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Hong A, Oliva M, Köppl D, Bannai H, Boucher C, Gagie T. Pfp-fm: an accelerated FM-index. Algorithms Mol Biol 2024; 19:15. [PMID: 38600518 PMCID: PMC11005213 DOI: 10.1186/s13015-024-00260-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
FM-indexes are crucial data structures in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [1] observed in 2007 that word-based indexes often use fewer random accesses than character-based indexes, and thus support faster searches. Since DNA lacks natural word-boundaries, however, it is necessary to parse it somehow before applying word-based FM-indexing. In 2022, Deng et al. [2] proposed parsing genomic data by induced suffix sorting, and showed that the resulting word-based FM-indexes support faster counting queries than standard FM-indexes when patterns are a few thousand characters or longer. In this paper we show that using prefix-free parsing-which takes parameters that let us tune the average length of the phrases-instead of induced suffix sorting, gives a significant speedup for patterns of only a few hundred characters. We implement our method and demonstrate it is between 3 and 18 times faster than competing methods on queries to GRCh38, and is consistently faster on queries made to 25,000, 50,000 and 100,000 SARS-CoV-2 genomes. Hence, it seems our method accelerates the performance of count over all state-of-the-art methods with a moderate increase in the memory. The source code for PFP - FM is available at https://github.com/AaronHong1024/afm .
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Affiliation(s)
- Aaron Hong
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA
| | - Marco Oliva
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA
| | - Dominik Köppl
- Faculty of Engineering, University of Yamanashi, Kōfu, 400-8510, Japan
- M &D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hideo Bannai
- M &D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, 32611, USA.
| | - Travis Gagie
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
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2
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Arasti S, Mirarab S. Median quartet tree search algorithms using optimal subtree prune and regraft. Algorithms Mol Biol 2024; 19:12. [PMID: 38481327 PMCID: PMC10938725 DOI: 10.1186/s13015-024-00257-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/13/2024] [Indexed: 03/17/2024] Open
Abstract
Gene trees can be different from the species tree due to biological processes and inference errors. One way to obtain a species tree is to find one that maximizes some measure of similarity to a set of gene trees. The number of shared quartets between a potential species tree and gene trees provides a statistically justifiable score; if maximized properly, it could result in a statistically consistent estimator of the species tree under several statistical models of discordance. However, finding the median quartet score tree, one that maximizes this score, is NP-Hard, motivating several existing heuristic algorithms. These heuristics do not follow the hill-climbing paradigm used extensively in phylogenetics. In this paper, we make theoretical contributions that enable an efficient hill-climbing approach. Specifically, we show that a subtree of size m can be placed optimally on a tree of size n in quasi-linear time with respect to n and (almost) independently of m. This result enables us to perform subtree prune and regraft (SPR) rearrangements as part of a hill-climbing search. We show that this approach can slightly improve upon the results of widely-used methods such as ASTRAL in terms of the optimization score but not necessarily accuracy.
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Affiliation(s)
- Shayesteh Arasti
- Computer Science and Engineering Department, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Siavash Mirarab
- Electrical and Computer Engineering Department, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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Quintano M, Moura RT, Kraka E. Exploring Jahn-Teller distortions: a local vibrational mode perspective. J Mol Model 2024; 30:102. [PMID: 38478107 DOI: 10.1007/s00894-024-05882-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
The characterization of normal mode (CNM) procedure coupled with an adiabatic connection scheme (ACS) between local and normal vibrational modes, both being a part of the Local Vibrational Mode theory developed in our group, can identify spectral changes as structural fingerprints that monitor symmetry alterations, such as those caused by Jahn-Teller (JT) distortions. Employing the PBE0/Def2-TZVP level of theory, we investigated in this proof-of-concept study the hexaaquachromium cation case,[ Cr ( OH 2 ) 6 ] 3 + /[ Cr ( OH 2 ) 6 ] 2 + , as a commonly known example for a JT distortion, followed by the more difficult ferrous and ferric hexacyanide anion case,[ Fe ( CN ) 6 ] 4 - /[ Fe ( CN ) 6 ] 3 - . We found that in both cases CNM of the characteristic normal vibrational modes reflects delocalization consistent with high symmetry and ACS confirms symmetry breaking, as evidenced by the separation of axial and equatorial group frequencies. As underlined by the Cremer-Kraka criterion for covalent bonding, from[ Cr ( OH 2 ) 6 ] 3 + to[ Cr ( OH 2 ) 6 ] 2 + there is an increase in axial covalency whereas the equatorial bonds shift toward electrostatic character. From[ Fe ( CN ) 6 ] 4 - to[ Fe ( CN ) 6 ] 3 - we observed an increase in covalency without altering the bond nature. Distinct π back-donation disparity could be confirmed by comparison with the isolated CN- system. In summary, our study positions the CNM/ACS protocol as a robust tool for investigating less-explored JT distortions, paving the way for future applications.
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Affiliation(s)
- Mateus Quintano
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX, 75275-0314, USA
| | - Renaldo T Moura
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX, 75275-0314, USA
- Department of Chemistry and Physics, Center of Agrarian Sciences, Federal University of Paraiba, Areia, PB, 58397-000, Brazil
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX, 75275-0314, USA.
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Vazquez-Guerrero P, Tuladhar R, Psychalinos C, Elwakil A, Chacron MJ, Santamaria F. Fractional order memcapacitive neuromorphic elements reproduce and predict neuronal function. Sci Rep 2024; 14:5817. [PMID: 38461365 PMCID: PMC10925066 DOI: 10.1038/s41598-024-55784-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/27/2024] [Indexed: 03/11/2024] Open
Abstract
There is an increasing need to implement neuromorphic systems that are both energetically and computationally efficient. There is also great interest in using electric elements with memory, memelements, that can implement complex neuronal functions intrinsically. A feature not widely incorporated in neuromorphic systems is history-dependent action potential time adaptation which is widely seen in real cells. Previous theoretical work shows that power-law history dependent spike time adaptation, seen in several brain areas and species, can be modeled with fractional order differential equations. Here, we show that fractional order spiking neurons can be implemented using super-capacitors. The super-capacitors have fractional order derivative and memcapacitive properties. We implemented two circuits, a leaky integrate and fire and a Hodgkin-Huxley. Both circuits show power-law spiking time adaptation and optimal coding properties. The spiking dynamics reproduced previously published computer simulations. However, the fractional order Hodgkin-Huxley circuit showed novel dynamics consistent with criticality. We compared the responses of this circuit to recordings from neurons in the weakly-electric fish that have previously been shown to perform fractional order differentiation of their sensory input. The criticality seen in the circuit was confirmed in spontaneous recordings in the live fish. Furthermore, the circuit also predicted long-lasting stimulation that was also corroborated experimentally. Our work shows that fractional order memcapacitors provide intrinsic memory dependence that could allow implementation of computationally efficient neuromorphic devices. Memcapacitors are static elements that consume less energy than the most widely studied memristors, thus allowing the realization of energetically efficient neuromorphic devices.
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Affiliation(s)
- Patricia Vazquez-Guerrero
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, 78349, USA
| | - Rohisha Tuladhar
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, 78349, USA
| | | | - Ahmed Elwakil
- Department of Electrical and Computer Engineering, University of Sharjah, PO Box 27272, Sharjah, UAE
- Department of Electrical and Software Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Maurice J Chacron
- Department of Physiology, McGill University, Quebec, H3G 1Y6, Canada
| | - Fidel Santamaria
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, 78349, USA.
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Wi S, Li C, Pham K, Lee W, Frydman L. Short and long range 2D 15N- 15N NMR correlations among peptide groups by novel solid state dipolar mixing schemes. J Biomol NMR 2024; 78:19-30. [PMID: 38102490 DOI: 10.1007/s10858-023-00429-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/06/2023] [Indexed: 12/17/2023]
Abstract
A recently developed homonuclear dipolar recoupling scheme, Adiabatic Linearly FREquency Swept reCOupling (AL FRESCO), was applied to record two-dimensional (2D) 15N-15N correlations on uniformly 15N-labeled GB1 powders. A major feature exploited in these 15N-15N correlations was AL FRESCO's remarkably low RF power demands, which enabled seconds-long mixing schemes when establishing direct correlations. These 15N-15N mixing schemes proved efficient regardless of the magic-angle spinning (MAS) rate and, being nearly free from dipolar truncation effects, they enabled the detection of long-range, weak dipolar couplings, even in the presence of strong short-range dipolar couplings. This led to a connectivity information that was significantly better than that obtained with spontaneously proton-driven, 15N spin-diffusion experiments. An indirect approach producing long-range 15N-15N correlations was also tested, relying on short (ms-long) 1HN-1HN mixings schemes while applying AL FRESCO chirped pulses along the 15N channel. These indirect mixing schemes produced numerous long-distance Ni-Ni±n (n = 2 - 5) correlations, that might be useful for characterizing three-dimensional arrangements in proteins. Once again, these AL FRESCO mediated experiments proved more informative than variants based on spin-diffusion-based 1HN-1HN counterparts.
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Affiliation(s)
- Sungsool Wi
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32304, USA.
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Karen Pham
- Department of Chemistry, University of Colorado at Denver, Denver, CO, 80217-3364, USA
| | - Woonghee Lee
- Department of Chemistry, University of Colorado at Denver, Denver, CO, 80217-3364, USA
| | - Lucio Frydman
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32304, USA.
- Department of Chemical and Biological Physics, Weizmann Institute of Sciences, Rehovot, Israel.
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6
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Chaudhary BP, Struppe J, Moktan H, Zoetewey D, Zhou DH, Mohanty S. Reconstitution and resonance assignments of yeast OST subunit Ost4 and its critical mutant Ost4V23D in liposomes by solid-state NMR. J Biomol NMR 2024:10.1007/s10858-024-00437-8. [PMID: 38421550 DOI: 10.1007/s10858-024-00437-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
N-linked glycosylation is an essential and highly conserved co- and post-translational protein modification in all domains of life. In humans, genetic defects in N-linked glycosylation pathways result in metabolic diseases collectively called Congenital Disorders of Glycosylation. In this modification reaction, a mannose rich oligosaccharide is transferred from a lipid-linked donor substrate to a specific asparagine side-chain within the -N-X-T/S- sequence (where X ≠ Proline) of the nascent protein. Oligosaccharyltransferase (OST), a multi-subunit membrane embedded enzyme catalyzes this glycosylation reaction in eukaryotes. In yeast, Ost4 is the smallest of nine subunits and bridges the interaction of the catalytic subunit, Stt3, with Ost3 (or its homolog, Ost6). Mutations of any C-terminal hydrophobic residues in Ost4 to a charged residue destabilizes the enzyme and negatively impacts its function. Specifically, the V23D mutation results in a temperature-sensitive phenotype in yeast. Here, we report the reconstitution of both purified recombinant Ost4 and Ost4V23D each in a POPC/POPE lipid bilayer and their resonance assignments using heteronuclear 2D and 3D solid-state NMR with magic-angle spinning. The chemical shifts of Ost4 changed significantly upon the V23D mutation, suggesting a dramatic change in its chemical environment.
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Affiliation(s)
- Bharat P Chaudhary
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA
| | | | - Hem Moktan
- Department of Physics, Oklahoma State University, Stillwater, OK, 74078, USA
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David Zoetewey
- Department of Chemistry, Physics and Astronomy, Georgia College and State University, Milledgeville, GA, 31061, USA
| | - Donghua H Zhou
- Department of Physics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Smita Mohanty
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
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7
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Guilderson TP, Glynn DS, McCarthy MD. Tropical decadal variability in nutrient supply and phytoplankton community in the Central Equatorial Pacific during the late Holocene. Sci Rep 2024; 14:4161. [PMID: 38378879 PMCID: PMC10879156 DOI: 10.1038/s41598-024-54635-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/14/2024] [Indexed: 02/22/2024] Open
Abstract
We have reconstructed baseline δ15N and δ13C of export production at Kingman Reef in the Central Equatorial Pacific (CEP) at sub-decadal resolution, nearly continuously over the last 2000 years. The changes in δ15N reflects the strength of the North Equatorial Counter Current (NECC) relative to the South Equatorial Current (SEC), and to a lesser extent, the North Equatorial Current (NEC). Seasonal to multi-decadal variation in the strength of these currents, through the redistribution of heat, have global climate impacts and influence marine and terrestrial ecosystems. We use modern El Niño-La Nina dynamics and the Tropical Pacific Decadal Variability (TPDV) pattern, which is defined in the CEP, as a framework for analyzing the isotopic data. The CEP δ15N and δ13C records exhibit multi-decadal (50-60 year) variability consistent with TPDV. A large multi-centennial feature in the CEP δ15N data, within age-model uncertainties, is consistent with one of the prolonged dry-pluvial sequences in the American west at the end of the Medieval Climate Anomaly, where low TPDV is correlated with drier conditions. This unique record shows that the strength of the NECC, as reflected in baseline δ15N and δ13C, has at quasi-predictable intervals throughout the late Holocene, toggled the phytoplankton community between prokaryotes and picoplankton versus eukaryotes.
