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Book ; Online: The DESI $N$-body Simulation Project -- II. Suppressing sample variance with fast simulations

2022

Abstract: ... fast quasi-$N$-body solvers combined with accurate simulations to produce accurate summary statistics ...

Abstract	Dark Energy Spectroscopic Instrument (DESI) will construct a large and precise three-dimensional map of our Universe. The survey effective volume reaches $\sim20\Gpchcube$. It is a great challenge to prepare high-resolution simulations with a much larger volume for validating the DESI analysis pipelines. \textsc{AbacusSummit} is a suite of high-resolution dark-matter-only simulations designed for this purpose, with $200\Gpchcube$ (10 times DESI volume) for the base cosmology. However, further efforts need to be done to provide a more precise analysis of the data and to cover also other cosmologies. Recently, the CARPool method was proposed to use paired accurate and approximate simulations to achieve high statistical precision with a limited number of high-resolution simulations. Relying on this technique, we propose to use fast quasi-$N$-body solvers combined with accurate simulations to produce accurate summary statistics. This enables us to obtain 100 times smaller variance than the expected DESI statistical variance at the scales we are interested in, e.g. $k < 0.3\hMpc$ for the halo power spectrum. In addition, it can significantly suppress the sample variance of the halo bispectrum. We further generalize the method for other cosmologies with only one realization in \textsc{AbacusSummit} suite to extend the effective volume $\sim 20$ times. In summary, our proposed strategy of combining high-fidelity simulations with fast approximate gravity solvers and a series of variance suppression techniques sets the path for a robust cosmological analysis of galaxy survey data. Comment: Matched version accepted by MNRAS, should be clearer
Keywords	Astrophysics - Cosmology and Nongalactic Astrophysics
Subject code	520 ; 612
Publishing date	2022-02-12
Publishing country	us
Document type	Book ; Online
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Article ; Online: Visible spectrum photofragmentation of O₃⁻(H₂O)n, n ≤ 16.

Lehman, Julia H / Lineberger, W Carl

The Journal of chemical physics

2014 Volume 141, Issue 15, Page(s) 154312

Abstract: Photofragmentation of ozonide solvated in water clusters, O3(-)(H2O)n, n ≤ 16, has been studied ... for close to 40% of photoproducts by n = 16. The remainder of the photoproducts exist as O(-)-based; no O2 ...

Abstract	Photofragmentation of ozonide solvated in water clusters, O3(-)(H2O)n, n ≤ 16, has been studied as a function of photon energy as well as the degree of solvation. Using mass selection, the effect of the presence of the solvent molecule on the O3(-) photodissociation process is assessed one solvent molecule at a time. The O3(-) acts as a visible light chromophore within the water cluster, namely the O3(-)(H2O) total photodissociation cross-section exhibits generally the same photon energy dependence as isolated O3(-) throughout the visible wavelength range studied (430-620 nm). With the addition of a single solvent molecule, new photodissociation pathways are opened, including the production of recombined O3(-). As the degree of solvation of the parent anion increases, recombination to O3(-)-based products accounts for close to 40% of photoproducts by n = 16. The remainder of the photoproducts exist as O(-)-based; no O2(-)-based products are observed. Upper bounds on the O3(-) solvation energy (530 meV) and the O(-)-OO bond dissociation energy in the cluster (1.06 eV) are derived.
Language	English
Publishing date	2014-10-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.4898373
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Article ; Online: Sialic acid catabolism by N-acetylneuraminate pyruvate lyase is essential for muscle function.

Wen, Xiao-Yan / Tarailo-Graovac, Maja / Brand-Arzamendi, Koroboshka / Willems, Anke / Rakic, Bojana / Huijben, Karin / Da Silva, Afitz / Pan, Xuefang / El-Rass, Suzan / Ng, Robin / Selby, Katheryn / Philip, Anju Mary / Yun, Junghwa / Ye, X Cynthia / Ross, Colin J / Lehman, Anna M / Zijlstra, Fokje / Abu Bakar, N / Drögemöller, Britt /

Moreland, Jacqueline / Wasserman, Wyeth W / Vallance, Hilary / van Scherpenzeel, Monique / Karbassi, Farhad / Hoskings, Martin / Engelke, Udo / de Brouwer, Arjan / Wevers, Ron A / Pshezhetsky, Alexey V / van Karnebeek, Clara Dm / Lefeber, Dirk J

JCI insight

2018 Volume 3, Issue 24

Abstract: ... in the N-acetylneuraminate pyruvate lyase gene (NPL). In vitro, NPL activity and sialic acid catabolism ... were affected, with a cell-type-specific reduction of N-acetyl mannosamine (ManNAc). A knockdown of NPL ... of NPL: N-acetyl glucosamine (GlcNAc) and ManNAc; the latter also rescuing the cardiac phenotype ...

