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1. Sequential non-determinism in tile self-assembly: a general framework and an application to efficient temperature-1 self-assembly of squares

Author

Furcy, David and Summers, Scott M.

Subjects
Computer Science - Data Structures and Algorithms, Computer Science - Computational Geometry
Abstract

In this paper, we work in a 2D version of the probabilistic variant of Winfree's abstract Tile Assembly Model defined by Chandran, Gopalkrishnan and Reif (SICOMP 2012) in which attaching tiles are sampled uniformly with replacement. First, we develop a framework called ``sequential non-determinism'' for analyzing the probabilistic correctness of a non-deterministic, temperature-1 tile assembly system (TAS) in which most (but not all) tile attachments are deterministic and the non-deterministic attachments always occur in a specific order. Our main sequential non-determinism result equates the probabilistic correctness of such a TAS to a finite product of probabilities, each of which 1) corresponds to the probability of the correct type of tile attaching at a point where it is possible for two different types to attach, and 2) ignores all other tile attachments that do not affect the non-deterministic attachment. We then show that sequential non-determinism allows for efficient and geometrically expressive self-assembly. To that end, we constructively prove that for any positive integer $N$ and any real $\delta \in (0,1)$, there exists a TAS that self-assembles into an $N \times N$ square with probability at least $1 - \delta$ using only $O\left( \log N + \log \frac{1}{\delta} \right)$ types of tiles. Our bound improves upon the previous state-of-the-art bound for this problem by Cook, Fu and Schweller (SODA 2011).

Published
2024

2. Self-Assembly of Patterns in the abstract Tile Assembly Model

Author

Drake, Phillip, Patitz, Matthew J., Summers, Scott M., and Tracy, Tyler

Subjects
Computer Science - Emerging Technologies, Computer Science - Computational Complexity, Computer Science - Computational Geometry
Abstract

In the abstract Tile Assembly Model, self-assembling systems consisting of tiles of different colors can form structures on which colored patterns are ``painted.'' We explore the complexity, in terms of the numbers of unique tile types required, of assembling various patterns. We first demonstrate how to efficiently self-assemble a set of simple patterns, then show tight bounds on the tile type complexity of self-assembling 2-colored patterns on the surfaces of square assemblies. Finally, we demonstrate an exponential gap in tile type complexity of self-assembling an infinite series of patterns between systems restricted to one plane versus those allowed two planes.

Published
2024

3. Identification of genetic drivers of plasma lipoprotein size in the Diversity Outbred mouse population.

Author

Price, Tara, Emfinger, Christopher, Schueler, Kathryn, King, Sarah, Nicholson, Rebekah, Beck, Tim, Yandell, Brian, Summers, Scott, Holland, William, Krauss, Ronald, Keller, Mark, and Attie, Alan

Subjects
HDL, LDL, VLDL, apolipoproteins, ceramides, genetic architecture, genomics, lipoproteins/metabolism, Female, Humans, Mice, Animals, Collaborative Cross Mice, Genome-Wide Association Study, Lipoproteins, Quantitative Trait Loci, Phenotype, Lipoproteins, VLDL
Abstract

Despite great progress in understanding lipoprotein physiology, there is still much to be learned about the genetic drivers of lipoprotein abundance, composition, and function. We used ion mobility spectrometry to survey 16 plasma lipoprotein subfractions in 500 Diversity Outbred mice maintained on a Western-style diet. We identified 21 quantitative trait loci (QTL) affecting lipoprotein abundance. To refine the QTL and link them to disease risk in humans, we asked if the human homologs of genes located at each QTL were associated with lipid traits in human genome-wide association studies. Integration of mouse QTL with human genome-wide association studies yielded candidate gene drivers for 18 of the 21 QTL. This approach enabled us to nominate the gene encoding the neutral ceramidase, Asah2, as a novel candidate driver at a QTL on chromosome 19 for large HDL particles (HDL-2b). To experimentally validate Asah2, we surveyed lipoproteins in Asah2-/- mice. Compared to wild-type mice, female Asah2-/- mice showed an increase in several lipoproteins, including HDL. Our results provide insights into the genetic regulation of circulating lipoproteins, as well as mechanisms by which lipoprotein subfractions may affect cardiovascular disease risk in humans.