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Affiliation(s)
- T P Guilderson
- Ocean Sciences Department, University of California - Santa Cruz, 1156 High Street, Santa Cruz, CA, USA.
| | - D S Glynn
- Ocean Sciences Department, University of California - Santa Cruz, 1156 High Street, Santa Cruz, CA, USA
| | - M D McCarthy
- Ocean Sciences Department, University of California - Santa Cruz, 1156 High Street, Santa Cruz, CA, USA
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8
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Lin K, Chang YC, Billmann M, Ward HN, Le K, Hassan AZ, Bhojoo U, Chan K, Costanzo M, Moffat J, Boone C, Bielinsky AK, Myers CL. A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds. Sci Rep 2024; 14:2508. [PMID: 38291084 PMCID: PMC10828508 DOI: 10.1038/s41598-024-51735-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
Current approaches to define chemical-genetic interactions (CGIs) in human cell lines are resource-intensive. We designed a scalable chemical-genetic screening platform by generating a DNA damage response (DDR)-focused custom sgRNA library targeting 1011 genes with 3033 sgRNAs. We performed five proof-of-principle compound screens and found that the compounds' known modes-of-action (MoA) were enriched among the compounds' CGIs. These scalable screens recapitulated expected CGIs at a comparable signal-to-noise ratio (SNR) relative to genome-wide screens. Furthermore, time-resolved CGIs, captured by sequencing screens at various time points, suggested an unexpected, late interstrand-crosslinking (ICL) repair pathway response to camptothecin-induced DNA damage. Our approach can facilitate screening compounds at scale with 20-fold fewer resources than commonly used genome-wide libraries and produce biologically informative CGI profiles.
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Affiliation(s)
- Kevin Lin
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Ya-Chu Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Khoi Le
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Arshia Z Hassan
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Urvi Bhojoo
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Katherine Chan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Institute for Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
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Stern CM, McPherson I, Dreier MJ, Coniglio K, Palmer LP, Gydus J, Graver H, Germine LT, Tabri N, Wang SB, Breithaupt L, Eddy KT, Thomas JJ, Plessow F, Becker KR. Avoidant/restrictive food intake disorder differs from anorexia nervosa in delay discounting. J Eat Disord 2024; 12:19. [PMID: 38287459 PMCID: PMC10823699 DOI: 10.1186/s40337-023-00958-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Avoidant/restrictive food intake disorder (ARFID) and anorexia nervosa (AN) are the two primary restrictive eating disorders; however, they are driven by differing motives for inadequate dietary intake. Despite overlap in restrictive eating behaviors and subsequent malnutrition, it remains unknown if ARFID and AN also share commonalities in their cognitive profiles, with cognitive alterations being a key identifier of AN. Discounting the present value of future outcomes with increasing delay to their expected receipt represents a core cognitive process guiding human decision-making. A hallmark cognitive characteristic of individuals with AN (vs. healthy controls [HC]) is reduced discounting of future outcomes, resulting in reduced impulsivity and higher likelihood of favoring delayed gratification. Whether individuals with ARFID display a similar reduction in delay discounting as those with AN (vs. an opposing bias towards increased delay discounting or no bias) is important in informing transdiagnostic versus disorder-specific cognitive characteristics and optimizing future intervention strategies. METHOD To address this research question, 104 participants (ARFID: n = 57, AN: n = 28, HC: n = 19) completed a computerized Delay Discounting Task. Groups were compared by their delay discounting parameter (ln)k. RESULTS Individuals with ARFID displayed a larger delay discounting parameter than those with AN, indicating steeper delay discounting (M ± SD = -6.10 ± 2.00 vs. -7.26 ± 1.73, p = 0.026 [age-adjusted], Hedges' g = 0.59), with no difference from HC (p = 0.514, Hedges' g = -0.35). CONCLUSION Our findings provide a first indication of distinct cognitive profiles among the two primary restrictive eating disorders. The present results, together with future research spanning additional cognitive domains and including larger and more diverse samples of individuals with ARFID (vs. AN), will contribute to identifying maintenance mechanisms that are unique to each disorder as well as contribute to the optimization and tailoring of treatment strategies across the spectrum of restrictive eating disorders.
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Affiliation(s)
- Casey M Stern
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, 2 Longfellow Place, Suite 200, Boston, MA, 02114, USA
| | - Iman McPherson
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, USA
| | - Melissa J Dreier
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, 2 Longfellow Place, Suite 200, Boston, MA, 02114, USA
- Department of Psychology, Rutgers University, New Brunswick, USA
| | - Kathryn Coniglio
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, 2 Longfellow Place, Suite 200, Boston, MA, 02114, USA
- Department of Psychology, Rutgers University, New Brunswick, USA
| | - Lilian P Palmer
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, 2 Longfellow Place, Suite 200, Boston, MA, 02114, USA
| | - Julia Gydus
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, USA
| | - Haley Graver
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, 2 Longfellow Place, Suite 200, Boston, MA, 02114, USA
| | - Laura T Germine
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, USA
- Department of Psychiatry, Harvard Medical School, Cambridge, USA
| | - Nassim Tabri
- Department of Psychology, Carleton University, Ottawa, Canada
- Mental Health and Well-Being Research and Training Hub, Carleton University, Ottawa, Canada
| | - Shirley B Wang
- Department of Psychology, Harvard University, Cambridge, USA
| | - Lauren Breithaupt
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, 2 Longfellow Place, Suite 200, Boston, MA, 02114, USA
- Department of Psychiatry, Harvard Medical School, Cambridge, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, USA
| | - Kamryn T Eddy
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, 2 Longfellow Place, Suite 200, Boston, MA, 02114, USA
- Department of Psychiatry, Harvard Medical School, Cambridge, USA
| | - Jennifer J Thomas
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, 2 Longfellow Place, Suite 200, Boston, MA, 02114, USA
- Department of Psychiatry, Harvard Medical School, Cambridge, USA
| | - Franziska Plessow
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Cambridge, USA
| | - Kendra R Becker
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, 2 Longfellow Place, Suite 200, Boston, MA, 02114, USA.
- Department of Psychiatry, Harvard Medical School, Cambridge, USA.
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10
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Carroll SL, Schmidt GM, Waller JS, Graves TA. Evaluating density-weighted connectivity of black bears (Ursus americanus) in Glacier National Park with spatial capture-recapture models. Mov Ecol 2024; 12:8. [PMID: 38263096 DOI: 10.1186/s40462-023-00445-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024]
Abstract
BACKGROUND Improved understanding of wildlife population connectivity among protected area networks can support effective planning for the persistence of wildlife populations in the face of land use and climate change. Common approaches to estimating connectivity often rely on small samples of individuals without considering the spatial structure of populations, leading to limited understanding of how individual movement links to demography and population connectivity. Recently developed spatial capture-recapture (SCR) models provide a framework to formally connect inference about individual movement, connectivity, and population density, but few studies have applied this approach to empirical data to support connectivity planning. METHODS We used mark-recapture data collected from 924 genetic detections of 598 American black bears (Ursus americanus) in 2004 with SCR ecological distance models to simultaneously estimate density, landscape resistance to movement, and population connectivity in Glacier National Park northwest Montana, USA. We estimated density and movement parameters separately for males and females and used model estimates to calculate predicted density-weighted connectivity surfaces. RESULTS Model results indicated that landscape structure influences black bear density and space use in Glacier. The mean density estimate was 16.08 bears/100 km2 (95% CI 12.52-20.6) for females and 9.27 bears/100 km2 (95% CI 7.70-11.14) for males. Density increased with forest cover for both sexes. For male black bears, density decreased at higher grizzly bear (Ursus arctos) densities. Drainages, valley bottoms, and riparian vegetation decreased estimates of landscape resistance to movement for male and female bears. For males, forest cover also decreased estimated resistance to movement, but a transportation corridor bisecting the study area strongly increased resistance to movement presenting a barrier to connectivity. CONCLUSIONS Density-weighed connectivity surfaces highlighted areas important for population connectivity that were distinct from areas with high potential connectivity. For black bears in Glacier and surrounding landscapes, consideration of both vegetation and valley topography could inform the placement of underpasses along the transportation corridor in areas characterized by both high population density and potential connectivity. Our study demonstrates that the SCR ecological distance model can provide biologically realistic, spatially explicit predictions to support movement connectivity planning across large landscapes.
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Affiliation(s)
- Sarah L Carroll
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Greta M Schmidt
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - John S Waller
- Glacier National Park, P.O. Box 128, West Glacier, MT, 59936, USA
| | - Tabitha A Graves
- U.S. Geological Survey, Northern Rocky Mountain Science Center, PO Box 169, West Glacier, MT, 59936, USA
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11
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Draizen EJ, Readey J, Mura C, Bourne PE. Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data. BMC Bioinformatics 2024; 25:11. [PMID: 38177985 PMCID: PMC10768222 DOI: 10.1186/s12859-023-05586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Machine learning (ML) has a rich history in structural bioinformatics, and modern approaches, such as deep learning, are revolutionizing our knowledge of the subtle relationships between biomolecular sequence, structure, function, dynamics and evolution. As with any advance that rests upon statistical learning approaches, the recent progress in biomolecular sciences is enabled by the availability of vast volumes of sufficiently-variable data. To be useful, such data must be well-structured, machine-readable, intelligible and manipulable. These and related requirements pose challenges that become especially acute at the computational scales typical in ML. Furthermore, in structural bioinformatics such data generally relate to protein three-dimensional (3D) structures, which are inherently more complex than sequence-based data. A significant and recurring challenge concerns the creation of large, high-quality, openly-accessible datasets that can be used for specific training and benchmarking tasks in ML pipelines for predictive modeling projects, along with reproducible splits for training and testing. RESULTS Here, we report 'Prop3D', a platform that allows for the creation, sharing and extensible reuse of libraries of protein domains, featurized with biophysical and evolutionary properties that can range from detailed, atomically-resolved physicochemical quantities (e.g., electrostatics) to coarser, residue-level features (e.g., phylogenetic conservation). As a community resource, we also supply a 'Prop3D-20sf' protein dataset, obtained by applying our approach to CATH . We have developed and deployed the Prop3D framework, both in the cloud and on local HPC resources, to systematically and reproducibly create comprehensive datasets via the Highly Scalable Data Service ( HSDS ). Our datasets are freely accessible via a public HSDS instance, or they can be used with accompanying Python wrappers for popular ML frameworks. CONCLUSION Prop3D and its associated Prop3D-20sf dataset can be of broad utility in at least three ways. Firstly, the Prop3D workflow code can be customized and deployed on various cloud-based compute platforms, with scalability achieved largely by saving the results to distributed HDF5 files via HSDS . Secondly, the linked Prop3D-20sf dataset provides a hand-crafted, already-featurized dataset of protein domains for 20 highly-populated CATH families; importantly, provision of this pre-computed resource can aid the more efficient development (and reproducible deployment) of ML pipelines. Thirdly, Prop3D-20sf's construction explicitly takes into account (in creating datasets and data-splits) the enigma of 'data leakage', stemming from the evolutionary relationships between proteins.