Abstract	Sialic acids are important components of glycoproteins and glycolipids essential for cellular communication, infection, and metastasis. The importance of sialic acid biosynthesis in human physiology is well illustrated by the severe metabolic disorders in this pathway. However, the biological role of sialic acid catabolism in humans remains unclear. Here, we present evidence that sialic acid catabolism is important for heart and skeletal muscle function and development in humans and zebrafish. In two siblings, presenting with sialuria, exercise intolerance/muscle wasting, and cardiac symptoms in the brother, compound heterozygous mutations [chr1:182775324C>T (c.187C>T; p.Arg63Cys) and chr1:182772897A>G (c.133A>G; p.Asn45Asp)] were found in the N-acetylneuraminate pyruvate lyase gene (NPL). In vitro, NPL activity and sialic acid catabolism were affected, with a cell-type-specific reduction of N-acetyl mannosamine (ManNAc). A knockdown of NPL in zebrafish resulted in severe skeletal myopathy and cardiac edema, mimicking the human phenotype. The phenotype was rescued by expression of wild-type human NPL but not by the p.Arg63Cys or p.Asn45Asp mutants. Importantly, the myopathy phenotype in zebrafish embryos was rescued by treatment with the catabolic products of NPL: N-acetyl glucosamine (GlcNAc) and ManNAc; the latter also rescuing the cardiac phenotype. In conclusion, we provide the first report to our knowledge of a human defect in sialic acid catabolism, which implicates an important role of the sialic acid catabolic pathway in mammalian muscle physiology, and suggests opportunities for monosaccharide replacement therapy in human patients.
MeSH term(s)	Adult ; Animals ; Disease Models, Animal ; Edema, Cardiac/metabolism ; Gene Expression Regulation, Developmental ; Gene Knockdown Techniques ; Genetic Diseases, Inborn/genetics ; Genetic Diseases, Inborn/metabolism ; HEK293 Cells ; Hexosamines/metabolism ; Humans ; Male ; Muscle, Skeletal/growth & development ; Muscle, Skeletal/metabolism ; Muscular Diseases/genetics ; Muscular Diseases/metabolism ; Muscular Diseases/physiopathology ; Mutation ; N-Acetylneuraminic Acid/metabolism ; Oxo-Acid-Lyases/genetics ; Oxo-Acid-Lyases/metabolism ; Oxo-Acid-Lyases/therapeutic use ; Sialic Acid Storage Disease/metabolism ; Young Adult ; Zebrafish/embryology
Chemical Substances	Hexosamines ; mannosamine (2636-92-2) ; Oxo-Acid-Lyases (EC 4.1.3.-) ; N-acetylneuraminate lyase (EC 4.1.3.3) ; N-Acetylneuraminic Acid (GZP2782OP0)
Language	English
Publishing date	2018-12-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.122373
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Book ; Online: Quantifying resolution in cosmological N-body simulations using self-similarity

Joyce, Michael / Garrison, Lehman / Eisenstein, Daniel

2020

Abstract: ... tool to quantify the resolution at small scales of cosmological N-body simulations. Analysing two-point ... with a hypothesis that it is set by two-body collisionality. A corollary of our results is that N-body simulations ...

Abstract	We demonstrate that testing for self-similarity in scale-free simulations provides an excellent tool to quantify the resolution at small scales of cosmological N-body simulations. Analysing two-point correlation functions measured in simulations using ABACUS, we show how observed deviations from self-similarity reveal the range of time and distance scales in which convergence is obtained. While the well-converged scales show accuracy below 1 percent, our results show that, with a small force softening length, the spatial resolution is essentially determined by the mass resolution. At later times the lower cut-off scale on convergence evolves in comoving units as $a^{-1/2}$ ($a$ being the scale factor), consistent with a hypothesis that it is set by two-body collisionality. A corollary of our results is that N-body simulations, particularly at high red-shift, contain a significant spatial range in which clustering appears converged with respect to the time-stepping and force softening but has not actually converged to the physical continuum result. The method developed can be applied to determine the resolution of any clustering statistic and extended to infer resolution limits for non-scale-free simulations. Comment: 14 pages, 9 figures, submitted, comments welcome
Keywords	Astrophysics - Cosmology and Nongalactic Astrophysics
Subject code	612
Publishing date	2020-04-15
Publishing country	us
Document type	Book ; Online
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Article ; Online: Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results.