Published
2023

5. Vitamin B2 enables regulation of fasting glucose availability.

Author

Masschelin, Peter M, Saha, Pradip, Ochsner, Scott A, Cox, Aaron R, Kim, Kang Ho, Felix, Jessica B, Sharp, Robert, Li, Xin, Tan, Lin, Park, Jun Hyoung, Wang, Liping, Putluri, Vasanta, Lorenzi, Philip L, Nuotio-Antar, Alli M, Sun, Zheng, Kaipparettu, Benny Abraham, Putluri, Nagireddy, Moore, David D, Summers, Scott A, McKenna, Neil J, and Hartig, Sean M

Subjects
Liver, Animals, Mice, Flavin-Adenine Dinucleotide, Glucose, Fatty Acids, Flavoproteins, PPAR alpha, Fasting, Oxidation-Reduction, Non-alcoholic Fatty Liver Disease, FAD, cell biology, gluconeogenesis, inborn errors of metabolism, metabolism, mouse, nuclear receptor, Nutrition, Liver Disease, Digestive Diseases, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Biochemistry and Cell Biology
Abstract

Flavin adenine dinucleotide (FAD) interacts with flavoproteins to mediate oxidation-reduction reactions required for cellular energy demands. Not surprisingly, mutations that alter FAD binding to flavoproteins cause rare inborn errors of metabolism (IEMs) that disrupt liver function and render fasting intolerance, hepatic steatosis, and lipodystrophy. In our study, depleting FAD pools in mice with a vitamin B2-deficient diet (B2D) caused phenotypes associated with organic acidemias and other IEMs, including reduced body weight, hypoglycemia, and fatty liver disease. Integrated discovery approaches revealed B2D tempered fasting activation of target genes for the nuclear receptor PPARα, including those required for gluconeogenesis. We also found PPARα knockdown in the liver recapitulated B2D effects on glucose excursion and fatty liver disease in mice. Finally, treatment with the PPARα agonist fenofibrate activated the integrated stress response and refilled amino acid substrates to rescue fasting glucose availability and overcome B2D phenotypes. These findings identify metabolic responses to FAD availability and nominate strategies for the management of organic acidemias and other rare IEMs.

Published
2023

7. Publisher Correction: Ramadan intermittent fasting is associated with ameliorated inflammatory markers and improved plasma sphingolipids/ceramides in subjects with obesity: lipidomics analysis

Author

Madkour, Mohamed Ibrahim, Islam, Md Torikul, Tippetts, Trevor S., Chowdhury, Kamrul H., Lesniewski, Lisa A., Summers, Scott A., Zeb, Falak, Abdelrahim, Dana N., AlKurd, Refat, Khraiwesh, Husam M., AbuShihab, Katia H., AlBakri, Asma, Obaideen, Khaled, and Faris, MoezAlIslam E.

Published
2023
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8. Ramadan intermittent fasting is associated with ameliorated inflammatory markers and improved plasma sphingolipids/ceramides in subjects with obesity: lipidomics analysis

Author

Madkour, Mohamed Ibrahim, Islam, Md Torikul, Tippetts, Trevor S., Chowdhury, Kamrul H., Lesniewski, Lisa A., Summers, Scott A., Zeb, Falak, Abdelrahim, Dana N., AlKurd, Refat, Khraiwesh, Husam M., AbuShihab, Katia H., AlBakri, Asma, Obaideen, Khaled, and Faris, MoezAlIslam E.

Published
2023
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11. Association between pre-diagnostic circulating lipid metabolites and colorectal cancer risk: a nested case–control study in the European Prospective Investigation into Cancer and Nutrition (EPIC)

Author

Harewood, Rhea, Rothwell, Joseph A., Bešević, Jelena, Viallon, Vivian, Achaintre, David, Gicquiau, Audrey, Rinaldi, Sabina, Wedekind, Roland, Prehn, Cornelia, Adamski, Jerzy, Schmidt, Julie A., Jacobs, Inarie, Tjønneland, Anne, Olsen, Anja, Severi, Gianluca, Kaaks, Rudolf, Katzke, Verena, Schulze, Matthias B., Prada, Marcela, Masala, Giovanna, Agnoli, Claudia, Panico, Salvatore, Sacerdote, Carlotta, Jakszyn, Paula Gabriela, Sánchez, Maria-Jose, Castilla, Jesús, Chirlaque, María-Dolores, Atxega, Amaia Aizpurua, van Guelpen, Bethany, Heath, Alicia K., Papier, Keren, Tong, Tammy Y.N., Summers, Scott A., Playdon, Mary, Cross, Amanda J., Keski-Rahkonen, Pekka, Chajès, Véronique, Murphy, Neil, and Gunter, Marc J.

Published
2024
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14. Improved lower and upper bounds on the tile complexity of uniquely self-assembling a thin rectangle non-cooperatively in 3D

Author

Furcy, David, Summers, Scott M., and Withers, Logan

Subjects
Computer Science - Data Structures and Algorithms, Computer Science - Computational Geometry
Abstract