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Affiliation(s)
- Eli J Draizen
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
- School of Data Science, University of Virginia, Charlottesville, VA, USA.
| | | | - Cameron Mura
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
- School of Data Science, University of Virginia, Charlottesville, VA, USA.
| | - Philip E Bourne
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
- School of Data Science, University of Virginia, Charlottesville, VA, USA
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12
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Athey TL, Tward DJ, Mueller U, Younes L, Vogelstein JT, Miller MI. Preserving Derivative Information while Transforming Neuronal Curves. Neuroinformatics 2024; 22:63-74. [PMID: 38036915 PMCID: PMC10917852 DOI: 10.1007/s12021-023-09648-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2023] [Indexed: 12/02/2023]
Abstract
The international neuroscience community is building the first comprehensive atlases of brain cell types to understand how the brain functions from a higher resolution, and more integrated perspective than ever before. In order to build these atlases, subsets of neurons (e.g. serotonergic neurons, prefrontal cortical neurons etc.) are traced in individual brain samples by placing points along dendrites and axons. Then, the traces are mapped to common coordinate systems by transforming the positions of their points, which neglects how the transformation bends the line segments in between. In this work, we apply the theory of jets to describe how to preserve derivatives of neuron traces up to any order. We provide a framework to compute possible error introduced by standard mapping methods, which involves the Jacobian of the mapping transformation. We show how our first order method improves mapping accuracy in both simulated and real neuron traces under random diffeomorphisms. Our method is freely available in our open-source Python package brainlit.
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Affiliation(s)
- Thomas L Athey
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Daniel J Tward
- Department of Computational Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Department of Neurology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ulrich Mueller
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Laurent Younes
- Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA
- Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Joshua T Vogelstein
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Michael I Miller
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
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13
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Bano R, Mears P, Golding I, Chemla YR. Flagellar dynamics reveal fluctuations and kinetic limit in the Escherichia coli chemotaxis network. Sci Rep 2023; 13:22891. [PMID: 38129516 PMCID: PMC10739816 DOI: 10.1038/s41598-023-49784-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The Escherichia coli chemotaxis network, by which bacteria modulate their random run/tumble swimming pattern to navigate their environment, must cope with unavoidable number fluctuations ("noise") in its molecular constituents like other signaling networks. The probability of clockwise (CW) flagellar rotation, or CW bias, is a measure of the chemotaxis network's output, and its temporal fluctuations provide a proxy for network noise. Here we quantify fluctuations in the chemotaxis signaling network from the switching statistics of flagella, observed using time-resolved fluorescence microscopy of individual optically trapped E. coli cells. This approach allows noise to be quantified across the dynamic range of the network. Large CW bias fluctuations are revealed at steady state, which may play a critical role in driving flagellar switching and cell tumbling. When the network is stimulated chemically to higher activity, fluctuations dramatically decrease. A stochastic theoretical model, inspired by work on gene expression noise, points to CheY activation occurring in bursts, driving CW bias fluctuations. This model also shows that an intrinsic kinetic ceiling on network activity places an upper limit on activated CheY and CW bias, which when encountered suppresses network fluctuations. This limit may also prevent cells from tumbling unproductively in steep gradients.
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Affiliation(s)
- Roshni Bano
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patrick Mears
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ido Golding
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yann R Chemla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Sajedi S, Ebrahimi G, Roudi R, Mehta I, Heshmat A, Samimi H, Kazempour S, Zainulabadeen A, Docking TR, Arora SP, Cigarroa F, Seshadri S, Karsan A, Zare H. Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package. Sci Rep 2023; 13:21721. [PMID: 38066050 PMCID: PMC10709411 DOI: 10.1038/s41598-023-48237-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package ( https://bioconductor.org/packages/iNETgrate/ ) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach.
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Affiliation(s)
- Sogand Sajedi
- Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, 78229, USA
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, San Antonio, TX, 78229, USA
| | - Ghazal Ebrahimi
- Bioinformatics Program, The University of British Columbia, Vancouver, BC, Canada
| | - Raheleh Roudi
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Isha Mehta
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Amirreza Heshmat
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hanie Samimi
- School of Architecture, University of Utah, Salt Lake City, UT, 84112, USA
| | - Shiva Kazempour
- Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, 78229, USA
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, San Antonio, TX, 78229, USA
| | - Aamir Zainulabadeen
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA
| | - Thomas Roderick Docking
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Sukeshi Patel Arora
- Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Francisco Cigarroa
- Malu and Carlos Alvarez Center for Transplantation, Hepatobiliary Surgery and Innovation, The University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, San Antonio, TX, 78229, USA
- Department of Neurology, University of Texas, San Antonio, TX, 78229, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, 02139, USA
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Habil Zare
- Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, 78229, USA.
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, San Antonio, TX, 78229, USA.
- Department of Cell Systems & Anatomy, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
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Koçillari L, Celotto M, Francis NA, Mukherjee S, Babadi B, Kanold PO, Panzeri S. Behavioural relevance of redundant and synergistic stimulus information between functionally connected neurons in mouse auditory cortex. Brain Inform 2023; 10:34. [PMID: 38052917 PMCID: PMC10697912 DOI: 10.1186/s40708-023-00212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/02/2023] [Indexed: 12/07/2023] Open
Abstract
Measures of functional connectivity have played a central role in advancing our understanding of how information is transmitted and processed within the brain. Traditionally, these studies have focused on identifying redundant functional connectivity, which involves determining when activity is similar across different sites or neurons. However, recent research has highlighted the importance of also identifying synergistic connectivity-that is, connectivity that gives rise to information not contained in either site or neuron alone. Here, we measured redundant and synergistic functional connectivity between neurons in the mouse primary auditory cortex during a sound discrimination task. Specifically, we measured directed functional connectivity between neurons simultaneously recorded with calcium imaging. We used Granger Causality as a functional connectivity measure. We then used Partial Information Decomposition to quantify the amount of redundant and synergistic information about the presented sound that is carried by functionally connected or functionally unconnected pairs of neurons. We found that functionally connected pairs present proportionally more redundant information and proportionally less synergistic information about sound than unconnected pairs, suggesting that their functional connectivity is primarily redundant. Further, synergy and redundancy coexisted both when mice made correct or incorrect perceptual discriminations. However, redundancy was much higher (both in absolute terms and in proportion to the total information available in neuron pairs) in correct behavioural choices compared to incorrect ones, whereas synergy was higher in absolute terms but lower in relative terms in correct than in incorrect behavioural choices. Moreover, the proportion of redundancy reliably predicted perceptual discriminations, with the proportion of synergy adding no extra predictive power. These results suggest a crucial contribution of redundancy to correct perceptual discriminations, possibly due to the advantage it offers for information propagation, and also suggest a role of synergy in enhancing information level during correct discriminations.
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Affiliation(s)
- Loren Koçillari
- Istituto Italiano Di Tecnologia, 38068, Rovereto, Italy.
- Department of Excellence for Neural Information Processing, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251, Hamburg, Germany.
- Department of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany.
| | - Marco Celotto
- Istituto Italiano Di Tecnologia, 38068, Rovereto, Italy
- Department of Excellence for Neural Information Processing, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251, Hamburg, Germany
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Nikolas A Francis
- Department of Biology and Brain and Behavior Institute, University of Maryland, College Park, MD, 20742, USA
| | - Shoutik Mukherjee
- Department of Electrical and Computer Engineering and Institute for Systems Research, University of Maryland, College Park, MD, 20742, USA
| | - Behtash Babadi
- Department of Electrical and Computer Engineering and Institute for Systems Research, University of Maryland, College Park, MD, 20742, USA
| | - Patrick O Kanold
- Department of Biomedical Engineering and Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Stefano Panzeri
- Department of Excellence for Neural Information Processing, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251, Hamburg, Germany.
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16
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Ghaemi Z, Nafiu O, Tajkhorshid E, Gruebele M, Hu J. A computational spatial whole-Cell model for hepatitis B viral infection and drug interactions. Sci Rep 2023; 13:21392. [PMID: 38049515 PMCID: PMC10695947 DOI: 10.1038/s41598-023-45998-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 10/26/2023] [Indexed: 12/06/2023] Open
Abstract
Despite a vaccine, hepatitis B virus (HBV) remains a world-wide source of infections and deaths. We develop a whole-cell computational platform combining spatial and kinetic models describing the infection cycle of HBV in a hepatocyte host. We simulate key parts of the infection cycle with this whole-cell platform for 10 min of biological time, to predict infection progression, map out virus-host and virus-drug interactions. We find that starting from an established infection, decreasing the copy number of the viral envelope proteins shifts the dominant infection pathway from capsid secretion to re-importing the capsids into the nucleus, resulting in more nuclear-localized viral covalently closed circular DNA (cccDNA) and boosting transcription. This scenario can mimic the consequence of drugs designed to manipulate viral gene expression. Mutating capsid proteins facilitates capsid destabilization and disassembly at nuclear pore complexes, resulting in an increase in cccDNA copy number. However, excessive destabilization leads to premature cytoplasmic disassembly and does not increase the cccDNA counts. Finally, our simulations can predict the best drug dosage and its administration timing to reduce the cccDNA counts. Our adaptable computational platform can be parameterized to study other viruses and identify the most central viral pathways that can be targeted by drugs.
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Affiliation(s)
- Zhaleh Ghaemi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- National Science Foundation Science and Technology Center for Quantitative Cell Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Oluwadara Nafiu
- Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Emad Tajkhorshid
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- National Science Foundation Science and Technology Center for Quantitative Cell Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- National Science Foundation Science and Technology Center for Quantitative Cell Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jianming Hu
- Department of Microbiology and Immunology, Pennsylvania State University, Hershey, PA, 17033, USA
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Al-Danoon O, Mohanty S. Backbone and side chain NMR assignments and secondary structure calculation of the pheromone binding protein3 of Ostrinia nubilalis, an agricultural pest. Biomol NMR Assign 2023; 17:223-227. [PMID: 37498448 DOI: 10.1007/s12104-023-10145-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023]
Abstract
Ostrinia nubilalis, also known as European Corn Borer (ECB), is a serious pest in Europe and North America, as well as in Central Asia and Northern Africa. It damages a variety of agricultural crops such as corn, oats, buckwheat, millet, and soybeans. causing annually at least one billion dollars in loss. The Ostrinia nubilalis pheromone-binding protein3 (OnubPBP3), preferentially expressed in the male moth antenna, has been implicated in the detection of the female-secreted pheromone blend during the mating process. Understanding the structure of and function of OnubPBP3, including the mechanism of pheromone binding and its release at the dendritic olfactory neuron (ORN), is essential if integrated pest management through sensory inhibition is to be achieved. We report here the backbone and side-chain resonance assignments of OnubPBP3 at pH 6.5 using various triple resonance NMR experiments on a 13C, 15N-labeled protein sample. The secondary structure of OnubPBP3 consists of six α-helices and an unstructured C-terminus based on backbone chemical shifts.
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Affiliation(s)
- Omar Al-Danoon
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Smita Mohanty
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
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18
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Reinhold JM, Halbert E, Roark M, Smith SN, Stroh KM, Siler CD, McLeod DS, Lahondère C. The role of Culex territans mosquitoes in the transmission of Batrachochytrium dendrobatidis to amphibian hosts. Parasit Vectors 2023; 16:424. [PMID: 37974288 PMCID: PMC10655354 DOI: 10.1186/s13071-023-05992-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/29/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Mosquitoes are the deadliest organisms in the world, killing an estimated 750,000 people per year due to the pathogens they can transmit. Mosquitoes also pose a major threat to other vertebrate animals. Culex territans is a mosquito species found in temperate zones worldwide that feeds almost exclusively on amphibians and can transmit parasites; however, little is known about its ability to transmit other pathogens, including fungi. Batrachochytrium dendrobatidis (Bd) is a topical pathogenic fungus that spreads through contact. With amphibian populations around the world experiencing mass die-offs and extinctions due to this pathogen, it is critical to study all potential modes of transmission. Because Cx. territans mosquitoes are in contact with their hosts for long periods of time while blood-feeding, we hypothesize that they can transmit and pick up Bd. METHODS In this study, we first assessed Cx. territans ability to transfer the fungus from an infected surface to a clean one under laboratory conditions. We also conducted a surveillance study of Bd infections in frogs and mosquitoes in the field (Mountain Lake Biological station, VA, USA). In parallel, we determined Cx. territans host preference via blood meal analysis of field caught mosquitoes. RESULTS We found that this mosquito species can carry the fungus to an uninfected surface, implying that they may have the ability to transmit Bd to their amphibian hosts. We also found that Cx. territans feed primarily on green frogs (Rana clamitans) and bullfrogs (Rana catesbeiana) and that the prevalence of Bd within the frog population at our field site varied between years. CONCLUSIONS This study provides critical insights into understanding the role of amphibian-biting mosquitoes in transmitting pathogens, which can be applied to disease ecology of susceptible amphibian populations worldwide.
