1,541 results on '"Borowski P"'
Search Results
2. Enhancing cognitive performance prediction by white matter hyperintensity connectivity assessment
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Petersen, Marvin, Coenen, Mirthe, DeCarli, Charles, De Luca, Alberto, van der Lelij, Ewoud, Weiner, Michael, Aisen, Paul, Petersen, Ronald, Jack, Clifford R, Jagust, William, Landau, Susan, Rivera-Mindt, Monica, Okonkwo, Ozioma, Shaw, Leslie M, Lee, Edward B, Toga, Arthur W, Beckett, Laurel, Harvey, Danielle, Green, Robert C, Saykin, Andrew J, Nho, Kwangsik, Perrin, Richard J, Tosun, Duygu, Sachdev, Pallavi, Drake, Erin, Montine, Tom, Conti, Cat, Weiner, Michael W, Nosheny, Rachel, Sacrey, Diana Truran, Fockler, Juliet, Miller, Melanie J, Conti, Catherine, Kwang, Winnie, Jin, Chengshi, Diaz, Adam, Ashford, Miriam, Flenniken, Derek, Rafii, Michael, Raman, Rema, Jimenez, Gustavo, Donohue, Michael, Salazar, Jennifer, Fidell, Andrea, Boatwright, Virginia, Robison, Justin, Zimmerman, Caileigh, Cabrera, Yuliana, Walter, Sarah, Clanton, Taylor, Shaffer, Elizabeth, Webb, Caitlin, Hergesheimer, Lindsey, Smith, Stephanie, Ogwang, Sheila, Adegoke, Olusegun, Mahboubi, Payam, Pizzola, Jeremy, Jenkins, Cecily, Saito, Naomi, Hussen, Kedir Adem, Amaza, Hannatu, Thao, Mai Seng, Parkins, Shaniya, Ayo, Omobolanle, Glittenberg, Matt, Hoang, Isabella, Germano, Kaori Kubo, Strong, Joe, Weisensel, Trinity, Magana, Fabiola, Thomas, Lisa, Guzman, Vanessa, Ajayi, Adeyinka, Benedetto, Joseph Di, Talavera, Sandra, Felmlee, Joel, Fox, Nick C, Thompson, Paul, Forghanian-Arani, Arvin, Borowski, Bret, Reyes, Calvin, Hedberg, Caitie, Ward, Chad, Schwarz, Christopher, and Reyes, Denise
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Biological Psychology ,Psychology ,Dementia ,Alzheimer's Disease Related Dementias (ADRD) ,Clinical Research ,Vascular Cognitive Impairment/Dementia ,Acquired Cognitive Impairment ,Behavioral and Social Science ,Neurodegenerative ,Basic Behavioral and Social Science ,Cerebrovascular ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Neurosciences ,Aging ,Brain Disorders ,2.1 Biological and endogenous factors ,Neurological ,Humans ,Male ,Female ,White Matter ,Aged ,Middle Aged ,Cross-Sectional Studies ,Magnetic Resonance Imaging ,Cognitive Dysfunction ,Cognition ,Neuropsychological Tests ,Connectome ,Brain ,Alzheimer’s Disease Neuroimaging Initiative ,cerebral small vessel disease ,dementia ,lesion network mapping ,magnetic resonance imaging ,vascular cognitive impairment ,white matter hyperintensities ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Neurology & Neurosurgery ,Biomedical and clinical sciences ,Health sciences - Abstract
White matter hyperintensities of presumed vascular origin (WMH) are associated with cognitive impairment and are a key imaging marker in evaluating brain health. However, WMH volume alone does not fully account for the extent of cognitive deficits and the mechanisms linking WMH to these deficits remain unclear. Lesion network mapping (LNM) enables us to infer if brain networks are connected to lesions and could be a promising technique for enhancing our understanding of the role of WMH in cognitive disorders. Our study employed LNM to test the following hypotheses: (i) LNM-informed markers surpass WMH volumes in predicting cognitive performance; and (ii) WMH contributing to cognitive impairment map to specific brain networks. We analysed cross-sectional data of 3485 patients from 10 memory clinic cohorts within the Meta VCI Map Consortium, using harmonized test results in four cognitive domains and WMH segmentations. WMH segmentations were registered to a standard space and mapped onto existing normative structural and functional brain connectome data. We employed LNM to quantify WMH connectivity to 480 atlas-based grey and white matter regions of interest (ROI), resulting in ROI-level structural and functional LNM scores. We compared the capacity of total and regional WMH volumes and LNM scores in predicting cognitive function using ridge regression models in a nested cross-validation. LNM scores predicted performance in three cognitive domains (attention/executive function, information processing speed, and verbal memory) significantly better than WMH volumes. LNM scores did not improve prediction for language functions. ROI-level analysis revealed that higher LNM scores, representing greater connectivity to WMH, in grey and white matter regions of the dorsal and ventral attention networks were associated with lower cognitive performance. Measures of WMH-related brain network connectivity significantly improve the prediction of current cognitive performance in memory clinic patients compared to WMH volume as a traditional imaging marker of cerebrovascular disease. This highlights the crucial role of network integrity, particularly in attention-related brain regions, improving our understanding of vascular contributions to cognitive impairment. Moving forward, refining WMH information with connectivity data could contribute to patient-tailored therapeutic interventions and facilitate the identification of subgroups at risk of cognitive disorders.
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- 2024
3. Calibrating the clock of JWST
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Shaw, A. W., Kaplan, D. L., Gandhi, P., Maccarone, T. J., Borowski, E. S., Britt, C. T., Buckley, D. A. H., Burdge, K. B., Charles, P. A., Dhillon, V. S., French, R. G., Heinke, C. O., Hynes, R. I., Knigge, C., Littlefair, S. P., Pawar, Devraj, Plotkin, R. M., Ressler, M. E., Santos-Sanz, P., Shahbaz, T., Sivakoff, G. R., and Stevens, A. L.
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Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
JWST, despite not being designed to observe astrophysical phenomena that vary on rapid time scales, can be an unparalleled tool for such studies. If timing systematics can be controlled, JWST will be able to open up the sub-second infrared timescale regime. Rapid time-domain studies, such as lag measurements in accreting compact objects and Solar System stellar occultations, require both precise inter-frame timing and knowing when a time series begins to an absolute accuracy significantly below 1s. In this work we present two long-duration observations of the deeply eclipsing double white dwarf system ZTF J153932.16+502738.8, which we use as a natural timing calibrator to measure the absolute timing accuracy of JWST's clock. From our two epochs, we measure an average clock accuracy of $0.12\pm0.06$s, implying that JWST can be used for sub-second time-resolution studies down to the $\sim100$ms level, a factor $\sim5$ improvement upon the pre-launch clock accuracy requirement. We also find an asymmetric eclipse profile in the F322W2 band, which we suggest has a physical origin., Comment: 16 pages, 13 figures, accepted for publication in AJ
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- 2024
4. Discarding Lavrentiev's Gap in Non-automonous and Non-Convex Variational Problems
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Borowski, Michał, Bousquet, Pierre, Chlebicka, Iwona, Lledos, Benjamin, and Miasojedow, Błażej
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Mathematics - Analysis of PDEs ,Mathematics - Functional Analysis - Abstract
We establish that the Lavrentiev gap between Sobolev and Lipschitz maps does not occur for a scalar variational problem of the form: \[ \textrm{to minimize} \qquad u \mapsto \int_\Omega f(x,u,\nabla u)\text{d}x \,, \] under a Dirichlet boundary condition. Here, $\Omega$ is a bounded Lipschitz open set in $\mathbb{R}^N$, $N\geq 1$ and the function $f$ is required to be measurable with respect to the spacial variable, continuous with respect to the second one, and continuous and comparable to convex with respect to the last variable. Moreover, we assume that $f$ satisfies a natural condition balancing the variations with respect to the first variable and the growth with respect to the last one. Remarkably, typical conditions that are usually imposed on $f$ to discard the Lavrentiev gap are dropped here: we do not require $f$ to be bounded or convex with respect to the second variable, nor impose any condition of $\Delta_2$-kind with respect to the last variable.
