James, Popp, Jürgen J., Bovy, Jo, Speagle, Josh, Dickinson, Hugh, Fortson, Lucy, Géron, Tobias, Kruk, Sandor, Lintott, Chris J., Mantha, Kameswara, Mohan, Devina, O'Ryan, David, and Slijepevic, Inigo V.
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Computer Science - Computer Vision and Pattern Recognition ,Astrophysics - Astrophysics of Galaxies - Abstract
We present the first systematic investigation of supervised scaling laws outside of an ImageNet-like context - on images of galaxies. We use 840k galaxy images and over 100M annotations by Galaxy Zoo volunteers, comparable in scale to Imagenet-1K. We find that adding annotated galaxy images provides a power law improvement in performance across all architectures and all tasks, while adding trainable parameters is effective only for some (typically more subjectively challenging) tasks. We then compare the downstream performance of finetuned models pretrained on either ImageNet-12k alone vs. additionally pretrained on our galaxy images. We achieve an average relative error rate reduction of 31% across 5 downstream tasks of scientific interest. Our finetuned models are more label-efficient and, unlike their ImageNet-12k-pretrained equivalents, often achieve linear transfer performance equal to that of end-to-end finetuning. We find relatively modest additional downstream benefits from scaling model size, implying that scaling alone is not sufficient to address our domain gap, and suggest that practitioners with qualitatively different images might benefit more from in-domain adaption followed by targeted downstream labelling., Comment: 10+6 pages, 12 figures. Appendix C2 based on arxiv:2206.11927. Code, demos, documentation at https://github.com/mwalmsley/zoobot
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- 2024
16. Galaxy merger challenge: A comparison study between machine learning-based detection methods
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Margalef-Bentabol, B., Wang, L., La Marca, A., Blanco-Prieto, C., Chudy, D., Domínguez-Sánchez, H., Goulding, A. D., Guzmán-Ortega, A., Huertas-Company, M., Martin, G., Pearson, W. J., Rodriguez-Gomez, V., Walmsley, M., Bickley, R. W., Bottrell, C., Conselice, C., and O'Ryan, D.
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Astrophysics - Astrophysics of Galaxies - Abstract
Various galaxy merger detection methods have been applied to diverse datasets. However, it is difficult to understand how they compare. We aim to benchmark the relative performance of machine learning (ML) merger detection methods. We explore six leading ML methods using three main datasets. The first one (the training data) consists of mock observations from the IllustrisTNG simulations and allows us to quantify the performance metrics of the detection methods. The second one consists of mock observations from the Horizon-AGN simulations, introduced to evaluate the performance of classifiers trained on different, but comparable data. The third one consists of real observations from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP) survey. For the binary classification task (mergers vs. non-mergers), all methods perform reasonably well in the domain of the training data. At $0.1
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- 2024
17. Causal knowledge engineering: A case study from COVID-19
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Mascaro, Steven, Wu, Yue, Pearson, Ross, Woodberry, Owen, Ramsay, Jessica, Snelling, Tom, and Nicholson, Ann E.
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Computer Science - Artificial Intelligence - Abstract
COVID-19 appeared abruptly in early 2020, requiring a rapid response amid a context of great uncertainty. Good quality data and knowledge was initially lacking, and many early models had to be developed with causal assumptions and estimations built in to supplement limited data, often with no reliable approach for identifying, validating and documenting these causal assumptions. Our team embarked on a knowledge engineering process to develop a causal knowledge base consisting of several causal BNs for diverse aspects of COVID-19. The unique challenges of the setting lead to experiments with the elicitation approach, and what emerged was a knowledge engineering method we call Causal Knowledge Engineering (CKE). The CKE provides a structured approach for building a causal knowledge base that can support the development of a variety of application-specific models. Here we describe the CKE method, and use our COVID-19 work as a case study to provide a detailed discussion and analysis of the method., Comment: 22 pages (plus 19 pages in appendices), 9 figures, submitted for review
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- 2024
18. Effects of galaxy environment on merger fraction
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Pearson, W. J., Santos, D. J. D., Goto, T., Huang, T. -C., Kim, S. J., Matsuhara, H., Pollo, A., Ho, S. C. -C., Hwang, H. S., Małek, K., Nakagawa, T., Romano, M., Serjeant, S., Suelves, L., Shim, H., and White, G. J.
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Astrophysics - Astrophysics of Galaxies - Abstract
Aims. In this work, we intend to examine how environment influences the merger fraction, from the low density field environment to higher density groups and clusters. We also aim to study how the properties of a group or cluster, as well as the position of a galaxy in the group or cluster, influences the merger fraction. Methods. We identified galaxy groups and clusters in the North Ecliptic Pole using a friends-of-friends algorithm and the local density. Once identified, we determined the central galaxies, group radii, velocity dispersions, and group masses of these groups and clusters. Merging systems were identified with a neural network as well as visually. With these, we examined how the merger fraction changes as the local density changes for all galaxies as well as how the merger fraction changes as the properties of the groups or clusters change. Results. We find that the merger fraction increases as local density increases and decreases as the velocity dispersion increases, as is often found in literature. A decrease in merger fraction as the group mass increases is also found. We also find groups with larger radii have higher merger fractions. The number of galaxies in a group does not influence the merger fraction. Conclusions. The decrease in merger fraction as group mass increases is a result of the link between group mass and velocity dispersion. Hence, this decrease of merger fraction with increasing mass is a result of the decrease of merger fraction with velocity dispersion. The increasing relation between group radii and merger fraction may be a result of larger groups having smaller velocity dispersion at a larger distance from the centre or larger groups hosting smaller, infalling groups with more mergers. However, we do not find evidence of smaller groups having higher merger fractions., Comment: 15 pages, 10 figures, 8 tables, 2 appendices, accepted for publication in Astronomy & Astrophysics
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- 2024
19. Effects of AFQ056 on language learning in fragile X syndrome
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Berry-Kravis, Elizabeth, Abbeduto, Leonard, Hagerman, Randi, Coffey, Christopher S, Cudkowicz, Merit, Erickson, Craig A, McDuffie, Andrea, Hessl, David, Ethridge, Lauren, Tassone, Flora, Kaufmann, Walter E, Friedmann, Katherine, Bullard, Lauren, Hoffmann, Anne, Veenstra-VanderWeele, Jeremy, Staley, Kevin, Klements, David, Moshinsky, Michael, Harkey, Brittney, Long, Jeff, Fedler, Janel, Klingner, Elizabeth, Ecklund, Dixie, Costigan, Michele, Huff, Trevis, Pearson, Brenda, and Investigators, NeuroNEXT FXLEARN
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Biomedical and Clinical Sciences ,Rare Diseases ,Intellectual and Developmental Disabilities (IDD) ,Behavioral and Social Science ,Fragile X Syndrome ,Clinical Research ,Pediatric ,Brain Disorders ,Clinical Trials and Supportive Activities ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Mental health ,Adult ,Animals ,Child ,Humans ,Single-Blind Method ,Learning ,Language ,Cleft Palate ,Indoles ,Malignant Hyperthermia ,Myotonia Congenita ,NeuroNEXT FXLEARN Investigators ,Clinical trials ,Neurodevelopment ,Neuroscience ,Translation ,Medical and Health Sciences ,Immunology ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
BACKGROUNDFXLEARN, the first-ever large multisite trial of effects of disease-targeted pharmacotherapy on learning, was designed to explore a paradigm for measuring effects of mechanism-targeted treatment in fragile X syndrome (FXS). In FXLEARN, the effects of metabotropic glutamate receptor type 5 (mGluR5) negative allosteric modulator (NAM) AFQ056 on language learning were evaluated in 3- to 6-year-old children with FXS, expected to have more learning plasticity than adults, for whom prior trials of mGluR5 NAMs have failed.METHODSAfter a 4-month single-blind placebo lead-in, participants were randomized 1:1 to AFQ056 or placebo, with 2 months of dose optimization to the maximum tolerated dose, then 6 months of treatment during which a language-learning intervention was implemented for both groups. The primary outcome was a centrally scored videotaped communication measure, the Weighted Communication Scale (WCS). Secondary outcomes were objective performance-based and parent-reported cognitive and language measures.RESULTSFXLEARN enrolled 110 participants, randomized 99, and had 91 who completed the placebo-controlled period. Although both groups made language progress and there were no safety issues, the change in WCS score during the placebo-controlled period was not significantly different between the AFQ056 and placebo-treated groups, nor were there any significant between-group differences in change in any secondary measures.CONCLUSIONDespite the large body of evidence supporting use of mGluR5 NAMs in animal models of FXS, this study suggests that this mechanism of action does not translate into benefit for the human FXS population and that better strategies are needed to determine which mechanisms will translate from preclinical models to humans in genetic neurodevelopmental disorders.TRIAL REGISTRATIONClincalTrials.gov NCT02920892.FUNDING SOURCESNeuroNEXT network NIH grants U01NS096767, U24NS107200, U24NS107209, U01NS077323, U24NS107183, U24NS107168, U24NS107128, U24NS107199, U24NS107198, U24NS107166, U10NS077368, U01NS077366, U24NS107205, U01NS077179, and U01NS077352; NIH grant P50HD103526; and Novartis IIT grant AFQ056X2201T for provision of AFQ056.