We investigate a fundamental question regarding a benchmark class of shapes in one of the simplest, yet most widely utilized abstract models of algorithmic tile self-assembly. Specifically, we study the directed tile complexity of a $k \times N$ thin rectangle in Winfree's abstract Tile Assembly Model, assuming that cooperative binding cannot be enforced (temperature-1 self-assembly) and that tiles are allowed to be placed at most one step into the third dimension (just-barely 3D). While the directed tile complexities of a square and a scaled-up version of any algorithmically specified shape at temperature 1 in just-barely 3D are both asymptotically the same as they are (respectively) at temperature 2 in 2D, the bounds on the directed tile complexity of a thin rectangle at temperature 2 in 2D are not known to hold at temperature 1 in just-barely 3D. Motivated by this discrepancy, we establish new lower and upper bounds on the directed tile complexity of a thin rectangle at temperature 1 in just-barely 3D. We develop a new, more powerful type of Window Movie Lemma that lets us upper bound the number of "sufficiently similar" ways to assign glues to a set of fixed locations. Consequently, our lower bound, $\Omega\left(N^{\frac{1}{k}}\right)$, is an asymptotic improvement over the previous best lower bound and is more aesthetically pleasing since it eliminates the $k$ that used to divide $N^{\frac{1}{k}}$. The proof of our upper bound is based on a just-barely 3D, temperature-1 counter, organized according to "digit regions", which affords it roughly fifty percent more digits for the same target rectangle compared to the previous best counter. This increase in digit density results in an upper bound of $O\left(N^{\frac{1}{\left\lfloor\frac{k}{2}\right\rfloor}}+\log N\right)$, that is an asymptotic improvement over the previous best upper bound and roughly the square of our lower bound.

Published
2020

15. Ceramides Increase Fatty Acid Utilization in Intestinal Progenitors to Enhance Stemness and Increase Tumor Risk

Author

Li, Ying, Chaurasia, Bhagirath, Rahman, M. Mahidur, Kaddai, Vincent, Maschek, J. Alan, Berg, Jordan A., Wilkerson, Joseph L., Mahmassani, Ziad S., Cox, James, Wei, Peng, Meikle, Peter J., Atkinson, Donald, Wang, Liping, Poss, Annelise M., Playdon, Mary C., Tippetts, Trevor S., Mousa, Esraa M., Nittayaboon, Kesara, Anandh Babu, Pon Velayutham, Drummond, Micah J., Clevers, Hans, Shayman, James A., Hirabayashi, Yoshio, Holland, William L., Rutter, Jared, Edgar, Bruce A., and Summers, Scott A.

Published
2023
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19. Women with Fragile X–associated Tremor/Ataxia Syndrome

Author

Schneider, Andrea, Summers, Scott, Tassone, Flora, Seritan, Andreea, Hessl, David, Hagerman, Paul, and Hagerman, Randi

Subjects
Biomedical and Clinical Sciences, Neurosciences, Clinical Sciences, Rare Diseases, Intellectual and Developmental Disabilities (IDD), Basic Behavioral and Social Science, Fragile X Syndrome, Mental Health, Clinical Research, Pediatric, Brain Disorders, Neurodegenerative, Behavioral and Social Science, Neurological, Mental health, FXTAS, FMR1female premutation, FXTAS, FMR1 female premutation, Clinical sciences
Abstract

BackgroundFragile X-associated tremor and ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder linked to the FMR1 premutation.ObjectivesFXTAS in women is far less common than in men, and this study represents the largest sample reported to date.MethodsA total of 53 female premutation carriers with FXTAS (meanage, 66.83 years; FXTAS stages 2-5) and 55 age-matched and demographic background-matched control participants (meanage, 61.94 years) underwent a comprehensive molecular, physiological, neuropsychological, and psychiatric assessment.ResultsThe large sample of female premutation carriers showed a wide range of variability of clinical signs and symptom progression. The imaging results showed a middle cerebellar peduncles sign in only 6 patients; another symptom included high-signal intensity in the splenium of the corpus callosum, and diffuse cerebral deep white matter changes (e.g., in the pons) are more common. The rate of psychiatric disorders, especially depression, is higher than in the general population. There is a clear impairment in executive functioning and fine motor skills in connection with a higher FXTAS stage.ConclusionsThe manifestation of FXTAS symptoms in female carriers can be diverse with a milder phenotype and a lower penetrance than those observed in male premutation carriers. The middle cerebellar peduncles sign is present in only a small percentage of the sample, and we propose that the imaging criteria for FXTAS in women need to be expanded.

Published
2020

20. Mitochondrial pyruvate carrier is required for optimal brown fat thermogenesis

Author

Panic, Vanja, Pearson, Stephanie, Banks, James, Tippetts, Trevor S, Velasco-Silva, Jesse N, Lee, Sanghoon, Simcox, Judith, Geoghegan, Gisela, Bensard, Claire L, van Ry, Tyler, Holland, Will L, Summers, Scott A, Cox, James, Ducker, Gregory S, Rutter, Jared, and Villanueva, Claudio J