Lesbon, Jéssika Cristina Chagas / Poleti, Mirele Daiana / de Mattos Oliveira, Elisângela Chicaroni / Patané, José Salvatore Leister / Clemente, Luan Gaspar / Viala, Vincent Louis / Ribeiro, Gabriela / Giovanetti, Marta / de Alcantara, Luiz Carlos Junior / Teixeira, Olivia / Nonato, Maria Cristina / de Lima, Loyze Paola Oliveira / Martins, Antonio Jorge / Dos Santos Barros, Claudia Renata / Marqueze, Elaine Cristina / de Souza Todão Bernardino, Jardelina / Moretti, Debora Botequio / Brassaloti, Ricardo Augusto / de Lello Rocha Campos Cassano, Raquel /

Mariani, Pilar Drummond Sampaio Correa / Slavov, Svetoslav Nanev / Dos Santos, Rafael Bezerra / Rodrigues, Evandra Strazza / Santos, Elaine Vieira / Borges, Josiane Serrano / de La Roque, Debora Glenda Lima / Kitajima, Joao Paulo / Santos, Bibiana / Assato, Patricia Akemi / da Silva da Costa, Felipe Allan / Banho, Cecilia Artico / Sacchetto, Livia / Moraes, Marilia Mazzi / Palmieri, Melissa / da Silva, Fabiana Erica Vilanova / Grotto, Rejane Maria Tommasini / Souza-Neto, Jayme A / Nogueira, Mauricio Lacerda / Coutinho, Luiz Lehman / Calado, Rodrigo Tocantins / Neto, Raul Machado / Covas, Dimas Tadeu / Kashima, Simone / Elias, Maria Carolina / Sampaio, Sandra Coccuzzo / Fukumasu, Heidge

Viruses

2021 Volume 13, Issue 12

Abstract: The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to ... ...

Abstract	The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the
MeSH term(s)	Brazil/epidemiology ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19 Nucleic Acid Testing ; Coronavirus Nucleocapsid Proteins/genetics ; Coronavirus RNA-Dependent RNA Polymerase/genetics ; DNA Primers ; False Negative Reactions ; Genome, Viral/genetics ; Humans ; Mutation ; Phosphoproteins/genetics ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification
Chemical Substances	Coronavirus Nucleocapsid Proteins ; DNA Primers ; Phosphoproteins ; RNA, Viral ; nucleocapsid phosphoprotein, SARS-CoV-2 ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; NSP12 protein, SARS-CoV-2 (EC 2.7.7.48)
Language	English
Publishing date	2021-12-10
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13122474
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Article ; Online: Correction: Lesbon et al. Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results.

Viruses

2022 Volume 14, Issue 9

Abstract: The authors hereby request the inclusion of two authors (Olivia Teixeira and Maria Cristina Nonato) in the recently published article ... ...

Abstract	The authors hereby request the inclusion of two authors (Olivia Teixeira and Maria Cristina Nonato) in the recently published article in
Language	English
Publishing date	2022-09-05
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14091967
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Article ; Online: The N Terminus of the PduB Protein Binds the Protein Shell of the Pdu Microcompartment to Its Enzymatic Core.

Lehman, Brent P / Chowdhury, Chiranjit / Bobik, Thomas A

Journal of bacteriology

2017 Volume 199, Issue 8

Abstract: ... In this report, we show that the N-terminal 37 amino acids of the PduB protein have a critical role in binding ... were constructed that deleted short regions of the N terminus of PduB. Growth tests indicated ... region of the N terminus of PduB required for MCP assembly is a putative helix spanning residues 6 to 18 ...

Abstract	Bacterial microcompartments (MCPs) are extremely large proteinaceous organelles that consist of an enzymatic core encapsulated within a complex protein shell. A key question in MCP biology is the nature of the interactions that guide the assembly of thousands of protein subunits into a well-ordered metabolic compartment. In this report, we show that the N-terminal 37 amino acids of the PduB protein have a critical role in binding the shell of the 1,2-propanediol utilization (Pdu) microcompartment to its enzymatic core. Several mutations were constructed that deleted short regions of the N terminus of PduB. Growth tests indicated that three of these deletions were impaired MCP assembly. Attempts to purify MCPs from these mutants, followed by gel electrophoresis and enzyme assays, indicated that the protein complexes isolated consisted of MCP shells depleted of core enzymes. Electron microscopy substantiated these findings by identifying apparently empty MCP shells but not intact MCPs. Analyses of 13 site-directed mutants indicated that the key region of the N terminus of PduB required for MCP assembly is a putative helix spanning residues 6 to 18. Considering the findings presented here together with prior work, we propose a new model for MCP assembly.
MeSH term(s)	Amino Acid Sequence ; Anti-Bacterial Agents ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Cobamides/pharmacology ; Gene Expression Regulation, Bacterial/physiology ; Gene Expression Regulation, Enzymologic/physiology ; Hydro-Lyases/genetics ; Hydro-Lyases/metabolism ; Mutation ; NAD ; Salmonella typhimurium/cytology ; Salmonella typhimurium/genetics ; Salmonella typhimurium/metabolism ; Vitamin B 12/pharmacology
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Cobamides ; NAD (0U46U6E8UK) ; Hydro-Lyases (EC 4.2.1.-) ; cobamamide (F0R1QK73KB) ; Vitamin B 12 (P6YC3EG204)
Language	English
Publishing date	2017-04-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00785-16
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Article ; Online: Gel purification of radiolabeled nucleic acids via phosphorimaging: Dip-N-Dot.