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- 2024
20. Do galaxy mergers prefer under-dense environments?
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Sureshkumar, U., Durkalec, A., Pollo, A., Pearson, W. J., Farrow, D. J., Narayanan, A., Loveday, J., Taylor, E. N., and Suelves, L. E.
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
Galaxy mergers play a crucial role in galaxy evolution. However, the correlation between mergers and the local environment of galaxies is not fully understood. We aim to address the question of whether galaxy mergers prefer denser or less dense environments by quantifying the spatial clustering of mergers and non-mergers. We use two different indicators to classify mergers and non-mergers - classification based on a deep learning technique ($f$) and non-parametric measures of galaxy morphology, Gini-$M_{20}$ ($g$). We used a set of galaxy samples in the redshift range 0.1 < z < 0.15 from the Galaxy and Mass Assembly (GAMA) survey with a stellar mass cut of log (M*/Msun) > 9.5. We measured and compared the two-point correlation function (2pCF) of mergers and non-mergers classified using the two merger indicators $f$ and $g$. We measured the marked correlation function (MCF), in which the galaxies are weighted by $f$ to probe the environmental dependence of galaxy mergers. We do not observe a statistically significant difference between the clustering strengths of mergers and non-mergers obtained using 2pCF. However, using the MCF measurements with $f$ as a mark, we observe an anti-correlation between the likelihood of a galaxy being a merger and its environment. Our results emphasise the advantage of MCF over 2pCF in probing the environmental correlations. Based on the MCF measurements, we conclude that the galaxy mergers prefer to occur in the under-dense environments on scales greater than 50 kpc/h of the large-scale structure (LSS). We attribute this observation to the high relative velocities of galaxies in the densest environments that prevent them from merging., Comment: 13 pages, 9 figures, accepted for publication in A&A
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- 2024
21. Benchmarking the algorithmic performance of near-term neutral atom processors
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McInroy, K., Pearson, N., and Pritchard, J. D.
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Quantum Physics - Abstract
Neutral atom quantum processors provide a viable route to scalable quantum computing, with recent demonstrations of high-fidelity and parallel gate operations and initial implementation of quantum algorithms using both physical and logical qubit encodings. In this work we present a characterization of the algorithmic performance of near term Rydberg atom quantum computers through device simulation to enable comparison against competing architectures. We consider three different quantum algorithm related tests, exploiting the ability to dynamically update qubit connectivity and multi-qubit gates. We calculate a quantum volume of $\mathbf{\mathit{V_{Q}}=2^{9}}$ for 9 qubit devices with realistic parameters, which is the maximum achievable value for this device size and establishes a lower bound for larger systems. We also simulate highly efficient implementations of both the Bernstein-Vazirani algorithm with >0.95 success probability for 9 data qubits and 1 ancilla qubit without loss correction, and Grover's search algorithm with a loss-corrected success probability of 0.97 for an implementation of the algorithm using 6 data qubits and 3 ancilla qubits using native multi-qubit $\mathbf{CCZ}$ gates. Our results indicate Rydberg atom processors are a highly competitive near-term platform which, bolstered by the potential for further scalability, can pave the way toward useful quantum computation., Comment: 14 pages, 7 figures
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- 2024
22. JWST NIRSpec+MIRI Observations of the nearby Type IIP supernova 2022acko
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Shahbandeh, M., Ashall, C., Hoeflich, P., Baron, E., Fox, O., Mera, T., DerKacy, J., Stritzinger, M. D., Shappee, B., Law, D., Morrison, J., Pauly, T., Pierel, J., Medler, K., Andrews, J., Baade, D., Bostroem, A., Brown, P., Burns, C., Burrow, A., Cikota, A., Cross, D., Davis, S., de Jaeger, T., Do, A., Dong, Y., Hsiao, E., Dominguez, I., Galbany, L., Janzen, D., Jencson, J., Hoang, E., Karamehmetoglu, E., Khaghani, B., Krisciunas, K., Kumar, S., Lu, J., Mazzali, P., Morrell, N., Patat, F., Pearson, J., Pfeffer, C., Wang, L., Yang, Y., Cai, Y. Z., Camacho-Neves, Y., Elias-Rosa, N., Lundquist, M., Maund, J., Phillips, M., Rest, A., Retamal, N., Stangl, S., Shrestha, M., Stevens, C., Suntzeff, N., Telesco, C., Tucker, M., Foley, R., Jha, S., Kwok, L., Larison, C., LeBaron, N., Moran, S., Rho, J., Salmaso, I., Schmidt, J., and Tinyanont, S.
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Astrophysics - High Energy Astrophysical Phenomena ,Astrophysics - Solar and Stellar Astrophysics - Abstract
We present JWST spectral and photometric observations of the Type IIP supernova (SN) 2022acko at ~50 days past explosion. These data are the first JWST spectral observations of a core-collapse SN. We identify ~30 different H I features, other features associated with products produced from the CNO cycle, and s-process elements such as Sc II and Ba II. By combining the JWST spectra with ground-based optical and NIR spectra, we construct a full Spectral Energy Distribution from 0.4 to 25 microns and find that the JWST spectra are fully consistent with the simultaneous JWST photometry. The data lack signatures of CO formation and we estimate a limit on the CO mass of < 10^{-8} solar mass. We demonstrate how the CO fundamental band limits can be used to probe underlying physics during stellar evolution, explosion, and the environment. The observations indicate little mixing between the H envelope and C/O core in the ejecta and show no evidence of dust. The data presented here set a critical baseline for future JWST observations, where possible molecular and dust formation may be seen.
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- 2024
23. Attenuation proxy hidden in surface brightness-colour diagrams. A new strategy for the LSST era
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Małek, K., Junais, Pollo, A., Boquien, M., Buat, V., Salim, S., Brough, S., Demarco, R., Graham, A. W., Hamed, M., Mullaney, J. R., Romano, M., Sifón, C., Aravena, M., Benavides, J. A., Busà, I., Donevski, D., Dorey, O., Hernandez-Toledo, H. M., Nanni, A., Pearson, W. J., Pistis, F., Ragusa, R., Riccio, G., and Román, J.