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- 2024
5. Overview of ADNI MRI
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Jack, Clifford R, Arani, Arvin, Borowski, Bret J, Cash, Dave M, Crawford, Karen, Das, Sandhitsu R, DeCarli, Charles, Fletcher, Evan, Fox, Nick C, Gunter, Jeffrey L, Ittyerah, Ranjit, Harvey, Danielle J, Jahanshad, Neda, Maillard, Pauline, Malone, Ian B, Nir, Talia M, Reid, Robert I, Reyes, Denise A, Schwarz, Christopher G, Senjem, Matthew L, Thomas, David L, Thompson, Paul M, Tosun, Duygu, Yushkevich, Paul A, Ward, Chadwick P, Weiner, Michael W, and Initiative, Alzheimer's Disease Neuroimaging
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Biomedical and Clinical Sciences ,Neurosciences ,Clinical Sciences ,Bioengineering ,Aging ,Clinical Research ,Biomedical Imaging ,Acquired Cognitive Impairment ,Neurodegenerative ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Alzheimer's Disease ,Dementia ,Brain Disorders ,Humans ,Alzheimer Disease ,Magnetic Resonance Imaging ,Neuroimaging ,Brain ,ADNI ,Alzheimer's disease imaging ,Alzheimer's disease MRI ,magnetic resonance imaging ,Alzheimer's Disease Neuroimaging Initiative ,Geriatrics ,Clinical sciences ,Biological psychology - Abstract
The magnetic resonance imaging (MRI) Core has been operating since Alzheimer's Disease Neuroimaging Initiative's (ADNI) inception, providing 20 years of data including reliable, multi-platform standardized protocols, carefully curated image data, and quantitative measures provided by expert investigators. The overarching purposes of the MRI Core include: (1) optimizing and standardizing MRI acquisition methods, which have been adopted by many multicenter studies and trials worldwide and (2) providing curated images and numeric summary values from relevant MRI sequences/contrasts to the scientific community. Over time, ADNI MRI has become increasingly complex. To remain technically current, the ADNI MRI protocol has changed substantially over the past two decades. The ADNI 4 protocol contains nine different imaging types (e.g., three dimensional [3D] T1-weighted and fluid-attenuated inversion recovery [FLAIR]). Our view is that the ADNI MRI data are a greatly underutilized resource. The purpose of this paper is to educate the scientific community on ADNI MRI methods and content to promote greater awareness, accessibility, and use. HIGHLIGHTS: The MRI Core provides multi-platform standardized protocols, carefully curated image data, and quantitative analysis by expert groups. The ADNI MRI protocol has undergone major changes over the past two decades to remain technically current. As of April 25, 2024, the following numbers of image series are available: 17,141 3D T1w; 6877 FLAIR; 3140 T2/PD; 6623 GRE; 3237 dMRI; 2846 ASL; 2968 TF-fMRI; and 2861 HighResHippo (see Table 1 for abbreviations). As of April 25, 2024, the following numbers of quantitative analyses are available: FreeSurfer 10,997; BSI 6120; tensor based morphometry (TBM) and TBM-SYN 12,019; WMH 9944; dMRI 1913; ASL 925; TF-fMRI NFQ 2992; and medial temporal subregion volumes 2726 (see Table 4 for abbreviations). ADNI MRI is an underutilized resource that could be more useful to the research community.
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- 2024
6. Design and validation of the ADNI MR protocol.
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Arani, Arvin, Borowski, Bret, Felmlee, John, Reid, Robert, Thomas, David, Gunter, Jeffrey, Stables, Lara, Buckner, Randy, Jung, Youngkyoo, Tosun, Duygu, Weiner, Michael, and Jack, Clifford
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Alzheimers Disease Neuroimaging Initiative ,Alzheimers disease ,amyloid‐related imaging abnormalities monitoring ,clinical neuroimaging ,magnetic resonance imaging protocols ,neuroimaging ,patient screening ,Humans ,Alzheimer Disease ,Magnetic Resonance Imaging ,Neuroimaging ,Brain ,Biomarkers ,Research Design - Abstract
Phase four of the Alzheimers Disease Neuroimaging Initiative (ADNI4) magnetic resonance imaging (MRI) protocols aim to maintain longitudinal consistency across two decades of data acquisition, while adopting new technologies. Here we describe and justify the studys design and targeted biomarkers. The ADNI4 MRI protocol includes nine MRI sequences. Some sequences require the latest hardware and software system upgrades and are continuously rolled out as they become available at each site. The main sequence additions/changes in ADNI4 are: (1) compressed sensing (CS) T1-weighting, (2) pseudo-continuous arterial spin labeling (ASL) on all three vendors (GE, Siemens, Philips), (3) multiple-post-labeling-delay ASL, (4) 1 mm3 isotropic 3D fluid-attenuated inversion recovery, and (5) CS 3D T2-weighted. ADNI4 aims to help the neuroimaging community extract valuable imaging biomarkers and provide a database to test the impact of advanced imaging strategies on diagnostic accuracy and disease sensitivity among individuals lying on the cognitively normal to impaired spectrum. HIGHLIGHTS: A summary of MRI protocols for phase four of the Alzheimers Disease Neuroimaging Initiative (ADNI 4). The design and justification for the ADNI 4 MRI protocols. Compressed sensing and multi-band advances have been applied to improve scan time. ADNI4 protocols aim to streamline safety screening and therapy monitoring. The ADNI4 database will be a valuable test bed for academic research.
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- 2024
7. Rapid Mid-Infrared Spectral-Timing with JWST. I. The prototypical black hole X-ray Binary GRS 1915+105 during a MIR-bright and X-ray-obscured state
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Gandhi, P., Borowski, E. S., Byrom, J., Hynes, R. I., Maccarone, T. J., Shaw, A. W., Adegoke, O. K., Altamirano, D., Baglio, M. C., Bhargava, Y., Britt, C. T., Buckley, D. A. H., Buisson, D. J. K., Casella, P., Segura, N. Castro, Charles, P. A., Corral-Santana, J. M., Dhillon, V. S., Fender, R., Gúrpide, A., Heinke, C. O., Igl, A. B., Knigge, C., Markoff, S., Mastroserio, G., McCollough, M. L., Middleton, M., Miller, J. M., Miller-Jones, J. C. A., Motta, S. E., Paice, J. A., Pawar, D. D., Plotkin, R. M., Pradhan, P., Ressler, M. E., Russell, D. M., Russell, T. D., Santos-Sanz, P., Shahbaz, T., Sivakoff, G. R., Steeghs, D., Tetarenko, A. J., Tomsick, J. A., Vincentelli, F. M., George, M., Gurwell, M., and Rao, R.
