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Analysis of the time evolution of auditory steady-state responses (ASSR) recorded in rats Resource Report Resource Website |
Pavel Prado, Eduardo Martínez-Montes, Matías Zañartu | DOI:10.17504/protocols.io.wejfbcn | Auditory steady-state responses (ASSRs) are brain oscillations locked to the periodic properties of acoustic stimuli. Audiological tests based on the acquisition of ASSR are useful for estimating the hearing sensitivity, mainly because multiple hearing frequencies can be simultaneously assessed, and the auditory response can be objectively detected using statistical tests. Typically, the extraction of the auditory response from the measured signal essentially relies on averaging epochs of the EEG, time-locked to the stimulus. Such a manipulation assumes that the auditory response is steady over time and that averaging increases the signal-to-noise ratio of the measurement. Since the time-domain averaging of epochs within a recording does not allow to discriminate between methodological and physiological related variations in the amplitude of the ASSR, we designed a protocol for analyzing the dynamics of the auditory response during the acquisition procedure. The protocol allows us to compute the ASSR amplitude at a given time window without being compromised by those computed in the preceding EEG segments. In other words, the ASSR amplitudes are extracted from individual epochs, without those epochs being time-domain averaged with the preceding EEG segments. As a result, adaptation and other non-stationary behaviors of the ASSR can be studied. | Advanced Center for Electrical and Electronic Engineering (AC3E), Universidad Técnica Federico Santa María, Cuban Neuroscience Center, Department of Electronic Engineering, Universidad Técnica Federico Santa María, Valparaíso, Chile | http://eeglab.onuniverse.com/ | 2 | 2018 | Pavel Prado, Eduardo Martínez-Montes, Matías Zañartu 2018. Analysis of the time evolution of auditory steady-state responses (ASSR) recorded in rats. protocols.io https://dx.doi.org/10.17504/protocols.io.wejfbcn | 2021-04-15 09:14:54 | |||
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Tetraselmis transformation by microprojectile bombardment Resource Report Resource Website |
Fulei Luan, Xiaoxue Wen, Patrick Beardslee and Heriberto Cerutti | DOI:10.17504/protocols.io.hjtb4nn | Protist Research to Optimize Tools in Genetics (PROT-G) | Procedure for the transformation of the nuclear genome of Tetraselmis striata by microprojectile bombardment. | Faktorová D, Nisbet RER, Robledo JAF, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget F, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano J, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Vanclová AMGN, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Smith GJ, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, Dassow Pv, Haar Tvd, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J, Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods 17(5). doi: 10.1038/s41592-020-0796-x | University of Nebraska-Lincoln, University of Nebraska-Lincoln, University of Nebraska-Lincoln | https://doi.org/10.1038/s41592-020-0796-x | 1 | 2017 | Fulei Luan, Xiaoxue Wen, Patrick Beardslee and Heriberto Cerutti 2017. Tetraselmis transformation by microprojectile bombardment. protocols.io https://dx.doi.org/10.17504/protocols.io.hjtb4nn | 2021-04-15 09:14:57 | |
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Investigation of ancestral alleles in the Bovinae subfamily Resource Report Resource Website |
Maulana Naji, Yuri Utsunomiya, Johann Sölkner, Benjamin Rosen, Gábor Mészáros | DOI:10.17504/protocols.io.bh99j996 | In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). Defining AA and DA at polymorphic sites is useful to test hypotheses regarding molecular evolutionary processes, including estimation of allelic age, formation of linkage disequilibrium patterns and selection signatures. In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily (gaur, yak, bison, wisent, gayal, and cattle) to the cattle reference genome (ARS.UCD-1.2). We then identified sequence variants in three outgroups, i.e. yak, bison and gayal-gaur-banteng. Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups resulting in ~32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0.1% (high count) and regions without any occurrence of AA (null count). As mutation occurs across autosome independently, high count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. Gene ontology terms were inferred for functionality of referred regions. For both cattle, high count regions were associated to basal lipid metabolism which is essential on surviving of various condition pressures. Mutated regions were associated to productive traits in taurine such as higher metabolism, cell development and behaviors. While for zebu, mutation appeared for adaptation to marginal environment showed mainly by function in immune response domain. Our findings suggest that retaining and losing AA in some genes or regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience. | University of Natural Resources and Life Sciences Vienna, Austria, Sao Paulo State University, Brazil, University of Natural Resources and Life Sciences Vienna, Austria, Agricultural Research Service USDA, USA, University of Natural Resources and Life Sciences Vienna, Austria | 1 | 2020 | Maulana Naji, Yuri Utsunomiya, Johann Sölkner, Benjamin Rosen, Gábor Mészáros 2020. Investigation of ancestral alleles in the Bovinae subfamily. protocols.io https://dx.doi.org/10.17504/protocols.io.bh99j996 | 2021-04-15 09:14:40 | ||||
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DNA extraction from gram negative bacteria for ONT MinION sequencing Resource Report Resource Website |
Louise Judd | DOI:10.17504/protocols.io.p5mdq46 | High molecular weight DNA extraction from all kingdoms | This is the protocol I have developed to genterate High'ish' Molecular Weight gDNA from gram negative bacterial speices to use for ONT MinION sequencing.This protocol was intially developed for the high throughput extraction of bacterial gDNA for Illumina short read sequencing. To perform our high throughput work we utislise Beckman Coulter Biomek liquid handling robots and the Beckman Coutler gDNA extraction kit Genfind v2. This kit utilises magnetic pariticles and is relatively gentle. We have found that gDNA extracted using this method has a high'ish' molecular weight. On a fragment analyser the GNDA is typically a clean single peak >60 kb (the limits of the fragment analyser). ONT MinION libraries generated wiht this gDNA typically have N50s in excess of 20 kb and the data is suitable for the assembly automated of almost bacterial genomes we have tested to date. This protocol will not give you the ultra long 'whale' reads that others have reported but it is a good compromise between HMW DNA, speed and ease of use and capacity to scale up to high throughput. NOTEWe have found that gDNA extracted using this method often have underepresentation of smaller plamids ( | University of Melbourne | 1 | 2018 | Louise Judd 2018. DNA extraction from gram negative bacteria for ONT MinION sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.p5mdq46 | 2021-04-15 09:14:57 | |||
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Analysis of protein structure using Molprobity Resource Report Resource Website |
Chris Berndsen | James Madison University | 1 | 2020 | Chris Berndsen 2020. Analysis of protein structure using Molprobity. protocols.io https:// | 2021-04-15 09:14:37 | ||||||
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UC Davis - Acquisition/Acclimation/Quarantine Resource Report Resource Website |
K.C. Kent Lloyd | DOI:10.17504/protocols.io.xfifjke | Mouse Metabolic Phenotyping Centers | SummaryThe purpose of this standard operating procedure (SOP) is to provide steps for the acquisition, acclimation and quarantine of animals obtained from other institutions or laboratories and introduced to the MBP Vivarium with minimal risk to the current mouse colony population. This procedure applies to the import/export staff, veterinary staff and any principal investigator requesting animals. | University of California, Davis | https://www.mmpc.org/shared/document.aspx?id=117&docType=Protocol | 1 | 2019 | K.C. Kent Lloyd 2019. UC Davis - Acquisition/Acclimation/Quarantine. protocols.io https://dx.doi.org/10.17504/protocols.io.xfifjke | 2021-04-15 09:14:57 | ||
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Polyacrylamide Gel System For Electrophoresis Of Proteins Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.ep7bdrn | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Polyacrylamide Gel System For Electrophoresis Of Proteins. protocols.io https://dx.doi.org/10.17504/protocols.io.ep7bdrn | 2021-04-15 09:14:53 | ||||
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Synthesis of PF-06928215 and analogues Resource Report Resource Website |