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Astrophysics - Astrophysics of Galaxies - Abstract
Large future sky surveys, such as the LSST, will provide optical photometry for billions of objects. This paper aims to construct a proxy for the far ultraviolet attenuation (AFUVp) from the optical data alone, enabling the rapid estimation of the star formation rate (SFR) for galaxies that lack UV or IR data. To mimic LSST observations, we use the deep panchromatic optical coverage of the SDSS Photometric Catalogue DR~12, complemented by the estimated physical properties for the SDSS galaxies from the GALEX-SDSS-WISE Legacy Catalog (GSWLC) and inclination information obtained from the SDSS DR7. We restricted our sample to the 0.025-0.1 z-spec range and investigated relations among surface brightness, colours, and dust attenuation in the far UV range for star-forming galaxies obtained from the spectral energy distribution (SED). {Dust attenuation is best correlated with (u-r) colour and the surface brightness in the u band ($\rm \mu_{u}$). We provide a dust attenuation proxy for galaxies on the star-forming main sequence, which can be used for the LSST or any other type of broadband optical survey. The mean ratio between the catalogue values of SFR and those estimated using optical-only SDSS data with the AFUVp prior calculated as $\Delta$SFR=log(SFR$_{\tiny{\mbox{this work}}}$/SFR$_{\tiny{}\texttt{GSWLC}}$) is found to be less than 0.1~dex, while runs without priors result in an SFR overestimation larger than 0.3~dex. The presence or absence of theAFUVp has a negligible influence on the stellar mass estimation (with $\Delta$M$_{star}$ in the range from 0 to $-0.15$ dex). Forthcoming deep optical observations of the LSST Deep Drilling Fields, which also have multi-wavelength data, will enable one to calibrate the obtained relation for higher redshift galaxies and, possibly, extend the study towards other types of galaxies, such as early-type galaxies off the main sequence., Comment: 18 pages, accepted for publication in Astronomy and Astrophysics
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- 2024
24. Grain Size Effects on UV-MIR (0.2-14 micron) Spectra of Carbonaceous Chondrite Groups
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Cantillo, David C., Reddy, Vishnu, Battle, Adam, Sharkey, Benjamin N. L., Pearson, Neil C., Campbell, Tanner, Satpathy, Akash, De Florio, Mario, Furfaro, Roberto, and Sanchez, Juan
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Astrophysics - Earth and Planetary Astrophysics ,Physics - Geophysics - Abstract
Carbonaceous chondrites are among the most important meteorite types and have played a vital role in deciphering the origin and evolution of our solar system. They have been linked to low-albedo C-type asteroids, but due to subdued absorption bands, definitive asteroid-meteorite linkages remain elusive. A majority of these existing linkages rely on fine-grained (typically < 45 micron) powders across a limited wavelength range in the visible to near-infrared (0.35-2.5 microns). While this is useful in interpreting the fine-grained regolith of larger main-belt objects like Ceres, recent spacecraft missions to smaller near-Earth asteroids (NEAs), such as Bennu and Ryugu, have shown that their surfaces are dominated by larger grain size material. To better interpret the surfaces of these smaller, carbonaceous NEAs, we obtained laboratory reflectance spectra of seven carbonaceous chondrite meteorite groups (CI, CM, CO, CV, CR, CK, C2-ungrouped) over the ultraviolet to mid-infrared range (0.2-14 microns). Each meteorite contained five grain size bins (45-1000 microns) to help constrain spectral grain size effects. We find a correlation between grain size and absolute reflectance, spectral slope, band depth, and the Christiansen feature band center. Principal component analysis of grain size variation illustrates a similar trend to lunar-style space weathering. We also show that the Bus-DeMeo asteroid taxonomic classification of our samples is affected by grain size, specifically shifting CM2 Aguas Zarcas from a Ch-type to B-type with increasing grain size. This has implications for the parent body of the OSIRIS-REx target, Bennu. With Aguas Zarcas, we present results from Hapke modeling., Comment: 40 pages, 15 figures, published in the Planetary Science Journal
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- 2024
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25. Hidden high ionization lines in the low luminosity type II SN 2021gmj
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Retamal, Nicolas Meza, Dong, Yize, Bostroem, K. Azalee, Valenti, Stefano, Galbany, Lluis, Pearson, Jeniveve, Hosseinzadeh, Griffin, Andrews, Jennifer E., Sand, David J., Jencson, Jacob E., Janzen, Daryl, Lundquist, Michael J., Hoang, Emily T., Wyatt, Samuel, Brown, Peter J., Howell, D. Andrew, Newsome, Megan, Gonzalez, Estefania Padilla, Pellegrino, Craig, Terreran, Giacomo, Kouprianov, Vladimir, Hiramatsu, Daichi, Jha, Saurabh W., Smith, Nathan, Haislip, Joshua, Reichart, Daniel E., Shrestha, Manisha, and Rosales-Ortega, F. Fabián
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Astrophysics - High Energy Astrophysical Phenomena - Abstract
We present comprehensive optical observations of SN~2021gmj, a type II supernova (SN~II) discovered within a day of explosion by the Distance Less Than 40~Mpc (DLT40) survey. Follow up observations show that SN~2021gmj is a low luminosity SN~II (LL~SN~II), with a peak magnitude $M_V = -15.45$ and Fe II velocity of $\sim 1800 \ \mathrm{km} \ \mathrm{s}^{-1}$ at 50 days past explosion. Using the expanding photosphere method we derive a distance of $17.8^{+0.6}_{-0.4}$~Mpc. From the tail of the light-curve we obtain a radioactive nickel mass of $0.014 \pm 0.001$ $\mathrm{M}_{\odot}$. The presence of circumstellar material (CSM) is suggested by the early light curve, early spectra and the presence of high velocity H$\alpha$ in absorption. Analytical shock-cooling models of the early light curve cannot reproduce the fast rise, also supporting the idea that the early emission is partially powered by the interaction of the SN ejecta and CSM. The inferred low CSM mass of 0.025 $\mathrm{M}_{\odot}$ in our hydrodynamic-modeling light curve analysis is also consistent with our spectroscopic observations. We observe a broad feature near 4600 A, which may be high ionization lines of C, N or/and He II. This feature is reproduced by radiation hydrodynamic simulations of red supergiants with extended atmospheres. Several LL~SNe~II show similar spectral features implying that high density material around the progenitor may be common among them., Comment: Submitted to ApJ
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- 2024
26. A comparative study of the fundamental metallicity relation: the impact of methodology on its observed evolution
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Pistis, F., Pollo, A., Figueira, M., Vergani, D., Hamed, M., Małek, K., Durkalec, A., Donevski, D., Salim, S., Iovino, A., Pearson, W. J., Romano, M., and Scodeggio, M.