Subjects
Biochemistry and Cell Biology, Biological Sciences, Industrial Biotechnology, Nutrition, Obesity, Diabetes, Metabolic and endocrine, Affordable and Clean Energy, Adipocytes, Brown, Adipose Tissue, Brown, Animals, Anion Transport Proteins, Cold Temperature, Glucose, Male, Metabolomics, Mice, Mice, Inbred C57BL, Mitochondrial Membrane Transport Proteins, Monocarboxylic Acid Transporters, Oxidation-Reduction, Serum, Thermogenesis, biochemistry, chemical biology, glucose oxidations, glycolysis, ketones, mitochondria, mouse, pyruvate, thermogenesis, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Brown adipose tissue (BAT) is composed of thermogenic cells that convert chemical energy into heat to maintain a constant body temperature and counteract metabolic disease. The metabolic adaptations required for thermogenesis are not fully understood. Here, we explore how steady state levels of metabolic intermediates are altered in brown adipose tissue in response to cold exposure. Transcriptome and metabolome analysis revealed changes in pathways involved in amino acid, glucose, and TCA cycle metabolism. Using isotopic labeling experiments, we found that activated brown adipocytes increased labeling of pyruvate and TCA cycle intermediates from U13C-glucose. Although glucose oxidation has been implicated as being essential for thermogenesis, its requirement for efficient thermogenesis has not been directly tested. We show that mitochondrial pyruvate uptake is essential for optimal thermogenesis, as conditional deletion of Mpc1 in brown adipocytes leads to impaired cold adaptation. Isotopic labeling experiments using U13C-glucose showed that loss of MPC1 led to impaired labeling of TCA cycle intermediates. Loss of MPC1 in BAT increased 3-hydroxybutyrate levels in blood and BAT in response to the cold, suggesting that ketogenesis provides an alternative fuel source to compensate. Collectively, these studies highlight that complete glucose oxidation is essential for optimal brown fat thermogenesis.

Published
2020

21. Phospholipid methylation regulates muscle metabolic rate through Ca2+ transport efficiency

Author

Verkerke, Anthony RP, Ferrara, Patrick J, Lin, Chien-Te, Johnson, Jordan M, Ryan, Terence E, Maschek, J Alan, Eshima, Hiroaki, Paran, Christopher W, Laing, Brenton T, Siripoksup, Piyarat, Tippetts, Trevor S, Wentzler, Edward J, Huang, Hu, Spangenburg, Espen E, Brault, Jeffrey J, Villanueva, Claudio J, Summers, Scott A, Holland, William L, Cox, James E, Vance, Dennis E, Neufer, P Darrell, and Funai, Katsuhiko

Subjects
Medical Physiology, Biomedical and Clinical Sciences, Obesity, Nutrition, 2.1 Biological and endogenous factors, Aetiology, Oral and gastrointestinal, Musculoskeletal, Affordable and Clean Energy, Animals, Calcium, Diet, High-Fat, Energy Metabolism, Ion Transport, Methylation, Mice, Mice, Knockout, Muscle, Skeletal, Phosphatidylethanolamine N-Methyltransferase, Phospholipids, Sarcoplasmic Reticulum Calcium-Transporting ATPases, Medical biochemistry and metabolomics, Medical physiology, Nutrition and dietetics
Abstract

The biophysical environment of membrane phospholipids affects structure, function, and stability of membrane-bound proteins.1,2 Obesity can disrupt membrane lipids, and in particular, alter the activity of sarco/endoplasmic reticulum (ER/SR) Ca2+-ATPase (SERCA) to affect cellular metabolism.3-5 Recent evidence suggests that transport efficiency (Ca2+ uptake / ATP hydrolysis) of skeletal muscle SERCA can be uncoupled to increase energy expenditure and protect mice from diet-induced obesity.6,7 In isolated SR vesicles, membrane phospholipid composition is known to modulate SERCA efficiency.8-11 Here we show that skeletal muscle SR phospholipids can be altered to decrease SERCA efficiency and increase whole-body metabolic rate. The absence of skeletal muscle phosphatidylethanolamine (PE) methyltransferase (PEMT) promotes an increase in skeletal muscle and whole-body metabolic rate to protect mice from diet-induced obesity. The elevation in metabolic rate is caused by a decrease in SERCA Ca2+-transport efficiency, whereas mitochondrial uncoupling is unaffected. Our findings support the hypothesis that skeletal muscle energy efficiency can be reduced to promote protection from obesity.

Published
2019

25. A dominant negative ADIPOQ mutation in a diabetic family with renal disease, hypoadiponectinemia, and hyperceramidemia

Author

Simeone, Christopher A., Wilkerson, Joseph L., Poss, Annelise M., Banks, James A., Varre, Joseph V., Guevara, Jose Lazaro, Hernandez, Edgar Javier, Gorsi, Bushra, Atkinson, Donald L., Turapov, Tursun, Frodsham, Scott G., Morales, Julio C. Fierro, O’Neil, Kristina, Moore, Barry, Yandell, Mark, Summers, Scott A., Krolewski, Andrzej S., Holland, William L., and Pezzolesi, Marcus G.