Les Dakin | DOI:10.17504/protocols.io.jfxcjpn | Discovery of PF-06928215 as a high affinity inhibitor of cGAS enabled by a novel fluorescence polarization assay Cyclic GMP-AMP synthase (cGAS) initiates the innate immune system in response to cytosolic dsDNA. After binding and activation from dsDNA, cGAS uses ATP and GTP to synthesize 2 ʹ, 3 ʹ -cGAMP (cGAMP), a cyclic dinucleotide second messenger with mixed 2ʹ-5ʹ and 3ʹ-5ʹ phosphodiester bonds. Inappropriate stimulation of cGAS has been implicated in autoimmune disease such as systemic lupus erythematosus, thus inhibition of cGAS may be of therapeutic benefit in some diseases; however, the size and polarity of the cGAS active site makes it a challenging target for the development of conventional substrate-competitive inhibitors. We report here the development of a high affinity (KD = 200 nM) inhibitor from a low affinity fragment hit with supporting biochemical and structural data showing these molecules bind to the cGAS active site. We also report a new high throughput cGAS fluorescence polarization (FP)-based assay to enable the rapid identification and optimization of cGAS inhibitors. This FP assay uses Cy5-labelled cGAMP in combination with a novel high affinity monoclonal antibody that specifically recognizes cGAMP with no cross reactivity to cAMP, cGMP, ATP, or GTP. Given its role in the innate immune response, cGAS is a promising therapeutic target for autoinflammatory disease. Our results demonstrate its druggability, provide a high affinity tool compound, and establish a high throughput assay for the identification of next generation cGAS inhibitors. | Hall J, Brault A, Vincent F, Weng S, Wang H, Dumlao D, Aulabaugh A, Aivazian D, Castro D, Chen M, Culp J, Dower K, Gardner J, Hawrylik S, Golenbock D, Hepworth D, Horn M, Jones L, Jones P, Latz E, Li J, Lin L, Lin W, Lin D, Lovering F, Niljanskul N, Nistler R, Pierce B, Plotnikova O, Schmitt D, Shanker S, Smith J, Snyder W, Subashi T, Trujillo J, Tyminski E, Wang G, Wong J, Lefker B, Dakin L, Leach K (2017) Discovery of PF-06928215 as a high affinity inhibitor of cGAS enabled by a novel fluorescence polarization assay. PLoS ONE 12(9): e0184843. doi: 10.1371/journal.pone.0184843 | Pfizer | https://doi.org/10.1371/journal.pone.0184843 | 1 | 2017 | Les Dakin 2017. Synthesis of PF-06928215 and analogues. protocols.io https://dx.doi.org/10.17504/protocols.io.jfxcjpn | 2021-04-15 09:14:53 | ||
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Genotyping of the rs1695 polymorphism of the GSTP1 gene by PCR-RFLP Resource Report Resource Website |
Jéssica Barletto de Sousa Barros, Kamilla de Faria Santos, Rômulo Morais Azevedo, Rayana Pereira Dantas de Oliveira, Ana Carolina Dourado Leobas, Dhiogo da Cruz Pereira Bento, Rodrigo da Silva Santos, Angela Adamski da Silva Reis | DOI:10.17504/protocols.io.bqgqmtvw | Glutathione S-transferases (GSTs) are enzymes that act in the cellular detoxification of harmful compounds. Due to the role of the GSTP1 isoenzyme in the brain, the presence of the single nucleotide polymorphism (SNP) rs1695 in the GSTP1 gene may play an important role in the development of neurodegenerative diseases through oxidative stress, one of the main pathogenic mechanisms associated with the degeneration and death of motor neurons.Thus, this protocol provides a standardized methodology for genotyping the rs1695 polymorphism in the GSTP1 gene through polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (PCR- RFLP). This polymorphism consists of the exchange of adenine for guanine at position 313 (codon 105), which causes the substitution of amino acid isoleucine (Ile) for valine (Val), resulting in a decreased Pi enzyme activity. Polymorphism genotyping techniques have been of great interest in determining the genetic association of several polymorphisms with different diseases, and therefore this protocol may facilitate future genetic studies. | Barros JBdS, Santos KdF, Azevedo RM, Oliveira RPDd, Leobas ACD, Bento DdCP, Santos RdS, Reis AAdS (2021) No association of GSTP1 rs1695 polymorphism with amyotrophic lateral sclerosis: A case-control study in the Brazilian population. PLoS ONE 16(2): e0247024. doi: 10.1371/journal.pone.0247024 | Laboratory of Molecular Pathology, Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás (UFG), Goiânia, GO, Brazil., Laboratory of Molecular Pathology, Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás (UFG), Goiânia, GO, Brazil., Laboratory of Molecular Pathology, Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás (UFG), Goiânia, GO, Brazil., Laboratory of Molecular Pathology, Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás (UFG), Goiânia, GO, Brazil., Laboratory of Molecular Pathology, Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás (UFG), Goiânia, GO, Brazil., Rehabilitation and Readaptation Medical Center Dr. Henrique Santillo (CRER), Goiânia, Goiás, Brazil., Laboratory of Molecular Pathology, Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás (UFG), Goiânia, GO, Brazil., Laboratory of Molecular Pathology, Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás (UFG), Goiânia, GO, Brazil. | https://doi.org/10.1371/journal.pone.0247024 | 1 | 2021 | Jéssica Barletto de Sousa Barros, Kamilla de Faria Santos, Rômulo Morais Azevedo, Rayana Pereira Dantas de Oliveira, Ana Carolina Dourado Leobas, Dhiogo da Cruz Pereira Bento, Rodrigo da Silva Santos, Angela Adamski da Silva Reis 2021. Genotyping of the rs1695 polymorphism of the GSTP1 gene by PCR-RFLP. protocols.io https://dx.doi.org/10.17504/protocols.io.bqgqmtvw | 2021-04-15 09:14:53 | ||
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Double Digestion and Dephosphorylation of Plasmid Resource Report Resource Website |
Igem Dusseldorf | DOI:10.17504/protocols.io.79phr5n | Heinrich-Heine Universität Düsseldorf | 1 | 2019 | Igem Dusseldorf 2019. Double Digestion and Dephosphorylation of Plasmid. protocols.io https://dx.doi.org/10.17504/protocols.io.79phr5n | 2021-04-15 09:14:38 | |||||
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Mammalian Cell Culture: Subculturing Resource Report Resource Website |
Kenneth Schackart, Kattika Kaarj | DOI:10.17504/protocols.io.xukfnuw | 481b Laboratory | This protocol details how to subculture nearly confluent mammalian cells grown in a T-25 flask. | University of Arizona, University of Arizona | 1 | 2019 | Kenneth Schackart, Kattika Kaarj 2019. Mammalian Cell Culture: Subculturing. protocols.io https://dx.doi.org/10.17504/protocols.io.xukfnuw | 2021-04-15 09:14:40 | |||
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Real-Time PCR protocol to screen for SARS-COV-2 variants of concern (B.1.1.7, P.1 and B.1.1.35) Resource Report Resource Website |
Camila Romano, Jaqueline De Jesus, Alvina Clara Felix, Anderson V de Paula, Pâmela S Andrade, Franciane M de Oliveira, Darlan Cândido, Nuno Faria, William M de Souza, Ester C Sabino | DOI:10.17504/protocols.io.bszbnf2n | Coronavirus Method Development Community | The recently emerged variants of concern (VOC) B.1.1.7 in UK, B.1.1.35 in South Africa and P.1 in Brazil have increased transmissibility and are rapidly spreading worldwide. These variants have several substitutions that allow them to bypass the immune responses and are up to 10 times more contagious than the previous circulating SARS-COV-2 lineages. While in some regions P.1 predominates (as several estates in Brazil), in other countries B.1.1.7 or B.1.1.35 are most prevalent. Therefore, real-time surveillance of VOC is the key for rapid public health responses. In this matter, RT-PCR protocols that are capable of detecting VOCs easily and rapidly are needed. We developed and validated a protocol that detect simultaneously the 3 most widespread VOC. Although this protocol does not discriminate among the VOCs, it can reliably detect mixed infection. Importantly, our protocol successfully identified a co-infection by two SARS-COV-2 lineages (P.1 and B.1), confirmed through complete genome sequencing. | Institute of Tropical Medicine, University of Sao Paulo, Institute of Tropical Medicine, University of Sao Paulo, Institute of Tropical Medicine, University of Sao Paulo, Institute of Tropical Medicine, University of Sao Paulo, Institute of Tropical Medicine, University of Sao Paulo, Institute of Tropical Medicine, University of Sao Paulo, Department of Zoology, University of Oxford, Oxford, United Kingdom, Department of Zoology, University of Oxford, Oxford, United Kingdom, Department of Zoology, University of Oxford, Oxford, United Kingdom, Institute of Tropical Medicine, University of Sao Paulo | 1 | 2021 | Camila Romano, Jaqueline De Jesus, Alvina Clara Felix, Anderson V de Paula, Pâmela S Andrade, Franciane M de Oliveira, Darlan Cândido, Nuno Faria, William M de Souza, Ester C Sabino 2021. Real-Time PCR protocol to screen for SARS-COV-2 variants of concern (B.1.1.7, P.1 and B.1.1.35) . protocols.io https://dx.doi.org/10.17504/protocols.io.bszbnf2n | 2021-04-15 09:14:38 | |||
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During data acquisition Resource Report Resource Website |