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Astrophysics - Astrophysics of Galaxies - Abstract
We used 5487 star-forming galaxies at redshift z~0.63 extracted from the VIPERS and 143774 comparison galaxies in the local Universe from the GSWLC catalog. We employed two families of methods: parametric and non-parametric. In the former approaches, we compared the FMR projections plagued by observational biases on differently constructed control samples at various redshifts. Then, the metallicity difference between different redshifts in M*-SFR bins. In the latter approach, we related the metallicity and the normalized sSFR. The methodologies implemented to construct fair, complete samples for studying the MZR and the FMR produced consistent results showing a small, but still statistically significant evolution of both relations up to z~0.63. In particular, we observed a systematic trend where the median metallicity of the sample at z=0.63 is lower than that of the local sample at the same M* and SFR. The average difference in the metallicity of the low and intermediate redshifts is approximately 1.8 times the metallicity standard deviation of the median, of the intermediate redshift sample, in M*-SFR bins. We confirmed this result using the Kolmogorov-Smirnov test. When we applied the M*-completeness criterion to catalogs, the metallicity difference in redshifts decreased to approximately 0.96 times the metallicity standard deviation of the median, thus not statistically significant. This result may be dominated by the limited parameter space, being the lower M* galaxies where the difference is larger out from the analysis. A careful reading of the results, and their underlying selection criteria, are crucial in studies of the mass-metallicity and FMRs., Comment: Accepted for publication in A&A, 22 pages, 20 figures
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- 2023
27. A Preconditioned Interior Point Method for Support Vector Machines Using an ANOVA-Decomposition and NFFT-Based Matrix-Vector Products
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Wagner, Theresa, Pearson, John W., and Stoll, Martin
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Mathematics - Numerical Analysis ,Computer Science - Machine Learning ,Mathematics - Optimization and Control ,05C50, 65F08, 65F10, 65T50, 90C20 - Abstract
In this paper we consider the numerical solution to the soft-margin support vector machine optimization problem. This problem is typically solved using the SMO algorithm, given the high computational complexity of traditional optimization algorithms when dealing with large-scale kernel matrices. In this work, we propose employing an NFFT-accelerated matrix-vector product using an ANOVA decomposition for the feature space that is used within an interior point method for the overall optimization problem. As this method requires the solution of a linear system of saddle point form we suggest a preconditioning approach that is based on low-rank approximations of the kernel matrix together with a Krylov subspace solver. We compare the accuracy of the ANOVA-based kernel with the default LIBSVM implementation. We investigate the performance of the different preconditioners as well as the accuracy of the ANOVA kernel on several large-scale datasets., Comment: Official Code https://github.com/wagnertheresa/NFFTSVMipm
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- 2023
28. Achievement Level Description Review for the National Assessment of Educational Progress Grade 8 Science, U.S. History, and Civics Assessments
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National Assessment Governing Board, NCS Pearson, Inc., Moyer, Eric L., and Galindo, Jennifer
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The National Assessment Governing Board (the Board) contracted with Pearson to design and implement a review of the achievement level descriptions (ALDs) for National Assessment of Educational Progress (NAEP) Grade 8 assessments in Science, U.S. History, and Civics. This document describes the procedural and technical aspects and outcomes of the operational ALD Review study. This study commenced after Pearson had completed an ALD Review study for Mathematics and Reading in 2022, which itself was undertaken on behalf of the Board for the reasons noted in the Background section of this report. In particular, this report addresses the Board's updated achievement levels policy that called for the development of Reporting ALDs, which state what student performance associated with each NAEP achievement level likely can demonstrate related to the assessment content, and how these align with the existing content ALDs included in the frameworks and achievement level policy definitions. [For the 2022 report, "Achievement Level Description Review for the National Assessment of Educational Progress Mathematics and Reading Assessments. Final Process Documentation and Technical Report," see ED627620.]
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- 2023
29. Neighborhood-level characteristics as effect modifiers on the efficacy of the MyPEEPS mobile intervention in same-sex attracted adolescent men.
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Cordoba, Evette, Garofalo, Robert, Kuhns, Lisa, Pearson, Cynthia, Scott Batey, D, Janulis, Patrick, Jia, Haomiao, Bruce, Josh, Hidalgo, Marco, Hirshfield, Sabina, Radix, Asa, Belkind, Uri, Duncan, Dustin, Kim, Byoungjun, and Schnall, Rebecca
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Adolescent health ,Community health ,Gay/bisexual/transgender persons ,Geospatial epidemiology ,HIV prevention ,HIV/AIDS ,Mens health ,Young sexual minority men - Abstract
To estimate the effect of neighborhood-level modification on the efficacy of the MyPEEPS Mobile intervention on the reduction of condomless anal sex acts among same-sex attracted adolescent men. A series of generalized linear mixed model was used to examine if the effect of the MyPEEPS Mobile intervention on condomless anal sex acts was moderated by neighborhood-level factors using data from the 2019 American Community Survey US Census Bureau. The magnitudes of intervention were significantly smaller at both 6- and 9-month follow-up among adolescents living in neighborhood with high proportions of Hispanic or Latino residents (IRR6M = 1.02, 95 % CI: 1.01, 1.02; IRR9M = 1.03, 95 % CI: 1.01, 1.05) and high proportions of families with income below the poverty level (IRR6M = 1.07, 95 % CI: 1.01, 1.12; IRR9M = 1.05, 95 % CI: 1.01, 1.10), which indicated that living in communities with a higher concentration of residents living under poverty or of Hispanic/and Latino ethnicity significantly modified the effective of program intervention on condomless sex among adolescent MSM. Understanding how neighborhood characteristics modify the effect of HIV prevention interventions may be useful in better targeting delivery and tailoring content of interventions based on neighborhood level characteristics such as the ones identified in this study.
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- 2024
30. Foldy: An open-source web application for interactive protein structure analysis.
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Roberts, Jacob, Nava, Alberto, Pearson, Allison, Incha, Matthew, Valencia, Luis, Ma, Melody, Rao, Abhay, and Keasling, Jay
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Humans ,Software ,Proteins ,Amino Acids - Abstract
Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldys interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldys interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.
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- 2024
31. Characterization and Diversification of AraC/XylS Family Regulators Guided by Transposon Sequencing
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Pearson, Allison N, Incha, Matthew R, Ho, Cindy N, Schmidt, Matthias, Roberts, Jacob B, Nava, Alberto A, and Keasling, Jay D
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Biochemistry and Cell Biology ,Bioinformatics and Computational Biology ,Biological Sciences ,Genetics ,Escherichia coli ,Bacterial Proteins ,Promoter Regions ,Genetic ,Pseudomonas putida ,Plasmids ,Gene Expression Regulation ,Bacterial ,Escherichia coli Proteins ,AraC Transcription Factor ,Medicinal and Biomolecular Chemistry ,Biomedical Engineering ,Biochemistry and cell biology ,Bioinformatics and computational biology - Abstract
In this study, we explored the development of engineered inducible systems. Publicly available data from previous transposon sequencing assays were used to identify regulators of metabolism in Pseudomonas putida KT2440. For AraC family regulators (AFRs) represented in these data, we posited AFR/promoter/inducer groupings. Twelve promoters were characterized for a response to their proposed inducers in P. putida, and the resultant data were used to create and test nine two-plasmid sensor systems in Escherichia coli. Several of these were further developed into a palette of single-plasmid inducible systems. From these experiments, we observed an unreported inducer response from a previously characterized AFR, demonstrated that the addition of a P. putida transporter improved the sensor dynamics of an AFR in E. coli, and identified an uncharacterized AFR with a novel potential inducer specificity. Finally, targeted mutations in an AFR, informed by structural predictions, enabled the further diversification of these inducible plasmids.
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- 2024
32. The selection landscape and genetic legacy of ancient Eurasians
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Irving-Pease, Evan K, Refoyo-Martínez, Alba, Barrie, William, Ingason, Andrés, Pearson, Alice, Fischer, Anders, Sjögren, Karl-Göran, Halgren, Alma S, Macleod, Ruairidh, Demeter, Fabrice, Henriksen, Rasmus A, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew H, Speidel, Leo, Stern, Aaron J, Scorrano, Gabriele, Ramsøe, Abigail, Schork, Andrew J, Rosengren, Anders, Zhao, Lei, Kristiansen, Kristian, Iversen, Astrid KN, Fugger, Lars, Sudmant, Peter H, Lawson, Daniel J, Durbin, Richard, Korneliussen, Thorfinn, Werge, Thomas, Allentoft, Morten E, Sikora, Martin, Nielsen, Rasmus, Racimo, Fernando, and Willerslev, Eske
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Biological Sciences ,Genetics ,History ,Heritage and Archaeology ,Human Society ,Archaeology ,Historical Studies ,Anthropology ,Good Health and Well Being ,Humans ,Alzheimer Disease ,Affect ,Alleles ,Agriculture ,Europe ,General Science & Technology - Abstract
The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.