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Astrophysics - High Energy Astrophysical Phenomena ,Astrophysics - Solar and Stellar Astrophysics - Abstract
We present mid-infrared (MIR) spectral-timing measurements of the prototypical Galactic microquasar GRS 1915+105. The source was observed with the Mid-Infrared Instrument (MIRI) onboard JWST in June 2023 at a MIR luminosity L(MIR)~10^{36} erg/s exceeding past IR levels by about a factor of 10. By contrast, the X-ray flux is much fainter than the historical average, in the source's now-persistent 'obscured' state. The MIRI low-resolution spectrum shows a plethora of emission lines, the strongest of which are consistent with recombination in the hydrogen Pfund (Pf) series and higher. Low amplitude (~1%) but highly significant peak-to-peak photometric variability is found on timescales of ~1,000 s. The brightest Pf(6-5) emission line lags the continuum. Though difficult to constrain accurately, this lag is commensurate with light-travel timescales across the outer accretion disc or with expected recombination timescales inferred from emission line diagnostics. Using the emission line as a bolometric indicator suggests a moderate (~5-30% Eddington) intrinsic accretion rate. Multiwavelength monitoring shows that JWST caught the source close in-time to unprecedentedly bright MIR and radio long-term flaring. Assuming a thermal bremsstrahlung origin for the MIRI continuum suggests an unsustainably high mass-loss rate during this time unless the wind remains bound, though other possible origins cannot be ruled out. PAH features previously detected with Spitzer are now less clear in the MIRI data, arguing for possible destruction of dust in the interim. These results provide a preview of new parameter space for exploring MIR spectral-timing in XRBs and other variable cosmic sources on rapid timescales., Comment: Dedicated to the memory of our colleague, Tomaso Belloni. Submitted 2024 June 21; Comments welcome
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- 2024
8. Can triad forestry reconcile Europe’s biodiversity and forestry strategies? A critical evaluation of forest zoning
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Nagel, Thomas A., Rodríguez-Recio, Mariano, Aakala, Tuomas, Angelstam, Per, Avdagić, Admir, Borowski, Zbigniew, Bravo-Oviedo, Andrés, Brazaitis, Gediminas, Campagnaro, Thomas, Ciach, Michał, Curovic, Milic, Doerfler, Inken, Fotakis, Dimitrios, Govedar, Zoran, Gregor, Konstantin, Gültekin, Yaşar Selman, Heilmann-Clausen, Jacob, Hoffmann, Johanna, Hofmeister, Jeňýk, Jansone, Diāna, Jansons, Āris, Kepfer-Rojas, Sebastian, Lachat, Thibault, Lapin, Katharina, Lõhmus, Asko, Manton, Michael, Mikac, Stjepan, Mikoláš, Martin, Mohren, Frits, Nordén, Björn, Odor, Peter, Oettel, Janine, Paillet, Yoan, Panayotov, Momchil, Roibu, Catalin-Constantin, Sitzia, Tommaso, Svoboda, Miroslav, Tanács, Eszter, Trentanovi, Giovanni, Vacchiano, Giorgio, van der Sluis, Theo, Zlatanov, Tzvetan, and Burrascano, Sabina
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- 2024
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9. International survey on diagnostic reference levels based on clinical indications in plain radiography
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Schegerer, Alexander A., Stamm, Georg, Aberle, Christoph, Ammon, Josefin, Bazrafshan, Babak, Borowski, Markus, Eßeling, Rainer, Madsack, Bärbel, Menz, Roman, Müller, Constance, Oberhofer, Nadia, Renger, Bernhard, Singer, Julian, Verius, Michael, Walz, Michael, and Jungnickel, Kerstin
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- 2024
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10. Cytogenetics and DNA barcode in Hoplias gr. malabaricus (Characiformes, Erythrinidae) reveals correlation between karyomorphs and valid species
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Perin, Diana Paula, Máh, Denise Felicetti, Haerter, Chrystian Aparecido Grillo, Tonello, Sandro, Souza Machado, Amanda de, Paiz, Leonardo Marcel, da Silva, Maelin, Pietricoski, Luciana Borowski, Benvegnú, Dalila Moter, Margarido, Vladimir Pavan, Blanco, Daniel Rodrigues, and Lui, Roberto Laridondo
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- 2024
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11. Enhanced low-cost lipopeptide biosurfactant production by Bacillus velezensis from residual glycerin
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Brito, Henrique A., Napp, Amanda P., Pereira, Evandro, Bach, Evelise, Borowski, João V. B., Passaglia, Luciane M. P., Melo, Vania M. M., Moreira, Raphael, Foster, E. Johan, Lopes, Fernanda C., and Vainstein, Marilene H.
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- 2024
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12. Cultivation of Microalgae in Liquid Digestate to Remove Nutrients and Organic Contaminants
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Sobolewska, Ewelina, Borowski, Sebastian, and Nowicka-Krawczyk, Paulina
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- 2024
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13. Genetic associations with dementia‐related proteinopathy: Application of item response theory
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Katsumata, Yuriko, Fardo, David W, Shade, Lincoln MP, Wu, Xian, Karanth, Shama D, Hohman, Timothy J, Schneider, Julie A, Bennett, David A, Farfel, Jose M, Gauthreaux, Kathryn, Mock, Charles, Kukull, Walter A, Abner, Erin L, Nelson, Peter T, Carrillo, Maria, Reiman, Eric M, Chen, Kewei, Masterman, Donna, Green, Robert C, Ho, Carole, Fleisher, Adam, Saykin, Andrew J, Nho, Kwangsik, Apostolova, Liana G, Risacher, Shannon L, Jackson, Jonathan, Forghanian-Arani, Arvin, Borowski, Bret, Ward, Chad, Schwarz, Christopher, Jack, Clifford R, Jones, David, Gunter, Jeff, Kantarci, Kejal, Senjem, Matthew, Vemuri, Prashanthi, Reid, Robert, Petersen, Ronald, Hsiao, John K, Potter, William, Masliah, Eliezer, Ryan, Laurie, Bernard, Marie, Silverberg, Nina, Kormos, Adrienne, Conti, Cat, Veitch, Dallas, Flenniken, Derek, Sacrey, Diana Truran, Choe, Mark, Ashford, Miriam, Chen, Stephanie Rossi, Faber, Kelley, Nudelman, Kelly, Wilme, Kristi, Foroud, Tatiana M, Trojanowki, John Q, Shaw, Leslie M, Korecka, Magdalena, Figurski, Michal, Khachaturian, Zaven, Barnes, Lisa, Malone, Ian, Fox, Nick C, Beckett, Laurel, Weiner, Michael W, Jagust, William, Landau, Susan, Knaack, Alexander, DeCarli, Charles, Harvey, Danielle, Fletcher, Evan, González, Hector, Jin, Chengshi, Tosun‐Turgut, Duygu, Neuhaus, John, Fockler, Juliet, Nosheny, Rachel, Koeppe, Robert A, Yushkevich, Paul A, Das, Sandhitsu, Mathis, Chet, Toga, Arthur W, Zimmerman, Caileigh, Gessert, Devon, Shcrer, Elizabeth, Miller, Garrett, Coker, Godfrey, Jimenez, Gustavo, Salazar, Jennifer, Pizzola, Jeremy, Crawford, Karen, Hergesheimer, Lindsey, Donohue, Michael, and Rafii, Michael
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Biomedical and Clinical Sciences ,Biological Psychology ,Clinical Sciences ,Neurosciences ,Psychology ,Prevention ,Alzheimer's Disease Related Dementias (ADRD) ,Genetics ,Brain Disorders ,Aging ,Alzheimer's Disease ,Lewy Body Dementia ,Neurodegenerative ,Dementia ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Acquired Cognitive Impairment ,2.1 Biological and endogenous factors ,Neurological ,Humans ,alpha-Synuclein ,TDP-43 Proteinopathies ,Proteostasis Deficiencies ,DNA-Binding Proteins ,Biological Products ,Alzheimer Disease ,Membrane Proteins ,Nerve Tissue Proteins ,Alzheimer's Disease Neuroimaging Initiative ,National Alzheimer's Coordinating Center ,ARHGEF28 ,Alzheimer's Coordinating Center ,Alzheimer's Disease Sequencing Project ,Alzheimer's disease neuropathologic changes ,Item response theory ,Lewy ,RGNEF ,Religious Orders Study ,Rush Memory and Aging Project ,SDHAF1 ,TMEM68 ,neuropathology ,Geriatrics ,Clinical sciences ,Biological psychology - Abstract
IntroductionAlthough dementia-related proteinopathy has a strong negative impact on public health, and is highly heritable, understanding of the related genetic architecture is incomplete.MethodsWe applied multidimensional generalized partial credit modeling (GPCM) to test genetic associations with dementia-related proteinopathies. Data were analyzed to identify candidate single nucleotide variants for the following proteinopathies: Aβ, tau, α-synuclein, and TDP-43.ResultsFinal included data comprised 966 participants with neuropathologic and WGS data. Three continuous latent outcomes were constructed, corresponding to TDP-43-, Aβ/Tau-, and α-synuclein-related neuropathology endophenotype scores. This approach helped validate known genotype/phenotype associations: for example, TMEM106B and GRN were risk alleles for TDP-43 pathology; and GBA for α-synuclein/Lewy bodies. Novel suggestive proteinopathy-linked alleles were also discovered, including several (SDHAF1, TMEM68, and ARHGEF28) with colocalization analyses and/or high degrees of biologic credibility.DiscussionA novel methodology using GPCM enabled insights into gene candidates for driving misfolded proteinopathies.HighlightsLatent factor scores for proteinopathies were estimated using a generalized partial credit model. The three latent continuous scores corresponded well with proteinopathy severity. Novel genes associated with proteinopathies were identified. Several genes had high degrees of biologic credibility for dementia risk factors.