Lukas Snoek, Tinka Beemsterboer | DOI:10.17504/protocols.io.nmudc6w | Spinoza Centre, REC-L | Protocol to make sure the data acquisition process will yield data that can be processed by the centre's quality control and preprocessing pipelines. | Spinoza Centre, REC-L, Spinoza Centre, REC-L | 2 | 2018 | Lukas Snoek, Tinka Beemsterboer 2018. During data acquisition. protocols.io https://dx.doi.org/10.17504/protocols.io.nmudc6w | 2021-04-15 09:14:37 | |||
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Mathematical models for understanding the genetic diversity of the new coronavirus: LaBECom's analytical protocols Resource Report Resource Website |
Pierre Teodosio Felix, Robson da Silva Ramos, Dallynne Bárbara Ramos Venâncio, Cícero Batista do Nascimento Filho, Antônio João Paulino | DOI:10.17504/protocols.io.bmbvk2n6 | Coronavirus Method Development Community, LaBECom | In this work, we evaluated the levels of genetic diversity in 38 complete genomes of SARS-CoV-2, publicly available on the National Center for Biotechnology Information (NCBI) platform and from six countries in South America (Brazil, Chile, Peru, Colombia, Uruguay and Venezuela with 16, 11, 1, 1, 1, 7 haplotypes, respectively), all with an extension of 29,906 bp and Phred values ≥ 40. These haplotypes were previously used for phylogenetic analyses, following the alignment protocols of the MEGA X software; where all gaps and unconserved sites were extracted for the construction of phylogenetic trees. The specific methodologies for Paired FSTestimators, Molecular Variance (AMOVA), Genetic Distance, mismatch, demographic and spatial expansion analyses, molecular diversity and evolutionary divergence time analyses, were obtained using 20,000 random permutation. | Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA | 1 | 2020 | Pierre Teodosio Felix, Robson da Silva Ramos, Dallynne Bárbara Ramos Venâncio, Cícero Batista do Nascimento Filho, Antônio João Paulino 2020. Mathematical models for understanding the genetic diversity of the new coronavirus: LaBECom's analytical protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.bmbvk2n6 | 2021-04-15 09:14:55 | |||
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Macrophage Phagocytosis Assay Resource Report Resource Website |
Zahra Islam | DOI:10.17504/protocols.io.gb6bsre | CMSI protocols | A macrophage phagocytosis assay designed for use with recombinant, fluorescently labelled bacteria. This assay was optimised using recombinant GFP-labelled E. coli expressing eukaryotic-like proteins (ELPs) derived from sponge-symbionts. | The University of New South Wales, Australia | 1 | 2017 | Zahra Islam 2017. Macrophage Phagocytosis Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.gb6bsre | 2021-04-15 09:14:39 | |||
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Embedding living larvae in low-melting agarose for imaging and recovery thereafter Resource Report Resource Website |
Pringle Lab, Christian Renicke | DOI:10.17504/protocols.io.qxbdxin | Aiptasia-Symbiodiniaceae Model System | This protocol describes how to use agarose with a low gelling point (27-30°C; often called low-melting agarose) to immobilize Aiptasia larvae for microscopy.Larvae stay alive and in one place for prolonged periods of several hours but continue to mainly spin around the longitudal axis. After imaging, larvae can easily be retrieved from the agarose and transferred back to artificial sea water. | Stanford University, Stanford University | 1 | 2018 | Pringle Lab, Christian Renicke 2018. Embedding living larvae in low-melting agarose for imaging and recovery thereafter. protocols.io https://dx.doi.org/10.17504/protocols.io.qxbdxin | 2021-04-15 09:14:38 | |||
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Experimental test of the intrinsic dimensionality of Hounsfield unit measurements Resource Report Resource Website |
Zachary Levine, Adele Peskin, Andrew Holmgren, Edward Garboczi | DOI:10.17504/protocols.io.sw3efgn | Purpose: The immediate purpose is to determine the maximum number of tube voltages which are useful for acquiring information in medical computed tomography (CT) along with specific linear combinations of quantities of chemical elements which are observable with the current generation of medical CT machines. The larger purpose is to encourage the development of CT reconstruction algorithms based on the material basis described herein and, ultimately, to tie the measurand of CT to the International System of Units (SI). Methods and Materials: Experimentally, we scanned samples at four tube voltages, namely 80 kV, 100 kV, 120 kV, and 140 kV on a medical CT. The samples included 30 small plastic bottles of powders