Published
2022
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27. New bounds on the tile complexity of thin rectangles at temperature-1

Author

Furcy, David, Summers, Scott M., and Wendlandt, Christian

Subjects
Computer Science - Computational Geometry
Abstract

In this paper, we study the minimum number of unique tile types required for the self-assembly of thin rectangles in Winfree's abstract Tile Assembly Model (aTAM), restricted to temperature-1. Using Catalan numbers, planar self-assembly and a restricted version of the Window Movie Lemma, we derive a new lower bound on the tile complexity of thin rectangles at temperature-1 in 2D. Then, we give the first known upper bound on the tile complexity of ``just-barely'' 3D thin rectangles at temperature-1, where tiles are allowed to be placed at most one step into the third dimension. Our construction, which produces a unique terminal assembly, implements a just-barely 3D, zig-zag counter, whose base depends on the dimensions of the target rectangle, and whose digits are encoded geometrically, vertically-oriented and in binary.

Published
2018

28. Hierarchical Growth is Necessary and (Sometimes) Sufficient to Self-Assemble Discrete Self-Similar Fractals

Author

Hendricks, Jacob, Opseth, Joseph, Patitz, Matthew, and Summers, Scott

Subjects
Computer Science - Emerging Technologies, Computer Science - Computational Geometry
Abstract

In this paper, we prove that in the abstract Tile Assembly Model (aTAM), an accretion-based model which only allows for a single tile to attach to a growing assembly at each step, there are no tile assembly systems capable of self-assembling the discrete self-similar fractals known as the "H" and "U" fractals. We then show that in a related model which allows for hierarchical self-assembly, the 2-Handed Assembly Model (2HAM), there does exist a tile assembly systems which self-assembles the "U" fractal and conjecture that the same holds for the "H" fractal. This is the first example of discrete self similar fractals which self-assemble in the 2HAM but not in the aTAM, providing a direct comparison of the models and greater understanding of the power of hierarchical assembly.

Published
2018

31. Getting S.P.I.F.F.Y

Author

Summers, Scott

Subjects
Educational technology, Technology in education, Library and information science
Abstract

'Librarians have the wit and grit to get things done,' says Scott Summers, a former high school English teacher and school librarian who now brings that experience to his work [...]

Published
2024

33. Fractal Dimension of Assemblies in the Abstract Tile Assembly Model

Author

Hader, Daniel, Patitz, Matthew J., Summers, Scott M., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Kostitsyna, Irina, editor, and Orponen, Pekka, editor

Published
2021
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34. Ceramides are fuel gauges on the drive to cardiometabolic disease.

Author

Wilkerson, Joseph L., Tatum, Sean M., Holland, William L., and Summers, Scott A.

Subjects
HEART metabolism disorders, CERAMIDES, CORONARY artery disease, SPHINGOLIPIDS, CELL metabolism
Abstract

Ceramides are signals of fatty acid excess that accumulate when a cell's energetic needs have been met and its nutrient storage has reached capacity. As these sphingolipids accrue, they alter the metabolism and survival of cells throughout the body including in the heart, liver, blood vessels, skeletal muscle, brain, and kidney. These ceramide actions elicit the tissue dysfunction that underlies cardiometabolic diseases such as diabetes, coronary artery disease, metabolic-associated steatohepatitis, and heart failure. Here, we review the biosynthesis and degradation pathways that maintain ceramide levels in normal physiology and discuss how the loss of ceramide homeostasis drives cardiometabolic pathologies. We highlight signaling nodes that sense small changes in ceramides and in turn reprogram cellular metabolism and stimulate apoptosis. Finally, we evaluate the emerging therapeutic utility of these unique lipids as biomarkers that forecast disease risk and as targets of ceramide-lowering interventions that ameliorate disease. [ABSTRACT FROM AUTHOR]

Published
2024
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39. Optimal self-assembly of finite shapes at temperature 1 in 3D

Author

Furcy, David and Summers, Scott M.

Subjects
Computer Science - Computational Geometry, Computer Science - Data Structures and Algorithms
Abstract

Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for an arbitrary finite, connected shape $X \subset \mathbb{Z}^2$, there is a tile set that uniquely self-assembles into a 3D representation of a scaled-up version of $X$ at temperature 1 in 3D with optimal program-size complexity (the "program-size complexity", also known as "tile complexity", of a shape is the minimum number of tile types required to uniquely self-assemble it). Moreover, our construction is "just barely" 3D in the sense that it only places tiles in the $z = 0$ and $z = 1$ planes. Our result is essentially a just-barely 3D temperature 1 simulation of a similar 2D temperature 2 result by Soloveichik and Winfree (SICOMP 2007).