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- 2024
33. Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations
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Barrie, William, Yang, Yaoling, Irving-Pease, Evan K, Attfield, Kathrine E, Scorrano, Gabriele, Jensen, Lise Torp, Armen, Angelos P, Dimopoulos, Evangelos Antonios, Stern, Aaron, Refoyo-Martinez, Alba, Pearson, Alice, Ramsøe, Abigail, Gaunitz, Charleen, Demeter, Fabrice, Jørkov, Marie Louise S, Møller, Stig Bermann, Springborg, Bente, Klassen, Lutz, Hyldgård, Inger Marie, Wickmann, Niels, Vinner, Lasse, Korneliussen, Thorfinn Sand, Allentoft, Morten E, Sikora, Martin, Kristiansen, Kristian, Rodriguez, Santiago, Nielsen, Rasmus, Iversen, Astrid KN, Lawson, Daniel J, Fugger, Lars, and Willerslev, Eske
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Biological Sciences ,Genetics ,History ,Heritage and Archaeology ,Archaeology ,Historical Studies ,Neurosciences ,Autoimmune Disease ,Multiple Sclerosis ,Brain Disorders ,Neurodegenerative ,Human Genome ,Aetiology ,2.1 Biological and endogenous factors ,Inflammatory and immune system ,Neurological ,Humans ,Neurodegenerative Diseases ,Cluster Analysis ,Population Density ,Child ,Preschool ,Europe ,General Science & Technology - Abstract
Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated1. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age2, along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment.
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- 2024
34. 100 ancient genomes show repeated population turnovers in Neolithic Denmark
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Allentoft, Morten E, Sikora, Martin, Fischer, Anders, Sjögren, Karl-Göran, Ingason, Andrés, Macleod, Ruairidh, Rosengren, Anders, Schulz Paulsson, Bettina, Jørkov, Marie Louise Schjellerup, Novosolov, Maria, Stenderup, Jesper, Price, T Douglas, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Sørensen, Lasse, Nielsen, Poul Otto, Rasmussen, Peter, Jensen, Theis Zetner Trolle, Refoyo-Martínez, Alba, Irving-Pease, Evan K, Barrie, William, Pearson, Alice, Sousa da Mota, Bárbara, Demeter, Fabrice, Henriksen, Rasmus A, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Johannsen, Niels Nørkjær, Ramsøe, Abigail Daisy, Schork, Andrew Joseph, Ruter, Anthony, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, Brinch Petersen, Erik, Kannegaard, Esben, Hansen, Jesper, Buck Pedersen, Kristoffer, Pedersen, Lisbeth, Klassen, Lutz, Meldgaard, Morten, Johansen, Morten, Uldum, Otto Christian, Lotz, Per, Lysdahl, Per, Bangsgaard, Pernille, Petersen, Peter Vang, Maring, Rikke, Iversen, Rune, Wåhlin, Sidsel, Anker Sørensen, Søren, Andersen, Søren H, Jørgensen, Thomas, Lynnerup, Niels, Lawson, Daniel J, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Kjær, Kurt H, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Kristiansen, Kristian, and Willerslev, Eske
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Biological Sciences ,Genetics ,History ,Heritage and Archaeology ,Human Society ,Archaeology ,Historical Studies ,Anthropology ,Humans ,Genomics ,Genotype ,Denmark ,Emigrants and Immigrants ,Scandinavians and Nordic People ,General Science & Technology - Abstract
Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.
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- 2024
35. Population genomics of post-glacial western Eurasia
- Author
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Allentoft, Morten E, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise Schjellerup, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis Zetner Trolle, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V, Cuenca-Solana, David, Lordkipanidze, David O, En’shin, Dmitri, Salazar-García, Domingo C, Price, T Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V, Usmanova, Emma R, Cappellini, Enrico, Brinch Petersen, Erik, Kannegaard, Esben, Radina, Francesca, Eylem Yediay, Fulya, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N, Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, and Silvestrini, Mara
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Biological Sciences ,Genetics ,History ,Heritage and Archaeology ,Human Society ,Historical Studies ,Anthropology ,Biotechnology ,Humans ,Genomics ,Diploidy ,Agriculture ,Europe ,Metagenomics ,General Science & Technology - Abstract
Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
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- 2024
36. Development of Corynebacterium glutamicum as a monoterpene production platform
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Luckie, Bridget A, Kashyap, Meera, Pearson, Allison N, Chen, Yan, Liu, Yuzhong, Valencia, Luis E, Carrillo Romero, Alexander, Hudson, Graham A, Tao, Xavier B, Wu, Bryan, Petzold, Christopher J, and Keasling, Jay D
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Biological Sciences ,Industrial Biotechnology ,Monoterpenes ,Corynebacterium glutamicum ,Mevalonic Acid ,Terpenes ,Metabolic Engineering ,Monoterpene biosynthetic production ,Geraniol ,Citronellol ,Eucalyptol ,Linalool ,Citral ,Citronellic acid ,Biotechnology ,Biochemistry and cell biology ,Industrial biotechnology - Abstract
Monoterpenes are commonly known for their role in the flavors and fragrances industry and are also gaining attention for other uses like insect repellant and as potential renewable fuels for aviation. Corynebacterium glutamicum, a Generally Recognized as Safe microbe, has been a choice organism in industry for the annual million ton-scale bioproduction of amino acids for more than 50 years; however, efforts to produce monoterpenes in C. glutamicum have remained relatively limited. In this study, we report a further expansion of the C. glutamicum biosynthetic repertoire through the development and optimization of a mevalonate-based monoterpene platform. In the course of our plasmid design iterations, we increased flux through the mevalonate-based bypass pathway, measuring isoprenol production as a proxy for monoterpene precursor abundance and demonstrating the highest reported titers in C. glutamicum to date at 1504.6 mg/L. Our designs also evaluated the effects of backbone, promoter, and GPP synthase homolog origin on monoterpene product titers. Monoterpene production was further improved by disrupting competing pathways for isoprenoid precursor supply and by implementing a biphasic production system to prevent volatilization. With this platform, we achieved 321.1 mg/L of geranoids, 723.6 mg/L of 1,8-cineole, and 227.8 mg/L of linalool. Furthermore, we determined that C. glutamicum first oxidizes geraniol through an aldehyde intermediate before it is asymmetrically reduced to citronellol. Additionally, we demonstrate that the aldehyde reductase, AdhC, possesses additional substrate promiscuity for acyclic monoterpene aldehydes.
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- 2024
37. Hypoxemic Respiratory Failure and Coccidioidomycosis-Associated Acute Respiratory Distress Syndrome
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Heidari, Arash, Kaur, Simmer, Pearson, Skyler J, Munoz, Augustine, Sandhu, Harleen, Mann, Gursimran, Schivo, Michael, Zeki, Amir A, Bays, Derek J, Wilson, Machelle, Albertson, Timothy E, Johnson, Royce, and Thompson, George R
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Biomedical and Clinical Sciences ,Clinical Sciences ,Infectious Diseases ,Clinical Research ,Rare Diseases ,Lung ,Acute Respiratory Distress Syndrome ,Prevention ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Respiratory ,Good Health and Well Being ,ARDS ,Coccidioides ,fungal pneumonia ,glucocorticoids ,steroids ,Clinical sciences ,Medical microbiology - Abstract
BackgroundSevere coccidioidomycosis presenting with respiratory failure is an uncommon manifestation of disease. Current knowledge of this condition is limited to case reports and small case series.MethodsA retrospective multicenter review of patients with coccidioidomycosis-associated acute respiratory distress syndrome (CA-ARDS) was conducted. It assessed clinical and laboratory variables at the time of presentation, reviewed the treatment course, and compared this cohort with a national database of patients with noncoccidioidomycosis ARDS. Survivors and nonsurvivors of coccidioidomycosis were also compared to determine prognostic factors.ResultsIn this study, CA-ARDS (n = 54) was most common in males, those of Hispanic ethnicity, and those with concurrent diabetes mellitus. As compared with the PETAL network database (Prevention and Early Treatment of Acute Lung Injury; n = 1006), patients with coccidioidomycosis were younger, had fewer comorbid conditions, and were less acidemic. The 90-day mortality was 15.4% for patients with coccidioidomycosis, as opposed to 42.6% (P < .0001) for patients with noncoccidioidomycosis ARDS. Patients with coccidioidomycosis who died, as compared with those who survived, were older, had higher APACHE II scores (Acute Physiology and Chronic Health Evaluation), and did not receive corticosteroid therapy.ConclusionsCA-ARDS is an uncommon but morbid manifestation of infection. When compared with a national database, the overall mortality appears favorable vs other causes of ARDS. Patients with CA-ARDS had a low overall mortality but required prolonged antifungal therapy. The utility of corticosteroids in this condition remains unconfirmed.