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- 2024
14. Evaluation of the German living guideline “Protection against the Overuse and Underuse of Health Care” – an online survey among German GPs
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Warkentin, Lisette, Scherer, Martin, Kühlein, Thomas, Pausch, Felix, Lühmann, Dagmar, Muche-Borowski, Cathleen, and Hueber, Susann
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- 2024
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15. Methylation patterns at the adjacent CpG sites within enhancers are a part of cell identity
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Taryma-Leśniak, Olga, Bińkowski, Jan, Przybylowicz, Patrycja Kamila, Sokolowska, Katarzyna Ewa, Borowski, Konrad, and Wojdacz, Tomasz Kazimierz
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- 2024
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16. Evaluation of the efficacy of Simparica Trio® in the prevention of the transmission of Babesia canis by infected Dermacentor reticulatus to dogs
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Borowski, Stasia, Viljoen, Alta, D’Hanis, Lina, Mahabir, Sean, and Geurden, Thomas
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- 2024
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17. scg-cli -- a Tool Supporting Software Comprehension via Extraction and Analysis of Semantic Code Graph
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Borowski, Krzysztof and Baliś, Bartosz
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Computer Science - Software Engineering - Abstract
We present scg-cli, a~command line tool facilitating software comprehension. The tool extracts semantic information about code structure and dependencies from the Java and Scala projects, and structures it as a~Semantic Code Graph (SCG), an information model underlying scg-cli. The SCG data, once written into a~portable, open protobuf-based format, can be used by the scg-cli command line tool to obtain project metrics, find the most critical code entities, and compute project partitionings. The results of this analysis and the SCG data can be exported for further investigation by external tools such as Gephi software (visualization) and, notably, as a Jupyter Notebook environment with helper APIs to enable advanced analysis of the project using data analytics methods. We explain functionalities of the scg-cli tool and demonstrate its capabilities by showing an example analysis of an open-source Java project commons-io.
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- 2023
18. Semantic Code Graph -- an information model to facilitate software comprehension
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Borowski, Krzysztof, Baliś, Bartosz, and Orzechowski, Tomasz
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Computer Science - Software Engineering - Abstract
Software comprehension can be extremely time-consuming due to the ever-growing size of codebases. Consequently, there is an increasing need to accelerate the code comprehension process to facilitate maintenance and reduce associated costs. A crucial aspect of this process is understanding and preserving the high quality of the code dependency structure. While a variety of code structure models already exist, there is a surprising lack of models that closely represent the source code and focus on software comprehension. As a result, there are no readily available and easy-to-use tools to assist with dependency comprehension, refactoring, and quality monitoring of code. To address this gap, we propose the Semantic Code Graph (SCG), an information model that offers a detailed abstract representation of code dependencies with a close relationship to the source code. To validate the SCG model's usefulness in software comprehension, we compare it to nine other source code representation models. Additionally, we select 11 well-known and widely-used open-source projects developed in Java and Scala and perform a range of software comprehension activities on them using three different code representation models: the proposed SCG, the Call Graph (CG), and the Class Collaboration Network (CCN). We then qualitatively analyze the results to compare the performance of these models in terms of software comprehension capabilities. These activities encompass project structure comprehension, identifying critical project entities, interactive visualization of code dependencies, and uncovering code similarities through software mining. Our findings demonstrate that the SCG enhances software comprehension capabilities compared to the prevailing CCN and CG models. We believe that the work described is a step towards the next generation of tools that streamline code dependency comprehension and management.
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- 2023
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19. Unplugged: Planting and Growing the Seed of Replacement in Four-Year Old-Children
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Simpson, Amber, Borowski, Rebecca, Colquhoun, Ashleigh, and Hu, Zhengqi
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- 2024
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20. A fast in silico model for preoperative risk assessment of paravalvular leakage
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Spanjaards, Michelle, Borowski, Finja, Supp, Laura, Ubachs, René, Lavezzo, Valentina, and van der Sluis, Olaf
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- 2024
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21. Enhancement of Biogas Production from Vegetable Waste by Application of Mineral Fertilizers
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Borowski, Sebastian, Cieciura-Włoch, Weronika, and Liczbiński, Przemysław
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- 2024
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22. White matter hyperintensities are higher among early‐onset Alzheimer's disease participants than their cognitively normal and early‐onset nonAD peers: Longitudinal Early‐onset Alzheimer's Disease Study (LEADS)
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Eloyan, Ani, Thangarajah, Maryanne, An, Na, Borowski, Bret J, Reddy, Ashritha L, Aisen, Paul, Dage, Jeffrey L, Foroud, Tatiana, Ghetti, Bernardino, Griffin, Percy, Hammers, Dustin, Iaccarino, Leonardo, Jack, Clifford R, Kirby, Kala, Kramer, Joel, Koeppe, Robert, Kukull, Walter A, La Joie, Renaud, Mundada, Nidhi S, Murray, Melissa E, Nudelman, Kelly, Rumbaugh, Malia, Soleimani‐Meigooni, David N, Toga, Arthur, Touroutoglou, Alexandra, Atri, Alireza, Day, Gregory S, Duara, Ranjan, Graff‐Radford, Neill R, Honig, Lawrence S, Jones, David T, Masdeu, Joseph, Mendez, Mario F, Musiek, Erik, Onyike, Chiadi U, Rogalski, Emily, Salloway, Stephen, Sha, Sharon, Turner, Raymond S, Wingo, Thomas S, Wolk, David A, Womack, Kyle, Beckett, Laurel, Gao, Sujuan, Carrillo, Maria C, Rabinovici, Gil, Apostolova, Liana G, Dickerson, Brad, Vemuri, Prashanthi, and Consortium, and the LEADS
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Biological Psychology ,Psychology ,Neurodegenerative ,Alzheimer's Disease ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Cerebrovascular ,Behavioral and Social Science ,Dementia ,Acquired Cognitive Impairment ,Vascular Cognitive Impairment/Dementia ,Brain Disorders ,Neurosciences ,Aging ,Alzheimer's Disease Related Dementias (ADRD) ,2.1 Biological and endogenous factors ,Neurological ,Humans ,Alzheimer Disease ,White Matter ,Amyloid beta-Peptides ,tau Proteins ,Magnetic Resonance Imaging ,Cognitive Dysfunction ,Amyloidogenic Proteins ,Amyloid ,Alzheimer's disease ,amyloid ,EOAD ,tau PET ,tau positron emission tomography ,white matter hyperintensities ,WMH ,LEADS Consortium ,Clinical Sciences ,Geriatrics ,Clinical sciences ,Biological psychology - Abstract
IntroductionWe compared white matter hyperintensities (WMHs) in early-onset Alzheimer's disease (EOAD) with cognitively normal (CN) and early-onset amyloid-negative cognitively impaired (EOnonAD) groups in the Longitudinal Early-Onset Alzheimer's Disease Study.MethodsWe investigated the role of increased WMH in cognition and amyloid and tau burden. We compared WMH burden of 205 EOAD, 68 EOnonAD, and 89 CN participants in lobar regions using t-tests and analyses of covariance. Linear regression analyses were used to investigate the association between WMH and cognitive impairment and that between amyloid and tau burden.ResultsEOAD showed greater WMHs compared with CN and EOnonAD participants across all regions with no significant differences between CN and EOnonAD groups. Greater WMHs were associated with worse cognition. Tau burden was positively associated with WMH burden in the EOAD group.DiscussionEOAD consistently showed higher WMH volumes. Overall, greater WMHs were associated with worse cognition and higher tau burden in EOAD.HighlightsThis study represents a comprehensive characterization of WMHs in sporadic EOAD. WMH volumes are associated with tau burden from positron emission tomography (PET) in EOAD, suggesting WMHs are correlated with increasing burden of AD. Greater WMH volumes are associated with worse performance on global cognitive tests. EOAD participants have higher WMH volumes compared with CN and early-onset amyloid-negative cognitively impaired (EOnonAD) groups across all brain regions.