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Affiliation(s)
- Joanna M Reinhold
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- The Fralin Life Science, InstituteVirginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | | | - Megan Roark
- University of Virginia's College at Wise, Wise, VA, 24293, USA
| | - Sierra N Smith
- Sam Noble Oklahoma Museum of Natural History and School of Biological Sciences, The University of Oklahoma, Norman, OK, 73072, USA
| | - Katherine M Stroh
- Sam Noble Oklahoma Museum of Natural History and School of Biological Sciences, The University of Oklahoma, Norman, OK, 73072, USA
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and School of Biological Sciences, The University of Oklahoma, Norman, OK, 73072, USA
| | - David S McLeod
- Murphy Deming College of Health Sciences, Mary Baldwin University, Staunton, VA, 24401, USA
| | - Chloé Lahondère
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- The Fralin Life Science, InstituteVirginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Center of Emerging, Zoonotic and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- The Global Change Center, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
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Barton SA, Kent M, Hecht EE. Neuroanatomical asymmetry in the canine brain. Brain Struct Funct 2023; 228:1657-1669. [PMID: 37436502 DOI: 10.1007/s00429-023-02677-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/01/2023] [Indexed: 07/13/2023]
Abstract
The brains of humans and non-human primates exhibit left/right asymmetries in grey matter morphology, white matter connections, and functional responses. These asymmetries have been implicated in specialized behavioral adaptations such as language, tool use, and handedness. Left/right asymmetries are also observed in behavioral tendencies across the animal kingdom, suggesting a deep evolutionary origin for the neural mechanisms underlying lateralized behavior. However, it is still unclear to what extent brain asymmetries supporting lateralized behaviors are present in other large-brained animals outside the primate order. Canids and other carnivorans evolved large, complex brains independently and convergently with primates, and exhibit lateralized behaviors. Therefore, domestic dogs offer an opportunity to address this question. We examined T2-weighted MRI images of 62 dogs from 33 breeds, opportunistically collected from a veterinary MRI scanner from dogs who were referred for neurological examination but were not found to show any neuropathology. Volumetrically asymmetric regions of gray matter included portions of the temporal and frontal cortex, in addition to portions of the cerebellum, brainstem, and other subcortical regions. These results are consistent with the perspective that asymmetry may be a common feature underlying the evolution of complex brains and behavior across clades, and provide neuro-organizational information that is likely relevant to the growing field of canine behavioral neuroscience.
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Affiliation(s)
- Sophie A Barton
- Department of Human Evolutionary Biology, Harvard University, Cambridge, 02138, USA.
| | - Marc Kent
- College of Veterinary Medicine, University of Georgia, Athens, 30602, USA
| | - Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, Cambridge, 02138, USA
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20
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Alloy LB, Walsh RFL, Smith LT, Maddox MA, Olino TM, Zee PC, Nusslock R. Circadian, Reward, and Emotion Systems in Teens prospective longitudinal study: protocol overview of an integrative reward-circadian rhythm model of first onset of bipolar spectrum disorder in adolescence. BMC Psychiatry 2023; 23:602. [PMID: 37592214 PMCID: PMC10436678 DOI: 10.1186/s12888-023-05094-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Bipolar spectrum disorders (BSDs) are associated with a heightened sensitivity to rewards and elevated reward-related brain function in cortico-striatal circuitry. A separate literature documents social and circadian rhythm disruption in BSDs. Recently, integrated reward-circadian models of BSDs have been proposed. These models draw on work indicating that the two systems influence each other and interact to affect mood functioning. When dysregulated, reward and circadian system signaling may combine to form a positive feedback loop, whereby dysregulation in one system exacerbates dysregulation in the other. Project CREST (Circadian, Reward, and Emotion Systems in Teens) provides a first systematic test of reward-circadian dysregulation as a synergistic and dynamic vulnerability for first onset of BSD and increases in bipolar symptoms during adolescence. METHODS This NIMH-funded R01 study is a 3-year prospective, longitudinal investigation of approximately 320 community adolescents from the broader Philadelphia area, United States of America. Eligible participants must be 13-16 years old, fluent in English, and without a prior BSD or hypomanic episode. They are being selected along the entire dimension of self-reported reward responsiveness, with oversampling at the high tail of the dimension in order to increase the likelihood of BSD onsets. At Times 1-6, every 6 months, participants will complete assessments of reward-relevant and social rhythm disruption life events and self-report and diagnostic assessments of bipolar symptoms and episodes. Yearly, at Times 1, 3, and 5, participants also will complete self-report measures of circadian chronotype (morningness-eveningness) and social rhythm regularity, a salivary dim light melatonin onset (DLMO) procedure to assess circadian phase, self-report, behavioral, and neural (fMRI) assessments of monetary and social reward responsiveness, and a 7-day ecological momentary assessment (EMA) period. During each EMA period, participants will complete continuous measures of sleep/wake and activity (actigraphy), a daily sleep diary, and three within-day (morning, afternoon, evening) measures of life events coded for reward-relevance and social rhythm disruption, monetary and social reward responsiveness, positive and negative affect, and hypo/manic and depressive symptoms. The fMRI scan will occur on the day before and the DLMO procedure will occur on the first evening of the 7-day EMA period. DISCUSSION This study is an innovative integration of research on multi-organ systems involved in reward and circadian signaling in understanding first onset of BSD in adolescence. It has the potential to facilitate novel pharmacological, neural, and behavioral interventions to treat, and ideally prevent, bipolar conditions.
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Affiliation(s)
- Lauren B Alloy
- Department of Psychology and Neuroscience, Temple University, Philadelphia, USA.
| | - Rachel F L Walsh
- Department of Psychology and Neuroscience, Temple University, Philadelphia, USA
| | - Logan T Smith
- Department of Psychology and Neuroscience, Temple University, Philadelphia, USA
| | - Mackenzie A Maddox
- Department of Psychology and Neuroscience, Temple University, Philadelphia, USA
| | - Thomas M Olino
- Department of Psychology and Neuroscience, Temple University, Philadelphia, USA
| | - Phyllis C Zee
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Evanston, USA
| | - Robin Nusslock
- Department of Psychology, Northwestern University, Evanston, USA
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21
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Rajput AA, Mostafavi A. Latent sub-structural resilience mechanisms in temporal human mobility networks during urban flooding. Sci Rep 2023; 13:10953. [PMID: 37414862 PMCID: PMC10326012 DOI: 10.1038/s41598-023-37965-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/30/2023] [Indexed: 07/08/2023] Open
Abstract
In studying resilience in temporal human networks, relying solely on global network measures would be inadequate; latent sub-structural network mechanisms need to be examined to determine the extent of impact and recovery of these networks during perturbations, such as urban flooding. In this study, we utilize high-resolution aggregated location-based data to construct temporal human mobility networks in Houston in the context of the 2017 Hurricane Harvey. We examine motif distribution, motif persistence, temporal stability, and motif attributes to reveal latent sub-structural mechanisms related to the resilience of human mobility networks during disaster-induced perturbations. The results show that urban flood impacts persist in human mobility networks at the sub-structure level for several weeks. The impact extent and recovery duration are heterogeneous across different network types. Also, while perturbation impacts persist at the sub-structure level, global topological network properties indicate that the network has recovered. The findings highlight the importance of examining the microstructures and their dynamic processes and attributes in understanding the resilience of temporal human mobility networks (and other temporal networks). The findings can also provide disaster managers, public officials, and transportation planners with insights to better evaluate impacts and monitor recovery in affected communities.
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Affiliation(s)
- Akhil Anil Rajput
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX, USA
| | - Ali Mostafavi
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX, USA.
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22
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Zarei HR, Ghanbarpour Mamaghani M, Ergun O, Yu P, Winchester L, Chen E. Matching medical staff to long term care facilities to respond to COVID-19 outbreak. BMC Health Serv Res 2023; 23:583. [PMID: 37287022 DOI: 10.1186/s12913-023-09594-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 05/23/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Staff shortage is a long-standing issue in long term care facilities (LTCFs) that worsened with the COVID-19 outbreak. Different states in the US have employed various tools to alleviate this issue in LTCFs. We describe the actions taken by the Commonwealth of Massachusetts to assist LTCFs in addressing the staff shortage issue and their outcomes. Therefore, the main question of this study is how to create a central mechanism to allocate severely limited medical staff to healthcare centers during emergencies. METHODS For the Commonwealth of Massachusetts, we developed a mathematical programming model to match severely limited available staff with LTCF demand requests submitted through a designed portal. To find feasible matches and prioritize facility needs, we incorporated restrictions and preferences for both sides. For staff, we considered maximum mileage they are willing to travel, available by date, and short- or long-term work preferences. For LTCFs, we considered their demand quantities for different positions and the level of urgency for their demand. As a secondary goal of this study, by using the feedback entries data received from the LTCFs on their matches, we developed statistical models to determine the most salient features that induced the LTCFs to submit feedback. RESULTS We used the developed portal to complete about 150 matching sessions in 14 months to match staff to LTCFs in Massachusetts. LTCFs provided feedback for 2,542 matches including 2,064 intentions to hire the matched staff during this time. Further analysis indicated that nursing homes and facilities that entered higher levels of demand to the portal were more likely to provide feedback on the matches and facilities that were prioritized in the matching process due to whole facility testing or low staffing levels were less likely to do so. On the staffing side, matches that involved more experienced staff and staff who can work afternoons, evenings, and overnight were more likely to generate feedback from the facility that they were matched to. CONCLUSION Developing a central matching framework to match medical staff to LTCFs at the time of a public health emergency could be an efficient tool for responding to staffing shortages. Such central approaches that help allocate a severely limited resource efficiently during a public emergency can be developed and used for different resource types, as well as provide crucial demand and supply information in different regions and/or demographics.
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Affiliation(s)
- Hamid Reza Zarei
- Department of Mechanical & Industrial Engineering, Northeastern University, Boston, MA, USA.
| | | | - Ozlem Ergun
- Department of Mechanical & Industrial Engineering, Northeastern University, Boston, MA, USA
| | - Patricia Yu
- Executive Office of Health and Human Services, Boston, MA, USA
| | - Leanne Winchester
- Graduate School of Nursing, University of MA Chan Medical School - Commonwealth Medicine, Worcester, MA, USA
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23
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Li Y, Yuan Q, Guo D, Lou C, Cui X, Mei G, Petek H, Cao L, Ji W, Feng M. 1D Electronic Flat Bands in Untwisted Moiré Superlattices. Adv Mater 2023; 35:e2300572. [PMID: 37057612 DOI: 10.1002/adma.202300572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/03/2023] [Indexed: 06/16/2023]
Abstract
After the preparation of 2D electronic flat band (EFB) in van der Waals (vdW) superlattices, recent measurements suggest the existence of 1D electronic flat bands (1D-EFBs) in twisted vdW bilayers. However, the realization of 1D-EFBs is experimentally elusive in untwisted 2D layers, which is desired considering their fabrication and scalability. Herein, the discovery of 1D-EFBs is reported in an untwisted in situ-grown two atomic-layer Bi(110) superlattice self-aligned on an SnSe(001) substrate using scanning probe microscopy measurements and density functional theory calculations. While the Bi-Bi dimers of Bi zigzag (ZZ) chains are buckled, the epitaxial lattice mismatch between the Bi and SnSe layers induces two 1D buckling reversal regions (BRRs) extending along the ZZ direction in each Bi(110)-11 × 11 supercell. A series of 1D-EFBs arises spatially following BRRs that isolate electronic states along the armchair (AC) direction and localize electrons in 1D extended states along ZZ due to quantum interference at a topological node. This work provides a generalized strategy for engineering 1D-EFBs in utilizing lattice mismatch between untwisted rectangular vdW layers.