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- 2024
38. Systemic advantage has a meaningful relationship with grade outcomes in students early STEM courses at six research universities.
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Castle, Sarah, Byrd, W, Koester, Benjamin, Pearson, Meaghan, Bonem, Emily, Caporale, Natalia, Cwik, Sonja, Fiorini, Stefano, Li, Yangqiuting, Mead, Chris, Rypkema, Heather, Sweeder, Ryan, Valdivia Medinaceli, Montserrat, Whitcomb, Kyle, Brownell, Sara, Levesque-Bristol, Chantal, Molinaro, Marco, Singh, Chandralekha, McKay, Timothy, Matz, Rebecca, and Denaro, Kameryn
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Course grades ,Generation status ,Grade anomaly ,Income ,Introductory courses ,Race/ethnicity ,STEM ,Sex ,Systemic advantage index ,Undergraduate - Abstract
BACKGROUND: Large introductory lecture courses are frequently post-secondary students first formal interaction with science, technology, engineering, and mathematics (STEM) disciplines. Grade outcomes in these courses are often disparate across student populations, which, in turn, has implications for student retention. This study positions such disparities as a manifestation of systemic inequities along the dimensions of sex, race/ethnicity, income, and first-generation status and investigates the extent to which they are similar across peer institutions. RESULTS: We examined grade outcomes in a selected set of early STEM courses across six large, public, research-intensive universities in the United States over ten years. In this sample of more than 200,000 STEM course enrollments, we find that course grade benefits increase significantly with the number of systemic advantages students possess at all six institutions. The observed trends in academic outcomes versus advantage are strikingly similar across universities despite the fact that we did not control for differences in grading practices, contexts, and instructor and student populations. The findings are concerning given that these courses are often students first post-secondary STEM experiences. CONCLUSIONS: STEM course grades are typically lower than those in other disciplines; students taking them often pay grade penalties. The systemic advantages some student groups experience are correlated with significant reductions in these grade penalties at all six institutions. The consistency of these findings across institutions and courses supports the claim that inequities in STEM education are a systemic problem, driven by factors that go beyond specific courses or individual institutions. Our work provides a basis for the exploration of contexts where inequities are exacerbated or reduced and can be used to advocate for structural change within STEM education. To cultivate more equitable learning environments, we must reckon with how pervasive structural barriers in STEM courses negatively shape the experiences of marginalized students. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40594-024-00474-7.
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- 2024
39. The Science of Precision Prevention: Research Opportunities and Clinical Applications to Reduce Cardiovascular Health Disparities.
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Pearson, Thomas, Vitalis, Debbie, Pratt, Charlotte, Campo, Rebecca, Armoundas, Antonis, Au, David, Beech, Bettina, Brazhnik, Olga, Chute, Christopher, Davidson, Karina, Diez-Roux, Ana, Fine, Lawrence, Gabriel, Davera, Groenveld, Peter, Hall, Jaclyn, Hamilton, Alison, Hu, Hui, Ji, Heng, Kind, Amy, Kraus, William, Krumholz, Harlan, Mensah, George, Merchant, Raina, Mozaffarian, Dariush, Murray, David, Neumark-Sztainer, Dianne, Goff, David, and Petersen, Maya
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data science ,health equity ,health promotion ,implementation science ,personalized medicine ,precision analytics - Abstract
Precision prevention embraces personalized prevention but includes broader factors such as social determinants of health to improve cardiovascular health. The quality, quantity, precision, and diversity of data relatable to individuals and communities continue to expand. New analytical methods can be applied to these data to create tools to attribute risk, which may allow a better understanding of cardiovascular health disparities. Interventions using these analytic tools should be evaluated to establish feasibility and efficacy for addressing cardiovascular disease disparities in diverse individuals and communities. Training in these approaches is important to create the next generation of scientists and practitioners in precision prevention. This state-of-the-art review is based on a workshop convened to identify current gaps in knowledge and methods used in precision prevention intervention research, discuss opportunities to expand trials of implementation science to close the health equity gaps, and expand the education and training of a diverse precision prevention workforce.
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- 2024
40. Longitudinal analysis of physical function in older adults: The effects of physical inactivity and exercise training.
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Manning, Kenneth, Hall, Katherine, Sloane, Richard, Magistro, Daniele, Rabaglietti, Emanuela, Castle, Steven, Kopp, Teresa, Giffuni, Jamie, Katzel, Leslie, McDonald, Michelle, Miyamoto, Miles, Pearson, Megan, Jennings, Stephen, Bettger, Janet, Morey, Miriam, and Lee, Cathy
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clinical ,cohort ,physical activity ,physical performance ,sedentary ,Humans ,Aged ,Aged ,80 and over ,Sedentary Behavior ,Exercise ,Aging - Abstract
Lack of exercise contributes to systemic inflammation and is a major cause of chronic disease. The long-term impact of initiating and sustaining exercise in late life, as opposed to sustaining a sedentary lifestyle, on whole-body health measures such as physical performance is not well known. This is an exploratory study to compare changes in physical performance among older adults initiating exercise late in life versus inactive older adults. Data from two observational cohorts were included in this analysis, representing two activity groups. The Active group cohort comprises older adults (n = 318; age 72.5 ± 7.2 years) enrolled in a supervised exercise program, Gerofit. The inactive group comprises older adults (n = 146; age 74.5 ± 5.5 years) from the Italian study Act on Ageing (AOA) who self-reported being inactive. Participants in both groups completed physical performance battery at baseline and 1-year including: 6-min walk test, 30-s chair stand, and timed up-and-go. Two-sample t-tests measured differences between Gerofit and AOA at baseline and 1-year across all measures. Significant between-group effects were seen for all performance measures (ps = 0.001). The AOA group declined across all measures from baseline to 1 year (range -18% to -24% change). The Gerofit group experienced significant gains in function for all measures (range +10% to +31% change). Older adults who initiated routine, sustained exercise were protected from age-related declines in physical performance, while those who remained sedentary suffered cumulative deficits across strength, aerobic endurance, and mobility. Interventions to reduce sedentary behaviors and increase physical activity are both important to promote multi-system, whole-body health.
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- 2024
41. A multifunctional Wnt regulator underlies the evolution of rodent stripe patterns.
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Johnson, Matthew, Li, Sha, Guerrero-Juarez, Christian, Miller, Pearson, Brack, Benjamin, Mereby, Sarah, Moreno, Jorge, Feigin, Charles, Gaska, Jenna, Rivera-Perez, Jaime, Ploss, Alexander, Shvartsman, Stanislav, Mallarino, Ricardo, and Nie, Qing
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Mice ,Animals ,Rodentia ,Reproducibility of Results ,Pigmentation - Abstract
Animal pigment patterns are excellent models to elucidate mechanisms of biological organization. Although theoretical simulations, such as Turing reaction-diffusion systems, recapitulate many animal patterns, they are insufficient to account for those showing a high degree of spatial organization and reproducibility. Here, we study the coat of the African striped mouse (Rhabdomys pumilio) to uncover how periodic stripes form. Combining transcriptomics, mathematical modelling and mouse transgenics, we show that the Wnt modulator Sfrp2 regulates the distribution of hair follicles and establishes an embryonic prepattern that foreshadows pigment stripes. Moreover, by developing in vivo gene editing in striped mice, we find that Sfrp2 knockout is sufficient to alter the stripe pattern. Strikingly, mutants exhibited changes in pigmentation, revealing that Sfrp2 also regulates hair colour. Lastly, through evolutionary analyses, we find that striped mice have evolved lineage-specific changes in regulatory elements surrounding Sfrp2, many of which may be implicated in modulating the expression of this gene. Altogether, our results show that a single factor controls coat pattern formation by acting both as an orienting signalling mechanism and a modulator of pigmentation. More broadly, our work provides insights into how spatial patterns are established in developing embryos and the mechanisms by which phenotypic novelty originates.