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- 2023
23. Determinants of cognitive and brain resilience to tau pathology: a longitudinal analysis
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Bocancea, Diana I, Svenningsson, Anna L, van Loenhoud, Anna C, Groot, Colin, Barkhof, Frederik, Strandberg, Olof, Smith, Ruben, Weiner, Michael W, Aisen, Paul, Petersen, Ronald, Jack, Clifford R, Jagust, William, Trojanowki, John Q, Toga, Arthur W, Beckett, Laurel, Green, Robert C, Saykin, Andrew J, Morris, John C, Perrin, Richard J, Shaw, Leslie M, Khachaturian, Zaven, Carrillo, Maria, Potter, William, Barnes, Lisa, Bernard, Marie, González, Hector, Ho, Carole, Hsiao, John K, Jackson, Jonathan, Masliah, Eliezer, Masterman, Donna, Okonkwo, Ozioma, Ryan, Laurie, Silverberg, Nina, Fleisher, Adam, Sacrey, Diana Truran, Fockler, Juliet, Conti, Cat, Veitch, Dallas, Neuhaus, John, Jin, Chengshi, Nosheny, Rachel, Ashford, Miriam, Flenniken, Derek, Kormo, Adrienne, Montine, Tom, Conti, Cat B, Rafii, Michael, Raman, Rema, Jimenez, Gustavo, Donohue, Michael, Gessert, Devon, Salazar, Jennifer, Zimmerman, Caileigh, Cabrera, Yuliana, Walter, Sarah, Miller, Garrett, Coker, Godfrey, Clanton, Taylor, Hergesheimer, Lindsey, Smith, Stephanie, Adegoke, Olusegun, Mahboubi, Payam, Moore, Shelley, Pizzola, Jeremy, Shaffer, Elizabeth, Harvey, Danielle, Forghanian-Arani, Arvin, Borowski, Bret, Ward, Chad, Schwarz, Christopher, Jones, David, Gunter, Jeff, Kantarci, Kejal, Senjem, Matthew, Vemuri, Prashanthi, Reid, Robert, Fox, Nick C, Malone, Ian, Thompson, Paul, Thomopoulos, Sophia I, Nir, Talia M, Jahanshad, Neda, DeCarli, Charles, Knaack, Alexander, Fletcher, Evan, Tosun-Turgut, Duygu, Chen, Stephanie Rossi, Choe, Mark, and Crawfor, Karen
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Health Sciences ,Dementia ,Brain Disorders ,Cerebrovascular ,Aging ,Neurosciences ,Alzheimer's Disease Related Dementias (ADRD) ,Neurodegenerative ,Biomedical Imaging ,Vascular Cognitive Impairment/Dementia ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Alzheimer's Disease ,Behavioral and Social Science ,Clinical Research ,Acquired Cognitive Impairment ,2.1 Biological and endogenous factors ,1.1 Normal biological development and functioning ,Mental health ,Neurological ,Humans ,Alzheimer Disease ,Longitudinal Studies ,tau Proteins ,Cross-Sectional Studies ,Cerebral Cortical Thinning ,Positron-Emission Tomography ,Brain ,Cognition ,Apolipoproteins E ,Alzheimer's disease ,tau ,resilience ,cognition ,PET ,MRI ,Alzheimer’s Disease Neuroimaging Initiative ,Alzheimer’s disease ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Neurology & Neurosurgery ,Biomedical and clinical sciences ,Health sciences ,Psychology - Abstract
Mechanisms of resilience against tau pathology in individuals across the Alzheimer's disease spectrum are insufficiently understood. Longitudinal data are necessary to reveal which factors relate to preserved cognition (i.e. cognitive resilience) and brain structure (i.e. brain resilience) despite abundant tau pathology, and to clarify whether these associations are cross-sectional or longitudinal. We used a longitudinal study design to investigate the role of several demographic, biological and brain structural factors in yielding cognitive and brain resilience to tau pathology as measured with PET. In this multicentre study, we included 366 amyloid-β-positive individuals with mild cognitive impairment or Alzheimer's disease dementia with baseline 18F-flortaucipir-PET and longitudinal cognitive assessments. A subset (n = 200) additionally underwent longitudinal structural MRI. We used linear mixed-effects models with global cognition and cortical thickness as dependent variables to investigate determinants of cognitive resilience and brain resilience, respectively. Models assessed whether age, sex, years of education, APOE-ε4 status, intracranial volume (and cortical thickness for cognitive resilience models) modified the association of tau pathology with cognitive decline or cortical thinning. We found that the association between higher baseline tau-PET levels (quantified in a temporal meta-region of interest) and rate of cognitive decline (measured with repeated Mini-Mental State Examination) was adversely modified by older age (Stβinteraction = -0.062, P = 0.032), higher education level (Stβinteraction = -0.072, P = 0.011) and higher intracranial volume (Stβinteraction = -0.07, P = 0.016). Younger age, higher education and greater cortical thickness were associated with better cognitive performance at baseline. Greater cortical thickness was furthermore associated with slower cognitive decline independent of tau burden. Higher education also modified the negative impact of tau-PET on cortical thinning, while older age was associated with higher baseline cortical thickness and slower rate of cortical thinning independent of tau. Our analyses revealed no (cross-sectional or longitudinal) associations for sex and APOE-ε4 status on cognition and cortical thickness. In this longitudinal study of clinically impaired individuals with underlying Alzheimer's disease neuropathological changes, we identified education as the most robust determinant of both cognitive and brain resilience against tau pathology. The observed interaction with tau burden on cognitive decline suggests that education may be protective against cognitive decline and brain atrophy at lower levels of tau pathology, with a potential depletion of resilience resources with advancing pathology. Finally, we did not find major contributions of sex to brain nor cognitive resilience, suggesting that previous links between sex and resilience might be mainly driven by cross-sectional differences.
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- 2023
24. Absence and presence of Lavrentiev's phenomenon for double phase functionals upon every choice of exponents
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Borowski, Michał, Chlebicka, Iwona, De Filippis, Filomena, and Miasojedow, Błażej
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Mathematics - Analysis of PDEs - Abstract
We study classes of weights ensuring the absence and presence of the Lavrentiev's phenomenon for double phase functionals upon every choice of exponents. We introduce a new sharp scale for weights for which there is no Lavrentiev's phenomenon up to a counterexample we provide. This scale embraces the sharp range for $\alpha$-H\"older continuous weights. Moreover, it allows excluding the gap for every choice of exponents $q,p>1$.
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- 2023
25. Comparison of Monophosphine and Bisphosphine Precatalysts for Ni-Catalyzed Suzuki-Miyaura Cross-Coupling: Understanding the Role of the Ligation State in Catalysis.
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Borowski, Julia, Newman-Stonebraker, Samuel, and Doyle, Abigail
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Ni catalysis ,Suzuki-Miyaura ,cross-coupling ,ligand effects ,phosphines - Abstract
Practical advances in Ni-catalyzed Suzuki-Miyaura cross-coupling (SMC) have been limited by a lack of mechanistic understanding of phosphine ligand effects. While bisphosphines are commonly used in these methodologies, we have observed instances where monophosphines can provide comparable or higher levels of reactivity. Seeking to understand the role of ligation state in catalysis, we performed a head-to-head comparison study of C(sp2)-C(sp2) Ni SMCs catalyzed by mono and bisphosphine precatalysts using six distinct substrate pairings. Significant variation in optimal precatalyst was observed, with the monophosphine precatalyst tending to outperform the bisphosphines with electronically deactivated and sterically hindered substrates. Mechanistic experiments revealed a role for monoligated (P1Ni) species in accelerating the fundamental organometallic steps of the catalytic cycle, while highlighting the need for bisligated (P2Ni) species to avoid off-cycle reactivity and catalyst poisoning by heterocyclic motifs. These findings provide guidelines for ligand selection against challenging substrates and future ligand design tailored to the mechanistic demands of Ni-catalyzed SMCs.