Published
2015

40. Scaled tree fractals do not strictly self-assemble

Author

Barth, Kimberly, Furcy, David, Summers, Scott M., and Totzke, Paul

Subjects
Computer Science - Computational Geometry
Abstract

In this paper, we show that any scaled-up version of any discrete self-similar {\it tree} fractal does not strictly self-assemble, at any temperature, in Winfree's abstract Tile Assembly Model., Comment: 13 pages, 3 figures, Appeared in the Proceedings of UCNC-2014, pp 27-39; Unconventional Computation and Natural Computation - 13th International Conference, UCNC 2014, London, ON, Canada, July 14-18, 2014, Springer Lecture Notes in Computer Science ISBN 978-3-319-08122-9

Published
2014
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41. Optimal program-size complexity for self-assembly at temperature 1 in 3D

Author

Furcy, David, Micka, Samuel, and Summers, Scott M.

Subjects
Computer Science - Computational Geometry, Computer Science - Emerging Technologies
Abstract

Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for all $N \in \mathbb{N}$, there is a tile set that uniquely self-assembles into an $N \times N$ square shape at temperature 1 with optimal program-size complexity of $O(\log N / \log \log N)$ (the program-size complexity, also known as tile complexity, of a shape is the minimum number of unique tile types required to uniquely self-assemble it). Moreover, our construction is "just barely" 3D in the sense that it works even when the placement of tiles is restricted to the $z = 0$ and $z = 1$ planes. This result affirmatively answers an open question from Cook, Fu, Schweller (SODA 2011). To achieve this result, we develop a general 3D temperature 1 optimal encoding construction, reminiscent of the 2D temperature 2 optimal encoding construction of Soloveichik and Winfree (SICOMP 2007), and perhaps of independent interest.

Published
2014

42. New Bounds on the Tile Complexity of Thin Rectangles at Temperature-1

Author

Furcy, David, Summers, Scott M., Wendlandt, Christian, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Thachuk, Chris, editor, and Liu, Yan, editor

Published
2019
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43. Plasma Ceramides as Biomarkers for Microvascular Disease in Diabetes: Evaluating the Relationship Between Ceramide and Multiple Outcomes

Author

Junqueira, Débora Leonor, primary, Cavalcanti, Alexandre Biasi, additional, Sallum, Juliana Maria Ferraz, additional, Yasaki, Erika, additional, Jesuíno, Isabella de Andrade, additional, Stach, Alline, additional, Negrelli, Karina, additional, Silva, Leila de Oliveira, additional, Lopes, Marcela Almeida, additional, Caixeta, Adriano, additional, Chan, Mark, additional, Ching, JIANHONG, additional, Carvalho, Valdemir Malechco, additional, Faccio, Andrea Tedesco, additional, Tsutsui, Jeane, additional, Rizzatti, Edgar, additional, Fonseca, Rafael Almeida, additional, Summers, Scott, additional, Fonseca, Henrique Almeida, additional, Rochitte, Carlos Eduardo, additional, Krieger, José, additional, and de Carvalho, Leonardo Pinto, additional

Published
2023
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45. The ChatGPT Artificial Intelligence Chatbot: How Well Does It Answer Accounting Assessment Questions?