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- 2023
42. Large-area photon calorimeter with Ir-Pt bilayer transition-edge sensor for the CUPID experiment
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Singh, V, Beretta, M, Hansen, EV, Vetter, KJ, Benato, G, Marini, L, Capelli, C, Fujikawa, BK, Schmidt, B, Chang, CL, Kolomensky, Yu G, Welliver, B, Kwok, WK, Pearson, J, Welp, U, Lisovenko, M, Wang, G, Yefremenko, V, Zhang, J, and Novosad, V
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Nuclear and Plasma Physics ,Particle and High Energy Physics ,Physical Sciences ,Engineering ,Physical sciences - Abstract
CUPID is a next-generation neutrinoless double-β decay experiment that will require cryogenic light detectors to improve background suppression, via the simultaneous readout of heat and light channels from its scintillating crystals. In this work, we showcase light detectors based on an alternative Ir-Pt bilayer transition-edge sensor. We have performed a systematic study to improve the thermal coupling between the photon absorber and the sensor, and thereby its responsivity. Our first devices meet CUPID's baseline noise requirement of
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- 2023
43. Effects of a clinic-based reproductive empowerment intervention on proximal outcomes of contraceptive use, self-efficacy, attitudes, and awareness and use of survivor services: a cluster-controlled trial in Nairobi, Kenya.
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Uysal, Jasmine, Boyce, Sabrina, Undie, Chi-Chi, Liambila, Wilson, Wendoh, Seri, Pearson, Erin, Johns, Nicole, and Silverman, Jay
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contraceptives ,family planning ,intervention ,intimate partner violence ,reproductive coercion ,Female ,Humans ,Contraceptive Agents ,Kenya ,Self Efficacy ,Family Planning Services ,Attitude - Abstract
This study was undertaken to evaluate the effect of a reproductive empowerment contraceptive counselling intervention (ARCHES) adapted to private clinics in Nairobi, Kenya on proximal outcomes of contraceptive use and covert use, self-efficacy, awareness and use of intimate partner violence (IPV) survivor services, and attitudes justifying reproductive coercion (RC) and IPV. We conducted a cluster-controlled trial among female family planning patients (N = 659) in six private clinics non-randomly assigned to ARCHES or control in and around Nairobi, Kenya. Patients completed interviews immediately before (baseline) and after (exit) treatment and at three- and six-month follow-up. We use inverse probability by treatment weighting (IPTW) applied to difference-in-differences marginal structural models to estimate the treatment effect using a modified intent-to-treat approach. After IPTW, women receiving ARCHES contraceptive counselling, relative to controls, were more likely to receive a contraceptive method at exit (86% vs. 75%, p
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- 2023
44. Mapping 'Brain Coral' Regions on Mars using Deep Learning
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Pearson, Kyle A., Noe, Eldar, Zhao, Daniel, Altinok, Alphan, and Morgan, Alex
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics ,Computer Science - Machine Learning ,Electrical Engineering and Systems Science - Image and Video Processing - Abstract
One of the main objectives of the Mars Exploration Program is to search for evidence of past or current life on the planet. To achieve this, Mars exploration has been focusing on regions that may have liquid or frozen water. A set of critical areas may have seen cycles of ice thawing in the relatively recent past in response to periodic changes in the obliquity of Mars. In this work, we use convolutional neural networks to detect surface regions containing "Brain Coral" terrain, a landform on Mars whose similarity in morphology and scale to sorted stone circles on Earth suggests that it may have formed as a consequence of freeze/thaw cycles. We use large images (~100-1000 megapixels) from the Mars Reconnaissance Orbiter to search for these landforms at resolutions close to a few tens of centimeters per pixel (~25--50 cm). Over 52,000 images (~28 TB) were searched (~5% of the Martian surface) where we found detections in over 200 images. To expedite the processing we leverage a classifier network (prior to segmentation) in the Fourier domain that can take advantage of JPEG compression by leveraging blocks of coefficients from a discrete cosine transform in lieu of decoding the entire image at the full spatial resolution. The hybrid pipeline approach maintains ~93% accuracy while cutting down on ~95% of the total processing time compared to running the segmentation network at the full resolution on every image. The timely processing of big data sets helps inform mission operations, geologic surveys to prioritize candidate landing sites, avoid hazardous areas, or map the spatial extent of certain terrain. The segmentation masks and source code are available on Github for the community to explore and build upon., Comment: Submitted for publication, seeking comments from the community. Code available: https://github.com/pearsonkyle/Mars-Brain-Coral-Network
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- 2023
45. A Foundation Model for Cell Segmentation
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Israel, Uriah, Marks, Markus, Dilip, Rohit, Li, Qilin, Schwartz, Morgan, Pradhan, Elora, Pao, Edward, Li, Shenyi, Pearson-Goulart, Alexander, Perona, Pietro, Gkioxari, Georgia, Barnowski, Ross, Yue, Yisong, and Van Valen, David
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Quantitative Biology - Quantitative Methods - Abstract
Cells are the fundamental unit of biological organization, and identifying them in imaging data - cell segmentation - is a critical task for various cellular imaging experiments. While deep learning methods have led to substantial progress on this problem, models that have seen wide use are specialist models that work well for specific domains. Methods that have learned the general notion of "what is a cell" and can identify them across different domains of cellular imaging data have proven elusive. In this work, we present CellSAM, a foundation model for cell segmentation that generalizes across diverse cellular imaging data. CellSAM builds on top of the Segment Anything Model (SAM) by developing a prompt engineering approach to mask generation. We train an object detector, CellFinder, to automatically detect cells and prompt SAM to generate segmentations. We show that this approach allows a single model to achieve state-of-the-art performance for segmenting images of mammalian cells (in tissues and cell culture), yeast, and bacteria collected with various imaging modalities. To enable accessibility, we integrate CellSAM into DeepCell Label to further accelerate human-in-the-loop labeling strategies for cellular imaging data. A deployed version of CellSAM is available at https://label-dev.deepcell.org/.
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- 2023
46. SN 2022jox: An extraordinarily ordinary Type II SN with Flash Spectroscopy
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Andrews, Jennifer E., Pearson, Jeniveve, Hosseinzadeh, Griffin, Bostroem, K. Azalee, Dong, Yize, Shrestha, Manisha, Jencson, Jacob E., Sand, David J., Valenti, S., Hoang, Emily, Janzen, Daryl, Lundquist, M. J., Meza, Nicolas, Wyatt, Samuel, Jha, Saurabh W., Simpson, Chris, Farah, Joseph, Gonzalez, Estefania Padilla, Howell, D. Andrew, McCully, Curtis, Newsome, Megan, Pellegrino, Craig, and Terreran, Giacomo
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Astrophysics - High Energy Astrophysical Phenomena ,Astrophysics - Solar and Stellar Astrophysics - Abstract
We present high cadence optical and ultraviolet observations of the Type II supernova (SN), SN 2022jox which exhibits early spectroscopic high ionization flash features of \ion{H}{1}, \ion{He}{2}, \ion{C}{4}, and \ion{N}{4} that disappear within the first few days after explosion. SN 2022jox was discovered by the Distance Less than 40 Mpc (DLT40) survey $\sim$0.75 days after explosion with followup spectra and UV photometry obtained within minutes of discovery. The SN reached a peak brightness of M$_V \sim$ $-$17.3 mag, and has an estimated $^{56}$Ni mass of 0.04 M$_{\odot}$, typical values for normal Type II SNe. The modeling of the early lightcurve and the strong flash signatures present in the optical spectra indicate interaction with circumstellar material (CSM) created from a progenitor with a mass loss rate of $\dot{M} \sim 10^{-3}-10^{-2}\ M_\odot\ \mathrm{yr}^{-1}$. There may also be some indication of late-time CSM interaction in the form of an emission line blueward of H$\alpha$ seen in spectra around 200 days. The mass-loss rate is much higher than the values typically associated with quiescent mass loss from red supergiants, the known progenitors of Type II SNe, but is comparable to inferred values from similar core collapse SNe with flash features, suggesting an eruptive event or a superwind in the progenitor in the months or years before explosion., Comment: ApJ, accepted 2024 Feb 14
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- 2023
47. A Numerical Optimisation Framework for Parameter Identification of the SIRD Model
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Miniguano-Trujillo, Andrés, Pearson, John W., and Goddard, Benjamin D.