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- 2023
26. Mobility of the lumbo-pelvic-hip complex (spinopelvic mobility) and sagittal spinal alignment - implications for surgeons performing hip arthroplasty
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Łaziński, Mariusz, Niemyjski, Włodzimierz, Niemyjski, Michał, Olewnik, Łukasz, Drobniewski, Marek, Synder, Marek, and Borowski, Andrzej
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- 2024
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27. Planetary Health in der Allgemeinmedizin: Bestandsaufnahme und Perspektiven
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Lenzer, Benedikt, Muche-Borowski, Cathleen, Bühn, Stefanie, and Schwienhorst-Stich, Eva-Maria
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- 2024
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28. Utilizing a Pretrained Language Model (BERT) to Classify Preservice Physics Teachers' Written Reflections
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Wulff, Peter, Mientus, Lukas, Nowak, Anna, and Borowski, Andreas
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Computer-based analysis of preservice teachers' written reflections could enable educational scholars to design personalized and scalable intervention measures to support reflective writing. Algorithms and technologies in the domain of research related to artificial intelligence have been found to be useful in many tasks related to reflective writing analytics such as classification of text segments. However, mostly shallow learning algorithms have been employed so far. This study explores to what extent deep learning approaches can improve classification performance for segments of written reflections. To do so, a pretrained language model (BERT) was utilized to classify segments of preservice physics teachers' written reflections according to elements in a reflection-supporting model. Since BERT has been found to advance performance in many tasks, it was hypothesized to enhance classification performance for written reflections as well. We also compared the performance of BERT with other deep learning architectures and examined conditions for best performance. We found that BERT outperformed the other deep learning architectures and previously reported performances with shallow learning algorithms for classification of segments of reflective writing. BERT starts to outperform the other models when trained on about 20 to 30% of the training data. Furthermore, attribution analyses for inputs yielded insights into important features for BERT's classification decisions. Our study indicates that pretrained language models such as BERT can boost performance for language-related tasks in educational contexts such as classification.
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- 2023
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29. Absence of Lavrentiev's gap for anisotropic functionals
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Borowski, Michał, Chlebicka, Iwona, and Miasojedow, Błażej
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Mathematics - Analysis of PDEs ,Mathematics - Functional Analysis ,46E30 - Abstract
We establish the absence of the Lavrentiev gap between Sobolev and smooth maps for a non-autonomous variational problem of a general structure, where the integrand is assumed to be controlled by a function which is convex and anisotropic with respect to the last variable. This fact results from new results on good approximation properties of the natural underlying unconventional function space. Scalar and vector-valued problems are studied.
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- 2022
30. Boundedness of Wolff-type potentials and applications to PDEs
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Borowski, Michał, Chlebicka, Iwona, and Miasojedow, Błażej
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Mathematics - Analysis of PDEs - Abstract
We provide a short proof of a sharp rearrangement estimate for a generalized version of a potential of Wolff--Havin--Maz'ya type. As a consequence, we prove a reduction principle for that integral operators, that is, a characterization of those rearrangement invariant spaces between which the potentials are bounded via a one-dimensional inequality of Hardy-type. Since the special case of the mentioned potential is known to control precisely very weak solutions to a broad class of quasilinear elliptic PDEs of non-standard growth, we infer the local regularity properties of the solutions in rearrangement invariant spaces for prescribed classes of data.
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- 2022
31. Fetal growth restriction induced by maternal gal-3 deficiency is associated with altered gut-placenta axis
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Xie, Yiran, Zhao, Fangqi, Wang, Yiru, Borowski, Sophia, Freitag, Nancy, Tirado-Gonzalez, Irene, Hofsink, Naomi, Matschl, Urte, Plösch, Torsten, Garcia, Mariana G., and Blois, Sandra M.
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- 2024
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32. A data‐driven examination of apathy and depressive symptoms in dementia with independent replication
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Da Silva, Miguel Vasconcelos, Melendez‐Torres, Gerardo Javier, Ismail, Zahinoor, Testad, Ingelin, Ballard, Clive, Creese, Byron, Weiner, Michael, Aisen, Paul, Petersen, Ronald, Jack, Clifford R, Jagust, William, Trojanowki, John Q, Toga, Arthur W, Beckett, Laurel, Green, Robert C, Saykin, Andrew J, Morris, John, Shaw, Leslie M, Liu, Enchi, Montine, Tom, Thomas, Ronald G, Donohue, Michael, Walter, Sarah, Gessert, Devon, Sather, Tamie, Jiminez, Gus, Harvey, Danielle, Bernstein, Matthew, Fox, Nick, Thompson, Paul, Schuff, Norbert, DeCArli, Charles, Borowski, Bret, Gunter, Jeff, Senjem, Matt, Vemuri, Prashanthi, Jones, David, Kantarci, Kejal, Ward, Chad, Koeppe, Robert A, Foster, Norm, Reiman, Eric M, Chen, Kewei, Mathis, Chet, Landau, Susan, Cairns, Nigel J, Householder, Erin, Reinwald, Lisa Taylor, Lee, Virginia, Korecka, Magdalena, Figurski, Michal, Crawford, Karen, Neu, Scott, Foroud, Tatiana M, Potkin, Steven, Shen, Li, Kelley, Faber, Kim, Sungeun, Nho, Kwangsik, Kachaturian, Zaven, Frank, Richard, Snyder, Peter J, Molchan, Susan, Kaye, Jeffrey, Quinn, Joseph, Lind, Betty, Carter, Raina, Dolen, Sara, Schneider, Lon S, Pawluczyk, Sonia, Beccera, Mauricio, Teodoro, Liberty, Spann, Bryan M, Brewer, James, Van der Swag, Helen, Fleisher, Adam, Heidebrink, Judith L, Lord, Joanne L, Mason, Sara S, Albers, Colleen S, Knopman, David, Johnson, Kris, Doody, Rachelle S, Meyer, Javier Villanueva, Chowdhury, Munir, Rountree, Susan, Dang, Mimi, Stern, Yaakov, Honig, Lawrence S, Bell, Karen L, Ances, Beau, Morris, John C, Carroll, Maria, Leon, Sue, Mintun, Mark A, Schneider, Stacy, and Oliver, Angela
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Clinical and Health Psychology ,Biomedical and Clinical Sciences ,Psychology ,Depression ,Mental Health ,Brain Disorders ,Mental Illness ,Neurological ,Mental health ,Alzheimer's Disease Neuroimaging Initiative ,apathy ,dementia ,depression ,latent class analysis ,Genetics ,Neurosciences ,Biological psychology - Abstract
Apathy is one of the most common neuropsychiatric symptoms (NPS) and is associated with poor clinical outcomes. Research that helps define the apathy phenotype is urgently needed, particularly for clinical and biomarker studies. We used latent class analysis (LCA) with two independent cohorts to understand how apathy and depression symptoms co-occur statistically. We further explored the relationship between latent class membership, demographics, and the presence of other NPS. The LCA identified a four-class solution (no symptoms, apathy, depression, and combined apathy/depression), reproducible over both cohorts, providing robust support for an apathy syndrome distinct from depression and confirming that an apathy/depression syndrome exists, supported by the model fit test with the four-class solution scores evidencing better fitting (Bayesian information criterion adjusted and entropy R 2). Using a data-driven method, we show distinct and statistically meaningful co-occurrence of apathy and depressive symptoms. There was evidence that these classes have different clinical associations, which may help inform diagnostic categories for research studies and clinical practice.HighlightsWe found four classes: no symptoms, apathy, depression and apathy/depression.Apathy conferred a higher probability for agitation.Apathy diagnostic criteria should include accompanying neuropsychiatric symptoms.
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- 2023
33. How well can U.S. military veterans’ suicidal ideation be predicted from static and change-based indicators of their psychosocial well-being as they adapt to civilian life?