Burton, Aaron S / Madix, Rowan A / Vaidya, Nilesh / Riley, Craig A / Hayden, Eric J / Chepetan, Andre / Arenas, Carolina Díaz / Larson, Brian C / Lehman, Niles

Analytical biochemistry

2009 Volume 388, Issue 2, Page(s) 351–352

Abstract: ... the radiolabeled molecule. A more cost-effective method is to physically inject the gel with a "Dip-N-Dot" solution ...

Abstract	RNA and DNA oligonucleotides radiolabeled with (32)P or (33)P often require gel electrophoresis to remove undesired side and/or degradation products. Common ways to visualize these molecules after electrophoresis are by ultraviolet (UV) shadowing, which necessarily reduces the specific activity of the oligonucleotide, and by autoradiography using film, which is cumbersome and increases the cost of generating the radiolabeled molecule. A more cost-effective method is to physically inject the gel with a "Dip-N-Dot" solution of dye and radionuclide after electrophoresis but prior to phosphorimaging. The gel can be overlaid on its computer-generated image, allowing the labeled molecules to be visualized quickly.
MeSH term(s)	Autoradiography/methods ; Electrophoresis/methods ; Nucleic Acids/analysis ; Nucleic Acids/chemistry ; Phosphorus Radioisotopes/chemistry
Chemical Substances	Nucleic Acids ; Phosphorus Radioisotopes
Language	English
Publishing date	2009-05-15
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2009.02.010
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Article: Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results

Lesbon, Jéssika Cristina Chagas / Poleti, Mirele Daiana / de Mattos Oliveira, Elisângela Chicaroni / Patané, José Salvatore Leister / Clemente, Luan Gaspar / Viala, Vincent Louis / Ribeiro, Gabriela / Giovanetti, Marta / de Alcantara, Luiz Carlos Junior / de Lima, Loyze Paola Oliveira / Martins, Antonio Jorge / dos Santos Barros, Claudia Renata / Marqueze, Elaine Cristina / de Souza Todão Bernardino, Jardelina / Moretti, Debora Botequio / Brassaloti, Ricardo Augusto / de Lello Rocha Campos Cassano, Raquel / Mariani, Pilar Drummond Sampaio Correa / Slavov, Svetoslav Nanev /

dos Santos, Rafael Bezerra / Rodrigues, Evandra Strazza / Santos, Elaine Vieira / Borges, Josiane Serrano / de La Roque, Debora Glenda Lima / Kitajima, Joao Paulo / Santos, Bibiana / Assato, Patricia Akemi / da Silva da Costa, Felipe Allan / Banho, Cecilia Artico / Sacchetto, Livia / Moraes, Marilia Mazzi / Palmieri, Melissa / da Silva, Fabiana Erica Vilanova / Grotto, Rejane Maria Tommasini / Souza-Neto, Jayme A. / Nogueira, Mauricio Lacerda / Coutinho, Luiz Lehman / Calado, Rodrigo Tocantins / Neto, Raul Machado / Covas, Dimas Tadeu / Kashima, Simone / Elias, Maria Carolina / Sampaio, Sandra Coccuzzo / Fukumasu, Heidge

Viruses. 2021 Dec. 10, v. 13, no. 12

2021

Abstract: ... Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 ... Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection ... different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution ...

Abstract	The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19.
Keywords	COVID-19 infection ; RNA-directed RNA polymerase ; Severe acute respiratory syndrome coronavirus 2 ; frameshift mutation ; genes ; genomics ; monitoring ; nucleocapsid ; nucleotides ; pandemic ; pathogenicity ; phenotype ; protein content ; reverse transcriptase polymerase chain reaction ; vaccines ; viruses ; Brazil
Language	English
Dates of publication	2021-1210
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13122474
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Article ; Online: Preface to the special issue.

Lehman, Michael N

Journal of neuroendocrinology

2022 Volume 34, Issue 5, Page(s) e13150

Language	English
Publishing date	2022-05-20
Publishing country	United States
Document type	Editorial
ZDB-ID	1007517-3
ISSN	1365-2826 ; 0953-8194
ISSN (online)	1365-2826
ISSN	0953-8194
DOI	10.1111/jne.13150
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