containing various compounds spanning the atomic numbers from 1 to 20, along with a similar bottle of water and one of air. Using the known chemical formulas and measured masses, we formed a matrix giving the number of Hounsfield units per (mole per cubic meter) at each tube voltage for each of 13 chemical elements. Theoretically, we took the XCOM cross sections, combined them with the tungsten anode spectral model using interpolating cubic splines (TASMICS), with a one-parameter filter, and a simple detector model, and created a similar matrix for the first 20 chemical elements. In the training phase, we found a best-fit parameter. We define the molar Hounsfield unit (HU) potency as the difference in HU values that an added mole per cubic meter in a given voxel would add to the measured HU value. We built a matrix of molar potencies for each chemical element and tube voltage and performed a singular value decomposition (SVD) on these. In a validation phase, we compared the model predictions to Hounsfield unit measurements on three CT calibration phantoms taken from the literature. Results: We found that we could predict the measured HU potency for the chemical elements within our model. The singular values and singular vectors of the model and powder measurements are in substantial agreement. Application of the Bayesian Information Criterion (BIC) shows that exactly two singular values and singular vectors describes the results over four tube voltages. We were able to give a good account of the HU values measured for the calibration phantoms at several tube voltages for several vendors within our model without introducing additional parameters. Conclusions: Measurements at two tube voltages are necessary and sufficient to extract the available material dependent information in medical CT. The linear combination of elements that can be observed using a medical CT have been characterized, providing a material basis for use in dual-energy reconstruction. This approach provides groundwork for improved reconstruction and for the link of Hounsfield units to the SI. | National Institute of Standards and Technology, National Institute of Standards and Technology, National Institute of Standards and Technology, National Institute of Standards and Technology | 1 | 2018 | Zachary Levine, Adele Peskin, Andrew Holmgren, Edward Garboczi 2018. Experimental test of the intrinsic dimensionality of Hounsfield unit measurements. protocols.io https://dx.doi.org/10.17504/protocols.io.sw3efgn | 2021-04-15 09:14:55 | ||||
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U Mass - Body composition (organs) Resource Report Resource Website |
Jason Kim | DOI:10.17504/protocols.io.xsnfnde | Mouse Metabolic Phenotyping Centers | The EchoMRI 3-in-1 uses ¹H- magnetic resonance spectroscopy to noninvasively measure fat mass, lean mass, and water mass in individual organs. Fat, lean, and water mass composition in specific organs is altered in obesity. | University of Massachusetts | https://mmpc.org/shared/document.aspx?id=148&docType=Protocol | 1 | 2019 | Jason Kim 2019. U Mass - Body composition (organs). protocols.io https://dx.doi.org/10.17504/protocols.io.xsnfnde | 2021-04-15 09:14:53 | ||
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High molecular weight gDNA extraction after Mayjonade et al. optimised for eucalyptus for nanopore sequencing Resource Report Resource Website |
Miriam Schalamun | DOI:10.17504/protocols.io.i6vche6 | High molecular weight DNA extraction from all kingdoms | Extraction of high quality DNA for long read sequencing e.g. the Oxford Nanopore Optimized for DNA extraction from eucalyptus grandis and eucalyptus pauciflora. This protocol contains an optional Chloroform clean up step which is necessary for eucalyptus but might not be for other tissue. For long DNA fragments don't vortex the DNA sample. | 7 | 2017 | Miriam Schalamun 2017. High molecular weight gDNA extraction after Mayjonade et al. optimised for eucalyptus for nanopore sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.i6vche6 | 2021-04-15 09:14:38 | ||||
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NEBExpress Ni Spin Column Reaction Protocol (NEB #S1427) Resource Report Resource Website |
New England Biolabs | New England Biolabs | https://www.neb.com/protocols/2019/08/28/nebexpress-ni-spin-column-reaction-protocol-neb-s1427 | 1 | 2020 | New England Biolabs 2020. NEBExpress Ni Spin Column Reaction Protocol (NEB #S1427). protocols.io https:// | 2021-04-15 09:14:55 |
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