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Affiliation(s)
- Yafei Li
- School of Physics and Technology and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Qing Yuan
- School of Physics and Technology and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Deping Guo
- Beijing Key Laboratory of Optoelectronic Functional Materials & Micro-Nano Devices, Department of Physics, Renmin University of China, Beijing, 100872, P. R. China
- Key Laboratory of Quantum State Construction and Manipulation (Ministry of Education), Renmin Universiry of China, Beijing, 100872, P. R. China
| | - Cancan Lou
- School of Physics and Technology and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Xingxia Cui
- School of Physics and Technology and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Guangqiang Mei
- School of Physics and Technology and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Hrvoje Petek
- Department of Physics and Astronomy and the IQ Initiative, University of Pittsburgh, Pittsburgh, 15260, USA
| | - Limin Cao
- School of Physics and Technology and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Wei Ji
- Beijing Key Laboratory of Optoelectronic Functional Materials & Micro-Nano Devices, Department of Physics, Renmin University of China, Beijing, 100872, P. R. China
- Key Laboratory of Quantum State Construction and Manipulation (Ministry of Education), Renmin Universiry of China, Beijing, 100872, P. R. China
| | - Min Feng
- School of Physics and Technology and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
- Institute for Advanced Study, Wuhan University, Wuhan, 430072, P. R. China
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24
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Majumdar S, Basu S, McGue M, Chatterjee S. Simultaneous selection of multiple important single nucleotide polymorphisms in familial genome wide association studies data. Sci Rep 2023; 13:8476. [PMID: 37231056 PMCID: PMC10213008 DOI: 10.1038/s41598-023-35379-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 05/17/2023] [Indexed: 05/27/2023] Open
Abstract
We propose a resampling-based fast variable selection technique for detecting relevant single nucleotide polymorphisms (SNP) in a multi-marker mixed effect model. Due to computational complexity, current practice primarily involves testing the effect of one SNP at a time, commonly termed as 'single SNP association analysis'. Joint modeling of genetic variants within a gene or pathway may have better power to detect associated genetic variants, especially the ones with weak effects. In this paper, we propose a computationally efficient model selection approach-based on the e-values framework-for single SNP detection in families while utilizing information on multiple SNPs simultaneously. To overcome computational bottleneck of traditional model selection methods, our method trains one single model, and utilizes a fast and scalable bootstrap procedure. We illustrate through numerical studies that our proposed method is more effective in detecting SNPs associated with a trait than either single-marker analysis using family data or model selection methods that ignore the familial dependency structure. Further, we perform gene-level analysis in Minnesota Center for Twin and Family Research (MCTFR) dataset using our method to detect several SNPs using this that have been implicated to be associated with alcohol consumption.
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Affiliation(s)
- Subhabrata Majumdar
- University of Minnesota Twin Cities, Minneapolis, USA.
- AI Risk and Vulnerability Alliance, Seattle, USA.
| | - Saonli Basu
- University of Minnesota Twin Cities, Minneapolis, USA
| | - Matt McGue
- University of Minnesota Twin Cities, Minneapolis, USA
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25
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Hunt GR, Hood S, Gabert L, Lenzi T. Can a powered knee-ankle prosthesis improve weight-bearing symmetry during stand-to-sit transitions in individuals with above-knee amputations? J Neuroeng Rehabil 2023; 20:58. [PMID: 37131231 PMCID: PMC10155411 DOI: 10.1186/s12984-023-01177-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/19/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND After above-knee amputation, the missing biological knee and ankle are replaced with passive prosthetic devices. Passive prostheses are able to dissipate limited amounts of energy using resistive damper systems during "negative energy" tasks like sit-down. However, passive prosthetic knees are not able to provide high levels of resistance at the end of the sit-down movement when the knee is flexed, and users need the most support. Consequently, users are forced to over-compensate with their upper body, residual hip, and intact leg, and/or sit down with a ballistic and uncontrolled movement. Powered prostheses have the potential to solve this problem. Powered prosthetic joints are controlled by motors, which can produce higher levels of resistance at a larger range of joint positions than passive damper systems. Therefore, powered prostheses have the potential to make sitting down more controlled and less difficult for above-knee amputees, improving their functional mobility. METHODS Ten individuals with above-knee amputations sat down using their prescribed passive prosthesis and a research powered knee-ankle prosthesis. Subjects performed three sit-downs with each prosthesis while we recorded joint angles, forces, and muscle activity from the intact quadricep muscle. Our main outcome measures were weight-bearing symmetry and muscle effort of the intact quadricep muscle. We performed paired t-tests on these outcome measures to test for significant differences between passive and powered prostheses. RESULTS We found that the average weight-bearing symmetry improved by 42.1% when subjects sat down with the powered prosthesis compared to their passive prostheses. This difference was significant (p = 0.0012), and every subject's weight-bearing symmetry improved when using the powered prosthesis. Although the intact quadricep muscle contraction differed in shape, neither the integral nor the peak of the signal was significantly different between conditions (integral p > 0.01, peak p > 0.01). CONCLUSIONS In this study, we found that a powered knee-ankle prosthesis significantly improved weight-bearing symmetry during sit-down compared to passive prostheses. However, we did not observe a corresponding decrease in intact-limb muscle effort. These results indicate that powered prosthetic devices have the potential to improve balance during sit-down for individuals with above-knee amputation and provide insight for future development of powered prosthetics.
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Affiliation(s)
- Grace R Hunt
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA.
| | - Sarah Hood
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Lukas Gabert
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
- Rocky Mountain Center for Occupational and Environmental Health, Salt Lake City, UT, USA
| | - Tommaso Lenzi
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
- Rocky Mountain Center for Occupational and Environmental Health, Salt Lake City, UT, USA
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26
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Demidova EV, Serebriiskii IG, Vlasenkova R, Kelow S, Andrake MD, Hartman TR, Kent T, Virtucio J, Rosen GL, Pomerantz RT, Dunbrack RL, Golemis EA, Hall MJ, Chen DYT, Daly MB, Arora S. Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing. BMC Genomics 2023; 24:212. [PMID: 37095444 PMCID: PMC10123997 DOI: 10.1186/s12864-023-09310-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/13/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined. METHODS Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes. RESULTS Analysis of whole-exome sequencing (WES) data found enrichment of candidate pathogenic germline variants in DNA repair and replication genes, including multiple DNA polymerases. Induction of DNA damage in peripheral blood monocytes (PBMCs) significantly elevated numbers of [Formula: see text]H2AX foci, a marker of double-stranded breaks, in PBMCs from eoRCC patients versus PBMCs from matched cancer-free controls. Knockdown of candidate variant genes in Caki RCC cells increased [Formula: see text]H2AX foci. Immortalized patient-derived B cell lines bearing the candidate variants in DNA polymerase genes (POLD1, POLH, POLE, POLK) had DNA replication defects compared to control cells. Renal tumors carrying these DNA polymerase variants were microsatellite stable but had a high mutational burden. Direct biochemical analysis of the variant Pol δ and Pol η polymerases revealed defective enzymatic activities. CONCLUSIONS Together, these results suggest that constitutional defects in DNA repair underlie a subset of eoRCC cases. Screening patient lymphocytes to identify these defects may provide insight into mechanisms of carcinogenesis in a subset of genetically undefined eoRCCs. Evaluation of DNA repair defects may also provide insight into the cancer initiation mechanisms for subsets of eoRCCs and lay the foundation for targeting DNA repair vulnerabilities in eoRCC.
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Affiliation(s)
- Elena V Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
- Kazan Federal University, Kazan, 420008, Russia
| | - Ilya G Serebriiskii
- Kazan Federal University, Kazan, 420008, Russia
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Ramilia Vlasenkova
- Kazan Federal University, Kazan, 420008, Russia
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Simon Kelow
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mark D Andrake
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Tiffiney R Hartman
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
- Arcadia University, Glenside, PA, USA
| | - Tatiana Kent
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - James Virtucio
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Gail L Rosen
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Richard T Pomerantz
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Roland L Dunbrack
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Erica A Golemis
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Michael J Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
- Department of Clinical Genetics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - David Y T Chen
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Mary B Daly
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
- Department of Clinical Genetics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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27
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Jiménez-Marín B, Rakijas JB, Tyagi A, Pandey A, Hanschen ER, Anderson J, Heffel MG, Platt TG, Olson BJSC. Gene loss during a transition to multicellularity. Sci Rep 2023; 13:5268. [PMID: 37002250 PMCID: PMC10066295 DOI: 10.1038/s41598-023-29742-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/09/2023] [Indexed: 04/03/2023] Open
Abstract
Multicellular evolution is a major transition associated with momentous diversification of multiple lineages and increased developmental complexity. The volvocine algae comprise a valuable system for the study of this transition, as they span from unicellular to undifferentiated and differentiated multicellular morphologies despite their genomes being similar, suggesting multicellular evolution requires few genetic changes to undergo dramatic shifts in developmental complexity. Here, the evolutionary dynamics of six volvocine genomes were examined, where a gradual loss of genes was observed in parallel to the co-option of a few key genes. Protein complexes in the six species exhibited novel interactions, suggesting that gene loss could play a role in evolutionary novelty. This finding was supported by gene network modeling, where gene loss outpaces gene gain in generating novel stable network states. These results suggest gene loss, in addition to gene gain and co-option, may be important for the evolution developmental complexity.
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Affiliation(s)
- Berenice Jiménez-Marín
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
- Interdepartmental Genetics Graduate Program, Kansas State University, Manhattan, KS, 66506, USA
| | - Jessica B Rakijas
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Antariksh Tyagi
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Aakash Pandey
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Jaden Anderson
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Matthew G Heffel
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
- Interdepartmental Genetics Graduate Program, Kansas State University, Manhattan, KS, 66506, USA
| | - Thomas G Platt
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
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Gillette S, Yin L, Kianian PMA, Pawlowski WP, Chen C. Corn360: a method for quantification of corn kernels. Plant Methods 2023; 19:23. [PMID: 36894953 PMCID: PMC9996904 DOI: 10.1186/s13007-023-00995-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The rapidly advancing corn breeding field calls for high-throughput methods to phenotype corn kernel traits to estimate yield and to study their genetic inheritance. Most of the existing methods are reliant on sophisticated setup, expertise in statistical models and programming skills for image capturing and analysis. RESULTS We demonstrated a portable, easily accessible, affordable, panoramic imaging capturing system called Corn360, followed by image analysis using freely available software, to characterize total kernel count and different patterned kernel counts of a corn ear. The software we used did not require programming skills and utilized Artificial Intelligence to train a model and to segment the images of mixed patterned corn ears. For homogeneously patterned corn ears, our results showed accuracies of 93.7% of total kernel count compared to manual counting. Our method allowed to save an average of 3 min 40 s per image. For mixed patterned corn ears, our results showed accuracies of 84.8% or 61.8% of segmented kernel counts. Our method has the potential to greatly decrease counting time per image as the number of images increases. We also demonstrated a case of using Corn360 to count different categories of kernels on a mixed patterned corn ear resulting from a cross of sweet corn and sticky corn and showed that starch:sweet:sticky segregated in a 9:4:3 ratio in its F2 population. CONCLUSIONS The panoramic Corn360 approach enables for a portable low-cost high-throughput kernel quantification. This includes total kernel quantification and quantification of different patterned kernels. This can allow for quick estimate of yield component and for categorization of different patterned kernels to study the inheritance of genes controlling color and texture. We demonstrated that using the samples resulting from a sweet × sticky cross, the starchiness, sweetness and stickiness in this case were controlled by two genes with epistatic effects. Our achieved results indicate Corn360 can be used to effectively quantify corn kernels in a portable and cost-efficient way that is easily accessible with or without programming skills.