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Mathematics - Optimization and Control - Abstract
We consider a numerical framework tailored to identifying optimal parameters in the context of modelling disease propagation. Our focus is on understanding the behaviour of optimisation algorithms for such problems, where the dynamics are described by a system of ordinary differential equations associated with the epidemiological SIRD model. We examine properties of the solution operator and determine existence of optimal parameters for the problem considered. Further, first-order optimality conditions are derived, the solution of which provides a certificate of goodness of fit, which is not always guaranteed with parameter tuning techniques. We then propose strategies for the numerical solution of such problems, based on projected gradient descent, Fast Iterative Shrinkage-Thresholding Algorithm (FISTA), and limited memory BFGS trust region approaches. We carry out a thorough computational study for a range of problems of interest, determining the relative performance of these numerical methods. Our results provide insights into the efficacy of these strategies, contributing to ongoing research into optimising parameters for accurate and reliable disease spread modelling. Moreover, our approach paves the way for calibration of more intricate compartmental models., Comment: 26 pages, 7 figures, 3 tables
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- 2023
48. JWST MIRI/MRS Observations and Spectral Models of the Under-luminous Type Ia Supernova 2022xkq
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DerKacy, J. M., Ashall, C., Hoeflich, P., Baron, E., Shahbandeh, M., Shappee, B. J., Andrews, J., Baade, D., Balangan, E. F, Bostroem, K. A., Brown, P. J., Burns, C. R., Burrow, A., Cikota, A., de Jaeger, T., Do, A., Dong, Y., Dominguez, I., Fox, O., Galbany, L., Hoang, E. T., Hsiao, E. Y., Janzen, D., Jencson, J. E., Krisciunas, K., Kumar, S., Lu, J., Lundquist, M., Evans, T. B. Mera, Maund, J. R., Mazzali, P., Medler, K., Retamal, N. E. Meza, Morrell, N., Patat, F., Pearson, J., Phillips, M. M., Shrestha, M., Stangl, S., Stevens, C. P., Stritzinger, M. D., Suntzeff, N. B., Telesco, C. M., Tucker, M. A., Valenti, S., Wang, L., and Yang, Y.
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Astrophysics - High Energy Astrophysical Phenomena ,Astrophysics - Solar and Stellar Astrophysics - Abstract
We present a JWST mid-infrared spectrum of the under-luminous Type Ia Supernova (SN Ia) 2022xkq, obtained with the medium-resolution spectrometer on the Mid-Infrared Instrument (MIRI) $\sim130$ days post-explosion. We identify the first MIR lines beyond 14 $\mu$m in SN Ia observations. We find features unique to under-luminous SNe Ia, including: isolated emission of stable Ni, strong blends of [Ti II], and large ratios of singly ionized to doubly ionized species in both [Ar] and [Co]. Comparisons to normal-luminosity SNe Ia spectra at similar phases show a tentative trend between the width of the [Co III] 11.888 $\mu$m feature and the SN light curve shape. Using non-LTE-multi-dimensional radiation hydro simulations and the observed electron capture elements we constrain the mass of the exploding white dwarf. The best-fitting model shows that SN 2022xkq is consistent with an off-center delayed-detonation explosion of a near-Chandrasekhar mass WD (M$_{\rm ej}$ $\approx 1.37$ M$_{\odot}$) of high-central density ($\rho_c \geq 2.0\times10^{9}$ g cm$^{-3}$) seen equator on, which produced M($^{56}$Ni) $= 0.324$ M$_{\odot}$ and M($^{58}$Ni) $\geq 0.06$ M$_{\odot}$. The observed line widths are consistent with the overall abundance distribution; and the narrow stable Ni lines indicate little to no mixing in the central regions, favoring central ignition of sub-sonic carbon burning followed by an off-center DDT beginning at a single point. Additional observations may further constrain the physics revealing the presence of additional species including Cr and Mn. Our work demonstrates the power of using the full coverage of MIRI in combination with detailed modeling to elucidate the physics of SNe Ia at a level not previously possible., Comment: 31 pages, 18 figures, accepted to ApJ; updated to accepted version
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- 2023
49. Design and Performance of Parallel-channel Nanocryotrons in Magnetic Fields
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Draher, Timothy, Polakovic, Tomas, Li, Yi, Pearson, John, Dibos, Alan, Meziani, Zein-Eddine, Xiao, Zhili, and Novosad, Valentine
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Condensed Matter - Superconductivity ,Physics - Applied Physics - Abstract
We introduce a design modification to conventional geometry of the cryogenic three-terminal switch, the nanocryotron (nTron). The conventional geometry of nTrons is modified by including parallel current-carrying channels, an approach aimed at enhancing the device's performance in magnetic field environments. The common challenge in nTron technology is to maintain efficient operation under varying magnetic field conditions. Here we show that the adaptation of parallel channel configurations leads to an enhanced gate signal sensitivity, an increase in operational gain, and a reduction in the impact of superconducting vortices on nTron operation within magnetic fields up to 1 Tesla. Contrary to traditional designs that are constrained by their effective channel width, the parallel nanowire channels permits larger nTron cross sections, further bolstering the device's magnetic field resilience while improving electro-thermal recovery times due to reduced local inductance. This advancement in nTron design not only augments its functionality in magnetic fields but also broadens its applicability in technological environments, offering a simple design alternative to existing nTron devices., Comment: 6 pages, 5 figures. Accepted by Applied Physics Letters. Supplemental information includes additional supporting figures and tables
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- 2023
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50. A JWST survey of the Trapezium Cluster & inner Orion Nebula. I. Observations & overview
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McCaughrean, M. J. and Pearson, S. G.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Astrophysics of Galaxies - Abstract
We present a near-IR survey of the Trapezium Cluster and inner Orion Nebula using the NASA/ESA/CSA James Webb Space Telescope. The survey with the NIRCam instrument covers 10.9 x 7.5 arcminutes (~1.25 x 0.85 pc) in twelve wide-, medium-, and narrow-band filters from 1-5 microns and is diffraction-limited at all wavelengths, providing a maximum spatial resolution of 0.063 arcsec at 2 microns, corresponding to ~25 au at Orion. The suite of filters chosen was designed to address a number of scientific questions including the form of the extreme low-mass end of the IMF into the planetary-mass range to 1 Jupiter mass and below; the nature of ionised and non-ionised circumstellar disks and associated proplyds in the near-IR with a similar resolution to prior HST studies; to examine the large fragmented outflow from the embedded BN-KL region at very high resolution and fidelity; and to search for new jets and outflows from young stars in the Trapezium Cluster and the Orion Molecular Cloud 1 behind. In this paper, we present a description of the design of the observational programme, explaining the rationale for the filter set chosen and the telescope and detector modes used to make the survey; the reduction of the data using the JWST pipeline and other tools; the creation of large colour mosaics covering the region; and an overview of the discoveries made in the colour images and in the individual filter mosaics. Highlights include the discovery of large numbers of free-floating planetary-mass candidates as low as 0.6 Jupiter masses, a significant fraction of which are in wide binaries; new emission phenomena associated with the explosive outflow from the BN-KL region; and a mysterious "dark absorber" associated with a number of disparate features in the region, but which is seen exclusively in the F115W filter. Further papers will examine those discoveries and others in more detail., Comment: 39 pages, 18 figures, 1 table
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- 2023
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