Author

Wood, David A., primary, Achhpilia, Muskan P., additional, Adams, Mollie T., additional, Aghazadeh, Sanaz, additional, Akinyele, Kazeem, additional, Akpan, Mfon, additional, Allee, Kristian D., additional, Allen, Abigail M., additional, Almer, Elizabeth D., additional, Ames, Daniel, additional, Arity, Viktor, additional, Barr-Pulliam, Dereck, additional, Basoglu, K. Asli, additional, Belnap, Andrew, additional, Bentley, Jeremiah W., additional, Berg, Terje, additional, Berglund, Nathan R., additional, Berry, Erica, additional, Bhandari, Avishek, additional, Bhuyan, Md Nazmul Hasan, additional, Black, Paul W., additional, Blondeel, Eva, additional, Bond, David, additional, Bonrath, Annika, additional, Borthick, A. Faye, additional, Boyle, Erik S., additional, Bradford, Marianne, additional, Brandon, Duane M., additional, Brazel, Joseph F., additional, Brockbank, Bryan G., additional, Burger, Marcus, additional, Byzalov, Dmitri, additional, Cannon, James N., additional, Caro, Cecil, additional, Carr, Abraham H., additional, Cathey, Jack, additional, Cating, Ryan, additional, Charron, Kimberly, additional, Chavez, Stacy, additional, Chen, Jason, additional, Chen, Jennifer C., additional, Chen, Jennifer W., additional, Cheng, Christine, additional, Cheng, Xu, additional, Christensen, Brant E., additional, Church, Kimberly Swanson, additional, Cicone, N. J., additional, Constance, Patience, additional, Cooper, Lauren A., additional, Correia, Candice L., additional, Coyne, Joshua, additional, Cram, W. Alec, additional, Curtis, Asher, additional, Daigle, Ronald J., additional, Dannemiller, Steve, additional, Davenport, Stephan A., additional, Dawson, Gregory S., additional, De Meyst, Karen J. L., additional, Dell, Scott, additional, Demirkan, Sebahattin, additional, Denison, Christine A., additional, Desai, Hrishikesh, additional, DeSimone, Steven, additional, Diehl, Leah M., additional, Dimes, Ruth, additional, Dong, Bei, additional, Donnelly, Amy, additional, du Pon, Adam, additional, Duan, Huijue Kelly, additional, Duffey, Ada, additional, Dunn, Ryan T., additional, Durkin, Mary P., additional, Dzuranin, Ann C., additional, Eberle, Rachel M., additional, Ege, Matthew S., additional, El Mahdy, Dina, additional, Esplin, Adam, additional, Eulerich, Marc, additional, Everaert, Patricia, additional, Farah, Nusrat, additional, Farish, Lauren, additional, Favere-Marchesi, Michael, additional, Fayard, Dutch, additional, Filosa, Jessica R., additional, Ford, Melinda, additional, Franz, Diana R., additional, Fulmer, Bachman P., additional, Fulmer, Sarah, additional, Furner, Zhan Z., additional, Gantman, Sonia, additional, Garner, Steve, additional, Garrett, Jace, additional, Geng, Xin, additional, Golden, Joanna, additional, Goldman, William, additional, Gomez, Josue, additional, Gooley, Mark, additional, Granitto, Shawn P., additional, Green, Karen Y., additional, Greenman, Cindy L., additional, Gupta, Gaurav, additional, Guymon, Ronald N., additional, Hale, Kevin, additional, Harper, Christopher J., additional, Hartt, S. Allen, additional, Hawk, Holly, additional, Hawkins, Steven R., additional, Hawkins, Erin M., additional, Hay, David C., additional, Heinzelmann, Rafael, additional, Henderson, Cassy D., additional, Hendricks, Bradley E., additional, Heninger, William G., additional, Hill, Mary S., additional, Holden, Nicole, additional, Holderness, D. Kip, additional, Holt, Travis P., additional, Hoopes, Jeffrey L., additional, Hsieh, Sheng-Feng, additional, Huang, Feiqi, additional, Huang, Hua-Wei, additional, Huang, Ting-Chiao, additional, Huels, Brian W., additional, Hunter, Kara, additional, Hurley, Patrick J., additional, Inger, Kerry, additional, Islam, Sharif, additional, Ison, Isaac, additional, Issa, Hussein, additional, Jackson, Andrew B., additional, Jackson, Scott C., additional, Janvrin, Diane J., additional, Jimenez, Peggy D., additional, Johanson, Daniel, additional, Judd, J. Scott, additional, Kawada, Brett S., additional, Kelton, Andrea Seaton, additional, Kern, Sara, additional, Kerr, Jon N., additional, Keune, Marsha B., additional, Kim, Mindy, additional, Knox, Brian D., additional, Kogan, Gregory, additional, Kotb, Amr, additional, Krane, Ronja, additional, Kremin, Joleen, additional, Krieg, Kimberly S., additional, Kugel, Jonathan, additional, Kulset, Ellen M., additional, Kuruppu, Chamara, additional, LaDuca, Garrison, additional, Lamberton, Barbara A., additional, Lamboy-Ruiz, Melvin A., additional, Lang, Bradley, additional, Larocque, Stephannie A., additional, Larson, Melissa P., additional, Lawson, Bradley P., additional, Lawson, James G., additional, Lee, Lorraine, additional, Lenk, Margarita M., additional, Li-Kuehne, Michelle, additional, Liljegren, Jonathan, additional, Lin, Yi-Hung, additional, Liu, Wu-Po, additional, Liu, Zishang, additional, Lock, Brandon, additional, Long, James H., additional, Loraas, Tina, additional, Lowensohn, Suzanne, additional, Loy, Thomas R., additional, Lyngstadaas, Hakim, additional, Maas, Wim, additional, MacGregor, Jason E., additional, Madsen, Dag Øivind, additional, Malone, Carissa L., additional, Margolin, Maximilian, additional, Marshall, Mary E., additional, Martin, Rachel M., additional, Mpofu, Colleen McClain, additional, McCoy, Chris, additional, McGuigan, Nicholas C., additional, McSwain, Dwayne N., additional, Meckfessel, Michele D., additional, Mellon, Mark J., additional, Melton, Olivia S., additional, Mercado, Julie M., additional, Mitsuda, Steven, additional, Modugu, Kennedy, additional, Moehrle, Stephen, additional, Chaghervand, Amirali Moeini, additional, Moffitt, Kevin, additional, Moon, Joon Seok, additional, Muehlmann, Brigitte, additional, Murray, Johnna, additional, Mwaungulu, Emmanuel S., additional, Myers, Noah, additional, Naegle, J. 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Mike, additional, Turner, Michael C., additional, Vagner, Brandon, additional, Vakilzadeh, Hamid, additional, van der Geest, Jesse, additional, van Pelt, Victor, additional, Vandervelde, Scott D., additional, Vega, Jose, additional, Vera-Muñoz, Sandra, additional, Villanueva, Brigham, additional, Vincent, Nishani Edirisinghe, additional, Wagener, Martin, additional, Walton, Stephanie, additional, Warne, Rick C., additional, Watanabe, Olena V., additional, Watson, David, additional, Watson, Marcia Weidenmier, additional, Weber, Jill, additional, Weirich, Thomas, additional, West, Ashley N., additional, Wilford, Amanda L., additional, Wilson, Aaron B., additional, Winrow, Brian, additional, Winrow, Timothy, additional, Winrow, Tasia S., additional, Wiseman, Denise, additional, Witte, Annie L., additional, Wood, Bryan D., additional, Wood, Jessica, additional, Woolley, Darryl, additional, Wright, Nicole S., additional, Wu, Juan, additional, Xiong, Xiaomei, additional, Yatsenko, Dimitri, additional, Yazzie, Courtney E., additional, Young, Glen M., additional, Zhang, Chanyuan, additional, Zimmerman, Aleksandra B., additional, and Zoet, Emily, additional