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Affiliation(s)
- Samantha Gillette
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Lu Yin
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Penny M A Kianian
- PepsiCo Inc., 210 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
| | | | - Changbin Chen
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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29
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Orndorff PB, Poddar S, Owens AM, Kumari N, Ugaz BT, Amin S, Van Horn WD, van der Vaart A, Levitus M. Uracil-DNA glycosylase efficiency is modulated by substrate rigidity. Sci Rep 2023; 13:3915. [PMID: 36890276 PMCID: PMC9995336 DOI: 10.1038/s41598-023-30620-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/27/2023] [Indexed: 03/10/2023] Open
Abstract
Uracil DNA-glycosylase (UNG) is a DNA repair enzyme that removes the highly mutagenic uracil lesion from DNA using a base flipping mechanism. Although this enzyme has evolved to remove uracil from diverse sequence contexts, UNG excision efficiency depends on DNA sequence. To provide the molecular basis for rationalizing UNG substrate preferences, we used time-resolved fluorescence spectroscopy, NMR imino proton exchange measurements, and molecular dynamics simulations to measure UNG specificity constants (kcat/KM) and DNA flexibilities for DNA substrates containing central AUT, TUA, AUA, and TUT motifs. Our study shows that UNG efficiency is dictated by the intrinsic deformability around the lesion, establishes a direct relationship between substrate flexibility modes and UNG efficiency, and shows that bases immediately adjacent to the uracil are allosterically coupled and have the greatest impact on substrate flexibility and UNG activity. The finding that substrate flexibility controls UNG efficiency is likely significant for other repair enzymes and has major implications for the understanding of mutation hotspot genesis, molecular evolution, and base editing.
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Affiliation(s)
- Paul B Orndorff
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Souvik Poddar
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Institute Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, 85287, USA
| | - Aerial M Owens
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, 85287, USA
| | - Nikita Kumari
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Institute Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, 85287, USA
| | - Bryan T Ugaz
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Institute Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, 85287, USA
| | - Samrat Amin
- Magnetic Resonance Research Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Wade D Van Horn
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, 85287, USA.
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA.
| | - Marcia Levitus
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- The Biodesign Institute Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, 85287, USA.
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30
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Mohammed Taha H, Aalizadeh R, Alygizakis N, Antignac JP, Arp HPH, Bade R, Baker N, Belova L, Bijlsma L, Bolton EE, Brack W, Celma A, Chen WL, Cheng T, Chirsir P, Čirka Ľ, D’Agostino LA, Djoumbou Feunang Y, Dulio V, Fischer S, Gago-Ferrero P, Galani A, Geueke B, Głowacka N, Glüge J, Groh K, Grosse S, Haglund P, Hakkinen PJ, Hale SE, Hernandez F, Janssen EML, Jonkers T, Kiefer K, Kirchner M, Koschorreck J, Krauss M, Krier J, Lamoree MH, Letzel M, Letzel T, Li Q, Little J, Liu Y, Lunderberg DM, Martin JW, McEachran AD, McLean JA, Meier C, Meijer J, Menger F, Merino C, Muncke J, Muschket M, Neumann M, Neveu V, Ng K, Oberacher H, O’Brien J, Oswald P, Oswaldova M, Picache JA, Postigo C, Ramirez N, Reemtsma T, Renaud J, Rostkowski P, Rüdel H, Salek RM, Samanipour S, Scheringer M, Schliebner I, Schulz W, Schulze T, Sengl M, Shoemaker BA, Sims K, Singer H, Singh RR, Sumarah M, Thiessen PA, Thomas KV, Torres S, Trier X, van Wezel AP, Vermeulen RCH, Vlaanderen JJ, von der Ohe PC, Wang Z, Williams AJ, Willighagen EL, Wishart DS, Zhang J, Thomaidis NS, Hollender J, Slobodnik J, Schymanski EL. The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry. Environ Sci Eur 2022; 34:104. [PMID: 36284750 PMCID: PMC9587084 DOI: 10.1186/s12302-022-00680-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Background The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for "suspect screening" lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA's CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101). Conclusions The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the "one substance, one assessment" approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/). Supplementary Information The online version contains supplementary material available at 10.1186/s12302-022-00680-6.
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Affiliation(s)
- Hiba Mohammed Taha
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Reza Aalizadeh
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Nikiforos Alygizakis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
| | | | - Hans Peter H. Arp
- Norwegian Geotechnical Institute (NGI), Ullevål Stadion, P.O. Box 3930, 0806 Oslo, Norway
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Richard Bade
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD 4102 Australia
| | | | - Lidia Belova
- Toxicological Centre, University of Antwerp, Antwerp, Belgium
| | - Lubertus Bijlsma
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Castelló, Spain
| | - Evan E. Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Werner Brack
- UFZ, Helmholtz Centre for Environmental Research, Leipzig, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt Am Main, Germany
| | - Alberto Celma
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Castelló, Spain
- Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Wen-Ling Chen
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, 17 Xuzhou Rd., Zhongzheng Dist., Taipei, Taiwan
| | - Tiejun Cheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Parviel Chirsir
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Ľuboš Čirka
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
- Faculty of Chemical and Food Technology, Institute of Information Engineering, Automation, and Mathematics, Slovak University of Technology in Bratislava (STU), Radlinského 9, 812 37 Bratislava, Slovak Republic
| | - Lisa A. D’Agostino
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, 10691 Stockholm, Sweden
| | | | - Valeria Dulio
- INERIS, National Institute for Environment and Industrial Risks, Verneuil en Halatte, France
| | - Stellan Fischer
- Swedish Chemicals Agency (KEMI), P.O. Box 2, 172 13 Sundbyberg, Sweden
| | - Pablo Gago-Ferrero
- Institute of Environmental Assessment and Water Research-Severo Ochoa Excellence Center (IDAEA), Spanish Council of Scientific Research (CSIC), Barcelona, Spain
| | - Aikaterini Galani
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Birgit Geueke
- Food Packaging Forum Foundation, Staffelstrasse 10, 8045 Zurich, Switzerland
| | - Natalia Głowacka
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
| | - Juliane Glüge
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Ksenia Groh
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Sylvia Grosse
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Peter Haglund
- Department of Chemistry, Chemical Biological Centre (KBC), Umeå University, Linnaeus Väg 6, 901 87 Umeå, Sweden
| | - Pertti J. Hakkinen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Sarah E. Hale
- Norwegian Geotechnical Institute (NGI), Ullevål Stadion, P.O. Box 3930, 0806 Oslo, Norway
| | - Felix Hernandez
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Castelló, Spain
| | - Elisabeth M.-L. Janssen
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Tim Jonkers
- Department Environment and Health, Amsterdam Institute for Life and Environment, Vrije Universiteit, Amsterdam, The Netherlands
| | - Karin Kiefer
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Michal Kirchner
- Water Research Institute (WRI), Nábr. Arm. Gen. L. Svobodu 5, 81249 Bratislava, Slovak Republic
| | - Jan Koschorreck
- German Environment Agency (UBA), Wörlitzer Platz 1, Dessau-Roßlau, Germany
| | - Martin Krauss
- UFZ, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jessy Krier
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Marja H. Lamoree
- Department Environment and Health, Amsterdam Institute for Life and Environment, Vrije Universiteit, Amsterdam, The Netherlands
| | - Marion Letzel
- Bavarian Environment Agency, 86179 Augsburg, Germany
| | - Thomas Letzel
- Analytisches Forschungsinstitut Für Non-Target Screening GmbH (AFIN-TS), Am Mittleren Moos 48, 86167 Augsburg, Germany
| | - Qingliang Li
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - James Little
- Mass Spec Interpretation Services, 3612 Hemlock Park Drive, Kingsport, TN 37663 USA
| | - Yanna Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (SKLECE, RCEES, CAS), No. 18 Shuangqing Road, Haidian District, Beijing, 100086 China
| | - David M. Lunderberg
- Hope College, Holland, MI 49422 USA
- University of California, Berkeley, CA USA
| | - Jonathan W. Martin
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, 10691 Stockholm, Sweden
| | - Andrew D. McEachran
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd, Santa Clara, CA 95051 USA
| | - John A. McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235 USA
| | - Christiane Meier
- German Environment Agency (UBA), Wörlitzer Platz 1, Dessau-Roßlau, Germany
| | - Jeroen Meijer
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Frank Menger
- Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Carla Merino
- University Rovira i Virgili, Tarragona, Spain
- Biosfer Teslab, Reus, Spain
| | - Jane Muncke
- Food Packaging Forum Foundation, Staffelstrasse 10, 8045 Zurich, Switzerland
| | | | - Michael Neumann
- German Environment Agency (UBA), Wörlitzer Platz 1, Dessau-Roßlau, Germany
| | - Vanessa Neveu
- Nutrition and Metabolism Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Kelsey Ng
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
- RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Muellerstrasse 44, Innsbruck, Austria
| | - Jake O’Brien
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD 4102 Australia
| | - Peter Oswald
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
| | - Martina Oswaldova
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
| | - Jaqueline A. Picache
- Department of Chemistry, Center for Innovative Technology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235 USA
| | - Cristina Postigo
- Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- Technologies for Water Management and Treatment Research Group, Department of Civil Engineering, University of Granada, Campus de Fuentenueva S/N, 18071 Granada, Spain
| | - Noelia Ramirez
- University Rovira i Virgili, Tarragona, Spain
- Institute of Health Research Pere Virgili, Tarragona, Spain
| | | | - Justin Renaud
- Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | | | - Heinz Rüdel
- Fraunhofer Institute for Molecular Biology and Applied Ecology (Fraunhofer IME), Schmallenberg, Germany
| | - Reza M. Salek
- Nutrition and Metabolism Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Saer Samanipour
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, Amsterdam, 1090 GD The Netherlands
| | - Martin Scheringer
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
- RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
| | - Ivo Schliebner
- German Environment Agency (UBA), Wörlitzer Platz 1, Dessau-Roßlau, Germany
| | - Wolfgang Schulz
- Laboratory for Operation Control and Research, Zweckverband Landeswasserversorgung, Am Spitzigen Berg 1, 89129 Langenau, Germany
| | - Tobias Schulze
- UFZ, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Manfred Sengl
- Bavarian Environment Agency, 86179 Augsburg, Germany
| | - Benjamin A. Shoemaker
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Kerry Sims
- Environment Agency, Horizon House, Deanery Road, Bristol, BS1 5AH UK
| | - Heinz Singer
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Randolph R. Singh
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
- Chemical Contamination of Marine Ecosystems (CCEM) Unit, Institut Français de Recherche pour l’Exploitation de la Mer (IFREMER), Rue de l’Ile d’Yeu, BP 21105, 44311 Cedex 3, Nantes France
| | - Mark Sumarah
- Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Paul A. Thiessen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Kevin V. Thomas
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD 4102 Australia
| | | | - Xenia Trier
- Section for Environmental Chemistry and Physics, Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Annemarie P. van Wezel
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Roel C. H. Vermeulen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Jelle J. Vlaanderen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | | | - Zhanyun Wang
- Technology and Society Laboratory, Empa-Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Antony J. Williams
- Computational Chemistry and Cheminformatics Branch (CCCB), Chemical Characterization and Exposure Division (CCED), Center for Computational Toxicology and Exposure (CCTE), United States Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711 USA
| | - Egon L. Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | | | - Jian Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Nikolaos S. Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Juliane Hollender
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | | | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
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Burbano Lombana DA, Zino L, Butail S, Caroppo E, Jiang ZP, Rizzo A, Porfiri M. Activity-driven network modeling and control of the spread of two concurrent epidemic strains. Appl Netw Sci 2022; 7:66. [PMID: 36186912 PMCID: PMC9514203 DOI: 10.1007/s41109-022-00507-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The emergency generated by the current COVID-19 pandemic has claimed millions of lives worldwide. There have been multiple waves across the globe that emerged as a result of new variants, due to arising from unavoidable mutations. The existing network toolbox to study epidemic spreading cannot be readily adapted to the study of multiple, coexisting strains. In this context, particularly lacking are models that could elucidate re-infection with the same strain or a different strain-phenomena that we are seeing experiencing more and more with COVID-19. Here, we establish a novel mathematical model to study the simultaneous spreading of two strains over a class of temporal networks. We build on the classical susceptible-exposed-infectious-removed model, by incorporating additional states that account for infections and re-infections with multiple strains. The temporal network is based on the activity-driven network paradigm, which has emerged as a model of choice to study dynamic processes that unfold at a time scale comparable to the network evolution. We draw analytical insight from the dynamics of the stochastic network systems through a mean-field approach, which allows for characterizing the onset of different behavioral phenotypes (non-epidemic, epidemic, and endemic). To demonstrate the practical use of the model, we examine an intermittent stay-at-home containment strategy, in which a fraction of the population is randomly required to isolate for a fixed period of time.