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Vogt, Dawne, Rosellini, Anthony J., Borowski, Shelby, Street, Amy E., O’Brien, Robert W., and Tomoyasu, Naomi
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- 2024
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34. Explorative behavior allows the successful finding of ephemeral food resources in the wild
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Wirowska, Martyna, Iwińska, Karolina, Borowski, Zbigniew, Brzeziński, Marcin, Solecki, Paweł, and Boratyński, Jan S.
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- 2024
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35. The accessory heads of the quadriceps femoris muscle may affect the layering of the quadriceps tendon and potential graft harvest lengths
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Olewnik, Łukasz, Zielinska, Nicol, Aragones, Paloma, Ruzik, Kacper, Paulsen, Friedrich, Borowski, Andrzej, and LaPrade, Robert F.
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- 2023
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36. Impact of Mineral Fertilizers on Anaerobic Digestion of Vegetable Waste
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Borowski, Sebastian, Cieciura-Włoch, Weronika, Boniecki, Paweł, and Bednarek, Agata
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- 2023
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37. Diverse Models of Capitalism and Synchronization of Business Cycles
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Borowski, Jakub, Czerniak, Adam, and Farkas, Beáta
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- 2023
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38. The Polygenic Risk Score Knowledge Base offers a centralized online repository for calculating and contextualizing polygenic risk scores
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Weiner, MW, Aisen, P, Petersen, R, Jack, CR, Jagust, W, Trojanowki, JQ, Toga, AW, Beckett, L, Green, RC, Saykin, AJ, Morris, JC, Perrin, RJ, Shaw, LM, Khachaturian, Z, Carrillo, M, Potter, W, Barnes, L, Bernard, M, González, H, Ho, C, Hsiao, JK, Jackson, J, Masliah, E, Masterman, D, Okonkwo, O, Perrin, R, Ryan, L, Silverberg, N, Fleisher, A, Sacrey, DT, Fockler, J, Conti, C, Veitch, D, Neuhaus, J, Jin, C, Nosheny, R, Ashford, M, Flenniken, D, Kormos, A, Monine, T, Rafii, M, Raman, R, Jimenez, G, Donohue, M, Gessert, D, Salazar, J, Zimmerman, C, Cabrera, Y, Walter, S, Miller, G, Coker, G, Clanton, T, Hergesheimer, L, Smith, S, Adegoke, O, Mahboubi, P, Moore, S, Pizzola, J, Shaffer, E, Sloan, B, Harvey, D, Forghanian-Arani, A, Borowski, B, Ward, C, Schwarz, C, Jones, D, Gunter, J, Kantarci, K, Senjem, M, Vemuri, P, Reid, R, Fox, NC, Malone, I, Thompson, P, Thomopoulos, SI, Nir, TM, Jahanshad, N, DeCarli, C, Knaack, A, Fletcher, E, Tosun-Turgut, D, Chen, SR, Choe, M, Crawford, K, Yushkevich, PA, Das, S, Koeppe, RA, Reiman, EM, Chen, K, Mathis, C, Landau, S, Cairns, NJ, Householder, E, Franklin, E, Bernhardt, H, Taylor-Reinwald, L, Tojanowki, JQ, Korecka, M, and Figurski, M
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Biological Sciences ,Genetics ,Prevention ,Human Genome ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Genetic Predisposition to Disease ,Genome-Wide Association Study ,Humans ,Knowledge Bases ,Multifactorial Inheritance ,Polymorphism ,Single Nucleotide ,Risk Factors ,Alzheimer’s Disease Neuroimaging Initiative ,Biological sciences ,Biomedical and clinical sciences - Abstract
The process of identifying suitable genome-wide association (GWA) studies and formatting the data to calculate multiple polygenic risk scores on a single genome can be laborious. Here, we present a centralized polygenic risk score calculator currently containing over 250,000 genetic variant associations from the NHGRI-EBI GWAS Catalog for users to easily calculate sample-specific polygenic risk scores with comparable results to other available tools. Polygenic risk scores are calculated either online through the Polygenic Risk Score Knowledge Base (PRSKB; https://prs.byu.edu ) or via a command-line interface. We report study-specific polygenic risk scores across the UK Biobank, 1000 Genomes, and the Alzheimer's Disease Neuroimaging Initiative (ADNI), contextualize computed scores, and identify potentially confounding genetic risk factors in ADNI. We introduce a streamlined analysis tool and web interface to calculate and contextualize polygenic risk scores across various studies, which we anticipate will facilitate a wider adaptation of polygenic risk scores in future disease research.
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- 2022
39. Strengths and vulnerabilities: Comparing post-9/11 U.S. veterans’ and non-veterans’ perceptions of health and broader well-being
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Vogt, Dawne, Borowski, Shelby, Maguen, Shira, Blosnich, John R, Hoffmire, Claire A, Bernhard, Paul A, Iverson, Katherine M, and Schneiderman, Aaron
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Health Services and Systems ,Health Sciences ,Behavioral and Social Science ,Good Health and Well Being ,Military service ,Post-9/11 veterans ,Survey ,Health and health behavior ,Employment ,Finances ,Social relationships ,Well-being ,Public Health and Health Services ,Epidemiology ,Public health ,Sociology - Abstract
BackgroundPrior research has examined how the post-military health and well-being of both the larger veteran population and earlier veteran cohorts differs from non-veterans. However, no study has yet to provide a holistic examination of how the health, vocational, financial, and social well-being of the newest generation of post-9/11 U.S. military veterans compares with their non-veteran peers. This is a significant oversight, as accurate knowledge of the strengths and vulnerabilities of post-9/11 veterans is required to ensure that the needs of this population are adequately addressed, as well as to counter inaccurate veteran stereotypes.MethodsPost-9/11 U.S. veterans' (N = 15,160) and non-veterans' (N = 4,533) reported on their health and broader well-being as part of a confidential web-based survey in 2018. Participants were drawn from probability-based sampling frames, and sex-stratified weighted logistic regressions were conducted to examine differences in veterans' and non-veterans' reports of health, vocational, financial, and social outcomes.ResultsAlthough both men and women post-9/11 veterans endorsed poorer health status than non-veterans, they reported greater engagement in a number of positive health behaviors (healthy eating and exercise) and were more likely to indicate having access to health care. Veterans also endorsed greater social well-being than non-veterans on several outcomes, whereas few differences were observed in vocational and financial well-being.ConclusionDespite their greater vulnerability to experiencing health conditions, the newest generation of post-9/11 U.S. veterans report experiencing similar or better outcomes than non-veterans in many aspects of their lives. Findings underscore the value of examining a wider range of health and well-being outcomes in veteran research and highlight a number of important directions for intervention, public health education, policy, and research related to the reintegration of military veterans within broader civilian society.