Published
2023
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46. Phospholipid isotope tracing reveals β-catenin-driven suppression of phosphatidylcholine metabolism in hepatocellular carcinoma

Author

VanSant-Webb, Chad, primary, Low, Hayden K, additional, Kuramoto, Junko, additional, Stanley, Claire E, additional, Qiang, Hantao, additional, Su, Audrey, additional, Ross, Alexis N, additional, Cooper, Chad G, additional, Cox, James, additional, Summers, Scott, additional, Evason, Kimberley, additional, and Ducker, Gregory S, additional

Published
2023
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47. Supplemental Table 4 from New-Onset Diabetes after an Obesity-Related Cancer Diagnosis and Survival Outcomes in the Women's Health Initiative

Author

Karra, Prasoona, primary, Hardikar, Sheetal, primary, Winn, Maci, primary, Anderson, Garnet L., primary, Haaland, Benjamin, primary, Krick, Benjamin, primary, Thomson, Cynthia A., primary, Shadyab, Aladdin, primary, Luo, Juhua, primary, Saquib, Nazmus, primary, Strickler, Howard D., primary, Chlebowski, Rowan, primary, Arthur, Rhonda S., primary, Summers, Scott A., primary, Holland, William L., primary, Jalili, Thunder, primary, and Playdon, Mary C., primary

Published
2023
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48. Supplemental Table 1 from New-Onset Diabetes after an Obesity-Related Cancer Diagnosis and Survival Outcomes in the Women's Health Initiative

Author

Karra, Prasoona, primary, Hardikar, Sheetal, primary, Winn, Maci, primary, Anderson, Garnet L., primary, Haaland, Benjamin, primary, Krick, Benjamin, primary, Thomson, Cynthia A., primary, Shadyab, Aladdin, primary, Luo, Juhua, primary, Saquib, Nazmus, primary, Strickler, Howard D., primary, Chlebowski, Rowan, primary, Arthur, Rhonda S., primary, Summers, Scott A., primary, Holland, William L., primary, Jalili, Thunder, primary, and Playdon, Mary C., primary

Published
2023
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49. Data from New-Onset Diabetes after an Obesity-Related Cancer Diagnosis and Survival Outcomes in the Women's Health Initiative

Author

Karra, Prasoona, primary, Hardikar, Sheetal, primary, Winn, Maci, primary, Anderson, Garnet L., primary, Haaland, Benjamin, primary, Krick, Benjamin, primary, Thomson, Cynthia A., primary, Shadyab, Aladdin, primary, Luo, Juhua, primary, Saquib, Nazmus, primary, Strickler, Howard D., primary, Chlebowski, Rowan, primary, Arthur, Rhonda S., primary, Summers, Scott A., primary, Holland, William L., primary, Jalili, Thunder, primary, and Playdon, Mary C., primary

Published
2023
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50. Supplemental Table 3 from New-Onset Diabetes after an Obesity-Related Cancer Diagnosis and Survival Outcomes in the Women's Health Initiative

Author

Karra, Prasoona, primary, Hardikar, Sheetal, primary, Winn, Maci, primary, Anderson, Garnet L., primary, Haaland, Benjamin, primary, Krick, Benjamin, primary, Thomson, Cynthia A., primary, Shadyab, Aladdin, primary, Luo, Juhua, primary, Saquib, Nazmus, primary, Strickler, Howard D., primary, Chlebowski, Rowan, primary, Arthur, Rhonda S., primary, Summers, Scott A., primary, Holland, William L., primary, Jalili, Thunder, primary, and Playdon, Mary C., primary

Published
2023
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