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Affiliation(s)
- Daniel Alberto Burbano Lombana
- Center for Urban Science and Progress, Tandon School of Engineering, New York University, 370 Jay Street, Brooklyn, NY 11201 USA
- Department of Mechanical and Aerospace Engineering, Tandon School of Engineering, New York University, Six MetroTech Center, Brooklyn, NY 11201 USA
- Department of Electrical and Computer Engineering, Rutgers University, 94 Brett Rd, Piscataway, NJ 08854 USA
| | - Lorenzo Zino
- Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sachit Butail
- Department of Mechanical Engineering, Northern Illinois University, DeKalb, IL 60115 USA
| | - Emanuele Caroppo
- Department of Mental Health, Local Health Unit Roma 2, 00159 Rome, Italy
- University Research Center He.R.A., Universitá Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Zhong-Ping Jiang
- Department of Electrical and Computer Engineering, Tandon School of Engineering, New York University, 370 Jay Street, Brooklyn, NY 11201 USA
| | - Alessandro Rizzo
- Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca Degli Abruzzi, 24, 10129 Turin, Italy
- Institute for Invention, Innovation and Entrepreneurship, Tandon School of Engineering, New York University, Six MetroTech Center, Brooklyn, NY 11201 USA
| | - Maurizio Porfiri
- Center for Urban Science and Progress, Tandon School of Engineering, New York University, 370 Jay Street, Brooklyn, NY 11201 USA
- Department of Mechanical and Aerospace Engineering, Tandon School of Engineering, New York University, Six MetroTech Center, Brooklyn, NY 11201 USA
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, Six MetroTech Center, Brooklyn, NY 11201 USA
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32
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Wu M, Wang S, Pan S, Terentis AC, Strasswimmer J, Zhu X. Deep learning data augmentation for Raman spectroscopy cancer tissue classification. Sci Rep 2021; 11:23842. [PMID: 34903743 PMCID: PMC8668947 DOI: 10.1038/s41598-021-02687-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/22/2021] [Indexed: 11/08/2022] Open
Abstract
Recently, Raman Spectroscopy (RS) was demonstrated to be a non-destructive way of cancer diagnosis, due to the uniqueness of RS measurements in revealing molecular biochemical changes between cancerous vs. normal tissues and cells. In order to design computational approaches for cancer detection, the quality and quantity of tissue samples for RS are important for accurate prediction. In reality, however, obtaining skin cancer samples is difficult and expensive due to privacy and other constraints. With a small number of samples, the training of the classifier is difficult, and often results in overfitting. Therefore, it is important to have more samples to better train classifiers for accurate cancer tissue classification. To overcome these limitations, this paper presents a novel generative adversarial network based skin cancer tissue classification framework. Specifically, we design a data augmentation module that employs a Generative Adversarial Network (GAN) to generate synthetic RS data resembling the training data classes. The original tissue samples and the generated data are concatenated to train classification modules. Experiments on real-world RS data demonstrate that (1) data augmentation can help improve skin cancer tissue classification accuracy, and (2) generative adversarial network can be used to generate reliable synthetic Raman spectroscopic data.
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Affiliation(s)
- Man Wu
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, USA
| | - Shuwen Wang
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, USA
| | - Shirui Pan
- Faculty of Information Technology, Monash University, Melbourne, Australia
| | - Andrew C Terentis
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, USA
| | - John Strasswimmer
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, USA
- Department of Integrated Medical Science, Florida Atlantic University, Boca Raton, USA
| | - Xingquan Zhu
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, USA.
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Denervaud S, Christensen AP, Kenett YN, Beaty RE. Education shapes the structure of semantic memory and impacts creative thinking. NPJ Sci Learn 2021; 6:35. [PMID: 34887430 PMCID: PMC8660875 DOI: 10.1038/s41539-021-00113-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 10/27/2021] [Indexed: 06/01/2023]
Abstract
Education is central to the acquisition of knowledge, such as when children learn new concepts. It is unknown, however, whether educational differences impact not only what concepts children learn, but how those concepts come to be represented in semantic memory-a system that supports higher cognitive functions, such as creative thinking. Here we leverage computational network science tools to study hidden knowledge structures of 67 Swiss schoolchildren from two distinct educational backgrounds-Montessori and traditional, matched on socioeconomic factors and nonverbal intelligence-to examine how educational experience shape semantic memory and creative thinking. We find that children experiencing Montessori education show a more flexible semantic network structure (high connectivity/short paths between concepts, less modularity) alongside higher scores on creative thinking tests. The findings indicate that education impacts how children represent concepts in semantic memory and suggest that different educational experiences can affect higher cognitive functions, including creative thinking.
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Affiliation(s)
- Solange Denervaud
- Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland.
- Center for Biomedical Imaging (CIBM), Lausanne, Switzerland.
| | | | - Yoed N Kenett
- Faculty of Industrial Engineering and Management, Technion-Israel Institute of Technology, Haifa, Israel
| | - Roger E Beaty
- Department of Psychology, Pennsylvania State University, Philadelphia, PA, USA
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Ossmy O, Han D, Kaplan BE, Xu M, Bianco C, Mukamel R, Adolph KE. Children do not distinguish efficient from inefficient actions during observation. Sci Rep 2021; 11:18106. [PMID: 34518566 PMCID: PMC8438080 DOI: 10.1038/s41598-021-97354-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 07/13/2021] [Indexed: 11/08/2022] Open
Abstract
Observation is a powerful way to learn efficient actions from others. However, the role of observers' motor skill in assessing efficiency of others is unknown. Preschoolers are notoriously poor at performing multi-step actions like grasping the handle of a tool. Preschoolers (N = 22) and adults (N = 22) watched video-recorded actors perform efficient and inefficient tool use. Eye tracking showed that preschoolers and adults looked equally long at the videos, but adults looked longer than children at how actors grasped the tool. Deep learning analyses of participants' eye gaze distinguished efficient from inefficient grasps for adults, but not for children. Moreover, only adults showed differential action-related pupil dilation and neural activity (suppressed oscillation power in the mu frequency) while observing efficient vs. inefficient grasps. Thus, children observe multi-step actions without "seeing" whether the initial step is efficient. Findings suggest that observer's own motor efficiency determines whether they can perceive action efficiency in others.
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Affiliation(s)
- Ori Ossmy
- Department of Psychology, Center for Neural Science, New York University, 6 Washington Place, Room 403, New York, NY, 10003, USA.
| | - Danyang Han
- Department of Psychology, Center for Neural Science, New York University, 6 Washington Place, Room 403, New York, NY, 10003, USA
| | - Brianna E Kaplan
- Department of Psychology, Center for Neural Science, New York University, 6 Washington Place, Room 403, New York, NY, 10003, USA
| | - Melody Xu
- Department of Psychology, Center for Neural Science, New York University, 6 Washington Place, Room 403, New York, NY, 10003, USA
| | - Catherine Bianco
- Department of Psychology, Center for Neural Science, New York University, 6 Washington Place, Room 403, New York, NY, 10003, USA
| | - Roy Mukamel
- School of Psychological Sciences, Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Karen E Adolph
- Department of Psychology, Center for Neural Science, New York University, 6 Washington Place, Room 403, New York, NY, 10003, USA
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35
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Pinto-Ledezma JN, Cavender-Bares J. Predicting species distributions and community composition using satellite remote sensing predictors. Sci Rep 2021; 11:16448. [PMID: 34385574 PMCID: PMC8361206 DOI: 10.1038/s41598-021-96047-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Biodiversity is rapidly changing due to changes in the climate and human related activities; thus, the accurate predictions of species composition and diversity are critical to developing conservation actions and management strategies. In this paper, using satellite remote sensing products as covariates, we constructed stacked species distribution models (S-SDMs) under a Bayesian framework to build next-generation biodiversity models. Model performance of these models was assessed using oak assemblages distributed across the continental United States obtained from the National Ecological Observatory Network (NEON). This study represents an attempt to evaluate the integrated predictions of biodiversity models-including assemblage diversity and composition-obtained by stacking next-generation SDMs. We found that applying constraints to assemblage predictions, such as using the probability ranking rule, does not improve biodiversity prediction models. Furthermore, we found that independent of the stacking procedure (bS-SDM versus pS-SDM versus cS-SDM), these kinds of next-generation biodiversity models do not accurately recover the observed species composition at the plot level or ecological-community scales (NEON plots are 400 m2). However, these models do return reasonable predictions at macroecological scales, i.e., moderately to highly correct assignments of species identities at the scale of NEON sites (mean area ~ 27 km2). Our results provide insights for advancing the accuracy of prediction of assemblage diversity and composition at different spatial scales globally. An important task for future studies is to evaluate the reliability of combining S-SDMs with direct detection of species using image spectroscopy to build a new generation of biodiversity models that accurately predict and monitor ecological assemblages through time and space.
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Affiliation(s)
- Jesús N Pinto-Ledezma
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1479 Gortner Ave, Saint Paul, MN, 55108, USA.
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1479 Gortner Ave, Saint Paul, MN, 55108, USA
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36
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Halperin RF, Hegde A, Lang JD, Raupach EA, Legendre C, Liang WS, LoRusso PM, Sekulic A, Sosman JA, Trent JM, Rangasamy S, Pirrotte P, Schork NJ. Improved methods for RNAseq-based alternative splicing analysis. Sci Rep 2021; 11:10740. [PMID: 34031440 PMCID: PMC8144374 DOI: 10.1038/s41598-021-89938-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/13/2021] [Indexed: 01/04/2023] Open
Abstract
The robust detection of disease-associated splice events from RNAseq data is challenging due to the potential confounding effect of gene expression levels and the often limited number of patients with relevant RNAseq data. Here we present a novel statistical approach to splicing outlier detection and differential splicing analysis. Our approach tests for differences in the percentages of sequence reads representing local splice events. We describe a software package called Bisbee which can predict the protein-level effect of splice alterations, a key feature lacking in many other splicing analysis resources. We leverage Bisbee's prediction of protein level effects as a benchmark of its capabilities using matched sets of RNAseq and mass spectrometry data from normal tissues. Bisbee exhibits improved sensitivity and specificity over existing approaches and can be used to identify tissue-specific splice variants whose protein-level expression can be confirmed by mass spectrometry. We also applied Bisbee to assess evidence for a pathogenic splicing variant contributing to a rare disease and to identify tumor-specific splice isoforms associated with an oncogenic mutation. Bisbee was able to rediscover previously validated results in both of these cases and also identify common tumor-associated splice isoforms replicated in two independent melanoma datasets.