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- 2022
40. Does ridesourcing respond to unplanned rail disruptions? A natural experiment analysis of mobility resilience and disparity
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Borowski, Elisa, Soria, Jason, Schofer, Joseph, and Stathopoulos, Amanda
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Physics - Physics and Society ,Statistics - Applications - Abstract
Urban rail transit networks provide critical access to opportunities and livelihood in many urban systems. Ensuring that these services are resilient (that is, exhibiting efficient response to and recovery from disruptions) is a key economic and social priority. Increasingly, the ability of urban rail systems to cope with disruptions is a function of a complex patchwork of mobility options, wherein alternative modes can complement and fill service gaps. This study analyzes the role of ridesourcing in providing adaptive mobility capacity that could be leveraged to fill no-notice gaps in rail transit services, addressing the question of distributional impacts of resilience. Using a natural experiment, we systematically identify 28 major transit disruptions over the period of one year in Chicago and match them, both temporally and spatially, with ridesourcing trip data. Using multilevel mixed modeling, we quantify variation in the adaptive use of on-demand mobility across the racially and economically diverse city of Chicago. Our findings show that the gap-filling potential of adaptive ridesourcing during rail transit disruptions is significantly influenced by station-, community-, and district-level factors. Specifically, greater shifts to ridesourcing occur during weekdays, nonholidays, and more severe disruptions, in community areas that have higher percentages of White residents and transit commuters, and in the more affluent North district of the city. These findings suggest that while ridesourcing appears to provide adaptive capacity during rail disruptions, its benefits do not appear to be equitable for lower-income communities of color that already experience limited mobility options., Comment: 20 pages, 6 figures. arXiv admin note: substantial text overlap with arXiv:2010.15889
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- 2022
41. Protection or Peril of Following the Crowd in a Pandemic-Concurrent Flood Evacuation
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Borowski, Elisa and Stathopoulos, Amanda
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Economics - Econometrics ,Statistics - Applications - Abstract
The decisions of whether and how to evacuate during a climate disaster are influenced by a wide range of factors, including sociodemographics, emergency messaging, and social influence. Further complexity is introduced when multiple hazards occur simultaneously, such as a flood evacuation taking place amid a viral pandemic that requires physical distancing. Such multi-hazard events can necessitate a nuanced navigation of competing decision-making strategies wherein a desire to follow peers is weighed against contagion risks. To better understand these nuances, we distributed an online survey during a pandemic surge in July 2020 to 600 individuals in three midwestern and three southern states in the United States with high risk of flooding. In this paper, we estimate a random parameter logit model in both preference space and willingness-to-pay space. Our results show that the directionality and magnitude of the influence of peers' choices of whether and how to evacuate vary widely across respondents. Overall, the decision of whether to evacuate is positively impacted by peer behavior, while the decision of how to evacuate is negatively impacted by peers. Furthermore, an increase in flood threat level lessens the magnitude of these impacts. These findings have important implications for the design of tailored emergency messaging strategies. Specifically, emphasizing or deemphasizing the severity of each threat in a multi-hazard scenario may assist in: (1) encouraging a reprioritization of competing risk perceptions and (2) magnifying or neutralizing the impacts of social influence, thereby (3) nudging evacuation decision-making toward a desired outcome., Comment: 31 pages, 7 figures
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- 2022
42. Absence and presence of Lavrentiev’s phenomenon for double phase functionals upon every choice of exponents
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Borowski, Michał, Chlebicka, Iwona, De Filippis, Filomena, and Miasojedow, Błażej
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- 2024
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43. Controlling monotonicity of nonlinear operators
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Borowski, Michał and Chlebicka, Iwona
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Mathematics - Analysis of PDEs - Abstract
Controlling the monotonicity and growth of Leray--Lions' operators including the $p$-Laplacian plays a fundamental role in the theory of existence and regularity of solutions to second order nonlinear PDE. We collect, correct, and supply known estimates including the discussion on the constants. Moreover, we provide a comprehensive treatment of related results for operators with Orlicz growth. We pay special attention to exposition of the proofs and the use of elementary arguments.
- Published
- 2021
44. Interactive Analysis of CNN Robustness
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Sietzen, Stefan, Lechner, Mathias, Borowski, Judy, Hasani, Ramin, and Waldner, Manuela
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Computer Science - Human-Computer Interaction - Abstract
While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users' insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models., Comment: Accepted at Pacific Graphics 2021
- Published
- 2021
45. How Dance Promotes the Development of Social and Emotional Competence
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Borowski, Teresa G.
- Abstract
Social and emotional competencies (SEC) are critical for success in school and life, as they include the ability to interact with others, regulate one's emotions and behavior, solve problems, and communicate effectively. Research and practice show that dance experiences enhance social-emotional development, yet less is known about the mechanisms through which this occurs. To address this, 110 SEC and dance articles were reviewed to inform the development of a Theory of Change to explain how dance may promote SEC. Self-intimation, nonverbal expression and communication, embodied cognition and learning, synchrony, and a supportive learning environment emerged as the key components of dance practice that may facilitate SEC. Evidence for these components and research, practice, and policy implications are discussed.
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- 2023
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46. How Well do Feature Visualizations Support Causal Understanding of CNN Activations?
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Zimmermann, Roland S., Borowski, Judy, Geirhos, Robert, Bethge, Matthias, Wallis, Thomas S. A., and Brendel, Wieland
- Subjects
Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Computer Science - Human-Computer Interaction ,Computer Science - Machine Learning - Abstract
A precise understanding of why units in an artificial network respond to certain stimuli would constitute a big step towards explainable artificial intelligence. One widely used approach towards this goal is to visualize unit responses via activation maximization. These synthetic feature visualizations are purported to provide humans with precise information about the image features that cause a unit to be activated - an advantage over other alternatives like strongly activating natural dataset samples. If humans indeed gain causal insight from visualizations, this should enable them to predict the effect of an intervention, such as how occluding a certain patch of the image (say, a dog's head) changes a unit's activation. Here, we test this hypothesis by asking humans to decide which of two square occlusions causes a larger change to a unit's activation. Both a large-scale crowdsourced experiment and measurements with experts show that on average the extremely activating feature visualizations by Olah et al. (2017) indeed help humans on this task ($68 \pm 4$% accuracy; baseline performance without any visualizations is $60 \pm 3$%). However, they do not provide any substantial advantage over other visualizations (such as e.g. dataset samples), which yield similar performance ($66\pm3$% to $67 \pm3$% accuracy). Taken together, we propose an objective psychophysical task to quantify the benefit of unit-level interpretability methods for humans, and find no evidence that a widely-used feature visualization method provides humans with better "causal understanding" of unit activations than simple alternative visualizations., Comment: Presented at NeurIPS 2021. Shared first and last authorship. Project website at https://brendel-group.github.io/causal-understanding-via-visualizations/
- Published
- 2021
47. Correction to: Utilizing a Pretrained Language Model (BERT) to Classify Preservice Physics Teachers’ Written Refections
- Author
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Wulff, Peter, Mientus, Lukas, Nowak, Anna, and Borowski, Andreas
- Published
- 2024
- Full Text
- View/download PDF
48. Behavioral Signatures of Memory Resources for Language: Looking beyond the Lexicon/Grammar Divide
- Author
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Divjak, Dagmar, Milin, Petar, Medimorec, Srdan, and Borowski, Maciej
- Abstract
Although there is a broad consensus that both the procedural and declarative memory systems play a crucial role in language learning, use, and knowledge, the mapping between linguistic types and memory structures remains underspecified: by default, a dual-route mapping of language systems to memory systems is assumed, with declarative memory handling idiosyncratic lexical knowledge and procedural memory handling rule-governed knowledge of grammar. We experimentally contrast the processing of morphology (case and aspect), syntax (subordination), and lexical semantics (collocations) in a healthy L1 population of Polish, a language rich in form distinctions. We study the processing of these four types under two conditions: a single task condition in which the grammaticality of stimuli was judged and a concurrent task condition in which grammaticality judgments were combined with a digit span task. Dividing attention impedes access to declarative memory while leaving procedural memory unaffected and hence constitutes a test that dissociates which types of linguistic information each long-term memory construct subserves. Our findings confirm the existence of a distinction between lexicon and grammar as a generative, dual-route model would predict, but the distinction is graded, as usage-based models assume: the hypothesized grammar-lexicon opposition appears as a continuum on which grammatical phenomena can be placed as being more or less "ruly" or "idiosyncratic." However, usage-based models, too, need adjusting as not all types of linguistic knowledge are proceduralized to the same extent. This move away from a simple dichotomy fundamentally changes how we think about memory for language, and hence how we design and interpret behavioral and neuroimaging studies that probe into the nature of language cognition.
- Published
- 2022
- Full Text
- View/download PDF
49. Increasingly cautious sampling, not the black colouration of unpalatable prey, is used by fish in avoidance learning
- Author
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Kaczmarski, Mikołaj, Kaczmarek, Jan M., Kowalski, Krzysztof, Borowski, Karol, Kęsy, Jacek, and Kloskowski, Janusz
- Published
- 2023
- Full Text
- View/download PDF
50. The transfer of digitalized teaching-learning and assessment tools in higher education: approaches and best practices
- Author
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König, Johannes, Lindmeier, Anke, Zlatkin-Troitschanskaia, Olga, and Borowski, Andreas
- Published
- 2023
- Full Text
- View/download PDF
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