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Affiliation(s)
- Rebecca F Halperin
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
| | - Apurva Hegde
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jessica D Lang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Elizabeth A Raupach
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Christophe Legendre
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Winnie S Liang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | | | | | - Jeffrey M Trent
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Nicholas J Schork
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
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Boyle PM, Yu J, Klimas A, Williams JC, Trayanova NA, Entcheva E. OptoGap is an optogenetics-enabled assay for quantification of cell-cell coupling in multicellular cardiac tissue. Sci Rep 2021; 11:9310. [PMID: 33927252 PMCID: PMC8085001 DOI: 10.1038/s41598-021-88573-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/31/2021] [Indexed: 12/23/2022] Open
Abstract
Intercellular electrical coupling is an essential means of communication between cells. It is important to obtain quantitative knowledge of such coupling between cardiomyocytes and non-excitable cells when, for example, pathological electrical coupling between myofibroblasts and cardiomyocytes yields increased arrhythmia risk or during the integration of donor (e.g., cardiac progenitor) cells with native cardiomyocytes in cell-therapy approaches. Currently, there is no direct method for assessing heterocellular coupling within multicellular tissue. Here we demonstrate experimentally and computationally a new contactless assay for electrical coupling, OptoGap, based on selective illumination of inexcitable cells that express optogenetic actuators and optical sensing of the response of coupled excitable cells (e.g., cardiomyocytes) that are light-insensitive. Cell-cell coupling is quantified by the energy required to elicit an action potential via junctional current from the light-stimulated cell(s). The proposed technique is experimentally validated against the standard indirect approach, GapFRAP, using light-sensitive cardiac fibroblasts and non-transformed cardiomyocytes in a two-dimensional setting. Its potential applicability to the complex three-dimensional setting of the native heart is corroborated by computational modelling and proper calibration. Lastly, the sensitivity of OptoGap to intrinsic cell-scale excitability is robustly characterized via computational analysis.
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Affiliation(s)
- Patrick M Boyle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
| | - Jinzhu Yu
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
| | - Aleksandra Klimas
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Department of Biomedical Engineering, George Washington University, 800 22nd Street NW, Suite 5000, Washington, DC, 20052, USA
| | - John C Williams
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
| | - Natalia A Trayanova
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
- Alliance for Cardiovascular Diagnostic and Treatment Innovation, Johns Hopkins University, Baltimore, MD, USA
| | - Emilia Entcheva
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA.
- Department of Biomedical Engineering, George Washington University, 800 22nd Street NW, Suite 5000, Washington, DC, 20052, USA.
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38
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Earley EJ, Johnson RE, Sensinger JW, Hargrove LJ. Joint speed feedback improves myoelectric prosthesis adaptation after perturbed reaches in non amputees. Sci Rep 2021; 11:5158. [PMID: 33664421 PMCID: PMC7970849 DOI: 10.1038/s41598-021-84795-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
Accurate control of human limbs involves both feedforward and feedback signals. For prosthetic arms, feedforward control is commonly accomplished by recording myoelectric signals from the residual limb to predict the user's intent, but augmented feedback signals are not explicitly provided in commercial devices. Previous studies have demonstrated inconsistent results when artificial feedback was provided in the presence of vision; some studies showed benefits, while others did not. We hypothesized that negligible benefits in past studies may have been due to artificial feedback with low precision compared to vision, which results in heavy reliance on vision during reaching tasks. Furthermore, we anticipated more reliable benefits from artificial feedback when providing information that vision estimates with high uncertainty (e.g. joint speed). In this study, we test an artificial sensory feedback system providing joint speed information and how it impacts performance and adaptation during a hybrid positional-and-myoelectric ballistic reaching task. We found that overall reaching errors were reduced after perturbed control, but did not significantly improve steady-state reaches. Furthermore, we found that feedback about the joint speed of the myoelectric prosthesis control improved the adaptation rate of biological limb movements, which may have resulted from high prosthesis control noise and strategic overreaching with the positional control and underreaching with the myoelectric control. These results provide insights into the relevant factors influencing the improvements conferred by artificial sensory feedback.
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Affiliation(s)
- Eric J Earley
- Department of Biomedical Engineering, Northwestern University, Chicago, IL, USA.
- Center for Bionic Medicine, Shirley Ryan AbilityLab, Chicago, IL, USA.
| | - Reva E Johnson
- Department of Mechanical Engineering and Bioengineering, Valparaiso University, Valparaiso, IN, USA
| | - Jonathon W Sensinger
- Institute of Biomedical Engineering, University of New Brunswick, Fredericton, NB, Canada
- Department of Electrical and Computer Engineering, University of New Brunswick, Fredericton, NB, Canada
| | - Levi J Hargrove
- Department of Biomedical Engineering, Northwestern University, Chicago, IL, USA
- Center for Bionic Medicine, Shirley Ryan AbilityLab, Chicago, IL, USA
- Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL, USA
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39
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Gilbert DA, Murray PD, De Rojas J, Dumas RK, Davies JE, Liu K. Reconstructing phase-resolved hysteresis loops from first-order reversal curves. Sci Rep 2021; 11:4018. [PMID: 33597639 PMCID: PMC7889904 DOI: 10.1038/s41598-021-83349-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/11/2021] [Indexed: 11/09/2022] Open
Abstract
The first order reversal curve (FORC) method is a magnetometry based technique used to capture nanoscale magnetic phase separation and interactions with macroscopic measurements using minor hysteresis loop analysis. This makes the FORC technique a powerful tool in the analysis of complex systems which cannot be effectively probed using localized techniques. However, recovering quantitative details about the identified phases which can be compared to traditionally measured metrics remains an enigmatic challenge. We demonstrate a technique to reconstruct phase-resolved magnetic hysteresis loops by selectively integrating the measured FORC distribution. From these minor loops, the traditional metrics-including the coercivity and saturation field, and the remanent and saturation magnetization-can be determined. In order to perform this analysis, special consideration must be paid to the accurate quantitative management of the so-called reversible features. This technique is demonstrated on three representative materials systems, high anisotropy FeCuPt thin-films, Fe nanodots, and SmCo/Fe exchange spring magnet films, and shows excellent agreement with the direct measured major loop, as well as the phase separated loops.
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Affiliation(s)
- Dustin A Gilbert
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN, 37919, USA.
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, 37919, USA.
| | - Peyton D Murray
- Physics Department, University of California, Davis, CA, 95616, USA
| | - Julius De Rojas
- Physics Department, University of California, Davis, CA, 95616, USA
| | | | - Joseph E Davies
- Advanced Technology Group, NVE Corp, Eden Prairie, MN, 55344, USA
| | - Kai Liu
- Physics Department, University of California, Davis, CA, 95616, USA
- Department of Physics, Georgetown University, Washington, DC, 20057, USA
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40
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Abstract
Triconodontidae are considered the first carnivorous crown mammals. A virtual reconstruction of the masticatory cycle in the Late Jurassic Priacodon showed that triconodontid dental function is characterized by precise cutting on elongated crests. The combination of traits linked to both carnivorous diets (e.g. fore-aft cutting edges) and insectivorous diets (transverse crests and lobes) suggests a varied faunivorous diet appropriate to the small body size of most triconodontids. Total length of molar shear decreased with wear, suggesting a dietary shift during ontogeny. Embrasure occlusion is confirmed for P. fruitaensis as indicated by premolar positioning, facet orientation, and collision areas. Embrasure occlusion is considered a general feature of all Eutriconodonta, whereas the previously assumed Morganucodon-like pattern is limited to few early mammaliaforms. Unlike modern carnivores, significant roll of around 10° of the active hemimandible occurred during the power stroke. Roll was likely passive in Triconodontidae in contrast to active roll described for extant therians. The triconodontid molar series was highly uniform and adapted to a precise fit, with self-sharpening lower molar cusps. Whereas the uniformity ensured good cutting capabilities, it likely put the dentition under greater constraints, conserving the highly stereotyped nature of triconodontid molars for 60-85 Ma.
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Affiliation(s)
- Kai R K Jäger
- Section Palaeontology, Institute of Geosciences, Rheinische Friedrich-Wilhelms-Universität Bonn, Nussallee 8, 53115, Bonn, Germany.
| | - Richard L Cifelli
- Oklahoma Museum of Natural History, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Thomas Martin
- Section Palaeontology, Institute of Geosciences, Rheinische Friedrich-Wilhelms-Universität Bonn, Nussallee 8, 53115, Bonn, Germany
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41
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Pastore VP, Zimmerman TG, Biswas SK, Bianco S. Annotation-free learning of plankton for classification and anomaly detection. Sci Rep 2020; 10:12142. [PMID: 32699302 PMCID: PMC7376023 DOI: 10.1038/s41598-020-68662-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/16/2020] [Indexed: 11/09/2022] Open
Abstract
The acquisition of increasingly large plankton digital image datasets requires automatic methods of recognition and classification. As data size and collection speed increases, manual annotation and database representation are often bottlenecks for utilization of machine learning algorithms for taxonomic classification of plankton species in field studies. In this paper we present a novel set of algorithms to perform accurate detection and classification of plankton species with minimal supervision. Our algorithms approach the performance of existing supervised machine learning algorithms when tested on a plankton dataset generated from a custom-built lensless digital device. Similar results are obtained on a larger image dataset obtained from the Woods Hole Oceanographic Institution. Additionally, we introduce a new algorithm to perform anomaly detection on unclassified samples. Here an anomaly is defined as a significant deviation from the established classification. Our algorithms are designed to provide a new way to monitor the environment with a class of rapid online intelligent detectors.
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Affiliation(s)
- Vito P Pastore
- Industrial and Applied Genomics, AI and Cognitive Software, IBM Research - Almaden, San Jose, CA, USA.
- NSF Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA.
| | - Thomas G Zimmerman
- Industrial and Applied Genomics, AI and Cognitive Software, IBM Research - Almaden, San Jose, CA, USA
- NSF Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA
| | - Sujoy K Biswas
- Industrial and Applied Genomics, AI and Cognitive Software, IBM Research - Almaden, San Jose, CA, USA
- NSF Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA
| | - Simone Bianco
- Industrial and Applied Genomics, AI and Cognitive Software, IBM Research - Almaden, San Jose, CA, USA
- NSF Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA
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42
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Santarém MCA, Borkent A, Felippe-Bauer ML. Taxonomic Revision of Neotropical Downeshelea Wirth and Grogan Predaceous Midges (Diptera: Ceratopogonidae). Insects 2019; 11:E9. [PMID: 31861882 PMCID: PMC7023372 DOI: 10.3390/insects11010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 11/16/2022]
Abstract
The genus Downeshelea was described by Wirth and Grogan based on the diagnostic characters of the Monohelea multilineata species group. The first descriptions of species were based on body coloration, which resulted in confusion and misunderstanding of their identification. The aim of this study was to provide an updated diagnosis and description of Downeshelea, describe 18 new species, and redescribe 10 previously poorly described species. New records of species, a key for identification of all New World species, and a table with important morphometric data to distinguish both males and females of the various species are provided along with distribution maps of the 46 known New World species.
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Affiliation(s)
- Maria Clara A. Santarém
- Coleção de Ceratopogonidae, Laboratório de Diptera, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, Rio de Janeiro 21040–900, Brazil;
- Programa de Pós-Graduação em Biodiversidade e Saúde, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, Rio de Janeiro 21040–900, Brazil
| | - Art Borkent
- Research Associate American Museum of Natural History, 691–8 th Ave. SE, Salmon Arm, BC V1 E 2 C2, Canada;
| | - Maria Luiza Felippe-Bauer
- Coleção de Ceratopogonidae, Laboratório de Diptera, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, Rio de Janeiro 21040–900, Brazil;
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Abstract
The high cost of synthetic polymers has been a key impediment limiting the widespread adoption of polymer drag reduction techniques in large-scale engineering applications, such as marine drag reduction. To address consumable cost constraints, we investigate the use of high molar mass biopolysaccharides, present in the mucilaginous epidermis of plant seeds, as inexpensive drag reducers in large Reynolds number turbulent flows. Specifically, we study the aqueous mucilage extracted from flax seeds (Linum usitatissimum) and compare its drag reduction efficacy to that of poly(ethylene oxide) or PEO, a common synthetic polymer widely used as a drag reducing agent in aqueous flows. Macromolecular and rheological characterisation confirm the presence of high molar mass (≥2 MDa) polysaccharides in the extracted mucilage, with an acidic fraction comprising negatively charged chains. Frictional drag measurements, performed inside a bespoke Taylor-Couette apparatus, show that the as-extracted mucilage has comparable drag reduction performance under turbulent flow conditions as aqueous PEO solutions, while concurrently offering advantages in terms of raw material cost, availability, and bio-compatibility. Our results indicate that plant-sourced mucilage can potentially serve as a cost-effective and eco-friendly substitute for synthetic drag reducing polymers in large scale turbulent flow applications.
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Affiliation(s)
- Anoop Rajappan
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Gareth H McKinley
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.
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